title: mf-lon WT, 4h P.I. (AtC) replicate_2

description: Library name: ARN14

data_processing:
Rockhopper software
Sequences were mapped to E.coli MG1655 (NC_000913.3) and read counts were extracted using Rockhopper. RPKMs were calculated based on the total number of reads without rRNAs.
Assembly: E.coli MG155 genome used was NC_000913.3
Supplementary files format and content: tab delimited text file includes raw counts and RPKM values for each sample

treatment_protocol: Exponential growth cultures were diluted in LB and were induced for 4h with 50ng/mL AtC.

value: MG1655pro lacZ::PLtetO-mf-lon

value: AtC 50ng/mL

value: 4H P.I


title: mf-lon TopA-PDT, 4h P.I. (AtC) replicate_2

status: Public on Aug 27 2025

type: SRA

city: Paris Cedex 05

first: Celine

last: Borde

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de france

description: Library name: ARN18

library_source: transcriptomic

molecule: total RNA

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Bacteria were grown in rich medium,LB, at 30°C with agitation.

extract_protocol:
Total RNA was extracted by an aqua-phenol extraction and ethanol precipitation.
Libraries were prepared by Novogene as 150 bp paired-end reads, using an rRNA depletion kit and the Prokaryotic Directional mRNA Library Preparation Kit.

tag: cell type

value: Escherichia coli

tag: genotype

tag: treatment

tag: time


title: prostate_cancer_primary_421 (STAMPEDE)

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

country: USA

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

treatment_protocol: Not Applicable

tag: gleason score

tag: age at randomization

tag: psa at randomization (ng/ml)

tag: tissue

value: FFPE prostate cancer


title: 4DNEXK1UBWZO, Homo sapiens - HCT116, condition 3 anti-DDX39B, treated with Auxin, B1 T1

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
Library name: 4DNEXK1UBWZO
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-DDX39B_Auxin, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXK1UBWZO/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSPK4WZYH/, Results include

library_source: genomic

data_processing:
Raw sequencing reads were first mapped to the human genome (UCSC hg38) using Bowtie 2 version 2.0.2 with default parameters. For cell lines derived from females like U2OS, Chromosome Y was excluded in the reference genome to reduce mapping bias.
PCR duplicates reads were removed using samtools version 0.1.19 with default parameters.
We normalized and processed the TSA-Seq data using a sliding window approach as follows. The normalized SON-TSA score was calculated as the log 2 ratio of (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). This approach can be interpreted as the fold change between the pulldown sample and the input corrected by the total number of mapped reads in each sample. The window slides on the genome with a step size of 100 bp.
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw) files

molecule: genomic DNA

extract_protocol:
Cell were fixed with 1.6% paraformaldehyde for 20 minutes. After quenching, TSA-reaction (proximity-labelling) and cell lysis, genomic DNA was sonicated using Biorupter Pico sonicator (Diagenode).
TSA-Seq libraries were constructed using TruSeq ChIP Library Preparation Kit (Illumina). 3-10 ng DNA was used as the starting material for input and ip samples. Libraries were amplified for 8 cycles  in a thermocycler. Post amplification, libraries were purified using  Beckman Coulter AMPure XP beads. Concentrations of individual libraries were estimated by Qubit high sensitivity DNA kit and also by qPCR and then pooled accordingly. Pooled libraries were sequenced from one end of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.  Fastq files were generated and demultiplexed with the bcl-convert v4.1.7 Conversion Software (Illumina).

tag: cell line

value: immortalized cell line

value: condition3 anti-DDX39B_Auxin


title: 4DNEXRYNND7E, Homo sapiens - HCT116, input-condition 3 anti-DDX39B, treated with Auxin, B2 T1

description:
Library name: 4DNEXRYNND7E
TSA-seq in HCT116 (Homo sapiens), input-condition3 -anti-DDX39B_Auxin, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXRYNND7E/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSE1H2XNF/, Results include

value: input-condition3 anti-DDX39B_Auxin

tag: input-reference


title: 4DNEXT9SZLLC, Homo sapiens - HCT116, input-condition 3 anti-DDX39B, treated with Auxin, B1 T1

description:
Library name: 4DNEXT9SZLLC
TSA-seq in HCT116 (Homo sapiens), input-condition3 -anti-DDX39B_Auxin, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXT9SZLLC/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSPK4WZYH/, Results include


title: 4DNEXRJXPV9D, Homo sapiens - HCT116, condition 3 anti-THRAP3, treated with DMSO, B2 T1

description:
Library name: 4DNEXRJXPV9D
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_DMSO, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXRJXPV9D/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSISGQ1MP/, Results include

value: condition3 anti-THRAP3_DMSO


title: G12, Rituximab, rep3

city: La Jolla

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr. IBRFII, 5220E

department: Bioengineering; Pediatrics

institute: University of California, San Diego

description: Library name: G12_R3

data_processing:
The samples were quality controlled using FastQC and the adapter sequences trimmed using Trimmomatic
The sequences were demultiplexd with bcl2fastq v2.20 Conversion Software.
Reads were mapped to the CHO GCF_003668045.1_CriGri-PICRR genome, aligned and quantified with Salmon.
Assembly: CHO GCF_003668045.1_CriGri-PICRR
Supplementary files format and content: cvs files include TPM values for each sample

organism: Cricetulus griseus

source_name: CHO-S

growth_protocol: A panel of ten cell CHO-S clones expressing Rituximab were obtained. A Laminin-alpha1 knock-out CHO-S clone line was obtained to use as a control. CHO-S cells were grown in 125ml Erlenmeyer shaker flasks with baffled bottom (Fisher Scientific, USA) in a humidified 37oC incubator with shaking at 130 RPM at 5% CO2 with CD CHO Medium (Gibco, USA) supplemented with 8mM L-Glutamine (Gibco) and 1x anti-clumping agent (Gibco). The Rituximab producing clones were grown in media containing 250 ug/ml Geneticin Selective Antibiotic (G418 sulfate; Gibco) for selection.

extract_protocol:
RNA was harvested and extracted using the RNAeasy Kit (Qiagen)
RNA quality was analyzed using the Agilent Tapestation 4200, and only samples with an RNA Integrity Number (RIN) exceeding 8.0 were selected for library construction. Libraries were prepared using the Illumina Stranded mRNA Sample Prep Kit with Illumina RNA UD Indexes (Illumina, San Diego, CA), following the manufacturer's guidelines.

value: CHO-S

value: Chinese Hamster Ovaries


title: G12, Rituximab, rep2

description: Library name: G12_R2


title: prostate_cancer_primary_422 (STAMPEDE)


title: 4DNEX12K8VKH, Homo sapiens - U2OS, input-condition3enhancementG - anti-DDX39B, B1 T1

description:
Library name: 4DNEX12K8VKH
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-DDX39B, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX12K8VKH/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include

value: input- condition3 anti-DDX39B


title: 4DNEXPLM4LXZ, Homo sapiens - HCT116, input-condition 3 anti-THRAP3, treated with DMSO, B2 T1

description:
Library name: 4DNEXPLM4LXZ
TSA-seq in HCT116 (Homo sapiens), input-condition3 -anti-THRAP3_DMSO, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXPLM4LXZ/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSISGQ1MP/, Results include

value: input-condition3 anti-THRAP3_DMSO


title: G12, Rituximab, rep1

description: Library name: G12_R1


title: 4DNEXN3KWQ62, Homo sapiens - HCT116, input-condition 3 anti-THRAP3, treated with DMSO, B1 T1

description:
Library name: 4DNEXN3KWQ62
TSA-seq in HCT116 (Homo sapiens), input-condition3 -anti-THRAP3_DMSO, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXN3KWQ62/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSQEOM67N/, Results include


title: prostate_cancer_primary_420 (STAMPEDE)


title: prostate_cancer_primary_418 (STAMPEDE)


title: 4DNEXXG6VOHI, Homo sapiens - HCT116, condition 3 anti-THRAP3, treated with Auxin, B2 T1

description:
Library name: 4DNEXXG6VOHI
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_Auxin, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXXG6VOHI/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSE1H2XNF/, Results include

value: condition3 anti-THRAP3_Auxin


title: F1, Rituximab, rep3

description: Library name: F1_R3


title: prostate_cancer_primary_419 (STAMPEDE)


title: 4DNEXN7N2M4T, Homo sapiens - HCT116, input-condition 3 anti-THRAP3, treated with Auxin, B2 T1

description:
Library name: 4DNEXN7N2M4T
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_Auxin, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXN7N2M4T/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSE1H2XNF/, Results include

value: input-condition3 anti-THRAP3_Auxin


title: F1, Rituximab, rep2

description: Library name: F1_R2


title: 4DNEXZZXTUXO, Homo sapiens - HCT116, condition 3 anti-THRAP3, treated with Auxin, B1 T1

description:
Library name: 4DNEXZZXTUXO
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_Auxin, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXZZXTUXO/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSPK4WZYH/, Results include


title: prostate_cancer_primary_417 (STAMPEDE)


title: Rep1_I_48H

city: Richmond

first: Paige

middle: E

last: Allen

state: VA

address: 1220 East Broad MMRB 4-055

department: Microbiology and Immunology

institute: Virginia Commonwealth University

description: Library name: Rep1_I_48H

data_processing:
Original image data file from high-throughput sequencing platform was transformed to sequenced reads by CASAVA base recognition (Base Calling).
Reads with adaptor contamination, with > 10% uncerntain nucleotides (N), and/or with >50% low quality nucleotides (Base quality less than 5) were removed.
Spliced Transcripts Alignment to a Reference (STAR) program was employed to map raw reads to human reference genome (GRCh38/hg38).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file contains fpkm for all samples

growth_protocol: EA.hy926 cells at 100% confluency were synchronously infected with O. tsutsugamushi or left uninfected. RNA was collected from ninfected or infected cells at 8 h, 48 h, and 72 h.

extract_protocol:
At 8, 48, and 72 h p.i., spent medium was removed and the cells washed with 1X PBS before trypsinization. Dislodged cells were pelleted at 1000 xg for 3 min, and total RNA was extracted using RNeasy mini kit (Qiagen [74104], Hilden, Germany).
RNA library was constructed using mRNA Seq V2 Library Prep Kit following manufacturers protocol.

treatment_protocol: No treatment

value: Immortalized human vascular endothelial cells

value: infected with O. tsutsugamushi

tag: batch


title: Rep1_U_72H

description: Library name: Rep1_U_72H


title: E10, Rituximab, rep3

description: Library name: E10_R3


title: Rep1_U_48H

description: Library name: Rep1_U_48H


title: prostate_cancer_primary_416 (STAMPEDE)


title: prostate_cancer_primary_415 (STAMPEDE)


title: Rep1_I_8H

description: Library name: Rep1_I_8H

value: 8 h


title: 4DNEXDN3FR3Z, Homo sapiens - HCT116, condition 3 anti-THRAP3, treated with DMSO, B1 T1

description:
Library name: 4DNEXDN3FR3Z
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_DMSO, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXDN3FR3Z/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSQEOM67N/, Results include


title: E10, Rituximab, rep2

description: Library name: E10_R2


title: E10, Rituximab, rep1

description: Library name: E10_R1


title: MCF7 TP53 R181C/- Nutlin 24hr c

city: Philadelphia

first: Kara

last: Maxwell

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
Library name: Sample 54
MCF7_R181C_S1G11_24hr_c raw RNA Seq Counts

data_processing:
RNA-seq: Reads were aligned with STAR version 2.4.1d
RNA-seq: Reads were counted with HTSeq version 2.0.5
Assembly: GRCh38
Supplementary files format and content: RNA-seq: tab-delimited text file includes raw counts for each Sample

growth_protocol: HCT116 cells were grown in McCoy's 5A Media supplemented with 10% fetal bovine serum (FBS) and 1% Penn-Strep (PS). MCF7 cells were cultured in EMEM supplemented with 10% FBS and 1% PS. All cells were grown in humidified incubator with 5% carbon dioxide (CO2) at 37C.

extract_protocol:
RNA was harvested using RNeasy mini kit (QIAGEN). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit following manufacturer's protocols.

treatment_protocol: 10 uM of Nutlin-3a was added to cells when they were 70% confluent - the cells were harvested either 8 hours or 24 hours post-treatment. The 0 hour samples were treated with DMSO.

