Instruction of Use Kit

www.roche-applied-science.
com
MagNA Pure 96 Cellular RNA
Large Volume Kit
y Version 07
Content version: June 2012
Prefilled reagents for the isolation of cellular RNA from up to 1 10
6
cultured
cells, or up to 800 l whole blood, or whole blood stabilized in PAXgene Blood
RNA tubes, or up to 25 mg fresh- frozen tissue, or tissue stabilized in RNAlater,
or from 1 10 m sections from formalin-fixed, paraffin-embedded tissue, using
the MagNA Pure 96 Instrument.
Cat. No. 05 467 535 001
Kit for 3 96 isolations
Store the kit at 15 to 25C
Keep the kit away from magnets.
When properly stored, kit
components are stable until the
expiration date printed on the label.
For life science research only.
Not for use in diagnostic procedures.
Table of Contents
2 www.roche-applied-science.com
1. What this Product Does ................................................................................................. 3
Number of Tests 3
Kit Contents 3
Storage and Stability 3
Additional Equipment and Reagents Required 4
Application 5
Assay Time 5
2. How to Use this Product ............................................................................................... 6
2.1 Before You Begin 6
Precautions 6
Purification Protocols 8
Sample Material 10
Reagents 11
Preparation of Working Solutions 11
Controls 11
2.2 Pre-Isolation Steps 12
Cultured Cells 12
PAXgene Tubes 12
Whole blood 12
Tissue homogenization for fresh-frozen tissue and tissue stabilized in RNAlater 12
Deparaffinization of FFPE tissue sections 13
2.3 Isolation Procedure 13
General Remarks 13
Procedure 14
Storage of RNA Eluates 14
3. Results ............................................................................................................................ 14
Experimental Results 14
4. Troubleshooting ............................................................................................................ 15
5. Additional Information on this Product ................................................................... 17
How this Product Works 17
Test Principle 17
Quality Control 17
6. Supplementary Information ........................................................................................ 18
6.1 Conventions 18
Text Conventions 18
Symbols 18
Abbreviations 18
6.2 Changes to Previous Version 18
6.3 Ordering Information 19
6.4 Trademarks 20
6.5 Disclaimer of License 20
6.6 Regulatory Disclaimer 20
What this Product Does
www.roche-applied-science.com 3
MagNA Pure 96 Cellular RNA Large Volume Kit y Version 07
1. What this Product Does
Number of Tests 3 96 isolations from up to 1 10
6
cultured cells.
3 96 isolations of 400 l whole blood or a half PAXgene tube.
3 48 isolations of 800 l whole blood or a whole PAXgene tube.
3 48 isolations from up to 25 mg fresh-frozen tissue.
3 96 isolations from up to 20 mg fresh-frozen tissue or tissue stabilized in
RNAlater.
3 96 isolations from 110 m sections from formalin-fixed,
paraffin-embedded tissue.
The kit is designed to process up to 288 samples in a maximum of twelve
runs. For details, see section Isolation Protocols.
Kit Contents
Storage and
Stability
Kit components are stable at +15 to +25C until the expiration date printed
on the label.
The kit is shipped at ambient temperature.
Component Label Content
Tray 1 Reagent Tray 1 3 trays
Container 1 Wash Buffer I 1 container
for removing impurities
Container 2 Wash Buffer II 1 container
for removing impurities
Tray 2 Reagent Tray 2 3 trays
Container 1 Lysis/Binding
Buffer
1 container
for cell lysis and binding of RNA
Container 2 Proteinase K 1 container
for digestion of proteins
Container 3 Proteinase K
Incubation Buffer
1 container
for digestion of proteins
Container 4 DNase Incubation
Buffer
1 container
for digestion of DNA
Container 5 Elution Buffer 1 container
for elution of RNA
Bottle 1 Magnetic Glass
Particles
6 bottles
MGP suspension
for binding RNA
Bottle 2 DNase 6 glass vials
lyophilizate
for digestion of DNA
Bottle 3 DNase Incubation
Buffer
3 bottles
for reconstitution of DNase
Reagents, including reconstituted DNase, can be stored unsealed for
32hours at +15 to +25C on the stage of the instrument.
Store reconstituted DNase at +2 to +8C for up to 28 days. Seal the cap of
the bottle with parafilm after each use on the MagNA Pure 96 Instrument.
