title: CHC086T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: TRANSPLANT

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status


title: RNA-seq: iPSC line 2 condition: iPSC replicate: 1

status: Public on Apr 05 2019

type: SRA

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

library_source: transcriptomic

data_processing:
The first three bases of all forward reads were removed using the trimmomatic software (Bolger et al., 2014) (parameters: SE HEADCROP:3), as recommended by the manufacturer of the SMARTer Stranded RNA Sample Prep Kit.
Reads were mapped to the combined hg19-rn6 reference genome using STAR (Dobin and Gingeras, 2002) with default parameters.
All rn6-mapping reads and all h19-mapping reads with a mapping quality other than 255 were removed from the bam file (Number of mapped reads in Table S7). htseq-count (Anders et al., 2013) was used for quantifying the gene expression (parameters: --order=pos --stranded=yes --mode=union --type=exon --idattr=gene_id). For this, hg19 transcript definitions from GENCODE 27 (Harrow et al., 2012) were used.
Genome_build: Combined hg19/rn6 reference genome
Supplementary_files_format_and_content: BigWig coverage file aligned to combined hg19/rn6 reference

molecule: total RNA

organism: Homo sapiens

source_name: iPSC line 2

growth_protocol: iPSC lines were obtained by lentiviral transduction of two of the fibroblast lines with the mouse OSKM (Oct4, Sox2, Klf4, Myc) cocktail. iPSC lines were cultured in 6 well plates coated with vitronectin (Gibco) in E8 medium (Gibco) containing 50 μg/mL G418 (Sigma-Aldrich) and 0.5 μg/mL puromycin (Sigma-Aldrich). iPSC cultures were regularly passaged using 0.5 mM UltraPure EDTA (Gibco).

extract_protocol:
RNA was isolated with the RNeasy Mini kit (Qiagen) according to the manufacturer's instructions. The RNA isolation included on-column DNA digestion. Before the RNA isolation, iPSCs and fibroblasts were lysed after harvesting the cells, whereas the iNeurons were lysed in situ
RNA-seq library preparation was performed with the SMARTer Stranded Total RNA Sample Prep Kit (low input mammalian) (Clontech), according to the manufacturer's instructions. 50 ng of total RNA was depleted for rRNA using the RiboGone method included in the kit. The resulting rRNA-depleted RNA input was less than 10 ng and we followed the additional steps in the protocol of the manufacturer for this amount of input material. 12 amplification cycles were used for the PCR. The fragment length distribution was determined using TapeStation (Agilent) and the last bead size selection of the protocol (with 1.0x beads) was repeated once more in case the libraries contained PCR product with sizes smaller than 100 bp. The library concentration was quantified using KAPA library quantification kit (KAPA Biosystems).

tag: cell type

value: iPSC

tag: cell line

value: iPSC line 2 (IPS1500024/293, derived from CL1500024)


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus_rep3

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

country: USA

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
genome build: dm3-reporter combined genome
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings. All samples were first trimmed to 50 bp. Custom barcode sequences were removed from the first 9bp of each ChIP-nexus read or the first 4 bp of each gene-specific 5' RNA sequencing read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3. Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were separated by strand and reduced to a single base at the 5' end. Genome-wide coverage counts were calculated for each strand and normalized to reads per million.
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: transfected Kc167 cells

growth_protocol: Kc167 cells were cultured at 25C in HyClone SFX-Insect Cell Culture Media

extract_protocol:
Cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 250~500 bp. ~ 10 million cells was used for one ChIP-nexus.
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using NEBNext End repair module. A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module. Adapters with 5’ overhangs were ligated to the adenylated fragments. Libraries were then transformed to blunt end by Klenow 3'-5' exo- polymerase and T4 DNA polymerase. The resulting blunted DNA was digested by lambda exonuclease and RecJf. Digested single strand DNA was then reverse cross-linked and purified. Purified single-stranded DNA was then circularized with CircLigase, annealed with oligonucleotides complementary to the BamHI restriction site and linearized by BamHI digestion. Linearized single strand DNA was then PCR-amplified.

treatment_protocol: Kc167 cells were transfected with a reporter containing promoter sequence of interests. Cells were cultured at 25C for 48 h and treated with Triptolide (500 uM, dissolved in DMSO) or DMSO (2% v/v) at RT for 1h.

value: Kc167 cells

tag: chip antibody

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

tag: treatment

value: 500 uM Triptolide 1h


title: MDA-MB-231_dox 48h_3

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Reads were mapped on hg38 human genome with gencode v22 as gene annotation using STAR
PSI/PIR for each splicing event was calculated by R package ASpli
gene expression were quantified using RSEM v1.3.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene expression/splicing values for each sample

source_name: Triple-negative breast cancer cell line

growth_protocol: MCF10A cells were cultured in MEBM media (Lonza) supplemented with BPE, hEGF, insulin, hydrocortisone (Lonza, Bulletkit), 50 µg cholera toxin (Sigma) and 1% Pen/Strep. MDA-MB-231 cells were cultured in high glucose DMEM (Thermofisher), supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Cells were trypsinized, peletted, and RNA was harvested using Nucleospin (Macherey). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF10A cells were transfected with GapmeRs (Exiqon) designed against the candidate lncRNA or a scramble GapmeR using Lipofectamine 2000 (Thermofisher). The cells were cultured in a 1% O2 hypoxic chamber. MDA-MB-231 cells were used to create a stable cell line expressing a tetracycline inducible shRNA against the candidate lncRNA. shRNA induction was accomplished by treating the cells with doxycycline (1µg/µl) for 48 hours or 8 days, refreshing doxycycline every 48h.


title: RNA-seq: iPSC line 1 condition: iPSC replicate: 1

source_name: iPSC line 1

value: iPSC line 1 (IPS1500030/C2, derived from CL1500023)


title: MDA-MB-231_dox 48h_2


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus_rep3

value: 2% v/v DMSO 1h


title: RNA-seq: Fibroblast line 2 condition: Fibroblast replicate: 2

source_name: Fibroblast line 2

growth_protocol: The human skin fibroblast lines were obtained from three anonymized healthy individuals. The fibroblasts were cultured in tissue culture flasks (Corning) in Dulbecco’s modified Eagle’s medium containing 20 % (vol/vol) fetal bovine serum, 1 % (vol/vol) penicillin/streptomycin and 1 % (vol/vol) sodium pyruvate (all from Sigma-Aldrich), from here on referred to as fibroblast medium. Cells were regularly passaged using 0.25 % trypsin (BD Biosciences).

value: Skin derived fibroblast

value: Fibroblast line 2 (CL1500024)


title: MDA-MB-231_dox 8 days_1


title: CHC080T

type: RNA

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description:
MUTHEC
test

data_processing: Expression level (Ct values) was assessed using the Fluidigm Real-Time PCR Analysis software (4.1.3). Gene expression data were expressed using the 2-DDCt method relative to ribosomal 18S (R18S) and the expression level of the corresponding gene in normal liver samples. Final results were reported in 2- delta delta CT representing fold change compared to normal livers

label: taqman assay

source_name: liver tumor

label_protocol: We performed reverse transcription of 500 ng of total RNA using the High-Capacity Transcription Kit (Life Technologies) and assess gene expression using TaqMan predesigned assays (Life Technologies) on Fluidigm 96 dynamic arrays with the Bio-Mark Real-Time PCR system.

extract_protocol: Total RNA from frozen surgical samples was extracted using Maxwell 16 LEV simplyRNA Tissue kit (Promega, cat#AS1280) and from frozen biopsies using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, cat #80224) according to the manufacturer’s instructions. DNAs were quantified using a Qubit 2.0 fluorometer (Qubit dsDNA BR assay kit, LifeTechnologies – ThermoFisher Scientifics) and quality was assessed as previously described. RNA was quantified using a spectrophotometer at 260nm (Nanodrop) and quality of RNA was controlled by Qiaxcell gel electrophoresis (Qiagen).

tag: gender

value: M

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

value: NM

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: nras status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: CHC072T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: C

