title: NCCLu_185


title: prostate_cancer_primary_281 (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: Scramble control, vehicle treatment, rep 1

type: SRA

city: Seattle

first: Melissa

last: Krueger

state: WA

address: 850 Republican St, Box 358052

department: Pulmonary, Critical Care and Sleep Medicine Division

institute: University of Washington

description:
Library name: S1
S1

library_source: transcriptomic

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

source_name: ABM good immortalized human cardiomyocytes, Cat# T0519

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

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

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

tag: cell line

tag: cell type

value: human cardiomyocytes

tag: genotype

value: Scramble Control

tag: treatment

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


title: prostate_cancer_primary_280 (STAMPEDE)


title: NCCLu_162

city: Goyang-si

first: Sehwa

last: Hong

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

department: Research Institute

country: South Korea

institute: National cancer center

library_source: transcriptomic single cell

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

source_name: Pleural fluid

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

value: Pleural fluid

tag: disease

value: Lung cancer

tag: histopathology

value: Adenocarcinoma

tag: cancer stage

value: IV

tag: therapeutic response

value: Response


title: Scramble control, PMA treatment, rep 2

description:
Library name: S5
S5

value: ABM good immortalized human cardiomyocytes, Cat# T0519

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


title: CERS2 KD, vehicle treatment, rep 2

description:
Library name: C22
C22

value: CERS2 KD


title: prostate_cancer_primary_279 (STAMPEDE)


title: CERS2 KD, vehicle treatment, rep 1

description:
Library name: C21
C21


title: WT, Vg7 subset, rep4

city: New York

first: Sara

last: Alonso

state: New York

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: GK645_Vg7

data_processing:
Fastq files were processed using Kallisto (version 0.46.1) with 100 bootstraps for raw read counts and an average fragment length of 100 bp (20 bp standard deviation), then indexed to the mouse (mm9) genome. Transcript abundance HDF5 binary files were imported with tximport and then processed using DESeq2 (version 1.32) for calculating FPKM normalization and for differential expression analysis in R. Genes for analysis were filtered for an average FPKM of >1.
Assembly: mm9
Supplementary files format and content: Hierarchial Data Form (.h5) includes normalized counts for all samples.

organism: Mus musculus

source_name: Small intestine

extract_protocol:
RNA was extracted and purified using a RNeasy mini kit (Qiagen).
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina by PolyA selection method. The cDNA libraries were sequenced using NextSeq 500 instrument (Illumina, San Diego, CA).

value: Small intestine

value: gd intraepithelial lymphocyte

value: WT


title: MED15 T603D MCF7, TGFβ-0h, RNA-seq, rep3

city: Shanghai

first: Yuanming

last: Zheng

address: 220 Handan Rd., Shanghai

country: China

institute: fudan university

description: Library name: MCF7_T603D_rep3

data_processing:
Raw reads were trimmed for adptor sequence/low quality sequence using Trim Galore (parameter -q 20 --phred33 --stringency 3 --length 20 -e 0.1 )
The filtered clean reads were mapped to the human reference genome hg19 or mm10 with HISAT2
Raw counts were count by HTSeq count
Gene quantification and the differential expression analysis were performed with DEseq2
Assembly: Hg19/mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes CPM values for each sample

source_name: cell line

extract_protocol:
Total RNA was extracted from cells lysed with TRIzol
We used a commercial RNA library kit to prepare the RNAseq library according to the manufacturer’s specifications (VAHTS® Universal V8 RNA-seq LibraryPrep Kit) for Illumina. Briefly, mRNA was captured with mRNA capture beads before fragmentation

value: cell line

value: Human breast cancer

value: MED15 T603D

value: 10% FBS DMEM


title: Scramble control, vehicle treatment, rep 2

description:
Library name: S2
S2

value: human cardiomyocytes

value: Scramble Control


title: WT, Vg1 subset, rep4

description: Library name: GK645_Vg1


title: MED15 T603D MCF7, TGFβ-0h, RNA-seq, rep1

description: Library name: MCF7_T603D_rep1


title: MED15 T603D MCF7, TGFβ-0h, RNA-seq, rep2

description: Library name: MCF7_T603D_rep2


title: prostate_cancer_primary_278 (STAMPEDE)

value: FFPE prostate cancer


title: CERS2 KD, PMA treatment, rep 3

description:
Library name: C26
C26


title: WT MCF7, TGFβ-0h, RNA-seq, rep3

description: Library name: MCF7_WT_rep3


title: WT, Vg7 subset, rep3

description: Library name: GK642_Vg7


title: prostate_cancer_primary_276 (STAMPEDE)


title: WT, Vg1 subset, rep3

description: Library name: GK642_Vg1


title: WT MCF7, TGFβ-0h, RNA-seq, rep1

description: Library name: MCF7_WT_rep1


title: MED15 T603A HaCaT, TGFβ-3h, RNA-seq, rep3

description: Library name: HaCaT_T603A_3h_rep3

value: HaCaT

value: Human Keratinocytes Cells

value: MED15 T603A

value: 10% FBS DMEM TGFβ 3h


title: CERS2 KD, vehicle treatment, rep 3

description:
Library name: C23
C23

value: ABM good immortalized human cardiomyocytes, Cat# T0519

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


title: WT MCF7, TGFβ-0h, RNA-seq, rep2

description: Library name: MCF7_WT_rep2


title: prostate_cancer_primary_277 (STAMPEDE)


title: WT, Vg7 subset, rep2

description: Library name: GK641_Vg7


title: MED15 T603A HaCaT, TGFβ-3h, RNA-seq, rep1

description: Library name: HaCaT_T603A_3h_rep1


title: prostate_cancer_primary_275 (STAMPEDE)


title: MED15 T603A HaCaT, TGFβ-0h, RNA-seq, rep3

description: Library name: HaCaT_T603A_0h_rep3

value: 10% FBS DMEM TGFβ 0h


title: MED15 T603A HaCaT, TGFβ-0h, RNA-seq, rep1

description: Library name: HaCaT_T603A_0h_rep1


title: WT, Vg7 subset, rep1

description: Library name: GK640_Vg7

value: Small intestine


title: prostate_cancer_primary_273 (STAMPEDE)


title: MED15 T603A HaCaT, TGFβ-0h, RNA-seq, rep2

description: Library name: HaCaT_T603A_0h_rep2


title: WT HaCaT, TGFβ-3h, RNA-seq, rep2

description: Library name: HaCaT_WT_3h_rep2


title: WT HaCaT, TGFβ-3h, RNA-seq, rep3

description: Library name: HaCaT_WT_3h_rep3


title: WT, Vg1 subset, rep1

description: Library name: GK640_Vg1

value: gd intraepithelial lymphocyte


title: WT HaCaT, TGFβ-0h, RNA-seq, rep3

description: Library name: HaCaT_WT_0h_rep3

value: WT


title: prostate_cancer_primary_272 (STAMPEDE)


title: prostate_cancer_primary_271 (STAMPEDE)


title: gdHYP, Vg7 subset, rep4

description: Library name: GFXJ915_Vg7

value: gdHYP


title: WT HaCaT, TGFβ-3h, RNA-seq, rep1

description: Library name: HaCaT_WT_3h_rep1

value: cell line


title: WT HaCaT, TGFβ-0h, RNA-seq, rep2

description: Library name: HaCaT_WT_0h_rep2


title: MED15 T603A HaCaT, TGFβ-3h, RNA-seq, rep2

description: Library name: HaCaT_T603A_3h_rep2


title: prostate_cancer_primary_274 (STAMPEDE)


title: WT HaCaT, TGFβ-0h, RNA-seq, rep1

description: Library name: HaCaT_WT_0h_rep1


title: gdHYP, Vg1 subset, rep4

description: Library name: GFXJ915_Vg1


title: gdHYP, Vg7 subset, rep3

description: Library name: GFXJ914_Vg7


title: WT T603A HaCaT, TGFβ3h, Input

description: Library name: input-WT-3b

library_source: genomic

data_processing:
Raw reads were trimmed for adptor sequence/low quality sequence using Trim Galore (parameter -q 20 --phred33 --stringency 3 --length 20 -e 0.1 )
Assembly: Hg19
Supplementary files format and content: BigWig file format

molecule: genomic DNA

source_name: HaCaT

extract_protocol:
Cells were crosslinked with 0.9% formaldehyde for 9 min at room temperature, and the formaldehyde was quenched with glycine at a final concentration of 125 μM. After 5 min, the cells were washed twice with ice-cold PBS and collected with a cell scraper. The cell pellets were lysed and sonicated in lysis buffer (1% SDS, 50 mM Tris–HCl (pH 7.4), and 10 mM EDTA), and the chromatin was fragmented into 200–500 bp fragments using a COVARIS S220 sonicator
The DNA was subjected to library construciton (NEBNext Ultra II DNA Library Prep Kit, NEB, E7645B, USA) for Illumina sequencing

value: 10% FBS DMEM TGFβ3h


title: MED15 T603A  T603A HaCaT, TGFβ3h, Input

description: Library name: input-A-3


title: WT, Vg1 subset, rep2

description: Library name: GK641_Vg1


title: WT HaCaT, TGFβ3h, FOXA1 ChIP, rep1

description: Library name: FOXA1-WT-3


title: prostate_cancer_primary_269 (STAMPEDE)


title: gdHYP, Vg1 subset, rep3

description: Library name: GFXJ914_Vg1


title: MED15 T603A HaCaT, TGFβ3h, FOXA1 ChIP, rep2

description: Library name: FOXA1-A-3b


title: prostate_cancer_primary_268 (STAMPEDE)


title: prostate_cancer_primary_267 (STAMPEDE)


title: MED15 T603A HaCaT, TGFβ3h, FOXA1 ChIP, rep1

description: Library name: FOXA1-A-3


title: gdHYP, Vg7 subset, rep2

description: Library name: GFXJ911_Vg7


title: prostate_cancer_primary_266 (STAMPEDE)


title: WT HaCaT, TGFβ3h, POLII ChIP, rep2

description: Library name: POL2-WT-3b


title: MED15 T603A HaCaT, TGFβ3h, POLII ChIP, rep1

description: Library name: POL-A-3


title: MED15 T603A HaCaT, TGFβ3h, POLII ChIP, rep2

description: Library name: POL2-A-3b


title: TD-KOROPI84H-biol rep 3

city: fujisawa-shi

first: Hirotsugu

last: Asano

state: kanagawa

address: 2-26-1, Muraokahigashi

country: Japan

institute: K Pharma

description: Library name: TD-KOROPI84H-3

data_processing:
For quality control, raw FASTQ files were processed using fastp (version 0.23.2; -q 15 -n 5 -l 15 -w 8, and other parameters were set to default)
Following quality control, sequencing reads of FASTQ files were mapped to the human GRCH38 genome (GENCODE GRCh38.p13) using HISAT2 (version 2.1.0)
The differential expression analysis was conducted using DESeq2 (version 1.34.0)
Assembly: hg38
Supplementary files format and content: Tab-delimited CSV files include count, RPKM values, and TPM values for each sample.

