title: CHC1157T

description:
MUTHEC
test

tag: gender

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

value: NM

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: 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


title: h9.4_CD19

status: Public on Apr 05 2019

type: SRA

city: Lund

first: Axel

last: Hyrenius Wittsten

address: Klinikgatan 28

department: Division of Clinical Genetics

country: Sweden

institute: Lund University

library_source: transcriptomic

data_processing:
Bcl2FastQ software was used for basecalling.
Paired-end reads from RNA sequencing were aligned using STAR.
Fragments per kilobase of transcript per million mapped fragments (FPKM) and gene FPKM was calculated using Cufflink and log2 transformed.
FPKM cutoff of ≥0.5 was used to define “expressed” genes and genes not expressed in at least one sample were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including filtered log2 FPKM values.

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
AllPrep DNA/RNA Mini Kit (Cat# 80204)
llumina TruSeq RNA Sample Prep Kit v2 (Cat# RS-122-2001).

tag: genotype/variation

tag: cell type

value: CD34+ CB cells

tag: tissue

value: Bone marrow


title: reporter_dmso_5m_dps_pepck_rpb3_chipnexus_rep2

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
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 and cultured at 25C for 48 h.

tag: cell line

value: Kc167 cells

tag: treatment

value: 2% v/v DMSO 5 min

tag: chip antibody

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


title: h9.4_CD19CD33


title: CHC1156T

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: F

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

tag: serumalphafoeto (ui)

tag: tert status

value: M

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

value: p.G87In_Frame_Del + p.A142T

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


title: CN61_E2

city: Cambridge

first: Sanja

last: Vickovic

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

data_processing:
ST Pipeline v0.8.5
Image alignment in ImageJ
ST aligner v0.1
ST Annotator v0.2
Genome_build: GRCm38.v79
Supplementary_files_format_and_content: counts: tab-delimited text files include raw UMI filtered counts for each ST spot; processed using ST Pipeline v0.8.5
Tissue jpg image: Aligned and processed HE stainesd image in a coordinate system; colnames in the counts files; processed using ST aligner v0.1
Annotation file: columns for the counts file are associate with an anatomical region tab used ST Annotator v0.2
Barcode file: Barcode file needed for spatial demultiplexing of each sample; used in ST Pipeline v0.8.5. Column1 corresponds to the first 18 bp in the R1.fastq.gz; Column2 corresponds to x and Columns3 to y in a (x.y) Cartesian system on an ST array. In processed files 1, 2 and 4 the x_y values can be rouned and will correspond to Columns 2 and 3 (x,y) in the respective barcode files.

molecule: polyA RNA

organism: Mus musculus

source_name: RNA-Seq of Mus musculus: p100 male spinal cord

extract_protocol:
Spatial Transcriptomics
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: h9.15_CD19

tag: genotype/variation

value: Empty-mCherry+Empty-GFP

tag: cell type


title: h9.15_CD33


title: reporter_dmso_5m_dps_pepck_dve_downstream_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: CN61_C1


title: h9.14_CD33


title: CN62_E2


title: reporter_triptolide_5m_dps_pepck_pk_downstream_rpb3_chipnexus_rep1

value: 500 uM Triptolide 5 min


title: CHC114T

description:
MUTHEC
test

tag: gender

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

value: NM

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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation


title: CHC1151T

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

value: Splice_Site g.chr16:396147C>T

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC1152T

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

value: Splice_Site g.chr19:10600531T>A

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


title: reporter_triptolide_5m_dps_pepck_pk_downstream_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody

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


title: reporter_triptolide_5m_dps_pepck_dve_downstream_rpb3_chipnexus_rep1


title: h9.14_CD19

tag: genotype/variation

tag: cell type

value: CD34+ CB cells

tag: tissue

value: Bone marrow


title: CHC1148T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

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: 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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CN60_E2

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: reporter_dmso_5m_dps_pepck_pk_downstream_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

value: 2% v/v DMSO 5 min

tag: chip antibody


title: h9.13_CD33

tag: genotype/variation

value: Empty-mCherry+Empty-GFP

tag: cell type


title: CHC1147T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

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

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


title: h9.13_CD19

tag: genotype/variation

tag: cell type

tag: tissue


title: CHC1153T

description:
MUTHEC
test

tag: gender

value: M

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: 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

