title: Chd9KD_Rep1_RNAseq

description: Total RNA

value: Chd9 knockdown for 48 hours


title: Urine progenitor renal cells_dead donor 221

status: Public on May 08 2025

type: genomic

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description: Progenitor Renal Cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Minfi R package standard protocol
Processed data: Minfi preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: urine progenitor renal cells, dead donor

label_protocol: Standard Illumina labelling protocol

growth_protocol: Urinary renal progenitor cells (uRPC) and progenitor renal cells from nephrectomy (PEC) isolation was performed as previously described (Manonelles A et al, Front Physiol 2018 DOI:/10.3389/fphys.2018.01412; Lazzeri E et al. J Am Soc Nephrol 2015 doi: 10.1681/ASN.2014010057). Patients with sample contamination were also considered as screening failure. After cell isolation and expansion, samples with ≥80% CD133+CD24+ positivity by FACs analysis were suitable to study.

extract_protocol: Total DNA was isolated by standard procedures

tag: group

value: dead donor

tag: cell type

value: Urine progenitor renal cells


title: Chd9KD_Rep2_RNAseq

type: SRA

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

country: USA

institute: University of Pittsburgh

description: Total RNA

library_source: transcriptomic

data_processing:
Barcode adapter sequences removed using cutadapt and trimmed using trimmomatic.
Reads mapped to mm10 genome using STAR, with options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS.
Counts were generated using featureCounts, with options -B -t "exon" -g "gene_name" -F GTF -p -s 2 for Gencode mouse V23 features, with options -B -F SAF -p -s 2 for stranded features, and options -B -F SAF -p -s 0 for unstranded features.
In R/Bioconductor environment, raw count matrices were corrected for batch effects using Combat-seq and differential expression analysis was performed using DEseq2 for all replicates of each condition.
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Excel file containing all DEseq2 results for each condition for RNAseq.
Supplementary files format and content: Tab-delimited matrix of raw RNAseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited matrix of Combatseq corrected raw RNA-seq counts for each sample for all features.
Supplementary files format and content: Tab-delimited table containing information for Combatseq batch corrected for RNAseq data.

molecule: total RNA

organism: Mus musculus

growth_protocol: ES-E14TG2a (E14) embryonic stem cells from male Mus musculus origin were grown at 37°C and 5% CO2 in DMEM base medium (Sigma) supplemented with 10% FBS (Sigma, 18N103), 1X nonessential amino acids (Corning), 2mM L-glutamine (Corning), β-mercaptoethanol (Acros Organics), and LIF on 10-cm plates precoated with 0.2% gelatin. Cells were passaged every ~48 h using trypsin (Corning) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma TC hood cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened to confirm no mycoplasma presence.

extract_protocol:
48 h post transfection, media was aspirated from transfected plates and replaced with 10 mL of 500 nM 4-thio-uridine (4sU) containing ESC media and the plates incubated at 37°C with 5% CO2 for 5 min. After 5 min, the 4sU-containing media was aspirated and the cells were washed with PBS, trypsinized, and then pelleted by centrifugation. Total RNA was collected from cell pellets with a TRIzol extraction followed by an isopropanol/salt precipitation and resuspended in 100 µL 1XTE, according to ThermoFisher’s recommendations. 100 µg of total RNA was diluted to a concentration of 240 ng/µL at a volume of 416.67 µL in 1XTE and then fragmented with a Bioruptor Pico (Diagenode) on high power for one 30 second cycle. The fragmented RNA was then separated using thiol-specific biotinylation followed by streptavadin bead treated to isolate 4sU-labelled RNA from total RNA. 1 ug of total RNA and 100 ng nascent RNA from each sample were used to build RNA-seq and TT-seq libraries, respectively.
Total RNA was rRNA depleted using antisense oligos and purified. Total RNA-seq libraries were built using a strand-specific RNA-seq library build protocol.

treatment_protocol: After 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Cells were treated with 4sU and harvested 48 h post-transfection.

tag: cell line

value: embryonic stem cells

tag: genotype

value: wild-type

tag: treatment


title: Cro_con_E2C_Pol_2

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

library_source: genomic

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig file for each sample

source_name: embryo

extract_protocol:
A total of 100-200 early embryos were used in each ChIP-seq experiment
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

tag: tissue

value: embryo


title: Chd8KD_Rep1_RNAseq

description: Total RNA

value: Chd8 knockdown for 48 hours


title: Urine progenitor renal cells_alive donor 220

description: Progenitor Renal Cells

source_name: urine progenitor renal cells, alive donor

value: alive donor


title: Cro_con_E2C_Pol_1


title: Chd7KD_Rep2_RNAseq

description: Total RNA

value: Chd7 knockdown for 48 hours


title: Urine progenitor renal cells_alive donor 212

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 204

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 183

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 182

description: Progenitor Renal Cells


title: Chd5KD_Rep2_RNAseq

description: Total RNA

value: Chd5 knockdown for 48 hours


title: Chd5KD_Rep1_RNAseq

description: Total RNA


title: Urine progenitor renal cells_alive donor 175

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 156

description: Progenitor Renal Cells


title: Chd3KD_Rep2_RNAseq

description: Total RNA

value: Chd3 knockdown for 48 hours


title: Urine progenitor renal cells_dead donor 145

description: Progenitor Renal Cells


title: Chd3KD_Rep1_RNAseq

description: Total RNA


title: Urine progenitor renal cells_dead donor 141

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 138

description: Progenitor Renal Cells


title: Chd2KD_Rep2_RNAseq

description: Total RNA

value: Chd2 knockdown for 48 hours


title: Urine progenitor renal cells_dead donor 118

description: Progenitor Renal Cells


title: Chd2KD_Rep1_RNAseq

description: Total RNA


title: Chd1lKD_Rep1_RNAseq

description: Total RNA

value: Chd1l knockdown for 48 hours


title: Chd1KD_Rep2_RNAseq

description: Total RNA

value: Chd1 knockdown for 48 hours


title: Urine progenitor renal cells_dead donor 099

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 106

description: Progenitor Renal Cells


title: Btaf1KD_Rep2_RNAseq

description: Total RNA

value: Btaf1 knockdown for 48 hours


title: Chd1lKD_Rep2_RNAseq

description: Total RNA


title: Chd1KD_Rep1_RNAseq

description: Total RNA


title: Urine progenitor renal cells_alive donor 098

description: Progenitor Renal Cells


title: Urine progenitor renal cells_alive donor 179

description: Progenitor Renal Cells


title: Chd7KD_Rep1_RNAseq

description: Total RNA


title: Chd4KD_Rep2_RNAseq

description: Total RNA

value: Chd4 knockdown for 48 hours


title: Urine progenitor renal cells_dead donor 083

description: Progenitor Renal Cells


title: Chd4KD_Rep1_RNAseq

description: Total RNA


title: AtrxKD_Rep1_RNAseq

description: Total RNA

value: Atrx knockdown for 48 hours


title: AtrxKD_Rep2_RNAseq

description: Total RNA


title: ControlKD_Rep17_TTseq

description: 4sU-labelled RNA

data_processing:
Barcode adapter sequences removed using cutadapt and trimmed using trimmomatic.
Reads mapped to mm10 genome using STAR, with options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS.
Counts were generated using featureCounts, with options -B -t "exon" -g "gene_name" -F GTF -p -s 2 for Gencode mouse V23 features, with options -B -F SAF -p -s 2 for stranded features, and options -B -F SAF -p -s 0 for unstranded features.
In R/Bioconductor environment, raw count matrices were corrected for batch effects using Combat-seq and differential expression analysis was performed using DEseq2 for all replicates of each condition.
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Excel file containing all DEseq2 results for each condition for TTseq.
Supplementary files format and content: Tab-delimited matrix of raw TTseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited matrix of Combatseq corrected raw TTseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited table containing information for Combatseq batch corrected for TT-seq data.
Supplementary files format and content: bed file for all non-coding features in this study.

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Extracted nuclei were transposed for 30 minutes with Tn5 transposome in buffer containing digitonin, NP-40, and Tween-20.
Nascent RNA was rRNA depleted using antisense oligos, purified. Nascent RNA-seq libraries were built using the NEBNext Ultra II RNA Library Prep kit according to the manufacturer's modifications, but with modifications to account for higher volume input.

value: Control KD for 48 hours


title: Urine progenitor renal cells_dead donor 064

description: Progenitor Renal Cells

value: dead donor


title: Urine progenitor renal cells_alive donor 062

description: Progenitor Renal Cells

value: Urine progenitor renal cells


title: ControlKD_Rep15_TTseq

description: 4sU-labelled RNA

value: embryonic stem cells


title: Urine progenitor renal cells_dead donor 060

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 086

description: Progenitor Renal Cells


title: Urine progenitor renal cells_alive donor 058

description: Progenitor Renal Cells


title: ControlKD_Rep14_TTseq

description: 4sU-labelled RNA

value: wild-type


title: Urine progenitor renal cells_dead donor 119

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 100

description: Progenitor Renal Cells


title: ControlKD_Rep16_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep12_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_alive donor 044

description: Progenitor Renal Cells


title: ControlKD_Rep13_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep11_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_dead donor 048

description: Progenitor Renal Cells


title: ControlKD_Rep10_TTseq

description: 4sU-labelled RNA


title: Btaf1KD_Rep1_RNAseq

description: Total RNA


title: Urine progenitor renal cells_dead donor 036

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 031

description: Progenitor Renal Cells


title: ControlKD_Rep8_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep7_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep9_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_dead donor 032

description: Progenitor Renal Cells


title: ControlKD_Rep6_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_dead donor 030

description: Progenitor Renal Cells


title: ControlKD_Rep5_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_dead donor 028

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 020

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 008

description: Progenitor Renal Cells


title: ControlKD_Rep3_TTseq

description: 4sU-labelled RNA


title: Urine progenitor renal cells_dead donor 001

description: Progenitor Renal Cells


title: Urine progenitor renal cells_dead donor 045

description: Progenitor Renal Cells


title: Zranb3KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Zranb3 knockdown for 48 hours


title: ControlKD_Rep1_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep2_TTseq

description: 4sU-labelled RNA


title: TAO-shLSD1-1

city: HangZhou

first: Yuyan

last: Xu

address: Yuhang Tang Road

institute: Zhejiang university

description: Library name: Sample 9

data_processing:
RNA-seq:Clean data were obtained by processing RNA-seq raw data in fastq format using fast qv0.23.2. The default parameters were used to trim reads containing adapters and filter low-quality reads and reads containing N bases. Then, the clean data were aligned to GRCm39/GRCh38 (UCSC) genome assemblies using STAR v.2.7.10a with default parameters. The uniquely mapped read pairs were counted using feature Counts v2.0.1. The output gene count matrix was quantile normalized using the R package DESeq2 v1.32.0. log transformation of the count matrix was performed for principal component analysis (PCA). The significance and fold change of DEGs between samples were estimated using the R package DEseq2, where an adjusted P-value < 0.05 and absolute log2Foldchange value ≥ 1 were selected. KEGG and GO enrichment analysis of the DEGs were performed using clusterProfiler v4.6.0. The gene number and P-value of the KEGG and GO terms were visualized using clusterProfiler v4.6.0. The heat maps and bar plots of significant DEGs were constructed using heatmap v1.0.12 and ggplot2 v3.4.0, respectively.
Cut-Tag:Raw sequencing data was filtered by fastp (version 0.23.1), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean reads were mapped to the reference genome of Homo from Homo-sapiens.GRCh38.dna.toplevel.fa using bowtie2 (version 2.2.6) with default parameters. Sambamba (version 0.7.1) is used for sam/bam format conversion and PCR duplicate reads removal. The RSeQC（version 2.6）was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2). DeepTools (version 2.4.1) was used to visualize the distribution of reads on upstream and downstream of TSS. The MACS2 software（Version 2.2.7.1）was used for peak calling. The bedtools（version 2.30.0）was used for peaks annotation and peak distribution analysis. The different peaks were identified by csaw (version 1.24.3). The Homer（version 4.10）was used for motifs analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: Homo sapiens GRCh38 release-109/GRCh38.106
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample/Characteristic peaks on chromosomal regions of each gene in all samples
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Library strategy: CUT&Tag

source_name: Adipose tissue

growth_protocol: LSD1 in TAO adipocytes was knocked out with shRNA. Subsequently, non-TAO, TAO and LSD1 knock out TAO adipocytes were seeded into the six-well plate with the same number of cells, and when the cells were overgrown, they were digested and collected by Trple for RNA sequencing and Cut-tag.

