title: Mesenteric MSC IL33+ Replicate 1

city: Cambridge

first: Noe

last: Rodriguez Rodriguez

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

institute: MRC Laboratory of Molecular Biology

data_processing:
Sequence alignment using Tophat2 with Partek Flow
Analysis was performed using Partek® Genomics Suite® software, version 6.16
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample.

source_name: white adipose tissue

extract_protocol:
Cells were flow-cytometry-sorted into RPMI-1640, 10% fetal calf serum (FCS) plus penicillin/streptomycin, 2-mercaptoethano and transferred to Trizol (Life Technologies). RNA was extracted using RNeasy kits and reagents (Qiagen), DNA was digested using Turbo DNase (Ambion). RNA was concentrated using an RNeasy Micro Kit (Qiagen) and assessed using a Bioanalyzer (Agilent)
RNA was processed for RNA sequencing using Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220 and barcoded using Ovation Ultralow Library Systems (Nugen)

value: C57BL/6 IL33-citrine reporter

value: white adipose tissue

value: Mesenteric MSC IL33+

tag: sorted cell

value: ex vivo sorted cells


title: Lung Epcam+ epithelial cells Replicate 3

status: Public on Jun 24 2019

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: lung

tag: strain

tag: tissue

value: lung

tag: cell type

value: Lung Epcam+ epithelial cells


title: WAT CD31+ endothelial cells Replicate 2

value: WAT CD31+ endothelial cells


title: Mesenteric MSC IL33- Replicate 2

value: Mesenteric MSC IL33-


title: WAT CD31+ endothelial cells Replicate 1


title: Lung MSC IL33+ cells Replicate 3

value: Lung MSC IL33+ cells


title: Mesenteric MSC IL33+ Replicate 2


title: Mesenteric MSC IL33- Replicate 1


title: Mesenteric MSC IL33- Replicate 3


title: Lung Epcam+ epithelial cells Replicate 1


title: Lung MSC IL33+ cells Replicate 2


title: Lung MSC IL33+ cells Replicate 1


title: Mesenteric MSC IL33+ Replicate 3


title: WAT CD31+ endothelial cells Replicate 3


title: Lung Epcam+ epithelial cells Replicate 2


title: cisLiver8D2

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

country: USA

institute: University of North Carolina  at Chapel Hill

description: replicate 2

library_source: genomic

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: mm10
Supplementary_files_format_and_content: no

molecule: genomic DNA

source_name: Liver

extract_protocol: Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-cisplatin antibodies.  This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 4000 platform.

tag: treatment

value: cisplatin

tag: genotype

value: wild type

tag: age

value: post natal day 6 months


title: CIS12HL2

description: replicate 2

growth_protocol: NHF1, XPC, CSB, GM12878 and Wild-type mouse skin fibroblast cells were grown in DMEM (Life Technologies, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gemini, Woodland, CA). Cells were maintained in an incubator at 37°C under 5% CO2.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers was separated from chromosomal high molecular weight DNA by centrifugation
Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-CPD antibodies.  Then photolyase repairs the CPD damage. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 4000 platform.

treatment_protocol: Cells were grown to about 80% confluence in 150mm dishes. Media was removed, cells were washed with PBS, irradiated with 20 J/m2 of UV, and then warm, fresh media was added and cells were incubated for 3hr at 37°C (MSF), 1hr at 37°C (NHF1, XPC, CSB). GM12878 were treated with cisplatin 2hr at 37°C. Cells were then harvested and processed using the XR-seq procedure


title: CIS24HL2

description: replicate 2


title: CIS48HL2

description: replicate 2


title: CIS16HL2

description: replicate 2


title: CIS4HL2

description: replicate 2


title: CIS8HL2

description: replicate 2


title: CIS20HL2

description: replicate 2


title: CIS2HL2

description: replicate 2


title: E-cad-KO rep4

city: Baltimore

first: Andrew

last: Ewald

state: MD

address: 855 N. Wolfe Street, 452 Rangos Bldg.

department: Cell Biology

institute: Johns Hopkins University

data_processing:
Alignment to the transcriptome by the Bowtie2-Tophat2 pipeline
Counting reads in each sample mapping to each gene by HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated list of read pairs mapping to each gene

source_name: MMTV-PyMT mouse mammary tumor

growth_protocol: Organoids were cultured for 48h in 3D collagen I in a DMEM-based medium supplemented with b-FGF2

extract_protocol:
Collagen gels with organoids were flash frozen. RNA was extracted using the RNeasy kit
RNA libraries were prepared for sequencing using standard protocols using Illumina TruSeq stranded mRNA kit

treatment_protocol: Freshly isolated organoids were treated with adeno-Cre overnight, following which they were embedded in collagen I

value: mammary tumor

value: FVB/NJ

value: MMTV::PyMT; (R26)pCA::mT/mG; Cdh1fl/fl

value: adeno-Cre transduced


title: CIS10DLiver1

description: replicate 1


title: E-cad-KO rep5


title: olaparib-rep1

city: Boston

first: Li

last: Jia

state: MA

address: 20 Shattuck Street

department: Surgery

institute: Brigham and Women's Hospital

description: processed data file: PARPi.csv

data_processing:
bcl2fastq v2.18 used for base calling with default parameters
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2 (v2.1.0) with default setting.
Raw counts (counts per million, cpm) were generated by HTseq (v0.6.1) using the union method with default parameters. Genes that had at least 1 read per million in at least half of the samples were kept for further analysis.
The number of reads were normalized using the EdgeR package (3.12.0) for R.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited csv files include normalized counts per million for each Sample

organism: Homo sapiens

source_name: prostate cancer cell line

growth_protocol: LNCaP cells were maintaned in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA-Seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit (New England BioLabs; E7530) according to the manufacturer’s instructions

treatment_protocol: LNCaP cells were treated with vehicle control or 10 uM of each PARP inhibitors for 24 hours. And for gene knockdown experiments, LNCaP cells were transfected with indicated siRNA for 72 hours.

value: prostate cancer cell line

tag: cell line

value: LNCaP

value: olaparib


title: CIS8DLiver1

description: replicate 1


title: E-cad-KO rep3


title: WT rep4

value: MMTV::PyMT; (R26)pCA::mT/mG; Cdh1+/+


title: CIS6DLiver1

description: replicate 1


title: CIS48HL1

description: replicate 1


title: CIS4DLiver1

description: replicate 1


title: CIS40HL1

description: replicate 1


title: CIS24HL1

description: replicate 1


title: CIS20HL1

description: replicate 1


title: CIS44HL1

description: replicate 1


title: CIS36HL1

description: replicate 1


title: CIS8HL1

description: replicate 1


title: CIS12HL1

description: replicate 1


title: CIS2HL1

description: replicate 1


title: CIS16HL1

description: replicate 1


title: WT rep2


title: RNA (CD8+/GFP+) in vitro effector TCR SV40-I CD8 T cells overexpressing GFP replicate#2

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Naïve TCR SV40-I transgenic CD8 T cells were stimulated with anti-CD3/CD28, retrovirally transduced with a GFP-only constuct, and expanded with IL-2 in vitro.

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Differentially expressed genes (DEG) were determined with DESeq2. The q-value cut-offs for the final lists of DEG were as follows: TOX-GFP vs. GFP: 849 DEG with q-value smaller than 0.10, TAG vs. OT1: 2347 DEG with q-value smaller than 0.05, and WT vs. TOX KO: 679 DEG with q-value smaller than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: mouse splenocytes

extract_protocol:
Samples for RNA-seq were sorted directly into Trizol LS (Invitrogen). The volume was adjusted to 1ml with PBS and samples frozen and stored at -80°C. RNA was extracted using RNeasy mini kit (Qiagen) per instructions provided by the manufacturer. After ribogreen quantification and quality control of Agilent BioAnalyzer, total RNA underwent amplification using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing (12 cycles of amplification for 2-10 ng of total RNA). Subsequently, 10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 4000, in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 4000, in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).

tag: cd8 t cells

value: TCR SV40-I transgenic CD8 T cells

tag: biological context

value: in vitro overexpression


title: E-cad-KO rep2


title: CIS32HL1

description: replicate 1


title: E-cad-KO rep1


title: WT rep3


title: CIS4HL1

description: replicate 1


title: RNA (CD8+/GFP+) in vitro effector TCR SV40-I CD8 T cells overexpressing TOX-GFP replicate#2

description: Naïve TCR SV40-I transgenic CD8 T cells were stimulated with anti-CD3/CD28, retrovirally transduced with a TOX-GFP constuct, and expanded with IL-2 in vitro.


title: RNA (CD8+/GFP+) in vitro effector TCR SV40-I CD8 T cells overexpressing TOX-GFP replicate#1


title: RNA (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#2

value: malignant liver lesions


title: RNA (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#1


title: RNA (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#3


title: RNA (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#2


title: WT rep1


title: CIS28HL1

description: replicate 1


title: RNA (CD8+/GFP+) in vitro effector TCR SV40-I CD8 T cells overexpressing GFP replicate#1


title: RNA (CD8/Ly5.1) TCR OT-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#3

value: TCR OT-I transgenic CD8 T cells


title: RNA (CD8/Ly5.1) TCR OT-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#2


title: RNA (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#1


title: RNA (CD8+/Thy1.1+/PD1lo/LAG3lo/CD39lo) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#3


title: RNA (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#2

value: Naive CD8 T cells


title: RNA (CD8+/Thy1.1+/PD1lo/LAG3lo/CD39lo) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#1


title: RNA (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#3


title: RNA (CD8+/Thy1.1+/PD1lo/LAG3lo/CD39lo) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#2


title: RNA (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#1


title: RNA (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#3


title: LNCaP_5_R1881

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

data_processing:
FastQC
Trimmomatic
FastQC
Kallisto
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Seperated Value files with RAWCOUNTS/TPM/FPKM values for each sample in two cell lines. This file is can directly be used for further differentially gene expression and pathway analyses

source_name: LNCaP cells

growth_protocol: Cells were maintened in RPMI 1640 supplemented with penicillin, streptomycin, sodium pyruvate, and 10% fetal bovine serum

extract_protocol:
RNA were purified using the RNeasy plus purification kit from QIAGEN.
NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina

treatment_protocol: Cells were seeded in RPMI 1640 media cotaining 5% of charcola stripped serum for 48h to allow seroid deprivation. Medica was then changed, and fresh media with 10nM R1881 or vehicle (96% EtOH) was added. After 24h treatment cell, cells were harvested.

tag: cell lines

value: Synthetic Androgen (R1881)


title: LNCaP_4_R1881


title: K562_PolIISer5phos_rabbitAb_pAG_std_total_10min_(20190219_SH_HsSc_S5_10T_0211)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 10 min digestion, total

data_processing:
Library strategy:  CUT&RUN
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed).