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: CN60_D2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dmso_5m_dps_pepck_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: CN60_D1


title: h8.6_CD33

tag: genotype/variation

tag: cell type


title: CN61_D2


title: reporter_triptolide_5m_dps_act5c_pk_downstream_rpb3_chipnexus_rep2

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.

value: 500 uM Triptolide 5 min


title: CHC1146T

description:
MUTHEC
test

tag: gender

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

tag: apob status

tag: apob mutation

tag: atm status


title: CHC1145T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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: atm mutation


title: h8.6_CD19

tag: genotype/variation

tag: cell type

value: CD34+ CB cells

tag: tissue


title: h8.6_CD19CD33

value: Bone marrow


title: h8.4_CD33


title: L6CN59_D1

description:
*_1_stdata_aligned_counts_IDs.txt corresponds to B6SJLSOD1-WT and *_2_stdata_aligned_counts_IDs.txt to B6SJLSOD1-G93A; both produced with ST Pipeline v0.8.5
1000L6_barcodes.txt

source_name: RNA-Seq of Mus musculus: p70 female spinal cord

tag: mouse id

tag: genotype

value: mixed genotype:B6SJLSOD1-WT and B6SJLSOD1-G93A

tag: age

tag: Sex

value: female


title: reporter_triptolide_5m_dps_act5c_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody

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


title: reporter_dmso_5m_dps_act5c_rpb3_chipnexus_rep2


title: CN56_E1

value: spinal cord


title: reporter_triptolide_5m_dps_pepck_rpb3_chipnexus_rep1


title: h8.1_CD33


title: CHC113T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

tag: type

value: RESECTION

value: no

tag: alcohol

tag: hemochromatosis

value: yes

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: 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: 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: CHC1140T

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

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

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: atm mutation


title: reporter_scp_rna_5_sequencing

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

extract_protocol:
Total RNA was isolated from 0.5 million transfected cells.
Gene specific cDNA was generated using SuperScript™ II Reverse Transcriptase and primer against GFP. Reverse transcription products were then treated with RNAse A and RNAse H at RT for 30 min and cDNA were purified with Ethanol precipitation. The library preparation procedure for gene specific 5’ RNA sequencing is the same as the library preparation for ChIP-nexus, except that a new BamHI cutting oligo and new barcoded primers were used.

tag: cell line

tag: chip antibody

value: no antibody

tag: treatment


title: CHC1142T

description:
MUTHEC
test

tag: gender

value: M

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: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation


title: h8.12_CD33

tag: genotype/variation

value: Empty-mCherry+Empty-GFP

tag: cell type

tag: tissue


title: CN56_D1

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CN56_C2


title: h8.12_CD19


title: reporter_dps_dve_rna_5_sequencing

tag: cell line

tag: chip antibody

tag: treatment


title: reporter_dmso_5m_dps_act5c_pk_downstream_rpb3_chipnexus_rep2

value: 2% v/v DMSO 5 min


title: reporter_dps_cg12730_rna_5_sequencing


title: CN53_E1


title: reporter_dps_pk_rna_5_sequencing


title: CHC1139T

description:
MUTHEC
test

tag: gender

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: CHC1137T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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

value: p.C362Mfs + p.S1391Ifs

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


title: CN60_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: CHC1138T

description:
MUTHEC
test

tag: gender

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: 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

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: CN53_D2

tag: tissue

tag: mouse id

tag: genotype

value: mixed genotype:B6SJLSOD1-WT and B6SJLSOD1-G93A

tag: age

tag: Sex

value: female


title: CN56_D2


title: CN53_D1


title: reporter_dps_comm2_rna_5_sequencing

tag: cell line

value: Kc167 cells

tag: chip antibody

tag: treatment


title: CHC1135T

description:
MUTHEC
test

tag: gender

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


title: CHC1105T

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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: L6CN52_D2

