title: 13/99_CA

tag: age group


title: ChIP_Late_2C_H3K36me3_rep1

status: Public on May 01 2019

type: SRA

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

description:
processed data file:
Late_2C_H3K36me3.bed.gz

library_source: genomic

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

molecule: genomic DNA

organism: Mus musculus

source_name: embryo

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h.

tag: tissue

value: embryo

tag: developmental stage

tag: chip antibody

value: H3K36me3 (Active Motif, Cat.61021)


title: ChIP_MII_H3K36me3_rep2

description:
processed data file:
MII_H3K36me3.bed.gz

source_name: oocyte

value: oocyte

value: MII


title: ChIP_MII_H3K36me3_rep1


title: 13/96_CA

type: RNA

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.

hyb_protocol: Standard Illumina hybridization protocol. Hybridization performed in AROS (Denmark) http://arosab.com/services/microarrays/gene-expression/ .

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalised using lumi library in R 2.15.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Crohn’s disease, adult

label_protocol: Standard Illumina labeling protocol.

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

tag: condition

value: Crohn's disease

value: adult

value: whole blood


title: ChIP_1C_H3K36me3_rep1

description:
processed data file:
1C_H3K36me3.bed.gz


title: 2/121_WY

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.

source_name: Ulcerative colitis, child

value: ulcerative colitis

value: child


title: ATAC_THP1_24hrPMA_rep1

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2212 Garland Ave.

department: Biochemistry

country: USA

institute: Vanderbilt University

description: ATAC-seq of THP1 Monocytes: 24hrs 162nM PMA treatment

data_processing:
Trimming: All sequencing library reads were trimmed of adapters using TrimGalore script wrapper for Cutadapt (Martin, 2011) and FastQC. Version: trim_galore 0.4.0. Command: trim_galore --fastqc --fastqc_args "--outdir ${FASTQC_DIR}" --clip_R1 9 --clip_R2 9 --paired --retain_unpaired --output_dir ${TRIM_DIR} ${R1} ${R2}
Mapping: Standard ATAC reads were mapped with bowtie2. Version: bowtie2 2.2.6. Command: bowtie2 -p 8 --no-discordant --no-mixed -X 1000 -x ${INDEX} -1 ${R1} -2 ${R2} -S ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All bisulfite converted samples were mapped with WALT. Version: WALT v1.0. Command: walt -m 8 -t 6 -i ${INDEX} -1 ${R1} -2 ${R2} -o ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All RNA-seq reads were mapped with STAR. Version: STAR_2.6.1a. Command: STAR --runThreadN 4 --genomeDir /data/hodges_lab/human_genome/GRCh38_Gencode24 --sjdbGTFfile /data/hodges_lab/human_genome/GRCh38_Gencode24/gencode.v24.primary_assembly.annotation.gtf --readFilesCommand zcat --readFilesIn --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
ATAC peak calling: All peak calling was done with MACS2. Version: MACS2 2.1.1. Command: macs2 callpeak -t ${MAPPED_DIR}/${MAPPED}.shifted.bam -f BAMPE -n ${MACS_DIR}/${MAPPED} -g hs -q 0.005 -B --SPMR --keep-dup all --broad --broad-cutoff 0.005
DNA methylation analysis: The Methpipe suite of tools was used for all CpG methylation analysis. Version: Methpipe 3.4.3
Differential RNA-seq analysis: DESeq2 was use to calculate differential RNA expression across the time course. Version: DESeq2 1.18.1. R-Version: 3.4.3
Differential ATAC-seq analysis: TCseq was used to calculate differential chromatin accessibility across the time course. Version: 1.6.1. R-version: 3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are broadPeak output bed files from MACS2, meth files are a tab delimited text file of CpG methylation values for all symmetic CpGs in hg19, meth files are generated as output from Methpipe
Supplementary_files_format_and_content: DEseq2 normalized transcript abundance table

source_name: THP-1 Monocyte

growth_protocol: THP1 monocytes were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 units penicillin/streptomycin and 1mM sodium pyruvate. During routine culture THP1 cells were maintained at a density of 0.5-2E6 cells/mL. All cells were regularly screened for mycoplasma contamination using the Lonza MycoAlert kit.

extract_protocol: THP1 cell suspension volume corresponding to 2E5 cells was pelleted in a 1.5mL tube at 4°C, 500 R.C.F for 5 minutes. Supernatant was aspirated and the pellet resuspended in 150µL cold ATAC lysis buffer (10mM Tris-HCl pH = 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL-630). This suspension was agitated by pipetting up/down with a 200µL micropipette tip 8 times. Subsequently, this suspension was pelleted at 4°C, 500 R.C.F for 10 minutes. Supernatant was discarded and pellet immediately resuspended in 190µL transposition reaction mix (10mM Tris-HCl pH=7.5, 5mM MgCl2, 10% Dimethylformamide) by pipetting up/down with a 200µL micropipette tip 3 times. After resuspension 10µL of pre-assembled Tn5 transposome was added. Tube was flicked gently to mix all components and incubated at 37°C, 30 minutes, 700RPM in an Eppendorf Thermomixer. Immediately after the 30-minute incubation ATAC reactions were terminated by adding 1mL Zymo DNA binding buffer and vortexing. This binding buffer and ATAC reaction mixture was purified according to manufacturer instruction in the Zymo DNA Clean and Concentrator-5 kit. Final elution was in 12.5µL nuclease free H2O. Libraries were barcoded and amplified with 8 cycles of PCR amplification

treatment_protocol: Differentiation of THP1 monocytes was induced with RPMI medium carrying PMA at a concentration of 100ng/mL (162nM). THP1 monocyte PMA stimulation time points were harvested with a combination of aspiration (for suspended cells) and trypsin (for adherent cells). The final collection of each time point was pelleted at 4°C, 500 R.C.F for 5 minutes. After pelleting cells were resuspended in ice cold PBS and cell counted using an automated cell counter (Biorad). This cell suspension was divided as input material for RNA extraction, genomic DNA extraction and ATAC reactions.

tag: pma stimulation time point

value: 24 hr


title: ATAC_THP1_0hrPMA_rep1

description: ATAC-seq of THP1 Monocytes: 0hrs 162nM PMA treatment

value: 0 hr


title: ChIP_FGO_H3K36me3_rep1

description:
processed data file:
FGO_H3K36me3.bed.gz

value: FGO


title: Salmeterol 0.3 nM + RNO-treated rep4

city: Calgary

first: Radhika

last: Joshi

state: Alberta

address: 2500 UNIVERSITY DR NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

library_source: transcriptomic

data_processing:
Basecalls were performed using RTA v2
demultiplexing FASTQ conversion was performed using bcl2fastq v2.18.0.12
Sequenced reads were mapped to the reference human transcriptome (GRCh37/hg19) and quantified using Kallisto with 100 bootstraps per sample
Differential expression analysis was performed using the R package Sleuth and transcripts per million (TPM) values were calculated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes transcripts per million (TPM) values for each sample for each gene described by its HGNC symbol

source_name: BEAS-2B Cells

growth_protocol: BEAS-2B cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10 % Canada origin FBS, L-glutamine (2.5 mM) and NaHCO3 (0.15 % w/v) followed by overnight incubation in serum-free medium.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) and quantified using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE) according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional kit (New England Biolabs Inc., Ipswich, MA) with the poly(A) mRNA magnetic isolation module according to the manufacturer’s instructions. The prepared libraries were validated using the D1000 Screen Tape assay on an Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA) and quantified by Kapa qPCR Library Quantification kit for Illumina (Kapa Biosystems, Boston, MA).

treatment_protocol: Confluent BEAS-2B cells were treated for two hours with vehicle, RNO (1 µM), a maximal concentration of Salmeterol (100 nM), two sub-maximal concentrations of Salmeterol (0.3 nM and 0.5 nM), and their combination with RNO (Salm0.3 + RNO, Salm0.5 + RNO)

tag: cell type

value: BEAS-2B human airway epithelial cell line

tag: treatment

value: Salmeterol 0.3 nM + RNO


title: 13/91_CA


title: Salmeterol 0.3 nM + RNO-treated rep3


title: 13/101_CA


title: ChIP_GO_P10_H3K36me3_rep2

description:
processed data file:
GO_P10_H3K36me3.bed.gz


title: Ependymal EGF 2

city: Durham

first: Khadar

last: Abdi

state: NC

address: 300 North Duke St.

department: DMPI

institute: Duke University

description: Gene expression data from EGF treated cultures

hyb_protocol: Hybridization of targets were prepared from total RNA using a MessagAmp Premier RNA Amplificaiton Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 7G according to the standard Affymetrix GeneChip manufacturer instructions.

data_processing: Affymetrix Gene Chip microarray data underwent strict quality control processing using the simpleaffy package in the Bioconductor2 suite from the R statistical programming environment. Log-scale Robust Multiarray Analysis (RMA) from the  affy package was used to normalize the data and eliminate systematic differences across the arrays. Differential expression of genes across the conditions was identified from a moderated test statistic employed by the limma package. The False Discovery Rate (FDR) method was used to correct for multiple hypothesis testing.  Affymetrix Gene Chip microarray data underwent strict quality control processing using the simpleaffy package in the Bioconductor2 suite from the R statistical programming environment. Log-scale Robust Multiarray Analysis (RMA) from the  affy package was used to normalize the data and eliminate systematic differences across the arrays. Differential expression of genes across the conditions was identified from a moderated test statistic employed by the limma package. The False Discovery Rate (FDR) method was used to correct for multiple hypothesis testing. logFc = log2 fold-change.

source_name: ependymal culture MLN4924 treated

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Total RNA was labeled and hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: Ependymal cultures were differentiated from radial glial progenitors and grown in either differentiation media contain DMEM/F12, 2% FBS, penstrep or the same media with EGF included.

extract_protocol: Total RNA was extracted from ependymal cultures using RNA easy minikit (Invitrogen) and cDNA was prepared using Superscript Vilo cDNA synthesis kit (Invitrogen).

treatment_protocol: Cultures were treated with EGF at the point were differentiation media is included. We used 20 ng/ml EGF.

tag: sample type

value: primary culture

value: ependymal cell culture


title: ChIP_GO_P14_H3K36me3_rep1

description:
processed data file:
GO_P14_H3K36me3.bed.gz


title: ChIP_GO_P10_H3K36me3_rep1


title: Ependymal EGF 3


title: 13/90_CA


title: Ependymal EGF 1


title: Ependymal untreated 4

description: Gene expression data from untreated cultures

source_name: ependymal culture DMSO treated


title: Salmeterol 0.3 nM + RNO-treated rep1


title: Ependymal EGF 4


title: 13/89_CA


title: 13/88_CA


title: ChIP_GO_P7_H3K36me3_rep2

description:
processed data file:
GO_P7_H3K36me3.bed.gz


title: Ependymal untreated 3


title: 13/87_CA


title: 13/86_CA


title: Salmeterol 0.3 nM-treated rep4

value: Salmeterol 0.3 nM


title: Salmeterol 0.3 nM + RNO-treated rep2


title: ChIP_GO_P7_H3K36me3_rep1


title: Ependymal untreated 2


title: Salmeterol 0.3 nM-treated rep3


title: 13/82_CA


title: ChIP_GO_P14_H3K36me3_rep2


title: MethylC_FGO_Setd2_KO_5mC_rep1

description:
processed data file:
FGO_Setd2_KO_5mC.bed.gz

data_processing:
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: For STEM-seq, the bedgraph files contains the average DNA methylation level of 2kb bin.

