title: GC muscle_KO_06

city: Philadelphia

first: Damaris

last: Lorenzo

state: Pennsylvania

address: 1112 BRB II/III, 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: Library name: Sample 12

data_processing:
Raw data (raw reads) of FASTQ format were  processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Reference genome and gene model annotation files were directly downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped to each gene. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Assembly: mm10
Supplementary files format and content: tab-delimeted text file includes RPKM values for each sample

growth_protocol: Skeletal muscle AnkB KO mice and littermate control mice were kept on the same cage. All mice were housed at 22 ± 2 °C on 12-hour light/dark cycles and given food and water ad libitum until tissue collection.

extract_protocol:
Flash-frozen muscles were thawed on ice and homogenized in QIAzol Lysis Reagent (Qiagen, 79306) using a bead homogenizer. RNA was isolated using the RNeasy Mini kit (Qiagen, 74106) per manufacturers recommendations with on-column DNAse digestion. Integrity of RNA samples was evaluated using the Agilent 2100 bioanalyzer.
1 μg of total RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: skeletal muscle

value: male

value: bulk gastrocnemius muscle

value: Ank2f/f; HSA-Cre+

tag: age

value: 4 months old


title: 41s

status: Public on Sep 03 2025

type: SRA

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Library name: RNA_S8112Nr118

library_source: transcriptomic

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the H. sapiens reference genome provided by ENSEMBL, (grch38) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from Ensembl GRCh38 genome (version 109) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version 1.42).
Assembly: grch38
Supplementary files format and content: htseq-count output: tab delimited raw counts

molecule: total RNA

organism: Homo sapiens

source_name: normal bladder

extract_protocol:
Total RNA that was isolated from fresh frozen BC tumor and BM tissues using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer's instructions. Isolated RNA concentration and its purity were assessed by NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) determining the A260/280 and A260/230 ratios, respectively. RNA integrity number (RIN) and distribution value 200 (DV200) were assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA isolates were stored at -80° C. Next, 10 ng of RNA was used to prepare the RNA libraries.
During the library preparation, rRNA was depleted using KAPA RNA HyperPrep with RiboErase and KAPA Globin Depletion Hybridization Oligos (Roche, Basel, Switzerland). SMART-Seq Stranded Kit (Takara Bio, Kusatsu, Japan) was used for low input RNA quantities. The libraries were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Depths of 30 million (6Gb) paired-end 100 bp reads were generated for each sample.

tag: tissue

value: normal bladder

tag: Sex

tag: Stage

value: Ta

tag: grade

value: LOW


title: GC muscle_KO_05

country: USA

description: Library name: Sample 11

organism: Mus musculus

source_name: skeletal muscle

tag: cell type

tag: genotype


title: GC muscle_KO_04

description: Library name: Sample 10


title: mESC, EZH2-A677T mutant, H3K27ac (ChIP), rep2

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: The Smurfit Institute, The University of Dublin Trinity College, College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: Library name: A677T_H3K27ac_rep2

library_source: genomic

data_processing:
Chromosome names for the human genome were modified with the prefix hg38_ and a metagenome was created by concatenating the mouse and human reference genomes (mm10 and hg38, respectively) before indexing with Bowtie 2 version 2.3.5. Reads were aligned to the metagenome using Bowtie 2 with default parameters, with the exception of –no-unal.
Non-unique read alignments were filtered out using SAMtools version 1.10 to exclude those with an alignment quality of <2, and the hg38_  prefix appended to chromosome names was used to separate reads as aligned to the reference mouse or spike-in human genomes.
Spike-in normalization factors were calculated for each ChIP using the formula for normalized reference-adjusted reads per million (RRPM); 1 per million spike-in reads.
BigWig files were generated using the bamCoverage tool from the deepTools suite version 3.5.0 with a bin size of 10 and scaled using the RRPM normalization factor derived for each sample.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: Mouse embryonic stem cells

extract_protocol:
Enriched DNA fragments were Rnase (Thermo Fisher) and Proteinase K (Sigma) treated prior to purification using Qiagen MinElute PCR Purification Kit (Qiagen; 28006).
ChIP-purified DNA was quantified by fluorimetry using the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher), and 0.5–50 ng of DNA/ChIP was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (NEB E7645) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2; NEB E7335 and E7500). Library DNA was quantified using the Qubit, and size distributions were ascertained on a TapeStation (Agilent) using the D1000 ScreenTape assay reagents (Agilent; 5067- 5583).

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant

tag: antibody


title: GC muscle_KO_03

description: Library name: Sample 9


title: RT112, 1% hypoxia_1

type: RNA

city: Bangor

first: Tim

last: Smith

address: Dean Street Bangor LL57 1UT

country: United Kingdom

institute: Bangor University

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK).

scan_protocol: Affymetrix protocol

data_processing: Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RMA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

label: biotin

source_name: RT112, 1% hypoxia

label_protocol: 8ng/microlitre (9ul) added to deep 96 well plates frozen and sent to Clariom S for RNA determination

growth_protocol: Eagle's Minimum Essential Medium + 10% FBS

extract_protocol:
Cells lysed using lysis buffer (in hypoxia if hypoxic samples)
Samples RNA extracted using Qiagen RNA extraction kits

treatment_protocol: Incubated 24h in 5%CO2:95% air (21%O2) then kept at this or transferred to hypoxia cabinets at 1%, 0.2% or 0.1% O2for 24h.

tag: cell line

tag: treatment

value: 1%O2 (hypoxia)


title: mESC, EZH2-WT, H3K27ac (ChIP), rep2

description: Library name: WT_H3K27ac_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: SG TCR, B6, Male 2

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

description: Library name: TCR-B6M2

data_processing:
Corresponded to GSE268532, scRepertoire (v2.0.4) was used to analyze TCR V(D)J data from the 10x Cell Ranger.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values (CSV) files contained filtered contig annotations.
Library strategy: scTCR-seq

source_name: Salivary gland

extract_protocol:
Salivary glands of C57BL/6.NOD-Aec1/2 (51 weeks old, n=2 female, 2 male) and B6 (64 weeks old, n=2 female, 2 male) mice were explanted and digested in a buffer containing 1 mg/ml DNase (Sigma-Aldrich, St. Louis, MO) and 1 mg/ml Collagenase Type 4 (Worthington, Lakewood, NJ, USA) in RPMI (Lonza, Allendale, NJ) complete media (10% FBS, 2 mM L-glutamine, 0.05 mM β-mercaptoethanol). Tissues were placed in a MACS C tube (Miltenyi Biotec, San Diego, CA) for desiccation on GentleMACS V1.02 for a pulse of 38 seconds. After a 10-minute incubation at 37°C, the digest buffer was removed and placed into 4°C RPMI complete media. The process was repeated twice. Single-cell suspensions were centrifuged (2500 rpm, 10 min, 4°C) and resuspended in PBS for filtration through a 70-μm sterile cell strainer (Fisher, Pittsburgh, PA). After a wash with PBS, cells were resuspended again in PBS for lymphocyte isolation with Lympholyte-M cell separation media (Cedar Lane, Burlington, Canada) per the manufacturer's instructions. Single-cell suspensions were stained for DAPI, and live cells were sorted with a sorter (SH800S, Sony, San Jose, CA) into RPMI containing 10% FBS on ice for single-cell sequencing library preparation.
A total of 8 samples were loaded onto a Chromium Next GEM Chip G, analyzed by the Chromium Controller (10x Genomics, Pleasanton, CA) for Gel Beads-in-emulsion (GEMs) generation and reverse transcription. The generated cDNA was purified with SPRIselect (Beckman Coulter Inc, Indianapolis, IN) and used for 5′ gene expression with V(D)J library construction. The cDNAs and libraries were examined for quality control using D5000 ScreenTape (Agilent Technologies, Waldbronn, Germany), and Qubit (Thermo Fisher Scientific, Waltham, MA) was used for quantification. To achieve 5000 reads per cell for the V(D)J library, the libraries were sequenced using the Illumina NovaSeq6000 system (Illumina, San Diego, CA).

value: Salivary gland


title: 40s

description: Library name: RNA_S8112Nr117

value: HIGH


title: RT4, Control_3

source_name: RT4, Control

value: 21%O2 (normoxia)


title: RT4, 0.1% hypoxia_2

source_name: RT4, 0.1% hypoxia

value: 0.1%O2 (hypoxia)


title: 37s

description: Library name: RNA_S8112Nr116

value: TA


title: RT112, Control_1

source_name: RT112, Control


title: mESC, EZH2-A733T mutant, H3K27me2 (ChIP)

description: Library name: A733T_H3K27me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A733T mutant


title: GC muscle_KO_02

description: Library name: Sample 8

value: skeletal muscle

value: male


title: 35s

description: Library name: RNA_S8112Nr115


title: RT4, 0.2% hypoxia_2

source_name: RT4, 0.2% hypoxia

value: 0.2%O2 (hypoxia)


title: RT4, 1% hypoxia_2

source_name: RT4, 1% hypoxia


title: SG TCR, B6, Male 1

description: Library name: TCR-B6M1


title: mESC, EZH2-Y728 mutant, H3K27ac (ChIP), rep2

description: Library name: Y728_H3K27ac_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: 57s

description: Library name: RNA_S8112Nr125

value: normal bladder


title: GC muscle_KO_01

description: Library name: Sample 7

value: bulk gastrocnemius muscle

value: Ank2f/f; HSA-Cre+

value: 4 months old


title: 34s

description: Library name: RNA_S8112Nr114

value: Ta(m)

value: LOW


title: mESC, EZH2-Y728 mutant, H3K27me2 (ChIP), rep2

description: Library name: Y728_H3K27me2_rep2

value: Mouse embryonic stem cells


title: 30s

description: Library name: RNA_S8112Nr113


title: RT4, 1% hypoxia_3

value: 1%O2 (hypoxia)