source_name: CUT&RUN

tag: antibody

value: RNAPII_Ser5phos Cell Signalling Technology Rabbit mAb cat# 12523

value: K562 human immortalised myelogenous leukemia cell line


title: K562_PolIISer5phos_rabbitAb_pAG_std_total_2min_(20190219_SH_HsSc_S5_2T_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 2 min digestion, total


title: K562_PolIISer5phos_mouseAb_pAG_std_total_10min_(20190219_SH_HsSc_S5m10T_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 10 min digestion, total

value: RNAPII-Ser5phos Abcam 5408 mouse mAb


title: K562_PolIISer5phos_mouseAb_pAG_std_supn_10min_(20190219_SH_HsSc_S5m10_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 10 min digestion, supernatant


title: K562_PolIISer5phos_rabbitAb_pAG_std_supn_10min_(20190219_SH_HsSc_S5_10_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 10 min digestion, supernatant


title: K562_PolIISer5phos_mouseAb_pAG_std_supn_2min_(20190219_SH_HsSc_S5m2_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 2 min digestion, supernatant


title: LNCaP_2_Control

value: 96 % Ethanol


title: K562_H3K27me3_CST_pAG_1to8000_std_supn_30min_(20180605_SH_HsSc_8_AG_16k_0521)

description: CUT&RUN for H3K27me3 using 1:8000 pAG/MN with standard-salt protocol, 30 min digestion

value: H3K27me3 Cell Signalling Technology Rabbit mAb cat# 9733


title: K562_H3K27me3_CST_pAG_1to1000_std_supn_30min_(20180605_SH_HsSc_5_AG_2k_0521)

description: CUT&RUN for H3K27me3 using 1:1000 pAG/MN with standard-salt protocol, 30 min digestion


title: LNCaP_1_Control


title: K562_H3K27me3_CST_pA_1to500_std_supn_30min_(20180605_SH_HsSc_1_6_500_0521)

description: CUT&RUN for H3K27me3 using 1:500 pA/MN with standard-salt protocol, 30 min digestion


title: LAPC4_5_R1881

source_name: LAPC4 cells


title: RNA (CD8/Ly5.1) TCR OT-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#1


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_pellet_10min_(20190219_SH_HsSc_S5_10Lp_0211)

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed).


title: LNCaP_6_R1881


title: LAPC4_4_R1881


title: K562_PolIISer5phos_mouseAb_pAG_std_total_2min_(20190219_SH_HsSc_S5m2T_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 2 min digestion, total


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_10min_(20190219_SH_HsSc_S5_10L_0211)


title: LAPC4_3_Control


title: K562_PolIISer5phos_rabbitAb_pAG_std_supn_2min_(20190219_SH_HsSc_S5_2_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 2 min digestion, supernatant


title: LAPC4_2_Control


title: LAPC4_1_Control


title: K562_H3K4me2_Upstate_pA_std_total_2min_(20190219_SH_HsSc_K4m2T_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with standard protocol, 2 min digestion, total DNA extraction

value: Rabbit H3K4me2 Upstate 07-030


title: K562_H3K4me2_Upstate_pA_std_total_10min_(20190219_SH_HsSc_K4m2LT_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with high-calcium/low-salt protocol, 2 min digestion, total DNA extraction


title: K562_PolIISer5phos_mouseAb_pAG_hi-Ca_pellet_10min_(20190219_SH_HsSc_S5m10Lp_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 10 min digestion, pellet


title: CLLM5-H3K27me3-Ab 2

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

data_processing:
Cleaned reads were aligned to hg19 reference genome, with Bowtie2 using default parameters.
Aligned reads were used to call peaks with MACS2 with a minimum FDR cutoff 0.05
Removal of duplicates and reads mapping to blacklisted regions was done with Picard and NGSUtils.
ChIP-Enrich is used to associate the peaks to EZH2 target genes
Poly-Enrich is used to associate the peaks to H3K27me3 genes
Genome_build: hg19
Supplementary_files_format_and_content: BED

source_name: Peripheral blood mononuclear cell

extract_protocol:
For ChIP seq chromatin was extracted from CLL B cells and normal B cells, sonicated and specific antibody was used to pulldown the ChIP DNA.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tumor type

value: Chronic lymphocytic leukemia

tag: tumor classification

value: IGHV Mutated CLL

tag: ngs seq

value: ChIP seq

tag: chip antibody

value: H3K27me3 Ab


title: LNCaP_3_Control

value: LNCaP


title: K562_PolIISer5phos_mouseAb_pAG_hi-Ca_pellet_2min_(20190219_SH_HsSc_S5m2Lp_0211)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 2 min digestion, pellet


title: K562_H3K4me2_Upstate_pA_std_2min_(20190219_SH_HsSc_K4m2_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with standard protocol, 2 min digestion


title: CLLM4-EZH2-Ab 2

value: EZH2 Ab


title: CLLM4-H3K27me3-Ab 2


title: K562_H3K4me2_Upstate_pA_std_10min_(20190219_SH_HsSc_K4m2L_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with high-calcium/low-salt protocol, 2 min digestion


title: K562_H3K4me2_Upstate_pA_hi-Ca_total_10min_(20190219_SH_HsSc_K4m10LT_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with high-calcium/low-salt protocol, 10 min digestion, total DNA extraction


title: K562_H3K4me2_Upstate_pA_hi-Ca_2min_(20190219_SH_HsSc_K4m10_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with standard protocol, 10 min digestion


title: CLLUM6-H3K27me3-Ab

value: IGHV Unmutated CLL


title: K562_H3K4me2_Upstate_pA_hi-Ca_10min_(20190219_SH_HsSc_K4m10L_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with high-calcium/low-salt protocol, 10 min digestion


title: CLLUM6-EZH2-Ab


title: K562_PolIISer5phos_rabbitAb_pAG_std_total_30min_(20190207_SH_HsSc_S5_012919)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 30 min digestion, total DNA


title: CLLUM5-H3K27me3-Ab


title: CLLUM4-H3K27me3-Ab


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_supn_3min_(20190129_SH_HsSc_S5_3_012119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 3 min digestion, supernatant


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_total_30min_(20190207_SH_HsSc_S5L_012919)


title: CLLUM5-EZH2-Ab


title: CLLM5-EZH2-Ab 2


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_pellet_9min_(20190129_SH_HsSc_S5_9p_12119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 9 min digestion, pellet


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_pellet_3min_(20190129_SH_HsSc_S5_3p_12119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 3 min digestion, pellet


title: Input-normal-B-cell

value: Normal healthy control

value: Normal B cells

value: No Antibody (INPUT DNA)


title: Input-CLLUM


title: K562_PolIISer5phos_mouseAb_pAG_hi-Ca_total_30min_(20190207_SH_HsSc_S5mL_012919)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 30 min digestion, total DNA


title: CLLM3-H3K27me3-Ab 2


title: K562_H3K4me2_Upstate_pA_hi-Ca_total_2min_(20190219_SH_HsSc_K4m10T_0211)

description: CUT&RUN for H3K4me2 using pAG/MN with standard protocol, 10 min digestion, total DNA extraction


title: Normal-Bcell-EZH2-Ab


title: CLLUM4-EZH2-Ab


title: K562_PolIISer5phos_mouseAb_pAG_std_total_30min_(20190207_SH_HsSc_S5m_012919)


title: CLLUM3-H3K27me3-Ab


title: K562_PolIISer5phos_mouseAb_pAG_hi-Ca_pellet_9min_(20190129_SH_HsSc_S5m9p_12119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 9 min digestion, pellet


title: K562_IgG_hi-Ca_(20180314_SH_HsSc_IgG_0305)

description: CUT&RUN for IgG using high-calcium/low-salt protocol, 30 min digestion

value: Guinea Pig anti-Rabbit (Heavy & Light Chain), Antibodies Online ABIN101961


title: CLLM3-EZH2-Ab 2


title: Input-CLLM


title: K562_PolIISer5phos_mouseAb_pAG_hi-Ca_pellet_3min_(20190129_SH_HsSc_S5m3p_12119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using mouse monoclonal antibody with high-calcium/low-salt protocol, 3 min digestion, pellet

value: RNAPII_Ser5phos Cell Signalling Technology Rabbit mAb cat# 12523


title: K562_H3K27Ac_Milli_pA_hi-Ca_9min_(20181026_SH_HsSc_KAc_9m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with high-calcium/low-salt protocol, 9 min digestion

value: H3K27Ac Millipore MABE647 Lot VP1707111

value: K562 human immortalised myelogenous leukemia cell line


title: CLLUM2-H3K27me3-Ab


title: CLLUM2-EZH2-Ab


title: CLLUM1-H3K27me3-Ab


title: K562_H3K27Ac_Milli_pA_hi-Ca_3min_(20181026_SH_HsSc_KAc_3m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with high-calcium/low-salt protocol, 3 min digestion


title: K562_PolIISer5phos_rabbitAb_pAG_hi-Ca_supn_9min_(20190129_SH_HsSc_S5_9_012119)

description: CUT&RUN for RNA Polymerase II C-terminal domain Serine-5 phosphate using rabbit monoclonal antibody with high-calcium/low-salt protocol, 9 min digestion, supernatant


title: NormBcell-H3K27me3Ab


title: CLLUM1-EZH2-Ab


title: K562_H3K27Ac_Milli_pA_hi-Ca_1min_(20181026_SH_HsSc_KAc_1m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with high-calcium/low-salt protocol, 1 min digestion


title: K562_H3K27Ac_Milli_pAG_hi-Ca_9min_(20181026_SH_HsSc_KAc_G9m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with high-calcium/low-salt protocol, 9 min digestion


title: K562_H3K27Ac_Milli_pA_hi-Ca_27m_(20181026_SH_HsSc_KAc_27m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with high-calcium/low-salt protocol, 27 min digestion


title: CLLM3-H3K27me3-Ab


title: CLLM3-EZH2-Ab


title: CLLM2-EZH2-Ab


title: K562_NPAT_pAG_hi-Ca_30min_total_(20190207_SH_HsSc_NPATL_012919)

description: CUT&RUN for NPAT using high-calcium/low-salt protocol, 30 min digestion

value: NPAT Thermo-Fisher PA5-66839; antibody:RNAPII_Ser5phos Cell Signalling Technology Rabbit mAb cat# 12523


title: CLLM1-H3K27me3-Ab


title: CLLM1-EZH2-Ab


title: CLLUM3-EZH2-Ab


title: K562_H3K27Ac_Milli_pAG_hi-Ca_27m_(20181026_SH_HsSc_KAc_G27m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with high-calcium/low-salt protocol, 27 min digestion


title: K562_H3K27Ac_Abcam_std_9min_(20171122_SH_HsSc_AcAb9m_1109)

description: CUT&RUN for H3K27Ac using standard protocol, 9 min digestion


title: K562_H3K27Ac_Abcam_std_3min_(20171122_SH_HsSc_AcAb3m_1109)

description: CUT&RUN for H3K27Ac using standard protocol, 3 min digestion


title: K562_H3K27Ac_Abcam_std_27min_(20171122_SH_HsSc_AcAb27m_1109)

description: CUT&RUN for H3K27Ac using standard protocol, 27 min digestion


title: K562_H3K27Ac_Milli_pAG_hi-Ca_1min_(20181026_SH_HsSc_KAc_G1m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with high-calcium/low-salt protocol, 1 min digestion


title: K562_H3K27Ac_Abcam_std_20sec_(20171122_SH_HsSc_AcAb20s_1109)

description: CUT&RUN for H3K27Ac using standard protocol, 20 sec digestion


title: K562_H3K27Ac_Abcam_std_1min_(20171122_SH_HsSc_AcAb1m_1109)

description: CUT&RUN for H3K27Ac using standard protocol, 1 min digestion


title: K562_H3K27Ac_Abcam_hi-Ca_9min_(20180306_SH_HsSc_Kac_9m_0227)

description: CUT&RUN for H3K27Ac using high-calcium/low-salt protocol, 9 min digestion


title: K562_H3K27Ac_Abcam_hi-Ca_3min_(20180306_SH_HsSc_Kac_3m_0227)

