title: Human7_ChIP_Pol2_ZIKVpositive_24h

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads were mapped to the human genome (hg38) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF) mode using default parameters to identify spreading or focal peaks, respectively.
Gene expression was measured using HOMER with the following parameters analyzeRepeats rna hg38 -count exons -noadj -pc 3 -condenseGenes followed by DESeq normalized abundance measurements
ChIP-Seq: Tab-delimited BED files containing peak positions for each ChIP-seq experiment (one peak file per set of replicates, hg38) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene name, 8:Annotation/Divergence, 9:gene ID, 10: gene type, 10-43: FPKM for each experiment.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq tab-delimited text files include FPKM values for each Sample and pooled samples at each time point, Tab-delimited BED files containing peak positions for each ChIP-seq experiment

source_name: Human blood monocytes derived

extract_protocol:
For RNA-seq acrophages were washed once with 1XPBS, gently scraped off in 1XPBS, pelleted at 4C and stained with zombie violet viability dye [BioLegend] in the dark. Cells were washed once with FACS buffer (1X PBS, 3% fetal bovine serum, and 1 mM EDTA) and fixed and permeabilized with 4% PFA [Electron Microscopy Sciences, 15710-S], 0.1% saponin [Sigma-Aldrich, 47036] in molecular grade PBS supplemented with 1:100 RNasin Plus RNase Inhibitor [Promega, N2615] for 30’ at 4C. Cells were washed in Wash Buffer: 1XPBS containing 0.2% BSA, 0.1% saponin, and 1:100 RNasin Plus RNase Inhibitor and blocked for 10’ with Human Fc Block (1:500) [BioLegend] in Staining Buffer: 1XPBS containing 1%BSA, 0.1% saponin, and RNasin Plus RNase Inhibitor. HMDMs were then stained with 4G2 antibody [BioXcell] conjugated to AF647 [Thermo Scientific Cat#A20186] for 30’ at 4C, washed twice, resuspended at 5-10E6 cells/ml in Sort Buffer (PBS containing 0.5% BSA, and 1:25 RNasin Plus RNase Inhibitor) and sorted into ZIKV+ and ZIKV- cells on the FACSAria [BD Biosciences] at La Jolla Institute for Allergy for Immunology. Gates were set with reference to negative controls. After sorting, cells were pelleted at at 4C, supernatant discarded and total RNA isolated using Ambion’s RecoverAll Total Nucleic Acid Isolation Kit [AM1975], starting at the protease digestion step. All steps were performed per manufacturer recommendations with the following modification. Cells were incubated in digestion buffer for 3 hours at 50C supplemented with RNasin Plus RNase Inhibitor. RNA was treated with in column DNase per manufacturer instructions, eluted and RNA quality determined by BioAnalyzer using the Eukaryote Total RNA Pico Chip. Samples with RIN values greater than 8.0 were used for library preparation. For ChIP-seq macrophages were cross-linked with 1% formaldehyde for 15 minutes in the presence of 1 mM sodium butyrate and quenched with 0.125M glycine. Preparation of HMDMs for FACS was performed as described above for RNA-seq except that 1x cOmplete protease inhibitors (Roche) and 1 mM sodium butyrate [Sigma] were included in all buffers instead of RNasin Plus RNase Inhibitor. Following FACS cells were washed, pelleted and snap-frozen.
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted were prepared using the TruSeq kit (Illumina) according to the supplied protocol. ChIP-seq was essentially performed as described (Heinz et al., 2013), except that libraries were prepared using NEB Ultra II DNA library prep kit reagents.

tag: human donor

value: monocyte derived macrophage

tag: chip antibody

value: RPB2 protein of RNApol2, GeneTex #GTX102535

tag: viral infection

value: ZIKV-infected

tag: viral strain

tag: time post infection viral infection


title: shIFIT1-I 0h_A9104

status: Public on Sep 10 2018

type: RNA

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: THP-1 cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: THP1 monocytes were propagated in RPMI media with 10% FBS, 10 mM HEPES, and Betamercaptoethanol in 5% CO2 at 37oC.

extract_protocol: RNA was isolated with an RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol and eluted in RNase free TE buffer

treatment_protocol: Wild type THP1 and IFIT1 shRNA cells (3.5x105 per well) were transfected with NT siRNA and IFIT1 siRNA respectively in 24-well plates, and differentiated with 10 ng/ml PMA for 72 hours. Cells were stimulated with 100 ng/ml LPS for 0h, 1h, 2h, 4h, 6h and 24h

tag: sirna

tag: shRNA

tag: treatment

value: LPS

tag: treatment time

tag: experiment

value: I


title: Vastus_lateralis_muscle_male_1_trained_pos

city: São Paulo

first: Carlos

last: Ugrinowitsch

state: SP

address: Av. Prof. Mello Moraes, 65. Cidade Universitária, Butantã.

department: Departamento de Esporte

country: Brazil

institute: Escola de Educação Física e Esporte - USP

description: Sample name: IND_1_T_4

hyb_protocol: Direct hybridization assay for whole genome expression (Human HT-12 v4 Expression BeadChip, Illumina, CA, USA).

scan_protocol: Microarray scanning was done using iScan array scanner following standard Illumina protocol.

data_processing: Detection p-values were calculated with function detectionPValues() from limma 3.32.10. Function neqc() from limma was used to perform normexp background correction using negative control probes, and quantile normalization using negative and positive control probes. After normalization, intensities were log2 transformed and control probes were removed.

source_name: Vastus lateralis muscle

label_protocol: The amount of (normalized) RNA was determined by RiboGreen quantitation (Quant-iT RiboGreen RNA Assay Kit, Thermo Fisher Scientific, Rockville, MD, USA) before input into the Ambion Illumina Total Prep Kit (Thermo Fisher Scientific, Rockville , MD, USA) for amplification, cRNA synthesis and biotinylation. The cRNA generated was quantified and normalized by the RiboGreen fluorescence method.

extract_protocol: Tissues were homogenized with 1mL TRIzol (Life Technologies, Burlington, ON, Canada) using Lysing Matrix D tubes (MP Biomedicals, Solon, OH, USA), with FastPrep-24 Tissue and Cell Homogenizer (MP Biomedicals) during 40s at 6m/s. 200μL of chloroform (Sigma-Aldrich) was added, the tubes vigorously agitated for 15s and rested for 5min. Samples were centrifuged at 12000 g, 4ºC for 10min and the aqueous phase containing RNA was collected and transferred to a RNeasy minispin column. The RNA was purified according to the Total RNA Kit 1 (Omega Bio-Tek, Norcross, GA, USA) manufacturer instructions.

tag: tissue

value: Vastus lateralis muscle

tag: Sex

value: male

value: trained

value: pos


title: shIFIT1-I 24h_A9109


title: THP1-II 2h_A9124

value: NT

value: II


title: THP1-II 4h_A9125


title: THP1-I 24h_A9103


title: shIFIT1-I 6h_A9108


title: THP1-I 4h_A9101


title: shIFIT1-I4h_A9107


title: Human7_ChIP_Pol2_ZIKVnegative_24h

type: SRA

city: La Jolla

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

library_source: genomic

molecule: genomic DNA

growth_protocol: Human blood was obtained from healthy volunteers and separated using Histopaque 1077 spun at 300xg for 30-60’ at 4C. The buffy coat was washed once, red blood cells lysed and monocytes isolated by negative selection using the pan monocyte isolation kit [Miltenyi Biotech cat. #130-096-537]. Cells were seeded onto tissue coated plates and differentiated for 7 days in complete macrophage media (macrophage serum-free media [Gibco cat #12065] supplemented with 1% penicillin/ streptomycin, 1% nutridoma-SP [Roche cat #11011375001], 1% fungizone [Gibco cat#15290-018], and 100ng/ml human macrophage-colony stimulating factor (M-CSF) [Peprotech cat# 300-25]) at 37o C, 5% CO2. Media was changed every 2-3days.

treatment_protocol: On day 7 of culture, macrophages were infected with Zika virus clinical isolates SD001 or FSS13025 at indicated multiplicity of infection (MOI) with or without antibody-dependent enhancement (ADE) (MOI= 1 + 0.6% (v/v) DENV human immune serum). The virus was incubated with HMDMs for 2 hours with rocking every 10-15’ at 37oC, 5% CO2. The supernatant was removed, and cells were washed 3x with 1XPBS, before addition of fresh warm complete macrophage media. Both RNA-seq and flow cytometry confirmed that no infectious DENV is present in the human immune serum.

tag: cell type

value: ZIKV-bystander


title: Vastus_lateralis_muscle_male_4_trained_pos

description: Sample name: IND_4_T_4


title: Human7_ChIP_Pol2_Mock_24h

value: mock infected


title: AML2_PB

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and batch corrected to account for technical variation of isolation of human cells from patients versus xenografts using Partek Genomics Suite 6.6 software.

source_name: human AML

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

value: mononuclear cells

value: PB

tag: leukemic engraftment capacity

value: Engrafter


title: Human6_ChIP_Pol2_ZIKVnegative_24h


title: Human6_ChIP_Pol2_Mock_24h


title: Human6_RNA_ZIKVpositive_24h

library_source: transcriptomic


title: DosR mutant treated with HC106A, Rep 2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.30)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie  was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis CDC1551 genome
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the edgeR package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .csv spreadsheets and represents the average of 2 biological replicates
Supplementary_files_format_and_content: Normalized counts and differential expression WT or DosR mutant treated with HC104A or HC106A or DMSO

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 was grown at 37ºC in T-25 vented, standing tissue culture flasks in 8 mL of buffered 7H9 medium to an OD600 of 0.1.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were subsequently treated with 40 µM HC104A or HC106A. For the control, cultures treated with an equal amount of DMSO.  Following a 6D incubation period, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

tag: strain

tag: agent

tag: genotype/variation

value: DosR mutant


title: Human6_RNA_ZIKVpositive_18h

tag: human donor

value: monocyte derived macrophage


title: DosR mutant treated with HC104A, Rep 2


title: DosR mutant treated with HC104A, Rep 1


title: DosR mutant treated with HC106A, Rep 1


title: Human6_RNA_ZIKVpositive_12h


title: DosR mutant treated with DMSO, Rep 2

value: DMSO


title: Human6_RNA_ZIKVnegative_24h


title: SUD10-MEF2B-D83V_HAFLAG

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-12 for CB4 MEF2B, 10^-5 for CB5 MEF2B, 10^-8 for HAFLAG, 10^-10 for WT MEF2B, and 10^-12 for D83V MEF2B.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: Diffuse Large B Cell Lymphoma (DLBCL) cell line engineered to express Flag-HA-MEF2B-D83V mutant

growth_protocol: SUDHL10 cell line was infected with Lentiviral expression vector co-expressing GFP and Flag-HA-MEF2B-D83V mutant from a bidirectional promoter. GFP positive cells were sorted and maintained as stable line.

extract_protocol:
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 4ug of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 100 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Purified cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.

