title: 251486840587_1_4

description: DENV4, Day 1,  replicate 1

source_name: DENV4, Day 1,  replicate 1


title: SW948 Cell line Input ChIP-seq

status: Public on May 22 2021

type: SRA

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

country: USA

institute: Broad Institute of MIT and Harvard

description:
COAD-C015_G
Input DNA

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9.
Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background.
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: *_bed: Bed peak files

molecule: genomic DNA

organism: Homo sapiens

source_name: ATCC

growth_protocol: Cells were cultured in DMEM, 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin at 37c, 5% CO2.

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 300-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-50.

treatment_protocol: Cells did not undergo any treatment.

tag: cell line

tag: tissue

value: Colon

tag: chip-antibody


title: 251486840580_1_3

type: RNA

city: Riverside

first: Juliet

last: Morrison

state: CA

address: 900 University Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

description: DENV4, Day 1,  replicate 2

hyb_protocol: Probe labeling and microarray slide hybridization for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting and raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1).

data_processing: Extracted raw data was partitioned into liver and spleen samples and separately background corrected using the “norm-exp” method with an offset of 1 and quantile normalized using the limma package in the R environment

molecule: total RNA

organism: Mus musculus

source_name: DENV4, Day 1,  replicate 2

extract_protocol: RNA was extracted from tissues homogenized in Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Mice were infected with 1×106 plaque-forming units (pfu) of DENV1, 2, 3 or 4 strain by i.p. injection in 100μL of PBS. Drug-treated animals were given 0.6mg per mouse per day of ketotifen (Sigma) or an equivalent volume of saline by i.p. injection. The first dose was administered 1h after infection, with daily drug injections thereafter at 24h intervals.

value: Spleen


title: SW948 Cell line H3K27ac ChIP-seq

description:
COAD-C015_C
ChIP-DNA

value: H3K27ac (Abcam ab4729)


title: 251486840569_1_2

description: DENV4, Day 3,  replicate 1

source_name: DENV4, Day 3,  replicate 1

label_protocol: Probe labeling and microarray slide hybridization for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions


title: DLD1 Cell line Input ChIP-seq

description:
COAD-C013_G
Input DNA


title: 251486840568_1_2

description: DENV4, Day 3,  replicate 2

source_name: DENV4, Day 3,  replicate 2


title: S19: 45D_WT_N

city: Bethesda

first: Edward

last: Giniger

state: MD

address: Bldg 35,Rm 1C-1002; 35 Convent Dr

department: NINDS

institute: NIH

hyb_protocol: Labeled cRNA were hybridized to the DroGene 1.0 ST GeneChip (Affymetrix, Santa Clara, CA) according to the manufacturer‚Äôs guidelines.

scan_protocol: The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 16,322 RMA normalized probe expression values.

label: biotin

organism: Drosophila melanogaster

source_name: head

label_protocol: Extracted RNA were processed and labeled according to the manufacturer‚Äôs guidelines for use with the DroGene 1.0 ST GeneChip (Affymetrix, GeneChip Whole Transcript Sense Target Labeling).

growth_protocol: 25 male flies were aliquoted into a vial containing standard Nutri-Fly food (N) or Nutri Fly food with antibiotic (A); five sets of 10 vials were collected for each genotype and time point (each replicate consisted of 50 male flies).  Flies were maintained at 25C, 50% humidity with a 12 hr/12 hr light/dark cycle, and were transferred to fresh vials every three days.  Once at the appropriate age, flies were anesthetized under CO2, then flash frozen in liquid nitrogen; samples were stored at -80C until all time points were collected.

extract_protocol: Isolated tissue samples were stored at -80C prior to phenol-chloroform extraction using the TRIzol reagent.  Samples were homogenized in TRIzol, chloroform was added, and the resultant mixture centrifuged; RNA was precipitated from the upper aqueous layer using isopropanol.  Following ethanol washes, the purified RNA was resuspended in RNAse-free water and stored at -80C.

treatment_protocol: Axenic wild type fly line was generated by washing eggs with 70% ethanol, bleaching, rinsing with sterile water, and the transferring the sterilized eggs to sterile food supplemented with propionic acid (0.48%) + Pen/Strep (1:100 dilution). Axenic line was maintained as bacteria free on this food for > 3 generations before collection of flies for aging and RNA isolation.

value: head

tag: age

value: 45 day old adult

tag: Sex

value: male

tag: treatment

value: conventional growth conditions


title: DLD1 Cell line H3K27ac ChIP-seq

description:
COAD-C013_C
ChIP-DNA


title: HCT15 Cell line H3K27ac ChIP-seq

description:
COAD-C021_C
ChIP-DNA


title: S21: 10D_WT_A

value: 10 day old adult

value: bacteria-free


title: S20: 45D_WT_N


title: SW403 Cell line Input ChIP-seq

description:
COAD-C012_G
Input DNA


title: 251486840586_1_1

description: DENV4, Day 3,  replicate 3

source_name: DENV4, Day 3,  replicate 3


title: S18: 45D_WT_N


title: SW403 Cell line H3K27ac ChIP-seq

description:
COAD-C012_C
ChIP-DNA


title: S22: 10D_WT_A


title: 251486840579_1_1

description: DENV4, Day 1,  replicate 3

source_name: DENV4, Day 1,  replicate 3


title: HCT116 Cell line Input ChIP-seq

description:
COAD-C004_G
Input DNA


title: HCT116 Cell line H3K27ac ChIP-seq

description:
COAD-C004_C
ChIP-DNA


title: SW837 Cell line Input ChIP-seq

description:
COAD-C003_G
Input DNA


title: SW480 Cell line H3K27ac ChIP-seq

description:
COAD-C002_C
ChIP-DNA


title: SW480 Cell line Input ChIP-seq

description:
COAD-C002_G
Input DNA


title: SW837 Cell line H3K27ac ChIP-seq

description:
COAD-C003_C
ChIP-DNA


title: S15: 30D_WT_N

value: 30 day old adult


title: COAD-N012 RNA-seq

description:
RNA-access
processed data file: DEGs_CRCT-Normal_All.txt

library_source: transcriptomic

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *ReadsPerGene.out.tab: Tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2.

source_name: Adjacent Normal

extract_protocol:
Total RNA was isolated from human tumor and normal colon samples using RNeasy Mini Kit. RNA samples were measured for quality and concentration using Agilent 4200 TapeStation. Libraries were constructed using TruSeq RNA Access Library Prep Kit according to Illumina's protocol. Libraries were sequenced using Illumina HiSeq 2000 sequencer.
mRNA libraries were prepared from 200 ng of total RNA using the TruSeq Stranded mRNA HT sample preparation kit. Samples were dual-indexed prior to pooling. Libraries were quantified by qPCR using the NGS Library Quantification Kit. Pooled libraries were sequenced using the HiSeq2000 (Illumina) according to the manufacturer’s instructions. A minimum of approximately 80 million paired-end reads per sample were obtained.

treatment_protocol: All tissue samples were obtained from Division of Gastrointestinal Medical Oncology patients’ databank at MD Anderson Cancer Center as frozen samples.

value: Adjacent normal colon

tag: patient


title: COAD-N016 RNA-seq


title: S16: 45D_WT_N


title: 251486840570_1_1

description: Mock, Day 1,  replicate 2

source_name: Mock, Day 1,  replicate 2


title: S14: 30D_WT_N


title: S13: 30D_WT_N


title: 251486840584_1_3

description: Mock, Day 1,  replicate 1

source_name: Mock, Day 1,  replicate 1


title: COAD-N004 RNA-seq


title: S12: 30D_WT_N


title: 251486840574_1_1

description: Mock, Day 3,  replicate 1

source_name: Mock, Day 3,  replicate 1


title: COAD-T017 RNA-seq

source_name: Tumor

value: Colorectal tumor


title: 251486840585_1_1

description: Mock, Day 1,  replicate 3

source_name: Mock, Day 1,  replicate 3


title: S11: 30D_WT_N


title: COAD-T016 RNA-seq


title: COAD-T015 RNA-seq


title: S10: 10D_WT_N


title: COAD-N017 RNA-seq


title: COAD-T014 RNA-seq


title: COAD-T012 RNA-seq


title: 251486840577_1_1

description: DENV2, Day 1,  replicate 1

source_name: DENV2, Day 1,  replicate 1


title: COAD-N014 RNA-seq


title: 251486840580_1_4

description: Mock, Day 3,  replicate 2

source_name: Mock, Day 3,  replicate 2


title: S9: 10D_WT_N


title: COAD-T004 RNA-seq


title: 251486840567_1_3

description: Mock, Day 3,  replicate 3

source_name: Mock, Day 3,  replicate 3


title: S8: 10D_WT_N


title: COAD-T001 RNA-seq


title: S7: 10D_WT_N


title: 251486840585_1_3

description: DENV1, Day 1,  replicate 2

source_name: DENV1, Day 1,  replicate 2

value: Liver


title: S6: 10D_WT_N


title: Flow + 1

city: New Haven

first: Juan

last: Wang

state: CT

address: 10 Amistad Street

institute: Yale University

description:
HyperplasiaRNASeqFeatureCount.txt
controlvlowflow_padj0.05.txt
37DnS-LF_330_247

data_processing:
FASTQ reads were trimmed of overrepresented poly(A) sequences with Trimmomatic after FASTQC analysis and paired reads with a trimmed reads less than 30 bp long were discard
Alignment and feature couting was performed with Rsubread (Bioconductor), genes with no counts across all conditions were filtered out
Variance stabilizing transform and differential expression analysis was performed by DESeq2
Genome_build: Sscrofa11.1 release 99
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: coronary artery

extract_protocol:
Vessels were harvested, flash frozen in liquid nitrogen, and RNA extracted with the RNeasy Mini kit with on-column DNase treatment (Qiagen)
Libraries were prepared by the Yale Center for Genomics Analysis using the Pair End Sequencing Prep Kit

value: coronary artery


title: Flow + 2

description:
HyperplasiaRNASeqFeatureCount.txt
controlvlowflow_padj0.05.txt
38DnS-LF_367_210


title: Flow ++ 2

description:
HyperplasiaRNASeqFeatureCount.txt
controlvhiflow_padj0.05.txt
DnS-24_333_244


title: IL2 IL4 TCR CD8 rep3_run4

city: Denver

first: Brian

middle: Patrick

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 5.0.3.
Sequence reads of at least 30 nt length were mapped to the mm9 release of the mouse genome using STAR (version 2.5.1b) with splice site data from the mouse Ensembl annotation version 67.
Reads mapping unambiguously to each gene in the mouse Ensembl 67 annotation were quantified using the featureCounts program from the subread package (version 1.5.0-p1).
Statistical comparisons were performed using the DESeq2 package (version 1.8.1) under R version 3.2.0.
Genome_build: mm9
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text table (output from featureCounts, as well as aggregated over multiple sequencing runs)

molecule: polyA RNA

source_name: Spleen

growth_protocol: Mononuclear cells (MNCs) were isolated from the spleens of OT-1 mice followed by stimulation with 1 µg/ml SIINFEKL peptide for 1.5 hours. Two days later, living cells were isolated using Histopaque (Sigma-Aldrich, St. Louis, MO) and cultured in complete RPMI 1640 medium that contained recombinant mouse IL-2 (20 ng/ml, R&D, Minneapolis, MN) or appropriate cytokines.

