eamag/protocols-with-steps huggingface dataset:
TITLE: Study protocol: can viral load predict a symptomatic congenital CMV infection? A systematic review and meta-analysis
AUTHORS: Serena Salomè, Roberta Gammella, Clara Coppola, Pasquale Dolce, Letizia Capasso, Daniel Blasquez-Gamero

[DESCRIPTION]
CMV is the most common cause of congenital infection.
Although only approximately 10% of infected newborns are symptomatic at birth,
a clinical disease may develop later in infancy. An early diagnosis of
symptomatic cCMV is important for successful treatment.
Our objective was to
evaluate if a higher viral load in different biological fluids correlates with
symptomatic disease. We will perform a systematic searches of Medline, Embase,
and SCOPUS from 1976 to December 2023. Methods will follow the Preferred Reporting
Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) guidelines and
 it has been registered with the
International Prospective Register of Systematic Reviews (PROSPERO) on 03/05/24
(Registration number CRD42024537242). Our primary outcome will be to evaluate
if great CMV load in blood and urine may predict newborns at risk of symptoms. As
secondary outcome, we will search if higher CMV may influence long term
prognosis and if there is a specific threshold

[STEPS]
1.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<div>
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
</div>

[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>0 mM Ca<sup>2+</sup> hemolymph-like (HL)-3 solution:</strong></p>
<ul>
<li>70 mM NaCl</li>
<li>5 mM KCl</li>
<li>10 mM MgCl<sub>2</sub></li>
<li>10 mM NaHCO<sub>3</sub></li>
<li>5 mM trehalose</li>
<li>5 mM HEPES (pH 7.2) </li>
<li>115 mM sucrose</li>
</ul>
<p> </p>
<p> </p>
<p><strong> 2 mM Ca<sup>2+</sup>/5 mM K<sup>+</sup>/7 mM glutamate solution:</strong></p>
<ul>
<li>70 mM NaCl</li>
<li>5 mM KCl</li>
<li>10 mM MgCl<sub>2</sub></li>
<li>10 mM NaHCO<sub>3</sub></li>
<li>5 mM trehalose</li>
<li>5 mM HEPES (pH 7.2)</li>
<li>115 mM sucrose</li>
<li>2 mM CaCl<sub>2</sub> </li>
<li>7 mM Monosodium glutamate</li>
</ul>
<p> </p>
<p><strong>4 μM Fluo-4 AM (Invitrogen)/100 mM Ca<sup>2+</sup>/HL-3 solution to be loaded with Fluo-4 AM dye</strong></p>
<p> </p>
<p> </p>

[STEPS]
?. 
?. 
?. 
?. 
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?. 
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?. 
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?. 
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?. 
?.
TITLE: Differentiation of NPC into cortical neurons
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh

[STEPS]
?. Ensure cells are plated at an appropriate density (e.g.: 150K/well in 12-well plate; 75- 50K/well for 48 well plates; 30K/well for 8-well chamber slides) in NIM on pre-coated PLO/laminin plates.
?. After , replace with cortical neuron differentiation medium (Neurobasal medium, 1x B27, 20 ng/mL BDNF, 20 ng/mL GDNF, 0.5mM cAMP, 1% Glutamax, 1% penicillin/streptomycin)
?. Feed cells  every 2-3 days for 30 days.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Supplement to seawater for growth of cyanobacteria.