description: CUT&RUN for H3K27Ac using high-calcium/low-salt protocol, 3 min digestion


title: K562_H3K27Ac_Abcam_hi-Ca_27min_(20180306_SH_HsSc_Kac_27m_0227)

description: CUT&RUN for H3K27Ac using high-calcium/low-salt protocol, 27 min digestion


title: K562_H3K27Ac_Milli_pAG_hi-Ca_3min_(20181026_SH_HsSc_KAc_G3m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with high-calcium/low-salt protocol, 3 min digestion


title: CLLM2-H3K27me3-Ab


title: K562_H3K27Ac_Abcam_hi-Ca_1min_(20180306_SH_HsSc_Kac_1m_0227)

description: CUT&RUN for H3K27Ac using high-calcium/low-salt protocol, 1 min digestion


title: K562_CTCF_pA_hi-Ca_9min_(20181026_SH_HsSc_CTCF_9m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with standard protocol, 9 min digestion

value: CTCF Millipore 07-729 Lot 2971000


title: K562_CTCF_pA_hi-Ca_3min_(20181026_SH_HsSc_CTCF_3m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with standard protocol, 3 min digestion


title: K562_CTCF_pA_hi-Ca_27m_(20181026_SH_HsSc_CTCF_27m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with standard protocol, 27 min digestion


title: K562_CTCF_pA_hi-Ca_1min_(20181026_SH_HsSc_CTCF_1m_1018)

description: CUT&RUN for H3K27Ac using pA/MN with standard protocol, 1 min digestion


title: K562_CTCF_pAG_hi-Ca_9min_(20181026_SH_HsSc_CTCF_G9m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with standard protocol, 9 min digestion


title: K562_CTCF_pAG_hi-Ca_3min_(20181026_SH_HsSc_CTCF_G3m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with standard protocol, 3 min digestion


title: K562_CTCF_pAG_hi-Ca_27m_(20181026_SH_HsSc_CTCF_G27m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with standard protocol, 27 min digestion


title: TSOD-BTS_7w_rep3

type: RNA

city: Toyama

first: Makito

last: Oku

address: 2630 Sugitani

department: Research Center for Pre-Disease Science

country: Japan

institute: University of Toyama

description: body weight 37.2 (g); blood sugar concentration 174.0 (mg/dL); testicular fat mass 1.66 (g)

hyb_protocol: A total of 0.6 ug of Cy3-labeled cRNA was fragmented at 60 ºC for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) at 65 ºC for 17 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature for 1 minute with GE Wash Buffer 1 (Agilent) and at 37 ºC for 1 minute with GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent G2505C Microarray Scanner System (Agilent) using the one color scan setting for 8x60k array slides (scan area 61 mm x 21.6 mm, scan resolution 3 um, the dye channel was set to Green, and photomultiplier tube (PMT) gain was set to 100 percent).

data_processing: Scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended Processed Signal intensities.

source_name: adipose tissue, TSOD mouse, BTS-treated, 7 weeks, replicate 3

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1 ug total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent).

growth_protocol: Mice were housed in groups of two or three per cage, maintained at 24±2 ºC on a 12-hour light and 12-hour dark cycle, and given normal chow diet (MF; Oriental Yeast Co., Ltd., Tokyo, Japan) and water ad libitum.

extract_protocol: Mice were dissected to collect epididymal white adipose tissue under anesthesia to minimize suffering. Total RNA was extracted using the RNeasy Total RNA Extraction kit (Qiagen, Valencia, CA, USA).

treatment_protocol: In the BTS-treated group, BTS (bofutsushosan) was administrated (1000 mg/kg body weight/day, per os) every day.

value: epididymal white adipose tissue

tag: gender

value: male

value: TSOD mouse

value: 7 weeks


title: TSOD-BTS_6w_rep1

description: body weight 29.4 (g); blood sugar concentration 206.0 (mg/dL); testicular fat mass 0.76 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 6 weeks, replicate 1

value: 6 weeks


title: TSOD-BTS_6w_rep2

description: body weight 32.7 (g); blood sugar concentration 265.0 (mg/dL); testicular fat mass 1.19 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 6 weeks, replicate 2


title: TSOD-BTS_5w_rep4

description: body weight 26.1 (g); blood sugar concentration 161.0 (mg/dL); testicular fat mass 0.49 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 5 weeks, replicate 4

value: 5 weeks


title: K562_CTCF_pAG_hi-Ca_1min_(20181026_SH_HsSc_CTCF_G1m_1018)

description: CUT&RUN for H3K27Ac using pAG/MN with standard protocol, 1 min digestion


title: TSOD-BTS_5w_rep1

description: body weight 26.3 (g); blood sugar concentration 164.0 (mg/dL); testicular fat mass 0.47 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 5 weeks, replicate 1


title: K562_H3K27Ac_Abcam_hi-Ca_20sec_(20180306_SH_HsSc_Kac_20s_0227)

description: CUT&RUN for H3K27Ac using high-calcium/low-salt protocol, 20 sec digestion


title: TSOD-BTS_5w_rep2

description: body weight 27.7 (g); blood sugar concentration 202.0 (mg/dL); testicular fat mass 0.57 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 5 weeks, replicate 2


title: TSOD-BTS_7w_rep4

description: body weight 34.4 (g); blood sugar concentration 156.0 (mg/dL); testicular fat mass 1.47 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 7 weeks, replicate 4


title: TSOD-BTS_7w_rep1

description: body weight 35.6 (g); blood sugar concentration 149.0 (mg/dL); testicular fat mass 1.48 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 7 weeks, replicate 1


title: TSOD-BTS_5w_rep3

description: body weight 26.9 (g); blood sugar concentration 176.0 (mg/dL); testicular fat mass 0.65 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 5 weeks, replicate 3


title: TSOD-BTS_4w_rep3

description: body weight 23.3 (g); blood sugar concentration 158.0 (mg/dL); testicular fat mass 0.27 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 4 weeks, replicate 3

value: 4 weeks


title: TSOD-BTS_6w_rep4

description: body weight 32.4 (g); blood sugar concentration 254.0 (mg/dL); testicular fat mass 1.16 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 6 weeks, replicate 4


title: TSOD-BTS_4w_rep2

description: body weight 22.5 (g); blood sugar concentration 155.0 (mg/dL); testicular fat mass 0.23 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 4 weeks, replicate 2


title: TSOD-BTS_4w_rep1

description: body weight 20.2 (g); blood sugar concentration 164.0 (mg/dL); testicular fat mass 0.20 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 4 weeks, replicate 1


title: TSOD-BTS_7w_rep2

description: body weight 34.6 (g); blood sugar concentration 148.0 (mg/dL); testicular fat mass 1.27 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 7 weeks, replicate 2


title: TSOD-BTS_6w_rep3

description: body weight 32.5 (g); blood sugar concentration 192.0 (mg/dL); testicular fat mass 1.31 (g)

source_name: adipose tissue, TSOD mouse, BTS-treated, 6 weeks, replicate 3


title: TSOD_7w_rep5

description: body weight 40.3 (g); blood sugar concentration 240.0 (mg/dL); testicular fat mass 1.64 (g)

source_name: adipose tissue, TSOD mouse, 7 weeks, replicate 5


title: KOPN8.EPZ5676.96h_Rep3

city: Berlin

first: Bernard

last: Haendler

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
RSEM was used to quantify reads in genes.
Expected counts were further analyzed in R, DESeq2 was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes expected counts (obtained with RSEM) for all samples

molecule: polyA RNA

source_name: KOPN-8 (ALL)

growth_protocol: HL-60, Jurkat, MOLM-13, MOLM14, NOMO-1, KOPN-8, EOL-1 and OCI-AML3 were cultured in RPMI 1640 (FG1215). OCI-AML2, OCI-AML5 and RS4-11 were cultured in Alpha-Medium (F0915). MV4-11 and SEM were cultured in IMDM (21980-032). All above listed media were supplemented with 10% fetal bovine serum. Cell lines were cultured at 37C in 5% CO2.

extract_protocol:
RNA was extracted using using RNeasy-Plus Mini kit (Qiagen #74134).
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: Cells were treated for 8h (P-TEFb - 0.05 µM, OTX015 - 1 µM), 24h (BAY-155 - 2 µM, Brequinar - 2 µM, DMSO – 0.1%) and 96h (EPZ-5676 - 3 µM, DMSO – 0.1%) prior to RNA extraction.

tag: agent

tag: concentration

tag: time point (hours)

tag: mll fusion type

value: MLL-ENL


title: KOPN8.EPZ5676.96h_Rep2


title: KOPN8.DMSO.96h_Rep3

value: DMSO

value: 0.10 percent


title: KOPN8.DMSO.96h_Rep1


title: TSOD_7w_rep3

description: body weight 40.3 (g); blood sugar concentration 186.0 (mg/dL); testicular fat mass 1.47 (g)

source_name: adipose tissue, TSOD mouse, 7 weeks, replicate 3

tag: tissue

tag: strain


title: KOPN8.EPZ5676.96h_Rep1


title: TSOD_6w_rep2

description: body weight 34.0 (g); blood sugar concentration 181.0 (mg/dL); testicular fat mass 0.97 (g)

source_name: adipose tissue, TSOD mouse, 6 weeks, replicate 2

tag: age


title: TSOD_7w_rep2

description: body weight 38.2 (g); blood sugar concentration 180.0 (mg/dL); testicular fat mass 1.41 (g)

source_name: adipose tissue, TSOD mouse, 7 weeks, replicate 2


title: TSOD_7w_rep4

description: body weight 38.2 (g); blood sugar concentration 177.0 (mg/dL); testicular fat mass 1.35 (g)

source_name: adipose tissue, TSOD mouse, 7 weeks, replicate 4


title: TSOD_7w_rep1

description: body weight 38.2 (g); blood sugar concentration 204.0 (mg/dL); testicular fat mass 1.44 (g)

source_name: adipose tissue, TSOD mouse, 7 weeks, replicate 1


title: KOPN8.DMSO.96h_Rep2

tag: cell line


title: TSOD_6w_rep3

description: body weight 34.7 (g); blood sugar concentration 167.0 (mg/dL); testicular fat mass 1.01 (g)

source_name: adipose tissue, TSOD mouse, 6 weeks, replicate 3


title: TSOD_6w_rep4

description: body weight 33.0 (g); blood sugar concentration 211.0 (mg/dL); testicular fat mass 0.83 (g)

source_name: adipose tissue, TSOD mouse, 6 weeks, replicate 4


title: TSOD_6w_rep1

description: body weight 34.8 (g); blood sugar concentration 185.0 (mg/dL); testicular fat mass 1.01 (g)

source_name: adipose tissue, TSOD mouse, 6 weeks, replicate 1


title: KOPN8.DMSO.24h_Rep2


title: KOPN8.DMSO.24h_Rep3


title: KOPN8.DMSO.24h_Rep1


title: TSOD_5w_rep4

description: body weight 28.6 (g); blood sugar concentration 175.0 (mg/dL); testicular fat mass 0.49 (g)

source_name: adipose tissue, TSOD mouse, 5 weeks, replicate 4


title: KOPN8.Brequinar.24h_Rep3

value: Brequinar


title: KOPN8.Brequinar.24h_Rep2


title: TSOD_5w_rep2

description: body weight 30.4 (g); blood sugar concentration 184.0 (mg/dL); testicular fat mass 0.54 (g)

