title: 19-L-958-13bp-WT-LT-3

value: wild type


title: JH191_S24_1

status: Public on Jan 21 2022

type: SRA

city: Dallas

first: Jeremiah

last: Herbert

state: Texas

address: 5323 Harry Hines Blvd., MC 8511

department: Green Center for Reproductive Biology

country: USA

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Raw sequencing fastq files were mapped to the human genome build hg38 using the bwa mem aligner (0.7.5), with the following options: (-M: samtools view -q10 -bS -o).
Genome browser tracks were generated using the bedtools (version 2.29.2) utilities: genomecov sort, then processed to bigwig files with bedGraphToBigWig.

molecule: genomic DNA

organism: Homo sapiens

source_name: HS3 KO 1B5

growth_protocol: Cells were cultured in accordance with ATCC guidelines, in Iscove′s Modified Dulbecco′s Medium (Sigma-Aldrich I3390) supplemented with 10% FBS , 1% Pen/Strep (Sigma-Aldrich P4333), and 1% GlutaMAX (ThermoFisher 35050061).

extract_protocol: Viable cells were pelleted by centrifugation at 500g for 5 min at 4°C, then cell membranes were lysed in RSB with 0.1% Tween-20, 0.01% Digitonin, and 0.1% NP-40. Cell nuclei were pelleted by centrifugation at 500g for 10 min at 4°C, and digested with Tn5 for 30 minutes at 37°C. Transposition reaction was cleaned up with Qiagen PCR Clean-Up, and sequencing adapters added by PCR with KAPA HiFi enzyme mix . Final libraries were cleaned up with two 1.2x SPRI Select beads purifications and assayed by Qubit and TapeStation before submission for sequencing.

treatment_protocol: When seeking maximal GFP expression in tagged lines, enhancer knockout cell lines were treated with 2µg/mL of puromycin for 7 days, then assayed with FACS, analyzing mean fluorescence intensity with FlowJo.

tag: cell line

value: K562 cell line

tag: genotype

value: bgl HS3 KO


title: wt_4_input [re-analysis]

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

description:
B2-1-2_S8_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv

library_source: transcriptomic

data_processing:
reads trimmed with trimmomatic
alignment performed with Bowtie2 to TAIR10.48 genome
indexing with samtools
gene counting performed with htseq
differential expression analysis with DEseq2
Genome_build: TAIR10.48
Supplementary_files_format_and_content: .csv, differential expression analysis results

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: wild type input

growth_protocol: Arabidopsis seeds were cultured in plates. Seeds planted in plates were sterilized by soaking in 5% NaClO for 4 min and then washed with sterile water for 5 times before being planted onto 0.5 × MS medium plus 1% sucrose. Plates were placed in the cold room (4°C, dark) for 2 days and then kept in the tissue culture room (16 h light: 8 h dark, 22°C) until used.

extract_protocol:
Total RNA was isolated using hot phenol extration. Poly(A) RNA was prepared according to the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB). m6A levels were measured by two-dimensional thin layer chromatography (TLC) analysis as described previously
The libraries from fragmented poly (A) RNA (100-150 nt) were prepared using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina) followed by size selection  using E-Gel SizeSelect II (Invitrogen), and quality checked on Agilent High Sensitivity DNA Chips (Agilent).

tag: developmental stage/tissue

value: 2 weeks old, whole seedlings

tag: ecotype

value: Columbia

value: wt


title: 19-L-958-13bp-WT-LT-2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-seq was performed with three biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation [University of California at Santa Cruz (UCSC) gene models] with Cufflinks (v2.2.1). The expression level of each gene was quantified as FPKM, and FPKM values of replicates were averaged.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

molecule: total RNA

organism: Mus musculus

growth_protocol: All mice were bred in-house under specific-pathogen-free (SPF) conditions in individually ventilated cages (IVC).

extract_protocol:
Total RNA from 1500 FACS-sorted LT-HSCs was extracted using Quick-RNA Kits (ZYMO) and resuspended in nuclease-free water.
cDNA synthesized and amplified from the total RNA was used the Smart-seq2 method as described previously (Picelli et al., 2014). Sequencing libraries were generated from 500pg cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s protocols. All the samples were sequenced on the Illumina HiSeq X Ten sequencers with 150 bp paired-end reads.

treatment_protocol: Bone marrow cells stained with fluorochrome-labeled HSC antibodies were sorted on an Influx cell sorter (BD Biosciences).

tag: stain

tag: age

value: 2 months

tag: genotype/variation

tag: tissue

value: bone marrow

tag: cell type

value: FACS-sorted LT-HSCs


title: 19-L-958-13bp-WT-LT-1


title: CALGB03-1037784-K-6

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
Sample_PRE_RNA_010
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

data_processing:
Basecalls by Casava.
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a.
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments.
Fixed upper quartile normalization.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: CALGB40603.389PreTreat.JUNCTION.salmon_gene_normalized.matrix_FOR_GEO.v2.txt: Tab-delimited, normalized, transcript abundance estimates.

source_name: Breast

extract_protocol: Fresh-frozen RNA was isolated with Qiagen RNeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002).

value: Breast carcinoma

tag: treatment

value: None - Pretreatment Neoadjuvant Therapy


title: wt_3_input

description:
B1-3-5_S7_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv


title: JH189_S22_1

source_name: HS3 KO 1B3


title: JH188_S21_1


title: JH190_S23_1


title: wt_1_input

description:
B1-3-8_S3_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv


title: wt_6_input [re-analysis]

description:
B2-2-8_S14_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv


title: JH186_S19_1

source_name: LCR KO 1H4 GFP+

value: Potential blg LCR KO


title: JH187_S20_1


title: TAP-Tagged ACSS2, Log Growth Replicate 1

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Demultiplexing: chIPseq tags generated with the NextSeq 550 platform were demultiplexed using native applications on BaseSpace.
Alignment: data were aligned to the sacCer3 reference genome using Bowtie2 v2.3.4.1, (parameters --local -X 1000).
Quality Control: aligned tags were filtered for poor alignments using samtools v1.1 (samtools view -q 5 -bS) and merged over NextSeq lanes (samtools merge -n), sorted by tag ID using samtools sort -n, then filtered for PCR duplicates using PICARD (java -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname).
Track Creation: supplied bigWigs were created for ChIP–seq data by first pooling replicates and generating coverage maps using BEDtools genomeCoverageBed -bg, then adjusting for library size using the RPM (reads per million) coefficient. The input signal was then subtracted from the ChIP signal. The resulting tracks were converted from bedGraph to bigWig files by first sorting by position (bedSort) then using the bedGraphToBigWig utility from the UCSC Genome Browser.
Genome_build: sacCer3
Supplementary_files_format_and_content: The supplied bigWigs show input-subtracted and library size-adjusted tag pile-ups for the four histone acetyl chIPs as well as ACSS2 and TAP-Tagged ACSS2.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Saccharomyces cerevisiae glycerol stocks were streaked onto 2% agar plates containing yeast nitrogen base (Difco #233520), synthetic complete amino acids mix (Bufferad #S0051) and 2% glucose. Following overnight incubation at 30°C, starter cultures were inoculated with single colonies and incubated overnight at 30°C. Secondary cultures were inoculated at OD600=0.2 and grown at 30°C until they reached OD600=1.

extract_protocol:
Cultures were cross-linked with 1% formaldehyde at RT for 10 min. Reaction was stopped by adding 135 mM glycine. Cultures were then pelleted, washed and resuspended in FA-lysis buffer containing protease/phosphatase inhibitors and 10 mM Na-butyrate. Cells were lysed using a 0.5 mm Zirconia/Silica beads (RPI #9834) in a Mini-Beadbeater high energy cell disruptor (BioSpec) at 4°C, for 6 times 60 seconds. Samples were cooled on ice for 2 min in-between beatings. Subsequently, lysates were sonicated for 20 min in BioRuptor (Diagenode), using high setting and 30 seconds ON/OFF cycles. Cell debris was removed by centrifugation at 10,000 rcf for 15 min at 4°C. Sonication efficiency was confirmed for each sample by running on 0.8% agarose gel. Equal aliquots of sonicated lysates were used per immunoprecipitation reaction with 5 ul of H3K9ac antibody (Active Motif 39317), 5 ul H3K14ac antibody (Active Motif 39697), 5 ul of H3K18ac antibody (Active Motif 39755), 4 ul H3K23ac antibody (Millipore 07-355), 5 ul H3K27ac antibody (Abcam ab4729), 5 ul of H4K12ac antibody (Abcam ab46983), 5 ul H4K16ac antibody (Millipore 07-329), 5 ul Acs2 antibody (Thermo MA5-14810) or 8 ul TAP antibody (Invitrogen CAB1001) preconjugated to Protein G Dynabeads (Life Technologies). Ten percent of the chromatin was saved as input DNA. ChIP reactions were incubated overnight at 4 °C with rotation and washed three times in wash buffer. Immunoprecipitated DNA was eluted from the beads, reversed cross-linked and purified together with the input DNA.
Exactly 20 ng DNA (either ChIP or input) was used to construct sequencing libraries using the NEBNext Ultra II DNA library preparation kit for Illumina (New England Biolabs; NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-end sequenced (75 bp) on the NextSeq 550 platform (Illumina) in accordance with the manufacturer’s protocol.

treatment_protocol: Proliferating cultures were pelleted and resuspended in autoclaved water containing 10 mM D3-acetate (Sigma 176079) to induce quiescence. After 7 days, quiescent cultures were pelleted and washed to remove any residual D3-acetate, and proliferation was induced by resuspending in liquid media.

tag: strain

value: pJD47 TAP-Tagged

tag: time point

value: LOG

tag: antibody

value: Invitrogen CAB1001


title: JH184_S17_1

source_name: LCR KO 3E9


title: JH182_S15_1

source_name: LCR KO 3B12


title: TAP-Tagged ACSS2, Exit 240 min Replicate 1


title: JH183_S16_1


title: TAP-Tagged ACSS2, Quiescent Replicate 1

value: Q


title: wt_2_input

description:
B1-3-1_S2_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv


title: JH181_S14_1

source_name: LCR KO 2E11


title: TAP-Tagged Input, Exit 30 min Replicate 1


title: TAP-Tagged Input, Exit 30 min Replicate 2


title: TAP-Tagged Input, Log Growth Replicate 1


title: TCPOBOP Treated_6hr_2

type: RNA

city: Monserrato

first: Rajesh

last: Pal

state: Cagliari

address: Cittadella Universitaria, SP. 8 Monserrato

department: Department of Biomedical Sciences

country: Italy

institute: University of Cagliari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BRB Array Tools version 4.6.0 for quality control and gene expression analysis. First, the quantile normalization algorithm was applied to the data set. Only genes whose expression differed by at least 1.5-fold from the median in at least 20% of the arrays and characterized by the 50th percentile of intensities >300 were retained. The false discovery rate–adjusted P values were calculated using the Benjamini-Hochberg procedure. To identify the differentially expressed genes, F-test and Multivariate Permutation Test were applied. Further, the genes were filtered based on their fold change values (±1.5).