extract_protocol:
Total RNA was extracted using the the NucleoSpin II RNA isolation kit (#740955, Macherey-Nagel, Dueren, Germany) following the manufacturer's protocol
Libraries were made from 200 ng input RNA using the RNA Library Preparation Kit (Kapa Biosystems #KK8420) and modified primers. Libraries were analyzed for size and quality using the High Sensitivity Bioanalyzer Kit (Agilent #5067-4626) and sequenced with on Life Technologies Ion Proton at the NJH Genomics Facility.

treatment_protocol: Cells were treated wtih IL-2 or IL-2+IL-4 (20 ng/ml, Peprotech, Rocky Hill, NJ). Medium with cytokines was changed every day on 4 consecutive days. Cells were then re-stimulated with 1 µg/ml SIINFEKL in medium containing 2 µM monensin (Calbiochem, La Jolla, CA) for 4 hours.

tag: cell type

value: CD8+T cells

tag: strain


title: S4: 3D_WT_N

value: 3 day old adult


title: S3: 3D_WT_N


title: S2: 3D_WT_N


title: Flow ++ 1

description:
HyperplasiaRNASeqFeatureCount.txt
controlvhiflow_padj0.05.txt
DnS-23-1_345_232


title: MLL-AF9 cells 1 µM Riok2i treated replicate 3

city: Copenhagen N

first: Jan-Erik

last: Messling

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Trimming (Trimmomatic (version 0.38.0)).
Alignment (RNA-Star (version 2.7.2b))
read counting (htseq-count (version 0.9.1))
differential expression analysis (DeSeq 2 (version 2.11.40.6))
Genome_build: mouse mm10
Supplementary_files_format_and_content: Deseq2 read count tables

source_name: acute myeloid leukemia cells

extract_protocol:
cells were pelleted and RNA was prepped using the RNeasy Mini Kit (Qiagen, Cat Nr.: 74106)
RNA libraries were made using the TruSeq RNA library prep kit (Illumina, Cat Nr.:RS-122-2001).

value: MLL-AF9 acute myeloid leukemia

tag: condition


title: IL2 IL4 TCR CD8 rep3_run3


title: MLL-AF9 cells 1 µM Riok2i treated replicate 2


title: IL2 IL4 TCR CD8 rep3_run2


title: 251486840573_1_1

description: DENV1, Day 1,  replicate 1

source_name: DENV1, Day 1,  replicate 1


title: Stent/Flow ++ 3

description:
ApRNASeqFeatureCount.txt
controlvdynamic_padj0.05.txt
32DS-7d_085_108


title: 251486840578_1_2

description: DENV1, Day 3,  replicate 1

source_name: DENV1, Day 3,  replicate 1


title: S1: 3D_WT_N

source_name: head


title: 251486840574_1_2

description: DENV1, Day 3,  replicate 3

source_name: DENV1, Day 3,  replicate 3


title: 251486840568_1_3

description: DENV1, Day 1,  replicate 3

source_name: DENV1, Day 1,  replicate 3


title: S5: 3D_WT_N


title: 251486840586_1_4

description: DENV2, Day 3,  replicate 2

source_name: DENV2, Day 3,  replicate 2


title: 251486840580_1_1

description: DENV2, Day 1,  replicate 4

source_name: DENV2, Day 1,  replicate 4


title: 251486840569_1_1

description: DENV2, Day 3,  replicate 3

source_name: DENV2, Day 3,  replicate 3


title: 251486840584_1_1

description: DENV2, Day 1,  replicate 1


title: 251486840584_1_2

description: DENV2&ketotifen, Day 1,  replicate 3

source_name: DENV2&ketotifen, Day 1,  replicate 3


title: 251486840572_1_1

description: DENV2, Day 1,  replicate 5

source_name: DENV2, Day 1,  replicate 5


title: 251486840570_1_2

description: DENV2, Day 3,  replicate 1

source_name: DENV2, Day 3,  replicate 1


title: MLL-AF9 cells 1 µM Riok2i treated replicate 1


title: IL2 IL4 TCR CD8 rep3_run1


title: MLL-AF9 cells DMSO treated replicate 3

value: DMSO


title: Stent/Flow ++ 2

description:
ApRNASeqFeatureCount.txt
controlvdynamic_padj0.05.txt
DS-28_381_196


title: Stent/Flow ++ 1

description:
ApRNASeqFeatureCount.txt
controlvdynamic_padj0.05.txt
DS-25_298_279


title: Stent/Flow - 2

description:
ApRNASeqFeatureCount.txt
controlvstatic_padj0.05.txt
36SS-3d_313_264


title: IL2 IL4 TCR CD8 rep1_run1


title: IL2 IL4 TCR CD8 rep2_run1


title: MLL-AF9 cells DMSO treated replicate 2


title: Stent/Flow - 1

description:
ApRNASeqFeatureCount.txt
controlvstatic_padj0.05.txt
34SS-3d-1_073_120


title: Riok2fl/fl MLL-AF9 cells OHT treated replicate 3

value: Riok2fl/fl with OHT


title: IL2 IL4 CD8 rep3_run3


title: IL2 IL4 CD8 rep3_run4


title: Native control 2

description:
ApRNASeqFeatureCount.txt
controlvdynamic_padj0.05.txt
controlvstatic_padj0.05.txt
controlvhiflow_padj0.05.txt
controlvlowflow_padj0.05.txt
HyperplasiaRNASeqFeatureCount.txt
CTL-25_310_267


title: 251486840579_1_3

description: DENV2&ketotifen, Day 1,  replicate 5

source_name: DENV2&ketotifen, Day 1,  replicate 5


title: Riok2fl/fl MLL-AF9 cells OHT treated replicate 2


title: 251486840574_1_3

description: DENV2&ketotifen, Day 1,  replicate 4

source_name: DENV2&ketotifen, Day 1,  replicate 4


title: 251486840570_1_3

description: DENV2&ketotifen, Day 3,  replicate 2

source_name: DENV2&ketotifen, Day 3,  replicate 2


title: IL2 IL4 CD8 rep3_run2


title: 251486840573_1_2

description: DENV1, Day 3,  replicate 2

source_name: DENV1, Day 3,  replicate 2


title: MLL-AF9 cells DMSO treated replicate 1


title: IL2 IL4 CD8 rep3_run1

source_name: Spleen


title: Riok2fl/fl MLL-AF9 cells OHT treated replicate 1

source_name: acute myeloid leukemia cells


title: 251486840572_1_2

description: DENV2&ketotifen, Day 3,  replicate 1

source_name: DENV2&ketotifen, Day 3,  replicate 1


title: SI_23843

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Base calling, read alignment and quantification were conducted with Cell Ranger (2.1.1) and pre-built reference genome (GRCh38-1.2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: h5

source_name: Kidney

extract_protocol:
Partial nephroctomy samples were dissociated using collagense based enzyme cocktail to obtain single cell suspension.
Single cell RNA libraries were prepared for sequencing using standard 10X genomics and Illumina protocols

tag: individual

value: Patient SS_2026

value: Tumor

tag: tumor subtype

value: Clear Cell RCC

value: Male


title: IL2 IL4 CD8 rep2_run1


title: Riok2fl/fl MLL-AF9 cells EtOH treated replicate 2

value: Riok2fl/fl with ETOH


title: IL2 IL4 CD8 rep1_run1


title: SI_22604

value: Patient SS_2022

value: Benign Adjacent


title: IL2 TCR CD8 rep3_run3


title: SI_22605


title: Riok2fl/fl MLL-AF9 cells EtOH treated replicate 1


title: 251486840581_1_3

description: DENV2&ketotifen, Day 3,  replicate 3

source_name: DENV2&ketotifen, Day 3,  replicate 3


title: 251486840585_1_4

description: DENV3, Day 1,  replicate 2

source_name: DENV3, Day 1,  replicate 2


title: SI_23459

value: Patient SS_2023


title: Riok2fl/fl MLL-AF9 cells EtOH treated replicate 3


title: 251486840577_1_4

description: DENV3, Day 1,  replicate 3

source_name: DENV3, Day 1,  replicate 3


title: 251486840585_1_2

description: DENV3, Day 1,  replicate 1

source_name: DENV3, Day 1,  replicate 1


title: 251486840571_1_3

description: DENV3, Day 3,  replicate 1

source_name: DENV3, Day 3,  replicate 1


title: CD8_IGG_PD1

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools
Peaks were called using SEACR (version1.1) (Meers et al., 2019) with options: 0.01 non stringent.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

source_name: GP33-41 tetramer+ or GP276-286 tetramer+ CD8 T cells

extract_protocol: 50000 to 100000 cells each CD8 subset were used for library construction using CUT&Tag ChIP-Seq approach (version 2) (Kaya-Okur, Wu et al. 2019) (step wise protocol can be found in https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).

treatment_protocol: Three LCMV-specific (GP33-41 tetramer+ or GP276-286 tetramer+) CD8 subsets were sort-purified from spleen and lymph nodes of C57BL/6 mice 3-5 weeks’ post LCMV-Cl13 infection.