source_name: adipose tissue, TSOD mouse, 5 weeks, replicate 2


title: TSOD_5w_rep1

description: body weight 28.8 (g); blood sugar concentration 169.0 (mg/dL); testicular fat mass 0.46 (g)

source_name: adipose tissue, TSOD mouse, 5 weeks, replicate 1


title: KOPN8.DMSO.8h_Rep3


title: KOPN8.DMSO.8h_Rep2


title: TSOD_5w_rep5

description: body weight 28.7 (g); blood sugar concentration 177.0 (mg/dL); testicular fat mass 0.50 (g)

source_name: adipose tissue, TSOD mouse, 5 weeks, replicate 5


title: TSOD_5w_rep3

description: body weight 31.5 (g); blood sugar concentration 186.0 (mg/dL); testicular fat mass 0.57 (g)

source_name: adipose tissue, TSOD mouse, 5 weeks, replicate 3


title: TSOD_4w_rep4

description: body weight 21.4 (g); blood sugar concentration 134.0 (mg/dL); testicular fat mass 0.16 (g)

source_name: adipose tissue, TSOD mouse, 4 weeks, replicate 4


title: TSOD_4w_rep5

description: body weight 22.6 (g); blood sugar concentration 142.0 (mg/dL); testicular fat mass 0.19 (g)

source_name: adipose tissue, TSOD mouse, 4 weeks, replicate 5


title: TSOD_4w_rep3

description: body weight 21.9 (g); blood sugar concentration 135.0 (mg/dL); testicular fat mass 0.18 (g)

source_name: adipose tissue, TSOD mouse, 4 weeks, replicate 3


title: TSOD_4w_rep1

description: body weight 21.8 (g); blood sugar concentration 144.0 (mg/dL); testicular fat mass 0.17 (g)

source_name: adipose tissue, TSOD mouse, 4 weeks, replicate 1


title: KOPN8.DMSO.8h_Rep1

source_name: KOPN-8 (ALL)


title: TSOD_4w_rep2

description: body weight 22.6 (g); blood sugar concentration 151.0 (mg/dL); testicular fat mass 0.19 (g)

source_name: adipose tissue, TSOD mouse, 4 weeks, replicate 2


title: KOPN8.BAY155.24h_Rep3


title: KOPN8.BAY155.24h_Rep2


title: KOPN8.BAY155.24h_Rep1


title: KOPN8.Brequinar.24h_Rep1


title: KOPN8.BAY1251152.8h_Rep2


title: KOPN8.OTX015.8h_Rep3


title: KOPN8.OTX015.8h_Rep2


title: KOPN8.OTX015.8h_Rep1


title: KOPN8.BAY1251152.8h_Rep1


title: TSOD_3w_rep5

description: body weight 12.1 (g); blood sugar concentration 124.0 (mg/dL); testicular fat mass 0.08 (g)

source_name: adipose tissue, TSOD mouse, 3 weeks, replicate 5

value: 3 weeks


title: MOLM14.DMSO.96h_Rep3

source_name: MOLM-14 (AML)

value: MLL-AF


title: MOLM14.DMSO.96h_Rep2


title: MOLM14.DMSO.96h_Rep1


title: MOLM14.EPZ5676.96h_Rep1


title: MOLM14.EPZ5676.96h_Rep2


title: TSOD_3w_rep4

description: body weight 13.3 (g); blood sugar concentration 128.0 (mg/dL); testicular fat mass 0.05 (g)

source_name: adipose tissue, TSOD mouse, 3 weeks, replicate 4


title: TSOD_3w_rep2

description: body weight 11.1 (g); blood sugar concentration 132.0 (mg/dL); testicular fat mass 0.05 (g)

source_name: adipose tissue, TSOD mouse, 3 weeks, replicate 2


title: TSNO_6w_rep5

description: body weight 27.3 (g); blood sugar concentration 171.0 (mg/dL); testicular fat mass 0.28 (g)

source_name: adipose tissue, TSNO mouse, 6 weeks, replicate 5

value: TSNO mouse


title: TSOD_3w_rep1

description: body weight 13.1 (g); blood sugar concentration 127.0 (mg/dL); testicular fat mass 0.05 (g)

source_name: adipose tissue, TSOD mouse, 3 weeks, replicate 1


title: TSNO_7w_rep5

description: body weight 29.0 (g); blood sugar concentration 143.0 (mg/dL); testicular fat mass 0.37 (g)

source_name: adipose tissue, TSNO mouse, 7 weeks, replicate 5


title: TSNO_7w_rep4

description: body weight 30.0 (g); blood sugar concentration 159.0 (mg/dL); testicular fat mass 0.46 (g)

source_name: adipose tissue, TSNO mouse, 7 weeks, replicate 4


title: TSNO_7w_rep3

description: body weight 29.0 (g); blood sugar concentration 151.0 (mg/dL); testicular fat mass 0.28 (g)

source_name: adipose tissue, TSNO mouse, 7 weeks, replicate 3


title: TSNO_7w_rep1

description: body weight 29.5 (g); blood sugar concentration 146.0 (mg/dL); testicular fat mass 0.27 (g)

source_name: adipose tissue, TSNO mouse, 7 weeks, replicate 1


title: MOLM14.DMSO.24h_Rep6


title: MOLM14.DMSO.24h_Rep5


title: TSNO_6w_rep4

description: body weight 26.3 (g); blood sugar concentration 146.0 (mg/dL); testicular fat mass 0.27 (g)

source_name: adipose tissue, TSNO mouse, 6 weeks, replicate 4


title: MOLM14.DMSO.24h_Rep4


title: MOLM14.Brequinar.24h_Rep3


title: TSNO_7w_rep2

description: body weight 27.5 (g); blood sugar concentration 148.0 (mg/dL); testicular fat mass 0.35 (g)

source_name: adipose tissue, TSNO mouse, 7 weeks, replicate 2


title: TSNO_6w_rep3

description: body weight 26.0 (g); blood sugar concentration 162.0 (mg/dL); testicular fat mass 0.27 (g)

source_name: adipose tissue, TSNO mouse, 6 weeks, replicate 3


title: MOLM14.Brequinar.24h_Rep2


title: TSNO_6w_rep2

description: body weight 27.6 (g); blood sugar concentration 150.0 (mg/dL); testicular fat mass 0.33 (g)

source_name: adipose tissue, TSNO mouse, 6 weeks, replicate 2


title: TSNO_6w_rep1

description: body weight 26.3 (g); blood sugar concentration 164.0 (mg/dL); testicular fat mass 0.23 (g)

source_name: adipose tissue, TSNO mouse, 6 weeks, replicate 1


title: TSNO_5w_rep3

description: body weight 21.1 (g); blood sugar concentration 154.0 (mg/dL); testicular fat mass 0.10 (g)

source_name: adipose tissue, TSNO mouse, 5 weeks, replicate 3


title: TSNO_5w_rep4

description: body weight 22.6 (g); blood sugar concentration 147.0 (mg/dL); testicular fat mass 0.13 (g)

source_name: adipose tissue, TSNO mouse, 5 weeks, replicate 4


title: TSNO_5w_rep5

description: body weight 23.0 (g); blood sugar concentration 146.0 (mg/dL); testicular fat mass 0.12 (g)

source_name: adipose tissue, TSNO mouse, 5 weeks, replicate 5


title: TSNO_4w_rep5

description: body weight 19.1 (g); blood sugar concentration 155.0 (mg/dL); testicular fat mass 0.08 (g)

source_name: adipose tissue, TSNO mouse, 4 weeks, replicate 5


title: MOLM14.DMSO.24h_Rep2

source_name: MOLM-14 (AML)


title: TSNO_5w_rep1

description: body weight 21.3 (g); blood sugar concentration 137.0 (mg/dL); testicular fat mass 0.10 (g)

source_name: adipose tissue, TSNO mouse, 5 weeks, replicate 1


title: MOLM14.Brequinar.24h_Rep1


title: MOLM14.DMSO.24h_Rep3


title: TSNO_4w_rep4

description: body weight 17.9 (g); blood sugar concentration 139.0 (mg/dL); testicular fat mass 0.06 (g)

source_name: adipose tissue, TSNO mouse, 4 weeks, replicate 4


title: MOLM14.BAY155.24h_Rep3


title: TSOD_3w_rep3

description: body weight 11.8 (g); blood sugar concentration 135.0 (mg/dL); testicular fat mass 0.05 (g)

source_name: adipose tissue, TSOD mouse, 3 weeks, replicate 3


title: MOLM14.DMSO.24h_Rep1


title: MOLM14.BAY155.24h_Rep2


title: MOLM14.BAY155.24h_Rep1


title: MOLM14.OTX015.8h_Rep3


title: TSNO_5w_rep2

description: body weight 23.1 (g); blood sugar concentration 155.0 (mg/dL); testicular fat mass 0.14 (g)

source_name: adipose tissue, TSNO mouse, 5 weeks, replicate 2


title: MOLM14.OTX015.8h_Rep1


title: MOLM14.BAY1251152.8h_Rep3


title: TSNO_4w_rep2

description: body weight 18.8 (g); blood sugar concentration 157.0 (mg/dL); testicular fat mass 0.07 (g)

source_name: adipose tissue, TSNO mouse, 4 weeks, replicate 2


title: OCIAML5.DMSO.96h_Rep3

source_name: OCI-AML5 (AML)

value: MLL-WT


title: OCIAML5.DMSO.96h_Rep2


title: MOLM14.BAY1251152.8h_Rep2


title: TSNO_4w_rep3

description: body weight 17.6 (g); blood sugar concentration 143.0 (mg/dL); testicular fat mass 0.06 (g)

source_name: adipose tissue, TSNO mouse, 4 weeks, replicate 3


title: TSNO_4w_rep1

description: body weight 18.5 (g); blood sugar concentration 157.0 (mg/dL); testicular fat mass 0.06 (g)

source_name: adipose tissue, TSNO mouse, 4 weeks, replicate 1


title: TSNO_3w_rep2

description: body weight 9.0 (g); blood sugar concentration 121.0 (mg/dL); testicular fat mass 0.01 (g)

source_name: adipose tissue, TSNO mouse, 3 weeks, replicate 2


title: OCIAML5.DMSO.96h_Rep1


title: MOLM14.OTX015.8h_Rep2


title: TSNO_3w_rep3

description: body weight 9.4 (g); blood sugar concentration 117.0 (mg/dL); testicular fat mass 0.02 (g)

source_name: adipose tissue, TSNO mouse, 3 weeks, replicate 3


title: TSNO_3w_rep4

description: body weight 10.4 (g); blood sugar concentration 115.0 (mg/dL); testicular fat mass 0.01 (g)

source_name: adipose tissue, TSNO mouse, 3 weeks, replicate 4


title: OCIAML5.EPZ5676.96h_Rep3


title: TSNO_3w_rep1

description: body weight 10.3 (g); blood sugar concentration 137.0 (mg/dL); testicular fat mass 0.02 (g)

source_name: adipose tissue, TSNO mouse, 3 weeks, replicate 1


title: TSNO_3w_rep5

description: body weight 9.2 (g); blood sugar concentration 119.0 (mg/dL); testicular fat mass 0.01 (g)

source_name: adipose tissue, TSNO mouse, 3 weeks, replicate 5


title: OCIAML5.EPZ5676.96h_Rep1


title: MOLM14.BAY1251152.8h_Rep1


title: OCIAML5.DMSO.24h_Rep6


title: OCIAML5.Brequinar.24h_Rep2


title: OCIAML5.Brequinar.24h_Rep1


title: OCIAML5.EPZ5676.96h_Rep2


title: OCIAML5.DMSO.24h_Rep3


title: OCIAML5.DMSO.24h_Rep2


title: HFD, hypoxia, replicate 6

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with Ozone-barrier slides.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: HFD, hypoxia, replicate 6