value: DLBCL cell line

tag: antibody

value: anti-Flag (M2, F3165, Sigma) and anti-HA (ab9110, Abcam)


title: TG_C57_2

city: Providence

first: Chun Geun

last: Lee

state: RI

address: 185 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

description: lung, Rt lobe

hyb_protocol: GeneChip Scanner 3000

scan_protocol: A “rotisserie” oven is used to carry out the hybridization of up to 64 arrays at one time.

data_processing: Affy Package (1.58.0) in R (3.3.2) was used to processing of raw data, no filtering was performed.

organism: Mus musculus

source_name: Lung

label_protocol: Ambion WT Expression Kit  was used for cDNA synthesis and IVT labeling

growth_protocol: Freshly harvested lungs in PBS

extract_protocol: Fresh lung tissue was homogenized in a Trisol solution and  followed by RNA purificaton using Qiagen RNA purification kit

treatment_protocol: All the mice were given 2weeks of Doxycycline in a drinking water for induction of TGF-b transgene expression

value: Two weeks Dox induction

tag: genotype

value: TG

tag: fibrosis

value: 1, prone; 2, resistant strains:2

tag: emphysematous


title: SUD10-MEF2B-D83V_MEF2B

value: anti-MEF2B (epitope aa102-121; Bethyl custom)


title: WT_C57_2

description: lung, Rt lobe

value: WT


title: TG_C57_1

description: lung, Rt lobe


title: WT_C3H_1

description: lung, Rt lobe

value: 1, prone; 2, resistant strains:1

value: nonEmp


title: Human6_RNA_ZIKVnegative_18h

tag: viral infection

value: ZIKV-bystander

tag: viral strain

tag: time post infection viral infection


title: TG_C3H_3

description: lung, Rt lobe

tag: treatment


title: TG_C3H_1

description: lung, Rt lobe


title: TG_C3H_2

description: lung, Rt lobe


title: WT_BC_1

description: lung, Rt lobe

value: BC

value: emp


title: WT_C57_1

description: lung, Rt lobe


title: TG_BC_2

description: lung, Rt lobe


title: AML2_BM

label_protocol: In accordance with manufacturer's protocols

value: mononuclear cells

value: BM


title: THP1-I 1h_A9099

tag: sirna

value: NT

tag: shRNA

value: LPS

tag: treatment time

tag: experiment

value: I


title: DosR mutant treated with DMSO, Rep 1

value: DMSO

value: DosR mutant


title: Human6_ChIP_Pol2_ZIKVpositive_24h

tag: cell type

value: monocyte derived macrophage

tag: chip antibody

value: RPB2 protein of RNApol2, GeneTex #GTX102535

value: ZIKV-infected


title: Human6_RNA_ZIKVnegative_12h


title: Wildtype treated with HC106A, rep 2

tag: strain

tag: agent

value: wildtype


title: SUD10-MEF2B-WT_HAFLAG

source_name: Diffuse Large B Cell Lymphoma (DLBCL) cell line engineered to express Flag-HA-MEF2B wild type

growth_protocol: SUDHL10 cell line was infected with Lentiviral expression vector co-expressing GFP and Flag-HA-MEF2B wild type from a bidirectional promoter. GFP positive cells were sorted and maintained as stable line.

tag: tissue

value: DLBCL cell line

value: anti-Flag (M2, F3165, Sigma) and anti-HA (ab9110, Abcam)


title: Wildtype treated with HC106A,  rep 1

tag: genotype/variation


title: Human6_RNA_Mock_24h

tag: human donor

value: mock infected


title: SUD10-MEF2B-WT_MEF2B

tag: antibody

value: anti-MEF2B (epitope aa102-121; Bethyl custom)


title: TG_AKR_3

description: lung, Rt lobe

value: Two weeks Dox induction

value: AKR

tag: genotype

value: TG

tag: fibrosis

value: 1, prone; 2, resistant strains:2

tag: emphysematous


title: Wildtype treated with HC104A, rep 2


title: SUD10-MEF2B-WT_Input


title: TG_BC_3

description: lung, Rt lobe

value: BC

value: 1, prone; 2, resistant strains:1

value: emp


title: Wildtype treated with HC104A, rep 1


title: CB5_MEF2B

source_name: germinal center B cells

growth_protocol: Tonsillar germinal center B cells were isolated by  by magnetic cell separation (CD38+, CD77+), as described in Klein et al, Proc Natl Acad Sci U S A, 2003.

value: tonsil


title: CB5_Input


title: Human5_RNA_ZIKVpositive_24h

tag: viral infection

tag: viral strain

tag: time post infection viral infection


title: SUD10-MEF2B-D83V_Input


title: Wildtype treated with DMSO, rep 2

value: DMSO


title: CB4_MEF2B


title: Wildtype treated with DMSO, rep 1


title: Human5_RNA_ZIKVnegative_24h

value: monocyte derived macrophage

value: ZIKV-bystander


title: TG_AKR_1

description: lung, Rt lobe

tag: treatment


title: Human5_RNA_ZIKVnegative_18h


title: TG_AJ_3

description: lung, Rt lobe

value: AJ


title: CB4_Input


title: Human5_RNA_ZIKVnegative_12h


title: L474_Oxygen_shock

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
The remaining reads of each library were aligned to the corresponding genomes using Bowtie2 v2.2.9 and alignments were filtered with Samtools v1.3.1 using a MAPQ cut-off of 15. Reads were assigned to genomic features using featureCounts v1.5.1.
TPMs were calculated using raw read counts obtained in featureCounts, with effective gene length equal to gene length in annotation.
Genome_build: D23580 experiments were aligned to D23580 genome and quantified using D23580 annotation. 4/74 experiments were aligned and quantified using 4/74 genome and annotation.
Supplementary_files_format_and_content: TPM values in tab-separated text columns

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: in vitro culture

growth_protocol: Growth conditions and treatment for 16 in vitro conditions are described previously (PMID 24331466). Growth conditions for intra-macrophage transcriptome are described in PMID 26561851.

extract_protocol:
Transcription and RNA turnover were stopped using 2/5 volumes of the cell suspension using ice-cold ‘‘stop solution’’ (19% ethanol, 1% acidic phenol [pH 4.3]) and incubated on ice for 30 min to prevent RNA degradation. RNA was isolated using TRIzol (Invitrogen) and digested with DNase I.
For RNA-seq, cDNA libraries were prepared and sequenced by Vertis Biotechnologie AG (Freising, Germany). RNA samples were fragmented with ultrasound (4 pulses of 30 sec at 4°C), treated with antarctic phosphatase, and rephosphorylated with polynucleotide kinase (PNK). RNA fragments were poly(A)-tailed and a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was carried out using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. cDNA was subsequently amplified by PCR to 20-30 ng/μL, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). cDNA samples were pooled in equimolar amounts, size-selected to 150 - 500 bp and sequenced on an Illumina HiSeq 2000 or Illumina NextSeq 500 system (single-end 50, 75, or 100 bp reads).

tag: growth conditions

value: oxygen shock

value: wildtype


title: L474_Peroxide_shock_InSPI2

treatment_protocol: Growth conditions and treatment for 16 in vitro conditions are described previously (PMID 24331466). Growth conditions for intra-macrophage transcriptome are described in PMID 26561851.

value: peroxide shock InSPI2


title: Human5_RNA_ZIKVpositive_18h

value: ZIKV-infected


title: Human5_RNA_ZIKVpositive_12h


title: M_3

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC hg19) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were mapped to exons to produce count tables which were converted to transcript per million (TPM) values.
Genome_build: hg19
Supplementary_files_format_and_content: TPM tables containing the normalized transcripts per million mapped reads (TPM) counts for genes.

source_name: Memory B cells

growth_protocol: Surgically removed tonsil tissue was immediately processed to isolate mononuclear cells by Ficoll.

extract_protocol:
Total RNA was isolated using the Trizol Reagent and cleaned up by  Qiagen RNAeasy kit, according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Tonsillar naïve, germinal center and memory B cells were isolated by  by magnetic cell separation, as described in Klein et al, Proc Natl Acad Sci U S A, 2003.

value: Tonsil

value: Memory B cells


title: M_2


title: L474_NO_shock_InSPI2

value: no shock InSPI2


title: M_1


title: TG_AJ_1

description: lung, Rt lobe

value: Two weeks Dox induction

value: TG


title: Human4_RNA_ZIKVpositive_18h


title: CB_3

source_name: Germinal Center B cells

value: Germinal Center B cells


title: WT_AJ_1

description: lung, Rt lobe

value: WT

value: 1, prone; 2, resistant strains:2


title: WT_AKR_1

description: lung, Rt lobe

value: AKR

value: emp


title: TG_AJ_2

description: lung, Rt lobe


title: L474_NonSPI2


title: Human4_RNA_ZIKVpositive_24h

value: monocyte derived macrophage


title: CB_2


title: L474_Macrophage-2

source_name: macrophage co-culture

value: macrophage co-culture


title: Human4_RNA_ZIKVnegative_24h

value: ZIKV-bystander


title: HSF1i.39.3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
annapon_counts.txt
annapon_l2tpm.txt
d577

data_processing:
HiSeq2000 using v3 chemistry. Software: Control software version 2.0.12.0, RTA version 1.17.21.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence aligned and transcripts quantified using star2.5.3a, rsem1.3.0 and samtools 1.3
Genome_build: canFam3 with ENSEMBL annotation
Supplementary_files_format_and_content: annapon_counts.txt  is parsed integer counts for samples from rsem
Supplementary_files_format_and_content: annapon_l2tpm.txt is parsed tpm for samples from rsem transformed to log2 space by adding 1 to TPM and calculating the log2 value

organism: Canis lupus familiaris

source_name: Madin Darby canine kidney (MDCK) cells transduced with inducible inhibitor of HSF1, HSF1i.39

growth_protocol: MDCK cells expressing doxycycline-inducible dn-cHSF1 construct were cultured at 37 °C or 39 °C in a 5% CO2 atmosphere in DMEM (CellGro) supplemented with 10% fetal bovine serum (CellGro) and 1% penicillin/streptomycin/glutamine (CellGro).