tag: infection

value: 3-5 weeks post LCMV-Cl13 infection

value: spleen and lymph nodes

tag: antibody

value: IGG

tag: sample type


title: IL2 TCR CD8 rep3_run2


title: SI_22368

value: Patient SS_2017


title: SI_21561

value: Patient SS_2016

value: Chromophobe RCC

value: Female


title: SI_22369


title: 251486840583_1_2

description: DENV3, Day 3,  replicate 4

source_name: DENV3, Day 3,  replicate 4

value: Liver


title: IL2 TCR CD8 rep2_run1

value: CD8+T cells


title: IL2 TCR CD8 rep3_run1


title: H3K4me3_PD1_2


title: CD8_IGG_CX3CR1


title: IL2 TCR CD8 rep1_run1


title: 251486840583_1_4

description: DENV4, Day 1,  replicate 1

source_name: DENV4, Day 1,  replicate 1


title: 251486840583_1_3

description: DENV4, Day 1,  replicate 2

source_name: DENV4, Day 1,  replicate 2


title: 251486840578_1_1

description: DENV4, Day 1,  replicate 3

source_name: DENV4, Day 1,  replicate 3


title: H3K4me3_PD1_1


title: 251486840567_1_1

description: DENV3, Day 3,  replicate 2

source_name: DENV3, Day 3,  replicate 2


title: SI_21255

value: Patient SS_2014

value: Benign Adjacent Cortex


title: IL2 CD8 rep3_run4


title: SI_19703

value: Patient SS_2007


title: IL2 CD8 rep3_run3


title: SI_19704

value: Tumor

value: Clear Cell RCC

value: Male


title: H3K4me3_LY108_1


title: 251486840568_1_1

description: DENV4, Day 3,  replicate 1

source_name: DENV4, Day 3,  replicate 1


title: H3K4me3_CX3CR1_2


title: IL2 CD8 rep3_run2


title: CD8_IGG_LY108


title: SI_18855

value: Patient SS_2006

value: Benign Adjacent


title: H3K4me3_CX3CR1_1

value: 3-5 weeks post LCMV-Cl13 infection


title: H3K27me3_PD1_2

value: spleen and lymph nodes


title: IL2 CD8 rep3_run1


title: IL2 CD8 rep2_run1


title: SI_21256

value: Benign Adjacent Medulla


title: 251486840571_1_2

description: DENV4, Day 3,  replicate 2

source_name: DENV4, Day 3,  replicate 2


title: SI_18856


title: IL2 CD8 rep1_run1

source_name: Spleen


title: SI_18854

value: Patient SS_2005


title: H3K4me3_LY108_2


title: 251486840577_1_3

description: Mock, Day 1,  replicate 2

source_name: Mock, Day 1,  replicate 2


title: H3K27me3_PD1_1


title: 251486840580_1_2

description: Mock, Day 1,  replicate 3

source_name: Mock, Day 1,  replicate 3


title: 251486840581_1_2

description: Mock, Day 1,  replicate 1

source_name: Mock, Day 1,  replicate 1


title: H3K27me3_LY108_2


title: H3K27me3_LY108_1


title: ZYFR14

city: Kifeng

first: Yifan

last: Zhu

state: Henan

address: Xi Men Da Jie 115

country: China

institute: Henan University Huaihe Hospital

description: P group

data_processing:
Pre-processing of sequencing reads was performed by FastQC v. 0.10.1 for cleaning low quality sequences and by Cutadapt to trim adaptor sequences
Then processed clean reads with more than 17 nucleotides in length were aligned against human Genome (hg19) and miRBase 20 using Bowtie v. 0.12.7
Subsequently, identification and quantification of known and predicted potential miRNAs were finished by miRDeep v. 2.0.0.5
The significance of differential expression of miRNAs was determined with edgeR between healthy volunteers (H group) and PDAC patients (P group)
The results were expressed as mean ± SD. Differences between the groups were evaluated by analysis of variance, and post hoc analysis by the Tukey–Kramer test. A p Value less than 0.05 was considered statistically significant.
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix, each column includes the expression value of each sample for miRNAs

source_name: plasma

extract_protocol:
Total RNA was extracted using Norgen Plasma/Serum Circulating RNA Purification Mini Kit 51000 following the manufacturer's procedure
The total RNA quantity and purity were analyzed by Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 0.2-0.7 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).

tag: diagnosis

value: PDAC

tag: sequencing protocol

value: small RNA-Seq

tag: Stage

value: stage IV


title: ZYFR15

description: P group

value: stage III


title: H3K27me3_CX3CR1_2

tag: tissue


title: IL2 IL4 TCR Input CD8 rep2

description: IL2/IL4/TCR Input ChIP-Seq rep2

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 4.0.2.
Sequence reads were mapped to the mm9 release of the mouse genome using tmap VN:4.4.6 from  Ion Torrent Suite 4.0.2.
Peaks were called using MACS version 2.1.1.20160309 for each IP and its corresponding Input sample, using the parameters   '-f BAM -g mm -q 0.001 -B --SPMR'.
Peaks were annotated to transcripts defined by Ensembl ensGene Build 67 based on proximity of peak to gene body or TSS using intersectBed from the bedtools v2.17.0-123-gb0155b2 software suite.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak files of H3Ac vs Input as output by MACS version 2.1.1.20160309 with the following 10 columns: chromosome name, start position of peak, end position of peak, name of peak, integer score for display, empty column, fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start. Note, the score in the 5th column is  equal to the integer part of 9th column (-log10qvalue) multiplied by 10 and may sometimes exceed 1000.

extract_protocol:
Chromatin was sheared using the isothermal Covaris S2 to produce approximately 100-300bp fragments for Ion Proton ChIP-seq. DNA-protein complexes were immunoprecipitated with an Pan-acetyl H3 (AcH3) antibody (Active Motif #39139), captured by magnetic beads, cross-links reversed, and the genomic DNA purified (Invitrogen Magnify ChIP Kit #49-2024).
Libraries were made according to the instructions using the Ion Xpress Plus Fragment Library Kit (# 4471252).  Libraries were analyzed for size and quality using the High Sensitivity Bioanalyzer Kit (Agilent #5067-4626) and sequenced with on Life Technologies Ion Proton at the NJH Genomics Facility.

value: Spleen

value: CD8+T cells

tag: chip antibody

value: none (input)


title: IL2 IL4 TCR H3ac CD8 rep2

description: IL2/IL4/TCR H3ac ChIP-Seq rep2

value: Anti-Pan Acetylation H3 antibody (Active Motif #39139)


title: IL2 IL4 TCR Input CD8 rep3

description: IL2/IL4/TCR Input ChIP-Seq rep3


title: IL2 IL4 TCR H3ac CD8 rep3

description: IL2/IL4/TCR H3ac ChIP-Seq rep3


title: ZYFR13

description: P group


title: ZYFR12

description: P group


title: H3K27me3_CX3CR1_1


title: ZYFR11

description: P group


title: IL2 IL4 TCR Input CD8 rep1

description: IL2/IL4/TCR Input ChIP-Seq rep1


title: H3K27ac_PD1_2


title: IL2 IL4 TCR H3ac CD8 rep1

description: IL2/IL4/TCR H3ac ChIP-Seq rep1


title: ZYFR10

description: C group

value: chronic pancreatitis

value: NOT applicable


title: 251486840570_1_4

description: Mock, Day 3,  replicate 3

source_name: Mock, Day 3,  replicate 3

value: Liver


title: IL2 TCR Input CD8 rep3

description: IL2/TCR Input ChIP-Seq rep3


title: H3K27ac_PD1_1


title: ZYFR9

description: C group


title: 251486840571_1_1

description: Mock, Day 3,  replicate 1

source_name: Mock, Day 3,  replicate 1


title: 251486840578_1_4

description: DENV4, Day 3,  replicate 3

source_name: DENV4, Day 3,  replicate 3


title: H3K27ac_LY108_2


title: IL2 TCR H3ac CD8 rep3

description: IL2/TCR H3ac ChIP-Seq rep3


title: ZYFR8

description: C group


title: IL2 TCR Input CD8 rep2

description: IL2/TCR Input ChIP-Seq rep2


title: ZYFR7

description: C group


title: ATAC7

city: Tokyo

first: Sanshiro

last: Kanazawa

address: 7-3-1, Hongo, Bunkyo-ku

department: Oral and Maxillofacial Surgery

country: Japan

institute: The University of Tokyo Hospital

data_processing:
The ATAC-seq libraries were sequenced on Illumina Hiseq X sequencer.
The sequence reads were aligned to the mouse genome reference sequence mm9 by bowtie aligner
Peak calling was performed by two-sample analysis on CisGenome software50 with a P-value cutoff of 10-5 comparing with the input control. Peaks were incorporated into further analysis displaying an FDR<0.01. Correlation heat map and PCA plot were generated by DiffBind software in R with default setting. Peak intersection was performed by BEDTools-Version-2.16.2.
Genome_build: mm9

source_name: bone marrow stromal cells

extract_protocol:
Bone marrow were removed, crush with a scissors and a pestle, and RNA was harvested using Trireagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow derived stromal cells

tag: genotype

value: wild type

value: bone marrow

tag: age

value: post natal 6 weeks


title: H3K27ac_CX3CR1_2

source_name: GP33-41 tetramer+ or GP276-286 tetramer+ CD8 T cells

value: 3-5 weeks post LCMV-Cl13 infection

value: spleen and lymph nodes


title: 251486840581_1_1

description: Mock, Day 3,  replicate 2

source_name: Mock, Day 3,  replicate 2


title: Input


title: ZYFR5

description: H group

value: healthy volunteer


title: H3K27ac_LY108_1


title: H3K27ac_CX3CR1_1


title: ZYFR6

description: C group

value: small RNA-Seq


title: IL2 TCR Input CD8 rep1

description: IL2/TCR Input ChIP-Seq rep1

tag: treatment


title: IL2 TCR H3ac CD8 rep2

description: IL2/TCR H3ac ChIP-Seq rep2


title: ATAC_LY108_2

data_processing:
Peaks were called using MACS2 (--no model --shift -100 --ext size 200 -q 0.01) (version 2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

source_name: polyclonal LCMV-specific CD8+ T cells (GFP+)

extract_protocol:
Libraries were prepared using 50,000 cells as described in published protocol (Buenrostro et al., 2015).
Libraries were prepared using 50,000 cells as described in published protocol (Buenrostro et al., 2015).

treatment_protocol: GzmB-cre+; RosamT/mG mice were used for ATAC-seq experiments. In these mice, activated CD8+ T cells express high levels of GzmB which initiates Cre recombinase expression. As a result, these GzmBhigh cells will turn from Tomato positive to GFP positive. Thus, GFP+ CD8+ T cells represent polyclonal LCMV-specific CD8+ T cells. 3-5 weeks’ post LCMV-Cl13 infection, three subsets of LCMV-specific CD8+ T cells from spleen and lymph nodes were FACS sorted using surface markers, Ly108 and CX3CR1.

value: GzmB-cre+; RosamT/mG mice

value: 3-5 weeks’ post LCMV-Cl13 infection


title: ATAC3


title: IL2 IL4 Input CD8 rep3

description: IL2/IL4 Input ChIP-Seq rep3

value: Spleen


title: ATAC6


title: ZYFR3

description: H group


title: ATAC5


title: IL2 TCR H3ac CD8 rep1

description: IL2/TCR H3ac ChIP-Seq rep1

value: CD8+T cells


title: ATAC_CX3CR1_LY108_DN_2


title: IL2 IL4 H3ac CD8 rep3

description: IL2/IL4 H3ac ChIP-Seq rep3


title: ZYFR2

description: H group


title: ATAC1


title: ATAC_LY108_1


title: ZYFR4

description: H group


title: ATAC4


title: ATAC2


title: IL2 IL4 Input CD8 rep2

description: IL2/IL4 Input ChIP-Seq rep2

value: none (input)


title: ZYFR1

description: H group


title: IL2 IL4 H3ac CD8 rep2

description: IL2/IL4 H3ac ChIP-Seq rep2

value: Anti-Pan Acetylation H3 antibody (Active Motif #39139)


title: LN_10_DE_2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 using RSEM aligner (v1.2.31) with default parameter (both paired-end and single read).
Gene level report were used for downstream analysis.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: RSEM gene level report  in tabular format, with column heading: gene_id, transcript_id(s), length,effective_length,expected_count,TPM,FPKM

growth_protocol: Hormone-sensitive LNCaP cells transduced with MOI of 10 lentiviral particles carrying shRNA against non-targeted control (NTC) or SIRT1 (shSIRT1 or 10) (Dharmacon, Lafayette, CO) were selected with 1 μg/ml puromycin. Stable knockdown (KD) clones were cultured and maintained in culture medium in the presence of 0.5 μg/ml puromycin.