extract_protocol:
RNA-seq:Cells were dissociated with Trypsin for 5 min, stopped with serum containing media, total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer's instructions.Embryos (five embryos per sample) were collected in a 0.2-mL PCR tube, and 4 µL lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTP, and oligo-dT primers) was added. The samples were immediately incubated at 72 °C for 3 min, and cDNA was produced using SuperScript II reverse transcriptase.
The RNA-seq transcriptome librariy of cell was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Embryos RNA-seq libraries were generated from early mouse embryos using the Smart-seq2 protocol.The cut-tag library of cells were made as following steps: treated with 10 μl of pre-washed ConA beads in a 1.5-ml low-binding tube. Next, 50 μl of antibody buffer containing 0.5 μg of antibody was added, and the mixture was incubated for 2 hours at room temperature. After two washes with dig-wash buffer, 50 μl of dig-wash buffer with 0.5 μg of secondary antibody was added, followed by a 30-minute incubation at room temperature. The samples were washed twice with 800 μl of dig-wash buffer, then 0.58 μl of pG–Tn5 and 100 μl of dig-300 buffer were added. After a 1-hour incubation at room temperature, another two washes with 800 μl of dig-wash buffer were performed. Tagmentation was carried out by adding 300 μl of tagmentation buffer, and the samples were incubated at 37 °C for 1 hour. The reaction was halted by adding 10 μl of 0.5 M EDTA, 3 μl of 10% SDS, and 2.5 μl of 20 mg/ml Proteinase K. Following phenol-chloroform extraction and ethanol precipitation, PCR was conducted to amplify the libraries, which were sequenced using Illumina Hi-Seq Xten or Hi-Seq 2500 systems, following the manufacturer’s guidelines.

value: Adipose tissue

value: Adipose cell


title: TAO-2

description: Library name: Sample 8

value: TAO


title: non-TAO-2

description: Library name: Sample 6

value: non-TAO


title: TAO-1

description: Library name: Sample 7


title: Zranb3KD_Rep1_TTseq

description: 4sU-labelled RNA


title: non-TAO-1

description: Library name: Sample 5


title: SrcapKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Srcap knockdown for 48 hours


title: Ttf2KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Ttf2 knockdown for 48 hours


title: Ttf2KD_Rep2_TTseq

description: 4sU-labelled RNA


title: RNA-TAO-shLSD1-2

description: Library name: Sample 4

data_processing:
RNA-seq:Clean data were obtained by processing RNA-seq raw data in fastq format using fast qv0.23.2. The default parameters were used to trim reads containing adapters and filter low-quality reads and reads containing N bases. Then, the clean data were aligned to GRCm39/GRCh38 (UCSC) genome assemblies using STAR v.2.7.10a with default parameters. The uniquely mapped read pairs were counted using feature Counts v2.0.1. The output gene count matrix was quantile normalized using the R package DESeq2 v1.32.0. log transformation of the count matrix was performed for principal component analysis (PCA). The significance and fold change of DEGs between samples were estimated using the R package DEseq2, where an adjusted P-value < 0.05 and absolute log2Foldchange value ≥ 1 were selected. KEGG and GO enrichment analysis of the DEGs were performed using clusterProfiler v4.6.0. The gene number and P-value of the KEGG and GO terms were visualized using clusterProfiler v4.6.0. The heat maps and bar plots of significant DEGs were constructed using heatmap v1.0.12 and ggplot2 v3.4.0, respectively.
Cut-Tag:Raw sequencing data was filtered by fastp (version 0.23.1), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean reads were mapped to the reference genome of Homo from Homo-sapiens.GRCh38.dna.toplevel.fa using bowtie2 (version 2.2.6) with default parameters. Sambamba (version 0.7.1) is used for sam/bam format conversion and PCR duplicate reads removal. The RSeQC（version 2.6）was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2). DeepTools (version 2.4.1) was used to visualize the distribution of reads on upstream and downstream of TSS. The MACS2 software（Version 2.2.7.1）was used for peak calling. The bedtools（version 2.30.0）was used for peaks annotation and peak distribution analysis. The different peaks were identified by csaw (version 1.24.3). The Homer（version 4.10）was used for motifs analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: Homo sapiens GRCh38 release-109/GRCh38.106
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample/Characteristic peaks on chromosomal regions of each gene in all samples
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample


title: ControlKD_Rep4_TTseq

description: 4sU-labelled RNA


title: Smarcal1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarcal1 knockdown for 48 hours


title: Smarcal1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: RNA-TAO-ctr-2

description: Library name: Sample 2


title: RNA-TAO-shLSD1-1

description: Library name: Sample 3


title: RNA-TAO-ctr-1

description: Library name: Sample 1


title: Smarcad1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarcad1 knockdown for 48 hours


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 4 hours, Replicate 3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: Library name: GB4h_R3

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: Assembly: HG38
Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

molecule: polyA RNA

growth_protocol: Day 0: Seeding cells in DMEM/F-12 GlutaMAX medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
NucleoSpin RNA Mini kit, (Macherey-Nagel, REF 740955.50) was used for RNA isolation.
mRNA-Seq (NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs))

treatment_protocol: Day 1: Treatment of cells with (R)-GNE-140 (7.5 µM) + BMS-986205 (6 µM) combination or DMSO (0.135 %). Day 1 + indicated hours post treatment : Harvesting cells by 2x PBS washing, scraping, pelleting 400 x g, 5 min, 4°C followed by snap freezing of cell pellet in liquid nitrogen until RNA isolation.

value: fallopian tube scretory epithelial cells


title: Smarcad1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, DMSO treatment for 4 hours, Replicate 3

description: Library name: DMSO4h_R3


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 4 hours, Replicate 2

description: Library name: GB4h_R2


title: TAO-shLSD1-2

description: Library name: Sample 10


title: Smarca5KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarca5 knockdown for 48 hours


title: Smarca5KD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, DMSO treatment for 4 hours, Replicate 2

description: Library name: DMSO4h_R2


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 4 hours, Replicate 1

description: Library name: GB4h_R1


title: Smarca4KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarca4 knockdown for 48 hours


title: Smarca4KD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, DMSO treatment for 4 hours, Replicate 1

description: Library name: DMSO4h_R1


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 120 hours

description: Library name: GB_120h


title: SrcapKD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 108 hours

description: Library name: GB_108h


title: ShprhKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Shprh knockdown for 48 hours


title: Smarca2KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Smarca2 knockdown for 48 hours


title: ShprhKD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 84 hours

description: Library name: GB_84h


title: Rad54l2KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Rad54l2 knockdown for 48 hours


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 72 hours

description: Library name: GB_72h


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 60 hours

description: Library name: GB_60h


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 48 hours

description: Library name: GB_48h


title: Rad54lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: embryonic stem cells

value: Rad54l knockdown for 48 hours


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 36 hours

description: Library name: GB_36h


title: Rad54lKD_Rep1_TTseq

description: 4sU-labelled RNA

value: wild-type


title: Rad54bKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Rad54b knockdown for 48 hours


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 24 hours

description: Library name: GB_24h


title: Rad54l2KD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 12 hours

description: Library name: GB_12h


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 8 hours

description: Library name: GB_8h


title: Rad54bKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ino80KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ino80 knockdown for 48 hours


title: Ino80KD_Rep1_TTseq

description: 4sU-labelled RNA


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 4 hours

description: Library name: GB_4h

source_name: fallopian tube scretory epithelial cells


title: HltfKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Hltf knockdown for 48 hours


title: PR79_1_WTA | 059 | Trp

city: Seoul

first: Sang Eun

last: Lee

state: Songpa-gu

address: 88, Olympic-ro 43-gil

department: Department of Cardiology

country: South Korea

institute: Asan Medical Center

data_processing:
In the initial step, raw sequencing FASTQ files are combined with a configuration file that outlines the processing parameters. Following this, the raw reads undergo computational processing to remove adapter sequences, producing trimmed reads, and paired-end reads are merged to create stitched reads. In the third step, these stitched reads are aligned to the RTS-ID barcodes in the reference assay, generating aligned reads and assigning counts to biological target names. Subsequently, PCR duplicates are removed by sorting based on the Unique Molecular Identifier (UMI) present in each read, resulting in deduplicated reads. Finally, DCC files are generated and compiled into a .zip file within a designated folder, ready for upload into the DSP Control Center for study creation in the DSP Data Analysis Suite.
Assembly: GRCh38
Supplementary files format and content: Process FASTQ sequencing files into digital count conversion (DCC) files
Library strategy: Nanostring GeoMX digital spatial profiler

source_name: Heart

extract_protocol:
Adult human heart samples were harvested between January 2018 and April 2021 and kept in paraffin blocks after formalin fixation. Control samples were obtained from autopsy cases with no history of HF or extracted from the left ventricle (LV) of the patients with normal LV function while receiving a heart transplant or a heart-lung transplan for isolated right ventricular failure or other reasons. Failing hearts were obtained from explanted hearts of recipients receiving a heart transplant, from excisional biopsy of patients receiving a LV assisant device, from myomectomy for obstructive HCMP, and from autopsy.
Formalin-fixed, paraffin-embedded sections were deparaffinized, went through antigen retrieval procedures, and then incubated with human WTA UV-cleavable RNA probes. They were co-stained with fluorescently conjugated antibody antibody morphologic markers against Troponin I, Vimentin, and CD31. After preparing tissue, bake slides with mounted sections in 60C drying oven for 30min to 3 hours. Deparaffinize and rehydrate FFPE tissue sections for 35 minutes. Target retriveal were performed for 25 minutes After exposing RNA targets, add 200 uL of hybridization solution made by manufacturer's buffer(Buffer R, Atlas Probe Mix, Custom assay1, Custom assay2, DEPC-treated H2O) in the hybridization chamber. Gently apply a Grace Bio-Labs HybriSlip and incubate at 37C for obernight at hybridization oven. Stringent wash was performed using 4X SSC with formamide and 2x SSC to remove off-target probes. Load prepared slides in to the GeoMX DSP instrument. Slides are scanned to capture fluorescent images used to select regions of interest(ROIs). The instrument collects UV-cleaved oligos from the ROIs into the wells of a collection plate.