extract_protocol:
The DNA extraction follows STEM-seq protocol
The STEM-seq libraries were generated following the protocol as described previously(Zhang et al., 2018).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG.  Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyts 98h, Germinal vesicle stage

tag: genotype


title: Ependymal untreated 1


title: 13/84_CA


title: 13/79_CA


title: 13/80_CA


title: Salmeterol 0.3 nM-treated rep1


title: MethylC_FGO_Dnmt3l_KO_5mC_rep2

description:
processed data file:
FGO_Dnmt3l_KO_5mC.bed.gz


title: Salmeterol 0.5 nM + RNO-treated rep4

value: Salmeterol 0.5 nM + RNO


title: MethylC_FGO_Setd2_Con_5mC_rep1

description:
processed data file:
FGO_Setd2_Con_5mC.bed.gz


title: Salmeterol 0.5 nM + RNO-treated rep3


title: Salmeterol 0.3 nM-treated rep2


title: MethylC_FGO_Dnmt3l_KO_5mC_rep1


title: MethylC_FGO_Setd2_Con_5mC_rep2


title: MethylC_FGO_Dnmt3l_Con_5mC_rep2

description:
processed data file:
FGO_Dnmt3l_Con_5mC.bed.gz


title: MethylC_FGO_Dnmt3l_Con_5mC_rep1


title: mouse_colon_mucosal_layer-VILCre_MCCf_Sulindac-rep4

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

hyb_protocol: cDNA probes were then hybridized to the Mouse Transcriptome Arrays 1.0 as per the manufacturer’s instructions (Affymetrix Ca, USA) at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia).

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using the AffymetrixPowerTools apt-probeset-summarize software (version 1.16.1) (using the -a rma option)

label: Biotin

source_name: Colon Mucosal Cells_VILcreMccf/f (MccΔIEC)_Sulindac

label_protocol: Total RNA was converted to cDNA. The cDNA was biotin labeled at the Ramaciotti Centre for Genomics at the University of New South Wales (UNSW, Sydney, Australia), following manufacturers instructions.

growth_protocol: Homozygous Mcc-loxP (Mccf/f) mice were generated and designated B6.Cg-Mcc<tm1Maija>/Ausb. These were crossed with mice carrying the Villin-cre transgene (B6.SJL-Tg(vil-cre)997Gum/J) to produce colon/intestinal cell specific Mcc knockout mice, VILcreMccf/f (MccΔIEC) and the sibling controls Mccf/f.

extract_protocol: Total RNA was isolated using Qiagen RNeasy mini (Qiagen GmbH, Germany) and measured on the 2100 Bioanalyzer (Agilent).

treatment_protocol: Six-week old mice were given a diet containing 320 ppm sulindac or control feed for 10 weeks. Mice were culled and the mucosal layer was harvested and snap-frozen for RNA extraction. For the sulindac-treated mice, the mucosa was only harvested from areas of inflammation in the proximal colon. For control-fed mice the matching normal tissue was harvested.

tag: strain background

tag: genotype/variation

value: VILcreMccf/f (Mcc VILCre KO)

tag: gender

value: male

tag: age

value: 6 wks

tag: diet

value: containing 320 ppm sulindac for 10 wks

value: inflamed colon mucosa

value: Colon Mucosal Cells


title: 2/46_CY

source_name: Crohn’s disease, child

value: Crohn's disease

value: whole blood


title: mouse_colon_mucosal_layer-VILCre_MCCf_Sulindac-rep3


title: mouse_colon_mucosal_layer-VILCre_MCCf_Sulindac-rep2


title: 13/78_CA

value: adult


title: 2/44_CY

value: child


title: mouse_colon_mucosal_layer-VILCre_MCCf_control-rep2

source_name: Colon Mucosal Cells_VILcreMccf/f (MccΔIEC)_control

value: control for 10 wks

value: normal colon mucosa


title: mouse_colon_mucosal_layer-VILCre_MCCf_Sulindac-rep1


title: 2/47_CY


title: Salmeterol 0.5 nM-treated rep4

value: BEAS-2B human airway epithelial cell line

value: Salmeterol 0.5 nM


title: 2/31_CY


title: mouse_colon_mucosal_layer-VILCre_MCCf_control-rep3


title: 2/32_CY


title: RNA_1C(48h)_Setd2_KO_RNA_rep1

description:
processed data file:
Setd2_KO_RNA_FPKM.txt.gz

data_processing:
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The RNA FPKM txt file contains FPKM value for each sample.

extract_protocol: The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stage (GV) oocytes were harvested at 48 h after PMSG. For D7, D10, D14 oocytes, corresponding postnatal female mouse were sacrificed and oocytes were harvested in M2.

value: embryo


title: mouse_colon_mucosal_layer-WT_MCCf_Sulindac-rep1

source_name: Colon Mucosal Cells_WT Mcc_Sulindac treated

value: controls Mccf/f


title: RNA_1C(48h)_Setd2_KO_RNA_rep2


title: Salmeterol 0.5 nM-treated rep3


title: 2/45_CY


title: mouse_colon_mucosal_layer-WT_MCCf_Sulindac-rep2


title: Salmeterol 0.5 nM + RNO-treated rep2

value: Salmeterol 0.5 nM + RNO


title: mouse_colon_mucosal_layer-WT_MCCf_Sulindac-rep3


title: mouse_colon_mucosal_layer-VILCre_MCCf_control-rep1

value: VILcreMccf/f (Mcc VILCre KO)


title: 13/76_CA


title: Salmeterol 0.5 nM-treated rep2


title: Salmeterol 0.5 nM-treated rep1


title: RNA_2C(48h)_Setd2_Con_RNA_rep1


title: RNA_2C(48h)_Setd2_Con_RNA_rep2


title: Salmeterol 100 nM-treated rep4

value: Salmeterol 100 nM


title: Salmeterol 100 nM-treated rep3


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep6

source_name: Colon Mucosal Cells_WT Mcc_control

value: male

value: 6 wks


title: RNA_1C_Setd2_KO_RNA_rep1


title: 2/116_CY


title: RNA_1C_Setd2_Con_RNA_rep2


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep5


title: 2/29_CY


title: RNA_1C_Setd2_Con_RNA_rep1


title: 8/68_PBC

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.

source_name: Primary biliary cholangitis, adult

value: primary biliary cholangitis


title: Salmeterol 100 nM-treated rep1


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep4

value: Colon Mucosal Cells


title: RNO-treated rep4

value: Roflumilast N-oxide (RNO)


title: SQH-A317-3

city: Detroit

first: Jessica

middle: Renee

last: Blount

state: MI

address: 540 E. Canfield, 3108 Scott Hall

department: Pharmacology

institute: Wayne State School of Medicine

data_processing:
Libraries were quantified on the Qubit and Agilent 2200 Tapestation using the DNA High Sensitivity Screen tape. The barcoded libraries were multiplexed at equimolar concentrations and sequenced with 50 bp reads in rapid mode on an Illumina HiSeq 2500.
Data was demultiplexed using Illumina's CASAVA 1.8.2 software
Reads were aligned to the Drosophila genome (Build dm3) and tabulated for each gene region
Differential gene expression analysis was used to compare transcriptome changes between conditions. Significantly altered genes (fold change ≥ 2; FDR ≤ 0.05) were used to identify affected pathways
Genome_build: dm3

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: All fly crosses were maintained in 25 degree, diurnal incubators

extract_protocol:
Whole flies were frozen in groups of 10 to extract all RNA on the same day. RNA was harvested using Trizol.
Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina)  was utilized for building RNA-seq libraries from 250 ng of total RNA in 5 µl of nuclease-free ultrapure water.

treatment_protocol: Ub6 transgene expression was driven by sqh-Gal4; all Ub6 flies were heterozygous for transgene and driver

value: 1 day old

tag: driver

value: Control

tag: insertion site


title: RNA_FGO_Setd2_KO_RNA_rep2

value: oocyte

value: FGO


title: Salmeterol 100 nM-treated rep2


title: SQH-A317-2


title: RNO-treated rep3


title: RNA_1C_Setd2_KO_RNA_rep2


title: 8/55_PBC

tag: age group

value: adult

value: whole blood


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep3

value: control for 10 wks

tag: tissue

value: normal colon mucosa


title: 11//27_K

description: RNA expression levels in the blood of control patient.

source_name: Control, adult

value: control


title: 11//26_K


title: SQH-A317-4


title: 11//16_K


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep2

value: controls Mccf/f


title: 11//30_K


title: RNA_FGO_Setd2_KO_RNA_rep1

tag: developmental stage


title: SQH-A317-1


title: 11/37_K


title: RNO-treated rep2

value: BEAS-2B human airway epithelial cell line


title: RNO-treated rep1


title: RNA_FGO_Setd2_Con_RNA_rep1


title: RNA_FGO_Setd2_Con_RNA_rep2


title: Vehicle-treated rep4

value: Vehicle


title: SQH-Stop-3


title: SQH-Stop-2


title: mouse_colon_mucosal_layer-WT_MCCf_control-rep1

value: male


title: SQH-Stop-1


title: Donor_1_d1

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

country: France

institute: INSERM

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1).
Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: purified Vgd1

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

tag: subject id

value: purified TCRVdelta 1 gammadelta T lymphocytes

tag: cmv status

value: CMV+


title: Donor_1_d2

source_name: purified Vgd2

value: purified TCRVdelta 2 gammadelta T lymphocytes


title: Vehicle-treated rep2


title: TM D3_B04

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via Vincenzo Vela 6

department: Molecular Immunology

country: Switzerland

institute: Institute For Research in Biomedicine

description: Sample 8

data_processing:
Sequencing was carried out on an Illumina HiSeq 3000
reads were aligned to hg19 human reference genome using Bismark v0.16.1 (PMID: 21493656 )
Genome-wide methylation call report was obtained using Bismark methylation extractor
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab delimited methylation file with .cov2cyt_detected.txt extension. Each  line has 6 fields: chromosome - start and end position - covering methylated reads - covering  unmethylated reads - CpG context type and actual CpG sequence.

source_name: Memory T lymphocyte_stimulated

growth_protocol:
sample preparation: Human perferal blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec).Memory T cell subsets were then sorted based on the expression of the following surface markers:  CD4+CD25–CD45RA–CCR7+/–
Primary human T lymphocytes were isolated from human periferal blood mononuclear cells and were either left resting or were stimulated for 3 days with anti-CD3 and anti-CD28 antibodies
sample preparation:

extract_protocol:
Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen)
Premium RRBS Kit (Diagenode)

treatment_protocol: Memory T lymphocytes were stimulated for 3 days with anti-CD3 and anti-CD28 antibodies prior to genomic DNA extraction

value: primary T lymphocytes derived from human periferal blood mononuclear cells (PBMC)

value: Memory T lymphocyte

tag: cell status

value: stimulated for 3 days with anti-CD3 and anti-CD28 antibodies.


