title: PBMC healthy donor scRNA-seq replicate 3-4

description: Library name: HC3-04_GEX


title: HCC PBMC patient B-17 timepoint C1D1 CITE-seq

status: Public on Dec 12 2025

type: SRA

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

country: USA

institute: University of California San Francisco

description: Library name: B-17-02_FB

library_source: transcriptomic

data_processing:
Cell Ranger version 7.0.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data. The feature barcoding library sequences were aligned to a customized reference genome provided by Biolegend containing the oligonucleotide sequences corresponding to each antibody. Cell Ranger generated a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
Library strategy: CITE-seq

molecule: total RNA

organism: Homo sapiens

source_name: Hepatocellular Carcinoma (HCC)

extract_protocol:
Blood samples were processed using Ficoll (Cytiva); after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered fetal bovine serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. 1.1x105 cells from each sample were combined into staining buffer (1 mmol/L EDTA and 2% heat-inactivated FBS in calcium/magnesium-free Dulbecco PBS; Thermo Fisher Scientific) and stained with one pooled cocktail containing a custom panel of 197 Total-Seq C antibody–oligonucleotide conjugates (BioLegend) as per standard protocols following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution, Biolegend).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 5ʹ Reagent Kits v2, according to manufacturer instructions. 10X Genomics 5′ v2 Library Construction kits for feature barcoding (protein antibodies) or CITE-seq were used to generate libraries per manufacturer instructions. All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression libraries and 5,000 reads per cell for feature barcode libraries.

tag: tissue

value: Hepatocellular Carcinoma (HCC)

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: genotype

tag: treatment

value: sorafenib + nivolumab

tag: time


title: HCC PBMC patient B-15 timepoint C1D1 scRNA-seq replicate 2

description: Library name: B-15-01_02_GEX

library_source: transcriptomic single cell

data_processing:
Cell Ranger version 7.0.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data. The feature barcoding library sequences were aligned to a customized reference genome provided by Biolegend containing the oligonucleotide sequences corresponding to each antibody. Cell Ranger generated a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.


title: PBMC healthy donor scRNA-seq replicate 2-4

description: Library name: HC2-04_GEX

value: HD

value: healthy donor


title: HCC PBMC patient B-07 timepoint C2D1 scRNA-seq replicate 2

description: Library name: B-07-04_02_GEX


title: HCC PBMC patient B-14 timepoint C1D1 scRNA-seq replicate 2

description: Library name: B-14-01_02_GEX


title: PBMC healthy donor scRNA-seq replicate 2-3

description: Library name: HC2-03_GEX


title: PBMC healthy donor scRNA-seq replicate 2-2

description: Library name: HC2-02_GEX


title: HCC PBMC patient B-14 timepoint C2D1 scRNA-seq replicate 2

description: Library name: B-14-03_02_GEX


title: HCC PBMC patient B-11 timepoint baseline scRNA-seq replicate 2

description: Library name: B-11-01_02_GEX

value: no treatment

value: baseline


title: HCC PBMC patient B-06 timepoint C3D1 scRNA-seq

description: Library name: B-06-06_GEX


title: HCC PBMC patient A-31 timepoint C2D1 scRNA-seq

description: Library name: A-31-02_GEX

value: nivolumab


title: HCC PBMC patient A-33 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-33-01_01_GEX

value: durvalumab+tremelimumab


title: HCC PBMC patient B-07 timepoint C1D1 scRNA-seq

description: Library name: B-07-02_GEX


title: HCC PBMC patient A-08 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-08-01_02_GEX


title: PBMC healthy donor scRNA-seq replicate 2-5

description: Library name: HC2-05_GEX


title: HCC PBMC patient B-03 timepoint C2D1 scRNA-seq

description: Library name: B-03-04_GEX


title: HCC PBMC patient B-04 timepoint baseline scRNA-seq

description: Library name: B-04-01_GEX


title: HCC PBMC patient B-06 timepoint C2D1 scRNA-seq

description: Library name: B-06-04_GEX


title: HCC PBMC patient B-14 timepoint C1D1 scRNA-seq replicate 1

description: Library name: B-14-01_01_GEX


title: PBMC healthy donor scRNA-seq replicate 1-8

description: Library name: HC1-08_GEX


title: PBMC healthy donor scRNA-seq replicate 2-1

description: Library name: HC2-01_GEX


title: HCC PBMC patient B-08 timepoint C2D1 scRNA-seq

description: Library name: B-08-04_GEX


title: HCC PBMC patient A-03 timepoint Long term follow up scRNA-seq replicate 2

description: Library name: A-03-01_02_GEX

value: temsirolimus + sorafenib

value: Long term follow up


title: HCC PBMC patient B-21 timepoint C3D1 scRNA-seq

description: Library name: B-21-05_GEX


title: HCC PBMC patient B-07 timepoint C2D1 scRNA-seq replicate 1

description: Library name: B-07-04_01_GEX


title: HCC PBMC patient A-02 timepoint C2D1 scRNA-seq

description: Library name: A-02-02_GEX


title: HCC PBMC patient B-22 timepoint C1D1 scRNA-seq

description: Library name: B-22-02_GEX


title: HCC PBMC patient B-08 timepoint Safety follow up scRNA-seq

description: Library name: B-08-08_GEX

value: Safety follow up


title: HCC PBMC patient B-05 timepoint C2D1 scRNA-seq

description: Library name: B-05-04_GEX


title: HCC PBMC patient B-01 timepoint baseline scRNA-seq

description: Library name: B-01-01_GEX


title: HCC PBMC patient A-03 timepoint Long term follow up scRNA-seq replicate 1

description: Library name: A-03-01_01_GEX


title: HCC PBMC patient B-21 timepoint C2D1 scRNA-seq

description: Library name: B-21-03_GEX


title: PBMC healthy donor scRNA-seq replicate 1-7

description: Library name: HC1-07_GEX


title: HCC PBMC patient A-30 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-30-01_02_GEX

value: atezolizumab + bevacizumab


title: HCC PBMC patient A-05 timepoint C4D1 scRNA-seq replicate 2

description: Library name: A-05-01_02_GEX


title: HCC PBMC patient B-13 timepoint C1D1 scRNA-seq

description: Library name: B-13-01_GEX


title: HCC PBMC patient B-23 timepoint C1D1 scRNA-seq

description: Library name: B-23-02_GEX


title: HCC PBMC patient B-06 timepoint Safety follow up scRNA-seq

description: Library name: B-06-07_GEX


title: HCC PBMC patient B-15 timepoint C1D1 scRNA-seq replicate 1

description: Library name: B-15-01_01_GEX


title: HCC PBMC patient A-02 timepoint C1D1 scRNA-seq

description: Library name: A-02-01_GEX


title: EPOP-WT EpiLCs, JARID2, Replicate 1, ChIP

city: Dallas

first: Xin

last: Liu

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Library name: wt_epilc_jarid2_rep1

library_source: genomic

data_processing:
The raw sequencing reads were trimmed by Cutadapt
The trimmed reads were mapped by Bowtie 2 with the “--very-sensitive” parameter
The aligned reads were filtered by SAMtools using the “-F 1804 -f 2 -q 30” parameter. Duplicates were removed by Picard
Duplicates were removed by Picard. ChIP-seq peaks were called by MACS2 using the “-f BAMPE -q 0.05 --broad” parameter.
Genome browser tracks bigwig files were generated by bamCoverage from deepTools.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Mus musculus

source_name: EpiLCs differentiated from E14 mESCs

growth_protocol: mESCs were cultured on 0.2% gelatin-coated plates in 2i/LIF medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with 1 × Pen/Strep, 0.05% BSA, 1 mM GlutaMAX, 100 μM β-mercaptoethanol, 0.5 × N2 supplement, 1 × B27 supplement, 1 μM MEK inhibitor PD0325901, 3 μM GSK3 inhibitor CHIR99021, and home-made LIF).  For the EpiLC differentiation, 1.5 million mESCs were plated on a 10 cm dish coated with human fibronectin (16.7 μg/ml) in N2B27 medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with containing 1 × Pen/Strep, 2 mM GlutaMAX, 50 μM β-mercaptoethanol, 0.5 × N2 supplement, 0.5 × B27 supplement, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR). The medium was replaced every day until 48 hours before cell collection.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Formaldehyde was quenched with 0.125 M Glycine for 5 minutes before two PBS washes. Chromatin was prepared using the SimpleChIP kit from Cell Signalig Technology.
Libraries were constructed using the NEBNext Ultra II kit from NEB with 8 ng DNA from ChIP.

tag: cell line

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of WT EPOP


title: PBMC healthy donor scRNA-seq replicate 1-6

description: Library name: HC1-06_GEX


title: HCC PBMC patient B-08 timepoint C7D1 scRNA-seq

description: Library name: B-08-07_GEX


title: HCC PBMC patient B-18 timepoint baseline scRNA-seq

description: Library name: B-18-01_GEX


title: EPOP-Mutant EpiLCs, JARID2, Replicate 2, ChIP

description: Library name: d5_epilc_jarid2_rep2

value: Re-expression of mutant EPOP


title: EPOP-Mutant EpiLCs, JARID2, Replicate 1, ChIP

description: Library name: d5_epilc_jarid2_rep1


title: HCC PBMC patient B-02 timepoint C2D1 scRNA-seq

description: Library name: B-02-04_GEX

value: Hepatocellular Carcinoma (HCC)


title: HCC PBMC patient B-06 timepoint C1D1 scRNA-seq

description: Library name: B-06-02_GEX

value: peripheral blood mononuclear cells (PBMCs)


title: JB mESC Zfp57-/- (Capture Hi-C)

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

country: France

institute: Institute for Integrative Biology of the Cell

description:
Library name: Capture Hi-C JB mESC Zfp57-/-
Hi-C followed by catpure

data_processing:
Read pairs were initially processed using AGeNT Trimmer to trim the adaptors and dark bases. The provided FastQ files were already processed by AGeNT Trimmer.
Trimmed read pairs were then processed using Hi-C pro to generate the Hi-C allelic matrices. Up to 3 technical libraries were generated from the same Hi-C biological material, were Captured in parallel (rep1, rep2, rep3) and independenly processed using HiC-pro. The allelic matrices outputed by HiC-pro were combined to generate the provided processed files.
Assembly: mm10 (N-masked GRCm38/mm10)
Supplementary files format and content: HiC-pro raw contact tables, for both alleles, at a 5kb resolution

source_name: mouse embryonic stem cells

growth_protocol: ESGRO Complete PLUS Clonal Grade Medium (Merck)

extract_protocol:
Experiments were performed using the Arima Hi-C+ kit (Arima Genomics), following the manufacturer’s instructions.
Sequencing libraries were prepared using the SureSelect XT HS2 DNA System kit (Agilent), and target enrichments was achieved on pools of 4 libraries using a custom panel targeting the genomic intervals chr7:142,240,000-143,530,000; chr12:108,840,000-110,050,000; chr4:98,670,000-99,260,000 (mm10). Capture Hi-C material was sequenced on the Illumina NextSeq 2000 system (2 x 60).

treatment_protocol: Cells were harvested using Accutase and crosslinked in 1% Formaldehyde for 10min followed by additon of Glycine to a final concentration of 167mM.