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation


title: RNA-seq: Fibroblast line 2 condition: Fibroblast replicate: 1

tag: cell type

tag: cell line


title: reporter_triptolide_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep2

tag: chip antibody

tag: treatment


title: reporter_triptolide_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep2


title: RNA-seq: Fibroblast line 1 condition: Fibroblast replicate: 2

source_name: Fibroblast line 1

value: Fibroblast line 1 (CL1500023)


title: MDA-MB-231_no dox 48h_3


title: reporter_dmso_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep2


title: CHC059T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC051T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation


title: RNA-seq: Fibroblast line 1 condition: Fibroblast replicate: 1

tag: cell type

tag: cell line


title: MDA-MB-231_no dox 48h_2


title: MDA-MB-231_no dox 48h_1


title: reporter_dmso_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep2

value: Kc167 cells

tag: chip antibody

tag: treatment


title: CHC050T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: CHC043T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation


title: MDA-MB-231_dox 48h_1

tag: cell line


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus_rep2

tag: chip antibody

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

tag: treatment


title: AB162507_HCMEC_2KOB2_S4_R1

city: Chapel Hill

first: Adriana

middle: Sujey

last: Beltran

address: 120 Mason farm Rd

department: Pharmacology

institute: UNC-CH

description:
HCMEC DeSEq
HCMEC_read_counts
AB162507_HCMEC_2KOB2_S4_R1

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using DeSeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files (.xlsx) contain RPKM values for HCMEC samples and read counts values for HUVEC samples, organized by official gene symbol

molecule: polyA RNA

growth_protocol: see SAMPLES

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libaries constructed with Illumina TruSeq RNA Library Prep Kit v2.  1 µg total RNA and 14 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

treatment_protocol: see SAMPLES

tag: culture media

value: EndoGRO™-MV Complete Media Kit (Milipore SCME004) supplementel with FGF2

tag: library preparation kit

value: KAPA Stranded mRNAseq kit


title: AB162507_HCMEC_3KOB12_S10_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB162507_HCMEC_3KOB12_S10_R1


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus_rep2

value: 500 uM Triptolide 1h


title: reporter_triptolide_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep3


title: AB162507_HCMEC_D3_WT_P6_S1_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB162507_HCMEC_D3_WT_P6_S1_R1


title: RNA-seq: TEX_UT_2

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

country: Canada

institute: Research Institute of McGill University Hospital Centre

data_processing:
For ChIP-seq data, reads were trimmed of TruSeq adaptor sequences using trimmomatic. Trimmed reads were then aligned to hg19 and dme5 using BWA-MEM, PCR duplicates were soft-clipped using Picard. BigWig files were generated  using Homer, and consist of uniquely aligned reads without PCR duplicates. Enrichment of H3K27me3 or H3K27ac were calculated as reads per million per kilobase mapped (RPKM) over all annotated ENSEMBL promoter (+/- 2.5kb), and multiplied by Rx ratio.
For RNA-seq data, reads were trimmed of TruSeq adaptor sequences using trimmomatic. Trimmed reads were then aligned to hg19 transcriptome using STAR aligner. PCR duplicates were flagged and bigWig files were generated using uniquely aligned reads without PCR duplicates. RNA-seq were then quantitated using reads anti-sense to all annotated ENSEMBL transcript as reads per million per kilobase mapped (RPKM) over exonic regions.
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg files

source_name: TEX

growth_protocol: TEX cells were grown in IMDM containing 4mM L-glutamine, 15% fetal bovine serum, 20ng/ml SCF, 2ng/ml IL-3 and penicillin/streptomycin.

extract_protocol:
For crosslinked  ChIP, cells were crosslinked (1% formaldehyde, 10mins) and sonicated. Protein:DNA complexes were immunoprecipitated with specific antibodies pre-bound to protein A or goat anti-mouse IgG magnetic beads. Eluted DNA underwent crosslink reversal, and were purified using Qiagen PCR purification columns. For RNA extraction, 1 million TEX cells were pelleted, washed with PBS and resuspended in 350ul RLT buffer (Qiagen-RNAeasy mini kit) with beta-mercaptoethanol. The suspension was then stored at -80oC until frozen. Sample was thawed and RNA extraction was performed using Qiagen's RNAeasy mini kit as per the manufacturer's instructions.
The eluted ChIP DNA undewent adaptor ligation based library construction for single-end 50bp Illumina sequencing on HiSeq 4000. RNA-seq library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts, paired-end sequencing (100 bp) was performed on the Illumina HiSeq 2500 or 4000 platform.

treatment_protocol: TEX cells were transduced with lentiviral particles at an MOI 3 to overexpress HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2 using the pSMAL lentivirus vector (Amendola et al. Nat Biotechnol, 2005; van Galen et al. Nature, 2014). 16h after transduction, media was changed. Cells were then expanded and sorted for transduced cells (GFP+).

tag: cell type

value: TEX

tag: transgene

value: Untransfected

tag: mutation


title: reporter_triptolide_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep1


title: RNA-seq: TEX_UT_1


title: RNA-seq: TEX_UT


title: CHC040T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: AB162507_HCMEC_1KOD9_S7_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB162507_HCMEC_1KOD9_S7_R1

tag: culture media

tag: library preparation kit


title: reporter_dmso_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

tag: treatment

value: 2% v/v DMSO 1h


title: RNA-seq: TEX_Luc2_2

tag: cell type

tag: transgene

value: Luciferase

tag: mutation


title: CHC034T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

tag: alcohol

value: no

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

value: Splice_Site g.chrX:20185706C>T

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

value: HD

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: CHC037T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: yes

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

value: c.-124C>T + Missense_N898S

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

value: NM

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation


title: reporter_triptolide_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: chip antibody

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

tag: treatment


title: AB161807_HCMEC-3KOB12_S12_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB161807_HCMEC-3KOB12_S12_R1

tag: culture media

value: EndoGRO™-MV Complete Media Kit (Milipore SCME004) supplementel with FGF2

tag: library preparation kit

value: KAPA Stranded mRNAseq kit


title: CHC031T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation


title: CHC030T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation


title: AB161807_HCMEC-2KOB2_S7_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB161807_HCMEC-2KOB2_S7_R1

tag: culture media

tag: library preparation kit


title: reporter_dmso_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

tag: treatment


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus_rep1

value: 500 uM Triptolide 1h


title: AB161807_HCMEC-1KOD9_S5_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB161807_HCMEC-1KOD9_S5_R1


title: CHC028T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: RNA-seq: TEX_H3-1H_WT_2

tag: cell type

value: TEX

tag: transgene

tag: mutation

value: WT


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

tag: treatment

value: 2% v/v DMSO 1h


title: RNA-seq: TEX_H3-1H_WT_1


title: CHC022T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: AB150723_HUVEC_shCCM1-2_3D

description:
HUVEC DeSeq
HUVEC_read_counts
AB150723_HUVEC_shCCM1-2_3D_sorted

source_name: HUVEC

tag: culture media

value: EGM-2 BulletKit (lonza)

tag: library preparation kit


title: CHC020T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: AB150706_HUVEC_shCCM3-2_3D_S9_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM3-2_3D_S9_R1_sorted_genome_alignments

tag: culture media

tag: library preparation kit


title: RNA-seq: TEX_H3-1H_WT

tag: cell type

tag: transgene

tag: mutation


title: AB161807_HCMEC_WT_R3_S3_R1

description:
HCMEC DeSEq
HCMEC_read_counts
AB161807_HCMEC_WT_R3_S3_R1


title: reporter_triptolide_5m_dps_act5c_rpb3_chipnexus_rep1

treatment_protocol: Kc167 cells were transfected with a reporter containing promoter sequence of interests. Cells were cultured at 25C for 48 h and treated with Triptolide (500 uM, dissolved in DMSO) or DMSO (2% v/v) at RT for 5 min.

tag: cell line

tag: chip antibody

tag: treatment

value: 500 uM Triptolide 5 min


title: RNA-seq: TEX_H3-1H_K27M_2


title: reporter_dmso_5m_dps_act5c_pk_downstream_rpb3_chipnexus_rep1

value: 2% v/v DMSO 5 min


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM2-5_3D_10mMY27632_18hr_S11_R1_sorted_genome_alignments


title: RNA-seq: TEX_Luc2

value: Luciferase


title: RNA-seq: TEX_Luc2_1


title: CHC018T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

value: NM

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

value: HD

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status


title: reporter_triptolide_5m_dps_act5c_pk_downstream_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: chip antibody