title: Vehicle-treated rep3

tag: cell type


title: 2//19_PBC

tag: condition

value: primary biliary cholangitis


title: 2//10_PBC


title: 10/36_K


title: SQH-GG-4

value: 1 day old


title: SQH-Stop-4


title: Vehicle-treated rep1

tag: treatment


title: 11/38_K

value: adult


title: SQH-GG-3


title: TM D0_B03

description: Sample 7

source_name: Memory T lymphocyte_resting

treatment_protocol: Resting memory T lymphocytes collected after isolation and directly used for genomic DNA extraction

value: resting


title: SQH-GG-2


title: TN D3_B02

description: Sample 6

source_name: Naïve T lymophocyte_stimulated

growth_protocol:
sample preparation: Human perferal blood mononuclear cells were separated from peripheral blood using Ficoll-Paque Plus (GE Healthcare). CD4+ T lymphocytes were further isolated by positive selection using magnetic microbeads (Miltenyi Biotec). Naive T cell subsets were then sorted based on the expression of the following surface markers: CD4+CD25–CD45RA+CCR7+.
Primary human T lymphocytes were isolated from human periferal blood mononuclear cells and were either left resting or were stimulated for 3 days with anti-CD3 and anti-CD28 antibodies
sample preparation:

treatment_protocol: Naïve T lymphocytes stimulated for 3 days with anti-CD3 and anti-CD28 antibodies prior to genomic DNA extraction

value: Naive T lymophocyte


title: k562_6h_C [SLAMseq]

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: treated

data_processing:
library strategy: SLAMseq (Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA)
reads were processed with the slam dunk pipeline (https://github.com/t- neumann/slamdunk 0.3.3.). The reads were aligned to the human genome GRCh38.
Genome_build: hg38
Supplementary_files_format_and_content: CPMs transcript quantifications for coding genes  were  generated by slamdunk pipeline all the 3’UTRs from a single genes were collapse into one single entry per 3’UTR (similar to the exons->gene relationship in a gtf-file) with the collapse tool of slamdunk.mdunk pipeline

growth_protocol: IMDM media with10% FBS,  with 2mM L-Glutamine, penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
SLAMseq Kinetics Kit - Catabolic Kinetics Module
QuantSeq 3’mRNA-seq library

treatment_protocol: 100uM 4sU feed 24h, then wash out 100uM 4sU for mRNA decay

tag: cell line

tag: passages

tag: time point


title: 8//13_K

value: whole blood


title: TN D0_B01

description: Sample 5

source_name: Naïve T lymophocyte_resting

treatment_protocol: Resting naïve T lymphocytes collected after isolation and directly used for genomic DNA extraction


title: k562_6h_B [SLAMseq]

description: treated


title: SQH-GG-1

tag: genotype/variation


title: TM D0_A11

description: Sample 3


title: TM D3_A12

description: Sample 4


title: k562_4h_C [SLAMseq]

description: treated


title: k562_6h_A [SLAMseq]

description: treated


title: k562_4h_B [SLAMseq]

description: treated


title: 10//21_K

value: control


title: TN D3_A10

description: Sample 2


title: k562_4h_A [SLAMseq]

description: treated


title: k562_2h_C [SLAMseq]

description: treated


title: TN D0_A09

description: Sample 1


title: 8//15_K


title: k562_2h_B [SLAMseq]

description: treated


title: 12/375_PSC

description: RNA expression levels in the blood of patient diagnosed with primary sclerosing cholangitis.

source_name: Primary sclerosing cholangitis, adult

value: primary sclerosing cholangitis


title: FACS_H-ag_No1

city: Kyoto

first: Mototsugu

last: Eiraku

state: Kyoto

address: 53 Shougoin Kawahara-chou Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Basecalls were performed using illumina RTA software (version 1.18.64) and reads were de-multiplexed using bclfastq (version 1.8.4).
Quality check of the reads was performs using FastQC (version 0.11.5).
Ascertaining the high quality of sequencing, reads were mapped to mm10 mouse genome assembly using HISAT (version 2.0.4) with default parameter settings.
Number of reads originating from genes were quantified by cuffdiff program in Cufflinks package (version 2.1.1). These count values were subsequently used to test for differential expression using edgeR (version 3.16.2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including total read counts for all samples

source_name: mESC-derived limb bud organoid

growth_protocol: mESCs maintained in LIF+2i conditioned medium. 3000 cells of mESC reaggregated in for each well of 96-well low-cell-adhesion plate and incubated in differentiation medium with BMP4 and matrigel from day 1 to 5. For forelimb differentiation, ES-aggregates cultivated in retinoic acids (RA) including medium on days 5-6. For hindlimb differentiation, ES-aggregates cultivated in RA antagonist including medium on days 6-6.5. These aggregates were self-differentiated into limb bud organoids which comprised of Hand2::GFP positive mesenchyme coverd by epidermis layer in serum-free medium with step-wise addition of BMP inhibitor (LDN193189) and Wnt3 on days 7-9.

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (Qiagen). Libraries were prepared using 600 ng of total RNA, according to the TruSeq Stranded mRNA LT Sample Prep Kit (illumina).

treatment_protocol: At day 9, to obtain a single–cell suspension, forelimb and hindlimb organoid were trypsinized and filtrated 40 µm nylon mesh cell strainer. Hand2::GFP positive mesenchyme was sorted by using FACS from whole limb organoids cell suspension.

tag: age

value: Day 9

tag: strain

value: EB5 Hand2::GFP +/-

value: mouse ES cells-derived hindlimb bud mesenchyme


title: FACS_H-ag_No3


title: 12/336_PSC


title: k562_0h_B [SLAMseq]

description: treated


title: k562_0h_C [SLAMseq]

description: treated


title: FACS_H-ag_No2


title: 12/218_PSC


title: k562_0h_A [SLAMseq]

description: treated


title: FACS_F-ag_No2

value: mouse ES cells-derived forelimb bud mesenchyme


title: FACS_F-ag_No1


title: 12//18_PSC


title: 12//4_PSC


title: LB_H_10.5_3

source_name: embryonic tissue

value: hindlimb bud


title: FACS_F-ag_No3


title: 12/137_PSC


title: 12/213_PSC


title: 11/33_K


title: 12/332_PSC


title: k562_2h_A [SLAMseq]

description: treated


title: LB_H_10.5_1


title: 12/361_PSC


title: 12/376_PSC


title: K562_ORFome_infected_5h_B

data_processing:
The ORF-ome reads were trimmed using cutadapt 1.16 to keep only the barcode sequence; the resulting trimmed reads were mapped to the ORF-ome barcodes using salmon 0.9.1.
Genome_build: specific orf-ome library
Supplementary_files_format_and_content: TPM quantifications for each orf-ome barcode, the corresponding open reading frame associated with each barcode sequence is given in the ORF_Sequence column.
Supplementary_files_format_and_content: ORFome_Ids.csv contains the barcode information related to the ORFome.

growth_protocol: IMDM media with 10% FBS for k562, DMEM with 10% FBS for 293t, with 2mM L-Glutamine, penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
RNA extract with Direct-zol RNA Kits, elute in 50ul H20
illumina RNA-seq libray construction with specific adaptors after ribo depletion

treatment_protocol: puromycin selection for ORFome postive cells 1 week. Actinomycin D to detect mRNA decay,

value: ORFome infected

value: Actinomycin D (5ug/ml)


title: K562_ORFome_infected_6h_B


title: LB_H_10_3


title: K562_ORFome_infected_5h_A


title: 12/379_PSC


title: ref6 ChBS-Input2-rep2

first: Xiaofeng

last: Cao

address: No.1 West Beichen Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description:
Bisulfite-treated genomic DNA
library strategy: ChIP-Bisulfite-Seq

data_processing:
Bases calling was performed with RTA (Real Time Analysis) software version 1.18.64.
ChIP-Bisulfite sequencing reads were both mapped to the TAIR10 genome with BS-seeker2 with the setting "-m 2", allowing two mismatches.
The methylation level of each base site covering at least four reads were computed as the ratio #C/(#C+#T).
Then the enriched regions of ChIP-Bisulfite-Seq were searched using MACS2 with the input of bisulfite reads mapping position information.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig(bw)

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: All Arabidopsis materials were grown on half-strength Murashige and Skoog (MS) medium with 1% sucrose at 22°C under long day conditions (LD, 16 hours light, 8 hours dark), and 10-day-old seedlings were used for ChIP-Seq experiments.

extract_protocol:
Chromatin immunoprecipitation with REF6 antibody was performed with Col, ddcc and ref6-5. 20ng DNA was used for ChIP-BS-seq.
Libraries were constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) together with methylated adaptor (NEB, #E7535S). After adaptor ligation, DNA was treated with bisulfite solution according to EpiTect Fast DNA Bisulfite Kit (QIAGEN, #59824). 0.2 ng λDNA was added to detect bisulfite treatment efficiency.

value: 10-day-old seedlings

tag: ecotype

value: Columbia

value: seedling

tag: genotype

tag: antibody

value: anti-REF6 antibody


title: LB_H_10_2

tag: tissue


title: ddcc REF6-ChBS-rep2

tag: developmental stage

value: drm1-2; drm2-2; cmt2-7; cmt3-11 quadruple mutant


title: K562_ORFome_infected_4h_A


title: K562_ORFome_infected_6h_A


title: 12/296_PSC

tag: age group

value: adult


title: 12/377_PSC


title: 12/315_PSC


title: K562_ORFome_infected_3h_B


title: WT REF6-ChBS-rep2

value: Col


title: 2//18_PBC

value: primary biliary cholangitis

value: whole blood


title: LB_F_10.5_2

value: forelimb bud


title: K562_ORFome_infected_3h_A


title: ref6 ChBS-Input1-rep1


title: LB_H_10_1


title: ddcc REF6-ChBS-rep1


title: K562_ORFome_infected_2h_B


title: K562_ORFome_infected_4h_B


title: LB_F_10.5_1


title: LB_H_10.5_2


title: 2//4_PBC


title: Salmeterol 0.5 nM + RNO-treated rep1

source_name: BEAS-2B Cells

value: BEAS-2B human airway epithelial cell line

value: Salmeterol 0.5 nM + RNO


title: WT REF6-ChBS-rep1


title: K562_ORFome_infected_2h_A


title: LB_F_10.5_3


title: ref6_REF6_ChIPSeq_rep3

data_processing:
Bases calling was performed with RTA (Real Time Analysis) software version 1.18.64.
Paired-end sequencing reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using Bowtie2 (version 2.2.8) in local alignment mode.
Multiple mapping reads, unmated reads and mate reads which map too far apart (> 4x fragment length) for paired-end reads, were excluded for downstream analysis.
In order to avoid double counting in overlapping regions for paired-end data, the first read mate was used to calculate normalized genome coverage tracks by deepTools2 (--normalizeTo1x 1.19e8 --extendReads * --binSize 1) after extending ChIP-seq reads to the average estimated fragment length, disregarding the second read mate.
ChIP-seq peaks were called using MACS2 (v 2.1.1) with the “--gsize 1.19e8 --keep-dup 1” option. Peaks were annotated to the gene with the closest TSS by ChIPseeker.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig(bw)

extract_protocol:
Chromatin Immunoprecipitation (ChIP) assays were performed using 3 g 10-day-old seedlings as previously described with minor modifications (Cui, X. et al., 2016, Nat Genet 48, 694-9). Antibody used in ChIP was anti-REF6 antibody. 1-2 ng DNA was used for ChIP-seq.
Libraries were constructed with the NEXTflex Rapid DNA-seq Prep Kit for Illumina Sequencing (BIOO Scientific, #5144-03) according to the manufacturer's protocol.