value: cancer cells

value: 10 uM Nutlin-3a

value: 24 hr


title: MCF7 TP53 R181C/- Nutlin 24hr b

description:
Library name: Sample 53
MCF7_R181C_S1G11_24hr_b raw RNA Seq Counts


title: prostate_cancer_primary_413 (STAMPEDE)

value: FFPE prostate cancer


title: 4DNEXBNTHPGO, Homo sapiens - HCT116, input-condition 3 anti-THRAP3, treated with Auxin, B1 T1

description:
Library name: 4DNEXBNTHPGO
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-THRAP3_Auxin, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXBNTHPGO/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSPK4WZYH/, Results include

value: immortalized cell line


title: prostate_cancer_primary_414 (STAMPEDE)


title: Rep1_I_72H

description: Library name: Rep1_I_72H


title: prostate_cancer_primary_411 (STAMPEDE)


title: prostate_cancer_primary_412 (STAMPEDE)


title: F1, Rituximab, rep1

description: Library name: F1_R1


title: MCF7 TP53 R181C/- Nutlin 8hr a

description:
Library name: Sample 49
MCF7_R181C_S1G11_8hr_a raw RNA Seq Counts

value: 8 hr


title: E9, Rituximab, rep3

description: Library name: E9_R3


title: MCF7 TP53 R181C/- Nutlin 8hr c

description:
Library name: Sample 51
MCF7_R181C_S1G11_8hr_c raw RNA Seq Counts


title: MCF7 TP53 R181C/- Nutlin 0hr c

description:
Library name: Sample 48
MCF7_R181C_S1G11_0hr_c raw RNA Seq Counts

value: DMSO

value: 0 hr


title: MCF7 TP53 R181C/- Nutlin 24hr a

description:
Library name: Sample 52
MCF7_R181C_S1G11_24hr_a raw RNA Seq Counts


title: E9, Rituximab, rep1

description: Library name: E9_R1

value: CHO-S


title: prostate_cancer_primary_410 (STAMPEDE)


title: MCF7 TP53 R181C/- Nutlin 0hr a

description:
Library name: Sample 46
MCF7_R181C_S1G11_0hr_a raw RNA Seq Counts


title: MCF7 TP53 R181C/- Nutlin 0hr b

description:
Library name: Sample 47
MCF7_R181C_S1G11_0hr_b raw RNA Seq Counts


title: E7, Rituximab, rep3

description: Library name: E7_R3

value: Chinese Hamster Ovaries


title: prostate_cancer_primary_408 (STAMPEDE)


title: MCF7 TP53 R181H/- Nutlin 24hr c

description:
Library name: Sample 45
MCF7_R181H_1C8_24hr_c raw RNA Seq Counts


title: Rep1_U_8H

description: Library name: Rep1_U_8H


title: MCF7 TP53 R181H/- Nutlin 24hr b

description:
Library name: Sample 44
MCF7_R181H_1C8_24hr_b raw RNA Seq Counts


title: E7, Rituximab, rep2

description: Library name: E7_R2


title: prostate_cancer_primary_409 (STAMPEDE)


title: prostate_cancer_primary_407 (STAMPEDE)


title: MCF7 TP53 R181H/- Nutlin 24hr a

description:
Library name: Sample 43
MCF7_R181H_1C8_24hr_a raw RNA Seq Counts


title: MCF7 TP53 R181H/- Nutlin 8hr c

description:
Library name: Sample 42
MCF7_R181H_1C8_8hr_c raw RNA Seq Counts


title: E7, Rituximab, rep1

description: Library name: E7_R1


title: MCF7 TP53 R181H/- Nutlin 8hr b

description:
Library name: Sample 41
MCF7_R181H_1C8_8hr_b raw RNA Seq Counts


title: prostate_cancer_primary_406 (STAMPEDE)


title: MCF7 TP53 R181H/- Nutlin 8hr a

description:
Library name: Sample 40
MCF7_R181H_1C8_8hr_a raw RNA Seq Counts


title: MCF7 TP53 R181H/- Nutlin 0hr c

description:
Library name: Sample 39
MCF7_R181H_1C8_0hr_c raw RNA Seq Counts


title: E6, Rituximab, rep3

description: Library name: E6_R3


title: MCF7 TP53 R181H/- Nutlin 0hr b

description:
Library name: Sample 38
MCF7_R181H_1C8_0hr_b raw RNA Seq Counts


title: E6, Rituximab, rep2

description: Library name: E6_R2


title: MCF7 TP53 R181H/- Nutlin 0hr a

description:
Library name: Sample 37
MCF7_R181H_1C8_0hr_a raw RNA Seq Counts


title: E6, Rituximab, rep1

description: Library name: E6_R1


title: prostate_cancer_primary_404 (STAMPEDE)


title: MCF7 TP53 +/- Nutlin 24hr a

description:
Library name: Sample 34
MCF7_WTKO_P2D5_24hr_a raw RNA Seq Counts


title: prostate_cancer_primary_405 (STAMPEDE)


title: MCF7 TP53 +/- Nutlin 8hr c

description:
Library name: Sample 33
MCF7_WTKO_P2D5_8hr_c raw RNA Seq Counts


title: B5, Rituximab, rep3

description: Library name: B5_R3


title: prostate_cancer_primary_403 (STAMPEDE)


title: MCF7 TP53 +/- Nutlin 8hr b

description:
Library name: Sample 32
MCF7_WTKO_P2D5_8hr_b raw RNA Seq Counts


title: MCF7 TP53 +/- Nutlin 8hr a

description:
Library name: Sample 31
MCF7_WTKO_P2D5_8hr_a raw RNA Seq Counts


title: B5, Rituximab, rep2

description: Library name: B5_R2


title: prostate_cancer_primary_402 (STAMPEDE)


title: MCF7 TP53 +/- Nutlin 0hr c

description:
Library name: Sample 30
MCF7_WTKO_P2D5_0hr_c raw RNA Seq Counts


title: B2, Rituximab, rep3

description: Library name: B2_R3


title: HCT116 TP53 R181C/- Nutlin 24hr c

description:
Library name: Sample 27
HCT116_R181C_D1_24hr_c raw RNA Seq Counts


title: MCF7 TP53 +/- Nutlin 0hr a

description:
Library name: Sample 28
MCF7_WTKO_P2D5_0hr_a raw RNA Seq Counts


title: prostate_cancer_primary_399 (STAMPEDE)


title: prostate_cancer_primary_401 (STAMPEDE)


title: HCT116 TP53 R181C/- Nutlin 24hr b

description:
Library name: Sample 26
HCT116_R181C_D1_24hr_b raw RNA Seq Counts


title: B2, Rituximab, rep2

description: Library name: B2_R2


title: MCF7 TP53 +/- Nutlin 24hr c

description:
Library name: Sample 36
MCF7_WTKO_P2D5_24hr_c raw RNA Seq Counts


title: MCF7 TP53 +/- Nutlin 24hr b

description:
Library name: Sample 35
MCF7_WTKO_P2D5_24hr_b raw RNA Seq Counts


title: HCT116 TP53 R181C/- Nutlin 24hr a

description:
Library name: Sample 25
HCT116_R181C_D1_24hr_a raw RNA Seq Counts


title: HCT116 TP53 R181C/- Nutlin 8hr c

description:
Library name: Sample 24
HCT116_R181C_D1_8hr_c raw RNA Seq Counts


title: prostate_cancer_primary_397 (STAMPEDE)


title: HCT116 TP53 R181C/- Nutlin 8hr b

description:
Library name: Sample 23
HCT116_R181C_D1_8hr_b raw RNA Seq Counts


title: HCT116 TP53 R181C/- Nutlin 0hr c

description:
Library name: Sample 21
HCT116_R181C_D1_0hr_c raw RNA Seq Counts


title: HCT116 TP53 R181C/- Nutlin 8hr a

description:
Library name: Sample 22
HCT116_R181C_D1_8hr_a raw RNA Seq Counts


title: B2, Rituximab, rep1

description: Library name: B2_R1


title: A6, Rituximab, rep2

description: Library name: A6_R2


title: HCT116 TP53 R181C/- Nutlin 0hr b

description:
Library name: Sample 20
HCT116_R181C_D1_0hr_b raw RNA Seq Counts


title: B5, Rituximab, rep1

description: Library name: B5_R1


title: prostate_cancer_primary_400 (STAMPEDE)


title: MCF7 TP53 +/- Nutlin 0hr b

description:
Library name: Sample 29
MCF7_WTKO_P2D5_0hr_b raw RNA Seq Counts


title: prostate_cancer_primary_396 (STAMPEDE)


title: HCT116 TP53 R181C/- Nutlin 0hr a

description:
Library name: Sample 19
HCT116_R181C_D1_0hr_a raw RNA Seq Counts


title: prostate_cancer_primary_395 (STAMPEDE)


title: prostate_cancer_primary_394 (STAMPEDE)


title: HCT116 TP53 R181H/- Nutlin 24hr c

description:
Library name: Sample 18
HCT116_R181H_3B3_24hr_c raw RNA Seq Counts


title: A6, Rituximab, rep1

description: Library name: A6_R1


title: HCT116 TP53 R181H/- Nutlin 24hr b

description:
Library name: Sample 17
HCT116_R181H_3B3_24hr_b raw RNA Seq Counts


title: A4, Rituximab, rep3

description: Library name: A4_R3


title: prostate_cancer_primary_393 (STAMPEDE)


title: HCT116 TP53 R181H/- Nutlin 8hr c

description:
Library name: Sample 15
HCT116_R181H_3B3_8hr_c raw RNA Seq Counts


title: prostate_cancer_primary_398 (STAMPEDE)


title: HCT116 TP53 R181H/- Nutlin 8hr b

description:
Library name: Sample 14
HCT116_R181H_3B3_8hr_b raw RNA Seq Counts


title: A4, Rituximab, rep2

description: Library name: A4_R2


title: A6, Rituximab, rep3

description: Library name: A6_R3


title: prostate_cancer_primary_392 (STAMPEDE)


title: HCT116 TP53 R181H/- Nutlin 8hr a

description:
Library name: Sample 13
HCT116_R181H_3B3_8hr_a raw RNA Seq Counts


title: HCT116 TP53 R181H/- Nutlin 0hr c

description:
Library name: Sample 12
HCT116_R181H_3B3_0hr_c raw RNA Seq Counts


title: prostate_cancer_primary_391 (STAMPEDE)


title: A4, Rituximab, rep1

description: Library name: A4_R1


title: CHO-S, Lama knockout, rep3

description: Library name: WT_R3

value: WT


title: HCT116 TP53 +/- Nutlin 24hr c

description:
Library name: Sample 9
HCT116_WT_KO_B1_24hr_c raw RNA Seq Counts


title: CHO-S, Lama knockout, rep2

description: Library name: WT_R2


title: HCT116 TP53 +/- Nutlin 24hr b

description:
Library name: Sample 8
HCT116_WT_KO_B1_24hr_b raw RNA Seq Counts


title: HCT116 TP53 +/- Nutlin 24hr a

description:
Library name: Sample 7
HCT116_WT_KO_B1_24hr_a raw RNA Seq Counts


title: HCT116 TP53 R181H/- Nutlin 0hr a

description:
Library name: Sample 10
HCT116_R181H_3B3_0hr_a raw RNA Seq Counts


title: CHO-S, Lama knockout, rep1

description: Library name: WT_R1


title: HCT116 TP53 +/- Nutlin 8hr b

description:
Library name: Sample 5
HCT116_WT_KO_B1_8hr_b raw RNA Seq Counts


title: HCT116 TP53 +/- Nutlin 8hr c

description:
Library name: Sample 6
HCT116_WT_KO_B1_8hr_c raw RNA Seq Counts


title: HCT116 TP53 +/- Nutlin 0hr c

description:
Library name: Sample 3
HCT116_WT_KO_B1_0hr_c raw RNA Seq Counts


title: HCT116 TP53 +/- Nutlin 8hr a

description:
Library name: Sample 4
HCT116_WT_KO_B1_8hr_a raw RNA Seq Counts


title: HCT116 TP53 R181H/- Nutlin 24hr a

description:
Library name: Sample 16
HCT116_R181H_3B3_24hr_a raw RNA Seq Counts


title: prostate_cancer_primary_389 (STAMPEDE)


title: HCT116 TP53 +/- Nutlin 0hr b

description:
Library name: Sample 2
HCT116_WT_KO_B1_0hr_b raw RNA Seq Counts


title: prostate_cancer_primary_387 (STAMPEDE)


title: HCT116 TP53 +/- Nutlin 0hr a

description:
Library name: Sample 1
HCT116_WT_KO_B1_0hr_a raw RNA Seq Counts


title: Olive Baboon, Sample 05, Sublingual, Male, Left Gland, Flash Frozen, RNA

city: Buffalo

first: Charikleia

last: Karageorgiou

state: NY

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

description: Library name: Bab-05-SL-Mal-L-FF-RNA

data_processing:
Mutltiple tools (FastQC, MultiQC, cutadapt, Hisat2, Kallisto, samtools, featureCounts, DESeq2)
Assembly: GCF_008728515.1; NCBI Papio anubis Annotation Release 104
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Papio anubis

source_name: Sublingual

extract_protocol:
RNA was isolated from 3 x 30µm sections of tissue using RNAqueous Micro Kit (Ambion) and total RNA samples were DNase-treated (Ambion). Sample yield and integrity was analyzed using a Bioanalyzer (Illumina)."
RNA sequencing was performed by standard operating procedure by GENEWIZ (https://www.genewiz.com/en) using Illumina HiSeq with a 2x150bp configuration.

