title: B6.ltbi.none.naive.0.JN3.5 (RNA-seq)

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description:
rawCountsWBRNAseq.tsv
Sample 28

data_processing:
For libraries prepared with the SMARTer Stranded Total RNA-Seq Kit (v2) - Pico Input Mammalian (samples 7-12) the first three nucleotides of R2 (v2 kit) were removed as described in the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual (063017)
Read ends consisting of 50 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2016-08-24) RNA-seq samples: gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1. ATAC-seq samples: gsnap -N 0 --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --pairmax-dna=2000
RNA-seq: Concordantly mapping read pairs that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
ATAC-seq: Start and end positions of concordant, uniquely mapping sequences were adjusted to extend 4 and 5 base pairs respectively to account for transposase adapter insertion (see Buenrostro et al. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. 11, 21.29.1–21.29.9 (John Wiley & Sons, Inc., 2001).  Peak calling was performed with MACS2 (2.1.0) using the start and end locations of the pairs to define fragment lengths. “Blacklisted” regions of known artificially high signal as defined by the ENCODE project were filtered out of peak regions (https://sites.google.com/site/anshulkundaje/projects/blacklists). Bigwig files were generated by running MACS256 (https://github.com/taoliu/MACS) peak calling and outputting a normalized bedgraph file followed by file conversion using the bedGraphToBigWig program (genome.ucsc.edu).
Genome_build: mm10 + Mtb H37Rv
Supplementary_files_format_and_content: rawCountsAMRNAseq.tsv contains the raw counts for samples 1-12 generated by subRead, tab-separated
Supplementary_files_format_and_content: B6.[cntl|LTBI].none.naive.0.JN2.[1-3].bw are bigwig files containing ATAC-seq pileups for samples 13-18 generated as described above.
Supplementary_files_format_and_content: rawCountsWBRNAseq.tsv contains the raw counts for samples 19-28 generated by subRead, tab-separated

source_name: Whole-blood

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
For RNA-seq, cDNA libraries were constructed and amplified using the SMART-Seq v4 ultra low RNA prep (samples 1-6, 19-28) or the SMARTer Stranded Total RNA-Seq Kit (v2) - Pico Input Mammalian (samples 7-12) per the manufacturer’s instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end). For ATAC-seq, libraries were prepared using the protocol described by Chen et al, Nat. Methods 13, 1013–1020 (2016) and then sequenced on an Illumina NextSeq (2 x 75, paired-end).

tag: ltbi status

value: ltbi

tag: infectious challenge

tag: infection status

value: naive

tag: time infected

tag: experiment label

value: Whole-blood


title: dCAP2-14

status: Public on Jun 08 2020

type: SRA

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

country: USA

institute: University of Southern California

library_source: genomic

data_processing:
Library strategy: NG Capture-C
RNA-seq analysis. The RNA-seq analysis pipeline was adapted according to the publication (Trapnell et al., 2012). Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1) and fastq_trimmer_by_quality (window size 3; min score >= 20). Mapping. Tool: TopHat2 (Galaxy Version 2.1.1). Quantification and differentially expressed gene analysis. Tools: Cufflinks package (Trapnell et al., 2010)–including Cufflinks (Galaxy Version 2.2.1.2), Cuffmerge (Galaxy Version 2.2.1.1), Cuffquant (Galaxy Version 2.2.1.1), and Cuffdiff (Galaxy Version 2.2.1.3). Deeptools bamCoverage (Galaxy Version 3.1.2.0.0) was used to normalize the reads to 1X sequencing depth and wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files of read coverages.
ChIP-seq analysis. Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1), fastq_quality_filter (Galaxy Version 1.0.2), fastq_trimmer_by_quality (Galaxy Version 1.1.1; window size 3; min score >= 20). Mapping. Tool: bowtie2 (Galaxy Version 2.3.4.2; genome: UCSC galGal4, --very-sensitive). Filtering. Tools: samtool_filter2 (Galaxy Version 1.8; -q 1), samtools_sort (Galaxy Version 2.0.1), samtools_rmdup (Galaxy Version 1.0.1; BAM is single-end). Peak-calling. Tools: MACS2 (Galaxy Version 2.1.1.20160309.4; for H3K27ac-ChIP, --gsize 1065365425 --nomodel --extsize 147 --bdg --broad --broad-cutoff 0.1; for CTCF/KLF-ChIP, --gsize 1065365425 --nomodel --extsize value obtained from macs2_predictd tool) and macs2_bdgcmp (Galaxy Version 2.1.1.20160309.0; -m FE and -m logLR -p 0.00001). To normalize MACS2 results from different libraries for comparison, we followed a “Build Signal Track” instruction from https://github.com/taoliu/MACS/wiki/Build-Signal-Track#Run_MACS2_bdgcmp_to_generate_foldenrichment_and_logLR_track.  Convert format. Tool: wig_to_bigWig (Galaxy Version 1.1.1).
NG Capture-C analysis. Double Capture-C results were analyzed according to the publication (Davies et al., 2016). The analysis pipeline was well documented and can be downloaded from “https://github.com/Hughes-Genome-Group/captureC/releases/download/VS2.0/UserManualforCaptureCanalysis.pdf". In brief, 1) download the CaptureC analyser package including CCanalyser3.pl, dpngenome3_1.pl, dpnII2E.pl from “https://github.com/Hughes-Genome-Group/captureC/releases", 2) generate in silico DpnII digested chicken genome ver. Ensemble galGal4 Release 72 with alpha and beta keratins, 3) perform adapter trimmer using the tool trim_galore (Dr. Felix Krueger at the Babraham Institute), 4) Merge overlapping reads by using the tool FLASH (Magoc and Salzberg, 2011), 5) in silico DpnII digest the FLASH-merged reads; 6) install Bowtie 1.2 (Langmead et al., 2009), 7) build up bowtie index using the original genome used in the Step 2, 8) align digested FLASH-merged reads (output of Step 5) using Bowtie1.2, and 9) run CCanalyser3.pl. wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files from wig files of CCanalyser3 outputs.
Genome_build: UCSC Genome Browser assembly ID: galGal4
Supplementary_files_format_and_content: Bigwig files were generated using the wig/bedgraph_to_bigwig tool. Detail processes of RNA-seq, ChIP-seq, and NG Capture-C are described above.

molecule: genomic DNA

organism: Gallus gallus

source_name: adult dorsal feather barb branch

growth_protocol: White Leghorn chicken eggs were used. Eggs were incubated in a humidified egg incubator with an automatic egg turner.

extract_protocol:
Please find detailed protocols for ChIP and Capture-C DNA preparaion in Methods of this publication. RNA extraction for RNA-seq: Total RNAs of indicated tissues were extracted followed by the standard Trizol extraction protocol (Invitrogen, Cat.15596026). ChIPed-DNA preparation for ChIP-seq: The protocol was adapted from Dr. Ruchi Bajpai’s laboratory (Bajpai et al., 2010). 3C library preparation for NG Capture-C: The protocol was adapted from Dr. Wange Lu’s laboratory (Davies et al., 2016; Davies et al., 2017).
For RNA-seq library preparation: TruSeq RNA Prep Kit v2 (Illumina, RS-122-2001/-2002). For ChIP-seq library preparation: NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs, Cat. E7442S), NEBNext Ultra Ligation Module (New England Biolabs, Cat. E7445S), and KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Cat. KK2601). For NG Capture-C library preparation: 5 µg of sheared 3C-DpnII DNA was used in adaptor ligation for pre-capture library using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, Cat. E6040). Adaptors were from NEBNext Multiplex Oligos for Illumina (NEB, Cat. E7500). The indexed 3C DNA was amplified using a primer pair of P5 (5’-aatgatacggcgaccaccga) and P7 (5’-caagcagaagacggcatacgagat) and purified using 1.8X AMPure XP beads. To perform the first capture, SeqCap EZ Hybridization and Wash Kit (Roche, Cat. 05634261001) was used. For one library, the indexed sequencing library, 5 µg of a Cot-1 DNA equivalent chicken Hybloc DNA (Applied Genetics Lab, Cat. CHB), 1 µl of 1xGen Universal Blocking Oligo—TS-p5 (1 nmole/µl), and 1 µl of 1xGen Universal Blocking Oligo—TS-p7(6nt) (1 nmole/µl) were mixed well and dried completely in a low retention PCR tube (Axygen, Cat. PCR-02-L-C). The dried pellet was then resuspended in Nimblegen Hybridization Buffer and Component A, mixed with 2 µl of a capture probe pool (3 pmole in total), and incubated for hybridization at 47℃ for 72 hours. After the first hybridization, biotinylated-probe-hybridized DNA (captured DNA) was mixed with 40 µl of prepared streptavidin magnetic beads (Invitrogen, Cat. 65001) and incubated at 47℃ for 45 min. The mixture was further washed using the SeqCap Wash Kit. The captured DNA was then purified using 1.8X AMPure XP beads and eluted in final 44 µl of nuclease-free water and amplified using the P5/P7 primer pair for 12 cycles. This 1st-captured DNA was finally cleaned up with 1.8X AMPure XP beads and eluted in 25 µl of water. To perform the second capture, the 1st-captured DNA was mixed with components described in the first capture part and incubated for hybridization at 47℃ for 24 hours. The double-captured DNA was then washed, pulled down by using the streptavidin beads, purified, amplified, and cleaned up as described before.

treatment_protocol: No treatment

tag: chip antibody

tag: skin region

value: dorsal back

tag: age

value: Day 23 plus 6-week feather regeneration

tag: skin/appendage layer

value: feather barb branch


title: B6.cntl.none.naive.0.JN3.5 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 27

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

value: cntl

tag: tissue


title: TAP_untagged_10xteto-ade6_rep1

city: Boston

first: Danesh

last: Moazed

state: MA

address: 240 Longwood Avenue, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

data_processing:
Pooled libraries were demultiplexed using Geneious and barcode sequences were trimmed from the reads.
Reads were aligned to the reference genome using bowtie with default parameters.
The mapped reads were normalized to counts per million using Deeptools and visualized in IGV.
Genome_build: ASM294v2
Supplementary_files_format_and_content: The mapped reads were normalized to counts per million using Deeptools, saved as bw files and visualized in IGV.

organism: Schizosaccharomyces pombe

growth_protocol: Yeast cultures were grown in rich (YES) medium to OD600 densities of 1-2.