title: RT112, 0.2% hypoxia_2

source_name: RT112, 0.2% hypoxia


title: mESC, EZH2-A677T mutant, H3K27me2 (ChIP), rep2

description: Library name: A677T_H3K27me2_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: RT4, Control_2

value: 21%O2 (normoxia)


title: RT4, 0.1% hypoxia_1

value: 0.1%O2 (hypoxia)


title: GC muscle_WT_05

description: Library name: Sample 5


title: mESC, EZH2-WT, H3K27me2 (ChIP), rep2

description: Library name: WT_H3K27me2_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: GC muscle_WT_04

description: Library name: Sample 4


title: 29s

description: Library name: RNA_S8112Nr112

value: Ta


title: mESC, EZH2-A733T mutant, H3K27me3 (ChIP)

description: Library name: A733T_H3K27me3

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A733T mutant


title: 16g

description: Library name: RNA_S8112Nr11

source_name: tumour bladder

value: tumour bladder

value: male


title: mESC, EZH2-Y728 mutant, H3K27me3 (ChIP), rep2

description: Library name: Y728_H3K27me3_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: 28MD_p

description: Library name: RNA_S8112Nr111

value: normal bladder


title: RT4, 0.2% hypoxia_1

value: 0.2%O2 (hypoxia)


title: GC muscle_WT_03

description: Library name: Sample 3

value: skeletal muscle

value: bulk gastrocnemius muscle


title: GC muscle_WT_02

description: Library name: Sample 2

value: 4 months old


title: RT4, Control_1


title: 26S

description: Library name: RNA_S8112Nr110


title: mESC, EZH2-A677T mutant, H3K27me3 (ChIP), rep2

description: Library name: A677T_H3K27me3_rep2


title: GC muscle_WT_06

description: Library name: Sample 6


title: RT4, 1% hypoxia_1


title: GC muscle_WT_01

description: Library name: Sample 1


title: HT1376, 0.1% hypoxia_3

source_name: HT1376, 0.1% hypoxia


title: 25S

description: Library name: RNA_S8112Nr109

value: LOW


title: 307_Cx_HE

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description: Library name: HE307

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against mm39
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Mus musculus Annotation Release 109
Assembly: mm39
Supplementary files format and content: refseq_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format
Supplementary files format and content: refseq_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format

source_name: Cerebral cortex

extract_protocol:
Norgen Biotek RNA/DNA/Protein Purification Plus Kit
TruSeq stranded total RNAs

value: Cerebral cortex

value: HE


title: mESC, EZH2-WT, Input

description: Library name: WT_Input

value: Mouse embryonic stem cells

value: Input


title: HT1376, 0.2% hypoxia_3

source_name: HT1376, 0.2% hypoxia


title: 21s

description: Library name: RNA_S8112Nr108


title: mESC, EZH2-heterozygote, Input

description: Library name: het_Input

value: Ezh2 heterozygous knockout mESCs


title: mESC, EZH2-WT, H3K27me3 (ChIP), rep2

description: Library name: WT_H3K27me3_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: 20MD_p

description: Library name: RNA_S8112Nr107

value: HIGH


title: mESC, EZH2-Y728 mutant, FLAG (ChIP)

description: Library name: Y728_FLAG

value: FLAG


title: HT1376, 1% hypoxia_3

source_name: HT1376, 1% hypoxia

value: 1%O2 (hypoxia)


title: 19s

description: Library name: RNA_S8112Nr106

value: male


title: mESC, EZH2-A677T mutant, FLAG (ChIP)

description: Library name: A677T_FLAG

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: 300_Cx_WT

description: Library name: WT300

value: WT


title: 18s

description: Library name: RNA_S8112Nr105

value: normal bladder

value: Ta


title: mESC, EZH2-K563E mutant, FLAG (ChIP)

description: Library name: K563E_FLAG

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: 302_Cx_HE

description: Library name: HE302


title: 299_Cx_WT

description: Library name: WT299


title: HT1376, 0.1% hypoxia_2

value: 0.1%O2 (hypoxia)


title: HT1376, Control_3

source_name: HT1376, Control

value: 21%O2 (normoxia)


title: mESC, EZH2-K634E mutant, FLAG (ChIP)

description: Library name: K634E_FLAG

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: 292_Cx_WT

description: Library name: WT292

value: Cerebral cortex


title: 15s

description: Library name: RNA_S8112Nr103

source_name: normal bladder

value: LOW


title: 16s

description: Library name: RNA_S8112Nr104

value: Ta(m)


title: 291_Cx_WT

description: Library name: WT291


title: HT1376, 0.2% hypoxia_2

value: 0.2%O2 (hypoxia)


title: mESC, EZH2-R679C mutant, FLAG (ChIP)

description: Library name: R679C_FLAG

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: mESC, EZH2-WT, FLAG (ChIP)

description: Library name: WT_FLAG

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT

value: FLAG


title: 290_Cx_HE

description: Library name: HE290

value: HE


title: 15g

description: Library name: RNA_S8112Nr10

value: tumour bladder

value: male


title: 306_Cx_HE

description: Library name: HE306


title: HT1376, 0.1% hypoxia_1


title: HT1376, 1% hypoxia_2

value: 1%O2 (hypoxia)


title: mESC, EZH2-heterozygote, FLAG (ChIP)

description: Library name: het_FLAG

value: Ezh2 heterozygous knockout mESCs


title: 280_Cx_WT

description: Library name: WT280

value: WT


title: HT1376, 0.2% hypoxia_1


title: 11s

description: Library name: RNA_S8112Nr101

value: normal bladder

value: Ta


title: HT1376, 1% hypoxia_1


title: mESC, EZH2-Y728 mutant, H3K36me2 (ChIP)

description: Library name: Y728_H3K36me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: 276_Cx_WT

description: Library name: WT276

value: Cerebral cortex


title: Case3_6wks

city: Daegu

first: Sang Jin

last: Lee

state: Daegu

address: 130 Dongdeok‑ro, Jung‑gu, Daegu 41944, Republic  of Korea

department: 2Department of Internal Medicine

country: South Korea

institute: Kyungpook National University School of Medicine, Daegu, Republic of Korea

description:
Library name: Case3_6wks
10x genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed with Cell Ranger version 3.0.1 (10X Genomics, CA) using human reference transcriptomes.
Assembly: Human PBMC
Supplementary files format and content: GZ files including matrix

source_name: blood

extract_protocol:
Single-cell suspensions of PBMCs were washed and resuspended in 0.04% BSA with PBS. Cells were counted automatically with Countess II (Thermo Fisher, Waltham, MA). scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. Briefly, the cells were diluted into the Chromium Next GEM Chip G to yield a recovery of approximately 3,000 single cells.
Following the library preparation, the libraries were sequenced in multiplex on the Novaseq 6000 sequencer (Illumina, San Diego, CA) to produce on average a minimum of 60,000 reads per single cell.

value: blood

value: PBMC

value: female

tag: state


title: mESC, EZH2-A677T mutant, H3K36me2 (ChIP)

description: Library name: A677T_H3K36me2

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: HT1376, Control_1

value: 21%O2 (normoxia)


title: 269_Cx_HE

description: Library name: HE269


title: HT1376, Control_2


title: mESC, EZH2-K563E mutant, H3K36me2 (ChIP)

description: Library name: K563E_H3K36me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: 268_Cx_WT

description: Library name: WT268


title: Case2_6wks

description:
Library name: Case2_6wks
10x genomics


title: 264_Cx_HE

description: Library name: HE264

value: HE


title: mESC, EZH2-K634E mutant, H3K36me2 (ChIP)

description: Library name: K634E_H3K36me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: 12S

description: Library name: RNA_S8112Nr102

value: male

value: Ta(m)

value: LOW


title: J82, 0.1% hypoxia_3

source_name: J82, 0.1% hypoxia

value: 0.1%O2 (hypoxia)


title: Case2_flare

description:
Library name: Case2_flare
10x genomics

value: flare


title: 244_Cx_HE

description: Library name: HE244


title: Case1_6wks

description:
Library name: Case1_6wks
10x genomics


title: mESC, EZH2-WT, H3K36me2 (ChIP)

description: Library name: WT_H3K36me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: mESC, EZH2-R679C mutant, H3K36me2 (ChIP)

description: Library name: R679C_H3K36me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: Case1_flare

description:
Library name: Case1_flare
10x genomics


title: J82, 0.2% hypoxia_3

source_name: J82, 0.2% hypoxia

value: 0.2%O2 (hypoxia)


title: ctrltreated0

city: Shanghai

first: Shiyun

last: Huang

address: Zhizaoju ROAD No.833

country: China

institute: Shanghai JiaoTong University

description: Library name: Sample 3

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36).
Read 2 contains the cDNA information.
Assembly: mm10
Supplementary files format and content: matrix files

molecule: polyA RNA

source_name: tumor

extract_protocol:
A single-cell suspension was prepared from the indicated tissues. For labeling, 40 μl of CD45 microbeads (Miltenyi) were added. After an incubation step (15 min at 4˚C) the antigen-antibody reaction was stopped by adding 800 μl ice-cold PBS. Then, the cell suspension mixture is loaded onto a MACS Column, which is placed in the magnetic field of a MACS Separator. The magnetically labeled CD45+ cells are retained within the column. The unlabeled cells run through; this cell fraction is thus depleted of CD45+ cells, the CD45-negative cells were in the eluent buffer. After removing the column from the magnetic field, the magnetically retained CD45+ cells can be eluted as the positively selected cell fraction and can be used for subsequent experiments.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Novaseq6000 platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: tumor

value: Immune cells and cancer cells

value: control


title: mESC, EZH2-Y728 mutant, CBX7 (ChIP), rep1

description: Library name: Y728_CBX7_rep1

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: siCDH3-3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: Sample9

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a).
Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30.
Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Assembly: GRCh38
Supplementary files format and content: gene/transcript reads count file, text format

source_name: Melanoma

growth_protocol: Cell lines were cultured in RPMI containing 10% FBS, 200 nM TPA (12-O-tetradecanoylphorbol-13-acetate), 10 nM endothelin-1, 200 pM cholera toxin, and 10 ng/mL human stem cell factor  at 37˚C in a humidified atmosphere containing 10% CO2.

