title: Young

last: Yamazaki

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Biochemistry

institute: Keio University School of Medicine

data_processing:
Adaptor sequences, contamination and low-quality reads were removed from raw reads.
Clean reads were aligned to GRCm38 reference genome using Hisat2 (v2.1.0) and counted using Stringtie (v1.3.4d).
Gene annotation was performed using an Ensembl gene annotation file downloaded from University of California Santa Cruz (UCSC) genome browser. Ensembl gene IDs were converted to gene names using biomaRt (v2.38.0) in R (v3.5.0).
Count per million (CPM) was used for comparison of gene expressions between samples.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text file includes ensemble gene IDs, gene names, and CPM for each sample.

source_name: skeletal muscle

extract_protocol:
Gastrocnemius and plantaris muscle were dissected from mice. Tissues were frozen and crushed on liquid nitrogen. Total RNA was extracted using Sepasol-RNA I Super G (Nacalai tesque Inc.).
RNA libraries were prepared for sequencing using standard BGI protocols.

value: gastrocnemius and plantaris muscle

value: 24 weeks old


title: GR19_V5

status: Public on Dec 21 2020

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2 used to obtain betas, probe filtering completed, sample outliers removed, dansen normalization performed, ComBat used to remove known batch effects, invariable probes removed, predicted cell type proportional differences regressed out.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: time

value: 3 days post vaccine

value: post-vaccine

tag: Sex

value: M

tag: tissue

value: Normal whole blood sample

tag: individual


title: D4_E7386_50_4

type: SRA

city: Tsukuba-shi

first: Kazuhiko

last: Yamada

address: 5-1-3 Tokodai

country: Japan

institute: Eisai Co., Ltd.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq was used to de-multiplex and convert reads to FASTQ.
Sequencing data were processed by using Trimmomatic (version 0.36) to remove all Illumina adaptor sequences and bases with low quality scores.
Filtered reads were mapped to the mouse genome (Mm10 and Ensembl 84) by using STAR software (version 2.5.0c) .
Gene expression levels, in transcripts per million, were estimated for all samples by using RSEM software (version 1.2.31).
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file including TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: MMTV-Wnt1 tumor tissue

extract_protocol:
RNA was purified using RNeasy kit (Qiagen) following manufacturer’s instructions. SureSelect Strand Specific RNA Library Prep Kit (Agilent) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MMTV-Wnt1 tumors were collected Day4 and Day 8 after treatment with E7386 at 25, 50 mg/kg.

tag: strain

tag: agent

tag: time point


title: D4_E7386_25_4


title: GR10_V7

value: 14 days post vaccine

value: F


title: Sample15-negative

type: RNA

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450-0002, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Transcriptome Analysis Console 4.0 software was used for normalization, detection and summarization purposes, applying RMA+DABG algorithm only to human probesets

label: biotin

source_name: Blood

label_protocol: FlashTaq biotin HSR RNA labeling kit

growth_protocol: PBMCs were isolated from whole blood and cryopreserved in liquid nitrogen until used for RNA isolation

extract_protocol: miRNeasy mini kit (Qiagen) for total RNA isolation

tag: cell type

value: PBMC

tag: disease state

value: Multiple Sclerosis

tag: ls-ocmb characterization

value: Negative


title: skeletal muscle EPA

city: Tokyo

first: Hiroki

data_processing:
Adaptor sequences, contamination and low-quality reads were removed from raw reads.
Clean reads were aligned to GRCm38 reference genome using Hisat2 (v2.1.0) and counted using Stringtie (v1.3.4d).
Gene annotation was performed using an Ensembl gene annotation file downloaded from University of California Santa Cruz (UCSC) genome browser. Ensembl gene IDs were converted to gene names using biomaRt (v2.38.0) in R (v3.5.0).
Count per million (CPM) was used for comparison of gene expressions between samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes ensemble gene IDs, gene names, and CPM for each sample.

tag: treatment

value: EPA

tag: age

value: 87 weeks old


title: D4_E7386_25_3


title: skeletal muscle, cont

value: control


title: GR10_V3

value: 0 days post vaccine

value: Baseline


title: C-NEC3

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

description: Gene expression data of colonic NEC organoid 3

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Raw expression data were normalized with RMA.

source_name: Colonic NEC organoid 3

label_protocol: Standard Affymetrix procedures

growth_protocol: Organoids were maintained in a medium containing Wnt-3A, R-spondin, Noggin, A83-01, EGF, IGF-1 and FGF-2.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit according to the manufacturer's instructions.

value: Colon


title: GR04_V4

value: 1 days post vaccine


title: D4_E7386_25_2


title: RNA-seq in MSC3 [MSC3.RNAseq]

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

country: USA

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 or mm10 using STAR. Mapped reads were filtered to exclude PCR duplicates and reads mapping to known ribosomal RNA coordinates, obtained from rmsk table in the UCSC database
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Gene expression was calculated using featureCounts. Only primary alignments with mapping quality of 10 or more were counted.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech).  1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the Truseq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell line/tissue

tag: source type

value: primary tissue; mesenchymal stem cells (MSCs)


title: D4_E7386_25_1


title: Sample09-negative


title: GR15_V6

value: 7 days post vaccine


title: RNA-seq in MSC2 [MSC2.RNAseq]


title: Sample07-negative


title: Sample10-negative


title: GR10_V5

value: 3 days post vaccine

value: post-vaccine


title: D4_Vehicle_4

value: Vehicle


title: Sample06-negative


title: RNA-seq in MSC1 [MSC1.RNAseq]


title: GR13_V3

value: Normal whole blood sample


title: Larynx, CH39

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
Reads were aligned against Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95 using STAR v. 2.5.4b with the following flags  --runThreadN 8 --runMode alignReads --outSAMunmapped Within --outSAMattrIHstart 0 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif --twopassMode Basic
Gene expression was quantitated using HTSeq (v 0.7.0) with the following flags for all libraries: -m union -s yes -t gene -i gene_id
Genome_build: Oryctolagus_cuniculus.OryCun2.0/ ENSEMBL 95
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

organism: Oryctolagus cuniculus

source_name: Larynx (vocal folds)

extract_protocol:
Total RNA of vocal folds (low humidity n=6, moderate humidity n=6) was extracted with commercial kit RNeasy Fibrous Tissue Mini Kit (QIAGEN).
Library construction was done using NuGEN's Universal Plus mRNA Kit. Each library was performed with 200 ng of RNA. Unique barcodes were used for each library.

treatment_protocol: Rabbits (n=6) were exposed to a low relative humidity environment for 8 hours. Control rabbits (n=6) were held in a moderate realtive humidity environment.

tag: breed

value: New Zealand White

value: Male

value: 7 months

value: Larynx (vocal folds)


title: GR18_V7

value: 14 days post vaccine

value: M


title: RNA-seq in synovial sarcoma spheroids 4 [SS4.spheres.RNAseq]

value: primary tissue; synovial sarcoma spheroids


title: RNA-seq in synovial sarcoma spheroids 3 [SS3.spheres.RNAseq]


title: D4_Vehicle_1


title: GR15_V3

value: 0 days post vaccine

value: F


title: GR13_V5


title: D4_Vehicle_2


title: Sample19-positive

value: PBMC

value: Multiple Sclerosis

value: Positive


title: RNA-seq in synovial sarcoma spheroids 2 [SS2.spheres.RNAseq]


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.2.RNAseq]

value: cell line

tag: genotype/variation

value: SYT-SSX then CRE recombinase


title: Sample14-positive


title: Sample02-negative

value: Negative


title: Sample11-positive


title: GR04_V6

value: 7 days post vaccine

value: post-vaccine


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.1.RNAseq]


title: GR19_V3

value: Baseline

value: Normal whole blood sample


title: GR13_V4

value: 1 days post vaccine


title: Sample05-positive


title: INPUT library in Ewing sarcoma spheroids 2 [ES2.spheres.INPUT]

library_source: genomic

data_processing:
Reads were aligned to hg19 or mm10 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

value: primary tissue


title: GR18_V5

value: 3 days post vaccine


title: THP-1 macrophages stimulated with nESAT6 for 24 hours

city: Chongqing

first: Fake

last: Li

state: Chongqing

address: Changjiangzhilu 10 Yuzhong District

department: Clinical Laboratory Medicine

country: China

institute: Daping Hospital

data_processing:
Quality control analysis of the raw sequence files was conducted with FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality-checked reads for each condition were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0)
Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15) and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...

source_name: THP-1 macrophages

growth_protocol: Human monocyte cell line THP-1 was cultured in RPMI 1640 basic medium (Gibco, life technologies, USA) supplemented with 2 mM L-glutamine, Penicillin (100 U/ml)-Streptomycin (100 µg/ml) Solution and 10% fetal bovine serum (FBS) (Catalog No. 04-121-1A, Biological Industries, Israel) at cultural density of 5 × 105 - 1 × 106/ml.

extract_protocol:
The total RNA were isolated with RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions
The libraries were prepared with KAPA Stranded mRNA-Seq Kit for Illumina (Kapa biosystems, USA) following the manufacturer's procedure. In Brief, high quality intact total RNA (200 ng in 50 µl RNase-free water) were input for Poly(A) RNA capture with magnetic oligo-dT beads. The RNA was fragmented to the desired size (about 300 bp) by heating in the presence of Mg++. The 1st strand cDNA was synthesized with random primers. The 2nd strand cDNA synthesis converted cDNA:RNA hybrid to double strand cDNA (dscDNA), while marking the 2nd strand with dUTP. Then dAMP was added to 3’-end of dscDNA fragments. Following by ligation of 3’-dTMP adapters (10 nM) to 3’-dAMP library fragments, and PCR amplification (14 cycles) of the adapter-ligated library DNA. The dUTP-marked strand was not amplified. Library fragment size distribution was confirmed by electrophoresis and library concentration was determined with Qubit 2.0 Fluorometric Quantitation (Thermo Fisher Scientific, USA). These libraries were sequenced using the Illumina Hiseq 3000 Sequencer (50 cycles, single read lane).

treatment_protocol: THP-1 macrophages were stimulated in triplicates with 0.8 µg/ml nESAT6 (ESAT6 purchased from Catlog No. ab124574, Abcam, USA) or 0.8 µg/ml nBSA  for 4 h or 24 h. Cells were placed in a humidified, 37℃ 5% CO2 incubator.

value: THP-1 macrophages

value: 24 hours


title: Sample04-positive


title: H3K4me3 ChIP-seq in Ewing sarcoma spheroids 2 [ES2.spheres.H3K4me3]