extract_protocol:
50 OD600 units of cells per ChIP were fixed with 1% formaldehyde for 15min, quenched with glycine and collected. Cell pellets were resuspended in lysis buffer (50mM  Hepes/KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X-100, 0.1% Na Deoxycholate, 0.1% SDS, 1mM PMSF, supplemented with protease inhibitors) and cells were lysed by the glass bead method, using MagNA Lyser (Roche) (3 pulses of 90s at 4500rpm, 1 pulse of 45s at 5000rpm). The lysates were sonicated by 3 pulses of 20s (amplitude 40%) in a Branson microtip sonifier with intermittent cooling on ice, to a fragment distribution of 200-1000 bp. Cell debris were removed by centrifugation (16000xg) at 4*C for 15min and the cleared lysates were incubated for 2 hours at 4*C with magnetic beads coupled to antibodies against the targets of interest. For H3K9me2 30µl Protein A Dynabeads (Invitrogen) were coupled with 2µg anti-H3K9me2 antibody (Ab1220, Abcam). For H3K9me3 ChIPs, 30µl Streptavidin Dynabeads M280 (Invitrogen) were coupled to 2µg of anti-H3K9me3 antibody (Diagenode C15500003) and blocked with 5µM biotin. For Crb3-TAP ChIPs, 4.5µg Dynabeads M-270 Epoxy beads (Invitrogen) were coupled to 1.5µg rabbit IgG (Sigma, #15006) and incubated with the cleared lysate. The beads-protein complexes were washed three times with lysis buffer, once with chilled TE buffer (10mM Tris/HCl, 1 mM EDTA) and eluted in elution buffer (50mM Tris/HCl pH 8.0, 1mM EDTA, 1% SDS) with heating (65oC) for 20min. Crosslinks were reversed at 65*C overnight and the eluates were treated with RNase A and Proteinase K (Roche).
For ChIP-seq, reverse crosslinked DNA treated with RNase A and proteinase K was purified using the Qiagen PCR purification kit. The DNA was then sonicated in a QSonica water bath sonicator (5 min with 15s ON/OFF pulses, 20% amplitude) to a fragment size of ~200bp, concentrated and quantified using Qubit dsDNA high sensitivity kit. 1-10ng of DNA were used to prepare libraries as described previously (Wong et al, 2013). Libraries were pooled and sequenced on Illumina HiSeq 2500 and Illumina NextSeq 500 platforms.

tag: genotype/variation

tag: medium

value: YES

tag: antibody

value: TAP (rabbit IgG Sigma, #15006)


title: HFD-3

city: Shanghai

first: dongsheng

last: xiao

address: No.151 Libing Road, Zhangjiang Hi-Tech Park Pudong, Shanghai 201203, P.R. China

country: China

institute: Shanghai Biotechnology Corporation

data_processing:
The main steps of applying Seqtk [1] for filtering are as follows:1) Remove the sequence of joints contained in reads；2) Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01, among, Q=-10logerror_ratio；3) Remove reads with length less than 25, 4) Remove ribosome RNA reads of the species.
Spliced mapping algorithm of TopHat (version:2.0.9) [2] was applied to Genome mapping of pre-processed reads，The alignment result generated by Mapping is BAM file
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
Cufflinks (version:2.2.1)  was applied to quantitative gene mapping results of tophat
Cuffdiff was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM  and counts

organism: Rattus norvegicus

source_name: Liver

growth_protocol: All rats were acclimated for 1 week before initiation of the experiment and maintained on a 12/12 h light/dark cycle with free access to food and water.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using TAKARA RNAiso Plus#9109. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were randomly divided into two groups (n=12 each): Control group (ND group), received regular rodent chow diet (59.6% carbohydrate, 8.5% fat and 20.3% protein in total calories); HFD group, fed a high fat diet (43% carbohydrate, 41% fat and 17% protein in total calories) for 24 weeks.

value: Sprague-Dawley

value: Liver

value: ~22 weeks

tag: diet

value: High Fat Diet

tag: genotype

value: wild type


title: dCAP2-13


title: HFD-2


title: dCAP2-12

source_name: adult wing feather barb branch

value: wing

value: Day 23 plus 4-week feather regeneration


title: B6.ltbi.none.naive.0.JN3.4 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 26


title: colorectal adenocarcinoma cells - T48

city: Bethesda

first: Markus

middle: Alexander

last: Brown

state: Maryland

address: 50 South Drive, Room 1408

department: Center for Cancer Research

institute: National Institutes of Health

data_processing:
Library strategy: Hi-C
Reads were aligned using BWA to reference genome hg19 with site parameter MboI
Reads with MAPQ > 30 were kept and data was further processed using Juicer tools
Resulting Hi-C contact matrices were ICE normalized
Genome_build: hg19
Supplementary_files_format_and_content: hic files generated using the Juicer Tools and Juicebox software

organism: Homo sapiens

source_name: SW480 colorectal cancer cell line

growth_protocol: SW480 cells were grown in RPMI medium supplemented to 10% FBS. Cells were split when they reached 70% confluency in a T75 flask, approximately three times a week.

extract_protocol:
Hi-C samples were generated according to Rao et al., 2014. Briefly, 3 million cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Chromatin was digested with MboI, restriction fragments were filled in with biotinylated nucleotides, and ligated. Crosslinks were reversed and ligated DNA was purified and sheared to a length of 300-500 bp. Biotinylated fragments were purified using streptavidin beads.
Library construction was completed using end-repair, adaptor ligation, and high-fidelity PCR.

treatment_protocol: Three replicates were treated with siRNA targeting TCF7L2 for the indicated amount of time. The siRNA was deliverd using the RNAiMAX lipofectamine reagent.

tag: cell line

value: SW480 - colorectal cancer

tag: sirna

value: siRNA TCF7L2

tag: time point (hour)


title: Input_wt_rep2

value: wt


title: colorectal adenocarcinoma cells - T0

value: siRNA Negative Control


title: dCAP2-11


title: B6.cntl.none.naive.0.JN3.4 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 25

tag: ltbi status

tag: infectious challenge

tag: infection status

value: naive

value: Whole-blood


title: HFD-1


title: ND-3

value: Normal Diet


title: BJ_Aph_2

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
A coverage determination was then made for every base in the genome using Bedtools v.2.28.0 such that a base covered by one read was recorded as having a coverage of 1/(read length).
Base coverages were used to obtain pseudo-read counts in regions of interest (genes) using bedtools 2 v2.28.0 (bedtools intersect with strand-specific option -s).
Genes were defined for coverage using a method described in Chepelev et al., Nucleic Acids Research, 2009. In short, the exons from all isoforms of a gene were merged to create one meta-transcript with inter-exonic regions defined as intronic. Pseudo-counts covering these meta-transcripts were normalized by reads per kilobase per million (RPKM) using the effective length (sum of lengths of exonic and intronic regions) and by the size of the library (uniquely mapped read count).
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression files for individual samples are tab-delimited text files where the first 6 columns conform to standard BED6 format. Coordinates are for the hg38 reference genome. Column definitions: (1) "chr" - chromosome; (2) "start"; (3) "end"; (4) "name" - gene symbol; (5) "score" (set to 0 as a placeholder); (6) "strand"; (7) "ensembl_gene" - Ensembl gene ID; (8) "effective_length" - sum of feature lengths in meta-transcript, i.e. exons and introns; (10) "count" - pseudo read count OR "rpkm" - RPKM = counts/(effective_length/1x10^3)/(mapped read count/1x10^6). Gene counts and RPKM matrices for combined samples are available as tab-delimited text files (genes.counts.matrix.txt and genes.rpkm.matrix.txt), where column 1 is gene name and column 2 is Ensembl gene ID.

growth_protocol: Human foreskin fibroblasts BJ-hTERT cells were grown in DMEM supplemented with 10% fetal bovine serum, 1000,000 U l-1 penicillin and 100 mg l-1 streptomycin. The cells were tested and found negative for mycoplasma.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated by incubation of the isolated total RNA with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic Dynabeads (Invitrogen) under gentle agitation at room temperature for 1 h.
libraries were prepared from the isolated Bru-labeled RNA using the strand-specific dUTP method (Illumina TruSeq Kit).

treatment_protocol: Cells were treated with 200 nM Aphidicolin in growth media for 24 hours prior to bromouridine (Bru) labeling. BrU was added to the media to a final concentration of 2 mM and incubated at 37°C for 30 min.

value: BJ-hTERT

tag: cell type

tag: labeling agent

value: Bromouridine (Bru)

tag: bru labeling time

tag: time between bru labeling period and rna extraction

value: 0 h

tag: molecule subtype

value: Bru-labeled RNA


title: BJ_Aph_1


title: colorectal adenocarcinoma cells - T72


title: B6.ltbi.none.naive.0.JN3.3 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 24

tag: strain

value: ltbi

tag: time infected

tag: experiment label

tag: tissue


title: ND-2

value: Sprague-Dawley

value: Liver

tag: age

value: ~22 weeks

tag: diet


title: dCAP2-10

source_name: E14 leg scale skin epidermis

tag: chip antibody

tag: skin region

value: leg scutate scale

tag: skin/appendage layer

value: epidermis


title: BJ_control_2

tag: cell line


title: dCAP2-9


title: B6.cntl.none.naive.0.JN3.3 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 23

tag: ltbi status

value: cntl

tag: infectious challenge


title: B6.ltbi.none.naive.0.JN3.2 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 22

tag: infection status


title: colorectal adenocarcinoma cells - T24

value: SW480 - colorectal cancer

tag: sirna

value: siRNA TCF7L2

tag: time point (hour)


title: dCAP2-8

source_name: E14 non-keratinized feather filament

value: dorsal back

value: non-keratinized feather filament base (2 mm)


title: ND-1

tag: genotype

value: wild type


title: BJ_control_1

tag: cell type

tag: labeling agent

tag: bru labeling time

tag: time between bru labeling period and rna extraction

tag: molecule subtype


title: dCAP2-7

tag: age


title: ATACseq_Sub10_GF_rep2

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: technical replicate 2

data_processing:
Burrows-Wheeler Alignment (BWA) tool (v07.10)
BAM files were generated with SAMtools (v0.1.19)
“Peaks” were predicted using the Model-based Analysis of ChIP-Seq (MACS2) tool (v2.0.10)
To remove the artifacts from the predicted peaks, we used the blacklisted genomic regions of the Encyclopedia of DNA Elements (ENCODE)
Fragment length was set to 150 nucleotides by the makeTagDirectory program of the Hypergeometric Optimization of Motif EnRichment (HOMER) package (v4.2)
Coverage (bedgraph) files were created by the makeUCSCfile.pl program of HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: subcutaneous gluteofemoral fat

extract_protocol:
Fat biospsies were collected, adipocytes were isolated by centrifugation. Nuclei were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina).DNA was purified with MinElute PCR Purification Kit (Qiagen).
Tagmented DNA was amplified with Kapa HiFi Hot Start Kit (Kapa Biosystems) using 16 PCR cycles. Amplified libraries were purified with Agencourt AMPure XP (Beckman Coulter). Fragment distribution of libraries was assessed with Agilent Bioanalyzer.

treatment_protocol: The technical replicates for ATAC-seq: For each subject, the cells were cultured, harvested and counted. From there, 2 aliquots (with the same number of cells) were separated and proceed in parallel. Lysis, DNA isolation and library prep were then performed separately but in the same time. They were run in the same lane during sequencing.

