title: HIF1A-KD EPC2-hTERT_4

city: Maynooth

first: Joanne

middle: Carol

last: Masterson

address: Biomedical Sciences Building, Maynooth University

department: Biology

country: Ireland

institute: Maynooth University

data_processing:
Total RNA (1μg) was sent to the Genomics and Microarray Core at University of Colorado Anschutz Medical Campus.
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample
Assembly: GRCh38/hg38
Supplementary files format and content: .txt file includes normalised reads for each sample

growth_protocol: shCtrl and HIF1A-KD EPC2-hTERT cells were generated by shRNA lentiviral transduction and maintained in defined keratinocyte serum free media supplemented with 50μg/ml bovine pituitary extract and 1ng/ml epidermal growth factor. Cells were seeded on a 0.4μm semi-permeable transwell membrane and allowed to grow to confluence for 2 days. Cells were then maintained in 1.8mM CaCl2-supplemented complete media for 5 days before being exposed to air for 4 days.

extract_protocol:
Total RNA was harvested using the RNeasy kit (Qiagen) and approximately 1μg of total RNA was used for sequencing
RNA libraries for RNA seq were constructed using the NEB Next Ultra RNA library Prep kit for Illumina

treatment_protocol: For treatments, cells were treated with DMSO vehicle or 1mM Dimethyloxalylglycine (DMSO, Cayman Chemicals) for 18hr before harvest.

value: Esophageal Epithelial Cell


title: ATAC-Me, H9, 4.5 day NPCdiff B

status: Public on Mar 31 2025

type: SRA

city: Nashville

first: Lindsey

last: Guerin

state: Tennessee

address: 2215 Garland Ave, 673B Light Hall

department: Biochemistry

country: USA

institute: Vanderbilt University

library_source: genomic

data_processing:
trimming via trim_galore v0.6.2
alignment via WALT v1.0
QC filtering via SAMtools/1.9
methylation quantification via methpipe-5.0.1
peak calling via Genrich, version 0.6
Assembly: hg38
Supplementary files format and content: .meth for methylation quantification

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: STEMdiff™ SMADi Neural Induction Kit and mTeSR

extract_protocol:
Tn5 incubation on in-tact cells, part of ATAC-Me protocol
ATAC-Me as outlined in Nature Protocols paper (Guerin et al. Nat Protocol 2021), https://www.nature.com/articles/s41596-021-00608-z
ATAC-Me

treatment_protocol: STEMdiff™ SMADi Neural Induction Kit

tag: cell line

tag: cell type

value: differentiated human embryonic stem cell/ neural progenitor cell


title: HIF1A-KD EPC2-hTERT_2

library_source: transcriptomic

molecule: total RNA

tag: genotype


title: Ponce-32T

city: Tampa

first: Manishkumar

middle: S

last: Patel

state: FL

address: 12902 USF Magnolia Drive

department: Tumor Microenvironment and Metastasis

institute: H. Lee Moffitt Cancer Center and Research Institute

description:
Library name: Ponce-32T
Tumor

data_processing:
Initial quality control was performed on the sequenced files using fastqc, fastp and multiqc. The sequence reads were aligned to the human genome (hg38) using Bowtie 2 with the default settings and were further sorted and indexed using SAMtools. The duplicated reads were removed using Picard command line tool and, raw read counts per gene were generated using the feature Counts tool from package subread.
Differentially methylated genes were identified using the DESeq2 package. All samples were normalized using DESeq2 internal normalization and further compared in unpaired manner with multiple-hypothesis testing. Genes with |log2 fold-change| >0.4 and adjusted p-value<0.05 were considered differentially methylated.
Assembly: GRCh38
Supplementary files format and content: .txt
Supplementary files format and content: The processed data file contains normalized counts for 22 prostate tumors and 24 adjacent normal samples across different genes.

source_name: Prostate

extract_protocol:
Genomic DNA samples were obtained from the FFPE prostate tumor tissues as described in the manufacturer’s instructions (QIAamp DNA FFPE Tissue kit, Qiagen, Germantown, MD). We used 7-50 ng of genomic DNA as starting material.
DNA was enriched by labeling and capturing as described previously in Song et al., 2011 (https://www.nature.com/articles/nbt.1732). The 5hmC DNA was amplified using universal primer (New England Biolabs, USA), index primer (New England Biolabs, USA) and HiFi HotStart ReadyMix (KAPA/Roche). Single-end 75 bp sequencing was performed on an Illumina NextSeq 500. 22 prostate tumors and 24 adjacent normal FFPE samples were sequenced after 5hmC enrichment.

tag: tissue

value: Prostate

value: FFPE Tissue


title: Spleen Treg, control 3

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

data_processing:
The data were mapped using STAR with default parameters. The gene expression raw counts were quantified by HOMER’s analyzeRepeats command with the option ‘-condenseGenes -count exons -noadj’. Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Assembly: mm10
Supplementary files format and content: text (.txt) file for the TPM counts for each gene.
Supplementary files format and content: Excel file including up- and down-regulated genes in obese vs. normal.

organism: Mus musculus

source_name: spleen

extract_protocol:
Treg cells were sorted into Trizol LS and RNA was extracted using the Zymo Direct-zol RNA microprep kit.
Libraries were prepared using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina.

value: spleen

value: Treg cells

value: control


title: ATAC-Me, H9, 4.5 day NPCdiff A


title: Ponce-56T

description:
Library name: Ponce-56T
Tumor


title: ATAC-Me, H9, 12 day NPCdiff A


title: shCtrl EPC2-hTERT_4

value: shCtrl


title: HIF1A-KD EPC2-hTERT_3


title: shCtrl EPC2-hTERT_2


title: Ponce-34T

description:
Library name: Ponce-34T
Tumor


title: ATAC-Me, H9, 3 day NPCdiff B


title: shCtrl EPC2-hTERT_3


title: Spleen Treg, control 2


title: Spleen Treg, control 1


title: PR-30T

description:
Library name: PR-30T
Tumor


title: PR-44T

description:
Library name: PR-44T
Tumor


title: HIF1A-KD EPC2-hTERT_1


title: shCtrl EPC2-hTERT_1


title: ATAC-Me, H9, 3 day NPCdiff A


title: PR-41T

description:
Library name: PR-41T
Tumor


title: ATAC-Me, H9, 2 day NPCdiff B


title: DMOG-treated ALI_4

data_processing:
Total RNA (1μg) was sent to the Genomics and Microarray Core at University of Colorado Anschutz Medical Campus.
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample
GRCh38/hg38
Assembly: Text file includes normalised reads for each sample
Supplementary files format and content: .txt file includes normalised reads for each sample

growth_protocol: EPC2-hTERT cells were maintained in defined keratinocyte serum free media supplemented with 50μg/ml bovine pituitary extract and 1ng/ml epidermal growth factor. Cells were seeded on a 0.4μm semi-permeable transwell membrane and allowed to grow to confluence for 2 days. Cells were then maintained in 1.8mM CaCl2-supplemented complete media for 5 days before being exposed to air for 4 days.

treatment_protocol: For treatments, cells were treated with DMSO vehicle or 1mM Dimethyloxalylglycine (DMOG, Cayman Chemicals) for 18hr before harvest.

value: WT

tag: treatment

value: 1mM DMOG


title: Liver Treg, obese 3

data_processing:
The sequence tag returned by the Illumina Pipeline was adapter trimmed by Trim Galore (Galaxy Version 0.6.7+galaxy0) and aligned to the mouse genome mm10 assembly by Bowtie2 (Galaxy Version 2.5.0+galaxy0). For subsequent visualization of ATAC-Seq signal, bigwig files were generated using the DeepTools bamCoverage using “Normalized to reads per kilobase per million (RPKM)” with bin size of 50bp (Galaxy Version 3.5.2+galaxy0). The data were visualized by preparing custom tracks on the University of California, Santa Cruz (UCSC) genome browser. Then the ATAC-seq openness peaks were identified by MACS2 callpeak (Galaxy Version 2.2.7.1+galaxy0). For quantification of the count number in peak region, the peak region files from 8 samples (4 lean, 4 obese) were aligned by Bedtools Multiple Intersect (Galaxy Version 2.30.0) to identify the common regions, and the regions that overlapped in at least 3 samples were identified as the final peak regions. The peaks with interval <20 bp were merged as one peak, resulting in total n=26423 peak regions. Next, the final peak region was set as “feature”, and quantified by featureCounts (Galaxy Version 2.0.3+galaxy1). The featureCounts value for a total of the 26423 peak regions in each sample was used as input counts for Deseq2 analysis to identify the alteration of openness (Galaxy Version 2.11.40.8+galaxy0). FDR< 0.05 and log2FC>0.4 was called as significant change.
Assembly: mm10
Supplementary files format and content: 1. bigwig format file for visualizing each sample. 2. Excel file including up- and down-regulated peaks in obese vs. normal.

source_name: liver

extract_protocol:
Treg cells were sorted into FBS and DNA was extracted using the Active Motif ATAC-seq kit.
Libraries were prepared using the Active Motif ATAC-seq kit.

value: liver

value: obese


title: Normal diet, control 1

city: Chuo-ku, Kumamoto-shi

first: Kodai

last: Nakamura

state: Kumamoto-ken

address: 2-2-1 Honjo

department: Institute of molecular embryology and genetics

country: Japan

institute: Kumamoto university

data_processing:
StrandNGS software 3.4 (by Tomy digital biology) was used for base-calling.
Assembly: mm10
Supplementary files format and content: Sequenced reads were trimmed for low-quality sequences and then mapped to UCSC mm10 mouse reference transcript and genome.
Supplementary files format and content: TPM (transcripts per million) was used as a normalization procedure to quantify the gene expressions in each sample.