extract_protocol:
Total RNA was isolated using Qiagen mIRNease kit
NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA)

treatment_protocol: Cell were transfected with Dharmacon siRNAs using JetPRIME transfection reagent

value: Melanoma

value: Immortalized melanocytes

value: siRNA


title: J82, 0.1% hypoxia_2


title: J82, 1% hypoxia_3

source_name: J82, 1% hypoxia

value: 1%O2 (hypoxia)


title: shtreated1

description: Library name: Sample 2


title: siCDH3-2

description: Library name: Sample8


title: Case3_flare

description:
Library name: Case3_flare
10x genomics

value: blood

value: PBMC

value: female


title: mESC, EZH2-A677T mutant, CBX7 (ChIP), rep1

description: Library name: A677T_CBX7_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: J82, 0.2% hypoxia_2


title: siCDH3-1

description: Library name: Sample7


title: mESC, EZH2-K563E mutant, CBX7 (ChIP)

description: Library name: K563E_CBX7

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: J82, 1% hypoxia_2


title: siCDH3-AS1-3

description: Library name: Sample6


title: ctrltreated1

description: Library name: Sample 1


title: Cyclosporin A-treated sample

city: Tokyo

first: Yasuhiro

last: Oda

address: 7-3-1 Hongo, Bunkyo

country: Japan

institute: The University of Tokyo Graduate School of Medicine

description: Library name: Sample 2

data_processing:
Cell Ranger software v8.0.0 (10x Genomics) was used for data processing.
Assembly: Mouse mm10
Supplementary files format and content: Filtered feature-barcode matrix

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Nuclear dissociation was performed using the Nuclei EZ Prep Kit. A sliced, snap-frozen kidney was minced and homogenized in ice-cold EZ Lysis Buffer. After incubation on ice, the homogenate was filtered through a 40-μm strainer and centrifuged. The pellet was resuspended with EZ Lysis Buffer, centrifuged, resuspended in Dulbecco’s phosphate buffered saline with 1% fetal bovine serum and filtered through a 5-μm strainer.
Formation of gel beads in emulsion, barcoding, cDNA amplification and library construction were performed according to the manufacturer’s instructions for Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics).

value: Kidney

value: an early-stage chronic calcineurin inhibitor nephrotoxicity mouse model

value: Cyclosporin A


title: mESC, EZH2-K634E mutant, CBX7 (ChIP)

description: Library name: K634E_CBX7

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: J82, Control_3

source_name: J82, Control

value: 21%O2 (normoxia)


title: Vehicle-treated sample

description: Library name: Sample 1

value: control

value: Vehicle


title: J82, 0.2% hypoxia_1

value: 0.2%O2 (hypoxia)


title: J82, Control_2


title: J82, 0.1% hypoxia_1

value: 0.1%O2 (hypoxia)


title: siCDH3-AS1-2

description: Library name: Sample5

value: Melanoma

value: Immortalized melanocytes


title: shtreated0

description: Library name: Sample 4

value: tumor

value: Immune cells and cancer cells


title: mESC, EZH2-R679C mutant, CBX7 (ChIP)

description: Library name: R679C_CBX7

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: mESC, EZH2-heterozygote, H3K36me2 (ChIP)

description: Library name: het_H3K36me2

value: Ezh2 heterozygous knockout mESCs


title: siCDH3-AS1-1

description: Library name: Sample4

value: siRNA


title: Old1_replicate_2

city: Freiburg im Breisgau

first: Luis

last: Hortells

address: Albertstraße 25

country: Germany

institute: University of Freiburg

description: 3' single nucleus RNA-seq (10x Genomics)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.7.0.0
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Sciatic nerve

extract_protocol:
From each mouse, both snap frozen femoral sciatic nerves were thawed in nuclei isolation media (NIM, 250 mM Sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl) with 25 mM DTT, 1X protease inhibitor (05056489001, Roche), 0.1% Triton X-100 and RNase inhibitor (N2515, Promega). Each pair of nerves was homogenized using a Kimble dounce tissue grinder (D8938, Merck) and the resulting suspension was filtered through a 30 μm CellTRics (Sysmex, MSA150914) into a LoBind Eppendorf tube (Eppendorf). Nuclei were pelleted (1000 x g, 10 min, 4oC) and washed with NIM + DTT + Protease inhibitor (05056489001, Roche) and RNase inhibitor (N2515, Promega). After the wash, nuclei were resuspended in sorting buffer (1 mM EDTA, 0.2 U/μL RNase inhibitor (N2515, Promega), 2% fatty acid-free BSA (A7030-100g, Sigma) in PBS). Finally, the nuclei were filtered again through a 30 μm CellTRics (Sysmex, MSA150914), and DRAQ7 (#7406, Cell Signalling) was added to the nuclei suspension for nuclei detection by flow cytomtery. 10,000-20,000 nuclei were sorted using a S3 Fluorescence-activated cell sorter (Bio-Rad).
Nuclei were resuspended and used for snRNA-seq library generation following the Single Cell 3’ Reagents Kits V3.1 User Guidelines (10x Genomics).

value: Sciatic nerve

tag: strain

value: ALL

value: WT

value: Old


title: Old1_replicate_3


title: mESC, EZH2-WT, CBX7 (ChIP), rep1

description: Library name: WT_CBX7_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: siNT-3

description: Library name: Sample3


title: siNT-2

description: Library name: Sample2


title: mESC, EZH2-Y728 mutant, SUZ12 (ChIP), rep1

description: Library name: Y728_SUZ12_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: siNT-1

description: Library name: Sample1


title: mESC, EZH2-A677T mutant, SUZ12 (ChIP), rep1

description: Library name: A677T_SUZ12_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: 16mo_replicate_2


title: J82, Control_1

value: 21%O2 (normoxia)


title: mESC, EZH2-K563E mutant, SUZ12 (ChIP)

description: Library name: K563E_SUZ12

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: SKOV3 cells, DHX36 RIP_IP3

city: Hefei

first: Yi

last: Liu

state: Anhui

address: 17th Lujiang Road

department: Department of Obstetrics and Gynecology

institute: The First Affiliated Hospital of USTC,Division of Life Sciences and Medicine,University of Science and Technology of China

description: peak

data_processing:
RNA-seq was conducted on an Illumina platform with 150-bp paired-end reads. Reads were aligned to GRCh38 using hisat2 (v2.2.1), and ENSG IDs were converted to gene symbols. Gene expression analysis was performed, with significance defined as a p-value < 0.05 and absolute log2FC ≥ 1. For RIP-seq analysis, sequencing reads were trimmed for adapters using fastp and then mapped to the human genome (hg38) using Bowtie2 with default parameters. To visualize sequencing reads across the genome, bam files were converted to bigWig files using bedtools and displayed in IGV. Peaks were then called using MACS2, and annotated using bedtools.
Assembly: hg38
Supplementary files format and content: Table files include counts value or peaks for each Sample.

growth_protocol: All fresh HGSOC tumor tissues were obtained at the operation time and post-surgery, the samples were the rapidly frozen in liquid nitrogen for storage. SKOV3 cell lines were cultured under standard conditions in the DMEM medium supplemented with 10% FBS (CLARK, FB25015) and 1% penicillin/streptomycin (Beyotime, C0222) at 37 °C under 5% CO2.

extract_protocol:
Total RNA was extracted from the exosomes using TRIzol reagent (Invitrogen) following the manufacturer's protocol. RNA concentration and quality were assessed with a Nanodrop spectrophotometer and confirmed by gel electrophoresis.The RNA from anti-DHX36 RIP was extracted with TRIzol reagent according to the protocol.
RNA-seq was conducted on an Illumina platform with 150-bp paired-end reads.For RIP-seq cDNA library preparation, purified RNAs were ligated to adapters, reverse transcribed, and PCR-amplified for approximately 25 cycles. The resulting libraries were then subjected to high-throughput sequencing using an Illumina Novoseq platform with a 150-nt run length.

treatment_protocol: For tumor-derived exosomes RNA-seq, the groups were diveded ased on patient platinum sensitivity and resistance groups (resistant: sensitive ratio of 3:4). For RNA-seq, CATED were overexpressed and compared to control cells. For RIP-seq, the SKOV3 WT cells were used.

value: ovarian cancer cells


title: 16mo_replicate_3


title: 16mo_replicate_1


title: UMUC3, 0.1% hypoxia_3

source_name: UMUC3, 0.1% hypoxia

value: 0.1%O2 (hypoxia)


title: UMUC3, 0.2% hypoxia_3

source_name: UMUC3, 0.2% hypoxia

value: 0.2%O2 (hypoxia)


title: J82, 1% hypoxia_1

value: 1%O2 (hypoxia)


title: SKOV3 cells, DHX36 RIP_IP2

description: peak


title: mESC, EZH2-K634E mutant, SUZ12 (ChIP)

description: Library name: K634E_SUZ12

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: Young_replicate_3

value: Young


title: mESC, EZH2-heterozygote, CBX7 (ChIP)

description: Library name: het_CBX7

value: Ezh2 heterozygous knockout mESCs


title: SKOV3 cells, DHX36 RIP_IP1

description: peak


title: UMUC3, 1% hypoxia_3

source_name: UMUC3, 1% hypoxia


title: Old1_replicate_1

value: Sciatic nerve


title: mESC, EZH2-R679C mutant, SUZ12 (ChIP)

description: Library name: R679C_SUZ12

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: UMUC3, 0.1% hypoxia_2


title: Young_replicate_2

value: ALL

value: WT


title: SKOV3 cells, DHX36 RIP_input3

description: peak


title: Young_replicate_1


title: mESC, EZH2-WT, SUZ12 (ChIP), rep1

description: Library name: WT_SUZ12_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: UMUC3, 0.2% hypoxia_2


