title: Brain + Aurantiochytrium 18W-13a 3

city: Tsukuba

first: Kazunori

last: Sasaki

address: AIST Tsukuba Central 5-2

institute: AIST

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing: Data analysis was performed using the expression console and Visualization and Integrated Discovery (DAVID) v6.8 (National Institute of Allergy and Infectious Diseases (NIAID).

source_name: brain treated with Aurantiochytrium 18W-13a

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Male ICR mice (35 - 40 g, Charles River, USA) were used for the in vivo study. All mice were housed individually. Animals were provided with free access to food and water, except when subjected to EEA administration or testing. The animal house was maintained at a 12-h light/dark period, and the temperature was kept at 22 ± 1°C throughout the study.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Double-stranded cDNA was synthesized from 100 ng of total RNA with the GeneAtlas 3´ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3´ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA).

treatment_protocol: EEA was dissolved in drinking water and was administrated by oral gavages in each treatment group for 14 days. The control group was administered an equivalent volume of tap water. In our study, imipramine (serotonin and noradrenaline reuptake inhibitor; DNRI) was used as a positive control. It was dissolved in distilled water and was orally administered to mice in a volume of 20 mg/kg body weight for 14 days

value: Aurantiochytrium 18W-13a

value: ICR

tag: gender

value: male

value: limbic area of brain


title: benign T cell [2_CD8]

status: Public on Mar 12 2019

type: genomic

city: Hannover

first: Anke

middle: Katharina

last: Bergmann

address: OE 6300, Carl-Neuberg-Str. 1

department: human genetics

country: Germany

institute: Medical School Hannover

description:
benign T cell
2_CD8

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

scan_protocol: Arrays were scanned using the Illumina iScan using standard recommended Illumina scanner settings

data_processing: GenomeStudio software (version2011.1; Methylation Analysis Module version 1.9.0, Illumina)

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: benign

label_protocol: Standard Illumina Protocol

extract_protocol: Whole genomic DNA was extracted from frozen tumor cells containing samples and the benign controls using the Gentra purification kit (Qiagen, Hilden, Germany).

tag: disease state

value: benign


title: benign T cell [1_CD8]

description:
benign T cell
1_CD8


title: Nano_OHC_012

type: SRA

city: Philadelphia

first: Paul

middle: T

last: Ranum

state: PA

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

country: USA

institute: The Children's Hospital of Philadelphia

description: Single-Cell SmartSeq2 Nanopore

library_source: transcriptomic

data_processing:
For Nanopore data processing, begin with the .fastq file for each cell output by the Nanopore MinION run.  Perform Demultiplexing (samples uploaded here have already been demultiplexed) and Alignment using Mandalorion v0.2 (alignment within the mandalorion package is run using gmap).  Four cells are multiplexed within each nanopore output .fastq.  Demultiplex and align each MinION run output .fastq individually because indexes are repeated between runs.
Perform isoform quantification with Mandalorion Define and Quantify Isoforms.
Mandalorion documentation: https://github.com/christopher-vollmers/Mandalorion and
Mandalorion supporting publication: https://www.nature.com/articles/ncomms16027?WT.feed_name=subjects_adaptive-immunity
Our corresponding publication discusses the use of Nanopore long read sequencing to resolve full length messenger RNA transcripts.  Nanopore generated .fastq format files are the raw input data and the output of the bioinformatics analysis are .psl alignment files and corresponding .fasta sequence files.
Genome_build: mm10
Supplementary_files_format_and_content: Output alignment files for individual nanopore reads are in .psl format with corresponding .fasta sequences.  The .psl file format is described here https://useast.ensembl.org/info/website/upload/psl.html.  .psl format alignment files can be visualized in a genome browser.  We prefer to use the IGV browser.

molecule: polyA RNA

organism: Mus musculus

source_name: Cochlea

extract_protocol:
Individual cells were dissociated from mouse cochlear tissue using a collagenase digestion and gentle tituration.  Cells were then isolated using pulled glass micropipettes, washed to remove extracellular contaminants and re-isolated.
Single cell reverse transciption and PCR amplification was performed using Smartseq2

tag: age

tag: background

tag: cell type

value: OHC


title: shCntrl.IFN-Neg.ChIP

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

library_source: genomic

data_processing:
Analysis of the ChIP-seq data was performed by assessing read quality using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and trimming reads using Trim-Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Single-end ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2.
Additional quality and filtering steps were undertaken; demarking duplicate reads with Picard Tools (http://picard.sourceforge.net) as well as by retaining reads that map uniquely to single loci.
Peak calling was performed using USeq (v8.6.0) [124], with window and extension sizes of 200 bp and 150 bp, respectively, utilizing non-specific input DNA as a control.
Genome_build: hg19
Supplementary_files_format_and_content: bed files – peaks

growth_protocol: Native ChIP was performed for HIRA as described [69] using an equimolar mixture of mouse mAbs to HIRA (WC15, WC19, WC117, WC 119, a gift from Professor Peter Adams (Beatson Institute for Cancer Research, University of Glasgow) or mouse mAb to HA tag (Covance, MMS-101R) as a species and class-matched negative control.

extract_protocol:
Fragmented chromatin was incubated with antibodies to HIRA and preimmobilized on Dynabeads.
Libraries were prepared from 10–20 ng of ChIP or input DNA using New England Biolabs ChIP-seq kit according to the manufacturer’s instructions
Resulting libraries were sequenced on an Illumina GAIIx to yield ∼30 million to 40 million raw reads.

treatment_protocol: For HIRA ChIP, native ChIP was performed using benzonase endonuclease for chromatin solubilization and fragmentation. After quenching with glycine, the cells were harvested and sonicated to produce soluble chromatin with DNA fragments in the range of 300–500 base pairs.

tag: genotype/variation

value: Short-hairpin control

tag: treatment

value: Control

tag: chip antibody

value: mouse mAbs to HIRA


title: benign T cell [4_CD4]

description:
benign T cell
4_CD4


title: benign T cell [3_CD8]

description:
benign T cell
3_CD8


title: benign T cell [1_CD4]

description:
benign T cell
1_CD4


title: HT1080_EWSR1-FLI1-EGFP_p4

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
Genome_build: ENSEMBL GRCh38
Supplementary_files_format_and_content: Tab-delimited file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis

molecule: total RNA

source_name: Fibrosarcoma cell line

growth_protocol: Culture media was supplemented with 5% or 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin. Stable expression of EGFP constructs were maintained by addition of 500 µg/ml Geneticin.

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit, including DNase treatment
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell line

tag: transfected gene


title: Brain + Aurantiochytrium 18W-13a 2

type: RNA

country: Japan

label: biotin

tag: strain

tag: tissue


title: benign T cell [3_GD]

description:
benign T cell
3_GD


title: DLG1_rep3

city: State College

first: Santhosh

last: Girirajan

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Trimmomatic (Bolger et al., 2014) v.0.36 was first used to trim reads as necessary, based on FastQC (bioinformatics.babraham.ac.uk/projects/fastqc) output.
TopHat2 v.2.1.1 (Kim et al., 2013) was used to align the raw sequencing data to the reference fly genome and transcriptome.
HTSeq-Count v.0.6.1 (Anders et al., 2015) was used to calculate raw read counts for each gene.
Genome_build: Dmel 6.08
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts for all transcripts (two-three technical replicates per biological sample in each file).

organism: Drosophila melanogaster

source_name: Drosophila whole head

growth_protocol: Flies were reared with Elav-Gal4 driver at 25°C on conventional cornmeal-sucrose-dextrose-yeast medium.

extract_protocol:
F1 female progeny were collected in groups of 40-50, quickly frozen in liquid nitrogen, and stored at −80°C. For RNA extraction, heads were separated from the bodies by repetitive cycles of freezing in liquid nitrogen and vortexing. Total RNA was isolated using TRIZOL (Invitrogen, Carlsbad, CA, USA).
We prepared cDNA libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

value: Drosophila whole head

tag: tissue-specific knockdown

value: neuronal

tag: RNAi driver

tag: human genotype

tag: fly genotype

tag: fly rnai line (vdrc)

tag: vdrc genetic background

value: GD


title: HSTL [7_TENOMIC184]

description:
benign B cell precursor
7_TENOMIC184

source_name: malignant

tag: disease state

value: malignant


title: benign T cell [4_CD8]

description:
benign T cell
4_CD8


title: DLG1_rep2


title: HSTL [3_TENOMIC181]

description:
benign B cell precursor
3_TENOMIC181


title: benign T cell [4_GD]

description:
benign T cell
4_GD


title: Nano_OHC_010

description: Single-Cell SmartSeq2 Nanopore

tag: age


title: HSTL [10_TENOMIC179]

description:
benign B cell precursor
10_TENOMIC179


title: Nano_OHC_009

description: Single-Cell SmartSeq2 Nanopore

tag: background


title: HT1080_EWSR1-FLI1-EGFP_p3


title: HT1080_EWSR1-FLI1-EGFP_p2


title: benign T cell [1_GD]

description:
benign T cell
1_GD


title: HSTL [8_TENOMIC037]

description:
benign B cell precursor
8_TENOMIC037


title: HSTL [11_TENOMIC663]

description:
benign B cell precursor
11_TENOMIC663


title: DLG1_rep1


title: Brain + Aurantiochytrium 18W-13a 1

tag: gender


title: HSTL [9_TENOMIC446]

description:
benign B cell precursor
9_TENOMIC446


title: HT1080_EWSR1-FLI1-EGFP_p1


title: Nano_OHC_008

description: Single-Cell SmartSeq2 Nanopore

tag: cell type


title: HSTL [1_Kab17]

description:
benign B cell precursor
1_Kab17


title: benign T cell [2_GD]

description:
benign T cell
2_GD


title: Brain + Imipramine 3

source_name: brain treated with Imipramine

tag: treatment

value: Imipramine


title: Patient 9

city: MURCIA

first: Raul

last: Teruel-Montoya

address: Ronda Garay s/n

department: Hematology and Medical Oncology Deparment

country: Spain

institute: Centro Regional de Hemodonación, Morales Meseguer University Hospital, IMIB-Arrixaca

description:
H_9
Cell microvesicles

data_processing:
For the normalization, it uses the average of two reference miRNA: hsa-miR-103a-3p and hsa-miR-191-5p.
Target gene signals normalized to reference miRNA (RMIR)s; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RMIR)
GSE122352_fold-change.txt reports patients/controls ratios.

