title: PL91_vc

source_name: genomic DNA from PL91 aCA placenta

value: Chorionic villi

value: F

tag: 850k sentrix_id


title: BH500(pYS5)_OD=10_Run3

status: Public on Nov 06 2018

type: SRA

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

country: USA

institute: National Institute of Health

library_source: transcriptomic

data_processing:
Bcl2fastq2 software was used for base-calling.
The sequenced reads were trimmed to remove the low quality bases with the following parameters Trim based on : Quality score; Min read length : 25; Max N : FALSE ; End min quality level (Phred) : 20 ; Trim from end : 3-prime (right end).
Bowtie2 method was used to align the RNA-seq reads with the reference organism Bacillus anthracis str ames AE017334.2.
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Data was normalized using TPM method and differential gene expression were predicted across comparisions using ANOVA.
Genome_build: ASM844v1
Supplementary_files_format_and_content: tab-delimited text file contains normalized values obtained after TPM normalization, addition +1 and log2 transformation.
tab-delimited text file contains results from ANOVA and includes fold change calculations among pYS5 LagPhase vs pSW4 LagPhase, pYS5 LogPhase vs pSW4 LogPhase, pYS5 LateLogPhase vs pSW4 LateLogPhase, along with p-value, FDR stepup etc.

molecule: total RNA

organism: Bacillus anthracis str. Ames

extract_protocol:
Culture samples were immediately treated with RNA protect and preserved in Trizol at -80 degree celcius and total RNA was extracted using hot phenol method.
The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used to prepare the complete RNA-seq library preparation. First strand cDNA synthesis was performed using NEBNext first strand synthesis reaction buffer, random primers, Protoscript II reverse. To the same reaction mix, second strand synthesis enzyme mix was added and second strand synthesis was. The synthesized cDNA strands were purified using a 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Later steps involved end repair of extracted cDNA, adapter ligation using blunt/TA ligase and cleavage by USER enzyme, purification with AMPure XP beads and PCR enrichment of cDNA library using different sets of Multilex oligos for Illumina. The enriched library was again purified with Agencourt AMPure XP beads, and its quality was checked on a Bioanalyzer using Agilent DNA high sensitivity chips according to the manufacturer’s instructions.

tag: strain

tag: growth phase

value: log phase

tag: protocol

value: transformed with pYS5

tag: expression

value: PA producer

tag: od at harvest


title: flower-day0, rep1

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

country: Germany

institute: Humboldt University

data_processing:
miRNA-seq reads were subjected to quality and adapter trimming using the Trim Galore tool (https://github.com/FelixKrueger/TrimGalore) with parameters ‘--length 17 --phred33’.
Clean reads were mapped to A. thaliana genome using the STAR algorithm with the following parameters: ‘--outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.03 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1 --genomeLoad NoSharedMemory’.
miRNAs were quantified in RPM (reads per million mapped reads) values based on the count number from STAR output. Annotation of miRNA genes were obtained from the miRBase database (release 21) (Griffiths-Jones et al. 2008).
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: Plants were grown in a climatized greenhouse under long day conditions(16 h light, 8 h dark).

extract_protocol:
RNAs were isolated by the Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, Germany) according to manufacturer.
2 μg total RNA was used to produce libraries using TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, USA). Pooled libraries were submitted to a NextSeq®550 sequencing platform (Illumina, USA) for sequencing.

treatment_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 mM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Inflorescences were harvested before treatment and 2, 4 and 8 days after induction.

tag: ecotype

value: Landsberg

tag: genotype/variation

value: pAP1:AP1:GR ap1 cal

tag: agent

value: not treated

tag: tissue

value: inflorescences

tag: time

value: 0 days after treatment


title: AAA0500907  [miRNA-Seq]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: G1_healthy controls

data_processing:
Quality Control: performed  by an in-house written quality control function, axShortReadQCAnax. This function formats and filters the reads based of their per-base reported quality
Adapters removing: using Trimmomatic v 0.32.
Alignment: aligned to miRBase v21 mature miRNA sequences using Bowtie 2 with parameters '--local','-L 16'
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
Feature Count
Expression normalization and Differential expression analysis using R bioconductor packages EdgeR and Limma
Genome_build: mature miRNAs (miRBase version 21)
Supplementary_files_format_and_content: tab-delimited text file of raw counts for mature miRNAs (miRBase version 21) across samples.  Tab delimited text files of edger , limma (voom) normalized counts

organism: Homo sapiens

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
TruSeq Small RNA Sample Prep Kit (Illumina Inc.)
Isolation of mature microRNA fraction

value: intestinal tissue

tag: disease state

value: healthy controls

tag: group


title: seedlings, rep3

source_name: seedlings

value: seedlings

value: vegetative stage


title: AAA0500906  [miRNA-Seq]

description: G2_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)

value: ulcerative colitis


title: BH500(pYS5)_OD=16_Run2

value: Late log phase


title: AAA0500905  [miRNA-Seq]

description: G3_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids  and who will have a poor response to treatment (non-responders, NR)


title: AAA0500928  [miRNA-Seq]

value: patients with active ulcerative colitis before receiving glucocorticoids and who have a good response to treatment (responders, R)


title: BH500(pYS5)_OD=3_Run3

value: lag phase


title: PL73_vc

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Using R version 3.4.1. One amnion sample was removed from the analysis as it was a poor quality sample (sample not included in these GEO records). Array probes targeting sex chromosomes, with evidence of cross-hybridization, 59 rs probes, polymorphic probes, poor quality probes (detection p value >0.01 in >20 % of samples or <3 bead replicates in >20 % of samples) were eliminated.
Processed data matrices include: average beta (normalized by functional normalization and combat corrected for batch variables)
Signal intensities file includes: Methylated (signal A) and unmethylated (signal B) signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from PL73 aCA placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: patient id

value: Chorionic villi

tag: pathology group

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_position


title: seedlings, rep2


title: PL123_vc

source_name: genomic DNA from PL123 aCA placenta

value: M

tag: 850k sentrix_id


title: AAA0500917  [miRNA-Seq]

description: G4_intestinal samples collected on the third day of treatment in treatment-responders (R) patients


title: AAA0500904  [miRNA-Seq]

value: patients with active ulcerative colitis before receiving glucocorticoids  and who will have a poor response to treatment (non-responders, NR)


title: AAA0500902  [miRNA-Seq]

description: G1_healthy controls


title: BH500(pYS5)_OD=3_Run2

tag: strain

tag: growth phase

tag: protocol

value: transformed with pYS5

value: PA producer


title: PL15_vc

source_name: genomic DNA from PL15 aCA placenta

value: chorioamnionitis


title: PL32_vc

source_name: genomic DNA from PL32 aCA placenta


title: RNAseq 8d, rep3

data_processing:
RNA-seq reads were mapped to A.thaliana reference genome (TAIR10) using STAR (version 020201).
Expression levels (in terms of FPKM, fragments per kilobase of transcript per million mapped reads) of all annotated protein-coding genes were estimated by RSEM (version 1.2.22).
Differentially expressed genes across the four developmental stages were identified by analysis of variance (ANOVA) based on FPKM values. Resulting p-values were adjusted for multiple comparisons by false discovery rate (FDR) (Benjamini and Hochberg 1995).
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx

tag: ecotype

value: Landsberg

value: pAP1:AP1:GR ap1 cal

value: DEX

value: inflorescences

value: 8 days


title: BH500(pYS5)_OD=16_Run1

tag: expression

tag: od at harvest


title: BH500(pYS5)_OD=10_Run1

value: log phase


title: PM116_vc

source_name: genomic DNA from PM116 aCA placenta

tag: tissue


title: PM20_vc

source_name: genomic DNA from PM20 aCA placenta


title: 8W-HFD

city: La Jolla

first: Vandana

state: CA

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
8W-HFD_S2_L001
De-novo assembly: Contig sequences from 8wksPW assembly.fa

data_processing:
Illumina software was used for base-calling (accuracy 99.9%)
We used Qiagen's CLC workbench 10.0 to process and analyze RNA-Seq data. https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/
200 million reads from all the samples were combined to generate a reference and de novo assembly was done using an algorithm based on de Bruijn graphs to obtain the contigs.
Reads from each sample were mapped to the assembly. RPKM numbers and fold change were calculated.
Genome_build: De-novo assembly of the samples was done using CLC genomics workbench (Qiagen Bioinformatics).
Supplementary_files_format_and_content: Fasta file includes assembled contigs for 3 or 8 weeks post weaning samples
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for HFD and HFDM at 3 or 8 weeks post weaning.

organism: Mus musculus

source_name: cecal microbiota

extract_protocol:
At the time of sacrifice, cecal contents were collected and immediately frozen. RNA from each mouse for each diet group was isolated individually using Ambion RiboPure Bacteria kit.
RNA libraries were prepared for sequencing using Truseq Stranded total RNA library preparation kit as per the standard Illumina protocols

treatment_protocol: Mice were weaned on high fat diet (HFD) or high fat diet with 2% mannose in drinking water (HFDM)

tag: age

value: 24 weeks

tag: weaned on

value: HFD with no mannose

value: cecal contents


title: 8W-HFDM

description:
8W-HFDM_S3_L001
De-novo assembly: Contig sequences from 8wksPW assembly.fa

value: HFD and 2% mannose in water started 8 weeks post weaning


title: RNAseq 8d, rep1

tag: genotype/variation

tag: agent

tag: time


title: BH500(pYS5)_OD=3_Run1

value: lag phase


title: PL62_vc

source_name: genomic DNA from PL62 aCA placenta

tag: patient id

value: Chorionic villi

tag: pathology group

tag: fetal sex

value: F


title: 3W-HFDM

description:
3W-HFDM_S4_L001
De-novo assembly: Contig sequences from 3wksPW assembly.fa

value: HFD and 2% mannose in water started 3 weeks post weaning


title: PM122_vc

source_name: genomic DNA from PM122 aCA placenta

value: M

tag: gestational age

tag: 850k plate

tag: 850k sentrix_position


title: RNAseq 4d, rep3

value: 4 days


title: SCE-EtOAc

type: RNA

city: Shinjuku-ku

first: kayoko

last: Kawaguchi

state: Tokyo

department: Pediatric Cardiology

country: Japan

institute: Tokyo Women'Medical University

hyb_protocol: The arrays were hybridized at 65C overnight.