label: Biotinylated UTP

source_name: Liver

label_protocol: RNA was amplified (TotalPrep RNA Amplification Kit; Illumina Inc., San Diego, CA), labeled, and hybridized on Illumina microarray MouseRef-8 Expression BeadChips v2

extract_protocol: Total RNA was isolated with the RNeasy Plus Mini isolation kit (Qiagen) from 3 livers of untreated and treated mice, subjected to PH or TCP treatment

treatment_protocol: TCPOBOP (Sigma-Aldrich), was dissolved in dimethyl sulfoxide/corn oil. A single dose of 3 mg/kg body weight was administered by gavage. PH was performed by removal of 70% of the liver mass as originally described by Higgins and Anderson. Miice were sacrificed 1, 3 and 6 hours after each treatment. Three mice were used per group at each time point

tag: Sex

value: Female

value: TCP

tag: time

value: Liver


title: TAP-Tagged ACSS2, Exit 30 min Replicate 2


title: TAP-Tagged Input, Exit 240 min Replicate 1


title: TCPOBOP Treated_6hr_1


title: TCPOBOP Treated_6hr_3


title: JH180_S13_1

value: K562 cell line


title: TAP-Tagged Input, Quiescent Replicate 2


title: JH185_S18_1


title: JH179_S12_1

source_name: LCR KO 1H6


title: TAP-Tagged Input, Quiescent Replicate 1


title: TAP-Tagged ACSS2, Exit 30 min Replicate 1


title: TAP-Tagged ACSS2, Quiescent Replicate 2


title: JH178_S11_1


title: TCPOBOP Treated_3hr_2


title: JH177_S10_1

source_name: LCR KO 1D5


title: ACSS2, Log Growth Replicate 2

value: Thermo MA5-14810


title: JH176_S9_1


title: TCPOBOP Treated_3hr_3


title: ACSS2, Log Growth Replicate 1


title: TCPOBOP Treated_1hr_2


title: TCPOBOP Treated_3hr_1


title: TCPOBOP Treated_1hr_3


title: JH175_S8_1

source_name: HS2-4 KO 1F5 GFP+

value: Potential bgl HS2-4 KO


title: Partial Hepatectomy_6hr_3

value: PH


title: ACSS2, Exit 240 min Replicate 2


title: TCPOBOP Treated_1hr_1


title: FNR MeA-Run2

city: Palo Alto

first: Joseph

middle: Riley

last: Knoedler

state: CA

address: 1201 Welch Road

department: Psychiatry and Behavioral Sciences

institute: Stanford Univesity

description: Nuclear RNA

data_processing:
Reads were aligned to the mm10 build of the mouse transcriptome, modified to include and quantify intronic reads using the kallisto-bustools pipeline
Cell x gene matrix was loaded into Seurat (R programming environment). Cells were retained if they contained > 500 unique molecular identifies (UMIs); genes were retained if they were detected in 3 or more cells
Cells were grouped into clusters by principle component analysis and Jaccard-Louvain clustering.
Low quality clusters (low UMI count, lack of significant markers, high mitochondrial gene count) were filtered and clustering re-run
Clusters with few Esr1+ cells or markers that indicated cells originated outside region of interest were filtered
Genome_build: mm10
Supplementary_files_format_and_content: For each region surveyed, a cell x gene matrix with all cells passing filtering criteria is provided along with a metadata file indicating cluster identity and condition of origin for each cell
Supplementary_files_format_and_content: Unfiltered count matrices for single nucleus RNAseq samples

source_name: MeA

growth_protocol: Mice were group-housed until euthansia

extract_protocol:
Nuclei were extracted by density gradient centrifugaion. GFP+ nuclei were isolated using an Aria FACS sorter.
Single nucleus libraries were generated on the 10X Chromium platform using the 3' RNA v3 kit.
Libraries were sequenced on either a HiSeq4000 or NovaSeq 6000

treatment_protocol: Female mice were ovariectomized. FR mice received two days of estrogen injection followed by one day of progesterone injection on day of euthanasia, while FNR mice received equivalent vehicle injections

value: Brain

tag: gender

value: OVX + Veh


title: JH174_S7_1


title: ACSS2, Exit 240 min Replicate 1


title: FNR VMH 3

description: immunoprecipitated mRNA from Esr1+ neurons

data_processing:
Optical duplicates were removed using clumpify.sh from bbtools
Reads were pseudoaligned and quantified to mouse polyadenylated transcripts (Gencode vM21) using kallisto
Tximport was used calculate gene-level abundance prior to analysis with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file for each sample showing transcript-level quantification
Supplementary_files_format_and_content: Matrix from each region profiled with filtered, normalized gene-level abundance !Sample_data_processing = Supplementary_files_format_and_content: DESeq2 output tables

source_name: VMH

extract_protocol:
Brain regions were microdissected, flash frozen on dry ice and subject to immunoprecipitation with HA antibody. RNA was extracted with QIAgen DNeasy kit. Sequencing libraries were constructed using the Nugen Universal mRNA kit (10 ng/sample)
Libraries were prepared for sequencing using standard Illumina sequencing protocols

tag: hormone status


title: Male BNST-Run1

description: Nuclear RNA

source_name: BNST

value: Male

value: Intact


title: FNR VMH 2


title: Partial Hepatectomy_6hr_2


title: ACSS2, Exit 30 min Replicate 2


title: JH173_S6_1

source_name: HS2-4 KO 4B5

tag: cell line


title: FNR VMH 1

tag: genotype


title: ACSS2, Exit 30 min Replicate 1


title: JH172_S5_1


title: FR VMH 3

value: OVX + E2/P


title: Partial Hepatectomy_3hr_3


title: Partial Hepatectomy_3hr_2


title: Partial Hepatectomy_6hr_1


title: Partial Hepatectomy_3hr_1


title: JH171_S4_1

source_name: HS2-4 KO 2H5


title: FR VMH 2


title: ACSS2, Quiescent Replicate 2


title: FR VMH 1


title: Male VMH Rep 3


title: Male VMH Rep 2


title: JH170_S3_1


title: ACSS2, Quiescent Replicate 1


title: JH162_S73

source_name: HBG-GdTaP 1A7

value: Single bgl locus parental, GFP-tagged


title: Input, Exit 240 min Replicate 2


title: Input, Exit 240 min Replicate 1


title: Partial Hepatectomy_1hr_3


title: JH168_S1_1

source_name: HS2-4 KO 2H3


title: JH163_S74


title: Male VMH Rep 1


title: Input, Log Growth Replicate 1


title: Control Liver_2

value: CO

value: control


title: Control Liver_3


title: Partial Hepatectomy_1hr_1


title: FNR POA Rep 3

source_name: POA


title: Input, Log Growth Replicate 2

value: LOG


title: JH169_S2_1


title: Input, Exit 30 min Replicate 1


title: Input, Exit 30 min Replicate 2


title: JH160_S71

source_name: K562 {delta}{beta}gl

value: Single bgl locus parental


title: FNR POA Rep 1

value: Female


title: ONCM, biological rep 2

city: Su-won

first: Min Jung

last: Kwon

address: 206, World cup-ro

country: South Korea

institute: Ajou University

data_processing:
Illumina platform
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: mouse DRG tissue

growth_protocol: Adult (8weeks) female C57Bl6 (25-30g) were used.

extract_protocol:
Total RNA was isolated using an Rneasy Microarray Tissue Mini kit (Qiagen) in accordance with the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: Cultured DRGs neurons from WT mouse and treated with PBS or 100 ng/ml of recombinant ONCM for 12 hr.

value: cultured DRG neurons

value: mouse DRG tissue

value: Oncomodulin

value: female


title: ONCM, biological rep 3


title: Partial Hepatectomy_1hr_2

value: Liver


title: PBS, biological rep 3

value: PBS as negative control


title: Input, Quiescent Replicate 2

source_name: S. cerevisiae

value: Q


title: JH159_S70

source_name: HS4 KO 1D3 GFP+

value: K562 cell line

value: Potential bgl HS4 KO


title: FR POA Rep 3

value: Brain


title: JH158_S69


title: Input, Quiescent Replicate 1


title: FR POA Rep 2

value: OVX + E2/P


title: PBS, biological rep 1


title: PBS, biological rep 2


title: JH157_S68

source_name: HS4 KO 2A11 GFP-


title: Male POA Rep 3

value: Male

value: Intact


title: H3K27ac, Log Growth Replicate 2

value: Abcam ab4729


title: JH161_S72


title: JH155_S66

source_name: HS4 KO 4H11


title: L3

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: tab-delimited text files include gene expression count for each Sample

organism: Argopecten irradians concentricus

source_name: adductor muscle

extract_protocol:
Adductor muscle tissues were dissected and stored in liquid nitrogen individually.Total RNA from each tank was isolated by TRIzol reagent (Invitrogen, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: low temperature

value: one year old


title: FNR POA Rep 2

value: Female

value: OVX + Veh


title: JH154_S65


title: L2


title: H3K27ac, Exit 240 min Replicate 1


title: Male POA Rep 2


title: H3K27ac, Exit 240 min Replicate 2


title: Male POA Rep 1


title: L1


title: ONCM, biological rep 1

value: cultured DRG neurons

value: mouse DRG tissue


title: JH153_S64

source_name: HS4 KO 4C5


title: FNR MeA Rep 3


title: H3K27ac, Exit 30 min Replicate 2


title: H3

value: high temperature


title: FR POA Rep 1


title: JH156_S67


title: H3K27ac, Exit 30 min Replicate 1


title: H1


title: FNR MeA Rep 2


title: JH151_S62

source_name: HS4 KO 3H4


title: H2


title: FNR MeA Rep 1

source_name: MeA


title: JH150_S61


title: H3K27ac, Log Growth Replicate 1

value: LOG


title: H3K27ac, Quiescent Replicate 1


title: C3

value: room temperature


title: H3K23ac, Log Growth Replicate 2

value: Millipore 07-355


title: JH149_S60

source_name: HS4 KO 3D9

value: K562 cell line


title: FR MeA Rep 3


title: FR MeA Rep 2


title: H3K23ac, Log Growth Replicate 1


title: C2


title: Male MeA Rep 3


title: JH147_S58

source_name: HS4 KO 3C4

value: Potential bgl HS4 KO


title: H3K23ac, Exit 240 min Replicate 2


title: JH148_S59


title: C1


title: FR MeA Rep 1

value: Brain


title: JH146_S57


title: JH152_S63


title: JH145_S56

source_name: HS4 KO 3B3


title: H3K23ac, Exit 30 min Replicate 2


title: H3K27ac, Quiescent Replicate 2

value: Q


title: H3K23ac, Exit 240 min Replicate 1


title: H3K23ac, Exit 30 min Replicate 1


title: Male MeA Rep 2

value: Male


title: Male MeA Rep 1

value: Intact


title: JH144_S55


title: FNR BNST Rep 3

source_name: BNST


title: H3K23ac, Quiescent Replicate 2


title: JH143_S54

source_name: HS4 KO 2G2


title: JH142_S53


title: H3K23ac, Quiescent Replicate 1


title: FNR BNST Rep 2


title: FNR BNST Rep 1


title: GDM-N-3

city: Nanjing

first: Juan

last: Wen

address: Tianfei Xiang 123#

institute: Women’s Hospital of Nanjing Medical University

description: RNA expression in cord blood exosomes from control

hyb_protocol: Each slide was hybridized with 1.65 mg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent Technologies) in Hybridization Oven (Agilent Technologies).