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen, Carlsbad, CA).
Approximately 500 ng total RNA was used for RNA-Seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide (Illumina, CA).

treatment_protocol: To identify SIRT1 target genes in LNCaP cells, LNCaP-NTC and SIRT1 KD (shSIRT1) cells were cultured in androgen supplemented conditions (FBS-supplemented medium). To determine SIRT1 function in prosate cancer progression, LNCaP-NTC and SIRT1 KD (10) cells were cultured in androgen supplemented conditions (FBS-supplemented medium) for 48 h. Following this, LNCaP-NTC and SIRT1 KD (10) cells were shifted to charcol-stripped serum (CSS)-supplemented medium (androgen deprived conditions) for 24 hours. Following 24h incubation under CSS conditions, cells were stimulated with vehicle control (VC), 1 nM Dihydrotestosterone  (D) (Millipore sigma, Burlington, MA) in the absence or presence of 10 µM Enzalutamide  (DE) (Selleckchem, Houston, TX) for additional 24 hours for total RNA preparation.

tag: cell line

value: LNCaP

value: hormone-sensitive prostate cancer cell line

tag: shRNA

value: shSIRT1 KD

value: CSS-supplemented medium with 1 nM Dihydrotestosterone stimulation plus 10 µM enzalutamide for 24 hr


title: IL2 IL4 Input CD8 rep1

description: IL2/IL4 Input ChIP-Seq rep1

tag: cell type

tag: strain


title: LN_10_DE_3


title: MCF10A_400Pa_HI_glucose_rep2

city: Berkeley

first: Greg

last: Timblin

department: MCB

institute: UC Berkeley

description: 24 h culture on 400 Pa surface with high glucose media (100k cells per 15 mm^2 coverslip cultured in a single well of a 24 well plate)

data_processing:
Unmanipulated reads were aligned to the human geneome (hg19) using RNA STAR, producing SAM files.
SAM files were converted to tag directories using HOMER.
For reporting and clustering, HOMER was used to calculate nomalized reads per gene (reads per kilobase per million mapped reads, or RPKM).
For differential expression analysis, HOMER was used to count raw reads per gene. The raw read counts were used as input to DESeq2 to call differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: xlxs spreadsheets of: 1) normalized read counts, and 2), 3) differential expression analysis results

source_name: mammary epithelial cell line

growth_protocol: MCF10A cells were sourced from ATCC, routinely tested and found to be free of mycoplasma contamination, and maintained below passage 22 in 5% CO2 at 37 ºC. MCF10A were cultured in [5 mM] glucose DMEM:F12 (1:1 mixture of F:12 [10mM] glucose and [0 mM] glucose DMEM) (Life Technologies, 11765054 and 11966025) supplemented with 5% Horse Serum (Gibco, 16050-122), 20 ng/mL epidermal growth factor (Peprotech), 10 µg/mL insulin (Sigma), 0.5 µg/mL hydrocortisone (Sigma), 100 ng/mL cholera toxin (Sigma, C8052-2MG), and 1x penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was isolated from biological samples with TRIzol (Invitrogen, 15596-018) according to the manufacturer’s instructions.
RNA-seq libraries (2 biological replicates per condition comprised of a pool of 4 PA-gel cultures each) were prepared from total RNA using KAPA mRNA HyperPrep Kit (Roche) and IDT dual indexed sequencing adaptors.

treatment_protocol: Cleaned (10% ClO, 1M HCL, then 100% EtOH) round #1 German glass coverslips (Electron Microscopy Services) were coated with 0.5% v/v (3-Aminopropyl)triethoxysilane (APTES, Sigma, 440140), 99.2% v/v ethanol, and 0.3% v/v glacial acetic acid for 2 h and then cleaned in 100% EtOH on an orbital shaker at 22 ºC. APTES activated coverslips were coated with PBS buffered acrylamide / bis-acrylamide (Bio-Rad, 1610140 and 1610142) solutions (3% / 0.05% for 400 Pa, 7.5% / 0.07% for 6k Pa, and 10% / 0.5% for 60k Pa) polymerized with TEMED (0.1% v/v) (Bio-Rad, 1610801) and Potassium Persulfate (0.1% w/v) (Fisher, BP180) to yield a final thickness of ~ 85 µm. PA-gels were washed with 70% EtOH and sterile PBS prior 3,4-dihydroxy-L-phenylalanine (DOPA) coating for 5 min at 22 ºC protected from light with sterile filtered DOPA in pH 10 [10 mM] Tris buffer (Wouters et al., 2016). DOPA coated PA-gels were washed 2x with sterile PBS and ECM functionalized with 5 µg/mL human fibronectin (Millipore, FC010) in sterile PBS 1 h at 37 ºC to generate an expected fibronectin coating density of 6 μM/cm2. Coverslips with coated gels were placed in wells of 24-well plates, and cells seeded at 100k cells per 15 mm^2 coverslip for 24h culrture before harvest/RNA extraction.

value: 400Pa + high glucose


title: ATAC_CX3CR1_LY108_DN_1


title: LN_10_DE_1


title: ATAC_CX3CR1_1


title: IL2 IL4 H3ac CD8 rep1

description: IL2/IL4 H3ac ChIP-Seq rep1


title: MCF10A_60kPa_rep2

description: 24 h culture on 60k Pa surface (100k cells per 15 mm^2 coverslip cultured in a single well of a 24 well plate)


title: LN_10_D_3

value: CSS-supplemented medium with 1 nM Dihydrotestosterone stimulation for 24 hr


title: sp6.mouse3.cs2.index.plate10.lib1

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
FACS sorted single cells
Merged_s1346.barcodes.tsv.gz
Merged_s1346.reads.tsv.gz
Merged_s1346.transcripts.tsv.gz

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using BWA MEM (version 0.7.10) with default parameters. In the reference transcriptome , all exons of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 were used for demultiplexing, reads 1 contain the cel-specific barcodes and the UMI-sequence and a polyT-stretch (see: CEL-seq.demultiplexing.barcodes.pdf). After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (Grun 2014,PMID: 24747814 and Muraro 2016,PMID: 27693023). For details, see the online methods and supplementary of the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: Read-, UMI(Barcode)-, Transcript-, count tables for mapped reads per cell as tab separated values (.tsv) for all cells. The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Every other column contains the read/UMI/transcript counts per cell.

source_name: Testis, adult

growth_protocol: Standard laboratory mice conditions.

extract_protocol:
Cells were sorted into Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius, after which illumina sequencing libraries were prepared by the SORT-Seq protocol (Muraro et al., 2016, PMID: 27693023). For details, see online methods and supplementary of the manuscript.
CEL-seq v1 and v2; See online methods and supplementary of the manuscript
Illumina TRU-seq; See online methods and supplementary of the manuscript

treatment_protocol: Manual isolation of the testis

tag: animal

value: index

tag: plate

tag: library


title: IL2 Input CD8 rep3

description: IL2 Input ChIP-Seq rep3


title: sp4.mouse3.cs2.gate.plate8.lib1

value: gate


title: sp3.mouse2.cs2.index.plate6.lib1


title: LN_10_D_2


title: ATAC_CX3CR1_2

tag: infection

value: spleen and lymph nodes


title: LN_10_D_1


title: IL2 H3ac CD8 rep3

description: IL2 H3ac ChIP-Seq rep3


title: MCF10A_400Pa_HI_glucose_rep1


title: Native control 1

description:
ApRNASeqFeatureCount.txt
controlvdynamic_padj0.05.txt
controlvstatic_padj0.05.txt
controlvhiflow_padj0.05.txt
controlvlowflow_padj0.05.txt
HyperplasiaRNASeqFeatureCount.txt
CTL-2_321_256

source_name: coronary artery

value: coronary artery


title: sp1.mouse1.cs1.index.plate5.lib4


title: MCF10A_6kPa_rep1

description: 24 h culture on 6k Pa surface (100k cells per 15 mm^2 coverslip cultured in a single well of a 24 well plate)


title: LN_10_VC_3

value: CSS-supplemented medium with vehicle control for Dihydrotestosterone and Enzalutamide


title: IL2 Input CD8 rep2

description: IL2 Input ChIP-Seq rep2


title: MCF10A_6kPa_rep2


title: MCF10A_60kPa_rep1


title: IL2 H3ac CD8 rep2

description: IL2 H3ac ChIP-Seq rep2


title: sp1.mouse1.cs1.index.plate5.lib3


title: MCF10A_1kPa_rep2

description: 24 h culture on 1k Pa surface (100k cells per 15 mm^2 coverslip cultured in a single well of a 24 well plate)


title: sp1.mouse1.cs1.index.plate5.lib2


title: IL2 Input CD8 rep1

description: IL2 Input ChIP-Seq rep1


title: MCF10A_1kPa_rep1


title: LN_10_VC_2


title: LN_10_VC_1


title: MCF10A_400Pa_rep2

description: 24 h culture on 400 Pa surface (100k cells per 15 mm^2 coverslip cultured in a single well of a 24 well plate)


title: sp1.mouse1.cs1.index.plate5.lib1


title: sp1.mouse1.cs1.index.plate3.lib4


title: IL2 H3ac CD8 rep1

description: IL2 H3ac ChIP-Seq rep1


title: LN_NTC_DE_3

value: scrambled


title: PP1861C: Bmc1_deletion_replicate3

city: Mainz

first: Peter

last: Baumann

address: Ackermannweg 4

country: Germany

institute: Johannes Gutenberg University of Mainz

data_processing:
Sequenced reads were trimmed with fastx_toolkit (0.0.14)
Reads were aligned nad counted with STAR (2.5.2b)
Differential expression analysis was perfromed with DESeq2 (v. 1.22.2) in R
Genome_build: ASM294v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Schizosaccharomyces pombe

source_name: unicellular organism

growth_protocol: Cell cultures (250 ml) were grown to a density of 6-8.5 × 106 cells per ml in YES broth media at 32 °C

extract_protocol:
Cells were washed once with H2O and quick-frozen by dripping the cell suspension into liquid nitrogen. Cells were lysed in a 6850 Freezer mill (SPEX SamplePrep) using seven cycles (2 min) at a rate of 10 per second with 2 min cooling time between cycles. RNA was extracted four times with 5 ml phenol: chloroform:isoamyl alcohol (25:24:1, equilibrated with 50 mM sodium acetate, pH 5.2) and once with chloroform:isoamyl alcohol (24:1, equilibrated with 50 mM sodium acetate, pH 5.2). RNA was ethanol precipitated and resuspended in H2O.
rRNA was depleted using Illumina's Ribo-Zero Magnetic Kit for Yeast as per standard protocol, followed by Illumina's TruSeq Stranded Total RNA LT Sample Prep Kit using the TruSeq Stranded Total RNA Reference Guide

tag: developmental stage

value: log phase growth

value: Bmc1 deletion (SPBC2A9.10::natMX6)


title: LN_NTC_DE_2


title: sp1.mouse1.cs1.index.plate3.lib3


title: SW620 H3K27ac HiChIP

data_processing:
Library strategy: HiChIP
Paired-end reads were processed using HiC-Pro (Servant et al., 2015) and Loops were called using HiChipper software (http://hichipper.readthedocs.io/en/latest/index.html).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedpe, mango files: Output files from hichipper.

source_name: ATCC

growth_protocol: ATCC cell lines were purchased from ATCC and maintained as per standard ATCC protocol.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. In situ Hi-C contacts were generated with MboI restriction enzyme, followed with biotin-dATP filling and ligation. H3K27Ac ChIP was performed on them. Further, DNA elution with biotin capture was done.
Libraries were prepared using the Nextera Tn5 transposase.