title: met1_REF6_ChIPSeq_rep2


title: K562_ORFome_infected_1h_B


title: K562_ORFome_infected_1h_A


title: ref6_REF6_ChIPSeq_rep2


title: K562_ORFome_infected_0h_B

value: untreated


title: Tailbud_No3

value: tail bud


title: LB_F_10_1


title: 2//24_PBC


title: 2/45_PBC


title: 2/47_PBC


title: met1_REF6_ChIPSeq_rep1


title: 2/60_PBC


title: 2//26_PBC


title: K562_ORFome_infected_0h_A


title: LB_F_10_3


title: Col_REF6_ChIPSeq_rep2


title: Tailbud_No1


title: 293_ORFome_infected_6h_B


title: ddcc_REF6_ChIPSeq_rep2


title: Ca_No3

value: cardiac


title: Tailbud_No2


title: LB_F_10_2


title: ref6_REF6_ChIPSeq_rep1

data_processing:
Bases calling was performed with RTA (Real Time Analysis) software version 1.18.64.
Paired-end sequencing reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using Bowtie2 (version 2.2.8) in local alignment mode.
Multiple mapping reads, unmated reads, and mated reads that mapped too far apart (> 4 X fragment length) for paired-end reads were excluded for downstream analysis. In order to avoid double counting in overlapping regions for paired-end data, the first read mate was used to calculate normalized genome coverage tracks by deepTools2 (--normalizeTo1x 1.19e8 --extendReads * --binSize 1) after extending ChIP-seq reads to the average estimated fragment length, disregarding the second read mate.
ChIP-seq peaks were called using MACS2 (v 2.1.1) with the “--gsize 1.19e8 --keep-dup 1” option. Peaks were annotated to the gene with the closest TSS by ChIPseeker.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig(bw)

source_name: seedlings


title: 5/37_PBC


title: 2//9_PBC


title: 293_ORFome_infected_5h_B

value: ORFome infected


title: 5/41_PBC


title: 293_ORFome_infected_6h_A

value: Actinomycin D (5ug/ml)


title: 5//23_PBC


title: 293_ORFome_infected_5h_A


title: Col_REF6_ChIPSeq_rep1

value: 10-day-old seedlings


title: 5//24_PBC


title: Ca_No1


title: 5/38_PBC


title: 5/32_PBC


title: 293_ORFome_infected_4h_B


title: 293_ORFome_infected_4h_A


title: BA_No2

value: branchial arch


title: BA_No3


title: Ca_No2


title: BA_No1


title: ddcc_REF6_ChIPSeq_rep1

value: Columbia

value: seedling


title: 293_ORFome_infected_3h_B


title: 293_ORFome_infected_2h_B


title: M28ΔRD2 (1)

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description:
RD2 deletion mutant derivative of MGAS6180
rRNA-depleted total RNA
processed data file: Processed_datasheet_6.xls

data_processing:
CLC Genomics Workbench version 7.5.1 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS315 genome.
Parameters for alignment were set up: Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using Kal’s Z-test with a false-discovery rate correction.
Genome_build: MGAS6180 genome (CP000056.1)
Supplementary_files_format_and_content: Processed_datasheet_6.xls: Excel file containing columns for the gene name (Feature ID), Kal's Z-test with FDR correction value, normalized means of expression values for each strain, gene start nucleotide number, gene stop nucleotide number, and expression ratios.

organism: Streptococcus pyogenes

growth_protocol: GAS strains were grown in THY broth to the exponential phase of growth (an O.D.600 of 0.5).

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the Ribo-Zero Gram-Positive rRNA Removal Kit (Epicentre).
The rRNA-depleted RNA was used to generate cDNA libraries using the ScriptSeq kit (Epicentre). Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end. A limited number of PCR cycles (n=12) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp). The size-selected and barcoded libraries were run on an Illumina HiSeq flowcell.

tag: strain/background

value: RD2 deletion mutant

tag: growth phase

value: Exponential

tag: media

value: THY broth


title: M28ΔRD2 (2)


title: 293_ORFome_infected_2h_A


title: 293_ORFome_infected_1h_B


title: MGAS6180 (1)

description:
Parental M28 GAS isolate
rRNA-depleted total RNA
processed data file: Processed_datasheet_6.xls

value: Parental


title: 293_ORFome_infected_3h_A


title: MGAS6180 (2)


title: Mt1-mmp(-/-) macrophage_IL4 treated_biological rep2

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description: Gene expression data from Mt1-mmp(-/-) macrophages stimulated with IL4

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse ST 2.1 strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.1.1. RMA was used to fit log2 transformed expression values.

source_name: macrophages polarized with IL4

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: bone marrow cells were cultured in alpha-MEM with 10% heat-inactivated fetal bovine serum (HI-FBS), 1% penicillin-streptomycin solution (ThermoFisher), and 10 ng/mL M-CSF (R&D Systems) overnight on tissue culture dishes. Nonadherent cells were plated onto non-tissue culture-treated dishes in media with M-CSF for an additional 5-7 days; media was replaced every 48 hours.

extract_protocol: RNA was isolated from macrophages using the NucleoSpin RNA kit (Macherey Nagel) as instructed.

treatment_protocol: bone marrow derived macrophages were treated with control media, 1ug/ml LPS or 20ng/ml IL-4 for 24 hours, rinsed with PBS twice before the addition of extraction buffer (NucleoSpin RNA kit--Macerey Nagel)

tag: cell type

value: bone marrow derived macrophage

tag: background strain

value: Swiss Black


title: Mt1-mmp(-/-) macrophage_IL4 treated_biological rep1


title: 13/118_WA

description: RNA expression levels in the blood of patient diagnosed with ulcerative colitis.

data_processing: Quantile normalised using lumi library in R 2.15.

source_name: Ulcerative colitis, adult

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

tag: condition

value: ulcerative colitis

value: adult

value: whole blood


title: 293_ORFome_infected_1h_A

tag: cell line

tag: passages

tag: treatment


title: 5/36_PBC

source_name: Primary biliary cholangitis, adult

value: primary biliary cholangitis


title: dbp2∆2-RNA Pol II ChIP

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

institute: Purdue University

data_processing:
Illumina adaptors were removed using Trimmomatic (version 0.36)
The processed reads were mapped to the S288C reference genome (R64-2-1, from Saccharomyces Genome Database) using Bowtie 2 (v 2.3.3.1)
Peaks of RNA Pol II were then determined by MACS2 (v 2.1.2)
The fold enrichment of each peak over the background signal was calculated using the ‘bdgcmp’ function in MACS2 and presented as normalized RNA Pol II occupancy
Genome_build: S288C reference genome (R64-2-1, from Saccharomyces Genome Database)
Supplementary_files_format_and_content: Peak files gererated by MACS2

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: dbp2 mutant yeast cells

growth_protocol: Yeast cells were grown in YP with 2% glucose at 30 °C to an O.D. of 0.5~0.7

extract_protocol:
3XFLAG-tagged RNA Pol II was immunoprecipitated using anti-FLAG M2 antibody and DNAs were purified after reverse crosslinking, proteinase K, and RNase treatment.
Libraries were prepared using NEXTflex ChIP-Seq Kit according to the manufacter's instuction.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 min at 25 °C with vigorous shaking. The reaction was stopped with 250 mM glycine. Cells were then cryo-lyzed and sonicated.

value: MATa dbp2::KanMx6 his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

tag: genotype/variation

value: dbp2 mutant


title: Mt1-mmp(+/+) macrophage_IL4 treated_biological rep2

description: Gene expression data from Mt1-mmp(+/+) macrophages stimulated with IL4


title: 13/66_WA


title: dbp2∆3-RNA Pol II ChIP

tag: strain


title: 13/65_WA


title: Mt1-mmp(+/+) macrophage_IL4 treated_biological rep1


title: Mt1-mmp(-/-) macrophage_LPS treated_biological rep2

description: Gene expression data from Mt1-mmp(-/-) macrophages stimulated with LPS

source_name: macrophages polarized with LPS


title: 5//9_PBC


title: 13/103_WA


title: Mt1-mmp(+/+) macrophage_LPS treated_biological rep2

description: Gene expression data from Mt1-mmp(+/+) macrophages stimulated with LPS


title: Mt1-mmp(-/-) macrophage_LPS treated_biological rep1


title: Mt1-mmp(+/+) macrophage_LPS treated_biological rep1


title: 13/50_WA


title: 13/39_WA


title: 293_ORFome_infected_0h_A

value: ORFome infected

value: untreated


title: dbp2∆3-input


title: dbp2∆1-RNA Pol II ChIP


title: rpe_6h_B

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18
Reads were aligned to UCSC genome hg38 with TopHat v2.0.13 , with “–library-type fr-firststrand” , using qiw gene models.
FPKM values were generated using Cufflinks v2.2.1 with “-u –max-bundle-frags 100000000”.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values for each gene and sample

growth_protocol: DMEM with 10% FBS for all, with 2mM L-Glutamine, penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
RNA extract with Direct-zol RNA Kits, elute in 50ul Dnase/Rnase free H2O
illumina RNA-seq libray construction standard protocol, with ribo depletion.

treatment_protocol: Actinomycin D to detect mRNA decay

value: RPE

value: wild type

value: 5ug/ml Actinomycin D


title: 293_ORFome_infected_0h_B


title: rpe_6h_A


title: rpe_5h_A


title: dbp2∆2-input


title: 13/36_WA


title: rpe_4h_A


title: dbp2∆1-input


title: 13/38_WA


title: Mt1-mmp(-/-) macrophage_untreated_biological rep2

description: Gene expression data from control Mt1-mmp(-/-) macrophages

source_name: macrophages in control media


title: WT3-RNA Pol II ChIP

source_name: wild-type yeast cells

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: wild-type


title: 13/35_WA


title: Mt1-mmp(-/-) macrophage_untreated_biological rep1


title: Mt1-mmp(+/+) macrophage_untreated_biological rep1

description: Gene expression data from control Mt1-mmp(+/+) macrophages


title: 13/28_WA


title: rpe_2h_A


title: WT2-RNA Pol II ChIP


title: WT3-input


title: WT2-input


title: rpe_0h_B


title: rpe_1h_A


title: WT1-RNA Pol II ChIP


title: WT1-input


title: 93A_Air_ctrl

city: Helsinki

first: Harri

last: Alenius

address: Haartmaninkatu 3

department: Human Microbiome Program

country: Finland

institute: University of Helsinki

description: Exposed for 1h to nanoparticle aerosol, incubated for 24h

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

source_name: Bronchial epithelium

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: MucilAir™ fully diﬀerentiated bronchial epithelial models (Epithelix Sárl, Geneva, Switzerland), reconstituted from primary human cells of healthy or asthmatic donors, were used. The cells were maintained on 24-well Transwell® culture supports at an air-liquid interface using MucilAir™ culture medium, supplemented with 1% amphotericin and 0.5% gentamicin, in a humidiﬁed incubator at 37 °C with 5% CO2.

