title: Kc167 cells, 1min digestion, exp.1, seq.1

value: Kc167 cells

value: approximately tetraploid cell line from Drosophila Genomics Resource Center (Stock Number:1)


title: Experiment A - 1.3 units AluI

status: Public on Aug 27 2019

type: SRA

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

country: USA

institute: National Institutes of Health

library_source: genomic

data_processing:
Sequences were aligned to the Mus musculus genome (mm10) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing the fraction of cut DNA at each AluI site along the mouse genome (for IGV genome browser)

molecule: genomic DNA

organism: Mus musculus

source_name: Experiment A - 1.3 units AluI

growth_protocol: Livers were dissected from female NIH/S mice (E13.5) and stored at -80C.

extract_protocol:
AluI digestion was stopped and the DNA was sonicated.
Purified sonicated DNA was prepared for Illumina paired-end sequencing using New England Biolabs kit E7370. 50-nt paired reads were obtained using an Illumina NextSeq-500 machine.
New method: Quantitative DNA accessibility assay - "qDA-seq"

treatment_protocol: Nuclei were prepared from homogenised liver and digested with increasing amounts of the restriction enzyme AluI.

tag: strain

value: NIH/S

tag: gender

value: Female

tag: age

tag: tissue

value: liver

tag: treatment

value: 1.3 units AluI


title: Experiment A - 5 units AluI

source_name: Experiment A - 5 units AluI

value: 5 units AluI


title: Experiment A - 2.5 units AluI

source_name: Experiment A - 2.5 units AluI

value: 2.5 units AluI


title: S2 cells, 15min digestion, exp.2, seq.1

data_processing:
DNA sequences were aligned to the D. melanogaster reference genome dm6 and S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, 2012) with parameters -X 1000 --very-sensitive.
Nucleosome counts (defined as the number of Drosophila DNA fragments with the length between 100-200 bp) and spike-in counts (number of S. cerevisiae DNA fragments with the length between 100-200 bp) were obtained using MATLAB (Bioinformatics toolbox).
Genome-wide profiles (tdf files) containing the spike-in normalized nucleosome counts were generated using MATLAB and igvtools.
Genome_build: dm6
Supplementary_files_format_and_content: tdf files containing the spike-in normalized genome-wide nucleosome counts (for IGV browser)

organism: Drosophila melanogaster

source_name: Drosophila S2 cells chromatin

growth_protocol: D. mel S2 cells were obtained from Invitrogen (10831-014) and grown in HyClone SFX-Insect media supplemented with 18 mM L-glutamine.

extract_protocol:
Drosophila S2 and Kc167 cell nuclei were isolated and subjected to MNase digestion for 1, 2, 5, 15, 40, 60 minutes. S. cerevisiae spike-in DNA was used for normalization.
Paired-end sequencing (PE25x25) was performed on barcoded libraries using an Illumina Hi-seq 2500
Quantitative MNase-Seq

treatment_protocol: MNase-seq was performed on unfixed cells as described (Ramachandran et al., 2017) with the following modifications: For each time point, ~2 million cells were suspended in 10 mM HEPES pH 7.4, 0.5 mM PMSF, 0.5% NP40 on ice in a 166 µL volume. MNase was added at a concentration of 2.5 U per million cells. The mixture was warmed to 37C before addition of 3.5 µL 100 mM CaCl2 (to 2 mM) to activate the MNase. Reactions were stopped by addition of 170 µL of 2XSTOP (4.345 ml TM2, 340 µL 5M NaCl, 200 µL 0.5M EDTA, 100 µL 0.2M EGTA, 25 µL RNase A and 2 pg/ml yeast mononucleosomal spike-in DNA). After phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation, the DNA pellet was dissolved in 50 µL 1 mM Tris-HCl pH 8, 0.1 mM EDTA and used directly for 1.5% agarose gel analysis and for making sequencing libraries as described (Ramachandran et al., 2017).

tag: strain name

value: S2 cells

tag: genotype

value: triplo-X tetraploid cell line from Invitrogen (10831-014)


title: TCDD rep 4

city: Charlottesville

first: Jason

last: Papin

state: VA

address: 415 Lane Rd

department: Biomedical Engineering

institute: University of Virginia

library_source: transcriptomic

data_processing:
Illumina 1.9 was used for basecalling
Sequenced reads were pseudo-aligned to the rno reference transcriptome using Kallisto v. 0.43. with parameters -b 100
Supplementary_files_format_and_content: tab-separated value files include estimated counts and transcripts per million for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Hepatocyte

extract_protocol:
After supernatants were collected, cells from each time point were treated with TRIzol® and then scraped and collected into tubes. Chloroform was added to each tube and after shaking, cells were poured into pre-spun phase-lock gel tubes (5PRIME). Tubes were then spun in a cold room, the upper phase was collected, and IPA and glycogen were added to each tube followed by gentle inversion. Supernatants were again spun in a cold room and the resulting pellet was washed twice with 75% ethanol. The pellet was semi-dried and then dissolved in nuclease-free H2O. RNA samples were treated with DNA-free DNA removal kit (Ambion/Invitrogen), according to manufacturer’s instructions, to remove any remaining DNA. RNA was quantified using the Qubit RNA broad range kit and sample integrity assessed using Agilent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hepatocytes were exposed to a hepatotoxicant, and general toxins at sub-toxic levels. Sub-toxic levels were defined as concentrations that resulted in minimal cell death but observed phenotypic changes (i.e., decreases in albumin production and increases in cytochrome p450 activity). The compounds were acetaminophen (APAP) at 3mM, trichloroethylene (TCE) at 1mM, and 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) at 1nM. Acetaminophen is a known hepatotoxicant, while TCDD and TCE are not considered primary heptatotoxicants, but do indeed induce hepatotoxicity. Solutions were made in WEM containing 0.1% DMSO with 0.1% DMSO as a control. Cells were exposed to the compounds for six hours.

value: TCDD


title: TCDD rep 3


title: Replicate 2 - No AluI

data_processing:
Library strategy: Quantitative DNA accessibility assay - "qDA-seq"
Sequences were aligned to the S.cerevisiae genome (sacCer3) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab. Genome-wide profiles (bigwig files) containing the fraction of cut DNA at each site and nucleosome occupancy were generated using Matlab and wigToBigWig tool.
MNase-seq reads were size selected, and we kept all mono-nucleosomal fragments with the lengths between 120 and 180 bp. Genome-wide coverage profiles were computed in Matlab, and they were normalized such that the average coverage for every chromosome is 1. Bigwig files were generated using wigToBigWig tool.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig files containing the fraction of cut DNA at each AluI site, and nucleosome occupancy.

organism: Saccharomyces cerevisiae

source_name: Yeast genomic plasmid library

growth_protocol: Not applicable (in vitro experiment).

extract_protocol:
AluI digestion was stopped and the DNA was sonicated.
Purified sonicated DNA was prepared for Illumina paired-end sequencing using New England Biolabs kit E7370. 50-nt paired reads were obtained using an Illumina NextSeq-500 machine.

treatment_protocol: Nucleosomes were assembled on a yeast genomic plasmid library at a ratio of 1 recombinant yeast histone octamer per 206 bp (80% w/w) by salt dialysis. The reconstituted chromatin was digested with AluI for 0, 20 or 40 minutes, or with 1.6 units micrococcal nuclease (MNase) for 3 minutes at 25degC.

value: No AluI

tag: source

value: Yeast genomic plasmid library (Thermo Scientific cat. # YSC4613).


title: S2 cells, 2min digestion, exp.2, seq.1


title: Replicate 1 - 20 minutes AluI

value: 20 minutes AluI


title: Replicate 1 - 40 minutes AluI

value: 40 minutes AluI


title: S2 cells, 1min digestion, exp.2, seq.1


title: Experiment A - 10 units AluI

source_name: Experiment A - 10 units AluI

value: 10 units AluI


title: TCDD rep 2


title: Experiment A - 0.3 units AluI

source_name: Experiment A - 0.3 units AluI

value: 0.3 units AluI


title: Replicate 1 - No AluI


title: Control rep 3

value: Control


title: Experiment B - 800 units AluI

data_processing:
Sequences were aligned to the S.cerevisiae genome (sacCer3) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and wigToBigWig.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files containing the fraction of cut DNA at each AluI site along the yeast genome (for IGV genome browser)

source_name: Experiment B - 800 units AluI

growth_protocol: Yeast cells were grown in synthetic complete medium and then arrested with alpha-factor.

treatment_protocol: Nuclei were prepared from the cells and digested with increasing amounts of the restriction enzyme AluI

value: 800 units AluI


title: EcN_incubated_with_T4_phages_2 h_Rep_3

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

data_processing:
Demultiplexing
Quality control Fastq quality trimming using FastX version 0.0.13 and a cut-off value of phred score 20
Size filtering: discarding reads shorter than 15 nt (READemption 0.4.2, Förstner et al., 2014)
Mapping: Reads were mapped to reference genome sequences using segemehl version 0.2.0-418 (READemption 0.4.2, Förstner et al., 2014)
Coverage calculation, normalization (READemption 0.4.2, Förstner et al., 2014) and differential gene expression profiling (DESeq2 version 1.16.1,  Love et al., 2014)
Supplementary_files_format_and_content: abundance measurements: text format, coverage files: wiggle format

organism: Escherichia coli

source_name: EcN_incubated_with_T4_phages_2 h

growth_protocol: The OD600 of bacterial overnight cultures (ONC) were determined and the cells were collected by centrifugation at 9,400 x g for 5 min at RT. The bacterial pellet was resuspended in LB medium to obtain ~1e8 CFUs/ml.

extract_protocol: Total EcN bacterial RNA was isolated from 3 ml cultures after 2 h of a static incubation period with or without phages. RNA was isolated with the RNase Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: 100 µl of the EcN culture (1e8 CFUs/ml) and 100 µl of a phage extract (~1e8 pfus/ml) were added to final volume of 1 ml LB medium in a 24 well plate. The plates were incubated in a static manner for 2 h of time at 37 °C.

value: Nissle 1917


title: Experiment A - 0 units AluI

source_name: Experiment A - 0 units AluI

value: NIH/S

value: Female

value: 0 units AluI


title: EcN_incubated_with_T4_phages_2 h_Rep_2


title: TCDD rep 1


title: Replicate 2 - 20 minutes AluI


title: Control rep 2


title: EcN_incubated_with_T4_phages_2 h_Rep_1


title: Experiment B - 400 units AluI

source_name: Experiment B - 400 units AluI

value: 400 units AluI


title: EcN_incubated_with_LB_medium_2 h_Rep_3

source_name: EcN_incubated_with_LB_medium_2 h


title: Experiment A - 0.6 units AluI

source_name: Experiment A - 0.6 units AluI

value: liver

value: 0.6 units AluI


title: EcN_incubated_with_LB_medium_2 h_Rep_2


title: MCF7 cells, siCtrl_sBLISS

city: Jerusalem

first: Idit

last: Hazan

address: Hadassah Medical School

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

data_processing:
Library strategy: sBLISS-seq
Quality control with trim_galore version 0.6.1.
Alignment to hsa hg38 genome with hisat2 version 2.1.0.
Conversion of BAM to SAM file with samtools version 1.9.
Deduplication of UMI with custom python (2.7) script utility ddupUMI.py, to create bed and bedgraph files.
Conversion of bedgraph files to bigwig with ucsc bedGraphToBigWig utility
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file where each score represents break count or log break count at that location

organism: Homo sapiens

source_name: MCF7, transfected with siRNA negative control

growth_protocol: MCF7 were grown in RPMI supplemented with 10% FBS,  glutamine, and penicillin/streptomycin

extract_protocol:
BLISS was prepared as described in Yan et al., Nature communications 2017 and sBLISS was prepared as described in Gothe et al Molecular Cell, 2019.
Libraries were prepared in Yan et al., Nature communications 2017 and in Gothe et al Molecular Cell, 2019.