value: mouse embryonic stem cells

value: JB1 (JF1 x C57BL/J6)


title: JB mESC WT (Capture Hi-C)

description:
Library name: Capture Hi-C JB mESC WT
Hi-C followed by catpure

value: JB1 WT (JF1 x C57BL/J6)


title: HCC PBMC patient B-11 timepoint baseline scRNA-seq replicate 1

description: Library name: B-11-01_01_GEX

value: no treatment


title: HCC PBMC patient B-17 timepoint Safety follow up scRNA-seq

description: Library name: B-17-07_GEX

value: sorafenib + nivolumab


title: HCC PBMC patient B-12 timepoint C1D1 scRNA-seq

description: Library name: B-12-01_GEX


title: HCC PBMC patient B-17 timepoint C2D1 scRNA-seq

description: Library name: B-17-04_GEX


title: BJ NPC WT (Capture Repli-seq)

description:
Library name: Capture Repli-seq BJ NPC WT
Repli-seq followed by capture

data_processing:
Sequencing reads were mapped using bowtie2 to a modified N-masked GRCm38/mm10 genome in which all variants for Mus musculus JF1 were replaced by the ambiguous base ‘N’ (N-masked genome prepared used SNPsplit tools [PMID: 27429743]; variant information obtained from the Mouse genome project). PCR duplicates were then removed using Samtools (version 1.6) rmdup, and reads were assigned to each of the parental genotypes (Bl6 or JF1) using SNPsplit (version 0.3.4). For the rest of the analyses, we followed the procedure described by Marchal et al. except for the span of loess smoothing parameter, which was fixed to 0.01.
Assembly: mm10 (N-masked GRCm38/mm10)
Supplementary files format and content: bedgraph showing log2 ratio of early / late signal for each alleles and for every sample

source_name: mouse neuronal precursor cells

extract_protocol:
For cell cycle analysis, cells were stained with 80 μg/mL propidium iodide (Invitrogen, P3566) at RT, in the presence of 0.4 mg/mL RNaseA (Roche, #10109169001) for 1h to degrade RNA in the cells. Flow cytometry was performed using an AriaII FACS machine (BD Biosciences) and early and late fractions, and ~250,000 cells were sorted according to the fluorescence strength of propidium iodide. Sorted cells were recovered in a lysis buffer (50 mM Tris-HCl pH=8, 10 mM EDTA, 0.5% SDS, 300 mM NaCl). Genomic DNA samples were extracted through incubation with 0.2 mg/mL Proteinase-K (Thermo Fisher, #EO0492) at 65°C for 2 h, followed by Phenol-Chloroform extraction and EtOH precipitation, and were sonicated into 100-500-bp fragments using a Bioruptor Pico machine (Diagenode), followed by denaturation at 95°C for 5 minutes.
BrdU-incorporated DNA was extracted from 250,000 cells and sonicated into 100-500 bp fragments using a Bioruptor Pico (Diagnode). Using NEBNext Ultra II Library Prep Kit for Illumina (New England Biolabs, E7645S) and NEBNext Multiplex Oligo for Illumina (New England Biolabs, E7645S), adaptors was ligated following manufacturer’s protocol. DNA was then Phenol-Chloroform purified, denatured (95°C, 5 min), and subjected to BrdU immunoprecipitation. DNA was purified subsequently and was indexed during the amplification stage, using multiplex oligos (New England Biolabs, E7645S) following a manufacturer’s method. DNA was then purified with AMPure XP beads (Thermo Fisher, #10136224). The obtained libraries were quantified with Qubit and their quality was assessed with Bioanalyzer 2100 (Agilent Technologies). 4 to12 Repli-seq libraries were pooled in equimolar quantities (1 µg in total) and captured simultaneously, using the Arima Capture Modules (Arima, #A311032, #A311033, #A311034) according to the SureSelect XT HS2 DNA Kits protocol provided by Agilent. Hybridization of Repli-seq libraries with the SureSelect probes was achieved in a thermal cycler with 60 cycles [1 min at 65°C, then 3 sec at 37°C] followed by over-night incubation at 21°C. The hybridized pool of libraries was pulled-down using Streptavidin beads and libraries were then amplified following the manufacturer’s instructions, with 12 PCR cycles. Finally, libraries were purified using AMpure XP beads (Beckman Coulter; 1:1 beads:sample ratio), quantified using Qubit dsDNA HS kit (Thermo-Fisher Scientific; Q33230) and their size distribution measured using the TapeStation with the D1000 kit (Agilent). The material was sequenced on an Illumina NextSeq 2000 (paired-end, 100 cycles) at the High-throughput sequencing facility of the I2BC (CNRS, Gif-sur-Yvette).

treatment_protocol: 50 μM bromodeoxyuridine (BrdU) for 1 hour at 37°C, followed by fixation in ice-cold 70% Ethanol

value: mouse neuronal precursor cells

value: BJ1 (C57BL/6J x JF1)

value: mouse neuronal precursor

value: BJ1 WT (C57BL/6J x JF1)


title: BJ mESC Delta-Meg3-C1

description:
Library name: Capture Repli-seq BJ mESC Delta-Meg3-C1
Repli-seq followed by capture


title: JB mESC Zfp57-/- Meg3pro-/- (Capture Repli-seq)

description:
Library name: Capture Repli-seq JB mESC Zfp57-/- Meg3 pro-/-
Repli-seq followed by capture

value: JB1 Zfp57-/- Meg3 pro-/-  (JF1 x C57BL/J6)


title: PBMC healthy donor scRNA-seq replicate 1-5

description: Library name: HC1-05_GEX

value: HD

value: healthy donor


title: HCC PBMC patient A-30 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-30-01_01_GEX

value: atezolizumab + bevacizumab


title: JB mESC Zfp57-/- (Capture Repli-seq)

description:
Library name: Capture Repli-seq JB mESC Zfp57-/-
Repli-seq followed by capture


title: BJ mESC WT (Capture Repli-seq)

description:
Library name: Capture Repli-seq BJ mESC WT
Repli-seq followed by capture


title: EPOP-WT EpiLCs, JARID2, Replicate 2, ChIP

description: Library name: wt_epilc_jarid2_rep2

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of WT EPOP


title: BJ NPC WT (Capture Hi-C)

description:
Library name: Capture Hi-C BJ NPC WT
Hi-C followed by catpure

data_processing:
Read pairs were initially processed using AGeNT Trimmer to trim the adaptors and dark bases. The provided FastQ files were already processed by AGeNT Trimmer.
Trimmed read pairs were then processed using Hi-C pro to generate the Hi-C allelic matrices. 3 technical libraries were generated from the same Hi-C biological material, were Captured in parallel (rep1, rep2, rep3) and independenly processed using HiC-pro. The allelic matrices outputed by HiC-pro were combined to generate the provided processed files.
Assembly: mm10 (N-masked GRCm38/mm10)
Supplementary files format and content: HiC-pro raw contact tables, for both alleles, at a 2.5kb resolution


title: BJ mESC WT (Capture Hi-C)

description:
Library name: Capture Hi-C BJ mESC WT
Hi-C followed by catpure


title: HCC PBMC patient B-05 timepoint C1D1 scRNA-seq

description: Library name: B-05-02_GEX

value: Hepatocellular Carcinoma (HCC)

value: peripheral blood mononuclear cells (PBMCs)


title: HCC PBMC patient B-23 timepoint C1D15 scRNA-seq

description: Library name: B-23-03_GEX


title: Cx3cr1-GFP+ cells from host retina upon transplantation - Sample 1

city: Boston

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description: Library name: AMf1

data_processing:
Cell ranger v. 7.0.1
velocyto v. 0.17.17
Assembly: 2024-A Mouse GRCm39 for mouse samples, 2024-a Human GRCh38 for human sample
Supplementary files format and content: Cell ranger output matrix (.mtx), barcodes (.tsv) and features (.tsv)
Supplementary files format and content: Velocyto output spliced/unspliced data matrix (.loom)

source_name: Retina

growth_protocol: The H9-BRN3B:tdTomatoThy1.2-hESCs cells were cultured on six-well plates coated with 2% Matrigel in mTeSR1 cell culture medium in a low oxygen condition (3.5% O2, 5% CO2, 95% humidity, 37C). Cell culture medium was replaced daily. Human RGCs were differentiated in 3D retinal organoid cultures as previously described. Briefly, the colonies of hESCs were enzymatically dissociated for 12 minutes to make a single-cell suspension during cell passaging. To initiate the formation of embryoid bodies, 7,500 hESCs per well was seeded in an ultra-low attachment 96-well U-bottom plate in a low oxygen condition for 24 hours and plate with EBs transferred to 20% O2 the next day. The differentiation medium was replaced daily and changed from a 3:1 mix of mTeSR1 and BE6.2-NIM [B27 + E6 at 2X concentration – neural induction medium: 1x L-glutamine, 1x sodium pyruvate, 1x antibiotic-antimycotic, 1x B27 without Vitamin A, 0.88 mg/mL NaCl, 38.8 mg/L insulin, 128 mg/L L-ascorbic acid, 28 μg/L selenium, 21.4 mg/L transferrin, and 38.8 mg/L NaHCO3 in DMEM/F12 (3500 mg/L dextrose)] to primarily BE6.2-NIM by day 8. To promote early retinal development, the medium was supplemented with 20 μM Y-27632 on day 0, 1% Matrigel from days 2 to 6, 3μM IWR-1-endo from days 1 to 4, and 55 ng/mL BMP4 on day 6. Following 48 hours, organoids were chopped and then placed on tissue culture-treated plastic in Long-Term Retinal Differentiation Medium (LT-RDM) [1x L-glutamine, 1x sodium pyruvate, 1x antibiotic-antimycotic, 1x B27, 1x non-essential amino acids, and 10% FBS in 50:50 1x DMEM/F12 (3500 mg/L Dextrose):DMEM (4500 mg/mL dextrose)] to support attachment of organoids and growth of retinal epithelium. The medium was exchanged every two days and transitioned to a 1:1 mix of LT-RDM and Retinal Differentiation Media (RDM) [LT-RDM without FBS] by day 17, with added 100nM smoothened agonist (SAG) from days 12 to 16. On day 17, the clusters of retinal tissue were moved to a poly (2-hydroxyethyl methacrylate) -coated flask for suspension culture in RDM supplemented with 100nM SAG. Starting on day 18, the medium was replaced every other day, gradually transitioning to pure LT-RDM by day 24. From day 26, the medium was enriched with 1mM taurine, and from day 32, it was supplemented with 250nM all-trans-retinoic acid. The LT-RDM was exchanged every other day until the retinal organoids were dissociated using Gentle MACS protocol and RGCs sorted with CD90.2 Dynabeads.

extract_protocol:
Three days following RGC transplantation, mice were euthanized, eyes enucleated and retinal tissue isolated and transferred into a tube containing PBS with 0.04% BSA on ice. Eight mouse retinas were pooled for each sample. The tissue was dissociated by mechanical and enzymatic methods using Gentle MACS protocols. Briefly, retinas were allowed to settle to the bottom of the tube and excess PBS carefully removed. Tissues were then rinsed with HBSS and transferred to a MACS M-tube and let to settle to the bottom of the tube before again removing excess HBSS. Tissues were then resuspended in 2ml of dissociation solution containing DNAse 1 (1mg/ml). The mixture was incubated at 37°C for 5min in a heating bath. The M-tube was then inverted ensuring that all retina tissues remained in solution, and the tube placed into the MACS tissue dissociator and the brain 1 program run. At the end of brain 1 program, the M-tube was removed from the MACS dissociator and incubated at 37°C for 5mins in a heating bath. The tube was then inverted again and placed back into the MACS dissociator and program brain 2 initiated, after which 10mL of isolation buffer was added to the dissociate and the mixture triturated 7-10 times with a 1000µl pipette tip. Then 12ml of the homogenate was transferred into a 15ml tube and cells pelleted at 200g for 5 mins at 4°C. The cell pellet was resuspended in 500µl of isolation buffer and filtered using a 70um cell strainer into a FACS tube for sorting. All tubes for this procedure were pre-blocked with 2% BSA in HBSS. Separate single stain samples for TdTomato+ and GFP+ were prepared and used to set the gates. The harvested cells were sorted separately for TdTomato +ve, and GFP +ve, and collected into separate collection tubes each containing 200μl of PBS with 0.04% BSA. The sorted cells were taken for single cell RNA sequencing library preparation.
Of the sorted cells, up to 10,000 viable cells per sample were used for single cell RNA library preparation following the 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol. Briefly, the droplet-based encapsulation method was used to encapsulate single cells with gel beads, partitioning oil, and a reverse transcription master mix generating GEMs. The generated GEMs were cleaned, gene expression libraries constructed and sequenced at a sequencing depth of 20,000 read pairs per cell, paired-end dual indexing (See manufactures instructions for detail).