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

tag: treatment


title: CHC016T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

value: M

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: RNA-seq: TEX_H3-1H_K27M_1

tag: cell type

value: TEX

tag: transgene

tag: mutation


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus

tag: cell line

tag: chip antibody

tag: treatment

value: 500 uM Triptolide 1h


title: CHC014T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation


title: AB150706_HUVEC_shCCM2-1_3D_S8_R1_

description:
HUVEC DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM2-1_3D_S8_R1_sorted_genome_alignments

tag: culture media

tag: library preparation kit

value: KAPA Stranded mRNAseq kit


title: CHC013T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM1-2_3D_10mMY27632_18hr_S2_R1_sorted_genome_alignments

tag: culture media

tag: library preparation kit


title: RNA-seq: TEX_H3-1F_WT_1

tag: cell type

tag: transgene

tag: mutation

value: WT


title: RNA-seq: TEX_H3-1F_WT


title: RNA-seq: TEX_H3-1H_K27M


title: AB150706_HUVEC_shCCM1-2_3D_S1_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM1-2_3D_S1_R1_sorted_genome_alignments

value: EGM-2 BulletKit (lonza)


title: AB150706_HUVEC_shCCM2-5_3D_R3_S10_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150706_HUVEC_shCCM2-5_3D_R3_S10_R1_sorted_genome_alignments


title: RNA-seq: TEX_H3-1F_WT_2


title: reporter_dmso_5m_dps_act5c_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

tag: treatment


title: AB150706_HUVEC_CONTROL_3D_R2_S3_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150706_HUVEC_CONTROL_3D_R2_S3_R1_sorted_genome_alignments


title: AB150225_HUVEC_shCCM3-2_3D_R3_S6_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM3-2_3D_R3_S6_R1_sorted_genome_alignments


title: RNA-seq: TEX_H3-1F_K27I_2


title: reporter_triptolide_1h_dps_comm2_rpb3_chipnexus


title: CHC008T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

value: RESECTION

value: no

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: setd2 status


title: RNA-seq: TEX_H3-1F_K27I

tag: cell type

tag: transgene

tag: mutation


title: CHC012T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: map1b status

tag: map1b mutation


title: RNA-seq: TEX_H3-1F_K27I_1

tag: cell type

tag: transgene

tag: mutation


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM3-2_3D_10mMY27632_18h_S5_R1_sorted_genome_alignments

tag: culture media

tag: library preparation kit


title: reporter_dps_dve_rpb3_chipnexus

treatment_protocol: Kc167 cells were transfected with a reporter containing promoter sequence of interests and cultured at 25C for 48 h.

tag: cell line

tag: chip antibody

tag: treatment


title: AB150225_HUVEC_shCCM2-5_3D_S3_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM2-5_3D_S3_R1_sorted_genome_alignments


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus

value: 2% v/v DMSO 1h


title: CHC010T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status


title: ChIP-seq: TEX-Luciferase-Rx_cells_ChIP1_H3K27me3_1

tag: cell type

tag: transgene

value: Luciferase

tag: mutation

tag: chip antigen


title: ChIP-seq: TEX-Luciferase-Rx_cells_ChIP1_Input_1

value: Input


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM2-5_3D_10mMY27632_18h_R3_S4_R1_sorted_genome_alignments

tag: culture media

tag: library preparation kit


title: reporter_dps_cg12730_rpb3_chipnexus

tag: cell line

value: Kc167 cells

tag: chip antibody

tag: treatment


title: reporter_dmso_1h_dps_comm2_rpb3_chipnexus

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)


title: reporter_scp_rpb3_chipnexus


title: AB150225_HUVEC_shCCM2-1_3D_S1_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM2-1_3D_S1_R1_sorted_genome_alignments


title: reporter_dps_comm2_rpb3_chipnexus


title: reporter_dps_pxb_rpb3_chipnexus


title: AB150225_HUVEC_shCCM1-2_3D_R3_S8_R

description:
HUVEC DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM1-2_3D_R3_S8_R1_sorted_genome_alignments


title: ChIP-seq: TEX-Luciferase-2-Rx_cells_ChIP1_H3K27ac_1


title: ChIP-seq: TEX-HIST1H3H-WT-Rx_cells_ChIP1_Input_1


title: ChIP-seq: TEX-Luciferase-Rx_cells_ChIP1_H3K27ac_1


title: reporter_dps_pepck_rpb3_chipnexus


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM1-2_3D_10mMY27632_18h_R3_S7_R1_sorted_genome_alignments


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_shCCM2-1_3D_10mMY27632_18h_R3_S2_R1_sorted_genome_alignments


title: reporter_dps_pino_rpb3_chipnexus


title: ChIP-seq: TEX-HIST1H3H-WT-Rx_cells_ChIP1_H3K27me3_1


title: AB150225_HUVEC_Control_3D_R1_S11_R1

description:
HUVEC DeSeq
HUVEC_read_counts
AB150225_HUVEC_Control_3D_R1_S11_R1_sorted_genome_alignments


title: ChIP-seq: TEX-HIST1H3H-WT-Rx_cells_ChIP1_H3K27ac_1


title: reporter_dps_pk_rpb3_chipnexus


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_Control_3D_10mMY27632_18h_R3_S12_R1_sorted_genome_alignments


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150225_HUVEC_Control_3D_10mMY27632_18h_R3_S10_R1_sorted_genome_alignments


title: AB150206_HUVEC_shCCM3-2_3D_R2

description:
HUVEC DeSeq
HUVEC_read_counts
AB150206_HUVEC_shCCM3-2_3D_R2_sorted


title: reporter_dps_act5c_rpb3_chipnexus


title: 1500 ppm of hexanal was exposed in rats (T3 group) 38

type: genomic

city: Seoul

first: Yoon

last: Cho

address: hwarang-ro 14

country: South Korea

institute: KIST

description: T3 group

hyb_protocol: After checking labeling efficiency, each 2.5ug to 5ug of cyanine 3-labeled and cyanine 5-labeled DNA target were mixed and then resuspended with 2X hybridization buffer, Cot-1 DNA, and Agilent 10X blocking agent, and de-ionized formamide. Before hybridization to the array, the 260ul hybridization mixtures were denatured at 95℃ for 3min and incubated at 37℃ for 30min. The hybridization mixtures were was centrifuged at 17,900 xg for 1min and directly pipetted onto the Agilent’s Rat CpG 2X400K. The arrays hybridized at 65oC for 40 h using Agilent Hybridization oven(Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA) and the data quantification was performed using Agilent Feature Extraction software (Agilent Technology, USA).

data_processing: Preprocessing of raw data and normalization steps were performed using Agilent Genomic Workbench software, according to the manufacturer’s instructions (Agilent, USA). The background-corrected intensity data were normalized with blank subtraction followed by intra-array LOWESS normalization.

organism: Rattus norvegicus

source_name: IP 38

label_protocol: The immunoprecipitated and input DNA were amplified by using whole genome amplification kit (GenomePlex® Complete Whole Genome Amplification Kit, Sigma, USA) as recommended by manufacturer. The amplified samples were purified by using QIAQuick PCR clean-up kit (Qiagen). Labeling reactions were performed with 4ug of purified amplified DNA and a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions in a volume of 50ul with a modified dNTP pool containing 120uM each of dATP, dGTP, and dCTP; 60uM dTTP; and 60uM Cy5-dUTP (for the IPsample) or Cy3-dUTP (for theinput sample).

extract_protocol: Genomic DNA was extracted from the homogenized lung tissue of rats using DNA Mini kit (Qiagen, Germany) following manufacturer's instructions

tag: gender

value: female

tag: agent

value: 1500 ppm of hexanal

source_name: input


description:
HUVEC +Y27632 DeSeq
HUVEC_read_counts
AB150206_HUVEC_shCCM3-2_3D_10mMY27632_18h_R2_sorted


title: ChIP-seq: TEX-HIST1H3H-WT-2-Rx_cells_ChIP1_H3K27ac_1

value: TEX


title: ChIP-seq: TEX-HIST1H3H-K27M-Rx_cells_ChIP1_H3K27ac_1


title: ChIP-seq: TEX-HIST1H3H-K27M-2-Rx_cells_ChIP1_H3K27ac_1


title: ATAC-seq: iNeuron line 2 condition: iNeuron replicate: 2

data_processing:
ATAC-seq reads were aligned to a combined human-rat reference genome (respectively hg19 and rn6) using BWA sampe (Li and Durbin, 2010) with default parameters.
All rn6-mapping reads and all h19-mapping reads with a mapping quality ≤ 40 were removed from the bam file (Number of mapped reads in Table S7).
Peak calling was performed on the bam files using the MACS2 algorithm (Zhang et al., 2015) (parameters: -f BAMPE -g hs --nomodel -q 0.001). Note that for the peak calling the two replicates of each cell line were taken together.
BigWig files were created using the deeptools command bamCoverage --bam  -o --binSize 1 --normalizeUsingRPKM --extendReads.
Genome_build: Combined hg19/rn6 reference
Supplementary_files_format_and_content: BigWig coverage file aligned to combined hg19/rn6 reference

