title: CD4 bb&g7g7 1

data_processing:
MKION VDJ sequence analysis v 1.0
Sequence reads were trimmed for short and long reads (>100nt, <800nt)
Out-of-frame sequences were recovered by repairing the TRAJ segment by mapping back to germline
Organize by clonotype and reformat columns into immunarch format
Assembly: mm9
Supplementary files format and content: Comma-separated text file including ranked TCR clonotype counts for each Sample
Library strategy: TCR-Seq

value: naive CD4 T cell


title: CD4 bb&g7g7 2

status: Public on Jun 16 2024

type: SRA

city: Denver

first: Philippa

last: Marrack

state: CO

address: 1400 Jackson St

department: Immunology & Genomic Medicine

country: USA

institute: National Jewish Health

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Peripheral lymph nodes

extract_protocol:
Mice were euthanized, and axillary, brachial, inguinal, mesenteric, lumbar, and caudal lymph nodes were collected and filtered through a sterile 100µM filter. Cells were resuspended and washed 3x in BSS in a 15 ml conical tube. Cells were counted and resuspended in BSS supplemented with 1% BSA and anti-mouse CD16/CD32 (Clone: 2.4G2), as a pre-treatment reagent to block non-antigen-specific interactions of immunoglobulins to the FcγIII and FcγII, and possibly FcγI. Lymphocytes were stained with antibodies specific to TCRβ, CD45R, CD4, CD8, CD44, CD62L, and CD25 for 30 mins, washed 3x in BSS wash buffer. Cells were resuspended at 107/ml and fluorescently sorted for naïve lymphocytes on an iCyt Synergy.
RNA was isolated from purified naïve CD4 T cells using the RNeasy Kit (Invitrogen).  cDNA was made using the SuperScript VILO Kit (Invitrogen). For sequencing of TCR α-chains, a two-step PCR was done which added the machine oligonucleotides as well as barcodes for the sequencing runs. The first PCR included a reverse oligonucleotide in the constant region of the α-chain and a mixture of forward oligonucleotides that together cover all the different TCRα family members. The sequence or sequences for each TRAV family are as follows: TRAV01: GAGGGAACCTTTGCTCGGGTC; TRAV02: TATGAAGGGCAAGAAGTGAAC; TRAV03: CArGTCTTCAGTTGCTTATGA; TRAV04: TGCTCTGAGATGCAATTTTwC; TRAV05a: GGTGGAACAGCTCCCTTCCTC; TRAV05b: ATGGCTGCAGCTGGATGGGA; TRAV06a: GGACAAGGTCCACAGCTCCT; TRAV06b: GGAGAAGGTCCACAGCTCCTC; TRAV06c: GTCCAATATCCTGGAGAAGG; TRAV07: AGCAGAGCCCAGAATCCCTCA; TRAV08: AAAGAGCCAATGGGGAGAAG; TRAV08, GAATAGTCAACTAGCAGAAG; TRAV09: AGCTGAGATGCAAsTATTCCT; TRAV10: ACTTACACAGATACTGCyTCA; TRAV11: CACAGGCAAAGGTCTTGTGTC; TRAV12: GCTGAACTGCACCTATCAGA; TRAV13: TGGTTCTGCAGGAGGGGGArA; TRAV14: GTCCCCAATCTCTGACAGTCT; TRAV15: ACTGTTCATATrAGACAAGT; TRAV16: TGGAGAAGACAACGGTGACA; TRAV17: GTTATTCATACAGTGCAGCAC; TRAV18: ACCGCACGCTGCAGCTCCTCA; TRAV19: TACCCTGACAACAGCCCCACA; TRAV21: GTAGCCACGCCACAATCAGTG. The second PCR included just one forward oligonucleotide to add the machine oligonucleotide and a reverse oligonucleotide to add the barcode. For TCR β-chains, one PCR was done that contained a forward oligonucleotide priming all three TRBV13 family members at an identical region, the sequencing machine oligonucleotide CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATGCTGAGGCTGATCCATTA, and a reverse oligonucleotide that primed the Cβ region and contained the machine oligonucleotide and the barcode, CCATCTCATCCCTGCGTGTCTCCGACTCAGCTAAGGTAACGATCTTGGGTGGAGTCACATTTCTC.

tag: tissue

value: Peripheral lymph nodes

tag: cell type

tag: genotype


title: CD4 bb&g7g7 3


title: CD4 bb&g7g7 4


title: CD4 b+/- 5


title: imDC

city: Guiyang

first: Dong

middle: mei

last: ling

state: Guizhou

address: Guizhou Medical University

department: School of Basic Medical Sciences

country: China

institute: Guizhou Medical University

data_processing:
DNBSEQ
clean reads were compared to the reference genome sequence using HISAT
Bowtie2 was used to compare clean reads to reference gene sequences to obtain comparison results
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: immature dendritic cells

growth_protocol: Male C57BL/6 mice (6 weeks old) were sacrificed after anesthesia, femur and tibia were dissected, bone marrow cells were washed with PBS solution, and red blood cells were removed from cell suspension with red blood cell lysate. Complete media (containing 10% FBS, 20 ng/mL of rmGM-CSF and 10 ng/mL of rmIL-4) were added to re-suspension cell suspensions, and cell suspensions were subpackaged and cultured in six-well plates, and the liquid was changed every other day and half, and immature DCs was obtained on day 6.

extract_protocol:
1×106 cell samples were taken into the grinding and crushing tube with corresponding number. Add 600μL Buffer RLT Plus, homogenize the grinding machine, and let it stand at room temperature for 5 min; At room temperature, centrifuge at 12,000×g for 3 min; All supernatants were transferred to AllPrep DNA spin column; Centrifuge at room temperature of 10,000×g for 30 s, and the liquid in the collection tube was purified and collected for RNA
The DNBs obtained were added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe anchoring polymerization (cPAS)

treatment_protocol: High purity imDCs was obtained after purification by CD11c+ magnetic beads, and H2O2 with concentration of 100 μM was added for 24 h to obtain imDCS-H2O2.

value: immature dendritic cells

tag: treatment

value: control


title: P21 male Lrrk2G2019S KI striatum 1

city: New York

first: Deanna

middle: L

last: Benson

state: NY

address: 1470 Madison Avenue, 9-114

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
L-MiniLIMS RNAseq_Strandedx6
1GS

data_processing:
Preprocessing and alignment was performed by Weill Cornell Epigenomics Core. FASTQC was used to analyze the quality of the FASTQ files. We analyzed the presence of adaptors and we trimmed the reads with quality scores below 30. For trimming we used Flexbar.
HISAT2 was used for alignment using the indexed mouse genome obtained from https://ccb.jhu.edu/software/hisat2/manual.shtml.
For converting the obtained SAM files into BAM files we used SAMtools.
Stringtie was used to generate the gene expression matrix
Supplementary files format and content: text file; FPKM data; WT = wildtype and GS = Lrrk2-G2019S KI; # refers to sample number

source_name: dorsal striatum

extract_protocol:
Qiagen miRNeasy mini kit; quantified using Qubit on 01/04/17 by MSSM Biorepository and Pathology Core
TruSeq RNA sample prep kit; Weill Cornell Epigenomics Core

treatment_protocol: postnatal day 21 mice, anesthetized, sac'd, striatum rapidly dissected and placed in RNAlater on 12/21/16

value: dorsal striatum


title: Supersusceptible Progressor animal 471

status: Public on Jun 15 2024

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 471.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.62.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 24.0.0).  Expression values were averaged together by animal prior to analysis.

label: biotin

source_name: homogenized lung tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Four-to-five-week old female Diversity Outbred mice (n=1009) from generations 15, 16, 21, 22, 34, 35, 37, and 42 were purchased from The Jackson Laboratory (Bar Harbor, ME) and group housed (n=5-7 mice per cage) on Innovive (San Diego, CA) or Allentown Inc (Allentown, NJ) ventilated, HEPA-filtered racks in the New England Regional Biosafety Laboratory (Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA). The light cycle was 12 hours of light; 12 hours of dark. Disposable caging was purchased sterile and re-usable caging was autoclaved prior to use. All cages were lined with sterile corn-cob bedding and sterile paper nestlets (Scotts Pharma Solutions, Marlborough, MA). Cages were changed at least every other week. Mice were provided with sterile mouse chow (Envigo, Indianapolis, IA) and sterile, acidified water ad libidum.

extract_protocol: One lung lobe from each mouse was homogenized in TRIzol™, stored at -80°C, and RNA was extracted using PureLink RNA Mini Kits (Life Technologies, Carlsbad, CA).

treatment_protocol: At eight-to-ten-weeks old, mice were infected with aerosolized M. tuberculosis strain Erdman using a custom-built CH Technologies system. Twenty-four hours after each aerosol run, 4-12 mice were euthanized by carbon dioxide, and the entire lungs homogenized in 5mL sterile phosphate buffered saline, and all homogenate plated onto OADC-supplemented 7H11 agar. After 3 weeks at 37°C, M. tuberculosis colony forming units were counted to determine the retained lung dose.

value: lung

tag: class

value: Supersusceptible Progressor

tag: batch

value: batch 3

value: y


title: Supersusceptible Progressor animal 375

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 375.


title: Supersusceptible Progressor animal 421

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 421.


title: Supersusceptible Progressor animal 365

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 365.

value: batch 2


title: imDC_r1


title: Supersusceptible Progressor animal 340

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 340.


title: Supersusceptible Progressor animal 419

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 419.


title: Supersusceptible Progressor animal 350

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 350.


title: Supersusceptible Progressor animal 411

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 411.


title: Supersusceptible Progressor animal 383

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 383.


title: Supersusceptible Progressor animal 355

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 355.