source_name: Skeletal muscle

extract_protocol:
Total RNA was obtained from the gastrocnemius and plantaris muscles of ND- and HID-fed mice using ISOGEN ll and the RNeasy kit.
Library preparation and RNA-Seq were performed by Novogene (Beijing, China)

value: Skeletal muscle

value: wild type

value: Normal diet


title: ATAC-Me, H9, 2 day NPCdiff A


title: Vehicle-treated ALI_4

value: DMSO


title: DMOG-treated ALI_3


title: Liver Treg, obese 1


title: Liver Treg, obese 2


title: ATAC-Me, H9, 1 day NPCdiff A


title: PR-53T

description:
Library name: PR-53T
Tumor


title: ATAC-Me, H9, 1 day NPCdiff B


title: PR-5T

description:
Library name: PR-5T
Tumor


title: PR-36T

description:
Library name: PR-36T
Tumor


title: Vehicle-treated ALI_3


title: Liver Treg, lean 4

value: lean


title: DMOG-treated ALI_2

value: Esophageal Epithelial Cell


title: PR-42T

description:
Library name: PR-42T
Tumor


title: Liver Treg, lean 3


title: ATAC-Me, H9, 12 hour NPCdiff A

value: differentiated human embryonic stem cell/ neural progenitor cell


title: ATAC-Me, H9, 12 hour NPCdiff B


title: PR-11T

description:
Library name: PR-11T
Tumor

value: Prostate


title: Liver Treg, obese 4


title: DMOG-treated ALI_1


title: Liver Treg, lean 2


title: U2OS, empty vector, treated with 175 nM Pevonedistat, 2N4N population, replicate 2

city: Zurich

first: Matthias

last: Altmeyer

address: Winterthurerstrasse 190

department: Department of Molecular Mechanisms of Disease

country: Switzerland

institute: University of Zurich

description:
Library name: Pevo_2N4N_replicate
SORT-Seq

library_source: transcriptomic single cell

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the reference genome Homo sapiens GRCh38 with STARSolo 2.7.11b (Kaminow et al., 2021). Mapping and generation of count tables were automated using the STARSolo 2.7.11b aligner. For mapping, no UMI cutoff was used and intronic reads were not included. Multi-gene reads were not counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: U-2 OS

growth_protocol: All cell lines were grown at 37°C under standard cell culture conditions (humidified atmosphere, 5 % CO2) in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (Corning) and 1% penicillin-streptomycin antibiotics. Stable U-2 OS PCNA-mEmerald 53BP1-mScarlet cells with overexpression of HRAS and their empty vector controls were maintained in the presence of 4 µg/ml blasticidin (InvivoGen), 500 µg/ml Geneticin (Gibco) and 100 µg/ml hygromycin B (Invitrogen). All cell lines used in this study were grown in sterile conditions and routinely tested for mycoplasma.

extract_protocol:
Single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016) with primers described previously (van den Brink et al., 2017). Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT).
Library preparation was done following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina).

treatment_protocol: Cells treated with Pevonedistat were incubated for 24 h with 175 nM Pevonedistat.

value: U-2 OS

value: cancer cells

value: 175 nM Pevonedistat 24 h


title: U2OS, empty vector, treated with 175 nM Pevonedistat, polyploid population, replicate 2

description:
Library name: Pevo_Polyploid_replicate
SORT-Seq


title: Vehicle-treated ALI_2


title: Vehicle-treated ALI_1


title: miR451aKO_Mandibular LN, sensitized+challenged, rep1

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

institute: Kumamoto University

data_processing:
Sequenceing read were chacked quality and trimmed for adaptor sequence by fastp(v0.23.2)
Trimmed reads were aligned to the GRcm39 mouse reference genome using HISAT2 (v2.2.1) and the aligned reads were counted with StringTie (version 2.2.1)
Assembly: GRcm39
Supplementary files format and content: csv file contains raw counts for each sample.

source_name: Mandibular lymph node

extract_protocol:
Total RNA was extracted using Rneasy Mini kit and 1ug total RNA was used for library construction.
NEBNext® UltraTM ll Directional RNA Library Prep Kit was used for library preparation.

treatment_protocol: WT or miR-451a KO mice were sensitized by applying 100 μl of freshly prepared 0.5 % of 1- fluoro-2,4-dinitrobenzene (DNFB) to the shaved abdomen on day 0, 1, 2. On day 9, the left ears were challenged with 20 μl of freshly prepared 1 % of DNFB.Twenty-four hours after challenge, tissue such as ear skin or mandibular lymph node were harvested and subjected to RNA extraction.

value: Mandibular lymph node

value: miR-451a KO

value: 0.5% DNFB sensitization to the shaved abdomen at day 0, 1, 2 and 1% DNFB challenge to left ears on day 9


title: ATAC-Me, H9, 6 hour NPCdiff A


title: ATAC-Me, H9, 0 day NPCdiff B

value: human embryonic stem cell


title: Liver Treg, lean 1

value: liver

value: Treg cells


title: miR451aKO_Mandibular LN, sensitized+challenged, rep3


title: U2OS, HRAS overexpression, 2N4N population, replicate 2

description:
Library name: HRAS_2N4N_replicate
SORT-Seq

value: untreated


title: ATAC-Me, H9, 6 hour NPCdiff B


title: Decidua, term pregnancy preeclampsia- nuclei (419-d)

city: Berlin

first: Florian

last: Herse

state: FOREIGN

address: Lindenberger Weg 80

department: Experimental and Clinical Research Center (ECRC)

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

data_processing:
The demultiplexing, processing, identification of Unique Molecular Identifiers (UMI) and barcode filtering of raw 3′ single nuclei-seq data was performed using Cell Ranger Single cell software (version 3.0.2) from 10x Genomics.
The transcripts were aligned against the pre-built human reference genome GRCh38 premRNA version 3.0.0, which was built from the GRCh38 precompiled reference (https://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz), and modified for use with snRNAseq data by extracting “transcripts” features from the gene model GTF and instead annotating these as “exon”, as described in the protocol defined by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#grch38_3.0.0)
Data filtering- removal of empty droplets & ambient RNA using CellBender 0.2.0 and further filtering using Seurat 3.1.4
Genome_build: GRCh38
Supplementary_files_format_and_content: txt.gz & H5 matrices

source_name: Decidua

growth_protocol: Not applicable.

extract_protocol:
Approximately 100-200mg frozen placental and corresponding, separately sampled decidual tissue was processed to generate 10X libraries. Sequenced on an Illumina HiSeq 4000 (pair-ended)
Single nuclei libraries were prepared according to the instructions of 10X Genomics Chromium Single Cell 3’ Reagent Kits v2 User Guide – CG00052
Single nuclei sequencing

treatment_protocol: Not applicable.

value: Decidua

tag: gestational day

tag: origin

value: maternal

tag: disease state

value: PE (pre-eclampsia)

tag: sample type

value: single nuclei RNA


title: miR451aKO_Mandibular LN, sensitized+challenged, rep2


title: ATAC-Me, H9, 0 day NPCdiff A


title: Decidua, term pregnancy preeclampsia- nuclei (274-d)


title: miR451aKO_Mandibular LN, sensitized, rep3

value: 0.5% DNFB sensitization to the shaved abdomen at day 0, 1, 2


title: PDO sample, #2136650

city: Shanghai

first: Keda

last: Yu

address: 270 Dongan road

country: China

institute: Fudan university Shanghai cancer center

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2
Assembly: Human genome hg38
Supplementary files format and content: tab-delimited files containing the FPKM values of the samples.

source_name: breast

extract_protocol:
Total RNA was isolated from each thymic sample using the RNAmini kit ( Qiagen, Germany)
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

value: breast


title: U2OS, empty vector, untreated, 2N4N population, replicate 2

description:
Library name: EV_2N4N_replicate
SORT-Seq


title: Decidua, term pregnancy preeclampsia- nuclei (389-d)


title: U2OS, HRAS overexpression, polyploid population, replicate 2

description:
Library name: HRAS_Polyploid_replicate
SORT-Seq


title: U-2 OS cells, Exp2_UT

first: Genome

last: Informatics

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

description: Library name: UZH-MS-s016

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using STARsolo
Poisson correction using UMIs was performed by Single Cell Discoveries
Data was processed using Seurat v5
Assembly: grch38
Supplementary files format and content: Tab-separated values files and matrix files, Seurat R data object

growth_protocol: All cell lines were grown at 37°C under standard cell culture conditions (humidified atmosphere, 5 % CO2) in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (Corning) and 1% penicillin-streptomycin antibiotics.