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Cy-3 labelled samples were pooled on an equimolar basis and served as reference pool; this comprised all samples present in the SuperSeries GSE53805.

extract_protocol: Total RNA was isolated from epididymal whiet adipose tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: C57BL/6JOlaHsd wildtype male mice were acclimatized in the facility by feeding purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks, followed by 12 weeks BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into 2 treatment groups: i) control group which remained under normoxia for 5 days, and ii) 5 days oxygen restriction to 13% ambient oxygen. On day 6, after 2 hour food removal at the start of the light phase, mice were killed immediately after taking them out of the indirect calorimetry system by decapitation. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen.

value: adult

source_name: reference pool


title: OCIAML5.DMSO.24h_Rep4


title: HFD, hypoxia, replicate 7

source_name: HFD, hypoxia, replicate 7


title: M-WT-1 [16-007-023]

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Illumina adapters were trimmed using Trimmonatic v0.33
Trimmed reads were aligned to mm10 genome using 2 passes of STARv 2.4a aligner
reads were quantified using featureCounts v1.4.6
differential expression analysis was performed using DESeq2 v1.22.2
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts_gene_counts.txt contains summarized read counts for each sample.

source_name: Male_WT_intestinal mucosa

extract_protocol:
Qiagen RNeasy Lipid Kit
Libraries were prepared using Illumina's Tru-Seq Stranded RNA protocol

tag: strain background

tag: genotype/variation

value: WT

tag: Sex

value: Male

value: 8 weeks

tag: tissue/cell type

value: intestinal mucosa


title: M-WT-4 [16-007-037]


title: F-WT-4 [16-007-039]

source_name: Female_WT_intestinal mucosa

value: Female


title: M-WT-2 [16-007-031]


title: M-WT-3 [16-007-036]


title: IPMK loss-of-function mutant hippocampus at P90, biological rep2

city: Daejeon

first: Jina

last: Park

address: 291 Daehak-ro, Yuseong-gu

department: Biological Science

country: South Korea

institute: KAIST

description: right hippocampus from IPMK cKO #1557

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45 °C for 16 h.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).
The file Complete_set_of_log_value_2.xlsx includes log2 values and statistics.

label: biotin

source_name: IPMK cKO, hippocampus

label_protocol: The sense cDNA was then fragmented and biotin labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Mouse hippocampi dissected from P90 male mouse brain

extract_protocol: Mouse brain hippocampi were dissected immediately after decapitation, and stored at RNAlater Stabilization Solution (Thermo) at 4℃. Four high quality samples containing highest amount of isolated RNA were selected from each experimental group using RNeasy Mini Kit (Qiagen), and stored at – 80 °C until used. For check quality of RNA, RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop), and Agilent 2100 Bioanalyzer (Agilent Technologies). The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit). DNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

value: male

value: hippocampus

tag: genotype

value: IPMK cKO


title: HFD, hypoxia, replicate 1

source_name: HFD, hypoxia, replicate 1

value: epididymal white adipose tissue


title: F-WT-3 [16-007-038]


title: OCIAML5.DMSO.24h_Rep1

value: DMSO


title: OCIAML5.BAY155.24h_Rep3


title: HFD, hypoxia, replicate 5

source_name: HFD, hypoxia, replicate 5


title: HFD, hypoxia, replicate 8

source_name: HFD, hypoxia, replicate 8


title: HFD, hypoxia, replicate 4

source_name: HFD, hypoxia, replicate 4


title: OCIAML5.Brequinar.24h_Rep3

source_name: OCI-AML5 (AML)


title: HFD, hypoxia, replicate 9

source_name: HFD, hypoxia, replicate 9


title: IPMK loss-of-function mutant hippocampus at P90, biological rep1

description: right hippocampus from IPMK cKO #1568


title: HFD, hypoxia, replicate 2

source_name: HFD, hypoxia, replicate 2


title: wild type hippocampus at P90, biological rep2

description: right hippocampus from IPMK WT #1558

source_name: wild type, hippocampus

value: wild type


title: wild type hippocampus at P90, biological rep1

description: right hippocampus from IPMK WT #1566


title: F-WT-2 [16-007-035]


title: F-WT-1 [16-007-034]


title: OCIAML5.BAY155.24h_Rep2


title: OCIAML5.BAY155.24h_Rep1


title: M-KO-4 [16-007-027]

source_name: Male_Slfn 3 KO_intestinal mucosa

value: Slfn 3 KO


title: M-KO-2 [16-007-025]


title: OCIAML5.OTX015.8h_Rep3


title: M-KO-1 [16-007-024]


title: F-KO-4 [16-007-033]

source_name: Female_Slfn 3 KO_intestinal mucosa


title: HFD, hypoxia, replicate 10

source_name: HFD, hypoxia, replicate 10


title: OCIAML5.OTX015.8h_Rep2


title: OCIAML5.BAY1251152.8h_Rep2


title: M-KO-3 [16-007-026]


title: OCIAML5.BAY1251152.8h_Rep3


title: F-KO-3 [16-007-032]


title: OCIAML5.BAY1251152.8h_Rep1


title: F-KO-1 [16-007-028]


title: SEM.EPZ5676.96h_Rep3

source_name: SEM (ALL)

value: SEM


title: SEM.DMSO.96h_Rep1

value: 0.10 percent

value: MLL-AF


title: F-KO-2 [16-007-029]


title: Conventional B6-CD45.2 CD8+ Tc1 cells Input Rep 2

city: Birmingham

first: Amy

last: Weinmann

state: AL

address: 1825 UNIVERSITY BLVD

department: Department of Microbiology

institute: University of Alabama at Birmingham

data_processing:
Sequenced reads were trimmed for adapter sequence, then mapped to the mm10 genome using Bowtie2 v2.2.59 with default parameters
For stringent alignment processing, 0-mismatched alignments were extracted using bamtools 'XM:0' parameter
Peaks were called using MACS2 v2.1.1.20160309
Diffferential peak analyses were conducted using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: Primary CD4+ or CD8+ T cells were isolated from lymph nodes and spleen from mice.  The cells were purified by negative selection and then stimulated with plate bound anti-CD3 and anti-CD28 in type I conditions (IL-12 and anti-IL-4). The cells were split on day 3 and maintained in type I conditions and IL-2.

extract_protocol:
ChIP assay was performed as described in Oestreich et al. 2014 and Chisolm et al. 2019.
Library construction was performed by Genewiz, and samples were subjected to sequencing with paired-end 150bp reads, with the exception of the conventional and germ-free CD8+ Tc1 Rep 1, which was sequenced with single-end 50bp reads.

value: Conventional C57BL/6J (CD45.2)

tag: vendor

value: The Jackson Laboratory

tag: cell type

value: CD8+ Tc1 cells


title: SEM.EPZ5676.96h_Rep2


title: Germ-free B6.SJL-CD45.1 CD8+ Tc1 cells Input Rep 2

value: UAB Gnotobiotic Core

tag: chip antibody


title: Germ-free B6.SJL-CD45.1 CD8+ Tc1 cells H3K27Ac Rep 2

value: H3K27Ac; Abcam; Cat# ab4729


title: SEM.EPZ5676.96h_Rep1


title: SEM.DMSO.96h_Rep3


title: SEM.DMSO.96h_Rep2


title: HFD, hypoxia, replicate 3

source_name: HFD, hypoxia, replicate 3

tag: gender

value: adult

source_name: reference pool


title: Germ-free B6.SJL-CD45.1 CD8+ Tc1 cells Input Rep 1


title: SEM.DMSO.24h_Rep6

tag: agent


title: Conventional B6-CD45.2 CD8+ Tc1 cells H3K27Ac Rep 2


title: OCIAML5.OTX015.8h_Rep1

tag: concentration

value: MLL-WT


title: SEM.DMSO.24h_Rep5

tag: time point (hours)


title: Conventional B6-CD45.2 CD8+ Tc1 cells Input Rep 1


title: OCIAML5.DMSO.24h_Rep5

tag: mll fusion type


title: Conventional B6-CD45.2 CD8+ Tc1 cells H3K27Ac Rep 1


title: Germ-free B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 1

value: CD4+ Th1 cells


title: SEM.Brequinar.24h_Rep2

value: Brequinar


title: SEM.DMSO.24h_Rep4


title: SEM.Brequinar.24h_Rep3


title: Conventional B6-CD45.2 CD4+ Th1 cells Input Rep 1


title: Germ-free B6.SJL-CD45.1 CD8+ Tc1 cells H3K27Ac Rep 1


title: Germ-free B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 2


title: SEM.DMSO.24h_Rep2


title: SEM.DMSO.24h_Rep3


title: Conventional B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 1


title: Germ-free B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 1


title: Conventional B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 2


title: SEM.BAY155.24h_Rep3


title: Jax SJL CD4+ Th1 cells Input Rep 1

source_name: Jax SJL CD4+ Th1 cells Input

value: Jax SJL/J (CD45.1)


title: SEM.BAY155.24h_Rep2


title: SEM.OTX015.8h_Rep2


title: SEM.OTX015.8h_Rep1


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 1

source_name: Jax B6.SJL-CD45.1 CD4+ Th1 cells Input

value: Jax B6.SJL-PtprcaPepcb/BoyJ (CD45.1)


title: SEM.DMSO.24h_Rep1

value: DMSO


title: SEM.BAY155.24h_Rep1


title: Jax B6-CD45.2 CD4+ Th1 cells Input Rep 1

source_name: Jax B6-CD45.2 CD4+ Th1 cells Input


title: Germ-free B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 2


title: SEM.OTX015.8h_Rep3


title: Jax SJL CD4+ Th1 cells H3K27Ac Rep 1

source_name: Jax SJL CD4+ Th1 cells H3K27Ac


title: SEM.BAY1251152.8h_Rep3


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 1


title: Jax B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 1

source_name: Jax B6-CD45.2 CD4+ Th1 cells H3K27Ac


title: SEM.BAY1251152.8h_Rep1


title: Jax SJL CD4+ Th1 cells Input Rep 2


title: OCIAML2.DMSO.96h_Rep2

source_name: OCI-AML2 (AML)


title: OCIAML2.DMSO.96h_Rep3


title: Jax B6-CD45.2 CD4+ Th1 cells Input Rep 2


title: Conventional B6-CD45.2 CD4+ Th1 cells Input Rep 2


title: SEM.Brequinar.24h_Rep1


title: OCIAML2.DMSO.96h_Rep1


title: OCIAML2.EPZ5676.96h_Rep3


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 2


title: OCIAML2.DMSO.24h_Rep6


title: CR B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 2

source_name: CR B6.SJL-CD45.1 CD4+ Th1 cells Input

value: Charles River B6.SJL-PtprcaPepcb/BoyCrCrl (CD45.1)

value: Charles River


title: Jax B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 2


title: CR B6-CD45.2 CD4+ Th1 cells Input Rep 2

source_name: CR B6-CD45.2 CD4+ Th1 cells Input

value: Charles River C57BL/6NCrl (CD45.2)