extract_protocol:
Cellular RNA was harvested using the Qiagen RNeasy Plus Mini Kit with QIAshredder homogenization columns.
Kapa mRNA HyperPrep

treatment_protocol: 1 ug/ml tetracycline in water for 48 hr or 0.1% DMSO for 48hr each group at 37 °C or 39 °C

tag: cell line

value: MDCK

tag: transduction

value: inducible inhibitor of HSF1

value: 1 ug/ml Doxycycline in water for 48 hours at 39 degrees C


title: CB_1

tag: cell type


title: L474_MEP

value: MEP

tag: strain

value: wildtype


title: L474_NaCl_shock

value: NaCl shock


title: L474_Macrophage-1


title: N_3

source_name: Naïve B cells

value: Tonsil

value: Naive B cells


title: Human4_RNA_ZIKVpositive_12h

value: ZIKV-infected


title: HSF1i.39.1

description:
annapon_counts.txt
annapon_l2tpm.txt
d575


title: WT_129_1

description: lung, Rt lobe

value: Two weeks Dox induction

value: 1, prone; 2, resistant strains:1

value: nonEmp


title: TG_129_2

description: lung, Rt lobe

value: TG


title: TG_129_3

description: lung, Rt lobe


title: Human4_RNA_ZIKVnegative_12h


title: L474_LSP

value: LSP


title: Human4_RNA_ZIKVnegative_18h

value: monocyte derived macrophage


title: TG_129_1

description: lung, Rt lobe


title: L474_Low_Fe2+_shock

value: low Fe2+ shock


title: Human4_RNA_Mock_24h

value: mock infected


title: THP1-II 1h_A9123

tag: sirna

value: NT

tag: shRNA

value: LPS

tag: treatment time

tag: experiment

value: II


title: DMSO.39.3

description:
annapon_counts.txt
annapon_l2tpm.txt
d574

source_name: Madin Darby canine kidney (MDCK) cells transduced with inducible inhibitor of HSF1, DMSO.39

value: MDCK

value: inducible inhibitor of HSF1

value: 0.1% DMSO for 48 hours at 39 degrees C


title: DMSO.39.2

description:
annapon_counts.txt
annapon_l2tpm.txt
d573


title: N_1

tag: tissue

value: Tonsil


title: Human3_RNA_SD001_ZIKVpositive_24h

tag: human donor


title: TG_AKR_2

description: lung, Rt lobe

value: AKR

tag: genotype

tag: fibrosis

value: 1, prone; 2, resistant strains:2

value: emp


title: TG_BC_1

description: lung, Rt lobe

value: Two weeks Dox induction

value: BC

value: 1, prone; 2, resistant strains:1

tag: emphysematous


title: DMSO.39.1

description:
annapon_counts.txt
annapon_l2tpm.txt
d568


title: L474_InSPI2

value: wildtype


title: HSF1i.37.3

description:
annapon_counts.txt
annapon_l2tpm.txt
d1100

source_name: Madin Darby canine kidney (MDCK) cells transduced with inducible inhibitor of HSF1, HSF1i.37

value: 1 ug/ml Doxycycline in water for 48 hours at 37 degrees C


title: JJ_AMIL_141062

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

data_processing:
Illumina 3' adaptors were trimmed using cutadapt version 1.4
FASTQ files were aligned to the Homo sapiens genome hg19 using Tophat version 2.0.11
Gene counts were obtained using the HTSeq algorithm version 0.6.1p1 in the intersection-strict mode.
Gene count normalization was carried out using DESeq2 version 1.12.4
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample. Supplementary files: tab-delimited matrix tables which include normalized gene count values for each cell line

growth_protocol: All cell lines were cultured in RPMI 1640 medium supplemented with 10% (JJN3) or 20% KMS12M) fetal bovine serum and antibiotics (Gibco). Cells were routinely checked for the presence of mycoplasma with MycoAlert  kit  (Lonza  GmBH)  and  only  mycoplasma-free  cells were used in the experiments.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit (Qiagen). The RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were  constructed following a TrueSeq Strand-Specific RNA Sequencing Library protocol  7  (Illumina).

treatment_protocol: KMS12-BM and JJN3 cells untreated or treated with amiloride (0.1 mM  and 0.4 mM, respectively) for 24 h was isolated and prepared for RNA-seq

tag: disease

value: plasma cell leukemia

tag: treated with

value: Amiloride 0.4 mM 24h


title: N_2

value: Naive B cells


title: HSF1i.37.2

description:
annapon_counts.txt
annapon_l2tpm.txt
d1099

tag: treatment


title: JJ_AMIL_141056


title: L474_ESP

tag: growth conditions

value: ESP


title: Human3_RNA_FSS_ZIKVnegative_24h

source_name: Human blood monocytes derived

value: monocyte derived macrophage

tag: viral infection

value: ZIKV-bystander

tag: viral strain

tag: time post infection viral infection


title: JJ_DM_141060

tag: cell line

value: Untreated (DMSO)


title: L474_EEP

value: EEP

tag: strain


title: HSF1i.37.1

description:
annapon_counts.txt
annapon_l2tpm.txt
d1098

value: MDCK

tag: transduction

value: inducible inhibitor of HSF1


title: JJ_AMIL_141050


title: Human3_RNA_Mock_24h

tag: cell type

value: mock infected


title: JJ_DM_141054


title: L474_Bile_shock

value: bile shock


title: Human1_RNA_SD001_ZIKVpositive_24h

value: ZIKV-infected


title: L474_Anaerobic_shock

value: anaerobic shock


title: DMSO.37.2

description:
annapon_counts.txt
annapon_l2tpm.txt
d1096

source_name: Madin Darby canine kidney (MDCK) cells transduced with inducible inhibitor of HSF1, DMSO.37

value: 0.1% DMSO for 48 hours at 37 degrees C


title: JJ_DM_141048


title: Human1_RNA_SD001_ZIKVnegative_24h


title: DMSO.37.3

description:
annapon_counts.txt
annapon_l2tpm.txt
d1097


title: Human3_RNA_SD001_ZIKVnegative_24h


title: L474_LEP

value: LEP

value: wildtype


title: L474_Anaerobic_growth

value: anaerobic growth


title: BM_AMIL_141065

value: multiple myeloma

value: Amiloride 0.1 mM 24h


title: DMSO.37.1

description:
annapon_counts.txt
annapon_l2tpm.txt
d1095


title: Human1_RNA_FSS_ZIKVpositive_24h


title: Human3_RNA_FSS_ZIKVpositive_24h


title: L474_25C


title: BM_AMIL_141059


title: BM_AMIL_141053


title: L474_NonSPI2-3


title: BM_DM_141063


title: IAV-5T in MDCK replicate 2

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

description:
IAV_alignments.xlsx
CO91-IAV5T-MDCK-Rep3_S7

data_processing:
Libraries were run on an Illumina NextSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Raw sequencing reads were aligned to the corresponding reference viral genome using Bowtie2 with default paramaters
BAM files from each lane were consolidated into a single file
The resulting aligned reads were visualized, and the read counts for each residue per site obtained, using the Integrative Genomics Viewer (IGV)
Relative read counts and variation analyses were performed using in-house Perl scripts. Major variant for each site was defined as the residue (nucleotide) with higher read counts compared to all other possible residues for the same site.
For the analysis of junction sites, raw sequencing reads were aligned to the corresponding reference viral genome using HISAT2
Resulting alignments were filtered for low mapping quality reads using samtools(-q 10), and junction counts were obtained using regtools
Further consolidation of junction sites and their corresponding counts was performed using in-house Perl scripts.
Genome_build: As these are recombinant viruses, they do not have references on UCSC or  NCBI that are perfect matches.  See viral_genome sequences linked to the Series record.
Supplementary_files_format_and_content: Processed excel spread sheets contain, for each sample, Variability Ratio, Total Read Number, Number of Minor Variable reads, Number of mapped reads, Percentage, Coverage, and Minor Variable Reads for each position in the indicated viral genome

source_name: MDCK

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: Influenza A virus, targeted


title: IAV-5T in MDCK replicate 1

description:
IAV_alignments.xlsx
CO85-IAV5T-MDCK-Rep2_S4


title: L474_Macrophage-3

value: macrophage co-culture


title: HSF1i.39.2

description:
annapon_counts.txt
annapon_l2tpm.txt
d576

value: 1 ug/ml Doxycycline in water for 48 hours at 39 degrees C


title: L474_NonSPI2-2


title: IAV-GFPt in MDCK replicate 2

description:
IAV_alignments.xlsx
CO92-IAV5R-MDCK-Rep3_S18

value: Influenza A virus, control


title: Human1_RNA_Mock_24h

value: monocyte derived macrophage


title: L474_InSPI2-4


title: D23580_Peroxide_shock_InSPI2

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

value: peroxide shock InSPI2


title: IAV-GFPt in MDCK replicate 1

description:
IAV_alignments.xlsx
CO86-IAV5R-MDCK-Rep2_S1


title: D23580_Oxygen_shock

value: oxygen shock


title: SeV-5T in BHK replicate 2

description:
SeV_alignments.xlsx
CO76-SeV5T-BHK-Rep3_S5

organism: Mesocricetus auratus

value: Sendai virus, targeted


title: L474_InSPI2-3


title: D23580_NO_shock_InSPI2

value: no shock InSPI2


title: L474_NonSPI2-4


title: BM_DM_141057

value: Untreated (DMSO)