[GUIDELINES]
Matt suggested higher concentrations of NaH2PO4-H2O so only need to use 0.5 ml per 1 L seawater:<br />0.1 M NaH<sub>2</sub>PO<sub>4</sub>-H2O   0.345g/25ml or 1.38g/100ml<br />Use 500µl per 1L seawater

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

[DESCRIPTION]
<p>The anecdotal evidence is outstanding on the uses of <em>Aristolochia</em> plants as traditional medicines and dietary supplements in many regions of the world. However, herbal materials derived from <em>Aristolochia</em> species have been identified as potent human carcinogens since the first case of severe renal disease after ingesting these herbal preparations. Any products containing <em>Aristolochia</em> species have thus been banned on many continents, including Europe, America and Asia. Therefore, the development of a method to identify these herbs is critically needed for customer safety. The present study evaluated DNA barcoding of the <em>rbc</em>L, <em>mat</em>K, ITS2 and <em>trn</em>H-<em>psb</em>A regions among eleven <em>Aristolochia</em> species collected in Thailand. Polymorphic sites were observed in all four DNA loci. Among those eleven <em>Aristolochia</em> species, three species (<em>A. pierrei</em>, <em>A. tagala</em> and <em>A. pothieri</em>) are used as herbal materials in Thai folk medicine, namely, in Thai “Krai-Krue”. “Krai-Krue” herbs are interchangeably used as an admixture in Thai traditional remedies without specific knowledge of their identities. A species-specific multiplex PCR based on nucleotide polymorphisms in the ITS2 region was developed as an identification tool to differentiate these three <em>Aristolochia</em> species and to supplement the HPTLC pattern in clarifying the origins of herbal materials. The combination of multiplex PCR and HPTLC profiling achieves accurate herbal identification with the goal of protecting consumers from the health risks associated with product substitution and contamination.</p>

[STEPS]
?. 
?. 
?. 
?.
TITLE: Expression and purification protocol of WIPI2d
AUTHORS: Chunmei  Chang

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the expression and purification protocol of WIPI2d.</div></div>

[STEPS]
?. [Protein expression]
Transfect the DNA in cells using polyethylenimine (Polysciences).
?. [Protein expression]
After 48- to 72-hour expression, harvest the cells.
?. [Protein purification]
Follow the Strep-Tactin batch purification by Size Exclusion Chromatography.
?. [Protein purification]
Incubate the supernatant with Strep-Tactin Sepharose resin at  with gentle shaking for , apply to a gravity column, and wash extensively with Wash Buffer.
4 °C
?. [Protein purification]
Elute the protein of interest with Elution Buffer and then apply onto a Superdex 200 column (16/60 prep grade) pre-equilibrated in SEC Buffer at .
4 °C
?. [Protein purification]
Pool and concentrate the peak fractions containing pure protein, snap-frozen in liquid nitrogen and store at .
-80 °C
?. [Protein purification]
Resuspend the cell pellet in Lysis Buffer and clear at  at  for .
Centrifuge: 16000 33
4 °C
TITLE: Expression and purification protocol of ULK1 Complex wt or K46I mutant
AUTHORS: Xiaoshan Shi

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Protocol describes the expression and purification of ULK1 Complex wt or K46I mutant.</div></div>

[STEPS]
?. [1-	Protein expression:]
ULK1 and FIP200/ATG13/ATG101 are transfected and expressed separately. Transfect DNA in cells at a concentration of 2.5–3 × 106/mL using polyethylenimine (Polysciences) and harvest after  expression. Resuspend cells in PBS and harvest them by pelleting at  for  at , wash them with PBS once, and then store at .
Centrifuge: 500 34
4 °C
-80 °C
?. [2-	Protein Purification:]
Glutathione Sepharose 4B and Strep-Tactin affinity purification followed by MBP-tag affinity purification.Incubate Supernatant (add 6M NaCl to a final concentration of 0.5M) respectively with either Glutathione resin or Strep-Tactin sepharose at  with gentle shaking for  or  respectively, apply to a gravity column, and wash extensively with Wash Buffer1.
4 °C
?. [1-	Protein expression:]
Resuspend the cell pellets in Lysis Buffer, gentlely shake them at  for  and clear them at  at  for .
4 °C
Centrifuge: 16.000 33
4 °C
?. [2-	Protein Purification:]
Eluate Proteins of interest with Elution Buffer 1 or 2 respectively and then mix them for  cleavage with Tobacco Etch Virus (TEV) protease at .
4 °C
?. [2-	Protein Purification:]
The mixture is subjected to a second step of affinity purification using the MBP tag. Pass the eluted sample (with Elution Buffer 3) again through a Strep-Tactin Sepharose (IBA Lifesciences) column to clear the MBP-TSF tag from ULK1. Use final protein for assay immediately after purification.
?. [2-	Protein Purification:]
Yield: about 0.1 mg per litter culture (600 ml FIP200/ATG13/ATG101 + 400 ml ULK1)Protein stability: The complex aggregates easily and is degraded easily, so we suggest using fresh samples.
TITLE: Vandy - Mouse Blood Pressure Telemetry
AUTHORS: Lin Zhong, Chee Lim