scan_protocol: slides were scanned by Agilent Microarray Scanner (Agilent Technologies) with default settings.

data_processing: Data were extracted with Feature Extraction software 12.0 (Agilent Technologies).

source_name: cord blood

label_protocol: Total RNA was then amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total exosomal RNA was extracted using Serum/Plasma Kit (QIAGEN, Germany).

value: blood exosomes

tag: disease state

value: control


title: JH141_S52

source_name: HS4 KO 2D11


title: H3K18ac, Log Growth Replicate 1

value: Active Motif 39755


title: H3K18ac, Log Growth Replicate 2


title: JH140_S51


title: FR BNSTpr Rep 3

value: Female

value: OVX + E2/P


title: FR BNSTpr Rep 2


title: FR BNSTpr Rep 1


title: H3K18ac, Exit 240 min Replicate 1


title: H3K18ac, Exit 240 min Replicate 2


title: GDM-M-2

description: RNA expression in cord blood exosomes from GDM-macrosomia

value: GDM-macrosomia


title: GDM-N-1


title: GDM-M-1


title: GDM-M-3


title: GDM-N-2


title: JH139_S50

source_name: HS4 KO 2A6


title: Control Liver_1

source_name: Liver

value: CO

value: Liver


title: JH138_S49


title: JH137_S48

source_name: HS4 KO 1G8


title: Male BNSTpr Rep 3


title: Male BNSTpr Rep 2


title: JH136_S47


title: Male BNSTpr Rep 1


title: H3K18ac, Exit 30 min Replicate 1

source_name: S. cerevisiae


title: H3K18ac, Exit 30 min Replicate 2


title: E9_H3K4me2_ChIP_input

city: Austin

first: Steven

middle: A.

last: Vokes

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mouse limb buds

extract_protocol:
limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
Libraries were prepared with the following number of amplification cycles, for each given experiment: CUT&Tag/Run- 14 cycles, ChIP- 15 cycles, ATAC- 11 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.
ChIP & CUT&RUN library- NEBNext Ultra II DNA Library Prep Kit; ATAC & CUT&Tag- NEBNext HF 2x PCR Master Mix; RNA-seq- NEBNext Ultra II RNA Library Prep Kit

tag: strain/background

value: Swiss Webster

value: ~4 litters FLs (600k cells)

tag: Stage

value: forelimb bud


title: JH134_S45

source_name: HS3 KO 1E3 GFP+

value: K562 cell line

value: Potential bgl HS3 KO


title: H3K18ac, Quiescent Replicate 1


title: H3K18ac, Quiescent Replicate 2


title: SHR AMYG Ov+E 5

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

country: Japan

institute: International Christian University

description: gene expression in the amygdala of female SHR five weeks after ovariectomy and after four weeks of estradiol supplementation

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60ºC for 30 minutes with 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Rat GE 8x60k v2 (Agilent) Microarrays for 17 hours at 65ºC 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 37ºC GE Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for Sureprint G3 unrestricted GE 8x60 (G4858A) slides (Scan Area 61x21.6 mm, Profile AgilentHD_GX_1 color,  Scan resolution 3μm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074036_D_F_20180103) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as “glsFeatNonUnifOL”and “glsBGNonUnifOL ”in at least 50% of all samples were excluded. Features that were not flagged as “gIsWellAboveBG“in half of the samples or more in each group were eliminated.

organism: Rattus norvegicus

source_name: SHR amygdala, ovariectomized+estradiol

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 4-weeks-old female SHR rats were incised and both ovaries were removed. Rats were given one week to recover after suture and were subcutaneously implanted Alzet minipump containing PEG (OV, n=4) or estradiol in PEG (0.33 mg/ml, releasing 2 μg estradiol/day/rat) (OV+E rats, n=5) for one month.

extract_protocol: The amygdala of each rat was homogenized in TRIzol reagent, the total RNAs were isolated according to the protocol supplied by the manufacturer (Life Technologies) and stored at −80ºC. The purity (260/230 and 260/280 ratio >1.7) and integrity (RIN > 7) for all total RNA samples were verified by using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer respectively.

treatment_protocol: All animals were allowed to eat and drink ad libitum until the day of the tissue collection. Animals were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium, placed on an ice-cold platform,  amygdala (right and left part) was dissected under a dissecting microscope, and stored at -80ºC until processing.  A single operator performed all dissections.

value: Amygdala

value: female

value: SHR

tag: age

value: 9 weeks old


title: SHR AMYG Ov+E 4

value: after ovariectomy and after four weeks of estradiol supplementation


title: SHR AMYG Ov+E 3


title: SHR AMYG Ov+E 1

value: after ovariectomy and after  four weeks of estradiol supplementation


title: SHR AMYG Ov+E 2


title: JH132_S43

source_name: HS3 KO 1A5 GFP-


title: H3K9ac, Log Growth Replicate 1

value: LOG

value: Active Motif 39317


title: H3K9ac, Log Growth Replicate 2


title: JH133_S44


title: SHR AMYG Ov 3

description: gene expression in the amygdala of female SHR five weeks after ovariectomy

source_name: SHR amygdala, ovariectomized

value: ovariectomy


title: PDX34a

city: New York

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine

data_processing:
The raw data were processed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
featureCounts of Rsubread_1.32.4 (PMID: 30783653) was used to calcuate the raw counts from bam files, then readcounts were normalized and logged using log2(count+1) with DESeq2_1.22.2 (PMID: 25516281)
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: comma delimited text file containing log normalized counts of consensus peaks across all 40 samples

source_name: prostate cancer PDX

growth_protocol: Organoid culture and seeding experiments were performed as described previously (PMID: 25201529, 26797458)

extract_protocol: The libraries were generated using the OMNI-ATAC protocol (PMID: 28846090), and the final library was purified with AMPure beads (Beckman Coulter, A63880).

tag: primary site

value: Prostate

tag: biopsy site

value: Circulating tumor cells

tag: sample type

value: prostate cancer PDX


title: H3K9ac, Exit 240 min Replicate 2


title: iSPTΔBT_1526 rep B

city: Tuebingen

first: Stacey

last: Heaver

address: Max-Planck-Ring 5

department: Microbiome Science

country: Germany

institute: Max Planck Institute for Biology Tuebingen

data_processing:
Sequence reads were trimmed to remove adapter, quality assessed using FastQC, quality filtered with bbduk (quality cutoff = 20)
Reads were aligned to the Ensembl Bacteroides thetaiotaomicron VPI-5482 genome with bowtie 2
Aligned reads were assigned using htseq-count (alignment quality cutoff = 10)
Supplementary_files_format_and_content: tab-delimited text files include log2-counts per million for each sample

organism: Bacteroides thetaiotaomicron

source_name: bacterial culture

growth_protocol: 15-hour anaerobic growth in Bacteroides minimal medium at 37 deg C

extract_protocol:
QIAzol lysis reagent and miRNeasy Mini Kit (Qiagen)
rRNA was removed with the Bacterial RiboMinus Transcriptome Isolation Kit (Invitrogen) and the library prepared with the TruSeq Stranded Total RNA Library Kit (Illumina)

treatment_protocol: Bacteria with the iSPT background strain were induced with 100 ng/mL anhydrotetracycline

value: VPI-5482 delta-tdk delta-BT0870 delta-BT1526; 3xBT1311p-tetR; P1TDP-BT0870

tag: treatment

value: induction 100 ng/mL aTC


title: E9_H3K4me2_ChIP_rep2

value: Swiss Webster

tag: tissue

value: ~4 litters FLs (600k cells)

value: forelimb bud


title: E9_H3K4me2_ChIP_rep1


title: SHR AMYG Ov 5

value: Amygdala

tag: strain


title: JH131_S42

source_name: HS3 KO 4E9

value: K562 cell line

value: Potential bgl HS3 KO


title: iSPTΔBT_1526 rep A


title: JH130_S41


title: H3K9ac, Exit 240 min Replicate 1

tag: time point

tag: antibody


title: JH135_S46


title: PDX16a

value: femur left


title: iSPT rep B

value: VPI-5482 delta-tdk delta-BT0870; 3xBT1311p-tetR; P1TDP-BT0870


title: H3K9ac, Exit 30 min Replicate 2


title: JH127_S40

source_name: HS3 KO 2D11


title: SHR AMYG Ov 1

value: female

value: SHR

value: 9 weeks old


title: iSPT rep A


title: PDX10a

value: Brain


title: JH126_S39


title: SHR AMYG Ov 2

value: ovariectomy


title: H3K9ac, Exit 30 min Replicate 1

value: Active Motif 39317


title: PDX09a

value: Prostate

value: Pleural Fluid

value: prostate cancer PDX


title: ΔBT_1522 rep B

value: VPI-5482 delta-tdk dBT_1522

value: induction n/a


title: PDX16b

value: ilium right


title: ΔBT_1522 rep A


title: JH124_S37

source_name: HS3 KO 2B6


title: H3K9ac, Quiescent Replicate 2

value: Q


title: H660

source_name: prostate cancer cell line

value: cervical lymph node

value: prostate cancer cell line


title: JH121_S36

source_name: HS3 KO 1H3

value: K562 cell line

value: Potential bgl HS3 KO


title: wild-type rep A

value: VPI-5482 delta-tdk


title: PDX01a

value: lymph node


title: H3K9ac, Quiescent Replicate 1


title: wild-type rep B


title: PC3

value: bone


title: JH119_S34

source_name: HS3 KO 1B11


title: JH120_S35


title: Log Growth Replicate 3

data_processing:
Demultiplexing: sequencing data were demultiplexed using native applications on BaseSpace.
Alignment: demultiplexed FASTQs were aligned by RNA-STAR v.2.5.2a to the sacCer3 assembly of the yeast genome (parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000).
Gene Quantification: aligned reads were mapped to genomic features using HTSeq v.0.6.1 after merging four lanes of NextSeq (parameters -r pos -s no -t exon -i gene_id).
Size Adjustment: library size adjustment and analysis of differential gene expression was done using DESeq2 (Wald’s test) using the time-course variable in the design; adjusted counts supplied in the Adjusted Values.txt table were obtained using counts(DESEQ_OBJECT, normalized=T)
Track Creation: supplied bigWigs were obtained by first pooling three replicates in each time point, then employing the BEDtools script genomeCoverageBed -bg to create a coverage map (bedGraph) of pooled RNA-seq signal, then multiplying tag counts in the map by the RPM coefficient for each pooled time point. Size-adjusted bedGraphs were then sorted into position order and rendered as bigWigs using the UCSC Genome Browser utilities bedSort and bedGraphToBigWig.
Genome_build: sacCer3
Supplementary_files_format_and_content: The supplied bigWig files are tracks showing the RPM-adjusted RNA-seq tag counts over the genome; the Adjusted Values.txt file contains tag counts per-gene, per-sample adjusted for library size using DESeq2.