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dps_pxb_rna_5_sequencing

tag: cell line

tag: chip antibody

tag: treatment


title: h11.14_CD33

tag: genotype/variation

tag: cell type

value: CD34+ CB cells

value: Bone marrow


title: h8.11_CD33


title: h11.5_CD33


title: reporter_dps_pepck_rna_5_sequencing


title: L6CN52_D1


title: h11.14_CD19


title: CHC1104T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

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: 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


title: h8.11_CD19

tag: genotype/variation

tag: cell type

tag: tissue


title: CHC1102T

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

value: NM

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: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: CN52_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: h11.14_CD19CD33

tag: genotype/variation

tag: cell type


title: L6CN51_E2


title: reporter_dps_act5c_rna_5_sequencing

tag: cell line

tag: chip antibody

value: no antibody

tag: treatment


title: h11.11_CD33


title: L6CN51_E1


title: reporter_triptolide_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep3

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

value: 500 uM Triptolide 1h


title: CHC1087T

description:
MUTHEC
test

tag: gender

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: 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


title: CN51_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC108T

description:
MUTHEC
test

tag: gender

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: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation


title: reporter_triptolide_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep3

tag: cell line

tag: chip antibody

tag: treatment


title: reporter_dmso_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep3

value: 2% v/v DMSO 1h


title: CHC1103T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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


title: reporter_triptolide_1h_dps_dve_rpb3_chipnexus_rep3

tag: cell line

tag: chip antibody

tag: treatment


title: reporter_dps_pino_rna_5_sequencing


title: CHC1085T

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

value: HD

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: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation


title: KO11_Dox

city: Zurich

first: Andreas

last: Postlmayr

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

data_processing:
CLC Genomics Workbench: Alignment to reference genome (Ensemb GRCm38.94)
CLC Genomics Workbench: TPM read normalisation
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text, Name, Chromosome, Region, Expression Value, TPM, RPKM, Exons, Gene ID, Gene length, ENSEMBL, Biotype, Unique gen reads, Total gene reads, Transcripts annotated, Detected transcripts, Exon length, Unique exon reads,Total exon reads, Ratio of unique to total (Exon reads), Unique Exon-Exon reads, Total Exon-Exon reads, Unique intron reads, Total intron reads, Ratio of intron to total gene reads

source_name: Mouse embryonic stem cells

extract_protocol:
RNA was harvested using Rneasy Kit (Qiagen) including on-column Dnase digest (Qiagen). PolyA RNA was enriched using oligodT beads.  Illumina TruSeq stranded mRNA Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transgenic system

value: Dox inducible Xist expression

tag: genotype

tag: 48h xist expression

value: Yes


title: KO15_Dox


title: h11.11_CD19CD33

tag: genotype/variation

tag: cell type

tag: tissue


title: h10.3_CD33


title: CHC1086T

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: 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: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: h11.11_CD19

tag: genotype/variation

tag: cell type

value: CD34+ CB cells

tag: tissue


title: CHC1084T

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


title: h10.3_CD19

tag: genotype/variation

tag: cell type

tag: tissue

value: Bone marrow


title: KO8_Dox

tag: transgenic system

tag: genotype

tag: 48h xist expression


title: h10.8_CD33


title: KO15_NT

value: No


title: reporter_dmso_1h_dps_dve_rpb3_chipnexus_rep3

tag: cell line

value: Kc167 cells

tag: chip antibody

tag: treatment


title: CHC1136T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

value: RESECTION

value: yes

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

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: 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

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: h10.3_CD19CD33

tag: genotype/variation

tag: cell type

tag: tissue


title: reporter_dmso_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep3

tag: cell line

tag: chip antibody

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

tag: treatment


title: reporter_triptolide_1h_dps_dve_inr_g_to_t_rpb3_chipnexus_rep2

value: 500 uM Triptolide 1h


title: KO11_NT

tag: transgenic system

tag: genotype

tag: 48h xist expression


title: CHC1081T

description:
MUTHEC
test

tag: gender

value: M

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

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

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


title: CHC107T

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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation


title: h10.10_CD33

tag: genotype/variation

tag: cell type

tag: tissue


title: reporter_dmso_1h_dps_dve_inr_g_to_t_rpb3_chipnexus_rep2

tag: cell line

tag: chip antibody

tag: treatment

value: 2% v/v DMSO 1h


title: CHC1079T

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: 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


title: KO8_NT

tag: transgenic system

value: Dox inducible Xist expression

tag: genotype

tag: 48h xist expression


title: WT3_Dox

value: WT

value: Yes


title: CHC1073T

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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: reporter_triptolide_1h_dps_dve_inr_g_to_a_rpb3_chipnexus_rep2

tag: cell line

tag: chip antibody

tag: treatment


title: WT2_Dox

tag: transgenic system

tag: genotype

tag: 48h xist expression


title: ATAC-seq: Fibroblast line 1 condition: OC3+Bclxl replicate: 1

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

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

source_name: Fibroblast line 1

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).