Remove parafilm again when DNase is reused on the instrument.
Parafilm is not needed for sealing the caps of MGP bottles.
One set of reagent trays (tray 1 and tray 2) can be used for up to four individ-
ual runs with the MagNA Pure 96 Instrument. Once opened, reagent trays
can be used for additional runs on the same MagNA Pure 96 Instrument
within 28 days after proper sealing, with sealing foil, and stored at +15 to
+25C.
It is only possible to reuse partially used reagent cartridges on the same
MagNA Pure 96 Instrument. The MagNA Pure 96 Software for each instru-
ment tracks inventory using reagent barcodes, and recognizes partially
used reagents and tip trays, handling them appropriately in the next run.
When reagent trays are not properly sealed, or stored for longer than
28days, evaporation may negatively affect performance.
When storing output plates outside the MagNA Pure 96 Instrument, or lon-
ger than 32 hours on the instrument stage, seal the plate with a sealing foil.
Additional
Equipment and
Reagents
Required
Additional equipment and reagents required when using the MagNA Pure 96
Cellular RNA Large Volume Kit with the MagNA Pure 96 Instrument:
MagNA Pure 96 System Fluid (Internal) or (External)*
MagNA Pure 96 Sealing Foil*
Standard laboratory equipment
Pipettes and nuclease-free, aerosol-preventive tips to predispense samples
into the MagNA Pure 96 Processing Cartridge: Standard length tips, or
optional, extra-long tips of 10 cm length.
Centrifuge tubes (e.g., for PAXgene Blood RNA tubes)
Phosphate buffered saline (PBS)
Optional, RNA/DNA Stabilization Reagent for Blood/Bone Marrow*
Optional, PAXgene Blood RNA tubes (Cat. No. 762165, available from
PreAnalytiX)
Optional, new lids for PAXgene Blood RNA tubes (e.g., flexible Vacucap
Closures (16 mm), available from VWR)
Optional, MagNA Pure LC RNA Tissue Lysis Buffer/Refill* (for fresh-frozen
tissue applications)
Optional, MagNA Lyser Instrument* or similar device for homogenization of
fresh-frozen tissue
Optional, MagNA Lyser Green Beads*
Optional, MagNA Pure DNA Tissue Lysis Buffer (for FFPE tissue applications)
Optional, Proteinase K (solution)* for FFPE tissue applications
Vortex mixer or multiple vortex mixer
Optional, Xylol, for FFPE tissue applications
Optional, Ethanol, for FFPE tissue applications
RNAlater
* available from Roche Applied Science
Application The MagNA Pure 96 Cellular RNA Large Volume Kit is specifically designed to
isolate highly purified cellular RNA from cultured cells, or whole blood stabi-
lized with the RNA/DNA Stabilization Reagent for Blood/Bone Marrow, or
whole blood stored in PAXgene Blood RNA tubes, or from fresh-frozen tissue,
or tissue stabilized in RNAlater, or from 1 10 m sections from forma-
lin-fixed, paraffin-embedded tissue, using the MagNA Pure 96 Instrument.
Purified RNA can be used for RT-PCR with LightCycler
Instruments or stan-
dard thermal block cyclers.
Assay Time MagNA Pure 96 Instrument setup requires approximately 5 to 10 min. Total
time for automated isolation of cellular RNA from 96 samples is approximately
75 min (85 min for isolation of cellular RNA from blood prepared in PAXgene
tubes), and 90 min for the isolation of cellular RNA from whole blood samples.
Additional hands-on time may be required for manual pre-isolation steps
(e.g., preparation of cultured cells), depending on the protocol. For
detailed information, see section Pre-Isolation Steps.
How to Use this Product
2. How to Use this Product
2.1 Before You Begin
Precautions I) Handling Requirements
Perform sample preparation, RT-PCR setup, and the RT-PCR run in separate
locations.
Do not use a kit after its expiration date has passed.
Wear disposable gloves and change them frequently.
Some buffers contain dangerous or hazardous compounds. For detailed
information, see Figure 1 (reagent tray 1), Figure 2 (reagent tray 2), and the
following table. Do not allow these reagents to touch the skin, eyes, or
mucous membranes. If contact does occur, wash the affected area immedi-
ately with large amounts of water. If the reagents are spilled, dilute the spill
with water before wiping it up.