value: SW620 (ATCC CCL-227)

value: Colorectal cancer cell line

tag: disease

value: Dukes' type C, colorectal adenocarcinoma

tag: modification or treatment

value: Untreated

tag: antibody


title: PP1861A: Bmc1_deletion_replicate1


title: PP1860C: WT_replicate3

description: WT control for bmc1 deletion

value: Wildtype


title: sp1.mouse1.cs1.index.plate3.lib2


title: sp1.mouse1.cs1.index.plate3.lib1


title: LS513 H3K27ac HiChIP

value: Dukes' type C, colorectal carcinoma


title: LN_NTC_DE_1

value: LNCaP

value: hormone-sensitive prostate cancer cell line

value: CSS-supplemented medium with 1 nM Dihydrotestosterone stimulation plus 10 µM enzalutamide for 24 hr


title: SW480 H3K27ac HiChIP

value: SW480 (ATCC CCL-228)

value: Dukes' type B, colorectal adenocarcinoma


title: LN_NTC_D_3

value: CSS-supplemented medium with 1 nM Dihydrotestosterone stimulation for 24 hr


title: LN_NTC_D_2


title: PP1860B: WT_replicate2

description: WT control for bmc1 deletion


title: HCT116 H3K27ac HiChIP

value: HCT116 (ATCC CCL-247)

value: Colorectal carcinoma


title: LN_NTC_D_1

value: scrambled


title: palmitate plus DMSO in T6PNE cells

city: San Diego

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

description: ApDMSO

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values

source_name: Pancreas

growth_protocol: T6PNE cultured with RPMI 1640 media with 10% FBS, 1% antibiotics, 5.5mM glucose

extract_protocol:
After 2days, cells harvested in RLT buffer (Qiagen)
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: T6PNE cells treated with DMSO or NCT (15uM) for 2 days including palmitate

tag: tissue

value: pancreas

value: Fetal

value: DMSO control


title: MCF10A_400Pa_rep1


title: PP1860A: WT_replicate1

description: WT control for bmc1 deletion

value: log phase growth


title: PP1861B: Bmc1_deletion_replicate2

value: Bmc1 deletion (SPBC2A9.10::natMX6)


title: MSC-1

data_processing:
Formation of Cell-Barcode bead containing droplets with 10x Genomics Chromium
Preparation of sequencing library. Sequence analysis by Illumina HiSeq. Acquire data of 3,000 cells / sample and 100,000 reads / cell.
Data analysis with Cell Ranger, ver 2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Bone marrow were removed, crush with a scissors and a pestle, and RNA was harvested using Trireagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
scRNA-Seq

value: bone marrow derived stromal cells

value: wild type

value: bone marrow

value: post natal 6 weeks


title: Input cell_BM

data_processing:
The RNA libraries were constructed by mRNA sequencing via polyA selection kit.
Sequencing was performed with Hiseq PE 2x150 (Illumina). The sequence reads were aligned and mapped using Partek Flow software v2.2 (Partek).
The raw reads were first subjected to pre-alignment Quality Assurance and Quality Control (QA/QC). Any base below a Phred value of 20 was trimmed from either side of the read and reads shorter than 25 nt length were removed. The processed reads were aligned by Tophat2-2.0.847 to mm9 reference genome.
Genome_build: mm9

extract_protocol:
Bone marrow were removed, crush with a scissors and a pestle, and RNA was harvested using Trireagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: PP1847C: Thc1_deletion_replicate3

value: Thc1 deletion (SPCC18b5.09c::his3)


title: LN_NTC_VC_2

value: LNCaP

value: hormone-sensitive prostate cancer cell line

value: CSS-supplemented medium with vehicle control for Dihydrotestosterone and Enzalutamide


title: cluster7


title: palmitate plus NCT  in T6PNE cells

description: BpNT

value: NCT treated


title: PP1847B: Thc1_deletion_replicate2


title: cluster6


title: Ex vivo CD4+ cells - activated - TBX21 M/M

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Cell ranger v3.0.1
Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample: filtered feature-barcode matrices from cell ranger output in h5 format

source_name: CD4+ cells enriched from PBMCs

extract_protocol:
10x Genomics (Chromium Single Cell 3' Reagent kit v2)
10x Genomics (Chromium Single Cell 3' Reagent kit v2)
scRNA (10x Genomics)

treatment_protocol: see SAMPLES section, treatment

value: TBX21 M/M

value: CD4+ cells

value: activated with anti-CD3/anti-CD28 monoclonal antibodies for 14 hours


title: Ex vivo CD4+ cells - activated - TBX21 WT/WT

value: TBX21 WT/WT


title: LN_shSIRT1_3

value: shSIRT1 KD

value: FBS-supplemented medium


title: LN_shSIRT1_2


title: Ex vivo CD4+ cells - untreated - TBX21 WT/WT

value: untreated


title: cluster5


title: PP138C: WT_replicate3

description: WT control for thc1 deletion

value: log phase growth

value: Wildtype


title: The effect of ZBTB11 overexpression on iPS derived cardiomyocytes

description:
bulk gene expression
iPS derived cardiomyocytes were transduced with AAV-ZBTB11, AAV-GFP, or not transduced. 7 days after transduction, cells were harvested and RNA-Seq was performed.

data_processing:
Paired-end sequencing was performed on the Illumina Nextseq500 platform. Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the hg19 human RefSeq transcriptome using BWA v07.10
Deseq2 v1.24.0 was used to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: excel; gene expression table per sample

source_name: iPS-Cardiomyocytes

growth_protocol: iPS-Cardiomyocytes were maintained in Essential 8 medium

extract_protocol:
Total RNA was extracted from cells 7 days after transduction using standard TriZol extraction.
Samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.

treatment_protocol: Cells were transduced with AAV-GFP (AAV Control), AAV-ZBTB11, or were not transduced (control)

value: IPS cells

tag: genotype/variation


title: LN_shSIRT1_1


title: Ex vivo CD4+ cells - untreated - TBX21 M/M

tag: genotype


title: LN_NTC_VC_1

value: scrambled


title: Isolated transmural sections from a single ARVC diseased heart.

description:
CEL-seq
ARVC.BarcodeCounts.tsv.gz
ARVC.ReadCounts.tsv.gz
ARVC.TranscriptCounts.tsv.gz

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using BWA MEM (version 0.7.10) with default parameters. In the reference transcriptome , all exons of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 were used for demultiplexing, reads 1 contain the cel-specific barcodes and the UMI-sequence and a polyT-stretch (see: CEL-seq.2.demultiplexing.barcodes.pdf). After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (Grun 2014,PMID: 24747814 and Muraro 2016,PMID: 27693023). For details, see the online methods and supplementary of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Read-, UMI(Barcode)-, Transcript-, count tables for mapped reads per cell as tab separated values (.tsv) for all sections. The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Every other column contains the read/UMI/transcript counts per sections.

source_name: transmural heart  section

growth_protocol: Isolated primary tissue.

extract_protocol:
mRNA extraction, barcoding, reverse transcription and in vitro transcription were performed as described (Junker et al., 2014, PMID: 25417113) using the Message Amp II kit (Ambion). See online methods and supplementary of the manuscript.
After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113), but with CEL-Seq v2 reverse transcription primers; See online methods and supplementary of the manuscript.
Illumina TRU-seq libraries were constructed CEL-Seq v1 (but with CEL-Seq sample barcodes), as in (Junker et al 2014); See online methods and supplementary of the manuscript.

treatment_protocol: A transmural cross-section of the heart was positioned perpendicular to the sectioning axis, frozen and cryo-sectioned as described (Junker et al., 2014) with a sectioning width of 20 mm. See online methods and supplementary of the manuscript

tag: diagnosis

value: ARVC

value: PKP2-mutant, premature stop codon

tag: age

value: adult


title: PP138A: WT_replicate1

description: WT control for thc1 deletion


title: PP138B: WT_replicate2

description: WT control for thc1 deletion


title: cluster4

value: bone marrow derived stromal cells

value: wild type

value: bone marrow

value: post natal 6 weeks


title: cluster3


title: LN_NTC_VC_3

tag: cell line

value: LNCaP

value: hormone-sensitive prostate cancer cell line

tag: treatment

value: CSS-supplemented medium with vehicle control for Dihydrotestosterone and Enzalutamide


title: LN_NTC_3

tag: cell type

tag: shRNA


title: Valley Oak (SW.786) stem RNA long read sequencing (isoseq)

city: Los Angeles

first: Sorel

middle: Tanya

last: Fitz-Gibbon

state: CALIFORNIA

address: 961 Wellesley Ave

department: Ecology & Evolutionary Biology

institute: University of California, Los Angeles

data_processing:
library strategy: Iso-Seq (Full-Length Isoform Sequencing), PacBio_SMRT
Raw reads for each of the three tissues were processed using PacBio’s Iso-Seq classify bioinformatics pipeline (Gordon et al, 2015), although clustering was skipped and replaced with later  filtering of the Minimap2 read alignments. Specifically, the two Iso-Seq classify bioinformatics pipeline steps were:  1. ccs  with --minLength=50 --maxLength=12000 --minPasses=1 --minPredictedAccuracy=0.8 --minZScore=-999 --maxDropFraction=0.8, and 2. pbtranscript classify with --min_seq_len 100
Intron-enabled alignments to the genome were produced with Minimap2 (Li 2018) using -ax splice -uf --secondary=no
"full length non-chimeric" reads from Iso-Seq bioinformatic pipeline,  aligned to Valley Oak genome v3.0
Genome_build: Valley Oak version 3.0; GCA_001633185.3