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: This experiment consisted of overexpressing ONECUT3 and Bclxl in human adult skin fibroblasts. On day -2 (two days before induction of ONECUT3 expression), cultured fibroblasts were detached using 0.25% trypsin, counted and resuspended in fibroblast medium. 20.000 fibroblasts were plated in 1ml fibroblast medium in each well of a twelve wells plate (Corning). On day -1, cells were transduced with ONECUT3 and Bclxl. Transduction was performed in fresh fibroblast medium in the presence of 8ug/ml polybrene (Sigma-Aldrich). On day 0, the medium was refreshed for medium containing 2ug/ml doxycycline (Sigma-Aldrich) to induce expression of the ONECUT transgene. This medium also contained 2ug/ml puromycin (Sigma-Aldrich)  and 8ug/ml blasticidin (Sigma-Aldrich). Cells were isolated on day 2.

tag: cell type

value: 2 days after induction of OC3 in skin derived fibroblasts

value: Fibroblast line 1 (CL1500023)


title: reporter_dmso_1h_dps_dve_inr_g_to_a_rpb3_chipnexus_rep2

value: Kc167 cells


title: ATAC-seq: Fibroblast line 1 condition: OC3+Bclxl replicate: 2


title: WT1_Dox


title: CHC1065T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

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: 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


title: CHC1069T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

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

value: HD

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: braf mutation

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: reporter_dmso_1h_dps_dve_act5c_inr_rpb3_chipnexus_rep2

tag: cell line

tag: chip antibody

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

tag: treatment


title: WT3_NT

tag: transgenic system

tag: genotype

tag: 48h xist expression

value: No


title: ATAC-seq: Fibroblast line 1 condition: OC2+Bclxl replicate: 1

treatment_protocol: This experiment consisted of overexpressing ONECUT2 and Bclxl in human adult skin fibroblasts. On day -2 (two days before induction of ONECUT2 expression), cultured fibroblasts were detached using 0.25% trypsin, counted and resuspended in fibroblast medium. 20.000 fibroblasts were plated in 1ml fibroblast medium in each well of a twelve wells plate (Corning). On day -1, cells were transduced with ONECUT2 and Bclxl. Transduction was performed in fresh fibroblast medium in the presence of 8ug/ml polybrene (Sigma-Aldrich). On day 0, the medium was refreshed for medium containing 2ug/ml doxycycline (Sigma-Aldrich) to induce expression of the ONECUT transgene. This medium also contained 2ug/ml puromycin (Sigma-Aldrich)  and 8ug/ml blasticidin (Sigma-Aldrich). Cells were isolated on day 2.

tag: cell type

value: 2 days after induction of OC2 in skin derived fibroblasts


title: ATAC-seq: Fibroblast line 1 condition: OC1+Bclxl replicate: 2

treatment_protocol: This experiment consisted of overexpressing ONECUT1 and Bclxl in human adult skin fibroblasts. On day -2 (two days before induction of ONECUT1 expression), cultured fibroblasts were detached using 0.25% trypsin, counted and resuspended in fibroblast medium. 20.000 fibroblasts were plated in 1ml fibroblast medium in each well of a twelve wells plate (Corning). On day -1, cells were transduced with ONECUT1 and Bclxl. Transduction was performed in fresh fibroblast medium in the presence of 8ug/ml polybrene (Sigma-Aldrich). On day 0, the medium was refreshed for medium containing 2ug/ml doxycycline (Sigma-Aldrich) to induce expression of the ONECUT transgene. This medium also contained 2ug/ml puromycin (Sigma-Aldrich)  and 8ug/ml blasticidin (Sigma-Aldrich). Cells were isolated on day 2.