organism:
Homo sapiens
Rattus norvegicus

source_name: iNeuron line 2

extract_protocol:
iPSCs were harvested using accutase (Sigma-Aldrich) and fibroblasts using 0.25% trypsin (Gibco). Approximately 50,000 cells were collected and washed once with ice-cold PBS. Cells were centrifuged at 300 g and the supernatant was removed. iNeurons were not harvested, but 1-2 wells of the 12-well plate cultures (containing 50,000-100,000 cells) were washed once with ice-cold PBS.  Isolation of the nuclei was performed by adding 500 μL lysis buffer (10 mM Tris/HCl [pH = 7.5], 10 mM NaCl, 3 mM MgCl2 and 0.2 % [vol/vol] IGEPAL, in Milli-Q water/PBS [1:1]) to the cell pellet (iPSCs and fibroblasts) or to the cells on the plate (iNeurons), followed by mechanically dissociating the cells using a pipette. Nuclei were centrifuged at 500 g for 30 minutes. The pellet was washed once with ice-cold PBS and centrifuged at 500 g for 15 minutes.
After removing most of the supernatant without disturbing the pellet, the nuclei were resuspended in a master mix of 10.5 μL nuclease-free water, 12.5 μL TD buffer and 2 μL Tn5 transposase (both Illumina Nextera DNA Library Prep kit) followed by incubation in a shaking heat block at 37 °C/650 rpm for 1 hour. After incubation, the reaction was cleaned by adding 5 μL clean-up buffer (0.9 M NaCl and 0.3 M EDTA [pH = 8] in nuclease-free water), 2 μL proteinase K (10 mg/mL) and 2 μL 5 % SDS. DNA was purified using normal-phase 2x AMPure bead purification (Beckman Coulter). The purified DNA was PCR amplified in 8 PCR cycles, followed by reverse-phase 0.55x AMPure bead purification (Beckman Coulter) and QIAquick column purification (Qiagen). The size-selected, purified PCR product was PCR amplified for another 8 PCR cycles, followed by QIAquick column purification (Qiagen). The fragment length distribution was determined using TapeStation (Agilent) and library concentration was quantified using KAPA library quantification kit (KAPA Biosystems).

treatment_protocol: iNeuron differentiation was performed as described previously (DOI: 10.3791/54900). Briefly, rtTA/Neurog2-positive iPSC lines were differentiated to iNeurons via doxycyclin-dependent Neurog2 overexpression over a period of 21 days.

value: iPSC-derived neuron

value: iNeuron line 2 (derived from IPS1500024/293)


title: ChIP-seq: TEX-HIST1H3F-WT-Rx_cells_ChIP1_Input_1

value: WT


title: 1500 ppm of hexanal was exposed in rats (T3 group) 36

description: T3 group

source_name: IP 36


title: 1500 ppm of hexanal was exposed in rats (T3 group) 37

description: T3 group

source_name: IP 37


title: ChIP-seq: TEX-HIST1H3F-WT-Rx_cells_ChIP1_H3K27me3_1


title: ChIP-seq: TEX-HIST1H3H-K27M-Rx_cells_ChIP1_H3K27me3_1


title: 1000 ppm of hexanal was exposed in rats (T2 group) 27

description: T2 group

source_name: IP 27

value: 1000 ppm of hexanal


title: 1000 ppm of hexanal was exposed in rats (T2 group) 28

description: T2 group

source_name: IP 28


title: ChIP-seq: TEX-HIST1H3H-K27M-Rx_cells_ChIP1_Input_1


title: ChIP-seq: TEX-HIST1H3F-WT-Rx_cells_ChIP1_H3K27ac_1


title: ATAC-seq: iNeuron line 1 condition: iNeuron replicate: 2

source_name: iNeuron line 1

value: iNeuron line 1 (derived from IPS1500030/C2)


title: Cord Blood_P20

city: Philadelphia

first: Zubair

middle: H

last: Aghai

state: PA

address: 833 Chestnut Street, Suite 1201

department: Pediatrics/ Neonatology

institute: Thomas Jefferson University/ Nemours

description: sst-RMA expression value derived from Expression Console software; gene level analysis

hyb_protocol: Affymetrix gene chips HTA 2.0 array was hybridized with fragmented and biotin-labeled target (5 ug) in 220 ul of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization for 16-18 h.

scan_protocol: Chips (HTA 2.0) were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Chp files were generated by Gene Level-SST-RMA normalization from Affymetrix cel file by using Expression Console Software 1.4. HCA group was compare with Control group by using Transcriptome Analysis Console software 3.1 and GeneSpring 14.9.1

label: biotin

source_name: Chorioamnionitis exposed neonate

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the Affymetrix GeneChip WT PLUS reagent kit

growth_protocol: Cord blood was collected in sterile EDTA tubes and Mononuclear Leucocytes were isolated by Ficoll-Paque Plus density gradient

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit from 2 million cells according to manufacturer's instruction

tag: tissue

value: cord blood

value: Mononuclear Leukocytes


title: Cord Blood_P18


title: Cord Blood_P25


title: ATAC-seq: iNeuron line 2 condition: iNeuron replicate: 1


title: ATAC-seq: iNeuron line 1 condition: iNeuron replicate: 1


title: Cord Blood_P29


title: ChIP-seq: TEX-HIST1H3F-K27I-Rx_cells_ChIP1_Input_1


title: ChIP-seq: TEX-HIST1H3F-WT-2-Rx_cells_ChIP1_H3K27ac_1


title: 1500 ppm of hexanal was exposed in rats (T3 group) 33

description: T3 group

source_name: IP 33

value: male


title: 1500 ppm of hexanal was exposed in rats (T3 group) 32

description: T3 group

source_name: IP 32


title: Cord Blood_P12


title: ChIP-seq: TEX-HIST1H3F-K27I-Rx_cells_ChIP1_H3K27me3_1


title: RNA-seq: iNeuron line 2 condition: iNeuron replicate: 2


title: 1000 ppm of hexanal was exposed in rats (T2 group) 22

description: T2 group

source_name: IP 22


title: RNA-seq: iNeuron line 2 condition: iNeuron replicate: 1


title: ChIP-seq: TEX-HIST1H3F-K27I-Rx_cells_ChIP1_H3K27ac_1


title: Cord Blood_P30

source_name: Healthy Neonate


title: 600 ppm of hexanal was exposed in rats (T1 group) 18

description: T1 group

source_name: IP 18

value: 600 ppm of hexanal


title: RNA-seq: iNeuron line 1 condition: iNeuron replicate: 2


title: ChIP-seq: TEX-HIST1H3F-K27I-2-Rx_cells_ChIP1_H3K27ac_1


title: 1500 ppm of hexanal was exposed in rats (T3 group) 31

description: T3 group

source_name: IP 31


title: 1000 ppm of hexanal was exposed in rats (T2 group) 26

description: T2 group

source_name: IP 26


title: RNA-seq: iNeuron line 1 condition: iNeuron replicate: 1


title: 600 ppm of hexanal was exposed in rats (T1 group) 13

description: T1 group

source_name: IP 13


title: 1000 ppm of hexanal was exposed in rats (T2 group) 23

description: T2 group

source_name: IP 23


title: 2mpf_Pancreas

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 5000 (all other options were used as per default).
To build the reference for Cell Ranger, zebrafish genome (GRCz10) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lincRNA –attribute=gene_biotype:antisense’). Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.
Genome_build: Zebrafish GRCz10
Supplementary_files_format_and_content: csv format with rows as genes and columns as cells

organism: Danio rerio

source_name: pancreatic-cells

extract_protocol:
Enzymatic Dissociation
The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 5000 cells. Subsequently, the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system (Zheng et al., 2016).  After the gel emulsion bead suspension underwent the reverse transcription reaction, emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles, following the guidelines of the 10x Genomics user manual.  The 10X Genomics single cell RNA-seq library preparation - involving fragmentation, dA-Tailing, adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol.