tag: body type

value: pear

value: adipocytes

tag: fat depot

value: subcutaneous gluteofemoral fat

tag: Sex

value: female


title: ATACseq_Sub10_GF_rep1

description: technical replicate 1


title: B6.ltbi.none.naive.0.JN3.1 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 20

tag: strain

value: naive

tag: time infected

tag: experiment label

tag: tissue

value: Whole-blood


title: dCAP2-6

source_name: E14 whole brain

tag: chip antibody

tag: skin region

value: brain

tag: skin/appendage layer

value: whole brain


title: B6.cntl.none.naive.0.JN3.1 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 19

tag: ltbi status

tag: infectious challenge

tag: infection status


title: dCAP2-5


title: ATACseq_Sub10_ABD_rep2

description: technical replicate 2

source_name: subcutaneous abdominal fat

tag: cell type

value: subcutaneous abdominal fat


title: B6.ltbi.none.naive.0.JN2.3 (ATAC-seq)

description: Sample 18

source_name: Alveolar macrophages

value: ltbi

value: Alveolar macrophages


title: dCAP2-4

source_name: E7 dorsal back skin epidermis

value: epidermis


title: ATACseq_Sub10_ABD_rep1

description: technical replicate 1


title: B6.ltbi.none.naive.0.JN2.2 (ATAC-seq)

description: Sample 17


title: dCAP2-3


title: B6.ltbi.none.naive.0.JN2.1 (ATAC-seq)

description: Sample 16


title: B6.cntl.none.naive.0.JN3.2 (RNA-seq)

description:
rawCountsWBRNAseq.tsv
Sample 21

value: cntl


title: B6.cntl.none.naive.0.JN2.3 (ATAC-seq)

description: Sample 15


title: dCAP2-2

source_name: E7 whole brain


title: ATACseq_Sub9_GF_rep2

description: technical replicate 2

value: apple


title: dCAP2-1


title: ATACseq_Sub9_ABD_rep2

description: technical replicate 2


title: B6.cntl.none.naive.0.JN2.2 (ATAC-seq)

description: Sample 14


title: dCAP1

value: dorsal back


title: ATACseq_Sub9_ABD_rep1

description: technical replicate 1


title: Chuong-ChIP-231

data_processing:
RNA-seq analysis. The RNA-seq analysis pipeline was adapted according to the publication (Trapnell et al., 2012). Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1) and fastq_trimmer_by_quality (window size 3; min score >= 20). Mapping. Tool: TopHat2 (Galaxy Version 2.1.1). Quantification and differentially expressed gene analysis. Tools: Cufflinks package (Trapnell et al., 2010)–including Cufflinks (Galaxy Version 2.2.1.2), Cuffmerge (Galaxy Version 2.2.1.1), Cuffquant (Galaxy Version 2.2.1.1), and Cuffdiff (Galaxy Version 2.2.1.3). Deeptools bamCoverage (Galaxy Version 3.1.2.0.0) was used to normalize the reads to 1X sequencing depth and wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files of read coverages.
ChIP-seq analysis. Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1), fastq_quality_filter (Galaxy Version 1.0.2), fastq_trimmer_by_quality (Galaxy Version 1.1.1; window size 3; min score >= 20). Mapping. Tool: bowtie2 (Galaxy Version 2.3.4.2; genome: UCSC galGal4, --very-sensitive). Filtering. Tools: samtool_filter2 (Galaxy Version 1.8; -q 1), samtools_sort (Galaxy Version 2.0.1), samtools_rmdup (Galaxy Version 1.0.1; BAM is single-end). Peak-calling. Tools: MACS2 (Galaxy Version 2.1.1.20160309.4; for H3K27ac-ChIP, --gsize 1065365425 --nomodel --extsize 147 --bdg --broad --broad-cutoff 0.1; for CTCF/KLF-ChIP, --gsize 1065365425 --nomodel --extsize value obtained from macs2_predictd tool) and macs2_bdgcmp (Galaxy Version 2.1.1.20160309.0; -m FE and -m logLR -p 0.00001). To normalize MACS2 results from different libraries for comparison, we followed a “Build Signal Track” instruction from https://github.com/taoliu/MACS/wiki/Build-Signal-Track#Run_MACS2_bdgcmp_to_generate_foldenrichment_and_logLR_track.  Convert format. Tool: wig_to_bigWig (Galaxy Version 1.1.1).
NG Capture-C analysis. Double Capture-C results were analyzed according to the publication (Davies et al., 2016). The analysis pipeline was well documented and can be downloaded from “https://github.com/Hughes-Genome-Group/captureC/releases/download/VS2.0/UserManualforCaptureCanalysis.pdf". In brief, 1) download the CaptureC analyser package including CCanalyser3.pl, dpngenome3_1.pl, dpnII2E.pl from “https://github.com/Hughes-Genome-Group/captureC/releases", 2) generate in silico DpnII digested chicken genome ver. Ensemble galGal4 Release 72 with alpha and beta keratins, 3) perform adapter trimmer using the tool trim_galore (Dr. Felix Krueger at the Babraham Institute), 4) Merge overlapping reads by using the tool FLASH (Magoc and Salzberg, 2011), 5) in silico DpnII digest the FLASH-merged reads; 6) install Bowtie 1.2 (Langmead et al., 2009), 7) build up bowtie index using the original genome used in the Step 2, 8) align digested FLASH-merged reads (output of Step 5) using Bowtie1.2, and 9) run CCanalyser3.pl. wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files from wig files of CCanalyser3 outputs.
Genome_build: UCSC Genome Browser assembly ID: galGal4
Supplementary_files_format_and_content: Bigwig files were generated using the wig/bedgraph_to_bigwig tool. Detail processes of RNA-seq, ChIP-seq, and NG Capture-C are described above.

source_name: E14 leg scale skin

value: leg scutate scale

value: whole skin


title: ATACseq_Sub8_GF_rep2

description: technical replicate 2

value: pear


title: E7.5 Decidua, NK cells, Biological replicate 3

type: RNA

city: Philadelphia

first: Scott

middle: Michael

last: Gordon

state: PA

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

description: E7.5 decidual NK cells (F4/80-CD122+)

hyb_protocol: Following fragmentation, five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips using the GeneChip Hybridization oven 645 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Microarray data were normalized by the Robust Multichip Average (RMA) algorithm and log2 transformed using the oligo package in R.  Linear modeling to obtain differentially expressed genes was performed with the limma package in R.

label: biotin

source_name: E7.5 decidual NK cells

label_protocol: Biotinylated ssDNA was prepared according to the standard WT Plus Affymetrix protocol

growth_protocol: Mice were housed according to a protocol approved by the Institutional Animal Care and Use Committee of Children's Hospital of Philadelphia

extract_protocol: Decidual capsules were grossly dissected from myometrium with fine forceps.  Qiagen Micro RNeasy mini total RNA extraction was performed according to the manufacturer's instructions

treatment_protocol: The morning that a copulation plug was first detected was considered E0.5, assuming copulation occurred during the dark cycle in our facility

tag: strain background

tag: gender

tag: gestational age

value: 6-8 weeks

value: E7.5 decidual NK cells (F4/80-CD122+)


title: B6.ltbi.H37Rv.mEmPos.24.AD52.2 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 12

value: mEmPos


title: E7.5 Decidua, NK cells, Biological replicate 2

description: E7.5 decidual NK cells (F4/80-CD122+)

value: female

tag: age


title: B6.cntl.none.naive.0.JN2.1 (ATAC-seq)

description: Sample 13

value: naive


title: ATACseq_Sub8_GF_rep1

description: technical replicate 1

tag: body type

value: adipocytes

tag: fat depot

value: subcutaneous gluteofemoral fat


title: E7.5 Decidua, NK cells, Biological replicate 1

description: E7.5 decidual NK cells (F4/80-CD122+)


title: ATACseq_Sub9_GF_rep1

description: technical replicate 1

tag: Sex


title: E7.5 Decidua, cMacs, Biological replicate 3

description: E7.5 decidual cMacs (F4/80bright CD122-)

source_name: E7.5 decidual cMacs


title: Chuong-ChIP-24

source_name: E9 leg scale skin


title: E7.5 Decidua, cMacs, Biological replicate 2

value: E7.5 decidual cMacs (F4/80bright CD122-)


title: E7.5 Decidua, cMacs, Biological replicate 1


title: E7.5 Decidua, CD122+Macs, Biological replicate 3

description: E7.5 decidual CD122+Macs (F4/80bright CD122+)

source_name: E7.5 decidual CD122+Macs


title: B6.ltbi.H37Rv.mEmNeg.24.AD52.2 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 11

tag: strain

value: ltbi

value: mEmNeg

tag: time infected


title: ATACseq_Sub8_ABD_rep2

description: technical replicate 2

value: subcutaneous abdominal fat


title: E7.5 Decidua, CD122+Macs, Biological replicate 2

value: E7.5 decidual CD122+Macs (F4/80bright CD122+)


title: E7.5 Decidua, CD122+Macs, Biological replicate 1


title: Chuong-ChIP-53

source_name: E9 dorsal back feather skin


title: ATACseq_Sub8_ABD_rep1

description: technical replicate 1


title: B6.ltbi.H37Rv.mEmPos.24.AD52.1 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 9

tag: experiment label

value: Alveolar macrophages


title: Chuong-ChIP-23

source_name: E7 dorsal back skin

tag: chip antibody

value: dorsal back


title: SAMPLE 8_MDA-MB-231 cells

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human breast cancer

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and 480 ng cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software GX14.9.1 (Agilent) using default parameters.
Signal intensities of <1 were set to 1, and each chip was normalized to the 75th percentiles of all measurements from that chips. Baseline transformation of these data was not performed.

source_name: MDA-MB-231 cells, passage 45

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Breast carcinoma cell lines, MCF7 (HTB-22), T-47D (HTB-133), MDA-MB-157 (HTB-24), and MDA-MB-231 (HTB-26) were obtained from ATCC and maintained according to the provider’s instructions.