title: NUDT21, TMEM106C, replicate 2

first: Madeline

last: Kowalski

address: 101 6th Ave

institute: New York Genome Center

library_source: other

data_processing:
We performed quantification using custom python scripts. We assigned reads to a sample and gene by matching the sample-specific barcode, allowing 1 bp mutation. We then searched for polyA tails in these reads (18 A nucleotides with up to 3 mutations). If a polyA tail was found, this was evidence of proximal cleavage and if no polyA tail was encountered, this was evidence of distal cleavage. For both proximal and distal reads, we additionally required that the last 20bp prior to the cleavage site or end of read were consistent with the expected genomic sequence. This approach enables us to quantify proximal polyA site usage at each locus for each sample.
Assembly: hg38
Supplementary files format and content: Matrix where each row is a sample, and each column represents a position relative to the start of the read, determined by the primer position upstream of the proximal polyA site. Each entry corresponds to the number of reads where cleavage was observed at that position in the construct for that sample (the last column indicates usage of the more distal polyA site, i.e. where no cleavage was observed)

molecule: other

organism: Homo sapiens

extract_protocol:
7 days post-transduction, RNA was extracted using the Zymo DirectZol RNA purification kit with DNase I treatment following the manufacturer’s protocol (Zymo R2052). We divided RNA into 1ug aliquots, using a separate aliquot for each targeted locus.
For each locus, the 1 µg of total RNA was reverse transcribed with SuperScript IV Reverse Transcriptase (Thermo Fisher 18090200) to generate cDNA following manufacturer instructions. The anchored poly dT primer for reverse transcription contained a Nextera Read 2 handle (NexteraR2-T18VN, 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTTTTTTTTTTTTTTTTTTVN-3’). After reverse transcription, RNA hydrolysis was performed using RNase H (Thermo Fisher 18021071) and then samples were purified using a DNA Clean & Concentrator-5 kit (Zymo D4013). In the first locus-specific PCR, purified cDNA was amplified with KAPA HiFi HotStart ReadyMix (Kapa Biosystems 07958935001) using the locus-specific primer (Figure S1) and adds a Truseq Read 1 handle and a reverse primer containing a sample-specific barcode (P7-index-NexteraR2) (Supplementary Table 3) with the following cycling conditions: 98 °C for 3 min; 15 cycles of 98 °C for 20 s, 65°C for 20 s and 72°C for 1 min 20 s; followed by 72°C for 5 min. After amplification, samples were 1X SPRI purified. In the second PCR to prepare samples for next-generation sequencing, the purified product from the previous PCR was amplified with KAPA HiFi HotStart ReadyMix (Kapa Biosystems 07958935001) using a forward PCR primer add sequencing adaptors (P5-TruseqR1, 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC*T*C-3’) and a reverse P7 PCR primer (5’-CAAGCAGAAGACGGCATACGAGAT-3’) with the following cycling conditions: 98 °C for 3 min; 15 cycles of 98 °C for 20 s, 60°C for 20 s and 72°C for 1 min 20 s; followed by 72°C for 5 min. Samples were sequenced using an Illumina MiSeq (300 cycle kit), allocating 200 cycles for R1.

treatment_protocol: CRISPRi-expressing HEK293FT cells were transduced with lentivirus for guides targeting NUDT21 or NT (single guide per condition, 2 transduction replicates)

tag: cell line


title: NUDT21, TMEM106C, replicate 1


title: Supersusceptible Progressor animal 351

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 351.


title: Supersusceptible Progressor animal 407

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 407.


title: NUDT21, SHMT1, replicate 2


description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 299 (batch 3).


title: NUDT21, SHMT1, replicate 1


title: Supersusceptible Progressor animal 434

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 434.


title: Supersusceptible Progressor animal 465

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 465.


title: Supersusceptible Progressor animal 437

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 437.


title: Supersusceptible Progressor animal 286

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 286.


title: NUDT21, PRDX3, replicate 2


title: Supersusceptible Progressor animal 281

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 281.


title: Supersusceptible Progressor animal 344

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 344.


title: Supersusceptible Progressor animal 279

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 279.


description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 299 (batch 2).


title: Supersusceptible Progressor animal 295

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 295.


title: Supersusceptible Progressor animal 316

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 316.


title: NUDT21, PRDX3, replicate 1


title: Supersusceptible Progressor animal 285

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 285.


title: NUDT21, LDHA, replicate 2


title: Supersusceptible Progressor animal 274

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 274.


title: Supersusceptible Progressor animal 272

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 272.


title: NUDT21, JKAMP, replicate 1


title: NUDT21, JKAMP, replicate 2


title: Supersusceptible Progressor animal 256

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 256.


title: NUDT21, CCT6A,  replicate 2


title: NUDT21, CCT6A,  replicate 1


title: NUDT21, CIAPIN1,  replicate 1


title: Supersusceptible Progressor animal 261

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 261.


title: Asymptomatic Controller animal 467

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 467.

value: Asymptomatic Controller

value: n


title: Supersusceptible Progressor animal 267

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 267.


title: Asymptomatic Controller animal 459

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 459.


title: NT, SHMT1,  replicate 2


title: NT, TMEM106C,  replicate 2


title: Asymptomatic Controller animal 455

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 455.


title: NT, SHMT1,  replicate 1


title: NT, TMEM106C,  replicate 1


title: NT, PRDX3,  replicate 2


title: Asymptomatic Controller animal 452

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 452.


title: NT, PRDX3,  replicate 1


title: Asymptomatic Controller animal 443

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 443.


title: Asymptomatic Controller animal 440

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 440.


title: Asymptomatic Controller animal 451

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 451.


title: NUDT21, CIAPIN1,  replicate 2


title: NT, LDHA,  replicate 2


title: Asymptomatic Controller animal 426

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 426.


title: Asymptomatic Controller animal 422

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 422.


title: Asymptomatic Controller animal 429

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 429.


title: Asymptomatic Controller animal 424

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 424.


title: NT, JKAMP,  replicate 1


title: NT, LDHA,  replicate 1


title: NT, JKAMP,  replicate 2


title: Mouse spleen genotype NOD.L7 rep1

city: Montréal

first: Capucine

last: Bourel

address: 2900 Bd Edouard-Montpetit

country: Canada

institute: Université de Montréal

description: pooled spleen from 3 mice

data_processing:
Sequence mapping:  Illumina Casava 1.8.2 and ElandV2 aligner
Gene expression levels were calculated with Casava as RPKM
Variants were detected using samtools version 0.1.18
Assembly: Mouse mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: spleen

extract_protocol:
Quiagen RNeasy kit
RNA libraries for RNA-seq were prepared using Truseq RNA library

value: spleen


title: NT, CIAPIN1,  replicate 2


title: NT, CIAPIN1,  replicate 1


title: NT, CCT6A, replicate 2


title: Asymptomatic Controller animal 417

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 417.


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 418 (batch 2).


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 418 (batch 3).


title: NT, CCT6A, replicate 1


title: Asymptomatic Controller animal 415

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 415.


title: N2dG-control_L1_1.fq.gz

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

library_source: genomic

data_processing:
base calling analysis using the standard Illuminapipeline and sample de-multiplexing according to index read data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Assembly: hg19
Supplementary files format and content: wig files were generated using deeptools

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
The genomic DNA were extracted using Monarch® Genomic DNA Purification Kit (New England Biolabs) and reacted with biotin-azide at room temperature for 6 h. The biotinylated genomic DNA was sheared using a Covaris S220 sonicator. The N2-heptynyl-dG DNA were enriched with Dynabeads™ MyOne™ Streptavidin C1 (Thermo). Purified DNA was quantified and verified on an Agilent 2100 Bioanalyzer. The library was then constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions.
The library was constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a HiSeq4000 system (Illumina).

treatment_protocol: HEK293T cells were treated with N2-heptynyl-dG for 3-h at a final concentration of 10 μM. The cells were then harvested immediately for N2-heptynyl-dG sequencing.

value: HEK293T cells

value: Human embryonic kidney

value: WT

value: 10 μM N2-heptynyl-dG treatment for 3-h


title: Asymptomatic Controller animal 394

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 394.


title: Asymptomatic Controller animal 398

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 398.


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 386 (batch 3).


title: Asymptomatic Controller animal 409

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 409.


title: N2dG-1_L1_1.fq.gz


title: Mouse spleen genotype NOD.g7 rep1

description: pooled spleen from 3 mice


title: Asymptomatic Controller animal 389

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 389.


title: Asymptomatic Controller animal 378

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 378.


title: N2dG-2_L1_1.fq.gz


title: Asymptomatic Controller animal 372

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 372.


title: Asymptomatic Controller animal 384

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 384.


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 386 (batch 2).


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 359 (batch 2).


title: Asymptomatic Controller animal 368

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 368.


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 359 (batch 3).


title: Asymptomatic Controller animal 367

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 367.


title: Not infected animal 481 (batch 3) [re-analysis]

description: Re-analysis of GSM8250488

value: Not infected


title: Asymptomatic Controller animal 336

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 336.


title: Not infected animal 481 (batch 2) [re-analysis]

description: Re-analysis of GSM8250487


title: Not infected animal 480 (batch 3) [re-analysis]

description: Re-analysis of GSM8250486


title: Not infected animal 482 (batch 2) [re-analysis]

description: Re-analysis of GSM8250489


title: Not infected animal 479 (batch 3) [re-analysis]

description: Re-analysis of GSM8250484


title: Asymptomatic Controller animal 329

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 329.


title: Asymptomatic Controller animal 318

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 318.


title: Asymptomatic Controller animal 305

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 305.


title: Asymptomatic Controller animal 311

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 311.


title: Not infected animal 479 (batch 2) [re-analysis]

description: Re-analysis of GSM8250483


title: Asymptomatic Controller animal 303

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 303.


title: Not infected animal 478 (batch 3) [re-analysis]

description: Re-analysis of GSM8250481


title: Not infected animal 479 (batch 1) [re-analysis]

description: Re-analysis of GSM8250482

value: batch 1


title: Not infected animal 478 (batch 2) [re-analysis]

description: Re-analysis of GSM8250480


title: Not infected animal 478 (batch 1) [re-analysis]

description: Re-analysis of GSM8250479


title: Asymptomatic Controller animal 300

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 300.


title: Asymptomatic Controller animal 260

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 260.


title: Asymptomatic Controller animal 296

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 296.


title: Not infected animal 480 (batch 2) [re-analysis]

description: Re-analysis of GSM8250485


title: Not infected animal 482 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 482 (batch 3).


title: Not infected animal 475 (batch 1) [re-analysis]

description: Re-analysis of GSM8250472


title: Asymptomatic Controller animal 288

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 288.


title: Not infected animal 477 (batch 2) [re-analysis]

description: Re-analysis of GSM8250477


title: Not infected animal 477 (batch 3) [re-analysis]

description: Re-analysis of GSM8250478


title: Not infected animal 476 [re-analysis]

description: Re-analysis of GSM8250475


title: Not infected animal 481 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 481 (batch 3).


title: Not infected animal 477 (batch 1) [re-analysis]

description: Re-analysis of GSM8250476


title: Asymptomatic Controller animal 265

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 265.