treatment_protocol: The mice were anesthetized intraperitoneally with 100 mg/kg ketamine hydrochloride and 20 mg/kg xylazine hydrochloride solution dilute with saline, and the animals were allowed to be fully sedated. Pupils were dilated with 1% tropicamide ophthalmic solution (Baush & Lomb Americas Inc., Bridgewater, NJ). One drop of 0.5% proparacaine hydrochloride ophthalmic solution (Bausch & Lomb Americas Inc., Bridgewater, NJ) was instilled onto the cornea surface 2 minutes before subretinal injection. Using a glass pipette, 20,000 viable tdTomato+ve  human ES-derived RGCs in 1ml was injected into one eye of each mouse. One drop of Neomycin and Polymyxin B Sulfates and Bacitracin Zinc Ophthalmic ointment (Bausch & Lomb Americas Inc., Bridgewater, NJ) was applied onto the surface of injected eye following the procedure.

value: Retina

tag: collection time

value: 3 days after RGC transplantation

value: Myeloid cells

tag: Sex

value: missing

value: Cx3cr1 wt/-; C57Bl6

tag: developmental stage

value: 6 montths

tag: batch

value: Batch 1


title: Cx3cr1-GFP+ cells from host retina upon transplantation - Sample 2

description: Library name: AMf2

value: 6 months

value: Batch 2


title: HCC PBMC patient A-07 timepoint C2D1 scRNA-seq replicate 2

description: Library name: A-07-02_GEX

value: nivolumab


title: HCC PBMC patient B-03 timepoint C7D1 scRNA-seq

description: Library name: B-03-07_GEX

value: sorafenib + nivolumab


title: EPOP-WT EpiLCs, MTF2, Replicate 2, ChIP


title: BJ mESC Sh-1 (Capture Repli-seq)

description:
Library name: Capture Repli-seq BJ mESC Sh-1
Repli-seq followed by capture

value: mouse embryonic stem cells

value: BJ1 (C57BL/6J x JF1)

value: BJ1 Sh-1 (C57BL/6J x JF1)


title: HCC PBMC patient A-21 timepoint baseline scRNA-seq

description: Library name: A-21-01_GEX

value: no treatment

value: baseline


title: EPOP-WT EpiLCs, H3K27me3, Replicate 2, ChIP

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of WT EPOP


title: HCC PBMC patient B-10 timepoint C1D1 scRNA-seq

description: Library name: B-10-01_GEX

value: Hepatocellular Carcinoma (HCC)

value: peripheral blood mononuclear cells (PBMCs)


title: HCC PBMC patient A-08 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-08-01_01_GEX


title: EPOP-WT EpiLCs, MTF2, Replicate 1, ChIP


title: EPOP-WT EpiLCs, Input, Replicate 2, ChIP


title: JB mESC WT (Capture Repli-seq)

description:
Library name: Capture Repli-seq JB mESC WT
Repli-seq followed by capture

value: JB1 (JF1 x C57BL/J6)

value: JB1 WT (JF1 x C57BL/J6)


title: HCC PBMC patient A-12 timepoint baseline scRNA-seq replicate 2

description: Library name: A-12-01_02_GEX


title: HCC PBMC patient B-09 timepoint baseline scRNA-seq

description: Library name: B-09-01_GEX


title: EPOP-WT EpiLCs, H3K27me3, Replicate 1, ChIP


title: HCC PBMC patient B-13 timepoint C2D1 scRNA-seq

description: Library name: B-13-03_GEX


title: EPOP-WT EpiLCs, Input, Replicate 1, ChIP


title: HCC PBMC patient B-02 timepoint C1D1 scRNA-seq

description: Library name: B-02-02_GEX


title: HCC PBMC patient B-14 timepoint C2D1 scRNA-seq replicate 1

description: Library name: B-14-03_01_GEX


title: EPOP-Mutant EpiLCs, MTF2, Replicate 1, ChIP

value: Re-expression of mutant EPOP


title: EPOP-Mutant EpiLCs, H3K27me3, Replicate 2, ChIP


title: HCC PBMC patient A-05 timepoint C4D1 scRNA-seq replicate 1

description: Library name: A-05-01_01_GEX


title: PBMC healthy donor scRNA-seq replicate 1-3

description: Library name: HC1-03_GEX

value: HD

value: healthy donor


title: HCC PBMC patient B-22 timepoint C2D15 scRNA-seq

description: Library name: B-22-04_GEX


title: EPOP-Mutant EpiLCs, Input, Replicate 2, ChIP


title: HCC PBMC patient B-12 timepoint C2D1 scRNA-seq

description: Library name: B-12-03_GEX


title: EPOP-Mutant EpiLCs, Input, Replicate 1, ChIP


title: HCC PBMC patient A-04 timepoint C2D1 scRNA-seq replicate 2

description: Library name: A-04-01_02_GEX

value: nivolumab


title: HCC PBMC patient B-17 timepoint C1D1 scRNA-seq

description: Library name: B-17-02_GEX

value: sorafenib + nivolumab


title: Visium, SSc10

city: Lebanon

first: Helen

middle: C

last: Jarnagin

state: NH

address: WTRB 6-84 1 Medical Center Drive

institute: Geisel School of Medicine

description:
Library name: SSc10-Spatial
FFPE Fixed Spatial transcriptome sequencing

data_processing:
Counts and peaks were appropriatly generated using 10X Genomics’ Cell Ranger ARC software (v2.0.2).
Assembly: Human hg38
Supplementary files format and content: GEX Data: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: ATAC Data: Cellranger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, atac_peak_annotation.tsv.gz, atac_peaks.bed,
Supplementary files format and content: Visium image data:aligned_fidcials.jpg, scalefactors_jason, tisssue_hires_image.png, tissue_lowres.png, tissue_positions.csv, detected_tissue_image.jpg
Supplementary files format and content: Visium transcriptomic data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: Spatial Transcriptomics

source_name: Whole skin

extract_protocol:
Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. The epidermis and dermis were manually separated. The epidermal layer was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS, and filtered through a 70uM strainer. The dermis was minced and digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in DMEM for 1.5 hours at 37°C, then filtered through a 70uM strainer. Cells were counted and then combined at a 1:1 ratio.
Using the 10X Multiome (ATAC + RNA) workflow, single-nuclei were isolated and captured on a Chromium X instrument, and Illumina sequencing libraries prepared following the manufacturer’s protocols (CG000338, CG000365). Libraries were sequenced on an Illumina NovaSeq 6000

value: Whole skin


title: HCC PBMC patient A-12 timepoint baseline scRNA-seq replicate 1

description: Library name: A-12-01_01_GEX


title: Visium, SSc9

description:
Library name: SSc9-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: HCC PBMC patient B-08 timepoint C1D1 scRNA-seq

description: Library name: B-08-02_GEX


title: HCC PBMC patient A-04 timepoint C2D1 scRNA-seq replicate 1

description: Library name: A-04-01_01_GEX


title: PBMC healthy donor scRNA-seq replicate 1-1

description: Library name: HC1-01_GEX


title: Visium, SSc8

description:
Library name: SSc8-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: HCC PBMC patient B-22 timepoint C3D1 scRNA-seq

description: Library name: B-22-05_GEX


title: Visium, SSc5

description:
Library name: SSc5-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: Visium, SSc3

description:
Library name: SSc3-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: HCC PBMC patient B-21 timepoint C1D1 scRNA-seq

description: Library name: B-21-01_GEX


title: HCC PBMC patient B-03 timepoint C1D1 scRNA-seq

description: Library name: B-03-02_GEX


title: HCC PBMC patient B-23 timepoint C3D1 scRNA-seq

description: Library name: B-23-04_GEX


title: Visium, SSc4

description:
Library name: SSc4-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: EPOP-Mutant EpiLCs, H3K27me3, Replicate 1, ChIP


title: E2319040

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

description: Library name: E2319040

data_processing:
Kallisto software (v0.50.0) was used for quantifying transcript abundance from RNA-seq data against the GRCh38 cDNA reference transcriptome from the Ensembl database (v101) (36).
Downstream analysis included only protein-coding genes and transcripts. Differential expression analysis was performed using the DESeq2 R package, and gene expressions were normalized through variance-stabilizing transformation
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files containing TPM data for every sample

source_name: whole blood

extract_protocol:
Blood samples were collected in EDTA blood tubes immediately before the first durvalumab injection. The tubes were frozen at −80 °C within 4 hours of collection. Subsequently, all samples were transferred to the Centre Georges-François Leclerc for total RNA extraction and analysis via short-read RNA sequencing. Four mL of whole blood harvested in EDTA tubes were frozen at −80 °C until extraction. Total RNA was extracted with the Maxwell RSC simplyRNA Blood Kit (Promega, Madison, WI, USA), following the manufacturer’s instructions. RNA quantity and quality were assessed by spectrometry with absorbance at 230 nm, 260 nm, and 280 nm.
Eight hundred nanograms of total RNA were depleted of ribosomal and globin RNA using the NEBNext Globin and rRNA Depletion Kit (New England Biolabs, Ipswich, MA, USA). The depleted RNA was then used for library preparation with the NEBNext Ultra II RNA Directional Library Prep Kit for Illumina (New England Biolabs). RNA sequencing was performed on a NextSeq2000 device (Illumina, San Diego, CA, USA), using 2 × 100 bp paired-end reads and multiplexed to obtain 20 million reads per sample. For us, 20 million reads is a good balance between sensitivity and cost-efficiency. Indeed, such a read depth is consistent with easy implementation of RNA-seq in routine workflows.

treatment_protocol: The patients included in this study were participants in a multicentric, prospective clinical trial, the IOPREDI study, a French ancillary cohort of the STRONG study (NCT03084471). Participants were recruited from patients treated at 17 French sites. A total of 218 patients (IOPREDI) were recruited between July 2018 and August 2019, and 164 accepted blood withdrawal for the present study. Patients were considered eligible if they presented with a locally advanced or metastatic urothelial or non-urothelial carcinoma of the urinary tract. Detailed inclusion and exclusion criteria are available on ClinicalTrials.gov. All patients signed informed consent to participate in the trial. The trial protocol was approved by an institutional review committee and by the relevant French regional ethical committee (CPP SUD-OUEST and OUTRE-MER 4).