scan_protocol: The arrays were scanned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2 or each SCE sample to that for the control sample was calculated for each gene, and then normalized using control genes. Normalized/processed data for each sample prior to ratio generation were not provided.

source_name: breast cancer cells

label_protocol: Five ug of total RNA was reverse-transcribed and labeled with Cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

tag: cell line

tag: cell type

value: breast cancer cell line

tag: treatment

value: Sparassis crispa-Extraction (SCE)-EtOAc


title: 3W-HFD

description:
3W-HFD_S2_L001
De-novo assembly: Contig sequences from 3wksPW assembly.fa

tag: strain


title: RNAseq 4d, rep2

tag: ecotype

value: Landsberg

value: pAP1:AP1:GR ap1 cal


title: PL25_vc

source_name: genomic DNA from PL25 aCA placenta

tag: tissue

value: chorioamnionitis

tag: 850k sentrix_id


title: SCE(100 µg/ml)

value: Sparassis crispa-Extraction (SCE) (100 ug/ml)


title: PL4_vc

source_name: genomic DNA from PL4 aCA placenta


title: seedlings, rep1

value: not treated

value: seedlings

value: vegetative stage


title: RNAseq 4d, rep1

value: DEX

value: inflorescences


title: BH500(pYS5)_OD=10_Run2

tag: growth phase

value: log phase

tag: protocol

value: transformed with pYS5

tag: expression

value: PA producer

tag: od at harvest


title: RNAseq 8d, rep2

tag: genotype/variation

tag: agent

tag: time

value: 8 days


title: E2-3

value: 17beta-estradiol (E2)


title: SCE(10 µg/ml)

value: Sparassis crispa-Extraction (SCE) (10 ug/ml)


title: Scc1 Input_1

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
Scc1 Sonication Input
ws1ss1_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

library_source: genomic

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Read alignment: BWA-mem v.0.7.16 -t 20
Read filtering: samtools v.1.8 view -hSb, sort, view -bh -@4 -q10
COVERNANT v0.3.2
Genome_build: Tb427v9
Supplementary_files_format_and_content: wiggle files

organism: Trypanosoma brucei brucei

source_name: whole liquid cell culture

growth_protocol: All replicates were grown in HMI-11 (37 °C, 5% CO2) and drug selection was applied where necessary.

extract_protocol:
300 million cells were harvested by centrifugation and fixed in the presence of 1% formaldehyde. Cells were washed and permeabilized with digitonin and chromatin sheared by sonication. An input sample was seperated from the chromatin and stored at -20 °C. The IP was performed by addition of Ig-coated magnetic beads (BB2 Antibody against the Ty1-tag) and incubation over night at 4°C whilst rotating. The DNA was subsequently washed and eluted from the beads. Crosslinks were reversed in both the ChIP and input sample. The samples were purified and the concentration was determined using Qubit.
ChIP and input samples were end-repaired using T4 DNA polymerase (NEB),
Klenow large Fragment (NEB) and T4 DNA Polynucleotide Kinase (NEB). Protruding A-bases were added to the 3` end using  Klenow fragment (3´ to 5´ exo minus) and dATP. TruSeq adapters were ligated to the cDNA fragments using Quick Ligase (NEB) and was purified using AMPure XP magnetic beads. Y-shaped adapters were converted to dsDNA with Illumina primers for 5 cycles, purified with magnetic beads  and library fragments of 200-500 bp were size selected from a 6% PAGE gel. The gel-purified library was further amplified for 10 cycles using Illumina primers and purified using magnetic beads. Libraries were quantified using Qubit and qPCR and were sequenced on an Illumina flow cell in an Illumina NextSeq apparatus following the manufacturer's instructions.

value: Lister 427 MITat 1.2

tag: genotype

tag: life cycle stage

value: Bloodstream form


title: Scc1 Input_2

description:
Scc1 Sonication Input
ws1ss1_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig


title: Scc1 ChIP_2

description:
Scc1 Sonication ChIP
ws1ss1_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800475_Scc1_Ty1_wt_soni_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800474_Scc1_Ty1_wt_soni_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: chip antibody


title: RNAseq 2d, rep1

value: Landsberg

value: 2 days


title: PL29_vc

source_name: genomic DNA from PL29 aCA placenta

tag: patient id

value: Chorionic villi

tag: pathology group

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_position


title: E2-2

tag: cell line

tag: cell type

value: breast cancer cell line

tag: treatment


title: PL104r_vc

source_name: genomic DNA from PL104 aCA technical replicate placenta

tag: tissue

tag: 850k sentrix_id


title: PL23_vc

source_name: genomic DNA from PL23 aCA placenta


title: RNAseq 0d, rep3

source_name: inflorescences

tag: ecotype

tag: genotype/variation

value: pAP1:AP1:GR ap1 cal

value: not treated

value: 0 days


title: Scc1 ChIP_1

description:
Scc1 Sonication ChIP
ws1ss1_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800469_Scc1_Ty1_wt_soni_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800468_Scc1_Ty1_wt_soni_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: strain


title: Scc1 Input_0

description:
Scc1 Sonication Input
ws1ss1_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: genotype


title: RNAseq 0d, rep2

tag: agent

value: inflorescences

tag: time


title: E2-1


title: PL78_vc

source_name: genomic DNA from PL78 aCA placenta

tag: patient id

value: chorioamnionitis

value: M


title: RNAseq 0d, rep1


title: Human-Mouse-multiplet

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the hg19 (human), mm10 (mouse) or hg19+mm10 (human and mouse, for multiplet tests) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Human reference genome NCBI build 38 (GRCh38) or a combined hg19 (hGRC37) + Mouse reference genome NCBI build 38, GRCm38 (mm10) for multiplet tests
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Adult testis

extract_protocol:
Suspensions of human seminiferous tubule cells were prepared from adult testicular tissue parenchyma by a two-step enzymatic digestion was as described previously (Hermann et al., 2007b; Hermann et al., 2009; Dovey et al., 2013). Briefly, testis tissue was digested with 2mg/ml collagenase type IV at 37oC with vigorous agitation, washed with HBSS to remove interstitial cells, followed by digestion with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I for 15 minutes at 37oC with trituration every 5 minutes, and quenched with 10% FBS. In all cases, cell suspensions were strained (40um pore size for mouse, 70um pore size for humans) and suspended in MEMα containing 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 106 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S), labeled with antibodies (see Key Resources Table), and subjected to FACS using  a FACS Aria (BD). Positive antibody labeling was determined by comparison to staining with isotype control antibodies. Human spermatogonia were isolated by sorting cells with the phenotype HLA-ABCnegative / CD49enegative / THY1dim / ITGA6+ / EpCAMdim dim (see Fig. 2C). These markers were chosen because previous results indicate they specifically label undifferentiated spermatogonia, including some with colonization potential based on xenotransplantation (Dovey et al., 2013; Altman et al., 2014; Smith et al., 2014; Valli et al., 2014). Adult Human testis cells were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, sorted spermatoginia,Sta-Put-enriched spermatocytes and spermatids, or unselected spermatogenic cells from adult human testicular tissue were used for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~8700 cells were loaded on the instrument with the expectation of collecting up to 5,000 GEMs containing single cells. For the multiplet test (Fig. S1), equal numbers of mouse and human cells were loaded. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v2 chemistry).

treatment_protocol: De-identified, surgical excess normal adult human testicular tissue was obtained through the Infertility Center of St. Louis from patients undergoing a diagnostic testicular biopsy (n=28) in preparation for microscopic vasectomy reversal (MVR) or testicular sperm extraction (TESE) for obstructive azoospermia with the informed consent of patients (see Supplemental Table 2). Testicular tissue was also recovered from male organ donors (n=2) through the Texas Organ Sharing Alliance and the University of Texas Transplant Center with informed consent of the next of kin. The University of Texas at San Antonio IRB determined that research on these tissues did not constitute human subjects research (IRB #12-098N and #17-074N). The age of the individuals was recorded (median = 42yr, mean = 41.6 ± 1.3yr), and while organ donors tended to be younger (34.3 ± 7.2yr) than biopsy patients (42.4 ± 1.2yr), the difference was not significant (p=0.32). Procured tissue was transported to the laboratory on ice in either Lactated Ringer’s solution or minimal essential medium alpha (MEMα) containing 10% fetal bovine serum. The amount of time tissues were exposed to cold ischemia prior to processing was recorded (median = 18.7hr; mean = 24.7 ± 3.8 hr).

tag: number of cells

value: 1:1 mixture mouse and human spermatogenic cells


title: Scc1 ChIP_0

description:
Scc1 Sonication ChIP
ws1ss1_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800344_Scc1_Ty1_wt_soni_Input_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800343_Scc1_Ty1_wt_soni_ChIP_0_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: life cycle stage

tag: chip antibody


title: RNAseq 2d, rep2

value: DEX


title: Cont-1

value: Control


title: 786-O VHL-/- KDM5C shRNA 1

status: Public on Nov 05 2018

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

description:
replicate 1
1_B3_6_Y6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw gene expression data were preprocessed in GenomeStudio and further processed using R limma package for force-positive background correction, log2 transformation and quantile normalization. Data quality control was performed by selecting present probes using the detection threshold of 0.05. The average value across the probesets of an annotated gene was used to generate the gene-level expression data matrix.