treatment_protocol: Cells were treated for 24 hours with 4 Gy of ionizing radiation, or left untreated

value: Untreated


title: U-2 OS cells, Exp2_IR

description: Library name: UZH-MS-s022

value: U-2 OS

value: IR


title: Villi, term pregnancy preeclampsia- nuclei (577-1-v)

source_name: Villi

value: Villi

value: fetal


title: PDO sample, #2134353


title: Villi, term pregnancy preeclampsia- nuclei (419-v)


title: miR451aKO_Mandibular LN, sensitized, rep2

value: Mandibular lymph node

value: miR-451a KO


title: Decidua, term pregnancy preeclampsia- nuclei (577-2-v)


title: WT_Mandibular LN, sensitized+challenged, rep3

value: Wild type

value: 0.5% DNFB sensitization to the shaved abdomen at day 0, 1, 2 and 1% DNFB challenge to left ears on day 9


title: PDO sample, #2141570


title: PDO sample, #2143454


title: miR451aKO_Mandibular LN, sensitized, rep1


title: U-2 OS cells, Exp1_IR

description: Library name: UZH-MS-s021

value: cancer cells


title: PDO sample, #2134420


title: WT_Mandibular LN, sensitized+challenged, rep2


title: Villi, term pregnancy preeclampsia- nuclei (389-v)


title: Decidua, term pregnancy control- nuclei (372-d)

value: C (control)


title: PDO sample, #471561


title: WT_Mandibular LN, sensitized+challenged, rep1


title: U-2 OS cells, Exp1_UT

description: Library name: UZH-MS-s015


title: PR-30N

description:
Library name: PR-30N
Normal

value: Prostate

value: FFPE Tissue


title: NCI-H2170 HA3CERB3L1 Cl10-Rep2

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

description: Library name: R190012

data_processing:
Pairwise differential gene expression analyses were carried out in which each HA-CREB3L1-expressing clonal line was analyzed compared with the corresponding parental cell line. Gene-level differential expression was analyzed using DESeq2 v1.22.2 in R 3.5.1. Only genes that had a 1.4-fold increase or decrease, and a significance value of p < 0.05, as determined using a Benjamini-Hochberg (B-H) adjusted Wald test, were included in the results
Assembly: GRCh38.p12
Supplementary files format and content: Tab delimited text file include raw counts and TPM values for each sample

source_name: NCI-H2170 HA-CREB3L1 #10

growth_protocol: RPMI 10% FBS. Cells were grown at 37C 5% CO2.

extract_protocol:
Total RNA was isolated from two replicate samples for each of the 6 cell lines using a MagMAX mirVana Total RNA Isolation Kit (ThermoFisher).
An average of 15 µg of RNA was obtained per sample (determined via Qubit HS RNA assay on a Qubit 4 fluorometer (ThermoFisher)), with an average RNA Integrity Number (RIN) of 10.0 (determined via RNA Screen Tape Analysis on a TapeStation 4150 instrument (Agilent)). All samples provided RNA of sufficient quality and quantity for sequencing library construction. Twelve barcoded Illumina sequencing libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina) and 150 ng input RNA per sample. The average fragment length was 287 bp (determined via DNA Screen Tape Analysis with D1000 reagents on a TapeStation 4150 instrument (Agilent)). The 12 barcoded libraries were pooled at equimolar amounts and 150 bp paired-end reads generated on a NextSeq 550 instrument (Illumina). An average of 35 million reads were obtained per library after filtering. Transcript quantification was performed using the Gencode 30 human reference transcriptome (from genome version GRCh38.p12) and Salmon v0.13.1 with the following options: -l A --validateMappings --rangeFactorizationBins 4 --numBootstraps 10 –seqBias –gcBias --biasSpeedSamp=5.

value: NCI-H2170 HA-CREB3L1 #10

value: Human lung cancer

tag: biological replicate


title: Decidua, term pregnancy control- nuclei (328-d)

value: Decidua

value: maternal

value: single nuclei RNA


title: WT_Mandibular LN, sensitized, rep3

value: 0.5% DNFB sensitization to the shaved abdomen at day 0, 1, 2


title: PDO sample, #2122418

value: breast


title: PDO sample, #2140962


title: NCI-H2170 HA3CERB3L1 Cl10-Rep1

description: Library name: R190011


title: WT_Mandibular LN, sensitized, rep2


title: NCI-H2170 HA3CREB3L1 Cl7-Rep2

description: Library name: R190010

source_name: NCI-H2170 HA-CREB3L1 #7

value: NCI-H2170 HA-CREB3L1 #7


title: PDO sample, #2122097


title: Villi, term pregnancy control- nuclei (372-v)

value: Villi

value: fetal


title: WT_Mandibular LN, sensitized, rep1

value: Mandibular lymph node


title: NCI-H2170-Rep2

description: Library name: R190008

value: WT


title: NCI-H2170 HA3CREB3L1 Cl7-Rep1

description: Library name: R190009


title: resistant cell line, #4


title: Villi, term pregnancy control- nuclei (328-v)


title: Villi, term pregnancy control- nuclei (327-v)


title: NCI-H2170-Rep1

description: Library name: R190007


title: NCI-H1703 HA3 CREB3L1 Cl2-Rep2

description: Library name: R190006

source_name: NCI-1703 HA-CREB3L1 #2

value: NCI-1703 HA-CREB3L1 #2


title: resistant cell line, #2


title: resistant cell line, #3


title: Villi, term pregnancy control- nuclei (TRM3-v)


title: resistant cell line, #1


title: Villi, term pregnancy control- nuclei (TRM2-v)


title: NCI-H1703 HA3 CREB3L1 Cl2-Rep1

description: Library name: R190005


title: NCI-H1703 HA3 CREB3L1 Cl1-Rep1

description: Library name: R190003

source_name: NCI-1703 HA-CREB3L1 #1

value: NCI-1703 HA-CREB3L1 #1


title: Villi, term pregnancy control- nuclei (TRM1-v)

value: C (control)


title: NCI-H1703 HA3 CREB3L1 Cl1-Rep2

description: Library name: R190004


title: U10_scRNA-seq

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: re-analysis of GSM5578041

data_processing:
cellranger 7.1.0 was used to demultiplex and map the raw sequencing data to references built by cellranger from CA_000001405.29 genome assembly and GENCODE v44 gene annotation or ureter urothelial cell-specific poly(A) site reference our pipeline (scPASU) created.
Assembly: GRCh38/hg38
Supplementary files format and content: Compressed Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: polyA RNA

source_name: human ureter

extract_protocol:
10x Chromium Next GEM Single Cell 3ʹ Kit v3.1 barcoded single cell RNA seq libraries were prepared for each sample and subjected to 150 base paired-end sequencing on Illumina NovaSeq. Each sample library was loaded on 4 lanes of flowcell generating 4 sets of fastq files
Library construction steps were performed according to the manufacturer's standard protocol

value: human ureter

tag: Sex

value: male

tag: disease

value: normal

tag: age


title: Decidua, first trimester pregnancy control- nuclei (17-021-d)


title: NCI-H1703-Rep2

description: Library name: R190002

value: Human lung cancer


title: Decidua, first trimester pregnancy control- nuclei (17-022-d)

value: Decidua


title: NCI-H1703-Rep1

description: Library name: R190001


title: Decidua, term pregnancy control- nuclei (327-d)

value: maternal


title: U7_scRNA-seq

description: re-analysis of GSM5578038

value: female


title: Day 24 biol rep 3

city: Manchester

first: Anzy

last: Miller

address: Oxford Road

country: United Kingdom

institute: University of Manchester

data_processing:
Trimmed reads were aligned to hg19 and Bioconductor edgeR package used to normalise counts.
Assembly: GRCh37/hg19
Supplementary files format and content: tab delimited file with raw counts for each sample
Supplementary files format and content: tab delimited file with rpkm values for each sample

extract_protocol:
RNA was extracted using the GenElute Total RNA kit
Unstranded, poly(A) selection, mRNA library preparation using True-seq kit

tag: time

value: Day 24

value: human induced pluripotent cells

value: Pancreatic endocrine differentiation


title: U8_scRNA-seq

description: re-analysis of GSM5578039


title: U6_scRNA-seq

description: re-analysis of GSM5578037


title: Day 24 biol rep 2


title: U4_scRNA-seq

description: re-analysis of GSM5578035


title: Villi, first trimester pregnancy control- nuclei (17-021-v)

value: Villi

value: single nuclei RNA


title: Day 18 biol rep 3

value: Day 18


title: Day 24 biol rep 1

value: WT


title: U3_scRNA-seq

description: re-analysis of GSM5578034


title: U5_scRNA-seq

description: re-analysis of GSM5578036


title: Villi, first trimester pregnancy control- nuclei (17-022-v)

value: fetal


title: Villi, first trimester pregnancy control- nuclei (17-025-v)


title: Day 18 biol rep 2


title: U2_scRNA-seq

description: re-analysis of GSM5578033


title: U9_scRNA-seq

description: re-analysis of GSM5578040


title: Day 18 biol rep 1


title: U1_scRNA-seq

description: re-analysis of GSM5578032


title: Day 15 biol rep 3

value: Day 15


title: 11. DOX+F

city: Haining

first: Mikael

last: Bjorklund

address: International Campus

institute: Zhejiang University-University of Edinburgh Institute

data_processing:
After removal of poor-quality reads, the remaining reads were mapped against human transcriptome (Ensembl v109) using Salmon to obtain transcript abundances. Gene level summaries were generated by tximport. Differential gene expression analysis was done using DESeq2 from vst normalized counts.
Assembly: human transcriptome Homo_sapiens.GRCh38.cdna.all.fa (Ensembl v109)
Supplementary files format and content: Vst normalized counts from DESeq2 output

growth_protocol: RPE1 cells were seeded at the density of 0.25x10e5 cells/ml in a 10cm dish. Cells were incubated at 37℃ 5% CO2.

extract_protocol:
Cells were washed twice with PBS and lysed in 1 ml TRIzol on ice. Lysates were frozen in liquid nitrogen and stored at -80℃.
RNA library preparation and sequencing was performed at Novogene (Beijing). Briefly, sequencing libraries were generated from total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat.No. E7530L) following manufacturer’s recommendations. After random fragmentation, 370~420 bp cDNA fragments were selected for paired end sequencing of 150bp.