title: OCIAML2.DMSO.24h_Rep4

value: 0.10 percent


title: CR B6-CD45.2 CD4+ Th1 cells Input Rep 1


title: CR B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 1


title: OCIAML2.Brequinar.24h_Rep3

value: MLL-AF


title: Jax SJL CD4+ Th1 cells H3K27Ac Rep 2


title: CR B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 2

source_name: CR B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac


title: OCIAML2.Brequinar.24h_Rep2


title: CR B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 2

source_name: CR B6-CD45.2 CD4+ Th1 cells H3K27Ac


title: OCIAML2.Brequinar.24h_Rep1


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Input Rep 2


title: CR B6.SJL-CD45.1 CD4+ Th1 cells H3K27Ac Rep 1


title: CR B6-CD45.2 CD4+ Th1 cells H3K27Ac Rep 1


title: OCIAML2.DMSO.24h_Rep2


title: OCIAML2.DMSO.24h_Rep1


title: Jax B6-CD45.2 CD4+ Th1 cells (Tac expt) Rep 2

description:
Samples serve as a control for the experiments with Taconic mice.
RawCounts_TacPep_JaxB6_default_stringent.txt

data_processing:
All RNA-seq analyses were performed using the UAB Cheaha HPC system
FastQ files were trimmed to remove primer adapters using Trim Galore! version 0.4.1. The trimmed sequences were then aligned to the mouse reference genome (mm10) from UCSC using RNA STAR version 2.5.4b with either default settings (mismatches allowed): ‘--alignEndsType EndtoEnd’, or stringent settings (no-mismatches): ‘–-outFilterMismatchNmax 0’ ‘--alignEndsType EndtoEnd’. To output a sorted BAM file, ‘--outSAMtype BAM SortedByCoordinate’ was used.
Gene counts were generated using FeatureCounts from the Rsubread Package in R version 3.5.1
Genome_build: mm10
Supplementary_files_format_and_content: txt files with raw counts for samples processed with either default or stringent alignment parameters

source_name: CD4+ T cells

growth_protocol: Primary CD4+ T cells were isolated from lymph nodes and spleen from mice.  The cells were purified by negative selection and then stimulated with plate bound anti-CD3 and anti-CD28 in type I conditions (IL-12 and anti-IL-4). The cells were split on day 3 and maintained in type I conditions and IL-2.

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Clontech)
cDNA libraries were prepared by Genewiz. For the B6-CD45.2, B6.SJL-CD45.1, SJL and Tbx21-/- 150bp experiments, libraries were prepared by rRNA depletion to detect strand specific reads, and then subjected to paired-end sequencing 150bp reads.  For the Tbx21-/- 50bp experiments, the libraries were based on polyA and did not denote strand, and then were subjected to single-end sequencing 50bp reads.


title: OCIAML2.BAY155.24h_Rep3


title: OCIAML2.EPZ5676.96h_Rep2


title: Jax B6-CD45.2 CD4+ Th1 cells (Tac expt) Rep 1


title: OCIAML2.EPZ5676.96h_Rep1


title: Tbx21-/- CD4+ Th1 cells day 3 (50bp) Rep 2

description: RawCounts_Tbx21ko_day3_50bp_default_stringent.txt


title: OCIAML2.BAY155.24h_Rep1


title: Jax B6-CD45.2 CD4+ Th1 cells (Tac expt) Rep 3


title: B6-CD45.2 CD4+ Th1 cells day 3 (50bp) Rep 2


title: OCIAML2.OTX015.8h_Rep3


title: OCIAML2.DMSO.24h_Rep5


title: Tbx21-/- CD4+ Th1 cells day 3 (50bp) Rep 1


title: OCIAML2.OTX015.8h_Rep2


title: Tbx21-/- CD4+ Th1 cells day 3 (150bp) Rep 2

description: RawCounts_Tbx21ko_day3_150bp_default_stringent.txt


title: B6-CD45.2 CD4+ Th1 cells day 3 (50bp) Rep 1


title: OCIAML2.OTX015.8h_Rep1


title: B6-CD45.2 CD4+ Th1 cells day 3 (150bp) Rep 2


title: OCIAML2.BAY1251152.8h_Rep3


title: OCIAML2.DMSO.24h_Rep3


title: SEM.BAY1251152.8h_Rep2

value: SEM


title: RS411.DMSO.96h_Rep3

source_name: RS411 (ALL)


title: OCIAML2.BAY1251152.8h_Rep1


title: RS411.DMSO.96h_Rep2


title: Het B6-CD45.2/CD45.1 CD4+ Th1 cells Rep 1

description: RawCounts_B6CD45Het_default_stringent.txt

value: F1:C57BL/6J x B6.SJL-PtprcaPepcb/BoyJ (CD45.1)

value: The Jackson Laboratory


title: OCIAML2.BAY155.24h_Rep2


title: Tac B6.SJL-CD45.1 CD4+ Th1 cells Rep 3

description: RawCounts_TacPep_JaxB6_default_stringent.txt

value: Taconic B6.SJL-Ptprca/BoyAiTac (CD45.1)

value: Taconic


title: RS411.DMSO.96h_Rep1


title: 83406-06

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

scan_protocol: Straight after a RNA quality measurement and with a known RNA concentration for each sample, 300ng were able to be hybridised to the NanoString nCounter GX Human Immunology v2 panel. After overnight hybridisation the samples were ready to load to the PrepStation where they were washed with a two-step magnetic bead-purification process and loaded in the 12-well cartridges. Afterwards the cartridges were loaded to the Digital Analyzer (DA, nCounter, NanoString Technologies Inc., Seattle, WA, USA). The DA resolution was set to high, meaning that 280 fields of view (FOV) were counted per sample. A comma-separated-value (.csv) file was obtained after processing.

data_processing: Data Quality Control was done using the R-package NanoStringQCPro (Nickles et al, 2015). The gene expression data were normalized by first taking the log2 on the raw data and then subtracting the individual median gene count from each sample. Next, the median of all sample medians was added to each specimen to ensure positive normalized count values for each gene.

source_name: tumor

extract_protocol: Formalin-fixed paraffin-embedded material was cut in five 10μm-thick pieces per sample. Extraction of RNA was done according to the manufacturer’s instructions (ExpressArt FFPE Clear RNAready Kit, AmpTec, Hamburg, Germany). The RNA quality was analyzed with the Agilent RNA 6000 Nano Chips (Agilent Technologies, Santa Clara, California, USA) following the product’s protocol.  Further material quality control is present after RNA processing at the nCounter instrument for digital multiplexed gene expression due to the company’s recommendations.

tag: patient diagnosis

value: Hodgkin lymphoma

tag: tissue

value: tumor

value: primary


title: Tbx21-/- CD4+ Th1 cells day 3 (150bp) Rep 1

tag: strain

value: CD4+ Th1 cells


title: 80023-11

value: relapse


title: Tac B6.SJL-CD45.1 CD4+ Th1 cells Rep 1


title: 81792-02


title: RS411.DMSO.24h_Rep6

tag: cell line


title: 81458-10


title: OCIAML2.BAY1251152.8h_Rep2


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Rep 4

description: RawCounts_CR_B6Pep_default_stringent.txt

value: Jax B6.SJL-PtprcaPepcb/BoyJ (CD45.1)


title: RS411.EPZ5676.96h_Rep1


title: 82529-08-a


title: 80824-07


title: 80436-09


title: 83389-06


title: RS411.DMSO.24h_Rep5

value: DMSO


title: 86558-02


title: 85901-04


title: 83249-07


title: Het B6-CD45.2/CD45.1 CD4+ Th1 cells Rep 2


title: Jax B6-CD45.2 CD4+ Th1 cells Rep 4


title: RS411.DMSO.24h_Rep4


title: CR B6.SJL-CD45.1 CD4+ Th1 cells Rep 3

value: Charles River B6.SJL-PtprcaPepcb/BoyCrCrl (CD45.1)


title: 84940-05


title: RS411.EPZ5676.96h_Rep2


title: RS411.Brequinar.24h_Rep3

value: Brequinar


title: 81250-06


title: 86426-04


title: B6-CD45.2 CD4+ Th1 cells day 3 (150bp) Rep 1


title: CR B6-CD45.2 CD4+ Th1 cells Rep 3

value: Charles River C57BL/6NCrl (CD45.2)

value: Charles River


title: CR B6.SJL-CD45.1 CD4+ Th1 cells Rep 2


title: RS411.Brequinar.24h_Rep2

value: MLL-AF


title: CR B6-CD45.2 CD4+ Th1 cells Rep 2


title: RS411.Brequinar.24h_Rep1


title: 80823-03


title: 82662-09-b


title: RS411.DMSO.24h_Rep3

value: 0.10 percent


title: RS411.DMSO.24h_Rep2


title: 80404-10-b


title: CR B6.SJL-CD45.1 CD4+ Th1 cells Rep 1


title: CR B6-CD45.2 CD4+ Th1 cells Rep 1


title: 80913-06


title: Jax SJL CD4+ Th1 cells Rep 3

description: RawCounts_Jax_B6PepSJL_default_stringent.txt

value: Jax SJL/J (CD45.1)


title: RS411.BAY155.24h_Rep3


title: 83881-02


title: 47142-92


title: 86105-98


title: 85443-14


title: RS411.DMSO.24h_Rep1


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Rep 3

value: The Jackson Laboratory


title: RS411.BAY155.24h_Rep2


title: 84585-07


title: Jax B6-CD45.2 CD4+ Th1 cells Rep 3


title: RS411.BAY155.24h_Rep1


title: 80405-95


title: 85572-99


title: Jax SJL CD4+ Th1 cells Rep 2


title: Tac B6.SJL-CD45.1 CD4+ Th1 cells Rep 2

value: Taconic B6.SJL-Ptprca/BoyAiTac (CD45.1)


title: Liver_prenatal_HF_wk28_rep8

city: Maastricht

first: Sven

last: Rouschop

address: Universiteitssingel 50

department: Pharmacology and Toxicology

institute: Maastricht University

description: HF diet: 45% kcal fat, of which 31% saturated, 36% mono-unsaturated, and 33% polyunsaturated fatty acids; 20% kcal protein; and 35% kcal carbohydrate

hyb_protocol: Labeled RNA was hybridized to Affymetrix Mouse Gene 1.1 ST arrays using an Affymetrix GeneTitan instrumuent according to manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan following the manufacturers' instructions.

data_processing:
Microarrays were analyzed using MADMAX pipeline for statistical analysis of microarray data. Microarrays were normalized with the robust multichip average (RMA) method and probes were annotated. Statistical analysis was performed on normalized signal intensities using a 2-tailed paired intensity-based moderated t-statistics (IBMT).
Series supplementary file contains normalized signal intensities per sample; Limma (log 2 based) fold change, and IBMT raw p-value and q-value for the analyses: HF_wk12 vs LF_wk12; LF_wk28 vs LF_wk12; HF_wk28 vs. HF_wk12, HF_wk28 vs. LF_wk28; and the corresponding gene name and Entrez ID

source_name: Liver, prenatal HF diet, week28

label_protocol: RNA (100 ng) was labelled with Whole Transcript Sense Target Assay according to manufacturer's protocol.

growth_protocol: Mice were housed under standard conditions at 25°C with a 12-12 hour light-dark cycle with ad libitum access to water and feed. Both parent mice received either a HF or LF diet, starting 6 weeks before mating and continuing throughout gestation and lactation. All offspring was weaned onto a HF diet.