tag: cell line

value: Breast Carcinoma Cell Line MCF7

value: 48hr after siCtrl transfection


title: MCF7 cells, DRB_sBLISS

source_name: MCF7, treated with 5,6-Dichlorobenzimidazole 1-beta-D-ribofuranoside (DRB)

value: Treated with 60uM DRB for 30min


title: MCF7 cells, siRAD51_sBLISS

source_name: MCF7, transfected with siRAD51

value: 48hr after siRAD51 transfection


title: Control rep 1


title: MCF7 cells, Mock_DRB_sBLISS

source_name: MCF7, DMSO treated

value: Treated with DMSO for 30min


title: EcN_incubated_with_LB_medium_2 h_Rep_1


title: CCl4 rep 3


title: Experiment B - 100 units AluI

source_name: Experiment B - 100 units AluI

value: 100 units AluI


title: CCl4 rep 1


title: Experiment B - 20 units AluI

source_name: Experiment B - 20 units AluI

value: 20 units AluI


title: MCF7 cells, E2_BLISS

data_processing:
Library strategy: BLISS-seq
Quality control with trim_galore version 0.6.1.
Alignment to hsa hg38 genome with hisat2 version 2.1.0.
Conversion of BAM to SAM file with samtools version 1.9.
Deduplication of UMI with custom python (2.7) script utility ddupUMI.py, to create bed and bedgraph files.
Conversion of bedgraph files to bigwig with ucsc bedGraphToBigWig utility
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file where each score represents break count or log break count at that location

source_name: MCF7,  treated with Estradiol (E2)

value: To induce estrogen signaling, cells were grown for two days on hormone-stripped media followed by 1hr treatment with 100nM E2,


title: Experiment B - 40 units AluI

source_name: Experiment B - 40 units AluI

value: 40 units AluI


title: MCF7 cells, Mock_E2_BLISS

value: As a control for E2 treatment, cella were grown for two days on hormone-stripped media followed by 1hr with EtOh.


title: APAP rep 4

source_name: Hepatocyte

value: APAP


title: MCF7 cells, Eto_BLISS

source_name: MCF7, treated with Etoposide (Eto)

value: Treated with 5uM Eto for 4hr


title: Experiment B - 5 units AluI

source_name: Experiment B - 5 units AluI

value: 5 units AluI


title: APAP rep 3


title: Experiment B - 10 units AluI

source_name: Experiment B - 10 units AluI

value: 10 units AluI


title: MCF7 cells, Mock_Eto_BLISS

value: Treated with DMSO for 4hr


title: APAP rep 2


title: MCF7 cells, siTEAD4_BLISS

source_name: MCF7, transfected with siTEAD4

value: 48hr after siTEAD4 transfection


title: Experiment B - 1 unit AluI

source_name: Experiment B - 1 unit AluI

value: 1 unit AluI


title: Experiment B - 2.5 units AluI

source_name: Experiment B - 2.5 units AluI

value: 2.5 units AluI


title: MCF7 cells, siXRCC4_BLISS

source_name: MCF7, transfected with siXRCC4

value: Breast Carcinoma Cell Line MCF7

value: 48hr after siXRCC4 transfection


title: Experiment B - 200 units AluI

source_name: Experiment B - 200 units AluI

value: 200 units AluI


title: CCl4 rep 2


title: MCF7 cells, siRAD51_BLISS

value: 48hr after siRAD51 transfection


title: 1009U muscle

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

data_processing:
cutadapt v1.15 was used for trimming with the options -e 0.2 -m 17 -q 10 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC
fastqQualityFilter.pl within the miRWoods package was used to remove reads with an average quality score less than 30
bowtie v1.2.11 was used with the options -n 1 -e 50 -l 18 -m 10 -a -S --best --strata to map the reads to the genome
addNHTags.pl within the miRWoods package was used to add a tag containing the number of hits to the genome for each read in the sam file
trimMiRReads.pl within the miRWoods package was used for further trimming of mapped reads within the sam file
samtools was used to convert the sam output from bowtie into a bamfile
miRWoods was run in order to predict microRNAs within each set
Gff files were created consisting of the precursor and the products.
Genome_build: Bos Taurus UMD 3.1.1 and Felis cattus 8.0
Supplementary_files_format_and_content: gff3 consisting of predicted microRNAs

organism: Felis catus

source_name: muscle

extract_protocol:
RNA was isolated from tissue by chloroform-isopropanol extraction.
Libraries were prepared using the Illumina TruSeq small RNA sample preparation kit (Illumina, San Diego, CA) for library preparation and size-separation by polyacrylamide gel electrophorese. Library size was determined with the Bioanalyzer 2100 HS-DNA chip and the KAPA biosystem’s library quantification kit, and libraries normalized to 2 nM.  Multiplexed samples (6/lane) were sequenced with a 50 cycle v3 sequencing kit on an Illumina HiSeq 3000 sequencer.

value: Muscle


title: APAP rep 1


title: MCF7 cells, siControl_BLISS

source_name: MCF7, transfected with siRNA negative control

value: 48hr after siCtrl transfection


title: Experiment B - 0 units AluI

source_name: Experiment B - 0 units AluI

value: 0 units AluI


title: Experiment A - 800 units AluI

source_name: Experiment A - 800 units AluI

value: 800 units AluI


title: 1093N skin

source_name: skin

value: Skin


title: 1009N skin


title: Experiment A - 200 units AluI

source_name: Experiment A - 200 units AluI


title: 1033U muscle


title: Experiment A - 400 units AluI

source_name: Experiment A - 400 units AluI

value: 400 units AluI


title: SP_5 (SP25)

type: genomic

city: PAMPLONA

first: Marien

last: Pascual

state: NAVARRA

address: AVDA. PIO XII, 55, LAB 1.04

department: Hemato-Oncology

country: Spain

institute: CIMA, Universidad de Nacarra

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA).

scan_protocol: according to Illumina protocol,  arrays were scanned using the iScan BeadChip scanner.

data_processing: Using the minfi R package available through Bioconductor

label: Cy5 and Cy3

source_name: Peripheral blood cells

label_protocol: Standard Infinium Methylation array protocol.

extract_protocol: genomic DNA from PBCs was extracted using QIAmp DNA Mini Kit following the manufacturer´s instructions (Qiagen, Hilden, Germany).

tag: disease state

value: control

tag: status

value: healthy

tag: cell type

value: Peripheral blood cells

tag: jak2 v617f


title: Experiment A - 5 units AluI

source_name: Experiment A - 5 units AluI

value: 5 units AluI


title: SP_3 (SP23)


title: SP_6 (SP46)


title: Experiment A - 100 units AluI

source_name: Experiment A - 100 units AluI

value: 100 units AluI


title: Experiment A - 40 units AluI

source_name: Experiment A - 40 units AluI

value: 40 units AluI


title: SP_2 (SP10)


title: Experiment A - 20 units AluI

source_name: Experiment A - 20 units AluI

value: 20 units AluI


title: SP_1 (SP9)


title: G1_6h_CT

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

institute: Bundeswehr Institute of Radiobiology

data_processing:
For differential gene expression analysis we followed the workflow described by Love et al.. In brief, sequence reads were aligned to the human transcriptome (Homo_sapiens.GRCh37.67) with Salmon (version 0.8.1) . Resulting data was summarized into matrices using tximport (version 1.4.0) and analyzed for differential gene expression using the default settings of DESeq2 (version 1.16.1). Genes were assumed to be differentially expressed with log2 fold changes of FPKM ratios > 1 (fragments per kilobase per million mapped fragments) and FDR < 0.1. Results were exported with DESeq2 and the R package “reporting tools” (version 2.1.16.0) .
Results were exported from R to Microsoft Excel and sorted in accordance to their fold changes and significance.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx-File, Results table from DESeq2 with gene-symbols

source_name: CT-exposure

extract_protocol:
After irradiation and incubation at 37°C for 1h and 6h, respectively, 2.5ml of blood were transferred to PAXgene™ Blood RNA tubes. Apart from irradiation matching non-irradiated sham controls samples were handled the very same way.
RNA Seq library preparation was performed with NebNext Ultra II Directional Kit. Library fragment length was determined with Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and concentration was measured with a Qubit 3.0 Fluorometer (Thermo Scientific, Waltham, MA, USA). Libraries were sequenced with 1 x 75 bp single end reads following the protocols for the NextSeq500 sequencing platform (NextSeq 500 High Output Kit 75bp; NextSeq System Guide; NextSeq Denature and Dilute Libraries Guide; Illumina, San Diego, CA, USA, Document # 15048776 v02, Document # 15046563 v02).

treatment_protocol: Peripheral blood from three healthy male donors was collected into EDTA-Monovettes. Three separate blood samples for each proband and the two investigated post-exposure time points were placed into a spine phantom set up in a Dual Source CT scanner (SOMATOM Force, Siemens Medical Solutions, Forchheim, Germany). Exposure was done according to the standard protocol for lumbar spine examinations. This resulted in an administered effective dose of 9.61mSv as estimated in accordance to the ICRP 103 protocol by means of the Monte Carlo model-based tool ImpactDose (CT Imaging GmbH, Erlangen,Germany).

