title: CHC1562T

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: CHC1561T

status: Public on Apr 05 2019

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

molecule: total RNA

organism: Homo sapiens

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: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

value: M

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: 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: setd2 mutation


title: R1_C71

type: SRA

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

country: USA

institute: University of Oklahoma Health Sciences Center

description:
processed data file:
mouse_rsem-TPM-genes_annotated.xlsx
single cell

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 2.18.0.12 software was used for basecalling.
Fastq files were trimmed using TrimGalore! version 0.5.0 with parameters: --paired, --trim1
Trimmed fastq files were aligned using RSEM version 1.2.31 with parameters: --star, --star-gzipped-read-file --paired-end
Count files were loaded into the Fluidigm Singular version 3.6.1 for identification of clusters and genes.
Genome_build: mm10 or GRch38
Supplementary_files_format_and_content: tab-delimited Excel file containing gene symbols with their respective TPM expression for each cell/barcode.

organism: Mus musculus

source_name: kidney

extract_protocol:
Immune cell populations were sorted using a BD FACS Aria II. Single cells were loaded into the C1 machine to prepare cDNA libraries as described below
Fluidigm single cell cDNA libraries were prepared according to standard procedures outlined in “Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing”. Briefly, sorted macrophages were resuspended into a final concentration of 300~350 cells/ul in D-PBS and mixed with Fluidigm suspension reagent to reach 55% final buoyancy as determined by pre-testing. Six ul of mixed cells were loaded into the Fluidigm C1 IFC plate for mRNA seq (10–17 μm capture site) (Fluidigm PN 100-5760). Captured single cells were confirmed via bright field microscopy. Next, lysis mix, transverse transcription mix and pre-amplification mix were loaded into the C1 plate as instructed and single cell pre-amplified cDNA libraries were generated by the C1 machine using the program “mRNA Seq: RT & Amp (1771x/1772x/ 1773x) script”. Illumina Sequencing Libraries were prepared from pre-amplified single cell cDNA with Nextera XT DNA Sample Preparation Kit (Illumina PN FC-131-1096), following sequential steps of tagmentation, PCR amplification and pooling, and cleaning of the libraries.

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

tag: age

value: 8 weeks old

tag: Sex

value: Male


title: L7CN95_C2

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

source_name: RNA-Seq of Mus musculus: p30 female spinal cord

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

value: spinal cord

tag: mouse id

tag: genotype

value: female


title: R1_C70


title: L7CN95_C1


title: CHC155T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

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


title: L7CN94_E1

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

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC1552T

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: 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: CHC1555T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: C

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status


title: CHC1556T

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: L7CN94_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: R1_C65

tag: cell type

tag: strain


title: L7CN94_D2


title: CHC1551T

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 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


title: CHC154T

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: R1_C69

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: CHC1550T

description:
MUTHEC
test

tag: gender

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: 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


title: CHC1549T

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: R1_C63

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: CHC1548T

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: 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


title: L7CN95_D1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: L7CN94_D1


title: R1_C60

tag: cell type

tag: strain


title: R1_C77


title: CHC1545T

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: L7CN94_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: L7CN94_C1


title: R1_C58

tag: cell type

tag: strain


title: R1_C56


title: reporter_dps_act5c_2kb_h3k4me3_chipseq_rep1

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

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. Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
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. Sequencing libraries were prepared following Illumina's instructions: 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 single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

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.

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody

value: anti-H3K4me3 rabbit polyclonal, Cell Signaling (#9727)


title: CN96_E2

source_name: RNA-Seq of Mus musculus: p120 female spinal cord


title: CHC1535T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

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

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: CHC1534T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

value: p.G91Tfs + p.A245Pfs + p.P640A

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC1539T

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

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: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status


title: R1_C54

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

tag: age

value: 8 weeks old

tag: Sex


title: CHC1540T

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: 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: 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: R1_C55

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex

value: Male


title: CHC1531T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation


title: CN95_C1

source_name: RNA-Seq of Mus musculus: p120 male spinal cord

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: reporter_dps_act5c_2kb_wce_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: reporter_dps_act5c_wce_rep1


title: CHC1530T

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: apob status

tag: apob mutation

tag: atm status


title: reporter_dps_act5c_h3k4me3_chipseq_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: CN96_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: CHC141T

description:
MUTHEC
test

tag: gender

value: F

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: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: R1_C52