value: 2 days after induction of OC1 in skin derived fibroblasts


title: CHC1063T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

value: no

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

value: NM

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: gnas status

tag: gnas mutation

tag: braf status

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: mll2 mutation

tag: setd2 status


title: WT2_NT

tag: transgenic system

value: Dox inducible Xist expression

tag: genotype

value: WT

tag: 48h xist expression


title: reporter_triptolide_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep2

tag: cell line

tag: chip antibody

tag: treatment

value: 500 uM Triptolide 1h


title: WT1_NT


title: ATAC-seq: Fibroblast line 1 condition: OC1+Bclxl replicate: 1

tag: cell type

value: Fibroblast line 1 (CL1500023)


title: CHC1072T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

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: nras status

tag: hras

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: setd2 mutation


title: reporter_dmso_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: chip antibody

tag: treatment

value: 2% v/v DMSO 1h


title: CHC1062T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

value: yes

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: braf status

tag: braf mutation

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: reporter_triptolide_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep2

tag: cell line

tag: chip antibody

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

tag: treatment


title: Alveolar macrophage_KO_rep3

city: Neuherberg

first: Elke

last: Glasmacher

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description: abundance.txt

data_processing:
For B cell samples, reads were mapped against the mouse genome mm9 (UCSC version mm9, NCBI37) using STAR. To quantify the number of reads mapping to annotated genes we used the featureCounts program from the subread package (v1.6.0)
For alveolar macrophage samples, reads were mapped against the mouse genome mm10 (GRCm38) using HISAT2. To quantify the number of reads mapping to annotated genes we used the featureCounts program from the subread package
Genome_build: alveolar cells: mm10,B cells: mm9
Supplementary_files_format_and_content: For B cell samples, reads were mapped against the mouse genome mm9 (UCSC version mm9, NCBI37) using STAR; For alveolar macrophage samples, reads were mapped against the mouse genome mm10 (GRCm38) using HISAT2

source_name: pulmonary alveolus (bronchoalveolar lavage)

extract_protocol:
alveolar cells were isolated using anti-CD11c positive selection with MicroBeads, directly lysed in buffer RLT Plus and RNA was isolated; For B cell isolation, CD19+ B cells were isolated from lymph nodes using anti-CD19 positive selection with MicroBeads. Cells were lysed directly in Trizol reagent and total RNA was isolated according to the manufacturers protocol
Library preparation and rRNA depletion was performed using the ‘TruSeq Stranded Total RNA Library Prep Kit’ (Illumina)

tag: genotype

tag: cell type

value: CD11c+ alveolar macrophage


title: CHC1061T

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

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: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras


title: CHC1060T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

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: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: ATAC-seq: Fibroblast line 1 condition: OC2+Bclxl replicate: 2

tag: cell type

value: 2 days after induction of OC2 in skin derived fibroblasts

tag: cell line


title: Alveolar macrophage_KO_rep2

description: abundance.txt

tag: genotype


title: ATAC-seq: Fibroblast line 1 condition: Bclxl replicate: 1

treatment_protocol: This experiment consisted of overexpressing Bclxl in human adult skin fibroblasts. On day -2, cultured fibroblasts were detached using 0.25% trypsin, counted and resuspended in fibroblast medium. 20.000 fibroblasts were plated in 1ml fibroblast medium in each well of a twelve wells plate (Corning). On day -1, cells were transduced with Bclxl. Transduction was performed in fresh fibroblast medium in the presence of 8ug/ml polybrene (Sigma-Aldrich). On day 0, the medium was refreshed for medium containing 2ug/ml doxycycline (Sigma-Aldrich). This medium also contained 8ug/ml blasticidin (Sigma-Aldrich). Cells were isolated on day 2.

value: Skin derived fibroblast overexpressing Bclxl


title: reporter_dmso_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep2

tag: chip antibody

tag: treatment


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

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).