value: peripheral blood

tag: time point (h)

tag: exposure (yes/no)

value: yes


title: G1_1h_CT


title: G2_6h_CT


title: G2_1h_CT


title: Experiment A - 10 units AluI

source_name: Experiment A - 10 units AluI

value: 10 units AluI


title: G1_6h_NULL

source_name: sham control

value: no


title: Experiment A - 0 units AluI

source_name: Experiment A - 0 units AluI


title: SP_4 (SP24)


title: G3_6h_NULL


title: Experiment A - 2.5 units AluI

source_name: Experiment A - 2.5 units AluI

value: 2.5 units AluI


title: G2_6h_NULL


title: Prim_MFI (Prim.MFI.6483)

source_name: Granulocytes from peripheral blood

value: myelofibrosis (MF)

value: primary MF

value: Granulocytes from peripheral blood

value: YES


title: Experiment A - 1 unit AluI

source_name: Experiment A - 1 unit AluI

value: 1 unit AluI


title: G3_1h_NULL


title: G1_1h_NULL


title: Prim_MFI (Prim.MFI.42941)

value: NO


title: Prim_MFI (Prim.MFI.45060)


title: G2_1h_NULL


title: Lung4GFP

city: Baltimore

first: Daniele

middle: Marie

last: Gilkes

state: MD

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

data_processing:
Preliminary analysis was performed by Quick Biology. The reads were then mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
Gene expression level was estimated using RSEM v1.2.15.
TMM (Trimmed Mean of M-values) was used to normalize gene expression.
Differentially expressed genes were identified using the edgeR program.
Genome_build: human genome assembly GRCh38
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

source_name: lung metastasis derived from MDA-MB-231 orthotopic mouse tumor

growth_protocol: Our dual-vector approach to fate-map hypoxia was delivered to MDA-MB-231 cells obtained directly from the ATCC.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: Metastatic lungs of NSG mice bearing orthotopic tumors implanted in the mammary fat pad and resected 2 weeks post-implantation, were mechanically harvested 2 weeks post tumor removal, disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research).

tag: lung sample #

tag: system reporter

value: GFP


title: A Klinefelter syndrome Chinese adult male_scRNAseq

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

country: China

institute: Genergy Bio-technology (Shanghai) Co., Ltd

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: blood

extract_protocol: For scRNA-seq, the PBMC were dissociated into single cells suspensions using Ficoll-Paque buffer (Sigma), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: peripheral blood mononuclear cells


title: Lung5GFP


title: Lung5DsRed

value: DsRed


title: shGR_INPUT2

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

data_processing:
Each library was pair-end-sequenced across two lanes of the NovaSEQ flowcell, resulting in the output of four related fastq files for each sample.
Reads were first trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘ref = adapters.fa ktrim = r qtrim = 10 k = 23 mink = 23 hdist = 1 maq = 10 minlen= 20 tpe tbo’.
Quality of each sample was assessed both pre- and post-trim FastQC (v. 0.0.13). The FastQC reports suggested the ChIP samples may be contaminated with non-human DNA due to the appearance of two distinct G/C distribution peaks centered at 42% and 68% mean G/C content (Input control samples exhibited a normal distribution).
To resolve these two peaks in the ChIP samples, bbsplit.sh (part of the BBMap Suite v. 38.05) was used with argument ‘ref = hg38.fa’ to separate reads that mapped to hg38 from those that did not. (NCBI BLAST was then used to determine the organism responsible for the unmapped reads, which indicated that the majority of these reads mapped to the Pseudomonas aeruginosa genome.)
The remaining hg38-specific reads were mapped to hg38 using hisat2 (v. 2.1.0) with argument ‘--no-spliced-alignment’ using indexes built with hisat2-build (same version), which resulted in over 91.6% mapping for all ChIP and Input control samples.
Resulting SAM files were converted to sorted and indexed BAM files using samtools (v. 1.8) view, sort, and index, respectively.
Sorted BAM files were converted to bedGraph format using genomeCoverageBed from bedtools (v. 2.25.0) with arguments ‘-bg -ibam -g hg38’
MACS2 (v. 2.1.1) callpeak with ‘--SPMR’ argument was applied to each biological replicate pair of ChIP and respective Input control samples to call significant peaks.
Genome_build: hg38
Supplementary_files_format_and_content: Processed fastq files have had contaminating reads removed and are thus hg38-specific. Bedgraph files are standard coverage files following mapping.

source_name: Beas-2B airway epithelial cells

growth_protocol: Beas-2B cells obtained from ATCC were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing L-glutamine and 4.5 g/L glucose and supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (PMID: 23508109) with a 5 minute fixation time in 1% methanol-free formaldehyde and 35 cycles (30-second bursts separated by 30-second incubations in ice water) of sonication. Twelve ug of GR-IA1 (Miles Pufall) or GR-356 (custom-made by Covance) antibody were used for immunoprecipitation.
One ng of purified ChIP DNA was used to prepare uniquely barcoded libraries with the Ovation Ultralow Library System from NuGEN. Libraries were pooled and sequenced in duplicate on an Illumina NovaSEQ using 2 x 150 bp paired-end reads.

treatment_protocol: Stable GR (or control) knockdown was achieved via lentiviral shRNA transduction performed as described previously (PMID: 28424165). Control- and shGR-transduced Beas-2B cells were plated on 10 cm tissue culture dishes at 1.25E6 cells/dish and grown to confluence (~days), then treated with vehicle (ethanol), TNF (20 ng/ml), dexamethasone (dex; 100 nM), or TNF+dex for 1 hour.

tag: lentiviral treatment

value: shGR

value: TNF

tag: ip antibody

value: none (Input)


title: Prim_MFI (Prim.MFI.39168)

value: Peripheral blood cells


title: Prim_MFI (Prim.MFI.45286)


title: G3_6h_CT

value: peripheral blood

value: yes


title: Lung4DsRed


title: shGR_INPUT1


title: Ctrl_INPUT2

value: shCtrl

value: vehicle


title: Ctrl_INPUT1


title: Prim_MFI (Prim.MFI.46209)

value: myelofibrosis (MF)


title: Prim_MFI (Prim.MFI.46865)

value: primary MF


title: GR-356_Ctrl_10D2

data_processing:
Data were processed using a Nextflow pipeline (https://github.com/Dowell-Lab/ChIP-Flow).
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files are standard non-normalized coverage files following mapping.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (PMID: 23508109) with a 5 minute fixation time in 1% methanol-free formaldehyde and 35 cycles (30-second bursts separated by 30-second incubations in ice water) of sonication. Twelve ug of GR-356 (custom-made by Covance) antibody were used for immunoprecipitation.
Libraries were prepared using a KAPA HyperPrep kit and sequenced on an Illumina NextSeq using a V2 High Output 1 x 75-cycle single-end kit.

treatment_protocol: Lentiviral shRNA transduction was performed as described previously (PMID: 28424165). Transduced Beas-2B cells were plated on 10 cm tissue culture dishes at 1.25E6 cells/dish and grown to confluence (~3 days), then treated with vehicle (ethanol) or dexamethasone (dex; 100 nM) for 10 minutes.

value: dex


title: GR-356_Ctrl_INPUT2


title: GR-356_Ctrl_INPUT1


title: GR-356_Ctrl_10D1


title: GR-356_shGR_TD2

value: TNF+dex


title: GR-356_shGR_TD1


title: GR-356_shGR_D2


title: ChIP-seq Input

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

data_processing:
Reads were aligned to mm9 genome using bowtie 2.2.8 with --non-deterministic flag
Unmapped reads were filtered using samtools 1.8
wig files were produced using RSeQC tool 2.6.3 and normalized to a coverage of 10 million 100nt reads for display
Peak calling was performed using MACS2 with the following commands: macs2 callpeak -t IP.bam -n Result_directory --nomodel --extsize 51 --nolambda -B --SPMR -g mm --verbose 0 –broad
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file with Normalized CTCF ChIp-seq data.

source_name: melanoma cells

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using CTCF antibody(Active Motif, Catalog No: 61311).  Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: ocular melanoma cells

tag: chip antibody


title: GR-356_Ctrl_10V1


title: ChIP-seq CTCF

value: CTCF


title: Prim_MFI (Prim.MFI.4780)

value: Granulocytes from peripheral blood

value: YES


title: HDF-loading-IP

first: Gao

last: Ya

address: Zhizaoju road No.639

department: School of medicine

institute: Shanghai Jiao Tong University

description: HDF-jiali-IP_vs_HDF-jiali-input_1e-5_10_30_peaks.bed

data_processing:
Basecalls performed use Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human genome (HG19) using BOWTIE software (V2.1.0).
Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-5. The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
The annotation of the peaks which were located within -2Kb to +2Kb around the corresponding gene TSS.
Genome_build: hg19
Supplementary_files_format_and_content: WIG file format was generated from ChIP-seq data, which can be visualized on UCSC genome browser or IGB browser (Integrated Genome Browser, Java Runtime Environment needed, http://www.bioviz.org/igb/)

source_name: Primary human dermal fibroblast

growth_protocol:
Primary human dermal fibroblast (HDFs) were isolated using the skin samples provided by Shanghai Ninth People’s Hospital with ethics approval. Isolation steps are as fallows. After excision，use sterile 1 x PBS to wash the skin sample three times, then put it into 0.25% trypsin solution overnight at 4 °C. Next day use scissors to remove the epidermis, and cut dermal skin to small pieces. Then 0.25% Collagenase IV solution digest at 37 °C for 4 hrs. Passing through 200-mesh sieve.HDFs were cultured in Gibco™ DMEM, high glucose, both supplemented with 10% fetal bovine serum and antibiotics (penicillin 100 IU/mL and streptomycin 100 mg/mL) in 5% CO2
at 37 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and ELK1-DNA complexes were isolated with Anti-ELK1 antibody[E277] - ChIP Grade (abcam,ab32106)
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

treatment_protocol: HDFs were plated at a density of 5 × 105 cells/cm2 in 2 mL of medium on six-well flexible silicone rubber BioFlex plates coated with collagen type I (Flexcell International Corporation, Hillsborough, NC, USA). Cells were cultured for 24 hrs for adhesion and to reach 50-70% confluence before mechanical tension was applied. Cyclic mechanical stretch (CMS) with a 0.5-Hz sinusoidal curve at 10-20% elongation was applied using a Flexcell○RFX-5000TM Tension System (Flexcell○R International Corporation, NC, USA). The cultures were incubated in a humidified atmosphere at 37 °C and 5% CO2 during the stretching. Cells were harvested immediately after the application of CMS stimulation was completed. Control cells were cultured on the same plates in the same incubator with no stretching.

tag: tissue

value: human dermal skin

tag: passages

tag: chip-antibody

tag: condition

value: mechanic loading


title: GR-356_Ctrl_10V2

tag: treatment


title: EGR1_ChIPseq_hBJV600E_DoxClob24_DMSO24_rep2

city: Gif sur Yvette

first: Jean-Yves

last: Thuret

address: CEA Saclay Bat 142

country: France

institute: CEA

description:
L8_8_DoxClob24_2_S8_all
processed data file: DoxClob24_vs_Prolif.narrowPeak

data_processing:
Demultiplexing was done with bcl2fastq2 V2-2.18.12, adapters removed with Cutadapt v1.15 and reads longer than 10bp were kept for analysis. FastQC v0.11.5 was used for quality control.
Reads were mapped to the human genome (hg19) using bwa-sampe (0.7.15-r1140), and samtools (1.3.1, using htslib 1.3.2) was used to sort, index and remove duplicate.
Peak-calling was performed using MACS2 (2.1.1.20160309, https://github.com/taoliu/MACS) using the BAMPE option, collecting all peaks irrespective of the reported q-value. Peaks with q-value lower than 1e-5 were selected with R.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format, containing differential peak calling with MACS2 at FDR<1e-5, conditions as described

source_name: hBJV600E_doxycycline and clobetasol_24 hours

growth_protocol: 10e6 cells were grown in two 15-cm dishes for each condition.

