title: prostate_cancer_primary_684 (STAMPEDE)


title: prostate_cancer_primary_679 (STAMPEDE)

status: Public on Aug 27 2025

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

molecule: total RNA

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: prostate_cancer_primary_689 (STAMPEDE)


title: prostate_cancer_primary_680 (STAMPEDE)


title: prostate_cancer_primary_683 (STAMPEDE)


title: prostate_cancer_primary_681 (STAMPEDE)


title: prostate_cancer_primary_678 (STAMPEDE)


title: prostate_cancer_primary_673 (STAMPEDE)


title: prostate_cancer_primary_677 (STAMPEDE)


title: prostate_cancer_primary_672 (STAMPEDE)


title: prostate_cancer_primary_671 (STAMPEDE)


title: prostate_cancer_primary_670 (STAMPEDE)


title: prostate_cancer_primary_669 (STAMPEDE)


title: prostate_cancer_primary_668 (STAMPEDE)


title: prostate_cancer_primary_676 (STAMPEDE)


title: prostate_cancer_primary_667 (STAMPEDE)


title: prostate_cancer_primary_666 (STAMPEDE)


title: prostate_cancer_primary_664 (STAMPEDE)


title: prostate_cancer_primary_665 (STAMPEDE)


title: prostate_cancer_primary_663 (STAMPEDE)


title: prostate_cancer_primary_662 (STAMPEDE)


title: prostate_cancer_primary_661 (STAMPEDE)


title: prostate_cancer_primary_659 (STAMPEDE)


title: prostate_cancer_primary_655 (STAMPEDE)


title: prostate_cancer_primary_654 (STAMPEDE)


title: prostate_cancer_primary_658 (STAMPEDE)


title: prostate_cancer_primary_650 (STAMPEDE)


title: prostate_cancer_primary_648 (STAMPEDE)


title: prostate_cancer_primary_651 (STAMPEDE)


title: prostate_cancer_primary_646 (STAMPEDE)


title: prostate_cancer_primary_640 (STAMPEDE)


title: prostate_cancer_primary_649 (STAMPEDE)


title: prostate_cancer_primary_642 (STAMPEDE)


title: prostate_cancer_primary_652 (STAMPEDE)


title: prostate_cancer_primary_657 (STAMPEDE)


title: prostate_cancer_primary_645 (STAMPEDE)


title: prostate_cancer_primary_653 (STAMPEDE)


title: prostate_cancer_primary_647 (STAMPEDE)


title: prostate_cancer_primary_638 (STAMPEDE)


title: prostate_cancer_primary_644 (STAMPEDE)


title: prostate_cancer_primary_637 (STAMPEDE)


title: prostate_cancer_primary_656 (STAMPEDE)


title: prostate_cancer_primary_634 (STAMPEDE)


title: prostate_cancer_primary_633 (STAMPEDE)


title: prostate_cancer_primary_636 (STAMPEDE)


title: prostate_cancer_primary_643 (STAMPEDE)


title: prostate_cancer_primary_641 (STAMPEDE)


title: prostate_cancer_primary_632 (STAMPEDE)


title: prostate_cancer_primary_639 (STAMPEDE)


title: prostate_cancer_primary_630 (STAMPEDE)


title: prostate_cancer_primary_631 (STAMPEDE)


title: prostate_cancer_primary_635 (STAMPEDE)


title: prostate_cancer_primary_629 (STAMPEDE)


title: prostate_cancer_primary_616 (STAMPEDE)


title: prostate_cancer_primary_620 (STAMPEDE)


title: prostate_cancer_primary_622 (STAMPEDE)


title: prostate_cancer_primary_626 (STAMPEDE)


title: prostate_cancer_primary_617 (STAMPEDE)


title: prostate_cancer_primary_624 (STAMPEDE)


title: prostate_cancer_primary_611 (STAMPEDE)


title: prostate_cancer_primary_628 (STAMPEDE)


title: prostate_cancer_primary_615 (STAMPEDE)


title: prostate_cancer_primary_610 (STAMPEDE)


title: prostate_cancer_primary_609 (STAMPEDE)


title: prostate_cancer_primary_608 (STAMPEDE)


title: prostate_cancer_primary_613 (STAMPEDE)


title: prostate_cancer_primary_606 (STAMPEDE)


title: prostate_cancer_primary_607 (STAMPEDE)


title: prostate_cancer_primary_627 (STAMPEDE)


title: prostate_cancer_primary_605 (STAMPEDE)


title: prostate_cancer_primary_604 (STAMPEDE)


title: prostate_cancer_primary_612 (STAMPEDE)


title: prostate_cancer_primary_603 (STAMPEDE)


title: prostate_cancer_primary_623 (STAMPEDE)


title: prostate_cancer_primary_618 (STAMPEDE)


title: prostate_cancer_primary_621 (STAMPEDE)


title: prostate_cancer_primary_602 (STAMPEDE)


title: prostate_cancer_primary_619 (STAMPEDE)


title: prostate_cancer_primary_614 (STAMPEDE)


title: prostate_cancer_primary_601 (STAMPEDE)


title: prostate_cancer_primary_625 (STAMPEDE)


title: prostate_cancer_primary_600 (STAMPEDE)


title: prostate_cancer_primary_598 (STAMPEDE)


title: prostate_cancer_primary_592 (STAMPEDE)


title: prostate_cancer_primary_596 (STAMPEDE)


title: prostate_cancer_primary_597 (STAMPEDE)


title: prostate_cancer_primary_599 (STAMPEDE)


title: prostate_cancer_primary_593 (STAMPEDE)


title: prostate_cancer_primary_586 (STAMPEDE)


title: prostate_cancer_primary_591 (STAMPEDE)


title: prostate_cancer_primary_581 (STAMPEDE)


title: prostate_cancer_primary_595 (STAMPEDE)


title: prostate_cancer_primary_576 (STAMPEDE)


title: prostate_cancer_primary_580 (STAMPEDE)


title: prostate_cancer_primary_585 (STAMPEDE)


title: prostate_cancer_primary_578 (STAMPEDE)


title: prostate_cancer_primary_582 (STAMPEDE)


title: prostate_cancer_primary_587 (STAMPEDE)


title: prostate_cancer_primary_574 (STAMPEDE)


title: prostate_cancer_primary_583 (STAMPEDE)


title: prostate_cancer_primary_579 (STAMPEDE)


title: prostate_cancer_primary_589 (STAMPEDE)


title: prostate_cancer_primary_584 (STAMPEDE)


title: prostate_cancer_primary_590 (STAMPEDE)


title: prostate_cancer_primary_577 (STAMPEDE)


title: prostate_cancer_primary_573 (STAMPEDE)


title: prostate_cancer_primary_572 (STAMPEDE)


title: prostate_cancer_primary_594 (STAMPEDE)


title: prostate_cancer_primary_571 (STAMPEDE)


title: prostate_cancer_primary_588 (STAMPEDE)


title: prostate_cancer_primary_575 (STAMPEDE)


title: prostate_cancer_primary_570 (STAMPEDE)


title: prostate_cancer_primary_569 (STAMPEDE)


title: prostate_cancer_primary_567 (STAMPEDE)


title: siBRG1+siBRM, BT549 cells, Biorep3

type: SRA

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

library_source: genomic

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 ATAC-seq data and MACS2 called peaks

molecule: genomic DNA

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:
50,000 cells were lysed in ATAC-RSB (resuspension buffer) (10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) supplemented with 0.1% IgePal-CA630 and 0.01% Digitonin before being washed three times in cold ATAC-RSB buffer. Nuclei were pelleted and resuspended in 50μL transposition mixture (17.75μL PBS, 5uL Nuclease Free Water, 25uL TD 2x reaction buffer, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 1.25μL TDE1 (Illumina, 20034197)) and incubated at 37 degrees in a thermomixer at 1000RPM for 30min. DNA was cleaned using Qiagen PCR Purification kit before PCR amplification for 10 cycles using Illumina index primers, 25μL Q5 High Fidelity 2x master mix (New England BioLabs, M0492) in a final volume of 50μL. Samples were size selected and purified using Ampure XP beads (Bechman Coulter, A63881).
Next-generation sequencing was performed using Illumina Novaseq 6000 to get ~25M 50bp 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

tag: sirna

tag: cell line

tag: cell type

value: TNBC

tag: genotype

value: WT

tag: treatment


title: siCtl, BT549 cells, Biorep4

value: siCtl


title: siBRG1+siBRM, BT549 cells, Biorep2


title: siBRG1+siBRM, BT549 cells, Biorep1


title: siBRG1+siBRM, BT549 cells, Biorep4


title: siCtl, BT549 cells, Biorep2


title: prostate_cancer_primary_562 (STAMPEDE)


title: prostate_cancer_primary_568 (STAMPEDE)


title: prostate_cancer_primary_565 (STAMPEDE)


title: prostate_cancer_primary_566 (STAMPEDE)


title: prostate_cancer_primary_555 (STAMPEDE)


title: prostate_cancer_primary_558 (STAMPEDE)


title: prostate_cancer_primary_559 (STAMPEDE)


title: prostate_cancer_primary_550 (STAMPEDE)


title: prostate_cancer_primary_551 (STAMPEDE)


title: prostate_cancer_primary_553 (STAMPEDE)


title: prostate_cancer_primary_556 (STAMPEDE)


title: prostate_cancer_primary_557 (STAMPEDE)


title: prostate_cancer_primary_560 (STAMPEDE)


title: prostate_cancer_primary_561 (STAMPEDE)


title: prostate_cancer_primary_563 (STAMPEDE)


title: prostate_cancer_primary_660 (STAMPEDE)


title: prostate_cancer_primary_564 (STAMPEDE)


title: siCtl, BT549 cells, Biorep3


title: prostate_cancer_primary_548 (STAMPEDE)


title: prostate_cancer_primary_549 (STAMPEDE)


title: prostate_cancer_primary_554 (STAMPEDE)


title: DEX+BRM014, BT549 cells, Biorep3


title: DEX+BRM014, BT549 cells, Biorep4


title: prostate_cancer_primary_552 (STAMPEDE)


title: DEX+BRM014, BT549 cells, Biorep2


title: DEX+BRM014, BT549 cells, Biorep1


title: DEX+DMSO, BT549 cells, Biorep4

value: 4h DEX (500nM) + DMSO


title: DEX+DMSO, BT549 cells, Biorep3


title: prostate_cancer_primary_544 (STAMPEDE)