extract_protocol: Livers were extracted, snap-frozen and stored at -80°C; Total mRNA was extracted using RNeasy Mini Kit according to manufacturer's protocol.

tag: prenatal diet

value: High fat

value: Male

value: Liver

tag: age

value: 28 weeks


title: RS411.OTX015.8h_Rep3


title: 83921-06

value: Hodgkin lymphoma

value: tumor

value: primary


title: Jax SJL CD4+ Th1 cells Rep 1

value: CD4+ Th1 cells


title: RS411.OTX015.8h_Rep1


title: RS411.BAY1251152.8h_Rep3


title: Liver_prenatal_HF_wk28_rep9


title: Liver_prenatal_LF_wk28_rep8

description: LF diet (standard chow): 9% kcal fat; 33% kcal protein; and 58% kcal carbohydrate

source_name: Liver, prenatal LF diet, week28

value: Low fat


title: Jax B6-CD45.2 CD4+ Th1 cells Rep 2


title: Liver_prenatal_HF_wk28_rep7


title: Liver_prenatal_HF_wk28_rep6


title: Liver_prenatal_LF_wk28_rep7


title: Liver_prenatal_HF_wk28_rep5


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Rep 1

value: Jax B6.SJL-PtprcaPepcb/BoyJ (CD45.1)


title: Liver_prenatal_HF_wk12_rep6

source_name: Liver, prenatal HF diet, week12

value: 12 weeks


title: Liver_prenatal_LF_wk28_rep9


title: Jax B6-CD45.2 CD4+ Th1 cells Rep 1


title: Liver_prenatal_HF_wk12_rep7


title: Jax B6.SJL-CD45.1 CD4+ Th1 cells Rep 2


title: Liver_prenatal_LF_wk12_rep6

source_name: Liver, prenatal LF diet, week12


title: RS411.BAY1251152.8h_Rep1


title: Liver_prenatal_LF_wk12_rep7


title: RS411.BAY1251152.8h_Rep2


title: HL60.DMSO.96h_Rep3

source_name: HL-60 (AML)

value: DMSO

value: MLL-WT


title: Liver_prenatal_LF_wk28_rep6


title: ATAC (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#4

data_processing:
Alignment and identification of open chromatin regions The data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools (Li et al. 2009, Broad Institute (2015)) to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin represented by enrichments of reads, peak calling was performed with MACS2 (Liu 2014). For every replicate, the narrowpeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Differentially accessible regions Regions where the chromatin accessibility changed between different conditions were identified with diffBind (Stark and Brown 2011): with the following options: minOverlap=4, bUseSummarizeOverlaps=T, minMembers=2, bFullLibrarySize=TRUE. 12,166 differentially accessible peaks were identified between WT and KO TCR-TAG; 19,071 differentially accessible peaks were identified between TCR-TAG and TCR-OT1.
Coverage files Individual coverage files per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --blackListFileName mm10.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 -p 1. To create merged coverage files of replicates of the same condition, we used multiBigwigSummary to obtain the sequencing-depth-normalized coverage values for 10 bp bins along the entire genome, i.e. for every condition, we obtained a table with the coverage values in every replicate within the same bin. Subsequently, we chose the mean value for every bin to represent the coverage in the resulting “merged” file (see github.com/friedue/Scott2019 for the actual code that was used).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for each sample

source_name: mouse splenocytes

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition was performed at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

tag: cd8 t cells

value: TCR SV40-I transgenic CD8 T cells

tag: biological context

value: malignant liver lesions


title: Liver_prenatal_HF_wk12_rep5


title: HL60.DMSO.96h_Rep2

value: 0.10 percent


title: ATAC (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#3


title: Liver_prenatal_LF_wk28_rep5


title: Liver_prenatal_HF_wk28_rep4


title: Liver_prenatal_LF_wk12_rep4


title: Liver_prenatal_LF_wk28_rep4


title: HL60.DMSO.96h_Rep1


title: RS411.OTX015.8h_Rep2

value: MLL-AF


title: Liver_prenatal_HF_wk28_rep3

value: High fat


title: ATAC (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#2


title: EOL1.DMSO.96h_Rep3

source_name: EOL-1 (AML)

value: MLL-TD


title: ATAC (CD8+/Thy1.1+/PD1hi/LAG3hi/CD39hi) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#1


title: ATAC (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#3


title: ATAC (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#2


title: EOL1.DMSO.96h_Rep2


title: Liver_prenatal_LF_wk28_rep3

value: Male

value: Liver


title: Liver_prenatal_LF_wk28_rep2

value: 28 weeks


title: EOL1.DMSO.96h_Rep1


title: Liver_prenatal_LF_wk12_rep5


title: ATAC (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#1


title: Liver_prenatal_HF_wk12_rep4


title: OCIAML3.DMSO.96h_Rep2

source_name: OCI-AML3 (AML)

value: NMP mut


title: Liver_prenatal_HF_wk28_rep1


title: Liver_prenatal_HF_wk28_rep2


title: ATAC (CD8/Ly5.1) TCR OT-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#2

value: TCR OT-I transgenic CD8 T cells


title: JS_6_2

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultral University

data_processing:
Clean reads (high quality reads) of 72 transcriptome libraries were filtered from raw reads by removing low-quality reads (the number of base with Qphred <= 20 is more than that of 50% all bases in one read) with ambiguous nucleotides and adaptor sequences, and Tophat2 (Kim et al., 2013) with default parameters was used to map clean reads to the reference genome C. sinensis (Xu et al., 2013). The prediction of novel transcripts was used Cufflinks and Cuffcompare (Trapnell et al., 2010). Gene expression levels were calculated by the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method using the HTSeq (v0.6.1) (Trapnell et al., 2010).
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/). version 2.
Supplementary_files_format_and_content: xls files were generated by Microsoft Excel,FPKM represent the expression of genes.

organism: Citrus sinensis

source_name: Fruit

extract_protocol:
Approximate 2 to 3 g of  powdered material was subjected to each RNA extraction, including 10 mL buffer  extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol  precipitation, 5 mL 75% ethanol cleaning and RNA purification as described  by liu et al.(2006)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Juice sac

tag: development stage

value: 220 DAF


title: ATAC (CD8/Ly5.1) TCR OT-I CD8 T cells isolated D20-21 from malignant liver lesions replicate#1


title: JS_6_3


title: Liver_prenatal_LF_wk12_rep2

value: Low fat


title: Liver_prenatal_LF_wk28_rep1


title: Liver_prenatal_LF_wk12_rep3

value: 12 weeks


title: OCIAML3.DMSO.96h_Rep1

value: DMSO


title: JS_6_1


title: Liver_prenatal_HF_wk12_rep2


title: ATAC (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#3

value: Naive CD8 T cells


title: Liver_prenatal_LF_wk12_rep1


title: Liver_prenatal_HF_wk12_rep1


title: JS_5_3

value: 180 DAF


title: JS_5_1


title: JS_5_2


title: OCIAML3.DMSO.96h_Rep3


title: ML2.DMSO.96h_Rep2

source_name: ML2 (AML)


title: ATAC (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#2

value: TCR SV40-I transgenic CD8 T cells


title: ATAC (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#1


title: JS_4_2

value: 150 DAF


title: JS_4_1


title: JS_4_3


title: ML2.DMSO.96h_Rep1

value: 0.10 percent

value: MLL-AF


title: JS_3_3

value: 120 DAF


title: Liver_prenatal_HF_wk12_rep3

value: High fat

value: Male


title: ATAC (CD8+/Thy1.1+/PD1lo/LAG3lo/CD39lo) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#2

value: malignant liver lesions


title: HL60.EPZ5676.96h_Rep3

value: MLL-WT


title: JS_3_1


title: ATAC (CD8+/Thy1.1+/PD1lo/LAG3lo/CD39lo) TCR SV40-I CD8 T cells isolated D8-9 from malignant liver lesions replicate#3


title: JS_2_3

value: 80 DAF


title: ML2.DMSO.96h_Rep3


title: JS_3_2

value: Juice sac


title: HL60.EPZ5676.96h_Rep1


title: R2G_8_rep2

first: Jun

last: You

address: Xudong 2nd Road

institute: Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences

description: Waterlogging tolerant genotype, waterlogging stress for 8 hours, replicate 2

data_processing:
Illumina Casava1.7 software used for basecalling.
The program FastQC was employed to determine the base quality of the raw reads (in FASTQ format) and we removed the paired-end reads containing more than 5% ambiguous residues (Ns) and those containing >10% bases with a Phred quality score of 10. Then, the raw reads were trimmed using Trimmomatic, version 0.32
The high-quality reads were mapped to the sesame (Sesamum indicum L.) reference genome v1.0 using the STAR software
Genome_build: GCF_000512975.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Sesamum indicum

source_name: root

extract_protocol:
Total RNA was extracted from 126 root samples using the TRIzol reagent (Invitrogen), and treated with DNase I and Oligo (dT) to isolate mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: developmental stage

value: flowering stage

tag: genotype

tag: condition

value: waterlogging stress for 8 hours


title: JS_1_3

value: 50 DAF


title: JS_2_2


title: R2G_8_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 8 hours, replicate 3


title: EOL1.EPZ5676.96h_Rep3

value: MLL-TD


title: HL60.EPZ5676.96h_Rep2


title: JS_1_1


title: JS_1_2


title: R2G_6_rep3

description: Waterlogging tolerant  genotype, waterlogging stress for 6 hours, replicate 3

value: waterlogging stress for 6 hours


title: SM_6_1

value: Segment membrane

value: 220 DAF


title: SM_6_2


title: SM_6_3


title: SM_5_3

value: 180 DAF


title: R2G_6_rep2

description: Waterlogging tolerant  genotype, waterlogging stress for 6 hours, replicate 2


title: OCIAML3.EPZ5676.96h_Rep3

value: NMP mut


title: SM_5_2


title: SM_5_1


title: OCIAML3.EPZ5676.96h_Rep2


title: SM_4_3

value: 150 DAF


title: SM_4_2


title: R2G_48_rep3

description: Waterlogging tolerant genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 3


title: OCIAML3.EPZ5676.96h_Rep1


title: R2G_8_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 8 hours, replicate 1


title: SM_3_3

value: 120 DAF


title: EOL1.EPZ5676.96h_Rep2


title: R2G_48_rep2

description: Waterlogging tolerant genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 2


title: ML2.EPZ5676.96h_Rep3

value: MLL-AF


title: SM_3_2


title: SM_3_1


title: SM_2_2


title: SM_2_3


title: R2G_46_rep3

description: Waterlogging tolerant genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 3


title: ML2.EPZ5676.96h_Rep2


title: SM_2_1


title: SM_1_3


title: HL60.DMSO.24h_Rep3

value: DMSO

value: 0.10 percent


title: SM_1_2


title: R2G_46_rep2

description: Waterlogging tolerant genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 2


title: R2G_46_rep1

description: Waterlogging tolerant genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 1


title: SM_1_1


title: EOL1.EPZ5676.96h_Rep1


title: R2G_6_rep1

description: Waterlogging tolerant  genotype, waterlogging stress for 6 hours, replicate 1


title: AL_6_2

value: Albedo


title: AL_6_3


title: HL60.DMSO.24h_Rep2

value: MLL-WT


title: R2G_44_rep3

description: Waterlogging tolerant genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 3

value: root


title: SM_4_1


title: R2G_48_rep1

description: Waterlogging tolerant genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 1

