title: mESC ATAC-seq, biological replicate 1

city: La Jolla

first: Miao

last: Yu

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
ATAC-seq reads were mapped to mm10 genome using bowtie 1.1.2 with flags "-X2000 --no-mixed --no-discordant". The reads were converted to bam files, sorted, and PCR duplicates and mitochondrial reads were removed using samtools. To account for the Tn5 insertion position, read end positions were moved 4bp towards the center of the fragment. Bigwig signal tracks and peak calls were generated using MACS2 2.1.1.20160309 and the following flags: "-nomodel -shift 37 -ext 73 -pval 1e-2 -B -SPMR -call-summits". To obtain the set of replicated peaks for each sample, the data were processed as described above for each replicate independently as well as pooled. Using bedtools 2.27.1, the pooled peaks were intersected against each replicate's peaks sequentially, and pooled peaks present in both replicates were considered to be 'replicated'.
supplementary files and format: The bed file contains the genomic coordinates of the replicated ATAC-seq peaks between the two biological replicates.
Genome_build: mm10

source_name: embryonic stem cells

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

extract_protocol:
100,000 freshly harvested F123 cells were resuspend in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and rotate at 4oC for 15 minutes. After lysis the nuclei was spun down at 500×g for 5 min at 4 °C. Then the reaction was carried out for 30 min at 37 °C in 1×TD buffer with 2.5 μL transposase from Nextera DNA Library Prep Kit (Illumina). After reaction completion DNA is purified using MinElute PCR Purification Kit (Qiagen).
PCR amplification was perform with 1×NEBNext PCR MasterMix and 1 μM i7-index and i5-index primers using the following PCR condition: 72 °C for 5 min; 98 °C for 30 s; and 8 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The amplified libraries are purified and size selected using 0.55× and 1.5× (total) of sample volume.

tag: strain

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


title: mESC ATAC-seq, biological replicate 2

status: Public on Apr 05 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: CHC2466T

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: M

tag: age

tag: diagnosis

value: HCC

tag: type

value: TRANSPLANT

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

tag: serumalphafoeto (ui)

tag: tert status

value: NM

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC2465T

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


title: L7CN68_C1

city: Cambridge

first: Sanja

last: Vickovic

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic

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: p120 male spinal cord

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

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: L7CN69_E1


title: L7CN69_C2


title: CHC2469T

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: 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: L7CN69_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2464T

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


title: Prdm12 KO 2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Quality control of sequencing data with FastQC 0.10.1
Alignment to mouse genome using STAR version 2.3.0e_r291
Convert SAM to BAM files using Samtools version 0.1.18
Read counting with featureCounts version 1.4.6-p1
Differential expression analysis using DESeq2 version 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Counts

source_name: Prdm12 KO

extract_protocol:
Tissues were microdissected in ice-cold PBS and stored at -80°C. RNA was extracted using the illustra RNAspin Mini RNA isolation kit from GE Healthcare (25-0500-70) and following the manufacturer protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

tag: genotype

tag: tissue

value: Dorsal root ganglia and spinal cord


title: L7CN70_E1

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

tag: mouse id

tag: Sex

value: female


title: CHC2463T

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: 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: Prdm12 KO 4

tag: strain

tag: age

tag: genotype

tag: tissue


title: Prdm12 WT 4

source_name: Prdm12 WT

value: Wild Type


title: L7CN70_E2

tag: mouse id

tag: Sex


title: L7CN70_D2


title: CHC2458T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: C

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status


title: Prdm12 WT 3

tag: strain

tag: age

tag: genotype

tag: tissue


title: CHC2460T

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: 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


title: CHC2459T

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: 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


title: CHC245T

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: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca 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: CHC2461T

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 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: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: CHC2462T

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: 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: L7CN70_D1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: L7CN69_D1


title: CHC2456T

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 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status


title: CHC2455T

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: jak1 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: CHC2457T