value: Heart

value: Cardiomyocytes

tag: ventricle

value: LV

tag: clinical phenotype_lv

tag: p hypertrophy

tag: p degeneration

tag: p fibrosis

tag: p disarray


title: Smarca2KD_Rep2_TTseq

description: 4sU-labelled RNA


title: HltfKD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 059 | vessel


title: HellsKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Hells knockdown for 48 hours


title: KRASG12V/MYC cancer cells, (R)-GNE-140 + BMS-986205 combination treatment for 96 hours

description: Library name: GB_96h


title: PR79_1_WTA | 058 | Trp

value: Control


title: Ercc6lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ercc6l knockdown for 48 hours


title: PR79_1_WTA | 057 | Full ROI


title: HellsKD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 056 | Full ROI


title: Ercc6lKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ercc6KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ercc6 knockdown for 48 hours


title: PR79_1_WTA | 055 | Trp


title: Ercc6KD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 054 | vessel


title: PR79_1_WTA | 054 | Trp


title: PR79_1_WTA | 052 | Full ROI


title: PR79_1_WTA | 053 | Full ROI


title: PR79_1_WTA | 051 | Full ROI

value: DCMP


title: Chd9KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd9 knockdown for 48 hours


title: Ep400KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ep400 knockdown for 48 hours


title: Chd9KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd8KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd8 knockdown for 48 hours


title: Ep400KD_Rep1_TTseq

description: 4sU-labelled RNA

value: embryonic stem cells


title: PR79_1_WTA | 050 | Full ROI


title: PR79_1_WTA | 049 | Trp


title: Chd8KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Chd7KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd7 knockdown for 48 hours


title: PR79_1_WTA | 048 | Trp


title: PR79_1_WTA | 048 | vessel


title: PR79_1_WTA | 049 | vessel


title: PR79_1_WTA | 047 | Trp


title: Chd5KD_Rep2_TTseq

description: 4sU-labelled RNA

value: wild-type

value: Chd5 knockdown for 48 hours


title: Chd7KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd5KD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 047 | vessel


title: Chd4KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd4 knockdown for 48 hours


title: Chd3KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd3 knockdown for 48 hours


title: PR79_1_WTA | 046 | Trp

value: Heart


title: Chd4KD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 046 | vessel


title: PR79_1_WTA | 045 | Trp

value: Cardiomyocytes


title: Chd3KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd2KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd2 knockdown for 48 hours


title: PR79_1_WTA | 044 | Trp

value: LV


title: PR79_1_WTA | 044 | fb

value: Fibroblasts


title: Chd1lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd1l knockdown for 48 hours


title: Chd2KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd1lKD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 044 | vessel


title: PR79_1_WTA | 043 | Trp


title: PR79_1_WTA | 043 | fb


title: Chd1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd1 knockdown for 48 hours


title: Chd1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Btaf1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Btaf1 knockdown for 48 hours


title: PR79_1_WTA | 042 | Trp

value: DCMP


title: Btaf1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 043 | vessel


title: AtrxKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Atrx knockdown for 48 hours


title: AtrxKD_Rep1_TTseq

description: 4sU-labelled RNA


title: PR79_1_WTA | 040 | Trp


title: PR79_1_WTA | 041 | vessel


title: PR79_1_WTA | 040 | vessel


title: PR79_1_WTA | 041 | Trp


title: Smarcal1KD_Rep1_ATACseq

data_processing:
Reads were trimmed to 25 bp and barcode adapter sequences removed using trim_galore.
Reads mapped to mm10 genome using bowtie2, allowing for 1 mismatch.
Duplicates were removed using Picard.
Reads were size-selected for nucleosome free region size fragments (1-100 bp).
Reads were processed in deepTools by using alignmentSieve with option --ATACshift and then bamCoverage to generate bigwig files detailing coverage genome-wide with options -bs 5 -e --centerReads -p 40 --smoothLength 20 --normalizeUsing RPGC --effectiveGenomeSize 2407883318 and occluding reads overlapping ENCODE black listed regions.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Extracted nuclei were transposed for 30 minutes with Tn5 transposome in buffer containing digitonin, NP-40, and Tween-20.
ATAC-seq libraries were amplified by high-fidelity PCR with barcoded Nextera indices.

treatment_protocol: After 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Nuclei were harvested 48 h post-transfection.

value: Smarcal1 knockdown for 48 hours


title: Smarcal1KD_Rep2_ATACseq

value: embryonic stem cells


title: PR79_1_WTA | 039 | Trp


title: PR79_1_WTA | 039 | vessel


title: PR79_1_WTA | 045 | vessel


title: Chd8KD_Rep1_ATACseq

value: Chd8 knockdown for 48 hours


title: PR79_1_WTA | 038 | Trp


title: Chd8KD_Rep2_ATACseq

value: wild-type


title: SrcapKD_Rep2_ATACseq

value: Srcapknockdown for 48 hours


title: PR79_1_WTA | 038 | vessel


title: SrcapKD_Rep1_ATACseq

value: Srcap knockdown for 48 hours


title: PR79_1_WTA | 037 | Trp


title: PR79_1_WTA | 036 | Trp


title: ControlKD_Rep2_ATACseq

value: Control knockdown for 48 hours


title: PR79_1_WTA | 035 | Trp

value: Heart

value: Control


title: WT_Rep3_CandR_IgG

data_processing:
Barcode adapter sequences removed.
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch.
Picard used to remove duplicates.
Low quality reads were removed (MAPQ <10).
Reads were divided into size classes: 1-120 for DNA binding proteins or 150-500 for histone variants or histone modifications.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol: After treatment, nuclei were extracted as outlined in CUT&RUN. Nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodies followed by proteinA-MNase. Cleavage of MNase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

treatment_protocol: For cross linked WT cells: cells were washed with 1X PBS, trypsinized, counted, and 1 million cells were collected in 1.5 mL microfuge tubes and placed on ice. Cells were centrifuged at 600 rcf at 4°C for 5 min, and the supernatant was removed without disturbing the pellet. The cell pellet was resuspended gently in 1 mL ESC media + 0.1% formaldehyde, inverted 3 times, and crosslinked for 5 min at RT. The reaction was then quenched with 100 uL of 2.5M glycine. For RNAi treated cells: after 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Nuclei were harvested 48 h post-transfection.

tag: antibody

value: IgG (Sigma-Aldrich 06-371)


title: PR79_1_WTA | 035 | vessel

value: LV


title: WT_Rep2_CandR_IgG


title: PR79_1_WTA | 034 | Trp

value: Cardiomyocytes

value: ICMP


title: WT_Rep1_CandR_IgG


title: WT_Rep3_CandR_Smarcal1

value: SMARCAL1 (Invitrogen PA5-28980)


title: PR79_1_WTA | 032 | Trp


title: WT_Rep1_CandR_Smarcal1


title: PR79_1_WTA | 032 | vessel


title: PR79_1_WTA | 031 | Trp


title: WT_Rep3_CandR_SRCAP

value: SRCAP (Kerafast ESL103)


title: PR79_1_WTA | 029 | Trp

value: DCMP


title: PR79_1_WTA | 028 | Trp


title: WT_Rep1_CandR_SRCAP


title: PR79_1_WTA | 030 | Full ROI


title: WT_Rep2_CandR_SRCAP


title: Smarcal1KD_Rep2_CandR_IgG


title: PR79_1_WTA | 031 | vessel


title: PR79_1_WTA | 029 | vessel


title: Smarcal1KD_Rep2_CandR_INTS5

value: INTS5 (Proteintech 14069-1-AP)


title: PR79_1_WTA | 028 | vessel


title: PR79_1_WTA | 027 | Trp


title: Smarcal1KD_Rep2_CandR_H3K27ac

value: Smarcal1 knockdown for 48 hours

value: H3K27ac (abcam ab4729)


title: Smarcal1KD_Rep1_CandR_INTS5

value: embryonic stem cells


title: Smarcal1KD_Rep1_CandR_IgG

value: wild-type


title: Smarcal1KD_Rep1_CandR_H3K27ac


title: PR79_1_WTA | 026 | vessel


title: ControlKD_Rep1_ATACseq


title: WT_Rep2_CandR_Smarcal1


title: PR79_1_WTA | 026 | Trp


title: PR79_1_WTA | 033 | Trp


title: Chd8KD_Rep1_CandR_IgG

value: Chd8 knockdown for 48 hours


title: Chd8KD_Rep2_CandR_IgG


title: PR79_1_WTA | 023 | Trp


title: Chd8KD_Rep1_CandR_NFYA

value: NFYA (Santa Cruz SC-17753)


title: Chd8KD_Rep2_CandR_NFYA


title: PR79_1_WTA | 023 | fb

value: Fibroblasts


title: Chd8KD_Rep2_CandR_H3K27ac


title: Chd8KD_Rep1_CandR_H3K27ac


title: PR79_1_WTA | 022 | Trp

value: Heart


title: PR79_1_WTA | 021 | Trp


title: PR79_1_WTA | 020 | Trp


title: SrcapKD_Rep2_CandR_H2AZ

value: Srcap knockdown for 48 hours

value: H2AZ (abcam ab4729)


title: PR79_1_WTA | 025 | Trp

value: LV


title: SrcapKD_Rep2_CandR_H3K27ac


title: PR79_1_WTA | 019 | Trp

value: Cardiomyocytes


title: PR79_1_WTA | 018 | Trp


title: SrcapKD_Rep1_CandR_H3K27ac


title: ControlKD_Rep2_CandR_IgG

value: Control knockdown for 48 hours

value: IgG (Sigma-Aldrich 06-371)


title: PR79_1_WTA | 018 | vessel


title: ControlKD_Rep1_CandR_IgG


title: PR79_1_WTA | 024 | Trp

value: ICMP


title: PR79_1_WTA | 025 | vessel


title: PR79_1_WTA | 017 | Trp

value: DCMP


title: PR79_1_WTA | 017 | vessel


title: ControlKD_Rep2_CandR_NFYA


title: PR79_1_WTA | 016 | Trp


title: ControlKD_Rep1_CandR_NFYA


title: PR79_1_WTA | 015 | Trp


title: ControlKD_Rep1_CandR_INTS5

value: INTS5 (Proteintech 14069-1-AP)


title: PR79_1_WTA | 014 | Trp


title: SrcapKD_Rep2_CandR_IgG


title: PR79_1_WTA | 013 | Trp


title: SrcapKD_Rep1_CandR_IgG


title: ControlKD_Rep1_CandR_H2AZ


title: PR79_1_WTA | 019 | vessel


title: SrcapKD_Rep1_CandR_H2AZ


title: PR79_1_WTA | 020 | vessel


title: PR79_1_WTA | 012 | Trp


title: ControlKD_Rep2_CandR_H3K27ac


title: PR79_1_WTA | 011 | Trp


title: ControlKD_Rep1_CandR_H3K27ac


title: PR79_1_WTA | 009 | Trp


title: PR79_1_WTA | 010 | Trp


title: ControlKD_Rep2_CandR_INTS5


title: PR79_1_WTA | 007 | Trp


title: PR79_1_WTA | 007 | vessel


title: ISX9-3h-2 for Fig. 5C and S5B

city: Boston

first: Ting

last: Zhao

state: MA

address: 185 Cambridge st, Simches Building, CPZN4400

institute: MGH

description: Library name: TZa20-2-6

data_processing:
Sequencing reads were aligned to hg19 reference genome using BWA v. 0.7.17-r1188 with command bwa sampe. Peaks were called using HOMER v. 4.10.3
Assembly: hg19
Supplementary files format and content: coverage track in bigwig format was prepared using bamCoverage function of the deepTools
Library strategy: CUT&Tag