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: GR04_V5

tag: time

tag: Sex

value: F

tag: tissue


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.2.RNAseq]

value: SYT-SSX then pLKO control


title: D4_Vehicle_3

tag: strain

tag: agent

value: Vehicle


title: GR09_V5

tag: individual


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.2.RNAseq]

value: SYT-SSX


title: INPUT library in Ewing sarcoma spheroids 1 [ES1.spheres.INPUT]


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.1.RNAseq]

value: cell line


title: RNA-seq in synovial sarcoma spheroids 1 [SS1.spheres.RNAseq]

value: primary tissue; synovial sarcoma spheroids


title: THP-1 macrophages stimulated with nBSA for 24 hours

tag: cell type

value: nBSA

tag: time point


title: RNA-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.1.RNAseq]


title: SMARCA2 ChIP-seq in Ewing sarcoma spheroids 2 [ES2.spheres.SMARCA2]

value: Active Motif


title: GR17_V7

value: 14 days post vaccine

value: post-vaccine


title: GR11_V5

value: Normal whole blood sample


title: H3K4me3 ChIP-seq in Ewing sarcoma spheroids 1 [ES1.spheres.H3K4me3]


title: GR09_V6

value: 7 days post vaccine


title: THP-1 macrophages stimulated with nBSA for 4 hours

value: 4 hours


title: RNA-seq in C3H10T1/2 cell line infected with control [C3H.control.2.RNAseq]

value: control


title: SMARCA2 ChIP-seq in Ewing sarcoma spheroids 1 [ES1.spheres.SMARCA2]

value: primary tissue


title: IgG RIP-seq

city: Hangzhou

first: Yujia

last: Wang

address: Yuhangtang Road No.388

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: bam/bam.bai/bw files with whole genomic peaks

source_name: Mouse peritoneal macrophage cells

growth_protocol: Mouse peritoneal macrophages were isolated from mice peritoneal cavities 4 days after 3% fluid thioglycollate medium (B&D) intraperitoneal injection. Cells were cultured in DMEM medium supplemented with 10% (v/v) fetal bovine serum (Gibco).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5×10^6 peritoneal macrophages were irradiated with 0.4 J/cm2 of 254 nm UV light and lysed with RIPA buffer (Beyotime), incubated on ice with frequent vortex for 30 minutes, and the lysate was obtained by centrifugation at 13,000 RPM for 10 min. Antibody of GSTM1 or IgG were added to the lysate, followed by incubation for 4 hours at 4C. Agarose beads were added to the sample and incubated for 2 hours at 4C. Beads were washed twice in RIPA buffer, four times in 1M RIPA buffer (50 mMTris, pH 7.4, 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, and 0.5% sodium deoxycholate). The beads were resuspended in RIPA buffer and treated with proteinase K at 45 C for 45 min.

value: Mouse peritoneal macrophage cells

tag: passages

value: primary cell

tag: rip antibody

value: Anti-IgG antibody


title: INPUT library in MSC2 [MSC2.INPUT]

tag: cell line/tissue


title: H3K4me3 ChIP-seq in MSC2 [MSC2.H3K4me3]

value: Millipore


title: USP7 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.USP7]

value: Bethyl


title: RYBP ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.RYBP]

value: RYBP

value: Sigma-Aldrich


title: Lnc GMR KO

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads using fastp (version 0.17.1)
HISAT2 (version 2.1.0)  was used to map the cleaned reads to the mouse GRCm38.p4 (mm10) reference genome.
After genome mapping, StringTie (version v1.3.4d ) was run with a reference annotation to generate FPKM values （Fragments Per Kilobase of exon model per Million mapped reads）for known gene models.
Differentially expressed genes were identified using DESeq2 (version 1.18.1) with R (version 3.4.3) . The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Lnc GMR KO_BMDM

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were differentiated from bone-marrow cells in RPMI 1640 medium containing10% (v/v) fetal bovine serum with recombinant 20 ng/ml murine M-CSF (PeproTech) cultured

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using Bioanalyzer 4200 (Agilent, santa Clara, CA, USA), and RNA integrity was determined using an Agilent 2100 system and an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
The next-generation libraries were prepared using VAHTS mRNA-Seq v2 Library Prep Kit for Illumina® (Vazyme). The Library quality was determined by Bioanalyzer 4200 (Agilent).Then the RNA-Seqlibraries was sequenced in HiSeq X10 system (Illumina) on a 150bp paired-end run.

treatment_protocol: VSV stimulation for 9 hours

tag: strain background

value: Lnc GMR KO

tag: stimulation

value: VSV 9h

tag: cell typ

value: bone marrow-derived macrophage (BMDM)


title: USP7 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.USP7]

value: cell line

tag: chip antibody


title: INPUT library in MSC1 [MSC1.INPUT]


title: GR07_V5

value: 3 days post vaccine

value: post-vaccine

value: M


title: RYBP ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.RYBP]

tag: chip antibody vendor


title: RNA-seq in C3H10T1/2 cell line infected with control [C3H.control.1.RNAseq]

tag: source type

tag: genotype/variation


title: H3K4me3 ChIP-seq in MSC1 [MSC1.H3K4me3]

tag: chip antibody cat. #


title: GR01_V3

tag: time

value: 0 days post vaccine

value: Baseline

tag: Sex

value: F

tag: tissue

value: Normal whole blood sample


title: 34_ANS_6HR_L

city: New Delhi

last: Mukherjee

state: Delhi

address: New Mehrauli Road, Munirka

department: School of Biotechnology

country: India

institute: Jawaharlal Nehru University (JNU)

data_processing:
Illumina HiSeq 2500 reads were trimmed for removing adapter sequences using Trimmomatic v.0.36. Read quality was checked for each sample using FastQC v0.10.1. Reference genome (E.coli BW25113)  (FASTA format) and annotation file (GFF format) was obtained from ENSEMBL database. The GFF annotation file was converted to GTF format using “Gffread” from Cufflinks suite and then  reference indices were created using Bowtie2 tool. BAM files generated by Bowtie2  tool after alignment were then used to calculate mapped reads abundance using RSEM. Normalization was done to rule out the effect of library size and reads length by estimating FPKM values for paired-end reads for each sample.  Differential expression was performed using edgeR software which is based on negative binomial distribution. We selected the genes having at least two log fold change value (log2 fold change ≥ 2) and false-discovery-rate (FDR) corrected P value < 0.05 to be considered as differentially expressed genes.
Genome_build: Escherichia_coli_bw25113.ASM75055v1
Supplementary_files_format_and_content: Processed data files were generated using RSEM. Abundance of each transcript is measured in the form of FPKM.

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Control BW25113 , ∆(elaA+cysW) double knock-out  & its respective single knock out strains transformed with pMAL-p2x plasmid containing L-Asparaginase gene  were grown in 50 ml flask containing TB media(10mM MgsO4 & 0.4% glycerol). After ~ 1.5 – 2.0 hours when O.D.600 reached 0.8-1.5, cultures were induced by adding 1mM IPTG for L-Asparaginase expression. After induction, the O.D. was monitored at 600 nm at regular intervals and samples were collected for two time-points i.e. pre-induction (0h) & post-induction (6h).

extract_protocol:
RNA was isolated for all the various time-point samples using Trizol method followed by Dnase I treatment. The total RNA concentration and quality  was determined by Agilent bioanalyzer 2100 expert. The good quality and quantity of total RNA was given to AgriGenome for further library preparation & RNA Sequencing.
Illumina HiSeq 2000/2500 Paired end run; 2 X 100 bp 30 million reads (3GB) per sample. ~3 ug of total RNA was used to prepare the RNA seq library. In short, mRNA molecules were purified using magnetic beads. Folllowing purification, mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA polymeraseI and RNase H. These cDNA fragments were used to generate RNA libraries. Bioanalyzer plots were used at every step to assess mRNA quality, enrichment success, fragmentation sizes,and final library sizes. The size distribution of the sequencing library was determined by AgilentTapestation or Bioanalyzer. After the libraries were constructed, paired end run were performed on Illumina’s HiSeq 2500 platform to obtain 2 x100bp reads.

treatment_protocol: No treatment

tag: strain

tag: genotype

value: cysW KO

value: post-induction (6h)


title: GR03_V7

value: 14 days post vaccine

tag: individual


title: 34_ANS_0HR_K

value: pre-induction (0h)


title: GR18_V4

value: 1 days post vaccine


title: THP-1 macrophages stimulated with nESAT6 for 4 hours

tag: cell type

value: THP-1 macrophages

tag: agent

tag: time point

value: 4 hours


title: H2AK119ub ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.H2AK119ub]

tag: cell line/tissue

value: Cell Signaling


title: GSTM1 RIP-seq

value: Mouse peritoneal macrophage cells

tag: passages

value: primary cell

tag: rip antibody

value: Anti-GSTMI antibody


title: RING1B ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.RING1B]

value: cell line

tag: chip antibody


title: SMARCA2 ChIP-seq in MSC1 [MSC1.SMARCA2]

value: primary tissue

tag: chip antibody vendor

value: Active Motif


title: 28_ANS_6HR_J

value: elaA KO


title: H3K27me3 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.H3K27me3]

value: Millipore


title: H3K36me3 ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K36me3]

value: Abcam


title: GR02_V3

value: 0 days post vaccine

value: Baseline

value: F

value: Normal whole blood sample


title: 28_ANS_0HR_I

value: pre-induction (0h)


title: INPUT library in synovial sarcoma spheroids 4 [SS4.spheres.INPUT]


title: H3K27ac ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.H3K27ac]


title: GR05_V6

value: 7 days post vaccine

value: post-vaccine

value: M


title: Lnc GMR WT

source_name: Lnc GMR WT_BMDM

tag: strain background

value: WT

tag: stimulation

value: VSV 9h

tag: cell typ

value: bone marrow-derived macrophage (BMDM)


title: GR10_V6

tag: time


title: H3K27me3 ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K27me3]

tag: chip antibody cat. #


title: 28_34_ANS_6HR_F

value: elaA+cysW doubleKO

value: post-induction (6h)


title: GR11_V7

value: 14 days post vaccine

tag: Sex

tag: tissue


title: SMARCA2 ChIP-seq in MSC2 [MSC2.SMARCA2]

value: primary tissue

value: Active Motif


title: GR05_V4

value: 1 days post vaccine


title: 28_34_ANS_0HR_D

tag: strain

tag: genotype


title: H3K27ac ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K27ac]


title: H3K9ac ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K9ac]

value: Abcam


title: GR02_V4

tag: individual


title: BW_ANS_6HR_B

description: Replicate

value: control


title: BW_ANS_6HR_C

description: Replicate


title: GR06_V5

value: 3 days post vaccine


title: SMARCA2 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.SMARCA2]

value: cell line


title: H3K4me3 ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K4me3]