value: Sublingual

tag: animal id

tag: Sex

value: Male


title: Olive Baboon, Sample 05, Submandibular, Male, Left Gland, Flash Frozen, RNA

description: Library name: Bab-05-SM-Mal-L-FF-RNA

source_name: Submandibular

value: Submandibular


title: Olive Baboon, Sample 05, Parotid, Male, Left Gland, Flash Frozen, RNA

description: Library name: Bab-05-PAR-Mal-L-FF-RNA

source_name: Parotid

value: Parotid


title: prostate_cancer_primary_388 (STAMPEDE)


title: HCT116 TP53 R181H/- Nutlin 0hr b

description:
Library name: Sample 11
HCT116_R181H_3B3_0hr_b raw RNA Seq Counts


title: Olive Baboon, Sample 05, Pancreas, Male, Flash Frozen, RNA

description: Library name: Bab-05-PANC-Mal-FF-RNA

source_name: Pancreas

value: Pancreas


title: Olive Baboon, Sample 05, Liver, Male, Flash Frozen, RNA

description: Library name: Bab-05-LIV-Mal-FF-RNA

source_name: Liver

value: Liver


title: prostate_cancer_primary_386 (STAMPEDE)


title: prostate_cancer_primary_390 (STAMPEDE)


title: hOrg_SMS_3

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: hOrg_SMS_3

data_processing:
Reads were trimmed and aligned to the human reference genome (GRCh38) using BWA-MEM. Paired-end alignments were filtered to retain valid Hi-C contacts.
Valid Hi-C pairs were parsed into contact matrices using HiC-Pro. ICE normalization was applied to generate genome-wide and chromosome-wide contact maps.
TADs and chromatin loops were identified using insulation score and HiCCUPS algorithms. Differential contact analysis was performed using HiCExplorer and custom R scripts.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Contact matrix in pairs file format

source_name: hOrg sample from SMS individual

growth_protocol: Patterned human cortical organoids were generated using the AggreWell system (StemCell technologies) according to manufacturer instructions.

extract_protocol:
Nuclei were extracted from crosslinked samples, followed by Hi-C proximity ligation. DNA was purified and subjected to end-repair, biotin pull-down, and library preparation with indexed adaptors.
Hi-C libraries were constructed using the Arima-HiC+ kit and amplified using NEBNext Ultra II reagents. Final libraries were size-selected and quality-checked using Bioanalyzer and Qubit before sequencing.

treatment_protocol: hiPSC and cortical organoid samples were crosslinked, lysed, and processed using Arima-HiC+ kit. Chromatin was digested, biotin-labeled, ligated, purified, and then sheared. Hi-C libraries were prepared according to the manufacturer's protocol.

value: neural

tag: disease

value: Smith-Magenis Syndrome

value: cortical organoid

tag: condition

value: SMS

value: F


title: hOrg_SMS_4

description: Library name: hOrg_SMS_4


title: hOrg_CTL_3

description: Library name: hOrg_CTL_3

source_name: hOrg sample from control individual

value: healthy

value: CTL


title: hOrg_SMS_2

description: Library name: hOrg_SMS_2


title: hOrg_CTL_2

description: Library name: hOrg_CTL_2


title: hOrg_CTL_4

description: Library name: hOrg_CTL_4

value: M


title: prostate_cancer_primary_383 (STAMPEDE)

value: FFPE prostate cancer


title: Olive Baboon, Sample 04, Submandibular, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-04-SM-Fem-L-FF-RNA

value: Female


title: prostate_cancer_primary_384 (STAMPEDE)


title: hIPSC_SMS_4

description: Library name: hIPSC_SMS_4

source_name: hiPSC sample from SMS individual

value: stem cell

value: hiPSC


title: Olive Baboon, Sample 04, Sublingual, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-04-SL-Fem-L-FF-RNA

value: Sublingual


title: hIPSC_SMS_2

description: Library name: hIPSC_SMS_2


title: hIPSC_SMS_3

description: Library name: hIPSC_SMS_3


title: hIPSC_SMS_1

description: Library name: hIPSC_SMS_1


title: prostate_cancer_primary_382 (STAMPEDE)


title: prostate_cancer_primary_381 (STAMPEDE)


title: hIPSC_CTL_4

description: Library name: hIPSC_CTL_4

source_name: hiPSC sample from control individual


title: Olive Baboon, Sample 04, Parotid, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-04-PAR-Fem-L-FF-RNA


title: hOrg_SMS_1

description: Library name: hOrg_SMS_1


title: hIPSC_CTL_3

description: Library name: hIPSC_CTL_3


title: prostate_cancer_primary_385 (STAMPEDE)


title: Olive Baboon, Sample 04, Pancreas, Female, Flash Frozen, RNA

description: Library name: Bab-04-PANC-Fem-FF-RNA


title: prostate_cancer_primary_380 (STAMPEDE)


title: prostate_cancer_primary_379 (STAMPEDE)


title: hIPSC_CTL_2

description: Library name: hIPSC_CTL_2


title: prostate_cancer_primary_378 (STAMPEDE)


title: Olive Baboon, Sample 04, Liver, Female, Flash Frozen, RNA

description: Library name: Bab-04-LIV-Fem-FF-RNA


title: M9C10_CM_2

city: MINNEAPOLIS

first: Sophie

last: Givens

state: MN

address: 312 Church Street SE, Room 7-256

department: Biomedical Engineering

institute: University of Minnesota

description: Library name: M9C10_CM_2_S17

data_processing:
The  University of Minnesota Research Informatics at MSI  analyzed the RNA Seq output. 2 x 50bp FastQ paired-end reads for 18 samples  were trimmed using Trimmomatic (v 0.33) enabled with the optional headcrop 3 and  “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC.
Sequencing reads were mapped to the human reference genome (GRCh38.109) using Hisat2.
Differentially expressed genes  were calculated using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo Sapiens GRCh38.109
Supplementary files format and content: A .txt file with the raw counts for each gene sequenced

molecule: polyA RNA

growth_protocol: Upon reaching 70-80% confluency, hiPSCs were dissociated using Accutase solution (Millipore Sigma A6964). The exhausted media was aspirated, and cells were washed with 1 mL of DPBS (-) calcium (-) magnesium. Then, 1 mL of room temperature Accutase solution was added to each well and incubated at 37°C for 8 minutes. The hiPSCs were then singularized by pipetting up and down with a P1000 micropipette and quenched using ½ mL of mTesR. The resulting cell suspension was transferred to a conical tube and counted on a hemocytometer using a 1:1 dilution of 0.4% trypan blue. The hiPSCs were then seeded onto a 12-well plate coated with 8.68 ug/cm2 Cultrex-RGF at a density of 0.5x106 cells per well in 1 mL of mTesR with 5uM Rock Inhibitor. The exhausted media was replaced every day with 2 mL of fresh mTesR until the cells reached 97-100% confluency (2-4 days). Upon reaching confluency (defined as day 0 of differentiation), the media was replaced with RPMI/B27(-insulin) (Fisher A1895601) containing varied CHIR99021 (Sigma SML1046) concentrations based on the hiPSC line (Table S1). On day 2, exactly 48 hours later, the media was replaced with RPMI/B27(-ins) containing 7.5 uM of IWP2 (Tocris 686770-61-6), followed by another media change with RPMI/B27(-ins) on day 4. The media was then replaced every two days until day 13 of differentiation, using fresh RPMI/B27(+ins) (Thermo 17504001). On day 13, the cardiomyocytes were replated onto 8.68 g/cm^2 Cultrex-RGF coated 12-well plates at a 1:2 ratio to facilitate lactate purification. Each well was washed with 1/2 mL of DPBS (-) calcium (-) magnesium. Subsequently, 1 mL of 37°C 0.25% trypsin-EDTA solution was added to each well and incubated at 37°C for 20 minutes. After incubation, cardiomyocytes were singularized by pipetting with a P1000 micropipette, then quenched with 2 mL of RPMI/B27(+ins) with 20% FBS. The resulting cell suspension was transferred to a conical tube, centrifuged at 200g for 5 minutes, and the supernatant was aspirated. Cells were resuspended in RPMI/B27(+ins) containing 10 uM Rock Inhibitor and seeded at 1mL cell suspension per well. On day 14, the replated cells were given 1 mL of RPMI/B27(+ins). Cardiomyocytes were then purified using lactate purification media composed of DMEM no glucose with 4 mM lactate. On day 15, the media was replaced with 1 mL lactate medium. On day 17, the cells were washed with 1/2 mL of DPBS (-) calcium (-) magnesium, and the media was replaced with 1 mL of lactate medium. On day 19, the cells were washed with 1/2 mL of DPBS (-) calcium (-) magnesium and switched into RPMI/B27 (+ins). The media was changed every three days with fresh RPMI/B27(+ins) until the cardiomyocytes RNA lysate was collected on day 40.

extract_protocol:
On day 40, cardiomyocytes were lysed in a solution of 700μL PureLink Lysis buffer containing 7μL Beta-mercaptoethanol. The cell lysis was quickly transferred to -80°C for storage. The RNA purification was done using the PureLinkTM RNA Mini Kit (Thermo 12183025). The DNA was removed using the on-column Ambion PureLink DNase Set (Thermo 12185010). Total eukaryotic RNA isolates are quantified using a fluorimetric RiboGreen assay. Total RNA integrity is assessed using capillary electrophoresis (e.g. Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN). For samples to pass the initial QC step, they need to quantify higher than 500 ng and have a RIN of 8 or greater.
Total RNA samples are converted to Illumina sequencing libraries using Illumina’s TruSeq RNA Sample Preparation Kit (Cat. # RS-122-2001 or RS-122-2002) or Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2101). (Please see www.illumina.com for a detailed list of kit contents and methods). In summary, the mRNA from a normalized input mass of total RNA is isolated using oligo-dT coated magnetic beads, fragmented, and then reverse transcribed into cDNA. The cDNA is blunt-ended, A-tailed, and indexed by ligating molecularly barcoded adaptors. Libraries are amplified using 15 cycles of PCR. The final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen) and via Q-PCR. Indexed libraries are then normalized, pooled, and size-selected to 320 bp (tight) using the PippinHT instrument.