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: 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 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status


title: Prdm12 WT 2

tag: strain

tag: age

tag: genotype

tag: tissue


title: Prdm12 KO 3


title: L7CN70_C2

tag: mouse id

tag: Sex


title: CHC2452T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

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: jak1 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: Prdm12 WT 1

tag: strain

tag: age

tag: genotype

tag: tissue


title: CHC2453T

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: irf2 status

tag: irf2 mutation

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status


title: CHC2450T

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: pik3ca mutation

tag: jak1 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: Prdm12 KO 1

tag: strain

tag: age

tag: genotype

tag: tissue


title: L7CN70_C1

tag: mouse id

tag: Sex


title: L7CN73_C1

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


title: L7CN75_E2

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


title: revitalized MSCs RNA-Seq rep3

city: Bronx

first: Fumio

last: Nakahara

state: NY

address: 1301 Morris Park Ave., Price Center Rm. 107

department: Dep. of Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Single- and paired-ended sequencing reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.4.1c).
Aligned reads were then quantified to the transcriptome (UCSC mm10 annotation) at the gene level using featureCounts (v1.4.6).
Read counts were then normalized to reads per kilobase per million (RPKM) and differentially expressed genes were identified using the Characteristic Direction method.
Genome_build: mm10

source_name: bone marrow mesenchymal-derived stromal cells

growth_protocol: CD45(-) Ter119(-) CD31(-) Scf-GFP(+) stromal cells from digested bone marrow were seeded in alpha-MEM media (Gibco) supplemented with 20 % fetal bovine serum (FBS; Gibco), 100 units/ml of penicillin and 100 µg/ml of streptomycin, 10 ng/ml of fibroblast growth factor (FGF)-basic (R&D Systems) and 2 mM of L-glutamine (Thermo Fisher Scientific).

extract_protocol:
Total RNA from 1,000-5,000 sorted MSCs was extracted using the RNeasy Plus Micro kit (QIAGEN), and assessed for integrity and purity using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT DNA Sample preparation Kit (Illumina). The libraries were then submitted for Illumina NextSeq 500 sequencing (150 bp single ended) according to the standard procedures (ENSEMBL Mus musculus reference genome GRCm38 release 77).

tag: cell type

value: revitalized MSCs (rMSCs)

tag: transduced gene

value: 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7)


title: revitalized MSCs RNA-Seq rep1


title: CHC242T

description:
MUTHEC
test

tag: gender

value: M

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: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status


title: CHC2448T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

value: no

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC2443T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: 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


title: revitalized MSCs RNA-Seq rep2

tag: cell type

tag: strain

tag: transduced gene


title: CHC239T

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

value: HD

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: CHC241T

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: 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: mll2 status


title: L7CN75_C1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: L7CN75_C2

value: male


title: control stroma RNA-Seq rep3

tag: cell type

value: control vector-transduced stroma

tag: strain

tag: transduced gene

value: control vector


title: control stroma RNA-Seq rep2


title: CHC2454T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: TRANSPLANT

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: CHC2353T

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: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status


title: CHC230T

description:
MUTHEC
test

tag: gender

tag: age

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: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: CHC228T

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: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status


title: CHC231T

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: gnas mutation

tag: braf status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: L7CN76_C2

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

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: control stroma RNA-Seq rep1

tag: cell type

tag: strain

tag: transduced gene


title: CHC2216T

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: CHC223T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation


title: L7CN78_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: Scf-GFP(+) cells RNA-Seq rep3

tag: cell type

value: freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(+)

tag: strain

tag: transduced gene


title: L7CN78_E1


title: CHC2210T

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: CHC2211T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: 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


title: CHC2213T

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: 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: CHC2215T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: atm mutation


title: CHC2208T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

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: 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: L7CN78_D2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: Scf-GFP(+) cells RNA-Seq rep1

tag: cell type

tag: strain

tag: transduced gene


title: Scf-GFP(+) cells RNA-Seq rep2


title: L7CN78_D1


title: CHC2207T

description:
MUTHEC
test

tag: gender

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: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status


title: Scf-GFP(-) cells RNA-Seq rep3

source_name: bone marrow stromal cell

tag: cell type

value: freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-)

tag: strain

tag: transduced gene


title: Scf-GFP(-) cells RNA-Seq rep2


title: L7CN78_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: L7CN78_C1


title: CHC215T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

value: NM

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: 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: CHC217T

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: setd2 mutation

tag: tsc1 status


title: CHC218T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

value: HD

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status


title: Scf-GFP(-) cells RNA-Seq rep1

tag: cell type

tag: strain

tag: transduced gene


title: CHC2200T

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: 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: CHC2202T

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: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca 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: CHC2152T

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: rps6ka3 status

tag: rps6ka3 mutation

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: CHC2150T

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: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca 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: CHC2145T

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: rps6ka3 status

tag: rps6ka3 mutation

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


title: CHC214T

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: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status


title: L7CN79_D1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: L7CN79_D2


title: revitalized MSCs ATAC-Seq rep2

data_processing:
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (mm10 including small contigs) using the BWA-MEM software (arXiv:1303.3997v1).
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis.
Read numbers were down-sampled so that peak calling was based on comparable numbers of reads for each sample.
We performed peak calling using MACS2 and calculated the irreproducible discovery rates (IDR) of the detected peaks between biological replicates to select the high confidence peaks (IDR < 0.05).
We selected peaks which were shared across at least two biological replicates with an IDR <0.05.
Genome_build: mm10

extract_protocol:
ATAC-seq was performed as previously described. 2,700-5,000 MSCs were sorted into 4°C 1× PBS and washed in cold 1× PBS, lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630) to obtain nuclei. Immediately after lysis, nuclei were spun at 500 g for 10 min using a refrigerated centrifuge. To perform Transpose reaction, immediately following the nuclei prep, the nuclei pellet was resuspended in the transposase reaction mix (2.5 μl 2× TD buffer, 0.25 μl transposase (Illumina) and 2.25 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C.
We amplified the library fragments using 5 μl of transposed DNA, 10 μl of nuclease-free H20, 25 μl of NEBnext High-Fidelity 2× PCR master mix (New England Biolabs), 2.5 μl of 25 μM custom PCR primers 1, and 2.5 μl of 25 μM Barcode PCR primers 2 (primer sequences are previously described), using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. We amplified the libraries for a total of 13 or 17 cycles. The appropriate number of cycles for PCR amplification was determined through qPCR as described. After the initial 5 cycles additional 8 or 12 cycles were performed depending on the yield measured by qPCR. All libraries were sequenced on the Illumina Hiseq 2500 with 100 bp paired-end reads.

tag: cell type

value: revitalized MSCs (rMSCs)

tag: strain

tag: transduced gene

value: 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7)


title: CHC2141T

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


title: CHC2206T

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: atm status


title: CHC2135T

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: 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: L7CN79_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: control stroma ATAC-Seq rep3

tag: cell type

value: control vector-transduced stroma

tag: strain

tag: transduced gene

value: control vector


title: CHC2132T

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: atm status


title: CHC2128T

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: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: L7CN80_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: CHC2127T

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: 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: atm status


title: control stroma ATAC-Seq rep2

tag: cell type

tag: strain

tag: transduced gene


title: revitalized MSCs ATAC-Seq rep3


title: CHC2123T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

value: TRANSPLANT

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: 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: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: L7CN80_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2124T

description:
MUTHEC
test

tag: gender

tag: diagnosis

value: HCC

tag: type

value: no

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: 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: atm status


title: L7CN80_D2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: Scf-GFP(+) cells ATAC-Seq rep2

tag: cell type

value: freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(+)

tag: strain

tag: transduced gene


title: control stroma ATAC-Seq rep1


title: L7CN80_D1

value: spinal cord


title: CHC2119T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

value: NM

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: L7CN79_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: CHC2122T

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: atm status


title: CHC211T

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: jak1 status

tag: jak1 mutation

tag: gnas status

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation


title: CHC2115T

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

value: p.G964_Q965insT In_Frame_Ins

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 mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: atm status


title: CHC2114T

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: gnas status

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm mutation


title: L7CN80_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: Scf-GFP(+) cells ATAC-Seq rep1

tag: cell type

tag: strain

tag: transduced gene


title: CHC2113T

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: atm status


title: Scf-GFP(-) cells ATAC-Seq rep2

tag: cell type

value: freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-)

tag: strain

tag: transduced gene


title: L7CN80_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: Scf-GFP(-) cells ATAC-Seq rep1


title: CHC2112T

description:
MUTHEC
test

tag: gender

value: F

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

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: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

value: Splice_Site g.chr4:74275071del

tag: apob status

tag: apob mutation


title: L7CN81_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2110Tbis

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: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: atm status


title: CHC210T

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: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: hras

tag: hnf1a status

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


title: CHC2103T

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: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: atm status


title: CHC2099T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: gnas status

tag: gnas mutation

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation


title: revitalized MSCs ATAC-Seq rep1

tag: cell type

value: revitalized MSCs (rMSCs)

tag: strain

tag: transduced gene

value: 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7)


title: CHC2098T

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: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: atm status


title: CHC206T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

value: TRANSPLANT

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: gnas status

tag: gnas mutation

tag: hras

tag: hnf1a status

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


title: L7CN81_C1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: female


title: L7CN83_E2

value: spinal cord


title: CHC205T

description:
MUTHEC
test

tag: gender

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

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

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: atm status


title: CHC2111T

description:
MUTHEC
test

tag: gender

value: F

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: 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: alb mutation

tag: apob status

tag: apob mutation


title: L7CN83_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex

value: male


title: CHC2052T

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: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: atm status


title: CHC204T

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: 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


title: L7CN83_D2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2048T

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: atm status


title: L7CN81_E1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2043T

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: alb mutation

tag: apob status

tag: apob mutation


title: L7CN81_D2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2039Tbis

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: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: atm status


title: CHC209T

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: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf 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: L7CN83_C2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: CHC2034T

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: atm status


title: CHC207T

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: 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


title: CHC203T

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: 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: atm status


title: CHC2029T

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: apob status

tag: apob mutation


title: CHC1994T

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: 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: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: 3-Aged tail total epidermis

city: Tokyo

last: Liu

address: 1-5-45 Yushima, Bunkyo-ku

department: Stem Cell Biology

country: Japan

institute: Tokyo Medical and Dental Universtiy

description: Gene expressions in aged tail total epidermis

hyb_protocol: 1.3 μg Cy3 labeled cDNA were fragmented, and hybridized at 65°C for 17 hr to an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (Design ID: 028005).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: For normalization of microarray data, intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features that were flagged as no errors (Detected flags) and excluded features that were not positive, not significant, not uniform, not above background, saturated or population outliers (Compromised and Not Detected flags).

source_name: Aged tail total epidermis

label_protocol: Total RNA was isolated using a RNA easy micro Kit (Qiagen) according to the manufacturer’s instructions. cDNA samples were prepared from 1-10 ng RNA using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA, USA) according to the manufacturer’s instructions. Amplified cDNAs were labeled with Cyanine 3 (Cy3) using a SureTag DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer's instructions.

extract_protocol: Total tail epidermal cells were harvested from young and aged mice by EDTA treatments.

treatment_protocol: Tail skin samples were immersed in EDTA (5mM) for 3.5hr to separate epidermis from dermis.

tag: development stage

value: Aged (25m)

tag: genotype/variation

value: wild type

tag: strain


title: 2-Aged tail total epidermis


title: L7CN84_E2

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: 2-Young tail total epidermis

description: Gene expressions in young tail total epidermis

source_name: Young tail total epidermis

value: Young (8w)


title: L7CN83_C1


title: CHC1992T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: A

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: CHC1991T

description:
MUTHEC
test

tag: gender

value: M

tag: age

tag: diagnosis

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: mll2 status

tag: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: 1-Aged tail total epidermis

tag: development stage

value: Aged (22m)

tag: genotype/variation

tag: strain


title: M3

first: Aaron

last: Goldman

state: MA

address: 65 Landsdowne St.

institute: mitra biotech

description: mutant 3

data_processing:
Fastq reads were analyzed for quality and converted to .fastq.gzc
Sequenced reads were mapped to the UCSC mm9 reference genome assembly and gene counts quantified using STAR v2.5.1b
Normalized read counts (FPKM) were calculated using cufflinks
Differential gene expression profiling was performed using DESeq2 (v1.10.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

source_name: Lung

growth_protocol: Cells were cultured as spheroids in a 3-D culture system and RNA isolated after 48 hours of growth

extract_protocol:
RNA was isolated after 48 hours of culture growth using manufacturer protocol (Qiagen). Illumina TruSeq Stranded mRNA Sample Prep Kits were used for library preparation from 500ng of purified total RNA.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Prep Kits.

tag: cell type

value: Lung Tumor

tag: genotype


title: CHC198T

description:
MUTHEC
test

tag: gender

tag: age

tag: diagnosis

value: HCC

tag: type

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

value: B

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation


title: L7CN84_E1

tag: tissue

value: spinal cord

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: M1

description: mutant 1

tag: cell type


title: M2

description: mutant 2


title: 1-Young tail total epidermis

tag: development stage

tag: genotype/variation

tag: strain


title: CHC1989T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: no

tag: alcohol

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

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: L7CN84_D1

tag: tissue

tag: mouse id

tag: genotype

tag: age

tag: Sex


title: WT

description: wild type

tag: cell type


title: mouse

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

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.

source_name: kidney

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: strain

value: kidney

value: CD45+ innate immune cells

value: 8 weeks old

value: Male


title: 3-Young tail total epidermis

tag: development stage

tag: genotype/variation


title: L7CN84_C1

value: male


title: L7CN85_E2

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

value: female


title: CHC1980T

description:
MUTHEC
test

tag: gender

tag: diagnosis

tag: type

value: TRANSPLANT

tag: alcohol

value: yes

tag: hemochromatosis

tag: metavir fibrosis

tag: bclc

tag: serumalphafoeto (ui)

tag: tert status

value: NM

tag: tert mutation

tag: ctnnb1 status

tag: ctnnb1 mutation

tag: tp53 status

tag: tp53 mutation

tag: arid1a status

tag: arid1a mutation

tag: axin1 status

tag: axin1 mutation

tag: cdkn2a status

tag: cdkn2a mutation

tag: arid2 status

tag: arid2 mutation

tag: il6st status

tag: il6st mutation

tag: rps6ka3 status

tag: rps6ka3 mutation

tag: nfe2l2 status

tag: nfe2l2 mutation

tag: keap1 status

tag: keap1 mutation

tag: pik3ca status

tag: pik3ca mutation

tag: irf2 status

tag: irf2 mutation

tag: jak1 status

tag: jak1 mutation

tag: gnas status

tag: gnas mutation

tag: braf status

tag: braf mutation

tag: stat3 status

tag: stat3 mutation

tag: kras status

tag: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: CHC1985T

description:
MUTHEC
test

tag: gender

tag: age

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: mll2 mutation

tag: setd2 status

tag: setd2 mutation

tag: tsc1 status

tag: tsc1 mutation

tag: tsc2 status

tag: tsc2 mutation


title: CHC1976T

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: kras mutation

tag: nras status

tag: hras

tag: hnf1a status

tag: hnf1a mutation

tag: alb status

tag: alb mutation

tag: apob status

tag: apob mutation

tag: atm status

tag: atm mutation

tag: cdkn1a status

tag: cdkn1a mutation

tag: map1b status

tag: map1b mutation

tag: mll2 status


title: CHC1979T

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: mll2 mutation

tag: setd2 status

tag: setd2 mutation