extract_protocol:
Cells were the resuspended in 1mL of cold IP buffer (10 mM Tris-HCl (pH8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine sodium salt) and sonicated in a Covaris S220 (Brighton, UK) with the following parameters: 150W, 10%, 200 bursts/cycle, 5x2 mins. 250µL of sonicated chromatin was diluted with 500µL of cold IP buffer containing addtionnally Roche protease inhibitor cocktail. 6 µg of anti-EGR1 Ab (sc-189X) was then added for each IP and incubated O/N with rotation at 4°C. 30 µL of protein G-sepharose beads that had been blocked by incubation with IP buffer containing 2% BSA were then added for each IP and incubated for 2 hours with rotation at 4°C. The beads were then washed once consecutively with WB1 (20 mM Tris-HCl (pH8), 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.25% Triton x-100), WB1 with 500 mM NaCl, WB 2 (10 mM Tris-HCl (pH8), 250 mM LiCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Igepal CA-630) and TE (10 mM Tris-HCl (pH8), 1 mM EDTA). The washed beads were then resuspended in 200 µL of TE+ 1% SDS. 1µL (20 µg) of proteinase K solution was added and the suspension was incubated with shaking O/N at 65°C in a Thermomixer (Eppendorf) to digest proteins and to reverse the formaldehyde crosslinks. Immunoprecipitated DNA was then purified by phenol/chloroform extraction and ethanol precipitation.
A DNA library for sequencing was prepared with a Diagenode IP-Star platform using their MicroPlex Library Preparation kit v2. Amplified DNA fragments with ligated sequence adapters were sized to approximately 325bp with AMPure XP beads (A63880, Beckman Coulter). The size of the final library fragments was verified on an Agilent Bioanalyzer and DNA concentrations were determined with an Invitrogen Qubit fluorimeter. Libraries were pooled in equimolar proportions and sequenced on an Illumina NextSeq500 instrument, using NextSeq 500/550 High Output 75 cycles kits; 43 (Paired-End) sequencing cycles were performed.

treatment_protocol: Cells were fixed in 1% final concentration of EM-grade formaldehyde for 10 mins then quenched by the addition of glycine to a final concentration of 0.2M for 10 mins. Celles were washed once with cold PBS then scraped in cold PBS, centrifuged, and washed again with cold PBS.

tag: cell line

value: human fibroblasts

tag: inducer

value: doxycycline 1000 ng mL-1

value: clobetasol 2nM

value: anti-EGR1 Ab (sc-189X)


title: GR-356_shGR_T2

value: shGR

value: TNF


title: Prim_MFI (Prim.MFI.37291)

source_name: Peripheral blood cells

tag: disease state

tag: status

value: Peripheral blood cells


title: HDF-control-input

description: HDF-control-IP_vs_HDF-control-input_1e-5_10_30_peaks.bed

value: control


title: G3_1h_CT

value: peripheral blood

value: yes


title: EGR1_ChIPseq_hBJV600E_DoxClob24_DMSO24_rep3

description:
L8_9_DoxClob24_3_S9_all
processed data file: DoxClob24_vs_Prolif.narrowPeak

tag: cell type


title: HDF-loading-input


title: EGR1_ChIPseq_hBJV600E_Dox24_DMSO24_rep3

description:
L8_6_Dox24_3_S6_all
processed data file: Dox24_vs_Prolif.narrowPeak

source_name: hBJV600E_doxycycline and DMSO_24 hours

value: DMSO


title: EGR1_ChIPseq_hBJV600E_DoxClob24_DMSO24_rep1

description:
L8_7_DoxClob24_1_S7_all
processed data file: DoxClob24_vs_Prolif.narrowPeak


title: GR-356_shGR_T1


title: GR-356_shGR_V2

value: vehicle


title: HDF-control-IP


title: Prim_MFI (Prim.MFI.38759)

source_name: Bone marrow cells

value: myelofibrosis (MF)

value: primary MF

value: Bone marrow cells

tag: jak2 v617f


title: Prim_MFI (Prim.MFI.33643)

value: YES


title: Prim_MFI (Prim.MFI.35955)


title: Prim_MFI (Prim.MFI.38791)


title: EGR1_ChIPseq_hBJV600E_Dox24_DMSO24_rep2

description:
L8_5_Dox24_2_S5_all
processed data file: Dox24_vs_Prolif.narrowPeak


title: GR-356_shGR_V1


title: Prim_MFI (Prim.MFI.36339)


title: GR-356_Ctrl_TD2

value: shCtrl

value: TNF+dex


title: EGR1_ChIPseq_hBJV600E_EtOH24_DMSO24_rep3

description:
L8_3_Prolif2_S3_all
processed data file: Dox24_vs_Prolif.narrowPeak

source_name: hBJV600E_ethanol and DMSO_24 hours

value: human fibroblasts

value: ethanol


title: GR-356_Ctrl_TD1


title: EGR1_ChIPseq_hBJV600E_EtOH24_DMSO24_rep2

description:
L8_2_Prolif2_S2_all
processed data file: Dox24_vs_Prolif.narrowPeak

value: anti-EGR1 Ab (sc-189X)


title: GR-356_Ctrl_D2

value: dex


title: MMCL_2_U133

type: RNA

city: Nantes

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

description: Gene expression data

hyb_protocol: Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Fluorescence intensities were quantified and analyzed using the GECOS software

data_processing: Gene expression data were normalized with the GCRMA algorithm

label: biotin

growth_protocol: Peripheral blood primary monocytes from healthy donors were obtained by elutriation (CIC Biotherapy 0503, Nantes, France). For in vitro generation of classically activated M1 and alternatively activated M2 macrophages, monocytes were differentiated with CSF2 (GM-CSF, 20 ng/ml, 5 days) or CSF1 (M-CSF, 50 ng/ml, 5 days) before activation with IFNγ (10 ng/ml, 2 days) or IL-10 (25 ng/ml, 2 days), respective. MMCL were generated with monocytes cocultured with CD19+ primary MCL cells during seven days.

extract_protocol: RNA was extracted using the RNeasy Kit (Qiagen, Hilden,Germany)

tag: cell

value: Macrophages


title: Prim_MFI (Prim.MFI.30954)


title: Prim_MFI (Prim.MFI.29397)

value: Peripheral blood cells


title: MMCL_4_U133

description: Gene expression data

source_name: monocytes cocultured with CD19+ primary MCL cells during seven days

label_protocol: Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA)


title: Prim_MFI (Prim.MFI.33042)


title: Prim_MFI (Prim.MFI.15561)

value: Granulocytes from peripheral blood

value: NO


title: GR-356_Ctrl_D1


title: Prim_MFI (Prim.MFI.29533)


title: 139781_B: 1492

city: Pittsburgh

first: Wei

last: Chen

state: PA

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
Quality control for raw fastq files were performed with FastQC
The low-quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt
Then the trimmed reads were aligned to human genome reference (hg19) with the RNA-seq aligner STAR
Subsequently, gene expression for each sample was quantified by counting the number of read fragments that were uniquely mapped to genes using the featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files count.txt and RPKM.txt that contain counts and FPKM values for all samples

source_name: buffy coat of cystic fibrosis (CF) patient

extract_protocol:
The buffy coats stored in -80ºC were thawed on ice for two hours and transferred into PAXgene tubes (PreAnalytiX), and the RNA was extracted using the PAXgene RNA extraction kit.
~500ng total RNA per sample was used for library prep using the TruSeq RNA Access Library Prep Kit (Illumina, Inc). Libraries were then quantified and normalized to 2nM prior to sequencing on a NextSeq 500 sequencer using NextSeq 500 High Output Kit -150 cycles (Illumina, Inc), generating about 60 million paired-end reads for each sample.

tag: subject identifier

value: PBMC

tag: diagnosis

value: cystic fibrosis (CF)


title: MMCL_3_U133

description: Gene expression data


title: GR-356_Ctrl_T2

tag: lentiviral treatment

value: TNF


title: EGR1_ChIPseq_hBJV600E_EtOH24_DMSO24_rep1

description:
L8_1_Prolif1_S1_all
processed data file: Dox24_vs_Prolif.narrowPeak

value: DMSO


title: Prim_MFI (Prim.MFI.16749)

value: myelofibrosis (MF)

value: primary MF


title: GR-356_shGR_D1

value: shGR

tag: ip antibody


title: 7754799_B: 1385


title: GR-356_Ctrl_T1

value: shCtrl


title: GR-356_Ctrl_V2

value: vehicle


title: 4404513_B: 1381


title: 971710_B: 1354


title: MFI_post_ET (MFI.Post.45185)

value: MFI post-ET

value: Bone marrow cells


title: MFI_post_PV (MFI.Post.42158)

value: MFI post-PV

value: YES


title: M2_3_U133

description: Gene expression data

source_name: monocytes were differentiated with CSF2 (GM-CSF, 20 ng/ml, 5 days) before activation with IL-10 (25 ng/ml, 2 days)

value: Macrophages


title: Prim_MFI (Prim.MFI.19536)


title: GR-356_Ctrl_V1


title: 9747279_B: 1169


title: GR-IA1_shGR_TD2

value: TNF+dex


title: MFI_post_PV (MFI.Post.4173)

value: Granulocytes from peripheral blood


title: 5072257_B: 1168


title: MFI_post_ET (MFI.Post.37210)

value: Peripheral blood cells


title: M1_2_U133

description: Gene expression data

source_name: monocytes were differentiated with  CSF1 (M-CSF, 50 ng/ml, 5 days) before activation with IFNγ (10 ng/ml, 2 days)


title: GR-IA1_shGR_TD1


title: MMCL_1_U133

description: Gene expression data


title: M2_2_U133

description: Gene expression data


title: MFI_post_ET (MFI.Post.39751)

value: NO


title: M1_3_U133

description: Gene expression data


title: Ucp2-/- (KO) sample 10

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Mouse Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V20 was used for annotation.

source_name: Ucp2-/- (KO) sample 10

label_protocol: 240 ng of total RNA is reverse transcribed  following the Gene chip® WT-Amp Plus kit (Affymetrix). Briefly, the resulting double stranded cDNA is used to produce single stranded RNA using T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Mice were sacrificed at week 15 after starting AOM/DSS protocol and colon tumors were collected

value: Colon tumors

tag: strain

tag: genotype


title: GR-IA1_shGR_D2

value: dex


title: 2983853_B: 1123

tag: tissue

value: PBMC

value: cystic fibrosis (CF)


title: M1_1_U133

description: Gene expression data


title: 7510751_B: 1081


title: GR-IA1_shGR_T2

value: TNF


title: EGR1_ChIPseq_hBJV600E_Dox24_DMSO24_rep1

description:
L8_4_Dox24_1_S4_all
processed data file: Dox24_vs_Prolif.narrowPeak

value: human fibroblasts

value: doxycycline 1000 ng mL-1

value: DMSO

tag: chip antibody

value: anti-EGR1 Ab (sc-189X)


title: M2_1_U133

description: Gene expression data


title: Ucp2-/- (KO) sample 9

source_name: Ucp2-/- (KO) sample 9


title: RH4 Entinostat 6h Single Cell

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: Paired-end

data_processing:
Sequencing data was processed following the Drop-seq Computational Protocol and using the Drop-seq software tools v.1.2 from the McCarroll lab using the default parameters for barcode extraction, QC, filtering, alignment, and generation of expression matrices.
Cells detecting a minimum of 300 genes were included in the expression matrix generation step.
The Seurat version 2.3.0 R package was used for downstream data analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_out_gene_exon_tagged.dge.txt: Gene expression matrices.