treatment_protocol: Described above

value: hiPSC-derived Cardiomyocyte

value: WT


title: M9C10_CM_3

description: Library name: M9C10_CM_3_S18


title: Olive Baboon, Sample 03, Submandibular, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-03-SM-Fem-L-FF-RNA

value: Submandibular


title: Olive Baboon, Sample 03, Sublingual, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-03-SL-Fem-L-FF-RNA


title: M7C16_CM_2

description: Library name: M7C16_CM_2_S14


title: prostate_cancer_primary_377 (STAMPEDE)


title: Olive Baboon, Sample 03, Parotid, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-03-PAR-Fem-L-FF-RNA

value: Parotid


title: M7C16_CM_1

description: Library name: M7C16_CM_1_S13


title: Olive Baboon, Sample 03, Pancreas, Female, Flash Frozen, RNA

description: Library name: Bab-03-PANC-Fem-FF-RNA

value: Pancreas


title: M4C8_CM_2

description: Library name: M4C8_CM_2_S11


title: prostate_cancer_primary_376 (STAMPEDE)


title: M4C8_CM_1

description: Library name: M4C8_CM_1_S10


title: M4C8_CM_3

description: Library name: M4C8_CM_3_S12


title: prostate_cancer_primary_375 (STAMPEDE)


title: Olive Baboon, Sample 03, Liver, Female, Flash Frozen, RNA

description: Library name: Bab-03-LIV-Fem-FF-RNA

value: Liver


title: F7C6_CM_3

description: Library name: F7C6_CM_3_S9


title: prostate_cancer_primary_374 (STAMPEDE)


title: F7C6_CM_2

description: Library name: F7C6_CM_2_S8


title: F7C6_CM_1

description: Library name: F7C6_CM_1_S7


title: prostate_cancer_primary_373 (STAMPEDE)


title: Olive Baboon, Sample 02, Submandibular, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-02-SM-Fem-L-FF-RNA


title: MCF7 TP53 R181C/- Nutlin 8hr b

description:
Library name: Sample 50
MCF7_R181C_S1G11_8hr_b raw RNA Seq Counts

value: cancer cells

value: 10 uM Nutlin-3a

value: 8 hr


title: M9C10_CM_1

description: Library name: M9C10_CM_1_S16


title: M7C16_CM_3

description: Library name: M7C16_CM_3_S15


title: E9, Rituximab, rep2

description: Library name: E9_R2

value: CHO-S

value: Chinese Hamster Ovaries


title: prostate_cancer_primary_372 (STAMPEDE)


title: F6C2_CM_1

description: Library name: F6C2_CM_1_S4


title: F6C2_CM_2

description: Library name: F6C2_CM_2_S5


title: F6C2_CM_3

description: Library name: F6C2_CM_3_S6


title: prostate_cancer_primary_371 (STAMPEDE)


title: F5C9_CM_3

description: Library name: F5C9_CM_3_S3


title: Olive Baboon, Sample 02, Parotid, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-02-PAR-Fem-L-FF-RNA


title: F5C9_CM_2

description: Library name: F5C9_CM_2_S2


title: hIPSC_CTL_1

description: Library name: hIPSC_CTL_1

value: healthy

value: CTL

value: F


title: GR ChIPseq siJUN replicate 3

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: Library name: RM_66_GR_sic_Jun_E3

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove PCR duplicates and low quality reads, before MACS2 was used to call peaks using defult settings, except summits were set to 300
Homer was used to generate files for plotting the data of the regions of interest.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files the ChIP-seq data or MACS2 called peaks in narrowPeak format

growth_protocol: BT549 cells were maintained in RPMI supplemented with 10% HI FBS and antibiotics and culutred at 37 degrees and 5% CO2

extract_protocol:
For each chromatin immunoprecipitation, cells from two 15cm plates were crosslinked at RT using 2mM disuccinimidyl glutarate (DSG) for 20min followed by 1% formaldehyde for 10min, which was quenched in 0.1M glycine for 10min. Cells were washed twice in cold PBS and scraped off in cold PBS containing protease inhibitors (Roche, Complete 11836170001 and Halt, Thermo Scientific, 78438). Crosslinked material was resuspended in lysis buffer 1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10min followed by 5min in lysis buffer 2 (10mM Tris-HCL pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) before resuspending in lysis buffer 3 (10mM Tris-HCL pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0,5% N-lauroylsarcosine). Samples were sonicated using Covaris Ultrasonicator ME220 until DNA fragments had a size between 150-500bp. Chromatin was immunoprecipitated overnight using protein A coated dynabeads (Dynabeads, 10002D) with specific antibodies. After washing the beads, chromatin was eluted and decrosslinked by incubating at 65 degrees over-night in elution buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS). Samples were treated with RNase A (20ng/mL) for 1h followed by proteinase K (200ng/mL) for 2h before DNA was purified by standard phenol-chloroform purification.
Purified DNA was submitted to library preparation using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E765). The samples were sequenced on a NovaSeq 6000 (Illumi-na) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 500nM DEX (dissolved in water) for 2h or 4h, 10μM BRM014 (dissolved in DMSO) for 4h, SMARTpool siRNA used for 72h knock-down of GATA6

value: TNBC

value: siJUN

tag: antibody

value: Cell Signaling (D6H2L) 12041 lot:3


title: Olive Baboon, Sample 02, Liver, Female, Flash Frozen, RNA

description: Library name: Bab-02-LIV-Fem-FF-RNA

value: Female


title: Olive Baboon, Sample 02, Pancreas, Female, Flash Frozen, RNA

description: Library name: Bab-02-PANC-Fem-FF-RNA


title: prostate_cancer_primary_370 (STAMPEDE)

value: FFPE prostate cancer


title: GR ChIPseq siJUN replicate 1

description: Library name: RM_66_GR_sic_Jun_E1

value: WT


title: Olive Baboon, Sample 01, Submandibular, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-01-SM-Fem-L-FF-RNA

value: Submandibular


title: GR ChIPseq siFra1 replicate 3

description: Library name: RM_66_GR_siFra_1_D3


title: prostate_cancer_primary_367 (STAMPEDE)


title: GR ChIPseq siFra1 replicate 2

description: Library name: RM_66_GR_siFra_1_D2


title: GR ChIPseq siFra1 replicate 1

description: Library name: RM_66_GR_siFra_1_D1


title: Olive Baboon, Sample 01, Sublingual, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-01-SL-Fem-L-FF-RNA

value: Sublingual


title: GR ChIPseq siCtl replicate 3

description: Library name: RM_66_GR_siCtl_C3

value: siCtl


title: prostate_cancer_primary_368 (STAMPEDE)


title: GR ChIPseq siCtl replicate 2

description: Library name: RM_66_GR_siCtl_C2


title: Olive Baboon, Sample 02, Sublingual, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-02-SL-Fem-L-FF-RNA


title: Olive Baboon, Sample 01, Parotid, Female, Left Gland, Flash Frozen, RNA

description: Library name: Bab-01-PAR-Fem-L-FF-RNA

value: Parotid


title: prostate_cancer_primary_366 (STAMPEDE)


title: RM_66_Input_Veh

description: Library name: RM_66_input_G_pool

value: Veh


title: GR ChIPseq siCtl replicate 1

description: Library name: RM_66_GR_siCtl_C1


title: Olive Baboon, Sample 01, Pancreas, Female, Flash Frozen, RNA

description: Library name: Bab-01-PANC-Fem-FF-RNA

value: Pancreas


title: prostate_cancer_primary_365 (STAMPEDE)


title: BRG1 ChIPseq KJPYR9 replicate 2

description: Library name: RM_66_BRG1_H2_KJPYR


title: Olive Baboon, Sample 01, Liver, Female, Flash Frozen, RNA

description: Library name: Bab-01-LIV-Fem-FF-RNA

value: Liver


title: GR ChIPseq siJUN replicate 2

description: Library name: RM_66_GR_sic_Jun_E2


title: BRG1 ChIPseq KJPYR9 replicate 1

description: Library name: RM_66_BRG1_H1_KJPYR


title: BRG1 ChIPseq Veh replicate 3

description: Library name: RM_66_BRG1_G3


title: 4DNEX4A3RB71, Homo sapiens - HCT116, DMSO control, B3 T1

description:
Library name: 4DNEX4A3RB71
RNA-seq in HCT116 (Homo sapiens), DMSO control, Biological replicate 3, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEX4A3RB71/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSPRHFI11/

data_processing:
Adapter trimming was performed on the 3′ ends of reads, using the first 33 nucleotides of the adapter sequences for trimming. FASTQ files were generated and demultiplexed using Illumina's bcl2fastq v2.20 software. High-quality reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner (Dobin et al., 2013), with the corresponding GTF annotation file obtained from Ensembl. Differential gene expression analysis was performed using the DESeq2 R package (Love et al., 2014), using DMSO-treated samples as controls. Genes with an adjusted p-value (Padj) ≥ 0.05 (Benjamini-Hochberg correction) were considered not significant and excluded from further analysis.
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw)  for plus and minus read counts, and tsv file for isoform and gene expression

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Catalog #74134, Qiagen), as per manufacturer's protocol. Purified RNA was treated with DNase I (Catalog #M0303S, New England Biolabs) for 20 minutes, followed by heat inactivation at 75°C in the presence of 5 µM EDTA.
RNA integrity was assessed at the DNA Services Facility, Roy J. Carver Biotechnology Center (University of Illinois at Urbana-Champaign), using an Agilent Bioanalyzer. All samples exhibited RNA Integrity Numbers (RIN) of 10. Ribosomal RNA was depleted using the FastSelect HMR kit (Qiagen). RNA-seq libraries were prepared with the KAPA HyperPrep Stranded mRNA Library Kit (Roche). The libraries were barcoded with Unique Dual Indexes (UDI’s) which have been developed to prevent index switching. The adaptor-ligated double-stranded cDNAs were amplified by PCR for 10 cycles with the Kapa HiFi polymerase (Roche). The final libraries were quantitated with Qubit (ThermoFisher) and the average cDNA fragment sizes were determined on a Fragment Analyzer. The libraries were diluted to 10nM and further quantitated by qPCR on a CFX Connect Real-Time qPCR system (Biorad) for accurate pooling of barcoded libraries and maximization of number of clusters in the flowcell. The pooled barcoded RNA-seq libraries were sequenced on a NovaSeq X Plus instrument using V1.0 sequencing chemistry for 151 paired-end cycles.

value: immortalized cell line

value: DMSO control


title: BRG1 ChIPseq Veh replicate 1

description: Library name: RM_66_BRG1_G1


title: BRG1 ChIPseq Veh replicate 2

description: Library name: RM_66_BRG1_G2


title: BT549 control siJUN + DEX treatment replicate 3

description: Library name: RM66_E3_sicJun_DEX

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove low quality read.
FeatureCounts were used to quantify raw read coverage before further analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Raw FeatureCounts

growth_protocol: BT549 and MDA-MB-231 cells were maintained in RPMI supplemented with 10% FBS and antibiotics and culutred at 37 degress and 5% CO2

extract_protocol:
Total RNA was harvested from cells with Tri-reagent (Sigma-Aldrich, 93289) and purified with chloroform on EconoSpin Columns (EconoSpin, 1910). Ribosomal RNA was depleted using the NEBNext rRNA depletion kit (Biolabs, E6310) before the library was prepared with the NEBNext RNA Library Prep kit (Biolabs, E7540).
Samples were sequenced on a NovaSeq 6000 (Illumina) to reach approximately 25M paired-end reads per sample.