molecule: polyA RNA

source_name: iPSC

growth_protocol: iPSCs were dissociated into single cells and plated on an iMatrix-511 with StemFit AK02N and Y-27632. The following day, iPSCs were transferred to a chemically transitional embryoid body-like state (CTraS) using 3 mM SB431542 (Tocris), 150 nM LDN-193189 (StemRD), and 3 mM CHIR99021 (Sigma-Aldrich). After 5 days, using TrypLE Select, the CTraS treated-iPSCs were dissociated to single cells, and plated on poly-D-lysine (Sigma-Aldrich) and Matrigel (Corning)-coated plates with MN medium, KBM neural stem cell medium (KBM; Kohjin Bio) containing 2% B27 supplement (Thermo Fisher Scientific), 10 ng/mL brain-derived neurotrophic factor (BDNF; Abcam), 10 ng/mL glial cell line–derived neurotrophic factor (GDNF; Alomone Labs), 2 mM retinoic acid (RA; Sigma-Aldrich), 200 ng/mL ascorbic acid (Sigma-Aldrich), 2 mM DAPT (Selleck), and 2 mM PD-0332991 (Selleck). For the first 5 days, 1 μg/mL doxycycline was administered

extract_protocol:
Total RNA was extracted by RNAeasy plus mini kit. 1.0ug of total RNA was used for sequence library construction.
A cDNA library was created using TruSeq Stranded mRNA Library

treatment_protocol: ROPI (10μM) was added to the MNs and half of the medium was replaced every 2–3 days.

value: iPSC

value: motor neuron

value: ROPI

tag: time


title: prostate_cancer_primary_270 (STAMPEDE)

value: FFPE prostate cancer


title: gdHYP, Vg7 subset, rep1

description: Library name: GFXJ909_Vg7


title: TD-KOROPI84H-biol rep 2

description: Library name: TD-KOROPI84H-2


title: prostate_cancer_primary_264 (STAMPEDE)


title: prostate_cancer_primary_265 (STAMPEDE)


title: WT HaCaT, TGFβ3h, FOXA1  ChIP, rep2

description: Library name: FOXA1-WT-3b

value: HaCaT


title: TD-KOROPI84H-biol rep 1

description: Library name: TD-KOROPI84H-1


title: gdHYP, Vg1 subset, rep1

description: Library name: GFXJ909_Vg1


title: prostate_cancer_primary_263 (STAMPEDE)


title: TDP43ROPI84H-biol rep 2

description: Library name: TDP43ROPI84H-2


title: TCRgd+ ZsG- IELs

city: Amherst

first: Leonid

last: Pobezinsky

state: MA

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

description: Library name: TCRgd_ZsG-neg_IELs

data_processing:
The 10x Could Analysis Cell Ranger Pipeline (Cellranger version 7.1.0) was used to align reads and generate feature-barcode matrices. Reads were aligned to Mus musculus reference genome (Mouse mm10 v3.0.0) with ZsGreen sequence added to the genome gtf file. The aggr pipeline was used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Compressed Tab-separated vales files and matrix files for scRNAseq counts, comma-separated files for scRNAseq metadata, and loom files for RNA velocity analysis.

source_name: Small Intestine

extract_protocol:
Whole small intestine was isolated from mice and kept on media (RPMI supplemented with 3% FBS, 1% L-glutamine, 1% Pen/Strep, 50uM beta-mercaptoethanol). After flushing the intestine, Peyer's patches were removed, and tissue tragments were agited on a plate stirrer at 37C 5% CO2 in serum-free media containing EDTA and DTT. Cell suspensions were filtered and washed with media, then counted on a hemocytometer. Cells were stained for CD45, TCRb, TCRd, and DAPI prior to sorting by the BD FACSAria Fusion instrument.
Single cell gene expression profiling was performed using the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) kit. Each cell suspension was loaded onto a well of Chip G on the 10x Genomics Chromium Controller System following the manufacturer's user manual (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions. Qualitative analysis of cDNA was performed using the 2100 Agilent Bioanalyzer High Sensitivity assay. The cDNA libraries were constructed using the 10x Chromium Single cell 3’ Library Kit v3.1 (dual index) according to the manufacturer’s protocol. Quality assessment of final libraries was done on Qubit fluorometer using a DNA High Sensitivity assay (Thermo Scientific) and a 2100 Agilent Bioanalyzer High Sensitivity assay (Agilent Technologies). Libraries were sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) sequencing kit, with the following read length: 28 bp Read1 for the 10x cell barcode and UMI, 90 bp Read 2 for the insert, and 10 bp I7 and I5 for the sample index. Phix (Illumina) was spiked in at 1% as per kit manual recommendation (10x Genomics).

value: Small Intestine

value: Vil Cre+ R26 ZsG+

value: CD45+ TCRgd+ ZsG- IELs


title: RC802ROPI84H-biol rep 3

description: Library name: RC802ROPI84H-3


title: TCRgd+ ZsG+ IELs

description: Library name: TCRgd_ZsG-pos_IELs

value: CD45+ TCRgd+ ZsG+ IELs


title: WT HaCaT, TGFβ3h, POLII ChIP, rep1

description: Library name: POL2-WT-3

value: Human Keratinocytes Cells


title: RC802ROPI84H-biol rep 2

description: Library name: RC802ROPI84H-2


title: prostate_cancer_primary_262 (STAMPEDE)


title: TD-KODM84H-biol rep 3

description: Library name: TD-KODMSO84H-3

value: DMSO


title: prostate_cancer_primary_259 (STAMPEDE)


title: prostate_cancer_primary_260 (STAMPEDE)


title: TD-KODM84H-biol rep 1

description: Library name: TD-KODM84H-1


title: TD-KODM84H-biol rep 2

description: Library name: TD-KODMSO84H-2


title: TDP43DMSO84H-biol rep 3

description: Library name: TDP43DMSO84H-3


title: Brachiocephalic artery, Dll1 Ab-treated 4

city: Kitakyushu

first: Jun-ichiro

last: Koga

state: --- Select One ---

address: 1-1, Iseigaoka, Yahatanishi-ku

institute: University of Occupatinal and Environmental Health, Japan

data_processing:
CLC genomic workbench (v10.1.1)
Assembly: Reads were mapped to reference genomes (hg19 for Human) using CLC Genomics Workbench.
Supplementary files format and content: xslx data including TPM data for each genes and samples

source_name: brachiocephalic artery

extract_protocol:
RNA was extracted using TRIZOL and dissolved in RNase-free H2O according to the reagent's instructions.
100 ng of total RNA per sample was used for library preparation. Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit, and libraries were constructed with the NEBNext Ultra II Directional RNA Library Prep Kit. Library quality was assessed with the Bioanalyzer DNA-sensitivity kit.

treatment_protocol: Atherosclerotic plaque formation was induced by a high-fat diet in ApoE-deficient mice from 12 weeks of age.

value: brachiocephalic artery

value: ApoE-deficient

value: Dll1 blocking antibody


title: TDP43DMSO84H-biol rep 2

description: Library name: TDP43DMSO84H-2


title: TCRab+ ZsG+ IELs

description: Library name: TCRab_ZsG-pos_IELs

value: CD45+ TCRab+ ZsG+ IELs


title: gdHYP, Vg1 subset, rep2

description: Library name: GFXJ911_Vg1

value: Small intestine

value: gd intraepithelial lymphocyte

value: gdHYP


title: TDP43ROPI84H-biol rep 3

description: Library name: TDP43ROPI84H-3

value: iPSC

value: motor neuron


title: Brachiocephalic artery, Dll1 Ab-treated 3


title: prostate_cancer_primary_261 (STAMPEDE)

value: FFPE prostate cancer


title: TDP43DMSO84H-biol rep 1

description: Library name: TDP43DMSO84H-1


title: RC802DMSO84H-biol rep 3

description: Library name: RC802DMSO84H-3


title: TDP43ROPI84H-biol rep 1

description: Library name: TDP43ROPI84H-1

value: ROPI


title: Brachiocephalic artery, Dll1 Ab-treated 2


title: RC802DMSO84H-biol rep 1

description: Library name: RC802DMSO84H-1


title: TCRab+ ZsG- IELs

description: Library name: TCRab_ZsG-neg_IELs

value: Small Intestine

value: CD45+ TCRab+ ZsG- IELs


title: prostate_cancer_primary_257 (STAMPEDE)


title: Brachiocephalic artery, Dll1 Ab-treated 1


title: RC802ROPI84H-biol rep 1

description: Library name: RC802ROPI84H-1


title: RC802DMSO84H-biol rep 2

description: Library name: RC802DMSO84H-2


title: TD-KOROPI36H-biol rep 3

description: Library name: TD-KOROPI36H-3


title: prostate_cancer_primary_256 (STAMPEDE)


title: Brachiocephalic artery, IgG-treated 4

value: non-immune IgG


title: TD-KOROPI36H-biol rep 2

description: Library name: TD-KOROPI36H-2


title: prostate_cancer_primary_255 (STAMPEDE)


title: prostate_cancer_primary_254 (STAMPEDE)


title: prostate_cancer_primary_258 (STAMPEDE)


title: prostate_cancer_primary_253 (STAMPEDE)


title: TDP43ROPI36H-biol rep 3

description: Library name: TDP43ROPI36H-3


title: TDP43ROPI36H-biol rep 2

description: Library name: TDP43ROPI36H-2


title: TDP43ROPI36H-biol rep 1

description: Library name: TDP43ROPI36H-1


title: RC802ROPI36H-biol rep 2

description: Library name: RC802ROPI36H-2


title: Brachiocephalic artery, IgG-treated 1


title: Brachiocephalic artery, IgG-treated 3


title: RC802ROPI36H-biol rep 1

description: Library name: RC802ROPI36H-1


title: Brachiocephalic artery, IgG-treated 2


title: RC802ROPI36H-biol rep 3

description: Library name: RC802ROPI36H-3


title: BAT_WT_PBS_4deg_8wk_#3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Brown adipose tissue

extract_protocol:
For RNA.seq on Tregs: The cells were double-sorted directly into 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). The cells were sorted as DAPI-CD45+Tcrb+CD4+Thy1.1+ from fat tissues of Foxp3.Th1.1 reporter mice at 8 weeks.  For whole tissue experimentes 2 ng RNA was added to 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

value: Brown adipose tissue

value: Whole tissue

value: DTR-

tag: age

tag: Sex

value: Male

tag: strain

value: PBS


title: TD-KODMSO36H-biol rep 2

description: Library name: TD-KODMSO36H-2

value: DMSO


title: prostate_cancer_primary_250 (STAMPEDE)


title: TD-KODMSO36H-biol rep 1

description: Library name: TD-KODMSO36H-1


title: TDP43DMSO36H-biol rep 3

description: Library name: TDP43DMSO36H-3


title: TD-KODMSO36H-biol rep 3

description: Library name: TD-KODMSO36H-3


title: prostate_cancer_primary_252 (STAMPEDE)


title: prostate_cancer_primary_251 (STAMPEDE)


title: TDP43DMSO36H-biol rep 2

description: Library name: TDP43DMSO36H-2


title: prostate_cancer_primary_249 (STAMPEDE)


title: BAT_WT_PBS_4deg_8wk_#2


title: BAT_WT_PBS_4deg_8wk_#1


title: BAT_DTR+_Isotype#8

value: DTR+

value: DT, Isotype control Ab


title: RC802DMSO36H-biol rep 3

description: Library name: RC802DMSO36H-3


title: prostate_cancer_primary_248 (STAMPEDE)


title: RC802DMSO36H-biol rep 2

description: Library name: RC802DMSO36H-2


title: TD-KOROPI36H-biol rep 1

description: Library name: TD-KOROPI36H-1


title: prostate_cancer_primary_247 (STAMPEDE)