Do not allow reagents containing guanidine thiocyanate to contact sodium
hypochlorite (bleach) solution or acids. These mixtures produce a highly toxic
gas. This precaution is particularly important to be aware of when cleaning
the MagNA Pure 96 Waste Cover.
Fig. 1: Reagent Tray 1 Fig. 2: Reagent Tray 2
Component Label Dangerous/Hazardous Compounds
Tray 1 Reagent Tray 1
Container 1 Wash Buffer I Guanidine hydrochloride
Ethanol
Container 2 Wash Buffer II Ethanol
Tray 2 Reagent Tray 2
II) Laboratory Procedures
Handle all samples as if potentially infectious. Use safe laboratory proce-
dures. As the sensitivity and titer of potential pathogens in sample material
can vary, the operator must optimize pathogen inactivation. Follow the
appropriate measures according to local safety regulations.
Do not eat, drink, or smoke in the laboratory area.
Do not pipette by mouth.
Wear protective disposable gloves, laboratory coats, and eye protection,
when handling samples and kit reagents.
Wash hands thoroughly after handling samples and reagents.
III) Waste Handling
Material Safety Data Sheets (MSDS) are available on the Roche Applied
Science homepage (www.roche-applied-science.com), or upon request from
the local Roche office.
Discard unused reagents and waste in accordance with country, federal,
state, and local regulations.
Wear protective disposable gloves, laboratory coats, and eye protection when
handling samples and kit reagents.
To discard reagents from the containers, follow the procedure below:
Container 1 Lysis/Binding
Buffer
Guanidine thiocyanate
Container 2 Proteinase K Proteinase K
Container 3 Proteinase K
Incubation Buffer
Urea
Container 4 DNase Incubation
Buffer
Container 5 Elution Buffer
Bottle 1 Magnetic Glass
Particles
Isopropanol
Bottle 2 DNase DNase
Bottle 3 DNase Incubation
Buffer
Pierce the foil in the corner of one container in the reagent tray with a
solid plastic disposable (e.g., a cell culture pipette).
Fold back the foil and discard the liquid in the specific container for
waste.
Discard the contents of all containers by repeating steps 1 and 2 until
all containers are empty.
Component Label Dangerous/Hazardous Compounds
Purification
Protocols
To perform RNA isolations with the MagNA Pure 96 Cellular RNA Large Vol-
ume Kit, pre-installed purification protocols are available. The elution volume
must be chosen using the software menu.
Regularly check for new versions of the purification protocols.
For downloading protocols that are currently not installed, follow the proce-
dure below:
For additional details, contact your local Roche representative.
Different protocols are optimized for a specific sample material.
Do not use a protocol for a sample material other than specified below.
Doing so will negatively affect the performance of the isolation process and
may lead to clumping and loss of MGPs, as well as cross-contamination of
samples, or even damage to the instrument.
Download the protocol (.zip file format) from
www.magnapure96.com/ (see Download System Protocols), and
save the file onto a USB stick.
Log on to the MagNA Pure 96 Software as admin user.
Insert the USB stick with the protocol into the corresponding drive.
Unzip the .zip file.
In the MagNA Pure 96 Software, select the Utilities tab.
In the Utilities tab, select the Tools sub-tab.
Click Import Protocol.
The Import Protocol dialog box opens.
In the Import Protocol dialog box, select the respective purification
protocol saved on the USB stick [Files of Type Protocols (.tdf)].
Click Open.
The selected purification protocol is imported.
Exit the MagNA Pure 96 Software and restart the control unit.
Restarting the control unit is a prerequisite for using newly
installed purification protocols.
Protocol Name Sample Material Elution Volume
1)
Cellular RNA LV Up to 1 10
6
cultured
cells resuspended in
200 l PBS
50, 100, or 200 l
RNA PAXgene LV PAXgene pellet resus-
pended in 400 l PBS
100 or 200 l
RNA PAXgene Half
Tube LV
half PAXgene pellet con-
tained in 200 l PBS
50 or 100 l
Use the most up-to-date protocol version available for purification of RNA.
Only specified types of sample material can be combined in the same run.
One set of reagent trays (tray 1 and tray 2) can be used for up to four indi-
vidual runs with the same MagNA Pure 96 Instrument. Pierced reagent
trays can be stored for 28 days after the first use.