source_name: FP-RMS cell line, PAX3-FOXO1

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
Drop-seq was subsequently performed as previously communicated (Macosko et al., 2015). Briefly, the treated cells were trypsinized, washed, filtered through a 40um filter, and resuspended in PBS with 0.01% BSA at a concentration of 100 cells/ul. Barcoded beads (ChemGenes Cat# Macosko-2011-10) were resuspended in complete lysis buffer at a concentration of 120 cells/ul. Cells, beads and oil (Bio-Rad #186-4006) were loaded into syringes and then pumped through a microfluidic chip (FlowJEM) at a rate of 4ml/h (beads and cells) or 12ml/h (oil) to create nanoliter-sized droplets containing a single bead and/or cell. The outflow of droplets was collected. Droplets were disrupted with perfluorooctanol (Sigma Cat# 370533-25G) to release the beads, which were then washed several times. Reverse transcription of the mRNAs bound to the capture beads was performed using Maxima H- RTase (Thermo Scientific Cat# EP0753) and Template Switch Oligos (Table S1). Single-stranded nucleotides were removed by exonuclease I treatment (Thermo Scientific Cat# EN0581). Beads were counted, and twenty PCR reactions each containing 8000 beads were prepared and performed using 2x Kapa HiFi Hotstart Readymix (Kapa Biosystems Cat# KK2605) and a custom SMART PCR primer. The resulting cDNA was purified and concentrated using AMPure XP beads (Beckman Coulter Cat# A63880).
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: Drug was dissolved in DMSO to a stock concentration of 10 mM, and additionally diluted in DMEM to a final concentration of 1 µM (or DMSO of equivalent final volume), exposing cells for 1, 6 hours before extracting RNA.

value: FP-RMS cell line

tag: treatment time

value: 6 hours

value: Entinostat 1 uM

tag: drug target

value: HDAC


title: Ucp2-/- (KO) sample 8

source_name: Ucp2-/- (KO) sample 8


title: GR-IA1_shGR_T1

value: shGR

tag: treatment


title: MFI_post_PV (MFI.Post.31796)

value: myelofibrosis (MF)

value: MFI post-PV


title: MFI_post_ET (MFI.Post.31222)

value: MFI post-ET

value: Peripheral blood cells

value: YES


title: steer3 coriumFeet

organism: Bos taurus

source_name: Corium

value: Corium


title: MFI_post_PV (MFI.Post.33177)


title: Prim_MFI (Prim.MFI.29662)

value: primary MF

value: Bone marrow cells


title: Ucp2-/- (KO) sample 7

source_name: Ucp2-/- (KO) sample 7

value: Colon tumors


title: steer2 brainStem

source_name: Brain Stem

value: Brain Stem


title: Ucp2-/- (KO) sample 6

source_name: Ucp2-/- (KO) sample 6


title: MFI_post_PV (MFI.Post.31354)


title: MFI_post_ET (MFI.Post.29933)

source_name: Granulocytes from peripheral blood

value: Granulocytes from peripheral blood

value: NO


title: RH4 DMSO 6h Single Cell

description: Paired-end

tag: cell line

value: FP-RMS cell line

value: DMSO 0.1%

value: control


title: RH4 Entinostat 1h Single Cell

description: Paired-end

value: 1 hours

value: Entinostat 1 uM

value: HDAC


title: GR-IA1_shGR_V2

source_name: Beas-2B airway epithelial cells

value: shGR

value: vehicle


title: Ucp2+/+ (WT) sample5

source_name: Ucp2+/+ (WT) sample5

value: WT


title: MFI_post_PV (MFI.Post.28530)

tag: disease state

value: myelofibrosis (MF)

value: MFI post-PV

value: YES


title: steer1 SLN

source_name: Submandibular Lymph Node

value: Submandibular Lymph Node


title: MFI_post_PV (MFI.Post.28013)

tag: status


title: MFI_post_PV (MFI.Post.26765)

tag: cell type


title: Comb1 (Both DBP and DiBP)

city: Zhenjiang

first: Hui

address: Xuefu Road

institute: jiangsu university

data_processing:
Data filtering was performed on Raw Data, the linker sequences and low-quality reads were removed to obtain high-quality Clean Data.
HISAT2 was used to sequence alignment.
The reads numbers mapped to each gene were counted by HTSeq v0.6.1.
The number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to estimate the gene expression levels of each gene which was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/danio_rerio/dna/Danio_rerio.GRCz10.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: Both DBP and DiBP

extract_protocol:
Ovaries were removed and snap frozen in liquid nitrogen, and total RNA was extracted through an RNeasy Mini Kit (Qiagen, USA). The sequencing libraries were established with 3 μg RNA per sample by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA).
RNA libraries were sequenced by the Illumina HiSeq X Ten with the pair-end mode (Genepioneer Biotechnologies Company)

value: AB

tag: age

value: 5 months old

value: ovary

value: wild type


title: GR-IA1_Ctrl_TD2

value: shCtrl

value: TNF+dex


title: steer1 retina

source_name: Retina

value: Retina


title: steer1 penis

source_name: Penis

value: Penis


title: GR-IA1_shGR_V1


title: GR-IA1_Ctrl_TD1


title: I1 (DiBP)

source_name: DiBP


title: B1 (DBP)

source_name: DBP


title: Ucp2+/+ (WT) sample4

source_name: Ucp2+/+ (WT) sample4

value: Colon tumors


title: GR-IA1_Ctrl_D2

value: dex


title: Ucp2+/+ (WT) sample3

source_name: Ucp2+/+ (WT) sample3


title: steer1 oralPapillae

source_name: Oral Papillae

value: Oral Papillae


title: CK1 (Control)

source_name: control


title: steer1 opticNerve

source_name: Optic Nerve

value: Optic Nerve


title: MFI_post_PV (MFI.Post.26055)

value: Granulocytes from peripheral blood

tag: jak2 v617f


title: MFI_post_ET (MFI.Post.13011)

value: myelofibrosis (MF)

value: MFI post-ET


title: GR-IA1_Ctrl_T1

value: TNF


title: Scrib_14d

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

data_processing:
Raw data mapping and primary analysis was performed in the Cell Ranger pipeline.
The first 26 bp of R1 contains the barcode and UMI.
Secondary analysis for marker gene expression pattern was performed with Seurat (Butler et al., 2018).
Reads were normalized with the log normalization function in Seurat. Briefly: for each cell, sum all UMI number across all genes, this number is S; for each gene, the normalisation result =  log1p(UMI number (of this gene)/S).
Genome_build: GCF_000001215.4
Supplementary_files_format_and_content: csv files include normalized abundance measurements for each Sample

source_name: Imaginal wing disc

growth_protocol: Around 50 embryos collected within 3 hours were put in an individual vial of fly food to avoid crowding and the larvae were raised at 25-degree incubator for appropriate lengths of time before dissection.

extract_protocol:
The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation.
Construction of 10x single cell libraries and sequencing on Illumina Hiseq platform were performed by Novogene.

tag: parental strain

value: Imaginal wing disc

value: After Egg Laying 14d


title: GR-IA1_Ctrl_T2


title: Scrib_5d

value: After Egg Laying 5d


title: steer1 dentalPulp

source_name: Dental Pulp

value: Dental Pulp


title: Scrib_8d

value: After Egg Laying 8d


title: GR-IA1_Ctrl_D1

value: shCtrl


title: Scrib_4d

value: After Egg Laying 4d


title: GR-IA1_Ctrl_V1

value: vehicle


title: steer1 eyeIris

source_name: Iris

value: Iris


title: steer1 boneMarrow

source_name: Bone Marrow

value: Bone Marrow


title: MFI_post_ET (MFI.Post.29102)

source_name: Granulocytes from peripheral blood

value: YES


title: GR-IA1_Ctrl_V2

source_name: Beas-2B airway epithelial cells


title: Ucp2+/+ (WT) sample1

source_name: Ucp2+/+ (WT) sample1

value: Colon tumors

value: WT


title: smoker 195, genotype

status: Public on Aug 26 2019

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method. CHP files were created from CEL files after running BRLMM_p

source_name: DNA obtained from blood

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

extract_protocol: DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: white

tag: Smoking status

value: smoker, 38 pack-years


title: wt AEC, Streptococcus pneumoniae, rep1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description:
inf wt
primary alveolar epithelial cells from male BALB/c mice

hyb_protocol: 2 µg of the labeled aDNA were hybridized for 22h at 65°C in Agilent hybridization chambers.

scan_protocol: The dried slides were scanned at 2 µm/pixel resolution using the InnoScan is900 (Innopsys, Carbonne, France).

data_processing: Image analysis was performed with Mapix 6.5.0 software, and calculated values for all spots were saved as GenePix results files. Mean spot signals were quantile normalized.

source_name: wt AEC, Streptococcus pneumoniae

label_protocol: Purified total RNA was amplified and labeled with Cy3 using the Agilent Low-Input RNA amplification and labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: AECs were isolated from mice lungs by digestion thru dispase and negative selection via anti-CD45, CD31 and CD16/32 following MACS procedure (Milteny Biotec GmbH, Bergisch Gladbach, Germany). Cells were grown over night in DMEM (1% P/S, 1% Glutamine, 10% FCS, 25mM HEPES buffer). 2h before treatment, medium was changed to DMEM (2% FCS, 1% Glutamine, 25mM HEPES buffer).