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Imlantable radiotelemetry devices allow for long-term continous monitoring of blood pressure and heart rate in conscious freely moving caged animals. This protocol describes the surgical implantation of a radio transmitter device in the mouse.</div></div>

[STEPS]
?. Mice are anesthetized with pentobarbital (50 mg/kg, IP).
?. The ventral neck and upper dorsum are shaved and disinfected with Betadine and then 70% alcohol.
?. The mouse is positioned supineon a heating pad and a 1.5 cm midline incision is made through the skin underlying the trachea.
?. The mouse is placed lateral decubitus and a 3” 16G needle is advanced through the left ventral neck to the upper dorsum , creating a tunnel.
?. The catheter of asterilized PA-C10 transmitter (DSI) is advanced through the needle from the dorsal to the ventral side and the needle is carefully removed leaving the catheter in the ventral neck area and the transmitter body in the dorsal area.
?. The mouse is again positioned supine and the left carotid artery is located and isolated from surrounding tissue.
?. Three pieces of non-absorbable 6-0 sutures are passed under the carotid artery. The cranial suture furthest from the aorta is positioned just below the bifurcation of the interior and exterior carotid arteries and a secure knot is tied to permanently occlude the vessel.
?. The suture closest to the aorta is gently lifted to temporarily occlude blood flow and a small puncture is made in the carotid artery just distal to the middle suture.
?. The catheter is inserted through the puncture and advanced towards the aorta until it reaches the occlusion sutures.
?. The middle suture is loosely tied to prevent the catheter from slipping out and to stop bleeding from the puncture hole.
?. The tension in the occlusion sutures is released and the catheter is advanced further beyond the suture towards the aorta until the catheter tip is approximately 2 mm into the aortic arch.
?. Tie the occlusion suture and the middle suture to seal the vessel wall around the catheter and anchor it in place.
?. Close the skin incision with a 6-0 suture.
?. The mouse is repositioned prone and starting from the needle puncture, a small incision is made and small surgical scissors are inserted into the incision to form a subcutaneous dorsal pocket using blunt dissection.
?. The pocket is irrigated with warm saline and the body of the transmitter is inserted into the pocket.
?. The dorsal skin incision is closed with a 6-0 suture.
?. The mouse is maintained on the heating pad until fully recovered from anesthesia.
?. Buprenorphine is administered SC immediately following surgery and every 8-12 hr for 72 hr.
?. Upon recovery, the mouse is placed in its cage and the cage is placed on a receiver platform (DSI) to confirm the fidelity of the blood pressure signal.
?. Mice are allowed to recover for 10 days after the surgical procedure before collection of blood pressure and heart rate data.
TITLE: Confocal imaging and digital image analysis
AUTHORS: Hong-Yuan Chu

[DESCRIPTION]
This protocol describes confocal imaging on a Nikon A1R confocal microscope and digital image analysis.

