eamag/protocols-with-steps huggingface dataset:
TITLE: Making your own electrocompetent cells
AUTHORS: New  England   Biolabs

[DESCRIPTION]
This protocol explains methods for making two 250 ml cultures of electrocompetent cells.


An Electroporation Protocol can be found here.

[BEFORE_START]
Sterile 10 % (can be autoclaved) is needed for the washes. The volume of  10 % needed is 2X the culture volume (for example, a 500 ml culture requires 1L of 10 %).

[STEPS]
1. Innoculate 1 colony from a fresh plate of the strain to be made electrocompetent into 10 mL in a 125 ml flask.
2. Incubate for 16-18 hours at 37 °C and 250 rpm.
3. Pre-warm two 1 L flasks containing 250 mL pre-warmed to 37 °C.
4. Add two drops of the overnight culture to each of the pre-warmed 250 ml flasks.
6. Place cultures on ice for 15 min. From this point on the cultures must be kept ice cold.
7. Pour each 250 ml culture into chilled 500 ml (or 1000 ml) centrifuge bottles.
8. Centrifuge at 5000 rpm, 10 min. 
9. Pour off the supernatant and aspirate any residual broth.
10. Add 250 mL to each of the centrifuge bottles and completely suspend the cells by pipetting up and down.
14. Pour off the supernatant and suspend the cells in the residual glycerol by pipetting up and down.
15. 
 

To freeze, add 100 µL to microcentrifuge tubes on ice.
16. Once you have used all of the culture, transfer the tubes to dry ice for 10 min. 
17. Once the cultures are frozen, transfer them to a -80°C freezer.
 

5. Shake at 37 °C and 250 rpm until the cultures reach an OD600 of 0.5-0.7. 
 


12. Pour off the supernatant.
 

12. Centrifuge at 5000 rpm, 10 min, 4 °C. 

11. Centrifuge at 5000 rpm, 10 min. 
13. Completely suspend the cells in 250 mL and re-centrifuge.
TITLE: MWP5 Final Project: 5 findability opportunities to access the portfolio dataset 
AUTHORS: Anastasiia  Iarkaeva

[DESCRIPTION]
This protocol was created as part of the Information Science Master's program project MWP5 Digital Information Management at the Humboldt University of Berlin.

It aims to help a potential user group of the decision-making stakeholders to find the examined dataset for cluster modeling (https://doi.org/10.6084/m9.figshare.12743639.v1).

Overall five opportunities are both described textually and shown visually. 

In all cases, except the DOI system, the search results can be reduced by applying multiple filters to find the wanted dataset faster and more precisely. 

[STEPS]
SECTION: DOI
1. 
Use the DOI to directly access the dataset. 
 

SECTION: PubMed Central
5. Searching via PubMed Central with the keywords “pubmed literature model” you will hit the data descriptor article as the first result.
SECTION: Figshare
2. Use figshare repository where the data is located to find the dataset.

For that, open the repository website and type or paste the keywords pubmed and literature which were selected from the dataset title STS Model of the PubMed Literature. 

The results can be filtered and sorted to reduce the amount of found datasets and to find a proper match, e.g. from 7109 to 2437 datasets here.
 

 
 
SECTION: DOI
1.1. For that, open the DOI system on doi.org, add "/" sign and the unique identifier of the dataset (doi: 10.6084/m9.figshare.12743639.v1) or the data descriptor article (doi: 10.1038/s41597-020-00749-y) as shown in the video.

You will be navigated to the requested source at once.
 

SECTION: DOI
1.2. Another opportunity to find the dataset in the DOI system is to use the search field by typing in or pasting the identifier as shown in the video.
 

SECTION: Google dataset search
4. Use Google dataset search which collects a lot of well-curated datasets' metadata if they conform to the standards defined by the schema.org consortium.

For that, open the Google dataset search engine and type or paste the keywords pubmed and literature. 

When you type, it will show a dropdown with the best match results that you can open right away as it is shown in the video below. 