treatment_protocol: Four replicates were treated immediately upon plating with or without 50 nM doxorubicin or 50 nM doxorubicin and 5 µM ferrostatin-1. Cells were incubated for 48h after which ferrostatin was replenished (5 µM). Cells were treated for 72h in total.

value: Doxorubicin (50nM)+5µM Ferrostatin-1


title: Day 15 biol rep 2


title: 12. DOX+F


title: Decidua, first trimester pregnancy control- nuclei (17-025-d)

value: C (control)


title: Day 15 biol rep 1


title: 10. DOX+F


title: Day 12 biol rep 3

value: Day 12


title: 9. DOX+F


title: Day 12 biol rep 2


title: ADSC 1st MSCGM-2

type: RNA

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Life and Environmental sciences

institute: University of Tsukuba

description: SAMPLE 11

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ng cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Exp v3 8x60K array kit(G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), added with Acetonitrile(Wako), then dried  immediately by pick up from Acetonitrile liquid.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting. The AgilentG3_GX_1Color was selected as scan protocol.

data_processing: The scanned images were analyzed using the GeneSpring 14.9 software (Agilent), using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Adipose derived stem cell, ADSC2152

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

growth_protocol: After thawing cell vials, ADSC2152 cells were passaged in 10 cm dishes at a density of 5000 cells/cm2 with each medium, at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from each harvested cells by ISOGEN (Nippon Gene, Toyama, Japan)following the manufacturer's protocols.  The extracted RNAs were quantified using Nanodrop ND-1000 UV-spectrophotometer (NanoDrop/Thermo Fisher).

treatment_protocol: When reaching around 80% confluence, these cells were harvested separately from each medium condition to extract RNA.

value: Adipose derived stem cell

tag: medium

value: MSCGM medium

tag: passage no.

value: Passage 5


title: 7. DOX

value: Doxorubicin (50nM)


title: EPSC_rep1

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Libraries were mapped tomm9 genome using STAR. Genes  expression levels were quantified using Cuffquant.
Assembly: mm9
Supplementary files format and content: FPKM table

source_name: mouse embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1 hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen) and Monarch total RNA miniprep kit (NEB)
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.

treatment_protocol: EPSC was transitioned back into ESC media for 1,2, or 3 days to generate 1dESC, 2dESC, or 3dESC, respectively. 20μM diethylstilbestrol (DES) was added to the ESC media daily to generate 3dESC_plus_DES. DMSO was used as vehicle control. 50nM siRNA was added to the ESC media to generate 3dESC_siEsrrb or 3dESC_siNT

value: mouse embryonic stem cells


title: ADSC 1st MP-2

description: SAMPLE 9

value: MesenPro medium


title: ESC1d_rep1


title: Day 9 biol rep 3

value: Day 9

value: human induced pluripotent cells


title: 8. DOX


title: ADSC 1st medD-1

description: SAMPLE 6

value: mediumD


title: Day 12 biol rep 1

value: Pancreatic endocrine differentiation


title: 6. DOX


title: ADSC 1st medD-2

description: SAMPLE 7


title: ADSC 1st MSCGM-1

description: SAMPLE 10


title: ADSC 1st MP-1

description: SAMPLE 8


title: Day 9 biol rep 2


title: 5. DOX


title: ESC2d_rep1


title: 4. CTRL

value: DMSO


title: Day 6 biol rep 3

value: Day 6

value: WT


title: Day 9 biol rep 1


title: BMAC

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

description: Library name: BMAC

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

organism: Sus scrofa

source_name: Bone marrow attached cell

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

value: Bone marrow attached cell


title: ESC3d_DES

value: Adding drug DES


title: 3. CTRL


title: ADSC 1st medB-2

description: SAMPLE 4

value: mediumB


title: ADSC 1st medB-1

description: SAMPLE 3


title: ADSC 1st medC-1

description: SAMPLE 5

value: mediumC


title: EPSC_siEsrrb

value: add siRNA of  Esrrb


title: Day 6 biol rep 2


title: ADSC 1st medA-2

description: SAMPLE 2

value: Adipose derived stem cell

value: mediumA


title: ESC3d_DMSO

value: Adding DMSO


title: 1. CTRL


title: ADSC 1st medA-1

description: SAMPLE 1

value: Passage 5


title: Day 3 biol rep 3

value: Day 3


title: PBMC

description: Library name: PBMC

source_name: peripheral blood mononuclear cells (PBMCs)


title: ESC3d_siNT

value: mouse embryonic stem cells

value: Adding siNT


title: ESC3d_rep1


title: Mo_C57B6_Test_EthanolVapor

city: Baltimore

first: Seth

middle: A

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
Library name: Replication 1.1, 1.2
10X Genomics

data_processing:
We demultiplexed the male vs. female cells within each pooled sample based on the universally expressed female-specific marker gene Xist. First, we performed zeropreserving imputation of read counts with ALRA87 to reduce dropouts. Then, cells with normalized Xist expression values greater than the median were assigned as female, and cells with expression values below the median were assigned as male. We validated that Y chromosome genes were expressed near-exclusively in cells assigned as male.
: Genome alignment (mm10), cell calling, and read counting were performed with cellranger count (v7.1.0), Doublets were detected and removed via scDblFinder.8
Assembly: mm10
Supplementary files format and content: Seurat rds and rdata objects

molecule: nuclear RNA

source_name: Dorsal Striatum

extract_protocol:
Distinct nuclei isolation protocols were used in the discovery dataset and in each of the two replication datasets. For the discovery dataset, cellular nuclei were isolated from frozen dorsal striatal tissue following a 10x Genomics Demonstrated Protocol (CG000124.RevE) with modifications. One hemisphere, dorsal striatum 1 mm punch, was used for 150ul lysis buffer for nuclei extraction. To remove cellular debris and large clumps, an Iodixanol density gradient was used. An 8.5% iodixanol (OptiPrepTM Density Gradient, Millipore) buffer serves as a cushion to remove membranes at 1000xg/10 min at 4C. Clean nucleus was collected in the pellet. Propidium iodide was used to determine the nuclei concentration using a bench cytometer MoxiGoII (Orflo) and nuclei aggregation and clumping were evaluated under 60X magnification in a fluorescent microscope and brightfield. For both replication datasets, nuclei were isolated from frozen brain tissue following a published protocol with our slight modifications.82,83 Briefly, frozen brain tissue was disaggregated by pipetting up and down in chilled extraction buffer consisting of Poly(1- 22 vinylpyrrolidone-co-vinyl acetate) (Sigma #190845), 0.1% TritonX-100, and 1% bovine serum albumen (BSA) in dissociation buffer (DB; 82 mM Na2SO4, 30mM K2SO4, 10mM Glucose, 2.5mM MgCl2,10mM Hepes pH7.4, and RNase inhibitor [Protector, Roche]). Pellets containing nuclei were resuspended in DB and filtered with 70 um and 40 um strainers. To separate nuclei from debris, the nuclei suspension was mixed in a 25% (final) iodixanol layer over a 27% iodixanol cushion, followed by centrifugation (13000g x 20min, 4° C), then nuclei were washed twice in DB.
Nuclei from one male mouse and one female mouse of the same ethanol treatment group were pooled. Approximately 20,000 nuclei per pooled sample were loaded into a Chromium X microfluidics controller (10x Genomics, Pleasanton, CA). 10x Genomics NextGEM 3’ GEX sequencing libraries were prepared from each sample following manufacturer’s instructions and sequenced at depth of 50M/sample on HiSeq4000 Sequencer. In the second replication dataset, nuclei were labeled with sample-specific oligonucleotide tag using CellPlex reagents, following a validated protocol (CG000391). Finally, nuclei were counted using a MoxiGoII (Orflo) cytometer, and the concentration was adjusted to 365 nuclei/ul in phosphate buffered saline with 2% BSA. 17,000 nuclei were loaded in each well of a Chromium Controller (10x Genomics). Nuclei from four male and four female mice were pooled in each sample. Sequencing libraries were prepared using NextGEM 3’ Gene Expression reagents (10x Genomics), following manufacturer’s instructions and sequenced on HiSeq4000 (Replication Dataset 1) and NovaSeq6000 (Replication Dataset 2) sequencers

value: Dorsal Striatum

value: EtOH


title: BM-MSC

description: Library name: BM-MSC

source_name: Bone marrow derived mesenchymal stem cell


title: Day 3 biol rep 2

value: human induced pluripotent cells

value: Pancreatic endocrine differentiation


title: EPSC_DES


title: SLC25A19_sg2B

city: Haining, Zhejiang Province

first: Zongsheng

last: Jiang

state: Select if applicable

address: Haizhou East Road, Haining, Zhejiang province

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

data_processing:
The reads were mapped to human genome (GRCh38.cdna) by Salmon (v1.10.1).
The normalized count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: This file is a plain-text, tab-separated file with a single header line (which names all of the columns).  Name — This is the name of the target transcript provided in the input transcript database (FASTA file).  Length — This is the length of the target transcript in nucleotides.  EffectiveLength — This is the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias (if they are being modeled).  TPM — This is salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.  NumReads — This is salmon’s estimate of the number of reads mapping to each transcript that was quantified. It is an “estimate” insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37 °C in 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) following manufacturer's protocol. 1.3 μg of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Sequencing  libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,  Catalog #: E7530L) following manufacturer’s recommendations and index codes were  added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in NEB  Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand  cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.  Remaining overhangs were converted into blunt ends via exonuclease/polymerase  activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin  loop structure were ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP  system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected,  adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then  PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers  and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library  quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR  (1.5 nM).  The qualified libraries were pooled and sequenced on Illumina platforms with PE150  strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to  effective library concentration and data amount required.