value: whole blood

tag: age

value: Male

tag: smoking history

value: Missing

tag: patient activity

value: Restricted

tag: histology

value: Urothelial (transitional cell) carcinoma

tag: disease stage

value: IV

tag: pdl1 staining

tag: clinical response_(recist)

value: Not evaluated

tag: pfs

tag: pfs events

tag: os

tag: os events

tag: irae

value: No


title: Visium, SSc7

description:
Library name: SSc7-Spatial
FFPE Fixed Spatial transcriptome sequencing

tag: tissue


title: CDDO_72h_3

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

description: Library name: CDDO_72h_3

data_processing:
Reads were aligned to the human genome version hg38 (GRCh38, Ensembl) using STAR and the resulting binary alignment mapped (bam) files were indexed using Samtools.
Read counts for each transcript (GRCh38, Ensembl) were generated using Subread (featureCounts).
Assembly: GRCh38, Ensembl
Supplementary files format and content: tab-deliminated text file with raw gene counts for each sample.

molecule: polyA RNA

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with GlutaMAX, 25 mM glucose, 1 mM pyruvate and 1% non-essential amino acids (NEAA) with supplemented 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin antibiotics. Cells were grown within a humified atmosphere at 37°C and 5% CO2 and maintained through regular passaging; experiments were performed on cells between passages 3-10.

extract_protocol:
Total RNA was isolated from cell monolayers using the Monarch Total RNA Miniprep Kit (NEB, USA) according to the manufacturer’s instructions.
RNAseq libraries (unstranded, polyA selection) were prepared using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: DMSO (0.1%) and 100 nM CDDO-Me for 24 h or 72 h before RNA extraction.

tag: cell line

tag: treatment

value: 100 nM CDDO-Me for 72 h


title: Visium, SSc1

description:
Library name: SSc1-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: E2319041

description: Library name: E2319041

tag: Sex

value: Former

value: Normal

value: PR

value: Yes


title: E2319038

description: Library name: E2319038


title: HCC PBMC patient A-07 timepoint C2D1 scRNA-seq replicate 1

description: Library name: A-07-01_GEX

value: Hepatocellular Carcinoma (HCC)

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: genotype

tag: time


title: Visium, SSc2

description:
Library name: SSc2-Spatial
FFPE Fixed Spatial transcriptome sequencing


title: E2319035

description: Library name: E2319035

tag: age

tag: smoking history

value: Current

tag: patient activity

value: SD


title: CDDO_72h_2

description: Library name: CDDO_72h_2


title: EPOP-Mutant EpiLCs, MTF2, Replicate 2, ChIP

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of mutant EPOP


title: HCC PBMC patient A-32 timepoint C1D1 scRNA-seq

description: Library name: A-32-01_GEX

value: atezolizumab + bevacizumab


title: Visium, SSc6

description:
Library name: SSc6-Spatial
FFPE Fixed Spatial transcriptome sequencing

value: Whole skin


title: CDDO_24h_2

description: Library name: CDDO_24h_2

value: 100 nM CDDO-Me for 24 h


title: CDDO_24h_3

description: Library name: CDDO_24h_3


title: CDDO_72h_1

description: Library name: CDDO_72h_1


title: E2319033

description: Library name: E2319033

value: whole blood

value: Male

value: Missing

value: Restricted

tag: histology

value: Urothelial (transitional cell) carcinoma

tag: disease stage

value: IV

tag: pdl1 staining

value: PD


title: CDDO_24h_1

description: Library name: CDDO_24h_1


title: DMSO Control_3

description: Library name: Control_3

value: DMSO (0.1%) for 72 h


title: E2319032

description: Library name: E2319032

value: Former

tag: clinical response_(recist)

tag: pfs

tag: pfs events

value: No


title: E2319031

description: Library name: E2319031

value: Normal

value: III

tag: os

tag: os events

tag: irae


title: E2319030

description: Library name: E2319030

tag: tissue

value: PR


title: DMSO Control_1

description: Library name: Control_1

tag: cell line

tag: treatment


title: HCC PBMC patient B-10 timepoint C2D1 scRNA-seq

description: Library name: B-10-03_GEX

value: Hepatocellular Carcinoma (HCC)

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: genotype

value: sorafenib + nivolumab


title: E2319029

description: Library name: E2319029

tag: age

tag: Sex

value: Not evaluated


title: E2319026

description: Library name: E2319026

value: whole blood

tag: smoking history

tag: patient activity


title: E2319027

description: Library name: E2319027

value: Male

tag: histology

tag: disease stage


title: DOX_2

description: Library name: DOX_2

treatment_protocol: DMSO (0.1%) or 100 nM doxorubicin for 48 h before RNA extraction.

value: 100 nM doxorubicin for 48 h


title: DOX_3

description: Library name: DOX_3


title: E2319024

description: Library name: E2319024

tag: pdl1 staining

value: Missing

tag: clinical response_(recist)

value: CR

value: Yes


title: E2319023

description: Library name: E2319023

value: Never

value: Restricted

value: Urothelial (transitional cell) carcinoma

value: PD

tag: pfs

tag: pfs events


title: Control_3

description: Library name: Control_3

value: DMSO (0.1%) for 48 h


title: E2319021

description: Library name: E2319021

value: Female

value: IV

tag: os

tag: os events

value: No


title: E2319022

description: Library name: E2319022

tag: tissue

value: III

tag: irae


title: E2319019

description: Library name: E2319019

value: Current

value: Normal


title: Control_1

description: Library name: Control_1

tag: cell line

tag: treatment


title: CDDO_DOX_3

description: Library name: CDDO_DOX_3

treatment_protocol: DMSO (0.1%) and 100 nM CDDO-Me for 24 h followed by 100 nM doxorubicin for a further 48 h (72 h total) before RNA extraction.


title: E2317045

description: Library name: E2317045

value: whole blood

value: Former


title: E2319017

description: Library name: E2319017

value: Male

value: Not evaluated


title: CDDO_DOX_2

description: Library name: CDDO_DOX_2

value: 100 nM CDDO-Me for 24 h followed by 100 nM doxorubicin for a further 48 h (72 h total)


title: E2318011

description: Library name: E2318011

value: SD


title: Control_2

description: Library name: Control_2


title: Control_2

description: Library name: Control_2

value: DMSO (0.1%) for 72 h


title: E2318010

description: Library name: E2318010

value: Never

value: Restricted


title: CDDO_DOX_1

description: Library name: CDDO_DOX_1


title: DMSO Control_2

description: Library name: Control_2


title: E2317054

description: Library name: E2317054

value: Urothelial (transitional cell) carcinoma

value: PD


title: E2317043

description: Library name: E2317043

value: In bed < 50% time

value: Missing


title: Control_1

description: Library name: Control_1


title: E2317038

description: Library name: E2317038

value: No


title: PA-H3K4me1-igg

city: Wuhan

first: Hui

last: Zhao

address: Luoyu Road

country: China

institute: Wuhan university

description:
Library name: PA-H3K4me1-igg
library name:PA-H3K4me1-igg

data_processing:
Sequencing was performed on the Illumina NovaSeq platform with PE150 configuration.
H3K4me1 and H3K27ac peaks were detected using Macs2 software (V2.1.1).
Differentially accessible regions were identified with the DESeq2 package (V1.34.0).
Motif enrichment analysis was performed using Homer software, and peaks were visualized with IGV (2.19.1).
Assembly: GRCh38.p14
Supplementary files format and content: Microsoft Excel spreadsheet format (.xlsx). Each file contains annotated genomic peaks from CUT&Tag sequencing, identified for a specific histone mark in a specific sample.
Library strategy: CUT&Tag

source_name: OSCC tissue

growth_protocol: Cancer-associated fibroblasts (CAFs) isolated from tissues of OSCC patients were cultured in high-glucose medium supplemented with 10% fetal bovine serum (FBS) and antibiotics, and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
DNA was extracted using the CUT&Tag Assay Kit (CST, #77552) following the manufacturer's protocol.
Following DNA extraction, libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L).

treatment_protocol: Live CAFs treated with or without 50 μM PA for 24h.

value: OSCC tissue

value: Cancer-associated fibroblast

tag: cell type

value: Fibroblast

tag: genotype

value: WT

value: The cell lines were then treated with 50 μM PA for 24 hours.

tag: batch

value: single batch


title: DOX_1

description: Library name: DOX_1

value: 100 nM doxorubicin for 48 h


title: E2317036

description: Library name: E2317036

value: whole blood

tag: age

tag: Sex

value: Female

tag: smoking history

value: IV

value: Yes


title: PA3-H3K27ac

description:
Library name: PA3-H3K27ac
library name:PA3-H3K27ac


title: PA3-H3K4me1

description:
Library name: PA3-H3K4me1
library name:PA3-H3K4me1


title: E2317035

description: Library name: E2317035

value: Male

value: Current

tag: patient activity

value: Restricted

tag: histology

tag: disease stage


title: PA2-H3K27ac

description:
Library name: PA2-H3K27ac
library name:PA2-H3K27ac


title: E2317024

description: Library name: E2317024

value: Former

value: Urothelial (transitional cell) carcinoma

tag: pdl1 staining

tag: clinical response_(recist)

value: Not evaluated

tag: pfs


title: Control_3

description: Library name: Control_3

value: DMSO (0.1%) for 72 h


title: E2317032

description: Library name: E2317032

value: Never

value: In bed < 50% time

value: Missing

value: PD

tag: pfs events

tag: os

tag: os events

value: No


title: PA-H3K27ac-igg

description:
Library name: PA-H3K27ac-igg
library name:PA-H3K27ac-igg

tag: tissue

value: OSCC tissue

tag: cell line

value: Cancer-associated fibroblast

value: Fibroblast

value: WT

value: The cell lines were then treated with 50 μM PA for 24 hours.

value: single batch


title: PA2-H3K4me1

description:
Library name: PA2-H3K4me1
library name:PA2-H3K4me1

tag: cell type

tag: treatment


title: PA1-H3K4me1

description:
Library name: PA1-H3K4me1
library name:PA1-H3K4me1

tag: genotype

tag: batch


title: E2316015

description: Library name: E2316015

value: whole blood

tag: age

tag: Sex

value: Male

value: IV

tag: irae

value: Yes


title: E2317023

description: Library name: E2317023

tag: smoking history

value: Former

tag: patient activity

value: Normal

tag: histology

value: Urothelial (transitional cell) carcinoma

value: III

value: SD


title: E2317042

description: Library name: E2317042

value: In bed < 50% time

tag: disease stage

tag: pdl1 staining

value: Missing

tag: clinical response_(recist)

value: Not evaluated


title: PA1-H3K27ac

description:
Library name: PA1-H3K27ac
library name:PA1-H3K27ac

value: OSCC tissue

value: Cancer-associated fibroblast


title: CON-H3K4me1-igg

description:
Library name: CON-H3K4me1-igg
library name:CON-H3K4me1-igg

value: Fibroblast

value: WT

value: Untreated cells served as the control group.


title: E2316012

description: Library name: E2316012

value: whole blood

value: PR

tag: pfs

tag: pfs events

tag: os


title: CON-H3K27ac-igg

description:
Library name: CON-H3K27ac-igg
library name:CON-H3K27ac-igg

tag: tissue

tag: cell line

value: single batch


title: E2316017

description: Library name: E2316017

value: Male

value: Current

value: Restricted

value: IV

tag: os events

value: No


title: E2316011

description: Library name: E2316011

value: Female

value: Urothelial (transitional cell) carcinoma

value: SD

value: Yes


title: CON3-H3K4me1

description:
Library name: CON3-H3K4me1
library name:CON3-H3K4me1

value: OSCC tissue

tag: cell type

tag: genotype

tag: treatment


title: E2316016

description: Library name: E2316016

tag: age

tag: Sex

value: Former

value: Normal

value: PD


title: E2316007

description: Library name: E2316007

tag: smoking history

value: Missing

tag: irae


title: CON1-H3K27ac

description:
Library name: CON1-H3K27ac
library name:CON1-H327ac

value: Cancer-associated fibroblast

value: Fibroblast

value: WT

value: Untreated cells served as the control group.