title: SeV-5T in BHK replicate 1

description:
SeV_alignments.xlsx
CO70-SeV5T-BHK-Rep2_S15


title: L474_ESP-4

value: ESP


title: BM_DM_141051


title: D23580_NonSPI2


title: L474_ESP-3


title: SeV-5R in BHK replicate 2

description:
SeV_alignments.xlsx
CO77-SeV5R-BHK-Rep3_S16

value: Sendai virus, control


title: D23580_NaCl_shock

value: NaCl shock


title: L474_ESP-2

value: wildtype


title: D23580_MEP

value: MEP


title: D23580_Macrophage-3


title: L474_Anaerobic_growth-4

value: anaerobic growth


title: L474_InSPI2-2


title: SFVGsplit-5T passage 4 replicate 3

description:
SFVG_alignments.xlsx
VV47-SFVG5T-BHK-pass4-Rep3_S7

value: Semliki Forest virus, targeted


title: SFVGsplit-5T passage 4 replicate 2

description:
SFVG_alignments.xlsx
VV45-SFVG5T-BHK-pass4-Rep2_S8


title: D23580_Macrophage-2


title: L474_Anaerobic_growth-3


title: L474_Anaerobic_growth-2


title: SeV-5R in BHK replicate 1

description:
SeV_alignments.xlsx
CO71-SeV5R-BHK-Rep2_S11


title: D23580_Macrophage-1


title: SFVGsplit-5R passage 4 replicate 3

description:
SFVG_alignments.xlsx
VV48-SFVG5R-BHK-pass4-Rep3_S4

value: Semliki Forest virus, control


title: SFVGsplit-5T passage 4 replicate 1

description:
SFVG_alignments.xlsx
VV43-SFVG5T-BHK-pass4-Rep1_S10


title: D23580_pBT1del_ESP-2

value: pBT1del ESP

value: pBT1 deletion


title: D23580_LSP

value: LSP


title: Human1_RNA_FSS_ZIKVnegative_24h

value: monocyte derived macrophage

value: ZIKV-bystander


title: D23580_Low_Fe2+_shock

value: low Fe2+ shock


title: SFVGsplit-5R passage 4 replicate 2

description:
SFVG_alignments.xlsx
VV46-SFVG5R-BHK-pass4-Rep2_S12


title: D23580_pBT1del_ESP-1


title: D23580_NonSPI2-4


title: SFVGsplit-5R passage 4 replicate 1

description:
SFVG_alignments.xlsx
VV44-SFVG5R-BHK-pass4-Rep1_S4


title: D23580_LEP

value: LEP


title: SFVGsplit-5T passage 0 replicate 2

description:
SFVG_alignments.xlsx
VV3-SFVG5T-BHK-pass0-Rep2_S13


title: D23580_NonSPI2-3


title: D23580_InSPI2


title: Human5_RNA_Mock_24h

value: mock infected


title: D23580_NonSPI2-2


title: SFVGsplit-5R passage 0 replicate 2

description:
SFVG_alignments.xlsx
VV4-SFVG5R-BHK-pass0-Rep2_S7


title: SFVGsplit-5T passage 0 replicate 1

description:
SFVG_alignments.xlsx
VV1-SFVG5T-BHK-pass0-Rep1_S2


title: D23580_InSPI2-4


title: D23580_ESP


title: D23580_EEP

value: EEP


title: SFVGsplit-5R passage 0 replicate 1

description:
SFVG_alignments.xlsx
VV2-SFVG5R-BHK-pass0-Rep1_S6


title: D23580_Bile_shock

value: bile shock


title: SINVsplit-5T-GFPFlag passage 4 replicate 3

description:
SINV_alignments.xlsx
VW47-SINVsplit5T-BHK-pass4-Rep3_S2

value: Sindbis virus, targeted


title: D23580_InSPI2-3


title: D23580_InSPI2-2


title: D23580_Anaerobic_growth


title: SINVsplit-5T-GFPFlag passage 4 replicate 2

description:
SINV_alignments.xlsx
VW45-SINVsplit5T-BHK-pass4-Rep2_S22


title: D23580_ESP-3

value: ESP


title: SINVsplit-5T-GFPFlag passage 4 replicate 1

description:
SINV_alignments.xlsx
VW43-SINVsplit5T-BHK-pass4-Rep1_S21


title: D23580_Anaerobic_shock

value: anaerobic shock

value: wildtype


title: D23580_25C


title: SINVsplit-5R-GFPFlag passage 4 replicate 2

description:
SINV_alignments.xlsx
VW48-SINVsplit5R-BHK-pass4-Rep3_S3

value: Sindbis virus, control


title: D23580_ESP-4


title: Genomic DNA from superficial MPNST  MPNST14

type: genomic

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: tumor sample

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differenitally methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

label: Cy5 and Cy3

source_name: Skin

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

tag: condition

value: superficial MPNST


title: Genomic DNA from desmoplastic melanoma DM14

description: tumor sample

value: desmoplastic melanoma


title: Genomic DNA from superficial MPNST  MPNST15

description: tumor sample


title: SINVsplit-5R-GFPFlag passage 4 replicate 1

description:
SINV_alignments.xlsx
VW44-SINVsplit5R-BHK-pass4-Rep1_S3


title: A4H

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
Cufflinks
Cuffdiff
Genome_build: hg19/rheMac8
Supplementary_files_format_and_content: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id

organism: Macaca mulatta

source_name: Macaca mulatta_Hypoxia

growth_protocol: CHIR 8uM x 2d + IWR 5uM x 2d + Glucose starvation on day 12 for 4 days. Cells were collected on day 30 of differentiation.

extract_protocol:
Trisol/ Qiagen RNA extract kit
Ion Total RNA Seq Kit v2 with ERCC RNA Spike-in Mix 1 added

treatment_protocol: Normoxia (control) vs. 24hr Hypoxia

value: Hypoxia

value: iPSC-Cardiomyocytes (iPSC-CM)


title: D23580_Anaerobic_growth-4

value: anaerobic growth


title: Genomic DNA from desmoplastic melanoma DM13

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM11

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM15

description: tumor sample


title: Genomic DNA from superficial MPNST  MPNST13

description: tumor sample


title: SINVsplit-5T-GFPFlag passage 0 replicate 2

description:
SINV_alignments.xlsx
VW3-SINVsplit5T-BHK-pass0-Rep2_S14


title: D23580_ESP-2


title: A12N

source_name: Macaca mulatta_Normoxia

value: Normoxia


title: Genomic DNA from superficial MPNST  MPNST12

description: tumor sample


title: SINVsplit-5T-GFPFlag passage 0 replicate 1

description:
SINV_alignments.xlsx
VW1-SINVsplit5T-BHK-pass0-Rep1_S20


title: Genomic DNA from superficial MPNST  MPNST10

description: tumor sample


title: D23580_Anaerobic_growth-2


title: Genomic DNA from desmoplastic melanoma DM12

description: tumor sample


title: Genomic DNA from superficial MPNST  MPNST8

description: tumor sample


title: cdk1-as1 S phase

city: Oslo

first: Jorrit

last: Enserink

address: Montebello

department: Molecular Cell Biology

country: Norway

institute: Oslo University Hospital

description:
tRNA
The cdk1-as1 allele encodes a form of Cdk1 in which the gatekeeper phenylalanine at position 88 is replaced with a much smaller glycine residue. This creates an enlarged ATP binding pocket that can accommodate the bulky, non-hydrolysable ATP analog 1-NM-PP1, which inhibits the kinase activity of Cdk1. However, the gene product of cdk1-as1 has a ten-fold reduction in ATP-binding affinity and a six-fold reduction in maximum ATP turnover rate, resulting in a profound hypomorphic phenotype even in absence of 1-NM-PP1.

data_processing:
rRNA was depleted from the samples.
Samples were sequenced using PE101 on HiSeq4000 (Illumina’s HiSeq Xten, Hong Kong, China)
10M clean reads per sample.
Small RNA sequencing
Size selection between 70 nt and 120 nt.
Genome_build: SacCer3 genome Reference
Supplementary_files_format_and_content: Xls files include for each tRNA identified, Locus, Gene ID, gene short, length, RPKM values, log2Fold Change, FDR and Log10 RPKM for each Sample,

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were synchronized by culturing in YPD to log phase, after which 15 mg/L α factor was added for 3 hrs. Synchronized cells were released into the cell cycle by washing away the pheromone and resuspending the cells in YPD or in YPD + nocodazole (10 mg/L) to prevent initiation of a new cell cycle. Cells were harvested after release from pheromone arrest when cells reached S-phase based on microscopy.Total RNA was isolated by using  QIAGEN kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell cycle phase

value: S phase

value: cdk1-as1 strain


title: Genomic DNA from superficial MPNST  MPNST11

description: tumor sample


title: Genomic DNA from superficial MPNST  MPNST9

description: tumor sample


title: A12H


title: A11N


title: A4N


title: SINVsplit-5R-GFPFlag passage 0 replicate 1

description:
SINV_alignments.xlsx
VW2-SINVsplit5R-BHK-pass0-Rep1_S11


title: Genomic DNA from superficial MPNST  MPNST2

description: tumor sample


title: Genomic DNA from superficial MPNST  MPNST5

description: tumor sample


title: A11H


title: Genomic DNA from superficial MPNST  MPNST3

description: tumor sample


title: Genomic DNA from superficial MPNST  MPNST6

description: tumor sample


title: PHH-T48-3

status: Public on Sep 09 2018

city: Shanghai

first: Baocun

last: Li

address: Medical College Road 138

country: China

institute: Fudan University

data_processing:
illumina GApipeline1.6 used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to hg19 whole genome using Hisat2(v2.0.1)
Reads Per Kilo basesof per exon per Million reads(RPKM) were calculated using a protocol from Mortazavi, A., B. A. Williams, et al. Nature methods, 2008.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Liver hepatocytes

growth_protocol: Primary human hepatocytes (PHH) (purchased from Bioreclamation IVT) was cultured in maintenance medium (Life Technologies) containing 2% DMSO and 2% FBS, the cells were plated on type I collagen coated 24-well plates at a concentration of 4.0 x 105 cells per well

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen), total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer,1 μg total RNA with RIN value above 7 was used for following library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PHH were infected with HBV at MOI of 150. After 24 h incubation, PHH cells were washed by PBS three times and treated with DMSO or Tazarotene for 8 h or 48 h

tag: tissue

value: Liver

value: primary human hepatocytes


title: PHH-T48-2


title: PHH-T48-1


title: PHH-T8-3


title: PHH-T8-2


title: PHH-T8-1


title: Genomic DNA from superficial MPNST  MPNST1

description: tumor sample


title: D23580_Anaerobic_growth-3

tag: genotype


title: Genomic DNA from superficial MPNST  MPNST7

description: tumor sample


title: PHH-D48-3


title: Genomic DNA from superficial MPNST  MPNST4

description: tumor sample


title: PHH-D48-2


title: Genomic DNA from desmoplastic melanoma DM10

description: tumor sample


title: PHH-D48-1


title: PHH-D8-3


title: PHH-D8-2


title: PHH-D8-1


title: Genomic DNA from desmoplastic melanoma DM7

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM8

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM9

description: tumor sample


title: SINVsplit-5R-GFPFlag passage 0 replicate 2

description:
SINV_alignments.xlsx
VW4-SINVsplit5R-BHK-pass0-Rep2_S18


title: Genomic DNA from desmoplastic melanoma DM6

description: tumor sample


title: CDK1 S phase

description:
tRNA
wildtype strain

value: CDK1 strain

value: wild type


title: Genomic DNA from desmoplastic melanoma DM4

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM5

description: tumor sample


title: T4F: genomic DNA from Father

city: Istanbul

first: ozkan

last: ozdemir

address: Kayisdagi Cad. No:32

department: Research and Development

country: Turkey

institute: Acibadem Labmed AŞ.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan Platform using standard recommended Illumina scanner setting

data_processing:
R bioconductor - The big melon package (Gorrie-Stone TJ, Saffari A, Malki K, Schalkwyk LC (2018). bigmelon: Illumina methylation array analysis for large experiments. R package version 1.6.0.)
Unmethylated and methylated signal intensities in Series supplementary file

source_name: genomic DNA from Father

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

tag: gender

value: Male

value: Peripheral Blood

tag: disease state

value: Normal


title: T15M: genomic DNA from Mother

source_name: genomic DNA from Mother

value: Female

value: Epilepsy


title: Genomic DNA from desmoplastic melanoma DM1

description: tumor sample


title: Genomic DNA from desmoplastic melanoma DM2

description: tumor sample


title: T7M: genomic DNA from Mother


title: T14D: genomic DNA from Offspring

source_name: genomic DNA from Offspring


title: T15F: genomic DNA from Father


title: T7D: genomic DNA from Offspring


title: T13D: genomic DNA from Offspring


title: T14M: genomic DNA from Mother


title: T15D: genomic DNA from Offspring


title: T4M: genomic DNA from Mother


title: T12S: genomic DNA from Offspring


title: T7F: genomic DNA from Father


title: T12M: genomic DNA from Mother


title: T11M: genomic DNA from Mother


title: T11D: genomic DNA from Offspring


title: T4S: genomic DNA from Offspring


title: T12F: genomic DNA from Father


title: T11F: genomic DNA from Father


title: T10F: genomic DNA from Father


title: T14F: genomic DNA from Father


title: T13F: genomic DNA from Father


title: T10D: genomic DNA from Offspring


title: Genomic DNA from desmoplastic melanoma DM3

description: tumor sample


title: T9D: genomic DNA from Offspring


title: T9M: genomic DNA from Mother


title: MB49

city: Orsay

first: Olivier

last: Ayrault

address: Institut Curie / CNRS UMR 3347 / INSERM U1021 Bldg. 110 – Centre Universitaire

country: France

institute: Institut Curie

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw data files were then processed by Genome Studio (Illumina) according to defaults using the OncoArray-500K-C manifest file.