title: DEX+DMSO, BT549 cells, Biorep2


title: BRM014, BT549 cells, Biorep3

value: 4h BRM014


title: prostate_cancer_primary_546 (STAMPEDE)


title: prostate_cancer_primary_545 (STAMPEDE)


title: BRM014, BT549 cells, Biorep4


title: BRM014, BT549 cells, Biorep1


title: DEX+DMSO, BT549 cells, Biorep1


title: BRM014, BT549 cells, Biorep2


title: DMSO, BT549 cells, Biorep4

value: 4h DSMO


title: siCtl, BT549 cells, Biorep1


title: DMSO, BT549 cells, Biorep3


title: prostate_cancer_primary_541 (STAMPEDE)


title: prostate_cancer_primary_542 (STAMPEDE)


title: DMSO, BT549 cells, Biorep2


title: prostate_cancer_primary_547 (STAMPEDE)


title: prostate_cancer_primary_538 (STAMPEDE)


title: DMSO, BT549 cells, Biorep1


title: prostate_cancer_primary_537 (STAMPEDE)


title: prostate_cancer_primary_540 (STAMPEDE)


title: prostate_cancer_primary_536 (STAMPEDE)


title: prostate_cancer_primary_539 (STAMPEDE)


title: prostate_cancer_primary_535 (STAMPEDE)


title: prostate_cancer_primary_533 (STAMPEDE)


title: prostate_cancer_primary_534 (STAMPEDE)


title: prostate_cancer_primary_543 (STAMPEDE)


title: siGATA6, +DEX, BT549 cells, Biorep2

value: 2h DEX (500nM)


title: siGATA6, +DEX, BT549 cells, Biorep1


title: prostate_cancer_primary_532 (STAMPEDE)


title: siGATA6, Veh, BT549 cells, Biorep3

value: Veh


title: siGATA6, Veh, BT549 cells, Biorep2


title: siGATA6, Veh, BT549 cells, Biorep1


title: prostate_cancer_primary_529 (STAMPEDE)


title: siCtl, +DEX, BT549 cells, Biorep3


title: prostate_cancer_primary_528 (STAMPEDE)


title: siCtl, +DEX, BT549 cells, Biorep2


title: prostate_cancer_primary_527 (STAMPEDE)


title: siGATA6, +DEX, BT549 cells, Biorep3


title: siCtl, +DEX, BT549 cells, Biorep1


title: siCtl, Veh, BT549 cells, Biprep3


title: siCtl, Veh, BT549 cells, Biprep2


title: siCtl, Veh, BT549 cells, Biprep1


title: prostate_cancer_primary_526 (STAMPEDE)


title: Wt83c7p37_no_graphene_light

first: Elena

last: Molokanova

address: 9500 Gilman Drive

institute: NeurANO Bioscience

description: Library name: Wt83c7p37_no_graphene_light

library_source: transcriptomic

data_processing:
Post-sequencing quality control, including adapter trimming and read filtering, was carried out using Rosalind, a cloud-based bioinformatics platform designed for RNA sequencing analysis. Subsequent differential gene expression analysis was also performed in Rosalind and R, comparing expression profiles across the experimental groups
Assembly: hg38
Supplementary files format and content: text file

source_name: brain organoid

growth_protocol: Briefly, hiPSCs were maintained with mTeSR on Matrigel-coated tissue culture dishes. iPSCs were dissociated into single cells using Accutase and plated in 6-well plates in mTeSR with 5µM ROCK 739 inhibitor (Y-27632) and SMAD inhibitors (SB431542 (10µM), Dorsomorphin (1µM) (all chemicals 740 are from Sigma). At this point, graphene dispersion (10-100 µg/mL) was added to wells for generation of graphene-interfaced organoids. Plates were continuously shaken with an orbital platform (95 rpm) from this point on. Media was changed daily through day 6. From days 7-11, media was changed every other day with M1 media [Neurobasal Medium (Life Technologies, 744 21103049) + 1% GlutaMAX (ThermoFisher Scientific, 35050061) + 1% Gem21 NeuroPlex (Gemini Bio, 400-160-010) + 1% N2 NeuroPlex (Gemini Bio, 400-163-005) + 1% NEAA (ThermoFisher Scientific, 11140050) + 1% PS (ThermoFisher Scientific, 15140122) + 10 μM SB + 1 μM Dorso] and embryoid bodies were split between new wells approximately once during this period to prevent overcrowding. From days 12-18, media was changed every day with M2 media [Neurobasal Medium + 1% GlutaMAX + 1% Gem21 NeuroPlex + 1% NEAA + 1% PS] + 20 ng/mL FGF2 (Peprotech, 100-25). From days 19-25, media was changed every other day with M2 + 20 751 ng/mL FGF2 + 20 ng/mL EGF (PeproTech, AF-100-15). From days 26-29, half media changes 23 were performed with M3 media [M2 medium + 10 ng/mL BDNF (PeproTech, 450-02) + 10 ng/mL GDNF (PeproTech, 450-10) + 10 ng/mL NT-3 (PeproTech, 450-03) + 200 μM L-ascorbic acid (Sigma-Aldrich, A4403) + 1 mM dibutyryl-cAMP (StemCell Technologies, 100-0244)] + 20 ng/mL 755 FGF2. On days 30-35, media was changed every 3-4 days with M3 media. On days 36-42, media was changed every 3-4 days with M2.5 media [M3 medium with half the concertation of factors]

extract_protocol:
hiPSC-derived brain organoids were carefully transferred to conical tubes, rinsed three times with Dulbecco's Phosphate-Buffered Saline (D-PBS) to remove residual media and debris, and snap-frozen in liquid nitrogen to preserve RNA integrity. The frozen samples were then stored at -80°C until further processing. RNA extraction was performed using  Qiagen’s RNeasy Plus Mini Kit, following the manufacturer’s protocol. The quality and integrity of the extracted RNA were assessed using the Agilent TapeStation system. Only samples with an RNA Integrity Number (RIN) greater than 7.0 were selected for library preparation to ensure high quality sequencing results.
Library preparation was conducted using the Illumina Stranded mRNA Prep Kit, which selectively enriches polyadenylated (poly-A) transcripts to capture mature mRNA. The prepared libraries were quantified and assessed for quality using Qubit 3.0 and TapeStation respectively before sequencing. Sequencing was performed on the Illumina NovaSeq X Plus 1017 platform using the 10B kit, generating paired-end 100 bp (PE100) reads with standard Illumina primers.

treatment_protocol: G-substrates (3-5 mm PDMS circles or 5-mm glass coverslips) were coated with 100µl/ml poly-L-ornithine and 10µg/ml laminin, and then placed inside a glass-bottom 96-well plate 759 (Greiner). Organoids (2-3 per coverslip) at 6 weeks of age were plated on G-substrates and maintained in Media 2 for 1-2 months. Media were changed twice a week. Before imaging, Media 2 was replaced with BrainPhys media (StemCell Technologies) supplemented with 1% N2, 2% 762 Gem21, and 1% pen/strep.

value: brain organoid

value: induced pluripotent stem cell

value: No rGO, Light


title: Wt83c7p33_no_graphene_light

description: Library name: Wt83c7p33_no_graphene_light


title: prostate_cancer_primary_524 (STAMPEDE)


title: prostate_cancer_primary_525 (STAMPEDE)


title: Wt83c7p33_graphene_light

description: Library name: Wt83c7p33_graphene_light

value: rGO, Light


title: prostate_cancer_primary_522 (STAMPEDE)


title: prostate_cancer_primary_531 (STAMPEDE)


title: Wt83c7p33_graphene_no_light

description: Library name: Wt83c7p33_graphene_no_light

value: rGO,  No Light


title: prostate_cancer_primary_521 (STAMPEDE)


title: prostate_cancer_primary_530 (STAMPEDE)


title: prostate_cancer_primary_518 (STAMPEDE)


title: prostate_cancer_primary_516 (STAMPEDE)


title: prostate_cancer_primary_520 (STAMPEDE)


title: Wt83c7p33_no_graphene_no_light

description: Library name: Wt83c7p33_no_graphene_no_light

value: No rGO, No Light


title: Wt83c7p37_graphene_no_light

description: Library name: Wt83c7p37_graphene_no_light


title: prostate_cancer_primary_523 (STAMPEDE)


title: Wt83c7p37_no_graphene_no_light

description: Library name: Wt83c7p37_no_graphene_no_light


title: prostate_cancer_primary_517 (STAMPEDE)


title: N_Cre_pos.3

city: Seattle

first: Elia

last: Tait Wojno

state: WA

address: 750 Republican Street

department: Immunology

institute: University of Washington

description: Library name: lib106120

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.  The FASTQs were aligned to the GRCm38 mouse reference genome, using STAR v.2.4.2a, and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools (v1.134). DESeq2 was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: Raw and normalized read counts from DESeq2

organism: Mus musculus

source_name: Cecum

extract_protocol:
Ttotal RNA was purified from sort-purified cecum LP CD4+ T cells using the Norgen Biotek Total RNA Purification Plus Micro Kit (Norgen Biotek).
Total RNA was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

treatment_protocol: Cecum CD4+ T cells were sort-purified from single- cell suspensions from 1-2 Mcpt8Cre- DNMAML F/F female mice on D0 or D14 p.i. with T. muris.

value: Cecum

value: CD4+ T cell

value: Cre positive

value: Naïve


title: prostate_cancer_primary_515 (STAMPEDE)

value: FFPE prostate cancer


title: N_Cre_neg.3

description: Library name: lib106119

value: Cre negative


title: prostate_cancer_primary_514 (STAMPEDE)


title: prostate_cancer_primary_513 (STAMPEDE)


title: prostate_cancer_primary_512 (STAMPEDE)


title: Tm_Cre_pos.2

description: Library name: lib106117

value: T. muris infection


title: prostate_cancer_primary_519 (STAMPEDE)


title: Tm_Cre_neg.2

description: Library name: lib106116


title: prostate_cancer_primary_510 (STAMPEDE)


title: prostate_cancer_primary_511 (STAMPEDE)


title: AD-bMSC, Knockout-Library, day10, Replicate 3, 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: Bovine subcutaneous adipose derived mesenchymal stem cells