source_name: Osteosarcoma patient-derived cells PDXC-OS052

extract_protocol:
CUT&Tag was performed using the CUT&Tag-IT™ Assay Kit (Active Motif, 53160) with H3K27ac antibody (Abcam, ab4729). Briefly, cells after 6 days’ treatment were first incubated with concanavalin A beads and primary antibodies followed by secondary antibody. Then the chromatin is digested by tagmentation using the protein A-Tn5 (pA-Tn5) transposome enzyme. After DNA purification and PCR amplification with adaptors, samples were sequenced on Illumina NextSeq2000
CUT&Tag was performed using the CUT&Tag-IT™ Assay Kit (Active Motif, 53160) with H3K27ac antibody (Abcam, ab4729). Briefly, cells after 6 days’ treatment were first incubated with concanavalin A beads and primary antibodies followed by secondary antibody. Then the chromatin is digested by tagmentation using the protein A-Tn5 (pA-Tn5) transposome enzyme. After DNA purification and PCR amplification with adaptors, samples were sequenced on Illumina NextSeq2000

value: ISX9 100µM

tag: time

value: 3 hours


title: ISX9-3h-1 for Fig. 5C and S5B

description: Library name: TZa20-2-5

value: Osteosarcoma patient-derived cells PDXC-OS052


title: DMSO-3h-1 for Fig. 5C and S5B [ATAC-Seq]

description: Library name: TZa20-1-1

data_processing:
Sequencing reads were aligned to hg19 reference genome using BWA v. 0.7.17-r1188 with command bwa sampe. Peaks were called using HOMER v. 4.10.3
Assembly: hg19
Supplementary files format and content: coverage track in bigwig format was prepared using bamCoverage function of the deepTools

extract_protocol: cells were first lysed in buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, and 0.1% Igepal CA-630). Then, cell pellets were incubated with transposition reaction mix (25µl Tagment DNA Buffer, 2.5µl TDE1 Tagment DNA Enzyme, and 22.5µl nuclease-free H2O) (Illumina, 20034197) for 30 min at 37°C in a thermomixer at 300rpm, followed by PCR reaction for 18 cycles.

value: DMSO


title: DMSO-3h-2 for Fig. 5C and S5B [ATAC-Seq]

description: Library name: TZa20-1-6


title: ISX9-3h-1 for Fig. 5C and S5B [ATAC-Seq]

description: Library name: TZa20-1-3


title: PR79_1_WTA | 006 | Trp


title: ControlKD_Rep2_CandR_H2AZ

value: embryonic stem cells

value: wild-type


title: DMSO-3h-2 for Fig. 5C and S5B

description: Library name: TZa20-2-2


title: PR79_1_WTA | 008 | Trp


title: DMSO-3h-1 for Fig. 5C and S5B

description: Library name: TZa20-2-1


title: PR79_1_WTA | 005 | Trp


title: PSS008 M+I -2 for Fig. S5K

description: Library name: TZa12-14

value: MGCD0103 1µM plus ISX9 20µM

value: 6 days


title: PR79_1_WTA | 008 | vessel

value: Heart


title: PR79_1_WTA | 005 | vessel


title: PSS008 M+I -1 for Fig. S5K

description: Library name: TZa12-13


title: PSS008 MGCD0103-2 for Fig. S5K

description: Library name: TZa12-12

value: MGCD0103 1µM


title: PR79_1_WTA | 003 | fb

value: Fibroblasts

value: LV


title: PSS008 ISX9-1 for Fig. S5K

description: Library name: TZa12-9

value: ISX9 20µM


title: PR79_1_WTA | 002 | Trp

value: Cardiomyocytes


title: PR79_1_WTA | 004 | vessel


title: PR79_1_WTA | 001 | vessel

value: ICMP


title: PSS008 DMSO-1 for Fig. S5K

description: Library name: TZa12-7


title: A498, shARNT, biol rep 3

city: SAN DIEGO

first: Rebecca

last: Mello

state: CA

address: 11093 CLAIREMONT MESA BLVD

institute: The Scripps Research Institute

data_processing:
STAR alignment with SeqMan NGen 17
Counts table with ArrayStar 17
DESeq2 using GenePattern online tool
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium + 10% fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco), and maintained in an atmosphere containing 5% CO2 at 37°C.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN #74104) and QIAshredder (QIAGEN #79654)
DNBSEQ stranded mRNA library by BGI

treatment_protocol: To generate cell lines expressing shRNA, lentiviral shRNA constructs encoded in PLKO.1 vectors were produced by transient transfection in HEK293T cells. Target cells were infected with lentivirus for 4-6 hours before selection in DMEM + 10% fetal bovine serum and 1% penicillin-streptomycin containing 2.5 µg/mL puromycin for 1 week. After initial selection, cells were maintained in DMEM containing 1.25 µg/mL.

value: Carcinoma; Renal Cell

value: ARNT knockdown


title: PSS008 ISX9-2 for Fig. S5K

description: Library name: TZa12-10


title: PR79_2_WTA | 068 | Full ROI

value: DCMP


title: PR79_2_WTA | 069 | Full ROI


title: ISX9-3h-2 for Fig. 5C and S5B [ATAC-Seq]

description: Library name: TZa20-1-8

value: ISX9 100µM

value: 3 hours


title: PSS008 MGCD0103-1 for Fig. S5K

description: Library name: TZa12-11

value: Osteosarcoma patient-derived cells PDXC-OS052


title: A498, shARNT, biol rep 2


title: P7F1_RNAseq_pDOX_Rep1

first: Gerard

last: Martinez-Cebrian

state: Barcelona

address: Edifici Josep carreras, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Institut Josep carreras

description: Library name: P7F1_RNAseq_pDOX_Rep1

data_processing:
For RNA-seq, raw sequencing reads were aligned to the human reference genome (hg38 assembly) with bowtie2 v2.3.5.1. Quantification of gene expression was performed with featureCounts from Subread v1.6.3 using uniquely mapping reads.
Assembly: hg38
Supplementary files format and content: Counts

source_name: induced pluripotent stem cell muscle progenitor

growth_protocol: Human iPS cells expressing PAX7 (muscle progenitors)(Wu et al., 2016) were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% penicillin/streptomycin (Corning), 50 μg/ml L-ascorbic acid (Sigma), 4.5mM 1-thioglycerol (Sigma), and 10 ng/ml recombinant human basic-FGF (Peprotech). These muscle progenitors were infected using lentiviral doxycycline-inducible or constitutive (EF1α promoter) constructs driving expression of a cDNA encoding the exact PAX7-FOXO1 or PAX3-FOXO1 fusion protein found in ARMS tumors. PAX7 transgene expression was induced by adding Dox (Sigma-Aldrich, final concentration 1 μg/ml), and then maintained throughout the protocol by replacing the medium (including dox) with 10 ng/ml human basic-FGF (Preprotech) every 2 days.

extract_protocol:
For RNAseq, total RNA was extracted from iPS control and iPS-MPPAX3/7-FOXO1 cells (in three technical replicates) using RNA Zymo-Spin columns (Zymo R1015). Before library preparation, rRNA was depleted with NEBNext rRNA Depletion Kit (NEB E6310).
RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) and sequenced (2x50bp paired end) using an Illumina NextSeq 2000 machine.

treatment_protocol: For cultures without Dox, cells were harvested at day 3 following Dox removal for analysis.

value: +Dox


title: P7F1_RNAseq_pDOX_Rep3

description: Library name: P7F1_RNAseq_pDOX_Rep3

value: induced pluripotent stem cell muscle progenitor


title: P7F1_RNAseq_pDOX_Rep2

description: Library name: P7F1_RNAseq_pDOX_Rep2


title: P3F1_RNAseq_pDOX_Rep3

description: Library name: P3F1_RNAseq_pDOX_Rep3


title: P3F1_RNAseq_pDOX_Rep2

description: Library name: P3F1_RNAseq_pDOX_Rep2


title: PR79_2_WTA | 067 | Full ROI


title: P3F1_RNAseq_pDOX_Rep1

description: Library name: P3F1_RNAseq_pDOX_Rep1


title: A498, shARNT, biol rep 1


title: Control_RNAseq_pDOX_Rep3

description: Library name: Control_RNAseq_pDOX_Rep3

value: WT


title: PR79_2_WTA | 066 | Full ROI


title: PR79_1_WTA | 004 | Trp


title: Control_RNAseq_pDOX_Rep2

description: Library name: Control_RNAseq_pDOX_Rep2


title: PR79_2_WTA | 065 | Full ROI


title: Control_RNAseq_pDOX_Rep1

description: Library name: Control_RNAseq_pDOX_Rep1


title: A498, shBMAL1, biol rep 3

value: BMAL1 knockdown


title: PR79_1_WTA | 001 | Trp

value: Heart


title: A498, shBMAL1, biol rep 2


title: PSS008 DMSO-2 for Fig. S5K

description: Library name: TZa12-8

value: DMSO

value: 6 days


title: PR79_2_WTA | 064 | Full ROI

value: RV


title: A498, shBMAL1, biol rep 1


title: PR79_2_WTA | 063 | Trp

value: LV


title: A498, shControl, biol rep 3


title: FHSC14_sgUSP22_CE1_H2AK119ub

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: Library name: H14ce_U1_H2ub119

data_processing:
The nf-core cutandrun pipeline was followed for quality trimming using TrimGalore and alignment to GRCh38 reference genome using Bowtie2. MACS2 was used to call broad peaks with and without IgG controls and an intersection of the two was considered the final peak set for each sample. For quality control, a combination of Samtools and the bedtools suite was used to calculate fragment length and number of reads in peaks. Peak annotation generated using Homer and Gencode v38 annotations. Read counts for each peak were generated using Subread featureCounts, tabulated and passed to Bioconductor edgeR for differential peaks (FDR < 0.05) expressed between groups of interest.
Assembly: hg38
Supplementary files format and content: bed files with peak coordinates
Library strategy: CUT&Tag

source_name: SCLC PDX tumor

growth_protocol: SCLC PDX models were grown subcutaneously in the flanks of immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice.