tag: batch


title: E2316006

description: Library name: E2316006

value: whole blood

value: Male

tag: patient activity

tag: histology

tag: disease stage

value: Not evaluated


title: CON3-H3K27ac

description:
Library name: CON3-H3K27ac
library name:CON3-H3K27ac

value: single batch


title: E2316008

description: Library name: E2316008

value: Female

value: In bed < 50% time

value: IV

tag: pdl1 staining

tag: clinical response_(recist)

tag: pfs

value: No


title: E2315038

description: Library name: E2315038

tag: tissue

value: Urothelial (transitional cell) carcinoma

tag: pfs events

tag: os

value: Yes


title: E2316005

description: Library name: E2316005

value: Former

value: Normal

tag: os events


title: E2316009

description: Library name: E2316009

value: CR


title: CON1-H3K4me1

description:
Library name: CON1-H3K4me1
library name:CON1-H3K4me1

value: OSCC tissue

tag: cell line

value: Cancer-associated fibroblast

tag: cell type

tag: genotype


title: CON2-H3K27ac

description:
Library name: CON2-H3K27ac
library name:CON2-H3K27ac

value: Fibroblast

value: WT

tag: treatment


title: CON2-H3K4me1

description:
Library name: CON2-H3K4me1
library name:CON2-H3K4me1

value: Untreated cells served as the control group.


title: E2315039

description: Library name: E2315039

value: whole blood

tag: age

tag: Sex

value: Male

tag: smoking history

value: Urothelial (transitional cell) carcinoma with variant histology

value: PR


title: EGFP-overexpressing HEK293T cells, 36h, rep2

first: Liu

last: Chen

address: No.1 Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agricultural University

description:
Library name: Sample_Control_Rep2
HEK293T cells transfected with empty pEGFP-N1 vector for 36 hours, replicate 2

data_processing:
Raw reads were processed with fastp (v0.20.0) to remove adapters, poly-N, and low-quality bases.
Clean reads were aligned to the human reference genome (GRCh38) using BWA v0.7.12
Peaks were identified using MACS2 v2.1.0
Motif analysis was conducted using HOMER v4.9.1
Following annotation with ChIPseeker, functional enrichment analyses were carried out: GO terms with GOseq and KEGG pathways with KOBAS.
Assembly: GRCh38
Supplementary files format and content: bigWig (.bw), narrowPeak
Library strategy: CUT&Tag

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were  maintained in DMEM supplemented with 10% (v/v) fetal bovine serum at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
The sequencing library was constructed by capturing cells/nuclei with ConA magnetic beads, permeabilizing them with digitonin, and performing antibody-guided in situ tagmentation using pA-Tn5 transposase to simultaneously fragment target-proximal DNA and add sequencing adapters. The library was then amplified by PCR and purified with AMPure beads.
CUT&Tag libraries were prepared using the CUT&Tag_Novogene Kit following the method described by Kaya-Okur et al. Cells were immobilized on concanavalin A-coated magnetic beads, and permeabilized with Digitonin. The pA-Tn5 transposome was guided by antibodies to tagment DNA near the target protein. Adapters were simultaneously added at both ends. Libraries were PCR-amplified and purified with AMPure XP beads. Library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: For each well of a 6-well plate, 4 μg of plasmid DNA and 10 μL of transfection reagent (Hieff Trans™ Liposomal)  were diluted in 250 μL of Opti-MEM, incubated at room temperature for 20 minutes, and then added dropwise to each well. Following transfection with either MmpE-pEGFP (experimental) or pEGFP-N1 (control), cells were incubated for 36 hours prior to harvest.

value: Human embryonic kidney

value: Epithelial cells

value: EGFP

value: HEK293T cells were transfected with pEGFP and analyzed at 36 hours

tag: chip antibody

value: GFP (proteintech, #66002-1-Ig )


title: MmpE-EGFP-overexpressing HEK293T cells, 36h, rep1

description:
Library name: Sample_MmpE_Rep1
HEK293T cells transfected with MmpE-pEGFP plasmid for 36 hours, replicate 1

value: MmpE-EGFP

value: HEK293T cells were transfected with MmpE-pEGFP and analyzed at 36 hours


title: EGFP-overexpressing HEK293T cells, 36h, rep1

description:
Library name: Sample_Control_Rep1
HEK293T cells transfected with empty pEGFP-N1 vector for 36 hours, replicate 1


title: E2315037

description: Library name: E2315037

value: Former

tag: patient activity

value: Normal

tag: histology

value: IV

tag: irae

value: Yes


title: CUT&Tag of EP300 in KMT2C-KO IOMM-Lee cells (replicate 1)

city: Nanjing

first: Liuchao

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road, Nanjing

institute: Nanjing medical universuty

description: Library name: EP300_KO_rep1

data_processing:
Raw data quality was assessed using FastQC (v0.11.9) with default parameters. Adapter trimming and quality filtering were performed using fastp (v0.23.2) with default parameters. Reads were aligned to the human genome (hg38) using Bowtie2 (v2.4.5) with the following settings: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 2000. Aligned reads were processed with Picard (v2.27.3) to remove PCR duplicates (REMOVE_DUPLICATES=true). Peak calling was performed using SEACR (v1.3) in stringent mode. Peak annotation was conducted using ChIPseeker (v1.32.0) with default parameters. Motif enrichment analysis was performed using HOMER (v4.11) with parameters: -size -100,100 -mask. Differential peak analysis was performed using DESeq2 (v1.40.2). Functional enrichment (GO/KEGG) analysis was conducted using clusterProfiler (v4.2.0) with default settings.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Peak files generated from CUT&Tag data. Peaks were called using SEACR (stringent mode). Each BED file contains genomic intervals with enriched signal: chromosome, start, end, peak score. One BED file is provided per sample.
Library strategy: CUT&Tag

source_name: IOMM-Lee

growth_protocol: IOMM-Lee meningioma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells (IOMM-Lee meningioma cell line) were harvested at ~1×10⁵ cells per reaction. Cells were bound to concanavalin A (ConA)–coated magnetic beads, permeabilized in digitonin buffer, and incubated with primary antibody (H3K27ac, H3K27me3, H3K4me1, CBP, EP300, KMT2C) at 4°C overnight. Cells were washed and incubated with secondary antibody for 1 h at room temperature. Subsequently, pAG-Tn5 transposome was added and incubated for 1 h at room temperature. Tagmentation was activated by addition of Mg²⁺ buffer for 1 h at 37°C. DNA fragments were released by proteinase digestion and purified using AMPure beads.
Tagmented DNA was amplified using NEBNext High-Fidelity 2× PCR Master Mix with Illumina-compatible indexed primers. PCR conditions: 72°C 5 min, 98°C 30 s, followed by 12 cycles of 98°C 10 s, 63°C 30 s, 72°C 1 min. Libraries were size-selected using AMPure beads (0.8× ratio) to enrich 200–700 bp fragments. Libraries were quantified by Qubit and checked on Agilent Bioanalyzer.

value: IOMM-Lee

value: meningioma

value: CUT&Tag of EP300


title: CUT&Tag of KMT2C in IOMM-Lee cells

description: Library name: KMT2C_CONTROL

value: CUT&Tag of KMT2C


title: E2315027

description: Library name: E2315027

value: whole blood

value: Female

value: Current

value: Restricted

value: Urothelial (transitional cell) carcinoma

tag: disease stage

tag: pdl1 staining

tag: clinical response_(recist)

value: PD


title: E2315036

description: Library name: E2315036

tag: tissue

value: Male

value: Never

value: In bed < 50% time

tag: pfs

tag: pfs events

value: No


title: E2315035

description: Library name: E2315035

value: Former

value: Not evaluated

tag: os

tag: os events


title: E2315033

description: Library name: E2315033

value: Urothelial (transitional cell) carcinoma with variant histology

value: IV


title: E2314023

description: Library name: E2314023

value: Normal

value: Yes


title: CUT&Tag of H3K4me1 in IOMM-Lee cells

description: Library name: H3K4me1_CONTROL_rep1

tag: cell line

value: IOMM-Lee

tag: cell type

value: meningioma

value: CUT&Tag of H3K4me1


title: CUT&Tag of EP300 in IOMM-Lee cells

description: Library name: EP300_CONTROL_rep1

tag: treatment

value: CUT&Tag of EP300


title: CUT&Tag of CBP in KMT2C-KO IOMM-Lee cells (replicate 1)

description: Library name: CBP_KO_rep1

tag: genotype

value: CUT&Tag of CBP


title: MmpE-EGFP-overexpressing HEK293T cells, 36h, rep2

description:
Library name: Sample_MmpE_Rep2
HEK293T cells transfected with MmpE-pEGFP plasmid for 36 hours, replicate 2

value: Human embryonic kidney

value: Epithelial cells

value: MmpE-EGFP

value: HEK293T cells were transfected with MmpE-pEGFP and analyzed at 36 hours

value: GFP (proteintech, #66002-1-Ig )


title: E2315020

description: Library name: E2315020

value: whole blood

tag: age

tag: Sex

value: Male

tag: smoking history

value: Urothelial (transitional cell) carcinoma

value: CR

value: No


title: CUT&Tag of CBP in IOMM-Lee cells

description: Library name: CBP_CONTROL_rep1


title: E2314024

description: Library name: E2314024

value: Never

tag: patient activity

value: In bed < 50% time

tag: histology

value: Adenocarcinoma typical

value: IV

value: Not evaluated


title: CUT&Tag of H3K4me1 in KMT2C-KO IOMM-Lee cells (replicate 1)

description: Library name: H3K4me1_KO_rep1

value: IOMM-Lee

value: meningioma

value: CUT&Tag of H3K4me1


title: E2314020

description: Library name: E2314020

value: Restricted

tag: disease stage

value: Missing

value: SD

tag: irae

value: Yes


title: CUT&Tag of H3K27me3 in IOMM-Lee cells

description: Library name: H3K27me3_CONTROL_rep1

value: CUT&Tag of H3K27me3


title: E2314022

description: Library name: E2314022

value: whole blood

value: Male

value: Former

value: Normal

tag: pdl1 staining

tag: clinical response_(recist)


title: E2314017

description: Library name: E2314017

tag: tissue

value: Never

value: Urothelial (transitional cell) carcinoma

value: PD

tag: pfs

value: No


title: CUT&Tag of H3K27ac in KMT2C-KO IOMM-Lee cells (replicate 1)

description: Library name: H3K27ac_KO_rep1

value: CUT&Tag of H3K27ac


title: CUT&Tag of H3K27me3 in KMT2C-KO IOMM-Lee cells (replicate 1)

description: Library name: H3K27me3_KO_rep1

value: IOMM-Lee


title: E2313011

description: Library name: E2313011

value: IV

tag: pfs events

tag: os


title: CUT&Tag of H3K27ac in CONTROL IOMM-Lee cells (replicate 3)

description: Library name: H3K27ac_CONTROL_rep3

tag: cell line

value: meningioma

value: CONTROL


title: E2314019

description: Library name: E2314019

value: Current

value: Restricted

value: Missing

value: Not evaluated

tag: os events


title: CUT&Tag of H3K27ac in KMT2C-KO IOMM-Lee cells (replicate 3)

description: Library name: H3K27ac_KO_rep3

tag: cell type

tag: treatment


title: E2314018

description: Library name: E2314018

value: whole blood

tag: age

value: In bed < 50% time


title: CUT&Tag of H3K27ac in KMT2C-KO IOMM-Lee cells (replicate 2)

description: Library name: H3K27ac_KO_rep2

tag: genotype


title: CUT&Tag of H3K27ac in CONTROL IOMM-Lee cells (replicate 2)

description: Library name: H3K27ac_CONTROL_rep2


title: E2314016

description: Library name: E2314016

tag: Sex

value: Male

tag: smoking history

value: Former

value: Yes


title: E2313010

description: Library name: E2313010

value: Never

tag: patient activity

value: Normal

tag: histology

value: Urothelial (transitional cell) carcinoma

value: PR


title: MKN1 cells_Treated_rep2

city: Gui Yang

first: Tai

last: Xie

address: No. 9 Beijing Road, Yunyan District, Guiyang City, Guizhou Province, P.R. China

institute: Guizhou Medical University

description:
Library name: Samples 11
Column name in gene_count_matrix.txt: MKN1-SC-2