label: Cy3, Cy5

source_name: human tumor

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: medulloblastoma

tag: material preparation

value: Frozen

tag: tumor subgroup

value: SHH


title: T8F: genomic DNA from Father


title: T8D: genomic DNA from Offspring


title: T9F: genomic DNA from Father


title: T8M: genomic DNA from Mother


title: T6F: genomic DNA from Father


title: MB48


title: MB55


title: T10M: genomic DNA from Mother


title: MB53


title: T5F: genomic DNA from Father


title: T6S: genomic DNA from Offspring


title: T3F: genomic DNA from Father


title: T13M: genomic DNA from Mother


title: T3M: genomic DNA from Mother


title: T5S: genomic DNA from Offspring


title: T6M: genomic DNA from Mother


title: T3D: genomic DNA from Offspring


title: MB46


title: T2F: genomic DNA from Father


title: T2M: genomic DNA from Mother


title: MB47


title: T5M: genomic DNA from Mother


title: MB54


title: T1M: genomic DNA from Mother


title: MB52


title: T1D: genomic DNA from Offspring


title: T2D: genomic DNA from Offspring


title: T1F: genomic DNA from Father


title: MB51


title: MB50


title: MB49

hyb_protocol: Illumina standard protocol

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: human medulloblastoma_SHH

label_protocol: Illumina standard protocol

tag: sample type

value: frozen tumor sample

value: human medulloblastoma


title: MB55


title: MB43


title: MB34

value: WNT


title: MB53

source_name: human medulloblastoma_G3


title: MB47


title: MB31


title: MB50


title: MB42

source_name: human medulloblastoma_NA


title: MB43


title: MB33


title: MB39

source_name: human medulloblastoma_G4


title: MB51


title: MB54


title: MB40


title: MB52


title: MB32


title: MB33

source_name: human medulloblastoma_WNT


title: MB39


title: MB30


title: MB24


title: MB40


title: MB31


title: wt_a_6h

first: Hajime

last: Murakami

address: 1275 york ave

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: For wild-derived S. cerevisiae strains YPS128 and UWOPS03-461.4, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for S. paradoxus YPS138, reads were mapped to the strain's genome assembly from SGRP (Saccharomyces Genome Resequencing Project, Wellcome Trust Sanger Institute); for S. mikatae IFO1815 and S. kudriavzevii ZP591, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: tab delimited text files include Spo11-oligo hitcount at each nucleotide position in the genome

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

value: epitope tag:Spo11-Flag

tag: meiotic time-point

value: meiotic time-point:6 hr in meiosis


title: MB30


title: MB34


title: wt_b_4h

description: Spo11-associated DNA oligonucleotides

value: meiotic time-point:4 hr in meiosis


title: MB48


title: MB41


title: MB25


title: wt_a_4h

description: Spo11-associated DNA oligonucleotides


title: MB25


title: MB22


title: MB27


title: MB24


title: Group D: Knockout day 21  biological replicate 3

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

description: Gene experession data from beta-catenin knockout mice at post-natal day 21

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

label: Biotin

source_name: Lung, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was prepared using the RNEasy Mini Kit and QIAshredder columns (QIAGEN, Valencia, CA)

value: male

value: beta-catenin knockout

tag: age

value: post-natal day 21


title: MB21


title: wt_b_6h

description: Spo11-associated DNA oligonucleotides


title: MB21


title: Group D: Knockout day 21  biological replicate 2


title: Group D: Knockout day 21  biological replicate 4


title: Group D: Knockout day 21  biological replicate 1


title: MB22


title: MB20


title: Group C: Stabilized day 21 biological replicate 4

description: Gene experession data from beta-catenin stabilized mice at post-natal day 21

value: beta-catenin stabilized


title: Group C: Stabilized day 21 biological replicate 1


title: MB19


title: MB17


title: Group C: Stabilized day 21 biological replicate 3


title: MB13


title: MB16


title: MB15


title: MB14


title: MB10


title: MB20


title: MB16


title: MB15


title: MB12


title: MB19


title: Group C: Stabilized day 21 biological replicate 2


title: MB13


title: MB14


title: Fig 3 liver 2-3

status: Public on Sep 08 2018

city: Carlsbad

first: Milos

last: Babic

address: 5922 Farnsworth Court, Suite 102

institute: BioSpyder Technologies Inc.

description:
MouseGeneCountsMaster.csv
F3liv2-3

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: TempO-Seq is a targeted sequencing assay, and sequencing results are aligned to a pseudo-transcriptome formed from known probe sequences (see Yeakley et al., PLoS One. 2017, 12(5):e0178302). For each species, the entire pseudo-transcriptome used for alignment is present in the corresponding master gene count files (Probe_ID and Probe_Sequence columns).
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

source_name: mouse liver FFPE

growth_protocol: For experiments involving cell pellets, MCF7 and MDA-MB-231 cells were grown in RPMI supplemented with 10% FBS

extract_protocol:
For cells that were not prepared as FFPE, cells were washed once with PBS, then lysed using TempO-Seq Lysis Buffer
TempO-Seq targeted expression assay. Addition of adapters by amplification.

treatment_protocol: For preparing FFPE cell pellets, live cells were washed twice with 1X PBS, and then fixed with 1% formaldehyde in 1X PBS for 30 minutes at room temperature

value: liver

tag: sample preparation

value: mouse FFPE tissue

tag: input

value: 2 mm ^2, 5 micron thick


title: Fig 3 liver 2-2

description:
MouseGeneCountsMaster.csv
F3liv2-2


title: MB11


title: MB08


title: MB17


title: Fig 3 liver 2-1

description:
MouseGeneCountsMaster.csv
F3liv2-1


title: Fig 3 liver 10-3

description:
MouseGeneCountsMaster.csv
F3liv10-3

value: 10 mm ^2, 5 micron thick


title: Fig 3 liver 10-1

description:
MouseGeneCountsMaster.csv
F3liv10-1


title: MB06

value: medulloblastoma


title: MB09


title: MB08

value: Frozen


title: MB07


title: Fig 3 liver 10-2

description:
MouseGeneCountsMaster.csv
F3liv10-2


title: Fig 2 muscle replicate 2

description:
MouseGeneCountsMaster.csv
F2mus2

source_name: mouse muscle FFPE

value: muscle


title: MB10

value: frozen tumor sample


title: Fig 2 lung replicate 2

description:
MouseGeneCountsMaster.csv
F2lun2

source_name: mouse lung FFPE

value: lung


title: Fig 2 muscle replicate 1

description:
MouseGeneCountsMaster.csv
F2mus1


title: Fig 2 lung replicate 1

description:
MouseGeneCountsMaster.csv
F2lun1


title: Fig 2 lung replicate 3

description:
MouseGeneCountsMaster.csv
F2lun3


title: MB07


title: Fig 2 muscle replicate 3

description:
MouseGeneCountsMaster.csv
F2mus3


title: Fig 2 breast replicate 1

description:
MouseGeneCountsMaster.csv
F2bre1

source_name: mouse breast FFPE

value: breast


title: B16-F10-Flv_input

city: Cincinnati

first: Kakajan

last: Komurov

state: OH

address: 3333 Burnet Ave OH 45229

department: Division of Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital

data_processing:
ChIP-Seq data processing: Chipseq reads were aligned to the mm10 reference genome using BWA-MEM (v0.7.12) .
Samtools (v 0.1.1 9) is then used to exclude reads that were either unaligned, were not primary alignments, failed vendor QC, are PCR duplicates or have quality < 10 (option: -F 1084) additionally only properly paired reads were retained (option: -f 2).
The BAM files post filtering are indexed and coverage around genebody, TSS and TES and 2000bp flanking regions is computed using ngs.plot (v 0.2.61). Briefly, reads from the BAM file are overlaid with regions of interest and coverage at single base resolution and the vector is normalized by length. Coverage vector is then fit to a spline and then 101 points are sampled at equal intervals and normalized by library size (per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: excel file; RNA pol2 coverage across genes in B16 control and 1week flavo treated B16 cell lines

source_name: Skin

growth_protocol: cultured inDMEM) containing 10% FBS with 0.1% antibiotic and antimycotic (Gibco)

extract_protocol:
Chromatin extrated cell cell lysate was sonicated and shered to 300bp to 1kb fragments using a Sonifier Cell Disruptor (Branson Ultrasonics #101-063-588). To 0.5ml sheared chromatin (after clarification of debrie), we added 150µl ChIP mix (440mM NaCl, 0.44% sodium deoxycholate, 4.4% Triton X-100) and antibody-coupled beads for immunoprecipitation overnight at 4C.
Precipitated DNA fragments were processed to ChIP-seq library using the ThruPLEX DNA-seq 12S kit (Takara #R400428) according to manufacturer’s instructions. 75bp paired end

treatment_protocol: B16/F10 cells pre-treated with flavopiridol (25nM) for one week

tag: disease

value: melanoma

tag: morphology

value: mixture of spindle-shaped and epithelial-like cells

tag: chip antibody


title: B16-F10-Flv_RNApol2

value: RNAPII (Active Motif:39097)


title: B16-F10_input


title: CAST/Eij_Female_NaiveCD4+Tcell_C6

first: Nicolas

last: Walker

address: Downing Street

department: Genetics

institute: University of Cambridge

data_processing:
These samples were not processed for quantitative gene expression analysis. They were used solely to further help map different mouse strain genomes and annotate genes described in https://www.biorxiv.org/content/early/2018/02/12/235838.  The genome sequence is NCBI BioProject PRJNA310854.
Genome_build: GRCm38

source_name: from CD4+CD62L+ T cells

growth_protocol: C57BL/6 mice at 6-8 weeks of age were used for spleen collection purposes.