extract_protocol:
SCLC PDX tumors were dissociated and viable cells were sorted by FACS. Approximately 40,000 cells per reaction were processed for CUT&Tag sequencing.
CUT&Tag libraries were prepared using the following protocol CUT&Tag-direct for whole cells with CUTAC  V.4 (Henikoff, 2023): https://www.protocols.io/view/cut-amp-tag-direct-for-whole-cells-with-cutac-x54v9mkmzg3e/v4

treatment_protocol: SCLC PDX models were treated for 48-hours with intraparotineal injections of cisplatin (5 mg/kg)+etoposide (10 mg/kg) or saline vehicle

value: SCLC PDX tumor

value: CE

tag: chip antibody

value: H2K119ub (Cell Signaling, 8240)


title: FHSC14_sgCtrl_CE2_H2AK119ub

description: Library name: H14ce_C2_H2ub119

value: sgCtrl


title: FHSC14_sgUSP22_CE2_H2AK119ub

description: Library name: H14ce_U2_H2ub119


title: FHSC14_sgUSP22_SAL2_H2AK119ub

description: Library name: H14_U2_H2ub119

value: SAL


title: PR79_2_WTA | 062 | Trp

value: Cardiomyocytes

value: ICMP


title: A498, shControl, biol rep 2

value: Carcinoma; Renal Cell


title: FHSC14_sgCtrl_SAL2_H2AK119ub

description: Library name: H14_C2_H2ub119


title: FHSC14_sgCtrl_SAL1_H2AK119ub

description: Library name: H14_C1_H2ub119


title: FHSC14_sgUSP22_CE3_H3K27me3

description: Library name: H14ce_U3_H3me27

value: H3K27me3 (Cell Signaling, 9733)


title: PR79_2_WTA | 061 | Trp

value: DCMP


title: 786O + VHL (WT8), shBMAL1, biolrep 3

value: Adenocarcinoma; Renal Cell


title: FHSC14_sgUSP22_CE1_H3K27me3

description: Library name: H14ce_U1_H3me27


title: PR79_2_WTA | 054 | vessel


title: FHSC14_sgCtrl_CE3_H3K27me3

description: Library name: H14ce_C3_H3me27


title: FHSC14_sgCtrl_CE2_H3K27me3

description: Library name: H14ce_C2_H3me27


title: 786O + VHL (WT8), shBMAL1, biolrep 2

value: BMAL1 knockdown


title: PR79_2_WTA | 050 | Full ROI

value: Heart


title: 786O + VHL (WT8), shBMAL1, biolrep 1


title: FHSC14_sgCtrl_CE1_H3K27me3

description: Library name: H14ce_C1_H3me27


title: FHSC14_sgUSP22_SAL3_H3K27me3

description: Library name: H14_U3_H3me27


title: FHSC14_sgCtrl_CE1_H2AK119ub

description: Library name: H14ce_C1_H2ub119


title: PR79_2_WTA | 049 | Full ROI


title: FHSC14_sgUSP22_SAL2_H3K27me3

description: Library name: H14_U2_H3me27


title: 786O + VHL (WT8), shControl, biolrep 3

value: WT


title: FHSC14_sgUSP22_SAL1_H2AK119ub

description: Library name: H14_U1_H2ub119


title: FHSC14_sgUSP22_SAL1_H3K27me3

description: Library name: H14_U1_H3me27


title: FHSC14_sgUSP22_CE2_H3K27me3

description: Library name: H14ce_U2_H3me27


title: PR79_2_WTA | 054 | fb

value: Fibroblasts


title: PR79_2_WTA | 048 | Trp


title: A498, shControl, biol rep 1


title: 786O + VHL (WT8), shControl, biolrep 2


title: PR79_2_WTA | 048 | fb


title: 786O + VHL (WT8), shControl, biolrep 1


title: PR79_2_WTA | 048 | vessel


title: FHSC14_IgG3

description: Library name: H14_C3_IgGRab1

value: normal Rabbit IgG (Cell Signaling, 2729)


title: SC11.2_OE_AAI

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

department: Department of Medicine

institute: Stony Brook University

library_source: transcriptomic single cell

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Assembly: mm10
Supplementary files format and content: A csv file containing normalized expression of genes based on cluster and group

molecule: nuclear RNA

source_name: Kidney cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: Kidney cortex

tag: strain

value: mixed

tag: Sex

value: male

value: AAI


title: FHSC14_sgCtrl_SAL3_H3K27me3

description: Library name: H14_C3_H3me27

value: SCLC PDX tumor

value: sgCtrl


title: 786O, shBMAL1, biolrep 3


title: PR79_2_WTA | 047 | Full ROI

value: LV


title: SC11.3_OE


title: FHSC14_IgG2

description: Library name: H14_C2_IgGRab1

value: SAL


title: SC11.1_Control_AAI


title: 786O, shBMAL1, biolrep 2


title: PR79_2_WTA | 046 | Trp

value: Cardiomyocytes

value: RV

value: Control


title: FHSC14_IgG1

description: Library name: H14_C1_IgGRab1


title: 786O, shBMAL1, biolrep 1

value: Adenocarcinoma; Renal Cell


title: SC11.4_Control


title: PR79_2_WTA | 046 | fb


title: 786O, shControl, biolrep 3


title: JHULX33_USP22_CE5

description:
Library name: JHULX33_USP22_CE5
LX33B_USP22_CE5

data_processing:
Reads were aligned to human genome assembly hg38 and GENCODE gene annotation v38 as well as mouse genome assembly mm10 and GENCODE gene annotation vM23 using STAR v2.7.7a with 2-pass mapping. Reads of mouse origin were removed using R package XenofilteR. Gene expression quantification was performed using FeatureCounts in Subread 2.0.0 and genes with low expression were excluded using edgeR function filterByExpr with min.count = 10 and min.total.count = 15. Following TMM normalization, differentially expressed genes between sample groups were identified using Bioconductor package edgeR 3.34.1 and were subjected to significance testing using GLM LRT method and Benjamini-Hochberg p-value correction.
Assembly: hg38
Supplementary files format and content: JHU-LX33 rawCounts.txt contains a gene-by-sample read count matrix. The total exonic length for each gene is included.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). mRNA was was poly(A) enriched using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs) kit. 50 ng RNA was used for library construction.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s protocol.

treatment_protocol: SCLC PDX models were treated for a 10 day weekly cycle with intraparotineal injections of cisplatin (5 mg/kg)+etoposide (10 mg/kg) or saline vehicle

value: CE


title: FHSC14_sgCtrl_SAL2_H3K27me3

description: Library name: H14_C2_H3me27

value: H3K27me3 (Cell Signaling, 9733)


title: JHULX33_USP22_CE4

description:
Library name: JHULX33_USP22_CE4
LX33B_USP22_CE4


title: Progenitor renal cells from nephrectomy_donor R13072018P2

description:
nKPC_10
R13072018P2

data_processing:
Reads were quality assessed and preprocessed using FASTQC (v0.11.7) and Trimmomatic (v0.36) software
Quasi-mapping and transcript quantification was performed with Salmon against GENCODE v35 human genome annotation
Assembly: GRCh38
Supplementary files format and content: Matrix with raw read count per sample (columns) per transcript (rows)
Supplementary files format and content: tpm_genes.gencV35.csv

source_name: Progenitor renal cells, nephrectomy

growth_protocol: Urinary renal progenitor cells  and progenitor renal cells from nephrectomy  isolation was performed as previously described (Manonelles A et al, Front Physiol 2018 DOI:/10.3389/fphys.2018.01412; Lazzeri E et al. J Am Soc Nephrol 2015 doi: 10.1681/ASN.2014010057). Patients with sample contamination were also considered as screening failure. After cell isolation and expansion, samples with ≥80% CD133+CD24+ positivity by FACs analysis were suitable to study.

extract_protocol:
Total DNA was isolated by standard procedures using using conventional phenol:chloroform:isoamylalcohol (Sigma) extraction
Illumina Sequencing Analysis Viewer, Illumina run specifications, FastQC, and Quality control alignment INS-017

treatment_protocol: Any additional treatment from growth conditions was applied to the biological material prior DNA extraction

value: Progenitor renal cells, nephrectomy


title: PR79_2_WTA | 046 | vessel

value: Heart


title: FHSC14_sgCtrl_SAL1_H3K27me3

description: Library name: H14_C1_H3me27


title: 786O, shControl, biolrep 2

value: WT


title: JHULX33_USP22_CE3

description:
Library name: JHULX33_USP22_CE3
LX33B_USP22_CE3


title: PR79_2_WTA | 045 | Trp


title: Progenitor renal cells from nephrectomy_donor R13164201

description:
nKPC_08
R13164201


title: Progenitor renal cells from nephrectomy_donor R23072019P3

description:
nKPC_09
R23072019P3


title: 786O, shARNT, biol rep 3

value: ARNT knockdown


title: Progenitor renal cells from nephrectomy_donor R23102018P4

description:
nKPC_07
R23102018P4


title: PR79_2_WTA | 045 | fb

value: Fibroblasts


title: JHULX33_USP22_CE1

description:
Library name: JHULX33_USP22_CE1
LX33B_USP22_CE1

value: Empty


title: 786O, shARNT, biol rep 2


title: Progenitor renal cells from nephrectomy_donor 09072018P2

description:
nKPC_06
09072018P2


title: PR79_2_WTA | 044 | vessel


title: 786O, shARNT, biol rep 1


title: JHULX33_Empty_CE5

description:
Library name: JHULX33_Empty_CE5
LX33B_Ctrl_CE5


title: JHULX33_Empty_CE4

description:
Library name: JHULX33_Empty_CE4
LX33B_Ctrl_CE4


title: PR79_2_WTA | 043 | Trp


title: 786O, shBMAL1, biol rep 3

value: BMAL1 knockdown


title: Progenitor renal cells from nephrectomy_donor R130718

description:
nKPC_04
R130718


title: PR79_2_WTA | 043 | fb


title: 786O, shControl, biolrep 1


title: JHULX33_Empty _CE3

description:
Library name: JHULX33_Empty _CE3
LX33B_Ctrl_CE3

value: SCLC PDX tumor


title: 786O, shBMAL1, biol rep 2


title: JHULX33_Empty_CE2

description:
Library name: JHULX33_Empty_CE2
LX33B_Ctrl_CE2


title: PR79_2_WTA | 044 | Trp


title: Progenitor renal cells from nephrectomy_donor R200519

description:
nKPC_02
R200519


title: Progenitor renal cells from nephrectomy_donor R10139962

description:
nKPC_03
R10139962


title: 786O, shControl, biol rep 3


title: JHULX33_USP22_CE2

description:
Library name: JHULX33_USP22_CE2
LX33B_USP22_CE2


title: PR79_2_WTA | 043 | vessel


title: JHULX33_Empty_CE1

description:
Library name: JHULX33_Empty_CE1
LX33B_Ctrl_CE1


title: Progenitor renal cells from nephrectomy_donor R121118

description:
nKPC_01
R121118


title: JHULX33_USP22_SAL5

description:
Library name: JHULX33_USP22_SAL5
LX33B_USP22_S5


title: 786O, shControl, biol rep 2


title: Progenitor renal cells from nephrectomy_donor R26062018P1

description:
nKPC_05
R26062018P1


title: Urine progenitor renal cells_DEAD donor 221

description:
221_DEAD
221

source_name: urine progenitor renal cells

value: urine progenitor renal cells


title: PR79_2_WTA | 040 | Trp

value: LV


title: JHULX33_USP22_SAL4

description:
Library name: JHULX33_USP22_SAL4
LX33B_USP22_S4

value: SAL


title: 786O, shControl, biol rep 1


title: PR79_2_WTA | 042 | Trp

value: Cardiomyocytes


title: PR79_2_WTA | 037 | Trp

value: DCMP


title: JHULX33_USP22_SAL3

description:
Library name: JHULX33_USP22_SAL3
LX33B_USP22_S3


title: Ldlr-/-, 16-week Western diet

city: New York

first: Chenyi

last: Xue

institute: Columbia University

description: Library name: RBM019

data_processing:
Fastq files were processed by Cell Ranger 5.0.1 from 10x genomics to generate count matrices of unique molecular identifiers (UMIs). Reads were mapped to mouse reference genome mm10 and transcriptome annotated by GENCODE vM23 from 10x prebuilt reference package version 2020-A.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: blood monocyte

extract_protocol:
RNA was extracted using 10x Genomics Chromium Single Cell 3' v3 protocol.
Library was constructed using 10x Genomics Chromium Single Cell 3' v3 protocol. 5000 cells and 100M reads were targeted per sample.