treatment_protocol: no treatment

value: iPSC

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


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


title: reporter_triptolide_1h_dps_dve_rpb3_chipnexus_rep2

value: 500 uM Triptolide 1h


title: Alveolar macrophage_KO_rep1

description: abundance.txt


title: Alveolar macrophage_WT_rep3

description: abundance.txt


title: reporter_triptolide_1h_dps_dve_act5c_inr_rpb3_chipnexus_rep2


title: reporter_dmso_1h_dps_dve_rpb3_chipnexus_rep2


title: ATAC-seq: Fibroblast line 1 condition: Bclxl replicate: 2

value: Fibroblast line 1 (CL1500023)


title: reporter_triptolide_1h_dps_dve_inr_g_to_t_rpb3_chipnexus_rep1


title: CHC1053T

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

value: NM

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: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras


title: Alveolar macrophage_WT_rep2

description: abundance.txt

tag: genotype

tag: cell type


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

source_name: iPSC line 1

tag: cell line

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


title: CHC1055T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


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

tag: cell type

tag: cell line


title: reporter_triptolide_1h_dps_dve_inr_g_to_a_rpb3_chipnexus_rep1

value: Kc167 cells

tag: chip antibody

tag: treatment


title: CHC1052T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

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: p.A43_P44dup In_Frame

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 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras


title: CHC104T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

value: TRANSPLANT

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: keap1 status

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

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

tag: setd2 status


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

source_name: Fibroblast line 2

tag: cell type

value: Skin derived fibroblast

tag: cell line

value: Fibroblast line 2 (CL1500024)


title: CHC1044T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

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: 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


title: reporter_dmso_1h_dps_dve_inr_g_to_a_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

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

tag: treatment

value: 2% v/v DMSO 1h


title: mESC ChIP-seq input, biological replicate 1

city: La Jolla

first: Miao

last: Yu

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
The H3K4me3 ChIP-seq data on F123 cells was analyzed using ENCODE Uniform processing pipeline for ChIP-seq (histone marks) (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Genome_build: mm10

source_name: embryonic stem cells

growth_protocol: F123 cells were cultured in DMEM (10013-CV, Corning), supplement with 15% knockout serum replacement (10828028, Invitrogen), 1×penicillin/streptomycin (15140122, Thermo Fisher Scientific), 1×non-essential amino acids (11140050, Thermo Fisher Scientific), 1×GlutaMax (35050061, Thermo Fisher Scientific), 1000 U/ml LIF (ESG1107, Millipore), 0.1 mM β-mercaptoethanol (M3128, Sigma). F123 cells were maintained on irradiated CF1 mouse embryonic fibroblasts (A34180, Thermo Fisher Scientific) and were passaged once on 0.1% gelatin-coated feeder-free plates before harvesting.

extract_protocol:
2 million fixed F123 cells were thawed on ice, resuspend in hypotonic lysis buffer (20 mM HEPES, pH 8.0, 10 mM KCl, 1 mM EDTA, 10% glycerol) with proteinase inhibitors and rotate at 4 °C for 15 minutes. The nuclei were then washed once with hypotonic lysis buffer with proteinase inhibitors and resuspend in 130 μL RIPA buffer (10 mM Tris, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) with proteinase inhibitors. After incubation on ice for 10 minutes, the nuclei were sheared using Covaris M220 with following setting: power, 75 W; duty factor, 10%; cycle per burst, 200; time, 10 minutes; temp, 7 °C. The cell lysate was cleared by centrifugation at 15,000×g for 20 min and supernatant was collected. The clear cell lysate was precleared with Protein G Sepharose beads (GE Healthcare) and for 3 hours at 4 °C with slow rotation. ~5% of precleared cell lysate was saved as input control. The rest of the lysate was mixed with 2.5 µg of H3K4me3 (04-745, Millipore) antibody and rotate at 4 °C for at least 12 hours. On the next day, 0.5% BSA-blocked Protein G Sepharose beads (prepared one day ahead) were added and rotated for another 3 hours at 4 °C. The beads were collected by centrifugation at 400×g for 1 min and then washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. Washed beads were treated with 10 µg Rnase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 hours at 37 °C, followed by reverse crosslinking in the presence of proteinase K (20 µg) overnight at 65 °C. After reverse crosslink the DNA was purified by Zymo DNA Clean&Concentrator.
10-100 ng ChIP DNA or input DNA was first end repaired at 20 °C for 30 minutes in 1×T4 DNA ligase buffer (NEB) with 0.5mM dNTP mix, 3U T4 DNA polymerase (NEB), 2.5U Klenow fragment (NEB) and 10U T4 PNK (NEB). The repaired DNA was then purified by Zymo DNA Clean&Concentrator and adenylated at 37 °C for 30 minutes in 1×NEBbuffer 2 (NEB) with 0.4mM dATP, 10U Klenow fragment (3’-5’ exo-) (NEB). The adenylated was purified by Zymo DNA Clean&Concentrator and ligated to the adapters (Illumina, TruSeq, 0.1 μL per 100ng DNA) at 16 °C for overnight in 1×T4 DNA ligase buffer (NEB) with 400U T4 DNA ligase. After purification with Zymo DNA Clean&Concentrator, DNA was amplified with KAPA HiFi HotStart ReadyMix PCR Kit for 12 cycles according to the manufacturer’s instructions. The amplified libraries were purified with Ampure Beads to extract fragments between 200-600bp for sequencing.