value: Millipore


title: H3K4me1 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.H3K4me1]


title: H2AK119ub ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.H2AK119ub]

value: Cell Signaling


title: V5 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then CRE recombinase [C3H.SYTSSX.CRE.V5]


title: H3K4me1 ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.H3K4me1]


title: GR03_V4

value: post-vaccine

value: F

value: Normal whole blood sample


title: GR06_V7

value: M


title: GR05_V7


title: RING1B ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.RING1B]


title: SMARCA2 ChIP-seq in synovial sarcoma spheroids 4 [SS4.spheres.SMARCA2]


title: GR07_V3

value: 0 days post vaccine

value: Baseline


title: H3K27me3 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.H3K27me3]


title: INPUT library in synovial sarcoma spheroids 3 [SS3.spheres.INPUT]


title: BW_ANS_0HR_A

value: pre-induction (0h)


title: GR01_V7

value: 14 days post vaccine


title: H3K27ac ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.H3K27ac]


title: Terminal tracheal cells _ Suc2_Dam_rep2

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Library strategy: DamID-seq
Sequencing data from TaDa experiments were processed using a previously described pipeline (Marshall et al., 2015)
Reads were mapped to release 6.11 of the Drosophila genome.
Transcribed genes were annotated from Pol II binding data using a custom Perl script (available at https://github.com/tonysouthall/Dam-RNA_POLII_analysis).
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Transcribed genes were identified based on meeting a threshold of 1% FDR and > 0.2 log2 ratios.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 normalised fold changes between the experimental and Dam-only control as a gff file produced by the damidseq_pipeline

organism: Drosophila melanogaster

source_name: Dam-control processed DNA from adult terminal tracheal cells expressing LT3-Dam in control intestine (Suc)

growth_protocol: Animals were crossed  at 18°C. F1 progeny were collected every 48 hrs and aged for a further 7 days at 18°C before transferring to 29°C to induce adult restricted Dam protein expression for 24 hrs.

extract_protocol:
60 midguts with associated TTCs per condition per biological replicate were dissected in cold PBS and stored at -80°C. Genomic DNA was isolated, RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: During the last 16 hrs at 29°C, flies were fed a Sucrose or Sucrose + Pe solution.

value: w-; dSRF-GAL4, UAS-CD8GFP/+; tub-GAL80ts/UAS-LT3-Dam

tag: treatment

value: untreated with sucrose solution (Suc) for 16 hrs

value: tracheal cells


title: H3K36me3 ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K36me3]

value: primary tissue

value: Abcam


title: Terminal tracheal cells _ Suc1_Dam_rep1


title: Terminal tracheal cells _ Suc1_DamPol_rep1

source_name: Dam-Pol II processed DNA from adult terminal tracheal cells expressing LT3-Dam Pol II in control intestine (Suc)

value: w-; dSRF-GAL4, UAS-CD8GFP/+; tub-GAL80ts/UAS-LT3-Dam-Pol II


title: H3K4me1 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.H3K4me1]

value: cell line


title: H3K27me3 ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K27me3]

value: Millipore


title: Terminal tracheal cells _ Pe2_DamPol_rep2

source_name: Dam-Pol II processed DNA from adult terminal tracheal cells expressing LT3-Dam Pol II in damaged intestine (Pe)

value: treated with bacteria solution (Pe) for 16hrs


title: SMARCA2 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.SMARCA2]

value: Active Motif


title: H3K27ac ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K27ac]


title: Terminal tracheal cells _ Pe2_Dam_rep2

source_name: Dam-control processed DNA from adult terminal tracheal cells expressing LT3-Dam in damaged intestine (Pe)


title: V5 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX then pLKO control [C3H.SYTSSX.pLKO.V5]


title: GR06_V4

value: 1 days post vaccine

value: post-vaccine


title: H3K9ac ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K9ac]


title: Terminal tracheal cells _ Pe1_DamPol_rep1


title: INPUT library in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.INPUT]


title: GR05_V5

value: 3 days post vaccine

value: M

value: Normal whole blood sample


title: Terminal tracheal cells _ Pe1_Dam_rep1


title: H3K4me3 ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K4me3]


title: GR01_V6

value: 7 days post vaccine

value: F


title: H2AK119ub ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H2AK119ub]

value: Cell Signaling


title: GR06_V6


title: H3K4me1 ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.H3K4me1]


title: RING1B ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.RING1B]


title: SMARCA2 ChIP-seq in synovial sarcoma spheroids 3 [SS3.spheres.SMARCA2]


title: H3K27me3 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H3K27me3]


title: H3K27ac ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H3K27ac]


title: PAO1_serum-azm_1

city: Burnaby

first: Amy

middle: H.

last: Lee

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PAO1 reference genome using STAR v2.6.1a  read count tables were generated from bam files using htseq-count v.2.5
Significance and fold changes calculated in R (3.6.2) using DEseq2 package with Likelihood Ratio Test
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa mid-log culture

growth_protocol: P. aeruginosa was inoculated into 25 mL of each growth medium at a startingOD of 0.05 and grown to mid log

extract_protocol:
Sixty minutes post-treatment, bacterial cells were collected and mixed 1:2 volume wise with RNA protect Bacteria Reagent (QIAGEN). RNA was extracted using RNeasy mini kit (QIAGEN).
RNA was quantified using a Nanodrop-1000 (ThermoFisher). RNA quality and quantity were assessed on an Agilent Bioanalyzer. rRNA was depleted (Ribo-Zero depletion kit, Illumina), and cDNA libraries were prepared using the KAPA RNA HyperPrep Kit (KAPA Biosystems) and sequenced through the University of British Columbia Sequencing Consortium (Illumina HiSeq-2500)

treatment_protocol: P. aeruginosa was grown in each medium to OD600 0.5, cultures were split into two equal volumes and effective concentrations of AZM were added to one of the two aliquots (samples denoted as AZM treated). To AZM cultures, AZM was added at an effective concentration to decrease growth without total inhibition (MHB: 16 ug/mL; RPMI: 8 ug/mL; serum: 6 ug/mL)

value: AZM treated

tag: media

value: RPMI-1640 +5% MHB + 20% human serum

tag: growth phase

value: mid-log


title: H3K36me3 ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K36me3]

tag: cell line/tissue

value: primary tissue

value: Abcam


title: GR02_V5


title: GR01_V4


title: PAO1_serum-azm_2


title: GR03_V3

value: 0 days post vaccine

value: Baseline


title: GR07_V6


title: PAO1_serum_3

value: untreated


title: H3K9ac ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H3K9ac]

value: cell line


title: PAO1_serum_2


title: H3K4me3 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H3K4me3]

value: Millipore


title: ccRCC patient-2

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

description: Gene expresison without any treatment

hyb_protocol: Labeled cRNA (1 μg) for each sample was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, followed by heating at 60°C for 30 min. Finally, 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. Hybridization solution (50 μl) was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hrs at 65°C in an Agilent hybridization oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using a DNA Microarray Scanner (part No. G2505C, Agilent, Santa Clara, CA, USA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering.

source_name: Peripheral Blood, ccRCC patient-2

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNA samples were then purified using RNeasy Mini Kit (Qiagen, Hilden, Germany). Concentration and specific activity of labeled cRNA samples (pmol Cy3/μg cRNA) were subsequently measured using a NanoDrop ND-1000.

extract_protocol: Whole blood was collected from each participant in EDTA tubes as an anticoagulant followed by centrifugation at 1,000 g for 10 min at 4°C. Plasma was then transferred to sterile polypropylene tubes on ice and centrifuged again at 10,000g for 10 min at 4°C to remove cell debris. Total RNA was extracted from plasma samples of 5 ccRCC patients and 5 normal control for microarray using Trizol Reagent (Invitrogen, Carlsbad, CA, USA), followed by purification using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: All five ccRCC patients received no treatment before enrolling into this study. Five healthy controls without a urological system disorder received physical examinationbefore enrolling in this study.

tag: disease state

value: clear cell renal cell carcinoma (ccRCC)

value: plasma

tag: gender

value: male

tag: age

tag: kidney

value: right

tag: tumor size

tag: tnm stage


title: H3K27ac ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K27ac]

tag: chip antibody

tag: chip antibody vendor

value: Active Motif


title: ccRCC patient-3

description: Gene expresison without any treatment

source_name: Peripheral Blood, ccRCC patient-3

value: female


title: PAO1_serum_1


title: ccRCC patient-4

description: Gene expresison without any treatment

source_name: Peripheral Blood, ccRCC patient-4


title: GR07_V7

source_name: Whole Blood

tag: time

value: 14 days post vaccine

value: post-vaccine

tag: Sex

value: M

value: Normal whole blood sample


title: INPUT library in synovial sarcoma spheroids 2 [SS2.spheres.INPUT]

value: primary tissue


title: H3K9ac ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K9ac]

value: Abcam

tag: chip antibody cat. #


title: ccRCC patient-1

description: Gene expresison without any treatment

source_name: Peripheral Blood, ccRCC patient-1

tag: tissue

value: left


title: PAO1_rpmi-azm_3

value: AZM treated

value: mid-log


title: GR03_V5

value: 3 days post vaccine

value: F

tag: individual


title: SMARCA2 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.SMARCA2]

value: cell line


title: H3K4me1 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.H3K4me1]


title: GR06_V3

value: 0 days post vaccine

value: Baseline


title: PAO1_rpmi-azm_2

tag: treatment


title: V5 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.V5.2]


title: H3K4me1 ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K4me1]


title: GR05_V3


title: GR02_V6

value: 7 days post vaccine


title: V5 ChIP-seq in C3H10T1/2 cell line infected with SYT-SSX [C3H.SYTSSX.V5.1]


title: PAO1_rpmi_3

value: untreated

tag: media


title: SMARCA2 ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.SMARCA2]

value: Active Motif


title: PAO1_rpmi-azm_1

tag: growth phase


title: INPUT library in C3H10T1/2 cell line infected with control [C3H.control.INPUT]

tag: cell line/tissue


title: PAO1_rpmi_2


title: H2AK119ub ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H2AK119ub]

value: Cell Signaling


title: INPUT library in synovial sarcoma spheroids 1 [SS1.spheres.INPUT]


title: GR03_V6

value: post-vaccine


title: H2AK119ub ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H2AK119ub]


title: HCT116_MT3

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

description: MT rep3

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: GRCh38(hg38)

source_name: colon cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

tag: cell line

tag: cell type

value: colon cancer cells

tag: genotype


title: healthy control-4

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-4

tag: disease state

value: healthy

value: plasma

tag: gender

value: male

tag: age


title: healthy control-2

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-2

value: female


title: HCT116_MT2

description: MT rep2


title: PAO1_mhb-azm_3

value: AZM treated

value: Mueller Hinton Broth (MHB)