value: Chronic myeloid leukemia


title: Day 3 biol rep 1

value: WT


title: mDorsalStriatum_ETOH_F_M_E4

description:
Library name: Discovery 15+16
10X Genomics


title: EPSC_siNT

value: adding siNT


title: ESC3dsiEsrrb


title: mDorsalStriatum_ETOH_F_M_E2

description:
Library name: Discovery 11+12
10X Genomics


title: SLC25A19_sg2A


title: Mo_C57B6_Control_WaterVapor

description:
Library name: Replication 1.3, 1.4
10X Genomics

value: Air


title: EPSC_DMSO


title: Day 0 biol rep 3

value: Day 0


title: SLC25A19_sg1B


title: Day 0 biol rep 2


title: SLC25A19_sg1C


title: Day 0 biol rep 1


title: 2. CTRL

value: DMSO


title: SLC25A19_sg2C


title: mDorsalStriatum_ETOH_F_M_E1

description:
Library name: Discovery 9+10
10X Genomics


title: mDorsalStriatum_Air_F_M_A4

description:
Library name: Discovery 7+8
10X Genomics


title: mDorsalStriatum_Air_F_M_A3

description:
Library name: Discovery 5+6
10X Genomics


title: CHIR_CHIR

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Raw RNA-seq reads contaminated with adapters and reads with low-quality bases were discarded to obtain the clean reads, and then clean reads were mapped against UCSC mouse reference mm10 using Tophat, and uniquely mapped reads were counted using HTSeq. Gene expression levels were quantified with RPKM (reads per kilobase million).
Assembly: Mus musculus (GRCm38)

source_name: digits of the hind limbs

growth_protocol: 9-day-old neonatal mice were mock-treated with PBS and vaseline ointment in a 10 μL volume (n > 5)

extract_protocol:
10 digits of the hind limbs from one mouse were amputated at the proximal level and collected together for RNA extraction and RNA-seq (5 dpi)
Libraries were prepared according to KAPA mRNA capture Kit and KAPA RNA HyperPrep Kit（for Illumina platform）

treatment_protocol: 9-day-old neonatal mice were infected with 10^4 TCID50 Coxsackievirus A10 in a 10 μL volume (n > 5) and vaseline or CHIR ointment

value: 9-day-old neonatal mice

value: Treat with agonist

value: digits of the hind limbs


title: NC_C

value: NC


title: CVA10_Vaseline

value: Treat with virus


title: mDorsalStriatum_ETOH_F_M_E3

description:
Library name: Discovery 13+14
10X Genomics


title: 2021-42-set5_mRNA_library

city: Marseille

first: Julien

last: Maurizio

address: Bd Jean Moulin

country: France

data_processing:
Reads from the mRNA library were mapped to GRch38-2020-A transcripts and cells using CellRanger software (v5.0.0), giving 2021-42-set3_mRNA_barcodes.tsv.gz, 2021-42-set3_mRNA_features.tsv.gz and 2021-42-set3_mRNA_matrix.mtx.gz, 2021-42-set5_mRNA_barcodes.tsv.gz, 2021-42-set5_mRNA_features.tsv.gz and 2021-42-set5_mRNA_matrix.mtx.gz files.
Reads from the HTO library were processed with CITE-seq-count (v1.4.3), giving 2021-42-set3_HTO_barcodes.tsv.gz, 2021-42-set3_HTO_features.tsv.gz and 2021-42-set3_HTO_matrix.mtx.gz, 2021-42-set5_HTO_barcodes.tsv.gz, 2021-42-set5_HTO_features.tsv.gz and 2021-42-set5_HTO_matrix.mtx.gz files
Data was loaded using R (v4.1.2) in a Seurat (v4.1.0) object for further processing
Filtering : Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed. Cells with more than 8% of mitochondrial-associated genes among their expressed genes were also removed.
Demultiplexing : We used HTO demux coupled with Souporcell (v2.0 ; https://github.com/wheaton5/souporcell) to assign each cells to its sample of origin; doublet cells and negative cells were removed
Expression data were normalized using the Seurat R package NormalizeData function.
Expression data were scaled and centred using the Seurat R package ScaleData function. PCA calculation was done using Seurat R package RunPCA function. Clusters were defined using Seurat R package FindNeighbors and FindClusters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

growth_protocol: Cells were cultured in StemSpan™ Serum-Free Expansion Medium II (SFEM II) supplemented with StemSpan™ Megakaryocyte Expansion Supplement (100X) for 6 (2021-42-set5) or 11 days (2021-42-set5

extract_protocol: 10x Genomics Chromium Single-Cell 5’ protocol

value: blood

value: CD34+ progenitors isolated from blood


title: PBS_Vaseline

value: PBS control


title: NC_B


title: 2021-42-set3_mRNA_library


title: mDorsalStriatum_Air_F_M_A2

description:
Library name: Discovery 3+4
10X Genomics

value: Dorsal Striatum


title: 2021-42-set5_HTO_library


title: mDorsalStriatum_Air_F_M_A1

description:
Library name: Discovery 1+2
10X Genomics


title: heart_10mg_rep5

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Aligned reads were imported to Partek Flow software for downstream analysis.
DEGs were identified with DESeq2 package implemented in Partek Flow
Assembly: Ensembl release 76
Supplementary files format and content: tab-delimited text file includes normalized gene counts for each sample

source_name: Heart

growth_protocol: Heart Tissue was stored in RNALater (Thermofisher) in 4 degree

extract_protocol:
RNA was extracted with the magnetic bead based MaxwellRSC 48 instrument using the Maxwell RSC simply RNA Tissue kit
Library was prepared according to manufacturer’s protocol with Clontech SMARTer method kit

value: Heart

value: 10mg/kg oxaliplatin


title: healthy individual 2

city: Guangzhou

first: Xiaobao

last: Huang

state: Guangdong

address: No. 58 Zhongshan Second Road, Guangzhou, Guangdong, China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing and single-cell 3’ gene counting by using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger, version 6.1.1).
Assembly: scRNA-seq data were aligned to Ensembl genome GRCh38 reference genome.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T cell

extract_protocol:
To isolate human circulating CD8+ T cells, we collected 10 mL peripheral blood from each subject. Then, the EasySep™ Direct Human CD8+ T Cell Isolation Kit (STEMCELL Technologies SARL), in combination with EasyEights Magnets (STEMCELL Technologies SARL), was used to isolate CD8+ T cells from the blood of patients with SJS/TEN and healthy controls, resulting in a CD8+ T cell suspension with a purity of > 90%.
Cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller according to the manufacturer's instructions. Single-cell libraries were then constructed according to the manufacturer's instructions. Single-cell suspensions were loaded to 10x Chromium to capture at least 2000 single cells according to the manufacturer's instructions of 10X Genomics Chromium Single-Cell 3'kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an llumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) at aminimum depth of 20,000 reads per cell.

value: CD8+ T cell

value: healthy


title: hBO_d45_MTX-3

city: Deajoen

first: Onju

last: Ham

address: 141 Gajeong-ro

institute: Korea Institute of Toxicology

data_processing:
The RNA-seq reads were trimmed using Trimmomatic 0.38 and quality checked with FastQC
Clean reads were mapped to the reference genome using HISAT2 version 2.1.0.
The raw read counts were calculated from unique and multiple alignments using StringTie version 2.1.3b.
The raw read count data were normalized by trimmed mean of M-values (TMM) method  using edgeR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: H9 is cultured in mTeSR plus with supplements. hCOs were cultured in 2% B27 contained Neurobasal [EB(d1~d6): 2.5 uM dorsomorphine+10uM SB431642, Neural induction: 20ng/ml bFGF and 20ng/ml EGF(d6~d25), Neural maturation (d25~d45): 20ng/ml BDNF and 20 ng/ml NT,long-term culture: no growth factor]

extract_protocol:
Total RNA was extracted from all cells using Maxwell® RSC simplyRNA Cells Kit
RNA libraries for RNA-seq were prepared using the SureSelect RNA Direct_Human following manufactuer's protocols

treatment_protocol: 0.5uM MTX was administered every other day from d16 until harvesting the samples.