tag: strain

value: F123 (F1 Mus musculus castaneus x S129/SvJae mouse ESC line)


title: CHC1041T

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

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: reporter_triptolide_1h_dps_dve_act5c_inr_rpb3_chipnexus_rep1

tag: cell line

tag: chip antibody

tag: treatment

value: 500 uM Triptolide 1h


title: mESC H3K4me3 ChIP-seq, biological replicate 2

description:
F123_H3K4me3_ChIPseq_pool.fc_signal.bw
F123_H3K4me3_ChIPseq_replicated.narrowPeak

data_processing:
The H3K4me3 ChIP-seq data on F123 cells was analyzed using ENCODE Uniform processing pipeline for ChIP-seq (histone marks) (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
supplementary files and format: bigwig file represents the signal track for fold change over control from pooled sample (rep1+rep2). Peak files are in narrowPeak format. Replicated peaks are the set of peak calls from the pooled replicates that are either observed in both replicates, or are observed in two pseudoreplicates (https://www.encodeproject.org/chip-seq/histone/).
Genome_build: mm10

tag: strain

value: H3K4me3 (04-745, Millipore)


title: reporter_dmso_1h_dps_dve_act5c_inr_rpb3_chipnexus_rep1

value: Kc167 cells


title: mESC H3K4me3 ChIP-seq, biological replicate 1


title: CHC1040T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

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: 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


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

tag: cell type

tag: cell line

value: Fibroblast line 1 (CL1500023)


title: RNA-seq: Fibroblast line 1 condition: OC3+Bclxl replicate: 1

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

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).

value: 2 days after induction of OC3 in skin derived fibroblasts


title: reporter_dmso_1h_dps_dve_inr_g_to_t_rpb3_chipnexus_rep1

tag: chip antibody

tag: treatment


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


title: reporter_triptolide_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep1


title: CHC103T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

value: TRANSPLANT

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: 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

tag: setd2 status


title: Alveolar macrophage_WT_rep1

description: abundance.txt

tag: genotype

tag: cell type

value: CD11c+ alveolar macrophage


title: mESC H3K4me3 PLAC-seq, biological replicate 2

description:
It contains fastq files with different read lengths (paired-end 50bp or 100bp).
F123_H3K4me3_PLACseq_combine.hic

data_processing:
Library strategy: PLAC-seq
To call long-range interactions with MAPS, PLAC-seq data was processed using MAPS pipeline (https://github.com/ijuric/MAPS). In brief, the raw sequencing reads were mapped using BWA-MEM to mm10 reference genome in single-end mode for each of the two ends separately. The independently mapped ends were then paired-up and the read pairs were kept if they satisfy certain criteria. Then “samtools rmdup” is used to remove PCR duplicates. To call long-range interactions with MAPS, all the unique read pairs are further filtered, only keeping the short-range (<=1Kb) intra-chromosomal reads (to measure IP efficiency) and long-range intra-chromosomal reads (>1Kb) falling into “AND” and “XOR” sets for downstream normalization and interaction calling. To call interactions from the same PLAC-seq and HiChIP datasets using hichipper, we performed the mapping and preprocessing using the default settings of HiC-Pro 2.7.6 and bowtie 2.3.0 as base mapper (recommended by hichipper), specifying digestion fragment size of 100 to 100,000. Genome fragment size files were obtained from the GitHub repository of hichipper (https://github.com/aryeelab/hichipper). Since the data in each run are from one sample and no merging was required, therefore we removed allValidPairs and mRStat files to make the HiC-Pro output consistent with the requirements of the hichipper input. We then used hichipper v0.4.4 to call interactions using ChIP-seq peaks as interaction anchors.
supplementary files and format: combine.hic files are generated using all the unique reads after PCR duplication removal from MAPS pipeline (replicate1+replicate2) via Juicebox.
Genome_build: mm10