extract_protocol: Cells were stabilized for another 24 h with 0.7 ml MucilAir culture medium at the basal site in a humidiﬁed incubator (ca. 37 °C, 5% CO2) after exposures. Total RNA was isolated from cell lysates with RNeasy Plus Mini Kit according to manufacturer's instructions (Qiagen, GmbH, Hilden, Germany). Desalting of the samples was required and thus, additional purification was performed by ethanol precipitation with 3M sodium acetate (Thermo Fisher Scientific Inc., Wilmington, NC, USA)

treatment_protocol: Prior to performing the experiments, the MucilAir™ cells were stabilized in culture for at least one week, while the medium was refreshed every 2–3 days. The basolateral culture medium was refreshed approximately 24 h before exposure. The MucilAir™ cells were rinsed with saline solution (0.9% NaCl,1.25 mM CaCl2 and 10 mM HEPES buﬀer) approximately 24 h before and again just before exposure to ensure that each individual model contained a mucus layer of comparable thickness. Right before exposure, the inserts were transferred to the exposure device. The stainless-steel wells of the exposure device contained MucilAir culture medium to feed the cell monolayer from the basal side during a 1-hour exposure.

tag: donor

value: G

value: Asthmatic

tag: nanoparticle

value: Air

tag: dose

value: 0 mg/m3

tag: dose description

value: control air

tag: time

value: 1 hour aerosolization + 24 hours incubation


title: 94A_CuO_COOH_m

value: E

value: mid


title: hela_6h_A

value: Hela


title: 90A_CuO_COOH_h

value: H

value: high


title: 13/14_WA

value: ulcerative colitis

tag: age group

value: adult

tag: tissue

value: whole blood


title: 91H_CuO_COOH_m

value: C

value: Healthy


title: 13//9_WA


title: 13/13_WA


title: hela_6h_B

value: wild type

value: 5ug/ml Actinomycin D


title: 13//4_WA


title: 85A_CuO_COOH_h

value: F

value: Asthmatic


title: rpe_0h_A

value: RPE

value: untreated


title: 84A_CuO_COOH_l

value: low

value: 1 hour aerosolization + 24 hours incubation


title: hela_5h_A


title: 13//6_WA


title: 79H_CuO_l

value: A

value: CuO


title: 82H_CuO_m

value: B

value: mid


title: 2/137_WY

source_name: Ulcerative colitis, child

value: ulcerative colitis

value: child


title: 88H_CuO_COOH_l


title: 2/2_WY

value: whole blood


title: rpe_3h_A


title: hela_4h_A

value: Hela


title: hela_3h_A


title: 13/27_WA

value: adult


title: hela_2h_A

value: wild type


title: hela_1h_A

value: 5ug/ml Actinomycin D


title: 2/106_WY


title: 2/133_WY


title: LKB liver-specific knockout mice treated with saline_B

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

description:
LKBko saline-B
Biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: liver

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: FVB

value: LKB1 lox/lox

tag: agent

value: saline

tag: age

value: 10 wks

tag: gender

value: male

value: liver


title: wild-type mice treated with AICAR_B

description:
WT AICAR-B
Biological replicate 2

value: wild-type

value: AICAR


title: LKB liver-specific knockout mice treated with AICAR_B

description:
LKBko AICAR-B
Biological replicate 2


title: LKB liver-specific knockout mice treated with saline_A

description:
LKBko saline-A
Biological replicate 1


title: 77A_CuO_l

value: D

value: Asthmatic

value: CuO

value: low

value: 1 hour aerosolization + 24 hours incubation


title: LKB liver-specific knockout mice treated with AICAR_A

description:
LKBko AICAR-A
Biological replicate 1


title: hela_0h_B

value: Hela

value: untreated


title: 293t_6h_chx_B

value: wild type

value: Cycloheximide


title: 74A_Air_ctrl

value: F

value: Air

value: 0 mg/m3

value: control air


title: wild-type mice treated with AICAR_A

description:
WT AICAR-A
Biological replicate 1

value: FVB

value: 10 wks

value: male


title: 2/108_WY

value: ulcerative colitis

value: child

value: whole blood


title: 71A_CuO_h

value: D

value: Asthmatic

value: CuO

value: high


title: hela_0h_A

value: Hela

value: untreated


title: 2/9_WY


title: 2/97_WY


title: 2/33_WY


title: wild-type mice treated with saline_B

description:
WT saline-B
Biological replicate 2

value: wild-type

value: saline

value: liver


title: wild-type mice treated with saline_A

description:
WT saline-A
Biological replicate 1


title: 69H_Air_ctrl

value: C

value: Healthy

value: Air

value: 0 mg/m3

value: 1 hour aerosolization + 24 hours incubation


title: 293t_6h_chx_A

value: wild type

value: Cycloheximide


title: 293t_6h_ad_B

value: 5ug/ml Actinomycin D


title: 72A_CuO_m

value: F

value: mid


title: 13/74_CA

description: RNA expression levels in the blood of patient diagnosed with crohn’s disease.

source_name: Crohn’s disease, adult

value: Crohn's disease

value: adult

value: whole blood


title: 75A_CuO_COOH_l

value: G

value: Asthmatic

value: low


title: 293t_6h_ad_A


title: 293t_3h_chx_A


title: 293t_3h_ad_A


title: 68H_CuO_h

value: A

value: CuO

value: high


title: 13/72_CA


title: 293t_1h_chx_A


title: wild-type mice treated with CCL4_B

description:
WT CCL4-B
Biological replicate 2

value: FVB

value: wild-type

value: 10 wks

value: male

value: liver


title: 66A_Air_ctrl

value: E

value: Air

value: 0 mg/m3

value: control air

value: 1 hour aerosolization + 24 hours incubation


title: LKB liver-specific knockout mice treated with CCL4_B

description:
LKBko CCL4-B
Biological replicate 2

value: LKB1 lox/lox


title: 13/64_CA

value: Crohn's disease

value: adult

value: whole blood


title: LKB liver-specific knockout mice treated with CCL4_A

description:
LKBko CCL4-A
Biological replicate 1


title: 13/69_CA


title: 13/67_CA


title: 13/57_CA


title: 293t_1h_ad_A

value: wild type

value: 5ug/ml Actinomycin D


title: 64A_Air_ctrl

value: H

value: Asthmatic


title: 63A_Air_ctrl

value: D


title: 62H_CuO_COOH_h

value: B

value: Healthy

value: high


title: 65A_CuO_m

value: CuO

value: mid


title: wild-type mice treated with CCL4_A

description:
WT CCL4-A
Biological replicate 1

value: FVB

value: wild-type

value: 10 wks

value: male

value: liver


title: LKB liver-specific knockout mice treated with mineral oil_A

description:
LKBko min.oil-A
Biological replicate 1

value: LKB1 lox/lox

value: mineral oil


title: 293t_0h_B

value: wild type

value: untreated


title: 59A_CuO_l

value: E

value: low

value: 1 hour aerosolization + 24 hours incubation


title: wild-type mice treated with mineral oil_A

description:
WT min.oil-A
Biological replicate 1


title: 293t_0h_A


title: LKB liver-specific knockout mice treated with mineral oil_B

description:
LKBko min.oil-B
Biological replicate 2


title: 13/41_CA

value: Crohn's disease

value: adult

value: whole blood


title: Donor2

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description:
Donor #2 stim/restim data
cytoplasmic mRNA

data_processing:
Encode CEL-Seq sample barcode and UMI into R2 read name; Custom Python script; CEL-Seq primers carry a sample barcode and unique molecule identifier (UMI), which is used for removing PCR duplicates.
Align to hg19 genome; tophat v2.0.14; The transcript annotation file contains all RefSeq transcripts with IDs starting with 'NM_', and includes annotation for T cell constant region genes TRAC, TRBC2, TRDC, TRGC1, and TRGC2.
Align to transcripts, PCR duplicate removal, and quantification; ESAT v1.0; ESAT is run in single-cell mode to remove PCR duplicates and separate the samples by sample barcode.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene.txt: Tab-delimited text files; ESAT output (raw transcript counts); Final raw gene expression counts from ESAT with PCR duplicates removed.

source_name: PBMCs

extract_protocol:
CEL-Seq2
CEL-Seq2

tag: cell type

value: Natural killer (NK) cells

tag: nk population

value: mixed sample (non-demultiplexed)


title: 13/34_CA

first: Krzysztof

last: Goryca

institute: Uniwersytet Warszawski

tag: condition


title: 13/52_CA


title: 13/40_CA


title: wild-type mice treated with mineral oil_B

description:
WT min.oil-B
Biological replicate 2

value: FVB


title: Donor1

description:
Donor #1 stim/restim data
cytoplasmic mRNA


title: non-diabetic sample h17181

description:
total RNA
UMICounts.txt
cytoplasmic mRNA

data_processing:
Extract sample reads from multiplexed Illumina sequencing run
custom Python script
Reads were extracted based on multiplexed sample index. Only reads with valid cell barcode and no 'N's in the UMI are extracted. The cell barcode and UMI are appended to the read name as a colon-delimited string.
Align to hg19 genome
tophat v2.0.14
aligned to hg19 with default parameters.
align to transcripts, PCR duplicate removal, and quantification
ESAT v1.0
The transcript annotation file contains all RefSeq transcripts with IDs starting with 'NM_', and includes annotation for T cell constant region genes TRAC, TRBC2, TRDC, TRGC1, and TRGC2.
clean up low-count UMIs
custom Python script
merges single-read UMIs with higher-count UMIs with Hamming distance of 1.
remove cells with fewer than 500 total transcripts
custom R script
Genome_build: hg19
Supplementary_files_format_and_content: rawCounts.txt
Supplementary_files_format_and_content: text file
Supplementary_files_format_and_content: each column contains the total observed transcripts for a cell for each gene specified in the row name.
Supplementary_files_format_and_content: raw transcript counts for single-cell data. All T1D cell column headers begin with h6416_T1D, all non-diabetic cell column headers begin with h17181_ND.

source_name: human pancreatic islet

extract_protocol:
InDrop single-cell protocol
InDrop library protocol, modified CEL-Seq2

value: pancreatic islet


title: 56H_Air_ctrl

value: B

value: Healthy

value: Air

value: 0 mg/m3

value: control air


title: 57H_CuO_l

value: C

value: CuO


title: 13/26_CA


title: T1D sample h6414


title: 58H_Air_ctrl

value: A


title: 13/31_CA


title: 55H_CuO_h

value: high


title: 13//8_CA


title: Localized tumor H3K27ac_2479_T

city: Boston

first: Matthew

last: Freedman

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Patient localized prostate tumor tissue