If you press the "enter" key it will show a page with search results that can be filtered to find a proper dataset.
 

SECTION: Dimensions
3. Use Dimensions Abstracting & Indexing database where the datasets from figshare are harvested automatically.

From the home page access right away the web retrieval system.

Use the keywords pubmed literature in the search bar.

Then the results can be filtered by multiple parameters, e.g. type of data, repository name, year, etc. Here the repository name filter was applied  - the number was reduced from 2732 to 30 results.

The third hit is the wanted dataset. 
 
If searching the keywords "pubmed literature model" the hit will appear already on the first page (6th here).
TITLE: Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii.
AUTHORS: Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span>: The blood clam, </span><span style = "font-style:italic;">Scapharca </span><span style = "font-style:italic;font-style:italic;">(</span><span style = "font-style:italic;">Anadara</span><span style = "font-style:italic;font-style:italic;">)</span><span style = "font-style:italic;"> broughtonii</span><span>, is an economically and ecologically important marine bivalve of the Family Arcidae. The efforts that have been made to study their population genetics, breeding, cultivation and stock enrichment were somewhat hindered by the lack of a reference genome. Here, we reported the complete genome sequence of </span><span style = "font-style:italic;">S. broughtonii,</span><span> a first reference genome of the Family Arcidae.</span></div><div class = "text-block"><span style = "font-weight:bold;">Funding</span><span>: A total of 75.79 Gb clean data was generated with the PacBio and Oxford Nanopore platforms, which represented approx. 86× coverage of the </span><span style = "font-style:italic;">S. broughtonii</span><span> genome. </span><span style = "font-style:italic;">De novo</span><span> assembly of these long reads resulted in an 884.5 Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb, respectively. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases of the assembled genome. Genome annotation revealed that a considerable part of the genome (46.1%) is composed by repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.</span></div><div class = "text-block"><span style = "font-weight:bold;">Conclusion</span><span>: We report here the chromosomal-level assembly of the </span><span style = "font-style:italic;">S. broughtonii</span><span> genome based on long read sequencing and Hi-C scaffolding. The genomic data could be served as reference genome for the Arcidae Family and will provide a valuable resource for the scientific community and aquaculture sector.</span></div></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>A real-time PCR to broadly detect Rickettsia species DNA. This method has been adapted from a publication by Jiang et al 2012, and  the oligonucleotides have been modified and a different PCR kit used.</p>

[GUIDELINES]
<ul>
<li>If using a different brand or model of real-time thermocycler, check the concentration of ROX is adequate.</li>
<li>Method assumes the user is familiar with the thermocycler and software used to run the protocol.</li>
</ul>

[STEPS]
?. 
?. 
?. 
?.
TITLE: Viral enrichment from wastewater samples 
AUTHORS: Iraola Lab

[STEPS]
?. Wastewater samples are centrifuged at    to remove debris
Centrifuge: 4500 33, 10 min, 4 10
Volume processed depends on user preferences and equipment. For information on sampling, check our previous protocol : Sampling and viral concentration for SARS-CoV-2 detection in wastewater
?. The supernatant is then filtered through a 0.45 µm membrane to remove eukaryotic and bacterial cells
Although the first step is optional, if your sample is very cloudy, it will take a lot of time for it to flow through the filter. Also, if you see the flow stops, your membrane might be clogged, and you should replace it.
?. of the flowthrough are then transferred to a 26,9 mL ultracentrifuge tube (compatible with Beckman Coulter Type 50.2 Ti Fixed-Angle Rotor) and spiked with  of PP7 phage (this enacts as a protocol validation method later in the analysis).
25 mL
5.9 µl
Make sure your tubes are correctly balanced before you set up the Ultracentrifuge, according to manufacturer's instructions
?. The pellet is then resuspended in   of Zymo DNA/RNA Shield, and stored at  or used for DNA/RNA extraction
200 µl
-80 °C
?. Then, the result is ultracentrifuged at
Centrifuge: 100000 34, 150 min, 4 10
?. The flowthrough is pasteurized to inactivate pathogens at  for
60 °C
Wastewater samples may contain potencially harmful pathogens, so always handle with gloves, work in a laminar flow cabinet, and pasteurize samples immediately after filtration. All equipment used up to this step must be washed in hypochlorite.
TITLE: Twist2 Snap Frozen Skeletal Muscle IF
AUTHORS: Griffen Wakelin