extract_protocol:
Cultures were pelleted and resuspended in QIAzol (Qiagen). Cells were lysed using a 0.5 mm Zirconia/Silica beads (RPI #9834) in a Mini-Beadbeater high energy cell disruptor (BioSpec) at 4°C, for 4 times 60 seconds. Samples were cooled on ice for 2 min in-between beatings. RNA was subsequently purified using RNeasy Mini kit (Qiagen).
1 ug of RNA was used to construct sequencing libraries using the NEBNext Ultra II RNA library preparation kit for Illumina (New England Biolabs; NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-end sequenced (75 bp) on the NextSeq 550 platform (Illumina) in accordance with the manufacturer’s protocol.

value: LOG


title: C4-2

value: LNCaP derived


title: Log Growth Replicate 2


title: Log Growth Replicate 1


title: 22Rv1

value: CWR22 derived


title: Exit 240 min Replicate 3


title: JH117_S32

source_name: HS3 KO 1B5


title: VCaP

value: Prostate

value: vertebrae


title: JH116_S31


title: JH118_S33


title: Exit 240 min Replicate 1


title: Exit 240 min Replicate 2


title: LNCaP

value: Left Supraclavicular Lymph Node


title: JH125_S38


title: DU145

value: brain


title: Exit 30 min Replicate 3


title: WCM1078

source_name: prostate cancer organoid

value: Lymph Node

value: prostate cancer organoid


title: Exit 30 min Replicate 2


title: JH113_S28

source_name: HS1 KO 3F6 GFP+

value: Potential bgl HS1 KO


title: JH112_S27


title: Exit 30 min Replicate 1

source_name: S. cerevisiae


title: JH114_S29

source_name: HS3 KO 1B3


title: WCM1262

value: Soft tissue


title: Quiescent Replicate 3

value: Q


title: WCM155

value: Liver


title: WCM154

value: Sternum


title: Quiescent Replicate 2


title: JH111_S26

source_name: HS1 KO 1A5 GFP-

value: K562 cell line


title: JH110_S25


title: MSK-PCa22


title: Quiescent Replicate 1


title: JH109_S24

source_name: HS1 KO 4C8


title: MSK-PCa20


title: JH108_S23


title: JH107_S22

source_name: HS1 KO 4B4


title: MSK-PCa19

value: Bone


title: 2102EP LP99

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 20.0.4, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Genome_build: Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
Supplementary_files_format_and_content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resulting p-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. A p-value of ≤0.05 was considered significant.

source_name: non-seminoma germ cell tumor, embryonal carcinoma

growth_protocol: 2102EP cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin)

extract_protocol:
RNA was isolated (including DNase I digestion) using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the â€˜Total RNA Standard Sensitivity Assayâ€™ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturerâ€™s protocol (â€˜VAHTS Stranded mRNA-Seq Library Prep Kitâ€™). 300Â ng totalÂ RNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.
RNA sequencing performed on the HiSeq 3000 system (Illumina Inc., San Diego, USA) with a read setup of 1x150Â basepairs (bp).

treatment_protocol: cells were treated with corresponding EC50 values of each epi-drug for 16 h

tag: agent

value: LP99 treatment


title: 2102EP PRT4165

value: PRT4165 treatment


title: MSK-PCa18


title: JH115_S30

data_processing:
Raw sequencing fastq files were mapped to the human genome build hg38 using the bwa mem aligner (0.7.5), with the following options: (-M: samtools view -q10 -bS -o).
Genome browser tracks were generated using the bedtools (version 2.29.2) utilities: genomecov sort, then processed to bigwig files with bedGraphToBigWig.

extract_protocol: Viable cells were pelleted by centrifugation at 500g for 5 min at 4°C, then cell membranes were lysed in RSB with 0.1% Tween-20, 0.01% Digitonin, and 0.1% NP-40. Cell nuclei were pelleted by centrifugation at 500g for 10 min at 4°C, and digested with Tn5 for 30 minutes at 37°C. Transposition reaction was cleaned up with Qiagen PCR Clean-Up, and sequencing adapters added by PCR with KAPA HiFi enzyme mix . Final libraries were cleaned up with two 1.2x SPRI Select beads purifications and assayed by Qubit and TapeStation before submission for sequencing.

value: Potential bgl HS3 KO


title: 2102EP MZ-1

value: MZ-1 treatment


title: JH106_S21


title: MSK-PCa17

value: Prostate


title: JH105_S20

source_name: HS1 KO 3D1, Rep 1+2


title: MSK-PCa16


title: MSK-PCa24


title: 2102EP JIB-04

value: JIB-04 treatment


title: 2102EP Chaetocin

value: Chaetocin treatment


title: MSK-PCa15

value: Ascites


title: JH79_S13

source_name: {delta}{beta}gl 45

value: Single bgl locus parental


title: 2102EP Quisinostat

value: Quisinostat treatment


title: 2102EP DMSO

value: solvent control


title: MSK-PCa13

value: Lymph Node

value: prostate cancer organoid


title: Single cell RNAseq Culture

city: Durham

first: Bradley

last: Goldstein

address: 203 Research Dr.

department: Department of Head and Neck Surgery & Communication Sciences

institute: Duke University School of Medicine

description: Culture

data_processing:
Raw base call files were analyzed using Cell Ranger v.4.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
The CellRanger v.4.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2020-A Ensembl 98 human genome.
Genome_build: GRCh38-2020-A Ensembl 98
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mx

source_name: adult human olfactory epithelium

extract_protocol:
Biopsy specimens were digested using collagenase I, dispase and DNAse, then further digested using papain and trypsin. Cells were filtered through a 70 μm strainer, pelleted and washed, and then treated with an erythrocyte lysis buffer and washed again. The cells were then resuspended in PBS with 0.1% bovine serum albumin and 0.2% anti-clumping agent (Invitrogen) and immediately processed for scRNA-seq.
Samples were processed for scRNA-seq using Chromium Single Cell 3′ Paired-End, Dual-Index Library & Gel Bead Kit v3.1 (10X Genomics) targeting 5000-10000 cells, then sequenced using NextSeq 150bp (Illumina) flow cells.

value: Normosmia


title: Single cell RNAseq Presbyosmic 3

description: Presbyosmic 3

value: Moderate Hyposmia


title: Single cell RNAseq Presbyosmic 2

description: Presbyosmic 2

value: Anosmia


title: MSK-PCa12


title: MSK-PCa11

value: Liver


title: 2102EP GSK343

value: GSK343 treatment


title: Single cell RNAseq Control 3

description:
Control 3
A subset of this sample was NOTCH1 sorted using an APC-conjugated antibody and cultured on 5% laminin in PneumaCult-Ex medium with glutamax supplement (Invitrogen), penicillin-streptomycin (Invitrogen), 10 μM Y27632, 20 ng/ml EGF, and 10 μM A83-01 (all from Stemcell Tech). The resulting cells underwent single cell RNA-seq analysis per the protocol below.


title: Single cell RNAseq Control 2

description: Control 2


title: MSK-PCa9


title: MSK-PCa8

value: Bone


title: JH104_S19

value: K562 cell line

value: Potential bgl HS1 KO


title: Single cell RNAseq Control 1

description: Control 1


title: MSK-PCa14

value: Prostate


title: MSK-PCa2


title: MSK-PCa1


title: T3: 5-FU tratemt HCT-8 rep3

city: shiyan

first: Xueyan

last: Xi

state: Hubei Province

address: Renmin Nanlu #30

institute: Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include count and FPKM values for each sample.

growth_protocol: The cells were maintained in a monolayer culture in RPMI-1640 mediums supplemented with 10% fetal bovine serum. The cells were cultured in an incubator at 37℃ in 5% CO2.

extract_protocol:
The control and 5-FU treated HCT-8 cancer cells were lysed with TRIzol reagent (Invitrogen, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: In this study, in order to mimic a dose schedule used in clinic (continuous infusion), 10% inhibitory concentration (IC10) of 5-FU was used to treat HCT-8 colon cancer cells.

tag: cancer

value: colon cancer

value: 5-fu treatment


title: Single cell RNAseq Presbyosmic 1

description: Presbyosmic 1


title: SARS2_siMAPK11_2

first: Jeffrey

last: Johnson

state: NY

address: 1 Gustave L. Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
SARS2_siRNA_host.csv
virus_counts.csv
position_read_counts.csv

data_processing:
automated base-calling performed with bcl2fastq (Illumina)
Reads were aligned using the RNA-Seq Alignment App in Basespace (Illumina) using hg19.
total counts for each sample were extracted and compiled into a csv file (SARS2_siRNA_human.csv)
Alignments to viral genomes was performed using bowtie2 app on Basespace (Langmead and Salzberg, 2012) using SARS-CoV-2 USA/WA1/2020 strain genome (GenBank: MN985325).
total counts for each lane were extracted and compiled into a csv file (virus_counts.csv)
Genome_build: hg19 and SARS-CoV-2 USA/WA1/2020 strain genome (GenBank: MN985325)
Supplementary_files_format_and_content: human total counts are in .csv file with counts for each gene for each sample; virus counts are total virus counts per lane per sample; virus bam files can be used for alignments against virus genome

source_name: Lung epithelial cells

growth_protocol: ACE2-expressing A549 cells were cultured in DMEM with 10% FBS and 1X pen/strep and plated into 12-well plates

extract_protocol:
Media was removed and cells were lysed in 0.5mL Trizol per well. Trizol lysate was transferred to tubes and frozen at -80C. RNA was extracted and DNase I treated using Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s protocol.
RNA-seq libraries of polyadenylated RNA were prepared with the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s protocols.

treatment_protocol: 2x105 cells were transfected with siRNA targeting non-targeting control or MAPK11 with RNAiMAX according to manufacturer's protocol, three replicates per condition. 48h post-transfection, cells were mock-infected or infected with SARS-CoV-2 MOI 0.75 in DMEM + 2% FBS + 1X pen/strep for 8h.