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: localized  tumor tissue

tag: chip antibody

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat.#

tag: chip antibody lot/batch#

tag: chromosome


title: 13/25_CA

city: Warszawa

address: Banacha 2c

value: Crohn's disease

value: adult


title: Localized normal H3K27ac_2479_N

source_name: Patient localized prostate normal tissue

value: localized  normal tissue


title: 54A_CuO_COOH_l

tag: donor

value: F

value: Asthmatic

tag: nanoparticle

value: low

value: 1 hour aerosolization + 24 hours incubation


title: 13//5_CA

value: whole blood


title: 50A_CuO_h

value: E

tag: dose

tag: dose description


title: 51A_CuO_COOH_m

value: D

value: mid

tag: time


title: 2/112_CY

source_name: Crohn’s disease, child

tag: age group

value: child

tag: tissue


title: 52H_CuO_COOH_m

value: Healthy


title: 2/96_CY


title: 67A_CuO_COOH_h

value: G


title: Localized tumor H3K27ac_2078_T


title: 13//1_CA


title: Localized normal H3K27ac_2078_N


title: Localized tumor AR_1609_T

value: AR

value: Santa Cruz Biotechnology


title: 48A_CuO_COOH_m


title: 47A_Air_ctrl

value: Air

value: 0 mg/m3

value: control air


title: 45H_CuO_l

value: B

value: CuO


title: liver, TrxR1/Gsr-null biological rep4 [TrxR1_Gsr-null_6813]

city: Bozeman

first: Edward

last: Schmidt

state: MT

address: 109 Lewis Hall

institute: Montana State University

description:
TrxR1_Gsr-null_6813
Gene expression data from liver.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16h at 45°C. Washes and staining were performed in a GCOS Fluidics Station 450.

scan_protocol: GeneChips were scanned with an Affymetrix 7G scanner. CEL and CHP files were generated using Affymetrix GCOS v1.4.

data_processing: CEL files were imported into FlexArray v.1.6.2 using GC-RMA pre-processing for analysis.

label_protocol: Ambion MesageAmp II-Biotin Enhanced Kit was used according to the manufacturer's instructions. 1 µg of total RNA was used as initial cDNA synthesis step.

growth_protocol: Not applicable.

extract_protocol: Ambion RiboPure Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Not applicable.

tag: strain/background

tag: genotype/variation

value: liver

value: female

tag: age

value: 4 weeks


title: Localized normal AR_1609_N

value: localized  normal tissue


title: 44H_Air_ctrl

value: 1 hour aerosolization + 24 hours incubation


title: 2/94_CY

value: Crohn's disease

value: whole blood


title: Localized tumor AR_1335_T

value: localized  tumor tissue


title: 2/48_CY

value: child


title: NPC (3) exposed to 10µM BDE-47 for 24h Exp3

type: genomic

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description:
BDE47_10μM_24h_Exp3
3999442105_R03C02

hyb_protocol: Converted DNA was amplified, fragmented and hybridized to Illumina Infinium 450k Bead Array

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

data_processing: BeadStudio software v3.2 and Illumina standard background subtraction and control probe normalization, converted to M values, using the minfi package and BRB Array Tools (National Cancer Institute)

label: Cy5 and Cy3

source_name: UCSF4 human embryonic stem cell line (hESC) derived human neural progenitor cells (NPCs)

label_protocol: Downstream processing of genomic DNA bisulfite conversion was performed using the EZ DNA Methylation Kit (ZymoResearch) and Infinium HumanMethylation450 bead arrays (Illumina) following the manufacturer’s protocols.

growth_protocol: Neural precursor cells (NPCs) were derived from hESCs (UCSF4, NIH registry code 0044) using a protocol developed by Swistowski et al., 2009 at the Buck Institute for Age Research,. NPCs were grown in Neurobasal Medium (Gibco), NEAA (2mM), L-Glutamine (2mM), penicillin/ streptomycin, B27, FGF2 (20ng/mL) and LIF (10ng/mL; Millipore) at 8% O2 and 5%CO2,  and passaged every 3-5 days in culture. For transcriptomic experiments, NPCs (passages <15) were plated at 500,000 cells/well (6-well plate).

extract_protocol: Immediately following a 24h exposure duration, NPCs were washed once with PBS and trypsinized (0.05%, Gibco, 5min). Cell pellets were washed 2X with PBS (centrifugation at 5min/800 rpm) and stored at -80oC. To extract genomic DNA, CTBs were digested with 1mg/ml proteinase K in lysis buffer (50mM Tris, pH 8.0, 1mM EDTA pH 8.0, 0.5% SDS) overnight at 55⁰C. Following RNase treatment, DNA was isolated using the Phenol-Chloroform Isoamyl Alcohol (PCI) method, followed by precipitation with ethanol, and resuspended in TE. The DNA concentration and quality were estimated by using a Nanodrop spectrometer (Thermo Scientific) and the Agilent RNA 6000 Nano LabChip Kit and Bioanalyzer 2100 system. DNA was extracted from exposed and control cultures from 3 independent experiments (~1-2 million cells/sample).

treatment_protocol: After 2 days of culture (~60-70% confluency) fresh media was supplied and NPCs were exposed to vehicle control (0.1% DMSO), 1µM BDE-47 or 10µM BDE-47 at a 1:1000 dilution.

tag: cell type

value: NPCs

tag: passage

tag: exposure

tag: exposure duration


title: 2/5_CY

tag: condition


title: Localized normal AR_1335_N

tag: chip antibody

value: AR

tag: chip antibody vendor

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: liver, TrxR1/Gsr-null biological rep2 [TrxR1_Gsr-null_6810]

description:
TrxR1_Gsr-null_6810
Gene expression data from liver.

tag: gender


title: liver, TrxR1/Gsr-null biological rep3 [TrxR1_Gsr-null_6811]

description:
TrxR1_Gsr-null_6811
Gene expression data from liver.


title: 41A_CuO_COOH_h

tag: donor

value: D

value: Asthmatic

tag: nanoparticle

tag: dose

tag: dose description

value: high


title: NPC (2) exposed to 1µM BDE-47 for 24h Exp2

description:
BDE47_1μM_24h_Exp2
3999442105_R05C01


title: 2/40_CY

tag: age group

tag: tissue


title: NPC (3) exposed to 0.1% DMSO for 24h Exp3

description:
DMSO_24h_Exp3
3999442105_R01C02


title: NPC (3) exposed to 1µM BDE-47 for 24h Exp3

description:
BDE47_1μM_24h_Exp3
3999442105_R02C02


title: 12/120_PBC

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.

value: primary biliary cholangitis

value: adult


title: 42H_CuO_COOH_h

value: A

value: Healthy

tag: time


title: 78A_CuO_m

value: G

value: CuO

value: mid


title: Lin-CD34-CD164low (Donor B)

first: Luca

last: Biasco

state: MA

address: 1 Jimmy Fund Way

institute: Dana-Farber/Boston Children’s Cancer and Blood Disorders Center

data_processing:
Raw sequencing data were processed using the previously described (Zilionis et al., Nature Protocols 2017) inDrops.py bioinformatics pipeline, available at https://github.com/indrops/indrops, using library version "v3".
The cDNA read was trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the human transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCh38.85).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols 2017).
Genome_build: GRCh38.85
Supplementary_files_format_and_content: The supplementary data files include raw unique molecular identifier (UMI)-filtered counts for each single-cell transcriptome that passed filtering. Following the first header row, each row corresponds to one cell barcode. Column 1 contains the library ID. Columns 2+ contain UMI counts for each gene.

source_name: Bone marrow hematopoietic progenitors

extract_protocol:
Using inDrops, cells were encapsulated into 4-nL droplets on ice and lysed using a final concentration of 0.4% NP-40. Single-cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications as described for the "FACS subsets" samples in Khoramian Tusi et al., Nature 2018.

treatment_protocol: Bone marrow (BM) samples were collected from adult healthy donors at Children’s Hospital in Boston with the approval of the Committee on Clinical Investigations Children’s Hospital Boston and consent from the subjects under the protocol #09-04-0167. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation (Lymphoprep, STEMCELL Technologies). CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Kit (Miltenyi Biotec) according to the manufacturer’s specifications or were purchased from commercial sources (AllCells). Seven HSPC sub-populations were purified from the CD34+ fraction of a healthy donor (Donor A) BM cells through a two-step four-way sorting using FACSAria II (BD Biosciences). The following combinations of cell surface markers were used to identify and separate the HSPC subsets. Hematopoietic stem cells (HSC): Lin-CD34+CD38-CD90+CD45RA-; multipotent progenitors (MPP): Lin-CD34+CD38-CD90-CD45RA-; multilymphoid progenitors (MLP): Lin-CD34+CD38-CD90-CD45RA+; pre-B lymphocytes / Natural Killer cells (PREB/NK): Lin-CD34+CD38+CD7-CD10+; megakaryocyte-erythroid progenitors (MEP): Lin-CD34+CD38+CD7-CD10-CD135-CD45RA-; common myeloid progenitors (CMP): Lin-CD34+CD38+CD7-CD10-CD135+CD45RA-; granulocyte-monocyte progenitors (GMP): Lin-CD34+CD38+CD7-CD10-CD135-CD45RA+. From healthy Donor B, four cell fractions were purified from BM MNCs through a four-way sorting using the following combinations of cell surface markers: Lin-CD34+CD164+; Lin-CD34lowCD164high; Lin-CD34-CD164high; Lin-CD34-CD164low. CD71 was included to identify erythroid progenitors. Immunophenotyping was performed on BM CD34+ cells labelled with CD164 in combination with HSPC subsets markers by using LSRFortessa (BD Biosciences). CD15 and CD19 were included to identify the lineage positive cells. The antibodies were as follows: CD34 PB, CD38 PE/Cy5, CD90 APC, CD10 PE/Cy7, CD135 PE, Lin BV510 (CD3, CD14, CD16, CD19, CD20, CD56 BV510), CD15 BV510, CD164 (clone 67D2) PE, CD164 FITC, CD71 PerCP/Cy5.5, CD41 APC, CD19 PE/Cy7 (all Biolegend); CD45RA APCH7, CD7 AF700, CD15 PE (all BD Biosciences), Glycophorin A (Miltenyi Biotec).

value: bone marrow

tag: purification

tag: cell type


title: Lin-CD34lowCD164high (Donor B)


title: 40A_CuO_h

value: H

value: 1 hour aerosolization + 24 hours incubation


title: liver, WT, biological rep4 [WT_10]

description:
WT_10
Gene expression data from liver.

tag: strain/background

tag: genotype/variation

value: WT

value: liver

value: female

tag: age

value: 4 weeks


title: NPC (2) exposed to 10µM BDE-47 for 24h Exp2

description:
BDE47_10μM_24h_Exp2
3999442105_R06C01

value: NPCs

tag: passage

tag: exposure

tag: exposure duration


title: 12/178_PBC

tag: condition

value: whole blood


title: genomic DNA from decidualized ESC

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

institute: Yamaguchi University School of Medicine

description: decidualized ESC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing:
BeadStudio software v3.2
The non_normalized.txt contains unmethylated and methylated signal intensities

source_name: decidualized ESC

label_protocol: Standard Illumina Protocol

growth_protocol: ESCs were incubated with estradiol and medroxyprogesterone acetate for 14 days to induce decidualization.