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: R1_C53


title: R1_C40


title: CN94_D2

tag: mouse id

tag: genotype


title: CN94_E1


title: CN94_D1


title: reporter_dps_rpl13a_2kb_wce_rep1

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: CHC1544T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

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: 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: CHC137T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: reporter_dps_rpl13a_2kb_h3k4me3_chipseq_rep1

tag: cell line

tag: treatment

tag: chip antibody

value: anti-H3K4me3 rabbit polyclonal, Cell Signaling (#9727)


title: reporter_dps_rpl13a_h3k4me3_chipseq_rep1


title: CN94_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dps_rpl13a_wce_rep1


title: CN93_E2


title: R1_C38

value: kidney

tag: cell type

value: macrophages

tag: strain


title: CHC123T

description:
MUTHEC
test

tag: gender

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 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: mll2 status

tag: mll2 mutation


title: R1_C34

tag: tissue

tag: cell type

tag: strain

tag: age

value: 8 weeks old

tag: Sex

value: Male


title: R1_C32


title: reporter_dps_act5c_2kb_rpb3_chipnexus_rep1

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

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.

tag: cell line

tag: treatment

tag: chip antibody

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


title: CHC129T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: CHC122T

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation


title: CN93_D2

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: R1_C25

tag: cell type

tag: strain


title: reporter_dps_act5c_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: CN93_E1


title: CHC121T

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


title: reporter_dps_rpl13a_2kb_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: CN93_D1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: R1_C23

tag: cell type

tag: strain


title: CHC1210T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: apob mutation

tag: atm status


title: R1_C24

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: R1_C16


title: CN92_E2

tag: mouse id

tag: genotype

value: female


title: reporter_triptolide_30m_scp_inr_g_to_t_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

value: 500 uM Triptolide 30 min

tag: chip antibody


title: CHC1209T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

value: Splice_Site g.chrX:20183016del

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status


title: CHC1211T

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: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: apob mutation

tag: atm status


title: CHC131T

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: 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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: R1_C15

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

tag: age

value: 8 weeks old

tag: Sex


title: reporter_dmso_30m_scp_inr_g_to_t_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

value: 2% v/v DMSO 30 min

tag: chip antibody

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


title: CHC1208T

description:
MUTHEC
test

tag: gender

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: 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

tag: map1b status

tag: map1b mutation


title: R1_C12

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex

value: Male


title: CN92_D1

value: spinal cord

tag: mouse id

tag: genotype


title: R1_0_C59


title: reporter_triptolide_30m_scp_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: CN92_C2

value: female


title: CN93_C1

value: male


title: CHC1207T

description:
MUTHEC
test

tag: gender

value: M

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

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: 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


title: R1_0_C07

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: CN90_C1

tag: mouse id

tag: genotype


title: reporter_dps_rpl13a_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody


title: AT-PCM1-2

city: Dallas

first: Samadrita

last: Bhattacharyya

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: PCM1-IP enriched PCM1+ nuclei was used for OMNI-ATAC library prep protocol

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
peaks were called using MACS version 2.1.0.20160309 with the following setting: Q-value < 0.05 and using the random background
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using HOMER. Scores represent normalized counts per 10 million.

source_name: Heart

extract_protocol:
Whole mouse hearts were harvested at P1. Nuclei was isolated using 2.2M sucrose cushion as described in details in the methodes section. MAN-IP was performed for samples PCM1 and Myc to enrich for specific cell-type nuclei and pure nuclei from 2.2M cushion was used as Input sample.
We used 2 independent biological replicates per experimental sample for library construction. To generate ATAC-Seq libraries, we followed the improved ATAC-Seq version called Omni-ATAC from Howard Chang lab (Corces et al., 2017). The detailed method is provided by the authors in the Supplementary protocol 1 in their published work. Very briefly, in this study, upon counting the nuclei using Countess II FL (using DAPI light cube) Automated Cell Counter, 50000 nuclei were pelleted in ATAC-Resuspension Buffer (recipe published in the same study) containing 0.1% Tween-20. The supernatant was carefully discarded. Nuclei pellet was incubated with transposase in the transposition mixture following the above-mentioned protocol. Transposed DNA was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014). This was followed by pre-amplification of transposed fragments, qPCR amplification, followed by KAPA library quantification to determine additional cycles for the final PCR amplification (none to very few additional cycles were required upon following the Omni-ATAC protocol). After final amplification, the ATAC-Seq library was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014) and submitted for Tape Station and Qubit analysis. 4nM of each ATAC-Seq library was used for paired-end sequencing on an Illumina NextSeq 500 Mid Output (130 M) flow cell. Image analysis and base calling were performed with Sanger/Illumina 1.9 pipeline.