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: CRISPR-KO Library

value: Proliferation

tag: sequencing batch

tag: time

value: day 10


title: N_Cre_neg.2

description: Library name: lib106114


title: prostate_cancer_primary_508 (STAMPEDE)


title: AD-bMSC, Knockout-Library, day10, Replicate 2, Amplicon-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells


title: AD-bMSC, Knockout-Library, day1, Replicate 3, Amplicon-seq

value: day 1


title: AD-bMSC, Knockout-Library, day10, Replicate 1, Amplicon-seq


title: prostate_cancer_primary_507 (STAMPEDE)


title: Tm_Cre_pos.1

description: Library name: lib106112


title: AD-bMSC, Knockout-Library, day1, Replicate 2, Amplicon-seq


title: AD-bMSC, Knockout-Library, day1, Replicate 1, Amplicon-seq


title: Plasmid Library, day0, Replicate 3, Amplicon-seq

source_name: Plasmid library

value: Plasmid library

value: control

value: day 0


title: prostate_cancer_primary_506 (STAMPEDE)


title: Tm_Cre_neg.1

description: Library name: lib106111


title: Plasmid Library, day0, Replicate 2, Amplicon-seq


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 10, Replicate 3, Amplicon-seq


title: N_Cre_pos.2

description: Library name: lib106115


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 10, Replicate 1, Amplicon-seq


title: N_Cre_neg.1

description: Library name: lib106109


title: prostate_cancer_primary_505 (STAMPEDE)


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 1, Replicate 3, Amplicon-seq


title: Tm_Cre_pos

description: Library name: lib106107


title: prostate_cancer_primary_509 (STAMPEDE)


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 1, Replicate 2, Amplicon-seq


title: prostate_cancer_primary_503 (STAMPEDE)


title: Tm_Cre_neg

description: Library name: lib106106


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


title: Differentiated SH-SY5Y cells treated with Naloxone, replicate 3

city: Freiburg im Breisgau

first: Aly

last: Abotaleb

country: Germany

institute: Medical Center – University of Freiburg

description:
Library name: Naloxone_rep3
M5_Naloxone_14.04

data_processing:
Raw sequencing reads were quality-checked with FastQC.
Reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 aligner.
Gene-level counts were generated using featureCounts.
Differential gene expression analysis was performed using DESeq2 in R.
Assembly: Homo sapiens GRCh38 (hg38).
Supplementary files format and content: Tab-delimited text file containing raw read counts per gene (featureCounts output).

source_name: SH-SY5Y cells differentiated with ATRA, then treated with Naloxone (Naloxone 200 nM, 15 min)

growth_protocol: SH-SY5Y human neuroblastoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and maintained at 37°C in 5% CO₂. For neuronal differentiation, cells were seeded for 24 h, then treated with 10 µM all-trans-retinoic acid (ATRA) in DMEM supplemented with 2% FBS and 1% penicillin-streptomycin for 7 days. Medium was refreshed every 48–72 h.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol, followed by DNase I treatment to remove genomic DNA contamination. RNA quality and integrity were assessed using Bioanalyzer (Agilent).
RNA-seq libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042) for 250–300 bp insert cDNA libraries, without strand-specific information. Sequencing was performed on the Illumina NovaSeq 6000 platform, generating paired-end 150 bp reads.

treatment_protocol: Differentiated neuron-like SH-SY5Y cells were treated with opioids (morphine, metamorphine, TRV130, β-endorphin, naloxone) or vehicle control for 15 minutes prior to RNA extraction.

value: Neuroblastoma

value: neuron-like cells (ATRA-differentiated)

value: wild type

value: Naloxone 200 nM, 15 min


title: prostate_cancer_primary_501 (STAMPEDE)


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 10, Replicate 2, Amplicon-seq


title: prostate_cancer_primary_502 (STAMPEDE)


title: N_Cre_pos

description: Library name: lib106105

value: Cecum

value: CD4+ T cell

value: Cre positive


title: Differentiated SH-SY5Y cells treated with Naloxone, replicate 2

description:
Library name: Naloxone_rep2
M5_Naloxone_1109


title: N_Cre_pos.1

description: Library name: lib106110

value: Naïve


title: Differentiated SH-SY5Y cells treated with β-Endorphin, replicate 2

description:
Library name: Beta-Endorphin_rep2
M4_b-Endorphin_1109

source_name: SH-SY5Y cells differentiated with ATRA, then treated with β-Endorphin (β-Endorphin 200 nM, 15 min)

value: β-Endorphin 200 nM, 15 min


title: N_Cre_neg

description: Library name: lib106104

value: Cre negative


title: Differentiated SH-SY5Y cells treated with β-Endorphin, replicate 3

description:
Library name: Beta-Endorphin_rep3
M4_b-Endorphin_14.04


title: Differentiated SH-SY5Y cells treated with β-Endorphin, replicate 1

description:
Library name: Beta-Endorphin_rep1
M4_b-Endorphin_0409


title: prostate_cancer_primary_500 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_504 (STAMPEDE)


title: prostate_cancer_primary_498 (STAMPEDE)


title: prostate_cancer_primary_499 (STAMPEDE)


title: Differentiated SH-SY5Y cells treated with TRV130, replicate 3

description:
Library name: TRV130_rep3
M3_TRV130_1109

source_name: SH-SY5Y cells differentiated with ATRA, then treated with TRV130 (TRV130 200 nM, 15 min)


title: Differentiated SH-SY5Y cells treated with TRV130, replicate 2

description:
Library name: TRV130_rep2
M3_TRV130_20409


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM AGB1 and 100nM dTAG13 treatment for 2hr, replicate1

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

institute: University of Copenhagen

description: Library name: 7

library_source: other

data_processing:
Processing of EU-seq data Adaptors were trimmed using Cutadapt. Read sequences were aligned to the mm10 mouse genome using bwa meme (version 1.0.4, PMID: 35253835) with soft clipping option for supplementary alignments. Low-mapping quality reads ( < q 10) were removed using samtools (version 1.4). Reads mapped to rRNA and tRNA regions, obtained from UCSC genome browser, were removed using Bedtools. The number of reads mapped to defined regions was counted using HTseq. Transcripts with low mapped reads (average reads ≤ 20 between replicates in both control and treatment conditions) were excluded from DGE analysis. Log2 fold-change (FC) were calculated with the default scaling method of DESeq2, using the median of relative abundance. Asymmetrical DGE profiles resulted in a bias towards the opposite direction of the asymmetry. To adjust for this, the median log2 FC value was subtracted from the DEseq output. Unless described otherwise, fold changes from distinct timepoints were summarized by calculating the averages. For the gene track visualization, we used deeptools and bigWigMerge (UCSC tool) to generate bigwig files using scaling factors calculated from DESeq2.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files and count data

molecule: other

source_name: E14 ES cells

growth_protocol: ESCs were cultured in the standard N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium (Thermo Fisher Scientific), supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1μM PD0325901, 3μM CT-99021 (custom-made by ABCR GmbH, Karlsruhe), 100μM 2-mercaptoethanol, 150μM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (made in house or from Thermo Fisher Scientific.

extract_protocol:
After the 5-EU labeling, cells were quickly washed once with PBS, and immediately lysed in RLT buffer, and RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. Labeled RNA was further enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The labelled RNA was subsequently enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
EU-seq libraries were prepared using the NEBNext® Ultra II RNA First Strand Synthesis Module (E7771) combined with NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module (E6111) or NEBNext® Ultra II Directional RNA Library prep kit for Illumina (E6111), following the manufacturer’s instructions.

treatment_protocol: To analyze nascent transcription changes under various conditions, cells were treated with DMSO or with the indicated chemicals for the specified time points. Unless indicated otherwise, A-485 at 10μM, AGB1 0.1 μM, dTAG13 0.1 μM, or IAA at 500 μM were used for treatment. Cells treated with or without chemicals were pulse-labeled with 0.5 mM 5-EU for 20 min before sample collection.

value: E14 ES cells

value: ES cells

value: bTAG-delN-CTCF/dTAG-CTCF-delC

tag: batch


title: Differentiated SH-SY5Y cells treated with TRV130, replicate 1

description:
Library name: TRV130_rep1
M3_TRV130_10409


title: Differentiated SH-SY5Y cells treated with Metamorphine, replicate 3

description:
Library name: Metamorphine_rep3
M2_Metamorphine_14.04

source_name: SH-SY5Y cells differentiated with ATRA, then treated with Metamorphine (Metamorphine 169 nM, 15 min)

value: Metamorphine 169 nM, 15 min


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM dTAG13 treatment for 2hr, replicate2

description: Library name: 6

value: 100nM dTAG13 treatment for 2h


title: Differentiated SH-SY5Y cells treated with Naloxone, replicate 1

description:
Library name: Naloxone_rep1
M5_Naloxone_0409


title: Differentiated SH-SY5Y cells treated with Morphine, replicate 3

description:
Library name: Morphine_rep3
M1_Morphine_14.04

source_name: SH-SY5Y cells differentiated with ATRA, then treated with Morphine (Morphine 193 nM, 15 min)

value: Morphine 193 nM, 15 min


title: Differentiated SH-SY5Y cells treated with Metamorphine, replicate 1

description:
Library name: Metamorphine_rep1
M2_Metamorphine_0409

value: Neuroblastoma


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM dTAG13 treatment for 2hr, replicate1

description: Library name: 5


title: Differentiated SH-SY5Y cells treated with Metamorphine, replicate 2

description:
Library name: Metamorphine_rep2
M2_Metamorphine_1109

value: neuron-like cells (ATRA-differentiated)


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM AGB1 and 100nM dTAG13 treatment for 2hr, replicate2

description: Library name: 8


title: Differentiated SH-SY5Y cells treated with Morphine, replicate 1

description:
Library name: Morphine_rep1
M1_Morphine_0409

value: wild type


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM AGB1 treatment for 2hr, replicate2

description: Library name: 4

value: 100nM AGB1 treatment for 2hr


title: Differentiated SH-SY5Y cells treated with Morphine, replicate 2

description:
Library name: Morphine_rep2
M1_Morphine_1109


title: Differentiated SH-SY5Y cells treated with Control, replicate 3

description:
Library name: Control_rep3
Control_14.04

source_name: SH-SY5Y cells differentiated with ATRA, then treated with Control (Water control, 15 min)

value: Water control, 15 min


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, 100nM AGB1 treatment for 2hr, replicate1

description: Library name: 3


title: Differentiated SH-SY5Y cells treated with Control, replicate 1

description:
Library name: Control_rep1
Control_0409


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, control, replicate1

description: Library name: 1

value: Control


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_11
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate12.