title: RC802DMSO36H-biol rep 1

description: Library name: RC802DMSO36H-1


title: TD-KOROPI6H-biol rep 3

description: Library name: TD-KOROPI6H-3


title: BAT_DTR+_Isotype#4


title: TD-KOROPI6H-biol rep 1

description: Library name: TD-KOROPI6H-1


title: prostate_cancer_primary_246 (STAMPEDE)


title: TDP43ROPI6H-biol rep 3

description: Library name: TDP43ROPI6H-3


title: prostate_cancer_primary_245 (STAMPEDE)


title: TDP43ROPI6H-biol rep 2

description: Library name: TDP43ROPI6H-2


title: TDP43ROPI6H-biol rep 1

description: Library name: TDP43ROPI6H-1


title: BAT_DTR+_aIFNg#2

value: DT, Anti-IFNy Ab


title: prostate_cancer_primary_244 (STAMPEDE)


title: TDP43DMSO36H-biol rep 1

description: Library name: TDP43DMSO36H-1


title: RC802ROPI6H-biol rep 3

description: Library name: RC802ROPI6H-3


title: RC802ROPI6H-biol rep 1

description: Library name: RC802ROPI6H-1


title: prostate_cancer_primary_243 (STAMPEDE)


title: BAT_DTR+_aIFNg#4


title: TD-KODMSO6H-biol rep 3

description: Library name: TD-KODMSO6H-3


title: BAT_DTR+_aIFNg#1


title: RC802ROPI6H-biol rep 2

description: Library name: RC802ROPI6H-2


title: BAT_PC61_M_wk8#3

value: WT

value: Anti-CD25 (PC61)


title: TD-KODMSO6H-biol rep 1

description: Library name: TD-KODMSO6H-1

value: iPSC

value: motor neuron


title: TD-KOROPI6H-biol rep 2

description: Library name: TD-KOROPI6H-2

value: ROPI


title: TD-KODMSO6H-biol rep 2

description: Library name: TD-KODMSO6H-2


title: BAT_PC61_M_wk8#2


title: prostate_cancer_primary_241 (STAMPEDE)

value: FFPE prostate cancer


title: TDP43DMSO6H-biol rep 3

description: Library name: TDP43DMSO6H-3


title: BAT_DTR+_Isotype#3


title: TDP43DMSO6H-biol rep 2

description: Library name: TDP43DMSO6H-2


title: prostate_cancer_primary_240 (STAMPEDE)


title: prostate_cancer_primary_242 (STAMPEDE)


title: prostate_cancer_primary_239 (STAMPEDE)


title: BAT_PC61_M_wk8#1


title: TDP43DMSO6H-biol rep 1

description: Library name: TDP43DMSO6H-1


title: BAT_ISO_M_wk8#3

value: Isotype control Ab


title: RC802DMSO6H-biol rep 3

description: Library name: RC802DMSO6H-3


title: prostate_cancer_primary_238 (STAMPEDE)


title: RC802DMSO6H-biol rep 2

description: Library name: RC802DMSO6H-2


title: RC802DMSO6H-biol rep 1

description: Library name: RC802DMSO6H-1


title: BAT_ISO_M_wk8#2


title: PBMC, Healthy donors, VDJ

city: Bethesda

first: Adrian

last: Wiestner

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

description:
Library name: HD_vdj
mutliplexed three donors
10x Genomics

data_processing:
Demultiplexing, index barcode processing to generate FASTQs per was performed using 'mkfastq' pipeline in Cellranger (v.7.1.0). This resulted in three sets of fastq sequences (GEX, CITE, TCR) per sample library. Cell calling and estimation of feature counts per cell was performed using 'multi' pipeline in Cellranger (v.7.1.0). The 'expect-cells' parameter was set to 3000 for mutli pipeline.
TCR reference: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Assembly: Human GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: barcode files (featureHTO_IFP-07.csv, featureHTO_IFP-09.csv, featureHTO_IFP-10.csv, featureHTO_IFP-14.csv, featureHTO_HD.csv)
Supplementary files format and content: filtered_matrix.h5 files (IFP-07_citemulti_feature_bc_matrix.h5, IFP-09_citemulti_feature_bc_matrix.h5, IFP-10_citemulti_feature_bc_matrix.h5, IFP-14_citemulti_feature_bc_matrix.h5, HD_citemulti_feature_bc_matrix.h5)

source_name: Peripheral blood

extract_protocol:
scRNA-seq: CD8+ T cells from peripheral blood were negatively selected using Miltenyi beads and sequenced at C1D1, C2D1 (after 1 cycle of pembrolizumab), and C9D1 (after 6 months of pembrolizumab) (10X Genomics).
scRNA-Seq: Libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10x Genomics) and sequenced on NovaSeq 6000 (Illumina).

treatment_protocol: ClinicalTrails.gov (NCT03204188)

value: Peripheral blood

value: PBMC

value: Healthy donor (M662, 14889, M52)


title: PBMC, Healthy donors, ADT

description:
Library name: HD_adt
mutliplexed three donors
10x Genomics

library_source: other

molecule: protein


title: prostate_cancer_primary_237 (STAMPEDE)


title: BAT_ISO_M_wk8#1

value: Brown adipose tissue

value: Whole tissue


title: PBMC, Healthy donors, GEX

description:
Library name: HD_gex
mutliplexed three donors
10x Genomics


title: BAT_DTR+_CL_M_8wk_#3

value: Male

value: DT, CL


title: CD8+ cells, IFP14, ADT

description:
Library name: IFP14_adt
multiplexed timepoints
10x Genomics

value: CD8+ T cells

value: mixed sample (C1D1, C2D1)


title: CD8+ cells, IFP14, VDJ

description:
Library name: IFP14_vdj
multiplexed timepoints
10x Genomics


title: CD8+ cells, IFP14, GEX

description:
Library name: IFP14_gex
multiplexed timepoints
10x Genomics


title: CD8+ cells, IFP10, VDJ

description:
Library name: IFP10_vdj
multiplexed timepoints
10x Genomics

value: mixed sample (C1D1, C2D1, C9D1)


title: CD8+ cells, IFP10, GEX

description:
Library name: IFP10_gex
multiplexed timepoints
10x Genomics


title: BAT_DTR+_CL_M_8wk_#1

value: DTR+


title: CD8+ cells, IFP10, ADT

description:
Library name: IFP10_adt
multiplexed timepoints
10x Genomics


title: prostate_cancer_primary_235 (STAMPEDE)


title: BAT_DTR-_PBS_M_8wk_#3

value: DTR-

value: DT, PBS


title: CD8+ cells, IFP09, VDJ

description:
Library name: IFP09_vdj
multiplexed timepoints
10x Genomics


title: CD8+ cells, IFP09, ADT

description:
Library name: IFP09_adt
multiplexed timepoints
10x Genomics


title: prostate_cancer_primary_234 (STAMPEDE)


title: prostate_cancer_primary_233 (STAMPEDE)


title: CD8+ cells, IFP09, GEX

description:
Library name: IFP09_gex
multiplexed timepoints
10x Genomics


title: BAT_DTR-_PBS_M_8wk_#2


title: CD8+ cells, IFP07, VDJ

description:
Library name: IFP07_vdj
multiplexed timepoints
10x Genomics


title: CD8+ cells, IFP07, ADT

description:
Library name: IFP07_adt
multiplexed timepoints
10x Genomics


title: prostate_cancer_primary_232 (STAMPEDE)


title: CD8+ cells, IFP07, GEX

description:
Library name: IFP07_gex
multiplexed timepoints
10x Genomics


title: prostate_cancer_primary_236 (STAMPEDE)


title: prostate_cancer_primary_231 (STAMPEDE)


title: BAT_DTR-_CL_M_8wk_#3


title: BAT_DTR+_CL_M_8wk_#2


title: prostate_cancer_primary_230 (STAMPEDE)


title: KOIR3

city: Tianjin

first: Zhengkun

last: Cai

address: Tianjin, State

institute: Tianjin Medical University Cancer Institute and Hospital

description: Library name: Sample3

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include Count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Two ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: CAD knockout (KO)


title: BAT_DTR-_CL_M_8wk_#2


title: prostate_cancer_primary_229 (STAMPEDE)


title: prostate_cancer_primary_228 (STAMPEDE)


title: KOIR2

description: Library name: Sample2


title: KOIR1

description: Library name: Sample1


title: BAT_DTR-_CL_M_8wk_#1


title: SAT_DTR+_D3_PBS#3

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue

value: DT


title: BE98

city: Aurora

first: Manoel

middle: Emilio

last: Lixandrao

state: Colorado

institute: University of Colorado Anschutz Medical Campus

data_processing:
Low-quality raw reads were trimmed out using fastp. After that, samples were aligned with STAR (ultrafast universal RNA-seq aligner) using GRCh38 (version 79) human genome build and were annotated with Ensembl. Read counts matrix were generated using featureCounts from Rsubread package available from Rstudio.
Assembly: GRCh38 (version 79)
Supplementary files format and content: Tab-delimited raw read counts matrix.

source_name: Skeletal muscle

extract_protocol:
TRIzol method. Homogenized samples were thawed on ice followed by the addition of 200µL of chloroform and thorough mixing, then a 5 min incubation at room temperature, followed by centrifugation for 15 min at 40ºC at 12000g. The clear, aqueous top layer was collected and total RNA was precipitated by adding 100% cold ethanol to the extracted portion until a final concentration of 35% ethanol was achieved. Samples were then incubated for 30 minutes at 20C and centrifuged for 15 minutes at 4C at 16000g. 75% ethanol was used to wash the RNA pellet twice, and the RNA pellet was left to air-dry after which it was resuspended in 20µL of nuclease-free, ultra-pure diethlpyrocarbonate-treated water.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: Skeletal muscle

tag: participant id

tag: condition


title: BE97


title: BE94


title: BAT_DTR-_PBS_M_8wk_#1


title: prostate_cancer_primary_226 (STAMPEDE)

tag: gleason score

tag: age at randomization

value: FFPE prostate cancer


title: prostate_cancer_primary_227 (STAMPEDE)

tag: psa at randomization (ng/ml)

tag: tissue


title: prostate_cancer_primary_225 (STAMPEDE)


title: NCIR3

description: Library name: Sample6

tag: cell line

value: control


title: BE90


title: NCIR2

description: Library name: Sample5

tag: genotype


title: BE86


title: BE80


title: SAT_DTR-_D3_PBS#3

tag: cell type

tag: treatment


title: NCIR1

description: Library name: Sample4


title: SAT_DTR+_D3_PBS#1


title: BE77


title: BE76


title: prostate_cancer_primary_224 (STAMPEDE)


title: BE6


title: SAT_DTR-_D3_PBS#2


title: BE5


title: BE59


title: prostate_cancer_primary_223 (STAMPEDE)


title: prostate_cancer_primary_222 (STAMPEDE)


title: SAT_DTR+_D3_PBS#2


title: BE50


title: BE38


title: SAT_DTR-_D3_PBS#1


title: BE36


title: BE35


title: BAT_DTR+_D3_PBS#2


title: prostate_cancer_primary_221 (STAMPEDE)


title: BAT_DTR+_D3_PBS#3


title: prostate_cancer_primary_220 (STAMPEDE)