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies GmbH)

treatment_protocol: Cells were treated with S.pneumoniae (NCTC 7466, MOI 1) for 6h or left untreated as control

tag: strain

value: BALB/c

tag: gender

value: male

value: primary alveolar epithelial cells

tag: genotype

value: wild type for PGLYRP4

tag: infection

value: Streptococcus pneumoniae


title: smoker 188, genotype

value: black

value: smoker, 17.5 pack-years


title: wt AEC, uninfected, rep1

description:
uninf wt
primary alveolar epithelial cells from male BALB/c mice

source_name: wt AEC, uninfected

value: uninfected


title: 6489493_B: 1161

source_name: buffy coat of cystic fibrosis (CF) patient

tag: subject identifier

tag: tissue

value: PBMC

tag: diagnosis

value: cystic fibrosis (CF)


title: smoker 159, genotype

value: smoker, 3.8 pack-years


title: smoker 155, genotype

value: smoker, 7.6 pack-years


title: smoker 169, genotype

value: smoker, 47 pack-years


title: smoker 152, genotype

value: M

value: smoker, 16 pack-years


title: smoker 161, genotype

value: smoker, 5 pack-years


title: smoker 164, genotype

value: smoker, 44.3 pack-years


title: Ucp2+/+ (WT) sample2

source_name: Ucp2+/+ (WT) sample2

value: Colon tumors

value: WT


title: PGLYRP4KO AEC, Streptococcus pneumoniae, rep1

description:
inf KO
primary alveolar epithelial cells from male BALB/c mice

source_name: PGLYRP4KO AEC, Streptococcus pneumoniae

value: BALB/c

value: male

value: primary alveolar epithelial cells

value: knockout for PGLYRP4


title: small airways, smoker 141, genotype

value: hispanic

value: smoker, 13 pack-years


title: PGLYRP4KO AEC, uninfected, rep1

description:
uninf KO
primary alveolar epithelial cells from male BALB/c mice

source_name: PGLYRP4KO AEC, uninfected

value: uninfected


title: small airways, smoker 136, genotype

value: smoker, 26 pack-years


title: small airways, smoker 186, genotype

value: black

value: smoker, 38 pack-years


title: smoker 177, genotype


title: smoker 134, genotype

value: F

value: white

value: smoker, 20 pack-years


title: smoker 120, genotype

value: M

value: smoker, 30 pack-years


title: small airways, smoker 122, genotype

value: smoker, 3 pack-years


title: smoker 123, genotype

value: smoker, 22.5 pack-years


title: GR-IA1_shGR_D1

tag: lentiviral treatment

value: shGR

tag: treatment

value: dex

tag: ip antibody


title: smoker 129, genotype

value: smoker, 11 pack-years


title: smoker 119, genotype

value: smoker, 33 pack-years


title: smoker 098, genotype

value: smoker, 36 pack-years


title: smoker 130, genotype

value: smoker, 12 pack-years


title: smoker 095, genotype

value: smoker, 32 pack-years


title: smoker 114, genotype

value: smoker, 22 pack-years


title: smoker 094, genotype

value: black

value: smoker, 45 pack-years


title: smoker 093, genotype

value: smoker, 29 pack-years


title: HASMC TGFB1 input

city: New Haven

first: Michael

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

institute: Yale University

data_processing:
ChIP-seq reads were aligned to human reference genome GRCh38 (build 38) using bwa-mem.
deepTools (version 3.0.0) was used to convert bam files to bigwig files (default options)
The matrices were then computed and used for creating average profiles and signal visualization around promoter region of -5/+5kb and bin size of 25
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated using deepTools bamCoverage function ; the output represents normalized coverage file.

source_name: primary cells

growth_protocol: HUVECs (passage 5–10; CC-2517, Lonza) were cultured in endothelial basal medium-2, supplemented with the EGM-2MV BulletKit (CC-3202, Lonza). HASMC (#C-007-5C Thermofiher Scientific) were cultured in M231 (#231-500, Thermofisher Scientific), supplemented with the SMGS (S-007-25, Thermofisher Scientific).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP DNA samples was used in a 23.3 μl combined end repair and A-tailing reaction using a KAPA Hyper Prep Kit (Kapa Biosciences) for 30 minutes at 20°C followed by 30 minutes at 65°C. 10 μl of ligase buffer, 3.7 μl of Adapters and 3.3 μl ligase (KAPA Hyper Prep Kit) were added and incubated at 20°C for 4 hours. Double-stranded DNA fragments were purified from this reaction using KAPA Pure Beads (Kapa Biosciences) and eluted in 22 μl 10 mM Tris pH8.0. Libraries were generated by PCR and size-selected on a 2% E-Gel EX agarose gel (Invitrogen) and fragments between 150 and 400 bp were extracted using a QIAEX II Gel Extraction Kit (Qiagen) performed at room temperature.

treatment_protocol: TGFb1 (0.5 ug/ml) every day

tag: cell type

value: HASMC (Human Aortic Smooth Muscle Cells)

tag: passages

tag: chip antibody

value: TGFB1 input control


title: small airways, smoker 087, genotype

tag: Age

value: M

value: hispanic


title: HASMC PBS input

value: PBS input control


title: HASMC TGFB1 Smad2

value: Smad2/3 (Cell Signaling 8685), Smad2/3 (R&D AF3797)

value: Treated with TGFB1


title: smoker 102, genotype

tag: Sex

value: F

value: white


title: smoker 103, genotype

tag: Ethnic group

value: smoker, 15 pack-years


title: small airways, smoker 069, genotype

tag: Smoking status

value: smoker, 70 pack-years


title: smoker 063, genotype

value: smoker, 47 pack-years


title: smoker 074, genotype

value: smoker, 20 pack-years


title: small airways, smoker 183, genotype

value: smoker, 38 pack-years


title: HASMC TGFB1 Pol II S2

value: RNA pol II CTD phospho Ser2 (Active Motif 61083)


title: HASMC TGFB1 Pol II S5

value: RNA pol II CTD phospho Ser5 (Active Motif 39749)


title: HASMC PBS Smad2

value: Treated with PBS


title: HASMC PBS Pol II S2

value: HASMC (Human Aortic Smooth Muscle Cells)


title: smoker 049, genotype

value: black

value: smoker, 18 pack-years


title: smoker 057, genotype

value: M

value: smoker, 24 pack-years


title: HASMC PBS Pol II S5


title: smoker 048, genotype

value: smoker, 37 pack-years


title: smoker 044, genotype

value: smoker, 25 pack-years


title: smoker 041, genotype


title: HUVEC PBS input

value: HUVEC (human umbilical endothelial cells)

value: PBS input control


title: HUVEC TGFB1 Smad2

value: Smad2/3 (Cell Signaling 8685), Smad2/3 (R&D AF3797)

value: Treated with TGFB1


title: HUVEC TGFB1 Pol II S5


title: HUVEC PBS Smad2


title: HUVEC TGFB1 input

value: TGFB1 input control


title: HUVEC TGFB1 Pol II S2


title: HUVEC PBS Pol II S5


title: small airways, smoker 027, genotype

value: white

value: smoker, 45 pack-years


title: small airways, smoker 033, genotype

value: smoker, 15 pack-years


title: smoker 001, genotype

value: F

value: smoker, 23 pack-years


title: smoker 040, genotype


title: non-smoker 094, genotype

value: non-smoker


title: non-smoker 085, genotype


title: non-smoker 078, genotype


title: non-smoker 083, genotype

value: black


title: Activated Macrophage treated with TGFb1 1

description: Primary cell types and treatment condition

data_processing:
RNA-Seq reads were aligned to the human reference genome (human genome build 38 GRCh38) using short reads aligner STAR
Quantification of gene expression was performed using RSEM with GENCODE annotation (human release 27)
Genes with 1 count per million in less than 10% of samples were removed
Read counts were normalized using the trimmed mean of M-values method (TMM) and differentially expressed genes were identified (edgeR R package)
Macrophage comparisons were batch corrected using ComBat (sva R package) to remove the effects of sequencing at different times
Differentially expressed genes with a false discovery corrected p-value <= 0.05 were used for further analysis (heatmaps and functional enrichment).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated using deepTools bamCoverage function ; the output represents normalized coverage file.

source_name: Activated Macrophage

growth_protocol: Total CD4+ T lymphocytes were purified from PBMCs using Dynabeads CD4 Positive Isolation Kit (Invitrogen) per the manufacturer’s protocol. To obtain the resting TEM subset, naive T cells, central memory T cells, and activated TEM were depleted from the purified total CD4+ populations using antibodies against human CD45RA (eBioscience, HI100), CCR7 (Biolegend, clone G043H7), CD62L (eBiosicence, clone DREG56), and HLA-DR (clone LB3.1), followed by removal of antibody-bound cells by magnetic separation using Dynabeads Pan Mouse IgG (Invitrogen). The isolated populations were routinely greater than 95% CD45RA–CCR7–CD62L–HLA-DR–CD45RO+CD4+ TEM lymphocytes. TEM were then cultured in RPMI 1640 media (Gibco) with 10% FBS, 2% L-glutamine, penicillin (100 U/ml), and streptomycin (100 μg/ml), thereafter referred to as complete RPMI media.

extract_protocol: RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Freshly isolated CD4+ TEM were resuspended in complete RPMI media at the concentration of 1 million cells/mL, and were activated with Dynabeads Human T-Activator CD3/CD28 (Gibco) per manufacturer’s instructions. Fresh TGF-β (5ng/mL, company) or vehicle control were added to the CD4+ TEM on Day 0, Day 1, Day 2, and Day 3 of culture. On Day 3, CD4+ TEM were collected for RNA isolation.

value: Activated Macrophage


title: Activated Macrophage treated with PBS 2

value: PBS


title: small airways, non-smoker 076, genotype

value: M

value: hispanic


title: non-smoker 072, genotype


title: non-smoker 071, genotype


title: Activated Macrophage treated with PBS 1


title: non-smoker 055, genotype


title: non-smoker 059, genotype


title: CD4+ effector memory T cells treated with TGFb1 1

source_name: CD4+ effector memory T cells

value: CD4+ effector memory T cells


title: non-smoker 065, genotype


title: CD4+ effector memory T cells treated with PBS 1


title: smooth muscle cells treated with TGFb1 2

source_name: smooth muscle cells (HASMC)

value: smooth muscle cells (HASMC)


title: Activated Macrophage treated with TGFb1 2


title: CD4+ effector memory T cells treated with PBS 2


title: non-smoker 047, genotype


title: CD4+ effector memory T cells treated with TGFb1 2


title: HUVEC PBS Pol II S2

value: HUVEC (human umbilical endothelial cells)

value: RNA pol II CTD phospho Ser2 (Active Motif 61083)

value: Treated with PBS


title: smooth muscle cells treated with PBS 1


title: small airways, non-smoker 050, genotype


title: smooth muscle cells treated with PBS 2


title: non-smoker 046, genotype


title: non-smoker 066, genotype


title: smooth muscle cells treated with TGFb1 1


title: endothelial cells treated with TGFb1 2

source_name: endothelial cells (HUVEC)

value: endothelial cells (HUVEC)


title: non-smoker 045, genotype


title: endothelial cells treated with TGFb1 1


title: non-smoker 042, genotype


title: non-smoker 039, genotype

value: white


title: small airways, non-smoker 036, genotype


title: non-smoker 044, genotype


title: MFI_post_PV (MFI.Post.2567)

address: AVDA. PIO XII, 55, LAB 1.04

institute: CIMA, Universidad de Nacarra

data_processing: Using the minfi R package available through Bioconductor

extract_protocol: genomic DNA from PBCs was extracted using QIAmp DNA Mini Kit following the manufacturer´s instructions (Qiagen, Hilden, Germany).