[DESCRIPTION]
This protocol details Twist2 immunofluorescent staining of fresh frozen mouse skeletal muscle.

[BEFORE_START]
Collect fresh muscle according to institution-specific guidelines and snap freeze in liquid nitrogen-cooled 2-methylbutane. The Twist2 stain does not work on PFA-fixed muscle without antigen retrieval.

[STEPS]
SECTION: Day 1
1. Thaw slides, dry for 30 mins, surround sections with  , and label
SECTION: Day 1
2. Fix with ice-cold 4 % (v/v)    for 5 min
SECTION: Day 1
3. Wash three times with 1X PBS for 5 min
SECTION: Day 1
4. Permeabilize with 0.2 % (v/v)    for 10 min
SECTION: Day 1
5. Wash three times with 1X PBS for 5 min
SECTION: Day 1
6. Block with 5 Mass / % volume     for 60 min at Room temperature
SECTION: Day 1
7. Incubate primary    1:500 in 1% BSA   at 4 °C 
SECTION: Day 2
8. Wash three times with 1X PBS for 5 min 

SECTION: Day 2
9. Incubate secondary   1:1000 and    1:1000 in 1% BSA for 120 min at Room temperature 
SECTION: Day 2
10. Wash three times with 1X PBS for 5 min 
SECTION: Day 2
11. Mount with aqueous mounting media such as  . Image within 2 days.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from J Mol Biol 13,269 (1965)</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: No Title
AUTHORS: 

[GUIDELINES]
Note: AmPure XP beads are normally used at 80:100 ratio* (beads:DNA) to remove fragments less than 100bp and retain all DNA above 100bp. If you lower that ratio. then DNA will not bind to the beads as efficiently (due to decreased amount of PEG present) and you will lose some of the DNA. To recover all DNA, make sure the starting DNA is not too concentrated and hold onto the residual sample after beads first adhere to magnet; in this way you can re-bind any unbound DNA to fresh beads. <br /><br />*see step 17 annotation for more info<br /><br />Agencourt® AmPure® XP beads:  Beckman Coulter #A63880<br />100bp DNA ladder:  New England Biolabs (NEB) #N3231S (comes with 6xGLB)<br />6x Blue Orange Loading Dye:  Promega #G190A (optional)<br />Magnetic Particle Concentrator (MPC):  Invitrogen Dyna-Mag2 #123-21D

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Goga Lab RT-qPCR protocol: QuantStudio6 Machine
AUTHORS: Jeremy.williams

[DESCRIPTION]
Guidelines for preparing RT-qPCR samples for QuantStudio 6 located in HSW7 lab space.

[BEFORE_START]
*Thaw on ice (leave time!) and keep all reagents on ice through preparation. Prepare the plate on ice.


[GUIDELINES]
*start with full tip boxes and use tips in coordination with your plate map, so you never get lost
*watch 1uL volumes in the pipet tip like a hawk - major source of variability
*cap and gently vortex your *mixture per primer set* every 12 replicates or so, sometimes things separate

[STEPS]
2. Use 'GogaLab-RTqPCR-Preparation' Excel spreadsheet to input your sample number and calculate reagent volumes.