label: Eva Green

source_name: Plasma Exosome

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Plasma exosomes

tag: disease status

value: Paroxysmal nocturnal hemoglobinuria


title: HSTL [2_Uk17]

description:
benign B cell precursor
2_Uk17


title: Nano_OHC_007

description: Single-Cell SmartSeq2 Nanopore


title: Nano_OHC_004

description: Single-Cell SmartSeq2 Nanopore


title: Nano_OHC_006

description: Single-Cell SmartSeq2 Nanopore


title: HSTL [4_TENOMIC182]

description:
benign B cell precursor
4_TENOMIC182


title: Nano_OHC_005

description: Single-Cell SmartSeq2 Nanopore


title: HSTL [6_TENOMIC014]

description:
benign B cell precursor
6_TENOMIC014


title: HSTL [5_TENOMIC183]

description:
benign B cell precursor
5_TENOMIC183


title: HT1080_EGFP_p4

tag: cell line

value: EGFP


title: Patient 7

description:
H_7
Cell microvesicles


title: Patient 8

description:
H_8
Cell microvesicles


title: HT1080_EGFP_p3

tag: transfected gene


title: Nano_OHC_003

description: Single-Cell SmartSeq2 Nanopore


title: Brain + Imipramine 2

tag: strain


title: Brain + water 2

source_name: brain treated with water

value: water

tag: tissue


title: Brain + water 3

value: ICR


title: Patient 6

description:
H_6
Cell microvesicles


title: Patient 5

description:
H_5
Cell microvesicles


title: Brain + Imipramine 1

value: male


title: Patient 4

description:
H_4
Cell microvesicles


title: Brain + water 1

value: limbic area of brain


title: Nano_OHC_002

description: Single-Cell SmartSeq2 Nanopore


title: HT1080_EGFP_p2


title: Nano_OHC_001

description: Single-Cell SmartSeq2 Nanopore


title: WTCHG_380869_250277: blank

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Pre-processing, gene and sample filtering, data visualization and analysis were performed using Scater (McCarthy et al, 2017),scran (Lun  et al, 2016), EdgeR (Robinson et al, 2010), WGCNA (Langefekder et al,2008) R packages. Data sets results comparisons were performed using GSEA ( Subramanian, Tamayo et al, 2005).TCR repertoire was inferred using TraCeR software (Stubbington et al,2016)
Hierarchical clustering analysis of cell transcription profiles was conducted in R employing highly variable genes (IQR >0.75(Gentleman et al., 2004)) and Euclidian distance.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_w_ercc.txt: Raw mapped genes read counts
Supplementary_files_format_and_content: sce_k_G1_tmm_voom_quant_norm_entrezIDs.txt: Normalized, voom transformed (log cpm) gene expression values. Filtered genes and samples.

organism: other sequences

source_name: blank

extract_protocol:
Extraction and reverse transcription was as described by Picelli et al. (Nature Protocols, 2014). Briefly, single cells were lysed with 2ul buffer containing 0.2% (vol/vol) Triton X-100 and 2Uµ-1 Rnase inhibitorand mixed 1µl oligo-dT primer and 1µl of dNTP mix. Samples were incubated at 72°C for 3 mins.  Reverse transcription mix containing SuperScript II (Invitrogen) reverse transcriptase 100 U, RNAase inhibitor 10 U, SuperScript II first-strand buffer, DTT 5mM, betaine 1 M, MgCl2 6mM, TSO 1 µM and nuclease free water, was added to the samples. Samples where incubated at 45°C for 90mins followed by 10 cycles of 50°C for 2mins and 42°C for 2 min.
Library preparation of purified amplified cDNA was performed using Nextera XT library preparation (Illumina, AUS). Following QC, 150 pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposons. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalization and pooling before loading onto the HiSeq 2500 (Illumina, AUS) for paired end sequencing.

treatment_protocol: MCMV (Strain Smith, ATCC: VR194) was  injected i.v. at a dose of 1 x 106 pfus. Spleen and gut was obtained day 28 post infection. Spleen was minced, passed through a 40µm filter and red blood cells lysed. To obtain IELs, Peyer’s patches and fecal content were first removed from intestines. The intestines were then flushed with PBS and cut open longitudinally. To separate IELs from intestinal tissue, intestinal tissue was incubated in HBSS supplemented with 5mM EDTA, 10% FCS, 25 mM HEPES for 20 min at 200 rpm at 37°C, passed through a 40 µm nylon filter and purified by Percoll (GE healthcare, Little Chalfont, UK) gradient centrifugation. CD8+ T-cells were enriched by negative selection using the Miltenyi Biotec GmbH CD8a+ T-cell isolation kit (Bergisch Gladbach, Germany) as per manufacturer’s instructions. After M38-tetramer and surface staining, tetramer+ CD3+ CD8+ single-cells were sorted in two 96-well plates using a SH800S cell sorter (Sony, Tokyo, Japan).

value: blank

tag: cell population

tag: genotype/variation

tag: sample number

tag: sample id


title: FBXO45_rep1

tag: tissue-specific knockdown

tag: RNAi driver

tag: human genotype

tag: fly genotype

value: Fsn

tag: fly rnai line (vdrc)


title: WTCHG_380869_229273: blank


title: HT1080_EGFP_p1


title: WTCHG_380869_206255: blank


title: Patient 3

description:
H_3
Cell microvesicles


title: WTCHG_380869_226249: blank


title: PDF.PGE2.6h.H3K27ac.rep2

status: Public on Mar 11 2019

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: replicate 2 of H3K27ac ChIP-seq in cells treated six hours with PGE-2

data_processing:
Reads were aligned to GRCh37 using bwa (version 0.6.2) After removal of PCR duplicates using Picard(http://broadinstitute.github.io/picard), read counts were normalized for sequencing depth and scaled to 10 million reads to generate bigwig files.
Genome_build: hg19

source_name: Adult normal Dermal fibroblast American Type Culture Collection (Catalog Number: PCS-201-012)

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

value: primary dermal fibroblasts

value: PGE-2 six hours

value: American Type Culture Collection (Catalog Number:PCS-201-012)

tag: chip antibody


title: PDF.PGE2.6h.H3K27ac.rep1

description: replicate 1 of H3K27ac ChIP-seq in cells treated six hours with PGE-2


title: Control 1

description:
C_1
Cell microvesicles

tag: cell type

value: Healthy


title: Control 4

description:
C_4
Cell microvesicles


title: PDF.control.H3K27ac.rep2

description: replicate 2 of H3K27ac ChIP-seq in untreated cells

tag: treatment

value: untreated


title: Patient 1

description:
H_1
Cell microvesicles

tag: disease status


title: BIN-67_MLL4_SMARCA4.T910M_ChIP-Seq

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 2.1.0, reporting only the highest scoring alignment for each sequence.
To create ChIP-seq coverage plots, bedGraph plots were created using MACS2 callpeak, sorted and then converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig script downloaded from UCSC

source_name: BIN-67 (SCCOHT)

growth_protocol: BIN-67 cell lines were grown in custom media (20% FBS, 40% DMEM, 40% DMEM/Ham’s F12). SCCOHT-1 cell lines were grown in RPMI supplemented with 10% FBS. All media was supplemented with pen/strep.

extract_protocol:
cells were fixed in 1% formaldehyde at 37 degrees Celsius for 10 minutes, quenched in 2.5 M glycine, and snap frozen. Cells were thawed and lysed and the prepared nuclei was placed in a Covaris miliTube and sonicated for 20 minutes on a Covaris AFA Sonicator at standard settings (140 PIP, 5 W, 10% duty factor). The equivalent of 10 million cells were used in each immunoprecpitation. Three micrograms of the following antibodies were used: anti-SMARCA4 (Abcam ab110641); anti-DPF2 (Abcam); anti-SMARCC1 (homemade rabbit antibody raised against amino acids 998-1073 of human protein); anti-SS18 (Cell Signaling Technologies D6I4Z); anti-ARID2 (Cell Signaling Technologies D8D8U); anti-H3K4me1 (Abcam); anti-H3K27ac (Abcam). IP’s were washed in 150 and 500 mM salt solution as well as a LiCl wash. Protein-DNA fragments were eluted using an SDS/DTT buffer and reverse crosslinked overnight. DNA was captured with SPRI beads (Agilent). Size selection was used to eliminate DNA too large for library prep. Rubicon library prep was used to generate libraries, and libraries were sequenced on Illumina NextSeq 500.
ChIP-sequencing libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols.

treatment_protocol: Virus was prepared using co-transfection of lentiviral packaging vectors along with SMARCA4 WT, T910M, K785R, and control in a pLEX307 vector backbone. Concentrated virus was added to 15 cm plates of BIN-67 cells at 70% confluency and selected for 2 days using puromycin. Four days later, cells were harvested for ChIP-seq.

tag: lentivirus

tag: cell line

value: MLL4, homemade (PMID:29404406)


title: BIN-67_MLL4_SMARCA4_ChIP-Seq


title: PDF.control.INPUT

description: INPUT library in untreated cells

value: INPUT


title: PDF.control.H3K27ac.rep1

description: replicate 1 of H3K27ac ChIP-seq in untreated cells


title: BIN-67_MLL3_Control_ChIP-Seq

value: Control

value: MLL3, homemade (PMID:29404406)


title: BIN-67_MLL4_Control_ChIP-Seq


title: BIN-67_MLL3_SMARCA4_ChIP-Seq


title: BIN-67_BAF155_Control_ChIP-Seq_Rep2

value: BAF155, homemade (PMID:28945250)


title: BIN-67_DPF2_SMARCA4_ChIP-Seq

value: DPF2, Abcam, ab134942


title: BIN-67_MLL3_SMARCA4.T910M_ChIP-Seq


title: Plasmacytoid dendritic cells sample 2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions.
A consensus peak set were called for the two biological samples compbined
Genome_build: hg19
Supplementary_files_format_and_content: Peak files associated with each population combined between replicates

source_name: human hematopoietic cells

growth_protocol: PBMCs were derived from a healthy donor

extract_protocol:
Digitonin-based lysis
FAST-ATAC-seq

tag: population


title: Myeloid dendritic cells sample 2


title: Myeloid dendritic cells sample 1


title: Plasmacytoid dendritic cells sample 1


title: Nano_OHC_011

description: Single-Cell SmartSeq2 Nanopore

tag: age

tag: background

value: OHC


title: Control 2

description:
C_2
Cell microvesicles

value: Plasma exosomes


title: BIN-67_H3K27me3_Control_ChIP-Seq

value: H3K27me3 (Cell Signaling Technologies, 9733S, 8)


title: BIN-67_H3K27ac_SMARCA4.T910M_ChIP-Seq


title: Patient 2

description:
H_2
Cell microvesicles

value: Paroxysmal nocturnal hemoglobinuria


title: BIN-67_45D_SMARCA4.K785R_ChIP-Seq


title: BIN-67_H3K4me1_Control_ChIP-Seq


title: BIN-67_ARID2_SMARCA4.K785R_ChIP-Seq

value: ARID2 (CST, D8D8U)


title: BIN-67_BAF155_SMARCA4.K785R_ChIP-Seq

value: BAF155 (Homemade, Fx3)