tag: disease state

value: myelofibrosis (MF)

tag: status

value: MFI post-PV

value: Granulocytes from peripheral blood

tag: jak2 v617f

value: YES


title: ATRX-deleted BJ rep2

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

data_processing:
Following standard quality control and adapter removal, the sequences were mapped to human genome (hg19 from UCSC genome browser) using Bowtie2 software package (version 2.3.0)
All reads with mapping quality lower than 30 were excluded from downstream analysis. Picard software package (version 2.1.0) was used to remove presumptive PCR duplicates. The total number of mapped reads after the filtering process was designated as the library size and used for normalization.
For telomere read analysis, the maximum number of times of consecutive appearance of telomere sequence (TTAGGG or the reverse complement CCCTAA) with exact match was counted
Genome_build: hg19 from UCSC genome browser
Supplementary_files_format_and_content: excel files include the telomere reads that contain indicated consecutive telomeric repeat numbers.

source_name: Fibroblast

growth_protocol: The wild-type and ATRX-depleted cells were maintained in Dulbecco’s modified Eagle’s media (DMEM) containing 10% FBS, 100 IU/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
ATAC-seq sample extraction was performed following the standard protocols (Buenrostro et al., 2013).
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols.

value: Skin

tag: age

value: newborn

tag: genotype

value: ATRX deletion


title: non-smoker 029, genotype

value: black

value: non-smoker


title: WT BJ rep2

tag: tissue

value: wild type


title: ATRX-deleted BJ rep1


title: WT BJ rep1


title: small airways, non-smoker 022, genotype

value: M


title: ATRX-deleted IMR90-Day 20  rep1

value: Lung

value: 16 weeks gestation


title: endothelial cells treated with PBS 1

value: PBS


title: non-smoker 034, genotype


title: endothelial cells treated with PBS 2


title: ATRX-deleted IMR90-Day 20  rep2


title: small airways, non-smoker 021, genotype

value: hispanic


title: ATRX-deleted IMR90-Day 10  rep2


title: non-smoker 035, genotype


title: non-smoker 019, genotype

value: F


title: ET189 [methylation]

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System

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

label: biotin/DNP

source_name: Human Tumor

label_protocol: standard Illumina protocol

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

tag: subject status

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

tag: subset

value: C19MC balanced

tag: sample type

value: Frozen


title: non-smoker 014, genotype

value: white


title: non-smoker 015, genotype


title: WT IMR90 rep2


title: ET187 [methylation]

value: C19MC amplified


title: ET185 [methylation]


title: ET184 [methylation]


title: WT IMR90 rep1


title: dox.ib2.3: Doxo+I-BET151-rep3

city: Grattan St.

first: Gretchen

last: Poortinga

state: Victoria

department: Division of Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina’s bcl2fastq (v2.17.1.14) software was used to demultiplex data and convert BCL files to FASTQ files and all subsequent analyses were performed in Galaxy
Adapters were trimmed using Trimmomatic (v0.36.4) with the settings Perform ILLUMINACLIP with TruSeq3 paired-end, HEADCROP 12, SLIDINGWINDOW, MINLEN 20, and then filtered with the Remove sequencing artifacts tool (v 1.0.1)
Reads were mapped to the human reference genome (hg38) (genome_snp_tran) using HISAT2 (v2.1.0), with the settings stranded forward, --pen-noncansplice 3, --pen-canintronlen Constant
Read counting was performed using featureCounts part of the subread v1.6.0 software package with the settings for stranded forward and using featureCounts built-in RefSeq hg38 annotation
The Galaxy limma-voom workflow (v3.34.9.4) was applied for data normalisation and differential gene expression analysis, where lowly expressed genes were filtered prior to differential expression analysis by requiring a cpm of 1.5 in at least 3 samples
Genome_build: hg38
Supplementary_files_format_and_content: tsv file includes normalised counts for each sample

molecule: polyA RNA

source_name: MV4-11 cell line

growth_protocol: MV4-11 cells were cultured in RPMI-1640 media supplemented with 20% FBS, GlutaMax (4mM L-alanyl-L-glutamine) and 1% antibiotic/antimycotic solution at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA isolation kit (Macherey-Nagel) as per manufacturer's instructions.
RNA libraries were prepared for sequencing according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen).

treatment_protocol: MV4-11 cells were treated with vehicle (DMSO and NaH2PO4, pH 4.5), CX-5461 (250 nM),  I-BET151 (500 nM) or the combination for 6 hours or with 1 μM doxorubicin for 2 hours, all in triplicate. As an additional control, we also treated cells with 1 μM doxorubicin combined with 500 nM I-BET151 for 2 hours.

value: MV4-11 cell line

tag: replicate

value: replicate 3

tag: treatment

value: 1 μM doxorubicin, 500 nM I-BET151

tag: timepoint

value: 2 hr


title: non-smoker 011, genotype

value: non-smoker


title: non-smoker 008, genotype


title: ET183 [methylation]


title: dox2.3: Doxo-rep3

value: 1 μM doxorubicin


title: ET182 [methylation]


title: non-smoker 006, genotype

value: M

value: black


title: ET181 [methylation]


title: ET188 [methylation]


title: non-smoker 013, genotype

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method. CHP files were created from CEL files after running BRLMM_p.

tag: sex

tag: ethnic group

value: Hispanic

tag: smoking status


title: non-smoker 060_090, genotype


title: non-smoker 023, genotype


title: cx.ib6.3: COMBO-rep3

value: 6 hr


title: ET180 [methylation]


title: non-smoker 005, genotype

tag: Age

tag: Sex

tag: Ethnic group


title: smoker 023, genotype

value: smoker, 20 pack-years


title: smoker 058, genotype

value: smoker, 80 pack-years


title: non-smoker 004, genotype

tag: Smoking status


title: smoker 240, genotype

value: F

value: smoker, 56.5 pack-years


title: ET178 [methylation]

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

value: Frozen


title: ET177 [methylation]

value: C19MC amplified


title: ET173 [methylation]

value: C19MC balanced

value: FFPE


title: cx6.3: CX-5461-rep3

value: MV4-11 cell line

value: replicate 3


title: ET172 [methylation]


title: ET179 [methylation]


title: ET171 [methylation]


title: ib6.3: I-BET151-rep3


title: non-smoker 001, genotype

value: non-smoker


title: non-smoker 003, genotype


title: v6.3: Veh-rep3

value: Vehicle


title: dox2.2: Doxo-rep2

value: replicate 2

value: 1 μM doxorubicin

value: 2 hr


title: ET168 [methylation]


title: non-smoker 002, genotype

value: M

value: white


title: ET169 [methylation]


title: ET170 [methylation]


title: dox.ib2.2: Doxo+I-BET151-rep2

value: 1 μM doxorubicin, 500 nM I-BET151


title: ET167 [methylation]


title: non-smoker 059_089, genotype

value: F

value: black


title: smoker 002, genotype

value: smoker, 21 pack-years


title: smoker 125, genotype

value: smoker, 19 pack-years


title: ET165 [methylation]

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

value: C19MC amplified

value: Frozen


title: cx.ib6.2: COMBO-rep2

value: MV4-11 cell line

value: 6 hr


title: ib6.2: I-BET151-rep2


title: ET146 [methylation]

value: FFPE


title: ET147 [methylation]


title: ET145 [methylation]


title: cx6.2: CX-5461-rep2


title: ET144 [methylation]


title: ET143 [methylation]


title: ET142 [methylation]


title: v6.2: Veh-rep2

value: Vehicle


title: ET139 [methylation]


title: ET166 [methylation]


title: ET140 [methylation]


title: dox.ib2.1: Doxo+I-BET151-rep1

value: replicate 1


title: ET141 [methylation]


title: cx.ib6.1: COMBO-rep1


title: ET137 [methylation]


title: ET138 [methylation]


title: ET136 [methylation]


title: dox2.1: Doxo-rep1

value: 1 μM doxorubicin


title: ib6.1: I-BET151-rep1


title: ET134 [methylation]

value: C19MC balanced


title: ET159

hyb_protocol: Affymetrix Human Genome U133 Plus 2.0 according to the manufacturers protocol

data_processing: MAS 5.0 normalization

label: Biotin

extract_protocol: Qiagen RNeasy mini kit

tag: tumor stage

value: Primary tumor


title: ET84R1

scan_protocol: Affymetrix Human Genome U133 Plus 2.0 according to the manufacturers protocol

value: Relapse


title: ET85

label_protocol: Affymetrix Human Genome U133 Plus 2.0 according to the manufacturers protocol


title: ET108


title: cx6.1: CX-5461-rep1


title: ET160


title: ET83


title: ET132 [methylation]


title: ET133 [methylation]


title: ET131 [methylation]


title: ET130 [methylation]


title: v6.1: Veh-rep1


title: ET127 [methylation]


title: ET126 [methylation]


title: ET128 [methylation]


title: ET129 [methylation]


title: ET135 [methylation]


title: ET125 [methylation]


title: Cryba1 cKO-5 Months

first: Sayan

last: Ghosh

address: 4401 Penn Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
Hopkins-Stepichva_S10
Hopkins-Stepichva_S16

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 8 -u -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G mm10refseq.gtf)
FPKM calulcation done using cufflinks v2.2.0 using annotation from RefSeq assembly mm10 p5 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.0
Genome_build: GRCm38/mm10 Assembly  (UCSC tophat version as downloaded February 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: Cryba1 cKO 5 Mo

growth_protocol: RPE cells harvested

extract_protocol:
RPE cells harvested from mice by disection
Approximately 900 ng total RNA was used to perform RNA-sequencing
Kapa Stranded mRNA-Seq, Illumina

treatment_protocol: Aged as mentioned

tag: strain background

tag: genotype/variation

value: Cryba1 cKO

tag: age

value: 5 months

value: Retinal Pigment Epithelium (RPE)


title: Cryba1 cKO-10 Months

description:
Hopkins-Stepichva_S14
Hopkins-Stepichva_S19

source_name: Cryba1 cKO 10 Mo

value: 10 months

tag: tissue


title: ET124 [methylation]

tag: subject status

tag: subset


title: ET86


title: ET84


title: ET79


title: ET123 [methylation]

tag: sample type


title: ET82


title: ET68


title: Cryba1-floxed (WT)-5 Months

description:
Hopkins-Stepichva_S3
Hopkins-Stepichva_S12

source_name: WT 5 Mo

value: Cryba1-floxed (WT)


title: ET72

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient


title: ET121 [methylation]

value: C19MC amplified


title: ET66


title: ET120 [methylation]


title: Cryba1-floxed (WT)-10 Months

description:
Hopkins-Stepichva_S7
Hopkins-Stepichva_S9

source_name: WT 10 Mo


title: ET122 [methylation]


title: ET113 [methylation]


title: ET117 [methylation]


title: ET118 [methylation]


title: ET115 [methylation]


title: ET112 [methylation]


title: uninduced control 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: control w/o dox-treatment

data_processing:
Basecalls performed using RTA 1.18.64
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
ChIP-seq reads were aligned to the hg19 genome assembly using BWA-MEM (v 0.7.15) with default parameters
peaks were called using MACS2 (v 2.1.1.20160309) with the following setting: -g hs --nomodel --extsize 250 -q 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generated using MACS2  (v 2.1.1.20160309); colums represent chromosome; start; end; name; score; strand; signalValue; -log10 pvalue; -log10 qvalue; peak

source_name: colorectal adenocarcinoma cell line

growth_protocol: 5x10^6 cells were seeded in 15 cm dishes and grown for 48 h in DMEM + 10% fetal calf serum + 10 mM Hepes + 1% MEM non-essential amino acids (v/v) + 1% penicillin/streptomycin (v/v).