tag: age

tag: strain

tag: disease state

value: Normal


title: Cord Blood_P24


title: 600 ppm of hexanal was exposed in rats (T1 group) 17

description: T1 group

source_name: IP 17

source_name: input


title: Cord Blood_P21


title: 600 ppm of hexanal was exposed in rats (T1 group) 11

description: T1 group

source_name: IP 11


title: 1000 ppm of hexanal was exposed in rats (T2 group) 21

description: T2 group

source_name: IP 21


title: 600 ppm of hexanal was exposed in rats (T1 group) 12

description: T1 group

source_name: IP 12


title: WT1

status: Public on Apr 04 2019

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

description: Replicate 1 for transcriptome of wild type stem fragment

data_processing:
Read quality was checked for each sample using FastQC v0.11.7
High-quality reads were imported into TopHat v2.0.14 for alignment against the Arabidopsis genome TAIR10 into BAM files
BAM files were used to count reads in R (https://cran.r-project.org/)
Statistical analysis was performed using DESeq2 package from the R/Bioconductor software
Genome_build: TAIR10
Supplementary_files_format_and_content: DESeq2 output and raw read count

organism: Arabidopsis thaliana

source_name: Stem base

growth_protocol: Prior to grafting: Seedlings were grown on Murashige and Skoog (MS) medium-plates containing 0.8 % phyto agar and 1 % sucrose in short day conditions (8 h light and 16 h dark) at 22°C for 5 days. Roots were exchanged by wild type roots of the same age by grafting as described in Melnyk and Meyerowitz 2015. Freshly grafted seedlings were kept for 6 days on wetted filter paper in sterile conditions to ensure reconnection of the vasculature and then transferred for another 7 days on MS-plates for recovery. After grafting: Well-connected grafts were transferred to soil and kept in short day conditions for another 3 days. After 21 days (3 weeks) plants were transferred to log day conditions (16 h light and 8 h dark) at 22 °C and 60 % humidity. Samples (1 cm stem fragments at the stem base) were collected from 15-20 cm high Arabidopsis plants.

extract_protocol:
RNA was extracted from 1-cm stem segments including the stem base. Three stem segments were pooled into one biological replicate. Tree biological replicates were collected per genotype. RNA was extracted by phenol/chlorophorm as described (Mallory and Vaucheret 2010, PlantCell) with the modifcation of two additional concluding 70% EtOH washes. 2 µg of total RNA were treated by DNase (Fermantas) and sumbitted for library preparation to the Deep Sequencing Core Facility provided by the Exzellenzkluster CellNetworks at the University of Heidelberg (http://www.cellnetworks.uni-hd.de/483065/Deep_Sequencing_Core_Facility).
RNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit with NEBnext Multiplex Oligos for Illumina. For Poly A selection the NEBNext Poly A selection module was used. RNA fragmentation time was 15 minutes, and 12 cycles of PCR were used for amplification. All library preparation steps were executed by the Deep Sequencing Core Facility provided by the Exzellenzkluster CellNetworks at the University of Heidelberg (http://www.cellnetworks.uni-hd.de/483065/Deep_Sequencing_Core_Facility)

value: stem base

tag: genotype of analyzed stem fragment

value: wild type

tag: genotype of root (attached by grafting)

tag: stem height at time of sample collection

tag: number of individual stem fragments pooled into one sample


title: S2

description: Replicate 2 for transcriptome of smxl4 smxl5 stem fragment

value: smxl4 smxl5


title: WT2


title: S3

description: Replicate 3 for transcriptome of smxl4 smxl5 stem fragment


title: Cord Blood_P15

tag: cell type


title: WT3


title: Cord Blood_P17


title: 600 ppm of hexanal was exposed in rats (T1 group) 16

description: T1 group

source_name: IP 16


title: S1

description: Replicate 1 for transcriptome of smxl4 smxl5 stem fragment


title: filtered clean air was exposed in rats (control group) 7

description: Control group

source_name: IP 7

value: filtered clean air


title: filtered clean air was exposed in rats (control group) 3

description: Control group

source_name: IP 3


title: filtered clean air was exposed in rats (control group) 8

description: Control group

source_name: IP 8

value: female


title: filtered clean air was exposed in rats (control group) 6

description: Control group

source_name: IP 6


title: CD8-Adverse CD8_P9

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description:
Gene expression data
Well-defined cell populations were FACS-purified from BM of newly diagnosed AML patients and also control subjects.

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol: Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

value: M


title: CD8-Adverse CD8_P8


title: CD8-Intermediate CD8_P7

value: F


title: filtered clean air was exposed in rats (control group) 2

description: Control group

source_name: IP 2


title: CD8-Adverse CD8_P6


title: CD8-Favorable CD8_P32


title: CD8-Intermediate CD8_P4


title: CD8-Intermediate CD8_P28


title: CD8-Adverse CD8_P30


title: CD8-Intermediate CD8_P24


title: CD8-Adverse CD8_P5


title: CD8-Favorable CD8_P17


title: CD8-Intermediate CD8_P23


title: CD8-Intermediate CD8_P21


title: CD8-Intermediate CD8_P22


title: CD8-Favorable CD8_P15


title: CD8-Adverse CD8_P3


title: filtered clean air was exposed in rats (control group) 1

description: Control group

source_name: IP 1


title: CD8-Intermediate CD8_P33


title: CD8-Adverse CD8_P19


title: CD8-Intermediate CD8_P29


title: CD8-Intermediate CD8_P18


title: CD8-Favorable CD8_P11


title: CD8-Favorable CD8_P16


title: CD8-Intermediate CD8_P20


title: CD8-Favorable CD8_P31


title: CD8-Ctrl CD8_C9


title: CD8-Favorable CD8_P14


title: CD8-Adverse CD8_P1


title: CD8-Favorable CD8_P12


title: CD8-Ctrl CD8_C8


title: CD8-Adverse CD8_P10


title: CD8-Ctrl CD8_C7


title: CD8-Ctrl CD8_C6


title: CD8-Favorable CD8_P13


title: CD8-Ctrl CD8_C11


title: CD8-Ctrl CD8_C10


title: LPC-Adverse CD38_P8

source_name: LPC-Adverse


title: LPC-Adverse CD38_P6


title: LPC-Adverse CD38_P3


title: CD8-Adverse CD8_P2


title: LPC-Intermediate CD38_P24

source_name: LPC-Intermediate


title: LPC-Intermediate CD38_P4


title: LPC-Intermediate CD38_P28


title: LPC-Favorable CD38_P31

source_name: LPC-Favorable


title: LPC-Intermediate CD38_P22


title: LPC-Adverse CD38_P2


title: LPC-Favorable CD38_P32


title: LPC-Adverse CD38_P19


title: LPC-Favorable CD38_P14


title: LPC-Intermediate CD38_P21


title: LPC-Favorable CD38_P13


title: LPC-Adverse CD38_P9


title: LPC-Adverse CD38_P5


title: LPC-Intermediate CD38_P23


title: LPC-Intermediate CD38_P29


title: LPC-Intermediate CD38_P20


title: LPC-Intermediate CD38_P33


title: LPC-Intermediate CD38_P18


title: LPC-Intermediate CD38_P7


title: LPC-Favorable CD38_P17


title: CD8-Ctrl CD8_C4


title: LPC-Favorable CD38_P11


title: LPC-Adverse CD38_P30


title: LPC-Favorable CD38_P15


title: LPC-Adverse CD38_P10


title: LPC-Adverse CD38_P1


title: HPC-Ctrl CD38_C8

source_name: HPC-Ctrl


title: LPC-Favorable CD38_P12


title: LSC-Adverse CD34_P6

source_name: LSC-Adverse


title: HPC-Ctrl CD38_C9


title: LSC-Adverse CD34_P9


title: HPC-Ctrl CD38_C11


title: HPC-Ctrl CD38_C4


title: HPC-Ctrl CD38_C6


title: LSC-Favorable CD34_P31

source_name: LSC-Favorable


title: LSC-Intermediate CD34_P20

source_name: LSC-Intermediate


title: LSC-Intermediate CD34_P4


title: LSC-Intermediate CD34_P21


title: LSC-Intermediate CD34_P33


title: HPC-Ctrl CD38_C7


title: LSC-Adverse CD34_P30


title: LSC-Adverse CD34_P8


title: LSC-Intermediate CD34_P24


title: LSC-Intermediate CD34_P7


title: LSC-Intermediate CD34_P23


title: LSC-Adverse CD34_P3


title: LSC-Intermediate CD34_P28


title: LPC-Favorable CD38_P16


title: LSC-Intermediate CD34_P22


title: LSC-Adverse CD34_P5


title: LSC-Favorable CD34_P32


title: HPC-Ctrl CD38_C10


title: LSC-Intermediate CD34_P18


title: LSC-Adverse CD34_P19


title: LSC-Favorable CD34_P16


title: LSC-Adverse CD34_P2


title: LSC-Favorable CD34_P15


title: LSC-Favorable CD34_P17


title: LSC-Favorable CD34_P13


title: TGP-210-RL_3

city: Jupiter

first: Matthew

last: Costales

state: FL

address: 130 Scripps Way, A359

institute: The Scripps Research Institute Florida

description:
sample name:
326-12

data_processing:
Illumina reads were trimmed and clipped for quality control in Trimmomatic v0.35.
Read quality was checked for each sample using FastQC v0.11.4.
Sequencing reads were mapped against the human reference genome (hg19, NCBI build 37) using Kallisto v0.42.4
Differential expression analysis was done using gene mode in Sleuth v0.30.0.
Genome_build: hg19, NCBI build 37
Supplementary_files_format_and_content: kallisto_table.csv: Comma-separated values file with Transcripts per million and scaled reads per base corresponding to each gene for each sample.