data_processing:
Processing of EU-seq data Adaptors were trimmed using Cutadapt. Read sequences were aligned to the mm10 mouse genome using bwa meme (version 1.0.4, PMID: 35253835) with soft clipping option for supplementary alignments. Low-mapping quality reads ( < q 10) were removed using samtools (version 1.4). Reads mapped to rRNA and tRNA regions, obtained from UCSC genome browser, were removed using Bedtools. The number of reads mapped to defined regions was counted using HTseq. Transcripts with low mapped reads (average reads ≤ 20 between replicates in both control and treatment conditions) were excluded from DGE analysis. Log2 fold-change (FC) were calculated with the default scaling method of DESeq2, using the median of relative abundance. Asymmetrical DGE profiles resulted in a bias towards the opposite direction of the asymmetry. To adjust for this, the median log2 FC value was subtracted from the DEseq output. Unless described otherwise, fold changes from distinct timepoints were summarized by calculating the averages. For the gene track visualization, we used deeptools and bigWigMerge (UCSC tool) to generate bigwig files using scaling factors calculated from DESeq2.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files
Supplementary files format and content: Count data

treatment_protocol: To analyze nascent transcription changes under various conditions, cells were treated with DMSO or with the indicated chemicals for the specified time points. Unless indicated otherwise, A-485 at 10μM, dTAG13 0.1 μM, or IAA at 500 μM were used for treatment. Cells treated with or without chemicals were pulse-labeled with 0.5 mM 5-EU for 20 min before sample collection.

value: 500uM IAA for 4hrs


title: prostate_cancer_primary_496 (STAMPEDE)


title: Wt83c7p37_graphene_light

description: Library name: Wt83c7p37_graphene_light

value: brain organoid

value: induced pluripotent stem cell

value: WT

value: rGO, Light


title: 4OHT-U2OS-ER-AsiSI-R2

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

description:
Library name: Sample 14
END-seq protocol from Wong et al., 2020

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2 and processed into counts per bin using CUT&RUN Tools 2.0 (Yu et al., 2022)
Raw data for each aligned dataset were normalized in each genomic bin by dividing the counts by total read count for each sample (counts per million) and exported as bigwig (file format) for further analysis.
Assembly: hg19
Supplementary files format and content: Processed data files contain sequenced break counts as a bigwig file normalized by total reads (counts per million)

growth_protocol: BJ-5ta cells were cultured in a complete medium (4:1 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM, Corning, 10-013-CV) and Medium 199 (M199, Gibco, 11150-059), supplemented with 10% FBS, 1% Pen-Strep, 1% L-glutamine and 0.01 mg/ml hygromycin B) at 37°C supplied with 5% CO2. GM12878 cells were cultured in complete Roswell Park Memorial Institute Medium 1640 (Gibco, 11875-093; 15% FBS, 1% Pen-Strep, 1% L-glutamine and 0.01 mg/ml hygromycin B) at 37°C supplied with 5% CO2.U2OS-ER-AsiSI cells were cultured in a complete DMEM GlutaMAX medium (Gibco, 10566-024), supplemented with 10% FBS, 1% Pen-Strep, 1 mM sodium pyruvate and 1 µg/mL puromycin) at 37°C supplied with 5% CO2. BJ-5ta-ER-AsiSI cells were cultured in a complete medium (4:1 mixture of DMEM and M199, supplemented with 10% FBS, 1% Pen-Strep, 1% L-glutamine, 0.01 mg/ml hygromycin B and 1 µg/mL puromycin) at 37°C supplied with 5% CO2.

extract_protocol:
END-seq was performed in U2OS-ER-AsiSI, BJ-5ta-ER-AsiSI, BJ-5ta and GM12878 cells following the END-seq protocol from Wong et al., 2020.
Library amplification was performed following the END-seq protocol from Wong et al., e2020.

treatment_protocol: For irradiation experiments, BJ-5ta adhesion cells were grown to confluency, and GM12878 suspension cells were grown to a density of 1 x 10^6 cells per 1 mL medium prior to X-ray exposure. For DNA damage induction, both cells were seeded without puromycin treatment and treated with 300 nM 4-hydroxytamoxifen (4OHT) for 4 h and 6 h, respectively.

value: Osteosarcoma

value: biological replicate 2


title: 4OHT-U2OS-ER-AsiSI-R1

description:
Library name: Sample 13
END-seq protocol from Wong et al., 2020

value: biological replicate 1


title: DMSO-U2OS-ER-AsiSI-R2

description:
Library name: Sample 16
END-seq protocol from Wong et al., 2020

value: DMSO


title: DMSO-U2OS-ER-AsiSI-R1

description:
Library name: Sample 15
END-seq protocol from Wong et al., 2020


title: prostate_cancer_primary_494 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_495 (STAMPEDE)


title: DMSO-BJ-5ta-ER-AsiSI-R2

description:
Library name: Sample 12
END-seq protocol from Wong et al., 2020

value: Fibroblast


title: DMSO-BJ-5ta-ER-AsiSI-R1

description:
Library name: Sample 11
END-seq protocol from Wong et al., 2020


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_10
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate11.

value: E14 ES cells

value: ES cells


title: prostate_cancer_primary_497 (STAMPEDE)


title: prostate_cancer_primary_492 (STAMPEDE)


title: Differentiated SH-SY5Y cells treated with Control, replicate 2

description:
Library name: Control_rep2
Control_1109

value: Neuroblastoma

value: neuron-like cells (ATRA-differentiated)

value: wild type


title: prostate_cancer_primary_490 (STAMPEDE)


title: prostate_cancer_primary_491 (STAMPEDE)


title: 4OHT-BJ-5ta-ER-AsiSI-R2

description:
Library name: Sample 10
END-seq protocol from Wong et al., 2020


title: Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC ESC, control, replicate2

description: Library name: 2

value: bTAG-delN-CTCF/dTAG-CTCF-delC

value: Control


title: Control-GM12878-R1

description:
Library name: Sample 7
END-seq protocol from Wong et al., 2020

value: Lymphoblast


title: prostate_cancer_primary_493 (STAMPEDE)


title: 4OHT-BJ-5ta-ER-AsiSI-R1

description:
Library name: Sample 9
END-seq protocol from Wong et al., 2020


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_9
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate10.

value: 500uM IAA for 4hrs


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_8
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate9.


title: prostate_cancer_primary_489 (STAMPEDE)


title: prostate_cancer_primary_487 (STAMPEDE)


title: X-ray-GM12878-R2

description:
Library name: Sample 6
END-seq protocol from Wong et al., 2020

value: X-ray, 5Gy


title: prostate_cancer_primary_486 (STAMPEDE)


title: prostate_cancer_primary_488 (STAMPEDE)


title: X-ray-GM12878-R1

description:
Library name: Sample 5
END-seq protocol from Wong et al., 2020


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_7
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate8.


title: Control-BJ-5ta-R1

description:
Library name: Sample 3
END-seq protocol from Wong et al., 2020


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_6
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate7.


title: Control-BJ-5ta-R2

description:
Library name: Sample 4
END-seq protocol from Wong et al., 2020


title: X-ray-BJ-5ta-R2

description:
Library name: Sample 2
END-seq protocol from Wong et al., 2020


title: X-ray-BJ-5ta-R1

description:
Library name: Sample 1
END-seq protocol from Wong et al., 2020


title: Control-GM12878-R2

description:
Library name: Sample 8
END-seq protocol from Wong et al., 2020


title: prostate_cancer_primary_485 (STAMPEDE)


title: Huh7_RB1_knockout_Vol_3

city: Seoul

first: Wonkyung

last: Kim

address: 88, Olympic-ro 43-gil

country: South Korea

institute: Asan medical center

description:
Library name: Rba6_Vol_3
Column name in cell_line_count_RNA.txt: Rba6_Vol_3

data_processing:
Xenograft RNA-sequencing data of RB1-/- PLC/PRF/5 xenograft samples (wild-type, n=3; vehicle control, n=3; Alisertib-treated, n=3; Ispinesib-treated, n=3; Volasertib-treated, n=3) were processed using a multi-step alignment approach. Initially, reads were aligned using STAR aligner v2.7.9a against a combined hybrid genome of human (hg19) and mouse (mm10) references to separate human tumor- derived reads from mouse stroma-derived reads. Using SAMtools v1.9, reads that specifically mapped to either the human or mouse genome were extracted and assigned to corresponding BAM files. Human-specific paired reads were then extracted using the SAMtools parameter -f 1 from BAM files that had been preprocessed by subtracting reads mapped to the mouse genome. Duplicate reads were subsequently identified and marked using Sambamba v0.8.2. The SamToFastq utility of Picard v2.26.6 was used to convert the processed BAM files back to paired-end FASTQ format.68 The resulting paired-end FASTQ files were re-aligned to the human genome (hg19) using the TCGA RNASeqV2 pipeline with upper quartile normalization. Cell line RNA-sequencing data of Huh7 RB1-/- and RB1+/+ cell lines were aligned to the human genome (hg19) using the TCGA RNASeqV2 pipeline with upper quartile normalization.
Assembly: hg19
Supplementary files format and content: tep-delimited text file includes raw counts for each sample.

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. mRNA was enriched with poly-T oligo-attached magnetic beads.
RNA sequencing libraries were prepared by Novogene using Illumina-compatible protocols. mRNA was enriched with poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. The libraries were completed through end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification.

value: hepatocellular carcinoma cells

value: Volasertib


title: Huh7_RB1_knockout_Tal_3

description:
Library name: Rba6_Tala_3
Column name in cell_line_count_RNA.txt: Rba6_Tala_1

value: Talazoparib


title: Huh7_RB1_knockout_Tal_2

description:
Library name: Rba6_Tala_2
Column name in cell_line_count_RNA.txt: Rba6_Tala_1


title: Huh7_RB1_knockout_Vol_1

description:
Library name: Rba6_Vol_1
Column name in cell_line_count_RNA.txt: Rba6_Vol_1


title: Huh7_RB1_knockout_Tal_1

description:
Library name: Rba6_Tala_1
Column name in cell_line_count_RNA.txt: Rba6_Tala_1


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_4
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate5.


title: Huh7_RB1_knockout_Isp_3

description:
Library name: Rba6_Isp_3
Column name in cell_line_count_RNA.txt: Rba6_Isp_3

value: Ispinesib


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_3
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate4.