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.  All RNA samples were subjected to in-column RNase-Free DNase treatment (Qiagen) to remove traces of DNA contamination. RNA integrity was subsequently assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) by using the RNA 6000 Pico Kit (Agilent Technologies). For each sample type 3 biological replicates were generated from male and female samples. AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 106 sorted naïve CD4+ T cells and resting B cells. All RNA samples were subjected to in-column RNase-Free DNase treatment (Qiagen) to remove traces of DNA contamination. RNA integrity was subsequently assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) by using the RNA 6000 Pico Kit (Agilent Technologies).
RNA was extracted from 1 million cells and spiked-in with synthetic ERCC ExFold RNA Spike-In Mixes (Ambion®) according to manufacturer’s instructions. RNA-sequencing libraries were prepared at the Wellcome Trust Sanger Institute using the bespoke pipeline and the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina) following manufacturer’s instructions with minor modifications. 400ng of RNA per sample type were subjected to rRNA-depletion with RiboZero Gold, fragmented for 6 min using metal-ion catalysed hydrolysis. Following the adaptor ligation step an Uracil-Specific Excision enzymatic treatment (NEB) was incorporated to introduce nicks in U positions of the second strand and ensure optimal stranded library preparation. The libraries were amplified with 8 cycles of PCR using the KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems), cleaned up with AMPure XP Beads, quantified and pooled in equimolar amounts. The pools were sequenced at the Wellcome Trust Sanger Institute on the Illumina HiSeq 2000 platform using 100bp paired-end read length.

tag: strain

value: CAST/Eij

value: spleen

tag: cell type

value: CD4+CD62L+ T cells

tag: Sex

value: female


title: CAST/Eij_Male_NaiveCD4+Tcell_D5

tag: tissue

value: male


title: CAST/Eij_Female_NaiveCD4+Tcell_C5


title: MB01

value: human medulloblastoma


title: MB05

value: SHH


title: MB04


title: CAST/Eij_Female_NaiveCD4+Tcell_C4


title: CAST/Eij_Male_RestingBcell_D3

source_name: from CD43- B cells

value: CD43- B cells


title: CAST/Eij_Male_RestingBcell_D1


title: CAST/Eij_Male_RestingBcell_D2


title: CAST/Eij_Male_NaiveCD4+Tcell_D4


title: MB05

value: medulloblastoma


title: MB02


title: CAST/Eij_Female_RestingBcell_C3


title: MB06


title: MB03

value: Frozen


title: CAST/Eij_Female_RestingBcell_C2


title: MB03


title: CAST/Eij_Female_RestingBcell_C1


title: MB01


title: B16-F10_RNApol2


title: Fig 6b mda20-2

description:
HumanGeneCountsMaster.csv
F6bmda20-2

source_name: human cell line FFPE

tag: cell line

value: embedded cell pellet FFPE

value: 20 mm ^2, 5 micron thick


title: Fig 6b mcf20-2

description:
HumanGeneCountsMaster.csv
F6bmcf20-2


title: Fig 6b mcf20-1

description:
HumanGeneCountsMaster.csv
F6bmcf20-1


title: Fig 6b mda20-3

description:
HumanGeneCountsMaster.csv
F6bmda20-3


title: Fig 6a fresh mda-1

description:
HumanGeneCountsMaster.csv
F6afreshmda-1

source_name: human cell line lysate

value: human cells lysed in TempO-Seq lysis buffer

value: 10 mm ^2, 5 micron thick


title: Fig 6a fresh mda-2

description:
HumanGeneCountsMaster.csv
F6afreshmda-2


title: Fig 6b mcf20-3

description:
HumanGeneCountsMaster.csv
F6bmcf20-3


title: Fig 6a fresh mcf-1

description:
HumanGeneCountsMaster.csv
F6afreshmcf-1


title: Fig 6a fresh mcf-3

description:
HumanGeneCountsMaster.csv
F6afreshmcf-3


title: Fig 6a ffpe mda-3

description:
HumanGeneCountsMaster.csv
F6affpemda-3


title: MB02

source_name: human tumor


title: MB04

source_name: human medulloblastoma_SHH

value: frozen tumor sample


title: Fig 6a fresh mcf-2

description:
HumanGeneCountsMaster.csv
F6afreshmcf-2


title: Fig 6a ffpe mda-1

description:
HumanGeneCountsMaster.csv
F6affpemda-1


title: Fig 6a ffpe mda-2

description:
HumanGeneCountsMaster.csv
F6affpemda-2


title: MB09


title: MB46


title: Fig 6a ffpe mcf-3

description:
HumanGeneCountsMaster.csv
F6affpemcf-3


title: Fig 6a ffpe mcf-2

description:
HumanGeneCountsMaster.csv
F6affpemcf-2


title: Fig 4 liver 2-93-3

description:
HumanGeneCountsMaster.csv
F4liv2-93-3

source_name: human liver FFPE

value: liver

value: human FFPE tissue pulled from archives and >24 years old

value: 25 mm ^2, 5 micron thick


title: Fig 6a ffpe mcf-1

description:
HumanGeneCountsMaster.csv
F6affpemcf-1


title: Fig 4 liver 2-93-2

description:
HumanGeneCountsMaster.csv
F4liv2-93-2


title: Fig 6a fresh mda-3

description:
HumanGeneCountsMaster.csv
F6afreshmda-3


title: Fig 4 liver 1-93-3

description:
HumanGeneCountsMaster.csv
F4liv1-93-3


title: Fig 6b mda20-1

description:
HumanGeneCountsMaster.csv
F6bmda20-1


title: Fig 4 liver 1-93-2

description:
HumanGeneCountsMaster.csv
F4liv1-93-2


title: Fig 2 breast replicate 3

description:
MouseGeneCountsMaster.csv
F2bre3

value: breast

value: mouse FFPE tissue


title: Fig 4 kidney 2-88-3

description:
HumanGeneCountsMaster.csv
F4kid2-88-3

source_name: human kidney FFPE

value: kidney


title: Fig 4 liver 1-93-1

description:
HumanGeneCountsMaster.csv
F4liv1-93-1


title: Fig 4 kidney 2-88-2

description:
HumanGeneCountsMaster.csv
F4kid2-88-2


title: Fig 4 kidney 1-88-2

description:
HumanGeneCountsMaster.csv
F4kid1-88-2


title: Fig 4 kidney 1-88-1

description:
HumanGeneCountsMaster.csv
F4kid1-88-1


title: Fig 4 kidney 2-88-1

description:
HumanGeneCountsMaster.csv
F4kid2-88-1


title: Fig 4 kidney 1-88-3

description:
HumanGeneCountsMaster.csv
F4kid1-88-3


title: Fig 4 colon 2-86-3

description:
HumanGeneCountsMaster.csv
F4col2-86-3

source_name: human colon FFPE

value: colon


title: Fig 4 colon 2-86-2

description:
HumanGeneCountsMaster.csv
F4col2-86-2


title: Fig 4 kidney 2-94-3

description:
HumanGeneCountsMaster.csv
F4kid2-94-3


title: Fig 4 kidney 2-94-1

description:
HumanGeneCountsMaster.csv
F4kid2-94-1


title: Fig 4 liver 2-93-1

description:
HumanGeneCountsMaster.csv
F4liv2-93-1


title: Fig 4 kidney 1-94-1

description:
HumanGeneCountsMaster.csv
F4kid1-94-1


title: Fig 4 kidney 1-94-2

description:
HumanGeneCountsMaster.csv
F4kid1-94-2


title: Fig 4 colon 2-86-1

description:
HumanGeneCountsMaster.csv
F4col2-86-1


title: Fig 4 colon 1-86-2

description:
HumanGeneCountsMaster.csv
F4col1-86-2


title: Fig 4 colon 1-86-3

description:
HumanGeneCountsMaster.csv
F4col1-86-3


title: Fig 4 kidney 1-94-3

description:
HumanGeneCountsMaster.csv
F4kid1-94-3


title: Fig 4 colon 1-86-1

description:
HumanGeneCountsMaster.csv
F4col1-86-1


title: Fig 7 paraffinized 3

description:
HumanGeneCountsMaster.csv
F7par3

source_name: human prostate FFPE

value: prostate

value: human FFPE tissue

value: 5 mm ^2, 5 micron thick


title: Fig 7 paraffinized 4

description:
HumanGeneCountsMaster.csv
F7par4


title: Fig 7 stained 2

description:
HumanGeneCountsMaster.csv
F7sta2


title: Fig 7 stained 1

description:
HumanGeneCountsMaster.csv
F7sta1


title: Fig 4 kidney 2-94-2

description:
HumanGeneCountsMaster.csv
F4kid2-94-2


title: Fig 7 paraffinized 2

description:
HumanGeneCountsMaster.csv
F7par2


title: Fig 7 paraffinized 1

description:
HumanGeneCountsMaster.csv
F7par1


title: Fig 7 deparaffinized 2

description:
HumanGeneCountsMaster.csv
F7dep2


title: Fig 7 deparaffinized 1

description:
HumanGeneCountsMaster.csv
F7dep1


title: Fig 2 prostate replicate 3

description:
HumanGeneCountsMaster.csv
F2pro3


title: Fig 2 prostate replicate 2

description:
HumanGeneCountsMaster.csv
F2pro2


title: Fig 2 colon replicate 3

description:
HumanGeneCountsMaster.csv
F2col3


title: Fig 2 colon replicate 2

description:
HumanGeneCountsMaster.csv
F2col2


title: Fig 2 prostate replicate 1

description:
HumanGeneCountsMaster.csv
F2pro1


title: Fig 2 pancreas replicate 3

description:
HumanGeneCountsMaster.csv
F2pan3

source_name: human pancreas FFPE

value: pancreas


title: Fig 2 pancreas replicate 2

description:
HumanGeneCountsMaster.csv
F2pan2


title: Fig 2 pancreas replicate 1

description:
HumanGeneCountsMaster.csv
F2pan1


title: Fig 2 breast replicate 2

description:
MouseGeneCountsMaster.csv
F2bre2


title: MD-MB-453

description: RNAseq

data_processing:
Normalized gene and isoform expression values (RPKM) of the hg19 transcriptome were obtained from fastq files using RSEM (v1.2.15) using the command rsem-calculate-expression and options  --bowtie2 --forward-prob 0
Genome_build: hg19
Supplementary_files_format_and_content: excel file with gene expression levels presented as RPKM values generated using RSEM

source_name: Mammary gland:Breast: derived from metastatic site. perecardial effusion

growth_protocol: cultured in improved minimum essential medium (Gibco) containing 20% FBS with 0.1% antibiotic and antimycotic (Gibco)

extract_protocol:
Total RNA was extracted from the cells using Tri reagent (Sigma). RNase-free DNase was used for removing all genomic DNA contamination. The RNA was precipitated by Isopropanol (Sigma), washed by ice cold 75% ethanol (Sigma), and air dried prior to resuspension in 20 µl of DEPC-treated water. Purity and concentration of RNA was measured by NanoDrops (Thermo Scientific). The 260/280 ratio was 1.90-2.00 and the 260/230 ratio was 2.00-2.20 for all RNA Samples.
Stranded sdingle end polyA RNAseq was carried out using illumina dUTP protocol

value: Metastatic Carcinoma

value: epithelial


title: T47D

description: RNAseq

source_name: Mammary gland:Breast: derived from metastatic site. pleural effusion

growth_protocol: cultured in RPMI 1640 (Gibco) containing 10% FBS with 0.1% antibiotic and antimycotic (Gibco)

value: Ductal Carcinoma


title: CAL51

description: RNAseq

source_name: Mammary gland:Breast: pleural effusion

value: BreastCarcinoma


title: SKBR3

description: RNAseq

value: Adenocarcinoma


title: MD-MB-415

description: RNAseq

growth_protocol: cells were grown in Leibovitz’s L-15 (Gibco) medium with 2mM L-glutamine supplemented with 10 μg/ml insulin (Sigma), 10 μg/ml glutathione (Calbiochem), 15% FBS and 0.1% antibiotic and antimycotic (Gibco)


title: UACC-812

description: RNAseq

source_name: Mammary gland:Breast

growth_protocol: cells were grown in Leibovitz’s L-15 (Gibco) medium with 2mM L-glutamine containing 20% fetal bovine serum (FBS) and 0.1% antibiotic and antimycotic (Gibco)


title: Henle-407 mock infection

city: Kalamazoo

first: Ben

middle: James

last: Koestler

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

institute: Western Michigan University

data_processing:
CLC Workbench version 9.5.1 used for mapping and analysis
Reads were pooled by sample
Mapping was performed to inter-genic regions and both strands, using a mismatch cost of 2, insertion cost of 3, deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8
We restricted the maximum number of hits per read to 1
RPKM was used for differential expression
Genome_build: S. flexneri 2457T genome (GenBank accession no. AE014073.1) and the pCP301 plasmid (GenBank accession no. AF386526.1)
Supplementary_files_format_and_content: .xlsx files contain Shigella reads that mapped to mock treatment, which were dropped from analysis, and differential gene expression between Shigella and Shigella with formate

source_name: Mock

growth_protocol: Shigella flexneri 2457T was grown in LB with DOC, then added to Henle-407 cells at an MOI of 20. After 60 minute incubation, Henle-407 cells were washed with PBS, and MEM+gentamycin was added to kill extracellular bacteria. Cells were incubated wih or without 20 mM formate for 2 hours prior to RNA extraction

extract_protocol:
RNABee was applied directly to infected cells for lysis, total RNA was extracted and DNAse treated.
RNA libraries were prepared for sequencing using standard Illumina protocols by the University of Texas at Austin GSAF, and RiboZero Gold was used to remove rRNA. Sequencing was performed twice, and reads were combined.