value: mid-log


title: GR01_V5

value: 3 days post vaccine

value: F

value: Normal whole blood sample


title: PAO1_serum-azm_3

value: RPMI-1640 +5% MHB + 20% human serum


title: GR07_V4

value: 1 days post vaccine

value: M


title: PAO1_rpmi_1

value: untreated


title: RING1B ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.RING1B]

value: primary tissue

tag: chip antibody

value: Cell Signaling


title: healthy control-5

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-5


title: GR02_V7

value: 14 days post vaccine

value: post-vaccine


title: H3K27me3 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H3K27me3]

value: cell line

tag: chip antibody vendor

value: Millipore


title: PAO1_mhb-azm_2


title: RING1B ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.RING1B]


title: H3K27me3 ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K27me3]


title: HCT116_ORF3

description: ORF rep3

value: colon

value: colon cancer cells

value: ORF


title: healthy control-1

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-1

value: healthy

value: plasma

value: male


title: H3K36me3 ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K36me3]

value: Abcam


title: H3K9ac ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H3K9ac]


title: H3K27ac ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H3K27ac]

value: Active Motif


title: HCT116_ORF2

description: ORF rep2


title: HCT116_MT1

description: MT rep1


title: H3K27ac ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K27ac]


title: PAO1_mhb_3

value: Mueller Hinton Broth (MHB)

value: mid-log


title: H3K4me3 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H3K4me3]


title: ccRCC patient-5

description: Gene expresison without any treatment

source_name: Peripheral Blood, ccRCC patient-5

value: clear cell renal cell carcinoma (ccRCC)

value: female

tag: kidney

value: right

tag: tumor size

tag: tnm stage


title: PAO1_mhb-azm_1

value: AZM treated


title: H3K4me3 ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K4me3]

value: primary tissue

tag: chip antibody cat. #


title: Terminal tracheal cells _ Suc2_DamPol_rep2

value: w-; dSRF-GAL4, UAS-CD8GFP/+; tub-GAL80ts/UAS-LT3-Dam-Pol II

value: untreated with sucrose solution (Suc) for 16 hrs

tag: tissue

value: tracheal cells


title: HCT116_ORF1

description: ORF rep1

value: colon

value: colon cancer cells


title: PAO1_mhb_2

tag: treatment

value: untreated


title: H3K4me3 ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K4me3]

value: Millipore


title: H3K9ac ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K9ac]


title: H3K4me1 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.H3K4me1]

value: cell line


title: HCT116_NC3

description: NC rep3

value: blank vector


title: PAO1_mhb_1

tag: media


title: HCT116_NC2

description: NC rep2


title: V5 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.V5]

value: Abcam


title: HCT116_NC1

description: NC rep1


title: SMARCA2 ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.SMARCA2]

value: Active Motif


title: Sample 2 WT

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

description: 10x raw data contains cell barcode and UMI, cell barcode and UMI, cDNA reads

data_processing:
Chromium data was demultiplexed with cellranger mkfastq v3.0.1
Gene-cell count matrix was generated by cellranger count v3.0.1 against Ensembl GRCm38.p5 reference genome.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz.

source_name: Hippocampus

extract_protocol:
Adult Wildtype hippocampal single cell suspensions were obtained by either mechanical dissociation at 4°C or 30 minutes enzymatic digestion at 37°C and subsequent percoll-gradient centrifugation for debris and myealin removal. The sample loaded onto the 10x genomics chip is a pool of hippocampal cells from 3 adult mice.
Library construction was performed according to the 10x Chromium Single Cell 3' Reagent Kit v3.

tag: strain

value: Brain

tag: developmental stage

value: 10 weeks old


title: IRF8KO cMoP rep1

status: Public on Dec 20 2020

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

data_processing:
The RNA-seq reads were aligned to a mouse reference genome (mm10/GRCm38) using STAR software.
Duplicate reads were removed by using Picard tools (http://broadinstitute.github.io/picard).
The expression levels were quantified using RSEM software.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: EXCEL file includes TPM values for all samples

source_name: bone marrow cells

extract_protocol:
Total RNA was prepared using an RNeasy Micro Kit (QIAGEN) from approximately 3,000 to 10,000 cells according to the manufactures' instructions.
cDNA was synthesized and amplified using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Amplified cDNA was purified using Ampure XP beads (Beckman Coulter) to remove primer dimers. RNA-seq libraries were prepared using a Nextera XT Kit (Illumina). The prepared libraries were sequenced on a NextSeq 500 (Illumina) to generate single-end 75 nucleotide reads.

value: common monocyte progenitors

tag: cell isolation

value: Primary isolated cells

value: bone marrow

tag: sorting methods

value: MACS selection followed by FACS sorting

tag: surface markers

value: CD3– CD19– Ly6G– NK1.1– CD117+ CD115+ CD135– Ly6C+ CD11b low


title: IRF8KO cMoP rep2

tag: cell type

tag: genotype


title: WT_Mo_rep2_CEBPA

data_processing:
ChIP-seq and input reads were mapped on a mouse reference genome sequence (mm10/GRCm38) using Bowtie software (version 1.1.2).
Mapped SAM format files were converted to tag directories using HOMER package (version 4.9).
ChIP-seq peaks were identified using HOMER findPeaks module with “-style histone” option for ChIP-seq analysis of H3K27ac and with “-style factor” option for ChIP-seq analysis of IRF8 or C/EBPα.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BED files include ChIP-seq peak regions

extract_protocol:
Sorted cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. The lysates were sonicated using a Diagenode Bioruptor-Pico sonication device (12 cycles of 30 seconds on and 30 seconds off).
An aliquot of sheared chromatin was immunoprecipitated with anti-H3K27ac antibody (MABI0309, Cosmo Bio) using Dynabeads M-280 sheep anti-mouse immunoglobulin G (IgG) (Thermo Fisher Scientific), anti-IRF8 antibody (C-19, Santa Cruz) using Dynabeads protein G (Thermo Fisher Scientific) or anti-C/EBPα antibody (D56F10, Cell Signaling Technology) using Dynabeads protein G (Thermo Fisher Scientific) at 4˚C. Then, ChIP-seq libraries were prepared with a TruSeq ChIP sample prep Kit (Illumina) or KAPA HyperPrep Kit (KAPA).

value: monocytes

value: Wild type

value: MACS selection

value: CD117– CD135– Ly6G– CD115+

value: anti-C/EBPα (D56F10, Cell Signaling Technology)


title: Sample 1 WT


title: IRF8KO MDP rep2

value: monocyte-dendritic cell progenitors

value: Lin– Sca-1– CD117+ IL-7R– CD115+


title: IRF8KO MDP rep1


title: WT_cDC1_rep1_CEBPA

source_name: splenocytes

value: classical type 1 dendritic cells

value: spleen

value: Thy1.2– B220– CD49b– CD8a+


title: IRF8KO GMP rep2

value: granulocyte-monocyte progenitors

value: Lin– CD117+ Sca-1– IL-7R– CD16/32+ CD115–


title: d+56kb Ly6C+Mo rep1

value: Ly6C+ monocytes

value: Irf8 +56 kb enhancer-deficient

value: CD117– Ly6G– CD11b high CD115+ Ly6C high


title: IRF8KO LMPP rep1

value: multipotent progenitors-4

value: Primary isolated cells

value: bone marrow

value: MACS selection followed by FACS sorting

value: Lin– CD117+ Sca-1+ CD135+


title: d+56kb Ly6C+Mo rep2


title: WT_cDC1_rep2_CEBPA

value: Wild type

value: MACS selection


title: IRF8KO GMP rep1


title: SMARCA2 ChIP-seq in C3H10T1/2 cell line infected with control [C3H.control.SMARCA2]

tag: cell line/tissue

value: cell line

value: Active Motif


title: H3K4me1 ChIP-seq in synovial sarcoma spheroids 1 [SS1.spheres.H3K4me1]

value: primary tissue

tag: chip antibody

value: Abcam


title: d+56kb MDP rep2

value: monocyte-dendritic cell progenitors

value: Lin– Sca-1– CD117+ IL-7R– CD115+


title: d+56kb cMoP rep1

value: common monocyte progenitors

value: CD3– CD19– Ly6G– NK1.1– CD117+ CD115+ CD135– Ly6C+ CD11b low


title: d+56kb MDP rep1

value: Irf8 +56 kb enhancer-deficient


title: d+56kb cMoP rep2


title: WT_Mo_rep1_CEBPA

value: monocytes

value: CD117– CD135– Ly6G– CD115+

value: anti-C/EBPα (D56F10, Cell Signaling Technology)


title: d+56kb LMPP rep2

value: multipotent progenitors-4

value: Primary isolated cells

value: bone marrow


title: d+56kb GMP rep1

value: granulocyte-monocyte progenitors

value: MACS selection followed by FACS sorting

value: Lin– CD117+ Sca-1– IL-7R– CD16/32+ CD115–


title: WT_Ly6C-Mo_rep2

value: Ly6C- monocytes

value: wild type

value: spleen

value: CD117- Ly6G- CD11b high CD115+ Ly6C low


title: WT_Neu_rep1

value: neutrophils

value: CD117- Ly6G high CD11b high


title: d+56kb LMPP rep1

value: Lin– CD117+ Sca-1+ CD135+


title: WT_Neu_rep2


title: WT_cDC2_rep2

value: classical type 2 dendritic cells

value: F4/80- MHC-class II high CD11c high XCR1- CD172a+


title: WT_cMoP_rep2

value: common monocyte progenitors


title: WT_Ly6C+Mo_rep1

value: Ly6C+ monocytes

value: CD117- Ly6G- CD11b high CD115+ Ly6C high


title: WT_cDC1_rep2

value: classical type 1 dendritic cells

value: Primary isolated cells

value: F4/80- MHC-class II high CD11c high XCR1+ CD172a-


title: WT_Ly6C+Mo_rep2

value: MACS selection followed by FACS sorting


title: IRF8KO LMPP rep2

value: multipotent progenitors-4

value: bone marrow


title: WT_CDP_rep2

value: common dendritic cell progenitors

value: wild type

value: Lin- Sca-1- CD117int IL-7R- CD115+ CD135+


title: WT_cDC1_rep1

value: spleen


title: WT_CDP_rep1


title: d+56kb GMP rep2

value: granulocyte-monocyte progenitors

value: Irf8 +56 kb enhancer-deficient

value: Lin– CD117+ Sca-1– IL-7R– CD16/32+ CD115–


title: WT_MDP_rep2

value: monocyte-dendritic cell progenitors


title: WT_GMP_rep2


title: WT_cMoP_rep1

value: common monocyte progenitors


title: WT_LMPP_rep1


title: WT_LMPP_rep2


title: WT_MPP3_rep2

value: multipotent progenitors-3


title: WT_GMP_rep1


title: healthy control-3

description: Gene expresison without any treatment

source_name: Peripheral Blood, healthy control-3

tag: disease state

value: healthy

value: plasma

tag: gender

value: female

tag: age


title: WT_MDP_rep1

value: Primary isolated cells


title: WT_MPP3_rep1

value: MACS selection followed by FACS sorting


title: WT_MPP2_rep2

value: multipotent progenitors-2


title: WT_ST-HSC_rep2

value: short-term hematopoietic stem cells

value: bone marrow


title: WT_Ly6C-Mo_rep1

value: Ly6C- monocytes

value: wild type

value: CD117- Ly6G- CD11b high CD115+ Ly6C low


title: WT_LT-HSC_rep1

value: long-term hematopoietic stem cells


title: WT_ST-HSC_rep1


title: WT_LT-HSC_rep2


title: WT_cDC1_rep1_IRF8

data_processing:
ChIP-seq and input reads were mapped on a mouse reference genome sequence (mm10/GRCm38) using Bowtie software (version 1.1.2).
Mapped SAM format files were converted to tag directories using HOMER package (version 4.9).
ChIP-seq peaks were identified using HOMER findPeaks module with “-style histone” option for H3K27ac ChIP-seq and with “-style factor” option for IRF8 ChIP-seq
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BED files include ChIP-seq peak regions