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_2
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate3.


title: prostate_cancer_primary_483 (STAMPEDE)


title: Huh7_RB1_knockout_Isp_2

description:
Library name: Rba6_Isp_2
Column name in cell_line_count_RNA.txt: Rba6_Isp_2


title: prostate_cancer_primary_484 (STAMPEDE)


title: prostate_cancer_primary_481 (STAMPEDE)


title: Huh7_RB1_knockout_Isp_1

description:
Library name: Rba6_Isp_1
Column name in cell_line_count_RNA.txt: Rba6_Isp_1


title: Huh7_RB1_knockout_Ali_3

description:
Library name: Rba6_Ali_3
Column name in cell_line_count_RNA.txt: Rba6_Ali_3

value: Alisertib


title: prostate_cancer_primary_482 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_480 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC52_1
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate1.


title: prostate_cancer_primary_479 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_5
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate6.


title: Huh7_RB1_knockout_Ali_2

description:
Library name: Rba6_Ali_2
Column name in cell_line_count_RNA.txt: Rba6_Ali_2


title: prostate_cancer_primary_478 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_11
EU-seq of GFP-AID-Rad21 ESC, control, replicate12.


title: Huh7_RB1_knockout_Vol_2

description:
Library name: Rba6_Vol_2
Column name in cell_line_count_RNA.txt: Rba6_Vol_2


title: Huh7_RB1_knockout_Ali_1

description:
Library name: Rba6_Ali_1
Column name in cell_line_count_RNA.txt: Rba6_Ali_1


title: Huh7_RB1_knockout_DMSO_3

description:
Library name: Rba6_DMSO_3
Column name in cell_line_count_RNA.txt: Rba6_DMSO_3

value: DMSO


title: Huh7_RB1_knockout_DMSO_2

description:
Library name: Rba6_DMSO_2
Column name in cell_line_count_RNA.txt: Rba6_DMSO_2


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_10
EU-seq of GFP-AID-Rad21 ESC, control, replicate11.

value: E14 ES cells


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_9
EU-seq of GFP-AID-Rad21 ESC, control, replicate10.

value: ES cells


title: Huh7_RB1_knockout_DMSO_1

description:
Library name: Rba6_DMSO_1
Column name in cell_line_count_RNA.txt: Rba6_DMSO_1


title: Huh7_SC12_DMSO_1

description:
Library name: SC12_DMSO_1
Column name in cell_line_count_RNA.txt: SC12_DMSO_1

value: WT


title: Huh7_SC12_DMSO_2

description:
Library name: SC12_DMSO_2
Column name in cell_line_count_RNA.txt: SC12_DMSO_2


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_8
EU-seq of GFP-AID-Rad21 ESC, control, replicate9.


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_IAA_500uM_TC240_CC53_1
EU-seq of GFP-AID-Rad21 ESC, treated with 500uM IAA for 4hr, replicate2.


title: xenograft_RB11_Tal_2

description:
Library name: P_RB11_Tal_2
Column name in xenograft_count_RNA.txt: P_RB11_Tal_2

source_name: xenograft

value: xenograft


title: xenograft_RB11_Tal_3

description:
Library name: P_RB11_Tal_3
Column name in xenograft_count_RNA.txt: P_RB11_Tal_3


title: prostate_cancer_primary_477 (STAMPEDE)


title: prostate_cancer_primary_476 (STAMPEDE)


title: prostate_cancer_primary_475 (STAMPEDE)


title: xenograft_RB11_Tal_1

description:
Library name: P_RB11_Tal_1
Column name in xenograft_count_RNA.txt: P_RB11_Tal_1


title: xenograft_RB18_Vol_2

description:
Library name: P_RB18_Vol_2
Column name in xenograft_count_RNA.txt: P_RB18_Vol_2_count


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_6
EU-seq of GFP-AID-Rad21 ESC, control, replicate7.


title: xenograft_RB18_Vol_3

description:
Library name: P_RB18_Vol3N
Column name in xenograft_count_RNA.txt: P_RB18_Vol3N_count


title: prostate_cancer_primary_474 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_5
EU-seq of GFP-AID-Rad21 ESC, control, replicate6.


title: xenograft_RB18_Vol_1

description:
Library name: P_RB18_Vol_1
Column name in xenograft_count_RNA.txt: P_RB18_Vol_1_count


title: xenograft_RB18_Isp_3

description:
Library name: P_RB18_Isp_3
Column name in xenograft_count_RNA.txt: P_RB18_Isp_3_count


title: prostate_cancer_primary_473 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_4
EU-seq of GFP-AID-Rad21 ESC, control, replicate5.


title: xenograft_RB18_Isp_2

description:
Library name: P_RB18_Isp_2
Column name in xenograft_count_RNA.txt: P_RB18_Isp_2_count


title: xenograft_RB18_Isp_1

description:
Library name: P_RB18_Isp_1
Column name in xenograft_count_RNA.txt: P_RB18_Isp_1_count


title: Huh7_SC12_DMSO_3

description:
Library name: SC12_DMSO_3
Column name in cell_line_count_RNA.txt: SC12_DMSO_3


title: xenograft_RB18_Ali_3

description:
Library name: P_RB18_Ali_3
Column name in xenograft_count_RNA.txt: P_RB18_Ali_3_count


title: prostate_cancer_primary_471 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_2
EU-seq of GFP-AID-Rad21 ESC, control, replicate3.


title: prostate_cancer_primary_470 (STAMPEDE)


title: xenograft_RB18_3

description:
Library name: P_RB18_3
Column name in xenograft_count_RNA.txt: P_RB18_3_count

value: control


title: xenograft_RB18_Ali_1

description:
Library name: P_RB18_Ali_1
Column name in xenograft_count_RNA.txt: P_RB18_Ali_1_count


title: xenograft_RB18_Ali_2

description:
Library name: P_RB18_Ali_2
Column name in xenograft_count_RNA.txt: P_RB18_Ali_2_count


title: prostate_cancer_primary_469 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_7
EU-seq of GFP-AID-Rad21 ESC, control, replicate8.


title: xenograft_RB18_2

description:
Library name: P_RB18_2
Column name in xenograft_count_RNA.txt: P_RB18_2_count


title: xenograft_SC12_3

description:
Library name: P_SC12_3
Column name in xenograft_count_RNA.txt: P_SC12_3_count


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_1
EU-seq of GFP-AID-Rad21 ESC, control, replicate2.


title: xenograft_RB18_1

description:
Library name: P_RB18_1
Column name in xenograft_count_RNA.txt: P_RB18_1_count


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC52_1
EU-seq of GFP-AID-Rad21 ESC, control, replicate1.


title: xenograft_SC12_2

description:
Library name: P_SC12_2
Column name in xenograft_count_RNA.txt: P_SC12_2_count


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_A485_10uM_TC60_CC56_2
EU-seq of GFP-AID-Rad21 NPC, treated with 10uM A-485 for 1hr, replicate2.

source_name: NPC

value: NPC

value: 10uM A-485 for 1hr


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_A485_10uM_TC60_CC56_1
EU-seq of GFP-AID-Rad21 NPC, treated with 10uM A-485 for 1hr, replicate1.


description:
Library name: EUSeq.GFP.AID.Rad21.ESC_Ctrl_TC0_CC53_3
EU-seq of GFP-AID-Rad21 ESC, control, replicate4.

value: Control


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC240_CC56_2
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 4hr, replicate2.

value: 500uM IAA for 4hrs


title: KO-3

city: Guangzhou

first: xuyi

last: deng

state: Guangdong

address: No. 1838, North Guangzhou Avenue

country: China

institute: Southern Medical University

description: Library name: samples 6

data_processing:
This project, Raw Reads, uses the Trimmomatic software for data filtering. The main parameters adopt the default reference values. For the software reference, please refer to the literature [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-20. ]
Assembly: hg38
Supplementary files format and content: All.HTSeq.counts.txt

source_name: HaCaT

extract_protocol:
RNA extraction of the samples was performed using Trizol (Thermo Fisher Scientific, 15596018).
Library construction was performed using the NEBNext UltraTM RNA Library Prep Kit (NEB #E7490), and the libraries were purified using beads (AMPure XP system).

value: HaCaT

value: keratinocytes

value: BCL11A knockout


title: WT-3

description: Library name: samples 3


title: KO-1

description: Library name: samples 4


title: KO-2

description: Library name: samples 5


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC240_CC56_1
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 4hr, replicate1.


title: WT-2

description: Library name: samples 2


title: prostate_cancer_primary_468 (STAMPEDE)


title: WT-1

description: Library name: samples 1


title: prostate_cancer_primary_472 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC120_CC56_2
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 2hr, replicate2.

value: 500uM IAA for 2hrs


title: prostate_cancer_primary_467 (STAMPEDE)


title: xenograft_SC12_1

description:
Library name: P_SC12_1
Column name in xenograft_count_RNA.txt: P_SC12_1_count

value: hepatocellular carcinoma cells


title: PBMC15MCAR-NKT 2

city: Los Angeles

first: Shuo

last: Li

state: CA

address: 630 Charles E Young Dr S

institute: UCLA

description: Library name: PBMC15MCAR-NKT 2

data_processing:
The raw bisulfite sequencing reads were trimmed by cutadapt to remove sequencing adapters.
The trimmed reads were then aligned to hg19 reference genome by Bismark.
Then duplicated reads from PCR amplification were identified and removed by Bismark.
The deduplicated reads were then sorted and indexed using samtools.
The methylation level was calculated at every CpG site by Bismark.
Assembly: hg19
Supplementary files format and content: methylation level (beta value) at CpG sites in the bed format

growth_protocol: The therapeutic cells were generated from an Ex Vivo HSC-derived CAR-NKT cell culture

extract_protocol:
Genomic DNA from samples was isolated with QIAGEN DNeasy Blood & Tissue kit following the corresponding manufacturer’s protocols.
The isolated genomic DNA was sonicated by Covaris system. Size selection by Ampure XP beads (Beckman-Coulter) was performed to enrich DNA fragments of around 250 bp in average sizes before library construction. In brief, 0.7 volume beads were added to the fragmented genomic DNA. After incubation, the supernatant was transferred to a new tube and an additional 1.3 volume beads were added (“0.5×–2× bead size selection”). After washing two times with 80% ethanol, genomic DNA was eluted with 40 ul EB buffer. Subsequently,  200ng genomic DNA was used for DNA library preparation with NEBNext Ultra II DNA library prep Kit (Cat#E7645). DNA library preparation has the following steps: DNA fragments end prep, adaptor ligation, size selection or purification of Adaptor-ligated DNA with Ampure XP beads, bisulfite conversion by Epitect Fast DNA Bisulfite Kits (QIAGEN, Cat#59826), PCR enrichment of Adaptor-ligated DNA, and purification of PCR product with 0.9x Ampure XP beads.  The average size of resulting DNA fragments was around 480bp, validated by Tapestation. The libraries were then subjected to sequencing on Illumina NovaSeq sequencer with 2x150bp configuration (Azenta).