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: Homo sapiens genome assembly hg38 (GRCh38)
Supplementary files format and content: Tab-delimited text file contains counts for each sample.

source_name: Homo sapiens

growth_protocol: AGS/MKN1 gastric cancer cells were cultured in RPMI-1640 medium (supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin) at 37°C in a humidified atmosphere containing 5% CO₂. Cells were passaged every 2-3 days until reaching 70-80% confluence.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the kit’s protocol: fragmented mRNA was used as the template (with random oligonucleotides as primers), the first cDNA strand was synthesized in the M-MuLV reverse transcriptase system, followed by RNA strand degradation via RNase H, and the second cDNA strand was synthesized using dNTPs in the DNA polymerase I system. After purification, the double-stranded cDNA underwent end repair, A-tailing, and ligation of sequencing adapters; cDNAs of approximately 250-300 bp were selected using AMPure XP beads, then amplified by PCR, and the PCR products were purified again with AMPure XP beads to obtain the final library.

value: Homo sapiens

value: Gastric adenosquamous carcinoma

value: WT

value: Cantharidin sodium treatment


title: MKN1 cells_Treated_rep3

description:
Library name: Samples 12
Column name in gene_count_matrix.txt: MKN1-SC-3


title: E2313007

description: Library name: E2313007

value: Female

tag: disease stage

value: IV

value: PD

tag: irae


title: CUT&Tag of H3K27ac in CONTROL IOMM-Lee cells (replicate 1)

description: Library name: H3K27ac_CONTROL_rep1

value: IOMM-Lee

value: meningioma

value: CONTROL

value: CUT&Tag of H3K27ac


title: E2313001

description: Library name: E2313001

value: whole blood

value: Former

value: Restricted

tag: pdl1 staining

tag: clinical response_(recist)

value: No


title: MKN1 cells_Treated_rep1

description:
Library name: Samples 10
Column name in gene_count_matrix.txt: MKN1-SC-1

tag: tissue


title: E2312021

description: Library name: E2312021

value: Urothelial (transitional cell) carcinoma

tag: pfs

tag: pfs events

value: Yes


title: E2312020

description: Library name: E2312020

value: Male

value: Current

value: Normal

tag: os


title: MKN1 cells_Untreated_rep3

description:
Library name: Samples 9
Column name in gene_count_matrix.txt: MKN1-3

value: Homo sapiens

tag: cell line

value: Gastric adenosquamous carcinoma

value: WT

value: Untreated


title: E2313003

description: Library name: E2313003

value: IV

value: Missing

value: PD

tag: os events


title: MKN1 cells_Untreated_rep2

description:
Library name: Samples 8
Column name in gene_count_matrix.txt: MKN1-2

tag: cell type

tag: treatment


title: MKN1 cells_Untreated_rep1

description:
Library name: Samples 7
Column name in gene_count_matrix.txt: MKN1-1

tag: genotype


title: E2312018

description: Library name: E2312018

tag: age

tag: Sex

value: In bed < 50% time

value: SD


title: AGS cells_Treated_rep3

description:
Library name: Samples 6
Column name in gene_count_matrix.txt: AGS-SC-3

value: AGS

value: Gastric adenocarcinoma epithelial cell

value: Cantharidin sodium treatment


title: E2312019

description: Library name: E2312019

value: whole blood

tag: smoking history

value: Never

tag: patient activity

value: Restricted

value: Undetermined

value: Not evaluated

value: No


title: E2312017

description: Library name: E2312017

value: Male

tag: histology

value: Urothelial (transitional cell) carcinoma

tag: disease stage

value: Yes


title: AGS cells_Untreated_rep3

description:
Library name: Samples 3
Column name in gene_count_matrix.txt: AGS-3

value: Homo sapiens

value: WT

value: Untreated


title: AGS cells_Treated_rep2

description:
Library name: Samples 5
Column name in gene_count_matrix.txt: AGS-SC-2


title: E2312015

description: Library name: E2312015

value: Former

value: In bed < 50% time

value: IV

tag: pdl1 staining

value: PD

tag: irae


title: E2312013

description: Library name: E2312013

tag: tissue

value: Current

tag: clinical response_(recist)


title: AGS cells_Untreated_rep2

description:
Library name: Samples 2
Column name in gene_count_matrix.txt: AGS-2

value: AGS

value: Gastric adenocarcinoma epithelial cell


title: E2312014

description: Library name: E2312014

value: whole blood

value: Restricted

tag: pfs

tag: pfs events


title: AGS cells_Treated_rep1

description:
Library name: Samples 4
Column name in gene_count_matrix.txt: AGS-SC-1

tag: cell line

value: Cantharidin sodium treatment


title: E2311049

description: Library name: E2311049

value: Missing

tag: os

tag: os events

value: No


title: Multiome, HC4, whole skin, ATAC

description:
Library name: HC4-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

data_processing:
Counts and peaks were appropriatly generated using 10X Genomics’ Cell Ranger ARC software (v2.0.2).
Assembly: Human hg38
Supplementary files format and content: GEX Data: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: ATAC Data: Cellranger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, atac_peak_annotation.tsv.gz, atac_peaks.bed,
Supplementary files format and content: Visium image data:aligned_fidcials.jpg, scalefactors_jason, tisssue_hires_image.png, tissue_lowres.png, tissue_positions.csv, detected_tissue_image.jpg
Supplementary files format and content: Visium transcriptomic data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: Whole skin


title: AGS cells_Untreated_rep1

description:
Library name: Samples 1
Column name in gene_count_matrix.txt: AGS-1

tag: cell type

tag: treatment


title: E2312011

description: Library name: E2312011

tag: age

value: Female

value: Never

value: Urothelial (transitional cell) carcinoma

value: SD


title: E2311045

description: Library name: E2311045

tag: Sex

value: Male

value: Former

value: Normal

value: Yes


title: Multiome, HC3, whole skin, ATAC

description:
Library name: HC3-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2311043

description: Library name: E2311043

tag: smoking history

value: IV

value: PD


title: Multiome, HC2, whole skin, ATAC

description:
Library name: HC2-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2311044

description: Library name: E2311044

tag: patient activity

value: In bed < 50% time


title: Multiome, HC4, whole skin, GEX

description:
Library name: HC4-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, HC2, whole skin, GEX

description:
Library name: HC2-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, HC3, whole skin, GEX

description:
Library name: HC3-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2311032

description: Library name: E2311032

value: whole blood

tag: histology


title: E2311036

description: Library name: E2311036

tag: disease stage


title: Multiome, SSc10, whole skin, GEX

description:
Library name: SSc10-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2310044

description: Library name: E2310044

value: Restricted

tag: pdl1 staining


title: Multiome, SSc9, whole skin, GEX

description:
Library name: SSc9-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2309044

description: Library name: E2309044

tag: irae


title: Multiome, SSc8, whole skin, ATAC

description:
Library name: SSc8-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

tag: tissue


title: Multiome, HC1, whole skin, GEX

description:
Library name: HC1-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2310037

description: Library name: E2310037

value: Current

tag: clinical response_(recist)

value: PR


title: E2309039

description: Library name: E2309039

tag: pfs

value: No


title: Multiome, SSc10, whole skin, ATAC

description:
Library name: SSc10-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: Whole skin


title: E2309038

description: Library name: E2309038

value: Female

tag: pfs events


title: E2309048

description: Library name: E2309048

value: Never


title: E2310045

description: Library name: E2310045

value: Urothelial (transitional cell) carcinoma


title: Multiome, HC1, whole skin, ATAC

description:
Library name: HC1-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, SSc7, whole skin, GEX

description:
Library name: SSc7-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2308039

description: Library name: E2308039


title: E2308038

description: Library name: E2308038

value: Missing


title: E2308037

description: Library name: E2308037

value: III

value: CR


title: E2309046

description: Library name: E2309046

value: Male

value: Former


title: Multiome, SSc9, whole skin, ATAC

description:
Library name: SSc9-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, SSc3, whole skin, ATAC

description:
Library name: SSc3-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2307019

description: Library name: E2307019

value: Normal

value: IV

value: Not evaluated


title: E2309045

description: Library name: E2309045

value: whole blood

value: PD


title: E2307016

description: Library name: E2307016


title: Multiome, SSc1, whole skin, GEX

description:
Library name: SSc1-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, SSc2, whole skin, ATAC

description:
Library name: SSc2-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, SSc2, whole skin, GEX

description:
Library name: SSc2-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2307027

description: Library name: E2307027


title: E2307014

description: Library name: E2307014

value: Restricted


title: Multiome, SSc1, whole skin, ATAC

description:
Library name: SSc1-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 2

city: Shanghai

first: Lina

last: Wang

email: qdwln95@163.com, lina-wang@sjtu.edu.cn

address: 639 Zhizaoju Road

institute: Shanghai JiaoTong University School of Medicine

description: Library name: T3-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: CAR-T cells derived from PBMC

extract_protocol:
Total RNA was then extracted using RNA Extraction Reagent (Cat# R401-01, Vazyme) following the manufacturer’s instructions.
The libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: CAR-T cells derived from PBMC


title: E2307007

description: Library name: E2307007

value: In bed < 50% time

value: PR

value: Yes


title: Multiome, SSc8, whole skin, GEX

description:
Library name: SSc8-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: Whole skin