[STEPS]
SECTION: Confocal imaging on a Nikon A1R confocal microscope
1. Turn on the power of laser, microscope, and computer.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
2. Open the NIS-Elements AR software.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
3. Set lightpath to Eyepiece to locate brain slice under 10x lens.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
4. Once the brain slice is located, switch the lighpath to camera.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
5. Check the pinhole size and make sure it is set to 1.2.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
6. Check for lasers of interest and make sure they are in use.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
7. For scanning, set resolution to 256x256 so that you can find the target regions as fast as possible.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
8. Adjust Z using knob to find slices.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
9. For the imaging of vGluT2, the immunostaining signals were taken between 5 and 8 µm below the surface of slice using a 100x objective lens with a 0.15 µm interval.
SECTION: Confocal imaging on a Nikon A1R confocal microscope
10. For the imaging of neuron density, NeuN-ir signals are collected using a 40x objective lens (1024 X1024 pixels; z step = 1 μm).
SECTION: Digital image analysis: Spine density analysis using Imaris
11. Convert the confocal images (.ND2) to imaris images (.ims) using the convert function of imairs.
SECTION: Digital image analysis: Spine density analysis using Imaris
12. Open the images in imaris.
SECTION: Digital image analysis: Spine density analysis using Imaris
13. Add a new filament and skip the automatic creation.
SECTION: Digital image analysis: Spine density analysis using Imaris
14. Select “AutoPath” algorithm method and put your pointer in the “Select” mode.
SECTION: Digital image analysis: Spine density analysis using Imaris
15. Press shift and right click at the beginning of the dendrite of interests.
SECTION: Digital image analysis: Spine density analysis using Imaris
16. Let the algorithm starts quantified in a starting point.
SECTION: Digital image analysis: Spine density analysis using Imaris
17. Move the cursor from the beginning to the end of the dendrite.
SECTION: Digital image analysis: Spine density analysis using Imaris
18. When reach the end of the dendrite, press shift and left click to specify the end of the dendrite, make sure the length of the dendrite is around 20-30 microns.
SECTION: Digital image analysis: Spine density analysis using Imaris
19. Re-construct and quantify the spines manually.
SECTION: Digital image analysis: Spine density analysis using Imaris
20. The spine density = amount of spines/length of dendrite.
TITLE: Water Filtration with Peristaltic Pump or Syringe & DNA Preservation
AUTHORS: Annette Engel, Audrey Paterson, Hannah Rigoni

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cells, particulates, and fine sediment (i.e., clay) in water are retained on filters during filtration. Filtered water can be collected for geochemical analyses and nucleic acids (referred to as environmental DNA or eDNA) can be extracted from the filters. This protocol describes water filtration with a 0.22 mm Sterivex (Millipore) filter cartridge by using a peristaltic pump or manually with a syringe, and the preservation of filtered material collected on the filter membrane using CTAB. </div></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>How to run MASH  version (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x" target="_blank" rel="noopener noreferrer">Ondov <em>et al.</em> 2016</a>) through the <a href="https://www.imicrobe.us/" target="_blank" rel="noopener noreferrer">iMicrobe</a> plaform.</p>
<p> </p>
<p>MASH is a  kmer-based sample-comparison tool using the MinHash algorithm to reduce the sample dimensionality and calculating a distance betwwen sample.</p>
<p> </p>
<p>More informations about MASH can be found here : <a href="https://mash.readthedocs.io/en/latest/" target="_blank" rel="noopener noreferrer">https://mash.readthedocs.io/en/latest/</a></p>

[BEFORE_START]
<ul>
<li>You need a working Cyverse account to connect to iMicrobe.To explore how to log into iMicrobe, read <a href="https://www.protocols.io/view/logging-into-imicrobe-us-rmmd446" target="_blank" rel="noopener noreferrer">the dedicated protocol</a>. <br /><br /></li>
<li>Your dataset of interest should be metagenomic reads, in a fasta or fastq format.<br /><br /></li>
<li>In iMicrobe, there is several ways to run an app on a dataset (from the cart, from your personnal datastore and form an URL). If you need more information on how to run an app, <a href="https://www.protocols.io/view/running-an-app-on-imicrobe-r9jd94n" target="_blank" rel="noopener noreferrer">read the protocol associated</a>.</li>
</ul>