label: biotin

source_name: cancer cell line 786-O

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: All cell lines were maintained at 37C incubator with 5% Co2 in glutamine-containing DMEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin.

extract_protocol: Total RNA was extracted with Trizol, then cleaed up with DNase I treatment with QIAGEN RNeasy mini kit.

treatment_protocol: No treatment.

value: VHL-/-

tag: shRNA suppression

value: KDM5C shRNA

tag: ChIP


title: 786-O VHL-/- PBRM1 shRNA 3

description:
replicate 3
2_B2_17_Y21

value: PBRM1 shRNA

tag: cell line


title: 786-O VHL-/- PBRM1 shRNA 2

description:
replicate 2
1_B2_11_Y13


title: 786-O VHL-/- KDM5C shRNA 2

description:
replicate 2
1_B3_12_Y14


title: 786-O VHL-/- PBRM1 shRNA 1

description:
replicate 1
1_B2_5_Y5


title: 786-O VHL-/- Scramble shRNA 1

description:
replicate 1
1_B1_4_Y4

value: scramble shRNA


title: 786-O VHL+/+ scramble shRNA 3

description:
replicate 3
2_A1_13_Y17

value: VHL+/+


title: 786-O VHL-/- Scramble shRNA 3

description:
replicate 3
2_B1_16_Y20


title: 786-O VHL+/+ PBRM1 shRNA 1

description:
replicate 1
1_A2_2_Y2


title: 786-O VHL-/- Scramble shRNA 2

description:
replicate 2
1_B1_10_Y12


title: 786-O VHL+/+ scramble shRNA 1

description:
replicate 1
1_A1_1_Y1


title: 786-O VHL+/+ PBRM1 shRNA 2

description:
replicate 2
1_A2_8_Y10


title: 786-O VHL-/- KDM5C shRNA 3

description:
replicate 3
2_B3_18_Y22


title: 786-O VHL+/+ scramble shRNA 2

description:
replicate 2
1_A1_7_Y9


title: 786-O VHL+/+ PBRM1 shRNA 3

description:
replicate 3
2_A2_14_Y18


title: 786-O VHL+/+ KDM5C shRNA 3

description:
replicate 3
2_A3_15_Y19


title: 786-O VHL+/+ KDM5C shRNA 2

description:
replicate 2
1_A3_9_Y11


title: 786-O VHL+/+ KDM5C shRNA 1

description:
replicate 1
1_A3_3_Y3


title: temporal [tumor WGBS-seq]

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

description:
processed data file:
NBr_average_methylation_values.bigWig

data_processing:
For each sample, reads were mapped to the human genome (hg19) with bwa-mem (0.7.8) with a customized WGBS pipeline [ref methyCtools]. CpGs overlapping variable sites with a minor allele frequency higher than 0.25 were removed. Low coverage CpGs with 2 or fewer reads in more than 50% of the cohort were also removed from the analysis.
The mean methylation of the two cytosines in a CpG dinucleotide (one C on forward strand and the other on reverse strand) was calculated by weighting their CpG coverage, i.e. m = (m1*c1 + m2*c2) / (c1+c2), where m1 and m2 are the number of methylated CpGs of the two neighbouring cytosines. Similarly the mean coverage for the CpG dinucleotide is calculated by weighting the coverage itself: c = (c1*c1 + c2*c2)/(c1+c2) where c1 and c2 are the CpG coverage at corresponding cytosines.
(c1+c2) where c1 and c2 are the CpG coverage at corresponding cytosines.
Finally, the bsseq R package (1.10.0) was applied to smooth the methylation data and impute the missing methylation values with default parameters. CH methylation was also smoothed by bsseq.
Methylation features (LMRs, PMDs, DMVs) were called for each sample and consensus sets for each subtype generated (see the manuscript for details).
Correlating region analysis was performed to integrate methylation and ssRNAseq (see other Series) data for the GB tumours. CR detection was applied in a gene centric manner. For each protein coding gene, a sliding window of 6 CpG sites (maximum 10kb width) moves from 50kb upstream to 50kb downstream of the gene, with a step size of 3 CpG sites. The Spearman correlation and a correlation statistical test between mean CpG methylation (beta) in the window and the expression of the gene (TPM) was calculated. The windows are further filtered by correlation FDR <= 0.05 and maximum mean difference between subtypes >= 0.2. Negative correlated regions (negCRs) are defined as showing negative correlation between methylation and expression (i.e., high methylation corresponds to low expression) and positive correlated regions (posCRs) as the converse. Subtype specific CRs are defined as follows: the mean methylation in the subtype is higher or lower than all other subtypes, with a FDR < 0.05 from pairwise t-tests. We further analysed only the sets of subtype-specific CRs of at least 1000 regions.
Genome_build: hg19
Supplementary_files_format_and_content: deepTools2 was used to produce methylation values bigWigs, where each CpG methylation is shown on the beta scale [0,1]. Subtype average values are also included. Per-CpG methylation (beta) and read coverage files are also included in the following format: for each chromosome analysed (chr1:chr22), three files are included: CG_positions_chr.txt.gz (chromosomal coordinates of the CpG di-nt), CG_coverage_chr.txt.gz (per-sample coverage matrix) and CG_methylation_bsseq_smoothed_chr.txt.gz (per-sample methylation (beta) matrix). Each chr's files has the same number of rows, in the same order. Subtype methylation feature bedfiles showing the location of consensus subtype DMVs, LMRs and PMDs are included. Finally, the CR analysis table containing CR positions, target gene, CR region methylation for each sample (beta), correlation, and subtype-specificity is included with bedfiles containing positions of all neg/posCRs and subtype-specific CR sets.

source_name: adult normal brain tissue from the temporal lobe

extract_protocol:
Nucleic acids were extracted from tumour tissue using Qiagen Allprep DNA/RNA/Protein Mini kit or a standard caesium chloride (CsCl) density gradient ultracentrifugation protocol. QC was performed using the Agilent Bioanalyser 2100 and the Nanodrop spectrophotometer.
Whole-genome bisulphite library preparation was carried out as described previously (see Hovestadt et al., Nature (2014) 510:537-541 https://doi.org/10.1038/nature13268). Briefly, 5 μg of genomic DNA was sheared using a Covaris device. After adaptor ligation, DNA fragments with insert lengths of 200–250 bp were isolated using an E-Gel electrophoresis system (Life Technologies) and the DNA was bisulphite converted overnight using the EZ DNA Methylation kit (Zymo Research). The fragments were PCR amplified using the FastStart High Fidelity PCR kit (Roche) for 6-8 cycles. Library aliquots were then purified and size selected with AMPure beads (New England BioLabs) and quality controlled with a Bioanalyzer (Agilent). Each library was sequenced using 2 lanes on an Illumina HiSeq 2000 in the DKFZ Genomics and Proteomics core facility.

tag: subtype

tag: gender

tag: age

tag: os (overall survival, month)

tag: progression

tag: pfs (progression-free survival, month)

tag: idh1 mutation status

tag: idh2 mutation status


title: alveolar_macrophage_B2KO_3

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

institute: Tohoku University

description: Gene expression alveolar macropahge from Bach2_KO mouse

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensities filtered on expression flags error (CV <50)

source_name: AM, B2KO

label_protocol: Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).

extract_protocol: RNA  was isolated with an RNeasy micro kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Bronchoalveolar lavage was collected from mouse and alveolar macropahges were sorted by flow cytometer.

tag: strain

value: female

tag: cell type

value: alveolar macrophage

tag: genotype/variation

value: B2 KO


title: alveolar_macrophage_DD_2

description: Gene expression alveolar macropahge from Bach1/Bach2_double_KO mouse

source_name: AM, DD

value: B1/B2 DKO


title: AK218 [tumor WGBS-seq]

description:
processed data file:
CR_analysis_full_table.txt
MES_average_methylation_values.bigWig
MES_methylation_features_DMV.bed
MES_methylation_features_LMR.bed
MES_methylation_features_PMD.bed

source_name: adult glioblastoma tumour

value: MES

value: dead

value: wt


title: AK205 [tumor WGBS-seq]

description:
processed data file:
CR_analysis_full_table.txt
RTK_II_average_methylation_values.bigWig


title: AK217 [tumor WGBS-seq]

description:
processed data file:
CR_analysis_full_table.txt
RTK_I_average_methylation_values.bigWig
RTK_I_methylation_features_DMV.bed
RTK_I_methylation_features_LMR.bed
RTK_I_methylation_features_PMD.bed


title: AK216 [tumor WGBS-seq]


title: parietal [tumor WGBS-seq]

source_name: adult normal brain tissue from the parietal lobe


title: AK213 [tumor WGBS-seq]

description:
processed data file:
CR_analysis_full_table.txt
IDH_average_methylation_values.bigWig
IDH_methylation_features_DMV.bed
IDH_methylation_features_LMR.bed
IDH_methylation_features_PMD.bed

value: IDH

value: male

value: alive


title: AK227 [tumor WGBS-seq]


title: alveolar_macrophage_DD_1


title: AK231 [tumor WGBS-seq]


title: AK236 [tumor WGBS-seq]


title: AK226 [tumor WGBS-seq]


title: occipital [tumor WGBS-seq]

source_name: adult normal brain tissue from the occipital lobe


title: alveolar_macrophage_B1KO_1

description: Gene expression alveolar macropahge from Bach1_KO mouse

source_name: AM, B1KO

value: B1 KO


title: AK188 [tumor WGBS-seq]


title: alveolar_macrophage_B2KO_1


title: alveolar_macrophage_DD_3


title: frontal [tumor WGBS-seq]

source_name: adult normal brain tissue from the frontal lobe


title: alveolar_macrophage_B1KO_2


title: alveolar_macrophage_B1KO_3


title: alveolar_macrophage_WT_3

description: Gene expression alveolar macropahge from WT mouse

source_name: AM, WT

value: WT


title: alveolar_macrophage_B2KO_2


title: alveolar_macrophage_WT_2


title: alveolar_macrophage_WT_1


title: AK195 [tumor WGBS-seq]