title: SKOV3 cells, DHX36 RIP_input2

description: peak


title: UMUC3, Control_3

source_name: UMUC3, Control


title: mESC, EZH2-heterozygote, SUZ12 (ChIP)

description: Library name: het_SUZ12


title: scRNAseqofimmunecells from day 7 of cGN

city: Bonn

first: Junping

last: Yin

state: State

address: Venusberg-Campus, 1

institute: uniklinikum bonn

data_processing:
fastq files were analyzed using Cellranger
count matrix data was analyzed using Seurat
Assembly: mm10
Supplementary files format and content: txt
Supplementary files format and content: csv

extract_protocol:
kidneys were digested using enzyme and further homogenized by using gentelMACS. CD45+ cells and CD3+ T cells were sorted for library preparation.
10x gene expression profiling

value: immune cell

value: wt

value: cGN


title: UMUC3, 1% hypoxia_2


title: UMUC3, Control_2

value: 21%O2 (normoxia)


title: scRNAseqofimmunecells from day 14 of cGN


title: SKOV3 cells, CATED overexpressing2

value: ovarian cancer cells

value: CATED overexpression


title: mESC, EZH2-A677T mutant, H3K27me3 (ChIP), rep1

description: Library name: A677T_H3K27me3_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: scRNAseqofimmunecells from day 3 of cGN


title: mESC, EZH2-K563E mutant, H3K27me3 (ChIP)

description: Library name: K563E_H3K27me3

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: SKOV3 cells, CATED overexpressing1


title: scRNAseqofimmunecells from day 0 (healthy)

value: untouched


title: mESC, EZH2-Y728 mutant, H3K27me3 (ChIP), rep1

description: Library name: Y728_H3K27me3_rep1

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: UMUC3, 0.1% hypoxia_1

value: 0.1%O2 (hypoxia)


title: SKOV3 cells, Control2

value: CATED control


title: UMUC3, 0.2% hypoxia_1

value: 0.2%O2 (hypoxia)


title: mESC, EZH2-K634E mutant, H3K27me3 (ChIP)

description: Library name: K634E_H3K27me3

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: SKOV3 cells, Control1


title: G_5HT6R_KD_M5

city: Xi'an

first: Junlin

address: No. 76 Yanta West Road

institute: Xian Jiaotong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts  for each Sample

source_name: mPFC

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Male

value: mPFC

tag: time

value: CPP extinction 2 weeks


title: mESC, EZH2-R679C mutant, H3K27me3 (ChIP)

description: Library name: R679C_H3K27me3

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: UMUC3, Control_1


title: G_5HT6R_KD_M3


title: SKOV3 cells, DHX36 RIP_input1

description: peak

value: WT


title: G_5HT6R_KD_M2


title: mESC, EZH2-WT, H3K27me3 (ChIP), rep1

description: Library name: WT_H3K27me3_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: mESC, EZH2-heterozygote, H3K27me3 (ChIP)

description: Library name: het_H3K27me3

value: Ezh2 heterozygous knockout mESCs


title: Ovarian cancer/tumor/R2

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer

value: platinum resistant


title: T24, 0.2% hypoxia_3

source_name: T24, 0.2% hypoxia


title: Ovarian cancer/tumor/R1


title: G_5HT6R_KD_M1


title: T24, 0.1% hypoxia_3

source_name: T24, 0.1% hypoxia


title: Scramble_M5

value: AAV-Scramble-Morphine


title: Ovarian cancer/tumor/S4

value: platinum sensitive


title: T24, 1% hypoxia_3

source_name: T24, 1% hypoxia

value: 1%O2 (hypoxia)


title: T24, Control_3

source_name: T24, Control

value: 21%O2 (normoxia)


title: Scramble_M4


title: T24, 0.1% hypoxia_2

value: 0.1%O2 (hypoxia)


title: Ovarian cancer/tumor/R3


title: Ovarian cancer/tumor/S2


title: mESC, EZH2-K634E mutant, H3K27ac (ChIP)

description: Library name: K634E_H3K27ac

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells


title: Scramble_M3


title: Scramble_M1


title: mESC, EZH2-R679C mutant, H3K27ac (ChIP)

description: Library name: R679C_H3K27ac


title: mESC, EZH2-K563E mutant, H3K27ac (ChIP)

description: Library name: K563E_H3K27ac

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: Ovarian cancer/tumor/S1


title: Scramble_S4

value: AAV-Scramble-Saline


title: mESC, EZH2-Y728 mutant, H3K27ac (ChIP), rep1

description: Library name: Y728_H3K27ac_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: T24, 0.2% hypoxia_2

value: 0.2%O2 (hypoxia)


title: T24, 1% hypoxia_2


title: Scramble_S5

value: Male

value: mPFC

value: CPP extinction 2 weeks


title: HSKMC_Human_skeletal_muscle_cell

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

institute: Chonnam Univ. Med. Sch.

data_processing:
The library was sequenced using HiSeq 2500 (Illumina), and FastQC was used for the initial quality check of the sequencing results. The reads with low quality were removed with Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). The expression counts were calculated using the STAR aligner with DCC algorithm followed by normalization by the total counts of circRNAs in each sample. We selected circRNAs with a mean read count of at least 1 across all samples.
Assembly: hg19
Supplementary files format and content: Microsoft Excel Worksheet file that includes normalized counts of sequencing reads.

source_name: Muscle

extract_protocol:
Tota RNA was extracted using Trizol. Ribosomal RNAs were removed from total RNA with Ribo-Zero Gold rRNA Removal Kit (Illumina).
TruSeq Stranded Total RNA Kit (Illumina) was used to construct an RNA-seq library.

value: Muscle

value: Primary

value: Myocyte

value: WT


title: HSKMM_Human_skeletal_muscle_myoblast

value: Myoblast


title: Scramble_S3


title: T24, Control_2


title: T24, 0.1% hypoxia_1


title: HSKMSC_Human_skeletal_muscle_satellite_cells

value: Satelite


title: UMUC3, 1% hypoxia_1

value: 1%O2 (hypoxia)


title: mESC, EZH2-Y728 mutant, H3K27me2 (ChIP), rep1

description: Library name: Y728_H3K27me2_rep1


title: Scramble_S2


title: Ovarian cancer/tumor/S3

value: high-grade serous ovarian cancer

value: platinum sensitive


title: SNU-2670HR / biol rep 3

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

description: SNU-2670HR cell lines were derived from parental SNU-2670 cells by maintaining them in medium with 20 or 50 μg/mL trastuzumab for about one year.

data_processing:
The raw reads were trimmed using Trimmomatic 0.38 and aligned to the Homo sapiens reference genome (GRCh38) using HISAT v2.1.0.
StringTie v2.1.3b was used to assemble the mapped reads into transcripts and calculate read counts per gene.
DESeq2 was used to identify differentially expressed genes (DEGs) with a | fold change | ≥ 2 and raw p < 0.05. Hierarchical clustering analysis was performed using complete linkage and Euclidean distance as similarity measures.
Functional and pathway analyses were performed using gProfiler software.
Assembly: GRCh38
Supplementary files format and content: Excel file (xlsx) containing count (FPKM, TPM) and normalized expression values, along with DEGs and their respective fold-changes between biological groups.

source_name: Gallbladder

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 µg/ml gentamycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol, and RNA integrity was calculated using the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA samples (RIN greater than 7.0) were used for RNA library construction. RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, lnc., San Diego, CA, USA, #RS-122-2101).
Only high-quality RNA samples (RIN greater than 7.0) were used for RNA library construction. RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, lnc., San Diego, CA, USA, #RS-122-2101). The libraries were quantified using KAPA Library Quantification kits and qualified using a TapeStation D1000 ScreenTape (Agilent Technologies, #5067-5582) before sequencing on an Illumina NovaSeq platform.

treatment_protocol: No treatment

value: Gallbladder

value: Biliary tract cancer

value: x


title: mESC, EZH2-A677T mutant, H3K27me2 (ChIP), rep1

description: Library name: A677T_H3K27me2_rep1

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: B16F10-luc2_Mitf_Tfeb_Tfe3_tKO_R3

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

data_processing:
Basecalling, demultiplexing were carried out by the Wellcome Trust Genomic Service, Oxford
Raw fastq reads for each samples were stitched using UNIX, quality controlled using fastqc (v0.11.9)
adaptor-, poly-A-, and 2 colour-trimmed as paired-end reads using trim_galore (v0.6.5; running python-base v.3.6.10, cutadapt v.2.10, java v.17.0.1, fastqc v.0.11.9, and pigz v.2.4)
Trimmed reads were mapped to the Mus_musculus reference genome (mm39) with STAR (version 2.7.8a)
Normalisation and differential gene expression analyses were performed as previously described (PMID: 31207090, 31733993, 31595650) using edgeR glmQLFTest.
Assembly: mm39
Supplementary files format and content: .txt (normalised gene expression)

growth_protocol: All cell lines were maintained in DMEM with 10% FBS in humidified incubator with 10% CO2

extract_protocol:
Total RNA samplewere prepared using RNeasy Mini Kit (QIAGEN #74106)  according to manufacturer protocol
500ng Total RNA was used to generate sequencing library using QuantSeq Forward kit (LEXOGEN #0.15.96) according to the supplier protocol
3' end RNA-seq

value: melanoma

value: Mitf, Tfeb and Tfe3 KO


title: RMC_EXOs

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description:
Library name: Sample 1
Exosomes were isolated from ASCs culture supernatant using a gradient ultracentrifugation approach. Specifically, ASCs were cultured in the complete medium until 60-70% confluence, then switched to StemPro™ MSC SFM supplemented with 1% antibiotics and cultured for 40 hours until 90% confluence. The collected culture supernatant underwent sequential centrifugation at 4°C: 300×g for 15 minutes to remove cells, 2000×g for 30 minutes to eliminate cell debris, and 10000×g for 30 minutes to remove additional impurities. The filtered supernatant (0.22 μm) was then ultracentrifuged at 120,000×g for 2 hours to pellet exosomes using an Optima XPN-100 ultracentrifuge (Beckman Coulter, USA). Isolated ASC-Exos were resuspended in sterile, RNase-free PBS and stored at -80°C for subsequent analyses.