title: NUDT21, LDHA, replicate 1


title: Not infected animal 253 [re-analysis]

description: Re-analysis of GSM8250429


title: Not infected animal 479 (batch 1)

description: Gene expression data from homogenized lung tissue of Not infected animal 479 (batch 1).


title: Not infected animal 474 [re-analysis]

description: Re-analysis of GSM8250471


title: Supersusceptible Progressor animal 471 [re-analysis]

description: Re-analysis of GSM8250558


title: Not infected animal 475 (batch 3) [re-analysis]

description: Re-analysis of GSM8250474


title: Not infected animal 482 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 482 (batch 2).


title: Not infected animal 480 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 480 (batch 3).


title: Not infected animal 478 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 478 (batch 3).


title: Not infected animal 475 (batch 2) [re-analysis]

description: Re-analysis of GSM8250473


title: Not infected animal 478 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 478 (batch 2).


title: Not infected animal 479 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 479 (batch 3).


title: Not infected animal 480 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 480 (batch 2).


title: Not infected animal 252 [re-analysis]

description: Re-analysis of GSM8250428


title: Not infected animal 251 [re-analysis]

description: Re-analysis of GSM8250427


title: Not infected animal 479 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 479 (batch 2).


title: Not infected animal 249 [re-analysis]

description: Re-analysis of GSM8250425


title: Not infected animal 250 [re-analysis]

description: Re-analysis of GSM8250426


title: Not infected animal 481 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 481 (batch 2).


title: Not infected animal 476

description: Gene expression data from homogenized lung tissue of Not infected animal 476.


title: Not infected animal 475 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 475 (batch 3).


title: Not infected animal 478 (batch 1)

description: Gene expression data from homogenized lung tissue of Not infected animal 478 (batch 1).


title: Supersusceptible Progressor animal 465 [re-analysis]

description: Re-analysis of GSM8250557


title: Supersusceptible Progressor animal 419 [re-analysis]

description: Re-analysis of GSM8250553


title: Supersusceptible Progressor animal 437 [re-analysis]

description: Re-analysis of GSM8250556


title: Not infected animal 477 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 477 (batch 2).


title: Not infected animal 477 (batch 3)

description: Gene expression data from homogenized lung tissue of Not infected animal 477 (batch 3).


title: Supersusceptible Progressor animal 421 [re-analysis]

description: Re-analysis of GSM8250554


title: Supersusceptible Progressor animal 383 [re-analysis]

description: Re-analysis of GSM8250550


title: Not infected animal 477 (batch 1)

description: Gene expression data from homogenized lung tissue of Not infected animal 477 (batch 1).


title: Supersusceptible Progressor animal 411 [re-analysis]

description: Re-analysis of GSM8250552


title: Supersusceptible Progressor animal 240

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 240.


title: Supersusceptible Progressor animal 355 [re-analysis]

description: Re-analysis of GSM8250547


title: Supersusceptible Progressor animal 434 [re-analysis]

description: Re-analysis of GSM8250555


title: Supersusceptible Progressor animal 350 [re-analysis]

description: Re-analysis of GSM8250545


title: Supersusceptible Progressor animal 231

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 231.


title: Supersusceptible Progressor animal 351 [re-analysis]

description: Re-analysis of GSM8250546


title: Supersusceptible Progressor animal 216

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 216.


title: Supersusceptible Progressor animal 212

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 212.


title: Not infected animal 475 (batch 1)

description: Gene expression data from homogenized lung tissue of Not infected animal 475 (batch 1).


title: Not infected animal 474

description: Gene expression data from homogenized lung tissue of Not infected animal 474.


title: Supersusceptible Progressor animal 365 [re-analysis]

description: Re-analysis of GSM8250548


title: Supersusceptible Progressor animal 375 [re-analysis]

description: Re-analysis of GSM8250549


title: Supersusceptible Progressor animal 239

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 239.


title: Supersusceptible Progressor animal 221

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 221.


title: Not infected animal 475 (batch 2)

description: Gene expression data from homogenized lung tissue of Not infected animal 475 (batch 2).


title: Supersusceptible Progressor animal 299 (batch 3) [re-analysis]

description: Re-analysis of GSM8250541


title: Supersusceptible Progressor animal 316 [re-analysis]

description: Re-analysis of GSM8250542


title: Supersusceptible Progressor animal 340 [re-analysis]

description: Re-analysis of GSM8250543


title: Supersusceptible Progressor animal 344 [re-analysis]

description: Re-analysis of GSM8250544


title: Supersusceptible Progressor animal 210

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 210.


title: Supersusceptible Progressor animal 207

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 207.


title: Controller animal 234

description: Gene expression data from homogenized lung tissue of Controller animal 234.

value: Controller


title: Supersusceptible Progressor animal 295 [re-analysis]

description: Re-analysis of GSM8250539


title: Supersusceptible Progressor animal 203

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 203.


title: Supersusceptible Progressor animal 274 [re-analysis]

description: Re-analysis of GSM8250534


title: Supersusceptible Progressor animal 286 [re-analysis]

description: Re-analysis of GSM8250538


title: Supersusceptible Progressor animal 201

description: Gene expression data from homogenized lung tissue of Supersusceptible Progressor animal 201.


title: Supersusceptible Progressor animal 267 [re-analysis]

description: Re-analysis of GSM8250532


title: Controller animal 229

description: Gene expression data from homogenized lung tissue of Controller animal 229.


title: Supersusceptible Progressor animal 407 [re-analysis]

description: Re-analysis of GSM8250551


title: Supersusceptible Progressor animal 272 [re-analysis]

description: Re-analysis of GSM8250533


title: Supersusceptible Progressor animal 285 [re-analysis]

description: Re-analysis of GSM8250537


title: Supersusceptible Progressor animal 261 [re-analysis]

description: Re-analysis of GSM8250531


title: Controller animal 222

description: Gene expression data from homogenized lung tissue of Controller animal 222.


title: Supersusceptible Progressor animal 281 [re-analysis]

description: Re-analysis of GSM8250536


title: Controller animal 233

description: Gene expression data from homogenized lung tissue of Controller animal 233.


title: Supersusceptible Progressor animal 299 (batch 2) [re-analysis]

description: Re-analysis of GSM8250540


title: Supersusceptible Progressor animal 279 [re-analysis]

description: Re-analysis of GSM8250535


title: Controller animal 232

description: Gene expression data from homogenized lung tissue of Controller animal 232.


title: Controller animal 227

description: Gene expression data from homogenized lung tissue of Controller animal 227.


title: Controller animal 225

description: Gene expression data from homogenized lung tissue of Controller animal 225.


title: Controller animal 215 (batch 2)

description: Gene expression data from homogenized lung tissue of Controller animal 215 (batch 2).


title: Supersusceptible Progressor animal 256 [re-analysis]

description: Re-analysis of GSM8250530


title: Supersusceptible Progressor animal 231 [re-analysis]

description: Re-analysis of GSM8250468


title: Controller animal 241

description: Gene expression data from homogenized lung tissue of Controller animal 241.


title: Controller animal 220

description: Gene expression data from homogenized lung tissue of Controller animal 220.


title: Controller animal 215 (batch 1)

description: Gene expression data from homogenized lung tissue of Controller animal 215 (batch 1).


title: Supersusceptible Progressor animal 240 [re-analysis]

description: Re-analysis of GSM8250470


title: Controller animal 214

description: Gene expression data from homogenized lung tissue of Controller animal 214.


title: Supersusceptible Progressor animal 239 [re-analysis]

description: Re-analysis of GSM8250469


title: Supersusceptible Progressor animal 221 [re-analysis]

description: Re-analysis of GSM8250467


title: Supersusceptible Progressor animal 216 [re-analysis]

description: Re-analysis of GSM8250466


title: Controller animal 211

description: Gene expression data from homogenized lung tissue of Controller animal 211.


title: Controller animal 198

description: Gene expression data from homogenized lung tissue of Controller animal 198.


title: Supersusceptible Progressor animal 207 [re-analysis]

description: Re-analysis of GSM8250463


title: Controller animal 205

description: Gene expression data from homogenized lung tissue of Controller animal 205.


title: Controller animal 204

description: Gene expression data from homogenized lung tissue of Controller animal 204.


title: Asymptomatic Controller animal 236

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 236.


title: Controller animal 209

description: Gene expression data from homogenized lung tissue of Controller animal 209.


title: Controller animal 241 [re-analysis]

description: Re-analysis of GSM8250460


title: Supersusceptible Progressor animal 201 [re-analysis]

description: Re-analysis of GSM8250461


title: Supersusceptible Progressor animal 212 [re-analysis]

description: Re-analysis of GSM8250465


title: Asymptomatic Controller animal 218

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 218.


title: Asymptomatic Controller animal 217

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 217.


title: Controller animal 233 [re-analysis]

description: Re-analysis of GSM8250458


title: Controller animal 229 [re-analysis]

description: Re-analysis of GSM8250456


title: Controller animal 234 [re-analysis]

description: Re-analysis of GSM8250459


title: Supersusceptible Progressor animal 203 [re-analysis]

description: Re-analysis of GSM8250462


title: Asymptomatic Controller animal 208

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 208.


title: Controller animal 227 [re-analysis]

description: Re-analysis of GSM8250455


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 206 (batch 2).


title: Asymptomatic Controller animal 213

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 213.


title: Supersusceptible Progressor animal 210 [re-analysis]

description: Re-analysis of GSM8250464


title: Asymptomatic Controller animal 200

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 200.


description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 206 (batch 1).


title: Asymptomatic Controller animal 202

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 202.


title: Controller animal 220 [re-analysis]

description: Re-analysis of GSM8250452


title: Controller animal 232 [re-analysis]

description: Re-analysis of GSM8250457


title: Controller animal 222 [re-analysis]

description: Re-analysis of GSM8250453


title: Asymptomatic Controller animal 199

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 199.


title: Controller animal 209 [re-analysis]

description: Re-analysis of GSM8250447


title: Controller animal 225 [re-analysis]

description: Re-analysis of GSM8250454


title: Controller animal 215 (batch 2) [re-analysis]

description: Re-analysis of GSM8250451


title: Controller animal 211 [re-analysis]

description: Re-analysis of GSM8250448


title: ES-E14TG2a, dTAG, 24 hour, Rep 3

city: Leicester

first: Shaun

last: Cowley

address: Henry Wellcome Building, Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Reads were mapped to mm10 using HISAT2 version 2.1.0 with default parameters
SAM files were then sorted and converted to BAM files using SAMtools version 1.9 with default parameters, SAMtools was also used to index BAM files
Read counts were generated using LiBiNorm version 2.4, run in htseq-count compatible mode using the Mus musculusGRCm38.92 genome annotation from Ensembl with parameters as follows: count -z -r pos -i gene_name -s reverse
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: ESCs were grown on tissue culture plates pre-treated with 0.1% gelatine in KO DMEM supplemented with 15% FBS, pen-strep glutamine, 2-Mercaptoethanol and leukemia inhibitory factor in humidified atmosphere at 37 C with 5% CO2.