value: siJUN+DEX


title: prostate_cancer_primary_369 (STAMPEDE)


title: prostate_cancer_primary_361 (STAMPEDE)


title: 4DNEXJDBWSNP, Homo sapiens - HCT116, DMSO control, B1 T1

description:
Library name: 4DNEXJDBWSNP
RNA-seq in HCT116 (Homo sapiens), DMSO control, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEXJDBWSNP/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSAIJQNVO/


title: prostate_cancer_primary_362 (STAMPEDE)


title: BT549 control siJUN + DEX treatment replicate 1

description: Library name: RM66_E1_sicJun_DEX


title: 4DNEXEIQCA8C, Homo sapiens - HCT116, 16h Auxin, B3 T1

description:
Library name: 4DNEXEIQCA8C
RNA-seq in HCT116 (Homo sapiens), 16h Auxin, Biological replicate 3, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEXEIQCA8C/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSB9S5TZR/

value: 16h Auxin


title: BT549 control siFRA1 + DEX treatment replicate 3

description: Library name: RM66_D3_siFra1_DEX

value: TNBC


title: BRG1 ChIPseq KJPYR9 replicate 3

description: Library name: RM_66_BRG1_H3_KJPYR


title: BT549 control siFRA1 + DEX treatment replicate 2

description: Library name: RM66_D2_siFra1_DEX


title: BT549 control siFRA1 + DEX treatment replicate 1

description: Library name: RM66_D1_siFra1_DEX


title: BT549 control siCtl + DEX treatment replicate 3

description: Library name: RM66_C3_siCtl_DEX

value: siCtl+DEX


title: F5C9_CM_1

description: Library name: F5C9_CM_1_S1

value: hiPSC-derived Cardiomyocyte


title: 4DNEXX7GZ7I9, Homo sapiens - HCT116, 16h Auxin, B2 T1

description:
Library name: 4DNEXX7GZ7I9
RNA-seq in HCT116 (Homo sapiens), 16h Auxin, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEXX7GZ7I9/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSHJIHF5R/


title: prostate_cancer_primary_360 (STAMPEDE)


title: prostate_cancer_primary_359 (STAMPEDE)


title: prostate_cancer_primary_363 (STAMPEDE)


title: BT549 control siCtl + DEX treatment replicate 2

description: Library name: RM66_C2_siCtl_DEX


title: 4DNEXGXBT684, Homo sapiens - HCT116, 16h Auxin, B1 T1

description:
Library name: 4DNEXGXBT684
RNA-seq in HCT116 (Homo sapiens), 16h Auxin, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEXGXBT684/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS226MKKB/


title: prostate_cancer_primary_364 (STAMPEDE)


title: 4DNEXT33TSI4, Homo sapiens - HCT116, DMSO control, B2 T1

description:
Library name: 4DNEXT33TSI4
RNA-seq in HCT116 (Homo sapiens), DMSO control, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-seq/4DNEXT33TSI4/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU6SDSTI/


title: BT549 control siJUN + VEH treatment replicate 3

description: Library name: RM66_E3_sicJun

value: siJUN


title: BT549 control siJUN + VEH treatment replicate 2

description: Library name: RM66_E2_sicJun


title: RNA, siHNRNPK, rep4

first: Ricardo

middle: A

last: Linares Saldana

address: 3400 civic center blvd

description:
Library name: siHNRNPK-4
formatted_HNRNPK_counts.txt

data_processing:
Raw fastq reads were aligned to the hg38 reference genome with RefSeq transcripts aligned by UCSC using STAR (Dobin et al. 2013)(v2.7.1a) with parameters: --outFilterMismatchNmax 3 --outFilterMultimapNmax 1.
Gene-level read counts were obtained using featureCounts (Liao, Smyth, and Shi 2014)(subread v2.0.6) with parameters: -t exon -g gene_id -p --countReadPairs -B -Q 20.
Raw counts were normalized to transcripts per million (TPM) using gene length obtained from featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml-1 penicillin, and 100 µg ml-1 streptomycin at 37°C with 5% CO2.

extract_protocol:
Maxwell RSC simple RNA Tissue kit using Automation Maxwell® RSC 48 Instrument.
For siNTC5-1, siNTC5-2, siHNRNPK-1, and siHNRNPK-2, libraries were prepared with Illumina TruSeq stranded mRNA kit. For siNTC5-3, siNTC5-4, siHNRNPK-3, and siHNRNPK-4, libraries were prepared with the Illumina Stranded mRNA, Ligation kit.

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium and pipetted onto siRNA (nontargeting control or HNRNPK). The mixture was incubated at room temperature for 20 minutes. HCT116 cells were harvested by trypsinization, resuspended in antibiotic-free medium, and plated onto siRNA duplexes for a final siRNA concentration of 25 nM. Cells were collected for extraction after 72 hours of RNAi treatment.

value: Human colon cancer

value: HNRNPK siRNA


title: BT549 control siJUN + DEX treatment replicate 2

description: Library name: RM66_E2_sicJun_DEX

value: WT


title: prostate_cancer_primary_358 (STAMPEDE)

value: FFPE prostate cancer


title: BT549 control siJUN + VEH treatment replicate 1

description: Library name: RM66_E1_sicJun


title: RNA, siHNRNPK, rep3

description:
Library name: siHNRNPK-3
formatted_HNRNPK_counts.txt


title: prostate_cancer_primary_356 (STAMPEDE)


title: BT549 control siFRA1 + VEH treatment replicate 2

description: Library name: RM66_D2_siFra1


title: BT549 control siFRA1 + VEH treatment replicate 3

description: Library name: RM66_D3_siFra1


title: prostate_cancer_primary_357 (STAMPEDE)


title: BT549 control siFRA1 + VEH treatment replicate 1

description: Library name: RM66_D1_siFra1


title: RNA, siControl, rep4

description:
Library name: siNTC5-4
formatted_HNRNPK_counts.txt

value: Nontargeting control siRNA


title: prostate_cancer_primary_355 (STAMPEDE)


title: BT549 control siCtl + VEH treatment replicate 3

description: Library name: RM66_C3_siCtl

value: siCtl


title: RNA, siControl, rep3

description:
Library name: siNTC5-3
formatted_HNRNPK_counts.txt


title: prostate_cancer_primary_353 (STAMPEDE)


title: BT549 control siCtl + VEH treatment replicate 2

description: Library name: RM66_C2_siCtl


title: BT549 control siCtl + DEX treatment replicate 1

description: Library name: RM66_C1_siCtl_DEX


title: BT549 control siCtl + VEH treatment replicate 1

description: Library name: RM66_C1_siCtl


title: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 3, ncRNA

city: Beijing

first: Jiayu

last: Wang

state: Beijing

address: 38 Xueyuan Rd , Haidian District,Beijing,China

department: School of Pharmaceutical Sciences

country: China

institute: Peking University Health Science Center

description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 3
35-6-3

data_processing:
Standard human reference libraries were adapted from the tRNAScan-SE library by appending CCA tails to the tRNAs from the genomic tRNA database (GtRNAdb, http://gtrnadb.ucsc.edu; Hsapi19). Isodecoders with identical scores were consolidated for ease of identity assignment. Raw reads were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by the cutadapt software (v1.9.3). Then, trimmed reads from all samples were aligned using bowtie2 software to the aforementioned tRNA library with sensitive options. Mapped reads on each tRNA were counted using samtools.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: All cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
Total RNA was subjected to small-RNA (< 200nt) extraction using the MirVana Isolation Kit (Thermo Fisher Scientific). The enriched small RNAs were then deacylated in 100 mM Tris-HCl (pH 9.0) and 1 mM EDTA at 37 °C for 30 min.
tRNA libraries were constructed with the GenSeq® Small RNA Library Prep Kit (GenSeq, Inc) according to the manufacturer’s instructions.

value: human embryonic kidney cells

value: tRNALeuCAG (tL) overexpressed


title: prostate_cancer_primary_354 (STAMPEDE)


title: T47D_MKK7_3_FAS+PALB_rep3

city: Darlinghurst

first: Leila

last: Eshraghi

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: FD02637241

data_processing:
Reads were sequenced on a NovaSeq 6000 instrument (Illumina), using 150 base pair paired-end sequencing chemistry. Sequencing was done on two lanes resulting in 4 fastq files per each sample. FASTQ files were quality checked by ‘FastQC’ (version 0.11.9). Sequence adaptors and quality filtering was performed using ‘AdapterRemoval’ (version 2.3.1).
Processed paired-end FASTQ reads were aligned to the reference genome assembly ‘GRCh38_2020-A_build’ using STAR (version 2.7.9) with the default parameters. Picard was used for marking duplicated reads.
Gene expression was quantified by counting the number of reads aligned to each Ensembl gene model using 'featureCounts' (version 2.0.1) available through the package Rsubread.
To normalise read counts (dedup_countTable_geneName.tsv) according to library size differences between the samples, Trimmed Mean of M-values (TMM) normalisation method from edgeR (version 3.32.1) was used.
Differentially expressed genes (DEGs) between the different treatment groups were identified using the limma-voom method (version 3.46.0)
Assembly: GRCh38_2020-A_build
Supplementary files format and content: "dedup_countTable_geneName.tsv" file includes raw counts for each sample after removing the duplicates (introduced by PCR) using . This count matrix was used for differentially gene expression and other downsream analysis.

growth_protocol: MCF-7 and T-47D cells were cultured in phenol-red free RPMI 1640 (Gibco) supplemented with 5% charcoal-stripped fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen) and 10 pM 17β-estradiol (Sigma-Aldrich; resuspended in absolute ethanol (EtOH)).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen). 1 μg RNA was used to prepare libraries.
RNA libraries for RNA-seq were prepared using the KAPA mRNA HyperPrep Kit (Roche).

treatment_protocol: pLenti and MKK7_3 knockout cells (MCF-7 or T-47D) were treated with 500 nM tamoxifen + 250 nM palbociclib (tam+palb), 25 nM fulvestrant + 125 nM palbociclib (fas+palb) or vehicle (Absolute ethanol (EtOH) and tetrahydrofuran (THF)) for 48 hours.

value: ER+ breast cancer cells

value: MKK7 (MAP2K7) knockdown

value: 25nM fulvestrant + 125nM palbociclib


title: T47D_MKK7_3_FAS+PALB_rep2

description: Library name: FD02637208


title: T47D_MKK7_3_FAS+PALB_rep1

description: Library name: FD02637117


title: T47D_MKK7_3_TAM+PALB_rep3

description: Library name: FD02637236

value: 500nM tamoxifen + 250nM palbociclib


title: T47D_MKK7_3_TAM+PALB_rep2

description: Library name: FD02637135


title: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 1, ncRNA

description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 1
35-6-1


title: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 2, ncRNA

description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 2
35-6-2


title: prostate_cancer_primary_352 (STAMPEDE)


title: T47D_MKK7_3_VEHICLE_rep3

description: Library name: FD02637231

value: Vehicle (EtOH and THF)


title: prostate_cancer_primary_350 (STAMPEDE)


title: T47D_MKK7_3_VEHICLE_rep1

description: Library name: FD02636860


title: HEK293T-EF1α-mCherry (WT), 2, ncRNA

description:
Library name: HEK293T-EF1α-mCherry (WT), 2
EMH-2


title: T47D_MKK7_3_VEHICLE_rep2

description: Library name: FD02637132


title: prostate_cancer_primary_349 (STAMPEDE)


title: prostate_cancer_primary_348 (STAMPEDE)


title: prostate_cancer_primary_351 (STAMPEDE)


title: T47D_pLenti_FAS+PALB_rep2

description: Library name: FD02637130

value: pLenti (wild-type)


title: HEK293T-EF1α-mCherry (WT), 1, ncRNA

description:
Library name: HEK293T-EF1α-mCherry (WT), 1
EMH-1


title: T47D_pLenti_FAS+PALB_rep3

description: Library name: FD02637230


title: T47D_pLenti_FAS+PALB_rep1

description: Library name: FD02636852


title: prostate_cancer_primary_347 (STAMPEDE)


description:
Library name: HEK293T-EF1α-mCherry, tRNAAlaGGC overexpressed(tA), 1
Colum name in RiboSeq_RAW_counts_AllSample.txt: R-35-4.2-1

library_source: other

data_processing:
Adapter sequences were removed from raw sequencing data using cutadapt software (v1.9.3). Tophat2 software was consequently used to algin the resulting high-quality clean reads to the human (GRCh38) reference genome. HTSeq software (v0.9.1) was then used to get the raw counts. Aligned reads were employed to predict the offset by riboWaltz.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
ribosome profiling was conducted following the protocol for GenSeq® Ribo Profile Kit (GenSeq, Inc). Briefly, cycloheximide-treated cells were lysed with lysis buffer and digested with nuclease. Ribosome protected fragments (RPFs) were obtained through size exclusion chromatography, size selection by polyacrylamide gel-electrophoresis (PAGE), and rRNA removal.
The purified RNA fragments were then end-repaired, ligated with 3’ adapters and reverse-transcribed into cDNA, which was subjected to PAGE-purification, circularization, and PCR-amplification.

treatment_protocol: Ten-million WT, tL and tA cells were transfected with 2 µg of spike plasmid using PEI (Polysciences), respectively.