To prevent evaporation and contamination of reagents after use, the
reagent trays have to be sealed with a sealing foil. Up to three sealing foils
can be used to cover the reagent trays.
1)
The concentration of cellular RNA in the eluate, and the sensitivity in
downstream applications can be increased by choosing a lower elution
volume. This may however reduce the elution efficiency, and overall RNA
yield compared to using higher elution volumes. To increase total yield, we
recommend elution volumes of 100 or 200 l.
2)
For some tissue samples more than the specified amount of homoge-
nized tissue can be used (e.g., brain).
* When using the RNA Blood LV 800 protocol, the sample volume is
divided to produce two samples and is processed in two separate wells of
the MagNA Pure 96 Processing Cartridge. If less samples than multiples of
8 are processed using the RNA Blood LV 800 protocol, it is required to
RNA Blood LV 400 400 l whole blood stabi-
lized with 500 l RNA/
DNA Stabilization
Reagent for Blood/Bone
Marrow
50, 100, or 200 l
RNA Blood LV 800* 800 l whole blood stabi-
lized with 1000 l RNA/
DNA Stabilization
Reagent for Blood/Bone
Marrow
100 or 200 l
RNA Tissue FF
Standard LV
up to 10 mg homogenized
tissue from fresh-frozen
or RNAlater stabilized tis-
sue samples in a volume
of 350 l
2)
50, 100, or 200 l
RNA Tissue FF
High LV**
up to 25 mg homogenized
tissue from fresh-frozen
tissue samples in a vol-
ume of 700 l
2)
100 or 200 l
RNA Tissue FFPE LV Deparaffinized and
digested FFPE tissue
sections in a volume of
150 l
50 or 100 l
Protocol Name Sample Material Elution Volume
1)
specify dummy sample data in the sample table and fill the corresponding
positions in the processing cartridge with 1800 l PBS until the next multi-
ple of 8 is reached.
** When using the RNA Tissue FF High LV protocol, the sample volume is
divided to produce two samples and is processed in two separate wells of
the MagNA Pure 96 Processing Cartridge.
Sample Material For optimal results in downstream procedures, particulary in real-time RT-PCR
do not process samples with higher volume or cell count than the selected
purification protocol is designed to handle. Doing so can affect the perfor-
mance of the isolation process, may lead to clumping and loss of MGPs, as
well as cross-contamination of samples, or even damage to the instrument.
Treat all samples as potentially infectious.
I) Cultured Cells
Cell pellets can be stored at 15 to 25C for several weeks.
Cultured cells resuspended in 200 l PBS.
Never use more sample material than this kit is designed to handle (e.g.,
use not more than 1 10
6
cells). Doing so will negatively affect the perfor-
mance of the isolation process.
II) PAXgene Blood RNA Tubes
Pellet of a whole PAXgene tube suspended in 400 l PBS (or optionally, only
half of that suspension). The PAXgene Blood RNA tube is designed to hold 2.5
ml whole blood.
III) Whole blood
The stabilized whole blood (see section 2.2 below) can be stored for 2 days
at +15 to +25C or for 1 month at - 80C.
IV) Fresh-frozen tissue
Up to 25 mg fresh-frozen tissue samples (e.g., liver, kidney, lung, muscle, tail of
mammalian species) can be used after homogenization.
For some tissue samples, so-called "easy-to-lyse" tissues, more than the
specified amount of homogenized tissue can be used (e.g., brain).
When purifying 25 mg fresh-frozen tissue samples with high amounts of
nucleic acids (e.g. spleen), an additional DNase digestion step may be
required.
V) Tissues stabilized in RNAlater
5 mg of RNAlater stabilized tissue can be used after homogenization.
VI) FFPE tissue
1 10 m sections from formalin-fixed, paraffin-embedded tissue.
Please be aware that section thickness as well as yield and quality of the
isolated RNA are strongly related to type of tissue, age of sample as well
as fixation protocol used.
Reagents Kit components, except DNase, are ready-to-use.
Ensure that kit components are equilibrated to +15 to +25C before use. If
reagents are used at temperatures outside this recommended range, the
kit may not function properly.
Preparation of
Working
Solutions
Before starting, prepare the working solutions as described below:
Reconstitute DNase just before first time use.