data_processing:
CASAVA  bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 6000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Assembly: reference sequence database was the bovine genome database
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Cervus nippon

source_name: ASCs

growth_protocol: Exosomes were isolated from ASCs culture supernatant before and after induction of chondrogenic differentiation using a gradient ultracentrifugation approach. For ASC-Exos: specifically, ASCs were cultured in the complete medium until 60-70% confluence, then switched to StemPro™ MSC SFM supplemented with 1% antibiotics and cultured for 40 hours until 90% confluence. The collected culture supernatant underwent sequential centrifugation. For Chr-ASC-Exos: ASCs were digested, counted, and treated with a pre-mixed induction solution (2.5×10-4M ascorbic acid, 1×10-7M dexamethasone). After centrifugation, cells were resuspended in the chondrogenic induction medium (10 ng/mL TGF-β1), centrifuged to form cell pellets, and incubated with periodic media changes starting from day 3. On the 7th day, the collected culture supernatant underwent sequential centrifugation at 4°C. 300×g for 15 minutes to remove cells, 2000×g for 30 minutes to eliminate cell debris, and 10000×g for 30 minutes to remove additional impurities. The filtered supernatant (0.22 μm) was then ultracentrifuged at 120,000×g for 2 hours to pellet exosomes using an Optima XPN-100 ultracentrifuge (Beckman Coulter, USA). Isolated ASC-Exos were resuspended in sterile, RNase-free PBS and stored at -80°C for subsequent analyses.

extract_protocol:
The total RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA samples were used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The supernatant was subjected to gradient centrifugation to harvest exosomes. Briefly, the process involved centrifugation at 4°C for 15 minutes at 300×g, followed by 30 minutes at 2000×g, then 30 minutes at 10000×g, and finally 2 hours at 120000×g.

value: antler

value: antler mesenchymal stem cell

value: ASC-Exos were collected from the supernatant of ASCs

tag: batch


title: mESC, EZH2-WT, H3K27ac (ChIP), rep1

description: Library name: WT_H3K27ac_rep1

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: mESC, EZH2-A677T mutant, H3K27ac (ChIP), rep1

description: Library name: A677T_H3K27ac_rep1


title: Chr_RMC_EXOs

description:
Library name: Sample 2
Exosomes were isolated from ASCs culture supernatant induction of chondrogenic differentiation using a gradient ultracentrifugation approach. Specifically, ASCs were cultured in the complete medium until 60-70% confluence, then switched to StemPro™ MSC SFM supplemented with 1% antibiotics and cultured for 40 hours until 90% confluence. ASCs were digested, counted, and treated with a pre-mixed induction solution (2.5×10-4M ascorbic acid, 1×10-7M dexamethasone). After centrifugation, cells were resuspended in the chondrogenic induction medium (10 ng/mL TGF-β1), centrifuged to form cell pellets, and incubated with periodic media changes starting from day 3. On the 7th day, the collected culture supernatant underwent sequential centrifugation at 4°C: 300×g for 15 minutes to remove cells, 2000×g for 30 minutes to eliminate cell debris, and 10000×g for 30 minutes to remove additional impurities. The filtered supernatant (0.22 μm) was then ultracentrifuged at 120,000×g for 2 hours to pellet exosomes using an Optima XPN-100 ultracentrifuge (Beckman Coulter, USA). Isolated ASC-Exos were resuspended in sterile, RNase-free PBS and stored at -80°C for subsequent analyses.

value: WT

value: Chr-ASC-Exos were collected from the supernatant of ASCs induced chondrogenic differentiation


title: B16F10-luc2_Mitf_Tfeb_Tfe3_tKO_R2


title: T24, 0.2% hypoxia_1

value: 0.2%O2 (hypoxia)


title: mESC, EZH2-heterozygote, H3K27ac (ChIP)

description: Library name: het_H3K27ac

value: Ezh2 heterozygous knockout mESCs


title: mESC, EZH2-K563E mutant, H3K27me2 (ChIP)

description: Library name: K563E_H3K27me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K563E mutant


title: mESC, EZH2-K634E mutant, H3K27me2 (ChIP)

description: Library name: K634E_H3K27me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-K634E mutant


title: T24, 1% hypoxia_1

value: 1%O2 (hypoxia)


title: B16F10-luc2_Mitf_Tfeb_Tfe3_tKO_R1


title: mESC, EZH2-R679C mutant, H3K27me2 (ChIP)

description: Library name: R679C_H3K27me2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-R679C mutant


title: SNU-2670 / biol rep 3

value: Gallbladder

value: Biliary tract cancer

value: x


title: B16F10-luc2_Tfeb_Tfe3_dKO_R3

value: melanoma

value: Tfeb and Tfe3 KO


title: Mock_3

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

description:
Library name: sample8
M3

data_processing:
After sequencing, perl script was used to filter the original data (Raw Data) to clean reads by removing contaminated reads for adapters and low-quality reads.
Clean reads were aligned to the Mus musculus genome using Hisat2. The number of reads mapped to each gene in each sample was counted by HTSeq and TPM was then calculated  to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited CSV files include TPM values for each sample

source_name: brain

extract_protocol:
Total RNA from brains were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)  and DNase I (NEB, USA) treated, respectively.
Sequencing libraries were generated using FCL PE150 V3.0 RNA Library Prep Kit for DNBSEQ T7RS following the manufacturer’s recommendations

value: brain

value: Mock


title: SNU-2670 / biol rep 2


title: mESC, EZH2-WT, H3K27me2 (ChIP), rep1

city: Dublin

first: Adrian

address: The Smurfit Institute, The University of Dublin Trinity College, College Green

institute: Trinity College Dublin

description: Library name: WT_H3K27me2_rep1

data_processing:
Chromosome names for the human genome were modified with the prefix hg38_ and a metagenome was created by concatenating the mouse and human reference genomes (mm10 and hg38, respectively) before indexing with Bowtie 2 version 2.3.5. Reads were aligned to the metagenome using Bowtie 2 with default parameters, with the exception of –no-unal.
Non-unique read alignments were filtered out using SAMtools version 1.10 to exclude those with an alignment quality of <2, and the hg38_  prefix appended to chromosome names was used to separate reads as aligned to the reference mouse or spike-in human genomes.
Spike-in normalization factors were calculated for each ChIP using the formula for normalized reference-adjusted reads per million (RRPM); 1 per million spike-in reads.
BigWig files were generated using the bamCoverage tool from the deepTools suite version 3.5.0 with a bin size of 10 and scaled using the RRPM normalization factor derived for each sample.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Enriched DNA fragments were Rnase (Thermo Fisher) and Proteinase K (Sigma) treated prior to purification using Qiagen MinElute PCR Purification Kit (Qiagen; 28006).
ChIP-purified DNA was quantified by fluorimetry using the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher), and 0.5–50 ng of DNA/ChIP was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (NEB E7645) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2; NEB E7335 and E7500). Library DNA was quantified using the Qubit, and size distributions were ascertained on a TapeStation (Agilent) using the D1000 ScreenTape assay reagents (Agilent; 5067- 5583).

value: Mouse embryonic stem cells


title: B16F10-luc2_Tfeb_Tfe3_dKO_R2


title: Mock_1

description:
Library name: sample7
M1


title: mESC, EZH2-heterozygote, H3K27me2 (ChIP)

description: Library name: het_H3K27me2


title: B16F10-luc2_Tfeb_Tfe3_dKO_R1


title: MBD2_6

description:
Library name: sample6
C6

value: MBD2 infected


title: T24, Control_1

city: Bangor

first: Tim

address: Dean Street Bangor LL57 1UT

institute: Bangor University

data_processing: Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RMA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

extract_protocol:
Cells lysed using lysis buffer (in hypoxia if hypoxic samples)
Samples RNA extracted using Qiagen RNA extraction kits

value: 21%O2 (normoxia)


title: NK cells, healthy donor AG25, PD-1 positive

city: Genoa

first: Matteo

last: Bozzo

address: Viale Benedetto XV, 5

department: Department of Earth, Environmental and Life Sciences

country: Italy

institute: University of Genoa

data_processing:
Sequence reads were trimmed for adaptor sequences/low-quality sequences using Trimmomatic 0.38
Trimmed sequences were mapped to the hg38 human genome with HISAT2 version 2.1.0
Stringtie version 2.1.3b was used for transcript assembly. Expression profile was calculated for each sample and gene as read count, FPKM and TPM
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts, FPKM and TPM values for each sample

source_name: NK cells

extract_protocol:
RNA was extracted using the miRNeasy Micro kit (Qiagen). 10 ng of total RNA was used to contruct the sequencing libraries.
mRNA libraries for RNA-seq were prepared using the Watchmaker RNA Library Prep Kit following the manufacturer's protocol.

value: NK cells

tag: cell subset

value: male

tag: disease state

value: healthy donor


title: Genistein treated MEF rep2

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library name: Genistein24h2

data_processing:
Unprocessed reads were first quality and adapter trimmed using cutadapt55 version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR56 version 2.5.2b, with settings as recommended by TEtranscripts57. Both repeats and genes were then quantified using TEtranscripts version 2.0.3
Assembly: mm10
Supplementary files format and content: counts.tsv

source_name: MEF

growth_protocol: Cells were maintained in high glucose DMEM containing 10% FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 5-10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.

treatment_protocol: MEF cells were treated with 50uM genistein for 24hours.