value: tRNAAlaGGC (tA) overexpressed


title: T47D_pLenti_TAM+PALB_rep2

description: Library name: FD02637126


title: prostate_cancer_primary_346 (STAMPEDE)


title: T47D_MKK7_3_TAM+PALB_rep1

description: Library name: FD02637102


title: T47D_pLenti_TAM+PALB_rep3

description: Library name: FD02637220


description:
Library name: HEK293T-EF1α-mCherry, tRNAAlaGGC overexpressed(tA), 2
Colum name in RiboSeq_RAW_counts_AllSample.txt: R-35-4.2-2


title: prostate_cancer_primary_344 (STAMPEDE)


title: prostate_cancer_primary_345 (STAMPEDE)


title: T47D_pLenti_TAM+PALB_rep1

description: Library name: FD02632903


title: MCF7_MKK7_3_FAS+PALB_rep2

description: Library name: FD02632618


title: MCF7_MKK7_3_FAS+PALB_rep3

description: Library name: FD02632876


title: MCF7_MKK7_3_TAM+PALB_rep1

description: Library name: FD02632520


title: LIG20-2

first: Li

last: xiaojiaoyang

address: Bei jing shi chao yang qu bei san huan dong lu 11

institute: Beijing University of Chinese Medicine

description: Library name: Sample 5

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low qulity reads were removed to obtain the clean reads.
The reference genome using HISAT2 v2.1.0.
Difference expression analysis was performed using the DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values Sample

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol.Then, RNA puritied and quantificated by NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions.

value: Human hepatic stellate cell


description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 1
Colum name in RiboSeq_RAW_counts_AllSample.txt: R-35-6-1


description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 2
Colum name in RiboSeq_RAW_counts_AllSample.txt: R-35-6-2


title: T47D_pLenti_VEHICLE_rep2

description: Library name: FD02637122


title: MCF7_MKK7_3_TAM+PALB_rep3

description: Library name: FD02632784


title: MCF7_MKK7_3_TAM+PALB_rep2

description: Library name: FD02632608


title: HEK293T-EF1α-mCherry (WT), 2

description:
Library name: HEK293T-EF1α-mCherry (WT), 2
Colum name in RiboSeq_RAW_counts_AllSample.txt: EMH-R-2


title: T47D_pLenti_VEHICLE_rep3

description: Library name: FD02637211


title: MCF7_MKK7_3_VEHICLE_rep1

description: Library name: FD02632518


title: T47D_pLenti_VEHICLE_rep1

description: Library name: FD02632901


title: MCF7_pLenti_FAS+PALB_rep3

description: Library name: FD02632651


title: LIG20-3

description: Library name: Sample 6


title: HEK293T-EF1α-mCherry (WT), 1

description:
Library name: HEK293T-EF1α-mCherry (WT), 1
Colum name in RiboSeq_RAW_counts_AllSample.txt: EMH-R-1


title: LIG20-1

description: Library name: Sample 4


title: MCF7_MKK7_3_VEHICLE_rep2

description: Library name: FD02632606


title: prostate_cancer_primary_340 (STAMPEDE)


title: prostate_cancer_primary_341 (STAMPEDE)


title: prostate_cancer_primary_342 (STAMPEDE)


title: prostate_cancer_primary_337 (STAMPEDE)


title: prostate_cancer_primary_336 (STAMPEDE)


title: prostate_cancer_primary_338 (STAMPEDE)


title: MCF7_MKK7_3_FAS+PALB_rep1

description: Library name: FD02632522


title: MCF7_pLenti_FAS+PALB_rep2

description: Library name: FD02632605


title: MCF7_MKK7_3_VEHICLE_rep3

description: Library name: FD02632660


title: MCF7_pLenti_FAS+PALB_rep1

description: Library name: FD02632507


title: prostate_cancer_primary_339 (STAMPEDE)


title: MCF7_pLenti_TAM+PALB_rep3

description: Library name: FD02632645


title: TGFB-1

description: Library name: Sample 1


title: MCF7_pLenti_TAM+PALB_rep2

description: Library name: FD02632535


title: MCF7_pLenti_VEHICLE_rep1

description: Library name: FD02632497


title: MCF7_pLenti_VEHICLE_rep2

description: Library name: FD02632534


title: TGFB-2

description: Library name: Sample 2


title: MCF7_pLenti_TAM+PALB_rep1

description: Library name: FD02632502


title: U2OS cells rep2 (Input)

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: Library name: INU2

data_processing:
Reads were trimmed using Cutadapt
The trimmed reads were then mapped to hg19 genome following the standard ChIP seq-pipeline.
The classic ChIP-seq pipeline consists of BWA (http://bio-bwa.sourceforge.net/) for alignment and samtools (http://www.htslib.org/) for duplicate removal (rmdup), sorting (sort) and indexing (index)
Coverage was computed using Deeptools BamCoverage and the data was exported in BigWig format (.bw)
Assembly: hg19
Supplementary files format and content: Coverage tracks in BigWig format

source_name: Bone

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
U2OS and DIvA U2OS cells were plated in 15 cm dishes at densities of 4.5 million cells in complete DMEM, supplemented with 5 μM 5-azacytidine and incubated for 12 hours. The following day, DNA double-strand breaks (DSBs) were induced using AsiSI by adding 4-hydroxytamoxifen to complete DMEM achieving a final concentration of 500 nM. The cells were incubated for 4 hours at 37°C. Ten minutes before the end of DSBs induction, DSP (dithiobis[succinimidyl propionate]) was freshly dissolved in DMSO at concentration of 100 mM and then diluting dropwise into 150 ml of pre-warmed PBS containing Ca²⁺/Mg²⁺ while stirring at 37°C, to a final concentration of 1 mM. After DSB induction, cells were washed once with PBS containing Ca²⁺/Mg²⁺, then incubated with DSP solution for 30 minutes at 37°C. Subsequently, formaldehyde was added directly to the media (final concentration 1%) and incubated for 15 minutes at 37°C. Crosslinking was quenched with Glycine (final concentration 125mM) for 15 minutes at room temperature. Cells were washed twice with ice-cold PBS without Ca²⁺/Mg²⁺, collected by scraping using ice-cold PBS containing 0.5% BSA and pelleted by centrifugation at 500 g for 5 minutes at 4°C. Then, pellets were gently resuspended in ice-cold Cell Lysis Buffer (CLB) (85 mM KCl, 5 mM PIPES, 0.5% NP-40, 1× Halt protease inhibitor cocktail (PI), and 1 mM PMSF in DEPC-treated water), prepared immediately prior to use. Cells were incubated on ice for 10 minutes, pelleted by centrifugation at 500 g for 5 minutes at 4°C, and then resuspended in Nuclear Lysis Buffer (NLB) (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1× Halt PI, and 1 mM PMSF, in DEPC-treated water). Nuclei were incubated at room temperature for 10 minutes prior to sonication. Chromatin was sheared using a Diagenode PICO Bioruptor at ultra-high power, with 30-second ON/OFF cycles for 30 minutes. The sonicated lysate was centrifuged on a table top centrifuge at 17,200 RCF for 10 minutes at 4°C to pellet insoluble material. The soluble chromatin was pre-cleared by incubating with 1:1 mixture of Protein A and Protein G magnetic beads in ChIP IP buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1× Halt PI, and 1 mM PMSF in DEPC-treated water) and incubated for 1 hour at 4°C with rotation. Each sample was then split into input controls, antibody samples, no-antibody control. The antibody samples received 5 μg of NSUN2 mouse monoclonal antibody (1 μg/μl), then were incubated overnight at 4°C with rotation at 16 rpm. On the following day, antibody-chromatin complexes were captured by conjugation to freshly washed Protein A/G magnetic beads. Beads were washed twice in ChIP IP buffer containing protease inhibitors and subsequently added to each sample and incubated for 2 hours at 4°C with rotation at 16 rpm. Beads were then subjected to a sequential wash with ChIP wash buffers A-D, each prepared fresh in DEPC-treated water and pre-chilled. Buffer A (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, and 1% Triton X-1000. Buffer B (500 mM NaCl 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, and 1% Triton X-1000). Buffer C (10 mM Tris-HCl pH 8.0, 2 mM EDTA, 250 mM LiCl, 1% sodium deoxycholate, and 1% NP-400. Buffer D (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Each wash was performed for 5 minutes at 4°C with rotation, followed by 3 minutes on a magnetic rack. Buffers A–C were used once, and buffer D was applied twice, transferring beads to fresh tubes during the final wash. Elution was carried out by incubating beads twice with 250 μl of Elution Buffer (100 mM NaHCO₃, 1% SDS in DEPC-treated water) at 65°C for 15 minutes on thermomixer with shaking at 1200 rpm, pooling eluates in fresh tubes. To perform digestion and de-crosslinking, Digestion Buffer (10×) containing 400 mM Tris-HCl pH 6.5 and 100 mM EDTA was added. RNase A (50 μg final concentration) was added to all samples and incubated at 60°C for 3 hours on thermomixer at 400 rpm. Afterward, NaCl and DTT were added to final concentrations of 300 mM and 5 mM, respectively. Proteinase K (50 μg final concentration) was then added and samples were incubated overnight at 65°C on thermomixer with shaking at 400 rpm. The following day, DNA was purified via phenol/chloroform extraction. DNA precipitation was performed adding Isopropanol (0.8 volumes), NaCl (300mM final concentration), MgCl₂ (10mM final concentration), and GlycoBlue (30μg final concentration), and samples were incubated for 2 hours at -20°C. DNA was pelleted by centrifugation on a table top centrifuge at 17,200 RFC for 30 minutes at 4°C. Pellets were washed twice with 100% ethanol and 70% ethanol. Then, pellets were air-dried for 2 hours and resuspended in 50 μl of TE buffer with low EDTA (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA in DEPC-treated water). DNA was quantified using the Qubit dsDNA High Sensitivity assay.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: 4hr 400nm 4OHT or equivalent DMSO

value: Bone

value: osteosarcoma

tag: group

value: Wildtype


title: T76_participant 12_SMA positive, biol rep 1

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description:
Library name: Sample 87
DSP-1001660008150-A-H08

data_processing:
GeoMx NGS Pipeline on Basespace
Assembly: GeoMx Human Whole Transcriptome Atlas
Supplementary files format and content: GNP_config.ini (samples in plate 1001660008150 are discussed in the manuscript)
Library strategy: Spatial Transcriptomics

source_name: skeletal muscle

growth_protocol: fresh frozen biopsies

extract_protocol:
hybridized RNA probes using GeoMx DSP instrument
Nanostring's GeoMx Human Whole Transcriptome Atlas kit and GeoMx Digital Spatial Profiler

tag: cell type

value: smooth muscle actin positive

value: skeletal muscle

value: Exercise+telmisartan


title: U2OS cells rep3 (Input)

description: Library name: INU3

tag: genotype

value: WT


title: T76_participant 12_SMA negative, biol rep 1

description:
Library name: Sample 86
DSP-1001660008150-A-H07

value: smooth muscle actin negative

tag: treatment


title: MCF7_pLenti_VEHICLE_rep3

description: Library name: FD02632634


title: prostate_cancer_primary_334 (STAMPEDE)