tag: sample type

value: WT P1 mouse hearts were used. 2.2M sucrose cushion-purified nuclei followed by PCM1 antibody mediated MAN-IP to enrich for PCM1+ nuclei was used.

value: PCM1+ nuclei enriched from PCM1-MAN-IP was used


title: reporter_dmso_30m_scp_inr_g_to_t_rpb3_chipnexus_rep1


title: CN89_C1


title: CHC1205T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: C

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 status


title: CHC1204T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: reporter_triptolide_30m_scp_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

value: 500 uM Triptolide 30 min

tag: chip antibody

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


title: AT-PCM1-1

tag: sample type

tag: genotype


title: reporter_dmso_30m_scp_rpb3_chipnexus_rep1

value: 2% v/v DMSO 30 min


title: CHC1203T

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: 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 status


title: CN81_E1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC1202T

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: CN81_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: AT-Myc-2

description: Myc-IP enriched Nkx2-5+ nuclei was used for OMNI-ATAC library prep protocol

tag: sample type

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Nkx2-5+ nuclei was used. Nkx2-5 Cre/+; R26RSun1-Myc-Egfp/+ P1 mouse hearts were used

value: Nkx2-5+ nuclei enriched from Myc-MAN-IP was used


title: reporter_dmso_30m_scp_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: CHC1206T

description:
MUTHEC
test

tag: gender

value: M

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: 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 status


title: reporter_triptolide_1h_dps_pk_inr_g_to_t_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

value: 500 uM Triptolide 1h

tag: chip antibody


title: CN92_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: AT-Input-2

description: Pure nuclei was used for OMNI-ATAC library prep protocol

tag: sample type

value: Pure nuclei from 2.2M cushion was used as Input sample.

value: Wildtype mouse hearts was used for nuclei prep


title: CN80_E1


title: reporter_triptolide_30m_scp_inr_g_to_t_rpb3_chipnexus_rep1


title: reporter_dmso_1h_dps_pk_inr_g_to_t_rpb3_chipnexus_rep2

value: 2% v/v DMSO 1h


title: CN80_D2


title: CHC1200T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: C

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: CN80_D1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: AT-Input-1

tag: sample type

value: Pure nuclei from WT P1 mouse heart from 2.2M cushion was used as Input sample.


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus_rep5

tag: cell line

tag: treatment

tag: chip antibody

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


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus_rep5


title: CHC119T

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

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 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

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: CN80_C2

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: CHC1199T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

value: HD

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: human

data_processing:
CellRanger version 2.2.0 mkfastq tool was used for basecalling, which created 4 fastq files per sample from the 4 lanes of the flowcell. So, R1 has 4 fastq files; R2 has 4 fastq files; and I (index) has 4 fastq files.
R1 with a 16nt 10X barcode and a 10nt UMI
CellRanger version 2.2.0 count was used to create the matrix table for further processing.
The matrix was then loaded into Seurat version 2.3.4 for normalization, clustering and visualization.
Genome_build: GRch38,Sscrofa11 Release 91, mm10, Rnor6 Release 92
Supplementary_files_format_and_content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

extract_protocol:
CD45+ innate immune cells (T/B cell negative CD45+ cells) were sorted using a BD FACS AriaII. Live single cells were loaded into the 10x genomics machine.
Full length cDNA libraries were prepared by incubation of Gel Bead-In-EMulsions (GEMs) in a thermocycler machine with Chromium v2. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction.

tag: population

value: Caucasian

tag: tissue

value: kidney

tag: cell type

value: CD45+ innate immune cells

tag: age

value: 60 years old

tag: Sex

value: Male


title: reporter_triptolide_1h_dps_pk_inr_g_to_t_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: treatment

value: 500 uM Triptolide 1h

tag: chip antibody


title: AT-Myc-1

tag: sample type

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Nkx2-5+ nuclei was used. Nkx2-5 Cre/+; R26RSun1-Myc-Egfp/+ P1 mouse hearts were used

tag: genotype

value: Nkx2-5+ nuclei enriched from Myc-MAN-IP was used


title: CN79_D1

tag: mouse id


title: CHC1197T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

value: HCC

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

value: M

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: atm status


title: reporter_dmso_1h_dps_pk_inr_g_to_t_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

value: 2% v/v DMSO 1h

tag: chip antibody

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


title: 1_C94

description:
processed data file:
human_rsem-TPM-genes_annotated.xlsx
single cell
Human lineage negative