value: flowering stage


title: AL_6_1


title: AL_5_1


title: AL_4_3


title: HL60.DMSO.24h_Rep1


title: R2G_44_rep1

description: Waterlogging tolerant genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 1


title: AL_5_3


title: HL60.Brequinar.24h_Rep3

value: Brequinar


title: HL60.Brequinar.24h_Rep2


title: R2G_44_rep2

description: Waterlogging tolerant genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 2


title: ML2.EPZ5676.96h_Rep1


title: AL_5_2


title: HL60.Brequinar.24h_Rep1


title: R2G_42_rep3

description: Waterlogging tolerant genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 3


title: AL_4_1


title: AL_4_2


title: R2G_42_rep2

description: Waterlogging tolerant genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 2


title: AL_3_2


title: R2G_42_rep1

description: Waterlogging tolerant genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 1


title: AL_3_1


title: AL_3_3


title: AL_2_3

value: 80 DAF


title: EOL1.DMSO.24h_Rep2

value: MLL-TD


title: EOL1.DMSO.24h_Rep3


title: AL_2_2


title: R2G_40_rep3

description: Waterlogging tolerant genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 3


title: AL_2_1


title: AL_1_3

value: 50 DAF


title: R2G_40_rep2

description: Waterlogging tolerant genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 2


title: EOL1.DMSO.24h_Rep1


title: AL_1_2


title: EOL1.Brequinar.24h_Rep3


title: EOL1.Brequinar.24h_Rep2


title: AL_1_1


title: R2G_40_rep1

description: Waterlogging tolerant genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 1


title: R2G_4_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 4 hours, replicate 2

value: waterlogging stress for 4 hours


title: EP_6_2

value: Epicarp

value: 220 DAF


title: EP_5_3

value: 180 DAF


title: EP_6_1


title: EOL1.Brequinar.24h_Rep1


title: EP_6_3


title: OCIAML3.DMSO.24h_Rep3

value: NMP mut


title: EP_4_2

value: 150 DAF


title: OCIAML3.DMSO.24h_Rep2


title: R2G_38_rep3

description: Waterlogging tolerant genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 3


title: EP_5_2


title: EP_4_1


title: R2G_4_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 4 hours, replicate 1


title: EP_5_1


title: OCIAML3.DMSO.24h_Rep1


title: EP_4_3


title: EP_3_2

value: 120 DAF


title: OCIAML3.Brequinar.24h_Rep3


title: R2G_38_rep2

description: Waterlogging tolerant genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 2


title: EP_3_1


title: EP_3_3


title: R2G_4_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 4 hours, replicate 3


title: R2G_38_rep1

description: Waterlogging tolerant genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 1


title: OCIAML3.Brequinar.24h_Rep2


title: R2G_36_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 36 hours, replicate 3

value: waterlogging stress for 36 hours


title: EP_2_3


title: EP_2_1


title: OCIAML3.Brequinar.24h_Rep1


title: ML2.DMSO.24h_Rep3

value: DMSO

value: 0.10 percent

value: MLL-AF


title: EP_1_1


title: R2G_36_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 36 hours, replicate 2

value: root


title: EP_1_2


title: R2G_36_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 36 hours, replicate 1

value: flowering stage


title: ML2.DMSO.24h_Rep2


title: ML2.DMSO.24h_Rep1


title: R2G_32_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 32 hours, replicate 3

value: waterlogging stress for 32 hours


title: R2G_32_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 32 hours, replicate 2


title: ML2.Brequinar.24h_Rep3

value: Brequinar


title: DLC16013134802

first: xuewen

last: xu

address: Shizishan street, No.1

institute: Huazhong Agricultural University

description:
Complete data.txt.gz
Sample 195

data_processing:
Clean reads were obtained from the released raw reads through the following quality control steps: 1) remove reads containing adaptor; 2) remove reads containing more than 5% N; 3) remove low-quality reads
Alignment of RNA-seq data was conducted using Hisat2 V2.0.5 with the genome assembly Sscrofa11.1 (GCA_000003025) as the reference.
The aligned reads for each sample were then assembled into transcripts with StringTie v1.3.3 .
The generated transcripts from different samples were merged using the “merge” function of StringTie and yielded the final annotation file (the merged.gtf file)
The differential expression analysis was conducted with Ballgown.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample

organism: Sus scrofa

source_name: longissimus dorsi muscle

growth_protocol: The experimental population was composed of 265 F1 animals from the crossing of 8 Duroc boars and 112 Luchuan sows, which were fed with the same diets at the same farm. All animals were slaughtered by a standardized procedure at the age of 210 days ± 6 days at the same abattoir.

extract_protocol:
Total RNA was extracted from longissimus dorsi muscle samples with Trizol reagent according to the product instructions. RNA samples were quantified using NanoDrop-2000 spectrophotometers (Thermo Scientific) and checked for purity and integrity using Agilent 2100 bioanalyzer.
The 150-bp paired-end RNA sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep kit for Illumina® (NEB, USA) according to the manufacturer’s protocols and sequenced on the Illumina Hiseq 4000 platform.

treatment_protocol: Twenty-five minutes postmortem, samples of the longissimus dorsi muscle at the thoracolumbar junction were taken for meat quality trait measurements and RNA extraction.

tag: breed

value: Duroc x Luchuan crossed pigs

value: longissimus dorsi muscle

tag: imf content


title: DLC16021115406

description:
Complete data.txt.gz
Sample 199


title: DLC16020135101

description:
Complete data.txt.gz
Sample 196


title: DLC16020135102

description:
Complete data.txt.gz
Sample 197


title: ML2.Brequinar.24h_Rep2

tag: agent

tag: concentration


title: DLC16020217313

description:
Complete data.txt.gz
Sample 198


title: R2G_32_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 32 hours, replicate 1


title: EP_2_2

value: 80 DAF


title: R2G_28_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 28 hours, replicate 3

value: waterlogging stress for 28 hours


title: DLC16012736306

description:
Complete data.txt.gz
Sample 193


title: DLC16012734903

description:
Complete data.txt.gz
Sample 190


title: DLC16012734904

description:
Complete data.txt.gz
Sample 191


title: EP_1_3

value: Epicarp

value: 50 DAF


title: DLC16012334403

description:
Complete data.txt.gz
Sample 188


title: ML2.Brequinar.24h_Rep1

tag: time point (hours)

tag: mll fusion type


title: HL60.BAY155.24h_Rep3

value: MLL-WT


title: DLC16012334309

description:
Complete data.txt.gz
Sample 186

tag: tissue


title: HL60.BAY155.24h_Rep2


title: DLC16012334404 (re-analyzed)

description:
Complete data.txt.gz
Sample 189


title: R2G_28_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 28 hours, replicate 1


title: DLC16012334306

description:
Complete data.txt.gz
Sample 185


title: R2G_24_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 24 hours, replicate 3

value: waterlogging stress for 24 hours


title: DLC16012334401

description:
Complete data.txt.gz
Sample 187


title: DLC16012036006

description:
Complete data.txt.gz
Sample 184


title: DLC16012734907

description:
Complete data.txt.gz
Sample 192


title: R2G_24_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 24 hours, replicate 2


title: EOL1.BAY155.24h_Rep3

value: MLL-TD


title: R2G_22_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 22 hours, replicate 3

value: waterlogging stress for 22 hours


title: EOL1.BAY155.24h_Rep2


title: DLC16011835807

description:
Complete data.txt.gz
Sample 182


title: DLC16011835803

description:
Complete data.txt.gz
Sample 181


title: DLC16011834006

description:
Complete data.txt.gz
Sample 180


title: DLC16011834004

description:
Complete data.txt.gz
Sample 179


title: DLC16011834003

description:
Complete data.txt.gz
Sample 178


title: EOL1.BAY155.24h_Rep1


title: DLC16011834001

description:
Complete data.txt.gz
Sample 177


title: OCIAML3.BAY155.24h_Rep3

value: NMP mut


title: R2G_28_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 28 hours, replicate 2


title: DLC16011833913

description:
Complete data.txt.gz
Sample 176


title: DLC16011833909

description:
Complete data.txt.gz
Sample 175


title: R2G_22_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 22 hours, replicate 2


title: OCIAML3.BAY155.24h_Rep2


title: DLC16011736409

description:
Complete data.txt.gz
Sample 172


title: R2G_22_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 22 hours, replicate 1


title: R2G_20_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 20 hours, replicate 3

value: waterlogging stress for 20 hours


title: DLC16011833908

description:
Complete data.txt.gz
Sample 174


title: JS_2_1

value: Juice sac


title: DLC16011736411

description:
Complete data.txt.gz
Sample 173


title: OCIAML3.BAY155.24h_Rep1


title: DLC16012036003

description:
Complete data.txt.gz
Sample 183


title: HL60.BAY155.24h_Rep1


title: DLC16011736404

description:
Complete data.txt.gz
Sample 171


title: R2G_24_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 24 hours, replicate 1

value: root


title: DLC16011736403

description:
Complete data.txt.gz
Sample 170


title: R2G_20_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 20 hours, replicate 2

value: flowering stage


title: DLC16011638013

description:
Complete data.txt.gz
Sample 169


title: R2G_20_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 20 hours, replicate 1


title: DLC16011638010

description:
Complete data.txt.gz
Sample 168


title: ML2.BAY155.24h_Rep2

value: MLL-AF


title: R2G_2_rep3

description: Waterlogging tolerant  genotype, waterlogging stress for 2 hours, replicate 3

value: waterlogging stress for 2 hours


title: DLC16011638007

description:
Complete data.txt.gz
Sample 167

value: Duroc x Luchuan crossed pigs


title: ML2.BAY155.24h_Rep1


title: DLC16011528913

description:
Complete data.txt.gz
Sample 165

value: longissimus dorsi muscle


title: DLC16011527706

description:
Complete data.txt.gz
Sample 163


title: HL60.OTX015.8h_Rep3


title: R2G_2_rep2

description: Waterlogging tolerant  genotype, waterlogging stress for 2 hours, replicate 2


title: R2G_2_rep1

description: Waterlogging tolerant  genotype, waterlogging stress for 2 hours, replicate 1


title: DLC16011527703

description:
Complete data.txt.gz
Sample 161


title: HL60.OTX015.8h_Rep2


title: R2G_18_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 18 hours, replicate 3

value: waterlogging stress for 18 hours


title: DLC16011328603

description:
Complete data.txt.gz
Sample 158


title: HL60.OTX015.8h_Rep1


title: DLC16011328306

description:
Complete data.txt.gz
Sample 157


title: DLC16011428801 (re-analyzed)

description:
Complete data.txt.gz
Sample 160


title: R2G_18_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 18 hours, replicate 2


title: HL60.BAY1251152.8h_Rep3


title: ML2.BAY155.24h_Rep3


title: DLC16011328301

description:
Complete data.txt.gz
Sample 154


title: DLC16011328302 (re-analyzed)

description:
Complete data.txt.gz
Sample 155


title: DLC16011328305

description:
Complete data.txt.gz
Sample 156


title: DLC16011327806

description:
Complete data.txt.gz
Sample 153


title: HL60.BAY1251152.8h_Rep2


title: DLC16011327804

description:
Complete data.txt.gz
Sample 152


title: HL60.BAY1251152.8h_Rep1


title: DLC16011638002

description:
Complete data.txt.gz
Sample 166


title: R2G_16_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 16 hours, replicate 3

value: waterlogging stress for 16 hours