value: MEF

value: mouse embryonic fibroblast

value: Genistein treated

value: Genistein


title: B16F10-luc2_Mitf_Tfeb_dKO_R3

value: Mitf and Tfeb KO


title: B16F10-luc2_Mitf_Tfeb_dKO_R2


title: SNU-2670HR / biol rep 1

value: Gallbladder

value: Biliary tract cancer

value: WT


title: MBD2_2

description:
Library name: sample5
C2


title: Genistein treated MEF rep1

description: Library name: Genistein24h1


title: NK cells, healthy donor AG25, PD-1 negative


title: MBD2_1

description:
Library name: sample4
C1


title: Mock_5

description:
Library name: sample9
M5


title: wild-type, control MEF rep2

description: Library name: Control2

value: wild-type

value: untreated


title: wild-type, control MEF rep1

description: Library name: Control1


title: 1035_JAK1_low

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

description: FFPE spatial transcriptome sequencing

data_processing:
The Visium sequencing data were processed by Space Ranger.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: ovarian cancer

extract_protocol:
FFPE tissues of HGSOC (5μm) was mounted into each capture area of Visium CytAssist for FFPE (6.5mm × 6.5mm).
Library construction was performed according to the standard Visium for the FFPE workflow.

tag: individual

value: ovarian cancer

tag: neoajuvant chemotherapy

value: No

tag: surgical outcome

value: Suboptimal

tag: 1st tfip


title: WT_3

description:
Library name: sample3
A3

tag: tissue

value: brain

value: WT infected


title: WT_1

description:
Library name: sample1
A1


title: B16F10-luc2_Mitf_Tfe3_dKO_R2

value: melanoma

value: Mitf and Tfe3 KO


title: B16F10-luc2_Mitf_Tfe3_dKO_R3


title: 9229_JAK1_high

description: FFPE spatial transcriptome sequencing

tag: age

tag: Stage

value: Yes

value: PR

value: Optimal


title: WT_2

description:
Library name: sample2
A2


title: B16F10-luc2_Mitf_Tfe3_dKO_R1

tag: cell type

tag: genotype


title: NK cells, High-Grade Serous Ovarian Carcinoma patient PIO3, PD-1 positive

value: NK cells

tag: Sex

value: female

value: High-Grade Serous Ovarian Carcinoma


title: B16F10-luc2_Tfeb_sKO_R3

tag: cell line

value: Tfeb-KO


title: DSS-induced colitis mouse with treatment of A. caccae and B. bifidum 2

city: Chuncheon

first: Seongwon

last: Pak

address: 12-1, Bonguisan-gil 22beon-gil, Chuncheon-si, Gangwon-do, Republic of Korea

department: Biomedical science

institute: Hallym university

description: Library name: DSS_AcBb-2

data_processing:
Reads with Low quality and adapters were trimmed using Trimmomatic0.38.
Paired-end reads were equally controlled by Q30.
The percentages of Q30 bases were higher than 95%.
Trimmed reads were mapped to Mus Musculus mm10 reference genome by HISAT2 and assembled using StringTie.
Assembly: mm10
Supplementary files format and content: xlsx file of Read counts, FPKM, and TPM value for each sample

source_name: Epithelial cells of colonic tissue

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Six-week-old male mice were given amoxicillin-containing drinking water (1 g/L, MP Biomedicals) for six days, followed by normal water. Subsequently, the mice were given 5 x 108 CFU of both A. caccae and B. bifidum bacteria via intragastric gavage twice, on alternate days, after two days at the time of switching to normal water. Colitis was induced by providing the mice with drinking water containing 2.5% dextran sodium sulfate (DSS) for seven days. Colonic epithelial cells (CD45-negative and EpCAM-positive cells) were isolated using magnetic beads(Miltenyi biotec) on day 9 after DSS consumption.

value: Epithelial cells of colonic tissue

value: epithelial cells

value: Wt (C57BL6/J)

tag: treatment

value: A.caccae & B. bifidum and DSS


title: SNU-2670 / biol rep 1

value: Gallbladder

value: Biliary tract cancer

value: WT

value: x


title: NK cells, High-Grade Serous Ovarian Carcinoma patient PIO3, PD-1 negative


title: B16F10-luc2_Mitf_Tfeb_dKO_R1

value: melanoma

value: Mitf and Tfeb KO


title: DSS-induced colitis mouse with treatment of A. caccae and B. bifidum 1

description: Library name: DSS_AcBb-1


title: 5836_JAK1_low

description: FFPE spatial transcriptome sequencing

value: ovarian cancer

value: No

value: Complete


title: B16F10-luc2_Tfeb_sKO_R1


title: NK cells, healthy donor AH112, PD-1 positive

value: NK cells

value: healthy donor


title: B16F10-luc2_Tfeb_sKO_R2


title: NK cells, healthy donor AH112, PD-1 negative

value: female


title: DSS-induced colitis mouse 3

description: Library name: DSS-3

value: DSS


title: B16F10-luc2_Tfe3_sKO_R3


title: CRD vs 16T

type: genomic

city: Daejeon

first: Tae Jeong

address: 44-6 10-ro Yuseong-gu

institute: Genomictree, Inc.

description: methylation profiling in 16T sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CRD

label_protocol: The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
preparation protocol: Fresh-frozen tumors and paired tumor-adjacent non-tumor tissues of prostate cancer patients
Genomic DNA extracted using QIAamp DNA Mini Kit according to manufacturer's instructions
enrichment protocol: 0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.

value: pooled DNA of 13 adjacent normal samples

tag: sample type

value: common reference DNA

value: enriched methylated DNA of tumor tissue

tag: subject status

value: prostate cancer patient

value: male

value: IV


title: DSS-induced colitis mouse 2

description: Library name: DSS-2

value: Epithelial cells of colonic tissue

value: epithelial cells

value: Wt (C57BL6/J)


title: 7132_JAK1_high

description: FFPE spatial transcriptome sequencing

value: Yes

value: PR

value: Optimal


title: NK cells, healthy donor AH77, PD-1 positive


title: CRD vs 15T

description: methylation profiling in 15T sample

value: III


title: DSS-induced colitis mouse with treatment of A. caccae and B. bifidum 3

description: Library name: DSS_AcBb-3

value: A.caccae & B. bifidum and DSS


title: DSS-induced colitis mouse 1

description: Library name: DSS-1


title: B16F10-luc2_Tfe3_sKO_R2

value: melanoma


title: B16F10-luc2_Tfe3_sKO_R1


title: NK cells, healthy donor AH77, PD-1 negative

value: NK cells

value: female

value: healthy donor


title: Healthy mouse 2

description: Library name: Healthy-2

value: No DSS


title: Healthy mouse 3

description: Library name: Healthy-3


title: CON7

city: xuzhou

first: tianya

last: liu

address: 99 Huaihai West Road,xuzhou,jiangsu province

institute: Affiliated Hospital of Xuzhou Medical University

description: NC 7

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
Reference genome and gene model annotation files were downloaded from genome website directly.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each samples

source_name: Lung

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lung

value: Human lung cells

value: WT

tag: disease

value: control


title: Healthy mouse 1

description: Library name: Healthy-1

value: Epithelial cells of colonic tissue


title: B16F10-luc2_Mitf_sKO_R3

value: Mitf-KO


title: CON8

description: NC 8


title: CRD vs 15NT

description: methylation profiling in 15NT sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male


title: B16F10-luc2_Mitf_sKO_R1


title: CRD vs 14T

description: methylation profiling in 14T sample

value: enriched methylated DNA of tumor tissue

value: III


title: B16F10-luc2_Mitf_sKO_R2

value: melanoma


title: CON6

description: NC 6


title: F_F_3

city: Hangzhou

first: Mengjie

address: Institute of Immunology and Bone Marrow Transplantation Center, The First 6 Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, 7 China.

institute: Zhejiang University

description: Library name: F_F_3

data_processing:
recommendations and index codes were added to attribute sequences to each sample.
Assembly: genome-version GRCm38
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.

source_name: Liver

extract_protocol:
The total RNA of liver tissues was isolated by using TRIzol reagent according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s

value: Liver

value: RKIPf/f

value: HFD


title: CON5

description: NC 5

value: Lung


title: CRD vs 13NT

description: methylation profiling in 13NT sample


title: B16F10-luc2_R3


title: CRD vs 13T

description: methylation profiling in 13T sample


title: B16F10-luc2_R2


title: F_F_1

description: Library name: F_F_1


title: CON3

description: NC 3

value: Human lung cells


title: B16F10-luc2_R1

value: WT


title: CON4

description: NC 4

value: control


title: Cre2

description: Library name: Cre2

value: Albcre-RKIPf/f


title: CRD vs 11NT

description: methylation profiling in 11NT sample


title: NK cells, FUS2

city: Xi’an

first: Wei

last: Dong

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi’an Jiaotong University

data_processing:
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. Differential expression analysis was performed using the DESeq2. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

source_name: Spleen

growth_protocol: NK cells (CD45+ CD3- NK1.1+) were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system (MoFlo Astrios EQ, Beckman Coulter, lnc, USA), and subjected to RNA-seq immediately.

extract_protocol:
RNA was extracted using TRIzol, and  RNA integrity was detected by Agilent 2100 Bioanalyzer.
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep following manufacture's protocols.