title: BAT_DTR+_D3_PBS#1


title: BE27


title: BE32


title: BE17


title: BE30


title: BE114


title: prostate_cancer_primary_219 (STAMPEDE)


title: BE12


title: prostate_cancer_primary_217 (STAMPEDE)


title: BE110


title: BE107


title: prostate_cancer_primary_218 (STAMPEDE)


title: BAT_DTR-_D3_PBS#2


title: BAT_DTR-_D3_PBS#1


title: BE106


title: prostate_cancer_primary_216 (STAMPEDE)


title: SAT_DTR+_D4#4


title: BE102


title: BE104


title: BE105


title: BD98


title: prostate_cancer_primary_214 (STAMPEDE)


title: SAT_DTR+_D4#3


title: BD94


title: SAT_DTR+_D4#2


title: BD90


title: prostate_cancer_primary_212 (STAMPEDE)


title: BD97


title: SAT_DTR+_D4#1


title: BD86


title: BD80


title: prostate_cancer_primary_215 (STAMPEDE)


title: BD77


title: prostate_cancer_primary_210 (STAMPEDE)


title: prostate_cancer_primary_213 (STAMPEDE)


title: SAT_DTR-_D4#3


title: prostate_cancer_primary_211 (STAMPEDE)


title: BD6


title: SAT_DTR-_D4#2


title: SAT_DTR-_D4#4


title: prostate_cancer_primary_208 (STAMPEDE)


title: SAT_DTR-_D4#1


title: BD59


title: BD36


title: BD38


title: BD35


title: BAT_DTR+_D4#4


title: BD32


title: prostate_cancer_primary_209 (STAMPEDE)


title: BD50


title: BD27


title: BD76


title: prostate_cancer_primary_206 (STAMPEDE)


title: prostate_cancer_primary_205 (STAMPEDE)


title: prostate_cancer_primary_204 (STAMPEDE)


title: BD17


title: prostate_cancer_primary_203 (STAMPEDE)


title: BAT_DTR+_D4#2


title: BAT_DTR+_D4#1


title: BD107


title: BD114


title: BD12


title: BD110


title: BD106


title: BAT_DTR-_D4#3


title: BD5


title: BAT_DTR-_D4#4


title: BD104


title: prostate_cancer_primary_207 (STAMPEDE)


title: BD105


title: prostate_cancer_primary_202 (STAMPEDE)


title: BD30


title: BAT_DTR+_D4#3


title: A98

value: Baseline


title: BD102


title: BAT_DTR-_D4#1

value: Brown adipose tissue


title: A97


title: A94


title: prostate_cancer_primary_199 (STAMPEDE)


title: prostate_cancer_primary_201 (STAMPEDE)


title: prostate_cancer_primary_200 (STAMPEDE)


title: prostate_cancer_primary_198 (STAMPEDE)


title: prostate_cancer_primary_197 (STAMPEDE)


title: SPLN_8wk_082421#3

source_name: Spleen

value: Spleen

value: WT


title: A90


title: A86


title: A77


title: A80


title: SPLN_8wk_082421#1

value: Male


title: BAT_DTR-_D4#2

value: Whole tissue


title: SPLN_8wk_082421#2


title: A76


title: A5


title: A59


title: A6


title: SAT_8wk_082421#3


title: SAT_8wk_082421#2


title: A50


title: prostate_cancer_primary_196 (STAMPEDE)


title: A36


title: prostate_cancer_primary_195 (STAMPEDE)


title: BAT_DTR-_D3_PBS#3


title: A38


title: SAT_8wk_082421#1


title: BAT_8wk_082421#2


title: A32


title: prostate_cancer_primary_193 (STAMPEDE)


title: prostate_cancer_primary_194 (STAMPEDE)


title: prostate_cancer_primary_191 (STAMPEDE)


title: prostate_cancer_primary_192 (STAMPEDE)


title: A30


title: BAT_8wk_082421#1


title: A27


title: A114


title: A17


title: A12


title: A106


title: A107


title: A110


title: A105


title: A35


title: prostate_cancer_primary_190 (STAMPEDE)


title: A104


title: A102


title: hDPCs, soft-1

city: chengdu

first: zhaowei

last: zhang

state: sichuan

address: No. 14, Section 3, Renmin South Road

institute: sichuan university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: All_gene_fpkm.txt

source_name: tooth

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tooth

value: dental pulp stem cells

value: soft


title: prostate_cancer_primary_188 (STAMPEDE)


title: prostate_cancer_primary_189 (STAMPEDE)


title: P292_15_V5_TG

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

description:
Medium with 100 nM TG
P292_15_V5_TG_log2 Signal

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Bos taurus

source_name: BFH12 cells

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The bovine SV40 large T-antigen-transduced fetal hepatocyte-derived cell line BFH12 was kindly provided by Dr. Axel Schoeniger (Institute of Biochemistry, University of Leipzig, Germany). Cells were cultured in Williams’ E medium (Bio&SELL, Nürnberg, Germany). containing 5% heat-inactivated FBS, 2 mM L-alanyl-L-glutamine, 100 nM dexamethasone, 0.2 U/mL insulin (all from Sigma-Aldrich, Taufkirchen, Germany) and 1% penicillin/streptomycin (Th. Geyer, Höxter, Germany) at 37°C in a humidified atmosphere containing 5% CO2. Medium was changed every 2-3 days, and cells were passaged every 7 days using Trypsin-EDTA (8 min at 37°C). BFH12 cell cultures were regularly tested for Mycoplasma spp. contamination using the PCR Venor GeM Classic kit (Miberva Biolabs, Berlin, Germany).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Karlsruhe) according to the manufacturer’s protocol. RNA quantity and quality were assessed spectrophotometrically using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz). The RIN values and the A260/A280 ratios of all total RNA samples (n = 15) were between 9.4-9.8 and 1.92-2.02, respectively.

treatment_protocol: BFH12 cells were seeded in 24-well plates at a density of 2.5-3 × 104 cells/well and incubated in culture medium until reaching 70-80% confluency. Subsequently, cells were treated with medium containing vehicle only (0.1% DSMO) or TM (100 ng/mL) and TG (100 nM) for 24 h. The culture medium was aspirated and the cells were washed once with PBS.

value: TG


title: P292_03_V1_TG

description:
Medium with 100 nM TG
P292_03_V1_TG_log2 Signal


title: hDPCs, stiff-1

value: stiff


title: P292_12_V4_TG

description:
Medium with 100 nM TG
P292_12_V4_TG_log2 Signal


title: P292_06_V2_TG

description:
Medium with 100 nM TG
P292_06_V2_TG_log2 Signal


title: prostate_cancer_primary_187 (STAMPEDE)


title: P292_09_V3_TG

description:
Medium with 100 nM TG
P292_09_V3_TG_log2 Signal


title: P292_14_V5_TM

description:
Medium with 100 ng/mL TM
P292_14_V5_TM_log2 Signal

value: TM


title: prostate_cancer_primary_185 (STAMPEDE)


title: prostate_cancer_primary_186 (STAMPEDE)


title: COHP_50519

city: Omaha

first: Chengfeng

last: Bi

state: Nebarska

address: 42nd and, Emile St

institute: University of Nebraska Medical Center

description: Excluded in Main study

data_processing:
Contaminating adapter squences were removed (Trimmomatic ,v0.36). Trimmed reads were aligned to the hg38 (STAR,v 2.5.3) and gene expression quantification using HTSeq (v.0.9.1).
HTSeq counts were converted into FPKM
Assembly: hg38
Supplementary files format and content: tab deliminited text file includes raw data counts for each sample
Supplementary files format and content: tab deliminnited text file includes FPKM counts for each sample

source_name: FFPE Lymph Biopsy

extract_protocol:
RNA was extrated using RNAstorm FFPE isolation Kit (CD501)
Libraries were prepared using the kappa Hyperprep Riboerase Kit from Roche

value: FFPE Lymph Biopsy


title: prostate_cancer_primary_184 (STAMPEDE)

source_name: FFPE prostate cancer


title: P292_11_V4_TM

description:
Medium with 100 ng/mL TM
P292_11_V4_TM_log2 Signal


title: COHP_50517

value: No

value: Yes

value: Loss


title: hDPCs, soft-3


title: COHP_50516


title: hDPCs, soft-2


title: P292_08_V3_TM

description:
Medium with 100 ng/mL TM
P292_08_V3_TM_log2 Signal


title: prostate_cancer_primary_183 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_182 (STAMPEDE)


title: hDPCs, stiff-3


title: COHP_50518


title: hDPCs, stiff-2


title: P292_05_V2_TM

description:
Medium with 100 ng/mL TM
P292_05_V2_TM_log2 Signal


title: P292_02_V1_TM

description:
Medium with 100 ng/mL TM
P292_02_V1_TM_log2 Signal


title: COHP_50514


title: COHP_50512


title: COHP_50513


title: prostate_cancer_primary_180 (STAMPEDE)


title: COHP_50509


title: COHP_50510


title: prostate_cancer_primary_181 (STAMPEDE)


title: COHP_50507


title: COHP_50506


title: COHP_50508


title: COHP_50505


title: COHP_50504


title: COHP_50515


title: prostate_cancer_primary_179 (STAMPEDE)


title: prostate_cancer_primary_177 (STAMPEDE)


title: VD3_MDM_DENV_24H_rep2

city: Medellin

first: Yordi

middle: Sebastián

last: Tamayo Molina

state: Antioquia

country: Colombia

institute: University of Antioquia

description:
Library name: VD3_MDM_DENV_24H_rep2
Colum_name_raw_counts_All_samples.txt: VD_24_R2

data_processing:
Clean reads were obtained by removing low-quality adapter, poly N-containing, and shorter-than-70 bp reads. The location of the reads on the reference genome was determined quickly and precisely by comparing reads with the reference genome (GRCh38 or dengue virus type 2 [NC_001474]) using HISAT2 software. The new transcripts were then assembled using String Tie software, and using the feature counts tool in Subread software, the raw count number in each sample was obtained.
Assembly: GRCh38
Supplementary files format and content: All processed data are provided in txt

source_name: Monocyte-derived macrophage

extract_protocol:
Total RNA was extracted using the Direct-zol™ RNA Miniprep Plus kit (Zymo Research, California, USA), following the manufacturer’s protocol.
RNA concentration was measured using Nanodrop spectrophotometry (Thermo Scientific, Massachusetts, USA). For bulk RNA-Seq, 1 μg of RNA was used per sample, and sequencing was performed on an Illumina HiSeq 2000 platform (Macrogen, Seoul, South Korea).