title: BIN-67_Input_SMARCA4.T910M_ChIP-Seq


title: BIN-67_45D_SMARCA4.T910M_ChIP-Seq


title: BIN-67_BRG1_SMARCA4.K785R_ChIP-Seq


title: BIN-67_Input_SMARCA4.K785R_ChIP-Seq


title: BIN-67_SS18_SMARCA4.T910M_ChIP-Seq

value: SS18 (Cell Signaling Technologies, D6I4Z)


title: BIN-67_ARID2_SMARCA4.T910M_ChIP-Seq


title: BIN-67_BRG1_SMARCA4.T910M_ChIP-Seq


title: BIN-67_45D_Control_ChIP-Seq


title: BIN-67_H3K27ac_SMARCA4_ChIP-Seq


title: BIN-67_H3K9me3_Control_ChIP-Seq


title: BIN-67_SS18_Control_ChIP-Seq


title: BIN-67_BRG1_Control_ChIP-Seq_Rep2


title: BIN-67_H3K4me1_SMARCA4_ChIP-Seq


title: BIN-67_BAF155_Control_ChIP-Seq


title: SCCOHT-1_45D_Null_ChIP-Seq

source_name: SCCOHT-1 (SCCOHT)


title: SCCOHT-1_BAF155_Null_ChIP-Seq


title: BIN-67_H3K27ac_Control_ChIP-Seq


title: BIN-67_45D_Null_ChIP-Seq


title: BIN-67_BAF155_Null_ChIP-Seq


title: BIN-67_SS18_SMARCA4_ChIP-Seq


title: BIN-67_H3K4me1_SMARCA4.T910M_ChIP-Seq


title: BIN-67_BAF155_SMARCA4_ChIP-Seq


title: BIN-67_Input_SMARCA4_ChIP-Seq


title: BIN-67_BRG1_SMARCA4_ChIP-Seq


title: BIN-67_Input_Control_ChIP-Seq


title: BIN-67_BRG1_Control_ChIP-Seq_Rep1


title: Bin67_K785R_RNA-Seq_Rep1

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2a Only uniquely mapping reads with at most two mismatches were retained.
RNA read counts were calculated using GFOLD
Genome_build: hg19
Supplementary_files_format_and_content: read count files for gene expression created using GFOLD

extract_protocol:
One million cells of each condition were harvested using Qiagen RNeasy kit and 1 ug was DNase treated and used in Illumina TruSeq Stranded mRNA library prep kit
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Virus was prepared using co-transfection of lentiviral packaging vectors along with SMARCA4 WT, T910M, K785R, and control in a pLEX307 vector backbone. Concentrated virus was added to 15 cm plates of BIN-67 cells at 70% confluency and selected for 2 days using puromycin. Two days later, cells were harvested for RNA-seq.


title: Bin67_SMARCA2_RNA-Seq_Rep2


title: Bin67_K785R_RNA-Seq_Rep2


title: BIN-67_ARID2_Control_ChIP-Seq


title: Bin67_Control_RNA-Seq_Rep2

value: Control (GFP)


title: Bin67_SMARCA2_RNA-Seq_Rep1


title: Bin67_Control_RNA-Seq_Rep1


title: Bin67_SMARCA4_RNA-Seq_Rep2


title: Bin67_SMARCA4_RNA-Seq_Rep3


title: Bin67_T910M_RNA-Seq_Rep2


title: FBXO45_rep3

tag: tissue

value: Drosophila whole head

value: neuronal

value: Fsn

tag: vdrc genetic background

value: GD


title: Bin67_SMARCA4_RNA-Seq_Rep1


title: BIN67_K785R_ATAC-Seq_Rep1

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
Quality read trimming was performed by Trimmmomatic v0.36
ATAC-seq reads were aligned to UCSC hg19 using Bowtie2 v2.29
Duplicate reads were removed using Picard v2.8
Reads were filtered for quality using SAMtools v1.19
Reads in regions considered 'excludable' were removed using BEDtools v2.26
To create ChIP-seq coverage plots, bedGraph plots were created using BEDtools genomeCoverageBed, sorted and then converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig script downloaded from UCSC

extract_protocol:
50,000 cells were harvested for each condition. ATAC-seq library prep was performed as in Buenrostro et al, 2015, CPMB.
Libraries were sequenced on a paired end Illumina NextSeq 500, with 4 samples on a single paired end lane

treatment_protocol: Virus was prepared using co-transfection of lentiviral packaging vectors along with SMARCA4 WT, T910M, K785R, and control in a pLEX307 vector backbone. Concentrated virus was added to 15 cm plates of BIN-67 cells at 70% confluency and selected for 2 days using puromycin. Two days later, cells were harvested for ATAC-seq.


title: BIN67_SMARCA2_ATAC-Seq_Rep2


title: Bin67_T910M_RNA-Seq_Rep1


title: BIN67_Control_ATAC-Seq_Rep2


title: BIN67_SMARCA2_ATAC-Seq_Rep1


title: BIN67_T910M_ATAC-Seq_Rep1


title: BIN-67_ARID2_SMARCA4_ChIP-Seq


title: BIN-67_SS18_SMARCA4.K785R_ChIP-Seq


title: BIN67_SMARCA4_ATAC-Seq_Rep2


title: BIN67_Control_ATAC-Seq_Rep1

treatment_protocol: Virus was prepared using co-transfection of lentiviral packaging vectors along with SMARCA4 WT, T910M, K785R, and control (GFP) in a pLEX307 vector backbone. Concentrated virus was added to 15 cm plates of BIN-67 cells at 70% confluency and selected for 2 days using puromycin. Two days later, cells were harvested for ATAC-seq.


title: Mouse_BCAA200_replicate6 [BCAA200M_197]

city: Sydney

first: Qiao-Ping

last: Wang

state: NSW

address: Johns Hopkins Dr

department: Charles Perkins Centre

country: Australia

institute: University of Sydney

description:
BCAA200M_197.txt
197_3_CAF1VANXX_CTTGTA_L001

data_processing:
Illumina Casava1.7 software used for basecalling.
The per base sequence quality for the 53,samples looked excellent with >91% bases above Q30
The reads were also screened for the presence of any Illumina,adaptor/overrepresented sequences and cross-species contamination
The cleaned sequence reads were then aligned against the Mus musculus genome (GRCm38).
The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were generated using Stringtie based on the formula: FPKM=106 C / (NL/103)
Genome_build: The transcripts were assembled with the Stringtie tool v1.2.4 utilizing the reads alignment with gencode M14
Supplementary_files_format_and_content: FPKM values for generating the heatmap and volcano plot

growth_protocol: 15 month old animals fed ad libitum on one of the 4 diets from 12 weeks of age until collection at 15 months.

extract_protocol:
Trizol
Illumina's TruSeq stranded RNA sample preparation protocol
Illumina's standard strategy

treatment_protocol: Four diets were isocaloric and with the same total macronutrient conent (18.8% protein, 63.4% carbohydrate, 17.8% fat, 14.4 MJ/Kg). Diets were modified from AIN93G by manipulating the BCAA content to the following: 200%, 100%(chow control), 50% or 20%.

tag: strain

value: 15 month

tag: gender

value: male

tag: bcaa content

value: twice BCAA content of control diet AIN93G

value: Hypothalamus


title: Mouse_BCAA200_replicate5 [BCAA200M_195]

description:
BCAA200M_195.txt
195_3_CAF1VANXX_GGCTAC_L001


title: Mouse_BCAA200_replicate4 [BCAA200M_175]

description:
BCAA200M_175.txt
175_3_CAF1VANXX_TAGCTT_L001


title: Mouse_BCAA200_replicate3 [BCAA200F_198]

description:
BCAA200F_198.txt
198_3_CAF1VANXX_GATCAG_L001

value: female


title: BIN67_SMARCA4_ATAC-Seq_Rep1


title: Mouse_BCAA200_replicate2 [BCAA200F_196]

description:
BCAA200F_196.txt
196_3_CAF1VANXX_ACTTGA_L001


title: Mouse_BCAA100_replicate5 [ChowM_25]

description:
ChowM_25.txt
25_3_CAF1VANXX_GCCAAT_L002

value: standard content of BCAAs


title: Mouse_BCAA100_replicate4 [ChowM_1]

description:
ChowM_1.txt
1_3_CAF1VANXX_TGACCA_L002


title: Mouse_BCAA200_replicate1 [BCAA200F_176]

description:
BCAA200F_176.txt
176_3_CAF1VANXX_CAGATC_L001


title: Mouse_BCAA100_replicate1 [ChowF_2]

description:
ChowF_2.txt
2_3_CAF1VANXX_ATCACG_L002


title: Mouse_BCAA50_replicate6 [BCAA50M_189]

description:
BCAA50M_189.txt
189_3_CAF1VANXX_GTGAAA_L001

value: containing one half of standard content of BCAAs


title: Mouse_BCAA100_replicate3 [ChowF_50]

description:
ChowF_50.txt
50_3_CAF1VANXX_TTAGGC_L002


title: Mouse_BCAA100_replicate2 [ChowF_26]

description:
ChowF_26.txt
26_3_CAF1VANXX_CGATGT_L002


title: Mouse_BCAA100_replicate6 [ChowM_49]

description:
ChowM_49.txt
49_3_CAF1VANXX_ACAGTG_L002


title: Mouse_BCAA20_replicate6 [BCAA20M_185]

description:
BCAA20M_185.txt
185_3_CAF1VANXX_GCCAAT_L001

value: containing one fifth of standard content of BCAAs


title: Mouse_BCAA50_replicate1 [BCAA50F_170]

description:
BCAA50F_170.txt
170_3_CAF1VANXX_AGTCAA_L001


title: Mouse_BCAA50_replicate2 [BCAA50F_172]

description:
BCAA50F_172.txt
172_4_CAF1VANXX_AGTTCC_L001


title: Mouse_BCAA50_replicate4 [BCAA50M_169]

description:
BCAA50M_169.txt
169_3_CAF1VANXX_CCGTCC_L001


title: Mouse_BCAA20_replicate2 [BCAA20F_184]

description:
BCAA20F_184.txt
184_3_CAF1VANXX_TTAGGC_L001


title: Mouse_BCAA20_replicate5 [BCAA20M_183]

description:
BCAA20M_183.txt
183_3_CAF1VANXX_ACAGTG_L001


title: Mouse_BCAA20_replicate1 [BCAA20F_164]

description:
BCAA20F_164.txt
164_3_CAF1VANXX_ATCACG_L001


title: Mouse_BCAA20_replicate3 [BCAA20F_186]

description:
BCAA20F_186.txt
186_4_CAF1VANXX_CGATGT_L001


title: SW620_6244R

city: Waltham

first: Aleksandra

last: Markovets

address: 35 Gatehouse Dr.