value: Spleen

value: NK1.1 cells

value: NK cells_FUS

value: FUS stimulation


title: CON1

description: NC 1


title: Cre1

description: Library name: Cre1


title: PAH8

description: LUN 8

value: PAH


title: CRD vs 12NT

description: methylation profiling in 12NT sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male


title: CRD vs 16NT

description: methylation profiling in 16NT sample

value: IV


title: F_F_2

description: Library name: F_F_2

value: Liver

value: RKIPf/f

value: HFD


title: CRD vs 12T

description: methylation profiling in 12T sample

value: enriched methylated DNA of tumor tissue

value: III


title: CRD vs 11T

description: methylation profiling in 11T sample


title: CON2

description: NC 2

value: Lung

value: Human lung cells

value: WT

value: control


title: Cre3

description: Library name: Cre3

value: Albcre-RKIPf/f


title: PAH7

description: LUN 7

value: PAH


title: stage 7 Otx1 overexpression repeat 2

city: ShenZhen

first: Luming

last: Zhang

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

institute: Southern University of Science and Technology

description:
Library name: Sample 76
Otx1-OE-RNA_featureCounts.txt

data_processing:
RNA-seq reads adaptors were trimmed by fastp with parameters -a AGATCGGAAGAGC --detect_adapter_for_pe -w 12 --length_required 30 -q 20.
Reads were mapped to the genome by STAR ver 2.7.0e.
Counts for known genes were obtained by featureCounts ver2.0.1 with parameters -s 2 -p -BC.
bigwig files were generated using deepTools bamCoverage with the following configurations --normalizeUsing RPKM -bs 5
Assembly: xenopus tropicalis v10.0
Supplementary files format and content: Counts matrix contain counts for known genes
Supplementary files format and content: bigwig files were used for visualization using the Integrative Genome Viewer ver 2.16.0

organism: Xenopus tropicalis

source_name: Embryos

extract_protocol:
Total RNA was isolated using RNA Isolator Total RNA Extraction Reagent (Vazyme) followed by isopropanol precipitation according to standard protocols.
Libraries were prepared using standard protocol provided by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme).

value: Embryos

tag: developmental stage

value: Stage 7

value: Otx1 overexpression

value: Otx1 mRNA injection


title: CRD vs 14NT

description: methylation profiling in 14NT sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male


title: CRD vs 10T

description: methylation profiling in 10T sample

value: enriched methylated DNA of tumor tissue


title: NK cells, FUS1

value: Spleen

value: NK1.1 cells

value: NK cells_FUS

value: FUS stimulation


title: SNU-2670HR / biol rep 2

value: Gallbladder

value: Biliary tract cancer

value: WT

value: x


title: stage 7 Otx1 overexpression repeat 1

description:
Library name: Sample 75
Otx1-OE-RNA_featureCounts.txt

value: Embryos

value: Stage 7


title: PAH6

description: LUN 6

value: Lung

value: Human lung cells

value: PAH


title: PAH5

description: LUN 5


title: stage 8 E2f1 overexpression repeat 2

description:
Library name: Sample 74
s8E2f1-OE-RNA_featureCounts.txt

value: Stage 8

value: E2f1 overexpression

value: E2f1 mRNA injection


title: NK cells, CONTROL2

value: NK cells_control

value: Control


title: NK cells, CONTROL3

value: Spleen

value: NK1.1 cells


title: CRD vs 9T

description: methylation profiling in 9T sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of tumor tissue

value: prostate cancer patient

value: male

value: III


title: stage 8 E2f1 overexpression repeat 1

description:
Library name: Sample 73
s8E2f1-OE-RNA_featureCounts.txt

value: Embryos


title: CRD vs 9NT

description: methylation profiling in 9NT sample

value: enriched methylated DNA of adjacent non-tumor tissue


title: CRD vs 5T

description: methylation profiling in 5T sample

value: II


title: NK cells, FUS3

value: NK cells_FUS

value: FUS stimulation


title: PAH4

description: LUN 4

value: Lung

value: Human lung cells

value: WT

value: PAH


title: CRD vs 8T

description: methylation profiling in 8T sample


title: stage8 cdknla rep2

value: Stage 8

value: Cdkn1a mRNA

value: Cdkn1a mRNA injected


title: stage8 cdknla rep1


title: CD8 T cells, fus1

growth_protocol: CD8 T  cells (CD45+ CD3+ CD8a+) were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system (MoFlo Astrios EQ, Beckman Coulter, lnc, USA), and subjected to RNA-seq immediately.

value: Spleen

value: CD8a+ T  cells

value: CD8a+ T  cells_fus

value: fus irradiation


title: stage8 wildtype rep2


title: PAH3

description: LUN 3


title: NK cells, CONTROL1

value: NK1.1 cells

value: NK cells_control

value: Control


title: CD8 T cells, fus2


title: stage8 wildtype rep1

value: Embryos


title: CD8 T cells, control3

value: CD8a+ T  cells_control

value: wt

value: control


title: PAH2

description: LUN 2

value: Lung

value: Human lung cells


title: 501_TFE3-HA_Torin_HA_R2

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Processed fastq files were mapped using STAR 2.7.8a {Dobin, 2013} against hg38 build
Mapped SAM-files were used for peak calling using the Homer 4.8 {Heinz, 2010}
Homer was used to generatedbigWig normalised to 1e7
Assembly: hg38
Supplementary files format and content: bigwig of normalised counts for uniqely aligned reads

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
Samples were prepared as described in PMID: 37770430 and 32531202. Briefly 30x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 120ug of the indicated antibodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column.
Libraries were prepared using recommended Illumina protocols
Libraries were constructed by the Oxford Genomics Centre using Takara DNA SMART ChIP-Seq Kit

treatment_protocol: 250nM Torin1, 6h

value: melanoma

value: 250nM Torin1, 6h


title: PAH1

description: LUN 1

value: WT

value: PAH


title: CD8 T cells, fus3

value: Spleen


title: CD8 T cells, control2

value: CD8a+ T  cells


title: CRD vs 8NT

description: methylation profiling in 8NT sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male

value: II


title: 501_TFE3-HA_Torin_HA_R1


title: stage8 E2f1_MO_cdknla rep2

value: Embryos

value: Stage 8

value: E21f MO+Cdkn1a mRNA

value: E2F1 MO and Cdkn1a mRNA injected


title: stage8 E2f1_MO_cdknla rep1


title: CD8 T cells, control1

value: CD8a+ T  cells_control

value: wt

value: control


title: 501_TFE3-HA_Torin_Input_R2

value: melanoma

value: 250nM Torin1, 6h


title: stage8 E2f1_MO rep2

value: E2f1 MO

value: E2F1 MO injected


title: 501_TFE3-HA_Torin_Input_R1


title: AGS cells, PI103+PD0325901, 4

city: Trondheim

first: Åsmund

last: Flobak

state: Norway

address: Prinsesse Kristinas gt 1, Gastrosenteret

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology - NTNU

description: Library name: af24

data_processing:
The final libraries were purified using the AMPure XP (Beckman Coulter, Inc., Indianapolis, IN, USA), quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., Wilmington, MA, USA), and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were quantified (KAPA Library Quantification Kit (Illumina/ABI Prism), normalized and pooled.
Quantitated libraries were further diluted to 2.5 nM and subject to clustering by a cBot Cluster Generation System on four HiSeq2000 flow cells (Illumina Inc. San Diego, CA, USA), according to the manufacturer's instructions.
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts (HGNC, rows) per sample (sample_id, column)
Supplementary files format and content: all_samples_gene_counts.csv

source_name: stomach

growth_protocol: AGS (human gastric adenocarcinoma, ATCC, Rockville, MD) were grown in Ham’s F12 medium (Invitrogen, Carlsbad, CA) supplemented with 5% fetal calf serum (FCS; Euroclone, Devon, UK), and 10 U/ml penicillin-streptomycin (Invitrogen).

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). 0.8 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Ligation Kit following manufacturer’s protocols.

treatment_protocol: Inhibitors (5Z)-7-oxozeaenol (0.5 µM), PD0325901 (0.035 µM), and PI103 (0.7 µM) were added (single or in combination) to be incubated in AGS cells for 24 hours. Combinatorial treatments were administered using half their full concentration. All inhibitors were obtained from Merck.

value: stomach

value: AGS

value: WT

tag: batch


title: Mucosa0h, scRNAseq

city: ChangChun

first: Zhengwen

last: An

state: JiLin

address: HeGuang Road 763

department: Department of Oral Biology

institute: Jilin University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger (7.0.1). (https://www.10xgenomics.com)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Buccal mucosa

extract_protocol:
WT mice (n=5, 6~8 weeks) were anesthetized via intramuscular injection of a zolazepam and tiletamine mixture (30 mg/kg, Zoletil 50; Virbac, Carros, France) and xylazine (10 mg/kg, Xylazine Hydrochloride Injection; Bayer, Leverkusen, Germany). The wound was inflicted using a 1.5 mm punch biopsy (Miltex, York, Inc. PA, USA) in the buccal mucosa, with the same size wounds created in the facial skin of the same mouse. At 48h after injury, the oral mucosa and skin wounds were harvested by 3.0 mm punch biopsy. Tissues were minced and digested at 37°C with 0.25% trypsin-EDTA for 10 minutes, and continues to digest at 37°C with RPMI 1640 media containing DNase I (Roche), collagenase type I (Worthington), and dispase (Sigma-Aldrich) for 1 h. Clumps and debris were removed by filtering cells through 70-μm mesh.
The single cell suspension was quantified and loaded into the 10X Chromium system, targeting approximately10,000 cells for barcoding in preparation for scRNA-seq using a Single Cell 3′ Library Kit (10X Genomics). Cells were successfully barcoded and their transcriptomes were sequenced using the  Illumina Novaseq System (Illumina, San Diego, CA).

value: Buccal mucosa

value: Mucosa cell


title: AGS cells, (5Z)-7-oxozeaenol, 4

description: Library name: af22


title: Skin48h, scRNAseq

description: 10X Genomics

source_name: Facial skin

value: Facial skin

value: Skin cell


title: 501_TFE3-HA_CTRL_HA_R1

value: CTRL


title: stage8 E2f1_rescue rep1

value: Embryos

value: Stage 8

value: E2f1 MO+E2f1 mRNA

value: E2F1 MO and E2f1 mRNA injected


title: Skin0h, scRNAseq

description: 10X Genomics


title: Mucosa48h, scRNAseq

description: 10X Genomics


title: AGS cells, PI103, 4

description: Library name: af20


title: CRD vs 10NT

description: methylation profiling in 10NT sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male

value: III


title: CRD vs 3T

description: methylation profiling in 3T sample

value: enriched methylated DNA of tumor tissue

value: II


title: CRD vs 5NT

description: methylation profiling in 5NT sample


title: AGS cells, PI103+(5Z)-7-oxozeaenol, 4

description: Library name: af23

value: stomach

value: AGS

value: WT

value: PI103 + (5Z)-7-oxozeaenol


title: 501_TFE3-HA_CTRL_Input_R2

value: melanoma

value: CTRL


title: CD4, NRIP1 KO, wRA, replicate 3, scRNAseq

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: 10X Genomics

data_processing:
10X multiome data was processed using Cell Ranger ARC mkfastq (v2.0.1) from 10x Genomics via the cumulus workflow.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in h5 format

source_name: spleen

extract_protocol:
Mouse splenic naïve CD4+ T cells were purified using EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL). Cells were then stimulated by plates coated with 2μg/ml anti-mouse CD3e and 2μg/ml anti-mouse CD28 antibodies, with or without 100nM atRA supplement in full RPMI 1640 medium
Samples were prepared according to the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol and Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression User Guide.