tag: infection

value: SARS-CoV-2 infected 8h

tag: transfection

value: siRNA against MAPK11

value: ACE2-expressing A549


title: SARS2_siNTC_2

value: siRNA against non-targeting control

tag: cell line


title: SARS2_siMAPK11_3


title: MSK-PCa10


title: T1: 5-FU tratemt HCT-8 rep1


title: SARS2_siNTC_1


title: C3: HCT-8 rep3

value: no treatment


title: MSK-PCa3

value: Lymph Node

value: prostate cancer organoid


title: Mock_siNTC_3

description:
SARS2_siRNA_host.csv
virus_counts.csv
N/A

value: Mock-infected 8h


title: C2: HCT-8 rep2


title: SARS2_siMAPK11_1


title: Mock_siNTC_2


title: SARS2_siNTC_3


title: T2: 5-FU tratemt HCT-8 rep2


title: LM2 cells, CECR2 sg1_Rep2

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

description:
sg1_ATAC_rep2
ctrl_sg1_ATAC_merge.bed
ctrl_sg1_ATAC_merge.count.txt

data_processing:
Illumina Casava software used for basecalling.
Reads were trimmed of adapters using Trimmomatic v0.39
Trimmed reads were aligned using Bowtie2 using standard parameters and a maximum fragment length of 2000
Duplicate and low-quality reads were filtered using SAMTools v1.123 with parameters -F 1804
Reads were then processed where only the most 5' base pair for each read was kept and forward strand reads were shifted +5bp, and reverse strand reads were shifted -4bp.
Peak calling was performed using MACS2 v2.2.4 with parameters -g hs --nomodel -s 1 --shift -75 --extsize 150.
For differential accessibility analysis, reads in the consensus peak set were counted for each replicate and analyzed with DESeq2 v1.32.
Bigwig files were generated using Deeptools v3.1.3 and visualized using IGV
Heatmaps were generated using Deeptools function plotHeatmap
Supplementary_files_format_and_content: bigwig, bed, counts

source_name: breast cancer cell line

growth_protocol: Cells were grown in monolayer in DMEM+10%FBS+1% Penicillin+puromycin at 37°C, 5% CO2

extract_protocol:
50,000 cells were treated with Transposase. Protocol as previously described in Corces et al (Nat.Methods 2017).
DNA libraries were prepared as previously described in Corces et al (Nat.Methods 2017).

value: LM2 (MDA-MB-231 derived metastatic cell line with increased lung metastasis potential)

tag: cell type

value: breast cancer cells

tag: genotype

value: CECR2 deletion 1


title: Warmed tissue of hepatocellular carcinoma

city: Shanghai

first: Bo

last: Zhai

address: No.160, Pujian Road

department: Interventional Oncology

institute: Shanghai Jiao Tong University, School of Medicine, Affiliated Renji Hospital

description:
Liver cancer tissue
Warmed

data_processing:
Illumina Casava software used for basecalling.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions.
Genome_build: Homo_sapiens.GRCh38.94.chr
Supplementary_files_format_and_content: fpkm.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: Surgical specimens

extract_protocol:
RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM).

value: Hepatocellular carcinoma tissue

value: Cryopreservation solutions (LT2601; Tissue Mate) and warming solutions (LT2602; Tissue Mate)


title: HEK293 cells, TNF alpha treated

city: Zuarinagar, near MES College, Vasco

middle: maria

last: Talukdar

state: Goa

address: BITS Pilani K.K Birla Goa Campus

department: Department of Biological Sciences

country: India

institute: BITS PILANI K.K BIRLA GOA CAMPUS

description: Sample 2

data_processing:
Raw data processing and QC done using FASTQC
Alignment of reads to reference genome using Tophat-2.02  and Cufflinks-2.1.1
Merging assemblies with Cuffmerge
Differential gene expression analysis using cuffdiff
Genome_build: GRCh37
Supplementary_files_format_and_content: GT_SO_4470_control_vs_AlphaA_DGE_Report.xlsx (Normalized Abundance measurement )
Supplementary_files_format_and_content: Control_vs_AlphaA.merged.gtf (Abundance measurement)
Supplementary_files_format_and_content: GT_SO_4470_control_vs_AlphaA.xlsx (Raw counts)

source_name: HEK293 (Human Embryonic kidney cells)

growth_protocol: HEK 293 cells were grown in 10% DMEM medium supplemented with 10% FBS

extract_protocol:
RNA was isolated using Qiagen RNeasy mini kit
cDNA library was prepared using NEXT flex rapid directional RNA-seq library protocolThe prepared library was quantified using Quibit and validated .
Ref-based transcriptome analysis

treatment_protocol: Sample 2 was treated with TNF alpha at 10ng/ml for 6 hours

value: HEK293 (Human Embryonic kidney cells)

value: Epithelial cells

value: TNF alpha


title: LM2 cells, CECR2 sg1_Rep1

description:
sg1_ATAC_rep1
ctrl_sg1_ATAC_merge.bed
ctrl_sg1_ATAC_merge.count.txt


title: HEK293 cells, Untreated/ Control

description: Sample 1

value: control


title: LM2 cells, Control_Rep2

description:
ctrl_ATAC_rep2
ctrl_sg1_ATAC_merge.bed
ctrl_sg1_ATAC_merge.count.txt

value: nontargeting control


title: Fresh tissue of hepatocellular carcinoma

description:
Liver cancer tissue
Fresh

value: Untreated


title: Mock_siNTC_1

value: ACE2-expressing A549


title: C1: HCT-8 rep1

value: colon cancer


title: SH-EP_MYCNER_TLR3_MYD88_clone2_rep_2

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
SH-EP cell line, sgRNAs targeting TLR3 and MYD88, replicate 2
RNAseq_counts.txt

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: SH-EP cell line

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus mini kit (74134) after homogenization by centrifugation in QIAShredder (79656) microcentrifuge tubes
200 ng of DNAse I treated, total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen, Vienna, Austria)

value: SH-EP

value: sgRNAs targeting TLR3 and MYD88

tag: replicate


title: PLC_HHT_2

first: Chen

last: Yang

address: Xietu Road

institute: Shanghai Cancer Institute

data_processing:
Illumina Casava 1.8.2 software used for basecalling. The quality score encoding is in +Phred 33.
Raw sequencing reads were mapped to the human genome (GRCh38) using STAR (version 2.4.2g1).
Gene-level read counts were generated using featureCounts from the subRead package with default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: PLC

extract_protocol:
Total RNA was extracted and purified using the Trizol reagent (Invitrogen)
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).

treatment_protocol: We first treated liver cancer cells with vehicle or HHT for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated liver cancer cells.  HHT-induced expression changes were obtained based on the resultant data.

value: PLC

value: liver cancer cell line

value: Homoharringtonine

value: Liver


title: PLC_HHT_1


title: LM2 cells, Control_Rep1

description:
ctrl_ATAC_rep1
ctrl_sg1_ATAC_merge.bed
ctrl_sg1_ATAC_merge.count.txt

value: LM2 (MDA-MB-231 derived metastatic cell line with increased lung metastasis potential)

value: breast cancer cells


title: PLC_ctrl_2

value: Control


title: SH-EP_MYCNER_Luc_Rosa_clone2_rep_2

description:
SH-EP cell line, Control sgRNAs targeting luciferase and Rosa26, replicate 2
RNAseq_counts.txt


title: SH-EP_MYCNER_TLR3_MYD88_clone1_rep_2


title: OlN3

city: Montréal

first: Alexis

last: Vivoli

state: Québec

address: 900 rue St denis

country: Canada

institute: Centre de recherche du centre hospitalié de l'université de montréal (CRCHUM)

description: Isolated islets

data_processing:
Demultiplexing of binary base call (BCL) files, alignment, read filtering, barcode and unique molecular identifier (UMI) counting were performed using the CellRanger analysis pipeline (v2.0) provided by 10x Genomics
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table of Filtered feature-barcode matrix (raw gene counts) for every gene and every sample

source_name: Islets of Langherans

extract_protocol:
Single-cell libraries were generated using the Chromium Single-cell 3′ library and gel bead kit v2 (10x genomics) following manufacturer's instruction
Libraries were prepared for sequencing according to 10x genomics instructions and were sequenced on the NovaSeq 6000 with 150 bp paired-end sequencing

value: Wistar rat

value: pancreatic islets

value: oleate


title: SH-EP_MYCNER_TLR3_Rosa_clone2_rep_2

city: Philadelphia

description:
SH-EP cell line, Control sgRNA targeting Rosa26 and sgRNA targeting TLR3, replicate 2
RNAseq_counts.txt


title: OlN4

description: Isolated islets


title: C8, leukocytes

type: genomic

city: Ribeirão Preto

first: Carla

middle: Barbosa

last: Nonino

address: Av. Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip 450 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Champ package for Rstudio was used to process data.

label: Cy5 and Cy3

source_name: leukocytes peripheral blood, without obesity

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the collected whole blood, the technique adopted was automated by magnetic spheres, using the Maxwell MDx equipment.

tag: age

tag: weight

tag: bmi

tag: waist

tag: zn ( ug/dl)

tag: zinc

tag: zn seric/bmi

tag: zn ingested/bmi

tag: zn ingested/weight

value: peripheral blood

value: leukocytes


title: C19, leukocytes

tag: glucose

tag: cholesterol

tag: hdl

tag: ldl

tag: triglycerides

tag: tissue


title: C17, leukocytes

tag: cell type


title: C10, leukocytes


title: C13, leukocytes


title: PC10, leukocytes

source_name: leukocytes peripheral blood, with obesity


title: C16, leukocytes


title: C9, leukocytes


title: C12, leukocytes


title: OlN2

description: Isolated islets

tag: strain

tag: treatment


title: SH-EP_MYCNER_TLR3_Rosa_clone1_rep_2

tag: cell line

value: Control sgRNA targeting Rosa26 and sgRNA targeting TLR3

tag: replicate


title: Huh7_HHT_2


title: C4, leukocytes

tag: age

tag: weight

tag: bmi

tag: waist


title: VMH_F_Post_Control_Rep1

city: Pasadena

first: Mengyu

last: Liu

state: California

address: 1200 E California Blvd

department: BBE

institute: Caltech

data_processing:
alignment using CellRanger v3.0
filtering out cells using CellRanger v3.0 "cell-calling algorithm"
Genome_build: mm10
Supplementary_files_format_and_content: Features table with every gene (.tsv)
Supplementary_files_format_and_content: Barcodes table with unique barcode for each cell (.tsv)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell (.mtx)

source_name: female ventral VMH

extract_protocol:
Method section in publication: 10.1016/j.neuron.2021.12.002
10x Chromium 3' v3 sequencing

tag: developmental stage

value: adult

tag: Sex

value: female

tag: reproductive state

value: post-lactating

tag: social behavior

value: control

value: brain


title: OlN1

description: Isolated islets


title: Huh7_HHT_1

value: liver cancer cell line


title: PLC_ctrl_1

value: PLC


title: P30, leukocytes

tag: glucose

tag: cholesterol

tag: hdl

tag: zn ( ug/dl)

tag: zinc

tag: zn seric/bmi

tag: zn ingested/bmi

tag: zn ingested/weight


title: PC1, leukocytes

tag: ldl

tag: triglycerides

tag: tissue

tag: cell type


title: P9, leukocytes

tag: age

tag: weight

tag: bmi

tag: waist


title: P17, leukocytes


title: PC2, leukocytes


title: C5, leukocytes


title: SH-EP_MYCNER_TLR3_MYD88_clone2_rep_1

description:
SH-EP cell line, sgRNAs targeting TLR3 and MYD88, replicate 1
RNAseq_counts.txt