extract_protocol:
Total RNA was extracted using a Promega Maxwell 16 and quality checked using an Agilent Bioanalyzer by the NUCLEUS facility at the University of Leicester.
Library construction was performed by Novogene Cambridge using the NEB Next Ultra RNA Library Prep kit.

treatment_protocol: ESCs were first treated with 1uM 4-hydroxytamoxifen for 5 days to remove endogenous HDAC1/2, these cells were then treated with 100 nM dTAGV-1 for 2/6/24 hours or with an equivlaent volume of DMSO.

value: Embryonic stem cells

value: dTAGV-1 100 nM 24 hour


title: Not infected animal 251

description: Gene expression data from homogenized lung tissue of Not infected animal 251.

value: lung


title: Asymptomatic Controller animal 194

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 194.


title: Not infected animal 249

description: Gene expression data from homogenized lung tissue of Not infected animal 249.


title: Not infected animal 252

description: Gene expression data from homogenized lung tissue of Not infected animal 252.


title: Controller animal 214 [re-analysis]

description: Re-analysis of GSM8250449


title: ES-E14TG2a, dTAG, 24 hour, Rep 2


title: Asymptomatic Controller animal 195

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 195.


title: Not infected animal 250

description: Gene expression data from homogenized lung tissue of Not infected animal 250.


title: Controller animal 204 [re-analysis]

description: Re-analysis of GSM8250445


title: Asymptomatic Controller animal 196

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 196.


title: Asymptomatic Controller animal 459 [re-analysis]

description: Re-analysis of GSM8250528


title: Asymptomatic Controller animal 197

description: Gene expression data from homogenized lung tissue of Asymptomatic Controller animal 197.


title: Asymptomatic Controller animal 467 [re-analysis]

description: Re-analysis of GSM8250529


title: ES-E14TG2a, dTAG, 6 hour, Rep 3

value: dTAGV-1 100 nM 6 hour


title: Controller animal 215 (batch 1) [re-analysis]

description: Re-analysis of GSM8250450


title: ES-E14TG2a, dTAG, 24 hour, Rep 1


title: Asymptomatic Controller animal 455 [re-analysis]

description: Re-analysis of GSM8250527

value: batch 3


title: ES-E14TG2a, dTAG, 6 hour, Rep 2


title: Asymptomatic Controller animal 452 [re-analysis]

description: Re-analysis of GSM8250526


title: Asymptomatic Controller animal 451 [re-analysis]

description: Re-analysis of GSM8250525


title: ES-E14TG2a, dTAG, 6 hour, Rep 1


title: ES-E14TG2a, dTAG, 2 hour, Rep 3

value: dTAGV-1 100 nM 2 hour


title: Asymptomatic Controller animal 443 [re-analysis]

description: Re-analysis of GSM8250524


title: ES-E14TG2a, dTAG, 2 hour, Rep 2


title: ES-E14TG2a, dTAG, 2 hour, Rep 1


title: Asymptomatic Controller animal 429 [re-analysis]

description: Re-analysis of GSM8250522


title: Asymptomatic Controller animal 440 [re-analysis]

description: Re-analysis of GSM8250523


title: ES-E14TG2a, DMSO, 24 hour, Rep 3

value: DMSO 24 hour


title: ES-E14TG2a, DMSO, 24 hour, Rep 1


title: ESC, dTAG, H3K27Ac, Rep1

data_processing:
Raw reads were trimmed using trimmomatic
Trimmed reads were aligned to the mm10 genome sequence using Bowtie 2 using –no-mixed and –no-discordant options
SAM files were converted to BAM files, then sorted using samtools before duplicates were removed using sambamba
BAM files were merged using samtools merge
Merged BAM files were converted to bigWigs using deeptools bamCoverage and input files were subtracted from ChIP files. bigWig files were then viewed on the genome browser
Assembly: mm10
Supplementary files format and content: bigWig - dense, contiuous data for display as a graph on the genome browser

extract_protocol:
Following cell lysis chromatin was fragmented by 5 minutes of MNase digestion.
Libraries were prepared for ChIP and matched input samples using the NEBNext Ultra II DNA library kit and indexed using NEBNext Multiplex Oligos.

tag: spike-in reference_organism

value: Drosophila melanogaster

tag: spike-in cell_line

tag: chip antibody

value: H3K27Ac (Cell Signalling Technology D5E4, Rabbit mAb #8173)

value: dTAGV-1 100nM 6 hour


title: ESC, dTAG, H3K27Ac, Rep3


title: ESC, dTAG, H3K27Ac, Rep2


title: Asymptomatic Controller animal 418 (batch 2) [re-analysis]

description: Re-analysis of GSM8250517

value: Asymptomatic Controller

value: batch 2

value: n


title: Asymptomatic Controller animal 418 (batch 3) [re-analysis]

description: Re-analysis of GSM8250518


title: ESC, dTAG, H2BK5Ac, Rep2

value: H2BK5Ac (Active Motif 39123)


title: Asymptomatic Controller animal 422 [re-analysis]

description: Re-analysis of GSM8250519


title: ESC, dTAG, H2BK5Ac, Rep3


title: Asymptomatic Controller animal 415 [re-analysis]

description: Re-analysis of GSM8250515


title: Asymptomatic Controller animal 426 [re-analysis]

description: Re-analysis of GSM8250521


title: Asymptomatic Controller animal 417 [re-analysis]

description: Re-analysis of GSM8250516


title: ES-E14TG2a, DMSO, 24 hour, Rep 2


title: ESC, dTAG, Input, Rep2


title: ESC, dTAG, Input, Rep3


title: ESC, dTAG, Input, Rep1


title: Asymptomatic Controller animal 398 [re-analysis]

description: Re-analysis of GSM8250513


title: Asymptomatic Controller animal 394 [re-analysis]

description: Re-analysis of GSM8250512


title: Asymptomatic Controller animal 409 [re-analysis]

description: Re-analysis of GSM8250514


title: Asymptomatic Controller animal 386 (batch 3) [re-analysis]

description: Re-analysis of GSM8250510


title: ESC, dTAG, H2BK5Ac, Rep1


title: Asymptomatic Controller animal 389 [re-analysis]

description: Re-analysis of GSM8250511


title: Not infected animal 253

description: Gene expression data from homogenized lung tissue of Not infected animal 253.

value: Not infected


title: ESC, DMSO, H2BK5Ac, ChIP, Rep3

value: DMSO 6 hour


title: ESC, DMSO, H3K27Ac, ChIP, Rep1


title: Asymptomatic Controller animal 424 [re-analysis]

description: Re-analysis of GSM8250520


title: ESC, DMSO, H3K27Ac, ChIP, Rep2


title: Asymptomatic Controller animal 384 [re-analysis]

description: Re-analysis of GSM8250508


title: Asymptomatic Controller animal 372 [re-analysis]

description: Re-analysis of GSM8250506


title: Asymptomatic Controller animal 368 [re-analysis]

description: Re-analysis of GSM8250505


title: Asymptomatic Controller animal 367 [re-analysis]

description: Re-analysis of GSM8250504


title: Asymptomatic Controller animal 378 [re-analysis]

description: Re-analysis of GSM8250507


title: ESC, DMSO, H2BK5Ac, ChIP, Rep2


title: ESC, DMSO, H2BK5Ac, ChIP, Rep1


title: ESC, DMSO, Input, Rep3


title: ESC, DMSO, Input, Rep1


title: ESC, DMSO, Input, Rep2


title: Asymptomatic Controller animal 386 (batch 2) [re-analysis]

description: Re-analysis of GSM8250509


title: Asymptomatic Controller animal 359 (batch 2) [re-analysis]

description: Re-analysis of GSM8250502


title: ESC, DMSO, H3K27Ac, ChIP, Rep3


title: Liver_72h_CCl4_rep5

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

data_processing:
The BAM files were generated by aligning the R1 FASTQ (without any further processing) using STAR (v2.7.9a) on a GRCm38 index.
The STAR default parameters were used. Unmapped reads were kept in the BAM. The BAMs were directly written sorted by coordinates.
Assembly: GRCm38 Mouse Genome from Ensembl
Supplementary files format and content: space-delimited text file includes counts for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from FACS sorted Neutrophils samples using the RNEasy Micro kit (Qiagen) according to manufacturer’s instructions.
The RNA quality was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies). All RNA samples displayed an RNA integrity numbers (RIN) score superior to 8. RNA samples were sent to the Genome Quebec Innovation Center for RNA-seq libraries preparation using the NEB mRNA stranded library preparation.

treatment_protocol:
NA
NA

value: Liver

value: Neutrophils

tag: time

value: 72h after ccl4


title: Liver_72h_CCl4_rep4


title: Liver_72h_CCl4_rep3


title: Liver_72h_CCl4_rep2


title: Asymptomatic Controller animal 329 [re-analysis]

description: Re-analysis of GSM8250500

value: lung


title: Asymptomatic Controller animal 336 [re-analysis]

description: Re-analysis of GSM8250501


title: Asymptomatic Controller animal 318 [re-analysis]

description: Re-analysis of GSM8250499


title: Liver_24h_CCl4_rep4

value: 24h after ccl4


title: Asymptomatic Controller animal 311 [re-analysis]

description: Re-analysis of GSM8250498

value: batch 3


title: Asymptomatic Controller animal 359 (batch 3) [re-analysis]

description: Re-analysis of GSM8250503


title: Asymptomatic Controller animal 305 [re-analysis]

description: Re-analysis of GSM8250497


title: Asymptomatic Controller animal 296 [re-analysis]

description: Re-analysis of GSM8250494


title: Liver_24h_CCl4_rep2


title: Liver_24h_CCl4_rep3


title: Liver_24h_CCl4_rep1


title: Spleen_0h_rep2

source_name: Spleen

value: Spleen


title: Asymptomatic Controller animal 288 [re-analysis]

description: Re-analysis of GSM8250493


title: Liver_72h_CCl4_rep1


title: Asymptomatic Controller animal 265 [re-analysis]

description: Re-analysis of GSM8250492


title: 93, Prefrontal cortex, WT, Female

city: Rovereto

first: Caterina

last: Montani

address: Corso Bettini 31

country: Italy

institute: IIT - Istituto Italiano di Tecnologia

data_processing:
Raw reads were transformed into raw counts using the STAR aligner with the mm10 genome (GRCm38 primary assembly obtained from the Gencode website) and counted with featureCounts using the gene annotation Gencode v24.
Assembly: mm10
Supplementary files format and content: Comma Separated Values File (csv) includes raw counts for each Sample

source_name: Prefrontal cortex

extract_protocol:
RNA was harvested using RNeasy Mini Kit and RNeasy Micro Kit (Qiagen), following manufacturer's protocols. For each sample of hypothalamus and PFC, 1000 ng and 500 ng were used as input quantity, respectively.
RNA libraries for RNA-seq were prepared using paired-end TruSeq® Stranded mRNA Sample Preparation kit (Illumina, San Diego, Ca, USA), following manufacturer's protocols.