extract_protocol: Total RNA was prepared by using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: cell line

value: Breast carcinoma cell line

tag: passage

value: passage 45


title: Chuong-ChIP-227

tag: skin region

tag: skin/appendage layer

value: non-keratinized feather filament base (2 mm)


title: B6.ltbi.H37Rv.mEmNeg.24.AD52.1 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 8

tag: ltbi status

tag: infectious challenge

tag: infection status


title: Chuong-ChIP-243

value: leg scutate scale

value: whole skin


title: B6.ltbi.H37Rv.naive.24.AD52.1 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 7

tag: cell type


title: SAMPLE 7_MDA-MB-231 cells

description: Gene expression in human breast cancer


title: Chuong-ChIP-230


title: B6.ltbi.none.naive.0.JN1.3 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 6


title: Chuong-ChIP-237


title: Chuong-ChIP-226


title: B6.ltbi.none.naive.0.JN1.2 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 5


title: SAMPLE 6_MDA-MB-157 cells

description: Gene expression in human breast cancer

source_name: MDA-MB-157 cells, passage 49

value: passage 49


title: B6.ltbi.H37Rv.naive.24.AD52.2 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 10


title: ATACseq_Sub7_ABD_rep2

description: technical replicate 2

value: pear

value: female


title: ATACseq_Sub6_GF_rep2

description: technical replicate 2

value: apple

value: adipocytes


title: B6.ltbi.none.naive.0.JN1.1 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 4

value: naive


title: ATACseq_Sub7_ABD_rep1

description: technical replicate 1


title: ATACseq_Sub6_ABD_rep2

description: technical replicate 2


title: ATACseq_Sub7_GF_rep2

description: technical replicate 2

value: subcutaneous gluteofemoral fat


title: B6.cntl.none.naive.0.JN1.2 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 2

value: cntl


title: B6.cntl.none.naive.0.JN1.3 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 3


title: Chuong-ChIP-242

value: anti-CTCF


title: SAMPLE 4_T-47D cells

description: Gene expression in human breast cancer

source_name: T-47D cells, passage 94

value: passage 94


title: SAMPLE 5_MDA-MB-157 cells

description: Gene expression in human breast cancer


title: ATACseq_Sub6_GF_rep1

description: technical replicate 1


title: ATACseq_Sub7_GF_rep1

description: technical replicate 1


title: SAMPLE 3_T-47D cells

description: Gene expression in human breast cancer


title: ATACseq_Sub6_ABD_rep1

description: technical replicate 1

value: subcutaneous abdominal fat


title: SAMPLE 1_MCF-7 cells

description: Gene expression in human breast cancer

source_name: MCF-7 cells, passage 153

value: passage 153


title: Chuong-ChIP-234

description: input gDNA control for related ChIP

value: input genomic DNA


title: B6.cntl.none.naive.0.JN1.1 (RNA-seq)

description:
rawCountsAMRNAseq.tsv
Sample 1

value: Alveolar macrophages


title: SAMPLE 2_MCF-7 cells

description: Gene expression in human breast cancer

value: Breast carcinoma cell line


title: Chuong-ChIP-236

source_name: E14 non-keratinized feather filament

value: dorsal back


title: ATACseq_Sub5_GF_rep1

description: technical replicate 1

source_name: subcutaneous gluteofemoral fat


title: ATACseq_Sub5_GF_rep2

description: technical replicate 2


title: Chuong-ChIP-225

value: whole skin


title: Chuong-ChIP-223

description: input gDNA control for related ChIP


title: ATACseq_Sub5_ABD_rep2

description: technical replicate 2

source_name: subcutaneous abdominal fat


title: ATACseq_Sub5_ABD_rep1

description: technical replicate 1


title: Kidney, Wildtype_replicate_4 (ALc1-13)

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: whole kidney

extract_protocol:
RNA was isolated from kidneys or cells with Trizol reagent (Life technologies) and further purified with the Directzol RNA MiniPrep kit from Zymo (R2050).
200ng of total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Ilumina (E7420L) was used. 15 cycles of PCR were done. Quality control of libraries was done via Bioanalyzer High Sensitivity DNA and Tape Station High Sensitivity D5000 Screen Tape. Quantification of the samples was done via qPCR using the BioRad CFX96. The reagent kit for qPCR was the Kapa Library Quantification Kit for Illumina (KK4824).

tag: genotype

value: WT

tag: tissue

value: whole kidney


title: Chuong-ChIP-229

value: leg scutate scale

tag: age


title: Chuong-ChIP-241

description: IgG control for related ChIP

value: anti-IgG


title: Kidney, Wildtype_replicate_1 (ALc1-9)


title: ATACseq_Sub4_GF_rep2

description: technical replicate 2

tag: body type

value: apple

value: adipocytes

tag: fat depot

value: female


title: Kidney, Wildtype_replicate_2 (ALc1-10)


title: ATACseq_Sub4_GF_rep1

description: technical replicate 1

value: subcutaneous gluteofemoral fat

tag: Sex


title: Chuong-ChIP-22


title: Chuong-ChIP-235

description: IgG control for related ChIP


title: Chuong-ChIP-34


title: Kidney, Knockout_replicate_4 (ALc1-16)

value: KO b-actinCreERT2+TFAP2Bfl/fl mice


title: Chuong-ChIP-20

description: input gDNA control for related ChIP


title: ATACseq_Sub4_ABD_rep2

description: technical replicate 2


title: 28_11-22-19_SMJ115

first: Emanuel

middle: José

last: Novais

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

hyb_protocol: Gene chips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit

scan_protocol: scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Chp files were generated by sst-rma normalization from Affymetrix cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

source_name: 5 to 6-month-old SM/J mouse

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: NP tissue was dissected from caudal discs of 6M and 23M BL6 mice (n=7), LG/J (n=5/6)

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

tag: strain

value: SM/J

value: 5 to 6-month-old

value: Nucleus Pulposus


title: ATACseq_Sub4_ABD_rep1

description: technical replicate 1

value: subcutaneous abdominal fat


title: Kidney, Knockout_replicate_3 (ALc1-15)


title: Chuong-ChIP-33

value: non-keratinized feather filament base (2 mm)


title: Kidney, Wildtype_replicate_3 (ALc1-12)


title: Kidney, Knockout_replicate_2 (ALc1-14)


title: ATACseq_Sub3_GF_rep2

description: technical replicate 2


title: 29_11-22-19_SMJ116


title: 30_11-22-19_SMJ117


title: Chuong-ChIP-19


title: ATACseq_Sub3_GF_rep1

description: technical replicate 1


title: 27_11-22-19_SMJ114


title: 25_11-22-19_SMJ112


title: Kidney, Knockout_replicate_1 (ALc1-11)


title: 14_3-1-19_C57BL6_(Clariom_S_Mouse)

description: Gene expression data from 23-month-old C57BL/6 mouse.

hyb_protocol: GeneChips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit.

scan_protocol: Scanned on an Affymetrix GeneChip Scanner 3000 7G, using Command Console Software.

data_processing: CHP files were generated by sst-rma normalization from Affymetrix CEL file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

source_name: C57BL/6 Nucleus Pulposus

growth_protocol: NP tissue was dissected from caudal discs of 6M and 23M BL6 mice (n=7), LG/J (n=4/6).

tag: strain/background


title: ATACseq_Sub3_ABD_rep1

description: technical replicate 1


title: Skeletal Muscle Exe3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

source_name: Skeletal Muscle

extract_protocol:
About 800 SCs were isolated by FACS and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice in the exercise groups were subjected to 4 weeks of running exercise (4 days/week, 30 min/day at 12 m/min)

value: Muscle satellite cells (SCs)

tag: cell states

value: Trained

tag: treatment

value: Exercise


title: 12_3-1-19_C57BL6_(Clariom_S_Mouse)


title: ATACseq_Sub2_GF_rep2

description: technical replicate 2

value: pear


title: ATACseq_Sub3_ABD_rep2

description: technical replicate 2


title: 26_11-22-19_SMJ113


title: ATACseq_Sub2_GF_rep1

description: technical replicate 1


title: Skeletal Muscle Exe1


title: Chuong-ChIP-26

tag: chip antibody

value: leg

value: whole skin


title: Chuong-ChIP-52

tag: skin region


title: Chuong-ChIP-32

description: input gDNA control for related ChIP

value: input genomic DNA

tag: skin/appendage layer


title: Skeletal Muscle Con4

value: Untrained

value: Control


title: Chuong-ChIP-21

description: input gDNA control for related ChIP

value: dorsal back


title: Skeletal Muscle Exe4


title: Chuong-ChIP-11


title: Skeletal Muscle Con3


title: ATACseq_Sub2_ABD_rep1

description: technical replicate 1

value: adipocytes

value: female


title: ATACseq_Sub1_GF_rep2

description: technical replicate 2

value: subcutaneous gluteofemoral fat


title: Skeletal Muscle Con2


title: ATACseq_Sub1_GF_rep1

description: technical replicate 1


title: Skeletal Muscle Con1


title: Chuong-ChIP-15

description: input gDNA control for related ChIP


title: ATACseq_Sub2_ABD_rep2

description: technical replicate 2


title: ATACseq_Sub1_ABD_rep2

description: technical replicate 2


title: Chuong-ChIP-51


title: Chuong-ChIP-1


title: WT_Rep2

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Mapping with TopHat
Genemodel / Quantification with CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: FPKM Table

source_name: WT_subventricular zone NPCs

extract_protocol:
described in Fatt, et al (Stem Cell Reports, 5:1-8, 2015)
Qiagen RNA extraction Kit including the DNA digestion step; Illumina Hiseq 2000  SR50

tag: strain background

tag: genotype/variation

value: wild type

tag: cell types

value: SVZ NPCs subjected to differentiation in the presence of metfomrin

tag: passages


title: WT_Rep1

growth_protocol: described in Fatt, et al (Stem Cell Reports, 5:1-8, 2015)


title: ATACseq_Sub1_ABD_rep1

description: technical replicate 1

tag: cell type

value: subcutaneous abdominal fat


title: 10_152_12-18-18_LGJ_(Clariom_S_Mouse)

description: Gene expression data from 23-month-old LG/J mouse.

source_name: LG/J Nucleus Pulposus

value: LG/J

tag: tissue

value: Nucleus Pulposus


title: RNAseq_Sub10_GF

data_processing:
The RNA-Seq samples quality was checked using the tool FastQC. After this step, a required trimming was executed reducing distortions on the “per base sequence content” at the beginning of the reads using Trimmomatic. The trimmed samples were aligned to the UCSC genome, assembly hg19, using STAR. Reads were required to be uniquely mapped using Samtools for filtering, sorting and indexing. RSeQC was used to assess quality of each sample. The RNA sequencing abundance, raw read counts and TPM values, was calculated with TPMCalculator using the default parameters. The differential gene expression analysis was executed using the Bioconductor packages Deseq2 and EdgeR. An adjusted p-value of 0.05 and a logarithmic fold change of 1.5 was used to identified differentially expressed genes.  All tools were executed using publicly available Common Workflows Language files and docker images with fixed tool versions
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include raw read count values and TPM values for each Sample

extract_protocol:
Fat biospsies were collected, adipocytes were isolated by centrifugation and freeze at -80C. RNA was isolated using the GentleMACS Dissociator system (Milteny Biotec, GmbH, Germany). Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Library preparation kit (Illumina Inc., San Diego, CA) as per the instructions

value: isolated from gluteofemoral fat depot


title: 11_3-1-19_C57BL6_(Clariom_S_Mouse)

tag: age


title: 11_153_12-18-18_LGJ_(Clariom_S_Mouse)


title: 10_3-1-19_C57BL6_(Clariom_S_Mouse)


title: 09_3-1-19_C57BL6_(Clariom_S_Mouse)


title: 08_150_12-18-18_LGJ_(Clariom_S_Mouse)


title: Chuong-ChIP-31

description: input gDNA control for related ChIP


title: 13_3-1-19_C57BL6_(Clariom_S_Mouse)