treatment_protocol: 20 mM formate was added to tissue culture medium after Shigella invasion for 2 hours

tag: host cell line

value: Henle-407 cells

tag: host cell type

value: epithelial cell

tag: treatment

value: mock infection


title: prostate_cancer_biopsy_sample_pid_12604

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

institute: GenomeDx

hyb_protocol: Following fragmentation, 3.5-7ug of cDNA were hybridized for 20 hr at 45C on GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000Dx V.2

data_processing:
The data were analyzed with the Affymetrix Power Tools packages, probeset summarization and normalization were performed using the single channel array normalization (SCAN) algorithm.
Decipher, a 22-marker prognostic gene-expression score, was determine from the Decipher prostate cancer classifier assay.

source_name: FFPE prostate cancer

label_protocol: Fragmented and biotinylated cDNA were prepared according to the NuGen Encore Biotin Module from total RNA.

growth_protocol: Biopsy core cell tissue were preservated by being Formalin-Fixed Paraffin-Embedded

extract_protocol: Extraction of total RNA from FFPE tissue was performed using the QIAGEN RNeasy kit and QIAcube .

treatment_protocol: Cores were incubated in deparaffinization solution at 56C

tag: disesase state

value: prostate cancer

tag: institution

value: Cleveland Clinic

tag: nccn

value: Low

tag: tumor stage

tag: percent positive cores

tag: psa

tag: gleason score

tag: primary gleason grade

tag: secondary gleason grade

value: prostate cancer biopsy


title: prostate_cancer_biopsy_sample_pid_14724

value: University of Calgary

tag: age


title: prostate_cancer_biopsy_sample_pid_13847


title: prostate_cancer_biopsy_sample_pid_5505

value: Favorable Intermediate


title: prostate_cancer_biopsy_sample_pid_5513


title: prostate_cancer_biopsy_sample_pid_5495


title: prostate_cancer_biopsy_sample_pid_5498


title: 3990-DS-0005

city: Huntsville

first: Dmytro

last: Starenki

state: Alabama

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: non-demultiplexed sample

data_processing:
Library strategy: TCR-seq
Demultiplexing, alignment, filtering, and annotation was performed by iRepertoire using a proprietary pipeline
Raw files were submitted to SRA without demultiplexing.  This is required for use with the iRepertoire protocol.
The barcode is found at position 62 of the read. The schema is: 58bp Illumina adapter A followed by a triple N-sequence and a 6 sequence barcode. Thus, the barcode starts at position 62.
Barcode IDs with barcode sequence and genotype are listed below:
MTBIvc-01  GTGTCA = control
MTBIvc-02  TCTGAC =  control
MTBIvc-03  TGACTA = control
MTBIvc-07  TCGCTC = control
MTBIvc-08  AGACAC = control
MTBIvc-09  ATGATA = control
MTBIvc-04  CGCTCT = MHCII-expressing
MTBIvc-05  AGATGA = MHCII-expressing
MTBIvc-06  ACTCAT = MHCII-expressing
MTBIvc-10  CGTGAT = MHCII-expressing
MTBIvc-11  TACGTA = MHCII-expressing
MTBIvc-12  TGAGCG = MHCII-expressing
Genome_build: The alignment is done to the reference T cell receptor genes downloaded from IMGT/GENE-DB, http://imgt.org/genedb/tableC.action. Murine assembly is GRCm38.p3.
Supplementary_files_format_and_content: TCR CDR3 nucleotide and aminoacid sequences, and V-D-J gene segment usage lists were generated by iRepertoire. The final column with header "copy" contains the number of reads per clone.

source_name: Murine breast cancer

growth_protocol: Mice were injected with 1 x 10^5 TS/A or TS/A-hCIITA tumor cells into the mammary fat pad.

extract_protocol:
Total RNA was purified from excised tumors using the RNeasy Mini kit (Qiagen). RNA quality was assessed using Bioanalyzer 2100 (Agilent) and final concentration determined by Qubit (Life Technologies).
T-cell receptor (TCR) sequencing was performed using the Mouse TCR beta, MTBIvc-X-P bulk kit from iRepertoire (Huntsville, AL). 500 ng of RNA was reverse transcribed using a One-Step reverse transcription and amplification kit (Qiagen). The PCR product was purified using Ampure XP magnetic beads (Agencourt), and amplified again (TopTaq PCR Kit, Qiagen), to add Illumina TruSeq adaptor sequences. Libraries were purified with Ampure XP magnetic beads.