Controls For control reactions, prepare the following:
Positive control, using a sample material positive for the target.
Negative control, using a sample material negative for the target.
Extraction control, using phosphate buffered saline (PBS) in place of a
sample.
Reagent Preparation/Comments Storage
DNase For each reagent tray set (tray 1 and tray
2, for 96 samples), reconstitute two glass
bottles of DNase (bottle 2) with 3 ml from
one bottle of DNase incubation buffer
(bottle 3). Close the bottles and mix well
by inverting. Do not vortex. Dissolved, a
clear to slightly opaque solution is
obtained. Transfer all liquid to the original
plastic bottle labeled DNase incubation
buffer (bottle 3), and place a check in the
box DNase added on the label. Close
the bottle with the original lid. Mix by
inverting the bottles five times.
Once reconstituted,
the DNase is stable
for 28 days at +2 to
+8C.
2.2 Pre-Isolation Steps
Cultured Cells For cultured cells grown in suspension, gently spin down cells (e.g., for 5 min
at 300 g). Wash the cell pellet using PBS. Cell pellets can be stored at 15
to 25C for several weeks. Remove culture media (or PBS) completely.
Resuspend cells in cold phosphate buffered saline (PBS) by pipetting or shak-
ing the tube until the cell pellet is resuspended. Monolayer cultured cells
should be collected using trypsinization, prior to the procedure described
above. The required sample volume is 200 l. Ensure there are not more than
1 10
6
cells/200 l.
PAXgene Tubes For collection, storage, and transportation of whole blood in PAXgene Blood
RNA tubes, follow the PAXgene instructions. The PAXgene Blood RNA tube is
designed to hold 2.5 ml whole blood.
After blood sample collection, centrifuge PAXgene Blood RNA tubes in a
swing-out rotor with round bottomed tube adapters at 3,000 to 5,000 g for
10 min. Decant the supernatent as completely as possible. A reddish to
brownish pellet will be clearly visible. Add 400 l PBS to the PAXgene Blood
RNA tube pellet. Close the tube using the PAXgene Blood RNA tube lid. Do
not mix up lids from different samples, decant only one PAXgene Blood RNA
tube at a time. Alternatively, use a new lid.
Vortex the pellet until it is resuspended completely. When using a multitube
vortexer, vortex full speed for multiples of 30 sec until the pellet is resus-
pended.
When purifying RNA using the RNA PAXgene LV protocol, transfer the
whole volume (400 l) of the resuspended pellet from one PAXgene Blood
RNA tube into one well of a MagNA Pure 96 Processing Cartridge.
When purifying RNA using the RNA PAXgene Half Tube LV protocol, trans-
fer 200 l of the pellet resuspended in 400 l from one PAXgene Blood RNA
tube into one well of a MagNA Pure 96 Processing Cartridge.
Maintain PAXgene Blood RNA tubes for at least 2 hours at +15 to +25C
before starting RNA isolation.
Do not use the content from more than one PAXgene Blood RNA tube per
isolation to avoid clumping during the purification run.
Whole blood Stabilize 400 l (or 800 l) whole blood with 500 l (or 1000 l) RNA/DNA
Stabilization Reagent for Blood/Bone Marrow*, and mix thoroughly.
Tissue
homogenization
for fresh-frozen
tissue and tissue
stabilized in
RNAlater
MagNA Lyser treatment: Transfer up to 10 mg (or up to 25 mg) tissue sample
into a MagNA Lyser Green Beads Tube containing 400 l (or 800 l)
MagNA Pure LC RNA Tissue Lysis Buffer.
For some tissue samples, so-called "easy-to-lyse" tissues, more than the
specified amount of homogenized tissue can be used (e.g., brain): Up to
20 mg homogenized tissue for the RNA Tissue FF Standard LV and up to
50 mg for the RNA Tissue FF High LV protocol. This requires validation by
the user.
Avoid cooling at this step. Homogenize the tissue in the MagNA Lyser Instru-
ment for 30 to 50 seconds (depending on the tissue type).
If necessary, chill on ice for 90 s and repeat the procedure.
To minimize activity of present nucleases, perform homogenization as fast
as possible. When homogenizing more than two samples, RIN values
obtained using the Agilent Instrument may be lower due to prolonged
time at +15 to +25C. Tissue thawing can produce RNA degradation by
RNases.