organism: Quercus lobata

source_name: stem

extract_protocol:
RNA extractions were performed between November 6-8, 2017 using a modified version of the Conifer RNA prep protocol from the Cronn Lab  (https://openwetware.org/wiki/Conifer_RNA_prep) and the Spectrum Plant Total RNA kit (Sigma, St. Louis, MO, USA).  Plant tissues (100 mg each of leaves, buds and stems) were flash frozen in liquid nitrogen and ground with a mortar and pestle to a fine powder. Powdered tissues were transferred to cold 2mL tubes and 1.8 mL of cold RNA Extraction Buffer + DTT was added. RNA Extraction Buffer consists of 8 M Urea, 3 M LiCl, 1% polyvinylpyrrolidone K-60, 5 mM DTT (add just before use, 1M stock). The tubes were then vortexed for 30 seconds, incubated at 4°C for 30 minutes, then centrifuged at 4°C for 30 minutes at 20,000 rcf. The supernatant was discarded and the pellet was used as the starting material for the Spectrum Plant Total RNA kit, protocol A, adding 750uL of Binding Solution, and performing on-column DNase I digestion. RNA quality and quantity were assessed using the Agilent RNA ScreenTape System on the Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA).
RNA from leaves, bud and stems were further prepared following the “Guidelines for Preparing cDNA Libraries for Isoform Sequencing (Iso-SeqTM) User Bulletin” (Pacific Biosciences of California, Inc., 2014) and the “Procedure & Checklist – Iso-Seq™ Template Preparation for Sequel™ Systems” (Pacific Biosciences of California, Inc., 2017).  PolyA+ RNA was extracted from total RNA using the Ambion® Poly(A) Purist™ MAG Kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol.  First strand cDNA synthesis was performed using the SMARTer® PCR cDNA Synthesis Kit (Takara Bio, Inc., Kusatsu, Shiga Prefecture, Japan), with three reactions using 3.5uL of PolyA+ RNA per tissue, for a total of nine first strand synthesis reactions.  Each of nine reactions were diluted with 90uL of EB buffer, then pooled according to tissue type.  PCR cycle optimization resulted in the following PCR conditions with 24 x 50uL reactions per tissue type: 95°C for 2 minutes for initial denaturation, then n cycles of 98°C for 20 seconds, 65°C for 15 seconds, 72°C for 4 minutes, where n=10 for leaf cDNA, n=12 for bud cDNA, n=14 for stem cDNA, then 72°C for 5 minutes for the final extension. Twelve reactions per tissue type were pooled for 1X AMPure XP (Beckman Coulter, Inc., Pasadena, CA, USA) bead purification, and 12 reactions per tissue type were pooled for 0.4X AMPure XP bead purification.  Samples were sent to the DNA Technologies & Expression Analysis Core Laboratory at the University of California, Davis for size selection, enrichment, library preparation, and sequencing.  A second bead size selection was performed, 1X and 0.4X (Fraction 1 & 2, respectively) for two size fractions and a size selection of 5-10kb using the BluePippin Size Selection System. Six libraries were made from these different size selections following the “Procedure & Checklist – Iso-Seq™ Template Preparation for Sequel™ Systems” protocol: Library 1:  Leaf full length (Fractions 1 & 2); Library 2:  Bud full length (Fractions 1 &2), Library 3:  Stem full length (Fractions 1 &2); Library 4:  Leaf fraction 3 (5-10kb size selection); Library 5:  Bud fraction 3 (5-10kb size selection); Library 6:  Stem fraction 3 (5-10kb size selection). Bud libraries were pooled for sequencing (5:1, full length:fraction3), leaf libraries were pooled for sequencing (5:1, full length:fraction3), and stem libraries were pooled for seqencing (5:1, full length:fraction3) for a total of three libraries that were each sequenced on a single cell. The cells were loaded on the Sequel by Magbead / v2 SMRT cell / P2.1C2.1 (polymerase and chemistry versions).

treatment_protocol: Bud, leaf and stem tissues from Quercus lobata SW786 were collected on October 28, 2017 at Sedgewick Reserve in Santa Barbara, CA and placed immediately on dry ice, then kept in the -80°C freezer until the day of extraction

value: USA:Santa Barbara


title: cluster2

tag: strain


title: LN_NTC_2

value: FBS-supplemented medium


title: PP1847A: Thc1_deletion_replicate1

value: Thc1 deletion (SPCC18b5.09c::his3)


title: ChIP_H3K27ac_077_rep2

city: Beijing

first: Hong

last: Wu

address: Yiheyuan Road 5#

institute: Peking University

description: H3K27ac ChIP-Seq of human: blast cells of T-ALL patient 077

data_processing:
RNA-seq reads were aligned to the hg19 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ATAC-seq reads were mapped with Bowtie2 using parameter -X 2000 --no-mixed --no-discordant --no-unal. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIP-seq reads were mapped with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 5 kb and 10 kb resolutions with default parameters (except -d 15000,20000) for pooled Hi-C matrices of the healthy T cell controls, ETP and non-ETP samples, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: .validpairs of BL-Hi-C data were generated by HiC-Pro;.hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count and FPKM for each sample

source_name: bone marrow

growth_protocol: Loucy, Jurkat and KE-37 cells were routinly cultured in RPMI-1640 with 10% fetal bovine serum. Maintain cultures at cell concentrations between 3 x 105 and 3 x 106 viable cells/mL.

extract_protocol:
Leukemia blast cells were prepared by density-gradient centrifugation of bone marrow samples, and CD19-CD14-CD235-CD45+CD7+ cells were further purified by FACS analysis using anti-human antibodies for RNA-seq and Hi-C library preparations. Peripheral blood samples were obtained from four healthy donors under the approval of the ethics committee of Peking University. T cells were purified using the EasySepTM Direct Human T Cell Isolation Kit (StemCell Technology #19661).
Hi-C was performed on one million cells/sample according to the BL-Hi-C protocol (PMID: 29158486 ). RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC  was performed on 50,000 Loucy cells according to the Omni-ATAC protocol  (PMID:28846090) with TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme TD501). H3K27ac ChIP of case 077 was performed on 10^5 cells, according to the protocol of Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD 901). H3K27ac ChIP of KE-37 was performed on 10^6 cells, according to the protocol of Zymo-Spin ChIP Kit from Zymo Research for Illumina (Zymo Research,D5209).

value: primary leukemic blasts

tag: subtype

value: ETP


title: ChIP_IgG_077

description: IgG ChIP-Seq of human: blast cells of T-ALL patient 077


title: Valley Oak (SW.786) leaf RNA long read sequencing (isoseq)

source_name: leaf


title: cluster1


title: ChIP_H3K27ac_077_rep1


title: Valley Oak (SW.786) bud RNA long read sequencing (isoseq)

source_name: bud


title: LN_NTC_1


title: V_U_8714_udLN

status: Public on May 21 2021

city: San Francisco

first: Tippi

last: MacKenzie

state: California

address: 550 16th Street

department: Surgery, Pediatrics, Center for Maternal-Fetal Precision Medicine

institute: University of California, San Francisco

description: 8714 Adig+ virgin, 6.1 weeks old (DOB 5/31/18)

data_processing:
STAR (v 2.5.2b) was used to align reads to the mouse genome. No adapter clipping or filtering was preformed before alignment
Reads uniquely mapped to known mRNAs were used to preform differential expression.
Pairwise comparisons were made between pregnant vs virgin mice in the thymus, spleen, uterine-draining lymph node, and non uterine-draining lymph node, using DESeq2
Genome_build: GRCm38.78
Supplementary_files_format_and_content: counts.star.MOUSE.txt= tab delimited text file containing samples and their raw (unnormalized) read counts per gene.

source_name: CD3- CD19- NK1.1- MHCII+ GFP+ cells

extract_protocol:
For bulk RNA sequencing, stromal cells were prepared for cell sorting by mincing thymus, lymph nodes, and spleen with razor blades and then digesting for 30 minutes at 37C in 100ug/mL DNase I (Roche) and Liberase TM (Roche) before filtering through a 70-micron cell-strainer. Density-gradient centrifugation was used to enrich for stromal cells, using a three-layer Percoll PLUS gradient (Sigma) with specific gravities of 1.115, 1.065, and 1.0. Cells isolated from between the 1.065 and 1.0 layer were resuspended in anti-Fc receptor blocking antibody clone 2.4G2 for 10 minutes, then incubated on ice for 30 minutes with antibody cocktail. 4',6-diamidino-2-phenylindole (DAPI) was added to exclude dead cells before sorting on a FACSAriaII (BD Biosciences, San Jose, CA ). CD3- CD19- NK1.1- MHCII+ GFP+ cells were sorted directly into cold RPMI with 2% FBS, washed with PBS twice, and then resuspended in lysis bffer and snap frozen for RNA isolation and sequencing.
SmartSeq/NexteraXT
bulk RNA-sequencing

value: uterine-draining lymph node

value: CD3- CD19- NK1.1- MHCII+ GFP+ cells

tag: mouse id

tag: pregnancy status


title: V_U_8763_udLN

description: 8763 Adig+ virgin, 8.3 weeks old (DOB 5/8/18)


title: P_N_8706_ndLN

description: 8706 Adig+ pregnant, E9.5, 8.1 weeks old (DOB 5/17/18)

value: non-uterine-draining lymph node


title: P_U_8762_udLN

description: 8762 Adig+ pregnant, E9.5, 8.3 weeks old (DOB 5/8/18)


title: P_U_8761_udLN

description: 8761 Adig+ pregnant, E9.5, 8.3 weeks old (DOB 5/8/18)


title: P_U_8706_udLN

value: Adig+ pregnant, E9.5, 8.1 weeks old (DOB 5/17/18)


title: V_S_8758_spleen_2

description: 8758 Adig+ virgin, 8.3 weeks old (DOB 5/8/18)

value: spleen


title: P_N_8762_ndLN

value: Adig+ pregnant, E9.5, 8.3 weeks old (DOB 5/8/18)


title: V_N_8714_ndLN

value: Adig+ virgin, 6.1 weeks old (DOB 5/31/18)


title: P_N_8761_ndLN


title: V_S_8758_spleen

value: Adig+ virgin, 8.3 weeks old (DOB 5/8/18)


title: V_U_8758_udLN


title: P_S_8706_spleen_2


title: V_S_8714_spleen


title: V_S_8763_spleen


title: P_S_8706_spleen


title: V_T_8763_thymus

value: thymus


title: V_N_8758_ndLN


title: V_T_8758_thymus


title: P_T_8706_thymus_2


title: V_N_8763_ndLN


title: P_T_8706_thymus


title: V_T_8758_thymus_2


title: P_S_8761_spleen


title: V_N_58355_nondLN

description: 58355 Adig+ virgin, 8.0 weeks old

value: Adig+ virgin, 8.0 weeks old


title: P_T_8762_thymus


title: P_T_8761_thymus


title: V_U_58355_udLN

description: 58355 Adig+ virgin, 8.0 weeks old


title: P_N_58348_nondLN

description: 58348 Adig+ pregnant, E9.5, 8.0 weeks old

value: Adig+ pregnant, E9.5, 8.0 weeks old


title: P_U_58343_udLN

description: 58343 Adig+ pregnant, E9.5, 8.0 weeks old


title: V_S_58355_spleen

description: 58355 Adig+ virgin, 8.0 weeks old


title: P_S_8762_spleen


title: P_U_58348_udLN


title: P_S_58348_spleen


title: P_S_58350_spleen

description: 58350 Adig+ pregnant, E9.5, 8.0 weeks old


title: V_U_58349_udLN

description: 58349 Adig+ virgin, 8.1 weeks old

value: Adig+ virgin, 8.1 weeks old


title: P_N_58343_nondLN


title: V_U_58351_udLN

description: 58351 Adig+ virgin, 8.0 weeks old


title: V_S_58351_spleen

description: 58351 Adig+ virgin, 8.0 weeks old


title: P_U_58350_udLN


title: V_T_8714_thymus


title: V_N_58351_nondLN

description: 58351 Adig+ virgin, 8.0 weeks old


title: P_N_58350_nondLN


title: P_T_58350_thymus


title: V_T_58355_thymus

description: 58355 Adig+ virgin, 8.0 weeks old


title: V_N_58349_nondLN

description: 58349 Adig+ virgin, 8.1 weeks old


title: P_T_58348_thymus


title: P_S_58343_spleen


title: P_T_58343_thymus


title: V_T_58349_thymus

description: 58349 Adig+ virgin, 8.1 weeks old


title: Auts2 cKO Frontal Cortex 3

city: Seattle

first: Anthony

middle: Scott

last: Castanza

state: Washington

address: 1959 NE Pacific St Box 357470

institute: University of Washington

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FK5.175500

data_processing:
75bp Illumina reads were mapped to the GRCm38.p4 mouse reference genome (Gencode M11) with STAR version 2.5 by the NWGC at University of Washington
RIP-Seq BAM Files were filtered using SAMtools in Galaxy with the following flags -mapped -noqcfail -nopcrdup
A blacklist file was generated by retreiving alignments for tRNA, rRNA, chrM, and chrY for Gencode M14 from BioMart which were masked from downstream analysis
BAM files were masked against the blacklist and Quantified against the Gencode M14 annotation using CuffDiff version 2.2.1 on Galaxy
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CuffDiff FPKM values for each Sample. CummeRbund sqlite files contain CuffDiff tracking and results database for each analysis