value: blood monocyte

value: 16-week Western diet


title: Urine progenitor renal cells_DEAD donor 219

description:
219_DEAD
219


title: 786O, shBMAL1, biol rep 1

value: Adenocarcinoma; Renal Cell


title: PR79_2_WTA | 037 | vessel


title: PR79_2_WTA | 038 | Trp

value: RV

value: Control


title: JHULX33_USP22_SAL2

description:
Library name: JHULX33_USP22_SAL2
LX33B_USP22_S2


title: Urine progenitor renal cells_ALIVE donor 212

description:
212_ALIVE
212


title: PR79_2_WTA | 036 | Trp

value: Heart


title: Ldlr-/-, 16-week chow diet

description: Library name: RBM018

value: 16-week chow diet


title: JHULX33_USP22_SAL1

description:
Library name: JHULX33_USP22_SAL1
LX33B_USP22_S1


title: Urine progenitor renal cells_DEAD donor 187

description:
187_DEAD
187


title: Ldlr-/-, 8-week Western diet

description: Library name: RBM017

value: 8-week Western diet


title: PR79_2_WTA | 035 | Trp

value: ICMP


title: JHULX33_Empty_SAL5

description:
Library name: JHULX33_Empty_SAL5
LX33B_Ctrl_S5

value: Empty


title: Urine progenitor renal cells_DEAD donor 183

description:
183_DEAD
183


title: Ldlr-/-, 8-week chow diet

description: Library name: RBM016

value: 8-week chow diet


title: PR79_2_WTA | 034 | Trp


title: JHULX33_Empty_SAL4

description:
Library name: JHULX33_Empty_SAL4
LX33B_Ctrl_S4

value: SCLC PDX tumor


title: Urine progenitor renal cells_DEAD donor 182

description:
182_DEAD
182

value: urine progenitor renal cells


title: Ldlr-/-, 0-week diet

description: Library name: RBM009F

value: 0-week diet


title: PR79_2_WTA | 034 | fb

value: Fibroblasts

value: LV


title: Urine progenitor renal cells_ALIVE donor 220

description:
220_ALIVE
220


title: WT, chow diet, rep3

description: Library name: RBM008F

value: wild-type

value: chow-diet


title: Urine progenitor renal cells_DEAD donor 179

description:
179_DEAD
179


title: JHULX33_Empty_SAL3

description:
Library name: JHULX33_Empty_SAL3
LX33B_Ctrl_S3

value: SAL


title: PR79_2_WTA | 034 | vessel


title: JHULX33_Empty_SAL2

description:
Library name: JHULX33_Empty_SAL2
LX33B_Ctrl_S2


title: WT, chow diet, rep2

description: Library name: RBM007F

value: blood monocyte


title: PR79_2_WTA | 033 | Trp

value: Cardiomyocytes

value: RV


title: Urine progenitor renal cells_DEAD donor 156

description:
156_DEAD
156


title: WT, chow diet, rep1

description: Library name: RBM006F


title: Urine progenitor renal cells_DEAD donor 143

description:
143_DEAD
143


title: PR79_2_WTA | 033 | vessel

value: Heart

value: Control


title: PDXC-OS052 ISX9-2 [C&T]

source_name: Osteosarcoma patient-derived cells PDXC-OS054

extract_protocol: CUT&Tag was performed using the CUT&Tag-IT™ Assay Kit (Active Motif, 53160) with H3K27ac antibody (Abcam, ab4729). Briefly, cells after 6 days’ treatment were first incubated with concanavalin A beads and primary antibodies followed by secondary antibody. Then the chromatin is digested by tagmentation using the protein A-Tn5 (pA-Tn5) transposome enzyme. After DNA purification and PCR amplification with adaptors, samples were sequenced on Illumina NextSeq2000

value: Osteosarcoma patient-derived cells PDXC-OS052

value: 100µM ISX9 for 6 days


title: JHULX33_Empty_SAL1

description:
Library name: JHULX33_Empty_SAL1
LX33B_Ctrl_S1

value: Empty


title: DKO mouse2

city: DALLAS

last: YAN

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Library name: KY6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were done using CellRanger 7 software (10x Genomics)
Assembly: mouse reference mm10 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebellum

extract_protocol:
Cerebellum tissues were homogenized in 2 mL of ice-cold Nuclei EZ lysis buffer (MilliporeSigma, cat # EZ PREP NUC-101) using Dounce homogenizers. Nuclei were centrifuged at 500×g at 4°C for 5 min, washed with ice-cold Nuclei EZ lysis buffer. After wash, the nuclei were resuspended in nuclei suspension buffer (NSB) consisting of 1x PBS, 1% BSA (Thermo Fisher Scientific, cat# AM2618,) and 0.2U/l RNase inhibitor (Thermo Fisher Scientific, cat# AM2694) and were filtered through a 40-μm Flowmi Cell Strainer (Bel-Art, cat# H13680-0040). Cell suspension was adjusted to a final concentration of 1000 nuclei/μl with NSB.
Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 5’ Reagent Kits (10x Genomics) according to the manufacturer’s protocol.

value: cerebellum

tag: age

value: 8 weeks

value: Male


title: Urine progenitor renal cells_DEAD donor 141

description:
141_DEAD
141

tag: cell type

value: urine progenitor renal cells


title: PDXC-OS052 ISX9-1 [C&T]

source_name: Osteosarcoma patient-derived cells PDXC-OS053


title: Urine progenitor renal cells_DEAD donor 138

description:
138_DEAD
138


title: PR79_2_WTA | 032 | Trp


title: PR79_2_WTA | 031 | Trp


title: DKO mouse1

description:
Library name: KY5
10x Genomics


title: PDXC-OS052 DMSO-2 [C&T]

value: DMSO for 6 days


title: PR79_1_WTA | 006 | vessel

value: LV

value: ICMP


title: Urine progenitor renal cells_DEAD donor 118

description:
118_DEAD
118


title: PDXC-OS052 DMSO-1 [C&T]


title: KO mouse2

description:
Library name: KY4
10x Genomics


title: KO mouse1

description:
Library name: KY3
10x Genomics


title: PR79_2_WTA | 030 | Trp


title: PR79_2_WTA | 030 | vessel


title: Urine progenitor renal cells_DEAD donor 106

description:
106_DEAD
106


title: PR79_2_WTA | 029 | Trp

value: DCMP


title: PDXC-OS052 ISX9-2 [ATAC-seq]


title: Urine progenitor renal cells_DEAD donor 100

description:
100_DEAD
100


title: Ctrl mouse1

description:
Library name: KY1
10x Genomics


title: PDXC-OS052 ISX9-1 [ATAC-seq]


title: Ctrl mouse2

description:
Library name: KY2
10x Genomics


title: PR79_2_WTA | 028 | Trp


title: Urine progenitor renal cells_DEAD donor 099

description:
099_DEAD
099


title: PDXC-OS052 ISX9-2

description:
TZa7-6
Cell lines RNASeq_raw_count.txt

data_processing:
RNA-seq reads were mapped to the hg19 reference genome using STAR v. 2.7.3a. Read counts for individual genes were produced using count feature in HTSeq v. 0.6.0
Assembly: hg19
Supplementary files format and content: genes based raw counts of sequencing reads  were prepeared using htseq

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit. mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: 100µM ISX9 6 days


title: PR79_2_WTA | 027 | Trp


title: Urine progenitor renal cells_ALIVE donor 098

description:
098_ALIVE
098


title: HFD_KO_5

city: Barcelona

first: Francesc

last: Villarroya

address: Diagonal 643

department: Biochemistry and Molecular Biomedicine

institute: University of Barcelona

description:
Library name: ABA34588
Column name in raw_counts.txt: HFD_KO_5

data_processing:
Adaptor ligation, purification of 100 base-pair cDNA fragments, amplification of these fragments, and library preparation were performed according to the manufacturer’s instructions (Illumina) and sequenced using Illumina NovaSeq 6000 platform at Centro Nacional de Análisis Genómico (Barcelona, Spain).
The sequenced 100-base pair paired-end reads were quality-checked using FastQC, and Quality control alignment. The obtained reads were subsequently aligned to the mouse reference genome (GRCm39) using STAR (2.7.8a) and the number of exon reads for all RefSeq genes were counted using RSEM (1.3.0).
Data analysis of the resulting count matrix was performed in R studio (4.3.1) to determine differentially expressed genes by DESeq application (V1.42.0).
Assembly: GRCm39
Supplementary files format and content: raw counts from samples

source_name: Brown adipose tissue

growth_protocol: Mice were housed at 22 °C under a 12-h light cycle  (lights on, from 08.00 am to 08.00 pm) with 50% ±5% relative humidity with free access to water and a standard diet.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit, 2ug of total RNA was used for the construction of seq libraries
Integrity of RNA samples was determined using Qubit RNA IQ Assay (Invitrogen). A purification of 2ug from the obtained mRNA was performed using TruSeq RNA sample prep kit v2 (Illumina). Adaptor ligation, purification of 100 base-pair cDNA fragments, amplification of these fragments, and library preparation were performed according to the manufacturer’s instructions (Illumina) and sequenced

treatment_protocol: Mice were maintained under standard rodent diet (2018, Teklad Diet, Envigo) conditions or, where indicated, fed a high-fat diet for 12 weeks (#D12451, 45% Kcal fat, Envigo).

value: Brown adipose tissue

value: Acbp BAd-KO

value: HFD


title: HFD_KO_4

description:
Library name: ABA34587
Column name in raw_counts.txt: HFD_KO_4


title: PDXC-OS052 ISX9-1

description:
TZa7-5
Cell lines RNASeq_raw_count.txt


title: Urine progenitor renal cells_ALIVE donor 097

description:
097_ALIVE
097


title: HFD_KO_3

description:
Library name: ABA34586
Column name in raw_counts.txt: HFD_KO_3


title: PR79_2_WTA | 026 | Trp

value: Heart

value: Cardiomyocytes

value: RV


title: 143B cells, ISX9 -2

description:
TZa15-10
CRISPRa_raw count screen.csv

data_processing:
The CRISPR screening data are processed and analyzed using the MAGeCK V0.5
Assembly: hg19
Supplementary files format and content: Raw sequencing data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA, then MAGeCK robust rank aggregation (RRA) method is used to identify negative and positive selected genes
Library strategy: DNA-seq

source_name: 143B cells

extract_protocol: Genomic DNA was isolated using NucleoSpin Blood Maxi kit. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 and products were purified with DNA Clean & Concentrator-100. sgRNA target regions (260-280bp) were further enriched by gel extraction after running agarose gel. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000 with 50-bp single-end-read settings.