tag: cell line

value: SH-EP

tag: treatment

value: sgRNAs targeting TLR3 and MYD88

tag: replicate


title: SH-EP_MYCNER_Luc_Rosa_clone1_rep_2

value: Control sgRNAs targeting luciferase and Rosa26


title: VMH_F_Virgin_Control_Rep2

tag: strain

tag: developmental stage

tag: Sex

tag: reproductive state

value: virgin

tag: social behavior


title: VMH_F_Virgin_NonAgg_Rep2

value: non aggressive


title: Huh7_ctrl_2

value: Control

value: Liver


title: Huh6_HHT_2

value: Homoharringtonine


title: SH-EP_MYCNER_Luc_Rosa_clone2_rep_1

description:
SH-EP cell line, Control sgRNAs targeting luciferase and Rosa26, replicate 1
RNAseq_counts.txt


title: C14, leukocytes

tag: glucose

tag: cholesterol

tag: hdl

tag: zn ( ug/dl)

tag: zinc

tag: zn seric/bmi

tag: zn ingested/bmi

tag: zn ingested/weight

value: peripheral blood

value: leukocytes


title: PC6, leukocytes

tag: age

tag: weight

tag: bmi

tag: waist

tag: ldl

tag: triglycerides

tag: tissue

tag: cell type


title: Huh6_HHT_1

tag: cell line

tag: treatment


title: Huh7_ctrl_1


title: PalN1

description: Isolated islets

tag: strain

value: Wistar rat

value: pancreatic islets

value: glucose + palmitate


title: VehN4

description: Isolated islets

value: glucose


title: VMH_F_Virgin_Control_Rep1

tag: developmental stage

value: adult

tag: Sex

value: female

tag: reproductive state

tag: social behavior

value: control

value: brain


title: SH-EP_MYCNER_TLR3_Rosa_clone2_rep_1

description:
SH-EP cell line, Control sgRNA targeting Rosa26 and sgRNA targeting TLR3, replicate 1
RNAseq_counts.txt

value: SH-EP

tag: replicate


title: VMH_F_Lac_Agg_Rep2

value: lactating

value: aggressive


title: P4, leukocytes

tag: glucose

tag: cholesterol

tag: hdl

tag: zn ( ug/dl)

tag: zinc

tag: zn seric/bmi

tag: zn ingested/bmi

tag: zn ingested/weight


title: VMH_F_Lac_Control_Rep2

tag: tissue


title: VMH_F_Virgin_NonAgg_Rep1

value: virgin

value: non aggressive


title: P6, leukocytes

tag: age

tag: weight

tag: bmi

tag: waist

tag: ldl

tag: cell type


title: SH-EP_MYCNER_TLR3_Rosa_clone1_rep_1

tag: cell line

tag: treatment

value: Control sgRNA targeting Rosa26 and sgRNA targeting TLR3


title: VehN3

description: Isolated islets

tag: strain


title: VehN2

description: Isolated islets


title: Huh6_ctrl_2

value: liver cancer cell line

value: Control

value: Liver


title: Huh6_ctrl_1


title: P41, leukocytes

tag: glucose

tag: cholesterol

tag: triglycerides

value: peripheral blood

value: leukocytes


title: VMH_F_Lac_NonAgg_Rep1

tag: developmental stage

tag: Sex

tag: reproductive state

tag: social behavior


title: SH-EP_MYCNER_Luc_Rosa_clone1_rep_1

value: Control sgRNAs targeting luciferase and Rosa26

tag: replicate


title: SH-EP_MYCNER_TLR3_MYD88_clone1_rep_1

value: sgRNAs targeting TLR3 and MYD88


title: HepG2_HHT_500nM_2

value: Homoharringtonine

tag: tissue


title: VehN1

description: Isolated islets

value: Wistar rat

value: pancreatic islets

value: glucose


title: BE2c_PRRX1_Dox_PolyIC_Rep2

description:
BE2c cell line, Doxycyline (1ug/mL) for 14 days and 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: BE2c cell line


title: VMH_F_Lac_Agg_Rep1

value: adult

value: female

value: brain


title: HepG2_HHT_500nM_1


title: BE2c_PRRX1_Dox_H2O_Rep2

description:
BE2c cell line, Doxycyline (1ug/mL) for 14 days and vehicle (water), replicate 2
RNAseq_counts.txt


title: HepG2_HHT_1uM_2


title: BE2c_PRRX1_DMSO_PolyIC_Rep2

description:
BE2c cell line, Vehicle (DMSO) and 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt


title: HepG2_HHT_1uM_1


title: BE2c_PRRX1_DMSO_H2O_Rep2

description:
BE2c cell line, Vehicle (DMSO) and vehicle (water), replicate 2
RNAseq_counts.txt

value: Vehicle (DMSO) and vehicle (water)


title: VMH_F_Lac_Control_Rep1

value: lactating

value: control


title: FR VMH

city: Palo Alto

first: Joseph

last: Knoedler

address: 1201 Welch Road

institute: Stanford Univesity

description: Nuclear RNA

data_processing:
Reads were aligned to the mm10 build of the mouse transcriptome, modified to include and quantify intronic reads using the kallisto-bustools pipeline
Cell x gene matrix was loaded into Seurat (R programming environment). Cells were retained if they contained > 500 unique molecular identifies (UMIs); genes were retained if they were detected in 3 or more cells
Cells were grouped into clusters by principle component analysis and Jaccard-Louvain clustering.
Low quality clusters (low UMI count, lack of significant markers, high mitochondrial gene count) were filtered and clustering re-run
Clusters with few Esr1+ cells or markers that indicated cells originated outside region of interest were filtered
Genome_build: mm10
Supplementary_files_format_and_content: For each region surveyed, a cell x gene matrix with all cells passing filtering criteria is provided along with a metadata file indicating cluster identity and condition of origin for each cell
Supplementary_files_format_and_content: Unfiltered count matrices for single nucleus RNAseq samples

source_name: VMH

extract_protocol:
Nuclei were extracted by density gradient centrifugaion. GFP+ nuclei were isolated using an Aria FACS sorter.
Single nucleus libraries were generated on the 10X Chromium platform using the 3' RNA v3 kit.
Libraries were sequenced on either a HiSeq4000 or NovaSeq 6000

value: Brain

tag: genotype

tag: gender

value: Female

value: OVX + E2/P


title: HepG2_HHT_10uM_2

value: liver cancer cell line

value: Liver


title: BE2c_Luc_DMSO_PolyIC_Rep2

value: Vehicle (DMSO) and 30ug/mL Poly (I:C) for 24 hours


title: BE2c_Luc_Dox_PolyIC_Rep2

value: Doxycyline (1ug/mL) for 14 days and 30ug/mL Poly (I:C) for 24 hours


title: HepG2_HHT_10uM_1

value: Homoharringtonine


title: HepG2_HHT_100nM_1


title: BE2c_Luc_Dox_H2O_Rep2

value: Doxycyline (1ug/mL) for 14 days and vehicle (water)


title: FNR POA

description: Nuclear RNA

source_name: POA

value: OVX + Veh


title: Male POA

description: Nuclear RNA

value: Male

value: Intact


title: Male VMH

description: Nuclear RNA


title: FR POA

description: Nuclear RNA


title: HepG2_HHT_100nM_2


title: BE2c_Luc_DMSO_H2O_Rep2


title: IMR5_PolyIC_Rep2

description:
IMR5 cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: IMR5 cell line

value: 30ug/mL Poly (I:C) for 24 hours


title: FNR MeA-Run1

description: Nuclear RNA

source_name: MeA


title: HepG2_ctrl_1

value: Control


title: HepG2_ctrl_2


title: IMR5_H2O_Rep2

description:
IMR5 cell line, Vehicle (water), replicate 2
RNAseq_counts.txt

value: Vehicle (water)


title: FR MeA

description: Nuclear RNA


title: Hep3B_HHT_2


title: SK-N-DZ_PolyIC_Rep2

description:
SK-N-DZ cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: SK-N-DZ cell line

value: SK-N-DZ


title: FNR VMH

description: Nuclear RNA


title: Male MeA

description: Nuclear RNA


title: SK-N-DZ_H2O_Rep2

description:
SK-N-DZ cell line, Vehicle (water), replicate 2
RNAseq_counts.txt


title: FNR BNST

description: Nuclear RNA

source_name: BNST


title: Hep3B_HHT_1


title: NLF_PolyIC_Rep2

description:
NLF cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: NLF cell line

value: NLF


title: Hep3B_ctrl_2


title: FR BNST

description: Nuclear RNA

value: Brain


title: Hep3B_ctrl_1


title: Male BNST-Run2

description: Nuclear RNA


title: Kelly_H2O_Rep2

description:
Kelly cell line, Vehicle (water), replicate 2
RNAseq_counts.txt

source_name: Kelly cell line

value: Kelly


title: E10.5_ShhGli3_ATAC_rep5

last: Vokes

address: 2500 Speedway, STOP A5000

institute: University of Texas at Austin

data_processing:
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mouse limb buds

extract_protocol:
limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
Libraries were prepared with the following number of amplification cycles, for each given experiment: CUT&Tag/Run- 14 cycles, ChIP- 15 cycles, ATAC- 11 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.
ChIP & CUT&RUN library- NEBNext Ultra II DNA Library Prep Kit; ATAC & CUT&Tag- NEBNext HF 2x PCR Master Mix; RNA-seq- NEBNext Ultra II RNA Library Prep Kit

tag: strain/background

value: 1 pair posterior FLs (30k cells)

tag: Stage

value: forelimb bud


title: NLF_H2O_Rep2

description:
NLF cell line, Vehicle (water), replicate 2
RNAseq_counts.txt


title: E10.5_ShhGli3_ATAC_rep4


title: RFP.H202.day7.201007

city: Baltimore

first: Peter

middle: C

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
alignment and quantification to GRCh38 using Rsubread
Fragments Per Kilobasee of transcript per Million fragments mapped (FPKM) was calculated for each gene as outlined in Trapnell et al., Nature Biotechnology, 2010.
Normalization using variance stabilizing regularized logarithm transformation (rlog) using DESeq2
Supplementary_files_format_and_content: FPKM

source_name: iBMEC-RFP

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C.  iBMECs were differentiated using sequential treatment of iPSC colonies with unconditioned media without bFGF (for six days) and endothelial media (for two days). iBMECs were seeded onto transwell membranes coated with 50 µg mL-1 human placental collagen IV and 25 µg mL-1 fibronectin from human plasma in endothelial media supplemented with ROCK inhibitor (10 µM Y27632).  After 24 h, media was switched to basal medium.  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. Basal media: human endothelial serum-free medium supplemented with 1% human platelet poor derived serum, 1% penicillin-streptomycin.

extract_protocol:
At 1 hour, 4 days, or 7 days after intiation of treatment, 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, oligo (dT) capture and enrichment by Novogene.

treatment_protocol: After 24 h in basal media, cells were treated with either 500 µM H2O2 exposure for one hour, then returned to basal media (acute); 100 µM H2O2 exposure continuously (chronic); vehicle (H2O) exposure for one hour then returned to basal media; or vehicle exposure continuously (control).