growth_protocol: MDA-MB-231 (HTB-26; ATCC) cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 media with L-glutamine & 25 mM HEPES (Corning) supplemented with 10% fetal bovine serum (FBS) (Sigma) and 1× Penicillin Streptomycin Solution (Corning).  Cells cultured in hypoxia were maintained at 37 °C, < 1% O2 in a nitrogen filled hypoxic chamber (Billups-Rothenberg, Inc.), and 5% CO2.  Cells were directly purchased from ATCC.

extract_protocol:
Cell culture media was removed and the monolayer was washed with DPBS.  Total RNA was extracted using a miRNeasy Mini Kit (Qiagen) using an on-column DNase I treatment, following the manufacturer's protocol.
A Qubit 2.0 Fluorometer (Invitrogen) and an Agilent Technologies 2100 Bioanalyzer with an RNA nano chip were used to quantify and assess the quality of RNA, respectively.  Only samples with RNA Integrity Number > 8.0 were used.  NEBNext rRNA depletion modules (Catalog #: E6310L, New England Biosciences) were used to deplete rRNA on 500 ng of total RNA, according to manufacturer’s instructions.  A NEBNext Ultra II Directional RNA kit (Catalog #: E7760, New England Biosciences) was used for library preparation according to the manufacturer’s instructions.  RNA samples were then chemically fragmented, primed with random hexamers, and reverse transcribed to convert fragmented RNA to first strand cDNA.  The RNA template was removed and dUTP was incorporated in place of dTTP, after which the second strand of cDNA was synthesized by end repair and 3’ end adenylation.  A hairpin loop adaptor was used to ligate an adaptor A corresponding T nucleotide on the hairpin loop adaptor was used to ligate an adaptor to the double-stranded cDNA.  Uracil-specific excision reagent (USER) enzyme was then used to remove the dUTP in the loop, as well as other incorporated U’s in the second strand.  Final libraries were generated by PCR amplifying adaptor ligated DNA with Illumina barcoding primers, where fragments with both 5’ and 3’ adaptors would be enriched in the final PCR step.  Libraries were normalized to 2 nM, validated by a Bioanalyzer DNA chip, pooled equally, and then sequenced on a NextSeq500 v2.5 flow cell (1.8 pM) using paired-end chemistry (2 × 40 bp).  Approximately 20-25 million reads were generated per sample with a base quality score >Q30 (less than 1 error per 1000 bp).

treatment_protocol: For compound treatment (TGP-210-RL or DMSO), compound stocks in DMSO were diluted in growth medium and added to cells for 24 h.

value: 24 h of TGP-210-RL treatment in hypoxia


title: Vehicle_3

description:
sample name:
326-4

value: 24 h of DMSO treatment in hypoxia


title: Vehicle_1

description:
sample name:
326-1


title: TGP-210-RL_2

description:
sample name:
326-11


title: TGP-210-RL_1

description:
sample name:
326-10


title: Vehicle_2

description:
sample name:
326-2


title: HepG2_HCF1si_3

city: Boston

first: John

middle: G

last: Flanagan

state: MA

address: 200 Longwood Ave, Building C2, Room 523

department: Cell Biology

institute: Harvard Medical School

data_processing:
RNA samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (v0.9.1a; https://bcbio-nextgen.readthedocs.org/en/latest/).
Adapter sequences were trimmed from reads using Cutadapt (v1.4.2) (Martin, 2011).
Trimmed reads were aligned to the hg19 genome using STAR (v2.4.1d) (Dobin et al., 2013).
Read quantitation was performed with featureCounts (v1.4.4) (Liao et al., 2014).
Differential expression of genes was performed using DESeq2 (v1.16.1) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: CSV matrix file of normalized counts generated using DESeq2.

source_name: HepG2_HCF-1 siRNA

growth_protocol: For RNA-seq, eight biological replicates were used for each condition. HepG2 cells were maintained in EMEM supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Total RNA from cells was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA-seq libraries were constructed using TruSeq Stranded mRNA (Illumina) according to manufacturer’s instruction.

treatment_protocol: For siRNA transfection, HepG2 cells were reverse transfected using siPORT NeoFX (Invitrogen). The transfection procedure was repeated two days later, and RNA extraction was performed two days after the second transfection.

value: HCF-1 siRNA


title: HepG2_consi_8

source_name: HepG2_control siRNA

value: control siRNA


title: HepG2_HCF1si_5


title: HepG2_HCF1si_4


title: HepG2_consi_7


title: HepG2_HCF1si_6


title: HepG2_HCF1si_7


title: HepG2_HCF1si_1


title: LSC-Adverse CD34_P1


title: HSC-Ctrl CD34_C8

source_name: HSC-Ctrl


title: HepG2_HCF1si_8


title: HSC-Ctrl CD34_C7


title: HSC-Ctrl CD34_C11


title: HSC-Ctrl CD34_C4


title: HepG2_consi_5


title: HepG2_consi_1


title: HepG2_consi_2


title: HSC-Ctrl CD34_C6


title: LSC-Adverse CD34_P10


title: HepG2_input_Pol2_starve_rep1

description:
input used for Pol2 rep-1 starve sample
20150624-11

data_processing:
ChIP-seq data quality was evaluated by using FASTQC (Andrews, 2010), and if required, reads were trimmed with Cutadapt (v1.4.2) (Martin, 2011).
High quality sequencing reads were mapped to the human genome UCSC build hg19 using Bowtie2 2.2.8 (Langmead and Salzberg, 2012). Alignments (BAM files) were filtered to retain only reads with a unique mapping to the genome.
Peaks were called with MACS2 2.1.1 (Zhang et al., 2008) using default parameters, and a narrow peak cutoff of P<0.001.
To assess the reproducibility of peaks across replicates, samples were run through the IDR pipeline (Babu et al., 2011), in which peak consistency was validated by use of pooled pseudo-replicates.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain genomic coordinates for peaks that were identified as reproducible, per the IDR analysis. BigWig files were generated from BAM files using Deeptools within the Galaxy platform (v1.0.4).

growth_protocol: For ChIP-seq, two biological replicates from independent experiments were used for each condition. HepG2 and SH-SY5Y cells were maintained in EMEM or a 1:1 mixture of EMEM and F-12 medium, respectively. Medium was supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Lysates were clarified from sonicated nuclei and IR-DNA or Pol2-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using Thruplex DNAseq kit (Rubicon) according to manufacturer’s instruction.

treatment_protocol: For serum starvation, medium was removed, cells were washed three times with PBS, and medium supplemented with 0.1% BSA was added to cells for 16h. Cells were stimulated with 10 nM insulin for 20min.

value: serum starvation


title: HepG2_consi_4


title: HepG2_input_IRb_starve_rep1

description:
input used for IRb rep-1 starve sample
20150624-5


title: LSC-Favorable CD34_P14


title: HepG2_HCF1si_2


title: HepG2_consi_3


title: HepG2_consi_6


title: HSC-Ctrl CD34_C10


title: HepG2_Pol2_starve_rep2

value: rabbit, anti-Pol2, CST_2629


title: HepG2_input_Pol2_rep1

description:
input used for Pol2 rep-1 sample
20150624-12


title: HepG2_Pol2_starve_rep1


title: DLS395_CEH-60_3F10_IP_r2

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

data_processing:
The adapter-trimmed ChIP-Seq reads were mapped to the WS260 genome with bowtie2 using the default parameters.
Low quality reads (view -bS -q 10) and duplicate reads (rmdup -s) were removed using the SAMtools package (Li et al., Bioinformatics, 2009).
ChIP-Seq peaks were identified from the filtered sequencing read files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.
ChIP-Seq enrichment calculations were performed using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016).  The enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Genome_build: WS260
Supplementary_files_format_and_content: BigWig ChIP enrichment files were generated from the processed alignment files using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016).  The ChIP enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Supplementary_files_format_and_content: NarrowPeak files were generated from the processed alignment files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.