value: 143B cells


title: 143B cells, ISX9 -1

description:
TZa15-9
CRISPRa_raw count screen.csv


title: Urine progenitor renal cells_DEAD donor 086

description:
086_DEAD
086


title: Urine progenitor renal cells_DEAD donor 083

description:
083_DEAD
083


title: PR79_2_WTA | 024 | Trp

extract_protocol:
Adult human heart samples were harvested between January 2018 and April 2021 and kept in paraffin blocks after formalin fixation. Control samples were obtained from autopsy cases with no history of HF or extracted from the left ventricle (LV) of the patients with normal LV function while receiving a heart transplant or a heart-lung transplan for isolated right ventricular failure or other reasons. Failing hearts were obtained from explanted hearts of recipients receiving a heart transplant, from excisional biopsy of patients receiving a LV assisant device, from myomectomy for obstructive HCMP, and from autopsy.
Formalin-fixed, paraffin-embedded sections were deparaffinized, went through antigen retrieval procedures, and then incubated with human WTA UV-cleavable RNA probes. They were co-stained with fluorescently conjugated antibody antibody morphologic markers against Troponin I, Vimentin, and CD31. After preparing tissue, bake slides with mounted sections in 60C drying oven for 30min to 3 hours. Deparaffinize and rehydrate FFPE tissue sections for 35 minutes. Target retriveal were performed for 25 minutes After exposing RNA targets, add 200 uL of hybridization solution made by manufacturer's buffer(Buffer R, Atlas Probe Mix, Custom assay1, Custom assay2, DEPC-treated H2O) in the hybridization chamber. Gently apply a Grace Bio-Labs HybriSlip and incubate at 37C for obernight at hybridization oven. Stringent wash was performed using 4X SSC with formamide and 2x SSC to remove off-target probes. Load prepared slides in to the GeoMX DSP instrument. Slides are scanned to capture fluorescent images used to select regions of interest(ROIs). The instrument collects UV-cleaved oligos from the ROIs into the wells of a collection plate.


title: 143B cells, DMSO -2

description:
TZa15-8
CRISPRa_raw count screen.csv

value: DMSO


title: PR79_2_WTA | 025 | Trp


title: HFD_KO_2

description:
Library name: ABA34585
Column name in raw_counts.txt: HFD_KO_2


title: Urine progenitor renal cells_ALIVE donor 062

description:
062_ALIVE
062


title: 143B cells, DMSO -1

description:
TZa15-7
CRISPRa_raw count screen.csv


title: HFD_WT_5

description:
Library name: ABA34571
Column name in raw_counts.txt: HFD_WT_5

value: Wild-type


title: PR79_2_WTA | 024 | vessel


title: Urine progenitor renal cells_DEAD donor 072

description:
072_DEAD
072


title: HFD_WT_4

description:
Library name: ABA34570
Column name in raw_counts.txt: HFD_WT_4


title: PR79_2_WTA | 024 | fb

value: Fibroblasts


title: Urine progenitor renal cells_DEAD donor 061

description:
061_DEAD
061


title: 143B cells, shELMSAN1-1 -2

description:
TZa17-2
RNA-seq raw count_ELMSAN1-OE and KD.csv

value: ELMSAN1 knockdown


title: PR79_2_WTA | 023 | Trp


title: HFD_WT_3

description:
Library name: ABA34569
Column name in raw_counts.txt: HFD_WT_3


title: Urine progenitor renal cells_DEAD donor 060

description:
060_DEAD
060

value: urine progenitor renal cells


title: 143B cells, shELMSAN1-1 -1

description:
TZa17-1
RNA-seq raw count_ELMSAN1-OE and KD.csv


title: PR79_2_WTA | 022 | Trp


title: Rh30 M+I -2 [ATAC-seq]

data_processing:
Sequencing reads were aligned to hg19 reference genome using BWA v. 0.7.17-r1188 with commandbwa sampe. Peaks were called using HOMER v. 4.10.3
Assembly: hg19
Supplementary files format and content: coverage track in bigwig format was prepared using bamCoverage function of the deepTools

source_name: Rhabdomyosarcoma cell line Rh30

value: Rhabdomyosarcoma cell line Rh30

value: MGCD0103 0.25µM plus ISX9 10µM for 6 days


title: Urine progenitor renal cells_ALIVE donor 058

description:
058_ALIVE
058


title: PR79_2_WTA | 022 | fb

data_processing:
In the initial step, raw sequencing FASTQ files are combined with a configuration file that outlines the processing parameters. Following this, the raw reads undergo computational processing to remove adapter sequences, producing trimmed reads, and paired-end reads are merged to create stitched reads. In the third step, these stitched reads are aligned to the RTS-ID barcodes in the reference assay, generating aligned reads and assigning counts to biological target names. Subsequently, PCR duplicates are removed by sorting based on the Unique Molecular Identifier (UMI) present in each read, resulting in deduplicated reads. Finally, DCC files are generated and compiled into a .zip file within a designated folder, ready for upload into the DSP Control Center for study creation in the DSP Data Analysis Suite.
Assembly: GRCh38
Supplementary files format and content: Process FASTQ sequencing files into digital count conversion (DCC) files
Library strategy: Nanostring GeoMX digital spatial profiler

value: LV

value: ICMP


title: HFD_WT_2

description:
Library name: ABA34568
Column name in raw_counts.txt: HFD_WT_2


title: Urine progenitor renal cells_DEAD donor 048

description:
048_DEAD
048


title: HFD_WT_1

description:
Library name: ABA34567
Column name in raw_counts.txt: HFD_WT_1


title: Rh30 M+I -1 [ATAC-seq]


title: HFD_KO_1

description:
Library name: ABA34572
Column name in raw_counts.txt: HFD_KO_1


title: Rh30 DMSO-2 [ATAC-seq]

value: DMSO for 6 days


title: Chow_KO_4

description:
Library name: ABA34542
Column name in raw_counts.txt: Chow_KO_4

value: Brown adipose tissue

value: Chow diet


title: Urine progenitor renal cells_DEAD donor 045

description:
045_DEAD
045


title: PR79_2_WTA | 021 | Trp


title: PR79_2_WTA | 022 | vessel


title: Rh30 DMSO-1 [ATAC-seq]


title: Urine progenitor renal cells_ALIVE donor 044

description:
044_ALIVE
044


title: Urine progenitor renal cells_DEAD donor 032

description:
032_DEAD
032


title: Chow_KO_2

description:
Library name: ABA34540
Column name in raw_counts.txt: Chow_KO_2

value: Acbp BAd-KO


title: PDXC-OS052 DMSO-1 [ATAC-seq]

source_name: Osteosarcoma patient-derived cells PDC-PSS008


title: Urine progenitor renal cells_DEAD donor 031

description:
031_DEAD
031


title: Chow_WT_4

description:
Library name: ABA34538
Column name in raw_counts.txt: Chow_WT_4


title: Rh30 M+I

value: MGCD0103 1µM plus ISX9 5µM for 4 days


title: PR79_2_WTA | 020 | vessel

value: Heart


title: PDXC-OS052 DMSO-2 [ATAC-seq]

value: Osteosarcoma patient-derived cells PDC-PSS008


title: Chow_WT_3

description:
Library name: ABA34537
Column name in raw_counts.txt: Chow_WT_3


title: Rh30 DMSO

value: DMSO for 4 days


title: Urine progenitor renal cells_DEAD donor 030

description:
030_DEAD
030


title: Chow_WT_2

description:
Library name: ABA34283
Column name in raw_counts.txt: Chow_WT_2


title: Urine progenitor renal cells_ALIVE donor 028

description:
028_ALIVE
028


title: SW1533 M+I

source_name: Chondrosarcoma cell line SW1533

value: Chondrosarcoma cell line SW1533

value: MGCD0103 0.2µM plus ISX9 5µM for 4 days


title: Chow_WT_1

description:
Library name: ABA34275
Column name in raw_counts.txt: Chow_WT_1

value: Wild-type


title: Urine progenitor renal cells_ALIVE donor 025

description:
025_ALIVE
025


title: PR79_2_WTA | 018 | Trp

value: Cardiomyocytes


title: SW1353 DMSO


title: Mouse esophagus, MGL WT 4

city: Graz

first: Rudolf

last: Schicho

address: Neue Stiftingtalstraße 6

country: Austria

institute: Medical University of Graz

description:
Library name: X8_MGL_WT
X8_wt

data_processing:
quality control - fastqc (0.11.9)
adapter trimming - Cutadapt
sequence alignement - STAR (2.7.10b)
Assembly: GRCm39
Supplementary files format and content: counts_gene_geo_final.txt, .txt file with raw counts from multiple samples

source_name: Mouse esophagus tissue

extract_protocol:
RNA was isolated from frozen mouse esophagus tissues of WT and MGL KO mice and analyzed using GENEWIZ (Azenta Life Sciences).
rRNA was removed by PolyA selection

value: Mouse esophagus tissue

value: MGL WT


title: Chow_KO_3

description:
Library name: ABA34541
Column name in raw_counts.txt: Chow_KO_3


title: Urine progenitor renal cells_DEAD donor 020

description:
020_DEAD
020

value: urine progenitor renal cells


title: Hs 819.T M+I

source_name: Chondrosarcoma cell line Hs 819.T

value: Chondrosarcoma cell line Hs 819.T

value: MGCD0103 1µM plus ISX9 10µM for 4 days


title: Mouse esophagus, MGL WT 3

description:
Library name: X7_MGL_WT
X7_wt


title: PR79_2_WTA | 017 | Trp

source_name: Heart

value: LV

value: ICMP


title: Urine progenitor renal cells_DEAD donor 008

description:
008_DEAD
008


title: PR79_2_WTA | 021 | vessel

value: RV


title: PR79_2_WTA | 016 | Trp

value: DCMP


title: Mouse esophagus, MGL WT 2

description:
Library name: X6_MGL_WT
X6_wt


title: PR79_2_WTA | 020 | Trp


title: KOS8 M+I

source_name: Osteosarcoma patient-derived cells PDC-KOS8

value: MGCD0103 1µM plus ISX9 20µM for 4 days


title: Hs 819.T DMSO


title: PR79_2_WTA | 019 | Trp

value: Heart


title: Urine progenitor renal cells_ALIVE donor 007

description:
007_ALIVE
007


title: PR79_2_WTA | 015 | fb

value: Fibroblasts

value: Control


title: PR79_2_WTA | 019 | fb


title: Mouse esophagus, MGL KO 4

description:
Library name: X4_MGL_KO
X4_ko

value: MGL KO


title: TMEM25_sh2_3

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

data_processing:
Adaptor and imcomplete sequences were removed by Trim Galore (ver. 0.6.6)
Short-read sequences were mapped on the human reference genome hg38 by STAR
mapped reads were counted by bedtools
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
RNA was extracted with Sepazol Super G RNA (Nakarai Tesque), followed by Dnase digestion with NucleoSpin RNA column kit. 700 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

tag: cell line

value: neural progenitor cells

value: TMEM25 knockdown


title: KOS7 M+I

source_name: Osteosarcoma patient-derived cells PDC-KOS7


title: PR79_2_WTA | 015 | vessel


title: TMEM25_sh2_2

tag: genotype


title: PR79_2_WTA | 014 | Trp

value: Cardiomyocytes


title: Mouse esophagus, MGL KO 3

description:
Library name: X3_MGL_KO
X3_ko

value: Mouse esophagus tissue


title: Mouse esophagus, MGL KO 2

description:
Library name: X2_MGL_KO
X2_ko


title: PR79_2_WTA | 013 | Trp


title: TMEM25_sh2_1


title: U-2 OS M+I

source_name: Osteosarcoma cell line U-2 OS

value: Osteosarcoma cell line U-2 OS

tag: treatment

value: MGCD0103 1µM plus ISX9 5µM for 4 days


title: TMEM25_sh1_3


title: PR79_2_WTA | 013 | vessel

tag: tissue


title: PR79_2_WTA | 015 | Trp

tag: ventricle


title: Lacrimal glands of scop mouse treated with tam,snRNA-seq

city: Qingdao

first: xiaoyu

last: li

state: Shandong

address: NO.5 Yanerdao Road

institute: Qingdao Eye Hospital of Shandong First Medical University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0(https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: matrix files

source_name: lacrimal gland

extract_protocol:
Fresh lacrimal glands were chopped to 1 mm3, homogenized with Nuclei EZ Lysis Buffer and filtered through a 40- μm cell strainer. The pellet was then resuspended in PBS after centrifugation at 500g for 5 minutes at 4°C. Red fluorescent protein (RFP)+ nuclei were collected individually in a 384-well plate for Smart-seq2 or 10x Genomics sequencing after resuspension in the MoFlo Astrios EQ Cell Sorter
The cells were partitioned into GEM generation, barcoded cDNA library construction, and prepared using the single-cell 3' mRNA kit (V3; 10X Genomics) as manufacturer’s directions. Then all libraries were subjected to quality tests (Fragment Analyzer 2100, Agilent Technologies) and sequencing (Platform: Illumina NovaSeq 6000;paired-end).