extract_protocol:
Sorted cells were fixed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. The lysates were sonicated using a Diagenode Bioruptor-Pico sonication device (12 cycles of 30 seconds on and 30 seconds off).
An aliquot of sheared chromatin was immunoprecipitated with anti-H3K27ac antibody (MABI0309, Cosmo Bio) using Dynabeads M-280 sheep anti-mouse immunoglobulin G (IgG) (Thermo Fisher Scientific) or anti-IRF8 antibody (C-19, Santa Cruz) using Dynabeads protein G (Thermo Fisher Scientific) at 4˚C. Then, ChIP-seq libraries were prepared with a TruSeq ChIP sample prep Kit (Illumina).

value: classical type 1 dendritic cells

value: Wild type

value: spleen

value: MACS selection

value: Thy1.2– B220– CD49b– CD8a+

value: anti-IRF8 (C-19, Santa Cruz)


title: WT_cDC1_rep2_IRF8


title: WT_Mo_rep1_IRF8

value: monocytes

value: CD117– CD135– Ly6G– CD115+


title: WT_cDC2_rep1

value: classical type 2 dendritic cells

value: Primary isolated cells

value: F4/80- MHC-class II high CD11c high XCR1- CD172a+


title: IRF8KO_LMPP_input_DNA

value: lymphoid-primed multipotent progenitors

value: MACS selection followed by FACS sorting

value: CD135+ CD150– IL-7R– Lin– CD117+ Sca-1+

value: input DNA


title: WT_Mo_rep2_IRF8

value: bone marrow


title: d+56kb_cMoP_input_DNA

value: common monocyte progenitors

value: Irf8 +56 kb enhancer-deficient

value: CD3– CD19– Ly6G– NK1.1– CD117+ CD115+ CD135– Ly6C+ CD11b low


title: IRF8KO_LMPP_rep1_H3K27ac

value: anti-H3K27ac (MABI0309, MAB Institute)


title: d+56kb_cMoP_rep2_H3K27ac


title: d+56kb_MDP_input_DNA

value: monocyte-dendritic cell progenitors

value: Lin– Sca-1– CD117+ IL-7R– CD115+


title: d+56kb_cMoP_rep1_H3K27ac


title: d+56kb_MDP_rep1_H3K27ac


title: d+56kb_MDP_rep2_H3K27ac


title: d+56kb_GMP_input_DNA

value: granulocyte-monocyte progenitors

value: Lin– CD117+ Sca-1– IL-7R– CD16/32+ CD115–


title: d+56kb_GMP_rep1_H3K27ac


title: d+56kb_GMP_rep2_H3K27ac


title: d+56kb_LMPP_input_DNA


title: WT_MPP2_rep1

value: multipotent progenitors-2

value: wild type


title: WT_cDC1_input_DNA

value: classical type 1 dendritic cells

value: Wild type

value: Primary isolated cells

value: spleen

value: F4/80– MHC-class II high CD11c high XCR1+ CD172a-


title: WT_LMPP_rep2_H3K27ac

value: lymphoid-primed multipotent progenitors

value: MACS selection followed by FACS sorting

value: CD135+ CD150– IL-7R– Lin– CD117+ Sca-1+


title: d+56kb_LMPP_rep2_H3K27ac

value: Irf8 +56 kb enhancer-deficient

value: bone marrow


title: WT_cDC1_rep2_H3K27ac

value: anti-H3K27ac (MABI0309, MAB Institute)


title: WT_LSK_rep2_H3K27ac

value: Lin- Sca1+ CD117+ cells

value: Lin- Sca1+ CD117+


title: WT_LMPP_rep1_H3K27ac


title: WT_cDC1_rep1_H3K27ac


title: WT_LSK_rep1_H3K27ac


title: IRF8KO_MDP_rep1 [ATAC-Seq]

data_processing:
ATAC-seq reads were mapped on a mouse reference genome sequence (mm10) using Bowtie software (version 1.1.2).
Mapped SAM format files were converted to TagDirectories using the makeTagDirectory module of the HOMER package (version 4.9) with the “-tbp 1” option to remove duplicate reads.
ATAC-seq peaks were identified by the findPeaks module of the HOMER package.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BED files include ATAC-seq peak regions

extract_protocol:
5,000 to 7,200 cells were directly sorted into 1.5-mL tubes and pelleted by centrifugation for 10 minutes at 300g. The cells were then incubated with transposase solution (25 µL of 2 x Tagment DNA buffer and 2.5µL of Tagment DNA Enzyme [Illumina Nextera DNA Library Prep Kit], 0.5 µL of 1% digitonin [Promega], and 22 µL of distilled water) at 37˚C for 30 minutes with shaking at 300 rpm. Transposed DNA was then purified using a MinElute Reaction Cleanup Kit (QIAGEN).
Purified transposed DNA was amplified using a NEBNext High Fidelity 2 x PCR Master Mix (New England Biolabs) with indexed primers. Libraries were purified using SPRIselect beads (Beckman Coulter) to remove primer dimers.

value: monocyte-dendritic cell progenitors

value: Lin– Sca-1– CD117+ IL-7R– CD115+


title: IRF8KO_MDP_rep2 [ATAC-Seq]


title: WT_CDP_rep2 [ATAC-Seq]

value: common dendritic cell progenitors

value: Lin– Sca-1– CD117int IL-7R– CD115+ CD135+


title: WT_CDP_rep1 [ATAC-Seq]


title: WT_MDP_rep2 [ATAC-Seq]


title: WT_LMPP_rep2 [ATAC-Seq]

value: short-term hematopoietic stem cells

value: Lin– CD117+ Sca-1+ CD135+


title: d+56kb_LMPP_rep1_H3K27ac

value: Primary isolated cells


title: WT_MDP_rep1 [ATAC-Seq]

value: Wild type


title: WT_LT-HSC_rep2 [ATAC-Seq]

value: long-term hematopoietic stem cells

value: Lin– CD117+ Sca-1+ CD135– CD48– CD150+


title: WT_LT-HSC_rep1 [ATAC-Seq]

value: MACS selection followed by FACS sorting


title: D8 [2019A704]

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

description:
processed data file:
TPM_count.xlsx
D8_vs_D17.xlsx

data_processing:
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Paired end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio)
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files (.xlsx) include TPM values for each Sample and DEGs

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay.  (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
Libraries were constructed using 500 ng of total RNA after Qubit quantification, the Kapa mRNA HyperPrep (Roche, #KR1352-v5.17) was used following manufacturer’s instructions. Profile and quality of the libraries were assessed on a Bioanalyzer High Sensitivity DNA array (Agilent Technologies) and quantified using  QubitTM with a dsDNA High Sensibility Kit (Thermofisher)

tag: cell type source

value: primary fibroblasts cell line

value: hIPSCs

tag: differentiation

value: Muscle Progenitors growth

tag: time point


title: WT_LMPP_rep1 [ATAC-Seq]

tag: tissue

value: bone marrow


title: D8 [2019A703]


title: D30 [2019A708]

description:
processed data file:
TPM_count.xlsx
D8_vs_D30.xlsx

value: Mature Muscle fibers


title: D17 [2019A706]

description:
processed data file:
TPM_count.xlsx
D17_vs_D30.xlsx

value: Muscle fibers with contractions


title: JMML_ID7_HSC

city: Oxford

first: Adam

last: Mead

address: Headington

department: WIMM

institute: UNiversity of Oxford

data_processing:
Alignment to hg19 with using STAR (version 2.4.2a).
Aligned reads were counted using featureCounts (version 1.4.5-p1) summarized to gene identifiers from the hg19 UCSC transcriptome
Transcripts per million (TPM) were calculated from raw cound in R 3.4.1
Genome_build: hg19
Supplementary_files_format_and_content: TPM

extract_protocol:
Purrified cells were FACS sorted directly into lysis buffer containing 0.4% Triton X-100 (Sigma-Aldrich), RNase inhibitor (Clontech), 2.5 mM dNTPs (Thermo Fisher) and 2.5 μM oligo-dT30VN primer (Biomers.net).
FACS purified populations were processed for RNA-seq using the Smart Seq2 protocol as previously described (Picelli et al, 2014)

value: Juvenile Myelomonocytic Leukemia (JMML)

value: hematopoietic stem and progenitor cells (HSPCs)

tag: facs purified population

value: HSC


title: WT_LMPP_input_DNA

value: lymphoid-primed multipotent progenitors

tag: strain

value: CD135+ CD150– IL-7R– Lin– CD117+ Sca-1+

value: input DNA


title: WT_LSK_input_DNA

value: Lin- Sca1+ CD117+ cells

value: Primary isolated cells

value: Lin- Sca1+ CD117+


title: D17 [2019A705]


title: JMML_ID7_GMP

value: GMP


title: JMML_ID5_HSC


title: JMML_ID5_GMP


title: Synthetic embryo sample at 4 days of development created with the standard method rep3