title: AK199 [tumor WGBS-seq]


title: AK185 [tumor WGBS-seq]


title: AK183 [tumor WGBS-seq]


title: AK165 [tumor WGBS-seq]


title: AK178 [tumor WGBS-seq]


title: AK173 [tumor WGBS-seq]


title: AK156 [tumor WGBS-seq]


title: AK158 [tumor WGBS-seq]


title: AK132 [tumor WGBS-seq]


title: AK142 [tumor WGBS-seq]


title: AK149 [tumor WGBS-seq]


title: AK134 [tumor WGBS-seq]


title: AK133 [tumor WGBS-seq]


title: AK139 [tumor WGBS-seq]


title: AK100 [tumor WGBS-seq]


title: AK124 [tumor WGBS-seq]


title: AK102 [tumor WGBS-seq]


title: AK099 [tumor WGBS-seq]


title: AK123 [tumor WGBS-seq]


title: AK117 [tumor WGBS-seq]


title: AK103 [tumor WGBS-seq]


title: AK088 [tumor WGBS-seq]


title: AK098 [tumor WGBS-seq]


title: AK091 [tumor WGBS-seq]


title: AK089 [tumor WGBS-seq]


title: AK081 [tumor WGBS-seq]


title: AK085 [tumor WGBS-seq]


title: AK167 [tumor WGBS-seq]


title: AK153 [tumor WGBS-seq]


title: AK079 [tumor WGBS-seq]


title: BH500(pSW4)_OD=3_Run2

tag: growth phase

value: lag phase

tag: protocol

value: control

tag: expression

value: Non-Producer

tag: od at harvest


title: AK076 [tumor WGBS-seq]


title: PL32r_vc

source_name: genomic DNA from PL32 aCA technical replicate placenta

tag: patient id

tag: tissue

value: Chorionic villi

tag: pathology group

value: chorioamnionitis

tag: fetal sex

value: F

tag: gestational age

tag: 850k plate

tag: 850k sentrix_id

tag: 850k sentrix_position


title: AK074 [tumor WGBS-seq]

tag: subtype

tag: gender

tag: age

tag: os (overall survival, month)

tag: progression

tag: pfs (progression-free survival, month)

tag: idh1 mutation status


title: AK071 [tumor WGBS-seq]

value: female

tag: idh2 mutation status


title: AK068 [tumor WGBS-seq]


title: AK055 [tumor WGBS-seq]


title: AK066 [tumor WGBS-seq]


title: AK053 [tumor WGBS-seq]


title: AK041 [tumor WGBS-seq]


title: AK035 [tumor WGBS-seq]

description:
processed data file:
CR_analysis_full_table.txt
RTK_II_average_methylation_values.bigWig
RTK_II_methylation_features_DMV.bed
RTK_II_methylation_features_LMR.bed
RTK_II_methylation_features_PMD.bed


title: AK006 [tumor WGBS-seq]


title: AK030 [tumor WGBS-seq]


title: AK005 [tumor WGBS-seq]


title: AK049 [tumor WGBS-seq]


title: AK043 [tumor WGBS-seq]


title: AK003 [tumor WGBS-seq]


title: parietal [tumor RNA-seq]

description:
processed data file
NBr_average_RNAseq_coverage.bigWig
RNAseq_expression_matrix_counts.txt.gz
RNAseq_expression_matrix_TPMs.txt.gz

data_processing:
Reads were aligned to the human genome (hg19 build) with the Gencode reference transcriptome (v19) using STAR (v2.3.0e).
Read counts for each gene were quantified as the total number of reads mapping to exons using htseq-count (0.6.0).
bigWig coverage files were generated using the deepTools2 suite.
Subtype average files were generated by calculating the average across all samples in that subtype.
Identification of genes differentially expressed between GB subtypes and NBr: Differential expression analysis was performed using DESeq2 (1.14.1). The FDR threshold for significant differential expression was set to 0.05.
For the subtype gene signature analysis in limma, raw read counts per gene were pre-filtered, retaining those genes with >10 reads in >6 samples for further analysis. Normalisation factors for the counts were calculated using the calcNormFactors function in ‘edgeR’ (3.20.1). voomWithQualityWeights from ‘limma’ (3.34.4) was used to transform the raw counts. limma differential expression analysis was used to compare the gene expression of each GBM subtype versus the other 3 (example contrast: IDH / ((MES+RTK I+RTK II)/3) ). Genes were defined as significant for a subtype if they passed a BH adjusted p-value threshold of 0.001.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage tracks for each sample, as well as subtype average bigWig coverage tracks. Additionally, expression matrices (tab-delimited text files) of TPMs and counts are supplied for the entire cohort. The samplesheets used in the RTN GRN analysis are also included, as well as the results of the limma subtype gene signature model.

extract_protocol:
Nucleic acids were extracted from tumour tissue using Qiagen Allprep DNA/RNA/Protein Mini kit or a standard caesium chloride (CsCl) density gradient ultracentrifugation protocol. QC was performed using the Agilent Bioanalyser 2100 and the Nanodrop spectrophotometer.
RNA-seq libraries were prepared as described using methods to preserve strand specificity and deplete rRNA (see Hovestadt et al., Nature (2014) 510:537-541 https://doi.org/10.1038/nature13268). Briefly, the TruSeq stranded total RNA kit was used to prepare libraries according to the manufacturer's protocol. Sequencing was carried out on the HiSeq 2000 platform with 1 lane per sample.


title: temporal [tumor RNA-seq]


title: occipital [tumor RNA-seq]


title: AK231 [tumor RNA-seq]

description:
processed data file
IDH_average_RNAseq_coverage.bigWig
RNAseq_expression_matrix_counts.txt.gz
RNAseq_expression_matrix_TPMs.txt.gz
RNAseq_subtype_signature_gene_analysis_limma_model_results.txt


title: AK236 [tumor RNA-seq]

description:
processed data file
MES_average_RNAseq_coverage.bigWig
RNAseq_expression_matrix_counts.txt.gz
RNAseq_expression_matrix_TPMs.txt.gz
RNAseq_subtype_signature_gene_analysis_limma_model_results.txt


title: frontal [tumor RNA-seq]


title: AK226 [tumor RNA-seq]

description:
processed data file
RTK_II_average_RNAseq_coverage.bigWig
RNAseq_expression_matrix_counts.txt.gz
RNAseq_expression_matrix_TPMs.txt.gz
RNAseq_subtype_signature_gene_analysis_limma_model_results.txt


title: AK227 [tumor RNA-seq]


title: AK218 [tumor RNA-seq]


title: AK217 [tumor RNA-seq]

description:
processed data file
RTK_I_average_RNAseq_coverage.bigWig
RNAseq_expression_matrix_counts.txt.gz
RNAseq_expression_matrix_TPMs.txt.gz
RNAseq_subtype_signature_gene_analysis_limma_model_results.txt


title: AK216 [tumor RNA-seq]


title: AK205 [tumor RNA-seq]


title: AK051 [tumor WGBS-seq]


title: AK195 [tumor RNA-seq]


title: AK015 [tumor WGBS-seq]


title: AK002 [tumor WGBS-seq]


title: AK188 [tumor RNA-seq]


title: AK072 [tumor WGBS-seq]


title: AK178 [tumor RNA-seq]


title: AK183 [tumor RNA-seq]


title: AK173 [tumor RNA-seq]


title: AK185 [tumor RNA-seq]


title: AK167 [tumor RNA-seq]


title: AK165 [tumor RNA-seq]


title: AK158 [tumor RNA-seq]


title: AK153 [tumor RNA-seq]


title: AK149 [tumor RNA-seq]


title: AK142 [tumor RNA-seq]


title: AK134 [tumor RNA-seq]


title: AK133 [tumor RNA-seq]


title: AK132 [tumor RNA-seq]


title: AK139 [tumor RNA-seq]


title: AK213 [tumor RNA-seq]


title: AK117 [tumor RNA-seq]


title: AK103 [tumor RNA-seq]


title: AK123 [tumor RNA-seq]


title: AK102 [tumor RNA-seq]


title: AK124 [tumor RNA-seq]


title: AK199 [tumor RNA-seq]


title: AK098 [tumor RNA-seq]


title: AK099 [tumor RNA-seq]


title: AK089 [tumor RNA-seq]


title: AK091 [tumor RNA-seq]


title: AK088 [tumor RNA-seq]


title: AK085 [tumor RNA-seq]


title: AK156 [tumor RNA-seq]


title: AK079 [tumor RNA-seq]


title: AK076 [tumor RNA-seq]


title: AK074 [tumor RNA-seq]


title: AK081 [tumor RNA-seq]


title: AK068 [tumor RNA-seq]


title: AK066 [tumor RNA-seq]


title: AK051 [tumor RNA-seq]


title: AK055 [tumor RNA-seq]


title: AK049 [tumor RNA-seq]


title: AK053 [tumor RNA-seq]


title: AK041 [tumor RNA-seq]


title: AK043 [tumor RNA-seq]


title: AK100 [tumor RNA-seq]


title: AK035 [tumor RNA-seq]


title: AK030 [tumor RNA-seq]


title: AK015 [tumor RNA-seq]


title: AK006 [tumor RNA-seq]


title: AK003 [tumor RNA-seq]


title: AK005 [tumor RNA-seq]


title: AK231_H3K9me3_ChIP-seq

description:
processed data file:
AK231_ChromHMM_18states.bed
AK231_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed

data_processing:
ChIP-seq datasets were processed using a custom pipeline implemented in Snakemake. Briefly, reads were trimmed using the Trimgalore tool (https://github.com/FelixKrueger/TrimGalore) and aligned using Bowtie with standard parameters. Duplicates and multi-mapping reads were removed using the samtools package and the XS flag in the bam files. Input control (WGS) and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite. Peaks were called using the callpeak mode in MACS2 (https://github.com/taoliu/MACS) for broad and narrow peaks. In addition, SICER was used to call peaks using the gap 600 and window 200 parameters. Various QC parameters (FRiP, PCR bottleneck coefficient, cross-strand correlation) were determined according to the ENCODE guidelines. In addition, visual QC was performed using the signal profile at TSS of annotated genes and the fingerprint method from the DeepTools2 suite.
Chromatin segmentation was defined using the ChromHMM tool. ChIP-seq data (H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3) and WGS data (input control) were binarized using ChromHMM’s “BinarizeBam” command. The Epigenome Roadmap 18-state model was used to segment the genome of each sample.  The consensus state for a subtype is defined as the state with the highest frequency in a given segment, and a minimum frequency of 50%.
The simplified 7-state model was defined by mapping the 18 states as follows: 1-4 to TSS (Tss), 5-6 to Transcription (Tx), 7-11 and 15 to Enhancer (Enh), 12-13 to Heterochromatin/Repeats (Het/Rpts), 14 to Bivalent TSS (TSSBiv), 16-17 to Polycomb Repressed (ReprPC), 18 to Quiescent (Qui).
Subtype superenhancer analysis: the union of H3K27ac peaks for each subtype’s samples were used as input regions for the ROSE2 superenhancer analysis pipeline, stitching together regions within 12.5kbp. Sample H3K27ac signal was calculated using ‘bigWigAverageOverBed’ (v2), and enhancers were ranked by the subtype average enrichment. SEs were defined using the default parameters for ROSE2.
GBM superenhancer landscape: the pan-GBM SE landscape was defined as the reduced union of the 4 subtype SE lists. Enrichment of H3K27ac for each sample was calculated with ‘bigWigAverageOverBed’. z-scores of the log10-transformed H3K27ac signal was used to hierarchically cluster SEs using 1-Pearson correlation as the distance and the ‘Ward.D2’ method. Target genes were assigned as follows: for each SE, we computed the Spearman correlation of the H3K27ac signal in the SE regions across all samples with the expression of all genes within a region of +/- 500kb, and selected the gene showing the highest correlation as being the most likely target gene. We additionally filtered using TADs by requiring the SE and the predicted target gene to be within a common TAD.
Subtype enhancer analysis: subtype enhancers were defined as regions where a H3K4me1 peak was called in at least 2 samples in that subtype falling more than 2kbp from a H3K4me3 peak, or a promoter otherwise. Regions closer than 10bp were merged, and those longer than 500bp were retained. Active enhancers were defined as regions where a H3K27ac peak was also called, otherwise the region was defined as a poised enhancer. Intensities of H3K27ac ChIPseq signal was calculated using ‘bigWigAverageOverBed’.
Identification of the GBM active enhancer landscape: The GBM active enhancer landscape was defined by taking the union of the 4 subtype active enhancer sets. The activity of enhancers was visualised in a heatmap using ‘ComplexHeatmap’ of the z-scores of the log2-transformed H3K27ac signal. Active enhancers were clustered on the average log2 H3K27ac signal in each subtype, using 1-Pearson correlation as the distance and the ‘Ward.D2’ hierarchical clustering method.
Subtype-activated enhancer analysis: subtype-activated active enhancers were identified using an ANOVA test on the average subtype log2-transformed H3K27ac signal. Enhancers with a BH-adjusted ANOVA p-value < 0.1 and a log2FC of H3K27ac signal > 1 were defined as activated in a subtype.
Assignment of target genes to enhancers: The ‘InTAD’ R package (unpub., v0.1.1) was used to identify target genes of active enhancers. Briefly, the correlation of log2-transformed H3K27ac signal and protein-coding gene (Gencode v19 annotation) expression (log2 RPKM+1) was calculated within ESC-defined topologically associated domains for all possible enhancer-gene interactions. Genes were allowed to overlap multiple TADs (option “selMaxTadOvlp=TRUE” in the combineInTAD function). The target for each enhancer was defined as follows: the closest gene (distance to TSS) with correlation > 0.4; otherwise, the gene with the highest correlation.
genome build: hg19
processed data files format and content: ChromHMM results for each sample are contained in two bedfiles: the full 18-state and the reduced 7-state model. For each IPed factor, 3 files are included: a bigWig coverage file and two peak call bedfiles. Additionally, subtype consensus files are included for the ChromHMM models (both 18 and 7 states).    Superenhancer analysis: the individual subtype SE lists (SUBTYPE_subtype_H3K27ac_superenhancers.bed) as well as the full landscape (GB_H3K27ac_superenhancers.bed), with subtype-specific SEs.    Active enhancer analysis: individual subtype active enhancer lists (SUBTYPE_enhancers_annotated_with_histone_signal) are indluced, as well as the full landscape (GB_active_enhancers.bed) as well as subtype-specific lists. The full enhancer matrix, consisting of this full landscape with annotated targeted genes, is also included (GB_active_enhancers_matrix_with_target_gene_predictions.csv).

extract_protocol:
H3K27Ac (AM#39133, Active Motif), H3K4me1 (AM#38297, Active Motif), H3K4me3 (AM#39159, Active Motif), H3K9me3 (AM#39161, Active Motif), H3K27me3 (#07-449, Millipore) and H3K36me3 (AM#61101, Active Motif) ChIP library preparation of GB samples was performed at Active Motif according to proprietary methods.
Libraries were multiplexed so that all libraries for each individual IP were sequenced on 1-4 lanes using the Illumina HiSeq 2000 platform.

tag: molecule subtype

value: genomic DNA and associated chromatin

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat.#

tag: chip antibody lot #


title: AK231_H3K4me3_ChIP-seq


title: AK231_H3K4me1_ChIP-seq

description:
processed data file:
AK231_ChromHMM_18states.bed
AK231_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed


title: AK216_H3K9me3_ChIP-seq

description:
processed data file:
AK216_ChromHMM_18states.bed
AK216_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed


title: AK231_H3K27ac_ChIP-seq

description:
processed data file:
AK231_ChromHMM_18states.bed
AK231_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed
IDH_subtype_H3K27ac_superenhancers.bed


title: AK231_H3K36me3_ChIP-seq


title: AK071 [tumor RNA-seq]

value: MES


title: AK072 [tumor RNA-seq]

value: dead


title: AK216_H3K4me3_ChIP-seq

value: wt


title: AK216_H3K4me1_ChIP-seq

description:
processed data file:
AK216_ChromHMM_18states.bed
AK216_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed


title: AK216_H3K27me3_ChIP-seq

value: Millipore


title: AK213_H3K4me1_ChIP-seq

description:
processed data file:
AK213_ChromHMM_18states.bed
AK213_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed

value: IDH

value: male


title: AK213_H3K9me3_ChIP-seq

description:
processed data file:
AK213_ChromHMM_18states.bed
AK213_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed

value: alive


title: AK216_H3K27ac_ChIP-seq

description:
processed data file:
AK216_ChromHMM_18states.bed
AK216_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed
RTK_II_subtype_H3K27ac_superenhancers.bed


title: AK002 [tumor RNA-seq]


title: AK199_H3K4me3_ChIP-seq

description:
processed data file:
AK199_ChromHMM_18states.bed
AK199_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed


title: AK213_H3K27ac_ChIP-seq

description:
processed data file:
AK213_ChromHMM_18states.bed
AK213_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed
IDH_subtype_H3K27ac_superenhancers.bed


title: AK199_H3K9me3_ChIP-seq


title: AK199_H3K4me1_ChIP-seq

description:
processed data file:
AK199_ChromHMM_18states.bed
AK199_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed


title: AK231_H3K27me3_ChIP-seq


title: AK213_H3K27me3_ChIP-seq


title: AK183_H3K9me3_ChIP-seq

description:
processed data file:
AK183_ChromHMM_18states.bed
AK183_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed


title: AK183_H3K4me1_ChIP-seq

description:
processed data file:
AK183_ChromHMM_18states.bed
AK183_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed


title: AK199_H3K27me3_ChIP-seq


title: AK183_H3K4me3_ChIP-seq


title: AK199_H3K36me3_ChIP-seq


title: AK183_H3K36me3_ChIP-seq


title: AK199_H3K27ac_ChIP-seq

description:
processed data file:
AK199_ChromHMM_18states.bed
AK199_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed
IDH_subtype_H3K27ac_superenhancers.bed


title: AK178_H3K9me3_ChIP-seq

description:
processed data file:
AK178_ChromHMM_18states.bed
AK178_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed


title: AK178_H3K4me3_ChIP-seq


title: AK178_H3K4me1_ChIP-seq

description:
processed data file:
AK178_ChromHMM_18states.bed
AK178_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed


title: AK183_H3K27ac_ChIP-seq

description:
processed data file:
AK183_ChromHMM_18states.bed
AK183_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed
RTK_I_subtype_H3K27ac_superenhancers.bed


title: AK178_H3K27ac_ChIP-seq

description:
processed data file:
AK178_ChromHMM_18states.bed
AK178_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed
RTK_II_subtype_H3K27ac_superenhancers.bed


title: AK178_H3K27me3_ChIP-seq


title: AK216_H3K36me3_ChIP-seq


title: AK183_H3K27me3_ChIP-seq


title: AK173_H3K9me3_ChIP-seq

description:
processed data file:
AK173_ChromHMM_18states.bed
AK173_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed


title: AK173_H3K4me3_ChIP-seq


title: AK173_H3K4me1_ChIP-seq

description:
processed data file:
AK173_ChromHMM_18states.bed
AK173_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed


title: AK213_H3K4me3_ChIP-seq


title: AK173_H3K36me3_ChIP-seq


title: AK213_H3K36me3_ChIP-seq


title: AK173_H3K27me3_ChIP-seq


title: AK173_H3K27ac_ChIP-seq

description:
processed data file:
AK173_ChromHMM_18states.bed
AK173_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed
RTK_I_subtype_H3K27ac_superenhancers.bed


title: AK158_H3K4me3_ChIP-seq

description:
processed data file:
AK158_ChromHMM_18states.bed
AK158_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed


title: AK158_H3K9me3_ChIP-seq


title: AK156_H3K4me3_ChIP-seq

description:
processed data file:
AK156_ChromHMM_18states.bed
AK156_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed


title: AK158_H3K36me3_ChIP-seq


title: AK156_H3K9me3_ChIP-seq


title: AK158_H3K4me1_ChIP-seq

description:
processed data file:
AK158_ChromHMM_18states.bed
AK158_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed


title: AK156_H3K27ac_ChIP-seq

description:
processed data file:
AK156_ChromHMM_18states.bed
AK156_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed
RTK_I_subtype_H3K27ac_superenhancers.bed


title: AK158_H3K27ac_ChIP-seq

description:
processed data file:
AK158_ChromHMM_18states.bed
AK158_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed
RTK_II_subtype_H3K27ac_superenhancers.bed


title: AK158_H3K27me3_ChIP-seq


title: AK156_H3K36me3_ChIP-seq


title: AK156_H3K27me3_ChIP-seq


title: AK153_H3K4me1_ChIP-seq

description:
processed data file:
AK153_ChromHMM_18states.bed
AK153_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed


title: AK153_H3K9me3_ChIP-seq

description:
processed data file:
AK153_ChromHMM_18states.bed
AK153_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed


title: AK178_H3K36me3_ChIP-seq


title: AK156_H3K4me1_ChIP-seq

description:
processed data file:
AK156_ChromHMM_18states.bed
AK156_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed


title: AK153_H3K4me3_ChIP-seq


title: AK153_H3K36me3_ChIP-seq


title: AK153_H3K27me3_ChIP-seq


title: AK149_H3K4me1_ChIP-seq

description:
processed data file:
AK149_ChromHMM_18states.bed
AK149_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed


title: AK149_H3K36me3_ChIP-seq

description:
processed data file:
AK149_ChromHMM_18states.bed
AK149_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed


title: AK149_H3K4me3_ChIP-seq


title: AK149_H3K27me3_ChIP-seq


title: AK149_H3K9me3_ChIP-seq


title: AK142_H3K9me3_ChIP-seq

description:
processed data file:
AK142_ChromHMM_18states.bed
AK142_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed


title: AK142_H3K4me1_ChIP-seq

description:
processed data file:
AK142_ChromHMM_18states.bed
AK142_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed


title: AK142_H3K4me3_ChIP-seq


title: AK149_H3K27ac_ChIP-seq

description:
processed data file:
AK149_ChromHMM_18states.bed
AK149_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed
RTK_I_subtype_H3K27ac_superenhancers.bed


title: AK142_H3K36me3_ChIP-seq


title: AK142_H3K27me3_ChIP-seq


title: AK139_H3K9me3_ChIP-seq

description:
processed data file:
AK139_ChromHMM_18states.bed
AK139_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed


title: AK142_H3K27ac_ChIP-seq

description:
processed data file:
AK142_ChromHMM_18states.bed
AK142_ChromHMM_simplified_7states.bed
RTK_I_ChromHMM_18states.bed
RTK_I_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_I_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_I_enhancers_annotated_with_histone_signal.bed
RTK_I_subtype_H3K27ac_superenhancers.bed


title: AK139_H3K4me1_ChIP-seq

description:
processed data file:
AK139_ChromHMM_18states.bed
AK139_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed


title: AK139_H3K27me3_ChIP-seq


title: AK139_H3K27ac_ChIP-seq

description:
processed data file:
AK139_ChromHMM_18states.bed
AK139_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed
MES_subtype_H3K27ac_superenhancers.bed


title: AK124_H3K4me3_ChIP-seq

description:
processed data file:
AK124_ChromHMM_18states.bed
AK124_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed


title: AK139_H3K4me3_ChIP-seq


title: AK124_H3K9me3_ChIP-seq


title: AK124_H3K4me1_ChIP-seq

description:
processed data file:
AK124_ChromHMM_18states.bed
AK124_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed


title: AK124_H3K27ac_ChIP-seq

description:
processed data file:
AK124_ChromHMM_18states.bed
AK124_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed
MES_subtype_H3K27ac_superenhancers.bed


title: AK100_H3K9me3_ChIP-seq

description:
processed data file:
AK100_ChromHMM_18states.bed
AK100_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed


title: AK124_H3K27me3_ChIP-seq


title: AK124_H3K36me3_ChIP-seq


title: AK100_H3K4me3_ChIP-seq


title: AK100_H3K4me1_ChIP-seq

description:
processed data file:
AK100_ChromHMM_18states.bed
AK100_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed


title: AK100_H3K36me3_ChIP-seq


title: AK100_H3K27ac_ChIP-seq

description:
processed data file:
AK100_ChromHMM_18states.bed
AK100_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed
RTK_II_subtype_H3K27ac_superenhancers.bed


title: AK153_H3K27ac_ChIP-seq

description:
processed data file:
AK153_ChromHMM_18states.bed
AK153_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed
MES_subtype_H3K27ac_superenhancers.bed


title: AK139_H3K36me3_ChIP-seq


title: AK091_H3K9me3_ChIP-seq

description:
processed data file:
AK091_ChromHMM_18states.bed
AK091_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed


title: AK091_H3K36me3_ChIP-seq


title: AK089_H3K4me3_ChIP-seq

description:
processed data file:
AK089_ChromHMM_18states.bed
AK089_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed


title: AK091_H3K27me3_ChIP-seq


title: AK091_H3K4me1_ChIP-seq

description:
processed data file:
AK091_ChromHMM_18states.bed
AK091_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed


title: AK091_H3K27ac_ChIP-seq

description:
processed data file:
AK091_ChromHMM_18states.bed
AK091_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed
MES_subtype_H3K27ac_superenhancers.bed


title: AK091_H3K4me3_ChIP-seq


title: AK089_H3K9me3_ChIP-seq


title: AK089_H3K36me3_ChIP-seq


title: AK076_H3K9me3_ChIP-seq

description:
processed data file:
AK076_ChromHMM_18states.bed
AK076_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed


title: AK089_H3K27me3_ChIP-seq


title: AK100_H3K27me3_ChIP-seq


title: AK076_H3K4me3_ChIP-seq


title: AK076_H3K36me3_ChIP-seq


title: AK071_H3K36me3_ChIP-seq

description:
processed data file:
AK071_ChromHMM_18states.bed
AK071_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed


title: AK076_H3K27me3_ChIP-seq


title: AK076_H3K27ac_ChIP-seq

description:
processed data file:
AK076_ChromHMM_18states.bed
AK076_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed
IDH_subtype_H3K27ac_superenhancers.bed


title: AK071_H3K9me3_ChIP-seq


title: AK071_H3K27me3_ChIP-seq


title: AK071_H3K4me3_ChIP-seq


title: AK071_H3K27ac_ChIP-seq

description:
processed data file:
AK071_ChromHMM_18states.bed
AK071_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed
MES_subtype_H3K27ac_superenhancers.bed


title: AK076_H3K4me1_ChIP-seq

description:
processed data file:
AK076_ChromHMM_18states.bed
AK076_ChromHMM_simplified_7states.bed
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed


title: AK089_H3K4me1_ChIP-seq

description:
processed data file:
AK089_ChromHMM_18states.bed
AK089_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed


title: AK066_H3K27me3_ChIP-seq

description:
processed data file:
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed


title: AK071_H3K4me1_ChIP-seq

description:
processed data file:
AK071_ChromHMM_18states.bed
AK071_ChromHMM_simplified_7states.bed
MES_ChromHMM_18states.bed
MES_ChromHMM_simplified_7states.bed
GB_active_enhancers_MES_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
MES_enhancers_annotated_with_histone_signal.bed


title: AK066_H3K4me1_ChIP-seq

description:
processed data file:
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed


title: AK066_H3K27ac_ChIP-seq

description:
processed data file:
IDH_ChromHMM_18states.bed
IDH_ChromHMM_simplified_7states.bed
GB_active_enhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_IDH_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
IDH_enhancers_annotated_with_histone_signal.bed
IDH_subtype_H3K27ac_superenhancers.bed


title: AK089_H3K27ac_ChIP-seq

description:
processed data file:
AK089_ChromHMM_18states.bed
AK089_ChromHMM_simplified_7states.bed
RTK_II_ChromHMM_18states.bed
RTK_II_ChromHMM_simplified_7states.bed
GB_active_enhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_active_enhancers_matrix_with_target_gene_predictions.csv
GB_H3K27ac_superenhancers_RTK_II_specific_FDR_0.1_log2FC_1.bed
GB_H3K27ac_superenhancers_matrix_with_target_gene_predictions.csv
RTK_II_enhancers_annotated_with_histone_signal.bed
RTK_II_subtype_H3K27ac_superenhancers.bed


title: AK066_H3K4me3_ChIP-seq


title: LN229_shControl_RNAseq

data_processing:
Reads were aligned to the human genome (hg19 build) with the Gencode reference transcriptome (v19) using STAR (v2.3.0e).
Read counts for each gene were quantified as the total number of reads mapping to exons using htseq-count (0.6.0).
bigWig coverage tracks were produced using deepTools2.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig coverage tracks

source_name: adherent glioblastoma-derived cell line

growth_protocol: The human glioblastoma cell line LN229 was obtained from ATCC (cat. CRL-2611). Cells were cultured in DMEM containing 1 g/L glucose (D5921, Sigma) supplemented with 10% tetracycline-free fetal bovine serum (Clontech), 1% penicillin and streptomycin (P/S) mix, and glutamine (0.5 mM).     The ZH487 glioblastoma spheroid primary cells were originally established at the University of Zurich Hospital.  ZH487 cells were cultured in Neurobasal medium (Cat. 12348017, NBM) supplemented with 2% B27 (cat. 12587010, retinoic acid-free, Invitrogen), EGF (20 ng/ml, AF-100-15, Peprotech), FGF (20 ng/ml, cat. 100-18B, Peprotech) and glutamine (0.5 mM).     DNA methylation array (Illumina EPIC) analysis classified the ZH487 primary tumour and derived cell line as part of the RTK I subtype.    All cell lines were cultured under 10% CO2 at 37℃ with humidity.    Cell identities were verified by the Multiplex human Cell line Authentication Test (MCA). Cells were also tested for mycoplasma contamination with the Multiplex cell test (Multiplexion GmbH, Friedrichshafen, Germany).