value: lacrimal gland

tag: group

value: dry eye mice induced by scopolamine (SCOP) and dry stress (DS)

value: tamsulosin


title: U-2 OS DMSO

value: DMSO for 4 days


title: Urine progenitor renal cells_DEAD donor 001

last: Bioinformatics

institute: Josep Carreras Leukemia Research Institute

description:
001_DEAD
001

source_name: urine progenitor renal cells

value: urine progenitor renal cells


title: Mouse esophagus, MGL WT 1

description:
Library name: X5_MGL_WT
X5_wt

value: MGL WT


title: TMEM25_sh1_1


title: PR79_2_WTA | 012 | vessel

value: RV

tag: clinical phenotype_lv

tag: p hypertrophy


title: Saos-2 DMSO

source_name: Osteosarcoma cell line Saos-2

value: Osteosarcoma cell line Saos-2


title: Mouse esophagus, MGL KO 1

description:
Library name: X1_MGL_KO
X1_ko


title: KOS8 DMSO

value: Osteosarcoma patient-derived cells PDC-KOS8


title: Lacrimal glands of healthy mouse,snRNA-seq

value: normal control


title: Saos-2 M+I

value: MGCD0103 0.2µM plus ISX9 1µM for 4 days


title: shControl_3

value: neural progenitor cells

value: WT


title: PR79_2_WTA | 011 | Trp

value: Heart

value: Cardiomyocytes

value: LV

tag: p degeneration

tag: p fibrosis


title: MG-63 M+I

source_name: Osteosarcoma cell line MG-63

value: Osteosarcoma cell line MG-63

value: MGCD0103 1µM plus ISX9 10µM for 4 days


title: KOS7 DMSO

value: Osteosarcoma patient-derived cells PDC-KOS7


title: CUT&RUN Mel18 knock out rep 2

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

institute: Northwestern University

description:
Mel18_KO_rep2
KO-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig

data_processing:
Sequencing quality was checked using FASTQC/MultiQC v0.11.5
Sequencing adptors were trimmed and low-quality reads were removed using Trimmomatic v0.40
Sequencing reads were mapped against reference genome mm10 using Bowtie2 v1.2.2
Duplicated alignments were filtered out with PICARD (http://broadinstitute.github.io/picard/)
H2AK119ub1-associated peaks were identified using MACS2 v2.1.1
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Bone marrow

extract_protocol:
H2AK119ub1-associated chromatin DNA was isolated using CUTANA CUT&RUN Kit from EpiCypher according to the manufactue's instruction
sequencing library was constructed using NEBNext Ultra II DNA library prep kit for Illumina
CUT&RUN coupled with next generation sequencing

value: Bone marrow

value: primary mouse cells

value: hematopoietic stem and progenitor cells

value: Mel18 knock out


title: shControl_2


title: PR79_2_WTA | 010 | Trp

tag: p disarray


title: CUT&RUN Mel18 knock out rep 1

description:
Mel18_KO_rep1
KO-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig


title: MG-63 DMSO

value: DMSO for 4 days


title: shControl_1


title: TMEM25_sh1_2

value: TMEM25 knockdown


title: PR79_2_WTA | 010 | vessel


title: HOS M+I

source_name: Osteosarcoma cell line HOS

value: Osteosarcoma cell line HOS


title: PR79_2_WTA | 012 | Trp

value: RV


title: CUT&RUN Mel18 knock out group control IgG

description:
Mel18_KO_IgG
KO-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig


title: vemurafenib Day 21 rep3

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC (v0.11.8) and mapped to the hg19 human genome using the STAR aligner (v2.5.3a) with default parameters.
Raw or TPM (Transcripts Per Kilobase Million) gene expression was quantified across all the exons of RefSeq genes with analyzeRepeats.pl in HOMER (v4.11.1), which used the top-expressed isoform as proxy for gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: SK-MEL-2 human melanoma cells

growth_protocol: SKMEL-2 cells were grown in EMEM (HyClone) supplemented with 10% fetal bovine serum (Atlanta Biologicals) and Penicillin-Streptomycin (Gibco).

extract_protocol:
The total RNA was extracted from SKMEL-2 human melanoma cells using E.Z.N.A. Total RNA Kit I (Omega Bio-Tek).
Libraries were sequenced on the HiSeq 2500 following standard protocols.

treatment_protocol: Cells were treated with the vehicle (DMSO), PLX8394 (10μM), or Vemurafenib (10 μM) for 0, 3, 7, 14, or 21 days.

tag: time point

value: Day 21

value: vemurafenib


title: Lacrimal glands of scop mouse,snRNA-seq

value: lacrimal gland

value: dry eye mice induced by scopolamine (SCOP) and dry stress (DS)


title: HOS DMSO


title: PDXC-OS052 M+I -2

value: Osteosarcoma patient-derived cells PDC-PSS008

value: MGCD0103 1µM plus ISX9 20µM for 6 days


title: CUT&RUN Wiild type bio rep 2

description:
WT_rep2
WT-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig

value: Wildtype


title: PR79_2_WTA | 008 | Trp

value: Heart

value: Cardiomyocytes

value: LV

value: ICMP


title: vemurafenib Day 21 rep1


title: vemurafenib Day 21 rep2


title: CUT&RUN Wiild type bio rep 1

description:
WT_rep1
WT-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig

value: Bone marrow

value: primary mouse cells

value: hematopoietic stem and progenitor cells


title: CUT&RUN Wild type group control IgG

description:
WT_IgG
WT-H2AK119Ub_CUTRUN_nodup.pval.signal.bigwig


title: PR79_2_WTA | 007 | Trp


title: PDXC-OS052 DMSO-2

value: DMSO for 6 days


title: PDXC-OS052 M+I -1


title: PLX8394 Day 21 rep3


title: PR79_2_WTA | 006 | Trp


title: ATAC-seq Mel18 knock out, mouse 5

data_processing:
Sequencing quality was checked using FASTQC/MultiQC v0.11.5
Sequencing adptors were trimmed and low-quality reads were removed using Trimmomatic v0.40
Sequencing reads were mapped against reference genome mm10 using Bowtie2 v1.2.2
Duplicated alignments were filtered out with PICARD (http://broadinstitute.github.io/picard/)
ATAC-seq peaks were identified using MACS2 v2.1.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and logCPM for each sample

extract_protocol:
Lin- cells were lysed and incubated with Tn5 rtransposase at 37 degree for 1hr. Genomic DNA was eluented then purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter). Recovered tagmented DNA was amplified and barcoded by PCR performed with KAPA HotStart Taq enzyme (Kapa Biosystems).
sequencing library was constructed using NEBNext Ultra II DNA library prep kit for Illumina

value: Mel18 knock out


title: PLX8394 Day 21 rep1


title: PR79_2_WTA | 005 | Trp


title: Female 4 Total cell RNA (Total)

city: College Station

first: Darrell

last: Pilling

state: Texas

address: 301 Old Main Drive

department: Biology

institute: Texas A&M University

description:
Library name: Female 4 Total
120619F2-Total_S6

data_processing:
RNA sequencing data were analyzed using the QuantSeq Data Analysis Pipeline on the BlueBee Genomic Platform. The quality of sequences was evaluated using FastQC software (version 0.11.5) after adapter trimming with BBDUK software (version 35.92).
Assembly: hg38
Supplementary files format and content: CSV files for total and fractionated datasets

source_name: blood

extract_protocol:
Human neutrophils were isolated from blood using  Polymorphprep
Neutrophils were lysed with polysome buffer. One fraction was retained as total lysate (total cell RNA), the rest was fractionated on sucrose gradients to collect free RNA, monosome RNA, and early and late polysome RNA.
RNAseq libraries were created using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), with 2 µg of RNA used as the starting material.
RNAseq libraries were created using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), with 2 µg of RNA used as the starting material. Libraries were sequenced using an Illumina NextSeq 500 platform

value: blood

value: neutrophil


title: PR79_2_WTA | 005 | vessel


title: ATAC-seq Mel18 knock out, mouse 4


title: DMSO Day 21 rep3

value: Day 21

value: vehicle (DMSO)


title: PR79_2_WTA | 009 | Trp

value: RV


title: Female 4 Late Polysome RNA (F10-12)

description:
Library name: Female 4 late polysome
120619F2-F10-12_S35


title: ATAC-seq Wiild type, mouse 3


title: PR79_2_WTA | 003 | Trp


title: DMSO Day 21 rep2


title: Female 4 Early Polysome RNA (F7-9)

description:
Library name: Female 4 early polysome
120619F2-F7-9_S28


title: PR79_2_WTA | 004 | Full ROI


title: PR79_2_WTA | 002 | Trp


title: ATAC-seq Wiild type, mouse 2


title: Female 4 Monosome RNA (F4-6)

description:
Library name: Female 4 monosome
120619F2-F4-6_S20


title: vemurafenib Day 14 rep3

value: Day 14

value: vemurafenib


title: Mel18 knock out, HSCs mouse 6 [WC-6_S50]

data_processing:
Sequencing quality was checked using FASTQC/MultiQC v0.11.5
Sequencing adptors were trimmed and low-quality reads were removed using Trimmomatic v0.40
Sequencing reads were mapped against reference genome mm10 using STAR v2.5
Differentially expressed genes were identified using edgeR v3.28.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and logRPKM for each sample

extract_protocol:
total RNA was isolated using Clontech SMART-Seq v4 Ultra Low Input RNA Kit
sequencing library was constructed using Nextera XT DNA Lib Kit for Illumina


title: ATAC-seq Wiild type, mouse 1

value: Wildtype


title: Female 4 Free RNA (F1-3)

description:
Library name: Female 4 free
120619F2-F1-3_S13


title: PR79_2_WTA | 001 | Trp

value: Heart


title: DMSO Day 21 rep1


title: ATAC-seq Mel18 knock out, mouse 6


title: vemurafenib Day 14 rep2


title: PDXC-OS052 DMSO-1

value: Osteosarcoma patient-derived cells PDC-PSS008


title: PLX8394 Day 21 rep2


title: Male 3 Total cell RNA (Total)

description:
Library name: Male 3 Total
120619M-Total_S4


title: Mel18 knock out, HSCs mouse 5 [WC-5_S49]


title: PR79_2_WTA | 001 | vessel

value: LV


title: Male 3 Late Polysome RNA (F10-12)

description:
Library name: Male 3 late polysome
120619M-F10-12_S33