source_name: Frontal Cortex

extract_protocol:
Rostral cortex was dissected under cold saline and flash frozen on dry ice. RNA was extracted with the Qiagen RNEasy Plus Universal Mini Kit.
RNA Libraries were prepared with standard Illumina TruSeq Protocols

tag: developmental stage

value: C57BL6/J EMX1-cre Auts2 cKO

value: Rostral Cortex


title: Auts2 Wildtype Frontal Cortex 4

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FW5.175494


title: Auts2 cKO Frontal Cortex 2

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FK4.175499


title: Auts2 cKO Frontal Cortex 1

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FK3.175498


title: Auts2 cKO Frontal Cortex 4

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FK5.175501


title: V_S_58349_spleen

description: 58349 Adig+ virgin, 8.1 weeks old


title: Auts2 Wildtype Frontal Cortex 1

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FW1.175490


title: V_T_58351_thymus

description: 58351 Adig+ virgin, 8.0 weeks old


title: Auts2 Wildtype Frontal Cortex 3

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FW4.175493


title: control-ChIP_HSV-1 8h IgG rep2 HFF, HSV-1 infected for 8h, replicate 2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
HFF, HSV-1 infected for 8h, replicate 2
HEK_IgG_HSV1_8h_br2.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome, and the HSV-1 strain 17 genome (NC_001806) using standard parameters.
Reads were then quantified using quasR (Gaidatzis et al, 2015). For HSV1, plus and minus strand reads per processed separately, and only samples from infected cells were counted.
Genome_build: hg19
Genome_build: HSV-1 NC_001806
Supplementary_files_format_and_content: tab-separated values

growth_protocol:
Primary human foreskin fibroblasts (HFF) cells (ATCC SCRC-1041) were maintained in DMEM (high glucose) supplemented with 10% FCS, Gentamycin, Glutamine and HEPES. Cells were cultured at 37°C and 5% CO2.
Knockouts of DUX4 were done using CRISPR/Cas9, with components transduced by lentiviruses, followed by puromycin selection

extract_protocol:
ChIPmentation (Schmidl et al. 2015, doi: 10.1038/nmeth.3542)
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs)
polyA RNA-seq, or total RNA-seq. with rRNA depletion as indicated

treatment_protocol: Cells were subjected to HSV-1 infection as indicated

tag: grna sequence forward

tag: grna sequence reverse

tag: grna name

tag: hsv1 infection

value: yes

tag: harvesting timepoint


title: control-ChIP_HSV-1 8h IgG rep3 HFF, HSV-1 infected for 8h, replicate 3

description:
HFF, HSV-1 infected for 8h, replicate 3
HEK_IgG_HSV1_8h_br3.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak

source_name: Primary human foreskin fibroblasts (HFF) cells


title: Input_mock rep2 HFF, mock-treated, replicate 2

description:
HFF, mock-treated, replicate 2
HEK_IN_mock_0h_br2.bw
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak

value: no


title: control-ChIP_HSV-1 14h IgG rep1 HFF, HSV-1 infected for 14h, replicate 1

description:
HFF, HSV-1 infected for 14h, replicate 1
HEK_IgG_HSV1_14h_br1.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: control-ChIP_HSV-1 8h IgG rep4 HFF, HSV-1 infected for 8h, replicate 4

description:
HFF, HSV-1 infected for 8h, replicate 4
HEK_IgG_HSV1_8h_br4.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: control-ChIP_HSV-1 14h IgG rep4 HFF, HSV-1 infected for 14h, replicate 4

description:
HFF, HSV-1 infected for 14h, replicate 4
HEK_IgG_HSV1_14h_br4.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: Input_HSV-1 8h rep2 HFF, HSV-1 infected for 8h, replicate 2

description:
HFF, HSV-1 infected for 8h, replicate 2
HEK_IN_HSV1_8h_br2.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: Input_mock rep1 HFF, mock-treated, replicate 1

description:
HFF, mock-treated, replicate 1
HEK_IN_mock_0h_br1.bw
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak


title: control-ChIP_HSV-1 8h IgG rep1 HFF, HSV-1 infected for 8h, replicate 1

description:
HFF, HSV-1 infected for 8h, replicate 1
HEK_IgG_HSV1_8h_br1.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: Input_HSV-1 8h rep1 HFF, HSV-1 infected for 8h, replicate 1

description:
HFF, HSV-1 infected for 8h, replicate 1
HEK_IN_HSV1_8h_br1.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: control-ChIP_HSV-1 14h IgG rep3 HFF, HSV-1 infected for 14h, replicate 3

description:
HFF, HSV-1 infected for 14h, replicate 3
HEK_IgG_HSV1_14h_br3.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: DUX4-ChIP_HSV-1 8h rep1 HFF, HSV-1 infected for 8h, replicate 1

description:
HFF, HSV-1 infected for 8h, replicate 1
HEK_DUX4_HSV1_8h_br1.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: DUX4-ChIP_HSV-1 8h rep2 HFF, HSV-1 infected for 8h, replicate 2

description:
HFF, HSV-1 infected for 8h, replicate 2
HEK_DUX4_HSV1_8h_br2.bw
Peaks_HSV1_8h_IG_peaks.narrowPeak
Peaks_HSV1_8h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: DUX4-ChIP_HSV-1 14h rep2 HFF, HSV-1 infected for 14h, replicate 2

description:
HFF, HSV-1 infected for 14h, replicate 2
HEK_DUX4_HSV1_14h_br2.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: DUX4-ChIP_HSV-1 14h rep1 HFF, HSV-1 infected for 14h, replicate 1

description:
HFF, HSV-1 infected for 14h, replicate 1
HEK_DUX4_HSV1_14h_br1.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: DUX4-ChIP_mock rep1 HFF, mock-treated, replicate 1

description:
HFF, mock-treated, replicate 1
HEK_DUX4_mock_0h_br1.bw
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak


title: DUX4-ChIP_mock rep2 HFF, mock-treated, replicate 2

description:
HFF, mock-treated, replicate 2
HEK_DUX4_mock_0h_br2.bw
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak
Peaks_mock_0h_IN_peaks.narrowPeak


title: Input_HSV-1 14h rep1 HFF, HSV-1 infected for 14h, replicate 1

description:
HFF, HSV-1 infected for 14h, replicate 1
HEK_IN_HSV1_14h_br1.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: control-ChIP_HSV-1 14h IgG rep2 HFF, HSV-1 infected for 14h, replicate 2

description:
HFF, HSV-1 infected for 14h, replicate 2
HEK_IgG_HSV1_14h_br2.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: 293T-DUX4ko-1-4-uninf 293T-DUX4 knockout sgRNA-1-4 treated, mock 18h

description:
293T-DUX4 knockout sgRNA-1-4 treated, mock 18h
RNAseq_hg19_readcounts.tsv

source_name: HEK 293T cells

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs)
polyA RNA-seq, or total RNA-seq. with rRNA depletion as indicated

value: TCGGACAGCACCCTCCCCG

value: CGCTGAGGGGTGCTTCCAG


title: 293T-DUX4ko-1-3-18hpi 293T-DUX4 knockout sgRNA-1-3 treated, HSV-1 18h

description:
293T-DUX4 knockout sgRNA-1-3 treated, HSV-1 18h
RNAseq_hg19_readcounts.tsv
RNAseq_HSV1_readcounts.tsv

value: CACCCGGGCAAAAGCCGGG

value: CCCGGCTTTTGCCCGGGTG


title: 293T-DUX4ko-1-3-uninf 293T-DUX4 knockout sgRNA-1-3 treated, mock 18h

description:
293T-DUX4 knockout sgRNA-1-3 treated, mock 18h
RNAseq_hg19_readcounts.tsv


title: 293T-DUX4ko-1-4-18hpi 293T-DUX4 knockout sgRNA-1-4 treated, HSV-1 18h

description:
293T-DUX4 knockout sgRNA-1-4 treated, HSV-1 18h
RNAseq_hg19_readcounts.tsv
RNAseq_HSV1_readcounts.tsv


title: Input_HSV-1 14h rep2 HFF, HSV-1 infected for 14h, replicate 2

description:
HFF, HSV-1 infected for 14h, replicate 2
HEK_IN_HSV1_14h_br2.bw
Peaks_HSV1_14h_IG_peaks.narrowPeak
Peaks_HSV1_14h_IN_peaks.narrowPeak
Peaks_HSV1_14h_8h_peaks.narrowPeak


title: Auts2 Wildtype Frontal Cortex 2

description:
AUTS2_Frontal_Cortex_RNA-Seq_FPKM_Table
Auts2_FC_cummeRbund_database
FW2.175491

tag: tissue


title: 293T-DUX4ko-p8-18hpi 293T-DUX4 knockout sgRNA-p8 treated, HSV-1 18h

description:
293T-DUX4 knockout sgRNA-p8 treated, HSV-1 18h
RNAseq_hg19_readcounts.tsv
RNAseq_HSV1_readcounts.tsv

value: CTGGAAGCACCCCTCAGCG

value: CGGGGAGGGTGCTGTCCGA


title: 293T-DUX4ko-p8-uninf 293T-DUX4 knockout sgRNA-p8 treated, mock 18h

description:
293T-DUX4 knockout sgRNA-p8 treated, mock 18h
RNAseq_hg19_readcounts.tsv


title: 293T-DUX4ko-v1-uninf 293T-DUX4 knockout sgRNA-v1 treated, mock 18h

description:
293T-DUX4 knockout sgRNA-v1 treated, mock 18h
RNAseq_hg19_readcounts.tsv


title: 293T-DUX4ko-v1-18hpi 293T-DUX4 knockout sgRNA-v1 treated, HSV-1 18h

description:
293T-DUX4 knockout sgRNA-v1 treated, HSV-1 18h
RNAseq_hg19_readcounts.tsv
RNAseq_HSV1_readcounts.tsv


title: 293T-wt-18hpi 293T, infected with HSV-1 für 18h

description:
293T, infected with HSV-1 für 18h
RNAseq_hg19_readcounts.tsv
RNAseq_HSV1_readcounts.tsv


title: 293T-wt-uninf 293T, untreated, replicate 1

description:
293T, untreated, replicate 1
RNAseq_hg19_readcounts.tsv


title: 10084-AE11-AE-2

city: Birmingham

first: Kai

last: Qin

state: Alabama

address: Microbiology/845 19th Street South

department: Department of Medicine

institute: University of Alabama at Birmingham

description:
Raw_counts.csv
Normalized_counts.csv

data_processing:
Demutiplexing raw data was performed using VGAS v1.0
Alignment was performed using CLCBio V12.0
The Gene Count Matrix was genereated using HTSeq-count v0.9.1 and GRCh38 2018 gene annotations
The count matrices of all Plates were merged using R v3.5
Filtering and normalization was accomplished using Seurat v2.3.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every single cell sample

source_name: CD8 T cells

growth_protocol: Antigen specific CD8 T cells were specifically enriched in vitro by culturing with auologous peptide pulsed monocytes for 2~3 weeks.