extract_protocol:
Total RNA was isolated using the RNeasy Microkit (Qiagen) according to the manufacturer's standard protocol.
Libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit v2 according to the manufacturer's instructions. Briefly, 1000ng of total RNA was used for the polyA-based selection and fragmented. The first-strand cDNA was synthesized with random hexamer and SuperScript II (Invitrogen) following with second-strand synthesis, then the double-stranded cDNA fragments were end-repaired, A-tailed on the 3′ end, ligated to indexed adapters and amplified with 6 cycles of PCR. The final libraries were validated using Qubit (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent Technologies). Subsequently, the libraries were diluted to 10nM and pooled in equimolar ratios. The pooled library was sequenced with the Illumina HiSeq2000 (50 bp single-end) system.

treatment_protocol: Inducible SOX10 knockdown cells were established by infecting cells with pLKO-Tet-On non-targeting (nt) shRNA and pLKO-Tet-On SOX10 shRNA (TRCN0000018988) lentiviral particles and puromycin selection (1 µg/ml) for 7 days. shRNA expression was induced by adding 0.1 µg/ml doxycycline to the medium for at least 7 days.

tag: cell line

tag: cell type

value: adherent glioblastoma-derived cell line

value: RTK_I cell-like line

tag: gender source

tag: genotype/variation

value: pLKO-Tet-On non-targeting (nt) shRN


title: LN229_shSOX10_H3

description:
processed data file:
LN229_shSOX10_ChromHMM_18states.bed
LN229_shSOX10_ChromHMM_simplified_7states.bed

data_processing:
ChIP-seq datasets were processed using a custom pipeline implemented in Snakemake. Briefly, reads were trimmed using the Trimgalore tool (https://github.com/FelixKrueger/TrimGalore) and aligned using Bowtie with standard parameters. Duplicates and multi-mapping reads were removed using the samtools package and the XS flag in the bam files. Input control (WGS) and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite. Peaks were called using the callpeak mode in MACS2 (https://github.com/taoliu/MACS) for broad and narrow peaks. In addition, SICER was used to call peaks using the gap 600 and window 200 parameters. Various QC parameters (FRiP, PCR bottleneck coefficient, cross-strand correlation) were determined according to the ENCODE guidelines. In addition, visual QC was performed using the signal profile at TSS of annotated genes and the fingerprint method from the DeepTools2 suite.
Chromatin segmentation was defined using the ChromHMM tool. ChIP-seq data (H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3) and WGS data (input control) were binarized using ChromHMM’s “BinarizeBam” command. The Epigenome Roadmap 18-state model was used to segment the genome of each sample.  The consensus state for a subtype is defined as the state with the highest frequency in a given segment, and a minimum frequency of 50%.
The simplified 7-state model was defined by mapping the 18 states as follows: 1-4 to TSS (Tss), 5-6 to Transcription (Tx), 7-11 and 15 to Enhancer (Enh), 12-13 to Heterochromatin/Repeats (Het/Rpts), 14 to Bivalent TSS (TSSBiv), 16-17 to Polycomb Repressed (ReprPC), 18 to Quiescent (Qui).
genome build: hg19
processed data files format and content: ChromHMM results for each sample are contained in two bedfiles: the full 18-state and the reduced 7-state model. For each IPed factor, 3 files are included: a bigWig coverage file and two peak call bedfiles.

extract_protocol:
Cells were cross-linked with 1% methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x Covaris buffer and the chromatin was sheared for an additional 15 min with the LE220 Covaris device. The soluble chromatin was then recovered, quantified and 2µg chromatin was used in each IP with 2µl of antibody (H3: ab1791; H3K4me1, ab8895; H3K4me3, ab8580; H3K9me3, ab8898; H3K27ac, ab4729; H3K36me3, ab9050; H3K27me3, ab6002; all Abcam). After IP and washes with Covaris buffer, Li-buffer and TE, precipitated chromatin was digested with proteinase K and purified with AMPure beads.
Illumina sequencing libraries were prepared from purified DNA with the NEBNext Ultra library preparation kit (NEB) according to standard protocols.

tag: subtype

value: Abcam


title: LN229_shSOX10_H3K4me3


title: LN229_shSOX10_H3K27ac


title: LN229_shSOX10_H3K27me3


title: LN229_shControl_H3K9me3

description:
processed data file:
LN229_shControl_ChromHMM_18states.bed
LN229_shControl_ChromHMM_simplified_7states.bed


title: LN229_shSOX10_H3K36me3


title: AK066_H3K9me3_ChIP-seq

tag: gender


title: LN229_shControl_H3K4me3


title: LN229_shSOX10_H3K9me3


title: LN229_shControl_H3K4me1


title: LN229_shControl_H3K27me3


title: LN229_shSOX10_H3K4me1


title: LN229_shControl_H3K27ac


title: LN229_shControl_H3K36me3


title: LN229_shSOX10_RNAseq

value: pLKO-Tet-On SOX10 shRNA (TRCN0000018988)


title: ST-16_S8_R1_001

city: Kearneysville

first: Chris

last: Dardick

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

data_processing:
Raw reads were processed and analyzed by Genewiz. Trimmed sequences were imported into CLC Genomics Workbench (version v10.0.1, Qiagen, Redwood City, CA, USA) for de novo transcriptome assembly and mapping to Solanum lycopersicum genome assembly SL 3.0 (https://www.ncbi.nlm.nih.gov/genome/?term=tomato) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10).
Genome_build: Solanum lycopersicum assembly SL 3.0 (2018 Solanaceae Genomics Project. https://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.4/)
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID-name, Region, TPM, Gene length, Unique gene reads, Total gene reads

organism: Nicotiana tabacum

source_name: Treated plantlets cultured for 10 days with MVOC exposure

growth_protocol: Premixed medium powder containing MS salts and vitamins (Murashige and Skoog, 1962, Physiol Plant 15,473) were acquired from Phytotechnology Laboratories (Cat No. M519, Overland Park, KS, USA). Culture medium was prepared by supplementing medium powder with 30 g/L sucrose with pH adjusted to 5.8 prior to autoclaving at 121°C for 20 min. Medium was distributed to Magenta GA7 vessel at 100 ml per vessel. After plants were inserted cultures were maintained at 25°C under a 16 h light and 8 h dark photocycle for 10 days prior to sample collection.

extract_protocol:
Total RNA was then extracted from 100 mg tissue powder using the RNeasyR Plant Mini Kit per manufacturer’s instructions (Qiagen, Redwood City, CA, USA). There were four biological replicates from each treatment. RNA sequencing was performed by Genewiz via Illumina HiSeq platform (100bp paired end reads) (South Plainfield, NJ, USA).
Library preparation and 50bp single-end sequencing on the Illumina HiSeq system was performed by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: Tobacco seeds were surface-sterilized by immersion in 4% (w/v) sodium hypochlorite solution for 10 min followed by 3 x rinse with sterile water. Seeds were then placed on the surface of MS medium in petri dish and cultured for six days. Germinated seedlings were then transferred to Magenta GA7 vessels containing MS medium without exposure to microbial volatile organic compounds (MVOCs). There were three replicate seedling plants per vessel and four replicate vessels per treatment. After 10 days of cultivation, tissue samples including the apical meristem and 3 to 4 terminal leaves from all three seedling plants per vessel were collected, placed in a 1.5 ml microcentrifuge tube and immediately immersed in liquid nitrogen.  Samples were pulverized into a fine powder using Geno/Grinder 2010 and stored at -80°C for RNA extraction use.