value: iBMEC-RFP

value: chronic exposure

tag: time point

value: day 7


title: RFP.vehicle.day7.201007

tag: cell line

value: vehicle control


title: E10.5_ShhGli3_ATAC_rep3

first: Steven


title: RFP.H2O2.day4.201004

tag: treatment

value: acute exposure

value: day 4


title: CHP-212_H2O_Rep2

description:
CHP-212 cell line, Vehicle (water), replicate 2
RNAseq_counts.txt

source_name: CHP-212 cell line


title: E10.5_ShhGli3_ATAC_rep2


title: GI-M-EN_PolyIC_Rep2

description:
GI-M-EN cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: GI-M-EN cell line

value: GI-M-EN


title: RFP.H2O2.day0.200930

value: day 0


title: E10.5_ShhGli3_ATAC_rep1


title: RFP.vehicle.day0.200930


title: GI-M-EN_H2O_Rep2

description:
GI-M-EN cell line, Vehicle (water), replicate 2
RNAseq_counts.txt


title: ZO1.H202.day7.201004


title: SK-N-AS_PolyIC_Rep2

description:
SK-N-AS cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: SK-N-AS cell line

value: SK-N-AS

value: 30ug/mL Poly (I:C) for 24 hours


title: E10.5_Shhnull_ATAC_rep2-SR

value: Shh-/-


title: ZO1.H2O2.day4.201001


title: ZO1.vehicle.day7.201004


title: E10.5_Shhnull_ATAC_rep2-PE


title: SH-EP_PolyIC_Rep2

description:
SH-EP cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt

source_name: SH-EP cell line

value: SH-EP


title: Kelly_PolyIC_Rep2

description:
Kelly cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt


title: E10.5_Shhnull_ATAC_rep1-SR


title: CHP-212_PolyIC_Rep2

description:
CHP-212 cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 2
RNAseq_counts.txt


title: SH-EP_H2O_Rep2

description:
SH-EP cell line, Vehicle (water), replicate 2
RNAseq_counts.txt

value: Vehicle (water)


title: ZO1.H2O2.day0.200927


title: E10.5_WT_ATAC_rep3

value: Swiss Webster


title: RFP.vehicle.day4.201004


title: E10.5_WT_ATAC_rep2


title: BE2c_PRRX1_Dox_PolyIC_Rep1

description:
BE2c cell line, Doxycyline (1ug/mL) for 14 days and 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt


title: ZO1.vehicle.day0.200927


title: BE2c_PRRX1_Dox_H2O_Rep1

description:
BE2c cell line, Doxycyline (1ug/mL) for 14 days and vehicle (water), replicate 1
RNAseq_counts.txt


title: E10_Shhnull_ATAC_rep3

value: 2 pairs posterior FLs (30k cells)


title: E10.5_WT_ATAC_rep1

value: 1 pair posterior FLs (30k cells)


title: BE2c_PRRX1_DMSO_PolyIC_Rep1

description:
BE2c cell line, Vehicle (DMSO) and 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt


title: ZO1.vehicle.day7


title: BE2c_PRRX1_DMSO_H2O_Rep1

description:
BE2c cell line, Vehicle (DMSO) and vehicle (water), replicate 1
RNAseq_counts.txt

value: Vehicle (DMSO) and vehicle (water)


title: E10_Shhnull_ATAC_rep2

value: forelimb bud


title: E10.5_Shhnull_ATAC_rep1-PE


title: ZO1.H202.day4


title: SK-N-AS_H2O_Rep2

description:
SK-N-AS cell line, Vehicle (water), replicate 2
RNAseq_counts.txt


title: BE2c_Luc_Dox_PolyIC_Rep1

value: Doxycyline (1ug/mL) for 14 days and 30ug/mL Poly (I:C) for 24 hours


title: E10_Shhnull_ATAC_rep1


title: BE2c_Luc_Dox_H2O_Rep1

value: Doxycyline (1ug/mL) for 14 days and vehicle (water)


title: E10_WT_ATAC_rep3


title: ZO1.H202.day0


title: ZO1.vehicle.day4

value: vehicle control


title: PalN4

description: Isolated islets

source_name: Islets of Langherans

tag: strain

value: Wistar rat

value: pancreatic islets

value: glucose + palmitate


title: BE2c_Luc_DMSO_PolyIC_Rep1

value: Vehicle (DMSO) and 30ug/mL Poly (I:C) for 24 hours


title: ZO1.vehicle.day4.201001

value: day 4


title: E10_WT_ATAC_rep2


title: BE2c_Luc_DMSO_H2O_Rep1


title: ZO1.vehicle.day0

value: day 0


title: PalN3

description: Isolated islets


title: ZO1.H2O2.day7.200329

value: chronic exposure

value: day 7


title: IMR5_PolyIC_Rep1

description:
IMR5 cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: 30ug/mL Poly (I:C) for 24 hours


title: E10_WT_ATAC_rep1

value: Swiss Webster


title: ZO1.vehicle.day7.200329


title: IMR5_H2O_Rep1

description:
IMR5 cell line, Vehicle (water), replicate 1
RNAseq_counts.txt

value: Vehicle (water)


title: ZO1.H2O2.day7


title: E9_ATAC_rep1

value: ~5 pairs FLs (30k cells)


title: E9_ATAC_rep2


title: SK-N-DZ_PolyIC_Rep1

description:
SK-N-DZ cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: SK-N-DZ


title: ZO1.H202.day4.200323

value: acute exposure


title: ZO1.H202.day0.200322


title: E10.5_Gli3null-ant_RNAseq_rep3

extract_protocol:
limbs were disscociated in TRIzol (Invitrogen 15596026), incubated at RT for 5 minutes and then stored at -80C prior to RNA isolation
Libraries were prepared with the following number of amplification cycles, for each given experiment: CUT&Tag/Run- 14 cycles, ChIP- 15 cycles, ATAC- 11 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.
ChIP & CUT&RUN library- NEBNext Ultra II DNA Library Prep Kit; ATAC & CUT&Tag- NEBNext HF 2x PCR Master Mix; RNA-seq- NEBNext Ultra II RNA Library Prep Kit

value: 2 pairs anterior FLs

value: forelimb bud


title: E10.5_Gli3null-ant_RNAseq_rep2


title: E10.5_Gli3null-ant_RNAseq_rep1


title: ZO1.vehicle.day4.200323

value: vehicle control


title: NLF_PolyIC_Rep1

description:
NLF cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: NLF


title: ZO1.vehicle.day0.200322


title: NLF_H2O_Rep1

description:
NLF cell line, Vehicle (water), replicate 1
RNAseq_counts.txt


title: E10.5_WT-ant_RNAseq_rep4


title: Kelly_PolyIC_Rep1

description:
Kelly cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: Kelly


title: E10.5_WT-ant_RNAseq_rep3


title: Kelly_H2O_Rep1

description:
Kelly cell line, Vehicle (water), replicate 1
RNAseq_counts.txt


title: NSV2

city: Seoul

first: Jong Hee

last: Lee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

institute: Samsung Medical Center

description: Visium

data_processing:
Then, prepared libraries were sequenced on Illumina NovaSeq 6000(Illumina, USA) targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: raw gene expression matrix

source_name: Skin

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on Illumina NovaSeq 6000(Illumina, USA) targeting 50,000 raw reads per cell.

tag: pathology

value: Adjacent normal

tag: location

value: Cheek

value: Female


title: E10.5_WT-ant_RNAseq_rep2

city: Austin


title: JH236_S29

city: Dallas

first: Jeremiah

last: Herbert

address: 5323 Harry Hines Blvd., MC 8511

department: Green Center for Reproductive Biology

institute: University of Texas Southwestern Medical Center

extract_protocol: Viable cells were pelleted by centrifugation at 500g for 5 min at 4°C, then cell membranes were lysed in RSB with 0.1% Tween-20, 0.01% Digitonin, and 0.1% NP-40. Cell nuclei were pelleted by centrifugation at 500g for 10 min at 4°C, and digested with Tn5 for 30 minutes at 37°C. Transposition reaction was cleaned up with Qiagen PCR Clean-Up, and sequencing adapters added by PCR with KAPA HiFi enzyme mix . Final libraries were cleaned up with two 1.2x SPRI Select beads purifications and assayed by Qubit and TapeStation before submission for sequencing.

value: K562 cell line

value: bgl HS2-4 KO


title: E10.5_WT-ant_RNAseq_rep1


title: JH237_S30


title: CHP-212_PolyIC_Rep1

description:
CHP-212 cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt


title: CHP-212_H2O_Rep1

description:
CHP-212 cell line, Vehicle (water), replicate 1
RNAseq_counts.txt


title: JH235_S28

value: bgl HS1-4 KO


title: E9_Gli3null_RNAseq_rep4

value: ~4 pairs pooled FLs


title: GI-M-EN_H2O_Rep1

description:
GI-M-EN cell line, Vehicle (water), replicate 1
RNAseq_counts.txt

value: GI-M-EN


title: GI-M-EN_PolyIC_Rep1

description:
GI-M-EN cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: 30ug/mL Poly (I:C) for 24 hours


title: JH234_S27


title: E9_Gli3null_RNAseq_rep2


title: SK-N-AS_PolyIC_Rep1

description:
SK-N-AS cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: SK-N-AS


title: JH233_S26

source_name: HS3,4 KO 1B3

value: bgl HS3,4 KO


title: E9_Gli3null_RNAseq_rep3


title: JH232_S25


title: SK-N-DZ_H2O_Rep1

description:
SK-N-DZ cell line, Vehicle (water), replicate 1
RNAseq_counts.txt

value: SK-N-DZ

value: Vehicle (water)


title: E9_WT_RNAseq_rep3

value: Swiss Webster

value: forelimb bud


title: SH-EP_PolyIC_Rep1

description:
SH-EP cell line, 30ug/mL Poly (I:C) for 24 hours, replicate 1
RNAseq_counts.txt

value: SH-EP


title: JH231_S24

source_name: HS4 KO 3H4

value: bgl HS4 KO


title: SK-N-AS_H2O_Rep1

description:
SK-N-AS cell line, Vehicle (water), replicate 1
RNAseq_counts.txt


title: JH230_S23


title: SH-EP_H2O_Rep1

description:
SH-EP cell line, Vehicle (water), replicate 1
RNAseq_counts.txt


title: E9_WT_RNAseq_rep1


title: JH229_S22

source_name: HS3 KO 2B6

value: bgl HS3 KO


title: Tcf7_2_NICD_TCFKO [Hi-C]