extract_protocol: Genomic DNA was isolated from 20 mg frozen tissues using the a Qiagen Genomic DNA kit (Qiagen, Valencia, CA, USA).

treatment_protocol: ESCs were incubated with or without E (10-8 mol/L) and MPA (10-6 mol/L) for 14 days at 37°C, 95% air, and 5% CO2.

tag: gender

value: Female

tag: disease

value: normal

value: decidualized ESC


title: 8//19_K

description: RNA expression levels in the blood of control patient.

source_name: Control, adult

value: control

value: adult


title: NPC (2) exposed to 0.1% DMSO for 24h Exp2

description:
DMSO_24h_Exp2
3999442105_R04C01


title: 39A_CuO_COOH_h

tag: donor

value: E

value: Asthmatic

tag: nanoparticle

value: high


title: Lin-CD34+CD164+ (Donor B)

value: bone marrow


title: Lin-CD34-CD164high (Donor B)


title: 2/69_CY

value: Crohn's disease

value: child


title: liver, WT, biological rep2 [WT_7]

description:
WT_7
Gene expression data from liver.

value: WT


title: liver, WT, biological rep1 [WT_6]

description:
WT_6
Gene expression data from liver.

value: liver


title: genomic DNA from non-decidualized ESC

description: non-decidualized ESC

source_name: non-decidualized ESC

value: non-decidualized ESC


title: 38A_Air_ctrl

value: D

value: Air

tag: dose

value: 0 mg/m3

tag: dose description

value: control air

value: 1 hour aerosolization + 24 hours incubation


title: 37A_CuO_COOH_m

value: H

value: mid


title: 8//8_K

value: control

tag: age group

value: adult

tag: tissue

value: whole blood


title: GMP (Donor A)

tag: purification

value: GMP


title: CMP (Donor A)

value: bone marrow

tag: cell type

value: CMP


title: 11//15_K


title: NPC (1) exposed to 10µM BDE-47 for 24h Exp1

description:
BDE47_10μM_24h_Exp1
3999442105_R03C01

value: NPCs


title: 36A_CuO_l

value: G

value: Asthmatic

value: CuO

value: low

tag: time


title: 8//11_K


title: 11/36_K


title: liver, Gsr-null biological rep5 [Gsr-null_8]

description:
Gsr-null_8
Gene expression data from liver.

tag: strain/background

tag: genotype/variation

value: Gsr-null

value: liver

value: male

value: 15-20 weeks


title: PreB/NK (Donor A)

value: PreBNK


title: liver, WT, biological rep3 [WT_8]

description:
WT_8
Gene expression data from liver.

value: WT

value: female

tag: age

value: 4 weeks


title: MEP (Donor A)

value: MEP


title: 35H_CuO_COOH_h

value: C

value: Healthy

value: high

value: 1 hour aerosolization + 24 hours incubation


title: NPC (1) exposed to 1µM BDE-47 for 24h Exp1

description:
BDE47_1μM_24h_Exp1
3999442105_R02C01

value: NPCs

tag: passage

tag: exposure


title: NPC (1) exposed to 0.1% DMSO for 24h Exp1

description:
DMSO_24h_Exp1
3999442105_R01C01

tag: exposure duration


title: MLP (Donor A)

value: bone marrow

value: MLP


title: HSC (Donor A)

value: HSC


title: MPP (Donor A)

value: MPP


title: liver, Gsr-null biological rep6 [Gsr-null_9]

description:
Gsr-null_9
Gene expression data from liver.

value: Gsr-null

value: liver

tag: gender


title: liver, Gsr-null biological rep3 [Gsr-null_6]

description:
Gsr-null_6
Gene expression data from liver.

value: male

value: 15-20 weeks


title: liver, Gsr-null biological rep4 [Gsr-null_7]

description:
Gsr-null_7
Gene expression data from liver.


title: 28A_Air_ctrl

value: E

tag: condition

value: Asthmatic

value: Air

value: 0 mg/m3

value: control air


title: 12/228_PBC

source_name: Primary biliary cholangitis, adult

value: primary biliary cholangitis

value: adult

value: whole blood


title: 32H_Air_ctrl

tag: donor

value: C

value: Healthy

value: 1 hour aerosolization + 24 hours incubation


title: liver, Gsr-null biological rep1 [Gsr-null_4]

description:
Gsr-null_4
Gene expression data from liver.


title: 33H_Air_ctrl

value: A

tag: nanoparticle


title: 26H_CuO_COOH_m

value: B

tag: dose

value: mid


title: 8/42_K

value: control


title: Pt22_H3K27ac

first: Jun

last: Qi

department: Cancer Biology

institute: Dana-Farber

description: ChIP-seq  or input from MCL, DHL and ALL tumors

data_processing:
FASTQs were aligned to assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1) with parameter '-k 1.'
Wiggles for visualization and peak calling was performed on aligned data using MACS version 1.4.2 using with matched input chromatin as control, with a p-value threshold of 1e-9.
For any genomic region, normalized read density was calculated using Bamliquidator (version 1.0) (https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files of tag pileup

source_name: primary patient samples from MCL, DHL and acute B-cell lymphoblastic lymphoma/leukemia (ALL) cells

extract_protocol:
Samples were homogenized with rotor-stator device. Lysates were sonicated via Bioruptor.
Protein-DNA complexes were isolated via immunoprecipitation and prepared for sequencing with Rubicon Thruplex DNA-seq kit.

treatment_protocol: treated for 6 hours, with cell density at 1e6/ml, DMSO was used as vehicle control

tag: chip antibody

value: H3K27AC (Abcam ab4729)

tag: treatment

value: 50nM THZ1


title: Pt22_H3K27ac_Input


title: liver, Gsr-null biological rep2 [Gsr-null_5]

description:
Gsr-null_5
Gene expression data from liver.

value: Gsr-null

tag: tissue

value: liver

value: male

value: 15-20 weeks


title: 12/298_PBC

tag: age group


title: 27H_CuO_h

description: Exposed for 1h to nanoparticle aerosol, incubated for 24h

value: CuO

tag: dose description

value: high


title: 8/14_K

value: adult


title: Pt17_H3K27ac_Input


title: 11/29_K

value: whole blood


title: 23H_CuO_COOH_l

value: low

tag: time


title: Pt24_H3K27ac_Input


title: 25A_CuO_l

value: H

value: Asthmatic


title: 21A_CuO_m

value: E

value: 1 hour aerosolization + 24 hours incubation


title: 11/11_K


title: 11/22_K


title: PAR_THZ1_50NM_POL2

source_name: Mantle cell lymphoma

value: POL2 (Fisher scientific NC0888291)


title: 20A_CuO_COOH_l

source_name: Bronchial epithelium

value: D


title: 8/32_K

value: control


title: 10/12_K


title: Pt24_H3K27ac

value: H3K27AC (Abcam ab4729)

value: 50nM THZ1


title: liver, WT, biological rep3 [WT_3]

description:
WT_3
Gene expression data from liver.

tag: strain/background

value: WT

value: liver


title: liver, WT, biological rep1 [WT_1]

description:
WT_1
Gene expression data from liver.

tag: genotype/variation

value: male

value: 15-20 weeks


title: Pt17_H3K27ac


title: liver, WT, biological rep5 [WT_5]

description:
WT_5
Gene expression data from liver.

tag: age


title: RCF_6mo_rep4

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

institute: Gifu University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1x Blocking Agent and 1x Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy3-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: The hybridized microarray slides were washed according to the manufacturer’s instructions and were scanned with an Agilent DNA Microarray Scanner (#G2565CA, Agilent Technologies, CA, USA) at a resolution of 5 μm.

data_processing: These data were normalized by the percentile shift 75% using GeneSpring GX version 11.5.1 software (Agilent Technologies).

label_protocol: The cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the lung by phenol-chloroform method using a Fast RNA Pro Red Kit (MP Biomedicals, California, USA) following the manufacturer's instructions. Total RNA was purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. The concentration and purity of the resulting RNA were evaluated by absorbance at 260 nm using an Agilent 2100 BioanalyzerTM (Agilent Technologies, California, USA).

treatment_protocol: After the mice were sacrificed, their lungs were rapidly removed and processed for DNA microarray analysis.

tag: strain

value: lung


title: RCF_6mo_rep3


title: 12/167_PSC

description: RNA expression levels in the blood of patient diagnosed with primary sclerosing cholangitis.

source_name: Primary sclerosing cholangitis, adult

value: primary sclerosing cholangitis

value: adult


title: PAR_THZ1_50NM_POL2_INPUT


title: liver, WT, biological rep2 [WT_2]

description:
WT_2
Gene expression data from liver.

source_name: liver


title: RCF_6mo_rep2


title: 18H_CuO_m

value: C

value: Healthy

value: CuO

value: mid


title: 17A_Air_ctrl

value: F

value: Asthmatic

value: Air

value: 0 mg/m3

value: control air

value: 1 hour aerosolization + 24 hours incubation


title: 12/234_PSC

value: whole blood


title: 15H_CuO_m

value: A


title: PAR_DMSO_POL2

value: POL2 (Fisher scientific NC0888291)


title: 14A_Air_ctrl

value: H


title: liver, TrxR1/Gsr-null biological rep1 [TrxR1_Gsr-null_6805]

description:
TrxR1_Gsr-null_6805
Gene expression data from liver.

value: liver

value: female

value: 4 weeks


title: L20_THZ1_50NM_POL2

value: 50nM THZ1


title: RCF_6mo_rep1

value: lung

value: male


title: 12/92_PSC

value: primary sclerosing cholangitis

value: adult


title: 12/281_PSC


title: CCF_6mo_rep2


title: CCF_6mo_rep3


title: L20_THZ1_50NM_POL2_INPUT


title: L20_DMSO_POL2


title: L20_DMSO_POL2_INPUT


title: CCF_6mo_rep1


title: VCF_6mo_rep4


title: 6H_CuO_COOH_l

value: C

value: Healthy

value: low


title: 12A_CuO_m

value: D

value: Asthmatic

value: CuO

value: mid


title: 9A_CuO_h

value: G

value: high

value: 1 hour aerosolization + 24 hours incubation


title: 5T

city: Memphis

first: Qingfei

last: Pan

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
RNASeq reads were mapped to mm10 by Tophat (2.1.0) at splice mode with default parameters. Based on the alignment, transcriptome reconstruction, alternative splicing detection and novel transcripts prediction were implemented by Cufflinks (2.2.1). Gene expression quantification were estimated by two approaches for more accurate values of FPKM, RSEM (1.2.15) and Salmon (0.8.2). The differentially expressed genes (DEGs) were predicted by three popular software, EBSeq (1.14.0), edgeR (3.16.5) and DEseq2 (1.14.1).
The GATK Best Practice was introduced to call the variants from the RNA-Seq data and filtered with the default parameters.
Genome_build: mm10/NCBIM38
Supplementary_files_format_and_content: FPKM, somaticVariants.vcf

source_name: CRC-tumor of AOM/DSS Mouse #1

growth_protocol: 15 male mice of C57BL/6N inbred strain in the same brood that shared with the same age of (7 weeks) and similar body weight (18–20 g) were used for this study.