treatment_protocol: The therapeutic cells were engineered with mesothelin-targeting CAR


title: PBMC15MCAR-NKT 3

description: Library name: PBMC15MCAR-NKT 3


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC120_CC56_1
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 2hr, replicate1.


title: prostate_cancer_primary_463 (STAMPEDE)


title: prostate_cancer_primary_465 (STAMPEDE)


title: HSPC-cell 2

description: Library name: HSPC-cell 2

source_name: HSPC-cell

value: HSPC-cell


title: prostate_cancer_primary_464 (STAMPEDE)

value: FFPE prostate cancer


title: HSPC-cell 3

description: Library name: HSPC-cell 3


title: prostate_cancer_primary_466 (STAMPEDE)


title: prostate_cancer_primary_462 (STAMPEDE)


title: prostate_cancer_primary_461 (STAMPEDE)


title: prostate_cancer_primary_460 (STAMPEDE)


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC60_CC56_2
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA  for 1hr, replicate2.

value: 500uM IAA for 1hr


title: RBE_CB5339_bio rep3

city: Amsterdam

first: Wu

last: Yang

address: B7, Plesmanlaan 121 1066CX Amsterdam

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: Sample 14
V1_3

data_processing:
CLC Genomics Workbench v11.0.1
Quality control of raw sequencing reads (FASTQ) and removal of adapter sequences.
Alignment of trimmed reads to the reference genome.
Estimation of gene/transcript abundance based on aligned reads.
Identification of significantly differentially expressed genes between experimental conditions.
Assembly: GRCh38 (hg38)
Supplementary files format and content: csv files include raw counts for each sample.

source_name: RBE

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research, R1055) with on-column DNase I digestion to eliminate genomic DNA contamination. RNA integrity was verified by Agilent 2100 Bioanalyzer (RIN > 8.0), and concentrations were quantified via Qubit 4.0 Fluorometer (Thermo Fisher Scientific).
For bulk RNA sequencing, 1 μg of total RNA per sample underwent library construction. Libraries were sequenced on an Illumina NovaSeq 6000 platform (150-bp paired-end, 30M reads/sample).

value: RBE

value: Cholangiocarcinoma cell


title: prostate_cancer_primary_459 (STAMPEDE)

source_name: FFPE prostate cancer


title: RBE_CB5339_bio rep2

description:
Library name: Sample 13
V1_2

value: WT


title: RBE_CB5339_bio rep1

description:
Library name: Sample 12
V1_1


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_IAA_500uM_TC60_CC56_1
EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 1hr, replicate1.


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_Ctrl_TC0_CC56_2
EU-seq of GFP-AID-Rad21 NPC, control, replicate2.


title: RBE_Veh_bio rep3

description:
Library name: Sample 10
CT1_3

value: DMSO


title: RBE_Veh_bio rep2

description:
Library name: Sample 9
CT1_2


title: PBMC15MCAR-NKT 1

description: Library name: PBMC15MCAR-NKT 1


title: RBE_Veh_bio rep4

description:
Library name: Sample 11
CT1_4


description:
Library name: EUSeq.GFP.AID.Rad21.NSC_Ctrl_TC0_CC56_1
EU-seq of GFP-AID-Rad21 NPC, control, replicate1.


title: RBE_Veh_bio rep1

description:
Library name: Sample 8
CT1_1


title: EU-seq of GFP-AID-Rad21 mouse ESC  treated with IAA for 4hr, replicate2.

data_processing:
Processing EU-seq data Adaptors were trimmed using Cutadapt. Read sequences were aligned to the mm10 mouse genome using bwa meme (version 1.0.4, PMID: 35253835) with soft clipping option for supplementary alignments. Low-mapping quality reads ( < q 10) were removed using samtools (version 1.4). Reads mapped to rRNA and tRNA regions, obtained from UCSC genome browser, were removed using Bedtools. The number of reads mapped to defined regions was counted using HTseq. Transcripts with low mapped reads (average reads ≤ 20 between replicates in both control and treatment conditions) were excluded from DGE analysis. Log2 fold-change (FC) were calculated with the default scaling method of DESeq290, using the median of relative abundance. Asymmetrical DGE profiles resulted in a bias towards the opposite direction of the asymmetry. To adjust for this, the median log2 FC value was subtracted from the DEseq output. Unless described otherwise, fold changes from distinct timepoints were summarized by calculating the averages. For the gene track visualization, we used deeptools and bigWigMerge (UCSC tool)91 to generate bigwig files using scaling factors calculated from DESeq2.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files
Supplementary files format and content: Count data
Library strategy: EU-seq

extract_protocol:
Following 5-EU labelling, cells were quickly washed (1x) with PBS, and immediately lysed in RLT buffer and RNA was prepared using RNeasy Mini Kit (Qiagen). The labelled RNA was subsequently enriched using the Click-iT® Nascent RNA Capture Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
EU-seq libraries were prepared using the NEBNext Ultra kit (NEB) as per manufacturer’s instructions and subsequently sequenced using a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: Cells were treated with DMSO or with 500nM triptolide for 120min. The inhibitor was added prior to or simultaneous to adding 5-ethynyl uridine (5-EU), as specified. Cells were pulse-labelled with 0.5 mM 5-EU for 20 min before sample collection.

value: E14 ES cells

value: ES cells


title: prostate_cancer_primary_458 (STAMPEDE)


title: EU-seq of GFP-AID-Rad21 mouse ESC  treated with IAA for 4hr, replicate1.


title: HSPC-cell 1

description: Library name: HSPC-cell 1


title: prostate_cancer_primary_457 (STAMPEDE)


title: HuCCT1_CB5339_bio rep2

description:
Library name: Sample 6
V_2


title: HuCCT1_CB5339_bio rep1

description:
Library name: Sample 5
V_1


title: HuCCT1_Veh_bio rep4

description:
Library name: Sample 4
CT_4


title: HuCCT1_Veh_bio rep2

description:
Library name: Sample 2
CT_2


title: HuCCT1_Veh_bio rep3

description:
Library name: Sample 3
CT_3


title: HuCCT1_CB5339_bio rep3

description:
Library name: Sample 7
V_3


title: HuCCT1_Veh_bio rep1

description:
Library name: Sample 1
CT_1


title: prostate_cancer_primary_455 (STAMPEDE)


title: EU-seq of GFP-AID-Rad21 mouse ESC control, replicate1.


title: prostate_cancer_primary_454 (STAMPEDE)


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 4hr, replicate2.

value: GFP-FKBP12F36V-Ctcf (Y226A/F228A)

value: 200nM dTAG13 for 4hrs


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 4hr, replicate1.


title: prostate_cancer_primary_452 (STAMPEDE)


title: prostate_cancer_primary_453 (STAMPEDE)


title: prostate_cancer_primary_456 (STAMPEDE)


title: LOCL-TL with RNA-Seq, AKAP1 knock out monoclonal cells, pulldown sample. Replicate 2

city: Cambridge

first: Jingchuan

last: Luo

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Library name: AKAP1_null_replicate2-pulldown

data_processing:
Data was processed as previously described (PMID: 25378630). Sequencing reads were demultiplexed, adapters removed, and reads shorter than 18 nt discarded. Remaining reads were aligned sequentially to rRNA, tRNA, and then Homo_sapiens.GRCh38.104 genome using Bowtie, retaining only uniquely mapped, zero-mismatch genomic alignments. Gene-level enrichments were computed by taking the log2 ratio of biotinylated footprint density (reads per million) within a gene coding sequence (CDS) over the corresponding density in the matched input ribosome profiling experiment.
Assembly: Homo_sapiens.GRCh38.104
Supplementary files format and content: Processed data includes counting the number of read alignments and calculating read densities (in RPKM) across genes, separately for exons, 5′ UTRs, coding regions, and 3′ UTRs of each gene.

molecule: polyA RNA

source_name: HEK293T cells

extract_protocol:
Direct-zol RNA Kits
proximity specific ribosome profiling protocol

value: HEK293T cells


title: LOCL-TL with RNA-Seq, AKAP1 knock out monoclonal cells, total input. replicate 2

description: Library name: AKAP1_null_replicate2-total


title: LOCL-TL with RNA-Seq, no cycloheximide treatment, pulldown sample. replicate 1

description: Library name: No CHX treatment - pulldown


title: EU-seq of GFP-AID-Rad21 mouse ESC control, replicate2.

value: Control


title: prostate_cancer_primary_451 (STAMPEDE)


title: PBMC_NK

first: Yichen

last: Zhu

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description:
Library name: Sample_01
10x Genomics

library_source: transcriptomic single cell

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: In vitro

extract_protocol:
Therapeutic cell products (Pre-infusion) were subjected to FACS sorting for isolating live cells including MCAR-T, PBMC-MCAR-NKT- IL15, PBMC-NK, and Allo15MCAR-NKT cells.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: In vitro

value: Pre-infusion

value: T cells


title: LOCL-TL with RNA-Seq, AKAP1 knock out monoclonal cells, total input. replicate 1

description: Library name: AKAP1_null_replicate1-total


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 2hr, replicate1.

value: 200nM dTAG13 for 2hrs


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 2hr, replicate2.


title: LOCL-TL with RNA-Seq, LARP4 knock out monoclonal cells, pulldown sample. replicate 2

description: Library name: LARP4_null_replicate2-pulldown


title: prostate_cancer_primary_450 (STAMPEDE)


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant control, replicate2.