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

value: Caucasian

tag: age

tag: Sex


title: CHC1198T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob 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

tag: setd2 mutation


title: reporter_triptolide_1h_dps_pk_rpb3_chipnexus_rep4

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: CN79_D2

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: CHC1201T

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: CN79_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dmso_1h_dps_pk_rpb3_chipnexus_rep4

tag: cell line

tag: treatment

tag: chip antibody


title: CN78_C2


title: 1_C83

tag: cell type

tag: strain

value: 60 years old

value: Male


title: CN78_C1


title: CHC1192T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

value: HD

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_triptolide_40m_dps_act5c_upstream_comm2_rpb3_chipnexus_rep3

tag: cell line

tag: treatment

value: 500 uM Triptolide 40 min

tag: chip antibody


title: 1_C92

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: reporter_dmso_40m_dps_act5c_upstream_comm2_rpb3_chipnexus_rep3

value: 2% v/v DMSO 40 min


title: CHC1191T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: 1_C73

tag: tissue

value: kidney

tag: cell type

tag: strain

tag: age

tag: Sex


title: CHC1194T

description:
MUTHEC
test

tag: gender

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: 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

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: 1_C81

tag: tissue

tag: cell type

value: macrophages

tag: strain

value: Caucasian

tag: age

tag: Sex


title: 1_C64


title: CHC1190T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: reporter_triptolide_40m_dps_comm2_rpb3_chipnexus_rep3

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody

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


title: CN77_D1

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

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: 1_C59

tag: cell type

tag: strain

value: 60 years old

value: Male


title: CHC1188T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: 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

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: CHC1189T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: 1_C57

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: reporter_dmso_40m_dps_comm2_rpb3_chipnexus_rep3

tag: cell line

tag: treatment

value: 2% v/v DMSO 40 min

tag: chip antibody


title: CN71_D1

tag: mouse id

tag: genotype


title: CN77_E1


title: CN71_C2


title: reporter_triptolide_40m_dps_comm2_tata_insertion_rpb3_chipnexus_rep2

value: 500 uM Triptolide 40 min


title: 1_C52


title: CHC1186T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: no

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: 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: CN70_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: 1_C46

value: kidney

tag: cell type

value: macrophages

tag: strain


title: reporter_triptolide_40m_dps_comm2_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

tag: chip antibody


title: CN77_E2


title: CHC1185T

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

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CN70_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dmso_40m_dps_comm2_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

tag: chip antibody


title: 1_C44

tag: cell type

tag: strain

value: Caucasian


title: CHC1183T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status


title: reporter_triptolide_40m_dps_act5c_upstream_comm2_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody

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


title: CN69_E1

source_name: RNA-Seq of Mus musculus: p30 male spinal cord

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: reporter_dmso_40m_dps_comm2_tata_insertion_rpb3_chipnexus_rep2


title: 1_C43

tag: cell type

tag: strain

value: 60 years old

value: Male


title: reporter_dmso_40m_dps_act5c_upstream_comm2_rpb3_chipnexus_rep1

value: 2% v/v DMSO 40 min


title: CN70_C1


title: 1_C34


title: reporter_triptolide_40m_dps_comm2_tata_insertion_rpb3_chipnexus_rep1

value: 500 uM Triptolide 40 min


title: 1_C42


title: CHC1181T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

value: HCC

tag: type

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC1184T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

value: yes

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: 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

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: reporter_dmso_40m_dps_comm2_tata_insertion_rpb3_chipnexus_rep1

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

tag: cell line

tag: treatment

tag: chip antibody


title: 1_C33

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

tag: age

tag: Sex


title: CN69_D1

tag: mouse id

tag: genotype


title: reporter_triptolide_40m_dps_comm2_rpb3_chipnexus_rep1

value: Kc167 cells


title: CHC1180T

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

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

value: Splice_Site g.chr12:46285561A>G

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: 1_C32

tag: tissue

tag: cell type

tag: strain

value: Caucasian

tag: age

tag: Sex


title: CN69_C2

value: spinal cord

tag: mouse id

tag: genotype

value: male


title: reporter_dmso_40m_dps_comm2_rpb3_chipnexus_rep1

tag: cell line

tag: treatment

tag: chip antibody

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


title: CHC1179T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: 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: CHC1178T