value: Pripheral blood mononuclear cells

value: Monocyte-derived macrophage

value: VD3 + Infected

tag: batch


title: COHP_50502


title: P292_01_V1_Con

description:
Medium with 0.1%DMSO
P292_01_V1_Con_log2 Signal

value: CON


title: COHP_50511


title: VD3_MDM_DENV_24H_rep1

description:
Library name: VD3_MDM_DENV_24H_rep1
Colum_name_raw_counts_All_samples.txt: VD_24_R1

value: WT


title: prostate_cancer_primary_176 (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: P292_07_V3_Con

description:
Medium with 0.1%DMSO
P292_07_V3_Con_log2 Signal


title: prostate_cancer_primary_175 (STAMPEDE)


title: COHP_50501


title: P292_04_V2_Con

description:
Medium with 0.1%DMSO
P292_04_V2_Con_log2 Signal


title: COHP_50500


title: prostate_cancer_primary_178 (STAMPEDE)


title: COHP_50503


title: prostate_cancer_primary_173 (STAMPEDE)


title: COHP_50499

description: Excluded in Main study


title: P292_13_V5_Con

description:
Medium with 0.1%DMSO
P292_13_V5_Con_log2 Signal


title: COHP_50498

description: Excluded in Main study


title: P292_10_V4_Con

description:
Medium with 0.1%DMSO
P292_10_V4_Con_log2 Signal


title: VD3_MDM_DENV_10H_rep1

description:
Library name: VD3_MDM_DENV_10H_rep1
Colum_name_raw_counts_All_samples.txt: VD_10_R1


title: COHP_50497


title: prostate_cancer_primary_174 (STAMPEDE)


title: COHP_50495

description: Excluded in Main study


title: COHP_50494


title: VD3_MDM_DENV_5.5H_rep1

description:
Library name: VD3_MDM_DENV_5.5H_rep1
Colum_name_raw_counts_All_samples.txt: VD_5.5_R1


title: prostate_cancer_primary_171 (STAMPEDE)


title: COHP_50493


title: VD3_MDM_DENV_3H_rep2

description:
Library name: VD3_MDM_DENV_3H_rep2
Colum_name_raw_counts_All_samples.txt: VD_3_R2


title: COHP_50491


title: COHP_50492


title: prostate_cancer_primary_170 (STAMPEDE)


title: VD3_MDM_DENV_3H_rep1

description:
Library name: VD3_MDM_DENV_3H_rep1
Colum_name_raw_counts_All_samples.txt: VD_3_R1


title: COHP_50490


title: COHP_50489


title: VD3_MDM_DENV_10H_rep2

description:
Library name: VD3_MDM_DENV_10H_rep2
Colum_name_raw_counts_All_samples.txt: VD_10_R2


title: VD3_MDM_DENV_1.5H_rep2

description:
Library name: VD3_MDM_DENV_1.5H_rep2
Colum_name_raw_counts_All_samples.txt: VD_1.5_R2


title: COHP_50487


title: prostate_cancer_primary_168 (STAMPEDE)


title: prostate_cancer_primary_172 (STAMPEDE)


title: prostate_cancer_primary_169 (STAMPEDE)


title: prostate_cancer_primary_167 (STAMPEDE)


title: COHP_50496


title: COHP_50486


title: VD3_MDM_DENV_5.5H_rep2

description:
Library name: VD3_MDM_DENV_5.5H_rep2
Colum_name_raw_counts_All_samples.txt: VD_5.5_R2


title: COHP_50484


title: COHP_50485


title: VD3_MDM_DENV_1.5H_rep1

description:
Library name: VD3_MDM_DENV_1.5H_rep1
Colum_name_raw_counts_All_samples.txt: VD_1.5_R1


title: prostate_cancer_primary_166 (STAMPEDE)


title: VD3_MDM_Mock_0H_rep2

description:
Library name: VD3_MDM_Mock_0H_rep2
Colum_name_raw_counts_All_samples.txt: VD_0_R2

value: Mock + VD3


title: COHP_50483


title: prostate_cancer_primary_165 (STAMPEDE)


title: COHP_50482


title: COHP_50481


title: VD3_MDM_Mock_0H_rep1

description:
Library name: VD3_MDM_Mock_0H_rep1
Colum_name_raw_counts_All_samples.txt: VD_0_R1


title: COHP_50480


title: prostate_cancer_primary_163 (STAMPEDE)


title: prostate_cancer_primary_164 (STAMPEDE)


title: COHP_50478


title: MDM_DENV_24H_rep2

description:
Library name: MDM_DENV_24H_rep2
Colum_name_raw_counts_All_samples.txt: C_24_R2

value: Infected


title: COHP_50488


title: COHP_50479


title: MDM_DENV_24H_rep1

description:
Library name: MDM_DENV_24H_rep1
Colum_name_raw_counts_All_samples.txt: C_24_R1


title: prostate_cancer_primary_162 (STAMPEDE)


title: MDM_DENV_10H_rep2

description:
Library name: MDM_DENV_10H_rep2
Colum_name_raw_counts_All_samples.txt: C_10_R2


title: COHP_50476


title: MDM_DENV_10H_rep1

description:
Library name: MDM_DENV_10H_rep1
Colum_name_raw_counts_All_samples.txt: C_10_R1


title: COHP_50477


title: COHP_50474


title: COHP_50475


title: COHP_50473


title: MDM_DENV_5.5H_rep2

description:
Library name: MDM_DENV_5.5H_rep2
Colum_name_raw_counts_All_samples.txt: C_5.5_R2


title: COHP_50472


title: COHP_50471


title: COHP_50470


title: prostate_cancer_primary_161 (STAMPEDE)


title: prostate_cancer_primary_160 (STAMPEDE)


title: MDM_DENV_5.5H_rep1

description:
Library name: MDM_DENV_5.5H_rep1
Colum_name_raw_counts_All_samples.txt: C_5.5_R1


title: COHP_50469


title: prostate_cancer_primary_159 (STAMPEDE)


title: MDM_DENV_3H_rep2

description:
Library name: MDM_DENV_3H_rep2
Colum_name_raw_counts_All_samples.txt: C_3_R2


title: Z138-R248Q-p53-2

data_processing:
The fastq files were aligned against hg38 reference using bowtie2 aligner
Escherichia_coli_K_12_MG1655 was used for Spike-in calibration
SEACR was used to call peaks
DeSeq2 was used to perform differential expression analysis
Assembly: hg38
Supplementary files format and content: Bigwig files are generated for each sample
Library strategy: Cut&Run

source_name: Lymphoid

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol: CUTANA™ ChIC / CUT&RUN Kit

treatment_protocol: 500nM of Amg-232 treatment was applied to Z-138 cells for 24 hours; 125 and 250 ng/ml of doxycline treatment was applied to Maver-1 and Mino cells, respectively, for 12 hours.

value: Lymphoid

value: B cell


title: prostate_cancer_primary_158 (STAMPEDE)


title: Z138-R248Q-p53-1


title: prostate_cancer_primary_157 (STAMPEDE)


title: Z138-R273C-p53-1


title: Z138-R273C-p53-2


title: MDM_DENV_3H_rep1

description:
Library name: MDM_DENV_3H_rep1
Colum_name_raw_counts_All_samples.txt: C_3_R1


title: Z138 -wt-p53-2


title: prostate_cancer_primary_156 (STAMPEDE)


title: MDM_DENV_1.5H_rep2

description:
Library name: MDM_DENV_1.5H_rep2
Colum_name_raw_counts_All_samples.txt: C_1.5_R2


title: Z138-R273C-H3K4Me3


title: MDM_DENV_1.5H_rep1

description:
Library name: MDM_DENV_1.5H_rep1
Colum_name_raw_counts_All_samples.txt: C_1.5_R1


title: Maver-p53-H3K4Me3


title: MDM_Mock_0H_rep2

description:
Library name: MDM_Mock_0H_rep2
Colum_name_raw_counts_All_samples.txt: C_0_R2

value: Mock


title: Z138-R273C-IgG


title: prostate_cancer_primary_155 (STAMPEDE)


title: Maver-p53-p53-2


title: Maver-p53-p53-1


title: prostate_cancer_primary_154 (STAMPEDE)


title: Maver-p53-IgG


title: MDM_Mock_0H_rep1

description:
Library name: MDM_Mock_0H_rep1
Colum_name_raw_counts_All_samples.txt: C_0_R1


title: Maver-Ctrl-H3K4Me3


title: prostate_cancer_primary_153 (STAMPEDE)


title: TFAP2A IP in normoxia, replicate 2

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis, Mezourlo

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

data_processing:
Quality Control using FASTQC
Read mapping against hg19 with BWA and Bowtie2
Peak calling with MACS
Assembly: hg19
Supplementary files format and content: BED containing peak cocordinates after BWA and BOWTIE2 alignment for each sample

source_name: HeLa

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

extract_protocol:
HeLa cells were incubated under normoxia or hypoxia for 24 h. Cross-linked chromatin was immunoprecipitated with Rabbit polyclonal anti-TFAP2A (ThermoFisher SCIENTIFIC, PA5-17359), used in a concentration of 2μg per reaction (1.5-2 x 10^6 cells). Eluted chromatin was extracted with phenol-choloform from normoxic and hypoxic cells from two biological replicates
Ion torrent genomic DNA library

treatment_protocol: For hypoxic experiments, cells were incubated for 24 hr in an INVIVO2 200 hypoxia workstation (Baker Ruskinn, Sanford, ME, USA) at 1% O2, 94% N2, and 5% CO2.

value: HeLa

value: cervical cancer

value: Normoxia, anti-TFAP2A (ThermoFisher SCIENTIFIC, PA5-17359)


title: Maver-Ctrl-p53-2


title: Maver-Ctrl-p53-1


title: prostate_cancer_primary_152 (STAMPEDE)

city: San Diego

first: Elai

last: Davicioni

institute: Veracyte, Inc


title: Maver-Ctrl-IgG

value: Marver-Ctrl-IgG


title: TFAP2A IP in normoxia, replicate 1


title: Mino-p53-p53-2

value: Mino


title: Mino-p53-H3K4Me3


title: prostate_cancer_primary_150 (STAMPEDE)


title: Z138 -wt-p53-1


title: TFAP2A IP in hypoxia, replicate 2

value: Hypoxia, anti-TFAP2A (ThermoFisher SCIENTIFIC, PA5-17359)


title: prostate_cancer_primary_149 (STAMPEDE)

value: FFPE prostate cancer


title: Mino-p53-p53-1


title: Mino-p53-IgG


title: Mino-Ctrl-p53-2


title: Mino-Ctrl-H3K4Me3


title: Mino-Ctrl-p53-1


title: prostate_cancer_primary_148 (STAMPEDE)


title: prostate_cancer_primary_147 (STAMPEDE)


title: Input chromatin, replicate 2

value: no treatment


title: prostate_cancer_primary_151 (STAMPEDE)


title: Mino-Ctrl-IgG

value: Mino-Ctrl-IgG


title: Input chromatin, replicate 1


title: CBP300_Rep_3

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.40 )
The filtered reads were aligned to the reference genomes using Bowtie2 (versionv2.5.4)
A user-friendly software RSEM (version 1.3.3) was applied for the quantification of the transcript abundance
Differentially expressed genes (DEGs) were identified by EBSeq (version 2.2.0)
The functional enrichment analysis of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among gene clusters was implemented in an R language
Assembly: Homo_sapiens.GRCh38.98
Supplementary files format and content: Matrix table with normalized count of mapped reads (TPM) for every gene and every sample

source_name: Cell Line

growth_protocol: HMEC-1 cells were mantained in MCDB131 medium (Gibco, 10372019) with 10 ng/mL hEGF (Sigma, #E9644), 1 g/mL hydrocortisone (Sigma, #H0888), 10 mM L-glutamine (Gibco, #25030149), and 10% heat inactivated FBS (Gibco, #10437-028).