title: KI_Rep2

source_name: KI_subventricular zone NPCs


title: 07_143_12-18-18_LGJ_(Clariom_S_Mouse)


title: 09_151_12-18-18_LGJ_(Clariom_S_Mouse)


title: Chuong-ChIP-25


title: RNAseq_Sub10_ABD

tag: body type

value: isolated from abdominal fat depot


title: 06_142_12-18-18_LGJ_(Clariom_S_Mouse)


title: Control Dam 3 Offsping Female 1 [CD3F1]

city: Birmingham

first: Colin

middle: A

last: Martin

state: AL

address: 1600 7th Ave S Lowder Bldg S300

department: Surgery

institute: University of Alabama at Birmingham

data_processing:
Library prep, Illumina sequencing, and data analysis was carried out at Novogene Genome Sequencing Company (Sacramento, CA). Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. All sequence alignments were performed using Tophat program
Reads were mapped to the reference genome GRCm38/mm10 using STAR v2.5. HTSeq v0.6.1 was used to count the read numbers mapped for each gene. And then FPKM of each gene was calculated based on the length of the gene and read counts mapped to the gene.
Differential expression analysis was performed using either biological replicates or not. First, data sets were grouped by stressed female, stressed male, control female, and control male; each group had n=3. Pairwise comparisons of matched groups (e.g. stressed female vs control female, stressed male vs control male, and all stressed vs all control) were performed using DESeq2 R package (2_1.6.3). Genes with Benjamini-Hochberg adjusted P values <0.05 were considered differentially expressed. Second, samples were compared without replicates (e.g. rep 1 stressed male vs rep 1 control male, etc.) using EdgeR v3.16.5.
As with the DESeq2 results, Benjamini-Hochberg corrected P values of <0.05 and absolute foldchange of 1 were set as the thresholds for significant differential expression. Correlation was calculated using the Spearman method after assigning genes with 0 FPKM a value of 0.001. Samples were clustered using FPKM with hierarchical clustering, SOM (Self-organization mapping), and k means using silhouette coefficient to adapt the optimal classification with default parameter in R
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel and text files showing gene counts, FPKM values for each Sample

source_name: Control Dam Offsping Female

growth_protocol: Pregnant C57B/L6J mice were purchased from The Jackson Labs at housed at the animal facility at University of Alabama at Birmingham. They were fed a standard diet, and given free access to food and water.

extract_protocol:
ileum tissues were stored in RNAlater solution at the time of harvest and total RNA was extracted following instructions in RNEasy RNA extraction kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pregnant dams were restrain stressed in a 50 cc ventilated falcon tube everyday for 2 hr from gestational day 7 to 19. The pups were euthanized at 2 weeks of age and ileum harvested for RNASeq analysis. Control dams were not stressed and maintained in their home cages undisturbed.

tag: sample group

value: control

value: post natal day 14

value: ileum


title: Control Dam 2 Offsping Female 1 [CD2F1]


title: KI_Rep1


title: RNAseq_Sub9_GF

value: apple

tag: fat depot

tag: Sex


title: 08_3-1-19_C57BL6_(Clariom_S_Mouse)

tag: strain/background


title: 07_3-1-19_C57BL6_(Clariom_S_Mouse)

description: Gene expression data from 6-month-old C57BL/6 mouse.


title: Control Dam 2 Offsping Male 1 [CD2M1]

source_name: Control Dam Offsping Male

tag: strain


title: Wildtype_replicate_4

data_processing:
Pseudoalignment with salmon, version ,0.8.2
Import and summarize salmon generated counts with tximport, version 1.2.0
Analyze differential expression with DESeq2 BioConductor package, version 1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: comma separated format, rawCounts matrix file contains raw counts as generated by Salmon and imported by tximport (these counts were used for the DESeq2 analysis), tpm matrix contains transcripts per million normalized counts as calculated by tximport

tag: genotype

value: Wildtype

value: whole kidney


title: RNAseq_Sub9_ABD


title: Knockout_replicate_4

value: Nephron specific Kctd1 knockout


title: 06_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Wildtype_replicate_3


title: RNAseq_Sub8_ABD

value: pear

value: adipocytes


title: Control Dam 1 Offsping Female 1 [CD1F1]


title: Control Dam 3 Offsping Male 1 [CD3M1]


title: Control Dam 1 Offsping Male 1 [CD1M1]


title: RNAseq_Sub8_GF

value: female


title: 05_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Stressed Dam 3 offsping Female 1 [SD3F1]

source_name: Stressed Dam offsping Female

value: prenatal stress


title: 04_165_12-18-18_LGJ_(Clariom_S_Mouse)

description: Gene expression data from 6-month-old LG/J mouse.


title: 04_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Wildtype_replicate_2


title: Stressed Dam 3 offspring Male 1 [SD3M1]

source_name: Stressed Dam offspring Male


title: Wildtype_replicate_1


title: Stressed Dam 2 offsping Female 1 [SD2F1]


title: RNAseq_Sub7_ABD


title: RNAseq_Sub7_GF


title: RNAseq_Sub6_GF


title: Knockout_replicate_2


title: Stressed Dam 2 offspring Male 1 [SD2M1]


title: 03_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Knockout_replicate_1


title: Knockout_replicate_3


title: 02_163_12-18-18_LGJ_(Clariom_S_Mouse)


title: 02_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Stressed Dam 1 offsping Female 1 [SD1F1]


title: Stressed Dam 1 offspring Male 1 [SD1M1]


title: RNAseq_Sub5_ABD


title: RNAseq_Sub4_GF


title: 01_162_12-18-18_LGJ_(Clariom_S_Mouse)


title: RNAseq_Sub5_GF


title: 03_164_12-18-18_LGJ_(Clariom_S_Mouse)


title: 01_3-1-19_C57BL6_(Clariom_S_Mouse)


title: Crypto infected lung CD45

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of naïve and Crypto infected lung CD45 cells, using 10X Cellranger v3.0.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes. *barcodes.tsv = Barcode sequences that correspond to column indices in matrix.mtx. *features.tsv = Gene IDs.

source_name: Total lung

growth_protocol: 6-8 week old CXCL2-GFP reporter heterozygous mouse

extract_protocol:
CD45+ cells were positively selected using anti-CD45 antibody and MACS ((Miltenyi Biotec) positive selection system. Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library.
Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library.
Single-cell libraries were sequenced on Novaseq 6000 S-Prime flowcell 150bp paired end flowcell. Libraries were sequenced in single index mode with the following read lengths: 28x8x91.

treatment_protocol: 3 mice were pooled for each group: For the Cryptococcus-infected sample group, 3 mice were infected with Cryptococcus neoformans 10^4 yeasts/mouse through oro-tracheal instillation for 9 hours and pooled to isolate CD45+ cells from lung. For the naïve sample group, 3 naïve mice were pooled.

value: lung

value: CD45+ cells single cells

tag: trangene

value: CXCL2-GFP reporter heterozygous


title: OtA0819-Mf_S_RN2013

city: Gloucester

first: Andrea

middle: G

last: Bodnar

address: 417 Main Street

institute: Gloucester Marine Genomics Institute, Inc.

data_processing:
Read quality was assessed using FastQC v0.10.1
Adapter removal and quality-based trimming Trimmomatic v0.38
De novo transcriptome assembly was performed using Trinity v2.8.5
Quality trimmmed and filtered read pairs mapped to Trinity transcriptome with Bowtie v2.3.4 using align_and_estimate_abundance.pl in Trinity
Expression quantification performed with RSEM using align_and_estimate_abundance.pl in Trinity
Count-based DGE analysis was performed with DESeq v1.20
Genome_build: de novo transcriptome assembly
Supplementary_files_format_and_content: Tab delimited text files containing matrix of raw read counts generated by RSEM expression quantification step

organism: Mesocentrotus franciscanus

source_name: Radial Nerve

extract_protocol:
RNA was extracted from tissue with TRIzol reagent following Invitrogen's instructions, followed by a clean-up with the Rneasy mini kit following Qiagen's instructions with a 15 minute DNase I digestion.
cDNA was prepared form RNA using the SMARTer cDNA synthethis kit (Clontech) and the sequencing libraries were constructed using the NEBNext Illumina library preparation kit (New England Bioloabs), following the manufacturer's instructions. Illumina libraries were assessed on an Agilent Bioanalyzer 2100, samples were pooled in equal concentrations, and sequencing was preformed on an Illumina HiSeq-2000 with 100 bp PE reads.

tag: size

value: small

tag: sampling years

value: Radial Nerve


title: OtA2890-Mf_L_RN2011R

value: large


title: RNAseq_Sub4_ABD

value: isolated from abdominal fat depot


title: Naïve lung CD45

description: Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library.


title: Ot7681-Mf_S_RN2011


title: RNAseq_Sub3_GF

value: isolated from gluteofemoral fat depot


title: RNAseq_Sub6_ABD


title: IRI6w3

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

description: single nucleus RNA-seq

data_processing: We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single nucleus sequencing data from mouse and human kidneys. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to reference genome (mm10 and hg19) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis. Subsequently, we applied SoupX to remove ambient RNA

source_name: Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 5-µm cell strainer (pluriSelect 43-50020-50) and counted. We used the inDrops protocol developed by Klein et al to generate single nucleus transcriptome.
We followed the guideline provided by the manufacturer (10x Genomics) to generate single nucleus transcriptomes
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure

tag: group

tag: replicates


title: OtA2889-Mf_L_RN2010R


title: Ot7679-Mf_S_RN2010


title: RNAseq_Sub2_GF


title: IRI6w2

description: single nucleus RNA-seq


title: RNAseq_Sub3_ABD


title: IRI6w1_2

description: single nucleus RNA-seq


title: OtA0818-Mf_L_ES2013

source_name: Esophagus

value: Esophagus


title: IRI6w1_1

description: single nucleus RNA-seq


title: RNAseq_Sub2_ABD


title: OtA0817-Mf_S_ES2013


title: IRI14d_3

description: single nucleus RNA-seq


title: RNAseq_Sub1_GF

source_name: subcutaneous gluteofemoral fat


title: Liver, NEMO/JNK1Δhepa double knockout mouse, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: NEMO/JNK1Δhepa double knockout

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).

source_name: Liver, NEMO/JNK1Δhepa double knockout mouse aged 8 weeks

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Alb-Cre and Jnk2-deficient mice on a C57BL/6 background were purchased from The Jackson Laboratory (Bar Harbor, ME). Jnk1LoxP/LoxP /Jnk2−/− (JNKΔhepa) mice were created as previously reported (Cubero et al., 2016; Das et al., 2007; Das et al., 2009). NEMO∆hepa/JNKΔhepa mice, and their respective controls (NEMO∆hepa and NEMOf/f mice) were created as described in the current manuscript.