Deparaffinization
of FFPE tissue
sections
To one 5 10 m section (1 cm 1 cm) in a 1.5 ml reaction tube add 800 l
Xylol, incubate for 5 min and mix by overhead shaking.
Add 400 l absolute ethanol and mix. Centrifuge 2 min at maximum speed
and discard supernatant.
Add 1 ml absolute ethanol and mix by overhead shaking. Centrifuge for
2min at maximum speed and discard supernatant.
Invert tube and blot briefly on a paper towel to get rid of residual ethanol. Dry
the tissue pellet for 10 min at +55C.
Add 110 l MagNA Pure DNA Tissue Lysis Buffer.
Add 50 l Proteinase K solution and mix. Then incubate at +55C until com-
plete dissolution of the tissue. The required sample volume is 150 l.
2.3 Isolation Procedure
General Remarks The following procedures are used to process 96 samples at the same time.
When other sample numbers than multiples of 8 (Software version 1.1 and 2.0)
or 24 (Software version 1.0) are used, the instrument will process the empty
positions until the next multiple of 8 or 24 is reached. For a detailed description
of the instrument setup and handling, refer to the MagNA Pure 96 System
Quick Guide and Customer Training Guide (software version 2.0).
Ensure that kit components are equilibrated to +15 to +25C before use.
When the reagents are used at temperatures outside this recommended
range, the purification may not function properly.
Ensure that all containers are inserted correctly into the reagent trays,
prior to placing them on the stage.
Ensure that instructions are followed for type and amount of sample mate-
rial (see section Sample Material). Using inappropriate types and
amounts of sample material may cause clumping, which may lead to low
yield and purity of cellular RNA, as well as cross-contamination and inhibi-
tion of downstream assays (e.g., RT-PCR).
After the run has finished, carefully inspect the instrument for any signs of
spillage. If spillage has occurred, clean the instrument as described in the
MagNA Pure 96 System Operators Guide.
Clean the waste cover after each run, as described in the
MagNA Pure 96 System Operators Guide. Do not use sodium hypochlo-
rite (bleach) solution or acids for the first cleaning step, because this may
produce highly toxic gas in combination with reagents containing guani-
dine thiocyanate.
Results
Procedure For a detailed description on how to prepare and perform a purification run,
refer to the MagNA Pure 96 System Quick Guide and Customer Training
Guide (Software version 2.0).
Storage of RNA
Eluates
To ensure stability of the eluted RNA, proceed immediately with RT-PCR
setup. Do not store the eluted RNA on the MagNA Pure 96 Stage for a lon-
ger period of time; up to 32 hours stability on the cooled sample rack posi-
tion 4 are possible.
For storage, close the output plate with the MagNA Pure 96 Sealing Foil and
store at 15 to 25C or 60 to 80C. Store the RNA in aliquots if neces-
sary, so that purified RNA is not repeatedly frozen and thawed.
For long-term storage, we recommend transferring eluates to an archive
plate.
After thawing eluates, mix gently by pipetting up and down ten times
before performing any downstream steps, e.g., RT-PCR or OD measure-
ments. Mixing volumes should be at least half of the eluate volume.
Results may not be reproducible when RNA is not premixed and distrib-
uted homogenously before pipetting.
3. Results
Experimental
Results
High quality results with the MagNA Pure 96 Cellular RNA Large Volume Kit
were demonstrated using HeLa, K562 cultured cells, whole blood, PAXgene
tubes, fresh-frozen tissues, tissue stabilized in RNAlater, and FFPE tissue sec-
tions. High yield, purity, and integrity of cellular RNA were obtained using
spectrophotometry, electrophoresis and RT-PCR.
Independent from the extraction method, RNA extracted from FFPE sec-
tions is often degraded due to formalin fixation.
Troubleshooting
4. Troubleshooting
Possible Cause Recommendation
Clumping of
beads or
presence of
beads in the out-
put plate
Too much or inappropri-
ate sample material or
inefficient homogenization.
Reduce sample material to values recom-
mended in the section Sample Material.
Use only the specified types of sample material
(see section Sample Material).
MGPs were magnetized
prior to use.
Avoid contact between MGPs and magnets
prior to use.
Store kit appropriately.
RNA is degraded Improper storage of
samples.
Use fresh-frozen samples, or tissue samples
stabilized in RNAlater.