department: Oncology, iMED

institute: AstraZeneca

data_processing:
Illumina default software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference with NCBI build37.2 annotation using TopHat v2.0.6 with parameters --mate-std-dev=188, --b2-sensitive, --mate-inner-dist=32
Analysis of differentially expressed genes was performed using DESeq and EdgeR statistical packages. Differentially expressed genes were considered those with q value <0.05 (“high significance”) and additional genes with P value < 0.01 considered if fold change was > 3 or CPM difference >4  (“Marginal”)
Variant calling was performed using GATK, filtering for variants in CDS regions (inc. splice), non-synonymous, mean base quality > 30, depth >= 5, mutant allele frequency >= 0.05 (5%), mean positions in reads >= 8.
Genome_build: NCBI build37.2
Supplementary_files_format_and_content: tab delimited files with raw counts for each sample

source_name: Colorectal cancer

growth_protocol: Cells were grown in DMEM (HCT116R, HCT116R_6244R, HKH2, HKH2_6244R, LoVo, LoVo_6244R) or Leibovitz's L-15 (SW480, SW480_6244R, SW620, SW620_6244R) containing 10% FBS, penicillin (100 U mL-1), streptomycin (100 mg mL-1) and 2 mM glutamine. Liebovitz’s L-15 media was additionally supplemented with 0.75 mg mL-1 sodium bicarbonate. Cells were incubated in a humidified incubator at 37°C and 5% (v/v) CO2. For selumetinib-resistant cell lines, cells were grown in these media with added 2 µM selumetinib (HCT116R_6244R and HKH2_6244R), 4 µM selumetinib (LoVo_6244R), or 1 µM selumetinib (SW480_6244R and SW620_6244R).

extract_protocol: rRNA was depleted and strand-specific RNA-seq libraries were prepared using the Epicentre strand-specific ScriptSeq RNA-Seq Library Preparation Kit (Illumina, Eindhoven, Netherlands)

treatment_protocol: Cells were treated with fresh normal growth medium (with or without selumetinib as described above) for 24 hours.

tag: parental or resistant

value: Selumetinib-resistant

tag: selumetinib resistance concentration (um)


title: SW620

value: Parental


title: Mouse_BCAA50_replicate3 [BCAA50F_174]

description:
BCAA50F_174.txt
174_3_CAF1VANXX_ATGTCA_L001


title: SW480_6244R


title: LoVo


title: SW480


title: HCT116R_6244R


title: Mouse_BCAA20_replicate4 [BCAA20M_165]

description:
BCAA20M_165.txt
165_3_CAF1VANXX_TGACCA_L001


title: HKH2


title: LoVo_6244R


title: HKH2_6244R


title: siHNRNPAB-18-rep2

city: Toronto

first: Junjie

last: Hua

state: Ontario

address: 101 College Street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Reads were aligned against the human genome assembly Hg19 using TopHat2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts were generated by Rsubread (version 1.24.2) using Refgene annotation downloaded from UCSC

source_name: V16A cells

growth_protocol: V16A cell line was established by the Zoubeidi lab and cultured in RPMI1640 media with 10% FBS supplement. No mycoplasma contamination was detected in these cell lines using MycoAlert Mycoplasma Detection kit (LT07-118, Lonza).

extract_protocol:
RNA was extracted using RNAeasy mini kit (QIAgen) following manufacturer's protocol.
Library was constructed using Illumina TRuSeq Stranded mRNA Library Preparation Kit following manufacturer's protocol, and subsequently sequenced (50 bp single-end reads).

treatment_protocol: Cells were transfected with control siRNA, or siRNA targeting PCAT19-long isoform or HNRNPAB using lipofectamine RNAiMAX reagents.

value: V16A cells

tag: tumor type

value: Prostate cancer


title: siHNRNPAB-18-rep1


title: HCT116R


title: siHNRNPAB-17-rep1


title: siCtrl-hn-rep2


title: GSK-3alpha S21A knock-in1

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave MSB-I543

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

hyb_protocol: Hybridization and processing of Affymetrix arrays were performed according to Affymetrix standard protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

data_processing: Intensity values of all probe sets were normalized by the Robust Multichip Analysis (RMA) method using the Affymetrix Expression Console Software.

source_name: GSK-3alpha S21A_heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Baseline

tag: genotype

value: GSK-3alpha S21A

value: 3.6 month

value: Heart


title: GSK-3beta S9A knock-in2

source_name: GSK-3beta S9A_heart

value: GSK-3beta S9A

value: 3.5 month


title: GSK-3alpha S21A knock-in2


title: Wild-type2_control_for_alpha

description: The CEL file for this sample is identical to the CEL file of GSM3059009 but the processed data were normalized only with GSK-3alpha knockin samples.

value: wildtype


title: Wild-type2_control_for_beta

description: The CEL file for this sample is identical to the CEL file of GSM3059005 but the processed data were normalized only with GSK-3beta knockin samples.


title: Wild-type1_control_for_beta

description: The CEL file for this sample is identical to the CEL file of GSM3059004 but the processed data were normalized only with GSK-3beta knockin samples.


title: Wild-type1_control_for_alpha

description: The CEL file for this sample is identical to the CEL file of GSM3059008 but the processed data were normalized only with GSK-3alpha knockin samples.


title: V16A cells, siPCAT19-long rep2

data_processing:
Reads were aligned against the human genome assembly Hg19 using TopHat2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts were generated by Rsubread (version 1.24.2) using Refgene annotation downloaded from UCSC, with miTranscriptome PCAT19 annotations manually added

treatment_protocol: Cells were transfected with control siRNA or siRNA targeting PCAT19-long using lipofectamine RNAiMAX reagents.


title: V16A cells, siPCAT19-long rep1


title: siCtrl-hn-rep1


title: V16A cells, siCtrl rep1


title: V16A cells, siCtrl rep2


title: Rneasy_unsorted

city: Gent

first: Siebe

last: Loontiens

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

description: RNA isolated from 1 zebrafish embryo at the age of 5 days. RNA was isolated with the RNeasy plus micro kit

data_processing:
Fastq files were aligned to GRCz10 with STAR v2_4_2a.
Gene quantification was done on the fly by STAR on Danio_rerio.GRCz10.91.gtf
Genome_build: GRCz10
Supplementary_files_format_and_content: tsv files with raw count data

organism: Danio rerio

source_name: Fli:GFP, whole embryo 5 days, RNeasy, sample 1

extract_protocol:
polyA RNA
cDNA was synthesized according to the SMART seq V4 (takara biosystems) technology, tagmentation and sample barcoding with the Nextera XT kit (illumina)

tag: cell type

value: fli:GFP, whole embryo

value: 5 days

tag: rna isolation kit

value: RNeasy plus micro kit


title: siHNRNPAB-17-rep2


title: RNAqueous_unsorted

description: RNA isolated from 1 zebrafish embryo at the age of 5 days. RNA was isolated with the RNAqueous micro kit

source_name: Fli:GFP, whole embryo 5 days, RNAqueous, sample 1

value: RNAqueous micro


title: RNeasy_sorted_2_replicate_b

description: RNA isolated from 20 000 sorted fli:GFP zebrafish cells at the age of 3 days. RNA was isolated with the RNeasy plus micro kit

source_name: Fli:GFP, sorted, 3 days, RNeasy sample 2, replicate b

value: fli:GFP, GFP sorted

value: 3 days


title: RNeasy_sorted_2_replicate_a

source_name: Fli:GFP, sorted, 3 days, RNeasy sample 2, replicate a


title: RNeasy_sorted_2

source_name: Fli:GFP, sorted, 3 days, RNeasy sample 1


title: RNAqueous_sorted_2_replicate_b

description: RNA isolated from 20 000 sorted fli:GFP zebrafish cells at the age of 3 days. RNA was isolated with the RNAqueous micro kit

source_name: Fli:GFP, sorted, 3 days, RNAqueous, sample 2, replicate b


title: RNAqueous_sorted_1

source_name: Fli:GFP, sorted, 3 days, RNAqueous, sample 1


title: RNAqueous_sorted_2_replicate_a

source_name: Fli:GFP, sorted, 3 days, RNAqueous, sample 2, replicate a


title: Irf4-/- CD4+ TEa T cells_Rat IgG treated_rep

city: Houston

first: Hedong

last: Zhang

state: TX

address: 6670 Bertner Ave

department: Immunobiology & Transplant Science Center

institute: Houston Methodist Hospital Research Institute

description: Gene expression in Irf4-/- TEa CD4+ T cells, repeat

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (074809) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner(G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_jul11 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalization was performed by dividing all data points with the signal value of the 75th percentile of all of non-control probes , as suggested by Agilent.

source_name: Irf4-/- CD4+ TEa cells sorted from splenocytes of transplant recipients, treated with Rat IgG

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: TCR(Vα2+Vβ6+)CD45.2+CD4+ TEa cells were isolated from splenocytes of WT TEa or Irf4−/− TEa mice by a FACSAria flow cytometer (BD Biosciences).

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: B6.SJL CD45.1+ congenic mice were adoptively transferred with either 5 x 10e6 CD45.2+ WT TEa or 5 x 10e6 CD45.2+ Irf4‒/‒ TEa cells on day -1, and transplanted with Balb/c hearts on day 0. CD45.1+ mice adoptively transferred with either CD45.2+ Irf4‒/‒ TEa cells were i.p. injected with 400 μg Rat IgG, or 200 μg anti-PD-L1 plus 200 μg anti-CTLA-4 (9D9) mAbs on days 0, 3, 5. On day 6, adoptively transferred CD45.2+ TEa cells were sorted from splenocytes of transplant recipients by the FACSAria flow cytometer.

value: Spleen

value: CD4+ T cells

tag: background strain

value: Irf4 Knock out

tag: transplantation type

tag: treatment

value: Rat IgG treated


title: WT CD4+ TEa T cells_Rat IgG treated

description: Gene expression in WT TEa CD4+ T cells

source_name: WT CD4+ TEa cells sorted from splenocytes of transplant recipients, treated with Rat IgG

value: Wildtype


title: X212589

type: protein

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

hyb_protocol: Hybridization was performed following the standard operating protocol. See www.roche.com

scan_protocol: Fluorescent signal of the secondary antibody was detected by scanning at 635 nm at 2 µm resolution and 15% gain, using an MS200 microarray scanner (Roche NimbleGen)

data_processing: The intensity value of Ig binding to peptide was extracted from peptide arrays and a background correction was applied. 2-D Loess was used for the spatial correction. The extracted intensity levels were quantile normalized to remove variations between arrays.