tag: growth stage

value: 10 days after germination

tag: mvoc exposure

value: Yes

tag: cultivar

value: Samsun


title: ST-12_S4_R1_001

source_name: Control plantlets cultured for 10 days without MVOC exposure


title: ST-9_S1_R1_001


title: ST-11_S3_R1_001


title: ST-10_S2_R1_001


title: ST-15_S7_R1_001


title: ST-14_S6_R1_001


title: WT_DT_M4

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
3' polyA RNA-seq
CellRanger 1.3.1
PCA (prcomp in R)
kNN-based graph clustering (R code)
Supplementary_files_format_and_content: 10X genomics CellRanger output
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

source_name: Wild type control mouse rep. 4 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M4]

extract_protocol:
3' polyA RNA seq
Full length RNAseq (SMART-Seq2)
10X Genomics Chromium Prep

value: WT mouse intestinal epithelial cells

tag: strain

tag: treatment

value: DT injection

tag: time point

value: Day 7

tag: genotype

value: WT


title: Foxp3DTR_DT_M4

source_name: T-reg depleted (Foxp3-DTR) mouse rep. 4 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [Foxp3DTR_DT_M4]

value: Foxp3-DTR mouse intestinal epithelial cells


title: Foxp3DTR_DT_M1

source_name: T-reg depleted (Foxp3-DTR) mouse rep. 1 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [Foxp3DTR_DT_M1]


title: WT_DT_M3

source_name: Wild type control mouse rep. 3 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M3]


title: Foxp3DTR_DT_M3

source_name: T-reg depleted (Foxp3-DTR) mouse rep. 3 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [Foxp3DTR_DT_M3]


title: Foxp3DTR_DT_M2

source_name: T-reg depleted (Foxp3-DTR) mouse rep. 2 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [Foxp3DTR_DT_M2]


title: WT_DT_M5

source_name: Wild type control mouse rep. 5 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M5]


title: WT_DT_M2

source_name: Wild type control mouse rep. 2 injected intraperitoneally with diphtheria toxin (DT) [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M2]


title: TCRb_KO_M2_C2

source_name: α/β T cell-depleted (TCRβ KO) mouse rep. 2, channel 2 [Fig. S6C,D] [TCRb_KO_M2_C2]

value: TCRbeta KO mouse intestinal epithelial cells

value: TCRbeta KO


title: Nude_M1_C1

source_name: Athymic, T cell-depleted "nude" mouse rep. 1, channel 1 [Fig. S6A,B] [Nude_M1_C1]

value: Nude mouse intestinal epithelial cells

value: Nude


title: Nude_M2_C2

source_name: Athymic, T cell-depleted "nude" mouse rep. 2, channel 2 [Fig. S6A,B] [Nude_M2_C2]


title: Nude_M2_C1

source_name: Athymic, T cell-depleted "nude" mouse rep. 2, channel 1 [Fig. S6A,B] [Nude_M2_C1]


title: Nude_M1_C2

source_name: Athymic, T cell-depleted "nude" mouse rep. 1, channel 2 [Fig. S6A,B] [Nude_M1_C2]


title: TCRb_KO_M1_C2

source_name: α/β T cell-depleted (TCRβ KO) mouse rep. 1, channel 2 [Fig. S6C,D] [TCRb_KO_M1_C2]


title: CD45_MHCIIGut--_M2_HpDay4

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse rep. 2, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIGut--_M2_HpDay4]

value: MHCIIgut-/- mouse intestinal epithelial cells

value: H. poly

value: Day 4

value: MHCIIgut-/-


title: TCRb_KO_M1_C1

source_name: α/β T cell-depleted (TCRβ KO) mouse rep. 1, channel 1 [Fig. S6C,D] [TCRb_KO_M1_C1]


title: CD45_MHCIIGut--_M3_HpDay4

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse rep. 3, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIGut--_M3_HpDay4]


title: CD45_MHCIIGut--_M1_HpDay4

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse rep. 1, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIGut--_M1_HpDay4]


title: CD45_MHCIIFlox_M3_HpDay4

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 3, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIFlox_M3_HpDay4]

value: MHCII flox-flox control mouse intestinal epithelial cells

value: MHCII-flox-flox


title: WT_DT_M1

source_name: Wild type control mouse rep. 1 injected intraperitoneally with diphtheria toxin (DT)  [Fig. 6C,F,G and Fig. S67F-I] [WT_DT_M1]


title: Cph2_INPUT_Rep3

city: Würzburg

first: Valentina

last: del Olmo Toledo

state: Bayern

address: Josef-Schneider-Str. 2/D15

institute: Institute of Molecular Infection Biology

data_processing:
Sequenced reads were aligned to the Candida albicans genome using Bwtie2 v2.2.8 with default parameters.
Duplicated and non-uniquely aligned reads were filtered out using Samtools v1.3.
Peak calling was performed using MACS2 with parameters: callpeak --name MACS2 --format=BAM --gsize 13874315 --bw 300 --mfold 5 50 --bdg --qvalue 0,05 --nomodel --extsize 200
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: *.filtered.sorted.nodup.wig: wig files were generated using samtools v1.3 with resolution of 10bp and minimum depth of 3.

organism: Candida albicans

source_name: yeast cells

growth_protocol: C. albicans cells were grown in standard YPD medium from an OD600 of 0.1 to an OD600 of 0.8 (4-5 hours).

extract_protocol:
Cell lysates were clarified from sonicated cells and Cph2-myc-DNA complexes were isolated with MYC antibody and Sepharose beads.
DNA libraries were prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® following the manufacturer's protocol.

value: myc-tagged Cph2

tag: chip tag

value: myc-tagged

tag: chip antibody


title: CD45_MHCIIFlox_M2_HpDay4

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 2, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIFlox_M2_HpDay4]


title: TCRb_KO_M2_C1

source_name: α/β T cell-depleted (TCRβ KO) mouse rep. 2, channel 1 [Fig. S6C,D] [TCRb_KO_M2_C1]


title: CD45_MHCIIGut--_M2_Homeostasis

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse 2 at homeostasis [Fig. 5E-I] [CD45_MHCIIGut--_M2_Homeostasis]


title: CD45_MHCIIFlox_M1_HpDay4

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 1, H. poly infection day 4 [Fig. 5E-I] [CD45_MHCIIFlox_M1_HpDay4]


title: CD45_MHCIIGut--_M3_Homeostasis

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse 3 at homeostasis [Fig. 5E-I] [CD45_MHCIIGut--_M3_Homeostasis]


title: Cph2_IP_Rep3

value: Ms mAb Anti-Human c-myc (clone 9E10.3, Thermo Fisher Scientific)


title: CD45_MHCIIGut--_M1_Homeostasis

source_name: Lamina propia immune cells from constitutive intestinal epithelial H2-Ab1-KO (MHCIIgut−/−) mouse 1 at homeostasis [Fig. 5E-I] [CD45_MHCIIGut--_M1_Homeostasis]


title: Cph2_IP_Rep1


title: WT_INPUT_Rep1

value: Wildtype

value: untagged


title: WT_IP_Rep1


title: Cph2_INPUT_Rep1


title: Cph2_IP_Rep2


title: CD45_MHCIIFlox_M1_Homeostasis

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 1 at homeostasis [Fig. 5E-I] [CD45_MHCIIFlox_M1_Homeostasis]


title: CD45_MHCIIFlox_M3_Homeostasis

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 3 at homeostasis [Fig. 5E-I] [CD45_MHCIIFlox_M3_Homeostasis]


title: anti_MHCII_M1_C2

source_name: MHCII-blocked (anti MHCII)  mouse rep. 1, channel 2, H. poly day 3 [Fig. 4F] [anti_MHCII_M1_C2]

value: WT mouse intestinal epithelial cells

value: Day 3

value: WT


title: Cph2_INPUT_Rep2


title: CD45_MHCIIFlox_M2_Homeostasis

source_name: Lamina propia immune cells from MHCII (H2-Ab1) flox-flox control mouse rep. 2 at homeostasis [Fig. 5E-I] [CD45_MHCIIFlox_M2_Homeostasis]


title: CPH2_del_mut_Rep2

description:
Total RNA with poly(A)+ selection.
processed data file: cph2_genes.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.5.3a with parameters --runThreadN 3 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.7.2.
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.14.1.
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw read counts for each sample.
Supplementary_files_format_and_content: *_genes.txt: Tab-delimited text files contain the mean of normalized counts, log2 fold change, log2 fold change standard error, wald statistics, p-value and adjusted p-value for each replicate pair after differential gene expression analysis sample.

growth_protocol: C. albicans reference strain and deletion mutants were grown under anaerobic conditions in Todd-Hewitt broth at 37°C for 24 h.

extract_protocol:
Total RNA was extracted using RiboPure(TM) RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by GATC Biotech (Konstanz, Germany). Briefly, the protocol included poly(A)+ RNA selection, mRNA  fragmentation, random primer cDNA synthesis, adaptor ligation and Illumina (HiSeq2500) sequencing.

value: CPH2 deletion mutant


title: anti_MHCII_M2_C1

source_name: MHCII-blocked (anti MHCII) mouse rep. 2, channel 1, H. poly day 3 [Fig. 4F] [anti_MHCII_M2_C1]


title: HMS1_del_mut_Rep1

description:
Total RNA with poly(A)+ selection.
processed data file: hms1_genes.txt

value: HMS1 deletion mutant


title: HMS1_del_mut_Rep2


title: anti_MHCII_M1_C1

source_name: MHCII-blocked (anti MHCII) mouse rep. 1, channel 1, H. poly day 3 [Fig. 4F] [anti_MHCII_M1_C1]


title: WT_Rep2

description: Total RNA with poly(A)+ selection.


title: anti_IgG_M2_C1

source_name: Control (anti IgG) mouse rep. 2, channel 1, H. poly day 3 [Fig. 4F] [anti_IgG_M2_C1]


title: anti_IgG_M1_C1

source_name: Control (anti IgG) mouse rep. 1, channel 1, H. poly day 3 [Fig. 4F] [anti_IgG_M1_C1]


title: anti_IgG_M1_C2

source_name: Control (anti IgG) mouse rep. 1, channel 2, H. poly day 3 [Fig. 4F] [anti_IgG_M1_C2]


title: MHCII_dGut_1

source_name: Inducible intestinal epithelial H2-Ab1-KO (MHCIIΔgut) mouse rep. 1 [Fig. 3C and Fig. S4C-F] [MHCII_dGut_1]

value: MHCIIdelta gut mouse intestinal epithelial cells

value: MHCIIdelta gut


title: MHCII_dGut_3

source_name: Inducible intestinal epithelial H2-Ab1-KO (MHCIIΔgut) mouse rep. 3 [Fig. 3C and Fig. S4C-F] [MHCII_dGut_3]


title: MHCII_dGut_5

source_name: Inducible intestinal epithelial H2-Ab1-KO (MHCIIΔgut) mouse rep. 5 [Fig. 3C and Fig. S4C-F] [MHCII_dGut_5]