4. Mix your forward and reverse primer pairs together, to a final dilution of 10uM forward and 10uM reverse. For example, add 10uL each of forward and reverse primers to 80uL PCR-quality DI for 100uL final volume.
3. Mix *total reagent volumes required* (see spreadsheet, green) for DI and PowerUP
5. Mix *mixtures per primer set* (blue) volumes together.
6. Pipet 1uL diluted cDNA into respective qPCR well, aiming for the sidewall of each respective well.
7. Add 19uL *mixture per primer set* into each respective well.
8. Seal plate, and spin down 1000rpm for 1 minute. Use bacterial, not tissue culture, centrifuge.   
9. Load plate into centrifuge and proceed using QuantStudio software suite.
SECTION: Prior to plate preparation:
1. Dilute stock IDT primers to 100uM (see note in Guidelines).
TITLE: Axy Prep 质粒DNA小量提取
AUTHORS: 张 雪

[STEPS]
?. 取菌液于2ml圆底EP管中，12000rcf，1min，弃上清
?. 加入250µl Buffer S1（细菌悬浮液，已加RNase A，4°C储存），振荡器悬浮细菌沉淀
?. 裂解：加入250µl Buffer S2（细菌裂解液），温和翻转4-6次，静置至形成透亮液体（不超过5min）
?. 中和：加入350µl Buffer S3（中和液），温和翻转6-8次，12000rcf，10min
?. 取上清于制备管（置于配套的2ml离心管中），12000rcf，1min，弃滤液
?. 结合：加入500µl Buffer W1（洗涤液），12000rcf，1min，弃滤液
?. 洗涤：加入700µl Buffer W2（去盐液，已加无水乙醇），12000rcf，1min，弃滤液
?. 重复上一步骤
?. 空离，12000rcf，1min
?. 洗脱：将制备管移入配套的1.5ml离心管中，在膜中央加入40µl ddH2O，室温下静置1-10min，随后12000rcf，1min
TITLE: qPCR Assay
AUTHORS: Kokila Shankar, Olivier George

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for running qPCR assays using previously generated cDNA. This protocol has been adapted from ThermoFisher (</span><a href="https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2Fcms_042179.pdf&title=UHJvdG9jb2w6IFBvd2VyIFNZQlIgR3JlZW4gUENSIE1hc3RlciBNaXggYW5kIFJULVBDUg==" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2Fcms_042179.pdf&title=UHJvdG9jb2w6IFBvd2VyIFNZQlIgR3JlZW4gUENSIE1hc3RlciBNaXggYW5kIFJULVBDUg==</span></a><span style = ":;">)</span></div></div>

[STEPS]
?. Make cDNA and H2O master mix by combining  cDNA with enough H2O for a total of  , and multiplying these values by the number of wells needed. Samples should be run in at least duplicate, but preferably triplicate.
20 ng
4.5 µl
Make sure to account for pipetting error and make slightly more master mix than needed (~5%)
?. Make SYBR and primer master mix by combining  SYBR,  forward primer, and  reverse primer, and multiplying these values by the amount of wells needed.
5 µl
0.25 µl
0.25 µl
Make sure to account for pipetting error and make slightly more master mix than needed (~5%)
?. Add  cDNA + H2O mix and  SYBR + primers mix to each well, for a total reaction volume of  . Mix master mixes frequently while pipetting, and make sure contents of each well are mixed properly.
4.5 µl
5.5 µl
10 µl
Having a template can be helpful to ensure everything gets pipetted correctly!
?. Seal plate thoroughly, spin down quickly (2400 rpm for   is enough), and run reaction at the following conditions: for  for  for Repeat steps 2-3 39XRun melt curveReaction is run using
95 °C
95 °C
59 °C
TITLE: T4PNK end-healing of RNA samples
AUTHORS: Jonathan Howard

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Resolution of 5' and 3' ends of sample RNA prior to library preparation.</div></div>