extract_protocol:
Activated antigen specific CD8 T cells (defined as CD69+/CD137+) were first disaggregated into a single-cell suspension and placed in 96 well plate containing lysis buffer containing a ribonuclease inhibitor.
Single cell RNA-sequencing methodology was adapted from two previously described protocols, Smart-seq2 and MARS-Seq. Following the first round PCR, fragmentation and end-repair were performed using the NEBNext Ultra II FS kit, as per the manufacturer’s instructions. Adaptors were ligated to amplicons using the NEBNext Ultra II FS kit, as per the manufacturer’s instructions. A second round PCR was undertaken using GoTaq and linker primer 1. Following this, a third round PCR was conducted with barcoded linker primer 2. PCR products were purified and pooled for next-generation sequencing. The Kapa library quantitation kit  was used to quantify the libraries prior to sequencing on the Illumina MiSeq sequencer using the 600V3 kit (Illumina Inc.), as per the manufacturer’s instructions.

treatment_protocol: At the end of enrichment, cell lines were stimulated by autologous peptide for 18h before surface staining.

tag: vaccine recipient

value: MRKAd5 vaccination

tag: antigen specificity

value: AEQASQEVKNW

tag: adaptation group

value: adapted

value: CD8 T cells


title: 10084-AI11-NAE-2

description:
Raw_counts.csv
Normalized_counts.csv

tag: treatment

value: AEIQKQGQGQW

value: non-adapted


title: 10386-AE11-AE-1

description:
Raw_counts.csv
Normalized_counts.csv

tag: cell type


title: 10386-KK9-NAE-2

description:
Raw_counts.csv
Normalized_counts.csv

value: KYKLKHIVW


title: 10386-KK9-NAE-1

description:
Raw_counts.csv
Normalized_counts.csv


title: 10084-AE11-AE-1

description:
Raw_counts.csv
Normalized_counts.csv


title: 10084-AI11-NAE-1

description:
Raw_counts.csv
Normalized_counts.csv


title: 10386-AE11-AE-2

description:
Raw_counts.csv
Normalized_counts.csv


title: Nov20_2

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

data_processing:
Illumina Casava2.2 software used for basecalling.
Sequenced reads were mapped to hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.26.8
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each Sample …

source_name: human clear cell renal cell skin metastasis

growth_protocol: Caki-1 cells were grown in DMEM medium supplemented with 10% FBS and 1% Pen/Strep antibiotics. Cells were splitted twice per week and diluted at a 1:20, 1:25 ratio. Caki-1-SR cells were splitted following the same protocol and cultured in the same medium supplemented with 1 uM sunitinib

extract_protocol:
Protocol given by the manufacturer; QIAGEN Rneasy Plus Mini Kit (50); Ref 74134
RNA libraries were prepared for sequencing using Illumina TruSeqHT stranded mRNA kit

treatment_protocol: Cells were treated for 2 or 24h with the combination of Rapta-C (2 uM), erlotinib (1 uM), metformin (1 uM) and parthenolide (5 uM).

tag: cell line

value: CTRL (2h)


title: Nov20_3

value: human clear cell renal cell skin metastasis

value: ODC (2h)


title: 4_Jan_21

value: ODC (24h)


title: 2_Jan_21


title: 3_Jan_21

value: CTRL (24h)


title: Nov20_5


title: Nov20_1


title: 5_Jan_21


title: 6_Jan_21


title: Nov20_4


title: RNA-Seq 48hr rep3

city: Stanford

first: Helen

middle: M

last: Blau

address: 269 Campus Dr

department: Baxter Laboratories

institute: Stanford University

description:
48hr rep3
sorted heterokaryons 48 hours post-fusion

data_processing:
Default Illumina base calling implementation
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR
transcript abundance was quantified using rsem, reported as transcripts per million (TPM)
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited text file, genes in rows, samples in columns. Header at the top delineating samples.

organism:
Homo sapiens
Mus musculus

source_name: human fibroblast + mouse ESC fusion

growth_protocol: Fibroblasts are grown in 10% FBS + DMEM. ESCs are grown with 10% FBS, 10% KSR, LIF, beta-mercaptoethanol in KO DMEM

extract_protocol:
RNEasy purification kit from Qiagen for RNA extraction
Tru-Seq V2 kit according to manufacturer's protocol

treatment_protocol: To induce dnAP-1 in fibroblasts, doxycycline was added at the beginning of the co-culture step at 1000 ng/ml

value: heterokaryon

value: no dnAP-1 (control)


title: RNA-Seq 3hr rep1 + dnAP-1

description:
3hr rep1 + dnAP-1
sorted heterokaryons 3 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1

value: dnAP-1 (Tet-On)


title: RNA-Seq 3hr rep2 + dnAP-1

description:
3hr rep2 + dnAP-1
sorted heterokaryons 3 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 16hr rep3 + dnAP-1

description:
16hr rep3 + dnAP-1
sorted heterokaryons 16 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 48hr rep1 + dnAP-1

description:
48hr rep1 + dnAP-1
sorted heterokaryons 48 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 48hr rep3 + dnAP-1

description:
48hr rep3 + dnAP-1
sorted heterokaryons 48 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 48hr rep2 + dnAP-1

description:
48hr rep2 + dnAP-1
sorted heterokaryons 48 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 16hr rep2 + dnAP-1

description:
16hr rep2 + dnAP-1
sorted heterokaryons 16 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: 1_Jan_21


title: RNA-Seq 16hr rep1 + dnAP-1

description:
16hr rep1 + dnAP-1
sorted heterokaryons 16 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 3hr rep3 + dnAP-1

description:
3hr rep3 + dnAP-1
sorted heterokaryons 3 hours post-fusion after 1mg/ml doxycycline to induce dnAP-1


title: RNA-Seq 48hr rep1

description:
48hr rep1
sorted heterokaryons 48 hours post-fusion


title: RNA-Seq 3hr rep2

description:
3hr rep2
sorted heterokaryons 3 hours post-fusion


title: RNA-Seq 16hr rep3

description:
16hr rep3
sorted heterokaryons 16 hours post-fusion


title: RNA-Seq 48hr rep2

description:
48hr rep2
sorted heterokaryons 48 hours post-fusion


title: RNA-Seq 16hr rep1

description:
16hr rep1
sorted heterokaryons 16 hours post-fusion


title: RNA-Seq 3hr rep1

description:
3hr rep1
sorted heterokaryons 3 hours post-fusion


title: RNA-Seq 16hr rep2

description:
16hr rep2
sorted heterokaryons 16 hours post-fusion


title: BoC35_5dC3_5_days_cetux_treatment

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cetux treatment

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumor Bo63 soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol: Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Nude mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg, treatment was imitated when tumor size reached approc. 100-200 mm³

value: patient derived colon cancer xenograft tissue

tag: response

value: partial response


title: BoC35_K3_untreated control

source_name: untreated control


title: BoC35_C1_2_cetux-secondary resistant

source_name: cetux-secondary resistant


title: BoC32_K1_untreated control

value: stable disease


title: BoC32_K2_untreated control


title: BoC35_K4_untreated control


title: BoC35_5dC1_5_days_cetux_treatment


title: BoC35_C1_3_cetux-secondary resistant


title: BoC32_5dC2_5_days_cetux_treatment


title: BoC32_K3_untreated control


title: BoC35_5dC4_5_days_cetux_treatment


title: BoC35_C1_1_cetux-secondary resistant


title: BoC32_C16_1_cetux-secondary resistant


title: BoC32_C6_2_cetux-secondary resistant


title: BoC32_C16_2_cetux-secondary resistant


title: BoC32_C2_2_cetux-secondary resistant


title: BoC32_5dC3_5_days_cetux_treatment


title: BoC20_K9_untreated control


title: BoC20_K3_untreated control


title: BoC20_C9_2_cetux-secondary resistant


title: BoC20_K1_untreated control


title: BoC32_5dC1_5_days_cetux_treatment


title: BoC32_C5_1_cetux-secondary resistant


title: BoC32_C5_2_cetux-secondary resistant


title: BoC20_K10_untreated control


title: BoC20_C1_2_cetux-secondary resistant


title: BoC20_C9_1_cetux-secondary resistant


title: BoC20_5dC4_5_days_cetux_treatment


title: BoC32_C2_1_cetux-secondary resistant


title: BoC32_C6_1_cetux-secondary resistant


title: BoC20_5dC2_5_days_cetux_treatment


title: BoC20_5dC1_5_days_cetux_treatment


title: BoC106_C2_1_cetux-secondary resistant


title: BoC20_C1_1_cetux-secondary resistant


title: BoC106_K2_untreated control


title: BoC106_C8_2_cetux-secondary resistant


title: BoC20_5dC3_5_days_cetux_treatment


title: BoC106_K4_untreated control


title: BoC106_C2_2_cetux-secondary resistant


title: BoC106_C8_1_cetux-secondary resistant


title: BoC106_5dC8_5_days_cetux_treatment


title: BoC106_K1_untreated control


title: BoC106_5dC1_5_days_cetux_treatment


title: BoC106_C6_1_cetux-secondary resistant


title: BoC10_K14_untreated control


title: BoC10_K6_untreated control


title: BoC10_C3_cetux-secondary resistant


title: BoC106_5dC2_5_days_cetux_treatment


title: BoC10 C2_2_cetux-secondary resistant


title: BoC10_C14_2_cetux-secondary resistant


title: BoC10_K7_untreated control


title: BoC106_C6_2_cetux-secondary resistant


title: BoC10_C2_1_cetux-secondary resistant


title: BoC10_5dC4_5_days_cetux_treatment


title: BoC10_C14_1_cetux-secondary resistant


title: BoC10_C4_2_cetux-secondary resistant


title: BoC71_K2_untreated control

value: complete response


title: BoC71_K7_untreated control


title: BoC10_5dC2_5_days_cetux_treatment


title: BoC10_C4_1_cetux-secondary resistant


title: BoC71_C6_2_cetux-secondary resistant


title: BoC10_5dC1_5_days_cetux_treatment


title: BoC71_5dC3_5_days_cetux_treatment


title: BoC71_C4_1_cetux-secondary resistant


title: BoC71_5dC1_5_days_cetux_treatment


title: BoC69_K3_untreated control


title: BoC69_C6_cetux-secondary resistant


title: BoC71_5dC2_5_days_cetux_treatment


title: BoC69_K1_untreated control


title: BoC71_C3_1_cetux-secondary resistant


title: BoC71_C6_1_cetux-secondary resistant


title: BoC71_K1_untreated control


title: BoC71_C1_1_cetux-secondary resistant


title: BoC69_C9_cetux-secondary resistant


title: BoC69_C7_cetux-secondary resistant


title: BoC69_C5_cetux-secondary resistant


title: BoC69_5dC1_5_days_cetux_treatment


title: BoC69_C10_cetux-secondary resistant


title: BoC71_C3_2_cetux-secondary resistant


title: BoC60_C5_3_cetux-secondary resistant


title: BoC60_K5_untreated control


title: BoC69_5dC3_5_days_cetux_treatment3