extract_protocol: Total RNA was isolated by Directzol RNA Miniprep (Zymo Research, Irvine, CA). RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for analysis only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free access to chow and water. Depending on the mouse model and experiment, livers were removed from mice at the age of 8 or 52 weeks, or at the indicated time points after treatment with diethylnitrosamine (DEN) or after bile duct ligation (BDL). After removal, tissues were immediately snap-frozen in liquid nitrogen and stored at -80 until RNA isolation.

tag: genotype/variation

value: NEMO/JNK1<delta>hepa double knockout

value: Liver

tag: treatment

value: 8 weeks

tag: mouseid


title: OtA0816-Mf_L_ES2011

tag: tissue


title: Liver, NEMO/JNK1Δhepa double knockout mouse, replicate 2

description: NEMO/JNK1Δhepa double knockout

tag: age


title: IRI14d_2

description: single nucleus RNA-seq


title: IRI14d1_2

description: single nucleus RNA-seq


title: ARID1A-KO2 FBS rep2

city: Baltimore

first: Yohan

last: Suryo Rahmanto

state: MD

address: CRB-2, Rm 376, 1550 Orleans St

institute: Johns Hopkins School of Medicine

data_processing:
Bioinformatics analysis was performed using Galaxy, an open access web-based program that contains a variety of next-generation sequencing analysis tools. Reads were processed, trimmed to 101 bp, and aligned to Homo sapiens reference genome build hg19 using TopHat gapped-read mapper (ver. 2.1.0). The aligned reads were processed with Cufflinks transcript assembly (ver. 2.2.1.0), and output of the resulting GTF files was amalgamated to UCSC hg19 RefSeq genes annotation files using Cuffmerge (ver. 2.2.1.0). Differential expression analysis was performed using Cuffdiff (ver. 2.2.1.3) to produce a list of genes whose expression changes were significant (FDR < 0.05) between the groups tested.
Genome_build: hg19

source_name: endometrial epithelial cells

growth_protocol: The cell lines used in this study were maintained at 37°C and 5% CO2, and included immortalized isogenic human endometrial epithelial ARID1AWT and ARID1AKO cells. ARID1AWT and ARID1AKO cells were cultured in RPMI 1640 medium supplemented with 15% FBS, 1% MEM non-essential amino acids, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from cultured human endometrial epithelial cells using the Qiagen RNeasy Plus Mini Kit.
RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA Nano Chip. RIN values ranged from 9.2 to 10.0 for human endometrial epithelial cells. RNA-sequencing was performed by GeneWiz, Inc. on the Illumina HiSeq2500 platform, in a 2x150 bp paired-end high output V4 chemistry configuration.

treatment_protocol: Two biological pairs of wild-type (ARID1AWT) and knockout (ARID1AKO) cells were used (PMID: 26953344). These pairs of isogenic ARID1A wildtype and knockout cell lines were established from human endometrial using a CRISPR/Cas9 genome editing method.

tag: cell type

value: endometrial epithelial cells

value: ARID1A KO

tag: biological replicate

tag: technical replicate

value: Complete Growth Media (15% FBS)


title: IRI14d1_1

description: single nucleus RNA-seq


title: ARID1A-KO2 FBS rep1


title: OtA0813-Mf_S_ES2010


title: Liver, NEMO/JNK1Δhepa double knockout mouse, replicate 1

description: NEMO/JNK1Δhepa double knockout


title: Liver, NEMO knockout mouse, replicate 2

source_name: Liver, NEMO knockout mouse aged 8 weeks

value: NEMO single knockout


title: IRI2d3

description: single nucleus RNA-seq


title: OtA0812-Mf_L_ALM2013

source_name: Aristotle's Lantern muscle

value: Aristotle's Lantern muscle


title: IRI2d2_2

description: single nucleus RNA-seq


title: ARID1A-WT2 FBS rep2

value: ARID1A WT


title: Liver, JNKΔhepa double knockout mouse, bile duct ligation, replicate 3

description: JNKΔhepa double knockout

source_name: Liver, JNKΔhepa double knockout mouse, after 28 days of bile duct ligation

value: JNK<delta>hepa double knockout

value: Bile duct ligation (BDL)

tag: treatment duration

value: 28 days


title: Liver, NEMO knockout mouse, replicate 3


title: RNAseq_Sub1_ABD

source_name: subcutaneous abdominal fat

tag: body type

value: pear

value: adipocytes

tag: fat depot

tag: Sex

value: female


title: OtA0815-Mf_S_ES2011

value: small


title: IRI2d2_1

description: single nucleus RNA-seq


title: OtA0810-Mf_L_ALM2011

value: large


title: ARID1A-KO2 Starved rep2

tag: genotype

value: Serum Starved (0% FBS, 24h)


title: OtA0811-Mf_S_ALM2013

tag: size


title: IRI2d1_2

description: single nucleus RNA-seq


title: ARID1A-WT2 FBS rep1


title: OtA0814-Mf_L_ES2010

tag: sampling years

value: Esophagus


title: OtA2888-Mf_L_RN2013R

value: Radial Nerve


title: IRI2d1_1

description: single nucleus RNA-seq

tag: group


title: Liver, JNKΔhepa double knockout mouse, bile duct ligation, replicate 2

description: JNKΔhepa double knockout

value: Liver


title: OtA0809-Mf_S_ALM2011


title: Liver, JNKΔhepa double knockout mouse, bile duct ligation, replicate 1

description: JNKΔhepa double knockout


title: Skeletal Muscle Exe2

source_name: Skeletal Muscle

value: Muscle satellite cells (SCs)

tag: cell states

value: Trained

value: Exercise


title: Liver, NEMO knockout mouse, replicate 1

tag: genotype/variation

value: NEMO single knockout

value: 8 weeks


title: Liver, control mouse, bile duct ligation, replicate 3

source_name: Liver, control mouse, after 28 days of bile duct ligation

value: Control

tag: treatment


title: OtA0808-Mf_L_ALM2010

value: Aristotle's Lantern muscle


title: ARID1A-WT2 Starved rep1

value: endometrial epithelial cells

value: ARID1A WT


title: OtA0807-Mf_S_ALM2010


title: Liver, control mouse, bile duct ligation, replicate 2

value: Bile duct ligation (BDL)

value: 28 days

tag: mouseid


title: Astrocyte_HD_Rep1_ATAC-seq

city: Atlanta

first: Isaac

last: Kremsky

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

data_processing:
ATAC-seq raw reads were trimmed using pyadapter_trim.py.
Reads were aligned to the “MacaM_Rhesus_Genome_Annotation_v7.8.2” genome using Tophat2 v2.1.0 with the flags, “--no-mixed –no-discordant” for RNA-seq, and using bowtie version 2 2.2.6 with the flag, “-X 2000” for ATAC-seq.
Non-uniquely mapped reads were excluded from both RNA-seq and ATAC-seq samples, and duplicates were removed from ATAC-seq samples using picard-tools-2.1.7 MarkDuplicates.
For ATAC-seq, only fragments < 115 bp in length were kept, as those indicate transcription factor binding.
.bam files were converted to .bed using “bamToBed -split” for RNA-seq, and .bedpe using “bamToBed -bedpe” for ATAC-seq.  The ATAC-seq .bedpe file was converted to a bed file containing only the beginning and end of each fragment.
.bed files were converted to bedGraph using “bedtools genomecov -scale”, where the scale factor was the total number of uniquely mapped reads for RNA-seq, and the total number of uniquely mapped, non-duplicate fragments for ATAC-seq.  The result is an RPM-normalized .bedGraph file for each replicate. .bedGraph files were then converted to bigwig using “bedGraphToBigWig”
Genome_build: MacaM_Rhesus_Genome_Annotation_v7.8.2
Supplementary_files_format_and_content: bigwig files of RPM-normalized signal.

organism: Macaca mulatta

source_name: Astrocytes

extract_protocol:
ell cultures were harvested, washed in cold 1x PBS, and counted. One hundred thousand cells were resuspended in 50 µL cold resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP-40 (Sigma), 0.1% Tween-20 (Sigma), and 0.01% digitonin (Abcam ab141501) and incubated for 3 min on ice. Following lysis, 1 mL RSB with 0.01% Tween-20 was added to the samples. Samples were centrifuged for 10 min at 4°C/500 x g and the supernatant was carefully removed. Nuclei were then resuspended in the transposase reaction mix (25 µL 2x TD buffer, 2.5 µL Tn5 transposase, 0.5 µL 10% Tween-20, 2.5 µL 1% digitonin [0.05% final concentration], and 19.5 µL water) and incubated at 37°C for 30 min in a thermomixer with shaking at 600 r.p.m. Following the reaction, samples were treated with Proteinase K (Fisher 25530015) at 55°C for 2 hr and genomic DNA was isolated via phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
Library preparation was performed using 2x KAPA HiFi mix (KAPA BIOSYSTEMS INC #kk4604) and 1 mM indexed primers under the following PCR conditions: 72°C for 5 min; 98°C for 30 sec; and 8-12 cycles at 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. ATAC-seq experiments were performed on two replicates

value: Astrocytes

tag: disease state

value: Huntington’s Disease


title: ARID1A-KO FBS rep2

description: FBS.tabular

data_processing:
Bioinformatics analysis was performed using Galaxy, an open access web-based program that contains variety of next-generation sequencing analysis tools. Reads were processed and aligned to Homo sapiens reference genome build hg19 using TopHat gapped-read mapper (ver. 2.1.0). The aligned reads were processed with Cufflinks transcript assembly (ver. 2.2.1.0), and output of the resulting GTF files was amalgamated to UCSC hg19 RefSeq genes annotation files using Cuffmerge (ver. 2.2.1.0). Differential expression analysis was performed using Cuffdiff (ver. 2.2.1.3) to produce a list of genes whose expression changes were significant (FDR < 0.05) between the groups tested.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff output

extract_protocol: Total RNA was isolated from cultured human endometrial epithelial cells and mouse uterine tissues using the Qiagen RNeasy Plus Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA Nano Chip. RIN values ranged from 9.5 to 10.0. RNA-sequencing was performed by GeneWiz, Inc. on the Illumina HiSeq2500 platform, in a 2x100 bp paired-end high output V4 chemistry configuration.