[STEPS]
?. [PNK treatment and cleanup]
Set up the following reaction components in a sterile PCR tube:     4 μl 5 × PNK pH 6.5 buffer     0.5 μl PNK     0.5 μl RNasin     5 μl Plus-AlkB/Minus-AlkBRNA sample    To 20 μL with Nuclease-free Water
?. [PNK treatment and cleanup]
Put reaction at 37C for 30 mins. This can be done in a thermocycler
?. [PNK treatment and cleanup]
Put samples on ice, add to the reaction:5 μL of 10x PNK reaction buffer (NEB-supplied buffer)5 μL of 10 mM ATP1 μL of T4PNK (additional)1 μL of RNase inhibitor (optional)Up to 50 μL with Nuclease-free Water
?. [PNK treatment and cleanup]
Put reaction at 37°C for 30 min.
?. [PNK treatment and cleanup]
Raise volume of T4PNK-treated RNA samples to 400 μL.
?. [PNK treatment and cleanup]
Collect the solution and add it together with 400μL acid phenol/chloroform to a 2 ml Phase Lock Gel Heavy tube. Mix by inversion in hand for 30 sec.
?. [PNK treatment and cleanup]
Separate the phases by spinning for 5 min at full speed and room temperature.
?. [PNK treatment and cleanup]
Transfer the aqueous layer into a new tube (be careful not to touch the gel matrix with the pipette or remove organic phase that may have not migrated below the gel matrix).
?. [PNK treatment and cleanup]
Precipitate by adding 0.75 μL glycoblue and 40μL 3 M sodium acetate pH 5.5. Mix, then add 1 ml 100% ethanol, mix again, and place at -20°C overnight.
?. [PNK treatment and cleanup]
Centrifuge at 15,000 rpm at 4°C for 20 min. Remove the supernatant and wash the pellet with 500 μL 80% ethanol and vortex for 30 sec. Spin again for 5 min. to pellet RNA again.
?. [PNK treatment and cleanup]
Remove ethanol wash completely (be careful to not remove pellet). Allow to air-dry at room temperature for 10 mins. Remove any excess ethanol in tube with additional pipetting.
?. [PNK treatment and cleanup]
Resuspend the pellet in 5 μL of nuclease-free H2O and transfer to new 0.2 mL RNase-free PCR tube.
TITLE: Expression and purification MBP-ATG9 Constructs
AUTHORS: Adam  Yokom

[DESCRIPTION]
Expression and purification from HEK cells of ATG13, ATG101 and FOLDON-ATG9A proteins

[STEPS]
SECTION: Expression
1. Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml
   
SECTION: Purification
8. Resuspended pellet in lysis buffer (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA, 10% Glycerol) with 1% Triton X-100 and protease inhibitor cocktail (Thermo Scientific, Waltham, MA) 
SECTION: Expression
2. Dilute PEI with Warm Hybridoma-SFM(1X)
SECTION: Purification
10. Clarify lysate by centrifugation 17000 rpm, 30 min, 4 °C

SECTION: Purification
12. Rock supernatant with equilibrated resin for 60 min at 4 °C
  
SECTION: Purification
11. Load supernatant flow thru gravity column onto washed Amylose resin
SECTION: Purification
13. Wash with 5 column volumes of lysis buffer (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA, 10% Glycerol)
SECTION: Purification
15. Concentrate elution and inject onto pre-equilibrated S200 10/30 column (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA)
SECTION: Purification
14. Elute with lysis buffer plus 40 mM Maltose for amylose resin
SECTION: Purification
16. Pool peak fractions, concentrate, snap freeze, and store at -80C 
SECTION: Expression
3. In a separate tube, dilute DNA with Hybridoma-SFM(1X)
SECTION: Expression
4. Add PEI to DNA dilution. Incubate mixture for 30 min  at 37 °C 

SECTION: Expression
5. Add mixture to cells. Let cells grow for 2880 min 

SECTION: Expression
6. Harvest Cells 500 rpm, 10 min, 4 °C 

SECTION: Expression
7. Wash pellet with cold PBS. Store pellet at -80C until purification. 
SECTION: Purification
9. Wash Amylose resin with lysis buffer, ~2mL/1 Liter of cells
TITLE: SPARC Serotonin (5-HT) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment
AUTHORS: Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the immunofluorescent labeling technique used to identify serotonin expression in CtB-labelled phrenic motor neurons and within a defined region of interest surrounding phrenic motor neurons.</div></div>