value: human brain cortical organoids

value: WT

value: Methotraxate (MTX)


title: heart_control_rep2

value: vehicle


title: hBO_d45_MTX-1


title: heart_10mg_rep3


title: patient 1

description: 10x Genomics

value: SJS/TEN


title: CD8+ T cells, CGRP, rep6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTMReverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: T lymphocyte

value: CGRP


title: heart_10mg_rep2


title: SLC25A19_sg1A

value: Chronic myeloid leukemia


title: CD8+ T cells, CGRP, rep5


title: heart_control_rep1


title: heart_10mg_rep1


title: hBO_d45_cont-1


title: hBO_d45_cont-2


title: Day 6 biol rep 1

value: Day 6

value: human induced pluripotent cells

value: Pancreatic endocrine differentiation


title: heart_control_rep4


title: Coxsackievirus A10 infection

data_processing:
RNA-seq reads were aligned to the mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: mm10
Supplementary files format and content: csv

source_name: hindfoot

growth_protocol: 9-day-old neonatal mice were mock-treated with PBS in a 10 μL volume (n > 5)

treatment_protocol: 9-day-old neonatal mice were infected with 10^5 TCID50 Coxsackievirus A10 in a 10 μL volume (n > 5)

value: digit tips

tag: strain

value: BALB/c

value: Coxsackievirus A10


title: NC_A

tag: cell line

value: NC


title: heart_control_rep3

value: Heart


title: healthy individual 1

description: 10x Genomics

tag: cell type

value: CD8+ T cell

value: healthy


title: 2021-42-set3_HTO_library

value: blood

value: CD34+ progenitors isolated from blood


title: CD8+ T cells, CGRP, rep2


title: PBS (control)

value: PBS


title: heart_10mg_rep4

tag: genotype

value: 10mg/kg oxaliplatin


title: hBO_d45_MTX-2

value: human brain cortical organoids

value: WT

value: Methotraxate (MTX)


title: patient 2

description: 10x Genomics

value: SJS/TEN


title: hBO_d25_MTX-2


title: Liver, AAV-TBG-Cre, rep3

city: Ann Arbor

first: Qiantao

last: Zheng

state: MI

address: 2800 Plymouth Road

department: Department of Molecular & Integrative Physiology

institute: University of Michigan

description:
Library name: 1213
Column name in AllSamples.GeneExpression.FPKM.xls: 1213_FPKM

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.And then we assembled those clean reads into Unigenes, followed with Unigene functional annotation and calculate the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differential expressed genes) between samples and do clustering analysis and functional annotations.
Sequencing Reads Filtering: We use internal software SOAPnuke to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format.
Genome Mapping: We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
Gene Expression Analysis: We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with  RSEM, which is a software package for estimating gene and isoform expression levels from RNA-Seq data. Calculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R.
Assembly: mm10
Supplementary files format and content: xls files include FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (Qiagen Cat#74104) and used for RNA-seq
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on DNBseq platform.

tag: tissue

value: Liver

value: METTL14 KO


title: CD8+ T cells, CGRP, rep1

value: T lymphocyte

tag: treatment

value: CGRP


title: CD8+ T cells, Vehicle, rep6

value: Vehicle


title: hBO_d45_cont-3


title: Liver, AAV-TBG-Cre, rep2

description:
Library name: 1212
Column name in AllSamples.GeneExpression.FPKM.xls: 1212_FPKM


title: hBO_d25_MTX-1


title: CD8+ T cells, CGRP, rep4


title: CD8+ T cells, Vehicle, rep5


title: HiC_RA-rep2

data_processing:
HiC reads were aligned to mm9 genome assembly using BWA with runHiC pipeline using the default settings (https://pypi.org/project/runHiC/)
Assembly: mm9
Supplementary files format and content: The cool file were the matrix of Hi-C for each Sample.

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). 2i cells were derived from ESC by culturing in NDiff227 basal media (TakaraBio) supplemented with 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 15 μM CHIR (Tocris) and 5 μM PD0325901 (Tocris) for at least 3 passages. EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1 hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). RA cells were cultured in LIF-serum medium, supplemented with 1 retinoic acid for 48 hours. All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
HiC was performed according to Arima HiC+ kit protocol (document part number: A160430 v00). After HiC reactions, the chromatins were sheared using Covaris S2 instrument with intensity setting 3 (equivalent to 105W), 5% duty cycle, and 200 cycles per burst for 7min. Then, sheared chromatins were decrosslinked for library preparation.
Libraries were prepared according to Illumina's instructions with optimised rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.

treatment_protocol: no treatment was applied

tag: agent

value: LIF serum media + 1uM Retinoic acid


title: CD8+ T cells, Vehicle, rep4


title: CD8+ T cells, CGRP, rep3


title: hBO_d25_cont-1


title: E14_EPSC_Esrrb-HiChIP

data_processing:
HiChIP reads were aligned to mm9 genome assembly using BWA, loops were called using FitHiChIP
Assembly: mm9
Supplementary files format and content: The cool file were the reads matrix for each Sample.
Library strategy: HiChIP

extract_protocol:
HiChIP was performed according to Arima HiC+ kit protocol (document part number: A160430 v00) with some modifications. Briefly, cells were crosslinked with 2% formaldehyde in PBS at room temperature for 10min, quenched for 5min and washed once with ice-cold PBS. After HiC reactions, the chromatins were sheared using Covaris S2 instrument with intensity setting 3 (equivalent to 105W), 5% duty cycle, and 200 cycles per burst for 7min. Following shearing, the chromatins were precleared using Dynabeads™ Protein A (Thermo Fisher Scientific, 10001D) for 1h at 4°C. Subsequently, 10µg of Esrrb antibody (PPH6705, Perseus Proteomics) was added to the precleared chromatins and incubated overnight at 4°C. Following the overnight incubation, BSA-blocked Dynabeads™ Protein A were added to the antibody-bound chromatins and incubated for 4h at 4°C, washed, eluted and decrosslinked according to Arima HiC+ kit protocol.
Libraries were prepared according to Illumina's instructions with optimised rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.

treatment_protocol: Lipofectamine (Invitrogen) was used for transfection of shRNA or CRISPRi plasmids according to the manufacturer’s instructions. cells were harvested for experiments after 3 days of knockdown.

value: EPSC media

tag: antibody

value: Esrrb antibody (Perseus Proteomics, PPH6705)


title: CD8+ T cells, Vehicle, rep3

value: CD8+ T cell


title: Liver, AAV-TBG-GFP, rep3

description:
Library name: 1211
Column name in AllSamples.GeneExpression.FPKM.xls: 1211_FPKM


title: hBO_d25_MTX-3


title: E14_2i_Esrrb-HiChIP

value: 2i LIF media


title: Liver, AAV-TBG-GFP, rep2

description:
Library name: 36
Column name in AllSamples.GeneExpression.FPKM.xls: 036_FPKM


title: CD8+ T cells, Vehicle, rep2


title: Liver, AAV-TBG-GFP, rep1

description:
Library name: 25
Column name in AllSamples.GeneExpression.FPKM.xls: 025_FPKM


title: CD8+ T cells, Vehicle, rep1


title: H9P43-2

value: human embryonic stem cells


title: E14_ESC_Esrrb_HiChIP

value: LIF serum media


title: HiC_EPSC-rep2


title: hBO_d25_cont-3


title: H9P43-1


title: CONTROL3

city: 深圳

first: Yilun

last: Liu

address: 深圳市福田区深圳北京大学香港科技大学医学中心

institute: Shenzhen PKU-HKUST Medical Center

data_processing:
clc genomics workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: Lung

extract_protocol:
After 5 days culture in transwell plates, the airway smooth muscle cells were lysed by Trizol and frozen on dry ice for sample delivery
HISAT was used to compare RNA sequences

value: Lung

value: Primary cell

value: smooth muscle cell

value: control


title: HiC_2i-rep2


title: U2OS, empty vector, treated with 175 nM Pevonedistat, 2N4N population

city: Zurich

first: Matthias

last: Altmeyer

address: Winterthurerstrasse 190

institute: University of Zurich

description: SORT-Seq

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the reference genome Homo sapiens GRCh38 with STARSolo 2.7.10b (Kaminow et al., 2021). Mapping and generation of count tables were automated using the STARSolo 2.7.10b aligner. For mapping, no UMI cutoff was used and intronic reads were not included. Multi-gene reads were not counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: U-2 OS

extract_protocol:
Single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016) with primers described previously (van den Brink et al., 2017). Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT).
Library preparation was done following the CEL-Seq2 protocol (Hashimshony et al., 2016) to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina).

value: U-2 OS

value: cancer cells

tag: population

value: 175 nM Pevonedistat 24 h


title: IPFHS07, scRNAseq

city: Hull

first: Eamon

middle: Connor

last: Faulkner

address: Cottingham Road

department: Centre for Biomedicine

institute: University of Hull

description: 10x Genomics

data_processing:
Base calls were converted to reads with the software Cell Ranger’s (v7.1) implementation mkfastq. Multiple fastq files from the same library and strand were catenated to single files.
Assembly: hg38
Supplementary files format and content: Tab-seperated files and Matrix files

source_name: HPMEC

extract_protocol:
Cultured HPMEC were washed with phosphate buffered saline (PBS). The HPMEC monolayers were then trypsinised, washed in PBS again and passed through a 40um cell strainer. The cell suspension was then frozen in foetal bovine serum (FBS) containing 10% Dimethylsulfoxide (DMSO) in liquid nitrogen until being processed for scRNAseq.
Single cells were barcoded using the 10× chromium single-cell platform, and complementary DNA (cDNA) libraries were prepared according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ LT Reagents Kits, 10× Genomics, USA). Cell suspensions, reverse transcription master mix, and partitioning oil were loaded on a single cell “A” chip with a targeted cell output of 1,000 cells per library, assuming 100% viability, and then run on the Chromium Controller. Reverse transcription was performed within the droplets at 53°C for 45 minutes. cDNA was amplified for 12 cycles total on a Bio-Rad C1000 Touch thermocycler. cDNA size selection was performed using SPRIselect beads (Beckman Coulter, USA) and a ratio of SPRIselect reagent volume to a sample volume of 0.6. cDNA was analysed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 minutes at 32°C, followed by end-repair and A-tailing at 65°C for 30 minutes. cDNA were double-sided size selected using SPRIselect beads. Sequencing adaptors were ligated to the cDNA at 20°C for 15 minutes. cDNA was amplified using a sample-specific index oligo as a primer, followed by another round of double-sided size selection using SPRIselect beads. Final libraries were analysed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes.