molecule: protein

source_name: serum

label_protocol: Labeling was performed following the standard operating protocol. See www.roche.com

growth_protocol: Human serum samples, without in vitro growth

extract_protocol: Serum samples were dilutedd 1:100 in binding buffer, following the standard operating protocol. See www.roche.com

treatment_protocol: Serum samples from patients

tag: histology

value: control

tag: phenotype


title: Irf4-/- CD4+ TEa T cells_checkpoint blockade treated

description: Gene expression in checkpoints blockade treated Irf4-/- TEa CD4+ T cells

source_name: Irf4-/- CD4+ TEa cells sorted from splenocytes of transplant recipients, treated with checkpoints blockade

value: checkpoint blockade treated


title: X212803

value: Squamous cell

value: case


title: Irf4-/- CD4+ TEa T cells_checkpoint blockade treated_rep

description: Gene expression in checkpoints blockade treated Irf4-/- TEa CD4+ T cells, repeat

value: Heart


title: X212590


title: X212602


title: X212579


title: X212600


title: X212801


title: X212571

value: Adenocarcinoma


title: X212572


title: X212800


title: X212603


title: X212567


title: X212592


title: WT CD4+ TEa T cells_Rat IgG treated_rep

description: Gene expression in WT TEa CD4+ T cells, repeat


title: X212566


title: X212591


title: X212563


title: X212562


title: Irf4-/- CD4+ TEa T cells_Rat IgG treated

description: Gene expression in Irf4-/- TEa CD4+ T cells


title: X212564


title: X212565


title: X212580


title: X212561


title: X212557


title: X212551


title: X212556


title: X212550


title: X212555


title: X212297

value: Other NSCLC


title: X212294


title: X212295


title: X212267


title: X212529


title: X212296


title: X212530


title: X212288


title: X212264


title: X212531


title: X212289


title: X212263


title: X212265


title: X212293


title: X212261


title: X212260


title: X212259


title: X212258


title: X212549


title: X212256


title: X212249


title: X212244


title: X212242


title: X212247


title: X212262


title: X212220


title: X212243


title: X212255


title: X212236


title: X212213


title: X211982


title: X211987


title: X211985


title: X212212


title: X211986


title: BIN-67_BAF155_SMARCA4.T910M_ChIP-Seq

source_name: BIN-67 (SCCOHT)

tag: lentivirus

tag: cell line

tag: chip antibody

value: BAF155 (Homemade, Fx3)


title: GSK-3beta S9A knock-in1

tag: strain

value: GSK-3beta S9A

tag: age

value: 3.5 month

tag: tissue


title: X211972


title: X212257


title: X212601


title: Rad21 ChIP-seq CTL

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

data_processing:
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

source_name: ChIP-seq under normal conditions

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-RNAPII or anti-Rad21 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol for ChIP-seq and Hi-C or using a Tn5 library prepartion protocol for HiChIP. Genomic fragments were end repaired, A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). For Tn5 protocol samples were incubated with Tn5 transposase in the presence of adaptors. Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

value: Embryonic Cell Line

tag: chip-antibody


title: X212216


title: X211971


title: Mouse_BCAA50_replicate5 [BCAA50M_187]

description:
BCAA50M_187.txt
187_3_CAF1VANXX_GTCCGC_L001

value: 15 month

tag: gender

value: male

tag: bcaa content

value: containing one half of standard content of BCAAs

value: Hypothalamus


title: X212245


title: Cap-H2 ChIP-seq FLV

source_name: ChIP-seq after 3 hours Flv treatment

value: 3 hours Flv treatment


title: X211963


title: X211989


title: X211988


title: RNAPII ChIP-seq CTL rep2

value: RNAPII (biolegend 664906)


title: Cap-H2 ChIP-seq CTL


title: X211962

value: control


title: RNAPII ChIP-seq Cap-H2 KD rep2

source_name: ChIP-seq after knockdown of Cap-H2

tag: genotype/variation

value: Cap-H2 knockdown


title: X211956


title: X211959


title: X211957


title: X211954

value: Squamous cell


title: X211964

value: case


title: RNAPII ChIP-seq Cap-H2 KD rep1

tag: cell type


title: X212215


title: RNAPII ChIP-seq Rad21 KD

source_name: ChIP-seq after knockdown of Rad21

value: Rad21 knockdown


title: X211950


title: X211951


title: X211944


title: RNAPII ChIP-seq CTL rep1


title: X211952


title: X211943


title: X211942


title: X211939

value: Adenocarcinoma


title: X211970


title: X211937


title: Sample_72N

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

country: China

institute: Wuhan University

data_processing:
Fastq files were aligned with  bowtie2 to remove rRNA
unmapped fastq files  were aligned with hisat2
Convert SAM to BAM using samtools with parameter -q 30
Remove pcr duplicates with picard
featureCounts were used to count reads
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count

source_name: adjacent normal tissue

extract_protocol:
The total RNA samples of three pairs of Clear Cell Renal cell carcinoma and adjacent normal tissues were treated with the RiboZero rRNA Removal Kit and RNase R for deleting rRNA and linear RNA, according to the manufacturer’s instructions.  The rRNA depleted and RNase R digested RNA samples were fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced by HiSeq2500 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols, total RNA with strand-specific, rRNA-depleted

tag: subject status

value: Clear Cell Renal cell carcinoma

tag: tissue type

value: adjacent normal tissue


title: X211935


title: X211960


title: X211933


title: Sample_65T

source_name: Clear Cell Renal cell carcinoma tissue

value: Clear Cell Renal cell carcinoma tissue


title: Sample_65N


title: Sample_72T


title: Rad21 ChIP-seq FLV


title: Sample_60T


title: Sample_60N


title: X211878


title: X211910


title: X211842


title: X211921


title: X211920


title: X211922


title: X211911


title: X211926


title: 22Rv1-H3K4me3-ChIP-seq

data_processing:
All ChIP-seq data were aligned using Bowtie2 (version 2.2.1) to the human genome of build version NCBI37/HG19
MACS2 was used for peak calling with the parameter "--SPMR" and "--keep-dup=1".
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated by UCSC bedGraphToBigWig tool from resultant bedgraph files.

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cell line wasobtained from the American Type Culture Collection (ATCC), and cultured in RPMI1640 media with 10% FBS supplement. No mycoplasma contamination was detected in these cell lines using MycoAlert Mycoplasma Detection kit (LT07-118, Lonza).

extract_protocol:
Nuclear lysates were obtained from sonicated nuclei, and protein-DNA complexes were subsequently isolated with the appropriate antibodies.
Library was constructed using Rubicon ThruPLEX-FD kit and sequenced (75 bp single-end reads).

value: 22Rv1 cells

tag: tumor type

value: Prostate cancer


title: X211839


title: X211865


title: X211840


title: Sample 30: elav-Gal4>UAS-ap,eya; AFT

city: Linkoping

first: Johannes

last: Stratmann

state: Ostergotland

address: Linkoping University Campus HU

department: Insitute for clinical and experimental medicine

institute: Linkoping Univeristy

description:
elav-Gal4>UAS-ap,eya
Experiment 5

data_processing:
Expression profiles and normalized abundance measurements of transcripts were determined using Kallisto (release 0.43.1) adjusted as transcripts per million (TPM) units. We have shown TPMs of all genes for all samples after merging the three replicates, in addtion we have shown the linear and log2 TPMs for each merged sample as well as the fold change and log2 fold change of TPMs (Control VS Experiment) for all genes falling into the 2FC difference between control and experiment.
Reference genome for RNA_seq aligment (Dmel CDS, BDGP6 from  ensemble.org)

source_name: whole embryo

extract_protocol:
Drosophila embryos at stages 16-AFT have been collected in 3 biological replicates per genoptype (>200 embryo); sampel collections were used for RNA extraction, using RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA sequencing was performed by (GeneWiz, New Jersey, NJ), in 2x150 bp paired end sequencing configuration for AFT samples or 1X50bp single read sequencing configuration for stage 16 samples , which yielded 30-50M reads/sample.

value: whole embryo

tag: embryonic stage

value: AFT

tag: strain/genotype

value: Drosophila melanogaster. UAS-Flag-Ap/+; elav-Gal4 (Bl#458)/UAS-eya-HPC4


title: X211841

tag: histology

tag: phenotype


title: X211837


title: X211835


title: 22Rv1-H3K4me1-ChIP-seq


title: X211819


title: X211927


title: Sample 25: elav-Gal4>UAS-col,lbe; AFT

description:
elav-Gal4>UAS-col,lbe
Experiment 4

value: Drosophila melanogaster. elav-Gal4 (Bl#458)/UAS-col-HA,UAS-myc-lbe


title: Sample 27: elav-Gal4>UAS-col,lbe; AFT

description:
elav-Gal4>UAS-col,lbe
Experiment 4


title: Sample 26: elav-Gal4>UAS-col,lbe; AFT

description:
elav-Gal4>UAS-col,lbe
Experiment 4


title: X211815


title: X211596


title: X211818


title: X211593

value: Other NSCLC


title: X211597


title: X211590


title: Sample 23: elav-Gal4>UAS-lbe; AFT

description:
elav-Gal4>UAS-lbe
Experiment 3

value: Drosophila melanogaster. elav-Gal4 (Bl#458)/UAS-myc-lbe


title: Sample 20: elav-Gal4>UAS-col; AFT

description:
elav-Gal4>UAS-col
Experiment 2

value: Drosophila melanogaster. elav-Gal4 (Bl#458)/UAS-col-HA


title: Sample 22: elav-Gal4>UAS-lbe; AFT

description:
elav-Gal4>UAS-lbe
Experiment 3


title: X211588


title: X211587


title: X211585

value: control


title: Sample 16: elav-Gal4/+ ; AFT

description:
elav-Gal4/+
Experiment 1

value: Drosophila melanogaster. elav-Gal4 (Bl#458)/OregonR (BDSC# 2376)