[GUIDELINES]
<p><strong>More informations and details about MASH can be found there : <a href="https://mash.readthedocs.io/en/latest/" target="_blank" rel="noopener noreferrer">https://mash.readthedocs.io/en/latest/</a></strong></p>
<p> </p>
<p> </p>
<p><strong>Several parameters are available to the user through the iMicrobe app.</strong> </p>
<ul>
<li><strong>kmer size :</strong><br />As in any k-mer based method, larger k-mers will provide more specificity, while smaller k-mers will provide more sensitivity. Larger genomes will also require larger k-mers to avoid k-mers that are shared by chance. The k-mer size can be tuned by the iMicrobe user using the "kmer size" parameter. The default setting is 21bp.</li>
<li><strong>Sketch size :</strong>For sequences to be compared with <span style="font-family: monospace;">MASH</span>, they must first be <cite>sketched</cite>, which creates vastly reduced representations of them. Sketch size corresponds to the number of (non-redundant) min-hashes that are kept. Larger sketches will better represent the sequence, but at the cost of larger sketch files and longer comparison times. The sketch size can be tuned by the iMicrobe user using the "Sketch size" parameter. The default setting is 1000.</li>
</ul>

[STEPS]
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Objective: To feed individual house flies a specific amount of bacteria in order to
determine bacteria “fate” (persistence, via enumeration; spatiotemporal location, via
microscopy) and house fly immune response (whole fly or tissue-specific, via downstream mRNA or protein expression analyses) 


 
  


[BEFORE_START]
Note: The bacteria culture conditions (e.g. media including antibiotics) will vary based on the
bacteria species and plasmid, if any.

[STEPS]
SECTION: Preparing House Flies for Bacterial Feeding
?. 
SECTION: Preparing House Flies for Bacterial Feeding
?. 
SECTION: Preparing House Flies for Bacterial Feeding
?. 
SECTION: Preparing House Flies for Bacterial Feeding
?. 
SECTION: Preparing bacterial culture
?. 
SECTION: Preparing bacterial culture
?. 
SECTION: Feeding House Flies on Culture Droplets
?. 
SECTION: Feeding House Flies on Culture Droplets
?. 
SECTION: Droplet enumeration
?.
TITLE: Transformation of E. coli  with  plasmid
AUTHORS: sanjana  

[DESCRIPTION]
This protocol can be used to transform electrocompetent E. coli cells with a plasmid.

[STEPS]
SECTION: Preparation
1. Wash cuvette with 100 % (v/v)  ethanol and UV in the hood for 20 min 

SECTION: Preparation
2. Pre-thaw electrocompetent cells and plasmid on wet ice for 10 min 

SECTION: Electroporation
3. Add 1 µL of plasmid DNA to 50 µL electrocompetent cells

SECTION: Electroporation
4. Transfer cell-DNA mixture into the cuvette and add equal amount (50 µL ) of MilliQ
SECTION: Electroporation
5. Let the cuvette sit in wet ice for 20 min 

SECTION: Electroporation
6. Place cuvette in BioRad pulser and pulse at 2.5 keV


SECTION: Electroporation
7. Within 40 s add 100 µL of 2X LB to the cuvette

SECTION: Incubation
8. Place cuvette in an incubator at 37 °C for 30 min 

SECTION: Incubation
9. Then use a bent pipette tip to spread the cuvette's contents onto a plate made with LB agar and the appropriate antibiotics. Spread until plate is dry
SECTION: Incubation
10. Place the plate in an incubator at 37 °C   