value: Prefrontal cortex

tag: strain

value: FVB/NJ

tag: developmental stage

value: adult

value: WT

tag: Sex

value: F


title: Spleen_0h_rep3


title: Spleen_0h_rep1


title: Asymptomatic Controller animal 236 [re-analysis]

description: Re-analysis of GSM8250443

value: Asymptomatic Controller

value: batch 2


title: Asymptomatic Controller animal 217 [re-analysis]

description: Re-analysis of GSM8250441

value: batch 1

value: n


title: 471, Hypothalamus, WT, Female

source_name: Hypothalamus

value: Hypothalamus


title: Asymptomatic Controller animal 300 [re-analysis]

description: Re-analysis of GSM8250495


title: Asymptomatic Controller animal 303 [re-analysis]

description: Re-analysis of GSM8250496


title: 462, Prefrontal cortex, Ube3a2x, Female


title: 462, Hypothalamus, Ube3a2x, Female


title: 423, Hypothalamus, WT, Male

value: M


title: Asymptomatic Controller animal 206 (batch 1) [re-analysis]

description: Re-analysis of GSM8250437


title: Asymptomatic Controller animal 213 [re-analysis]

description: Re-analysis of GSM8250440


title: Asymptomatic Controller animal 260 [re-analysis]

description: Re-analysis of GSM8250491


title: Asymptomatic Controller animal 200 [re-analysis]

description: Re-analysis of GSM8250435


title: Asymptomatic Controller animal 199 [re-analysis]

description: Re-analysis of GSM8250434


title: 420, Hypothalamus, Ube3a2x, Female


title: Asymptomatic Controller animal 218 [re-analysis]

description: Re-analysis of GSM8250442


title: Asymptomatic Controller animal 197 [re-analysis]

description: Re-analysis of GSM8250433


title: 420, Prefrontal cortex, Ube3a2x, Female


title: 417, Prefrontal cortex, Ube3a2x, Female


title: Asymptomatic Controller animal 208 [re-analysis]

description: Re-analysis of GSM8250439


title: 417, Hypothalamus, Ube3a2x, Female


title: 410, Hypothalamus, WT, Female


title: 404, Hypothalamus, Ube3a2x, Male


title: 468, Prefrontal cortex, Ube3a2x, Female


title: Asymptomatic Controller animal 206 (batch 2) [re-analysis]

description: Re-analysis of GSM8250438


title: 403, Prefrontal cortex, WT, Male


title: K562, replicate 2 gRNA

library_source: transcriptomic single cell

data_processing:
HEK and K562 scRNA-seq and Feature Barcoding data was processed using CellRanger (v6.0.0, ‘cellranger count’). HTO data was quantified using the CITE-seq-count package (v1.4.2).
Assembly: hg38
Supplementary files format and content: .Rds file (seurat object)

molecule: polyA RNA

extract_protocol:
We performed scRNA-seq (10x Genomics Chromium Single Cell 3’ Gene Expression v3 with Feature Barcoding technology for CRISPR screening) 6-7 days post-transduction. Before the run, cell viability was determined (>95%). We leveraged Cell Hashing in order to super-load (~40,000 cells/lane) the Chromium instrument
Gene expression and sgRNA feature libraries were constructed following the manufacturer’s protocol. Cell Hashing libraries (Hashtag-derived oligos, HTOs) libraries were prepared following the recommended protocol on cite-seq.com

treatment_protocol: We transduced 3x106 HEK293FT or K562 CRISPRi cells per 12-well with an MOI of < 0.1 (< 10% survival) ensuring high coverage (cells per sgRNA) of at least 1000x and a single integration probability > 95%. The cells were selected with 1µg/ml puromycin starting at 24 hours post-transduction for at least 48 hours for HEK293FT cells and at least 5 days for K562 cells. Cells were maintained with blasticidin and puromycin until the single-cell experiment 6-7 post transduction.


title: K562, replicate 2 GEX


title: Asymptomatic Controller animal 196 [re-analysis]

description: Re-analysis of GSM8250432


title: Asymptomatic Controller animal 194 [re-analysis]

description: Re-analysis of GSM8250430


title: 468, Hypothalamus, Ube3a2x, Female


title: K562, replicate 2 HTO


title: K562, replicate 1 HTO


title: K562, replicate 1 gRNA


title: Asymptomatic Controller animal 195 [re-analysis]

description: Re-analysis of GSM8250431


title: Controller animal 205 [re-analysis]

description: Re-analysis of GSM8250446

value: Controller

value: y


title: 397, Prefrontal cortex, WT, Female


title: Controller animal 198 [re-analysis]

description: Re-analysis of GSM8250444

value: lung


title: Not infected animal 482 (batch 3) [re-analysis]

description: Re-analysis of GSM8250490

value: Not infected


title: 272, Prefrontal cortex, Ube3a2x, Female


title: 403, Hypothalamus, WT, Male


title: Asymptomatic Controller animal 202 [re-analysis]

description: Re-analysis of GSM8250436


title: K562, replicate 1 GEX


title: HEK293FT, replicate 1 HTO


title: 272, Hypothalamus, Ube3a2x, Female


title: 267, Prefrontal cortex, Ube3a2x, Male


title: 398, Hypothalamus, WT, Female


title: 395, Prefrontal cortex, WT, Female


title: HEK293FT, replicate 1 GEX


title: 402, Prefrontal cortex, Ube3a2x, Male


title: HEK293FT, replicate 2 gRNA


title: HEK293FT, replicate 2 GEX


title: MPRA library, NUDT21 gB, replicate 2

data_processing:
Custom python scripts were used to demultiplex and quantify sequencing reads. The barcodes in Read 1 identified the experimental condition (i.e. replicate and gRNA identity), as well as a unique molecular identifier. The barcodes in Read 2 identify the proximal and distal site contexts that gave rise to the mRNA molecule being sequenced. The distal site barcodes were assigned using the first 4-8 bp of read 2 (see Supplementary Table 5). The next 20 bp after the distal site barcode were used to assign reads to a proximal site (each with a unique 20 bp barcode). Only reads that matched distal and proximal barcodes within 1 bp each were retained. We collapsed all reads with the same UMI, proximal, and distal site barcodes (allowing 1 bp mutations in the UMI sequence).  If an mRNA molecule is cleaved at the proximal site, we will observe a stretch of A nucleotides at the cleavage site in the sequence read. If the mRNA molecule is distally cleaved, the full read will consist of the 3’ UTR sequence. Therefore, for each read, we classified it as “proximal” if it contained a polyA stretch (18 A’s with up to 2 bp mismatches). Reads that did not contain a polyA stretch were classified as distal. We only retained reads where the last 20bp prior to the cleavage site or end of read were consistent (within a Levenshtein distance of 3) with the expected genomic sequence. We then obtained a quantification of proximal versus distal reads at each construct each sample and distal site.
Assembly: hg38
Supplementary files format and content: Text file where each row represents the number of proximal and distal reads observed for each construct within each sample, as well as information about each construct's native location and design.

extract_protocol:
48 hours post-transfection (7 days after original transduction with gRNAs), RNA was extracted using the Zymo DirectZol RNA purification kit with DNase I treatment following the manufacturer’s protocol (Zymo R2052). mRNA was isolated from 5 µg total RNA per sample using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490S).
mRNAs were reverse transcribed with SuperScript IV Reverse Transcriptase (Thermo Fisher 18090200) to generate cDNA following manufacturer instructions. The anchored poly dT primer for reverse transcription contained a Truseq Read 1 handle, an 8 bp sample barcode, and a unique molecule identifier (UMI) (TruseqR1-barcode-UMI-T18VN, see Supplementary Table 5 for primer sequences). After reverse transcription, RNA hydrolysis was performed using RNase H (Thermo Fisher 18021071) and then samples were purified using a DNA Clean & Concentrator-5 kit (Zymo D4013). Purified cDNA was amplified with KAPA HiFi HotStart ReadyMix (Kapa Biosystems 07958935001) using a forward primer containing additional Illumina adaptor sequences (P5-TruseqR1, 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC*T*C-3’) and reverse primer containing a sample-specific barcode (P7-index-NexteraR2) (). Amplification was monitored with qPCR so that the reaction could be stopped early to minimize PCR bias with the following cycling conditions: 98 °C for 3 min; 15 cycles of 98 °C for 20 s, 60°C for 20 s and 72°C for 1 min; followed by 72°C for 5 min. After amplification, samples were 1X SPRI purified. The MPRA library was sequenced using an Illumina NextSeq Mid-Output (300 cycle) kit: allocating 16 cycles to Read 1, and 200 cycles to Read 2.