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

value: FFPE prostate cancer


title: U2OS cells rep1 (Input)

description: Library name: INU1


title: prostate_cancer_primary_335 (STAMPEDE)


title: prostate_cancer_primary_333 (STAMPEDE)


title: T70_participant 12_SMA positive, biol rep 2

description:
Library name: Sample 84
DSP-1001660008150-A-H05

value: Baseline


title: T70_participant 12_SMA positive, biol rep 1

description:
Library name: Sample 82
DSP-1001660008150-A-H03


title: T70_participant 12_SMA negative, biol rep 2

description:
Library name: Sample 85
DSP-1001660008150-A-H06


title: T70_participant 12_SMA negative, biol rep 1

description:
Library name: Sample 83
DSP-1001660008150-A-H04


title: U2OS cells +4OHT rep3 (Input)

description: Library name: INA3

value: AsiSI

value: Damage induced


title: prostate_cancer_primary_332 (STAMPEDE)


title: prostate_cancer_primary_331 (STAMPEDE)


title: TGFB-3

description: Library name: Sample 3


title: T76_participant 12_SMA negative, biol rep 2

description:
Library name: Sample 88
DSP-1001660008150-A-H09


title: T66_participant 11_SMA negative, biol rep 2

description:
Library name: Sample 81
DSP-1001660008150-A-H02


title: prostate_cancer_primary_330 (STAMPEDE)


title: T66_participant 11_SMA positive, biol rep 2

description:
Library name: Sample 80
DSP-1001660008150-A-H01


title: U2OS cells +4OHT rep2 (Input)

description: Library name: INA2


title: T66_participant 11_SMA positive, biol rep 1

description:
Library name: Sample 78
DSP-1001660008150-A-G11


title: T66_participant 11_SMA negative, biol rep 1

description:
Library name: Sample 79
DSP-1001660008150-A-G12


title: U2OS cells +4OHT rep1 (Input)

description: Library name: INA1


title: U2OS cells rep3

description: Library name: U3


title: T60_participant 10_SMA positive, biol rep 2

description:
Library name: Sample 76
DSP-1001660008150-A-G09

value: Exercise+placebo


title: T60_participant 10_SMA negative, biol rep 1

description:
Library name: Sample 75
DSP-1001660008150-A-G08


title: prostate_cancer_primary_329 (STAMPEDE)


title: prostate_cancer_primary_328 (STAMPEDE)


title: U2OS cells rep2

description: Library name: U2


title: T60_participant 10_SMA positive, biol rep 1

description:
Library name: Sample 74
DSP-1001660008150-A-G07


title: T51_participant 11_SMA negative, biol rep 2

description:
Library name: Sample 73
DSP-1001660008150-A-G06


title: U2OS cells rep1

description: Library name: U1


title: T51_participant 11_SMA negative, biol rep 1

description:
Library name: Sample 71
DSP-1001660008150-A-G04


title: T51_participant 11_SMA positive, biol rep 2

description:
Library name: Sample 72
DSP-1001660008150-A-G05


title: U2OS cells +4OHT rep3

description: Library name: A3


title: T51_participant 11_SMA positive, biol rep 1

description:
Library name: Sample 70
DSP-1001660008150-A-G03


title: T48_participant 9_SMA negative, biol rep 2

description:
Library name: Sample 69
DSP-1001660008150-A-G02


title: prostate_cancer_primary_326 (STAMPEDE)


title: prostate_cancer_primary_325 (STAMPEDE)


title: T48_participant 9_SMA positive, biol rep 2

description:
Library name: Sample 68
DSP-1001660008150-A-G01


title: U2OS cells +4OHT rep2

description: Library name: A2


title: T60_participant 10_SMA negative, biol rep 2

description:
Library name: Sample 77
DSP-1001660008150-A-G10


title: U2OS cells +4OHT rep1

description: Library name: A1


title: T48_participant 9_SMA negative, biol rep 1

description:
Library name: Sample 67
DSP-1001660008150-A-F12


title: T44_participant 10_SMA negative, biol rep 2

description:
Library name: Sample 65
DSP-1001660008150-A-F10


title: prostate_cancer_primary_323 (STAMPEDE)


title: Non-endometriosis, follicle fluid, rep10

city: Shanghai

first: Yangshuo

last: Li

address: 168 Changhai Road

institute: Navy Medical University

data_processing:
Raw sequencing data were processed using Trimmomatic software to generate clean reads, which were then mapped to the GRCh38 reference genome using Hisat2. Expression count matrices were generated using FeatureCounts. Differential expression analysis between different sample groups was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: row_counts

source_name: follicle fluid

extract_protocol:
Bulk RNA-sequencing was performed on granulosa cells from infertile patients' follicular fluid. Follicular fluid was collected separately from patients with EMS-related infertility and male factor infertility, as described previously. Cells were pelleted by centrifugation at 4°C, 2000 rpm for 10 minutes, and resuspended in 10 ml PBS. The cell suspension was carefully layered over lymphocyte separation medium (1:1 volume) along the tube wall and centrifuged at 4°C, 2000 rpm for 20 minutes. The cloudy white layer was gently aspirated into a 15 ml centrifuge tube. After addition of red blood cell lysis buffer and gentle agitation to lyse red blood cells, the suspension was centrifuged at 4°C, 2000 rpm for 10 minutes. The resulting cell pellet was washed twice with PBS and RNA was extracted from granulosa cells using TRIzol reagent (Invitrogen) for subsequent Bulk RNA-seq.
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: follicle fluid


title: prostate_cancer_primary_324 (STAMPEDE)


title: prostate_cancer_primary_327 (STAMPEDE)


title: T44_participant 10_SMA negative, biol rep 1

description:
Library name: Sample 63
DSP-1001660008150-A-F08


title: T37_participant 9_SMA negative, biol rep 2

description:
Library name: Sample 61
DSP-1001660008150-A-F06


title: Non-endometriosis, follicle fluid, rep9


title: Non-endometriosis, follicle fluid, rep8


title: prostate_cancer_primary_322 (STAMPEDE)


title: T37_participant 9_SMA positive, biol rep 2

description:
Library name: Sample 60
DSP-1001660008150-A-F05


title: T37_participant 9_SMA negative, biol rep 1

description:
Library name: Sample 59
DSP-1001660008150-A-F04


title: Non-endometriosis, follicle fluid, rep7


title: prostate_cancer_primary_321 (STAMPEDE)


title: prostate_cancer_primary_320 (STAMPEDE)


title: T48_participant 9_SMA positive, biol rep 1

description:
Library name: Sample 66
DSP-1001660008150-A-F11


title: T44_participant 10_SMA positive, biol rep 1

description:
Library name: Sample 62
DSP-1001660008150-A-F07


title: T37_participant 9_SMA positive, biol rep 1

description:
Library name: Sample 58
DSP-1001660008150-A-F03


title: Non-endometriosis, follicle fluid, rep6


title: T64_participant 15_SMA negative, biol rep 1

description:
Library name: Sample 56
DSP-1001660008150-A-F01


title: T64_participant 15_SMA positive, biol rep 2

description:
Library name: Sample 57
DSP-1001660008150-A-F02


title: prostate_cancer_primary_319 (STAMPEDE)


title: T64_participant 15_SMA positive, biol rep 1

description:
Library name: Sample 55
DSP-1001660008150-A-E12


title: T46_participant 15_SMA positive, biol rep 3

description:
Library name: Sample 54
DSP-1001660008150-A-E11


title: prostate_cancer_primary_318 (STAMPEDE)


title: T44_participant 10_SMA positive, biol rep 2

description:
Library name: Sample 64
DSP-1001660008150-A-F09


title: Non-endometriosis, follicle fluid, rep5


title: Non-endometriosis, follicle fluid, rep4


title: T46_participant 15_SMA positive, biol rep 2

description:
Library name: Sample 52
DSP-1001660008150-A-E09


title: prostate_cancer_primary_317 (STAMPEDE)


title: prostate_cancer_primary_316 (STAMPEDE)


title: Non-endometriosis, follicle fluid, rep3


title: T46_participant 15_SMA positive, biol rep 1

description:
Library name: Sample 51
DSP-1001660008150-A-E08


title: prostate_cancer_primary_343 (STAMPEDE)


title: prostate_cancer_primary_315 (STAMPEDE)


title: T43_participant 13_SMA positive, biol rep 1

description:
Library name: Sample 49
DSP-1001660008150-A-E06


title: HEK293T-EF1α-mCherry (WT), 3, ncRNA

description:
Library name: HEK293T-EF1α-mCherry (WT), 3
EMH-3

value: human embryonic kidney cells


title: Non-endometriosis, follicle fluid, rep2


title: T42_participant 14_SMA negative, biol rep 1

description:
Library name: Sample 48
DSP-1001660008150-A-E05


title: T43_participant 13_SMA negative, biol rep 1

description:
Library name: Sample 50
DSP-1001660008150-A-E07


title: Non-endometriosis, follicle fluid, rep1


title: T27_participant 14_SMA positive, biol rep 1

description:
Library name: Sample 45
DSP-1001660008150-A-E02


title: T27_participant 14_SMA negative, biol rep 1

description:
Library name: Sample 46
DSP-1001660008150-A-E03


title: T25_participant 13_SMA negative, biol rep 1

description:
Library name: Sample 44
DSP-1001660008150-A-E01


title: endometriosis, follicle fluid, rep8


title: prostate_cancer_primary_312 (STAMPEDE)


title: endometriosis, follicle fluid, rep7


title: T8_participant  5_SMA negative, biol rep 2

description:
Library name: Sample 42
DSP-1001660008150-A-D11


title: T8_participant  5_SMA positive, biol rep 2

description:
Library name: Sample 41
DSP-1001660008150-A-D10


title: T46_participant 15_SMA negative, biol rep 1

description:
Library name: Sample 53
DSP-1001660008150-A-E10


title: T8_participant  5_SMA positive, biol rep 1

description:
Library name: Sample 39
DSP-1001660008150-A-D08


title: T8_participant  5_SMA negative, biol rep 1

description:
Library name: Sample 40
DSP-1001660008150-A-D09


title: prostate_cancer_primary_311 (STAMPEDE)


title: prostate_cancer_primary_310 (STAMPEDE)


title: endometriosis, follicle fluid, rep5


title: prostate_cancer_primary_309 (STAMPEDE)


title: T79_participant 6_SMA negative, biol rep 2

description:
Library name: Sample 38
DSP-1001660008150-A-D07


title: prostate_cancer_primary_314 (STAMPEDE)


title: T42_participant 14_SMA positive, biol rep 1

description:
Library name: Sample 47
DSP-1001660008150-A-E04


title: prostate_cancer_primary_313 (STAMPEDE)


title: T79_participant 6_SMA positive, biol rep 2

description:
Library name: Sample 37
DSP-1001660008150-A-D06


title: prostate_cancer_primary_308 (STAMPEDE)


title: T79_participant 6_SMA negative, biol rep 1

description:
Library name: Sample 36
DSP-1001660008150-A-D05


title: T79_participant 6_SMA positive, biol rep 1

description:
Library name: Sample 35
DSP-1001660008150-A-D04


title: endometriosis, follicle fluid, rep4


title: T73_participant 6_SMA negative, biol rep 1

description:
Library name: Sample 34
DSP-1001660008150-A-D03


title: T25_participant 13_SMA positive, biol rep 1

description:
Library name: Sample 43
DSP-1001660008150-A-D12


title: endometriosis, follicle fluid, rep3


title: T73_participant 6_SMA positive, biol rep 2

description:
Library name: Sample 33
DSP-1001660008150-A-D02


title: endometriosis, follicle fluid, rep2


title: prostate_cancer_primary_307 (STAMPEDE)


title: T73_participant 6_SMA positive, biol rep 1

description:
Library name: Sample 32
DSP-1001660008150-A-D01


title: T6_participant 4_SMA negative, biol rep 2

description:
Library name: Sample 31
DSP-1001660008150-A-C12


title: endometriosis, follicle fluid, rep1


title: endometriosis, follicle fluid, rep6


title: prostate_cancer_primary_306 (STAMPEDE)


title: Plasmid Library, day0, Replicate 1, Amplicon-seq

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

data_processing:
Raw fastq files were quality filtered followed by sgRNA abundance counting using MaGeCK count function
Ranking and scoring of sgRNA and genes by enrichment/depletion was performed using MaGeck test function
Comparison and validation of ranking and scoring of genes compared to the DepMap database
Genes were clustered based on their temporal expression profile of change in sgRNA abundance over time
Identified clusters were analysed for over-represented gene ontology terms using gProfiler
Assembly: ARS-UCD1.2
Supplementary files format and content: comma-sepearted txt file contains raw reads by sample and gene
Library strategy: CRISPR sgRNA-seq

organism: Bos taurus

source_name: Plasmid library

growth_protocol: Post-transduction, cells were passaged every 5 days, seeding 3.5e3 cells/cm2

extract_protocol:
Total DNA was extracted from 5x10^5 cells using QuickExtract reagent (Lucigen) followed by two consecutive PCR to amplify sgRNA amplicon
Extracted genomic DNA was amplified and added unique sample adapters, followed by SPRI-beads size selection and a second PCR adding NGS adapters, followed by a second SPRI-beads size selection

treatment_protocol: Cells were transduced with both Cas9 and CRISPR-knockout library, and were passaged for 30 days

value: Plasmid library

value: control

tag: sequencing batch

tag: time

value: day 0


title: T6_participant 4_SMA negative, biol rep 1

description:
Library name: Sample 29
DSP-1001660008150-A-C10


title: T6_participant 4_SMA positive, biol rep 1

description:
Library name: Sample 28
DSP-1001660008150-A-C09


title: T19_participant 5_SMA negative, biol rep 2

description:
Library name: Sample 27
DSP-1001660008150-A-C08


title: prostate_cancer_primary_305 (STAMPEDE)