value: ARID1A KO

value: Complete Growth Media (15% FBS)


title: ARID1A-KO FBS rep1

description: FBS.tabular


title: ARID1A-WT FBS rep2

description: FBS.tabular


title: Day3_HD_Rep2_ATAC-seq

source_name: Developing astrocytes

value: Developing astrocytes


title: Liver, JNKΔhepa double knockout mouse treated with DEN, replicate 3

description: JNKΔhepa double knockout

source_name: Liver, JNKΔhepa double knockout mouse treated with DEN for 40 days

value: JNK<delta>hepa double knockout

tag: tissue

value: Liver

value: Diethylnitrosamine (DEN)

value: 40 days


title: Day3_HD_Rep1_ATAC-seq

tag: cell type


title: ARID1A-KO2 Starved rep1

tag: biological replicate

value: Serum Starved (0% FBS, 24h)


title: Liver, control mouse, bile duct ligation, replicate 1


title: IRI4h3

description: single nucleus RNA-seq

tag: replicates


title: Liver, JNKΔhepa double knockout mouse treated with DEN, replicate 1

description: JNKΔhepa double knockout

tag: treatment duration


title: ARID1A-WT FBS rep1

description: FBS.tabular


title: ARID1A-KO Starved rep2

description: Starved.tabular


title: Astrocyte_WT_Rep3_RNA-seq

extract_protocol:
The RNA was extracted using Qiagen miRNeasy Mini Kit with DNase digestion. The RNA quantity and quality were validated using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis.
Amplified mRNA was fragmented, and barcodes were added using Illumina’s Nextera XT kits. Amplified Libraries were validated by Agilent 4200 Tapestation and quantified using a Qubit fluorimeter. Libraries were normalized, pooled and clustered on an Illumina HiSeq 3000/4000 Flowcell using the Illumina cBOT. The libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read reactions with multiplexing to achieve approximately 20 million reads per sample. RNA-seq experiments were performed in three different replicates.

value: wild type


title: ARID1A-WT2 Starved rep2

tag: technical replicate


title: IRI4h1

description: single nucleus RNA-seq


title: IRI4h2

description: single nucleus RNA-seq


title: ARID1A-KO Starved rep1

description: Starved.tabular


title: Astrocyte_WT_Rep2_RNA-seq


title: ARID1A-WT Starved rep2

description: Starved.tabular


title: Liver, JNKΔhepa double knockout mouse treated with DEN, replicate 2

description: JNKΔhepa double knockout


title: Liver, control mouse treated with DEN, replicate 3

source_name: Liver, control mouse treated with DEN for 40 days

value: Control


title: Liver, NEMO/JNKΔhepa triple knockout mouse, replicate 2

description: NEMO/JNKΔhepa triple knockout

source_name: Liver, NEMO/JNKΔhepa triple knockout mouse, aged 52 weeks

value: NEMO/JNK<delta>hepa triple knockout

tag: age

value: 52 weeks


title: Liver, control mouse treated with DEN, replicate 1


title: Liver, NEMO/JNKΔhepa triple knockout mouse, replicate 3

description: NEMO/JNKΔhepa triple knockout


title: ARID1A-WT Starved rep1

description: Starved.tabular

value: endometrial epithelial cells

value: ARID1A WT


title: Liver, NEMO/JNKΔhepa triple knockout mouse, replicate 1

description: NEMO/JNKΔhepa triple knockout


title: Liver, control mouse treated with DEN, replicate 2


title: Day3_WT_Rep2_RNA-seq


title: Day3_WT_Rep3_RNA-seq


title: Day3_WT_Rep1_RNA-seq


title: CON1-PB, CON2-PB

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
scRNA-seq
PolyA RNA
processed data file: CON-PB.matrix.mtx
processed data file: CON-PB.dense_umis.tsv

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment were performed with 10x Genomics Cell Ranger software.
Indexed BAM files contain position-sorted reads aligned to the genome.
Hashtag oligo (HTO) counts were quantified using CITE-seq-count.
HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells and demultiplexed using the HTODemux function in Seurat.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BALL-BM.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: BALL-PB.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: CON-BM.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: CON-PB.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: BALL-BM.dense_umis.tsv: hashtag count matrix
Supplementary_files_format_and_content: BALL-PB.dense_umis.tsv: hashtag count matrix
Supplementary_files_format_and_content: CON-BM.dense_umis.tsv: hashtag count matrix
Supplementary_files_format_and_content: CON-PB.dense_umis.tsv: hashtag count matrix
Supplementary_files_format_and_content: barcodes.mm10.tsv: raw barcodes
Supplementary_files_format_and_content: features.mm10.tsv: raw genes
Supplementary_files_format_and_content: mm.counts.raw.csv: combined raw counts matrix
Supplementary_files_format_and_content: mm.counts.normalized.csv: combined normalized counts matrix

source_name: peripheral blood mononuclear cells

extract_protocol:
Following disease onset, moribund mice were sacrificed with bone marrow and peripheral blood processed. Specifically, both tibia and femurs were flushed using centrifugation and subsequent red cell lysis, in parallel with peripheral blood red cell lysis. Murine Fc blocking (Purified Rat Anti-Mouse CD16/32, BD Pharmingen) was performed for 10 min on ice prior to fluorescence antibody staining for 30 mins at 4°C. Cells were subsequently washed in two cycles with 3 mL PBS with 2% FCS added to each tube followed by centrifugation at 300 x g at 4°C for 5 min with supernatant discarded. Finally, samples were re-suspended in 300 μL of PBS with 2% FCS per 2 x 106 cells, supplemented with DAPI (0.5 μg/mL) for live/dead staining.
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000075; Single Cell 3’ Chip Kit v3 PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

value: Healthy

value: peripheral blood mononuclear cells

tag: age (weeks)

tag: Sex

value: Female

tag: source

value: mixed sample (non-demultiplexed)

tag: source institute

value: Jackson Laboratories


title: CON1-BM, CON2-BM

description:
scRNA-seq
PolyA RNA
processed data file: CON-BM.matrix.mtx
processed data file: CON-BM.dense_umis.tsv

source_name: bone marrow

value: bone marrow


title: BALL8-PB, BALL9-PB

description:
scRNA-seq
PolyA RNA
processed data file: BALL-PB.matrix.mtx
processed data file: BALL-PB.dense_umis.tsv

value: B-ALL

tag: Stage

value: Moribund


title: U1: WT_Rep1

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

data_processing:
Reads were aligned to the XenBase X. tropicalis v9.1 reference genome using STAR v2.7.3 with default parameters and  --quantmode GeneCounts to generate raw reads counts.
Read counts were converted to counts per million and filtered to keep only those with more than 1 cpm in at least 3 samples (replicate size).
For exon-level counts,  a flattened GFF file was produced using the DEXseq v1.32.0 script "dexseq_prepare_annotation.py"; then, using the "dexseq_count.py" script, the falttened GFF,  bam files from STAR, and parameters '-p yes -r pos -s no -f bam' the exon-counts were generated.
Please refer to XenBase JgiToXenbaseGenePage_9.1.txt file for the most up-to-date annotations for each gene ID.
Genome_build: XenBase X. tropicalis v9.1

organism: Xenopus tropicalis

source_name: brain

growth_protocol: Standard X. tropicalis growth media

extract_protocol:
Trizol-based RNA extraction.
PolyA selection and and unstranded, low yield library preparation.

treatment_protocol: Uninjected or injected with CRISPR reagents targeting DYRK1A in both cells at the 2 cell stage

value: brain


title: Day3_HD_Rep3_RNA-seq

value: Developing astrocytes

value: Huntington’s Disease


title: Astrocyte_HD_Rep3_RNA-seq

value: Astrocytes


title: NPC_WT_Rep2_RNA-seq

source_name: Neural progenitor cells

value: Neural progenitor cells

value: wild type


title: U2: WT_Rep2

value: Control


title: D3: DYRK1A_Rep3

value: dyrk1a knockdown


title: BALL8-BM, BALL9-BM

description:
scRNA-seq
PolyA RNA
processed data file: BALL-BM.matrix.mtx
processed data file: BALL-BM.dense_umis.tsv


title: Astrocyte_HD_Rep1_RNA-seq


title: cryo.dhBMEC_2

city: BALTIMORE

first: Peter

middle: C

last: Searson

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
Base-calls were performed by Novogene using CASAVA base recognition.
Sequenced reads were mapped to hg38 whole genome using Rsubread v2.0.1 with default parameters.
Data were filtered using the filterByExpr function from edgeR v3.28.1, with samples grouped as iPSC, Fresh dhBMEC, and Cryo dhBMEC.
Normalization factors were calculated using the calcNormFactors function from edgeR v3.28.1 using the weighted trimmed mean of M-values (TMM) method.
Counts per Million of sample genes (CPM) were calculated using the cpm function from edgeR v3.28.1.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: one-year cryopreserved dhBMECs

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C. iPSC samples were passed onto Matrigel-coated plates at 10,000 cells/cm^2 and grown for three days in TESR-E8 with daily media switches.  dhBMECs were differentiated using sequential treatment of day 3 iPSC colonies with unconditioned media without bFGF (for six days) and endothelial media (for two days).  Unconditioned media without bFGF: DMEM/F12 supplemented with 20% knockout serum replacement, 1% non-essential amino acids, 0.5% GlutaMAX, and 0.836 μM beta-mercaptoethanol. Endothelial media: human endothelial cell serum-free medium supplemented with 1% human platelet poor derived serum, 2 ng mL-1 bFGF, and 10 mM all-trans retinoic acid.

extract_protocol:
dhBMECs were subcultured at the end of the differentiaiton (fresh) or after one-year cryopreservation on six-well plates coated with 50 μg mL-1 human placental collagen IV and 25 μg mL-1 fibronectin from human plasma in endothelial media supplemented with 1% penicillin-streptomycin and 10 mM ROCK inhibitor Y27632.  After one hour, media was switched for an additional 24 hours in the same media, before switching to 24 hours in human endothelial serum free media supplemented with 1% penicillin-streptomycin and 10 mM ROCK inhibitor. At day 2 of subculture (for dhBMECs) or day 3 of culture for iPSCs, cells were washed with 1x PBS and lysed using RLT buffer supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For cryopreservation, dhBMECs were resuspended into 60% endothelial media, 30% fetal bovine serum, and 10% dimethyl sulfoxide.  Vials were chilled to -80 °C using an isopropanol-filled Mr. Frosty container for 24 hours, and then transferred into liquid nitrogen vapor for long-term storage.  Vials were thawed at one year into endothelial media.

value: iPSC-derived brain microvascular endothelial cells (dhBMECs)

tag: cryopreservation status

value: one-year cryopreserved


title: Liver, control mouse, replicate 3

source_name: Liver, control mouse, aged 52 weeks

tag: genotype/variation

value: Liver

value: 52 weeks


title: cryo.dhBMEC_1


title: D2: DYRK1A_Rep2


title: Liver, control mouse, replicate 2

tag: treatment


title: U3: WT_Rep3


title: NPC_WT_Rep1_RNA-seq


title: NPC_HD_Rep3_RNA-seq


title: dhBMEC_3

source_name: freshly differentiated dhBMECs

value: fresh


title: dhBMEC_2


title: D1: DYRK1A_Rep1


title: HMI_Serum_starved-2

city: South Delhi

first: Sudha

last: Bhattacharya

state: Delhi

address: JNU Near Ber Sarai

department: School of Environmental Sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
RNA samples were sent to SciGenom Labs Private Limited, Cochin, Kerala for library preparation and sequencing of libraries using anIllumina HiSeq2500 (v3 Chemistry) platform (paired end, 100-bp read length). Project ID: NGS_P4173
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.36, then mapped to E. histolytica transcripts using RSEM (version 1.3.0) using --paired-end --bowtie2 -p 4
Genome_build: AAFB00000000.2
Supplementary_files_format_and_content: tab-delimited text files include expected count, TPM and FPKM values for each samples

organism: Entamoeba histolytica

growth_protocol: Trophozoites of E. histolytica strain HM-1:IMSS were axenically maintained in TYI-S-33 medium supplemented with 15% adult bovine serum (Biological industries, Israel), Diamond’s Vitamin mix, Tween 80 solution (Sigma–Aldrich) and antibiotics (0.3 units/ml penicillin and 0.25 mg/ml streptomycin) at 35.50C (Diamond et. al., 1978).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. These libraries were then subjected to paired-end sequencing on the Illumina HiSeq2500 (v3 Chemistry) platform using standard protocol at SciGenom Labs Private Limited, Cochin, Kerala

treatment_protocol:
For serum starvation, medium from early to mid-log phase grown trophozoites (48 hrs) was replaced with TYI-S-33 medium containing 0.5% adult bovine serum and incubation continued for 24hrs.
Serum replenishment was achieved by decanting total medium and replacing with complete TYI-S-33 medium. G-418 (Sigma) was added at 10 µg/ml for maintaining the transfected cell lines.