title: MPRA library, NIUDT21 gB, replicate 1


title: HEK293FT, replicate 1 gRNA


title: 267, Hypothalamus, Ube3a2x, Male


title: 258, Prefrontal cortex, Ube3a2x, Male


title: 266, Prefrontal cortex, WT, Male


title: 262, Prefrontal cortex, WT, Female


title: MPRA library, NUDT21 gA, replicate 2


title: 262, Hypothalamus, WT, Female


title: 259, Prefrontal cortex, WT, Female


title: 253, Prefrontal cortex, Ube3a2x, Male


title: HEK293FT, replicate 2 HTO


title: MPRA library, NUDT21 gA, replicate 1


title: MPRA library, CSTF3 gA, replicate 2


title: MPRA library, CSTF3 gB, replicate 2


title: MPRA library, NT gA, replicate 2


title: MPRA library, NT gB, replicate 1


title: 251, Hypothalamus, WT, Male


title: MPRA library, NT gB, replicate 2


title: MPRA library, CSTF3 gB, replicate 1


title: MPRA library, NT gA, replicate 1


title: 258, Hypothalamus, Ube3a2x, Male


title: MPRA library, CSTF3 gA, replicate 1


title: 256, Prefrontal cortex, WT, Male


title: 253, Hypothalamus, Ube3a2x, Male


title: 251, Prefrontal cortex, WT, Male


title: R435, scRNAsea

city: Edmonton

first: Patrick

middle: E

last: MacDonald

state: AB

address: 6-040 Li Ka Shing Centre

institute: University of Alberta

description:
10X Genomics
Islets were isolated from pancreases of cadaveric human donors at the Alberta Diabetes Institute IsletCore using standard procedures. The isolated islets were cultured prior to experimental use or distribution in CMRL 1066 (Corning) supplemented with 0.5% BSA (Equitech-Bio), 1% insulin-transferrin-selenium (Corning), 100 U/mL penicillin/streptomycin (Life Technologies), and L-glutamine (Sigma-Aldrich) at 22°C with 5% CO2 at a typical seeding density of 225 IEQ/cm2. Following release from the ADI IsletCore, islets were typically cultured in DMEM (11885, Gibco) supplemented with L-glutamine, 110 mg/l sodium pyruvate, 10% FBS (12483, Gibco), and 100 U/ml penicillin/streptomycin (15140, Gibco) at 37°C with 5% CO2.

data_processing:
Demultiplexing, barcode reading, gene counting, and aggregation were performed by Cell Ranger version 6.1.2
Assembly: GRCh38 (Ensembl release 104)
Supplementary files format and content: Barcodes, features, and matrix files from Cell Ranger

source_name: islets

extract_protocol:
Islets were hand picked to minimize acinar tissue contamination, and transferred to a 35 mm dish containing islet culture media. The islets were then re-picked from the 35 mm dish, transferred to a centrifuge compliant tube, and spun down at 150g for 5 min at RT. Supernatant was discarded. To dissociate the islets, islet pellet was resuspended in 2 mL cell dissociation buffer, gently pipetted up and down to mix, transferred to a 35 mm dish, and incubated at 37°C for 2 minutes. Dissociation buffer can be supplemented/replaced with Accutase or Trypsin for more aggressive dissociation if needed. After 2 minutes, islet dissociation was intermittently monitored every 1-2 minutes using a light microscope, with gentle pipetting to aid dissociation. Once dispersion was complete, the cells were strained 2x through a Flomi 40 μm cell strainer to remove any clumps, dispensed into a centrifuge compliant tube, and spun down at 150g for 5 minutes. The cell pellet were resuspended in 1x Ca2+ Mg2+ Free PBS + 0.04% BSA for 10x Chromium Single Cell Applications, and a trypan blue assay was performed to confirm cell viability of >90%, along with cell counting to determine cell concentration of the resuspension.
Library construction was performed according to the manufacturer's instructions (10X Genomics Chromium NEXT GEM Single Cell 3' Gene Expression Kit v3.1). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in emulsion (GEM), on a 10X Genomics Chromium Controller. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contained an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: islets

value: Male

value: primary islet cells

tag: bmi

tag: diabetesstatus

value: Non-diabetic

tag: age


title: MC-LR_6

city: Piscataway

first: Yingzheng

last: Wang

state: New Jersey

address: 170 Frelinghuysen Rd, Rm 406

department: Pharmacology and Toxicology

institute: Rutgers University

data_processing:
The potential rDNA and mtDNA contaminants were filtered using Bowtie 2.
The filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner.
Raw read counts were achieved by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm
Differential expression analysis was performed by using the DEseq2(R)
Assembly: whole mouse genome assembly-mm10
Supplementary files format and content: excel file with whole gene expression list

source_name: Ovary

extract_protocol:
Total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to manufacturer’s instructions.
The library preparation was performed by Novogene.

tag: tissue

value: Ovary

value: female

value: Follicle

value: 10 uM MC-LR


title: 245, Hypothalamus, WT, Male

value: FVB/NJ

value: adult

value: WT


title: K9

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

data_processing:
fastq.gzC was used to check quality of reads
Hisat2 and featureCounts was used to align and count reads.
DeSeq2 was used for differential expression analysis.
Assembly: hg18
Supplementary files format and content: Normalized read counts by DESeq2

source_name: Leiomyoma

extract_protocol:
TRIzol
mRNA-seq was performed by Novogene Corporation Inc.

value: Leiomyoma

value: Vehicle


title: K13


title: K6


title: MC-LR_3

tag: cell type


title: 245, Prefrontal cortex, WT, Male

value: Prefrontal cortex

tag: genotype

value: M


title: 238, Hypothalamus, Ube3a2x, Male

value: Hypothalamus


title: R434, scRNAseq

value: Female


title: R433, scRNAseq

value: islets


title: MC-LR_7

tag: treatment


title: 238, Prefrontal cortex, Ube3a2x, Male


title: Control_6


title: K12


title: MC-LR_5


title: K11


title: Control_4


title: MC-LR_4


title: iPSC1_D21

city: ShenZhen

first: Ran

last: YI

state: Guangdong

address: 1068 Xueyuan Avenue

department: The Brain Cognition and Brain Disease Institute

institute: Shenzhen Institute of Advanced Technology，Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The genes, barcodes, matrix files were made using the Cell Ranger software (version 7.0.0).
Assembly: A Homo sapiens transcriptome (GRch38) reference containing puromycin, rtTA, and the mouse Sox9 and Nfib genes was constructed using cellranger mkref pipeline.
Supplementary files format and content: Tab-separated values files and matrix files from cell ranger output.
Supplementary files format and content: CellLines.h5ad: Merged data of time course results (D0, 1, 3, 8, 14, 21).
Supplementary files format and content: TimeCourse.h5ad: Merged data of iPSC1 and iPSC2 cell lines.

extract_protocol:
On the day of collection, cultured cells were washed with DPBS and dissociated with 200 µL Accutase per well in a 6-well plate for 10 min at 37°C. The progression of cell detachment was constantly monitored under a microscope. Cells suspensions were collected into 1.5-mL tubes and centrifuged at 300 × g for 5 min to remove as much Accutase as possible without disturbing the cell pellets. The cells were resuspended in DPBS with 0.04% filtered Bovine Serum Albumin and 60 U/mL RNasin Plus Ribonuclease Inhibitor (Promega, N2615). After quantification by a Countess Automated Cell Counter (Invitrogen, C10281), cell suspensions were diluted to 700–1,200 cells/µL on ice for subsequent scRNA-seq library preparation.
The Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 & Gel Beads Kit (10x Genomics) were used according to the manufacturer’s guidelines. Briefly, single-cell suspensions, gel beads and partitioning oil were loaded onto the 10x Genomic Chromium Chip (Next GEM chip G) and subjected to the 10x Chromium Controller device during which single cells were encapsulated with individual Gel Beads-in-emulsion (GEMs). The number of cells targeted in each experiment was 10,000. Captured cells were lysed and the transcripts inside the individual GEMs were barcoded through reverse transcription. Constructed 10x libraries were quantified using a Qubit 4 Fluorometer (Invitrogen) with a Qubit 1x dsDNA HS Assay Kit (Invitrogen). Quality control for the 10x libraries was performed on a Fragment Analyzer 5200 (Agilent) with a DNF-474 HS NGS Fragment Kit (Agilent).

value: iPSC derived cells


title: MC-LR_2


title: K4


title: Control_2


title: Mono_iPSC1_D8

description: 10x Genomics


title: MC-LR_1


title: Control_8


title: K3


title: Mono_iPSC1_D3

description: 10x Genomics


title: K1


title: Mono_iPSC1_D1

description: 10x Genomics


title: Mono_iPSC1_D0

description: 10x Genomics


title: Control_7


title: thymus, WT

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 6000 or less than 1000, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: immune cells from thymus

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: thymus

value: immune cells


title: in situ Hi-C of DSMZ’s NB-4 cell line with no stimulation

city: Mitaka-shi

first: Tetsuko

last: Kobayashi

state: Tokyo

country: Japan

institute: Kyorin University

data_processing:
FASTQ files were processed through the Juicer software package.
Reads were aligned to the genome using BWA, and only reads with a MAPQ score >=30 were used for the subsequent analyses.
Compartments were identified at a 1 Mb resolution using Juicer Tool’s eigenvector program.
Topologically associating domains (TADs) were identified using Juicer’s Arrowhead software and chromatin loops were called using Juicer’s HiCCUPS software, both were run with default parameters.
Juicer’s output files were processed through Active Motif’s proprietary analysis program which generate Excel tables containing detailed information on gene annotations and the location of compartments, TADs, and loops.
Assembly: GRCh38/hg38
Supplementary files format and content: .fastq.gz, .hic, .bedpe, .bed.gz, .bed.gz.tbi, .txt.gz, .txt.gz.tbi

source_name: bone marrow

growth_protocol: 90 % RPMI 1640 + 10 % h.i. FBS. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Sample was processed using Arima-HiC Kit, Library Preparation using Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit [Arima A510008] .
Sample was lysed and crosslinked followed by restriction enzyme digestion and ligation. Ligated DNA was purified, sheared, and used for library generation using Active Motif Next Gen DNA Library Kit [Active Motif 53216].

value: bone marrow

value: acute promyelocytic leukemia

value: no treatment


title: iPSC2_D21

description: 10x Genomics


title: Human mini-colons collected at day 14 and day 21 and control organoids, biological rep 1 to 3, hashtag oligos library 2