extract_protocol:
In brief, 1-3 million crosslinked F123 cells were digested 2 hours at 37oC using 100 U of MboI followed by biotin fill-in and proximity ligation at room temperature for 4 hours. Then the nuclei were further lysed, sonicated and immunoprecipitated against the antibodies of choice. After immunoprecipitation, reverse crosslink was performed overnight at 65 oC after adding proteinase K to extract DNA.
DNA fragments containing ligation junctions were enriched with streptavidin beads followed by on-beads end repair, A-tail adding, adapter ligation and PCR amplification for 12-13 cycles.

tag: strain

tag: chip antibody


title: CHC1034T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: no

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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


title: mESC ChIP-seq input, biological replicate 2

tag: strain

tag: chip antibody


title: reporter_dmso_1h_dps_act5c_dve_downstream_fusion_rpb3_chipnexus_rep1

tag: cell line

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

tag: treatment

value: 2% v/v DMSO 1h


title: mESC H3K4me3 PLAC-seq, biological replicate 1

value: F123 (F1 Mus musculus castaneus x S129/SvJae mouse ESC line)


title: CHC1033T

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

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: 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


title: RNA-seq: Fibroblast line 1 condition: OC2+Bclxl replicate: 2

tag: cell type

value: 2 days after induction of OC2 in skin derived fibroblasts

tag: cell line


title: RNA-seq: Fibroblast line 1 condition: OC2+Bclxl replicate: 1


title: CHC1032T

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: 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


title: mESC CTCF PLAC-seq, biological replicate 1

tag: strain

tag: chip antibody

value: CTCF (sc-15914, Santa Cruz)


title: reporter_triptolide_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: treatment

value: 500 uM Triptolide 1h


title: reporter_dmso_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep1


title: mESC CTCF PLAC-seq, biological replicate 2


title: CHC1028T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

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: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC102T

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: 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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


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

tag: cell type

value: Skin derived fibroblast

tag: cell line

value: Fibroblast line 1 (CL1500023)


title: RNA-seq: Fibroblast line 1 condition: OC3+Bclxl replicate: 2

value: 2 days after induction of OC3 in skin derived fibroblasts


title: reporter_triptolide_1h_dps_dve_rpb3_chipnexus_rep1

tag: chip antibody

tag: treatment


title: RNA-seq: Fibroblast line 1 condition: OC1+Bclxl replicate: 1

value: 2 days after induction of OC1 in skin derived fibroblasts


title: reporter_dmso_1h_dps_dve_rpb3_chipnexus_rep1


title: MDA-MB-231_dox 8 days_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: Fibroblast line 1 condition: Bclxl replicate: 2

value: Skin derived fibroblast overexpressing Bclxl


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


title: reporter_triptolide_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep3

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


title: CHC101T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: TRANSPLANT

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: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: setd2 mutation

tag: tsc1 status


title: CHC100T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


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

tag: cell type

value: iPSC

tag: cell line

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


title: MDA-MB-231_no dox 8 days_3


title: MDA-MB-231_dox 8 days_2


title: CHC1010T

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

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: 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: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: reporter_dmso_1h_dps_act5c_upstream_pk_fusion_rpb3_chipnexus_rep3

tag: cell line

value: Kc167 cells

tag: chip antibody

tag: treatment

value: 2% v/v DMSO 1h


title: reporter_dmso_1h_dps_pk_tata_insertion_rpb3_chipnexus_rep3


title: CHC097T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status


title: MDA-MB-231_no dox 8 days_2

tag: cell line


title: RNA-seq: Fibroblast line 1 condition: OC1+Bclxl replicate: 2

tag: cell type

value: 2 days after induction of OC1 in skin derived fibroblasts

value: Fibroblast line 1 (CL1500023)


title: MDA-MB-231_no dox 8 days_1


title: CHC087T

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: 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: 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


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

tag: cell type

tag: cell line

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