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

institute: University of Cambridge

data_processing:
Pheniqs (biosails) demultiplexing
zUMIs 2.9.3e filtering, mapping,counting, velocity measurements
Scrublet doublet filtering
Scanpy/scVelo (scvelo 0.2.1) for downstream analysis
Seurat v3 for differential expression and gene
Genome_build: GRCm38 with 99 annotation
Supplementary_files_format_and_content: gene/barcode matrix in csv format
Supplementary_files_format_and_content: gene/barcode csv file of filtered cells
Supplementary_files_format_and_content: h5ad Scanpy object
Supplementary_files_format_and_content: csv file of annotations for each of the filtered cells

source_name: Stem cell derived embryo

growth_protocol: AggreWell plates (STEMCELL Technologies 34415) were prepared as described in (Sozen et al., 2018).To generate iETX-embryos, Doxycycline was added to CAG-GFP tetO-Gata4 ES cells for 6 hours. TS cells were trypsinised and were added to a gelatinised plate to deplete the MEFs for 20 minutes at 37°C. CAG-GFP WT ES cells and CAG-GFP tetO-Gata4 ES cells were subsequently trypsinised. Cell suspensions with 19,200 TS cells, 6000 CAG-GFP WT ES cell and 6,000 CAG-GFP tetO-Gata4 ES cells were mixed and pelleted by centrifugation. The cell pellet was resuspended in 1ml FC medium with 7.5nM ROCK inhibitor (Y27632, STEMCELL Technologies 72304). After adding the cell mixture drop-wise to the AggreWell, the plate was centrifuged at 100g for 3 minutes. On the next day, media change was performed twice by removing 1ml medium from each well and adding 1ml fresh FC medium without ROCK inhibitor. On Day 2, media change was performed once to replace 1ml medium with 1ml fresh FC medium. On Day 3, 1.2ml medium was removed from each well and 1.5ml IVC1 was added, after equilibrating for 20 minutes in the incubator. IVC1 (Bedzhov et al., 2014) is made of advanced DMEM/F12 (Gibco, 21331-020) supplemented with 20% (v/v) FBS, 2 mM GlutaMax, 1% v/v penicillin–streptomycin, 1X ITS-X Thermo Fisher Scientific, 51500-056), 8 nM β-estradiol, 200 ng/ml progesterone and 25 μM N-acetyl-L-cysteine. On Day 4, iETX-embryos in the AggreWell were transferred to CELLSTAR 6 well multiwell plate for suspension culture (Greiner Bio-One 657185) with 5ml of IVC1 (with FBS at 30% v/v) per well. On Day 5 IVC1 was replaced with fresh IVC2 (30% KSR-ThermoFisher Scientific 10828010).

extract_protocol:
Samples were dissociated to single cells by cutting with needles and then incubation in TrypLE Express dissociation solution for 15 minutes followed by reaction inactivation with media containing 15% fetal bovine serum, filtration and 2 washes in PBST (0.02% Tween-20.
inDrops v3

treatment_protocol: Not applicable

tag: type

value: Stem cell derived synthetic embryo

value: Mixed strain:CD1/MF1/C57BL/6

tag: developmental day

tag: ploidy

value: Euploid

tag: stem cells of origin

value: embryonic, trophoblast and extraembryonic endoderm stem cells

tag: transgenes

value: Embryonic stem cells:CAG-GFP/tetO-mCherry; trophoblast stem cells:Confetti (not active); Extraembryonic endoderm stem cells:wildtype


title: Synthetic embryo sample at 4 days of development created with the standard method rep1


title: Synthetic embryo sample at 4 days of development created with the standard method rep2


title: Mouse embryo at 6.5 days of development

source_name: Mouse embryo

value: Mouse embryos generated by natural mouse mating

value: Mixed strain:CD1/MF1

value: not applicable

value: Brachyury-GFP


title: Induced synthetic embryo sample at 4 days of development created with the novel method

value: embryonic stem cells transiently expressing Gata4, embryonic and trophoblast stem cells

value: Embryonic stem cells:CAG-GFP/tetO-mCherry; trophoblast stem cells:Confetti (not active); ES cells transiently expressing Gata4:CAG-GFP/tetO-mCherry; tetO=Gata4


title: Mouse embryo at 5.5 days of development


title: D30 [2019A707]

value: primary fibroblasts cell line

tag: cell type

value: hIPSCs

value: Mature Muscle fibers


title: IRF8KO_LMPP_rep2_H3K27ac

value: lymphoid-primed multipotent progenitors

tag: genotype

tag: cell isolation

value: Primary isolated cells

value: bone marrow

tag: sorting methods

value: MACS selection followed by FACS sorting

tag: surface markers

value: CD135+ CD150– IL-7R– Lin– CD117+ Sca-1+

value: anti-H3K27ac (MABI0309, MAB Institute)


title: JMML_ID15_GMP

value: Juvenile Myelomonocytic Leukemia (JMML)

value: hematopoietic stem and progenitor cells (HSPCs)

value: GMP


title: JMML_ID17_HSC

value: HSC


title: JMML_ID15_DP

value: DP


title: H3K27me3 ChIP-seq in synovial sarcoma spheroids 2 [SS2.spheres.H3K27me3]

data_processing:
Reads were aligned to hg19 or mm10 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell line/tissue

value: primary tissue

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: CB_CBD_GMP

tag: tissue

value: cord blood (CB)


title: CB_CBD_HSC

tag: facs purified population


title: CB_CBC_HSC


title: 88: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

city: Manchester

first: Xiangyu

middle: Jack

last: Ge

address: Oxford road

institute: University of Manchester

description: processed_data_file: 88_H3K4me3_healthy_KN_peaks.narrowPeak

data_processing:
CHiC were mapped to GRCh38 using HICUP, CHiCAGO was applied to the stimulatory conditions, treating each sample as a replicate. Interactions with CHiCAGO score over 5 were picked up and corresponding counts data were extracted from CHiCAGO results, for downstream differential interaction analysis using DESeq2.
Individual ATAC-seq reads were mapped to GRCh38 by Bowtie2. Duplicates were removed by Picard. Bam files of the stimulatory conditions were merged and MACS2 were applied to call peaks on each merged bam file.
RNA-seq data were mapped to GRCh38 by STAR. Gene expression quantification was done by RSEM, downstream normalizatioin and differential analysis was performed by DESeq2.
Hi-C reads were mapped to GRCh38 and processed by the HiC-Pro pipeline, the .hic files produced were then used for downstream TAD analysis using the R package TADCompare.
Hi-C reads were mapped to GRCh38 by HiCUP and then converted to HOMER format, runHiCpca.pl and findHiCCompartments.pl from HOMER were used to identify A/B compartments.
Genome_build: GRCh38
Supplementary_files_format_and_content: HGNC_FLS_norm_exp.txt: RNA-seq expression counts normalized by DESeq2.
Supplementary_files_format_and_content: narrowPeak/broadPeak: ATAC/ChIP-seq peaks as identified by MACS2 (chromosome, start, end, id, score, strand, signalValue, pValue, qValue, peak point-source)
Supplementary_files_format_and_content: allValidPairs.hic : Hi-C data processed by HiC-Pro.
Supplementary_files_format_and_content: Chicago_washU_text.txt : Significant Chi-C interactions (bait location, prey location, ChiCAGO score)
Supplementary_files_format_and_content: 18_segment.sorted.bed : ChromHMM state inference from 18 states based on 6 histone marks. (Segment_chr, segment_start, Segment_end, Inferred state)
Supplementary_files_format_and_content: All_stim/unstim_A/B.bed : Merged A/B compartments as identified by HOMER. (A/B compartment chr, A/B compartment start, A/B compartment end)
Supplementary_files_format_and_content: All_TADs_extended.sorted.bed : TADs identified with TADCompare, and their differential TAD status. (TAD chr, TAD start, TAD end, basal TAD score, stim TAD score, differential TAD score, differential status, enriched in condition, differential TAD type)

source_name: Primary FLS

extract_protocol:
Chromatin was prepared on pellets of fixed cells  using the iDeal ChIP seq kit for Histones (Diagenode). ChIP assays were performed using 1 million cells per IP and the following antibodies: H3K4me3 (0.5 μg, C15411003, Diagenode), H3K27me3 (1 μg, C15410195, Diagenode) and H3K27ac (1 μg, C15410196, Diagenode). A control library was processed in parallel using the same amount of control Diagenode ChIP’d DNA.
Libraries were prepared from 1 ng of IP and input DNA using the MicroPLEX v2 protocol, quantified by BioAnalyzer, purified (AMPure beads) and eluted in TE.

tag: sample id

tag: stimulation

tag: joint

value: Knee

tag: disease state

value: Healthy


title: 88: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_H3K27ac_healthy_KN_peaks.narrowPeak


title: 88: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_18_segments.sorted.bed


title: 88: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_H3K4me1_healthy_KN_peaks.broadPeak


title: 88: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_H3K27me3_healthy_KN_peaks.broadPeak


title: 88: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_H3K9me3_healthy_KN_peaks.broadPeak


title: 88: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 88_H3K36me3_healthy_KN_peaks.broadPeak


title: JMML_ID5_DP


title: CB_CBC_GMP


title: CB_CBB_HSC


title: JMML_ID15_HSC


title: 316: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K9me3_RA_MCP_peaks.broadPeak

value: MCP

value: Rheumatoid Arthritis


title: CB_CBB_GMP


title: 316: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K4me1_RA_MCP_peaks.broadPeak


title: 316: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K27me3_RA_MCP_peaks.broadPeak


title: 316: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K4me3_RA_MCP_peaks.narrowPeak


title: CB_CB37_HSC


title: JMML_ID17_DP


title: 316: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K36me3_RA_MCP_peaks.broadPeak


title: CB_CB34_GMP


title: CB_CB37_GMP


title: CB_CB34_HSC


title: 88: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: 316: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_18_segments.sorted.bed


title: JMML_ID3_HSC


title: 316: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 316_H3K27ac_RA_MCP_peaks.narrowPeak


title: JMML_ID3_GMP


title: 316: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: 343: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K9me3_OA_MCP_peaks.broadPeak

value: Osteoarthritis


title: JMML_ID1_HSC


title: 343: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K4me1_OA_MCP_peaks.broadPeak


title: JMML_ID1_GMP


title: JMML_ID3_DP


title: JMML_ID1_DP


title: 343: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K36me3_OA_MCP_peaks.broadPeak


title: 343: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K4me3_OA_MCP_peaks.narrowPeak


title: 343: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_18_segments.sorted.bed


title: 343: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K27me3_OA_MCP_peaks.broadPeak


title: 343: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: B87 + DMKG + Rita, replicate 2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Deseq2_normalized_gene_expression_with_annotations.txt

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide

molecule: polyA RNA

source_name: H460 cell line

growth_protocol: human non-small cell lung cancer (H460) cells were maintained at 37°C under 5% CO2, in RPMI 1640 GlutaMax medium supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES buffer, 100 units/ml penicillin G sodium and 100 µg/ml streptomycin sulfate. Culture media and supplements for cell culture were purchased from Gibco-Life Technologies (Carlsbad, CA, USA) and plasticware from Corning Inc. (Corning, NY, USA).