title: Sample 15: elav-Gal4>UAS-ap,eya; St16

description:
elav-Gal4>UAS-ap,eya
Experiment 5


title: Sample 19: elav-Gal4>UAS-col; AFT

description:
elav-Gal4>UAS-col
Experiment 2


title: X211591

value: case


title: X211583

value: Squamous cell


title: Sample 29: elav-Gal4>UAS-ap,eya; AFT

description:
elav-Gal4>UAS-ap,eya
Experiment 5


title: Sample 24: elav-Gal4>UAS-lbe; AFT

description:
elav-Gal4>UAS-lbe
Experiment 3


title: X211577


title: Sample 14: elav-Gal4>UAS-ap,eya; St16

description:
elav-Gal4>UAS-ap,eya
Experiment 5


title: X211581


title: X211589


title: Sample 11: elav-Gal4>UAS-col,lbe; St16

description:
elav-Gal4>UAS-col,lbe
Experiment 4


title: Sample 12: elav-Gal4>UAS-col,lbe; St16

description:
elav-Gal4>UAS-col,lbe
Experiment 4


title: X211574


title: Sample 13: elav-Gal4>UAS-ap,eya; St16

description:
elav-Gal4>UAS-ap,eya
Experiment 5


title: Sample 21: elav-Gal4>UAS-col; AFT

description:
elav-Gal4>UAS-col
Experiment 2


title: X211578


title: Sample 9: elav-Gal4>UAS-lbe; St16

description:
elav-Gal4>UAS-lbe
Experiment 3


title: Sample 17: elav-Gal4/+ ; AFT

description:
elav-Gal4/+
Experiment 1


title: Sample 18: elav-Gal4/+ ; AFT

description:
elav-Gal4/+
Experiment 1


title: X211582


title: Sample 7: elav-Gal4>UAS-lbe; St16

description:
elav-Gal4>UAS-lbe
Experiment 3


title: Sample 10: elav-Gal4>UAS-col,lbe; St16

description:
elav-Gal4>UAS-col,lbe
Experiment 4


title: X211572


title: X211576


title: Sample 6: elav-Gal4>UAS-col; St16

description:
elav-Gal4>UAS-col
Experiment 2


title: X211573


title: Sample 8: elav-Gal4>UAS-lbe; St16

description:
elav-Gal4>UAS-lbe
Experiment 3


title: X211569


title: Sample 5: elav-Gal4>UAS-col; St16

description:
elav-Gal4>UAS-col
Experiment 2


title: X211568


title: Sample 4: elav-Gal4>UAS-col; St16

description:
elav-Gal4>UAS-col
Experiment 2


title: X211567


title: Sample 3: elav-Gal4/+ ; St16

description:
elav-Gal4/+
Experiment 1


title: X211566


title: X211565


title: X211563

value: Adenocarcinoma


title: X211562


title: X211571


title: Sample 1: elav-Gal4/+ ; St16

description:
elav-Gal4/+
Experiment 1


title: BY4741A_INPUT_rep1

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Yeast chromatin immunoprecipitation and library construction were performed as described previously28. Resulting ChIP-seq libraries were single-read (SR) sequenced on the Illumina NextSeq 500 Sequencing System. ChIP-seq reads were trimmed from the 3′ end until the final base had a quality score > 30 and a minimal length of 20nt, using Trimmomatic29, and were aligned to the yeast genome (UCSC sacCer3, using Bowtie version 1.1.2)30. Only uniquely mapping reads with no more than two mismatches over the entire length of the read were considered for further analysis (options –m 1 –v 2). ChIP-seq reads were extended to 150 nt and were normalized to total reads aligned (reads per million, r.p.m.), and were formatted as bigWig coverage plots. Peaks were called from the aligned reads using MACS version 2.1.1 with options -B --nomodel --extsize 14731. Gene annotations and transcript start site information are from Ensembl release 78. Genes considered for analysis had to be at least 400nt long. Body promoter occupancy ratios (BPOR) were calculated for protein coding genes that had a called peak overlapping the TSS site for H3K4me2 and H3K4me3 individually by taking the average coverage in r.p.m. in the gene body (300 bp downstream of the TSS to the end of the gene) divided by the average coverage of the promoter region (100 upstream of the TSS to 300 downstream of the TSS).  P-values were then calculated with a two-sided Kolmogorov-Smirnov test. The empirical density distributions were calculated and plotted for all BPOR values. Metagene plots were obtained by approximating all genes to the same length. Peak centered heat maps were done with a 2kb window around the peak center. Both metagene and peak centered heatmps read coverage (r.p.m.) was binned into 25bp windows and averaged clustered with kmeans clustering. Heatmaps were made using Java TreeView version 1.6.432. Average profile plots were constructed using the colMeans function in R. For peak centered heatmap clusters, peaks were assigned to the nearest protein coding TSS, and GO term analysis was done using topGO version 2.26.0 (Alexa A and Rahnenfuhrer J (2016) topGO: Enrichment Analysis for Gene Ontology) using the Fisher’s exact test.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cell cultures were grown in YPD medium with OD600 ~1.0 (exponentially growing (LOG) phase).

extract_protocol:
Yeast cells were cracked with glass beads and bead-beater, and sonicated. Lysates were clarified with centrifugation and DNA-histone complexes were isolated with antibodies.
The libraries for sequencing were prepared with Illumina’s Tru-seq DNA sample prep kit.

treatment_protocol: Yeast cell cultures were fixed with 2% formaldehyde and fixation was quenched with 133mM Glycine.

tag: mutation

value: no antibody


title: X211564


title: cps25delta_LOG_H3K4me3_rep2

tag: chip antibody

value: Rb polyclonal homemade antibody #28


title: Sample 2: elav-Gal4/+ ; St16

description:
elav-Gal4/+
Experiment 1


title: X211554


title: set1delta_LOG_H3K4me2_rep1

tag: strain

value: Rb polyclonal homemade antibody #27


title: set1delta_LOG_H3K4me3_rep2


title: cps25delta_LOG_H3K4me3_rep1


title: X211555


title: set1delta_LOG_H3K4me3_rep1


title: cps25delta_LOG_H3K4me2_rep1


title: set1delta_LOG_H3K4me2_rep2


title: cps25delta_LOG_H3K4me2_rep2


title: X211548


title: X211550


title: X211551


title: X211549


title: X211547


title: cps25_WT_LOG_H3K4me3_rep1


title: cps25_WT_LOG_H3K4me2_rep2


title: cps25_WT_LOG_H3K4me3_rep2


title: X211546


title: X211553


title: X211552


title: X211544


title: cps25_WT_LOG_H3K4me2_rep1


title: X211542


title: X211538


title: cps25_A142D_LOG_H3K4me2_rep2


title: X211537


title: cps25_A142D_LOG_H3K4me3_rep2


title: mouse.male.cb.wt.untreated.7mo_31

city: South San Francisco

first: Carmela

last: Sidrauski

state: California

address: 1170 Veterans Blvd

institute: Calico Life Sciences

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.7mo_1

data_processing:
Alignment to mm10 reference genome using STAR 2.5.3a
Quantification of gene expression levels using MMSEQ
Collapse of transcripts to genes using mmcollapse of MMDIFF, conversion to TPM units
Differentiatl expression performed with MMDIFF
Genome_build: mm10
Supplementary_files_format_and_content: abundance.csv (abundance measurements) and results.csv (differential expression) files
[mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv]  Abundance measurements for RNA-seq time course
[mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv]  Differential expression test between WT ahd HO R191H animals using MMDIFF
[mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv]  Abundance measurements for 2BAct pharmacology, 1 month of treatment, profiled at 2 months of age
[mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv]  Differential expression test between WT vehicle-treated animals compared to 2BAct treated animals using MMDIFF

extract_protocol:
RNA-seq libraries were prepared using purified RNA isolated from frozen tissue using the RNeasy Mini kit. RNA quality and concentration were assayed using a Fragment Analyzer instrument.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit.

treatment_protocol: RNA extracted from cerebella of male HO R191H and WT mice at 2, 5, and 7 months. RNA extracted from cerebella of 2 month female HO R191H and WT mice, treated with either 2BAct or vehicle for 1 month. 2BAct was administered orally in rodent meal at 300 µgrams 2BAct/grams of meal.

value: Cb

tag: age

tag: Sex

value: male

tag: genotype

value: WT

tag: treatment

value: untreated

tag: replicate


title: cps25_A142D_LOG_H3K4me3_rep1


title: X211536


title: cps25_A142D_LOG_H3K4me2_rep1


title: X211534


title: X211533


title: X211531


title: mouse.male.cb.ho.untreated.7mo_48

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.7mo_3

tag: tissue


title: mouse.male.cb.ho.untreated.7mo_46

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.7mo_1


title: X211532


title: mouse.male.cb.wt.untreated.5mo_39

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.5mo_3


title: mouse.male.cb.wt.untreated.5mo_38

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.5mo_2


title: mouse.male.cb.wt.untreated.5mo_37

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.5mo_1


title: X211528


title: X211530


title: X211527


title: mouse.male.cb.wt.untreated.7mo_32

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.7mo_2


title: mouse.male.cb.ho.untreated.5mo_28

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.5mo_3


title: X211526


title: X211543


title: X211524


title: mouse.male.cb.ho.untreated.5mo_23

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.5mo_1


title: X211517


title: mouse.male.cb.ho.untreated.7mo_47

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.7mo_2


title: Sample 28: elav-Gal4>UAS-ap,eya; AFT

description:
elav-Gal4>UAS-ap,eya
Experiment 5

value: whole embryo

value: AFT

value: Drosophila melanogaster. UAS-Flag-Ap/+; elav-Gal4 (Bl#458)/UAS-eya-HPC4


title: mouse.male.cb.wt.untreated.2mo_59

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.2mo_3


title: mouse.male.cb.ho.untreated.5mo_26

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.5mo_2


title: X211511


title: X211529


title: mouse.male.cb.ho.untreated.2mo_55

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.2mo_3


title: mouse.male.cb.wt.untreated.2mo_57

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.2mo_1


title: X211508


title: X211505


title: mouse.male.cb.ho.untreated.2mo_54

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.2mo_2


title: mouse.male.cb.ho.untreated.2mo_52

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
ho.2mo_1


title: X211507


title: X211503


title: mouse.female.cb.wt.vehicle.2mo_129

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.vehicle_1

value: female

value: vehicle


title: mouse.female.cb.wt.vehicle.2mo_131

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.vehicle_2


title: X211502


title: mouse.female.cb.wt.vehicle.2mo_133

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.vehicle_3


title: mouse.male.cb.wt.untreated.2mo_58

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.2mo_2


title: X211525

value: control


title: X211501

value: Other NSCLC


title: X211500

value: case


title: mouse.female.cb.wt.4916.2mo_132

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.2BAct_3


title: mouse.female.cb.wt.4916.2mo_127

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.2BAct_2


title: mouse.male.cb.wt.untreated.7mo_33

description:
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_abundance.csv
mmdiff_collapsed_gene_mouse_vwm_male_cb_ho_vs_wt_results.csv
wt.7mo_3


title: X211498


title: X211499


title: mouse.female.cb.ho.vehicle.2mo_106

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.vehicle_2


title: X211504


title: mouse.female.cb.wt.4916.2mo_126

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
wt.2BAct_1


title: mouse.female.cb.ho.vehicle.2mo_107

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.vehicle_3


title: X211497


title: mouse.female.cb.ho.4916.2mo_115

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.2BAct_3


title: mouse.female.cb.ho.vehicle.2mo_105

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.vehicle_1


title: mouse.female.cb.ho.4916.2mo_112

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.2BAct_1


title: mouse.female.cb.ho.4916.2mo_114

description:
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_abundance.csv
mmdiff_collapsed_gene_mouse_vwm.cb_female_2BAct_results.csv
ho.2BAct_2


title: r4_d35_t15

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

institute: Imperial College

description: Mnase digested DNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1  T.acidophilum genome assembly obtained from ncbi using Bowtie2
Paired-end 100bp reads were first trimmed using BBDuk v37.64 (parameters: ktrim=r, k=21, hdist=1, edist=0, mink=11, qtrim=rl, trimq=30, minlength=10, ordered=t, qin=33) and then merged using BBmerge v37.64 (parameters: mininsert=10, mininsert0=10).
The merged reads were then mapped to the T. acidophilum DSM1728 genome (GCA_000195915.1) using Bowtie2 (-U).
Coverage tracks were computed using deeptools bamCoverage (RPGC normalization, effective genome size: 1564906bp), measuring coverage for reads of sizes 40-65bp and 70-100bp separately. Reads from the sonicated DNA control samples were mapped in paired-end mode. Coverage was computed independently of read size and smoothed over 10kbp to avoid introducing noise from the input into the MNase signal. Genome-wide coverage of MNase-digested samples was then divided by its corresponding undigested DNA sample to remove bias in coverage associated with replication. Lastly, coverage was converted into a Z-score using the scale function in R.
Genome_build: NC_002578.1
Supplementary_files_format_and_content: Detected peaks on normalized coverage files

organism: Thermoplasma acidophilum

source_name: Thermoplasma acidophilum cells

growth_protocol: T. acidophilum strain 122-1B2 was obtained from DSMZ (https://www.dsmz.de/) and cultured using the medium described in (Searcy and Stein 1980), supplemented to a final concentration of 2g/L yeast extract (BD Biosciences). The medium was boiled for five minutes and allowed to cool to 58°C before inoculation. Cultures were incubated at 59°C with shaking (90rpm) in an INFORS Thermotron incubator.