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 1

description: Library name: T3-1


title: E2309034

description: Library name: E2309034

value: Current

value: Urothelial (transitional cell) carcinoma

value: No


title: Multiome, SSc7, whole skin, ATAC

description:
Library name: SSc7-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 2

description: Library name: T2-2


title: Multiome, SSc6, whole skin, ATAC

description:
Library name: SSc6-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2308040

description: Library name: E2308040

value: Urothelial (transitional cell) carcinoma with squamous differentiation


title: Multiome, SS62, whole skin, GEX

description:
Library name: SSc6-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2306022

description: Library name: E2306022

value: Male

value: Never

value: III

value: SD


title: Multiome, SSc5, whole skin, GEX

description:
Library name: SSc5-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, SSc4, whole skin, ATAC

description:
Library name: SSc4-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2308034

description: Library name: E2308034

value: Former

value: IV


title: Multiome, SSc5, whole skin, ATAC

description:
Library name: SSc5-ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: E2308032

description: Library name: E2308032

value: whole blood


title: E2309040

description: Library name: E2309040

value: Restricted


title: Multiome, SSc4, whole skin, GEX

description:
Library name: SSc4-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: E2306018

description: Library name: E2306018

value: Missing

value: PD


title: E2307018

description: Library name: E2307018

value: In bed < 50% time

value: Not evaluated


title: E2306021

description: Library name: E2306021

value: Female

value: Yes


title: E2306019

description: Library name: E2306019

value: Normal

value: Urothelial (transitional cell) carcinoma with variant histology


title: E2307011

description: Library name: E2307011

value: Urothelial (transitional cell) carcinoma

value: No


title: E2307013

description: Library name: E2307013

value: Male

value: PR


title: Multiome, SSc3, whole skin, GEX

description:
Library name: SSc3-GEX
3' mRNA (v3.1 10X Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: Whole skin


title: LUAD tumoroid scRNA-seq

city: New York

first: Jin Suk

last: Park

state: NY

address: 417 East 68th St

institute: MSKCC

description:
Library name: Sample 1
10x Genomics

data_processing:
For scRNA-seq, all processing of the resulting data was performed using the Scanpy package. For quality control, cells with less than 200 genes detected and genes expressed by less than 3 cells were filtered out. Based on the library distribution, cells with less than 1,000, greater than 5% mitochondrial RNA content or less than 5% ribosomal RNA content were excluded from analysis. Housekeeping genes MALAT1 and GM42418 were also removed, with 9,949 cells from freshly isolated KP tumor and 11,064 cells for day-7 KP tumoroids passing the filters.
Assembly: hg38
Supplementary files format and content: Matrix files, ProcessedPeaks

source_name: Lung

extract_protocol:
Tumoroids were isolated from Matrigel using Cell Recovery Solution (Corning), dissociated using TryLE, and FACS sorted into single cells.
Single-cell RNA-seq was performed on 10x Genomics Chromium platform. The scRNA-seq libraries were prepared based on the manufacturer’s protocol for 3’ end reading. The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). The raw sequencing data were then demultiplexed and aligned to the mouse genome using 10X CellRanger pipeline. This generated an output matrix of mRNA counts per cell for every gene. We used the filtered matrix for all downstream analysis. For ChIP-seq, For library construction and sequencing, DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. The KAPA HTP Library Preparation Kit (Kapa Biosystems, Cat #: KK8234) was used to prepare Illumina sequencing libraries with 0.02-5 ng of input DNA and 8-14 cycles of PCR.

value: Lung

tag: cell line

value: PDX tumoroid

value: Lung adenocarcinoma


title: untransduced T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 1

description: Library name: T0-1

value: CAR-T cells derived from PBMC


title: E2306015

description: Library name: E2306015

value: whole blood

value: Former

value: Papillary urothelial carcinoma

value: IV

tag: os


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 3

description: Library name: T3-3


title: E2307010

description: Library name: E2307010

value: Restricted

tag: os events


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 3

description: Library name: T2-3

tag: cell type


title: E2306026

description: Library name: E2306026

value: PD


title: E2306025

description: Library name: E2306025

value: Female

value: Never

value: Normal

value: Undifferentiated carcinoma

value: Missing


title: E2306024

description: Library name: E2306024

value: Male

value: Urothelial (transitional cell) carcinoma

value: No


title: E2306010

description: Library name: E2306010

value: Yes


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 1

description: Library name: T2-1


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 2

description: Library name: T2-A-2


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 3

description: Library name: T3-A-3


title: anti-CD276 CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 3

description: Library name: T1-3


title: E2306012

description: Library name: E2306012


title: E2305027

description: Library name: E2305027

value: PR


title: anti-CD276 CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 2

description: Library name: T1-2

value: CAR-T cells derived from PBMC


title: E2306017

description: Library name: E2306017

value: whole blood

value: Current

value: Urothelial (transitional cell) carcinoma with variant histology


title: E2306016

description: Library name: E2306016

value: Former

value: IV


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 2

description: Library name: T3-A-2


title: untransduced T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 2

description: Library name: T0-2


title: anti-CD276 CAR-T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 1

description: Library name: T1-1


title: untransduced T cells incubated with A549 tumor cells (E:T = 1:2) for  five cycles (CAE), rep 3

description: Library name: T0-3


title: E2306014

description: Library name: E2306014

value: PD


title: E2305026

description: Library name: E2305026

value: Female

value: SD


title: E2305025

description: Library name: E2305025

value: Restricted


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 1

description: Library name: T2-A-1


title: E2306013

description: Library name: E2306013

value: Normal


title: E2305029

description: Library name: E2305029

value: Not evaluated


title: anti-CD276/NKG2DLs Bicephali CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 1

description: Library name: T3-A-1


title: anti-CD276 CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 2

description: Library name: T1-A-2


title: E2305024

description: Library name: E2305024

value: Male


title: E2305028

description: Library name: E2305028

value: Never

value: Urothelial (transitional cell) carcinoma


title: anti-CD276 CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 3

description: Library name: T1-A-3


title: untransduced T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 2

description: Library name: T0-A-2


title: anti-CD276 CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 1

description: Library name: T1-A-1


title: untransduced T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 1

description: Library name: T0-A-1


title: anti-NKG2DLs CAR-T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 3

description: Library name: T2-A-3


title: untransduced T cells incubated with A549 tumor cells for 24h at a 1:1 E/T ratio, rep 3

description: Library name: T0-A-3


title: E2305023

description: Library name: E2305023

value: Missing

value: No


title: SW780-shNT

city: Ningbo

first: Ye

last: Shazhou

state: Zhejiang Province

address: 59 Liuting street

institute: The Affiliated First Hospital of Ningbo University

description:
Library name: Sample 3
SW780_shSCD1_GFLOD.csv

data_processing:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDropTechnologies). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies).
Illumina Novaseq 6000 platform was used to randomly fragment mRNA and isolate small fragments of about 300 bp by magnetic bead screening. Under the action of reverse transcriptase, random hexamers were added to synthesize one-strand cDNA using mRNA as template, followed by two-strand synthesis to form a stable double-strand structure. The cDNA structure of the double strand was A sticky End, which was made into A flat End by adding End Repair Mix, and then an "A" base was added to the 3 'End for joining the Y-shaped connector. The library was enriched and 15 cycles were amplified by PCR. Then, recover the target band by 2% agarose gel, quantify by TBS380 (Picogreen), and mix on the machine according to the proportion of data. Bridge PCR amplification was performed on cBot to generate clusters. Sequencing was performed by Illumina HiSeq xten platform.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: SW780 cell line

growth_protocol: UMUC3 cells were cultured in MEM (Procell, PM150410). SW780 cells were maintained in DMEM (Procell, PM150210). All media were supplemented with 10% fetal bovine serum (FBS, F101-01, Vazyme, China) and 1% penicillin and streptomycin.

extract_protocol:
Total RNA of UMUC3 and SW780 cells with different treatment was harvested using Trizol reagent. TruSeq RNA Sample Preparation Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
The cluster formation and sequencing were performed on the Illumina NovaSeq 6000 platform following the manufacturer’s standard cBot and sequencing protocols.

treatment_protocol: We constructed SCD1 knockdown cells by lentivirus in UMUC3 and SW780 cells.

value: SW780 cell line

value: human bladder cancer cell

tag: genotype

value: WT


title: E2305021

description: Library name: E2305021

value: whole blood

tag: age


title: E2305020

description: Library name: E2305020

tag: Sex


title: SW780-shSCD1

description:
Library name: Sample 4
SW780_shSCD1_GFLOD.csv

value: SCD1 knockdown


title: E2305022

description: Library name: E2305022

tag: smoking history

value: Former

value: IV

value: Yes


title: E2306009

description: Library name: E2306009

value: Current

tag: patient activity

value: PD


title: E2305015

description: Library name: E2305015

value: In bed < 50% time

tag: histology


title: EW-1 cell line, WT, SOX2 (ChIP)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

description: Library name: EW-1_SOX6

data_processing:
Reads were trimmed with TrimGalore tool (v0.6.2)
Sequencing data were processed using nextflow ChIP-seq pipeline (Servant et al., 2023) (https://zenodo.org/records/10357860).
Briefly, reads were mapped with bwa (version 2.19.0) (Li and Durbin, 2010) to the human genome (version hg19). Duplicates or low-quality reads were removed.  Peaks were called with MACS2 (version 2.2.6) (Zhang et al., 2008) using the "narrow" option for transcription factors and the "broad" option for the H3K27ac histone mark. The fragment size was estimated from the data by MACS for transcription factors, while a fixed fragment size of 200 bp was used for histones. ChIP-seq data were normalized according to their respective input DNA samples
Assembly: hg19
Supplementary files format and content: narrowPeak for TF and broadPeak for H3K27ac mark

source_name: cell line

growth_protocol: EW-1, TC-71, MHH-ES-1, SK-N-MC, MSCVL were were cultured at 37°C in 5% CO2 using RPMI and supplemented with 10% fetal bovine serum (FBS) and antibiotics. For the CHLA-9, the cells were maintained with IMDM and 20% FBS, 4mM Glutamine, 1X insulin-transferrin-selenium (ITS) and antibiotics at 37°C in 5% CO2. MSC15 were cultured with alpha-MEM, 10% MSC FBS, 2ng/ml of FGF, 1% L-glutamine and antibiotics at 37°C in 5% CO2 and in hypoxic-like condition (1.5% O2).

extract_protocol:
Cells were fixed for 10 minutes with 1% methanol-free formaldehyde and the chromatin was sonicated for 20 cycles (30 seconds on, 30 seconds off) at the "high" setting. ChIP-Seq experiment was performed for IKZF2, POU3F2, SOX6, FLI1 and H3K27ac using Diagenod kit. Respective inputs were used as normalization controls for all models.
ChIP sequencing libraries were generated using the TruSeq ChIP library preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 (single -end, 100 bp).

treatment_protocol: Some cells were transfected by siRNA (non-targeting control, siCT or targeting the EWS-FLI1 fusion transcript, siEF1) using Lipofectamine RNAiMAX without antibiotics and they were harvested after 96 hours post transfection. For the shRNAs against the EWRS1-FLI fusion oncogenes, the cells were induced by addition of 1 µg/ml doxycycline to the cell culture medium for 7 days before ChIP-Seq experiment.

value: cell line

value: Ewing sarcoma cell line

tag: chip antibody


title: E2305009

description: Library name: E2305009

value: Male

value: Restricted

tag: disease stage

tag: pdl1 staining


title: E2305006

description: Library name: E2305006

tag: tissue

value: Urothelial (transitional cell) carcinoma

value: Not evaluated

tag: irae


title: EW-1 cell line, WT (Input)

description: Library name: EW-1_input


title: UMUC3-shSCD1

description:
Library name: Sample 2
UMUC3_shSCD1_GFLOD.csv

source_name: UMUC3 cell line

value: UMUC3 cell line


title: TC-71, siEF1, R2

description: Library name: TC-71_siEF1_96h_R2

data_processing:
Reads were aligned with STAR 2.5.3 (Dobin et al., 2013) to the human genome (GRCh37/hg19). The count matrix generated by STAR used the human gene annotation v19 of GENCODE.
Assembly: hg19
Supplementary files format and content: count matrix generated by STAR

growth_protocol: TC-71, RD-ES, MHH-ES-1, SKNMC were were cultured at 37°C in 5% CO2 using RPMI and supplemented with 10% fetal bovine serum (FBS) and antibiotics. For the CHLA-10, the cells were maintained with IMDM, 20% FBS, 4mM Glutamine, 1X insulin-transferrin-selenium (ITS) and antibiotics.