extract_protocol:
Total mRNA was isolated using miRNeasy Mini kit (Qiagen, #217084) per the instruction of manufacturer
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan

treatment_protocol: 10 ng/mL of rOSM; 30 ug/mL PF9363 + 10 ng/mL of rOSM ; 10 ug/mL CBP300 + 10 ng/mL of rOSM

value: Cell Line

value: Endothelial cells

value: OSM-treated + EP300 inhibitor

value: 10 ug/mL OSM + 10 ug/mL CBP300


title: CBP300_Rep_2

value: 10 ug/mL OSM + 10 ug/mLCBP300


title: prostate_cancer_primary_146 (STAMPEDE)


title: P2 and P3

city: Zhengzhou

first: Man

last: Luo

address: 195 Tongbai Road, Zhongyuan District

institute: Zhengzhou Central Hospital Affiliated to Zhengzhou University

description:
Library name: P2
multiplexed sample. Raw data contains reads for both sample P2 and P3.

data_processing:
Raw sequencing data were processed using the 10× Genomics Space Ranger pipeline  to generate FASTQ files
Assembly: mm10
Supplementary files format and content: matrix.zip:list of spatial barcodes, gene IDs and gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: ovary

extract_protocol:
Ovaries were collected at the end of the treatment period, immediately frozen in OCT compound for spatial transcriptomics.
Spatial transcriptome sequencing libraries were prepared with 10× Genomics Visium Spatial Gene Expression Slides&Reagent kit accorsing to manufacturer's construction.

value: ovary

value: ICR

value: DHEA


title: CBP300_Rep_1


title: P1

description: Library name: P1


title: PF9363_Rep_3

value: OSM-treated + KAT6A/B inhibitor

value: 10 ug/mL OSM + 30 ug/mL PF9363


title: PF9363_Rep_2


title: OSM_Rep_3

value: OSM-treated

value: 10 ug/mL OSM


title: PF9363_Rep_1


title: TFAP2A IP in hypoxia, replicate 1

value: HeLa

value: cervical cancer

value: WT


title: C2 and C3

description:
Library name: C2
multiplexed sample. Raw data contains reads for both sample C2 and C3.

value: control


title: OSM_Rep_2


title: C1

description: Library name: C1


title: prostate_cancer_primary_143 (STAMPEDE)

address: 9725 Lusk Blvd

value: FFPE prostate cancer


title: CT_Rep_3

value: Cell Line

value: Control

value: CT


title: OSM_Rep_1

value: Endothelial cells


title: CT_Rep_2


title: CT_Rep_1


title: Nac tissue, HSV-ZFP189WT

city: Richmond

first: Gabriella

middle: M

last: Silva

address: 1217 Marshall Street

institute: Virginia Commonwealth University

description:
Library name: HSV-ZFP189-WT-snRNAseq
HSV-ZFP189-WT

data_processing:
The sequencing data were processed using Cell Ranger software (version 7.1.0). The FASTQ files were aligned to the custom mouse reference genomes to generate feature-barcode matrices, and were further analyzed using the Seurat package (version 4.3). Initial quality control was performed to filter out low-quality nuclei (etc. number of features > 700, number of read > 3162, ratio of log10 features per UMI > 0.8, and percentage of mitochondrial gene expression < 5%).
Assembly: GRCmm39
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: brain, nucleus accumbens

extract_protocol:
Nuclei were  isolated following the 10X Genomics protocol on nuclei isolation of adult mouse brain tissue for single nuclei RNA sequencing. Briefly, tissue lysis and nuclei washing, myelin removal, and density gradient centrifugation were performed for nuclei isolation. Once nuclei were successfully isolated, we followed the 10x Genomics Chromium single cell 3’ gene expression pipeline. The nuclei suspension was loaded into a Chromium Chip B with partitioning oil, reverse transcription reagents, and gel beads containing 10X Genomics barcodes. Barcoded cDNA was generated for each sample then pooled together. Library construction and sequencing on an Illumina HiSeq series sequencer was performed at a depth of approximately 30,000 reads per nuclei.
To incorporate three different viral constructs into the reference genome for single-nucleus RNA sequencing analysis, we generated custom reference genomes for each viral construct (ZFP189VPR, ZFP189WT, and ZFP189NFD), following steps recommended by 10X Genomics. In brief, for each viral construct the viral construct sequence was added to the mouse reference genome (mm39) to create a combined fasta file. A corresponding gene annotation in GTF format was also created. The length of each viral sequence was calculated, and an exon annotation was added to the existing GENCODE vM32 annotation file to produce a comprehensive annotation file.

treatment_protocol: stereotaxic delivery of HSV-ZFP189VPR, HSV-ZFP189WT, or HSV-ZFP189NFD constructs

value: brain, nucleus accumbens


title: prostate_cancer_primary_142 (STAMPEDE)


title: H4_ZrQT

data_processing:
Contaminating adapter squences were removed (Trimmomatic ,v0.36). Trimmed reads were aligned to the hg38 (STAR,v 2.5.3) and gene expression quantification using HTSeq (v.0.9.1).
HTSeq counts were converted into FPKM
Assembly: hg38
Supplementary files format and content: FPKM_counts

extract_protocol:
Zymo Quick-RNA Miniprep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: MCL cell lines

value: Z138 R248Q  TRT


title: H3_ZRQT


title: prostate_cancer_primary_140 (STAMPEDE)


title: prostate_cancer_primary_141 (STAMPEDE)


title: Nac tissue, HSV-ZFP189NFD

description:
Library name: HSV-ZFP189-NFD-snRNAseq
RESUB-HSV-ZFP189-DN


title: prostate_cancer_primary_144 (STAMPEDE)


title: H2_ZRQC

value: CONTROL 2


title: Nac tissue, HSV-ZFP189WT, male, mouse 4

description: Library name: M-ZFP189WT-4-3D

data_processing:
Adapter sequences and low-quality bases removed with Trimmomatic (version 0.39). 4-base window of sequencing quality <15 and reads less than 50 bases were dropped.
High-quality reads aligned to Mus musculus GRCm39 reference genome using STAR (version 2.7.11a) with recommended parameters.
Assembly: GRCmm39
Supplementary files format and content: tab-delimited text files with raw counts for each sample

extract_protocol:
RNA was extracted and purified from snap-frozen brian tissue using RNeasy kit (Qiagen) per manufacturer's instructions.
Ribosomal RNA depletion and library preparation were performed with Illumina Ribo-Zero per manufacturer's instructions.


title: H1_ZRQC

value: CONTROL 1


title: Nac tissue, HSV-ZFP189WT, male, mouse 3

description: Library name: M-ZFP189WT-3-3D


title: prostate_cancer_primary_145 (STAMPEDE)


title: G4_ZHmT

value: Z138  HM R27C  TRT


title: G3_ZHmT


title: Nac tissue, HSV-ZFP189WT, male, mouse 2

description: Library name: M-ZFP189WT-2-3D


title: prostate_cancer_primary_138 (STAMPEDE)


title: prostate_cancer_primary_137 (STAMPEDE)


title: G2_ZHmC

value: Z138  HM R27C


title: G1_ZHmC


title: Nac tissue, HSV-ZFP189VPR

description:
Library name: HSV-ZFP189-VPR-snRNAseq
HSV-ZFP189-VPR


title: F4_ZKoT

value: Z138  KO P53  TRT


title: prostate_cancer_primary_139 (STAMPEDE)


title: Nac tissue, HSV-ZFP189WT, male, mouse 1

description: Library name: M-ZFP189WT-1-3D


title: F3_ZKoT


title: prostate_cancer_primary_135 (STAMPEDE)


title: F2_ZKoC


title: F1_ZKoC


title: Nac tissue, HSV-ZFP189VPR, male, mouse 4

description: Library name: M-ZFP189VPR-4-3D


title: E4_ZWtT

value: Z138 WT TRT


title: prostate_cancer_primary_134 (STAMPEDE)


title: n1-src splice blocking morpholinos rep 3

city: York

first: harry

middle: victor

last: isaacs

state: North Yorkshire

address: wentworth way

department: biology

country: United Kingdom

institute: university of york

description:
Library name: AMO3
n1-src AMO 3

data_processing:
Cutadapt was used to remove adapter sequences and primers
Salmon was used to map reads to the NCBI Xenopus tropicalis reference transcriptome v9.1
Differential gene expression was determined using Sleuth and the counts aggregation method. The reduced model was defined as ‘~batch’, and the full model ‘~batch + treatment’ to mitigate variation accounted for by embryo batch.
Assembly: NCBI Xenopus tropicalis reference transcriptome v9.1
Supplementary files format and content: gene counts in transcripts per million (TPM)

organism: Xenopus tropicalis

source_name: st16  whole embryos

growth_protocol: embryos were cultured in MRS/20 at 23 degrees

extract_protocol:
Total RNA was extracted from embryos with Trizol reagent (Invitrogen) as per manufacturer's instructions. RNA was further purified by LiCl precipitation and RNA integrity was checked using an Agilent 2100 Bioanalyzer.
NEBNext Poly(A) mRNA Magnetic Isolation Module was used to isolate Poly(A) mRNA from total RNA. NEBNext RNA Ultra II Directional RNA Library Prep Kit was used generate the cDNA libraries

treatment_protocol: Embryos were injected with 10 ng control morpholino or 10 ng of n1-src splice blocking morpholinos

value: st16  whole embryos

value: Nigerian

value: n1-src morpholino injected


title: Nac tissue, HSV-ZFP189VPR, male, mouse 3

description: Library name: M-ZFP189VPR-3-3D


title: E3_ZWtT


title: n1-src splice blocking morpholinos rep 2

description:
Library name: AMO2
n1-src AMO 2


title: Nac tissue, HSV-ZFP189VPR, male, mouse 1

description: Library name: M-ZFP189VPR-1-3D


title: n1-src splice blocking morpholinos rep 1

description:
Library name: AMO1
n1-src AMO 1


title: Nac tissue, HSV-ZFP189VPR, male, mouse 2

description: Library name: M-ZFP189VPR-2-3D


title: prostate_cancer_primary_132 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_136 (STAMPEDE)


title: control morpholino rep 3

description:
Library name: CMO3
CMO 3

value: control morpholino injected


title: Nac tissue, HSV-ZFP189NFD, male, mouse 4

description: Library name: M-ZFP189NFD-4-3D


title: E1_ZWtC

value: Z138 WT


title: E2_ZWtC


title: control morpholino rep 2

description:
Library name: CMO2
CMO 2


title: Nac tissue, HSV-ZFP189NFD, male, mouse 3

description: Library name: M-ZFP189NFD-3-3D


title: prostate_cancer_primary_131 (STAMPEDE)


title: D4_MvPT

value: MAVER P53 B

value: DOX 125


title: prostate_cancer_primary_130 (STAMPEDE)


title: prostate_cancer_primary_133 (STAMPEDE)


title: control morpholino rep 1

description:
Library name: CMO1
CMO 1


title: Nac tissue, HSV-ZFP189NFD, male, mouse 2

description: Library name: M-ZFP189NFD-2-3D

value: brain, nucleus accumbens


title: prostate_cancer_primary_129 (STAMPEDE)


title: D3_MvPT

value: MCL cell lines

value: MAVER P53 A


title: Nac tissue, HSV-ZFP189NFD, male, mouse 1

description: Library name: M-ZFP189NFD-1-3D


title: prostate_cancer_primary_128 (STAMPEDE)


title: CHIP034, H3K27me3, 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: CHIP034

data_processing:
Basecalling was performed with bcl2fastq v2.20. Reads were deduplicated, trimmed, and filtered for low complexity using fastp v0.23.2. High-quality reads (MAPQ >20) were aligned to the UCSC hg38 genome with Bowtie2 v2.5.1, and only uniquely mapped reads were retained using sambamba v1.0.0.
ChIP-seq coverage plots were generated by extending mapped reads to 120 bp to approximate fragment sizes, normalizing to counts per million (CPM), computing log₂ ratios over input, and z-scaling the resulting signal. The resulting bigwig files were generated using deeptools v3.1.3. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
Broad domains for LB1, H3K9me3, H3K9me3, and H3K27me3 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed files with domain calls per condition as described above.