Avoid the use of samples that have been
stored at ambient temperature.
Nuclease contamination Avoid contamination of disposables and
reagents with nucleases.
Tissue homogenization
was not fast enough.
Perform homogenization for fresh-frozen tis-
sues as rapidly as possible to avoid RNase deg-
radation. If necessary, chill on ice for 90 s and
repeat the procedure.
Poor or no RNA
yield
Sample did not contain
enough cells.
Count cells before use. For optimal number of
cells, refer to section Sample Material.
Storage of samples was
not optimal.
Use fresh-frozen samples, or tissue samples
stabilized in RNAlater.
Avoid the use of samples that have been
stored at ambient temperature.
Too much or wrong
sample material.
Reduce sample material to values recom-
mended in section Sample Material.
Use only specified types of sample material
Poor RNA purity Too many cells in the
sample
Reduce number of cells to the values recom-
mended in section Sample Material by dilut-
ing the sample.
Drops of sample material
on the walls of the wells
Pipette samples to the bottom of each well of
the processing cartridge.
Poor RT-PCR
performance
Poor purity of RNA Too much sample material used for isolation.
Adjust input material to the values recom-
mended in section Sample Material.
Avoid sample material on the walls of wells
when pipetting samples into the processing
cartridge.
Troubleshooting
Black particles in
the output plate
Magnetic glass particles
are present in the output
plate.
Low numbers of magnetic glass particles do
not affect PCR or RT-PCR assays on the
LightCycler
Instrument or conventional ther-

mal block cycler.
RT-PCR reagents and pro-
tocols were not optimal.
Verify reagents and protocols using a positive
and negative control.
Eluates show a
slight color
Drops of sample material
on the walls of the wells.
Pipette samples to bottom of wells of the pro-
cessing cartridge.
Use the automated sample transfer function to
pipette samples into the wells of another pro-
cessing cartridge. This ensures transfer with-
out contaminating the walls of wells with
sample material.
Too much or inappropri-
ate sample material.
Use only the specified types of sample material
Sediments in the
target plate
(PAXgene proto-
cols only)
Overloading due to high
blood cell content
Centrifuge the target plate (e.g., for 2 min at
1,500 g). Alternatively, use the RNA PAXgene
Half Tube LV protocol.
These sediments do not affect RT-PCR
assays.
Possible Cause Recommendation
Additional Information on this Product
5. Additional Information on this Product
How this Product
Works
The MagNA Pure 96 Cellular RNA Large Volume Kit is used together with the
MagNA Pure 96 Instrument to purify high-quality, intact RNA from up to
288 samples. Isolated RNA can be eluted in 50, 100, or 200 l (depending on
the Elution Volume selected in the MagNA Pure 96 Software). Purified RNA
meets the quality standards required for sensitive and quantitative RT-PCR
using the LightCycler
Instruments.
Test Principle RNA isolation uses MagNA Pure Magnetic Glass Particle Technology. The key
steps of a MagNA Pure 96 RNA isolation are:
Quality Control The kit is function tested using the following procedures:
Cellular RNA is isolated from K562 cells. High quality purified RNA is verified
using agarose gel electrophoresis, OD
260/280
, and RT-PCR using the
LightCycler
480 Instrument.
Sample material is lysed, nucleic acids are released, and nucleases
are denatured.
Nucleic acids bind to the silica surface of the MGPs, due to the chao-
tropic salt conditions and high ionic strength of the lysis/binding buf-
fer.
Genomic DNA is removed by incubation with DNase.
MGPs with bound RNA are magnetically separated from the rest of
the lysed sample.
Unbound substances (e.g., proteins, cell debris, PCR inhibitors) are
removed by washing steps.
Purified RNA is eluted from the MGPs.
Supplementary Information
6. Supplementary Information
6.1 Conventions
Text Conventions To make information consistent and easy to understand, the following text
conventions are used throughout this document:
Symbols In this document, the following symbols are used to highlight important infor-
mation:
Abbreviations In this document, the following abbreviations are used:
6.2 Changes to Previous Version
Editorial changes
New splitted protocol for the isolation of RNA from up to 25 mg fresh-frozen
tissue samples.
Text Convention Usage
Numbered stages
labeled , etc.
Stages in a process that usually occur in the order
listed.