extract_protocol:
RNA extraction using RNeasy Plus Mini Kit or Nucleospin RNA (Macherey-Nagel)
TruSeq Stranded mRNA

treatment_protocol: The cells were transfected by siRNA (non-targeting control, siCT or targeting the EWS-FLI1 fusion transcript, siEF1) using Lipofectamine RNAiMAX without antibiotics and they were harvested after 96 hours post transfection. For the shRNAs against the EWRS1-FLI fusion oncogenes, the cells were induced by addition of 1 µg/ml doxycycline to the cell culture medium for 7 days before RNA extraction.

value: KD

tag: treatment

tag: time of_treatment

value: 4 days


title: E2305007

description: Library name: E2305007

value: whole blood

value: Normal

tag: clinical response_(recist)

tag: pfs

tag: pfs events

value: No


title: UMUC3-shNT

description:
Library name: Sample 1
UMUC3_shSCD1_GFLOD.csv

tag: cell line

tag: cell type

value: human bladder cancer cell

value: WT


title: TC-71 cell line, KD, H3K27ac (ChIP)

description: Library name: TC-71_siEF1_H3K27ac


title: E2305019

description: Library name: E2305019

tag: age

value: Former

value: IV

value: Missing

tag: os

tag: os events


title: MSCVL cell line, WT, H3K27ac (ChIP)

description: Library name: MSCVL_H3K27ac

source_name: mesenchymal stem cells

value: mesenchymal stem cells

value: MSCVL

value: Mesenchymal Stem cell (normal)


title: TC-71, siEF1, R1

description: Library name: TC-71_siEF1_96h_R1

value: Ewing sarcoma cell line

tag: genotype


title: E2303027

description: Library name: E2303027

tag: Sex

value: Male

tag: smoking history

value: Never

tag: patient activity

value: In bed < 50% time

tag: histology

value: Urothelial (transitional cell) carcinoma


title: RD-ES, KD, R3

description: Library name: RD-ES_shEF1_D7pos_dox_R3

tag: tissue

value: RD-ES

value: KD

value: dox

value: 7 days


title: E2305004

description: Library name: E2305004

value: whole blood

tag: disease stage

tag: pdl1 staining

value: PD

tag: irae

value: No


title: E2305018

description: Library name: E2305018

value: Former

value: Restricted

value: Urothelial (transitional cell) carcinoma with squamous differentiation

value: IV

tag: clinical response_(recist)

value: SD


title: MHH-ES-1 cell line, KD, H3K27ac (ChIP)

description: Library name: MHH-ES-1_siEF1_H3K27ac

value: cell line

value: Ewing sarcoma cell line

tag: chip antibody


title: E2305014

description: Library name: E2305014

value: Male

value: Missing

tag: pfs

tag: pfs events

value: Yes


title: SK-N-MC cell line, KD, H3K27ac (ChIP)

description: Library name: SK-N-MC_siEF1_H3K27ac

tag: cell line

value: SK-N-MC

tag: cell type


title: E2305012

description: Library name: E2305012

tag: age

value: In bed < 50% time

value: Urothelial (transitional cell) carcinoma

value: Not evaluated

tag: os


title: RD-ES, WT, R1

description: Library name: RD-ES_shEF1_D0_R1

value: RD-ES

tag: genotype

value: WT

tag: treatment

tag: time of_treatment


title: EW-1 cell line, WT, POU3F2 (ChIP)

description: Library name: EW-1_POU3F2


title: E2303020

description: Library name: E2303020

value: whole blood

tag: Sex

tag: smoking history

value: Never

tag: patient activity

value: PD

tag: os events

value: No


title: E2303015

description: Library name: E2303015

tag: tissue

value: Current

value: Restricted

tag: histology

tag: disease stage

value: IV

tag: pdl1 staining


title: MHH, ES1, siCT, R2

description: Library name: MHH_ES1_siCT_96h_R2

value: Ewing sarcoma cell line

value: siCT

value: 4 days


title: EW-1 cell line, WT, IKZF2 (ChIP)

description: Library name: EW-1_IKZF2

value: cell line

tag: chip antibody


title: MHH, ES1, siCT, R1

description: Library name: MHH_ES1_siCT_96h_R1


title: E2305017

description: Library name: E2305017

value: Female

tag: clinical response_(recist)

tag: pfs

tag: pfs events

tag: irae


title: SK-N-MC, siEF1, R1

description: Library name: SK-N-MC_siEF1_96h_R1

tag: cell line

value: SK-N-MC

tag: cell type

value: KD


title: TC-71, siCT, R2

description: Library name: TC-71_siCT_96h_R2

tag: genotype

tag: treatment


title: TC-71, siCT, R1

description: Library name: TC-71_siCT_96h_R1

tag: time of_treatment


title: SK-N-MC, siCT, R1

description: Library name: SK-N-MC_siCT_96h_R1


title: E2303025

description: Library name: E2303025

tag: age

tag: Sex

value: Male

tag: smoking history

value: Urothelial (transitional cell) carcinoma

value: III

value: SD

tag: os

value: Yes


title: RD-ES, KD, R2

description: Library name: RD-ES_shEF1_D7pos_dox_R2

tag: tissue

value: RD-ES

value: dox

value: 7 days


title: E2303023

description: Library name: E2303023

value: whole blood

value: Current

tag: patient activity

value: Normal

tag: histology

tag: disease stage

value: PD

tag: os events

value: No


title: control siRNA-sample 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
FASTQ files were aligned to the mm10 genome assembly using STAR v.2.6.1a aligner
RNA-seq counts were preprocessed and analyzed for differential expression using the edgeR v.3.30.0, R package. p-values for differentially expressed genes were corrected using a False Discovery Rate (FDR) multiple testing correction method.
Assembly: mm10
Supplementary files format and content: gene counts

growth_protocol: KMWT1 glioma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted 48 hours post transfection using RNeasy plus kit (Qiagen)
Library construction and sequencing was performed at University of Cincinnati Genomics Core

treatment_protocol: Cells were transfected either wuith control or YY1 siRNA (SmartPool, Dharmacon).

value: glioma

value: control siRNA

tag: time point

value: 48 hours post transfection


title: E2303026

description: Library name: E2303026

value: Female

tag: pdl1 staining

tag: clinical response_(recist)

tag: pfs

tag: pfs events


title: E2303022

description: Library name: E2303022

value: Male

value: PR

tag: irae


title: RD-ES, WT, R3

description: Library name: RD-ES_shEF1_D0_R3

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genotype

value: WT

tag: treatment


title: E2305005

description: Library name: E2305005

tag: age

tag: Sex

tag: smoking history

value: Former

value: Restricted

value: Urothelial (transitional cell) carcinoma

value: IV


title: E2303021

description: Library name: E2303021

tag: tissue

value: whole blood

tag: patient activity

value: SD

tag: os

value: Yes


title: E2303018

description: Library name: E2303018

value: Current

value: Normal

tag: histology

tag: disease stage

value: III

value: Missing

tag: os events


title: RD-ES, WT, R2

description: Library name: RD-ES_shEF1_D0_R2

value: RD-ES

tag: time of_treatment


title: CHLA-10, WT , R3

description: Library name: CHLA-10_shEF1_D0_R3


title: CHLA-10, KD , R1

description: Library name: CHLA-10_shEF1_D7dox_R1

value: KD

value: dox

value: 7 days


title: E2303016

description: Library name: E2303016

value: Male

tag: pdl1 staining

tag: clinical response_(recist)

tag: pfs


title: MHH, ES1, siEF1, R2

description: Library name: MHH_ES1_siEF1_96h_R2

tag: cell line

value: Ewing sarcoma cell line

value: 4 days


title: MHH, ES1, siEF1, R1

description: Library name: MHH_ES1_siEF1_96h_R1

tag: cell type


title: YY1 siRNA-sample 6

value: glioma

tag: genotype

value: YY1 siRNA

tag: time point

value: 48 hours post transfection


title: SK-N-MC, siCT, R2

description: Library name: SK-N-MC_siCT_96h_R2

value: SK-N-MC

value: siCT

tag: treatment


title: control siRNA-sample 1

value: control siRNA


title: CHLA-10, WT , R2

description: Library name: CHLA-10_shEF1_D0_R2

value: WT


title: CHLA-10, KD , R3

description: Library name: CHLA-10_shEF1_D7dox_R3


title: YY1 siRNA-sample 5


title: E2303014

description: Library name: E2303014

value: whole blood

tag: age

tag: Sex

value: Former

value: Normal

value: Urothelial (transitional cell) carcinoma

value: IV

value: PR

tag: pfs events

tag: irae

value: Yes


title: SK-N-MC, siEF1, R2

description: Library name: SK-N-MC_siEF1_96h_R2

tag: tissue

value: KD


title: RD-ES, KD, R1

description: Library name: RD-ES_shEF1_D7pos_dox_R1

value: RD-ES

value: Ewing sarcoma cell line

value: dox

value: 7 days


title: E2303013

description: Library name: E2303013

value: Male

tag: smoking history

value: Never

tag: patient activity

value: Restricted

tag: histology

value: PD

tag: os


title: YY1 siRNA-sample 4

value: glioma

value: YY1 siRNA

value: 48 hours post transfection


title: E2302021

description: Library name: E2302021

value: whole blood

tag: disease stage

tag: pdl1 staining

tag: os events

value: No


title: E2302020

description: Library name: E2302020

value: Current

value: In bed < 50% time

value: Urothelial (transitional cell) carcinoma

value: IV

tag: clinical response_(recist)

value: Not evaluated

tag: pfs


title: Input DNA hepatocyte, replicate 1

description: Library name: ChIP-IgG-1

data_processing:
The data was processed using the Nextflow chipseq v.2.1.0 pipeline using the GRCh38 genome assembly.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, text

source_name: liver

extract_protocol:
ChIP was performed using IgG or V5 antibody and DNA was eluted from the immunoprecipitates.
Library was prepared using NEBNext Ultra II DNA library prepration kit

value: liver

tag: cell line

tag: cell type

value: HCC

value: input


title: TAF2-V5 ab hepatocyte, replicate 1

description: Library name: ChIP-V5-1

tag: treatment

value: TAF2-V5 ab


title: CHLA-10, KD , R2

description: Library name: CHLA-10_shEF1_D7dox_R2

value: Ewing sarcoma cell line

tag: genotype

value: KD

value: dox

tag: time of_treatment

value: 7 days


title: E2303012

description: Library name: E2303012

tag: age

tag: Sex

value: Male

value: Former

value: Normal

value: SD

tag: pfs events


title: control siRNA-sample 2

value: glioma

value: control siRNA

tag: time point

value: 48 hours post transfection


title: E2303011

description: Library name: E2303011

tag: tissue

value: whole blood

tag: smoking history

value: Current

tag: patient activity

value: Restricted

value: Urothelial (transitional cell) carcinoma

value: IV

value: PD

tag: irae

value: Yes


title: CHLA-10, WT , R1

description: Library name: CHLA-10_shEF1_D0_R1

value: Ewing sarcoma cell line

value: WT


title: E2303010

description: Library name: E2303010

value: Female

tag: histology

tag: disease stage

tag: pdl1 staining

value: PR

tag: os


title: E2302017

description: Library name: E2302017

value: Male

value: Never

tag: clinical response_(recist)

tag: pfs

tag: os events

value: No


title: Input DNA hepatocyte, replicate 2

description: Library name: ChIP-IgG-2

value: liver

tag: cell line

tag: cell type

value: HCC

tag: treatment

value: input