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:
ChIP-seq was performed as previously described(Shah et al. 2023; 2021). HCT116 cells were crosslinked in culture by addition of methanol-free formaldehyde (Pierce, final 1% v/v) for 10minutesat room temperature with gentle rotation. Crosslinking was quenched by addition of glycine (final 125 mM) for 5minuteswith gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (1500 rpm, 3 minutes at room temperature). Resulting pellets were flash frozen in liquid nitrogen and stored at −80°C. For ChIP, 30μL protein G magnetic beads (per ChIP sample; ThermoFisher) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250μL blocking buffer and 2μg antibody (Lamin B1, Abcam, ab16048; H3K9me2, Abcam, ab1220; H3K9me3, Abcam, ab8898; H3K27me3, Cell Signaling Technology, #9733) and rotated at 4°C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate or equivalent cell number) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors), and rotated at 4°C for 10 minutes, followed by centrifugation (1500 rpm at 4°C for 3 minutes). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (1500 rpm at 4°C for 3 minutes). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris). Samples were sonicated using a Covaris S220 sonicator (High Cell Chromatin Shearing: PIP 140W, CPB 200, Duty Factor 5%, 15 minutes). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4°C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bio-Rad Protein Assay Kit (Bio-Rad, Protein Assay Kit #5000002). Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50μL blocking buffer and added to 500μg input protein for overnight incubation with rotation at 4°C. 50μg lysate was stored at −20°C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) with inversion to mix followed by 2-minute incubation on ice for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes at room temperature before final resuspension in 210μL elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65°C for 30 minutes. 200μL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65°C with agitation for a minimum of 12 hours, but not more than 18 hours. 200μL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were treated with RNaseA (final 0.2mg/mL RNase; 37°C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55°C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
ChIP and input DNA were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit according to manufacturer’s instructions (NEB). Samples were indexed for multiplex sequencing with dual unique indices (NEBNext Multiplex Oligos for Illumina). Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (NEBNext Library Quant Kit). Libraries were pooled for multiplex sequencing, re-quantified, and sequenced on the Illumina NextSeq1000 platform (121bp single-end sequencing).

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

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, #9733)

value: HNRNPK siRNA


title: D2_MvP

value: DOX -VE


title: LOCL-TL with ribosome profiling, cytosol  located LOV-BirA, pulldown, replicate 2

city: Cambridge

first: Jingchuan

address: 455 Main Street

institute: Whitehead Institute

description: Library name: LOCL-TL_HEK_cytosol_LOV_BirA_pulldown_rep2

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.
Library strategy: Ribo-Seq

molecule: other

source_name: HEK293T cells

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

value: HEK293T cells


title: prostate_cancer_primary_126 (STAMPEDE)


title: D1_MvP


title: prostate_cancer_primary_127 (STAMPEDE)


title: CHIP033, Input, siHNRNPK, Rep1

description: Library name: CHIP033

value: Input


title: C4_MvCT

value: MAVER CTRL B


title: CHIP032, H3K27me3, siHNRNPK, Rep1

description: Library name: CHIP032


title: LOCL-TL with ribosome profiling, cytosol  located LOV-BirA, total input, replicate 2

description: Library name: LOCL-TL_HEK_cytosol_LOV_BirA_total_rep2


title: prostate_cancer_primary_125 (STAMPEDE)


title: LOCL-TL with ribosome profiling, cytosol located LOV-BirA, pulldown, replicate 1

description: Library name: LOCL-TL_HEK_cytosol_LOV_BirA_pulldown_rep1


title: C3_MvCT

value: MAVER CTRL A


title: prostate_cancer_primary_124 (STAMPEDE)


title: CHIP031, Input, siControl, Rep2

description: Library name: CHIP031

value: Nontargeting control siRNA


title: C2_MvC


title: CHIP035, Input, siHNRNPK, Rep2

description: Library name: CHIP035


title: LOCL-TL with ribosome profiling, mitochondrially located LOV-BirA, pulldown, replicate 2

description: Library name: LOCL-TL_HEK_mito_LOV_BirA_pulldown_rep2


title: LOCL-TL with ribosome profiling, mitochondrially located LOV-BirA, total input, replicate 2

description: Library name: LOCL-TL_HEK_mito_LOV_BirA_total_rep2


title: B4R_MPT

source_name: MINO

value: MINO

value: MINO P53 B

value: DOX 250


title: CHIP029, Input, siControl, Rep1

description: Library name: CHIP029


title: prostate_cancer_primary_123 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_121 (STAMPEDE)


title: prostate_cancer_primary_122 (STAMPEDE)


title: CHIP028, H3K27me3, siControl, Rep1

description: Library name: CHIP028


title: LOCL-TL with ribosome profiling, mitochondrially located LOV-BirA, pulldown, replicate 1

description: Library name: LOCL-TL_HEK_mito_LOV_BirA_pulldown_rep1


title: prostate_cancer_primary_120 (STAMPEDE)


title: B2R_MP


title: prostate_cancer_primary_119 (STAMPEDE)


title: B1R_MP

value: MINO P53 A


title: LOCL-TL with ribosome profiling, cytosol LOV-BirA, total input, replicate 1

description: Library name: LOCL-TL_HEK_cytosol_LOV_BirA_total_rep1


title: CHIP030, H3K27me3, siControl, Rep2

description: Library name: CHIP030


title: LOCL-TL with ribosome profiling, ER located LOV-BirA, pulldown, replicate 2

description: Library name: LOCL-TL_HEK_ER_LOV_BirA_pulldown_rep2


title: LOCL-TL with ribosome profiling, ER located LOV-BirA, total input, replicate 2

description: Library name: LOCL-TL_HEK_ER_LOV_BirA_total_rep2


title: CHIP025, Input, siHNRNPK, Rep2

description: Library name: CHIP025


title: A4R_MCT

value: MINO CTRL B


title: CHIP024, H3K9me3, siHNRNPK, Rep2

description: Library name: CHIP024

value: H3K9me3 (abcam, #ab8898)


title: A3R_MCT

value: MCL cell lines

value: MINO CTRL A


title: C1_MvC


title: CHIP006, Input, siControl, Rep3

description: Library name: CHIP006

value: Human colon cancer


title: prostate_cancer_primary_117 (STAMPEDE)


title: prostate_cancer_primary_116 (STAMPEDE)


title: CHIP023, Input, siHNRNPK, Rep1

description: Library name: CHIP023

value: HNRNPK siRNA


title: A2R_MC

value: DOX -VE


title: CHIP027, Input, siHNRNPK, Rep3

description: Library name: CHIP027


title: LOCL-TL with ribosome profiling, mitochondrially located LOV-BirA, total input, replicate 1

description: Library name: LOCL-TL_HEK_mito_LOV_BirA_total_rep1

value: HEK293T cells


title: B3R_MPT


title: CHIP022, H3K9me3, siHNRNPK, Rep1

description: Library name: CHIP022


title: A1R_MC


title: CHIP026, H3K9me3, siHNRNPK, Rep3

description: Library name: CHIP026


title: prostate_cancer_primary_114 (STAMPEDE)


title: CHIP021, Input, siControl, Rep3

description: Library name: CHIP021

value: Input


title: prostate_cancer_primary_118 (STAMPEDE)


title: LOCL-TL with ribosome profiling, ER located LOV-BirA, total input, replicate 1

description: Library name: LOCL-TL_HEK_ER_LOV_BirA_total_rep1


title: CHIP020, H3K9me3, siControl, Rep3

description: Library name: CHIP020


title: prostate_cancer_primary_113 (STAMPEDE)


title: LNA3 treated samples replicate 3

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

data_processing:
FastQC (v.0.11.8) was used to check the quality of the raw sequencing reads. Rsubread (v.2.6.4) was used to align the reads to the human reference genome hg38 and count the read for each RefSeq gene. The data was normalized as CPM (counts per million) values using EdgeR (v.3.34.1).
Assembly: hg38
Supplementary files format and content: csv file normalized reads count

source_name: cord blood

growth_protocol: CD4+ T cells were isolated from human umbilical cord blood samples collected from Turku University hospital from full-term normal delivery. Mononuclear cells were isolated using Ficoll density gradient centrifugation. CD4+ cells were then enriched using bead-based positive isolation (Dynal CD4 Positive Isolation Kit; Invitrogen). Cells were activated using plate-bound α-CD3 (3.75 μg/ml; Beckman Coulter, Cat. no. IM1304) and soluble α-CD28 (1 μg/ml; Beckman Coulter, Cat. no. IM1376) in RPMI medium (Lonza) supplemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/ml penicillin plus 50 μg/ml streptomycin; Sigma-Aldrich). All cultures were maintained at 37°C in a humidified atmosphere of 5% (v/v) CO2/air.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAGEN). The removal of genomic DNA was confirmed in-column with DNase treatment (RNase-Free DNase Set; QIAGEN) for 15 min, followed by an additional treatment of the samples with DNase I (Invitrogen). Nanodrop 2000 and BioRad Experion were used to measure the quantity and quality of RNA, respectively.
Libraries for RNA-Seq were prepared using Illumina Stranded mRNA Library Preparation, Illumina (1000000124518). The quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer, and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies).
Nine samples pooled on one and sequenced on  one lane with 2x150bp read length. Sequencing was performed at the Finnish Functional Genomics Centre using the NovaSeq 6000 SP v1.5 Next-Generation Sequencing platform.

treatment_protocol: LINC01871 was silenced using two LNAs targeting different regions of the gene (LNA2: 5´-TTCGGCCTTTGGTAGT-3´; LNA3: 5´-ACAGATCGTCCACGGC-3´) or non-targeting LNA (NT) (5´-AACACGTCTATACGC-3´). 300 pmol of LNAs were nucleofected into four million cells in 100 µl OptiMEM medium (Gibco by Life Technologies, Cat. no. 31985-047) using Amaxa nucleofector (Lonza). The cells were then rested for 24 h in RPMI 1640 medium (Sigma-Aldrich) supplemented with pen/strep, 2 mM L-glutamine and 10% FCS before activation.