Numbered instructions
labeled , etc.
Steps in a procedure that must be performed in
the order listed.
Symbol Description
Information Note:
Additional information about the current topic or procedure.
Important Note:
Information critical to the success of the procedure or use of the
product.
Abbreviation Meaning
MGPs Magnetic glass particles
PBS Phosphate buffered saline
RT-PCR Reverse transcription polymerase chain reaction
SW Software
6.3 Ordering Information
Roche Applied Science offers a large selection of reagents and systems for life
science research. For a complete overview of related products and guides, visit
and bookmark our homepage: www.roche-applied-science.com and our Spe-
cial Interest Sites including:
Automated Sample Preparation (MagNA Lyser Instrument, MagNA Pure
Compact System, MagNA Pure LC System, and MagNA Pure 96 System):
www.magnapure.com and www.magnapure96.com.
Real-time PCR Systems (LightCycler
Carousel-Based System,
LightCycler
480 System, LightCycler
1536 System, RealTime ready qPCR

assays, and Universal ProbeLibrary): www.lightcycler.com.
Product Pack Size Cat. No.
Instruments MagNA Pure 96 Instrument 1 instrument, control
unit and accessories
05 195 322 001
MagNA Lyser Instrument 1 instrument (110 V.)
1 instrument (220 V.)
plus 2 MagNA Lyser
Rotors, a MagNA Lyser
Rotor Cooling Block,
and a MagNA Lyser
Rotor Stand
03 358 968 001
03 358 976 001
Reagents and Kits MagNA Pure 96 DNA and Viral NA
Small Volume Kit
3 192 purifications 05 467 497 001
MagNA Pure 96 DNA and Viral NA
Large Volume Kit
3 96 purifications 05 467 454 001
RNA/DNA Stabilization Reagent
for Blood/Bone Marrow
1 Bottle 11 934 317 001
MagNA Pure 96 System Fluid
(Internal)
2 Containers 05 467 098 001
MagNA Pure 96 System Fluid
(External)
1 Container 05 467 578 001
MagNA Pure LC RNA Tissue Lysis
Buffer/Refill
1 Bottle 03 604 721 001
MagNA Pure DNA Tissue Lysis
Buffer
100 ml 04 805 160 001
Proteinase K (solution) 5 ml
25 ml
03 115 828 001
03 115 844 001
Disposables MagNA Pure 96 Tips (1000 l) 3840 (480 8) 05 392 900 001
MagNA Pure 96 Processing
Cartridge
36 05 435 315 001
6.4 Trademarks
LIGHTCYCLER, LC, MAGNA PURE, MAGNA LYSER, and REALTIME READY
are trademarks of Roche.
Exiqon and ProbeLibrary are registered trademarks of Exiqon A/S, Vedbaek,
Denmark.
All other product names and trademarks are the property of their respective
owners.
6.5 Disclaimer of License
This is a product licensed under patents owned by Qiagen.
6.6 Regulatory Disclaimer
For life science research only. Not for use in diagnostic procedures.
Disposables MagNA Pure 96 Sealing Foil 100 05 435 307 001
MagNA Pure 96 Output Plate 60 05 435 285 001
MagNA Lyser Green Beads 100 tubes prefilled
with ceramic beads
03 358 941 001
Product Pack Size Cat. No.
Contact and Support If you have questions or experience problems with this or any Roche Applied
Science (RAS) product, please contact our Technical Support staff. Our
scientists commit themselves to providing rapid and effective help.
We also want you to contact us if you have suggestions for enhancing RAS
product performance or using our products in new or specialized ways. Such
customer information has repeatedly proven invaluable to RAS and the world-
wide research community.
To ask questions, solve problems, suggest enhancements or report new appli-
cations, please visit our Online Technical Support Site at:
www.roche-applied-science.com/support
To call, write, fax, or email us, visit the Roche Applied Science home page,
www.roche-applied-science.com, and select your home country.
Country-specific contact information will be displayed.
On the Roche Applied Science home page select Printed Materials to find:
in-depth Technical Manuals
Lab FAQS : Protocols and references for life science research
our quarterly Biochemica Newsletter
Material Safety Data Sheets
Pack Inserts and Product Instructions
or to request hard copies of printed materials.
Roche Diagnostics GmbH
Roche Applied Science
68298 Mannheim
Germany
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