extract_protocol:
The extraction was made by Qiagen "Rneasy Plus Micro Kit (cat n. 74034) following the instructions of the manufacter.
Truseq mRNA stranded (Illumina)

treatment_protocol: The cells were plated at 350.000 in 6-wells plates. The day after, the cells were treated for 6h with DMKG (dimethyl α-ketoglutarate, 5mM, Sigma-Aldrich, St. Louis, MO, USA), B87 (BAY87-2243, 1µM, Bayer Pharma AG, Wuppertal, Germany), DMKG + B87, Nutlin-3 (30uM, Sigma-Aldrich), Rita (50uM, Sigma-Aldrich), DMKG + B87 + Rita, DMKG +B87 + Nutlin-3. Untreated cells are control. Each sample is from 2 wells made in quadruplicate.

value: non small cell lung cancer

tag: passages

tag: treatment

value: B87 + DMKG + Rita


title: B87 + DMKG + Rita, replicate 3

tag: cell type


title: B87 + DMKG + Rita, replicate 1


title: Rita, replicate 4

value: Rita


title: Rita, replicate 3


title: JMML_ID17_GMP


title: B87 + DMKG + Rita, replicate 4


title: Rita, replicate 2


title: 341: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K27me3_RA_SH_peaks.broadPeak

value: Shoulder


title: 341: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K4me1_RA_SH_peaks.broadPeak


title: 341: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K4me3_RA_SH_peaks.narrowPeak


title: Rita, replicate 1


title: B87 + DMKG + Nutlin-3, replicate 4

value: B87 + DMKG + Nutlin-3


title: 341: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K27ac_RA_SH_peaks.narrowPeak


title: 341: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K9me3_RA_SH_peaks.broadPeak


title: B87 + DMKG + Nutlin-3, replicate 3


title: 341: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_H3K36me3_RA_SH_peaks.broadPeak


title: 343: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 343_H3K27ac_OA_MCP_peaks.narrowPeak


title: 341: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 341_18_segments.sorted.bed


title: B87 + DMKG + Nutlin-3, replicate 2


title: B87 + DMKG + Nutlin-3, replicate 1


title: 341: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: 384: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K9me3_OA_SH_peaks.broadPeak


title: 384: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K4me1_OA_SH_peaks.broadPeak


title: 384: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K27me3_OA_SH_peaks.broadPeak


title: B87 + DMKG, replicate 4

value: B87 + DMKG


title: 384: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K4me3_OA_SH_peaks.narrowPeak


title: Nutlin-3, replicate 1


title: Nutlin-3, replicate 2


title: 384: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K36me3_OA_SH_peaks.broadPeak


title: B87 + DMKG, replicate 3


title: 384: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_18_segments.sorted.bed


title: B87 + DMKG, replicate 1


title: 384: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: DMKG, replicate 4

value: DMKG


title: DMKG, replicate 3


title: DMKG, replicate 2


title: 368: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K27me3_RA_KN_peaks.broadPeak


title: 368: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K4me1_RA_KN_peaks.broadPeak


title: DMKG, replicate 1

description: Deseq2_normalized_gene_expression_with_annotations.txt


title: Control, replicate 4

value: control


title: Nutlin-3, replicate 3


title: Control, replicate 3


title: Control, replicate 2


title: 368: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K36me3_RA_KN_peaks.broadPeak


title: 368: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K27ac_RA_KN_peaks.narrowPeak


title: 368: Input DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_18_segments.sorted.bed


title: 368: Input1 DNA ChIP-seq, Primary FLS, Unstimulated


title: Control, replicate 1


title: B87 + DMKG, replicate 2


title: 335: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K9me3_OA_KN_peaks.broadPeak


title: B87, replicate 2


title: 384: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 384_H3K27ac_OA_SH_peaks.narrowPeak


title: 335: H3K4me1 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K4me1_OA_KN_peaks.broadPeak


title: 335: H3K27me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K27me3_OA_KN_peaks.broadPeak


title: 368: H3K9me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K9me3_RA_KN_peaks.broadPeak


title: B87, replicate 4


title: 368: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 368_H3K4me3_RA_KN_peaks.narrowPeak


title: B87, replicate 1


title: SerD02

city: Durham

first: Aashutosh

last: Vihani

state: NC

address: 264 CARL Building

institute: Duke University

data_processing:
STAR read alignment
RSEM read quantification
EdgeR differential expression
Intact olfactory receptor subsetting
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files with differential expression statistics and rounded read counts

source_name: Whole olfactory mucosa

extract_protocol:
Whole olfactory mucosa was dissected and either sequenced or subjected to pS6-IP-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole olfactory mucosa

value: experimental


title: 335: H3K4me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K4me3_OA_KN_peaks.narrowPeak


title: SerD03


title: 335: Input1 DNA ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_18_segments.sorted.bed


title: SerD01


title: 335: Input DNA ChIP-seq, Primary FLS, Unstimulated


title: SerC12_GTAGAGGA


title: 335: H3K36me3 ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K36me3_OA_KN_peaks.broadPeak


title: 335: H3K27ac ChIP-seq, Primary FLS, Unstimulated

description: processed_data_file: 335_H3K27ac_OA_KN_peaks.narrowPeak


title: SerC10_CGAGGCTG


title: SerC11_AAGAGGCA


title: SF_435_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: HGNC_FLS_norm_exp.txt

extract_protocol:
Cultured FLS were treated with 10 ng/ml human recombinant TNF (Roche) for 24 h or were left untreated. Total RNA was isolated using the RNeasy Mini kit (Qiagen) including on-column DNAase I digestion.
RNA-seq libraries were prepared using the NEB Next Ultra Directional RNAseq Protocol with ribosomal depletion.

value: 10 ng/ml TNF for 24 hours


title: SF_435: RNA-seq, Primary FLS, unstimulated


title: SerC9_GCTACGCT


title: SerC8_CAGAGAGG


title: SF_415B: RNA-seq, Primary FLS, unstimulated


title: B87, replicate 3


title: SF_415B_TNF: RNA-seq, Primary FLS, TNF stimulated


title: SF_407_TNF: RNA-seq, Primary FLS, TNF stimulated


title: 4761_S10


title: SF_407: RNA-seq, Primary FLS, unstimulated


title: SF_346_TNF: RNA-seq, Primary FLS, TNF stimulated


title: 4761_S6


title: SF_346: RNA-seq, Primary FLS, unstimulated


title: 4761_S5


title: SF_336: RNA-seq, Primary FLS, unstimulated


title: SF_336_TNF: RNA-seq, Primary FLS, TNF stimulated


title: SF_292_TNF: RNA-seq, Primary FLS, TNF stimulated


title: 4575_S2

value: DHB


title: 4575_S1


title: 4761_S1


title: SF_429_TNF: ATAC-seq, Primary FLS, TNF stimulated

description: processed_data_file: Stim.merged_peaks.narrowPeak

extract_protocol: ATAC-seq libraries were prepared with 50,000 FLS cells as described in Buenrostro et al.


title: SF_429: ATAC-seq, Primary FLS, unstimulated

description: processed_data_file: Basal.merged_peaks.narrowPeak


title: 4429_S12


title: SF_424_TNF: ATAC-seq, Primary FLS, TNF stimulated


title: 4429_S5


title: SF_427_TNF: ATAC-seq, Primary FLS, TNF stimulated

value: Knee


title: 4429_S9


title: 4331_S12


title: 4761_S2


title: 4331_S11


title: SF_427: ATAC-seq, Primary FLS, unstimulated


title: SF_424: ATAC-seq, Primary FLS, unstimulated


title: SF_420_TNF: ATAC-seq, Primary FLS, TNF stimulated


title: SF_420: ATAC-seq, Primary FLS, unstimulated


title: 4331_S9


title: 4761_S9


title: SF_415B_TNF: ATAC-seq, Primary FLS, TNF stimulated


title: SF_415B: ATAC-seq, Primary FLS, unstimulated


title: 4331_S7


title: 4331_S8


title: SF_346_TNF: ATAC-seq, Primary FLS, TNF stimulated


title: 4331_S4


title: 4331_S5


title: 427_TNF: Hi-C, Primary FLS, TNF stimulated

description: processed_data_file: stim.allValidPairs.hic

extract_protocol:
Cultured human FLS from RA patients were treated with 10 ng/ml TNF for 24 h or were left untreated. Cells (1e7 to 3e7 per condition), were scratched in 10ml DMEM, spun down, suspended in 35ml DMEM and fixed (2% formaldehyde in DMEM, 10min, RT, with mixing on a rocker). The reaction was quenched with cold 0.125M glycine. Cells were incubated at RT for 5 min, followed by 15 min incubation on ice and centrifugation (1500 rpm, 10 min, 4 ⁰C). Pellets were suspended and washed in cold PBS (1500 rpm, 10 min, 4 ⁰C). Washed pellets were snap frozen and stored at -80 ⁰C.
Hi-C libraries from RA FLS samples, were generated as previously described in Lieberman-Aiden, E. et al.