tag: strain

tag: condition

value: Serum starved

value: axenic cell culture


title: cryo.dhBMEC_3


title: dhBMEC_1


title: NPC_WT_Rep3_RNA-seq

tag: disease state


title: Liver, control mouse, replicate 1

tag: tissue

tag: mouseid


title: HMI_Serum_starved

tag: cell type


title: NPC_HD_Rep2_RNA-seq


title: T-L

city: Berlin

first: Margarete

last: Baier

address: Königin-Luise-Straße 12-16

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

description: harvested after triggering

data_processing:
All raw reads obtained by cDNA library sequencing were quality controlled with the help of the SOAPnuke software (Chen et al. 2017). Residual adaptor sequences and reads with more than 5 % unclear base pairs were assigned as unclean reads.
The remaining clean reads were aligned to the Arabidopsis reference genome TAIR10 with a phred-value of 64 using HISAT v. 2.1.0 (Kim et al. 2015)
The number of reads for each transcript were normalized against the transcript length and the total number of reads per treatment (Fragments Per Kilobase Million - FPKM).
Genome_build: Arabidopsis genome annotation TAIR10
Supplementary_files_format_and_content: Excell-file including the FPKM values for all samples and all indentified genes

organism: Arabidopsis thaliana

source_name: complette rosette (vegetative state)

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown for 28 days individually in round pots (6 cm diameter) in soil at 20 ± 2 °C at a day - night regime of 10 h light / 14 h dark and an illumination rate of 100-110 μmol quanta m−2 s−1 (Lumilux Cool White fluorescence stripes).

extract_protocol:
For the RNASeq samples, entire rosettes of ten plants were harvested per treatment at the end of the 5-day-long lag-phase and 2 h after the cold and excess light triggering treatment, combined and immediately frozen in liquid N2 to stabilize the RNA against degradation.
For RNA library construction, the mRNA was enriched using oligo (dT) magnetic beads and depleted from rRNA by DNA/rRNA hybridization according to standard procedures of the Beijing Genomics Institute (Beijing, China). Afterwards, the mRNA was transcribed into cDNA and the second DNA strand was generated with random N6 primer. The double stranded cDNA was then 5´-end repaired, 3´-poly-A-tailed and ligated with an oligo-dT-adapter.
Single-end sequencing on the Illumina High-Seq4000 platform of the Bejing Genomics Institute

treatment_protocol: For priming, a 24 h cold stimulus was imposed to half of the 4-week-old plants by transferring them 2.5 h after the onset of light to a 4 ± 2 °C cold chamber with the same aeration, illumination and air humidity setting as the 20 °C chamber. Afterwards the primed plants were placed back to 20 °C and further cultivated side-by-side with non-primed plants in a randomized pattern. Cold triggering was started after a lag-phase of 5 days at 20 °C with 1/3 of the primed and 1/3 of the control plants by transfer of the plants to 4 °C (cold triggering) . For high light triggering, 1/3 of the primed and 1/3 of the naïve plants were exposed for 2 h to a photon flux density of 800 µmol quanta m-2 s-1 30 minutes after the onset of light using halogen lamps.

tag: ecotype

value: leaves

tag: treatment 1

value: non-primed

tag: treatment 2

value: light-triggered


title: iPSC_3

source_name: BC1 iPSC line

value: iPSC


title: NPC_HD_Rep1_RNA-seq

value: Huntington’s Disease


title: HMI_Serum_Replenished-2


title: T-C

description: harvested after triggering

value: cold-triggered


title: PSC_WT_Rep3_RNA-seq

source_name: Pluripotent stem cells

value: Pluripotent stem cells


title: HMI_Serum_Replenished


title: P

description: harvested at the end of the 5 day long lag phase between priming and triggering

value: cold-primed

value: non-triggered


title: PSC_WT_Rep2_RNA-seq

value: wild type


title: C


title: HMI_Normal

value: Normal


title: PSC_HD_Rep1_RNA-seq


title: HMI_Normal-2


title: Msi1-H2

status: Public on Jun 07 2020

city: Bejing

first: Xiaole

last: Sheng

address: Yuanmingyuan west Rd 2, Haidian district

institute: China Agricultural University

description: RNA from single cell

data_processing:
Chromium Single Cell 3’ v2 libraries were sequenced with a Novaseq 6000 sequencer, with the following sequencing parameters: read 1, 150 cycles; i7 index, 8 cycles and read 2, 150 cycles.
Raw Illumina data were demultiplexed and processed using Cell Ranger (10X Genomics version Cell Ranger 2.0.1)
In order to remove partial cells and doublets, cells with less than 1000 genes or more than 7000 genes were removed.
Cells with more than 10% of mitochondrial unique molecular identifiers (UMIs) were removed, as a high proportion of mitochondrial expression in cells is indicative of cell stress/damage during isolation.
In order to reduce gene expression noise, genes that are expressed in 6 cells or less are removed
Genome_build: mm10

source_name: intestinal epithelium

extract_protocol:
Intestinal epithelium were digested into single cells, the GFP+ cells were sorted by FACS.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at beijing capitalBio technology
Single Cell 3’ v2 chemistry - 10X Genomics

tag: sample type

tag: age

value: Adult

value: Tamoxifen for 2 days

tag: genotype

value: Msi1-CreERT2; R26-mTmG


title: Lgr5-H2

description: RNA from single cell

value: Lgr5-EGFP-IRES-CreERT2; R26-td


title: PT-L

description: harvested after triggering


title: Msi1-IR5

description: RNA from single cell

value: Tamoxifen for 15 hrs then Irradiation for 5 days


title: Msi1-IR3

description: RNA from single cell

value: Tamoxifen for 15 hrs then Irradiation for 3 days


title: PT-C

description: harvested after triggering

value: leaves


title: iPSC_1

value: fresh


title: Msi1-IR2

description: RNA from single cell

value: Tamoxifen for 15 hrs then Irradiation for 2 days


title: iPSC_2

value: iPSC


title: Msi1-IR1

description: RNA from single cell

value: Tamoxifen for 15 hrs then Irradiation for 1 day


title: Msi1-H15h

description: RNA from single cell

value: Tamoxifen for 15 hrs


title: sig-MeJA-24h-2

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Read counts of genes and their isoformes were calculated by HTseq-count Version 0.11.2
Genome_build: Capsicum annuum v1.6
Supplementary_files_format_and_content: tab-delimited text files include the values of read count for each sample

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

tag: cultivar

value: Bukang

value: six weeks

value: Leaves


title: sig-MeJA-24h-3


title: sig-MeJA-24h-1


title: sig-MeJA-12h-3


title: HEALTHY-PB1, HEALTHY-PB2, BALL-PB1, BALL-PB2

description:
scRNA-seq
PolyA RNA

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment were performed with 10x Genomics Cell Ranger software.
Indexed BAM files contain position-sorted reads aligned to the genome.
Hashtag oligo (HTO) counts were quantified using CITE-seq-count.
HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells and demultiplexed using the HTODemux function in Seurat.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: hPB.matrix.mtx: raw gene-barcode matrix
Supplementary_files_format_and_content: barcodes.hg38.tsv: raw barcodes
Supplementary_files_format_and_content: features.hg38.tsv: raw genes
Supplementary_files_format_and_content: hPB.dense_umis.tsv: hashtag count matrix
Supplementary_files_format_and_content: hPB.counts.raw.csv: combined raw counts matrix
Supplementary_files_format_and_content: hPB.counts.normalized.csv: combined normalized counts matrix

extract_protocol:
Frozen peripheral blood specimens were rapidly thawed and transferred into 50 mL conical tubes. 20 mL Pre-warmed RPMI 1640 (Corning) supplemented with 5% Fetal Bovine Serum (FBS) (Sigma Aldrich) and 2-Mercaptoethanol (2-ME, 55nM) (Thermo Fisher Scientific) was added drop-wise to tubes. Cell suspensions were subjected to centrifugation at 400 x g for 5 min at 4°C and supernatant was discarded. Pellets were re-suspended in 5mL RPMI 1640 with 5% FBS and 2-ME, and filtered using a 70 μm nylon mesh (Thermo Fisher Scientific) with residual cell clumps discarded. After centrifuging at 400 x g at 4°C for 5 min, the supernatant was discarded, and the cell pellet was re-suspended in PBS (Corning) with 2% FCS and placed on ice prior to staining for FACS. Single-cell BM suspensions were re-suspended in PBS with 2% FCS and Human TruStain FcX Blocking Solution (BioLegend) and incubated on ice for 10 mins. Cell suspensions were centrifuged at 400 x g at 4°C for 5 min, and supernatant discarded. Cell pellets were re-suspended in PBS with 2% FCS, FITC-conjugated anti-human CD45 (1:200, BD Pharmingen), APC-conjugated anti-human CD19 (1:200 concentration, BioLegend) and PE-conjugated anti-human CD10 (1:200, BioLegend), and incubated on ice for 30 mins. Following incubation, cell suspensions were subjected to two wash cycles involving re-suspension of cell pellets in 3 mL PBS with 2% FCS, followed by centrifuging at 400 x g at 4°C for 5 min, followed by supernatant removal. Finally, samples were re-suspended in 300 mL of PBS with 2% FCS per 2 x 106 cells, supplemented with DAPI (0.5 mg/mL) for live/dead staining. Cell sorting was performed using the SY3200™ highly automated parallel sorting (HAPS) cell sorter (Sony).
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000075; Single Cell 3’ Chip Kit v3 PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

value: mixed sample (non-demultiplexed)

tag: Stage

tag: age (years)

tag: Sex

value: Male

tag: source

tag: source institute


title: sig-MeJA-12h-1


title: sig-MeJA-6h-3


title: sig-MeJA-6h-2


title: sig-MeJA-6h-1