extract_protocol:
For immunoprecipitation, aliquots of 200 µg crosslinked chromatin were used. Each aliquot was filled up to 200 µl with nuclei lysis buffer and then diluted with sonication buffer to a final volume of 1 ml. Magnetic Protein-G beads, preblocked for at least 4 h with 250 µg/ml BSA, and the appropriate antibody (listed in 4.10.1) were added to the diluted chromatin. The samples were incubated on a rotating platform at 4°C overnight. The next day, beads were collected by using a magnetic rack. Beads were washed two times with sonication buffer, two times with buffer A, two times with buffer B and two times with TE buffer. Each time, 1 ml of buffer was used for washing and the samples were incubated for 10 min on a rotating platform at 4°C. After the last washing step, bound material was eluted from the beads in two sequential rounds by adding 150 µl elution buffer and incubating each time at 67°C for 10 min with continuous shaking. The two eluates were combined, 10 µg RNAse and 90 µMol NaCl added and the mix was incubated for 5 h at 67°C with gentle agitation to reverse the crosslinks, followed by addition of 80 µg Proteinase K and incubation for 1 h at 45°C. For the input sample, used as reference material, 20% of the initial chromatin was filled up to 300 µl with elution buffer and processed like the immunoprecipitated sample. DNA was purified using the Qiagen PCR Purification Kit or PeqGold Cycle Pure Kit and stored at -20°C until needed.
DNA libraries were prepared for 50 bp single-end sequencing on an Illumina HiSeq2000 system using standard Illumina protocols.

treatment_protocol: Cells were treated with 0.1 mg/ml doxycycline for 6h to induce Snail1-HA expression. Control cells were left untreated. Cells were corsslinked with formaldehyde (+MeOH) at a final concentratin of 1% for 5 min at room temperature. Crosslinking was stopped by the addition of glycine at a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with ice-cold PBS, cells were scraped off and transferred to a 15 ml tube. Cells were centrifuged for 5 min at 300 x g at 4°C, supernatant was removed and the pellet was washed with ice-cold PBS and centrifuged again for 5 min at 300 x g at 4°C. After centrifugation, supernatant was removed and pellets were stored at -80°C for chromatin preparation. Pellets were resuspended in 10 ml NP-40 lysis buffer with complete protease inhibitor and incubated on ice for 10 min. Pellets were resuspended in 10 ml NP-40 lysis buffer with complete protease inhibitor and incubated on ice for 10 min and mechanically disrupted by 50 strokes with a dounce homogenizer. Nuclei were pelleted by centrifugation for 5 min at 4 500 x g at 4°C, resuspended in an appropriate volume of nuclei lysis buffer supplemented with 1% SDS and incubated on ice for at least 10 min. To shear the chromatin to approximately 100-550 bp fragments, lysates were sonicated for 12 min in a Covaris S220 device (Covaris, Woburn, USA) with the following settings: peak incident power 150 watt, duty factor 10%, cycles/burst 200. After shearing, lysates were cleared from cellular debris by centrifugation for 10 min at 16 000 x g at 4°C and the chromatin concentration was measured using a NanoDrop 2000 device (Thermo Fisher Scientific, Dreieich, Germany).

tag: cell type

value: pN1-LS174T Snail1-HA cells

tag: chip antibody

value: abcam anti-HA (ChIP-grade) ab9110


title: ET36


title: ET111 [methylation]


title: ET119 [methylation]


title: ET31


title: ET30


title: uninduced control 1

description: control w/o dox-treatment


title: ET108_R1 [methylation]

value: Frozen


title: ET109 [methylation]

value: FFPE


title: ET116 [methylation]


title: ET106 [methylation]


title: Snail1-HA ChIP-seq 1

description: 6h dox-treatment


title: Snail1-HA ChIP-seq 2

description: 6h dox-treatment


title: ET107 [methylation]


title: ET56


title: ET20


title: ET19


title: ATRX-deleted IMR90-Day 10  rep1

value: Lung

value: 16 weeks gestation

tag: genotype

value: ATRX deletion


title: ET57

value: C19MC balanced


title: ET104 [methylation]


title: ET103 [methylation]


title: ET105 [methylation]


title: 15T145_D

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

data_processing:
Read files were quality-checked with FastQC.
Adapter sequences were removed with cutadapt v1.11 and only those reads longer than 15bp and shorter than 35bp were kept for further analysis.
Reads were aligned to the human genome (GRCh37/hg19) with Bowtie 1.0.0 and Samtools 0.1.18 allowing no mismatches and a maximum of 1 alignment per read.
Raw counts for miRNAs were obtained with HTSeq v0.5.3p9, using the miRBase v20 annotation for hg19
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Raw read counts obtained with HTSeq

source_name: Papillary thyroid carcinoma

extract_protocol:
Tissues were fresh frozen in OCT. RNA was harvested using Trizol reagent.
2µg of total RNA samples were used and  were processed with kit "NEXTflex Illumina Small RNA Sequencing Kit v3" (Bioo Scientific catalog# 5132) by following manufacturer instructions. Briefly, samples were sequentially ligated to randomized 3' and 5' adapters, with a truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with a MMuLV Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by 14 cycles of PCR. Amplified products were either purified by double-sided SPRI selection of by PAGE extraction, according to their BioAnalyzer size profile. Pooled purified fractions were applied to an Illumina flow cell for cluster generation, and sequenced on an Illumina HiSeq2000 by following manufacturer's protocols. Sequencing read ends contain a variable length of the 3' adapter, whose sequence is nnnnTGGAATTCTCGGGTGCCAAGG. As a consequence of the use of adapters with random tetramers, both the first four bases of the read and the four bases at the beginning of the 3' adapter are noninformative. Following 3' adapter trimming, those first and last four bases of the read were trimmed too.

value: Primary tumor

tag: disease

value: Papillary thyroid carcinoma


title: 15T145_I


title: ET16

value: Relapse


title: ET110 [methylation]


title: ET102 [methylation]


title: ET101 [methylation]


title: ET100 [methylation]


title: ET99 [methylation]


title: ET12


title: ET98 [methylation]


title: 15T144


title: ET97 [methylation]


title: ET96 [methylation]


title: 15T137

source_name: Follicular thyroid carcinoma

value: Follicular thyroid carcinoma


title: 15T136


title: ET92 [methylation]


title: 15T133


title: ET93 [methylation]


title: ET94 [methylation]


title: ET95 [methylation]


title: ET91 [methylation]


title: ET87 [methylation]


title: ET89 [methylation]


title: ET86 [methylation]


title: 15T143


title: 15T132


title: 15T129


title: 15T131


title: ET18


title: ET1


title: ET83 [methylation]


title: 15T128


title: ET88 [methylation]


title: ET1R1


title: ET77_R1 [methylation]


title: ET1R2

value: Secondary Relapse


title: ET77 [methylation]


title: ET77_R2 [methylation]


title: ET2


title: 15T125


title: alveolar macrophages, smoker 186

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: alveolar macrophages obtained from bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: sex

value: M

tag: ethnic group

value: black

tag: smoking status

value: smoker, 38 pack-years


title: alveolar macrophages, smoker 049

value: F

value: smoker, 23 pack-years


title: ET33

value: Embryonal Tumor/Multilayered Rosettes (ETMR) patient

value: C19MC amplified


title: alveolar macrophages, smoker 240

value: smoker, 56.5 pack-years


title: 15T120


title: ET85 [methylation]

value: Frozen


title: 12T40

source_name: Follicular adenoma

value: Follicular adenoma


title: 15T114


title: ET74_R1 [methylation]

value: FFPE


title: ET75 [methylation]


title: ET76 [methylation]


title: ET74 [methylation]

value: C19MC balanced


title: ET79 [methylation]


title: 15T127

value: Primary tumor


title: ET73_R1 [methylation]


title: ET73 [methylation]


title: 12T35

value: Papillary thyroid carcinoma


title: ET79_R2 [methylation]


title: ET72 [methylation]


title: ET79_R1 [methylation]


title: 12T34


title: ET69 [methylation]


title: ET68 [methylation]


title: ET67 [methylation]


title: ET68_R2 [methylation]


title: ET66 [methylation]


title: ET70 [methylation]


title: 12T32

source_name: Poorly differentiated thyroid carcinoma

value: Poorly differentiated thyroid carcinoma


title: 12T20

value: Follicular thyroid carcinoma


title: ET65 [methylation]


title: 12T27


title: 12T178_2

value: Metastasis_Lymph node


title: ET64 [methylation]


title: ET63 [methylation]


title: ET62 [methylation]


title: ET61 [methylation]


title: 12T178_1


title: ET59 [methylation]


title: ET60 [methylation]


title: 05T220


title: ET57 [methylation]


title: 05T212


title: ET55 [methylation]


title: 05T209


title: ET54 [methylation]


title: 05T205

source_name: Anaplastic thyroid carcinoma

value: Anaplastic thyroid carcinoma


title: ET52 [methylation]


title: ET58 [methylation]


title: ET53 [methylation]


title: ET56 [methylation]


title: ET71 [methylation]


title: ET49_R1 [methylation]


title: ET50 [methylation]


title: ET49 [methylation]


title: 05T153


title: 04T307

source_name: Normal thyroid

value: Thyroid

value: Normal thyroid


title: 04T305


title: ET48 [methylation]


title: ET47 [methylation]


title: ET45 [methylation]


title: ET44 [methylation]


title: ET43 [methylation]


title: ET43_R1 [methylation]


title: 04T172B


title: ET41 [methylation]


title: 04T144


title: 04T143


title: ET42 [methylation]


title: ET40_R1 [methylation]


title: ET51 [methylation]


title: ET38 [methylation]


title: ET37 [methylation]


title: ET36 [methylation]


title: 04T141


title: ET35 [methylation]


title: ET33 [methylation]


title: 04T139


title: ET34 [methylation]


title: ET32 [methylation]


title: ET46 [methylation]


title: 04T140


title: ET31 [methylation]


title: 04T131


title: ET30 [methylation]


title: 04T301


title: 04T249


title: ET29 [methylation]


title: ET42_R1 [methylation]


title: ET114 [methylation]


title: ET28 [methylation]


title: 04T111


title: 04T109


title: ET39 [methylation]


title: ET25 [methylation]


title: 04T108


title: ET26 [methylation]


title: ET24 [methylation]


title: ET23 [methylation]


title: ET21 [methylation]


title: 04T106


title: 04T138


title: ET20 [methylation]


title: 04T102


title: ET18 [methylation]


title: ET17 [methylation]


title: 04T099


title: ET16_R1 [methylation]


title: 04T103


title: ET19 [methylation]