title: LOCL-TL with RNA-Seq, LARP4 knock out monoclonal cells, total input. replicate 1

description: Library name: LARP4_null_replicate1-total


title: LOCL-TL with RNA-Seq, LARP4 knock out monoclonal cells, pulldown sample. replicate 1

description: Library name: LARP4_null_replicate1-pulldown


title: LOCL-TL with RNA-Seq, AKAP1 knock out monoclonal cells, pulldown sample. replicate 1

description: Library name: AKAP1_null_replicate1-pulldown


title: LOCL-TL with RNA-Seq, wild type cells with neg control gRNA, pulldown sample. replicate 2

description: Library name: neg control gRNA - replicate 2 pulldown


title: EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant control, replicate1.


title: LOCL-TL with RNA-Seq, wild type cells with neg control gRNA, total input. replicate 2

description: Library name: neg control gRNA - replicate 2 total


title: LOCL-TL with RNA-Seq, LARP4 knock out monoclonal cells, total input. replicate 2

description: Library name: LARP4_null_replicate2-total


title: prostate_cancer_primary_449 (STAMPEDE)


title: LOCL-TL with RNA-Seq, wild type cells with neg control gRNA, pulldown sample. replicate 1

description: Library name: neg control gRNA - replicate 1 pulldown


title: prostate_cancer_primary_446 (STAMPEDE)


title: prostate_cancer_primary_448 (STAMPEDE)


title: Stranded EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate2.

value: GFP-AID-Ctcf

value: 500uM IAA for 6hrs


title: prostate_cancer_primary_447 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_445 (STAMPEDE)


title: Stranded EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate1.


title: EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate2.


title: LOCL-TL with RNA-Seq, no cycloheximide treatment, total input. replicate 1

description: Library name: No CHX treatment - total


title: RNA, siHNRNPK, rep2

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description:
Library name: siHNRNPK-2
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: RNA, siHNRNPK, rep1

description:
Library name: siHNRNPK-1
formatted_HNRNPK_counts.txt


title: RNA, siControl, rep2

description:
Library name: siNTC5-2
formatted_HNRNPK_counts.txt

value: Nontargeting control siRNA


title: EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate1.


title: RNA, siControl, rep1

description:
Library name: siNTC5-1
formatted_HNRNPK_counts.txt


title: Stranded EU-seq of GFP-AID-Ctcf mouse ESC control, replicate2.


title: shGJA1_230831

city: Tokyo

first: Takuma

last: Takada

address: 8-1, Kawada-cho, Shinjuku-ku

country: Japan

institute: Tokyo Women's Medical University

description: Library name: Sample 12

data_processing:
This step was outsourced to Rhelixa (Tokyo, Japan).
Supplementary files format and content: deg_ann.txt

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany). More than 1.3 μg of total RNA were outsourced to Rhelixa (Tokyo, Japan).
This step was outsourced to Rhelixa (Tokyo, Japan).

value: human iPSC-derived cardiomyocytes

value: sh GJA1


title: scram_230831

description: Library name: Sample 9

value: scramble


title: Stranded EU-seq of GFP-AID-Ctcf mouse ESC control, replicate1.

value: E14 ES cells

value: ES cells


title: scram_230720

description: Library name: Sample 7


title: shGJA1_230202

description: Library name: Sample 11


title: prostate_cancer_primary_444 (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.


title: GJA1OE_230831

description: Library name: Sample 6

value: GJA1 OE


title: EU-seq of GFP-AID-Ctcf mouse ESC control, replicate2.

value: Control


title: LOCL-TL with RNA-Seq, wild type cells with neg control gRNA, total input. replicate 1

description: Library name: neg control gRNA - replicate 1 total

value: HEK293T cells


title: GJA1OE_230720

description: Library name: Sample 4


title: EU-seq of GFP-AID-Ctcf mouse ESC control, replicate1.


title: GFP_230831

description: Library name: Sample 3

value: GFP


title: Pol II ChIP-seq on  GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 4hrs, replicate2

data_processing:
Adaptor was trimmed using Cutadapt (doi:https://doi.org/10.14806/ej.17.1.200). Read sequences were aligned to the mm10 mouse or hg19 human genome using bwa meme (version 1.0.4, PMID: 35253835) with soft clipping option for supplementary alignments. Duplicated reads were annotated and removed using Picard toolkit tools. For the calculation of Pol2 ChIP-seq changes after CTCF degradation, we assumed that Pol2 binding remains unaffected at gene body regions that are not changed (NC) in EU-seq analysis. The scaling factors were calculated by DESeq2 default normalization methods using the Pol2 ChIP read counts at gene body regions of NC genes in the CTCF degradation experiments. The aggregate ChIP-seq profiles were plotted using deepTools2 (version 3.5.2, PMID: 27079975). For gene track visualization, IGV96 (version2.16) was used.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 2000 Sequencer (Illumina).

treatment_protocol: Cells were treated with DMSO or with 100nM dTAG13 for 4 hours.

value: GFP-dTAG-Ctcf

value: dTAG13 100nM for 4hrs.


title: shGJA1_230720

description: Library name: Sample 10


title: GFP_230202

description: Library name: Sample 2


title: scram_230202

description: Library name: Sample 8


title: GFP_230720

description: Library name: Sample 1


title: Pol II ChIP-seq on  GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 4hrs, replicate1


title: prostate_cancer_primary_439 (STAMPEDE)


title: prostate_cancer_primary_441 (STAMPEDE)


title: prostate_cancer_primary_443 (STAMPEDE)


title: prostate_cancer_primary_440 (STAMPEDE)


title: 4DNEXOV1X9O1, Homo sapiens - HCT116, input-condition3enhancementG - anti-SON, B2 T1

city: Boston

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
Library name: 4DNEXOV1X9O1
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXOV1X9O1/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include

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

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).

value: immortalized cell line

value: input-condition3  anti-SON

tag: input-reference


title: prostate_cancer_primary_442 (STAMPEDE)

last: Davicioni

institute: Veracyte, Inc

value: FFPE prostate cancer


title: 4DNEXB31RUO3, Homo sapiens - HCT116, condition3enhancementG - anti-SON, B2 T1

description:
Library name: 4DNEXB31RUO3
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXB31RUO3/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include

value: condition3  anti-SON


title: Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, control, replicate2

value: control


title: prostate_cancer_primary_438 (STAMPEDE)


title: GJA1OE_230202

description: Library name: Sample 5


title: 4DNEX61G44AI, Homo sapiens - HCT116, input-condition3enhancementG - anti-SON, B1 T1

description:
Library name: 4DNEX61G44AI
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX61G44AI/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include


title: 4DNEXLTCDBTP, Homo sapiens - HCT116, condition3enhancementG - anti-THRAP3, B2 T1

description:
Library name: 4DNEXLTCDBTP
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-THRAP3, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXLTCDBTP/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include

value: condition3  anti-THRAP3


title: Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, control, replicate1


title: prostate_cancer_primary_436 (STAMPEDE)


title: prostate_cancer_primary_437 (STAMPEDE)


title: 4DNEX3WUH84C, Homo sapiens - HCT116, condition3enhancementG - anti-THRAP3, B1 T1

description:
Library name: 4DNEX3WUH84C
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-THRAP3, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX3WUH84C/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include


title: 4DNEX6IY5FA9, Homo sapiens - HCT116, input-condition3enhancementG - anti-THRAP3, B2 T1

description:
Library name: 4DNEX6IY5FA9
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-THRAP3, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX6IY5FA9/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include

value: input-condition3  anti-THRAP3


title: ATAC-seq on  GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 3hrs, replicate2

data_processing:
Adaptor was trimmed using Cutadapt (doi:https://doi.org/10.14806/ej.17.1.200). Paired-end read sequences were aligned to mm10 genome using BWA meme (version 1.0.4)55 with soft clipping option for supplementary alignments. Duplicated read pairs were removed using Picard-tools (version 2.9.1, “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute). We filtered out low-quality reads with a MAPQ score less than 10 and non-primary alignments, and retained only the properly aligned read pairs, using samtools. Peak regions were called from the merged alignment files of both control and dTAG13-treated samples using LanceOtron and its default model (wide-and-deep_jan-2021). Peak height was calculated using bamCoverage with the following parameters (centerReads, bin size 20b, smooth length 400b, extend reads 200b, rpm normalization). Poorly- enriched peaks of peak summit height < 8 rpm were filtered out. For the calculation of ATAC accessibility changes, ATAC reads that were. mapped in the summit +/- 100b regions were counted. After filtering out the low-mapped regions (average reads ≤ 20 between replicates in both control and treatment conditions), log2 fold-change (FC) were calculated with the default scaling method of DESeq290, using the median of relative abundance.
Assembly: mm10
Supplementary files format and content: Gene track bigwig files
Supplementary files format and content: ATAC peak bed file

extract_protocol:
Cells were washed once in pre-warmed PBS, disaggregated using TrypLE (Thermo Fisher Scientific), and trypsinization was stopped by adding cold media. Two hundred thousand cells were transferred to LoBind microfuge tube (Eppendorf) and centrifuged at 500g for 5min at 4ºC. After centrifugation, the cells were suspended in buffer A (10mM HEPES pH 7.9, 10mM KCl, 1.5mM MgCl2, 0.34M Sucrose, 10% Glycerol, 10% Triton-X), mixed by tapping and incubated on ice for 7min. After centrifugation, buffer A was removed, and nuclei were suspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.3% Igepal). A quarter of nuclei was transferred to a new Lobind tube, briefly vortexed, incubated on ice for 15min, vortexed briefly again, and pelleted down at 600g for 10min at 4ºC. After removing lysis buffer, nuclei were recovered with 2.5 μL 2X TD buffer and 2.5 μL transposase (TDE1) mixture (Illumina). After pipetting several times, the nuclei were incubated for 30min at 37 ºC on a rocking mixer. The transposed DNA was purified using the MinElute PCR Purification kit (Qiagen) following the manufacture's protocol.
The transposed genomic region was PCR-amplified using Nextera Primers ( https://www.encodeproject.org/documents/860c95a8-fdc4-46bd-b9b5- d44242ff20ef/@@download/attachment/ATAC_garberlab_protocol.pdf ) and NEBNext High-Fidelity 2x PCR Master Mix (NEB). PCR product was purified using Agencourt® AMPure® XP beads (Beckman Coulter) and sequenced on a Next-Seq 2000 Sequencer (Illumina).

treatment_protocol: Cells were treated with DMSO or with 100nM dTAG13 for 3 hours.

value: dTAG13 100nM for 3hrs.