last: Davicioni

address: 9725 Lusk Blvd

tag: gleason score

tag: age at randomization


title: prostate_cancer_primary_304 (STAMPEDE)

tag: psa at randomization (ng/ml)

tag: tissue


title: T19_participant 5_SMA positive, biol rep 2

description:
Library name: Sample 26
DSP-1001660008150-A-C07


title: prostate_cancer_primary_303 (STAMPEDE)


title: T19_participant 5_SMA negative, biol rep 1

description:
Library name: Sample 25
DSP-1001660008150-A-C06


title: AD-bMSC, Late-WT, day125, Replicate 3, RNA-seq

data_processing:
Reads were quality controlled, aligned and counted at The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM).
Assembly: ARS-UCD1.2
Supplementary files format and content: comma-sepearted txt file contains raw reads by sample and gene

source_name: Bovine subcutaneous adipose derived mesenchymal stem cells

extract_protocol:
Total RNA was extracted from 5x10^6 cells using TRIzol reagent (Invitrogen) followed by Direct-zol RNA Miniprep Plus Kits (Zymo Research).
MARS-seq2.0

treatment_protocol: Cells were transduced with both Cas9 and CRISPR-knockout library, and were passaged for 100 days

value: Proliferation

value: day 125


title: T18_participant 4_SMA negative, biol rep 2

description:
Library name: Sample 23
DSP-1001660008150-A-C04


title: T18_participant 4_SMA positive, biol rep 2

description:
Library name: Sample 22
DSP-1001660008150-A-C03

value: smooth muscle actin positive


title: AD-bMSC, Late-WT, day125, Replicate 1, RNA-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells


title: T19_participant 5_SMA positive, biol rep 1

description:
Library name: Sample 24
DSP-1001660008150-A-C05

value: skeletal muscle

value: Exercise+telmisartan


title: AD-bMSC, Late-WT, day125, Replicate 2, RNA-seq

value: WT


title: T18_participant 4_SMA negative, biol rep 1

description:
Library name: Sample 21
DSP-1001660008150-A-C02

value: smooth muscle actin negative


title: prostate_cancer_primary_302 (STAMPEDE)

value: FFPE prostate cancer


title: T6_participant 4_SMA positive, biol rep 2

description:
Library name: Sample 30
DSP-1001660008150-A-C11

value: Baseline


title: T18_participant 4_SMA positive, biol rep 1

description:
Library name: Sample 20
DSP-1001660008150-A-C01


title: prostate_cancer_primary_301 (STAMPEDE)


title: T69_participant 24_SMA negative, biol rep 2

description:
Library name: Sample 19
DSP-1001660008150-A-B12


title: T69_participant 24_SMA positive, biol rep 2

description:
Library name: Sample 18
DSP-1001660008150-A-B11


title: AD-bMSC, Early-WT, day25, Replicate 3, RNA-seq

value: day 25


title: AD-bMSC, Early-WT, day25, Replicate 2, RNA-seq


title: T69_participant 24_SMA negative, biol rep 1

description:
Library name: Sample 17
DSP-1001660008150-A-B10

value: Exercise+placebo


title: AD-bMSC, Early-WT, day25, Replicate 1, RNA-seq


title: prostate_cancer_primary_299 (STAMPEDE)


title: T69_participant 24_SMA positive, biol rep 1

description:
Library name: Sample 16
DSP-1001660008150-A-B09


title: prostate_cancer_primary_300 (STAMPEDE)


title: prostate_cancer_primary_298 (STAMPEDE)


title: T56_participant 24_SMA negative, biol rep 2

description:
Library name: Sample 15
DSP-1001660008150-A-B08


title: T56_participant 24_SMA positive, biol rep 2

description:
Library name: Sample 14
DSP-1001660008150-A-B07


title: AD-bMSC, Knockout-Library, day125,  Replicate 3, RNA-seq

value: CRISPR-KO Library


title: T56_participant 24_SMA negative, biol rep 1

description:
Library name: Sample 13
DSP-1001660008150-A-B06


title: AD-bMSC, Knockout-Library, day125,  Replicate 2, RNA-seq


title: prostate_cancer_primary_297 (STAMPEDE)


title: T56_participant 24_SMA positive, biol rep 1

description:
Library name: Sample 12
DSP-1001660008150-A-B05


title: AD-bMSC, Knockout-Library, day125,  Replicate 1, RNA-seq


title: T29_participant 23_SMA negative, biol rep 1

description:
Library name: Sample 11
DSP-1001660008150-A-B04


title: T29_participant 23_SMA positive, biol rep 2

description:
Library name: Sample 10
DSP-1001660008150-A-B03


title: T29_participant 23_SMA positive, biol rep 1

description:
Library name: Sample 9
DSP-1001660008150-A-B01


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 30, Replicate 3, Amplicon-seq

value: day 30


title: T26_participant 22_SMA negative, biol rep 1

description:
Library name: Sample 8
DSP-1001660008150-A-A12


title: T26_participant 22_SMA positive, biol rep 1

description:
Library name: Sample 7
DSP-1001660008150-A-A10


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 30, Replicate 2, Amplicon-seq


title: T13_participant 23_SMA positive, biol rep 2

description:
Library name: Sample 6
DSP-1001660008150-A-A08


title: prostate_cancer_primary_296 (STAMPEDE)


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 30, Replicate 1, Amplicon-seq


title: T13_participant 23_SMA negative, biol rep 1

description:
Library name: Sample 5
DSP-1001660008150-A-A07


title: T13_participant 23_SMA positive, biol rep 1

description:
Library name: Sample 4
DSP-1001660008150-A-A06


title: prostate_cancer_primary_294 (STAMPEDE)


title: prostate_cancer_primary_293 (STAMPEDE)


title: prostate_cancer_primary_295 (STAMPEDE)


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 20, Replicate 3, Amplicon-seq

value: day 20


title: T10910_participant 22_SMA negative, biol rep 1

description:
Library name: Sample 3
DSP-1001660008150-A-A05


title: T10910_participant 22_SMA positive, biol rep 2

description:
Library name: Sample 2
DSP-1001660008150-A-A04


title: T10910_participant 22_SMA positive, biol rep 1

description:
Library name: Sample 1
DSP-1001660008150-A-A02


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 20, Replicate 2, Amplicon-seq


title: Silencer negative control, PMA treatment, rep 3

city: Seattle

first: Melissa

last: Krueger

state: WA

address: 850 Republican St, Box 358052

department: Pulmonary, Critical Care and Sleep Medicine Division

institute: University of Washington

description:
Library name: N6
N6

data_processing:
Fastq raw data were processed through fastp. Low quality reads and those containing either adapter or poly-N were removed from the data.
Reads were mapped to the reference genome using Hisat2 (v2.0.5).
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited file with raw gene counts
Supplementary files format and content: tab-delimited file with raw gene counts

source_name: ABM good immortalized human cardiomyocytes, Cat# T0519

growth_protocol: Human ventricular cardiomyocytes were maintained in Prigrow I medium supplemented with 10% fetal bovine serum (FBS) and 0.1% Penicillin/Streptomycin in a humidified incubator at 37ºC with 5% CO2.

extract_protocol:
Total RNA isolation was completed utilizing the MagMax-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher) following the spin procedure
Samples were sent to Novogene, who completed sample QC and library preparation

treatment_protocol:
10 nM of each respective siRNA plus 5.9 uL Lipofectamine 3000 were incubated with the cells for 24h
After the siRNA incubation, cells were treated with 4 µM phorbol 12-myristate 13-acetate (PMA, cayman chemical) or a comparative vehicle control (0.025% DMSO) in serum-free media and either maintained for 48h (CERS2 KD and controls) or retreated with 2 µM PMA 24h after the start of the initial treatment, leading to a total 48h hypertrophy treatment (CERS5/6 KD and controls)

tag: cell line

value: human cardiomyocytes

value: Silencer control

value: PMA treatment - 24h treatment with 4uM PMA (0.025% DMSO), followed by 24h treatment with 2uM PMA (0.012% DMSO) (total 48h treatment)


title: Silencer negative control, PMA treatment, rep 1

description:
Library name: N4
N4

value: ABM good immortalized human cardiomyocytes, Cat# T0519


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 20, Replicate 1, Amplicon-seq

value: Proliferation


title: prostate_cancer_primary_290 (STAMPEDE)

first: Elai

institute: Veracyte, Inc

source_name: FFPE prostate cancer


title: prostate_cancer_primary_292 (STAMPEDE)


title: Silencer negative control, PMA treatment, rep 2

description:
Library name: N5
N5


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 5, Replicate 3, Amplicon-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells

value: day 5


title: Silencer negative control, vehicle treatment, rep 3

description:
Library name: N3
N3

value: Vehicle treatment - 24h treatment with 0.025% DMSO, followed by 24h treatment with 0.012% DMSO (total 48h treatment)


title: Silencer negative control, vehicle treatment, rep 2

description:
Library name: N2
N2


title: Silencer negative control, vehicle treatment, rep 1

description:
Library name: N1
N1


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 5, Replicate 2, Amplicon-seq


title: CERS5.6 KD, PMA treatment, rep 3

description:
Library name: C566
C566

value: CERS56 KD


title: prostate_cancer_primary_288 (STAMPEDE)


title: CERS5.6 KD, PMA treatment, rep 2

description:
Library name: C565
C565


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 5, Replicate 1, Amplicon-seq


title: CERS5.6 KD, vehicle treatment, rep 3

description:
Library name: C563
C563


title: CERS5.6 KD, vehicle treatment, rep 2

description:
Library name: C562
C562


title: NCCLu_397

city: Goyang-si

first: Sehwa

last: Hong

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

department: Research Institute

country: South Korea

institute: National cancer center

library_source: transcriptomic single cell

data_processing:
Preprocessing (barcoding, gene counting, and demultiplexing) of sequenced results was made using BD Rhapsody WTA analysis pipeline v.1.11 on the Seven Bridges Genomics platform.
Raw gene expression matrices were converted to Seurat objects and further analyses were performed using the Seurat R package (v.4.3.0)
Assembly: hg38
Supplementary files format and content: Tab delimited values files, UMI count matrix files

source_name: Pleural fluid

extract_protocol:
Single-cell isolation was performed from pleural effusion by density gradient centrifugation. Isolated cells were cultured in AR5 medium (5% FBS, 1 X GlutaMax, 1X ITS, 1% penicillin/streptomycin, 50 nM hydrocortisone, 1 mM Na-pyruvate, and 1ng/ml EGF in RPMI) at 37°C  incubator. Short-term cultured single cells were preserved in freezing media (10% DMSO + 90% FBS) under -140°C until generating RNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pleural fluid

value: Lung cancer

tag: histopathology

value: Adenocarcinoma

tag: cancer stage

value: IV

tag: therapeutic response

value: Non-response


title: CERS5.6 KD, vehicle treatment, rep 1

description:
Library name: C561
C561


title: NCCLu_383

tag: disease

value: Response


title: Scramble control, PMA treatment, rep 3

description:
Library name: S6
S6

value: Scramble Control

value: PMA treatment - 48h treatment with 4uM PMA (0.025% DMSO)


title: prostate_cancer_primary_287 (STAMPEDE)

city: San Diego

value: FFPE prostate cancer


title: CERS5.6 KD, PMA treatment, rep 1

description:
Library name: C564
C564

value: human cardiomyocytes


title: NCCLu_376


title: Scramble control, vehicle treatment, rep 3

description:
Library name: S3
S3

value: Vehicle treatment - 48h treatment with 0.025% DMSO


title: Scramble control, PMA treatment, rep 1

description:
Library name: S4
S4

value: ABM good immortalized human cardiomyocytes, Cat# T0519


title: prostate_cancer_primary_291 (STAMPEDE)


title: prostate_cancer_primary_289 (STAMPEDE)


title: NCCLu_334


title: prostate_cancer_primary_286 (STAMPEDE)


title: prostate_cancer_primary_285 (STAMPEDE)


title: NCCLu_327


title: prostate_cancer_primary_284 (STAMPEDE)


title: prostate_cancer_primary_283 (STAMPEDE)


title: CERS2 KD, PMA treatment, rep 1

description:
Library name: C24
C24

value: CERS2 KD


title: prostate_cancer_primary_282 (STAMPEDE)


title: CERS2 KD, PMA treatment, rep 2

description:
Library name: C25
C25