extract_protocol:
All samples, including CRC-tumor and adjacent-normal, were frozen in liquid nitrogen and ground into powder after isolation from each mouse. Then the powder was equally divided into 2 parts: one was used for total RNA extraction by TRIzol-based protocol, and the other was used for total protein extraction by urea-based lysis buffer.
For RNA samples: TruSeq RNA Library Prep Kit v2 was used for library constrution after mRNA extraction. Briefly, the genomic DNA contamination was removed by DNase I digestion according to the manufacturer protocols, and the mRNAs were enriched with the oligo (dT) magnetic beads followed by cDNA synthesis with random hexamer-primer, end repair, adenine addition and adaptor ligation. The ligation products were amplified with PCR and their quality was evaluated by Agilent 2100 BioAnalyzer system and ABI StepOnePlus Real-Time PCR System. The library was captured by Illumina flow cell and sequenced by HiSeq 4000. For protein samples: after extraction, the protein was sequentially reduced by dithiothreitol, alkylated by iodoacetamide and digested by trypsin. Hydrophilic interaction liquid interaction chromatography was introduced to the desalted peptide for  fractionation. Label-free method was employed to profile these fractionated peptides by nano-LC and Orbitrap Fusion MS strategy.

treatment_protocol: 12 mice in the experimental group received a single intraperitoneal injection of AOM with a dose of 12.5 mg/kg body weight. One week later, these mice were given three cycles of the DSS treatment, each cycle lasting 3 weeks with feeding 2% DSS-dissolved water for 5 days and tap water for 16 days. 3 mice in the control group received no AOM/DSS treatments.

tag: weeks after aom injection

tag: sample type

value: CRC-tumor


title: J4_THZ1_50NM_POL2

value: POL2 (Fisher scientific NC0888291)


title: J4_THZ1_50NM_POL2_INPUT

value: 50nM THZ1


title: 12/205_PSC

department: CeNT

value: whole blood


title: 12/354_PSC


title: 13A_CuO_l

value: F


title: 5N

source_name: Adjacent-normal of AOM/DSS Mouse #1

value: Adjacent-normal


title: 12/339_PSC

value: primary sclerosing cholangitis

value: adult


title: 3A_CuO_h


title: 5A_CuO_COOH_l

value: E


title: VCF_6mo_rep3

value: lung

tag: gender

value: male


title: VCF_6mo_rep2


title: 12//22_PSC

tag: condition


title: Ctrl_6mo_rep3


title: 12/347_PSC


title: J4_DMSO_POL2


title: 12/154_PSC


title: 12/293_PSC


title: PAR_DMSO_POL2_INPUT


title: J4_DMSO_POL2_INPUT


title: 4N


title: 4T


title: VCF_6mo_rep1


title: 12/356_PSC


title: 3T


title: 12/355_PSC


title: I10_THZ1_50NM_POL2_INPUT


title: 1A_CuO_COOH_m

tag: donor

value: Asthmatic


title: I10_THZ1_50NM_POL2


title: 3N


title: I10_DMSO_POL2


title: 2T


title: I10_DMSO_POL2_INPUT


title: liver, WT, biological rep4 [WT_4]

description:
WT_4
Gene expression data from liver.

value: WT

value: liver

value: 15-20 weeks


title: Ctrl_6mo_rep2


title: 2N


title: 1T


title: PAR_THZ1_H3K27AC_INPUT


title: 1N


title: PAR_DMSO_H3K27AC_INPUT


title: PAR_DMSO_H3K27AC

value: H3K27AC (Abcam ab4729)


title: 12/251 _PSC


title: 3T3 NNMT Replicate 3

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

description:
NNMTvsCtrl_H3K27me3.bed
NNMT3_H3K27

data_processing:
Illumina CASAVA used for base calling
Reads were preprocessed with Trimmomatic 0.36 to remove low quality data and adapters before aligning to GRCm38 with BWA aln 0.7.17
Alignments were filtered and PCR duplicates were marked using sambamba 0.6.5.
Differential binding was performed with rgt-THOR 0.11.2 which can integrate biological replicates.
Genome_build: GRCm38
Supplementary_files_format_and_content: bed file containing peaks identified in cells expressing control or NNMT overexpression construct.
Column headers:
1: chrom
2. chromStart
3. chromEnd
4. name
5. score (always 1000)
6. strand (+ for gains in control; - for gains in NNMT)
7. thickStart (same as column 2)
8. thickEnd (same as column 3)
9. itemRgb (red for gains in control; green for gains in NNMT)
10. blockCount (always 0)
11. Ctrl1 read count:Ctrl2 read count:Ctrl3 read count;NNMT1 read count:NNMT2 read count:NNMT3 read count;p-value

source_name: mouse 3T3 fibroblasts expressing NNMT overexpression construct H3K27me3 ChIP

growth_protocol: Cells were grown in methionine-free DMEM supplemented to 10 micromolar methionine and 10% dialyzed FBS

extract_protocol:
Cells were fixed with 1% formaldehye, quenched with glycine, and nuclei isolated and chromatin sheared with micrococcal nuclease per manufacturer's suggestions (Cell Signaling SimpleChIP Enzymatic Chromatin IP Kit).
Libraries were constructed using standard NEB library preparation protocols.

treatment_protocol: Cells were grown for 48 hrs before collection of RNA.

tag: cell line

value: 3T3 fibroblast cell line

tag: genotype

value: NNMT overexpression


title: 3T3 NNMT Replicate 2

description:
NNMTvsCtrl_H3K27me3.bed
NNMT2_H3K27

tag: chip antibody


title: 3T3 Ctrl Input

description:
NNMTvsCtrl_H3K27me3.bed
Ctrl_input

source_name: mouse 3T3 fibroblasts expressing control construct input

value: Control

value: None (input)


title: 3T3 NNMT Input

description:
NNMTvsCtrl_H3K27me3.bed
NNMT_input

source_name: mouse 3T3 fibroblasts expressing NNMT construct input


title: L20_DMSO_H3K27AC_INPUT

tag: treatment


title: 12/303_PBC

value: primary biliary cholangitis

tag: tissue

value: whole blood


title: 12/299_PBC

tag: age group


title: 12/150_PSC


title: 3T3 NNMT Replicate 1

description:
NNMTvsCtrl_H3K27me3.bed
NNMT1_H3K27


title: 12/52_PBC


title: 12/374_PBC


title: 12/373_PBC


title: 3T3 Ctrl Replicate 3

description:
NNMTvsCtrl_H3K27me3.bed
Ctrl3_H3K27

data_processing:
Illumina CASAVA used for base calling
Reads were preprocessed with Trimmomatic 0.36 to remove low quality data and adapters before aligning to GRCm38 with BWA aln 0.7.17
Alignments were filtered and PCR duplicates were marked using sambamba 0.6.5.
Differential binding was performed with rgt-THOR 0.11.2 which can integrate biological replicates.
Genome_build: GRCm38
Supplementary_files_format_and_content: bed file containing peaks identified in cells expressing control or NNMT overexpression construct.
1: chrom
2. chromStart
3. chromEnd
4. name
5. score (always 1000)
6. strand (+ for gains in control; - for gains in NNMT)
7. thickStart (same as column 2)
8. thickEnd (same as column 3)
9. itemRgb (red for gains in control; green for gains in NNMT)
10. blockCount (always 0)
11. Ctrl1 read count:Ctrl2 read count:Ctrl3 read count;NNMT1 read count:NNMT2 read count:NNMT3 read count;p-value

source_name: mouse 3T3 fibroblasts expressing control construct H3K27me3 ChIP


title: PAR_THZ1_H3K27AC

value: 50nM THZ1


title: L20_DMSO_H3K27AC


title: J4_THZ1_H3K27AC_INPUT


title: 3T3 Ctrl Replicate 2

description:
NNMTvsCtrl_H3K27me3.bed
Ctrl2_H3K27


title: J4_THZ1_H3K27AC


title: L20_THZ1_H3K27AC_INPUT


title: L20_THZ1_H3K27AC


title: 3T3 Ctrl Replicate 1

description:
NNMTvsCtrl_H3K27me3.bed
Ctrl1_H3K27


title: J4_DMSO_H3K27AC_INPUT


title: 25m bio-rep3 tech-rep2

city: Austin

first: Claus

last: Wilke

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
alignment with hisat2
counting with bedtools multicov
computation of TPMs with R script
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes
Supplementary_files_format_and_content: tab-delimitted text files contain raw counts for each sample, outputted from bedtools multicov

organism:
Escherichia coli
Escherichia phage T7

source_name: cell culture

extract_protocol:
RNA was isolated using Trizol reagent (Thermo Fisher Scientific)
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent).

tag: t7 strain

value: wild type


title: J4_DMSO_H3K27AC


title: 12/297_PBC

data_processing: Quantile normalised using lumi library in R 2.15.

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

value: adult


title: 12//28_PBC


title: 12/369_PBC


title: I10_THZ1_H3K27AC_INPUT


title: 12/55_PBC


title: 12/33_PBC


title: 12/147_PBC


title: I10_DMSO_H3K27AC_INPUT


title: 15m bio-rep3 tech-rep2

tag: time


title: 20m bio-rep3 tech-rep2


title: I10_THZ1_H3K27AC


title: 12/322_PBC


title: 20m bio-rep3 tech-rep1


title: I10_DMSO_H3K27AC


title: Ex3_DNMAML_IL-4

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Quality check of the raw reads data files using FASTQC software.
Adapter and poor quality reads were removed using Trimmomatic.
The filtered reads were aligned to Human reference genome (EnsembleXX) using HISAT2 aligner software.
HTSeq program was implemented to obtain raw counts for all human genes.
T+B52he gene counts were used for differential expression analysis with the DESeq2 package.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: counts

source_name: THP-1 cell line

growth_protocol: THP-1 cell line was cultured in RPMI1640 medium supplemented with 10%FBS, HEPES, sodium pyruvate and antibiotics (penicillin and streptomycin)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cell line was retrovirally transduced with IRES (MSCV-GFP-IRES), NIC1 (MSCV-GFP-MYC-NIC1) or DNMAML (MSCV-GFP-DNMAML) overexpressing construct. GFP+ cells were sorted using cell sorter. For RNASeq, IRES, NIC1 and DNMAML overexpressing THP-1 cell were pretreated with PMA (5 ng/ml) for 48 h before stimulating with IL-4 (20 ng/ml) for 3 h.

tag: transduction

value: DNMAML

tag: agent


title: 12/75_PBC


title: 25m bio-rep3 tech-rep1


title: Ex2_DNMAML_IL-4


title: 10m bio-rep3 tech-rep1


title: 15m bio-rep3 tech-rep1


title: Ex1_DNMAML_IL-4


title: Ex3_NIC1_IL-4


title: 5m bio-rep3 tech-rep1


title: 5m bio-rep3 tech-rep2


title: 12/216_PBC


title: Ex2_NIC1_IL-4


title: 25m bio-rep2 tech-rep2