title: 4DNEX9T3MZIB, Homo sapiens - HCT116, input-condition3enhancementG - anti-THRAP3, B1 T1

description:
Library name: 4DNEX9T3MZIB
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-THRAP3, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX9T3MZIB/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include


title: prostate_cancer_primary_435 (STAMPEDE)


title: 4DNEXBRXYZAL, Homo sapiens - HCT116, condition3enhancementG - anti-SON, B1 T1

description:
Library name: 4DNEXBRXYZAL
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXBRXYZAL/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include


title: prostate_cancer_primary_433 (STAMPEDE)


title: 4DNEX23RKBJC, Homo sapiens - HCT116, condition3enhancementG - anti-DDX39B, B1 T1

description:
Library name: 4DNEX23RKBJC
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-DDX39B, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX23RKBJC/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include

value: condition3  anti-DDX39B


title: prostate_cancer_primary_434 (STAMPEDE)


title: ATAC-seq on  GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 3hrs, replicate1

value: E14 ES cells


title: 4DNEX8QC7GJ3, Homo sapiens - HCT116, input-condition3enhancementG - anti-DDX39B, B2 T1

description:
Library name: 4DNEX8QC7GJ3
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX8QC7GJ3/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include

value: input-condition3  anti-DDX39B


title: 4DNEXAIACHR8, Homo sapiens - HCT116, condition3enhancementG - anti-DDX39B, B2 T1

description:
Library name: 4DNEXAIACHR8
TSA-seq in HCT116 (Homo sapiens), condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXAIACHR8/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSU2F64A2/, Results include


title: 4DNEXAOSHMWX, Homo sapiens - U2OS, condition3enhancementG - anti-SON, B2 T1

description:
Library name: 4DNEXAOSHMWX
TSA-seq in U2OS (Homo sapiens), condition3  - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXAOSHMWX/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include


title: 4DNEXJCOFAFI, Homo sapiens - U2OS, condition3enhancementG - anti-SON, B1 T1

description:
Library name: 4DNEXJCOFAFI
TSA-seq in U2OS (Homo sapiens), condition3  - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXJCOFAFI/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS61886MX/, Results include


title: ATAC-seq on GFP-dTAG-Ctcf ESC, control, replicate1

value: ES cells


title: 4DNEX7XZLWAG, Homo sapiens - U2OS, input-condition3enhancementG - anti-SON, B2 T1

description:
Library name: 4DNEX7XZLWAG
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX7XZLWAG/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include


title: 4DNEXRW8HB51, Homo sapiens - HCT116, input-condition3enhancementG - anti-DDX39B, B1 T1

description:
Library name: 4DNEXRW8HB51
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-DDX39B, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXRW8HB51/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSDV7B4VL/, Results include


title: 4DNEXA8JDOX4, Homo sapiens - U2OS, condition3enhancementG - anti-THRAP3, B2 T1

description:
Library name: 4DNEXA8JDOX4
TSA-seq in U2OS (Homo sapiens), condition3  - anti-THRAP3, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXA8JDOX4/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include


title: prostate_cancer_primary_431 (STAMPEDE)


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-G703P-R2

city: Paris Cedex 05

first: Celine

last: Borde

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de france

description: Library name: ARN_31

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 for each sample

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.

treatment_protocol: Exponentially growing cultures were diluted in LB medium and induced with 0.2% arabinose for 3 hours to express TopoI (wild-type or mutant variants). Depletion and CRISPRi were induced during the final 1.5 hours of this period. (Final OD 0.5)

value: Escherichia coli

value: MG1655pro lacZ::PLtetO-mf-lon topA-PDT3A [pdCas9-Prom-TopoI] [pGB2-Para-TopoI-G703P]

value: AtC 50ng/mL (1h30) + arabinose 0.2% (3h)

value: 3h P.I. with arabinose and 1h30 P.I. with AtC


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-Y704A-R1

description: Library name: ARN_32

value: MG1655pro lacZ::PLtetO-mf-lon topA-PDT3A [pdCas9-Prom-TopoI] [pGB2-Para-TopoI-Y704A]


title: 4DNEXT1YKCIQ, Homo sapiens - U2OS, condition3enhancementG - anti-THRAP3, B3 T1

description:
Library name: 4DNEXT1YKCIQ
TSA-seq in U2OS (Homo sapiens), condition3  - anti-THRAP3, Biological replicate 3, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXT1YKCIQ/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include

value: immortalized cell line


title: 4DNEXBKRVEU7, Homo sapiens - U2OS, input-condition3enhancementG - anti-THRAP3, B3 T1

description:
Library name: 4DNEXBKRVEU7
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-THRAP3, Biological replicate 3, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXBKRVEU7/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include


title: 4DNEX6Q6KW56, Homo sapiens - U2OS, condition3enhancementG - anti-THRAP3, B1 T1

description:
Library name: 4DNEX6Q6KW56
TSA-seq in U2OS (Homo sapiens), condition3  - anti-THRAP3, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX6Q6KW56/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS61886MX/, Results include


title: prostate_cancer_primary_430 (STAMPEDE)

first: Elai

address: 9725 Lusk Blvd


title: ATAC-seq on GFP-dTAG-Ctcf ESC, control, replicate2

value: GFP-dTAG-Ctcf


title: 4DNEX5YGEMN1, Homo sapiens - U2OS, input-condition3enhancementG - anti-THRAP3, B2 T1

description:
Library name: 4DNEX5YGEMN1
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-THRAP3, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX5YGEMN1/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-G703P-R1

description: Library name: ARN_30


title: 4DNEXGX3N9EQ, Homo sapiens - U2OS, input-condition3enhancementG - anti-THRAP3, B1 T1

description:
Library name: 4DNEXGX3N9EQ
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-THRAP3, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXGX3N9EQ/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS61886MX/, Results include


title: prostate_cancer_primary_429 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_427 (STAMPEDE)


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-Gly5-R2

description: Library name: ARN_29

value: MG1655pro lacZ::PLtetO-mf-lon topA-PDT3A [pdCas9-Prom-TopoI] [pGB2-Para-TopoI-Gly5]


title: prostate_cancer_primary_428 (STAMPEDE)


title: prostate_cancer_primary_426 (STAMPEDE)


title: 4DNEXOPTBMIN, Homo sapiens - U2OS, condition3enhancementG - anti-DDX39B, B2 T1

description:
Library name: 4DNEXOPTBMIN
TSA-seq in U2OS (Homo sapiens), condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXOPTBMIN/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include


title: 4DNEXANF5MRL, Homo sapiens - U2OS, input-condition3enhancementG - anti-SON, B1 T1

description:
Library name: 4DNEXANF5MRL
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXANF5MRL/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS61886MX/, Results include

value: input-condition3  anti-SON


title: prostate_cancer_primary_432 (STAMPEDE)


title: 4DNEX5X6G38R, Homo sapiens - U2OS, input-condition3enhancementG - anti-DDX39B, B2 T2

description:
Library name: 4DNEX5X6G38R
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 2, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX5X6G38R/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include

value: input- condition3 anti-DDX39B


title: 4DNEXPJ7HY7K, Homo sapiens - U2OS, input-condition3enhancementG - anti-DDX39B, B2 T1

description:
Library name: 4DNEXPJ7HY7K
TSA-seq in U2OS (Homo sapiens), input-condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXPJ7HY7K/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-Gly5-R1

description: Library name: ARN_28


title: prostate_cancer_primary_425 (STAMPEDE)


title: 4DNEXK4ZYUBM, Homo sapiens - U2OS, condition3enhancementG - anti-DDX39B, B2 T2

description:
Library name: 4DNEXK4ZYUBM
TSA-seq in U2OS (Homo sapiens), condition3  - anti-DDX39B, Biological replicate 2, Technical replicate 2, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXK4ZYUBM/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS5PTAHOL/, Results include


title: 4DNEXGHGXFGJ, Homo sapiens - HCT116, condition 3 anti-DDX39B, treated with DMSO, B2 T1

description:
Library name: 4DNEXGHGXFGJ
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-DDX39B_DMSO, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXGHGXFGJ/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSISGQ1MP/, Results include

value: condition3 anti-DDX39B_DMSO


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-WT-R1

description: Library name: ARN_26

value: MG1655pro lacZ::PLtetO-mf-lon topA-PDT3A [pdCas9-Prom-TopoI] [pGB2-Para-TopoI-WT]


title: prostate_cancer_primary_424 (STAMPEDE)


title: 4DNEXW7H8IXY, Homo sapiens - HCT116, condition 3 anti-DDX39B, treated with DMSO, B1 T1

description:
Library name: 4DNEXW7H8IXY
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-DDX39B_DMSO, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXW7H8IXY/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSQEOM67N/, Results include


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-WT-R2

description: Library name: ARN_27


title: 4DNEX1FVNJVS, Homo sapiens - HCT116, input-condition 3 anti-DDX39B, treated with DMSO, B2 T1

description:
Library name: 4DNEX1FVNJVS
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-DDX39B_DMSO, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX1FVNJVS/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSISGQ1MP/, Results include

value: input-condition3 anti-DDX39B_DMSO


title: 4DNEXI2XBBL3, Homo sapiens - U2OS, condition3enhancementG - anti-DDX39B, B1 T1

description:
Library name: 4DNEXI2XBBL3
TSA-seq in U2OS (Homo sapiens), condition3  - anti-DDX39B, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXI2XBBL3/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSKR9NL37/, Results include

value: condition3 anti-DDX39B


title: prostate_cancer_primary_423 (STAMPEDE)


title: mf-lon TopoI-PDT CRISPRi pGB2-TopoI-Y704A-R2

description: Library name: ARN_33


title: 4DNEXRHVOH33, Homo sapiens - HCT116, input-condition 3 anti-DDX39B, treated with DMSO, B1 T1

description:
Library name: 4DNEXRHVOH33
TSA-seq in HCT116 (Homo sapiens), input-condition3  - anti-DDX39B_DMSO, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXRHVOH33/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSQEOM67N/, Results include


title: 4DNEXO78ZO1C, Homo sapiens - HCT116, condition 3 anti-DDX39B, treated with Auxin, B2 T1

description:
Library name: 4DNEXO78ZO1C
TSA-seq in HCT116 (Homo sapiens), condition3 -anti-DDX39B_Auxin, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXO78ZO1C/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSE1H2XNF/, Results include

value: condition3 anti-DDX39B_Auxin