value: spleen

value: NRIP1 KO

value: with atRA


title: 501_TFE3-HA_CTRL_Input_R1

first: Pakavarin

address: Old Road Campus Research Building (off Roosevelt Drive)

institute: Ludwig Institute for Cancer Research


title: CRD vs 1NT

description: methylation profiling in 1NT sample

value: pooled DNA of 13 adjacent normal samples


title: 501_TFE3-HA_CTRL_HA_R2


title: stage8 DBD rep2

value: Embryos

value: Stage 8

value: E2f1 MO+[delta]DBD mRNA

value: E2F1 MO and E2f1 [delta]DBD mutant mRNA injected


title: CD4, NRIP1 KO, wRA, replicate 2, scRNAseq

description: 10X Genomics


title: AGS cells, control, 4

description: Library name: af19


title: NK cells, High-Grade Serous Ovarian Carcinoma, PD-1 positive [PI015-PD1POS]

value: NK cells

tag: cell subset

value: female

tag: disease state

value: High-Grade Serous Ovarian Carcinoma


title: stage8 E2f1_MO rep1

value: E2f1 MO

value: E2F1 MO injected


title: AGS cells, PI103+PD0325901, 3

description: Library name: af18

value: stomach

value: AGS

value: WT


title: CD4, NRIP1 KO, wRA, replicate 1, scRNAseq

description: 10X Genomics


title: CRD vs 3NT

description: methylation profiling in 3NT sample

value: common reference DNA

value: enriched methylated DNA of adjacent non-tumor tissue

value: prostate cancer patient

value: male

value: II


title: CRD vs 2T

description: methylation profiling in 2T sample

value: pooled DNA of 13 adjacent normal samples

value: enriched methylated DNA of tumor tissue


title: AGS cells, PD0325901, 4

description: Library name: af21


title: NK cells, High-Grade Serous Ovarian Carcinoma, PD-1 negative [PI015-PD1NEG]


title: stage8 E2f1_rescue rep2

value: Embryos

value: Stage 8

value: E2f1 MO+E2f1 mRNA

value: E2F1 MO and E2f1 mRNA injected


title: CRD vs 2NT

description: methylation profiling in 2NT sample


title: stage7 cdknla rep1

value: Stage 7

value: Cdkn1a mRNA

value: Cdkn1a mRNA injected


title: AGS cells, PI103+(5Z)-7-oxozeaenol, 3

description: Library name: af17

value: stomach

value: PI103 + (5Z)-7-oxozeaenol


title: AGS cells, (5Z)-7-oxozeaenol, 3

description: Library name: af16

value: AGS

value: WT


title: CD4, NRIP1 WT, wRA, replicate 2, scRNAseq

description: 10X Genomics

value: spleen

value: NRIP1 WT

value: with atRA


title: NK cells, healthy donor, PD-1 positive [AH88-PD1POS]

value: NK cells

value: female

value: healthy donor


title: CD4, NRIP1 WT, wRA, replicate 3, scRNAseq

description: 10X Genomics


title: stage8 DBD rep1

value: Embryos

value: E2f1 MO+[delta]DBD mRNA

value: E2F1 MO and E2f1 [delta]DBD mutant mRNA injected


title: stage7 wildtype rep2


title: NK cells, healthy donor, PD-1 negative [AH88-PD1NEG]


title: stage7 wildtype rep1


title: AGS cells, PD0325901, 3

description: Library name: af15


title: CD4, NRIP1 WT, wRA, replicate 1, scRNAseq

description: 10X Genomics


title: CD4, NRIP1 KO, woRA, replicate 3, scRNAseq

description: 10X Genomics

value: NRIP1 KO

value: without atRA


title: AGS cells, control, 3

description: Library name: af13


title: shSTARD7-4_Rep3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v3.0 (https://nf-co.re/rnaseq/3.0/docs/usage) and using Gene set from Ensembl.org release 103.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

growth_protocol: DMEM high glucose + 10% Fetal Bovine Serum, 1% Penicillin/Streptomycin

extract_protocol:
Total RNAs were extracted from cultured cells using the column based extraction E.Z.N.A.® Total RNA Kit I (Omega Biotek)
RNA libraries were prepared using the Illumina mRNA stranded ligation Kit

value: Breast cancer

value: ERalpha positive

tag: condition


title: CD4, NRIP1 KO, woRA, replicate 2, scRNAseq

description: 10X Genomics


title: stage7 E2f1_MO_cdknla rep1

value: Stage 7

value: E21f MO+Cdkn1a mRNA

value: E2F1 MO and Cdkn1a mRNA injected


title: stage7 E2f1_MO_cdknla rep2


title: shSTARD7-4_Rep1


title: AGS cells, PI103+PD0325901, 2

description: Library name: af12

value: stomach

value: AGS

value: WT


title: AGS cells, PI103+(5Z)-7-oxozeaenol, 2

description: Library name: af11

value: PI103 + (5Z)-7-oxozeaenol


title: stage7 E2f1_MO rep2

value: E2f1 MO

value: E2F1 MO injected


title: CD4, NRIP1 KO, woRA, replicate 1, scRNAseq

description: 10X Genomics

value: spleen


title: shSTARD7-2_Rep3


title: CD4, NRIP1 WT, woRA, replicate 3, scRNAseq

description: 10X Genomics

value: NRIP1 WT


title: stage7 E2f1_MO rep1

value: Embryos


title: AGS cells, (5Z)-7-oxozeaenol, 2

description: Library name: af10


title: CD4, NRIP1 WT, woRA, replicate 2, scRNAseq

description: 10X Genomics


title: AGS cells, PD0325901, 2

description: Library name: af09


title: stage7 E2f1_rescue rep2

value: E2f1 MO+E2f1 mRNA

value: E2F1 MO and E2f1 mRNA injected


title: shCtrl_Rep3

value: shCtrl


title: CD4, NRIP1 WT, woRA, replicate 1, scRNAseq

description: 10X Genomics

value: without atRA


title: stage7 E2f1_rescue rep1


title: AGS cells, PI103, 2

description: Library name: af08


title: shSTARD7-2_Rep1

value: Breast cancer

value: ERalpha positive


title: CD4, NRIP1 KO, wRA, replicate 3, scATACseq

description: 10X Genomics

data_processing:
10X multiome data was processed using Cell Ranger ARC mkfastq (v2.0.1) from 10x Genomics via the cumulus workflow.
Peaks were called using MACS2 (v2.2.7.1) with default parameters
Assembly: mm10
Supplementary files format and content: Fragment files in tab-separated values format and tabix indexed files in tbi format
Supplementary files format and content: Called peaks in narrowPeak format

value: NRIP1 KO

value: with atRA


title: stage7 DBD rep2

value: Stage 7

value: E2f1 MO+[delta]DBD mRNA

value: E2F1 MO and E2f1 [delta]DBD mutant mRNA injected


title: shSTARD7-2_Rep2


title: AGS cells, PI103, 3

description: Library name: af14

value: stomach

value: AGS

value: WT


title: shSTARD7-4_Rep2


title: shCtrl_Rep2


title: AGS cells, control, 2

description: Library name: af07


title: CD4, NRIP1 KO, wRA, replicate 2, scATACseq

description: 10X Genomics

value: spleen


title: stage7 DBD rep1


title: shCtrl_Rep1


title: CRD vs 1T

description: methylation profiling in 1T sample

value: pooled DNA of 13 adjacent normal samples

value: common reference DNA

value: enriched methylated DNA of tumor tissue

value: prostate cancer patient

value: male

value: II


title: AGS cells, PI103+PD0325901, 1

description: Library name: af06


title: CD4, NRIP1 KO, wRA, replicate 1, scATACseq

description: 10X Genomics


title: stage6 wildtype rep2

value: Embryos

value: Stage 6


title: CD4, NRIP1 WT, wRA, replicate 3, scATACseq

description: 10X Genomics

value: NRIP1 WT


title: stage6 wildtype rep1


title: AGS cells, (5Z)-7-oxozeaenol, 1

description: Library name: af04


title: siLinear+5078 Poly N3

city: Kingston

first: Mark

middle: L.

last: Ormiston

state: Ontario

address: 18 Stuart Street

country: Canada

institute: Queen's University

data_processing:
Reads were trimmed and filtered for quality by Trimmomatic, and were aligned to the Human reference genome (GRCh38) using STAR. The abundance of each transcript was estimated using FeatureCounts.
Assembly: GrCH38
Supplementary files format and content: .csv file containing raw counts for each sample

source_name: HPAECs

growth_protocol: Primary HPAECs were maintained in EGM2 (containing 2% FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was isolated from sucrose using overnight ethanol precipitation, and pellets were subsequently subject to TRIzol/chloroform extraction.
mRNA stranded RNA

treatment_protocol: siRNA mediated knockdown of linear BMPR2 mRNAs, circ5078, both, or a control were performed on cells plated in 15cm dishes. The following day, cells were harvested, and lysates separated on 10-45% sucrose gradients. Input RNA was sequenced alongside RNA isolated from heavily translated fractions (8-13)

value: HPAECs

value: primary pulmonary artery endothelial cells

value: Polysome Fraction


title: AGS cells, PD0325901, 1

description: Library name: af03