tag: strain

value: BALB/c

tag: genotype

value: mixed sample (non-demultiplexed) control and MHCII-expressing

value: breast tumor


title: prostate_cancer_biopsy_sample_pid_5504

tag: tissue


title: prostate_cancer_biopsy_sample_pid_5499


title: prostate_cancer_biopsy_sample_pid_12449


title: prostate_cancer_biopsy_sample_pid_12612

value: High


title: prostate_cancer_biopsy_sample_pid_13838


title: prostate_cancer_biopsy_sample_pid_13811


title: Fig 2 colon replicate 1

description:
HumanGeneCountsMaster.csv
F2col1

value: colon

tag: sample preparation

value: human FFPE tissue

tag: input

value: 10 mm ^2, 5 micron thick


title: prostate_cancer_biopsy_sample_pid_14433


title: prostate_cancer_biopsy_sample_pid_13820


title: prostate_cancer_biopsy_sample_pid_13842


title: 3990-DS-0006

description: non-demultiplexed sample


title: prostate_cancer_biopsy_sample_pid_17294

value: Johns Hopkins


title: prostate_cancer_biopsy_sample_pid_17305


title: prostate_cancer_biopsy_sample_pid_17299


title: prostate_cancer_biopsy_sample_pid_17320


title: prostate_cancer_biopsy_sample_pid_17292


title: prostate_cancer_biopsy_sample_pid_17284


title: prostate_cancer_biopsy_sample_pid_17325


title: prostate_cancer_biopsy_sample_pid_14531

value: Cedars-Sinai


title: prostate_cancer_biopsy_sample_pid_14530


title: prostate_cancer_biopsy_sample_pid_14532


title: prostate_cancer_biopsy_sample_pid_12396


title: prostate_cancer_biopsy_sample_pid_5529


title: prostate_cancer_biopsy_sample_pid_5459


title: prostate_cancer_biopsy_sample_pid_14718


title: prostate_cancer_biopsy_sample_pid_14540


title: prostate_cancer_biopsy_sample_pid_5247


title: prostate_cancer_biopsy_sample_pid_14538


title: prostate_cancer_biopsy_sample_pid_5478


title: prostate_cancer_biopsy_sample_pid_12519


title: prostate_cancer_biopsy_sample_pid_12530


title: prostate_cancer_biopsy_sample_pid_5100


title: prostate_cancer_biopsy_sample_pid_17264


title: prostate_cancer_biopsy_sample_pid_17310


title: prostate_cancer_biopsy_sample_pid_12398


title: prostate_cancer_biopsy_sample_pid_5190


title: prostate_cancer_biopsy_sample_pid_14535


title: prostate_cancer_biopsy_sample_pid_4843


title: prostate_cancer_biopsy_sample_pid_12380


title: prostate_cancer_biopsy_sample_pid_5497


title: prostate_cancer_biopsy_sample_pid_5533


title: prostate_cancer_biopsy_sample_pid_5450


title: prostate_cancer_biopsy_sample_pid_5451


title: prostate_cancer_biopsy_sample_pid_14053


title: prostate_cancer_biopsy_sample_pid_12401


title: prostate_cancer_biopsy_sample_pid_5488


title: prostate_cancer_biopsy_sample_pid_5521


title: prostate_cancer_biopsy_sample_pid_12397


title: prostate_cancer_biopsy_sample_pid_4903


title: prostate_cancer_biopsy_sample_pid_5193


title: prostate_cancer_biopsy_sample_pid_5501


title: prostate_cancer_biopsy_sample_pid_12615


title: prostate_cancer_biopsy_sample_pid_14721


title: prostate_cancer_biopsy_sample_pid_12487


title: prostate_cancer_biopsy_sample_pid_5411


title: prostate_cancer_biopsy_sample_pid_5492


title: prostate_cancer_biopsy_sample_pid_5506


title: prostate_cancer_biopsy_sample_pid_14543


title: prostate_cancer_biopsy_sample_pid_5466


title: prostate_cancer_biopsy_sample_pid_4972


title: prostate_cancer_biopsy_sample_pid_5473


title: prostate_cancer_biopsy_sample_pid_14723


title: prostate_cancer_biopsy_sample_pid_14722


title: prostate_cancer_biopsy_sample_pid_5475


title: prostate_cancer_biopsy_sample_pid_13849


title: prostate_cancer_biopsy_sample_pid_5491


title: prostate_cancer_biopsy_sample_pid_13877


title: prostate_cancer_biopsy_sample_pid_12684


title: prostate_cancer_biopsy_sample_pid_14477


title: prostate_cancer_biopsy_sample_pid_5461


title: prostate_cancer_biopsy_sample_pid_5507


title: prostate_cancer_biopsy_sample_pid_5118


title: prostate_cancer_biopsy_sample_pid_14720


title: prostate_cancer_biopsy_sample_pid_5455


title: prostate_cancer_biopsy_sample_pid_5532


title: prostate_cancer_biopsy_sample_pid_13848


title: prostate_cancer_biopsy_sample_pid_5194


title: prostate_cancer_biopsy_sample_pid_12669


title: prostate_cancer_biopsy_sample_pid_14708


title: prostate_cancer_biopsy_sample_pid_5487


title: prostate_cancer_biopsy_sample_pid_12379


title: prostate_cancer_biopsy_sample_pid_14054


title: prostate_cancer_biopsy_sample_pid_5518


title: prostate_cancer_biopsy_sample_pid_14719


title: prostate_cancer_biopsy_sample_pid_12400


title: prostate_cancer_biopsy_sample_pid_5096


title: prostate_cancer_biopsy_sample_pid_5471


title: prostate_cancer_biopsy_sample_pid_5457


title: prostate_cancer_biopsy_sample_pid_5496


title: prostate_cancer_biopsy_sample_pid_5479


title: prostate_cancer_biopsy_sample_pid_4842


title: prostate_cancer_biopsy_sample_pid_14709


title: prostate_cancer_biopsy_sample_pid_14060


title: prostate_cancer_biopsy_sample_pid_5526


title: prostate_cancer_biopsy_sample_pid_5525


title: prostate_cancer_biopsy_sample_pid_13850


title: prostate_cancer_biopsy_sample_pid_4985


title: prostate_cancer_biopsy_sample_pid_5164


title: prostate_cancer_biopsy_sample_pid_5192


title: prostate_cancer_biopsy_sample_pid_5447


title: prostate_cancer_biopsy_sample_pid_5474


title: prostate_cancer_biopsy_sample_pid_5464


title: prostate_cancer_biopsy_sample_pid_14055


title: prostate_cancer_biopsy_sample_pid_5465


title: prostate_cancer_biopsy_sample_pid_5477


title: prostate_cancer_biopsy_sample_pid_14516


title: prostate_cancer_biopsy_sample_pid_14513


title: prostate_cancer_biopsy_sample_pid_13366

value: Spectrum Health


title: prostate_cancer_biopsy_sample_pid_13365


title: prostate_cancer_biopsy_sample_pid_5522


title: prostate_cancer_biopsy_sample_pid_13364


title: prostate_cancer_biopsy_sample_pid_14431


title: prostate_cancer_biopsy_sample_pid_5456


title: prostate_cancer_biopsy_sample_pid_12356


title: prostate_cancer_biopsy_sample_pid_14156


title: prostate_cancer_biopsy_sample_pid_5438


title: prostate_cancer_biopsy_sample_pid_12355


title: prostate_cancer_biopsy_sample_pid_17278


title: prostate_cancer_biopsy_sample_pid_14077


title: prostate_cancer_biopsy_sample_pid_17271


title: prostate_cancer_biopsy_sample_pid_17270


title: prostate_cancer_biopsy_sample_pid_14489


title: prostate_cancer_biopsy_sample_pid_14490


title: prostate_cancer_biopsy_sample_pid_14094


title: prostate_cancer_biopsy_sample_pid_14488


title: prostate_cancer_biopsy_sample_pid_14487


title: prostate_cancer_biopsy_sample_pid_14520


title: prostate_cancer_biopsy_sample_pid_13363


title: prostate_cancer_biopsy_sample_pid_14485


title: prostate_cancer_biopsy_sample_pid_14483


title: prostate_cancer_biopsy_sample_pid_14504


title: prostate_cancer_biopsy_sample_pid_14432


title: prostate_cancer_biopsy_sample_pid_14423


title: Mouse RELACS CTCF (16 tissues)

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: RELACS-barcoded nuclei extracted from each tissue, typically with 2 replicates

data_processing:
ChIP-seq reads were aligned to the mm10 and hs37d5 genome assembly using Bowtie2-2.2.8 with the following configuration: -X 1000 --local --fr --rg CN:mpi-ie_deep_sequencing_unit --rg PL:ILLUMINA
BigWig files were created with bamCoverage (deepTools 2.4.1) using `-e --normalizeTo1x -bs 50`
Genome_build: mouse: mm10, human: hs37d5
Supplementary_files_format_and_content: BigWig files contain coverage information generated from genomic alignments.

source_name: whole organ

growth_protocol: HepG2 (ATCC, HB-8065TM) were culture in EMEM (Lonza, 06-174) supplemented with 10% FBS, 2 mM L-Glutamine, 1.8 mM CaCl2, 1mM sodium pyruvate and penicillin-streptomycin mixture (100 units/ml, Lonza), at 37 ˚C at 5% CO2. S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C. Mouse experiments were performed on 9 weeks-old wild-type (WT) FVB/NJ littermate male mice fed chow diet and maintained on a 12h light cycle (lights on at 7 am).

extract_protocol:
RELACS: nuclei have been extracted, permeabilized and barcoded following RELACS protocol. Nuclei labeled with distinct barcodes have been pooled and lysed to complete chromatin preparation. Traditional ChIP-seq: after nuclei extraction chromatin has been fragmented by sonication. Immunoprecipitation has been performed using the antibody of interest.
RELACS libraries: as described in the paper, using A-tailing strategy and ligation of adapters containing nuclear barcodes. After ChIP and DNA purification library preparation has been completed by PCR amplification using NEB workflow (NEBNext Ultra II DNA library preparation kit (E7645L, NEB)). Traditional ChIP-seq libraries: NEBNext Ultra II DNA library preparation kit (E7645L, NEB)

tag: cell type

value: various (Adipocytes, Adipose, Brain, Duodenum, Heart, Liver, Lungs, Muscle, Pancreas, SVF, Spleen)

tag: provider/strain

value: wild-type (WT) FVB/NJ; 9 weeks old, male

tag: chip antibody

value: CTCF (Abcam, ab70303)


title: prostate_cancer_biopsy_sample_pid_14482

tag: disesase state

value: prostate cancer

tag: institution

value: Low


title: prostate_cancer_biopsy_sample_pid_14160

tag: nccn

tag: tumor stage

value: prostate cancer biopsy


title: prostate_cancer_biopsy_sample_pid_14157

value: Favorable Intermediate

tag: percent positive cores

tag: psa


title: prostate_cancer_biopsy_sample_pid_14507

tag: gleason score

tag: primary gleason grade


title: prostate_cancer_biopsy_sample_pid_14152

tag: age

tag: secondary gleason grade


title: prostate_cancer_biopsy_sample_pid_12540

value: MD Anderson Cancer Center


title: prostate_cancer_biopsy_sample_pid_13395


title: prostate_cancer_biopsy_sample_pid_14141


title: prostate_cancer_biopsy_sample_pid_14135


title: prostate_cancer_biopsy_sample_pid_14134


title: prostate_cancer_biopsy_sample_pid_14153


title: prostate_cancer_biopsy_sample_pid_14122


title: prostate_cancer_biopsy_sample_pid_14139


title: prostate_cancer_biopsy_sample_pid_14138


title: prostate_cancer_biopsy_sample_pid_14145


title: MCF10A Ctrl3

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using GenomeStudio

source_name: Cell line

label_protocol: Standard Illumina protocol

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit

tag: cell line

tag: genotype/variation

value: CTRL


title: KLE shMSH3 062 B

value: KLE


title: KLE shMSH6 603 C


title: MCF10A Ctrl2


title: KLE shMSH3 062 C


title: prostate_cancer_biopsy_sample_pid_14119

tag: tissue


title: KLE shMSH6 543 B


title: MCF10A MSH2KO 1

value: MSH2 KO


title: MCF10A MSH2KO 3


title: KLE shMSH6 603 A


title: prostate_cancer_biopsy_sample_pid_14133


title: KLE shMSH6 543 A


title: KLE shMSH6 603 B


title: prostate_cancer_biopsy_sample_pid_12500


title: prostate_cancer_biopsy_sample_pid_13418


title: prostate_cancer_biopsy_sample_pid_14117


title: KLE shMSH6 543 C


title: prostate_cancer_biopsy_sample_pid_12474


title: MCF10A Ctrl1


title: KLE shMSH2 670 C


title: MCF10A MSH2KO 2


title: prostate_cancer_biopsy_sample_pid_12646

value: Cleveland Clinic


title: KLE shMSH3 059 A


title: KLE shMSH2 384 C


title: prostate_cancer_biopsy_sample_pid_1519


title: KLE shMSH3 059 B


title: prostate_cancer_biopsy_sample_pid_12619

value: Unfavorable Intermediate


title: KLE shMSH3 062 A


title: KLE shMSH3 059 C


title: KLE shMSH2 670 A


title: KLE shMSH2 670 D


title: KLE shMSH2 670 B


title: prostate_cancer_biopsy_sample_pid_13836


title: prostate_cancer_biopsy_sample_pid_12575


title: KLE shMSH2 384 B


title: prostate_cancer_biopsy_sample_pid_13834


title: prostate_cancer_biopsy_sample_pid_12581


title: KLE shMLH1 642 C


title: prostate_cancer_biopsy_sample_pid_12453


title: prostate_cancer_biopsy_sample_pid_14427


title: prostate_cancer_biopsy_sample_pid_13830


title: KLE shMLH1 642 A


title: prostate_cancer_biopsy_sample_pid_12568


title: prostate_cancer_biopsy_sample_pid_12614


title: KLE shCTRL C

value: shCTRL


title: HCT116 MLH3


title: prostate_cancer_biopsy_sample_pid_13818


title: prostate_cancer_biopsy_sample_pid_2028


title: prostate_cancer_biopsy_sample_pid_13794


title: prostate_cancer_biopsy_sample_pid_12605


title: prostate_cancer_biopsy_sample_pid_12610


title: prostate_cancer_biopsy_sample_pid_12658


title: HCT116 MLH1


title: KLE shCTRL B


title: HCT116 MLH2


title: prostate_cancer_biopsy_sample_pid_2315


title: KLE shMSH2 384 A


title: KLE shMLH1 641 B


title: prostate_cancer_biopsy_sample_pid_12583


title: prostate_cancer_biopsy_sample_pid_12582


title: prostate_cancer_biopsy_sample_pid_12627


title: KLE shMLH1 641 C


title: HCCT116 Ctrl3


title: KLE shCTRL A


title: HCCT116 Ctrl1


title: prostate_cancer_biopsy_sample_pid_5269


title: prostate_cancer_biopsy_sample_pid_12450


title: prostate_cancer_biopsy_sample_pid_13828


title: prostate_cancer_biopsy_sample_pid_12566


title: prostate_cancer_biopsy_sample_pid_13819


title: HCCT116 Ctrl2


title: prostate_cancer_biopsy_sample_pid_13816


title: KLE shMLH1 641 A


title: prostate_cancer_biopsy_sample_pid_12438


title: prostate_cancer_biopsy_sample_pid_12569


title: prostate_cancer_biopsy_sample_pid_12565


title: PCMV6-5-8F-rep1

city: Nanning

first: Bo

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

institute: Guangxi Medical University

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: control

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: All cells were incubated at 37℃ in a humidified atmosphere containing 5% CO2 and cultured in Modified Eagles Medium/High glucose (DMEM) medium supplemented with 10% fetal bovine serum (FBS) in the presence of streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: The pCMV6-vector or BDH2 plasmid was transferred into NPC cell line 5-8F by liposome transfection. After 3 weeks of selection in 4 μg/ml of G418 resistant cell clones were grown up and the transfection efficiency was validated for BDH2 expression by RT-qPCR.

value: Nasopharyngeal carcinoma


title: BDH2-5-8F-rep3

source_name: ectopic expression of BDH2


title: prostate_cancer_biopsy_sample_pid_17256

value: Johns Hopkins