extract_protocol:
DNA was extracted by phenol chloroform extraction and precipitated with ethanol.
For MNase digestion experiments paired-end reads were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: T. acidophilum cells self-lyse at pH>6 (Robb et al. 1995). Pellets were therefore directly re-suspended in ice-cold MNase digestion buffer (10mM Tris, 5mM Ca2+, pH8) and homogenized by 20 passages through a Dounce homogenizer, on ice. Unfixed crude lysates were digested in the presence of 4U/mL of MNase (Thermo Fisher) at 37°C. Digestion was stopped by addition of EDTA to a final concentration of 20mM. Samples were incubated for an additional 30min at 37°C in the presence of RNAse A to a final concentration of 0.5mg/mL and then overnight at 65°C in the presence of SDS (1%) and proteinase K (125µg/mL). Undigested lysate was incubated as above but without addition of enzyme. Undigested DNA was then sonicated using a Covaris S220 sonicator with the following settings: peak power: 175, duty: 10, cycle/burst: 200 for 430s (target size: 150bp).

tag: time

value: 80 hours after inoculation

value: 15 min digestion


title: r4_d3_t15

description: Mnase digested DNA

value: 72 hours after inoculation


title: r3_d3_t15

description: Mnase digested DNA


title: r3_d3_t0

description: Sheared genomic DNA

value: Undigested


title: WT_TmBr_TBSp4_B2: WT tumor bearing_RNA-Seq_rep4

city: Bethesda

first: Stefano

last: Marenco

state: MD

address: Building 10, Room 4N306

institute: National Institute of Mental Health

description:
sample name in processed data file:
WT_TmBr_TBSp4_B2

data_processing:
RTA 1.18.64 software used for basecalling.
The sequencing reads were trimmed using Trimmomatic (version 0.30), demultiplexing was done using Bcl2fastq 1.8.4, then mapped to hybrid genome of mm10 and LCMV using STAR version 2.5.2b with two-pass alignment option
The mapped reads in the genomic features were counted by RSEM (version 1.2.22)
Genome_build: hybrid genome (GENECODE Mouse (mm10) and Lymphocytic choriomeningitis virus (NC_004291.1))
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each Sample.

source_name: NK cells

extract_protocol:
Lin-NK1.1+NKp46+ cells were sorted from spleens of naïve and B16F10 tumor-bearing mice. Total RNA was isolated from sorted cells using TRIzol (Ambion part of Life Technologies) following the manufacturer’s protocols. During RNA isolation, DNase treatment was additionally performed using the RNase-free DNase set (Qiagen). RNA quality was checked using an Agilent 2100 Expert bioanalyzer (Agilent Technologies). RNA quality was reported as a score from 1 to 10, and samples falling below the threshold of 8.0 were omitted from the study. cDNA library preparation involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go to the sequencer. The final purified product is then quantitated by qPCR before cluster generation and sequencing. Paired-end sequencing (2 × 150 bp) of stranded total RNA libraries was performed on one HiSeq run with Illumina HiSeq3000/4000 chemistry pair end sequencing. The samples have 99 to 148 million pass filter reads with a base call quality of above 92% of bases with Q30 and above.
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina bcl2fastq1.8.4 was used to demultiplex and convert binary base calls and qualities to fastq format. The sequencing reads were trimmed adapters and low-quality bases using Trimmomatic (version 0.30), the trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M9 using STAR (version 2.5) with two-pass alignment option. RSEM (version 1.2.22) was used for transcript quantification.

value: spleen

tag: cell type

value: natural killer (NK)

value: wildtype

tag: infected with

value: Lymphocytic choriomeningitis virus


title: WT_TmBr_TBSp2_B2: WT tumor bearing_RNA-Seq_rep3

description:
sample name in processed data file:
WT_TmBr_TBSp2_B2


title: r3_d2_t15

description: Mnase digested DNA

value: 48 hours after inoculation


title: WT_TmBr_3: WT tumor bearing_RNA-Seq_rep2

description:
sample name in processed data file:
WT_TmBr_3


title: r3_d2_t0

description: Sheared genomic DNA


title: r3_d1_t30

description: Mnase digested DNA

value: 24 hours after inoculation

value: 30 min digestion


title: r4_d2_t15

description: Mnase digested DNA


title: r3_d35_t0

description: Sheared genomic DNA


title: WT_TmBr_2: WT tumor bearing_RNA-Seq_rep1

description:
sample name in processed data file:
WT_TmBr_2


title: KO_TmBr_TBSp4_B2: Cd47-/- tumor bearing_RNA-Seq_rep4

description:
sample name in processed data file:
KO_TmBr_TBSp4_B2


title: KO_TmBr_TBSp1_B2: Cd47-/- tumor bearing_RNA-Seq_rep3

description:
sample name in processed data file:
KO_TmBr_TBSp1_B2


title: KO_TmBr_4: Cd47-/- tumor bearing_RNA-Seq_rep2

description:
sample name in processed data file:
KO_TmBr_4


title: r3_d1_t0

description: Sheared genomic DNA


title: r2_d35_t15

description: Mnase digested DNA


title: r3_d1_t15

description: Mnase digested DNA


title: WT_UnInf5: WT uninfected_RNA-Seq_rep6

description:
sample name in processed data file:
WT_UnInf5

extract_protocol:
Lin-NK1.1+NKp46+ cells were sorted from spleens of naïve and LCMV-Arm infected mice. Total RNA was isolated from sorted cells using TRIzol (Ambion part of Life Technologies) following the manufacturer’s protocols. During RNA isolation, DNase treatment was additionally performed using the RNase-free DNase set (Qiagen). RNA quality was checked using an Agilent 2100 Expert bioanalyzer (Agilent Technologies). RNA quality was reported as a score from 1 to 10, and samples falling below the threshold of 8.0 were omitted from the study. cDNA library preparation involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go to the sequencer. The final purified product is then quantitated by qPCR before cluster generation and sequencing. Paired-end sequencing (2 × 150 bp) of stranded total RNA libraries was performed on one HiSeq run with Illumina HiSeq3000/4000 chemistry pair end sequencing. The samples have 99 to 148 million pass filter reads with a base call quality of above 92% of bases with Q30 and above.
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina bcl2fastq1.8.4 was used to demultiplex and convert binary base calls and qualities to fastq format. The sequencing reads were trimmed adapters and low-quality bases using Trimmomatic (version 0.30), the trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M9 using STAR (version 2.5) with two-pass alignment option. RSEM (version 1.2.22) was used for transcript quantification.

value: uninfected


title: KO_TmBr_3: Cd47-/- tumor bearing_RNA-Seq_rep1

description:
sample name in processed data file:
KO_TmBr_3


title: C6244R-SEL 48h B

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

hyb_protocol: Samples were hybridized to Illumina Whole-Genome Gene Expression HumanHT-12 v4 Chips (Illumina, Eindhoven, Netherlands), washed and analytical probes bound according to manufacturer's instructions.

scan_protocol: Array scanning was performed using BeadArray Reader (Illumina, Eindhoven, Netherlands) and features extracted using Illumina BeadStudio software (Illumina, Eindhoven, Netherlands).

data_processing: The data was filtered using the detection p-value, at a threshold of >half of the sample to have detected signal for the probe to pass to the comparison stage. The data were then transformed using model-based variance-stabilizing transformation (VST) and normalized using quantile normalization, both using the lumi R software package. Differentially expressed genes were identified using limma bioconductor software package based on a moderated t-test.

source_name: COLO205 cells

label_protocol: Sample was amplified using Ambion Illumina TotalPrep RNA Amplification Kit and labelled as part of the Illumina Whole-Genome Gene Expression HumanHT-12 v4 Chip Kit (Illumina, Eindhoven, Netherlands) according to manufacturer’s instructions. Using these, mRNA was converted to single-stranded cDNA using a T7 Oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence. Single-stranded cDNA then underwent second-strand synthesis to produce a dsDNA template for transcription, and residual RNA then removed. cDNA was then amplified and labelled to yield biotinylated cRNA. Impurities were then removed from cRNA in preparation for analysis using Illumina Whole-Genome Gene Expression HumanHT-12 v4 chips.

growth_protocol: Human male COLO205 cells (RRID: CVCL_0218) are a colorectal cancer cell line harbouring the driving oncogene BRAFV600E. These cells are sensitive to inhibition of MEK1/2, the immediate targets of BRAFV600E, and we have made derivatives with resistance to the MEK1/2-inhibitor selumetinib (Sel; AZD6244) as described in Little et al., 2011 Sci. Signal. 4, ra17. These selumetinib-resistant COLO205 cells are termed C6244-R cells. COLO205 cells were grown in RPMI 1640 media supplemented with 10% (v/v) fetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL) and 2 mM glutamine (all from Gibco, Thermo Fisher Scientific, Paisley, UK), and C6244-R cells in the same media with addition of 1 µM selumetinib.

extract_protocol: At the of end treatment cells were lysed in TRI reagent (Sigma-Aldrich, Dorset, UK), typically 2 mL per 10 cm dish, and lysates mixed until a homogenous constituency was achieved. Lysates were transferred to sterile RNase free tubes, and 0.1 mL 1-bromo-3-chloropropane added per mL of lysate. The samples were mixed thoroughly and then allowed to stand for 5 min. Tubes were then centrifuged at 12000 x g for 15 min at 4°C, and the upper aqueous phase transferred to a fresh tube. 0.5 mL 2-propanol per mL original lysate was then added, tubes mixed and allowed to stand for 5 min. Samples were then centrifuged at 12000 x g for 10 min at 4°C, and RNA pellets washed with 75% (v/v) ethanol. Pellets were resuspended in RNase free water and RNA concentrations determined with Nanodrop spectrophotometer (Thermo Fisher Scientific, Loughborough, UK). RNA purity and concentration were checked using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Loughborough, UK) to determine the A260:A280 ratio.