value: HPMEC

value: Human Pulmonary Microvascular Endothelial Cell

tag: tissue origin

value: lung

value: Male

tag: cell donor_age

tag: serum donor_age

value: IPFHS


title: CONTROL2

address: 深圳市福田区深圳北京大学香港科技大学医学中心

value: WT


title: CONTROL1

address: 深圳市福田区深圳北京大学香港科技大学医学中心


title: U2OS, empty vector, treated with 175 nM Pevonedistat, polyploid population

description: SORT-Seq

value: Polyploid


title: hBO_d25_cont-2

value: human brain cortical organoids


title: CO-CULTURE3

address: 深圳市福田区深圳北京大学香港科技大学医学中心

value: CO CULTURE


title: Liver, AAV-TBG-Cre, rep1

description:
Library name: 35
Column name in AllSamples.GeneExpression.FPKM.xls: 035_FPKM

value: Liver

value: METTL14 KO


title: IPFHS06, scRNAseq

description: 10x Genomics

tag: Sex


title: H9P43-3

value: human embryonic stem cells


title: HVHS05, scRNAseq

description: 10x Genomics

value: HVHS


title: HiC_EPSC-rep1

value: EPSC media


title: CO-CULTURE2

address: 深圳市福田区深圳北京大学香港科技大学医学中心

value: Lung

value: Primary cell

value: smooth muscle cell


title: U2OS, HRAS overexpression, polyploid population

description: SORT-Seq

source_name: U-2 OS with HRAS overexpression

value: U-2 OS with HRAS overexpression

value: cancer cells

value: untreated


title: HVHS03, scRNAseq

description: 10x Genomics

value: HPMEC

value: Human Pulmonary Microvascular Endothelial Cell

value: lung

value: Male


title: HiC_2i-rep1

value: 2i LIF media


title: CO-CULTURE1

address: 深圳市福田区深圳北京大学香港科技大学医学中心

value: WT

value: CO CULTURE


title: HiC_ESC-rep1

value: LIF serum media


title: LV_KO, rep3

city: Dongguan

first: XUERONG

last: SUN

state: Guangdong Province

address: No. 1 Xincheng Avenue, Songshan Lake District

institute: Guangdong Medical University

data_processing:
The raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6), and the clean data was compared to the reference genome using HISTA2 (v2.1.0) software.
Ericscript (v0.5.5) was used for gene fusion detection, rMATS (V3.2.5) was used for variable splicing and differential variable splicing detection, and Bowtie2(v2.3.4.3) was used to compare clean data to the reference gene set.
RSEM (v1.3.1) software was used for gene expression quantification, pheatmap (v1.0.8) was used to draw the clustering heatmap of gene expression in different samples, and DESeq2 (v1.4.5) was used for differential gene detection under the condition of Q value≤0.05 or FDR≤0.001.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes FPKM, TPM and read count values for all samples

growth_protocol: Three wild-type and three Prxl2a knockout mice were normally fed up to 12 weeks.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SI MARTER mRNA-Seq Library Prep Kit following manufacturer's protoco

treatment_protocol: All the mice were systematically perfused with PBS solution to remove the blood. Then the tissues were routinely excised and frozen with liquid nitrogen.

value: Liver

value: Female

value: Prxl2a knockout


title: U2OS, empty vector, untreated, 2N4N population

description: SORT-Seq

value: U-2 OS


title: Pathological myoblast rep2

city: Paris

first: Florent

last: Hubé

address: 9 quai saint Bernard

department: LBD

institute: Sorbonne Université, CNRS, Paris, France

data_processing:
Trimmomatic (v0.32.3)
STAR (Galaxy Version 2.7.8a)
DESeq2 (Galaxy Version 2.11.40.6)
Assembly: hg38
Supplementary files format and content: Total_DM.xlsx

source_name: Muscle satellite cells undifferentiated

growth_protocol: We used pathological myoblast from myotonic dystrophy (DM). Cells were grown as previously described.

extract_protocol:
Tri Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: HiC_ESC-rep2


title: lcSSc-P3-Ljx_scRNA-seq

city: Shanghai

first: Hanlin

last: Yin

state: Please Select

address: 145 Middle Shandong Road

institute: Renji Hospital Affiliated to Shanghai Jiao Tong Univeristy School of Medicine

description: BD Rhapsody

data_processing:
Fastp was applied to all raw reads with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. UMI-tools() was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to human genome (Ensemble version 91) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample.
Assembly: GRCh38 Ensemble version 91
Supplementary files format and content: TXT file containing counts for each sample

source_name: skin

extract_protocol:
The 4mm skin tissues were surgically removed from the distal forearm and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 2.5mg/mL collagenase IV, 0.5mg/mL DNase I, and 2 mg/mL dispase for 1h at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec)
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. Cell-lysis buffer was added so that poly-adenylated RNA molecules hybridized to the beads. Beads were collected into a single tube for reverse transcription. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell label indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification workflow. In brief, second strand cDNA was synthesized, followed by ligation of the WTA adaptor for universal amplification. Eighteen cycles of PCR were used to amplify the adaptor-ligated cDNA products. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3′ end of the transcripts linked with the cell label and UMI. Sequencing libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). The library for each sample was sequenced by Illumina Nova-6000 (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: skin

value: female

tag: disease state

value: limited cutaneous systemic sclerosis (lcSSc)


title: U2OS, HRAS overexpression, 2N4N population

description: SORT-Seq

value: U-2 OS with HRAS overexpression

value: cancer cells


title: HiC_RA-rep1

value: LIF serum media + 1uM Retinoic acid


title: YY1_ChIP_in_shEV_Sample

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
peaks were called using MACS2 and bigiwg files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigwig file

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
10 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, with the formaldehyde then quenched by the addition of 200 mM glycine and cells then washed once with ice-cold PBS. Cell lysis was carried out with a buffer containing 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at 4°C before spinning down to collect the chromatin pellet. The pellet was then washed twice with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Sonication was conducted using the Branson sonifier 250 on ice (11 cycles, power amplitude of 35%, 30s pulses on with 59.9 s pulses off). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 5 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with phenol chloroform isoamyl alcohol followed by chloroform, ethanol precipitated in the presence of glycogen, and re-suspended in TE buffer.
The ChIP-Seq libraries were prepared using Illumina TruSeq ChIP Sample Prep Kit (Catalog #: IP-202-1012) as per manufacturer's instructions.

tag: shRNA

value: pSuper shRNA plasmid

value: Yy1 antibody (Invitrogen, PA5-29171)


title: dcSSc-P2-45Y-M_scRNA-seq

description: BD Rhapsody

value: male

value: diffuse cutaneous systemic sclerosis (dcSSc)


title: Pathological myoblast rep1


title: lcSSc-PFX_scRNA-seq

description: BD Rhapsody


title: LV_KO, rep2


title: LV_KO, rep1


title: HC2-45Y-M_scRNA-seq

description: BD Rhapsody

value: healthy


title: YY1_ChIP_in_shESRRB-sh1_Sample


title: LV_WT, rep3

value: Wildtype


title: HEK293_dsLACc_Parental_total_Rep2_Experiment3

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description:
small RNA
total RNA
dsRNA_variants_miRNA_quant.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with BBduk of the BBmap package using the following parameters ktrim=r k=23 mink=11 hdist=1
Mapping to the human genome (GRCh38) with STAR (--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --alignIntronMax 500 --alignIntronMin 50 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50)
Read counting to mirbase annotation with Rsubread (allowMultiOverlap=T, isPairedEnd=T, strandSpecific=2, countMultiMappingReads=T)
Read normalization with DEsep2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files of count per million (CPM) values

growth_protocol: All HEK293T cell lines were maintained at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) (Thermo Scientific) containing 4500 g/mL glucose, further supplemented with 10% fetal bovine serum (FBS) (Sigma Aaldrich), 100 U/mL of penicillin and 100 μg/mL of streptomycin (Sigma Aaldrich).

extract_protocol:
Ago-pulldown: Ago Affinity Purification by Peptides was performed in accordance with an earlier described protocols (Hauptmann et al., 2015). Ago-pulldown quality was validated by miR16/21 RT-qPCR. RNA extraction: 1.5-3*10^6 cells were trypsinized and washed twice with PBS before proceeding with RNA extraction. RNA was extarcted using TRI reagent (Sigma Aaldrich) according to manufacturer's recmmendations. Total RNA integrity and quality was validated on the Nanodrop 2000 (Thermo Scientific) and on an 1% agarose gel.
Libraries were prepared with total RNA and Ago-purified RNA, from approximately 2-3*10^6 cells, with the Lexogen small RNA-Seq Library Prep kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: All HEK293T cells were transfected with long dsRNA using Lipofectamine 3000 (Thermo Scientific) according to the manufacturers’ instructions.