organism: Caenorhabditis elegans

source_name: Whole animals

extract_protocol:
Animals were harvested in M9 buffer, washed, and ground to a find powder with a mortar and pestle in liquid Nitrogen.  Whole animal lysates were crosslinked with 1% formaldehyde for 5 minutes, and the genomic DNA was sheared using a Covaris E220 (Covaris).  The resulting chromatin was immunoprecipitated with anti-HA or anti-FLAG antibodies.
ChIP-Seq libraries were prepared for sequencing using the ThruPLEX DNA-Seq Kit (Rubicon Genomics) according to the manufacturer’s instructions.

tag: developmental stage

value: Day 1 adults

tag: genotype


title: DLS422_PQM-1_M2_IP_r4

value: anti-FLAG (M2, Sigma-Aldrich, F1804)


title: HepG2_IRb_starve_rep1

tag: cell line

value: rabbit, anti-IR_beta, sc-711


title: DLS435_CEH-60_3F10_IP_r2

tag: chip antibody


title: OP201_input_r4


title: OP201_PQM-1_M2_IP_r4


title: HSC-Ctrl CD34_C9


title: ceh-60_pqm-1_rhd90_d1Ad_rep2

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner v2.5.4. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.  The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Genome_build: WS260
Supplementary_files_format_and_content: gene level abundance measurements matrix (unnormalized)

extract_protocol: Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.  mRNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit v2 (1 μg of RNA as input) according to the manufacturer’s instructions.


title: ceh-60_pqm-1_rhd90_d1Ad_rep3


title: ceh-60_pqm-1_ok485_d1Ad_rep2


title: ceh-60_pqm-1_ok485_d1Ad_rep1


title: pqm-1_rhd90_d1Ad_rep3


title: pqm-1_rhd90_d1Ad_rep2


title: pqm-1_ok485_d1Ad_rep1


title: pqm-1_ok485_d1Ad_rep3


title: ceh-60_pqm-1_rhd90_d1Ad_rep1


title: pqm-1_ok485_d1Ad_rep2


title: ceh-60_d4Ad_rep3

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner v2.5.4.  The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Genome_build: WS260
Supplementary_files_format_and_content: A tab-delimited text file that includes gene level unnormalized read counts for each sample in matrix format

growth_protocol: C. elegans L1 animals were synchronized by egg prep and grown at 20°C on E. coli OP50 for ~72 hours until they reached day 1 of adulthood.  For isolation of day 4 adults, animals were washed off in M9 and transferred to new plates during each day of adulthood to prevent the accumulation of large amounts of progeny on the plates.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen.  Total RNA was isolated using Trizol.
mRNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit v2 (1 μg of RNA as input) according to the manufacturer’s instructions.

value: Day 4 adults


title: pqm-1_rhd90_d1Ad_rep1


title: ceh-60_d1Ad_rep3


title: ceh-60_d4Ad_rep1


title: ceh-60_d1Ad_rep2


title: ceh-60_pqm-1_ok485_d1Ad_rep3


title: N2_d4Ad_rep3


title: N2_d4Ad_rep2


title: D5_whole-embryo_Rep1

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Strasse 2

department: Faculty of Biology, Biozentrum

institute: Ludwig Maximilian University of Munich (LMU)

data_processing:
After demultiplexing and removal of adaptor sequences, ATAC-seq reads were aligned to a reference genome (UCSC: dm3) using Bowtie2 v.2.2.9, with the following settings: bowtie2 --local --very-sensitive-local.
Mapped reads were filtered for mapping quality (q > 10) and proper pairing (read paired & read mapped in proper pair) using SAMtools v.1.3.1, with the following settings: samtools view –f 0x3 – q 10.
ATAC-seq signal was defined as a number of Tn5 transposase cuts mapping to each base-pair. The cuts corresponded to 5' ends of ATAC-seq reads, with additional shifting by +4 bp for reads on the plus strand and -5 bp for reads on the minus strand.
Additionally, ATAC-seq signal was defined as coverage of short 1-100 bp fragmentation products (with in silico size selection) that corresponded to nucleosome-free regions (Schep et al., Genome Research, 2015).
ATAC-seq peaks were called with MACS2 v.2.1.1.2, based on the enrichment of Tn5 transposase cuts (smoothed by +/- 100 bp extension). ATAC-seq library from genomic DNA was used as a common control sample. Peak calling was performed separately for each replicate, with the q-value cut-off = 0.01 and the following non-default parameters: macs2 callpeak --keep-dup all -q 0.01 --nomodel --shift -100 --extsize 200 -f BAM -g dm -B.
Genome_build: UCSC dm3
processed data files format and content: BigWig files represent distribution of Tn5 transposase cuts after normalization to sequencing depth (CUTS_Normalized) and normalized coverage of 1-100 bp ATAC-seq fragments (COVERAGE_1-100-bp_Normalized). GFF3 files contain coordinates of ATAC-seq peaks called with MACS2.

source_name: Blastoderm (stage-5 embryo)

growth_protocol: Transgenic strains were expanded into population cages. After pre-clearing, embryos were collected on yeasted juice plates for 20 min and aged for additional 150 min, followed by harvesting and dechorionation (50% bleach, 2 min) for 20 min. The embryos were flash-frozen in liquid nitrogen exactly 190 min after the beginning of collections (2:50 – 3:10 h after egg laying). All collections were performed at controlled temperature of 25°C.

extract_protocol: Staged embryos were homogenized on ice with Dounce homogenizer. Tagged nuclei were isolated by antibody pull-down with Dynabeads protein G (ThermoFisher: 10009D) adsorbed to monoclonal anti-FLAG M2 antibody (Sigma-Aldrich: F1804). Fragmentation and amplification of ATAC-seq libraries were performed according to the standard protocol (Buenrostro et al., Current Protocols in Molecular Biology, 2015). Nuclei pellet corresponding to 340 ng of genomic DNA was resuspended in Nextera Tagment DNA Buffer and combined with 6 μl of Nextera Tn5 transposase (Illumina) to the final volume of 25 μl. After 12 PCR amplification cycles, ATAC-seq libraries were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 2.0x, right ratio: 0.5x). Whole-embryo control samples were generated according to the same protocol, but with exclusion of the step of antibody pull-down.

value: 2:50 - 3:10 h after egg laying

tag: assayed nuclei

value: whole-embryo

tag: genetic background

value: wild-type

tag: expression construct

tag: transgenic strain

value: D5 line A


title: gDNA_control_Rep1

data_processing:
After demultiplexing and removal of adaptor sequences, ATAC-seq reads were aligned to a reference genome (UCSC: dm3) using Bowtie2 v.2.2.9, with the following settings: bowtie2 --local --very-sensitive-local.
Mapped reads were filtered for mapping quality (q > 10) and proper pairing (read paired & read mapped in proper pair) using SAMtools v.1.3.1, with the following settings: samtools view –f 0x3 – q 10.
ATAC-seq peaks were called with MACS2 v.2.1.1.2, based on the enrichment of Tn5 transposase cuts (smoothed by +/- 100 bp extension). ATAC-seq library from genomic DNA was used as a common control sample. Peak calling was performed separately for each replicate, with the q-value cut-off = 0.01 and the following non-default parameters: macs2 callpeak --keep-dup all -q 0.01 --nomodel --shift -100 --extsize 200 -f BAM -g dm -B.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: GFF3 files contain coordinates of ATAC-seq peaks called with MACS2.

source_name: larval tissues

growth_protocol: Genomic DNA was isolated from larval tissues using a high-salt extraction method (Aljanabi, Nucleic Acids Research, 1997).

extract_protocol: Fragmentation and amplification of the ATAC-seq library was performed according to the standard protocol (Buenrostro et al., Current Protocols in Molecular Biology, 2015). 12 ng of genomic DNA was combined with 2.5 μl of Nextera Tn5 transposase in Nextera Tagment DNA Buffer (Illumina) to the final volume of 50 μl. After 12 PCR amplification cycles, the library was purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 2.0x, right ratio: 0.5x).