treatment_protocol: COLO205 and C6244-R cells were washed once with complete medium only, and then treated with either DMSO only containing medium or medium with 1 µM selumetinib for the indicated time points.

tag: cell line

value: Selumetinib-resistant COLO205 (C6244-R)

value: Sel-resistant

tag: agent

value: 48 hr


title: C6244R-SEL 48h C


title: r2_d3_t15

description: Mnase digested DNA


title: C6244R+SEL 48h C

value: Selumetinib


title: r2_d2_t15

description: Mnase digested DNA


title: C6244R+SEL 48h A


title: C6244R-SEL 48h A


title: WT_UnInf4_2x_B2: WT uninfected_RNA-Seq_rep5

description:
sample name in processed data file:
WT_UnInf4_2x_B2


title: r2_d1_t15

description: Mnase digested DNA


title: C6244R+SEL 48h B


title: C6244R-SEL 16h C

value: 16 hr


title: WT_UnInf2_2x: WT uninfected_RNA-Seq_rep3

description:
sample name in processed data file:
WT_UnInf2_2x


title: WT_UnInf4_B2: WT uninfected_RNA-Seq_rep4

description:
sample name in processed data file:
WT_UnInf4_B2


title: SW620 parental

description: Parental cell line SW620

hyb_protocol: The hybridization master mix was prepared by mixing 25 μl of Cot-1 (1mg/ml), 26 μl or Agilent 1-x Blocking Agent and 130 μl of Aligent 2x HiRPM Hybridization Buffer. The master mix was mixed with labeled experimental and control DNA and hybridized to the Agilent Human Genome CGH 2x400k Miscoarray (Agilent Technologies, Santa Clara, CA).  The arrays were incubated for 40 hours at 65°C in a rotating oven at 20 rpm. After hybridization slides were washed as stated in the protocol.

scan_protocol: All hybridized arrays were scanned on an Agilent G2505C scanner.

data_processing: Images were analized using Agilent Feature Extraction Software (version 10.7.3.1). Nexus Copy Number software v7.0 was used for data processing and visualization. Log2 ratio for each gene was calculated as mean of log2 values of all probes mapped to a particular gene.

source_name: Colorectal cancer cell line SW620

label_protocol: Genomic DNA extracted from experimental (cell lines) and normal control female gDNA (Promega, Madison, WI) samples was labeled using CytoSure HT Genomic DNA Labelling Kit (Oxford Gene Technology, Oxfordshire, UK)  following the OGT protocol for aCGH analysis with an adjustment to the post purification step. After labelled targets were combined in one tube, an additional 2 μl of water was added and directly proceeded to hybridization.

extract_protocol: Genomic DNA was prepared from the cell pellets using the Allprep DNA/RNA/miRNA Universal kit (Qiagen, Valencia, CA)

value: Colorectal cancer

tag: parental or resistant

value: Parental

tag: selumetinib resistance concentration

source_name: normal female gDNA, Promega

value: female

tag: disease state

value: normal


title: COLO205 48h C


title: COLO205 48h B


title: r1_d35_t0

description: Sheared genomic DNA

value: 80 hours after inoculation

value: Undigested


title: C6244R-SEL 16h A


title: SW480_6244R resistant

description: SW480 cells resistant to AZD6244

source_name: Colorectal cancer cell line SW480

value: Selumetinib-resistant


title: SW620_6244R resistant

description: SW620 cells resistant to AZD6244


title: C6244R-SEL 16h B


title: SW480 parental

description: Parental cell line SW480


title: HCT116R_6244R resistant

description: HCT116R cells resistant to AZD6244

source_name: Colorectal cancer cell line HCT116R


title: HKH2  parental

description: Parental cell line HKH2

source_name: Colorectal cancer cell line HKH2


title: COLO205 48h A


title: C6244R+SEL 16h A


title: COLO205 16h A


title: LoVo parental

description: Parental cell line LoVo

source_name: Colorectal cancer cell line LoVo

value: LoVo


title: C6244R+SEL 16h C


title: LoVo_6244R resistant

description: LoVo cells resistant to AZD6244


title: HCT116R parental

description: Parental cell line HCT116R


title: COLO205 16h C


title: Top2-1_Top1_TopAplasmid_2hr_Supercoil_INPUT

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Control data from naked genomic DNA used to eliminate the false positive binding of BTMP drug

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R array for 16 hours at 42 C in a hybridization oven at 60 rpm

scan_protocol: Arrays were scanned on Affymetrix geneChip Scanner 3000 7G

data_processing:
The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE)
Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

source_name: INPUT fraction of Biotin tagged psoralean of top2-1;top1△ TopA plasmid in GLU at 37 degree for 2hr15mins S Phase

label_protocol: Both IP and Input samples are amplified by using Whole genome amplificatio ki protocol ( Sigma-Aldrich WGA1-50RXN) pripor to labelling with Biotin-N11-ddATP (1nMole/ul).

growth_protocol: 1X10e7 cells were synchronized at G1 phase using Alpha-factor and cells were harvested for "G1" samples. For "S" phase samples cells were released into fresh medium after washing cells with 2X YP-medium. After 15 mins of the realese from alpha factor arrest cells were harvested for Chip protocols

extract_protocol:
Genomic DNA was isolated from Qiagen Gneomic-tip 100/G (Cat no 13343) & Genomic DNA buffer Set (Cat no 19060). Purified DNA was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. bTMP was added to purified DNA and incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). DNA is precipitated using isopropanol and washed with 70% ethannol. Dried Pellate was dissolved in buffer (50mM tris Ph 8.0, 10mM EDTA, 0.1% SDS) and incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).
Cells were collected blocked using Sodium Azide (0.1%). bTMP is added and cells were incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction is incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).

tag: category

value: BTMP DNA-Supercoil

tag: cell cycle

value: S Phase

tag: antibody

value: Glucose

tag: temperature

value: 37 degree for 2hr 15mins


title: r1_d3_t15

description: Mnase digested DNA

value: 72 hours after inoculation

value: 15 min digestion


title: Top2-1_Top1_TopAplasmid_2hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of top2-1;top1△ TopA pasmid expressed in GLU at 37 degree for 2hr15mins S Phase

value: Dynabeads My One Streptavidin-(Invitrogen)

tag: strain


title: WT_UnInf2_B2: WT uninfected_RNA-Seq_rep1

description:
sample name in processed data file:
WT_UnInf2_B2

value: spleen

value: natural killer (NK)

tag: phenotype

tag: genotype

value: wildtype

value: uninfected


title: C6244R+SEL 16h B

value: Selumetinib-resistant COLO205 (C6244-R)

value: Sel-resistant

value: Selumetinib

value: 16 hr


title: C6244R-SEL 4h C

value: 4 hr


title: WT_UnInf2A: WT uninfected_RNA-Seq_rep2

description:
sample name in processed data file:
WT_UnInf2A


title: r1_d35_t15

description: Mnase digested DNA

value: 80 hours after inoculation

tag: treatment


title: r1_d3_t0

description: Sheared genomic DNA

value: Undigested


title: WT_Inf4: WT LCMV infected_RNA-Seq_rep4

description:
sample name in processed data file:
WT_Inf4

tag: tissue

value: Lymphocytic choriomeningitis virus


title: Top2-1_Top1_TopAplasmid_1hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of top2-1;top1△ TopA plasmid in GLU at 37 degree for 1hr15mins S Phase

value: BTMP DNA-Supercoil

value: S Phase

value: Glucose

value: 37 degree for 1hr 15mins


title: r1_d2_t15

description: Mnase digested DNA

tag: time

value: 48 hours after inoculation

value: 15 min digestion


title: Top2-1_Top1_TopAplasmid_1hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of top2-1;top1△ TopA pasmid expressed in GLU at 37 degree for 1hr15mins S Phase

value: Dynabeads My One Streptavidin-(Invitrogen)


title: WT_Inf3: WT LCMV infected_RNA-Seq_rep3

description:
sample name in processed data file:
WT_Inf3

value: spleen

tag: cell type

value: natural killer (NK)

value: wildtype


title: WT_TopAplasmid_2hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt TopA plasmid in GLU at 37 degree for 2hr15mins S Phase

value: 37 degree for 2hr 15mins


title: COLO205 16h B

value: Parental


title: HKH2_6244R  resistant

description: HKH2 cells resistant to AZD6244

value: Colorectal cancer

value: Selumetinib-resistant

tag: Sex

value: female

value: normal


title: WT_TopAplasmid_2hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of wt TopA pasmid expressed in GLU at 37 degree for 2hr15mins S Phase


title: WT_Inf2: WT LCMV infected_RNA-Seq_rep2

description:
sample name in processed data file:
WT_Inf2

tag: infected with

value: Lymphocytic choriomeningitis virus


title: r1_d1_t0

description: Sheared genomic DNA

value: 24 hours after inoculation

value: Undigested


title: r1_d1_t15

description: Mnase digested DNA


title: KO_UnInf5: Cd47-/- uninfected_RNA-Seq_rep5

description:
sample name in processed data file:
KO_UnInf5

value: uninfected


title: WT_TopAplasmid_1hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt TopA plasmid in GLU at 37 degree for 1hr15mins S Phase

value: BTMP DNA-Supercoil

value: S Phase

value: Glucose

value: 37 degree for 1hr 15mins


title: r4d3

description: Total RNA depleted for ribosomal RNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1 T.acidophilum genome assembly obtained from ncbi
Transcripts were reconstructed and quantified using Rockhopper (McClure et al. 2013), using a  threshold of 0.9 for 5’ and 3’UTR detection.
Single-end reads were mapped to the T. acidophilum DSM1728 genome using Geneious 11.1.2 aligner.
Differential expression of transcript delineated by RockHopper was assessed using DESeq2
Genome_build: NC_002578.1
Supplementary_files_format_and_content: Results of 5 and 3 prime UTR detection as well as Operon prediction (RockHopper), Pairwise differential expression computed using DEseq2

extract_protocol:
Total RNA was extracted using an RNeasy kit (Qiagen) according to manufacturer’s instruction, including DNAse I treatment.
Ribosomal RNAs were depleted using Illumina’s Ribo-Zero rRNA Removal Kit (Bacteria) and RNA libraries prepared using the TruSeq Stranded Total RNA LT Kit

treatment_protocol: Pellets were re-suspended in 500µL RNAlater (Ambion), incubated for one hour at room temperature, pelleted again and snap-frozen.

value: 72 hours after inoculation


title: r4d2

description: Total RNA depleted for ribosomal RNA

value: 48 hours after inoculation