[STEPS]
?. Day 1: primary antibodies required:5-HT: Rabbit anti-5-HT (Immunostar #20080)Cholera toxin B-fragment: Goat anti-CT-B (Millipore #227040)
?. Place 40um transverse spinal cord sections into 1xPBS-Triton (0.1%) in 12 well cell culture plates
?. 5x washes in  1xPBS-Triton (0.1%) for 5 minutes each at room temperature
?. Antigen retrieval: place tissues into Heat-Induced Epitope Retrieval (TissuePro, Cat#: HIER01-32R) for 30 minutes at 85 degrees C
?. 5x washes in  1xPBS-Triton (0.1%) for 5 minutes each at room temperature
?. Blocking: place tissues in 5% Normal Donkey Serum (NDS) in 1xPBS-Triton (0.1%) for 60 minutes at room temperature
?. Primary Antibody Incubation: Incubate tissues in: 5%NDS in 1xPBS-Triton (0.1%), Rabbit anti-5-HT (1:2000), and Goat anti-Ct-B (1:2500) for 1 hour at room temperature
?. Continue primary antibody incubation overnight at 4 degrees C
?. Day 2: secondary antibodies required:AlexaFluor 488: donkey anti-goat (Invitrogen, Ref#A11055)AlexaFluor 594: donkey anti-rabbit (Invitrogen, Ref#A21207)
?. 5x washes in  1xPBS-Triton (0.1%) for 5 minutes each at room temperature
?. Secondary Antibody Incubation: Incubate tissues in: 5%NDS in 1xPBS-Triton (0.1%), donkey anti-goat (1:1000), and donkey anti-rabbit (1:500) for 2 hours at room temperature
?. 5x washes in  1xPBS for 5 minutes each at room temperature
?. Mount tissues on Superfrost Plus microscope slides
?. Allow slides to dry overnight
?. Coverslip with VectaShield Antifade Hard Set Mounting Medium (Cat#:H-1400)
TITLE: Preparation of ATP13A2 cryo-EM grids
AUTHORS: Sue  Sim, eunyong_park  

[DESCRIPTION]
Preparing cryo-EM grids using purified ATP13A2 samples

[STEPS]
SECTION: Preparing samples
1. Spin purified and concentrated ATP13A2 sample (5-7 mg/mL) after SEC at 17000 x g, 10 min, 4 °C 

SECTION: Preparing samples
2. Keep protein on ice
3. Plasma clean grids
3.1. Used gold holey carbon grids (Quantifoil R 1.2/1.3, 400 mesh) and PELCO easiGlow Glow Discharge Cleaning System (0.39 mBar, 25-30 mA, 40-45 sec)
4. Apply 3 μL of protein sample to grids and plunge freeze
4.1. Used Vitrobot Mark IV (FEI) operated at 4°C and 100% humidity and Whatman No.1 filter paper to blot samples
4.2. Our blotting settings were 3.5-4.5 second blot at force 25, but every Vitrobot is slightly different. Use optimal settings for your machine.
5. Store grids in liquid nitrogen until ready for imaging.
TITLE: Visium Direct Mount FFPE v2 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
The Visium Spatial Gene Expression for FFPE is designed to measure mRNA in tissue sections derived
from formalin fixed & paraffin embedded (FFPE) tissue samples and requires a Visium Spatial slide
with intact tissue sections as input. 

Tissue sections are processed with Visium Spatial Gene Expression assay performed by the University of Minnesota Imaging Center and sequenced by the University of Minnesota Genomics Center.



[STEPS]
SECTION: Deparaffinization, H&amp;E Staining, Imaging &amp; Decrosslinking
1.   

SECTION: Library Preparation &amp; Sequencing
2.   
 


SECTION: FASTQ Generation
3. BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0