value: larval tissues

value: purified genomic DNA


title: D7_whole-embryo_Rep2

value: D7 line B


title: D5_whole-embryo_Rep2

value: D5 line B


title: N2_d4Ad_rep1

value: wild type


title: D4_whole-embryo_Rep2

value: D4 line B


title: ceh-60_d1Ad_rep1


title: D4_whole-embryo_Rep1

value: D4 line A


title: N2_d1Ad_rep3


title: ceh-60_d4Ad_rep2


title: spleen_temp-crowding stress_27°C-100kg_bio-replicate1

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

description: Pool of 7 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

label_protocol: Seven individual RNA samples from spleen were pooled according to the different treatment groups. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured. All hybridisations include thus two biological and two technical replicates. The technical replicates in our study are exactly the same probes prepared for paired bio-replicate and were applied to an independent array.

growth_protocol: Fish were grown in water recirculation tanks at the Institute for Fisheries in Born, Germany.

extract_protocol: Spleen was sampled. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and Fluidigm assays.

treatment_protocol: Fish (26.2 ± 1.3 cm in length, and 230.2 ± 35.9 g in weight ) were randomly allocated to identical 309-L glass tanks (0.74 m length × 0.58 m width × 0.72 m height). The experimental procedures are illustrated in Fig. 1(Overall design diagram.pdf). The stocking density in four of the six experimental tanks (A1, A2, B1, B2) has been set to 30 kg/m3 (corresponding to 38 or 39 trout weighing 9.5 kg), while the stocking density in the other two of the six tanks (C1, C2) was 100 kg/m3 (corresponding to 96 or 119 trout weighing 35 kg). Two of the tanks with 30 kg of trout per cubic metre (A1, A2) served as control tanks and were kept at a constant temperature of 16 °C for the entire duration of the experiment. The water temperature in the other four tanks B1, B2 and C1, C2 was gradually elevated from 16 °C to 26 °C by 2 °C every day for a period of 6 days. On day 7, the temperature of 27 °C was kept for 24 h. Further husbandry conditions are detailed in reference (Rebl et al.,  2017: Microarray-predicted marker genes and molecular pathways indicating crowding stress in rainbow trout (Oncorhynchus mykiss). Aquaculture 473, 355–365). The water temperature and other relevant parameters were constantly recorded. Trout were fed ad libitum commercial dry pellets by automatic feeders. Throughout the experiment, no technical problems were registered.

tag: tissue

value: spleen

tag: gender

value: mixed

tag: age

value: ~10 months


title: spleen_temperature stress_27°C_tech-replicate1

description: Pool of 7 individual RNAs


title: D7_whole-embryo_Rep1

value: D7 line A


title: D7_domain_Rep2

value: D7 tagged domain


title: D1_whole-embryo_Rep1

value: D1 line A


title: spleen_reference_16°C_bio-replicate2

description: Pool of 7 individual RNAs


title: spleen_temperature stress_27°C_tech-replicate2

description: Pool of 7 individual RNAs


title: spleen_reference_16°C_tech-replicate1

description: Pool of 7 individual RNAs


title: N2_d1Ad_rep2

tag: strain

value: Day 1 adults


title: spleen_temp-crowding stress_27°C-100kg_tech-replicate1

description: Pool of 7 individual RNAs


title: spleen_temperature stress_27°C_bio-replicate2

description: Pool of 7 individual RNAs


title: spleen_reference_16°C_tech-replicate2

description: Pool of 7 individual RNAs


title: spleen_temp-crowding stress_27°C-100kg_bio-replicate2

description: Pool of 7 individual RNAs


title: spleen_temperature stress_27°C_bio-replicate1

description: Pool of 7 individual RNAs


title: spleen_temp-crowding stress_27°C-100kg_tech-replicate2

description: Pool of 7 individual RNAs


title: N2_d1Ad_rep1


title: D6_domain_Rep2

value: 2:50 - 3:10 h after egg laying

value: D6 tagged domain

value: D6 line B


title: spleen_reference_16°C_bio-replicate1

description: Pool of 7 individual RNAs


title: D5_domain_Rep2

value: D5 tagged domain

value: wild-type


title: D6_domain_Rep1

value: D6 line A


title: D1_whole-embryo_Rep2

value: whole-embryo

value: D1 line B


title: D5_domain_Rep1

value: D5 line A


title: D7_domain_Rep1


title: D4_domain_Rep2

value: D4 tagged domain

value: D4 line B


title: D4_domain_Rep1

value: D4 line A


title: RNA-seq in HAP1 cell line, replicate 3

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Transcriptome analysis was performed using the Tuxedo suite. TopHat2 was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e75, February 2014) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1) was used to assemble transcripts from spliced read alignments, using the Ensembl e73 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression was assessed with Cuffdiff v2.2.1. Transcriptome sets of all replicates for each sample group were combined with Cuffmerge. Finally, cummeRbund and biomaRt were used to perform quality assessment and refine analysis results.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair; tsv file contains FPKM values for each sample at gene level

source_name: HAP1 cell line

growth_protocol: HAP1 cell lines were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco), supplemented with 10% Fetal Bovine Serum (FBS; Gibco) and incubated in 5% CO2 atmosphere at 37°C.

extract_protocol:
For each immunoprecipitation 30 million nuclei were isolated. Cells were fixed with 1% paraformaldehyde for 10 min at room temperature. The fixation was stopped by addition of glycine. The collected pellet was sonicated using a Covaris S220 sonicator for 43 minutes to fragment the DNA to 200-700 bp. For immunoprecipitation, the sonicated chromatin was added to antibody-conjugated Protein A or G beads (Life Technologies) and incubated rotating at 4°C overnight. Used antibodies were: anti-MTHFD1 (C3, Santa Cruz), anti-BRD4 ((A301‐985A, Bethyl Labs), anti-H3K27Ac (ab4729, Abcam) and mouse IgG (sc-2025, Santa Cruz).
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Tagmentation was performed by resuspending the magnetic beads in 100 μl tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10 % v/v dimethylformamide) containing 2 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) followed by an incubation for 3 min at 37°C. Subsequently, formaldehyde crosslinks were reverted by incubation in elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA and 10 mM Tris-HCl pH 8.0) containing 2 µl of Proteinase K for 1 h at 55°C, and then at 65°C overnight. The DNA was purified using the QIAquick PCR Purification kit (Qiagen). The enrichment of the libraries was performed in a 50 µl-reaction using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) and 0.75 μM primers. Each DNA library was purified and size selected for a fragment length of 200-400 bp using SPRI AMPure XP beads (Beckman Coulter).
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

tag: cell linw

tag: knockout

value: WT


title: RNA-seq in HAP1 cell line, replicate 2


title: RNA-seq in HAP1 cell line, replicate 1


title: D1_domain_Rep2

value: D1 tagged domain


title: D3_domain_Rep1

value: D3 tagged domain

value: D3 line A


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone D3, replicate 3

value: MTHFD1, clone D3


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone D3, replicate 2


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone D3, replicate 1


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone C8, replicate 3

value: MTHFD1, clone C8


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone C8, replicate 2


title: D2_domain_Rep1

value: 2:50 - 3:10 h after egg laying

value: D2 tagged domain

value: D2 line A


title: RNA-seq in HAP1 cell line with MTHFD1 knockout, clone C8, replicate 1


title: S2R+ cells_T140min_S3

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

data_processing:
Sequencing reads in fastq  files obtained from the genome center were first filtered and trimmed and then  were mapped back to the Drosophila genome using TopHat.
sequence reads  were mapped back to the Drosophila genome using TopHat.
FPKM values were obtained with Cufflinks
Readcounts values were obtained using Htseq
Genome_build: Drosphila genome BDGP6
Supplementary_files_format_and_content: text files with FPKM values and read counts of all samples for each gene at each time point

growth_protocol: Drosophila S2R+ cells were incubated 12 hrs in serum-free Schneider’s Drosophila medium (Thermo Fisher Scientific, #21720-024).

extract_protocol:
RNA was harvested using Trizol reagent.
After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

treatment_protocol: Cells were treated with 25 mg/ml insulin, then lysed at 10 different time points at 20 min intervals (3 biological replicates per time point) after stimulation.

value: S2R+ cells

tag: treatment

value: insulin

tag: time

value: 140 min

tag: replicate


title: S2R+ cells_T160min_S3

tag: cell type

value: 160 min


title: S2R+ cells_T180min_S3

value: 180 min


title: S2R+ cells_T80min_S3

value: 80 min


title: S2R+ cells_T120min_S3

value: 120 min


title: S2R+ cells_T100min_S3

value: 100 min


title: S2R+ cells_T40min_S3

value: 40 min


title: ChIP-seq in HAP1 cell line for MTHFD1, replicate 2

value: WT


title: D3_domain_Rep2

tag: developmental stage

value: D3 tagged domain

value: wild-type