tag: parental cell line

value: pOSI17 PKR knock-out

value: Parental

tag: transfected long dsrna

value: dsLACc


title: lcSSc-P1-64Y-F_scRNA-seq

description: BD Rhapsody


title: HEK293_dsLACb_Parental_total_Rep2_Experiment3

value: dsLACb


title: HEK293_dsLACa_Parental_total_Rep2_Experiment3

value: dsLACa


title: LV_WT, rep1

value: Liver

value: Female


title: LV_WT, rep2


title: H37Rv::Rv1435cKO infected, Replicate 2

city: New Delhi

first: Dhiraj

last: Kumar

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: ICGEB, New Delhi

data_processing:
Reads mapped using Salmon against Gencode 40 human genome GRCh38
Used tximeta, fishpond and SummarizedExperiment to obtain genes expression based on GENCODE v40 annotation
Normalisation done using approach as described in fishpond library for swish methodology
Assembly: Human genome GRCh38
Supplementary files format and content: comma-separated text files include expression values for each Sample

source_name: THP-1 macrophages

extract_protocol:
Total RNA was isolate using MDI total mammalian RNA isolation Kit
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Library Prep Kit following manufacturer's protocols.

tag: type

value: Knockout restored

value: THP-1 macrophages

value: H37Rv::Rv1435cKO infected


title: sgMIR23Input

city: Singapore

first: Yingying

last: Zeng

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

value: CRISPRi plasmid (ORIGENE,  GE100083)


title: HC1-67Y-F_scRNA-seq

description: BD Rhapsody

value: skin

value: female


title: HEK293_dsGAPDHa_Parental_total_Rep2_Experiment3

tag: cell line

value: dsGAPDHa


title: H37Rv::Rv1435cKO infected, Replicate 1

tag: cell type


title: HEK293_dsGAPDHd_Parental_total_Rep2_Experiment3

value: dsGAPDHd


title: YY1_ChIP_in_shEV_Input

value: pSuper shRNA plasmid


title: sgMIR23ESRRB

value: Esrrb antibody (Perseus Proteomics, PPH6705)


title: BR_KO, rep3

source_name: Brain

value: Brain

tag: genotype

value: Prxl2a knockout


title: H37Rv infected, Replicate 2

value: Wildtype

value: H37Rv infected


title: BR_KO, rep2

tag: tissue


title: sgMIR22ESRRB


title: HEK293_dsGAPDHc_Parental_total_Rep2_Experiment3

value: pOSI17 PKR knock-out

value: Parental

value: dsGAPDHc


title: H37Rv infected, Replicate 1

tag: treatment


title: ScrmblInput


title: BR_KO, rep1

value: Female


title: Uninfected, Replicate 2

value: THP-1 macrophages

value: Uninfected


title: BR_WT, rep3


title: ScrmblESRRB

value: CRISPRi plasmid (ORIGENE,  GE100083)


title: Uninfected, Replicate 1


title: HEK293_dsGFPa_Parental_total_Rep2_Experiment3

value: dsGFPa


title: sgMIR23_Input


title: sgMIR23_Cas9_IP

value: Cas9 antibody (Diagenode, C15310258-100)


title: JB21120

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

description:
pHC14
JB21120

data_processing:
Illumina basecall files (*.bcl) were converted to fastqs using cellranger v3.0.2 which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to hg19 genome and transcriptome using the cellranger v3.0.2 pipeline, which generates a gene - cell expression matrix.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
Assembly: GRCh38
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format.  Transcriptomic counts matrices in Matrix Market CSR format.    Rows correspond to features in the order provided in features.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

source_name: BLOOD

extract_protocol:
10% DMSO + 90% FBS. PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells exhibiting a viability rate less than 70% were excluded. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII.
12,000 single cells were loaded into one lane of a 10X Genomics Chromium [Controller, X], targeting 6,000 barcoded single cells. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version [3, 3.1] chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000  targeting 100,000 raw read pairs per cell.

tag: cells

value: PBMCs

tag: groups

value: HC

tag: age (months)

tag: affection status

value: Healthy

value: F

value: B


title: BR_WT, rep2

value: Brain


title: HEK293_dsGFPb_Parental_total_Rep2_Experiment3

value: dsGFPb


title: HEK293_dsGFPc_Parental_total_Rep2_Experiment3

value: dsGFPc


title: JB21119

description:
pHC13
JB21119

value: BR


title: sgMIR22_Input


title: JB21104

description:
pHC12
JB21104

value: M


title: HEK293_dsGFPd_Parental_total_Rep2_Experiment3

value: pOSI17 PKR knock-out

value: Parental

value: dsGFPd


title: BA_KO, rep3

source_name: Dorsal brown adipose tissue

value: Dorsal brown adipose tissue

value: Female

value: Prxl2a knockout


title: sgMIR22_Cas9_IP

value: CRISPRi plasmid (ORIGENE,  GE100083)

tag: antibody

value: Cas9 antibody (Diagenode, C15310258-100)


title: BA_KO, rep2


title: JB21103

description:
pHC11
JB21103

value: PBMCs

value: HC

value: W


title: 4__H3K4me3_ChIP_Sample

value: wildtype

value: H3K4me3 antibody (Abcam, ab8580)


title: BA_KO, rep1


title: HEK293_dsLACa_Parental_total_Rep1_Experiment3

value: dsLACa


title: HEK293_Mock_Parental_total_Rep2_Experiment3

value: Mock


title: HEK293_dsGAPDHb_Parental_total_Rep2_Experiment3

value: dsGAPDHb


title: YY1_ChIP_in_shESRRB-sh1_Input

value: pSuper shRNA plasmid


title: JB20143

description:
pHC10
JB20143

value: Healthy

value: M

value: B


title: 3__Esrrb_ChIP_Sample

value: Esrrb antibody (Perseus Proteomics, PPH6705)


title: BA_WT, rep3

value: Dorsal brown adipose tissue

value: Female

value: Wildtype


title: HEK293_dsLACc_Parental_total_Rep1_Experiment3

value: pOSI17 PKR knock-out

value: Parental

value: dsLACc


title: JB20127

description:
pHC9
JB20127

value: PBMCs

value: HC


title: 2__H3K4me3_ChIP_Input

value: wildtype


title: BR_WT, rep1

value: Brain


title: BA_WT, rep2


title: HEK293_dsLACb_Parental_total_Rep1_Experiment3

value: dsLACb


title: 1__Esrrb_ChIP_Input


title: JB20080

description:
pHC8
JB20080

value: F

value: W


title: BA_WT, rep1


title: JB19069

description:
pHC7
JB19069

value: Healthy


title: Yy1_sh2

data_processing:
Libraries were mapped tomm9 genome using STAR.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the FPKM for every gene in every sample

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured in LIF-serum medium comprised of DMEM  high  glucose  (Hyclone)  supplemented  with  15%  ES  cell  FBS  (Gibco),  2mM  L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). 2i cells were derived from ESC by culturing in NDiff227 basal media (TakaraBio) supplemented with 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 15 μM CHIR (Tocris) and 5 μM PD0325901 (Tocris) for at least 3 passages. EPSC were derived from ESC by culturing in EPSC media developed by (Yang et al 2017), comprising of DMEM/F12 (Invitrogen), 20% KnockOut Serum Replacement (Invitrogen), 1× GPS, 1× non-essential amino acids, 0.1 mM β-ME, 103 U ml−1 hLIF, 3 μM CHIR99021 (Tocris), 1 μM PD0325901 (Tocris), 4 μM JNK Inhibitor VIII (Tocris), 10 μM SB203580 (Tocris), 0.3 μM A-419259 (Santa Cruz) and 5 μM XAV939 (Sigma). RA cells were cultured in LIF-serum medium, supplemented with 1 retinoic acid for 48 hours. All cultures were maintained at 37°C with 5% CO2. All cells were maintained on plates pre-coated with 0.1% gelatine (porcine).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen) and Monarch total RNA miniprep kit (NEB)
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.

value: pSuper shRNA plasmid


title: HEK293_dsGAPDHa_Parental_total_Rep1_Experiment3

value: dsGAPDHa


title: IAT_KO, rep3

source_name: Inguinal adipose tissue

value: Inguinal adipose tissue

value: Prxl2a knockout


title: Yy1_sh1


title: IAT_KO, rep2

value: Female


title: HEK293_dsGAPDHc_Parental_total_Rep1_Experiment3

value: dsGAPDHc


title: shEV


title: JB19066

description:
pHC6
JB19066

value: B


title: HEK293_dsGAPDHd_Parental_total_Rep1_Experiment3

value: pOSI17 PKR knock-out

value: Parental

value: dsGAPDHd


title: JB19058

description:
pHC5
JB19058

value: PBMCs

value: HC

value: M

value: BR


title: JB19057

description:
pHC4
JB19057

value: F


title: HEK293_dsGAPDHb_Parental_total_Rep1_Experiment3

value: dsGAPDHb


title: EPSC_shEV


title: HEK293_dsGFPa_Parental_total_Rep1_Experiment3

value: dsGFPa


title: HEK293_dsGFPb_Parental_total_Rep1_Experiment3

value: dsGFPb


title: IAT_WT, rep2

value: Wildtype


title: JB19056

description:
pHC3
JB19056

value: Healthy

value: W


title: IAT_KO, rep1

value: Inguinal adipose tissue

value: Female

value: Prxl2a knockout


title: JB19053

description:
pHC2
JB19053


title: EPSC_Esrrb_sh2

value: pSuper shRNA plasmid


title: IAT_WT, rep3


title: JB19050

description:
pHC1
JB19050

value: HC (healthy controls)


title: EPSC_Esrrb_sh1


title: HEK293_dsGFPc_Parental_total_Rep1_Experiment3

value: pOSI17 PKR knock-out

value: Parental

value: dsGFPc


title: IAT_WT, rep1


title: HEK293_dsGFPd_Parental_total_Rep1_Experiment3

value: dsGFPd


title: CRISPRi_sgScrmbl

value: CRISPRi plasmid (ORIGENE,  GE100083)