value: cord blood

value: CD4+ T cells

value: wild type


title: prostate_cancer_primary_112 (STAMPEDE)


title: SK_4XVG_A04, calcifediol, time 2

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: SK_4XVG_A04

data_processing:
Bulk RNA data were processed using  WARDEN workflow for the analysis of RNA-Seq differential expression (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: expression_matrix.txt

source_name: Blood

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Blood

value: CD14 Monocyte

value: calcifediol

tag: time (day)


title: CHIP019, H3K9me2, siControl, Rep3

description: Library name: CHIP019

value: H3K9me2 (abcam, #ab1220)

value: Nontargeting control siRNA


title: LNA3 treated samples replicate 2


title: SK_4XVG_A03, calcifediol, time 0

description: Library name: SK_4XVG_A03


title: SK_4XVG_A02, calcifediol, time 2

description: Library name: SK_4XVG_A02


title: CHIP017, H3K9me3, siControl, Rep2

description: Library name: CHIP017


title: prostate_cancer_primary_115 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_111 (STAMPEDE)


title: CHIP016, H3K9me2, siControl, Rep2

description: Library name: CHIP016


title: CHIP018, Input, siControl, Rep2

description: Library name: CHIP018


title: LNA2 treated samples replicate 2


title: SK_4VID_H10, calcifediol, time 2

description: Library name: SK_4VID_H10


title: LNA2 treated samples replicate 1


title: prostate_cancer_primary_109 (STAMPEDE)


title: SK_4XVG_A01, calcifediol, time 0

description: Library name: SK_4XVG_A01


title: prostate_cancer_primary_108 (STAMPEDE)


title: CHIP015, Input, siControl, Rep1

description: Library name: CHIP015


title: SK_4VID_H09, calcifediol, time 0

description: Library name: SK_4VID_H09


title: NT LNA treated samples replicate 3

value: NT


title: SK_4VID_H08, placebo, time 2

description: Library name: SK_4VID_H08

value: placebo


title: CHIP014, H3K9me3, siControl, Rep1

description: Library name: CHIP014

value: H3K9me3 (abcam, #ab8898)


title: NT LNA treated samples replicate 2


title: LNA3 treated samples replicate 1


title: prostate_cancer_primary_106 (STAMPEDE)


title: CHIP013, H3K9me2, siControl, Rep1

description: Library name: CHIP013

value: Human colon cancer


title: LNA2 treated samples replicate 3


title: prostate_cancer_primary_107 (STAMPEDE)


title: SK_4VID_H07, placebo, time 0

description: Library name: SK_4VID_H07


title: NT LNA treated samples replicate 1


title: CHIP012, Input, siHNRNPK, Rep3

description: Library name: CHIP012

value: HNRNPK siRNA


title: prostate_cancer_primary_110 (STAMPEDE)


title: SK_4VID_H06, calcitriol, time 2

description: Library name: SK_4VID_H06

value: calcitriol


title: prostate_cancer_primary_105 (STAMPEDE)


title: CHIP011, LMNB1, siHNRNPK, Rep3

description: Library name: CHIP011

value: LMNB1 (abcam, #ab16048)


title: DEX+BRM014 (24h), BT549 cells, Biorep3

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

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

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

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

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

value: TNBC

value: WT


title: SK_4VID_H04, calcitriol, time 2

description: Library name: SK_4VID_H04


title: CHIP010, Input, siHNRNPK, Rep2

description: Library name: CHIP010

value: Input


title: prostate_cancer_primary_104 (STAMPEDE)

state: California


title: SK_4VID_H03, calcitriol, time 0

description: Library name: SK_4VID_H03


title: DEX+DMSO (24h), BT549 cells, Biorep3

value: 24h DEX (500nM) + DMSO


title: CHIP008, Input, siHNRNPK, Rep1

description: Library name: CHIP008


title: SK_4VID_H02, calcitriol, time 2

description: Library name: SK_4VID_H02

value: Blood


title: DEX+DMSO (24h), BT549 cells, Biorep2


title: prostate_cancer_primary_101 (STAMPEDE)


title: prostate_cancer_primary_100 (STAMPEDE)


title: SK_4VID_H01, calcitriol, time 0

description: Library name: SK_4VID_H01

value: CD14 Monocyte


title: CHIP007, LMNB1, siHNRNPK, Rep1

description: Library name: CHIP007


title: DEX+DMSO (24h), BT549 cells, Biorep1


title: prostate_cancer_primary_103 (STAMPEDE)


title: CHIP004, Input, siControl, Rep2

description: Library name: CHIP004


title: SK_4VID_G12, calcifediol, time 2

description: Library name: SK_4VID_G12

value: calcifediol


title: BRM014 (24h), BT549 cells, Biorep3


title: DEX+BRM014 (24h), BT549 cells, Biorep2


title: CHIP003, LMNB1, siControl, Rep2

description: Library name: CHIP003


title: DEX+BRM014 (24h), BT549 cells, Biorep1


title: SK_4VID_H05, calcitriol, time 0

description: Library name: SK_4VID_H05


title: prostate_cancer_primary_102 (STAMPEDE)


title: CHIP009, LMNB1, siHNRNPK, Rep2

description: Library name: CHIP009


title: prostate_cancer_primary_98 (STAMPEDE)


title: SK_4VID_G11, calcifediol, time 0

description: Library name: SK_4VID_G11


title: CHIP002, Input, siControl, Rep1

description: Library name: CHIP002


title: prostate_cancer_primary_97 (STAMPEDE)


title: prostate_cancer_primary_96 (STAMPEDE)


title: prostate_cancer_primary_99 (STAMPEDE)


title: prostate_cancer_primary_95 (STAMPEDE)


title: SK_4VID_G09, calcifediol, time 0

description: Library name: SK_4VID_G09


title: CHIP001, LMNB1, siControl, Rep1

description: Library name: CHIP001


title: DMSO (24h), BT549 cells, Biorep3

value: 24h DMSO


city: Beijing

first: Jiayu

last: Wang

state: Beijing

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

department: School of Pharmaceutical Sciences

institute: Peking University Health Science Center

description:
Library name: HEK293T-EF1α-mCherry, tRNAAlaGGC overexpressed(tA), 3
35-4.2-3_1

data_processing:
Paired-end reads were harvested from sequencer and quality controlled by Q30. After 3’ adaptor-trimming and low-quality reads removing by cutadapt software (v1.9.3), cleaned reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get raw counts, and edgeR was used to perform normalization.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

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

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA), and subjected to mRNA isolation using GenSeq® mRNA Purification Kit (GenSeq, Inc.).
The purified mRNA was used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s recommendations.

value: human embryonic kidney cells

value: tRNAAlaGGC (tA) overexpressed


title: SK_4VID_G08, calcitriol, time 2

description: Library name: SK_4VID_G08


title: DMSO (24h), BT549 cells, Biorep2


description:
Library name: HEK293T-EF1α-mCherry, tRNAAlaGGC overexpressed(tA), 2
35-4.2-2_1


description:
Library name: HEK293T-EF1α-mCherry, tRNAAlaGGC overexpressed(tA), 1
35-4.2-1_1


title: DMSO (24h), BT549 cells, Biorep1


title: SK_4VID_G06, placebo, time 2

description: Library name: SK_4VID_G06


title: BRM014 (24h), BT549 cells, Biorep2


title: SK_4VID_G07, calcitriol, time 0

description: Library name: SK_4VID_G07


title: SK_4VID_G05, placebo, time 0

description: Library name: SK_4VID_G05


title: DEX+BRM014 (4h), BT549 cells, Biorep3


title: DEX+BRM014 (4h), BT549 cells, Biorep2


description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 2
35-6-2_1

value: tRNALeuCAG (tL) overexpressed


title: SK_4VID_G10, calcifediol, time 2

description: Library name: SK_4VID_G10


description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 3
35-6-3_1


title: BRM014 (24h), BT549 cells, Biorep1


title: DEX+BRM014 (4h), BT549 cells, Biorep1


title: SK_4VID_G04, calcifediol, time 2

description: Library name: SK_4VID_G04


description:
Library name: HEK293T-EF1α-mCherry, tRNALeuCAG overexpressed(tL), 1
35-6-1_1


title: prostate_cancer_primary_92 (STAMPEDE)

value: FFPE prostate cancer


title: SK_4VID_G03, calcifediol, time 0

description: Library name: SK_4VID_G03


title: prostate_cancer_primary_94 (STAMPEDE)


title: HEK293T-EF1α-mCherry (WT), 3

description:
Library name: HEK293T-EF1α-mCherry (WT), 3
EMH-3_1


title: prostate_cancer_primary_91 (STAMPEDE)


title: prostate_cancer_primary_89 (STAMPEDE)


title: prostate_cancer_primary_90 (STAMPEDE)


title: SK_4VID_G02, calcitriol, time 2

description: Library name: SK_4VID_G02


title: LOCL-TL with ribosome profiling, ER located LOV-BirA, pulldown, replicate 1

description: Library name: LOCL-TL_HEK_ER_LOV_BirA_pulldown_rep1

value: HEK293T cells


title: prostate_cancer_primary_93 (STAMPEDE)


title: HEK293T-EF1α-mCherry (WT), 2

description:
Library name: HEK293T-EF1α-mCherry (WT), 2
EMH-2_1


title: prostate_cancer_primary_87 (STAMPEDE)


title: DEX+DMSO (4h), BT549 cells, Biorep1

value: 4h DEX (500nM) + DMSO


title: SK_4VID_G01, calcitriol, time 0

description: Library name: SK_4VID_G01


title: prostate_cancer_primary_88 (STAMPEDE)


title: SK_4VID_F12, placebo, time 2

description: Library name: SK_4VID_F12

value: placebo


title: HEK293T-EF1α-mCherry (WT), 1

description:
Library name: HEK293T-EF1α-mCherry (WT), 1
EMH-1_1


title: BRM014 (4h), BT549 cells, Biorep3

value: 4h BRM014


title: Siha cells, BAG2, rep3

city: Wuhan

first: Jie

middle: Shi

last: Yao

state: Hubei

address: 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province

department: Department of Gynecological Oncology

institute: Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cervical cancer

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

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-02, Vazyme) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: cervical cancer

value: Siha

value: Tumor cells


title: BRM014 (4h), BT549 cells, Biorep2

value: TNBC

value: WT


title: prostate_cancer_primary_86 (STAMPEDE)


title: DEX+DMSO (4h), BT549 cells, Biorep3


title: Siha cells, BAG2, rep2


title: SK_4VID_F10, calcitriol, time 2

description: Library name: SK_4VID_F10

value: Blood

value: calcitriol


title: SK_4VID_F11, placebo, time 0

description: Library name: SK_4VID_F11

value: CD14 Monocyte


title: BRM014 (4h), BT549 cells, Biorep1


title: prostate_cancer_primary_85 (STAMPEDE)


title: SK_4VID_F09, calcitriol, time 0

description: Library name: SK_4VID_F09


title: DMSO (4h), BT549 cells, Biorep3

value: 4h DMSO


title: Siha cells, Vector, rep3


title: Siha cells, BAG2, rep1


title: SK_4VID_F08, placebo, time 2

description: Library name: SK_4VID_F08


title: DEX+DMSO (4h), BT549 cells, Biorep2


title: DMSO (4h), BT549 cells, Biorep2


title: prostate_cancer_primary_84 (STAMPEDE)


title: SK_4VID_F07, placebo, time 0

description: Library name: SK_4VID_F07


title: Siha cells, Vector, rep2


title: prostate_cancer_primary_82 (STAMPEDE)


title: prostate_cancer_primary_81 (STAMPEDE)


title: Siha cells, Vector, rep1


title: DMSO (4h), BT549 cells, Biorep1


title: SK_4VID_F06, calcifediol, time 2

description: Library name: SK_4VID_F06

value: calcifediol


title: siGATA6, +DEX, BT549 cells, Biorep3

tag: sirna

value: 2h Dex (500nM)


title: prostate_cancer_primary_83 (STAMPEDE)


title: siGATA6, +DEX, BT549 cells, Biorep2


title: prostate_cancer_primary_80 (STAMPEDE)