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CN69_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: 1_C29

tag: cell type

tag: strain

value: 60 years old

value: Male


title: 1_C28


title: reporter_triptolide_1h_dps_dve_tata_insertion_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

value: 500 uM Triptolide 1h

tag: chip antibody


title: CHC1174T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

value: HCC

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

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: CHC1182T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

value: yes

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: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CN68_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: CHC1177T

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: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: atm mutation


title: CHC1173T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

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


title: 1_C22

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

tag: age

tag: Sex


title: reporter_dmso_1h_dps_dve_tata_insertion_rpb3_chipnexus_rep2

tag: cell line

value: Kc167 cells

tag: treatment

value: 2% v/v DMSO 1h

tag: chip antibody


title: reporter_triptolide_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep4


title: CN69_D2

value: spinal cord

tag: mouse id

tag: genotype

value: male


title: 1_C20

value: Caucasian


title: CN67_D2


title: CN66_D1


title: 1_C17

value: 60 years old


title: 1_C15

value: Male


title: 1_C16


title: CN66_C1


title: CHC1166T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

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

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: reporter_triptolide_1h_dps_dve_rpb3_chipnexus_rep4

tag: cell line

tag: treatment

value: 500 uM Triptolide 1h

tag: chip antibody

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


title: CHC1169T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

value: HCC

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

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: 1_C14

tag: tissue

tag: cell type

tag: strain

tag: age

tag: Sex


title: CN65_C2

tag: mouse id

tag: genotype

value: female


title: CHC1163T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

tag: type

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: stat3 status

tag: stat3 mutation

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC1161T

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: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status


title: CN65_C1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dmso_1h_dps_dve_rpb3_chipnexus_rep4

tag: cell line

value: Kc167 cells

tag: treatment

value: 2% v/v DMSO 1h

tag: chip antibody


title: CHC1171T

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: 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: 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: CHC1168T

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


title: reporter_dmso_1h_dps_act5c_upstream_dve_fusion_rpb3_chipnexus_rep4

tag: cell line

tag: treatment

tag: chip antibody


title: 1_C13

tag: tissue

value: kidney

tag: cell type

value: macrophages

tag: strain

value: Caucasian

tag: age

value: 60 years old

tag: Sex


title: CN64_D1

tag: mouse id

tag: genotype

value: male


title: CN67_E2


title: 1_C04

value: Male


title: CHC115T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

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

value: Splice_Site g.chrX:20185706C>T

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 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


title: CN64_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: reporter_dmso_5m_dps_pepck_dve_downstream_rpb3_chipnexus_rep2

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

tag: cell line

tag: treatment

value: 2% v/v DMSO 5 min

tag: chip antibody

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


title: CHC1159T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

tag: type

value: yes

tag: alcohol

value: no

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: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status


title: reporter_triptolide_1h_dps_dve_tata_insertion_rpb3_chipnexus_rep1

tag: cell line

value: Kc167 cells

tag: treatment

value: 500 uM Triptolide 1h

tag: chip antibody


title: CN67_C1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: reporter_dmso_1h_dps_dve_tata_insertion_rpb3_chipnexus_rep1

value: 2% v/v DMSO 1h


title: CN64_C1

value: male


title: h9.6_CD33

city: Lund

first: Axel

last: Hyrenius Wittsten

address: Klinikgatan 28

department: Division of Clinical Genetics

country: Sweden

institute: Lund University

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.

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

value: Bone marrow


title: h9.4_CD33


title: CN63_E2


title: reporter_dmso_5m_dps_pepck_pk_downstream_rpb3_chipnexus_rep2


title: CHC1158T

description:
MUTHEC
test

tag: gender

value: M

tag: diagnosis

tag: type

value: RESECTION

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: reporter_triptolide_5m_dps_pepck_dve_downstream_rpb3_chipnexus_rep2

tag: cell line

tag: treatment

value: 500 uM Triptolide 5 min

tag: chip antibody


title: reporter_triptolide_5m_dps_pepck_rpb3_chipnexus_rep2


title: CN63_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex