title: multiplexed samples (tt2iLGo/hiTSC; DMSO/dm-aKG), GEX

description: gene expression (GEX): 3' mRNA library: R1 file contains cell barcode and UMI; R2 file contains transcript

data_processing:
Initial processing of scRNA-seq data was performed using Cell Ranger (v 6.1.2; 10X Genomics). Dual-indexed RNA and single-indexed hashtag oligo (HTO) libraries were processed in separate instances of cellranger mkfastq, using bcl2fastq (v2.20.0.422; Illumina).
FASTQ files were aligned to the human reference genome (GRCh38, v 2020-A as provided by 10x Genomics) with cellranger count (--expect-cells=8000), calling 8316 cells.
Resulting filtered feature-barcode matrices were loaded into Seurat (v 4.3.0), ignoring features that are detected in less than 3 cells. HTO assay was normalized with centered log-ratio (CLR) transformation, and Seurat's HTODemux function (with default parameters) was used to assign single cells back to their sample origins, resulting in 7001 cells classified as singlets.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: filtered feature-barcode matrix (combined gene expression and HTO counts) in Market Exchange Format: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Comma-separated values matrix of raw counts with cell barcodes as column names and gene names as row names (per sample, after HTODemux, before further cell QC)

growth_protocol: Naive ESC were cultured on gelatin-coated plates including a feeder layer of gamma-irradiated DR4 mouse embryonic fibroblasts (MEFs) (ATCC, SCRC-1045) in tt2iLGö medium. tt2iLGö medium consists of N2B27 basal medium supplemented with PD0325901 (1 μM, Axon Medchem, Axon 1408), CHIR99021 (0.3 μM, Axon Medchem, Axon1386), Gö 6983 (2 μM, Axon Medchem, Axon 2466) and human leukemia inhibitory factor (hLIF, 10 ng/mL, Qkine, Qk036)(Guo, von Meyenn et al. 2017). N2B27 basal medium contains DMEM/F12 with Glutamax (50%, Thermo Fisher Scientific, 31331028), neurobasal medium (50%, Fisher Scientific, 11570556), N2 supplement (1x, Merck Sigma Aldrich, SCM012), B27 supplement (0.5x, Thermo Fisher Scientific, 17504044), 2-mercaptoethanol (0.2 mM, Thermo Fisher Scientific, 31350010), and GlutaMAX™ (0.75 mM, Thermo Fisher Scientific, 25030024). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂) and passaged as single cells every three to four days. Cells were cultured for 24 hours with Y27632 (10 μM, Axon Medchem, Axon1683) after passaging. Medium was changed daily. hiTSC induction was performed according to Dong et al., with minor modifications. Briefly, prior to the induction, nESC were depleted from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Naive hESC then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium. After 24h, media was changed to hiTSC medium consisting of N2B27 supplemented with Bovine Serum Albumin (BSA) (0.3%, Sigma, A3294), heat-inactivated Fetal Bovine Serum (HI-FBS) (0.2%, Thermo Fisher Scientific, 12389782), Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1x, Gibco, 51500), L-ascorbic acid (1.5 μg/ml, Sigma, A8960-5G), recombinant human EGF (50 ng/ml, Qkine, Qk011), CHIR99021 (2 μM, Axon MedChem, Axon 1386), A83-01 (0.5 μM, Axon MedChem, Axon 1421), SB431542 (1 μM, Axon MedChem, Axon 1661), Valproic Acid (VPA) (0.8 mM, Axon MedChem, Axon 3127), and Y-27632 (10 μM, Axon MedChem, Axon 1683). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂).

extract_protocol:
Four samples were collected by 10 minutes of trypsinization and dissociated into single cells. Each sample was incubated with 0.5 μg of unique hashtag antibody for 20 min on ice. TotalSeq hashtag antibodies (A0253-A0256, Biolegend) were used to multiplex the samples (DOI: 10.1126/sciadv.adg4055). All 4 samples were sorted on a BD FACSymphony S6 (BD Bioscences) resulting in a total cell recovery of around 8000 cells, which were loaded onto a Chromium Next GEM chip (10x Genomics).
Library preparation was performed according to the Chromium Next GEM Single Cell 3’ v3.1 user guide with the addition of the hashtag library for demultiplexing. Combined libraries were sequenced using the NextSeq2000 P2-100 kit (Illumina) with Paired-end sequencing
10x scRNA-seq

treatment_protocol: For the tt2iLIFGö samples, naive ESC were depleted from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Cells then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium for 48 hours. Medium was changed to tt2iLGö supplemented with 0 or 4mM dm-αKG for 24h before cells were collected for scRNA-seq. hiTSC samples were acquired by depleting naive ESC from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Cells then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium supplemented with 0 or 4mM dm-αKG for 24 hours. Medium was then changed to hiTSC medium and cells were grown for 72 hours before collection for scRNA-seq.

value: mixed sample (non-demultiplexed):human embryonic stem cells/human induced trophoblast stem cells

value: mixed sample (non-demultiplexed):DMSO/4mM dm-aKG


title: YHB234_nash_f1_H3K27ac_cutrun

status: Public on Feb 27 2025

type: SRA

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

country: USA

institute: Vanderbilt University Medical Center

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F

library_source: genomic

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Alignment with Bowtie (V2.3.4.3) against hg38 with following parameters: --wrapper basic-0 -X2000 –mm; Data filtering steps: All alignments were filtered for unmapped and duplicated reads; Additional processing: Peak calling was performed using MACS2 (2.2.5) with following parameters: -g hs -p 0.01 --nomodel --shift 0 --extsize 70 --keep-dup all -B –SPMR. Reproducible peak sets were called using the IDR procedure, if no biological replicates were available pseudo-replicates were used, as implemented in the ENCODE ChIP-seq pipeline (v2.2.2). Resulting reproducible peak sets were merged and reads per sample counted using Rsubread (2.10.5). All downstream analysis was performed using R 4.2.1 Bigwig signal tracks were generated using bamCoverage from Deeptools (3.5.1.) with following parameters  --extendReads --centerReads -bs 1 –ignoreDuplicates
Assembly: hg38
Supplementary files format and content: peak read count table
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Human liver biopsy samples

extract_protocol:
Following CUT&RUN assay, DNA was extracted using phenol/chloroform/isoamyl alcohol followed by ethanol precipitation.
NEB DNA Ultra II Kit

treatment_protocol: Samples obtained at the time of bariatric surgery.

tag: tissue

value: Liver

tag: steatosis

tag: balloning

tag: lobular inflammation

tag: lobular necrosis

tag: fibrosis nas_tidy

tag: Stage

tag: Sex

value: F

tag: chip antibody


title: tt2iLGo, 4mM dm-αKG, rep3

city: Copenhagen

first: Jan

middle: Jakub

last: Żylicz

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Paired-end reads were aligned with STAR (v 2.7.2d) to the reference genome GRCh38.p13 with gene annotations from GENCODE release 32 (`--sjdbGTFfile gencode.v32.annotation.gtf`) and option `--quantMode GeneCounts` was set to count the number of reads per gene while mapping.
The 4th column of each sample's "ReadsPerGene.out.tab" file (corresponding to counts for the 2nd read strand aligned with RNA) was extracted and combined to a joint counts matrix.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.

molecule: polyA RNA

source_name: H9 (WA09, WiCell)

growth_protocol: Naive ESC were cultured on gelatin-coated plates including a feeder layer of gamma-irradiated DR4 mouse embryonic fibroblasts (MEFs) (ATCC, SCRC-1045) in tt2iLGö medium. tt2iLGö medium consists of N2B27 basal medium supplemented with PD0325901 (1 μM, Axon Medchem, Axon 1408), CHIR99021 (0.3 μM, Axon Medchem, Axon1386), Gö 6983 (2 μM, Axon Medchem, Axon 2466) and human leukemia inhibitory factor (hLIF, 10 ng/mL, Qkine, Qk036)(Guo, von Meyenn et al. 2017). N2B27 basal medium contains DMEM/F12 with Glutamax (50%, Thermo Fisher Scientific, 31331028), neurobasal medium (50%, Fisher Scientific, 11570556), N2 supplement (1x, Merck Sigma Aldrich, SCM012), B27 supplement (0.5x, Thermo Fisher Scientific, 17504044), 2-mercaptoethanol (0.2 mM, Thermo Fisher Scientific, 31350010), and GlutaMAX™ (0.75 mM, Thermo Fisher Scientific, 25030024). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂) and passaged as single cells every three to four days. Cells were cultured for 24 hours with Y27632 (10 μM, Axon Medchem, Axon1683) after passaging. Medium was changed daily.

extract_protocol:
RNA was collected and extracted using the Qiagen RNeasy Mini Kit (Qiagen, 74104) with on column DNAse treatment.
Libraries for sequencing were prepared using 500ng of total RNA and the NEBNext Poly(A) mRNA and NEBNext UltraII stranded RNA-seq library preparation kit. 10 cycles of amplification were performed.

treatment_protocol: Naive ESC were depleted from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Cells then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium for 48 hours. Medium was changed to tt2iLGö supplemented with 0 or 4mM dm-αKG or 1uM A-485 for 24h before cells were collected for mRNA-seq or induced towards hiTSC. Briefly, media was changed to hiTSC medium consisting of N2B27 supplemented with Bovine Serum Albumin (BSA) (0.3%, Sigma, A3294), heat-inactivated Fetal Bovine Serum (HI-FBS) (0.2%, Thermo Fisher Scientific, 12389782), Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1x, Gibco, 51500), L-ascorbic acid (1.5 μg/ml, Sigma, A8960-5G), recombinant human EGF (50 ng/ml , Qkine, Qk011), CHIR99021 (2 μM, Axon MedChem, Axon 1386), A83-01 (0.5 μM, Axon MedChem, Axon 1421), SB431542 (1 μM, Axon MedChem, Axon 1661), Valproic Acid (VPA) (0.8 mM, Axon MedChem, Axon 3127), and Y-27632 (10 μM, Axon MedChem, Axon 1683). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂).

tag: cell line

value: H9 (WA09, WiCell)

tag: cell type

value: human embryonic stem cells

tag: treatment

value: 4mM dm-aKG


title: hiTSC d3, 0mM dm-αKG, rep1

value: human induced trophoblast stem cells day 3

value: DMSO


title: RNA-seq_control_4

city: Buffalo

first: Dahong

last: Chen

state: Other

address: 955 Main Street

department: Biochemistry

institute: SUNY Buffalo

data_processing:
Reads were aligned to mouse m31reference with hisat2 or bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
Assembly: m31
Supplementary files format and content: bw files that are used for visulization

molecule: total RNA

organism: Mus musculus

source_name: rod

extract_protocol:
RNA was extracted by the Qiagen Micro-plus kit
CUT&Tag libraries were generated according to published protocols  Hatice S Kaya-Okur, Steven Henikoff 2020. Bench top CUT&Tag. protocols.io; ATAC-seq libraries were generated according to Chen et al., 2021, Nat. Commun.; RNA-seq libraries were generated according to the commertical instructions

value: rod

tag: genotype

value: Nrl>Tomato


title: tt2iLGo, 4mM dm-αKG, rep1


title: hiTSC d3, 4mM dm-αKG, rep1


title: ABJ468_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F

value: NAFL


title: tt2iLGo, 0mM dm-αKG, rep3


title: XSP436_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 3, stage: NASH_F23, sex: M

value: M


title: RNA-seq_control_3


title: tt2iLGo, 0mM dm-αKG, rep1


title: RFN819_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F

value: NOR


title: hiTSC d3, 1uM P300i, rep3


title: hiTSC d3, 1uM P300i, rep2


title: RNA-seq_control_7


title: hiTSC d3, 0uM P300i, rep3


title: IQG997_nash_f23_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: M


title: RNA-seq_control_2


title: RNA-seq_control_1


title: multiplexed samples (tt2iLGo/hiTSC; DMSO/dm-aKG), HTO

description: Hashtag-derived oligonucleotide (HTO): Cell Hashing library: R1 file contains cell barcode and UMI; R2 file contains Hashtag Antibody Derived Tag reads

library_source: other

molecule: protein

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0253 anti-human Hashtag 3, TotalSeq-A0254 anti-human Hashtag 4, TotalSeq-A0255 anti-human Hashtag 5, TotalSeq-A0256 anti-human Hashtag 6


title: hiTSC d3, 0uM P300i, rep2


title: GBP913_nor_H3K27ac_cutrun


title: JVQ477_nash_f1_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: M


title: TVO619_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: tt2iLGo, 1uM P300i, rep1


title: tt2iLGo, 1uM P300i, rep2


title: TPK_ADT-scATAC

city: shanghai

first: jiacheng

last: guo

address: yueyang road 320

country: China

institute: Shanghai Institute of Nutrition and Health

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Matrix files of prostate tumor epithelial cell sequencing results

source_name: prostate

extract_protocol:
Flow-sorted prostate epithelial cells.
The scRNA-seq libraries were generated using the 10´ Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. The experiments were performed by NovelBio Bio-Pharm Technology Co., Ltd.

value: prostate epithelium

value: prostate

value: ADT

tag: age


title: tt2iLGo, 0uM P300i, rep2


title: tt2iLGo, 0uM P300i, rep1


title: TPK_Sham-scATAC

description: 10x Genomics

value: sham


title: REI423_nor_H3K27ac_cutrun

value: Liver

value: F


title: tt2iLIFGo, dm-aKG, rep3

data_processing:
Basecalls and demultiplexing was performed by bcl2fastq v2.20.0.422.
Data was processed with the ENCODE ATAC-seq pipeline (v 2.2.2; https://github.com/ENCODE-DCC/atac-seq-pipeline). Samples with the same treatment were analyzed together as biological replicates in a single run (with "atac.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv", "atac.paired_end" : true, "atac.auto_detect_adapter" : true, and otherwise default parameters).
Briefly, ATAC-seq reads were trimmed using cutadapt, and aligned to GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta using bowtie2 (-k 5 -X2000). Alignments were filtered, removing PCR duplicates (using Picard’s MarkDuplicates) and reads mapping to the mitochondrial chromosome, converted to tagalign files and TN5 shifting applied.
Peak calling was performed on each replicate, as well as pooled data and pseudoreplicates of those using MACS2 (-g hs -p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits). IDR (Irreproducibility Discovery Rate) analysis was performed on the different sets, selecting the peaks passing IDR threshold of 5%. The 'optimal set' was found by comparing pooled pseudo-replicates. Lastly, blacklisted regions (https://www.encodeproject.org/files/ENCFF356LFX) were filtered out.
Optimal IDR peaks (idr.optimal_peak.narrowPeak.gz) from both pipeline runs were concatenated, trimmed to 200 bp around the summit, sorted and merged with bedtools v2.28.0 to generate a master peak file. This peak file was intersected with tagalign files from each sample using bedtools coverage -counts to generate a peak by sample matrix of raw counts.
Assembly: GRCh38
Supplementary files format and content: ENCODE narrowPeak format (BED6+4) file of optimal IDR peaks called for each treatment.
Supplementary files format and content: Tab-delimited text file with genomic region coordinates of the merged consensus ATAC peaks in the first 3 columns ('master peak file'), and raw read counts of the number of reads (from each replicate) aligning to these in the remaining 6 columns.

extract_protocol:
For ATAC-seq previous protocol was used (Grandi, Modi et al. 2022). Cells were trypsinized and resuspended in N2B27. After washing in PBS 50’000 cells were lysed for 3min on ice in lysis buffer (0.1% NP40; 0.1% Tween-20; 0.01% Digitonin; 10 mM Tris-HCl pH 7.4; 10 mM NaCl, 3 mM MgCl). Lysis was stopped with ATAC-wash buffer (0.1% Tween-20; 10 mM Tris-HCl pH 7.4; 10 mM NaCl, 3 mM MgCl). After pelleting the cells were resuspended in transposition mix [1x TD buffer (Illumina, cat. no. 20034197), 0.01% Digitonin; 0.1% Tween-20 in PBS; TDE1 TD enzyme (Illumina, cat. no. 20034197)] and incubated for 30min at 37°C in a thermomixer set on 1000 rpm. Transposition was terminated with DNA Binding Buffer DNA Clean and Concentrator-5 kit (Zymo Research, cat. no. D4014) and DNA was purified.
Libraries were prepared using barcoding adapters and the NebNext High-Fidelity 2x Master Mix (NEB cat. No. M0541S). Cycling conditions used were: 72°C 5min; 98°C 30sec; 11x(98°C 30sec; 63°C 30sec); 72°C 1min. Libraries were purified twice using DNA Clean and Concentrator kit.

treatment_protocol: Naive ESC were depleted from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Cells then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium for 48 hours. Medium was changed to tt2iLGö supplemented with 0 or 4mM dm-αKG for 24h before cells were collected for ATAC-seq.

value: H9 (WA09, WiCell)

value: human embryonic stem cells


title: tt2iLIFGo, dm-aKG, rep1

value: 4mM dm-aKG


title: TPK_ADT-scRNA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA


title: MRA483_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: tt2iLIFGo, dm-aKG, rep2


title: TPK_Sham-scRNA

description: 10x Genomics


title: tt2iLIFGo, DMSO, rep3

value: DMSO


title: BGB414_nor_H3K27ac_cutrun


title: tt2iLIFGo, DMSO, rep2


title: PPK_ADT-scRNA

description: 10x Genomics

value: PtenPC-/-; Kmt2cPC-/-


title: tt2iLIFGo, DMSO, rep1


title: JUT827_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: YSZ301_nash_f1_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: M


title: PPK-scRNA

description: 10x Genomics


title: PP_ADT-scRNA

description: 10x Genomics

value: PtenPC-/-


title: WLW163_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB14

city: Paris

first: Yimin

last: SHEN

state: Val-de-Marne

address: 27 Rue Juliette Dodu

country: France

institute: Fondation Jean Dausset-CEPH

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB14
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt

data_processing:
analyzed with different types of second and third generation sequencing protocols (see workflow of the different bioinformatic analyses ), then analyzed using the same microsatellite identification method based on the recognition of the 4 consecutive regions: (i), (ii), (iii) and (iv)
Assembly: other sequences
Supplementary files format and content: microsatellite profil text files

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Plasmid preparation
Illumina sequencing: QIAseq 1-Step Amplicon Library Kit (Qiagen), QIAseq FX DNA Library Kit (Qiagen), and xGen Prism DNA Library Prep Kit (Integrated DNA Technologies). PacBio sequencing: SMRTbell prep kit 3.0 (PacificBiosciences) and SMRTbell binding kit 2.0 (Pacific Biosciences). Nanopore sequencing : Native Barcoding Kit 96 V14 (Oxford Nanopore Technologies (ONT)) together with NEBNext® Ultra II End Repair / dA-tailing Module (New England Biolabs (NEB)), NEB Blunt/TA Ligase Master Mix (NEB), and NEBNext® Quick Ligation Module (NEB).

value: synthetic construct


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB13

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB13
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB19

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB19
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB18

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB18
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: PP-scRNA

description: 10x Genomics


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB12

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB12
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB10

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB10
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: LUH941_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F

value: NAFL


title: TPK_DNPC_TVB2640-B_RNA-seq

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The read length was 2×150 bp. The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per million mapped reads) using Perl. Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package in R between different groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM  values for each sample

extract_protocol:
RNA was extracted using Trizol purification from prostate epithelial cells or organoids, 1µg total RNA was used for the construction of sequencing libraries
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina) following manufacturer's protocols

value: prostate organoid


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB09

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB09
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: OKQ881_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F

value: NOR


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB19

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB19
Type V Simplex A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB17

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB17
Type V Simplex A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: GDJ739_nafl_H3K27ac_cutrun


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB14

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB14
Type V Simplex A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TPK_DNPC_Veh-A_RNA-seq

value: Veh.


title: JWQ775_nash_f1_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: TPK_DNPC_Veh-B_RNA-seq


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB18

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB18
Type V Simplex A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB17

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB17
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: TPK_Sham_TVB2640-B_RNA-seq


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB12

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB12
Type V Simplex A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB13

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB13
Type V Simplex A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB11

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB11
Type V Simplex A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB10

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB10
Type V Simplex A20/(AC)25/(AT)15
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TPK_Sham_TVB2640-A_RNA-seq


title: AUT782_nor_H3K27ac_cutrun


title: YDJ237_nafl_H3K27ac_cutrun

description: steatosis: 2, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Duplex,ONT_NB11

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.ONT_NB11
Type V Duplex (dx1:duplex read; dx-:simplex read with duplex offspring) A25/(AC)15/(AT)20
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.StandardDuplex.proportion.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Duplex.InhouseDuplex.proportion.txt


title: TypeV,NanoporeKit,Nanopore,PromethION,PCRcycles0,Simplex,Q25,ONT_NB09

description:
Library name: TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_Simplex_Q25.ONT_NB09
Type V Simplex A15/(AC)20/(AT)25
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.count.txt
TypeV_NanoporeKit_Nanopore_PromethION_PCRcycles0_StandardSimplex.proportion.txt


title: TPK_Sham_Veh-B_RNA-seq


title: TPK_DNPC_TVB2640-A_RNA-seq


title: TypeIV,SMRTbellprepkit3.0,PacBio,SequelII,PCRcycles0,CCS,Q20,PacBio_bc3

description:
Library name: TypeIV_SMRTbellprepkit3.0_PacBio_SequelII_PCRcycles0_CCS_Q20.PacBio_bc3
Type IV CCS Q20 (AC)15/A25


title: PNT686_nash_f1_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: TypeIV,SMRTbellprepkit3.0,PacBio,SequelII,PCRcycles0,CCS,Q20,PacBio_bc2

description:
Library name: TypeIV_SMRTbellprepkit3.0_PacBio_SequelII_PCRcycles0_CCS_Q20.PacBio_bc2
Type IV CCS Q20 (AT)25/(AC)20


title: QTB333_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: LA2_scRAGE_seq

city: Lebanon

first: Leena

last: Abdullah

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

description: flow cell=FLO-MIN114

data_processing:
Putative Cell IDs were extracted from the raw .fastq files and cross-checked against the Cell Ranger whitelist ("3M-february-2018.txt.gz"). The Cell IDs  were subjected to two error correction steps and  only corrected IDs that matched the Cell Ranger whitelist were kept. The fastq sequences per cell underwent error correction using Canu (PMID: 28298431).Post-Canu processing, every error-corrected read from a cell was subjected to IgBLAST (v1.20.0), with the organism set to mouse and using the IMGT germline libraries for V, D, and J sequences, along with auxiliary data files.
processed data files format and content: .csv file containing Cell IDs and their corresponding TCR annotation
Assembly: mm10

source_name: Spleen

extract_protocol:
RAGE-seq libraries were prepared using a modified version of the protocol described in the original RAGE-seq study (https://www.nature.com/articles/s41467-019-11049-4). After preparation of 10x RNA-seq and CARLIN libraries, the remaining cDNA from step 2.3 of the 10x 3’ v3.1 User Guide (CG000204 Rev D) was used as input into the RAGE-seq protocol. cDNA was amplified for 20 cycles and V(D)J sequences enriched with the xGen Hybridization Capture chemistry (IDT) using a custom probe set. Probes were designed against all mouse functional V, D, J and TCR/BCR constant regions obtained from the IMGT database . Following hybridization capture, libraries were further amplified for 20 cycles. Each RAGE-seq sample (1 per 10x library) was prepared for nanopore sequencing using the ligation sequencing kit for either the v10 (Sample LA1, SQK-LSK110) or v14 (Samples LA2 and LA3, SQK-LSK114) chemistry and sequenced using the corresponding FLO-MIN110 or FLO-MIN114 flow cells. Super accuracy basecalling was performed off instrument using dorado v0.2.1 on an Nvidia A40 GPU.
After 7 days of infection, CARLIN mice (LA1, LA2, LA3) were euthanized, and their spleens were harvested. The spleens were mashed and filtered to get a single cell suspension. Next, Erythrocytes were depleted and the samples were enriched for CD8+ T cells. The enriched CD8+ T cells were stained and finally, live, OVA-Tetramer-BV421 and OVA-Tetramer-PE double positive CD8+ T cells were sorted.

value: Spleen

value: CD8+ T cells

value: CARLIN (RRID:MMRRC_067061-JAX) x KH2/iCas9 (RRID:IMSR_JAX:029415) . The F1 generation (LA1,LA2,LA3) is heterozygous for the CARLIN barcode, tetO-Cas9 and rtTa locus.

value: mouse was infected with VSV-OVA for 7 days


title: LA3_scRAGE_seq

description: flow cell=FLO-MIN114


title: OBOB_FLO_mouse_R5

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2
Exon quantification pipeline (version 2.5, (51)) with STAR (version 2.7.3a)
PISCES (GitHub - Novartis/pisces) to quantify gene expression.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw count for each sample

growth_protocol: Animals were housed in standard mouse cages with standard chow diet ("OBOB_FLO") or standard chow diet along with injection of 0.15% Ethionine ("OBOB_Fibrotic")

extract_protocol:
Total RNA was extracted from whole livers with Trizol.
Poly A selected mRNA library

treatment_protocol: standard chow diet with 0.165% DL Ethionine in drinking water (Fibrotic) vs standard chow diet without Ethionine.

value: Liver

value: standard chow diet


title: LA1_scRAGE_seq

description: flow cell=FLO-MIN110


title: UHL541_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F

value: F


title: Persistent synergid cell, 24 HAP, rep3

city: Wuhan

first: Junyi

state: Hubei

address: Luoyu Road 152

department: Institute of Plant Sciences

institute: Central China Normal University

description: Library name: pSC24_3

data_processing:
Clean reads of samples were prepared using Cutadapt version 1.15 and an inhouse perl script.
Clean reads were mapped to the maize genome (AGPv5, Zm-B73-REFERENCE-NAM-5.0, http://ftp.ensemblgenomes.org/pub/plants/release-51/fasta/zea_mays/dna/) using Hisat2 version 2.0.5.
Gene expression levels were quantified as FPKM using featureCounts version 1.5.0-p3.
Assembly: Maize genome AGPv5
Supplementary files format and content: xls file includes raw counts for each Sample
Supplementary files format and content: xls file includes FPKM values for each Sample

organism: Zea mays

source_name: Persistent synergid cell 24 HAP

growth_protocol: Maize plants were cultivated in the greenhouses at 26°C under illumination of 24,000 lux with 16 h light/8 h dark cycles and a relative humidity of 60%.

extract_protocol:
mRNA was isolated from cell samples (25–28 cells for each biological replicate at each stage) using the Dynabeads mRNA DIRECTTM Micro Kit (Life Technologies). cDNA synthesis and amplification were performed using a SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Clontech). cDNA was purified using an Agencourt AMPure purification kit (Beckman Coulter). After purification and quantification, cDNA was used for library construction.
RNA-seq libraries were prepared using a NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions, and sequenced on an Illumina Novaseq platform using paired-end 150 bp flow cells.

value: Persistent synergid cell 24 HAP


title: Persistent synergid cell, 24 HAP, rep2

description: Library name: pSC24_2


title: OBOB_FLO_mouse_R4


title: PFX974_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F


title: Persistent synergid cell, 18 HAP, rep3

description: Library name: pSC18_3

source_name: Persistent synergid cell 18 HAP

value: Persistent synergid cell 18 HAP


title: Persistent synergid cell, 24 HAP, rep1

description: Library name: pSC24_1


title: OTW294_nor_H3K27ac_cutrun


title: OBOB_FLO_mouse_R3


title: TypeIV,SMRTbellprepkit3.0,PacBio,SequelII,PCRcycles0,CCS,Q20,PacBio_bc8

description:
Library name: TypeIV_SMRTbellprepkit3.0_PacBio_SequelII_PCRcycles0_CCS_Q20.PacBio_bc8
Type IV CCS Q20 (AT)15/(AC)25


title: Persistent synergid cell, 18 HAP, rep2

description: Library name: pSC18_2


title: DWS954_nor_H3K27ac_cutrun


title: TPK_Sham_Veh-A_RNA-seq

value: prostate


title: Persistent synergid cell, 18 HAP, rep1

description: Library name: pSC18_1


title: OBOB_FLO_mouse_R2


title: WRY133_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 2, fibrosis_nas_tidy: 3, stage: NASH_F23, sex: M

value: M


title: Persistent synergid cell, 12 HAP, rep3

description: Library name: pSC12_3

source_name: Persistent synergid cell 12 HAP

value: Persistent synergid cell 12 HAP


title: TypeIV,SMRTbellprepkit3.0,PacBio,SequelII,PCRcycles0,CCS,Q20,PacBio_bc1

description:
Library name: TypeIV_SMRTbellprepkit3.0_PacBio_SequelII_PCRcycles0_CCS_Q20.PacBio_bc1
Type IV CCS Q20 A15/A20/(AT)20

value: synthetic construct


title: Persistent synergid cell, 12 HAP, rep1

description: Library name: pSC12_1


title: OBOB_FLO_mouse_R1


title: YFH298_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M


title: XYG500_nash_f23_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: CQW242_nash_f1_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: Persistent synergid cell, 12 HAP, rep2

description: Library name: pSC12_2


title: Synergid cell, 0 HAP, rep2

description: Library name: SC_2

source_name: Synergid cell 0 HAP

value: Synergid cell 0 HAP


title: OBOB_Fibrotic_mouse_R6

value: standard chow diet along with addition of 0.165% DL Ethionine


title: OBOB_FLO_mouse_R6


title: Synergid cell, 0 HAP, rep1

description: Library name: SC_1


title: OBOB_Fibrotic_mouse_R5


title: OBOB_Fibrotic_mouse_R4


title: Synergid cell, 0 HAP, rep3

description: Library name: SC_3


title: OBOB_Fibrotic_mouse_R3


title: VVI446_nor_H3K27ac_cutrun

value: NOR


title: OBOB_Fibrotic_mouse_R2


title: YVA544_nafl_H3K27ac_cutrun

value: NAFL


title: SRC524_nor_H3K27ac_cutrun


title: OBOB_Fibrotic_mouse_R1


title: MCD_mouse_R12

growth_protocol: Animals were housed in standard mouse cages with methoinine-choline deficient diet or control diet for 20 weeks.

extract_protocol:
Total RNA was extracted from whole livers with Trizol.
poly A selected mRNA library.

treatment_protocol: Methionine-choline deficient diet vs. control chow diet.

value: methionine-choline deficient diet


title: Liver - P110aHepWT_LFD_ZT0 - Rep1

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 57 out of 71 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 51063 spots out of 62976 were selected.  The mean signal of the 24 first samples, 23 next and 24 last ones were substracted to individuals signals to correct the batch effect of the 3 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 46746 rows each corresponding to a unique ProbeName (provided as data Matrix).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mouse housing was controlled for temperature (23°C) and light (12-h light/12-h dark). All mice were males.

extract_protocol: Total cellular RNA was extracted with Tri reagent (Molecular Research Center).

treatment_protocol: Following killing by cervical dissociation, livers were removed, weighted and snap-frozen in liquid nitrogen and stored at -80°C.

tag: diet

value: LFD

tag: time

tag: washbatch


title: Liver - P110aHepKO_LFD_ZT0 - Rep1

tag: tissue


title: OQG452_nafl_H3K27ac_cutrun

tag: steatosis

tag: balloning

tag: lobular inflammation


title: MCD_mouse_R11


title: Liver - P110aHepWT_HFD_ZT04 - Rep3

value: HFD


title: SPM565_nash_f1_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: M

tag: lobular necrosis

tag: fibrosis nas_tidy

tag: Stage


title: SEG748_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F

tag: Sex

tag: chip antibody


title: MCD_mouse_R10

tag: treatment


title: Liver - P110aHepWT_HFD_ZT08 - Rep1

tag: genotype


title: RVO178_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: MCD_mouse_R9


title: Liver - P110aHepKO_LFD_ZT20 - Rep3


title: EFT620_nafl_H3K27ac_cutrun


title: HYC397_nor_H3K27ac_cutrun


title: MCD_mouse_R8


title: Liver - P110aHepKO_HFD_ZT04 - Rep1


title: Liver - P110aHepWT_LFD_ZT04 - Rep3


title: Liver - P110aHepWT_HFD_ZT20 - Rep3


title: Liver - P110aHepWT_LFD_ZT08 - Rep3


title: Liver - P110aHepWT_HFD_ZT0 - Rep1


title: Liver - P110aHepKO_LFD_ZT20 - Rep1


title: Liver - P110aHepKO_HFD_ZT08 - Rep3


title: Liver - P110aHepWT_HFD_ZT12 - Rep1


title: Liver - P110aHepWT_LFD_ZT16 - Rep3


title: Liver - P110aHepKO_HFD_ZT0 - Rep3


title: Liver - P110aHepKO_HFD_ZT16 - Rep2


title: Liver - P110aHepKO_LFD_ZT04 - Rep1


title: Liver - P110aHepWT_HFD_ZT16 - Rep3


title: JFL906_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 2, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: IMD704_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: MCD_mouse_R6


title: QKY201_nash_f1_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 2, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: MCD_mouse_R7


title: BQG343_nafl_H3K27ac_cutrun


title: MCD_mouse_R5


title: EXK318_nash_f23_H3K27ac_cutrun


title: MCD_mouse_R3


title: CFH377_nor_H3K27ac_cutrun


title: MCD_mouse_R2


title: LQF210_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: Liver - P110aHepKO_HFD_ZT20 - Rep1


title: Liver - P110aHepKO_LFD_ZT12 - Rep1


title: TypeIII,xGenPrismDNALibraryPrepKit,Illumina,NextSeq500,PCRcycles16,N6,NextSeq6_S15

description:
Library name: TypeIII_xGenPrismDNALibraryPrepKit_Illumina_NextSeq500_PCRcycles16_N6.NextSeq6_S15
Type III


title: Liver - P110aHepKO_LFD_ZT16 - Rep3


title: Liver - P110aHepWT_LFD_ZT12 - Rep2


title: Liver - P110aHepKO_HFD_ZT16 - Rep3


title: MCD_mouse_R4


title: Liver - P110aHepKO_LFD_ZT08 - Rep3


title: Liver - P110aHepKO_HFD_ZT12 - Rep3


title: Liver - P110aHepKO_LFD_ZT0 - Rep3


title: Liver - P110aHepWT_LFD_ZT20 - Rep1


title: Liver - P110aHepWT_LFD_ZT0 - Rep3


title: TypeIII,xGenPrismDNALibraryPrepKit,Illumina,NextSeq500,PCRcycles16,N6,NextSeq6_S14

description:
Library name: TypeIII_xGenPrismDNALibraryPrepKit_Illumina_NextSeq500_PCRcycles16_N6.NextSeq6_S14
Type III


title: Liver - P110aHepKO_HFD_ZT04 - Rep3


title: Liver - P110aHepWT_HFD_ZT08 - Rep2


title: KUV229_nor_H3K27ac_cutrun


title: MCD_Ctrl_mouse_R12

value: control diet


title: MCD_mouse_R1

value: Liver


title: Liver - P110aHepKO_HFD_ZT08 - Rep1


title: KXW719_nafl_H3K27ac_cutrun


title: TypeIII,xGenPrismDNALibraryPrepKit,Illumina,NextSeq500,PCRcycles16,N6,NextSeq6_S13

description:
Library name: TypeIII_xGenPrismDNALibraryPrepKit_Illumina_NextSeq500_PCRcycles16_N6.NextSeq6_S13
Type III


title: MCD_Ctrl_mouse_R11


title: TypeIII,xGenPrismDNALibraryPrepKit,Illumina,NextSeq500,PCRcycles16,N2,NextSeq2_S11

description:
Library name: TypeIII_xGenPrismDNALibraryPrepKit_Illumina_NextSeq500_PCRcycles16_N2.NextSeq2_S11
Type III


title: XPP673_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F


title: Liver - P110aHepKO_HFD_ZT0 - Rep2


title: MCD_Ctrl_mouse_R10


title: TypeIII,xGenPrismDNALibraryPrepKit,Illumina,NextSeq500,PCRcycles16,N2,NextSeq2_S10

description:
Library name: TypeIII_xGenPrismDNALibraryPrepKit_Illumina_NextSeq500_PCRcycles16_N2.NextSeq2_S10
Type III


title: MCD_Ctrl_mouse_R9


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy3_part4

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy3_part4
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: CIW710_nash_f1_H3K27ac_cutrun


title: MCD_Ctrl_mouse_R8


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy3_part3

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy3_part3
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepWT_LFD_ZT04 - Rep2


title: SLR4892_nor_H3K27ac_cutrun


title: MCD_Ctrl_mouse_R7


title: PGH821_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: Liver - P110aHepWT_HFD_ZT16 - Rep2


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy3_part2

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy3_part2
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepWT_HFD_ZT20 - Rep1


title: Liver - P110aHepKO_LFD_ZT12 - Rep2


title: MCD_Ctrl_mouse_R6


title: MCD_Ctrl_mouse_R5


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy2_part4

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy2_part4
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: MCD_Ctrl_mouse_R4


title: IOA210_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M


title: KQC337_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy2_part3

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy2_part3
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepKO_LFD_ZT04 - Rep2


title: MCD_Ctrl_mouse_R3


title: Liver - P110aHepWT_LFD_ZT16 - Rep1


title: Liver - P110aHepWT_HFD_ZT0 - Rep2


title: TTG258_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: MCD_Ctrl_mouse_R2


title: HML208_nash_f1_H3K27ac_cutrun

description: steatosis: 3, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 2, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy2_part2

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy2_part2
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepKO_LFD_ZT08 - Rep2


title: Liver - P110aHepWT_LFD_ZT08 - Rep2


title: FSM684_nor_H3K27ac_cutrun


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy1

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy1
Type II (BAM with UMI tag: RX,)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: MCD_Ctrl_mouse_R1


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy3_part1

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy3_part1
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: GNK557_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: FFD_Ctrl_mouse_R12

growth_protocol: Animals were housed in standard mouse cages with control diet or high fat diet for 20 weeks.

treatment_protocol: High fat diet vs. control chow diet.


title: YRI137_nafl_H3K27ac_cutrun


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq6_16cy2_part1

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq6_16cy2_part1
Type II (BAM with UMI tag: RX, split bam files by 4 subsamples)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq6_12cy2

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq6_12cy2
Type II (BAM with UMI tag: RX)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq6_12cy3

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq6_12cy3
Type II (BAM with UMI tag: RX)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: Liver - P110aHepKO_HFD_ZT20 - Rep3


title: FFD_Ctrl_mouse_R11


title: FFD_Ctrl_mouse_R10


title: CUG491_nash_f1_H3K27ac_cutrun

description: steatosis: 1, balloning: 2, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: M


title: GTX889_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: FFD_Ctrl_mouse_R9


title: LAH821_nafl_H3K27ac_cutrun


title: Liver - P110aHepKO_HFD_ZT12 - Rep2


title: FFD_Ctrl_mouse_R8


title: Liver - P110aHepKO_LFD_ZT16 - Rep2


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq2_S9

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq2_S9
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.proportion.txt


title: PWQ681_nash_f23_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 2, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: RJR816_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq2_S6

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq2_S6
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.proportion.txt


title: Liver - P110aHepWT_HFD_ZT12 - Rep2


title: Liver - P110aHepWT_HFD_ZT04 - Rep1


title: YNE987_nash_f23_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: FFD_Ctrl_mouse_R7


title: FFD_Ctrl_mouse_R6


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq1_S8

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq1_S8
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.proportion.txt


title: KQF393_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: FFD_Ctrl_mouse_R5


title: TypeII,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq6_12cy1

description:
Library name: TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq6_12cy1
Type II (BAM with UMI tag: RX)
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq1_S5

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq1_S5
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.maxFreq.proportion.txt


title: FFD_Ctrl_mouse_R4


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq2_S5

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq2_S5
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepKO_HFD_ZT04 - Rep2


title: Liver - P110aHepWT_LFD_ZT20 - Rep3


title: Liver - P110aHepKO_LFD_ZT0 - Rep2


title: Liver - P110aHepKO_LFD_ZT20 - Rep2


title: FFD_Ctrl_mouse_R3


title: YOX147_nafl_H3K27ac_cutrun

description: steatosis: 2, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: Liver - P110aHepWT_HFD_ZT08 - Rep3


title: Liver - P110aHepKO_HFD_ZT16 - Rep1


title: END612_nor_H3K27ac_cutrun


title: HSC001_TEAD3_12day_R2

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2
Exon quantification pipeline (version 2.5, (51)) with STAR (version 2.7.3a)
PISCES (GitHub - Novartis/pisces) to quantify gene expression.
Assembly: hg38 with ensembl version 98
Supplementary files format and content: tab-delimited file includes raw count for each sample

source_name: HSC

growth_protocol: Primary HSCs were obtained from Lonza and grown in collagen-coated flasks in human stellate cell growth medium (Lonza, MCST250) supplemented with 50 mM 2-Phospho-L-ascorbic acid (Merck, 49752).

extract_protocol:
Total RNA was extracted with Trizol
PolyA selected mRNA library

treatment_protocol: Cells were electroporated with individual RNPs then recovered for 12 days prior to RNA extraction.

tag: cell line

value: HSC


title: FFD_Ctrl_mouse_R1


title: HSC001_TEAD3_12day_R3


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq5_S10

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq5_S10
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: Liver - P110aHepKO_LFD_ZT12 - Rep3


title: DNL679_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M


title: FFD_mouse_R12

value: high fat diet


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq5_S7

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq5_S7
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: HSC001_TEAD3_12day_R1


title: HSC001_TBX3_12day_R3


title: FFD_mouse_R11


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq4_S10

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq4_S10
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: Liver - P110aHepKO_HFD_ZT0 - Rep1


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq1_S7

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq1_S7
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: FFD_Ctrl_mouse_R2


title: Liver - P110aHepWT_LFD_ZT04 - Rep1


title: Liver - P110aHepWT_LFD_ZT12 - Rep1


title: FFD_mouse_R10


title: HSC001_TBX3_12day_R2


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq3_S7

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq3_S7
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: FFD_mouse_R9


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq3_S10

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq3_S10
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: Liver - P110aHepWT_HFD_ZT16 - Rep1


title: HSC001_TBX3_12day_R1


title: FFD_mouse_R8


title: Liver - P110aHepWT_LFD_ZT16 - Rep2


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq4_S7

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq4_S7
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.maxFreq.proportion.txt


title: HSC001_RFX5_12day_R2


title: Liver - P110aHepKO_LFD_ZT04 - Rep3


title: FFD_mouse_R6


title: FFD_mouse_R7


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq2_S6

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq2_S6
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq1_S8

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq1_S8
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.proportion.txt


title: HSC001_RFX5_12day_R1


title: FFD_mouse_R4


title: HSC001_MSC_12day_R3


title: Liver - P110aHepWT_HFD_ZT0 - Rep3


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq2_S8

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq2_S8
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.proportion.txt


title: FFD_mouse_R5


title: Liver - P110aHepWT_LFD_ZT08 - Rep1


title: Liver - P110aHepWT_HFD_ZT20 - Rep2


title: HSC001_MSC_12day_R2


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq1_S5

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq1_S5
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.proportion.txt


title: HSC001_MSC_12day_R1


title: FFD_mouse_R3


title: Liver - P110aHepKO_HFD_ZT08 - Rep2


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq2_S5

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq2_S5
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles20,NextSeq2_S9

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.NextSeq2_S9
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles20.proportion.txt


title: FFD_mouse_R2


title: HSC001_RFX5_12day_R3


title: TypeII,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq2_S8

description:
Library name: TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq2_S8
Type II (BAM with UMI tag: RX)
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.count.txt
TypeII_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.maxFreq.proportion.txt


title: Liver - P110aHepKO_LFD_ZT16 - Rep1


title: HSC001_MEF2D_12day_R3


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles16,NextSeq1_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.NextSeq1_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles16.proportion.txt


title: HSC001_MEF2D_12day_R2


title: tumour mouse 102L, scRNAseq

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v4.0.0
Assembly: mm10
Supplementary files format and content: h5 feautre count matrix

source_name: Vhl/Trp53/Rb1 ccRCC

growth_protocol: Cells isolated from digested normal kidney or digested ccRCC tumours

extract_protocol:
Mixed CD45.1+ to CD45.1- in a 3:1 ratio
10X Genomics

treatment_protocol: Flow cytometry sorting to enrich for immune cells in the population

value: Vhl/Trp53/Rb1 ccRCC

value: Flow cytometry sorted cells from tissue

tag: cell type

value: Mixed CD45.1+ to CD45.1- in a 3:1 ratio

value: Vhl/Trp53/Rb1 mutant ccRCC


title: FFD_mouse_R1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq5_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq5_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt


title: HSC001_MEF2D_12day_R1


title: Liver - P110aHepWT_LFD_ZT20 - Rep2


title: tumour mouse 102R, scRNAseq

description: 10x Genomics


title: Liver - P110aHepKO_HFD_ZT20 - Rep2


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq5_S10

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq5_S10
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq4_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq4_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt


title: HSC001_HOXB4_12day_R3


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq4_S10

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq4_S10
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt


title: HSC001_HOXB4_12day_R2


title: Liver - P110aHepWT_HFD_ZT12 - Rep3


title: WT mouse 550, scRNAseq

description: 10x Genomics

source_name: Normal kidney

value: Normal kidney

value: Wild type normal


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq3_S10

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq3_S10
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt

value: synthetic construct


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles12,NextSeq3_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.NextSeq3_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles12.proportion.txt


title: bone marrow VpR2020 conditioned medium

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using trimmomatic (v 0.38) (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:3 TRAILING:10 MINLEN:25)
Sequences were aligned using the STAR aligner (v 2.5.2b) (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --quantMode GeneCounts)
Raw counts were generated using STAR --quantMode GeneCounts
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file of raw counts for each sample

source_name: bone marrow

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey Nagel).
RNA libraries were prepared using the Illumina TruSeq Stranded RNA library preparation kit.

treatment_protocol: bone marrow cultures were treated with control medium or conditioned medium deriving from VpR ccRCC cells

value: bone marrow

value: conditioned medium from VpR ccRCC cell line


title: HSC001_RUNX1_12day_R2


title: bone marrow VpR126 conditioned medium


title: HSC001_RUNX1_12day_R3


title: Liver - P110aHepWT_LFD_ZT0 - Rep2


title: Liver - P110aHepWT_HFD_ZT04 - Rep2


title: bone marrow VpR99 conditioned medium


title: HSC001_RUNX1_12day_R1


title: HSC001_HOXB4_12day_R1


title: TypeI,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles0,NextSeq6_S3

description:
Library name: TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.NextSeq6_S3
Type I
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.count.txt
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.proportion.txt


title: TypeI,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles0,NextSeq6_S2

description:
Library name: TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.NextSeq6_S2
Type I
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.count.txt
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.proportion.txt


title: Liver - P110aHepKO_LFD_ZT08 - Rep1


title: tumour mouse 538, scRNAseq

description: 10x Genomics


title: Liver - P110aHepKO_HFD_ZT12 - Rep1


title: HSC001_ZNF469_12day_R3


title: bone marrow VpR83 conditioned medium


title: bone marrow control medium rep2

value: control medium


title: Liver - p110aLKO_Fasted - Rep6

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35232 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32595 rows each corresponding to a unique ProbeName (provided as data Matrix).

tag: nutritional status

value: Fasted


title: Liver - p110aLKO_Fed - Rep3

value: Fed


title: HSC001_ZNF469_12day_R2


title: TypeI,QIAseqFXDNALibraryKit,Illumina,NextSeq500,PCRcycles0,NextSeq6_S1

description:
Library name: TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.NextSeq6_S1
Type I
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.count.txt
TypeI_QIAseqFXDNALibraryKit_Illumina_NextSeq500_PCRcycles0.proportion.txt


title: bone marrow control medium rep1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles10,NextSeq2_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.NextSeq2_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.proportion.txt


title: Liver - p110aLWT_Fasted - Rep5


title: Liver - p110aLWT_Fed - Rep6


title: HSC001_ZNF469_12day_R1


title: HSC001_RARG_12day_R3


title: Desc-RFP-Nkx2-5-Cre

city: New Haven

first: George

last: Tellides

state: CT

address: 10 Amistad st, 337B

department: Surgery

institute: Yale University

description: 2784 cells before, 987 cells after filtering

data_processing:
Samples were sequenced on Novaseq 6000
The data from sequencer was processed to obtain the fastq sequences using the "cellranger mkfastq" program provided by the vendor (10X genomics).
The raw reads were aligned to the mouse reference genome (mm10 with added sequences for GFP and tdTomato) and gene expression in cells was quantified using the "cellranger count" program provided by the vendor (10X genomics).
The gene expression data was further processing using the Seurat package (version 4.3), including data filtering, normalization, data dimension reduction, cell clustering, marker identification, cell type identity assignment, and data visualization.
keep cells with all criteria of: genes between 2000 and 6000, UMI between 5000 and 30000, and mitochondria percentage < 10%; keep genes detected in at least 10 cells
Assembly: mm10
Supplementary files format and content: filtered matrix, barcodes and features from Cellranger by 10x

source_name: descending aorta

growth_protocol: Mice were bred and housed under standard conditions

extract_protocol:
Root/Ascending aorta/aortic arch/Descending segments were enzymatically digested under cold conditions, stained with ITGA8, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye), ITGA8+, GFP or RFP positive (according to segments) SMCs were sorted into buffer with 0.04% BSA, and between 2,000 to 18,000 cells from individual aortic segments were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol: The root/ascending aorta/aortic arch/descending aorta segments were analyzed at 12 weeks of age

value: descending aorta

tag: strain

value: aortic SMC

tag: age


title: Liver - p110aLWT_Fasted - Rep4

value: Liver


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles10,NextSeq1_S6

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.NextSeq1_S6
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles10.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles5,NextSeq2_S4

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.NextSeq2_S4
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.proportion.txt


title: HSC001_RARG_12day_R2

value: HSC


title: Arch-RFP-Nkx2-5-Cre

description: 14485 cells before, 8367 cells after filtering

source_name: aortic arch

value: aortic arch


title: Liver - p110aLWT_Fed - Rep4


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles5,NextSeq1_S4

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.NextSeq1_S4
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles5.proportion.txt


title: Asc-RFP-Nkx2-5-Cre

description: 18991 cells before, 8577 cells after filtering

source_name: ascending aorta

value: ascending aorta


title: HSC001_RARG_12day_R1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles2,NextSeq2_S3

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.NextSeq2_S3
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.proportion.txt


title: Asc-GFP-Nkx2-5-Cre

description: 3969 cells before, 1771 cells after filtering


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles2,NextSeq1_S3

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.NextSeq1_S3
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles2.proportion.txt


title: HSC001_NR3C1_12day_R3


title: Root-RFP-Nkx2-5-Cre

description: 5774 cells before, 2884 cells after filtering

source_name: aortic root

value: aortic root


title: Liver - p110aLKO_Fed - Rep4

source_name: Liver


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles1,NextSeq2_S2

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.NextSeq2_S2
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.proportion.txt


title: Root-GFP-Nkx2-5-Cre

description: 8154 cells before, 3080 cells after filtering


title: Liver - p110aLKO_Fasted - Rep5


title: Liver - p110aLWT_Fed - Rep2


title: HSC001_NR3C1_12day_R1


title: Liver - p110aLWT_Fasted - Rep3


title: Arch-GFP-Wnt1-Cre2

description: 10506 cells before, 4710 cells after filtering

extract_protocol:
Root/Ascending aorta/aortic arch/Descending segments were enzymatically digested under cold conditions, stained with ITGA8, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye), ITGA8+, GFP or RFP positive (according to segments) SMCs were sorted into buffer with 0.04% BSA, and between 4,000 to 10,000 cells from individual aortic segments were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles1,NextSeq1_S2

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.NextSeq1_S2
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles1.proportion.txt


title: HSC001_COL1A1_12day_R3


title: Liver - p110aLKO_Fed - Rep5


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles0,NextSeq2_S1

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.NextSeq2_S1
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.proportion.txt


title: Asc-RFP-Wnt1-Cre2

description: 6539 cells before, 2450 cells after filtering


title: Liver - p110aLKO_Fasted - Rep1


title: HSC001_COL1A1_12day_R2


title: HSC001_COL1A1_12day_R1


title: Asc-GFP-Wnt1-Cre2

description: 8845 cells before, 4050 cells after filtering


title: Aggressive B-cell lymphoma R53R

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: Abdominal mass right iliac fossa

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: type of sample

value: Aggressive B-cell lymphoma

tag: gender

value: male

value: FFPE


title: Root-Wnt1-Cre2

description: 4040 cells before, 1841 cells after filtering

tag: tissue


title: HSC001_hNTO_12day_R3


title: Liver - p110aLWT_Fed - Rep1


title: LLC AR- + 20 GY IR, HTO Oligos Library, scRNAseq

city: Chicago

first: Arpit

last: Panda

state: IL

address: 924 E. 57th Street, Suite 104

department: Department of Chemistry

institute: University of Chicago

description:
RW-AP-10X-4s-PIF-04_barcodes.tsv.gz
RW-AP-10X-4s-PIF-04_features.tsv.gz
RW-AP-10X-4s-PIF-04_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v 7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Freshly collected lungs of tumor-bearing mice were minced and dissociated with 1 mg/mL collagenase IV and 200 μg/mL DNaseI at 37°C for 45 minutes. Red blood cells were removed with lysis buffer. Samples were then filtered through a 70 μm cell strainer and washed twice with sorting buffer (PBS supplemented with 2% FBS and 0.5 mM EDTA). The cells were re-suspended in staining buffer and were blocked with anti-FcR and stained with live/dead dye and extracellular antibodies. Live CD45+ cells were sorted with a BD FACSAria Fusion 5-18 and constantly kept on ice. Cells were re-blocked with anti-FcR and barcoded using TotalSeq™-B0301, B0302, B0303 and B0304 hashtag antibodies
Library construction was performed according to the manufacturer’s instruction (10x genomics)

value: Lung

value: CD45 positive

value: 20 GY IR


title: Aggressive B-cell lymphoma R48D

source_name: Intestine


title: HSC001_hNTO_12day_R2


title: Liver - p110aLKO_Fasted - Rep3


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,NextSeq500,PCRcycles0,NextSeq1_S1

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.NextSeq1_S1
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_NextSeq500_PCRcycles0.proportion.txt

source_name: synthetic construct

value: synthetic construct


title: LLC AR-, HTO Oligos Library, scRNAseq

description:
RW-AP-10X-4s-PIF-03_barcodes.tsv.gz
RW-AP-10X-4s-PIF-03_features.tsv.gz
RW-AP-10X-4s-PIF-03_matrix.mtx.gz

value: no irradiation


title: Liver - p110aLKO_Fed - Rep1


title: Liver - p110aLWT_Fasted - Rep1

value: Fasted


title: LLC WT + 20 GY IR, HTO Oligos Library, scRNAseq

description:
RW-AP-10X-4s-PIF-02_barcodes.tsv.gz
RW-AP-10X-4s-PIF-02_features.tsv.gz
RW-AP-10X-4s-PIF-02_matrix.mtx.gz


title: HSC_capturemicroc_Rep2

data_processing:
Alignment to hg38 via bwa meme (V2.2.1) with parameters -5SP  -T0;
ligation events were searched by pairtools (V1.0.2) with parameters --min-mapq 40 - walks-policy 5unique - maxinter-align-gap 30.
PCR duplicates removed with pairtools dedup; bam files generated with samtools (V1.13);
chromatin-chromatin interaction calling with CHiCAGO (V1.26.0).
Bait fragment (BF) and other end fragments (OEF) were generated at 5kb resolution.
Assembly: hg38
Supplementary files format and content: BED format of bait fragment (BF) and other end fragments (OEF) which were generated at 5kb resolution.

source_name: liver

growth_protocol: Cells were obtained from Lonza and grown in collagen-coated flasks in human stellate cell growth medium (Lonza, MCST250) supplemented with 50 mM 2-Phospho-L-ascorbic acid (Merck, 49752).

extract_protocol:
Dovetail genomics protocol
Dovetail Library Module for Illumina (25004), Dovetail Dual Index Primer Set #1 for Illumina (25010)
HiC-Promoter Capture

treatment_protocol: Unstimulated cells

value: liver

value: primary human hepatic cell

value: resting


title: Aggressive B-cell lymphoma R44R2

source_name: Abdominal mass


title: Liver - p110aLWT_Fasted - Rep6

value: Liver


title: Liver - p110aLWT_Fed - Rep5

value: Fed


title: Aggressive B-cell lymphoma R53D

source_name: abdominal mass


title: HSC_capturemicroc_Rep1

value: HSC


title: Aggressive B-cell lymphoma R44R


title: Liver - p110aLKO_Fed - Rep6


title: HSC001_NR3C1_12day_R2


title: Aggressive B-cell lymphoma R44D


title: LLC AR-, Gene Expression Library, scRNAseq


title: SKOV3 cells, normoxic device, 24 hr, rep2

city: Los Angeles

first: JEONG MIN

last: OH

state: California

address: 1042 Downey Way DRB 140

department: Biomedical Engineering

institute: University of Southern California

data_processing:
Partek Flow Genomic Analysis software version 11.0.24.0328 was used to build the following pipeline:
(i) pre-alignment QA/QC, (ii) trim bases from both ends base on minimum quality level (Phred) of 20 and a minimum read length of 25, (iii) alignment of mRNA-seq reads to the hg38 human genome using STAR, (iv) post-alignment QA/QC, (v) quantification to annotation model (Partek E/M), (vi) noise reduction filter to exclude features where the maximum ≤ 20, (vii) upper-quartile normalization after adding 1.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count for each sample

source_name: ovary

growth_protocol: Before the device culture, all cell lines were maintained in a humidified incubator at 37 °C with 5% CO2. OAW42, PC9, and LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U mL–1 penicillin and 100 μg mL–1 streptomycin (1% P/S). SKOV3, A549, MCF7, T47D, and PC3 cells were cultured in DMEM supplemented with 10% FBS and 1% P/S

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions.  Quality of the RNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). Only the RNA samples that have passed the QC were used.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were constructed with the NEBNExt Ultra II library kit (New England BioLabs Inc)

treatment_protocol: Each cancer cell type was resuspended in culture medium and injected into the poly-d-lysine coated middle chamber at initial seeding density of 60,000 cells per microdevice. Cells were allowed to attach in a humidified incubator at 37 °C and 5% CO2 for 2 hours. After confirming cell attachment, an additional culture medium was introduced through the side channels of the microdevice for continued incubation.

value: ovary

value: cancer cells


title: LLC AR- + 20 GY IR, Gene Expression Library, scRNAseq


title: SKOV3 cells, normoxic device, 24 hr, rep1


title: Aggressive B-cell lymphoma R37R

source_name: Medullary cone

value: Aggressive B-cell lymphoma


title: LLC WT + 20 GY IR, Gene Expression Library, scRNAseq


title: Aggressive B-cell lymphoma R36R

source_name: Abdominal LN

value: male


title: Aggressive B-cell lymphoma R46R

source_name: LN

value: FFPE


title: HSC001_hNTO_12day_R1

source_name: HSC


title: Liver - p110aLKO_Fasted - Rep4


title: Liver - p110aLKO_Fasted - Rep2


title: LLC WT, Gene Expression Library, scRNAseq

description:
RW-AP-10X-4s-PIF-01_barcodes.tsv.gz
RW-AP-10X-4s-PIF-02_features.tsv.gz
RW-AP-10X-4s-PIF-01_matrix.mtx.gz

value: Lung


title: LLC WT, HTO Oligos Library, scRNAseq

value: CD45 positive


title: Liver - p110aLWT_Fasted - Rep2


title: Aggressive B-cell lymphoma R36D

source_name: Gastric mucosa


title: IgG, Cut&Tag assay, Hepa1-6 cells

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Alignment: bowtie2 version 2.2.9
index: samtools 1.3.1
call peak: MACS2
plot: R 3.4.1
bowtie2 -q --phred33 --sensitive --end-to-end -I 0 -X 500 --fr -p 24
samtools view -bS $sample.sam > $sample.bam samtools sort $sample.bam -o $sample.sorted.bam samtools rmdup -s $sample.sorted.bam $sample.rmdup.sorted.bam samtools index $sample.rmdup.sorted.bam
macs2 callpeak -t nr4a1_R2.rmdup.sorted.bam  -f BAM -g mm -n macs2_Igg-Nr4a1_result -B -p 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: excel; ALKBH5_peaks; IgG_peaks
Library strategy: CUT&Tag

source_name: Hepa1-6 cells

growth_protocol: Hepa1-6 cells were cultured in DMEM containing 10% FBS.

extract_protocol:
CUT&Tag assay was performed by using a commercial kit (NovoNGS CUT&Tag 3.0 High-Sensitivity Kit, N259-YH01, Novoprotein Scientific Inc.).
CUT&Tag library

treatment_protocol: Hepa1-6 cells were infected with ad-FLAG-ALKBH5 adenovirus overnight.

value: Hepa1-6 cells

value: Hepatcoyte

value: ALKBH6-FLAG infection


title: Aggressive B-cell lymphoma R35R

source_name: Ileum


title: OAW42 cells, normoxic device, 24 hr, rep2


title: Liver - p110aLWT_Fed - Rep3


title: OAW42 cells, normoxic device, 24 hr, rep1


title: ALKBH5-FLAG, Cut&Tag assay, Hepa1-6 cells

value: ALKBH5-FLAG infection


title: LA3_scCARLIN_seq

description: 10X Genomics

data_processing:
Lineage barcodes were processed as previously described (McKenna et al., 2016 (PMID: 27229144), Raj et al. 2020 (PMID: 33068532)). Briefly, sequencing reads were merged on single-cell IDs and UMIs and editing outcomes were called at each target. These cell IDs were aligned with the 10X single-cell IDs to associate them with individual cells.
processed data files format and content: .csv file containing Cell IDs and their corresponding edited CARLIN array
Assembly: mm10

source_name: Spleen

extract_protocol:
CARLIN libraries were prepared as described in the original CARLIN study (PMID: 32413320). Briefly, 5ng of amplified cDNA from step 2.3 of the 10x 3’ v3.1 User Guide (CG000204 Rev D) was PCR amplified with CARLIN-specific, biotinylated primers (15 cycles), enriched with kilobaseBINDER streptavidin beads (Invitrogen, PN 60101), and further amplified (15 cycles) prior to 0.8x SPRIselect cleanup. Samples were indexed using the 10x Genomics “TT” dual-index plate (PN 1000215). Sequencing was performed on a NovaSeq6000 using SP 500 cycle flow cells (Read1: 28 cycles; Read2: 300 cycles; Index1: 10 cycles; Index2: 10 cycles)
After 7 days of infection, CARLIN mice (LA1, LA2, LA3) were euthanized, and their spleens were harvested. The spleens were mashed and filtered to get a single cell suspension. Next, Erythrocytes were depleted and the samples were enriched for CD8+ T cells. The enriched CD8+ T cells were stained and finally, live, OVA-Tetramer-BV421 and OVA-Tetramer-PE double positive CD8+ T cells were sorted.

value: Spleen

value: CD8+ T cells

value: CARLIN (RRID:MMRRC_067061-JAX) x KH2/iCas9 (RRID:IMSR_JAX:029415) . The F1 generation (LA1,LA2,LA3) is heterozygous for the CARLIN barcode, tetO-Cas9 and rtTa locus.

value: mouse was infected with VSV-OVA for 7 days


title: Liver - LWT_HFD_FED - Rep3

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 35083 spots out of 62976 were selected. The mean signal of the 24 first samples and 24 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32437 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

value: Liver

value: LWT

tag: diet

value: HFD

value: FED

tag: washbatch


title: Liver - p110aLKO_Fed - Rep2

value: Fed


title: OAW42 cells, µMeRe device (hypoxic), 24 hr, rep2

value: ovary

value: cancer cells


title: LA2_scCARLIN_seq

description: 10X Genomics


title: SKOV3 cells, µMeRe device (hypoxic), 24 hr, rep2


title: Aggressive B-cell lymphoma R31D

value: Aggressive B-cell lymphoma

value: male

value: FFPE


title: Aggressive B-cell lymphoma R29R


title: SKOV3 cells, µMeRe device (hypoxic), 24 hr, rep1


title: OAW42 cells, µMeRe device (hypoxic), 24 hr, rep1


title: Aggressive B-cell lymphoma R29D


title: LA1_scCARLIN_seq

description: 10X Genomics


title: T47D cells, normoxic device, 24 hr, rep1

source_name: breast

value: breast


title: Liver - LKO_CTRL_FASTED - Rep3

value: LKO

value: CTRL

value: FASTED