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Hi-C paired-end sequencing reads for each sample were filtered and aligned to the mouse genome (mm10) using the Juicer pipeline (version 1.6) with the restriction site coordinates of the restriction enzymes used in the Arima-HiC kit (cutting at GATC and GANTC). Aligned Hi-C contacts with an alignment score > 30 (MAPQ > 30) from individual replicates were combined using the “mega.sh” script provided with Juicer. Chromatin contact maps from pooled data were created using the “pre” command at custom (2.5 kb and 5 – 25 kb with a 1 kb increase) and default (50, 100, 250, 500 kb, 1, and 2.5 Mb) resolutions.
Chromatin contact domains were identified in KR normalized chromatin contact maps at 5 kb resolution using Arrowhead from Juicer tools  version 1.6. (Rao et al. 2014).
Chromatin loops were called at 2.5 and 5 to 25 kb resolutions (with a 1 kb increase) with HiCCUPS from Juicer tools version 1.6 (Rao et al. 2014) using custom parameters for peak size (p), window size (i) and distances for merging nearby pixels to a centroid (d).
For detailed description of methods and parameters, please refer to the material and method section of the main publication.
Genome_build: mm10
Supplementary_files_format_and_content: Contact matrices in 2 resolutions in hic format; TADs in 5Kb resolution in bedpe format, loops in all resolutions in bedpe format.

source_name: BM LSK (Lin- Sca1+ cKit+)

extract_protocol:
Low input in situ Hi-C was performed on 150,000 LSKs with Arima-HiC Kit (Arima) according to the manufacturers’ protocols.
DNA fragmentation was performed on Covaris E220 Evolution sonicator (Covaris Cat# 500429) with default settings for 400bp DNA size distribution.
Libraries for sequencing were prepared with Swift Biosciences Accel-NGS 2S Plus DNA Dual Indexing Library Kit (Swift Biosciences Cat# 21024 and #28096). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter). Library amplification was performed following DNA quantification with Invitrogen Qubit Fluorometer and KAPA Library Quantification Kit (Roche Cat# 07958927001).
sequencing protocol: Prepared libraries were sequenced using the sequencing platforms at Novogene with Illumina NovaSeq 6000 S4 and the 150 bp paired-end reads generating around 700 million paired reads per library.

tag: strain background

tag: transgene

value: R26 N1IC lox/+ Tcf7 lox/lox Mx1Cre

tag: cre

value: Mx1Cre induction 2ug/g b.w. poly(I:C)

tag: facs sorting

value: Target population from bone marrow:CD45.2+ eGFP+ Lin- Sca1+ cKit+

tag: group

tag: batch


title: JH228_S21

data_processing:
Raw sequencing fastq files were mapped to the human genome build hg38 using the bwa mem aligner (0.7.5), with the following options: (-M: samtools view -q10 -bS -o).
Genome browser tracks were generated using the bedtools (version 2.29.2) utilities: genomecov sort, then processed to bigwig files with bedGraphToBigWig.

value: K562 cell line


title: SK-N-DZ cell line, replicate 2

description: SK-N-DZ cell line, replicate 2

data_processing:
ATAC-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files and call significant peaks using “-style histone” and “-style factor” option
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq signal in bigwig track format

extract_protocol:
Cells were cooled slowly to minimize cell lysis with freezing. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA (Nextera Library Prep Kit, Illumina) was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

tag: replicate


title: NSV1

description: Visium

value: Adjacent normal

value: Leg

value: Male


title: SK-N-DZ cell line, replicate 1

description: SK-N-DZ cell line, replicate 1


title: JH227_S20

source_name: HS3 KO 1H3

tag: genotype


title: IMR5 cell line, replicate 2

description: IMR5 cell line, replicate 2

source_name: IMR5 cell line


title: JH226_S19


title: IMR5 cell line, replicate 1

description: IMR5 cell line, replicate 1


title: RNIC_3_NICD_TCFWT [Hi-C]

value: R26 N1IC lox/+ Mx1Cre


title: JH225_S18

source_name: HS3 KO 1B5


title: CTRL_2_NOTCHWT_TCFWT [Hi-C]

value: wild type

value: Controlled injection with 2ug/g body weight poly(I:C)

value: Target population from bone marrow:Lin- Sca1+ cKit+


title: CHP-212 cell line, replicate 2

description: CHP-212 cell line, replicate 2


title: Tcf7_1_NICD_TCFKO [Hi-C]


title: E9_Gli3null_RNAseq_rep1

tag: tissue

value: ~4 pairs pooled FLs


title: CHP-212 cell line, replicate 1

description: CHP-212 cell line, replicate 1


title: GI-M-EN cell line, replicate 2

description: GI-M-EN cell line, replicate 2

value: GI-M-EN


title: No Dox, Rep4

first: Mario

middle: R

last: Blanco

description: DNA associated with Xist RNA captured using hybridization capture

data_processing:
Raw fastq reads were trimmed and removed of Illumina adapters and low quality reads.
Filtered paired-end reads were aligned using STAR aligner and uniquely mapped reads kept for analysis.
Bigwig files were created using Deeptools suite to summarize read coverage.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files summarizing read-depth coverage per sample.

source_name: mouse embryonic stem cells

extract_protocol:
Lysate was prepared and diluted to hybridization conditions containing 3M guanidine thiocyanate, precleared by adding streptavidin-coated magnetic beads and incubating for 30 minutes at 37°C, mixed with biotin-labeled single stranded DNA capture probes, and incubated at 37°C for 2 hours. Streptavidin beads were used to capture the hybridized complexes. Next, captured chromatin complexes were eluted with RNaseH and crosslinks were reversed by adding Proteinase K to the probe-bead complexes and incubating overnight at 65°C.
DNA from captures was purified and subjected to standard Illumina sequencing procedures.

treatment_protocol: Cells were crosslinked with 3% Formaldehyde +DSG

tag: cell type

value: mouse embryonic stem cells

value: expressing Xist under a Dox inducible promoter

value: No Dox induction

tag: crosslinking

value: 3% Formaldehyde + DSG

tag: fraction

value: DNA from captures


title: No Dox, Rep3


title: RNIC_2_NICD_TCFWT [Hi-C]

value: Mx1Cre induction 2ug/g b.w. poly(I:C)


title: GI-M-EN cell line, replicate 1

description: GI-M-EN cell line, replicate 1

tag: cell line


title: JH221_S14

source_name: {delta}{beta}gl HBG-GdTaP 1A7

value: Single bgl locus parental, GFP-tagged


title: E9_WT_RNAseq_rep2

source_name: mouse limb buds

tag: strain/background

value: Swiss Webster

tag: Stage

value: forelimb bud


title: No Dox, Rep2

tag: treatment


title: 15-day old cecum infect 3

city: Yangzhou

first: 金俊

middle: 许金俊

last: 许

address: Floor 29, campus of Wenhui Road

institute: College of Veterinary Medicine, Yangzhou University

data_processing:
Illumina Casava1.8 software used for basecalling
The raw reads obtained by sequencing contains low-quality reads with connectors. In order to ensure the quality of information analysis, rawreads must be processed to get cleanreads.
The clean reads of each sample was screened, and the sRNA within a certain length was selected for follow-up analysis.
Reference sequence alignment analysis
The expression levels of known and new miRNAs in each sample were counted, and transcripts per million clean tags (TPM)
Genome_build: gallus_gallus_Ensembl_97
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cecum

extract_protocol:
The cecum samples aseptically collected from chickens were thoroughly rinsed in PBS and immediately frozen in liquid nitrogen. Then the cecum samples were stored at −80°C until RNA extraction.Total RNA was prepared from individual cecum samples using TRIzol Reagent according to the manufacturer's instruction. The small RNA libraries were prepared from a total of 2 μg total RNA isolated from each sample using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®
smallRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Histomonas meleagridis infect/control

tag: age

value: 15-day old

tag: agent

value: Histomonas meleagridis

value: cecum


title: JH220_S13

value: K562 cell line


title: 15-day old cecum infect 2


title: No Dox, Rep1


title: JH219_S12

source_name: {delta}{beta}gl 45

value: Single bgl locus parental


title: 15-day old cecum infect 1


title: 15-day old cecum control 3

value: control


title: NS02

description: scRNA-seq

data_processing:
Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Genome_build: hg38

extract_protocol:
the scar tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

tag: pathology

value: Normal scar

tag: location

value: Back

tag: gender

value: Male


title: 3X Dox, Rep2

value: mouse embryonic stem cells

value: expressing Xist under a Dox inducible promoter

value: Dox induction, 3X


title: No Dox, Input

value: No Dox induction

value: 3% Formaldehyde + DSG

value: input


title: 15-day old cecum control 2


title: 3X Dox, Rep1

value: DNA from captures


title: 1X Dox, Rep4

value: Dox induction, 1X


title: Pt2

description: Visium

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

value: Skin

value: Keloid

value: Abdomen

value: Female


title: JH224_S17

value: K562 cell line

value: bgl HS3 KO


title: 15-day old cecum control 1

value: 15-day old

value: control

value: cecum


title: 10-day old cecum infect 3

value: 10-day old

value: Histomonas meleagridis


title: JH223_S16

source_name: HS2 KO 4B5

value: bgl HS2 KO


title: Pt1

description: Visium

value: Ear

value: Male


title: CTRL_1_NOTCHWT_TCFWT [Hi-C]

tag: strain background

tag: transgene

value: wild type

tag: cre

value: Controlled injection with 2ug/g body weight poly(I:C)

tag: facs sorting

value: Target population from bone marrow:Lin- Sca1+ cKit+

tag: group


title: JH222_S15

tag: genotype


title: 10-day old cecum infect 2

tag: tissue


title: Ke02

description: scRNA-seq

value: Skin

value: Back


title: 1X Dox, Rep2

tag: cell type

value: mouse embryonic stem cells

value: expressing Xist under a Dox inducible promoter

value: Dox induction, 1X

tag: crosslinking

value: 3% Formaldehyde + DSG

tag: fraction

value: DNA from captures


title: 18-EndoC-E2-Val-SiPTPN2-IFNY.18

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
STAR alignment
HTseq count
DE analysis
analysis using Degust for log fold changes and statistics (limma-voom)
batch effect removal
LogfoldChange calculations
Genome_build: GRCh38

source_name: EndoC-𝛽H1 cells

growth_protocol: The human β-cell line EndoC-βH1 (kindly provided by Dr. R. Scharfmann, University of Paris, France) was cultured in Matrigel-fibronectin-coated plates

extract_protocol:
RNAeqsy mini kit (Qiagen #741014)
Tru stranded mRNA kit (illumina #20020594)

treatment_protocol: EndoC-βH1 and dispersed human islets have been transfected with small interfering RNAs (siRNAs) against STAT3, STAT1 or allstars Negative Control siRNA (negative control), Qiagen, Venlo, the Netherlands) (30nM) using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA)

value: PTPN2 silencing

value: Interferon-gamma


title: 10-day old cecum infect 1

value: 10-day old

value: cecum


title: 1X Dox, Rep3


title: 1X Dox, Rep1


title: 10-day old cecum control 2

value: control


title: 15-EndoC-E2-Val-SiQ-IFNY.15

value: Control


title: 1X Dox, Input

value: input


title: 16-EndoC-E2-Val-SiPTPN2-Ctl-.16


title: 10-day old cecum control 1


treatment_protocol: When seeking maximal GFP expression in tagged lines, enhancer knockout cell lines were treated with 2µg/mL of puromycin for 7 days, then assayed with FACS, analyzing mean fluorescence intensity with FlowJo.

tag: cell line

value: K562 cell line

value: Single bgl locus parental