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

description:
Cells injected in 10XG chip lane 2 - hashtag library
counts.tsv.gz
metadata.tsv.gz
barcodes.tsv.gz
features.tsv.gz
Minicolons_HTO2

data_processing:
The reads were aligned to hg38 with Cell Ranger v.6.0.1.
Raw count matrices were imported in Seurat 4.3.0 using RStudio 2022.12.0+353 and single live cells were selected on the basis of the number of detected genes (approximately 2,500–5,000) and fraction of mitochondrial genes (around 0.05–0.15). Demultiplexing of cells to their original sample-of-origin and identification of cross-sample doublets was performed using HTODemux function. The number of cells after filtering was 2050 (day 14 mini-colons), 5115 (day 21 mini-colons), 1475 (organoids matrigel), 1076 (organoids 20% collagen). The data were normalized to 10,000 counts per cell, and log1p-transformed using the natural logarithm (referred to as log(expression)) for further analysis (but the raw counts are given in the processed data file).
Dimensionality reduction was computed by scaling with regression of mitochondrial and RNA content, followed by PCA, followed by harmony alignment of the conditions, followed by UMAP, using Seurat.
Graph-based Louvain clustering (resolution of 1) using the FindClusters function of Seurat yielded 7 clusters that were assigned to known cell types by manual examination of differentially expressed genes and expression of canonical cell type markers.
Assembly: hg38
Supplementary files format and content: Matrix of raw counts (matrix market sparse matrix, same format as cell ranger)
Supplementary files format and content: Gene names associated with the count matrix (one per line, same format as cell ranger)
Supplementary files format and content: Cell barcodes associated with the previous matrix (one per line, same format as cell ranger)
Supplementary files format and content: Metadata associated with the cells as a tab separated values data frame. Includes QC statistics, dataset (10XG microfluidic chip lane), biological rep, cell types, hashtag oligo raw counts and assignments as well as dimensionality reductions.

source_name: Colon

growth_protocol: Human mini-colons were seeded in bioengineered chips. From day 7 apical medium was switched to ENR and basal medium to WNRGIFA+NRG1. Human mini-colons were maintained with daily perfusions to remove shed dead cells from the lumen and were collected at day 14 and day 21 of culture for scRNAseq.

extract_protocol:
14-day-old and 21-old human mini-colons in biological triplicates were extracted from the chips and dissociated to single cells using 4 mg/mL Protease VIII (Sigma) in dPBS containing 10 μM Y-27632 on ice for approximately 45 min with trituration using a P1000 micropipette every 10 minutes. Following one washing step in PBS+2% BSA (Gibco), cell suspensions were incubated for 20 min on ice with 6 different TotalSeq-C™ hashtag antibodies (1:500 dilution; A0251-A0256, Biolegend) that were used to tag the individual samples (three day 14 mini-colons and three day 21 mini-colons). Following incubation the samples were washed 3 times in PBS+2% BSA. All cell suspensions were resuspended in human organoid base medium, recounted, filtered through 20 um strainer and pooled together to achieve a uniform concentration of 2000 cells/ul in total volume of 22.5 ul.
After pooling and filtering (20 μm) the cell suspensions from six mini-colons, All cell suspensions were recounted to achieve a uniform concentration of 2000 cells per microliter before pooling for 10× capture. the single-cell sequencing library was constructed using 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) according to the manufacturer’s instructions.

treatment_protocol: Human mini-colons were differentiated in differentiation medium as indicated in the manuscript.

value: Colon

value: Organoids

value: Epithelium

value: Healthy

value: Control

tag: hashtag name

value: MiniColon_day14_1:A0251; MiniColon_day14_2:A0252; MiniColon_day14_3:A0253; MiniColon_day21_1:A0254; MiniColon_day21_2:A0255; MiniColon_day21_3:A0256; Organoids_Matrigel_1:A0257, Organoids_Matrigel_1:A0258, Organoids_Matrigel_3:A0259, Organoids_20%collagen_1:A0260, Organoids_20%collagen_2:A0262, Organoids_20%collagen_3:A0263

tag: hashtag barcode

value: MiniColon_day14_1:GTCAACTCTTTAGCG; MiniColon_day14_2:TGATGGCCTATTGGG; MiniColon_day14_3:TTCCGCCTCTCTTTG; MiniColon_day21_1:AGTAAGTTCAGCGTA; MiniColon_day21_2 AAGTATCGTTTCGCA; MiniColon_day21_3:GGTTGCCAGATGTCA, Organoids_Matrigel_1:TGTCTTTCCTGCCAG, Organoids_Matrigel_2:CTCCTCTGCAATTAC, Organoids_Matrigel_3:CAGTAGTCACGGTCA, Organoids_20%collagen_1:ATTGACCCGCGTTAG, Organoids_20%collagen_2:TAACGACCAGCCATA, Organoids_20%collagen_3:AAATCTCTCAGGCTC


title: Unpolarized BMDMs exosomes, biol rep 3

city: Taipa, Macau

first: Ruohan

last: Lou

address: Avenida da Universidade

country: Macau

institute: University of Macau

data_processing:
Fastx-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
The 3 'connector sequence in reads was removed, and the reads without inserted fragments were removed due to the joint self-connection, etc.
Cut the base with low quality of 3 'end sequencing (mass value less than 20).
Reads containing unknown base N were removed.
Remove reads that are too short in length (< 18nt).
Remove excessively long reads(> 32nt).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files

source_name: Exosomes

growth_protocol: BMDMs were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 10% L929 cell supernatant in humidified atmosphere containing 5% CO2 at 37 °C for 7 days.

extract_protocol:
RNA was harvested using miRNeasy kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for miRNA-seq were prepared using Illumina TruSeq Small RNA Library Kit following manufacturer's protocols.

treatment_protocol:
BMDMs were treated with 20 ng/mL interferon-γ (IFN-γ, Peprotech) and 100 ng/mL lipopolysaccharide (LPS, Sigma) for 1 day to differentiate into M1-like macrophages.
BMDMs were treated with 40 ng/mL Interleukin-4 (IL-4, Peprotech) for 1 day to differentiate into M2-like macrophages.

value: Exosomes

value: Bone marrow derived macrophages


title: spleen, CKO

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 5000 or less than 1000, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with NormalizeData function.
Merge function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (matrix.mtx, features.tsv, barcodes.tsv)

source_name: immune cells from spleen

value: RPA1 conditional knockout

value: spleen


title: Control_5

value: Ovary

value: female

value: Follicle

value: Vehicle


title: Unpolarized BMDMs exosomes, biol rep 2


title: Mono_iPSC1_D21

description: 10x Genomics

tag: cell line

value: iPSC derived cells


title: Pro-inflammatory BMDMs exosomes, biol rep 3

value: Pro-inflammatory differentiation


title: Control_3


title: Pro-inflammatory BMDMs exosomes, biol rep 2


title: Pro-inflammatory BMDMs exosomes, biol rep 1


title: RB9-MOLM14.HSN748

city: Indianapolis

first: Baskar

last: Ramdas

state: Indiana

address: 1044 West Walnut Street

department: Wells Center for Pediatric Research

institute: Indiana University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
Reads mapped to human genome using STAR, Uniquely mapped sequencing reads were assigned human genes and subject to differential analysis
Supplementary files format and content: differential analysis result with raw counts

growth_protocol: MOLM14 cells were grown in RPMI supplemented with 10% FBS

extract_protocol:
RNA was harvested using TRIZOL reagent. RNA with Agilent Bioanalyzer RIN of > 6 were selected for library preparation.
Library preparation was performed using New England Biolabs Single Cell/Low Input RNA Library Prep Kit for Illumina.

treatment_protocol: MOLM14 cells were incubated in the presence  of DMSO and 2nM HSN748 for 24 hours  HSN748 for 24 hours and extracted RNA to assess the effect of HSN748 on the gene expression changes through  RNASeq analysis.

value: FLT3 ITD


title: Anti-inflammatory BMDMs exosomes, biol rep 2

value: Anti-inflammatory differentiation


title: WT

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 4000 or less than 1000, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with NormalizeData function.
Merge function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell (gene-barcode counts, gene file, and cell barcode file)

source_name: immune cells from lymph nodes

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

tag: strain background

tag: genotype/variation

value: wild type

value: Lymph nodes


title: RB8-MOLM14.HSN748


title: RB7-MOLM14.HSN748


title: 96h

city: Seoul

first: Yong Kwon

last: Chae

address: Kyungheedaero 26

country: South Korea

institute: Kyung Hee University Dental Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: periodontal ligament

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: periodontal ligament


title: thymus, Rpa1 KO

value: Rpa1 conditional knockout

value: thymus

value: immune cells


title: 48h


title: CKO


title: tumor treated rep1

city: Beijing, China

first: Guojun

last: Li

address: 88 Kechuang Sixth Street, Beijing

institute: Chinese Academy of Sciences

description: PDX mice

data_processing:
The obtained sequencing data were subjected to quality control filtering using the NGSQCToolkit (v2.3.3) to eliminate reads with low quality bases and reads containing sequencing adapters.
The clean reads were then aligned to the reference genome hg19 using Bowtie software (version 2.2.4) with default parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: tumor

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (Qiagen Inc., Germantown, USA).
RNA libraries were constructed using the TruSeq RNA Exome kit (Illumina, Inc., San Diego, CA, USA) following manufacturer's protocols.

treatment_protocol: The G2 group was treated with JPHTF to observe tumor size compared to the untreated control group (G1).

value: tumor

value: human colorectal cancer cell

value: carring NRAS mut

value: JPHTF treatment


title: Human mini-colons collected at day 14 and day 21 and control organoids, biological rep 1 to 3, hashtag oligos library 1

description:
Cells injected in 10XG chip lane 1 - hashtag library
counts.tsv.gz
metadata.tsv.gz
barcodes.tsv.gz
features.tsv.gz
Minicolons_HTO1

value: Colon

value: Organoids

value: Epithelium

value: Healthy

value: Control

value: MiniColon_day14_1:A0251; MiniColon_day14_2:A0252; MiniColon_day14_3:A0253; MiniColon_day21_1:A0254; MiniColon_day21_2:A0255; MiniColon_day21_3:A0256; Organoids_Matrigel_1:A0257, Organoids_Matrigel_1:A0258, Organoids_Matrigel_3:A0259, Organoids_20%collagen_1:A0260, Organoids_20%collagen_2:A0262, Organoids_20%collagen_3:A0263

value: MiniColon_day14_1:GTCAACTCTTTAGCG; MiniColon_day14_2:TGATGGCCTATTGGG; MiniColon_day14_3:TTCCGCCTCTCTTTG; MiniColon_day21_1:AGTAAGTTCAGCGTA; MiniColon_day21_2 AAGTATCGTTTCGCA; MiniColon_day21_3:GGTTGCCAGATGTCA, Organoids_Matrigel_1:TGTCTTTCCTGCCAG, Organoids_Matrigel_2:CTCCTCTGCAATTAC, Organoids_Matrigel_3:CAGTAGTCACGGTCA, Organoids_20%collagen_1:ATTGACCCGCGTTAG, Organoids_20%collagen_2:TAACGACCAGCCATA, Organoids_20%collagen_3:AAATCTCTCAGGCTC