title: SF_346: ATAC-seq, Primary FLS, unstimulated


title: 4429_S8


title: 429_TNF: Hi-C, Primary FLS, TNF stimulated


title: 424_TNF: Hi-C, Primary FLS, TNF stimulated


title: 420_TNF: Hi-C, Primary FLS, TNF stimulated


title: 4331_S1


title: 4258_S11

value: bCaryophyllene


title: 4331_S2

value: ebFarnesene


title: 4258_S9


title: 415A_TNF: Hi-C, Primary FLS, TNF stimulated

value: Wrist

value: Rheumatoid Arthritis


title: 412_TNF: Hi-C, Primary FLS, TNF stimulated


title: 415B_TNF: Hi-C, Primary FLS, TNF stimulated

value: MCP


title: 4258_S7


title: 4258_S3


title: 4258_S5


title: 427: Hi-C, Primary FLS, unstimulated

description: processed_data_file: basal.allValidPairs.hic


title: 420: Hi-C, Primary FLS, unstimulated


title: 4331_S6


title: SerC7_CTCTCTAC


title: 3134_S2


title: 415B: Hi-C, Primary FLS, unstimulated


title: 4258_S1


title: 4331_S3


title: 415A: Hi-C, Primary FLS, unstimulated


title: 412: Hi-C, Primary FLS, unstimulated


title: 424: Hi-C, Primary FLS, unstimulated


title: 3046_S10


title: SF_292: RNA-seq, Primary FLS, unstimulated


title: 3134_S1


title: RiboSeq_ArfKO_shSCR_replicate_2

city: St. Louis

first: Kyle

middle: Aaron

last: Cottrell

state: MO

address: 660 S Euclid

institute: Washington University in St. Louis

description: raw files have been demultiplexed based on internal barcodes using cutadapt

data_processing:
Library strategy: Ribo-seq
fastx_clipper was used to remove adapter and filter out poor quality reads and short reads (fastx_clipper -a AGATCGGAAGAGCACACGTCTGAA -c -n -v -l 13)
UMItools (umi_tools extract --bc-pattern=NNNNNXXXXX --3prime) was used to remove UMI
fastx_barcode_splitter was used to split reads by 3' barcode and cutadapt was used to remove the barcode (cutadapt --cut -5)
Bowtie2 was used to remove reads mapping to ncRNAs (snRNA, tRNA, rRNA, miRNA)
Tophat (tophat --no-novel-juncs) was used align to reference genome (mm10)
HTSeq was used count reads within cds (htseq-count -t CDS)
Genome_build: mm10
Supplementary_files_format_and_content: .txt files containing read counts as determined by Htseq

source_name: embryonic fibroblast

growth_protocol: MEFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone) with 10% fetal bovine serum (Invitrogen), 2 mM glutamine (Hyclone), 0.1 mM nonessential amino acids (Hyclone), 1 mM sodium pyruvate (Hyclone), and 2 μg/ml gentamicin (Invitrogen)

extract_protocol:
RNA was extracted by Trizol and purified using the Zymo Research Direct-Zol RNA Cleanup kit. Ribosome profiling samples were processed as described in https://doi.org/10.1016/j.ymeth.2017.05.028.
For RNAseq, total RNA was fragmented by partial alkaline hydrolysis. Fragments between 17 and 34 nt were purified by PAGE. Library construction was performed as described in https://doi.org/10.1016/j.ymeth.2017.05.028.

treatment_protocol: Transduced with lentiviral shRNA (shARF or shSCR)

tag: mouse strain

tag: passage

value: embryonic fibroblast

tag: genotype

value: ArfKO

tag: transduction

value: shSCR


title: 3046_S11


title: RiboSeq_WT_shARF_replicate_2

value: WT

value: shARF


title: RiboSeq_WT_shARF_replicate_1


title: 3046_S7


title: 429: Hi-C, Primary FLS, unstimulated

value: Shoulder


title: 429_TNF: Capture Hi-C, Primary FLS, TNF stimulated

description: processed_data_file: Stim_Chicago_washU_text

data_processing:
Library strategy: CHiC
CHiC were mapped to GRCh38 using HICUP, CHiCAGO was applied to the stimulatory conditions, treating each sample as a replicate. Interactions with CHiCAGO score over 5 were picked up and corresponding counts data were extracted from CHiCAGO results, for downstream differential interaction analysis using DESeq2.
Individual ATAC-seq reads were mapped to GRCh38 by Bowtie2. Duplicates were removed by Picard. Bam files of the stimulatory conditions were merged and MACS2 were applied to call peaks on each merged bam file.
RNA-seq data were mapped to GRCh38 by STAR. Gene expression quantification was done by RSEM, downstream normalizatioin and differential analysis was performed by DESeq2.
Hi-C reads were mapped to GRCh38 and processed by the HiC-Pro pipeline, the .hic files produced were then used for downstream TAD analysis using the R package TADCompare.
Hi-C reads were mapped to GRCh38 by HiCUP and then converted to HOMER format, runHiCpca.pl and findHiCCompartments.pl from HOMER were used to identify A/B compartments.
Genome_build: GRCh38
Supplementary_files_format_and_content: HGNC_FLS_norm_exp.txt: RNA-seq expression counts normalized by DESeq2.
Supplementary_files_format_and_content: narrowPeak/broadPeak: ATAC/ChIP-seq peaks as identified by MACS2 (chromosome, start, end, id, score, strand, signalValue, pValue, qValue, peak point-source)
Supplementary_files_format_and_content: allValidPairs.hic : Hi-C data processed by HiC-Pro.
Supplementary_files_format_and_content: Chicago_washU_text.txt : Significant Chi-C interactions (bait location, prey location, ChiCAGO score)
Supplementary_files_format_and_content: 18_segment.sorted.bed : ChromHMM state inference from 18 states based on 6 histone marks. (Segment_chr, segment_start, Segment_end, Inferred state)
Supplementary_files_format_and_content: All_stim/unstim_A/B.bed : Merged A/B compartments as identified by HOMER. (A/B compartment chr, A/B compartment start, A/B compartment end)
Supplementary_files_format_and_content: All_TADs_extended.sorted.bed : TADs identified with TADCompare, and their differential TAD status. (TAD chr, TAD start, TAD end, basal TAD score, stim TAD score, differential TAD score, differential status, enriched in condition, differential TAD type)

extract_protocol:
Cultured human FLS from RA patients were treated with 10 ng/ml TNF for 24 h or were left untreated. Cells (1e7 to 3e7 per condition), were scratched in 10ml DMEM, spun down, suspended in 35ml DMEM and fixed (2% formaldehyde in DMEM, 10min, RT, with mixing on a rocker). The reaction was quenched with cold 0.125M glycine. Cells were incubated at RT for 5 min, followed by 15 min incubation on ice and centrifugation (1500 rpm, 10 min, 4 ⁰C). Pellets were suspended and washed in cold PBS (1500 rpm, 10 min, 4 ⁰C). Washed pellets were snap frozen and stored at -80 ⁰C.
The regions targeted by the capture HiC (CHiC) were generated based on the LD regions of the lead disease associated SNPs for RA, Juvenile Idiopathic Arthritis (JIA), Psoriatic arthritis (PsA) and Psoriasis (Ps).  This resulted in a total of 242 distinct risk variants.120bp capture baits were designed for all HindIII digestion fragments overlapping these regions as previously described in Martin et al.


title: 3046_S8


title: RiboSeq_ArfKO_shSCR_replicate_1


title: RiboSeq_WT_shSCR_replicate_2


title: RiboSeq_WT_shSCR_replicate_1


title: 3134_S4

value: control

value: CPD


title: 3134_S5

value: Whole olfactory mucosa

value: experimental


title: 424_TNF: Capture Hi-C, Primary FLS, TNF stimulated

value: 10 ng/ml TNF for 24 hours


title: RNAseq_ArfKO_shSCR_replicate_1

data_processing:
fastx_clipper was used to remove adapter and filter out poor quality reads and short reads (fastx_clipper -a AGATCGGAAGAGCACACGTCTGAA -c -n -v -l 13)
UMItools (umi_tools extract --bc-pattern=NNNNNXXXXX --3prime) was used to remove UMI
fastx_barcode_splitter was used to split reads by 3' barcode and cutadapt was used to remove the barcode (cutadapt --cut -5)
Bowtie2 was used to remove reads mapping to ncRNAs (snRNA, tRNA, rRNA, miRNA)
Tophat (tophat --no-novel-juncs) was used align to reference genome (mm10)
HTSeq was used count reads within cds (htseq-count -t CDS)
Genome_build: mm10
Supplementary_files_format_and_content: .txt files containing read counts as determined by Htseq


title: RNAseq_ArfKO_shSCR_replicate_2


title: 415B_TNF: Capture Hi-C, Primary FLS, TNF stimulated


title: 415A_TNF: Capture Hi-C, Primary FLS, TNF stimulated


title: 427_TNF: Capture Hi-C, Primary FLS, TNF stimulated

value: Knee


title: RNAseq_WT_shARF_replicate_2


title: RNAseq_WT_shARF_replicate_1


title: 412_TNF: Capture Hi-C, Primary FLS, TNF stimulated


title: RNAseq_WT_shSCR_replicate_2


title: 420_TNF: Capture Hi-C, Primary FLS, TNF stimulated


title: 3046_S2


title: 427: Capture Hi-C, Primary FLS, unstimulated

description: processed_data_file: Unstim_Chicago_washU_text


title: 3046_S4


title: 429: Capture Hi-C, Primary FLS, unstimulated


title: 3046_S1


title: 420: Capture Hi-C, Primary FLS, unstimulated


title: 424: Capture Hi-C, Primary FLS, unstimulated


title: 3046_S5


title: 5027_S5

extract_protocol:
Whole olfactory mucosa was dissected and sequenced
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: f

value: wt

value: sex-combined

tag: age


title: fpEC hyperglycemia

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

country: Austria

institute: Medical University of Graz

description: cells grown under hyperglycemia (25mM D-glucose) for 24h.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized gainst Affymetrix HU 133A chips.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data were normalized using Affymetrix Microarray Suite (MAS5.0) with standard settings and normalized globally.

label: Biotin

source_name: human placental arteries

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5µg total RNA (SuperScript double-stranded cDNA synthesis kit, Invitrogen and RNA transcript labeling kit, Enzo Diagnostics).

growth_protocol: cells were cultured in EBM (endothelial cell basal medium) supplemented with 5% FCS at 21% O2/5% CO2 at 37°C

extract_protocol: TRI REAGENT

treatment_protocol: normoglycemic (5.5mM D-glucose) vs hyperglycemic (25mM D-glucose) for 24h

value: primary fetoplacental endothelial cells (fpEC)

value: hyperglycemia


title: PreB_RNAseq_shRen_4

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
processed data files format and content: txt files with gene TPM

source_name: PreB cells

growth_protocol: preB cells were cultured in RPMI 1640 medium supplemented with 20% gibco FBS, 1% Pen/Strep and 10ng/ml mouse IL7.

extract_protocol: RNA was extracted with Trizol

treatment_protocol: 24h after isolation and culture, preB cells were transducted with eMLM-shRen or eMLM-shPhf23 through retroviral infection. 48h after infection, the transducted cells labelled with GFP were sorted out by FACS AriaIII. Immediately after sorting, the cells were centrifugated to obtain cell pellets, followed by Trizol addition.

value: PreB cells

tag: plasmids

tag: replicates


title: 415B: Capture Hi-C, Primary FLS, unstimulated

value: MCP

value: Rheumatoid Arthritis


title: RNAseq_WT_shSCR_replicate_1

value: embryonic fibroblast

value: WT

value: shSCR


title: 415A: Capture Hi-C, Primary FLS, unstimulated

value: Wrist


title: 5027_S3

tag: tissue

value: m


title: fpEC normoglycemia

description: cells grown under normoglycemia (5.5mM D-glucose).

value: normoglycemia


title: 5027_S2

value: Whole olfactory mucosa


title: 412: Capture Hi-C, Primary FLS, unstimulated


title: PreB_RNAseq_shRen_2


title: 5027_S6


title: PreB_RNAseq_shPhf23.877_4


title: 5027_S1