SECTION: Incubation
11. Make glycerol stocks of transformed cells and store for future use
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<strong>Primers</strong> (Fil&eacute;e et al, 2005)<strong>:</strong><br /><br />MZIA1bis primer F:&nbsp; GAT ATT TGI GGI GTT CAG CCI ATG A<br />MZIA6 primer R:&nbsp; CGC GGT TGA TTT CCA GCA TGA TTT C<br /><br /><strong>Reaction Mix</strong> (using LA Takara)<strong>:</strong><br /><br />
<table>
<tbody>
<tr>
<td>Water</td>
<td>8.25&mu;l</td>
</tr>
<tr>
<td>10x LA Buffer</td>
<td>2.5&mu;l</td>
</tr>
<tr>
<td>dNTP mix, 2.5mM each</td>
<td>5.0&mu;l</td>
</tr>
<tr>
<td>Primer A, 10&mu;M</td>
<td>4.0&mu;l</td>
</tr>
<tr>
<td>Primer B, 10&mu;M</td>
<td>4.0&mu;l</td>
</tr>
<tr>
<td>LA Takara HS 2.5U/&mu;l</td>
<td>0.25&mu;l</td>
</tr>
<tr>
<td>DNA (or viral lysates)</td>
<td>1.0&mu;l</td>
</tr>
<tr>
<td>Total</td>
<td>25&mu;l</td>
</tr>
</tbody>
</table>
<br /><br /><strong>Reaction Mix</strong> (using GoTaq)<strong>:</strong><br /><br />
<table>
<tbody>
<tr>
<td>Water</td>
<td>3.5&mu;l</td>
</tr>
<tr>
<td>Primer A, 10&mu;M</td>
<td>4.0&mu;l</td>
</tr>
<tr>
<td>Primer B, 10&mu;M</td>
<td>4.0&mu;l</td>
</tr>
<tr>
<td>GoTaq</td>
<td>12.5&mu;l</td>
</tr>
<tr>
<td>DNA (or viral lysates)<sup>1</sup></td>
<td>1.0&mu;l</td>
</tr>
<tr>
<td>Total</td>
<td>25&mu;l</td>
</tr>
</tbody>
</table>
<br /><br /><strong><strong>Cycling<br /><br /></strong></strong>
<table>
<tbody>
<tr>
<td>94&deg;C</td>
<td>3.5min</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>94&deg;C</td>
<td>15 sec</td>
<td rowspan="3"><br />30 cycles<br /><br /></td>
</tr>
<tr>
<td>38&deg;C + 0.3&deg;C</td>
<td>60 sec</td>
</tr>
<tr>
<td>72&deg;C</td>
<td>45 sec</td>
</tr>
<tr>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>72&deg;C</td>
<td>5 min</td>
<td>&nbsp;</td>
</tr>
<tr>
<td>4&deg;C</td>
<td>Hold</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
<br />Products in the range of 450-650 bp<br /><br /><sup>1</sup>When using CsCl purified samples (i.e. not dialyzed), must dilute the sample 1:2 to 1:10; undiluted CsCl will inhibit PCR reactions

[STEPS]
TITLE: Workflow for  bulk RNAseq of human placenta
AUTHORS: Scott   Lindsay-Hewett, Valentina  Stanley, Mana   Parast, Louise Laurent

[DESCRIPTION]
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate RNAseq data from human placenta.

[STEPS]
SECTION: Tissue preparation
1. As soon as possible after Cesarean section or vaginal delivery, prepare tissue according to the following protocol:

Human Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC

For this protocol, use tissue that has been stored in RNAlater.
SECTION: Total RNA isolation
2. Isolate total RNA using a bead beater to disrupt the tissue, followed by organic extraction and ethanol precipitation. Use the following protocol:

Total RNA extraction from frozen placenta tissue

After passing quality control, proceed to library construction.
SECTION: Library construction
3. Construct libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR), according to the following protocol:

Library construction for human placenta bulk RNAseq

After passing quality control, proceed to sequencing.
SECTION: Sequencing
4. For HuBMAP bulk RNAseq samples, the multiplexed pool was sequenced on a NovaSeq 6000 S4 lane using a 100bp paired-end run configuration. Reads were aligned using STAR, and transcript abundances were quantified using RSEM.