title: Mono_iPSC1_D14

description: 10x Genomics

value: iPSC derived cells


title: Human mini-colons collected at day 14 and day 21 and control organoids, biological rep 1 to 3, gene expression library 2

description:
Cells injected in 10XG chip lane 2 - gene expression library
counts.tsv.gz
metadata.tsv.gz
barcodes.tsv.gz
features.tsv.gz
Minicolons_GEX2


title: Control_1

value: Ovary

value: female

value: Follicle

value: Vehicle


title: Unpolarized BMDMs exosomes, biol rep 1

value: Exosomes

value: Bone marrow derived macrophages


title: RB2-MOLM14.DMSO

value: FLT3 ITD

value: DMSO


title: spleen, WT

value: WT

value: spleen

value: immune cells


title: RB1-MOLM14.DMSO


title: tumor treated rep3

description: PDX mice

value: tumor

value: human colorectal cancer cell

value: carring NRAS mut

value: JPHTF treatment


title: Human mini-colons collected at day 14 and day 21 and control organoids, biological rep 1 to 3, gene expression library 1

description:
Cells injected in 10XG chip lane 1 - gene expression library
counts.tsv.gz
metadata.tsv.gz
barcodes.tsv.gz
features.tsv.gz
Minicolons_GEX1

value: Colon

value: Organoids

value: Epithelium

value: Healthy

value: Control

value: MiniColon_day14_1:A0251; MiniColon_day14_2:A0252; MiniColon_day14_3:A0253; MiniColon_day21_1:A0254; MiniColon_day21_2:A0255; MiniColon_day21_3:A0256; Organoids_Matrigel_1:A0257, Organoids_Matrigel_1:A0258, Organoids_Matrigel_3:A0259, Organoids_20%collagen_1:A0260, Organoids_20%collagen_2:A0262, Organoids_20%collagen_3:A0263

value: MiniColon_day14_1:GTCAACTCTTTAGCG; MiniColon_day14_2:TGATGGCCTATTGGG; MiniColon_day14_3:TTCCGCCTCTCTTTG; MiniColon_day21_1:AGTAAGTTCAGCGTA; MiniColon_day21_2 AAGTATCGTTTCGCA; MiniColon_day21_3:GGTTGCCAGATGTCA, Organoids_Matrigel_1:TGTCTTTCCTGCCAG, Organoids_Matrigel_2:CTCCTCTGCAATTAC, Organoids_Matrigel_3:CAGTAGTCACGGTCA, Organoids_20%collagen_1:ATTGACCCGCGTTAG, Organoids_20%collagen_2:TAACGACCAGCCATA, Organoids_20%collagen_3:AAATCTCTCAGGCTC


title: tumor treated rep2

description: PDX mice


title: Anti-inflammatory BMDMs exosomes, biol rep 3

value: Exosomes

value: Bone marrow derived macrophages

value: Anti-inflammatory differentiation


title: CS12, YS, scRNA-seq

first: Guoju

last: You

state: Beijing

address: Shuangqing Road

institute: Tsinghua University

data_processing:
The Cell Ranger software pipeline (version 4.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes, map reads to the human reference genome,and filter data for valid cell barcodes and unique molecular identifiers
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every  cell

source_name: yolk sac

extract_protocol:
7-AAD– cells from one CS10 YS (in vivo) were sorted for scRNA-seq (10X Genomics). All generated CD45+ cells from cultured CS12b-YS were sorted for scRNA-seq (10X Genomics)
Libraries were prepared with Chromium Single cell 3' Reagent v2 Kits accoding to the manufacturer's instructions.

value: yolk sac

value: Hematopoietic cells

value: WT

value: in vitro culture


title: Anti-inflammatory BMDMs exosomes, biol rep 1


title: SH, scRNAseq

status: Public on Jun 14 2024

city: Wuhan

first: Mengyuan

state: Hubei

address: NO.1277 JieFang Avenue

department: Department of Critical Care Medicine

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: 10X Genomics

data_processing:
Sequencing data were aligned to the Macaca fascicularis 5.0 genome by STAR （v2.7.4a）. Counts of aligned UMI were used to quantify downstream gene expression levels. For scRNA-seq data, cells with less than 200 genes and top 10% of cells with the highest number of genes were removed. Additionally, cells with more than 15% mitochondrion reads were filtered out. We applied DoubletFinder to remove potential doublets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
The small intestines were carefully cleaned and opened longitudinally, washed with PBS, cut into 1.0–1.5 cm pieces and incubated in 20 ml of HBSS/10 mM HEPES, 8% FBS, 4 mM EDTA, and 0.5 mM dithiothreitol at 37 ℃ with constant agitation for 15 minutes twice. After washing with Ca2+ /Mg2+ -PBS to remove EDTA, the remaining pieces of small intestines were minced and digested in RPMI-1640 medium containing fetal bovine serum (FBS), collagenase Ⅳ (0.1 mg/mL) and DNase I (0.1 mg/mL) at 37 ℃ for 40 minutes. The tissue digestion was filtered through a 40 μm cell strainer, following by centrifugation at 400g for 5 min at 4 °C. CD45+ Cells were collected using FACS, and resuspended in PBS. Cell concentration was adjusted to 1000 cells /μl for library preparation.
Prepared single-cell suspensions were loaded on a chip of the Single Cell 3' Chip Kit (10X Genomics) and subjected to a Chromium Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsions (GEMs). cDNA amplification and library construction underwent using a Chromium Single Cell 3' Reagent Kits v2 (10x Genomics).

value: small intestine

value: CD45+ cells

value: sham-operated


title: tumor untreated rep3

description: PDX mice

value: tumor

value: human colorectal cancer cell

value: carring NRAS mut

value: Untreated control


title: RB3-MOLM14.DMSO

value: FLT3 ITD

value: DMSO


title: Pig heart tissue, Day28, Sample 1, Sequencing by CD Genomics

city: Scottsdale

first: Wuqiang

last: Zhu

state: AZ

address: 13400 E shea blvd

department: Cardiovascular Medicine

institute: Mayo Clinic

data_processing:
Assembly: Sscrofa10.2
Cross sample quality control check using metrics like percentage of uniquely mapped reads and GC content.
QC visualization was done using MultiQC (v1.11)
Index generation and paired-end alignment of each sample were performed using STAR (v2.7.9a).
Ensemble's reference genome Sscrofa10.2 was used for alignment.
circRNAs were called using CIRCexplorer2
Supplementary files format and content: tab delimited rawcounts files(txt). Each row is circRNA, and each column is a sample( total of 3 files, one from each batch)
Supplementary files format and content: tab seperated value(tsv) of miRNA expression count. Each row is a miRNA, and each column is a sample
Supplementary files format and content: tab seperated value(tsv) of mRNA expression count. Each row is a mRNA, and each column is a sample
Supplementary files format and content: Compressed zip files from CircAtlas databased, used for circRNA naming annotation.

organism: Sus scrofa

source_name: heart

growth_protocol: neonatal pigs were fed normally

extract_protocol:
The RNeasy Mini Kit (Qiagen) was used to extract total RNA from pig heart tissue
Construction of the library was performed according to the instructions provided by the manufacturer for the NEBNext Ultra II RNA (Directional) kit.
Plant and Animal Whole Transcriptome Sequencing

treatment_protocol: Heart tissue samples were harvested from neonatal pigs on days 1, 3, 7, and 28 after birth.

value: heart


title: Pig heart tissue, Day7, Sample 2, Sequencing by CD Genomics


title: Pig heart tissue, Day7, Sample 1,  Sequencing by CD Genomics


title: Pig heart tissue, Day7, Sample 3, Sequencing by CD Genomics


title: tumor untreated rep2

description: PDX mice


title: Pig heart tissue, Day1, Sample 3, Sequencing by CD Genomics


title: CS10, YS, scRNA-seq

description: 7-AAD– cells from one CS10 YS (in vivo)

value: in vivo


title: tumor untreated rep1

description: PDX mice


title: Pig heart tissue, Day1, Sample 1, Sequencing by CD Genomics


title: CS12, YS, CITE-seq

description: All generated CD45+ cells from cultured CS12a-YS, CS12a-EP, CS12a-YS (CD45+CD127+) and CS12a-YS (CD45+CD127–)

data_processing:
The Cell Ranger software pipeline (version 4.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes, map reads to the human reference genome,and filter data for valid cell barcodes and unique molecular identifiers
Assembly: hg19
Supplementary files format and content: Cellranger count output files: Matrix table with raw gene counts for every gene and every  cell

extract_protocol:
The generated cells from cultured CS12a-YS, CS12a-EP, CS12a-YS (CD45+CD127+) and CS12a-YS (CD45+CD127–) were sorted for CITE-seq.
Libraries were prepared with Chromium Single cell 3' Reagent v2 Kits accoding to the manufacturer's instructions. Antibody-bound oligos acted as synthetic transcripts that were captured by using 10X Chromium Next GEM Single Cell 3′ Kit v3.1 as per standard protocol and sequenced on the Illumina Novaseq 6000 system.


title: intestinal organoids from control Adipfl/fl mice(WT)

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

data_processing:
Library preparation and transcriptome sequencing on an MGISEQ-2000 platform were performed to generate 100-bp paired-end reads.
MGISEQ-2000 was used in counting the numbers of read mapping to each gene, and fragments per kilobase of transcript per million fragments mapped (FPKM) of each gene were calculated.
Data were analyzed after choosing an analysis tool on http://biosys.bgi.com. FC (fold change) was used to describes the difference of gene expression
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: intestine

growth_protocol: The prepared DMEM/F12-ENR medium (50 ng/ml EGF, 100 ng/ml Noggin and 500 ng/ml R-spondin) was added, and changed every other day.

extract_protocol:
Fresh small intestinal (5–10 cm length) was cut longitudinally, and flushed three times with cold PBS containing penicillin–streptomycin. After the villi were gently scraped with a sterile cover glass, the intestine tissue was cut into small pieces. After 2 mM EDTA incubation for 30 min on ice, crypts were dispersed by pipette, and then filtered using 70 mm cell strainer and collected in a tube, and counted and mixed with Matrigel
Total RNAs from cells were extracted according to the manual of TRIzol®reagent (Invitrogen, Shanghai, China)

value: intestine

value: Intestinal epithelial cells

value: Adipfl/fl


title: 0h

value: periodontal ligament