title: scTCR-seq of in vitro expanded HIV-1 latent clone P301d - Resting - rep1

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
Library name: P301_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone P301d

data_processing:
Binary base call (BCL) files from the NovaSeq 6000 sequencer were demultiplexed and converted to FASTQ format using Illumina's BCLtoFastq software.
FASTQ files were processed using Cellranger multi (v8.0.1). Reads were aligned to a modified version of the human genome hg38 that included HIV specific sequences from each HIV-1 provirus clone.
TCR sequences were assembled and annotated using Cellranger multi with the 10x VDJ human reference (GRCh38-alts-ensembl-7.1.0).
Downstream analysis was performed using Seurat (v5.3.0) in Rstudio (2024.12.0). Cells were filtered (200-2500 features, <10% mitochondrial content). Data was merged, normalized, and scaled using SCTransform.
Latent clones were identified based on identical combined TRA CDR3 and TRB CDR3 nucleotide sequences.
Assembly: hg38 (modified with HIV-1 provirus sequences)
Supplementary files format and content: Filtered feature-barcode matrices and V(D)J annotation files (CSV format) and airr_rearrangement.tsv (TSV format) generated by CellRanger.
Library strategy: TCR-Seq

source_name: peripheral blood

growth_protocol: CD4+CD45RA- T cells were isolated from PBMCs by negative selection. Cells were sorted by FACS at 5 cells/well in 96-well U-bottom plates containing activation media (R10, 50 U/ml IL-2, 100 ng/mL anti-human CD3 and CD28 antibodies) and 1x10^6 cells/mL feeder cells (irradiated PBMCs). Antiretroviral (ARV) drugs were added to prevent new infection. Cells were cultured at 37¬∞C with 5% CO2 for 3 to 4 weeks, with media exchange twice a week (maintenance media - R10+IL-2+ARVs). Cultures confirmed positive for the intact provirus were further expanded in activation media.

extract_protocol:
Cells were processed for single-cell analysis using the 10X Genomics platform, which lyses cells and captures mRNA onto Gel Beads.
Single-cell gene expression (GEX) and V(D)J libraries were prepared using the 10X Genomics platform. Chromium Single Cell Library & Gel Bead Kit (10X Genomics cat. PN-1000014) was used for GEX libraries, and Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10X Genomics cat. PN-1000005) was used for V(D)J libraries. Libraries were prepared following the 10X genomics protocol.

treatment_protocol: For activated samples, expanded clones were stimulated for 24 hours with 50 U/mL IL-2 and 100 ng/mL anti-CD3 and CD28 antibodies. Resting samples were analyzed in R10 media. All assays were performed in the presence of ARVs.

value: peripheral blood

value: CD4+CD45RA- T cells

value: HIV-1 infected (defective provirus)

value: Resting


title: THP1 EV, shDIS3L2

status: Public on Dec 16 2025

type: SRA

city: Frederick

first: Sandra

middle: L

last: Wolin

state: MD

address: FDC 560 BG RM 11-82C / 560 CHANDLER STREET

country: USA

institute: NCI

description:
Library name: EV_shDIS3L2
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)

library_source: transcriptomic

data_processing:
Illumina adapter sequences were trimmed with CutAdapt. After trimming, reads < 15 nt were discarded.
Transcript reads were quantified by Salmon utilizing sequences from GENCODE v45, high confidence tRNA sequences (GtRNAdb), and human repeat sequences from giri repbase.
UMI sequences were extracted from Read 1 using UMI-tools.
Reads were mapped to the human genome (GRCm38) using NovoAlign (Novocraft). Parameters included: gap opening penalty of 20 (-g), gap penalty of 4 (-x), and soft-clip penalty of 0. Reads were multi-mapped, allowing up to 100 mapping events.
Reads were deduplicated using UMI-tools
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured at 37°C with 5% CO2 and maintained in RPMI (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin-streptomycin, and 2 mM L-glutamine.

extract_protocol:
EV RNA was extracted with a Direct-Zol RNA Miniprep Kit and eluted into 25 μL water. Whole cell RNA was extracted from Trizol.
cDNA libraries were made from 50 ng RNA (either rRNA-depleted whole cell RNA or EV RNA) using a template switching reaction protocol. Briefly, 1 μM each of R2 RNA and R2R DNA oligonucleotides in 10 mM Tris-HCl pH 7.5, 1 mM EDTA were incubated at 82˚C for 2 min and cooled at 0.1°C/sec to 25°C to allow annealing. Afterwards, 20 μL reactions were set up containing 40 nM RNA, 100 nM DNA/RNA heteroduplex, 200 U Induro RT (NEB M0681S), 1 mM dNTPs, and 0.25 μL SuperAse-In in 300mM NaCl, 5mM MgCl2, 20mM Tris pH 7.5, 5mM DTT. Reactions were assembled with all components except the dNTPs in PCR tubes and were pre-incubated for 30 min at room temperature. Afterwards, dNTPs were added and reactions incubated at 60°C for 30 minutes, after which 5M NaOH was added to 0.25 M and the tube heated to 95°C for 3 minutes to terminate the reaction. Equimolar HCl was added to neutralize the NaOH and cDNA was purified with a Minelute Reaction Cleanup Kit (Qiagen). Next, thermostable 5′ AppDNA/RNA Ligase (NEB) was used to ligate a 5′-adenylated/3′-blocked adapter containing the complement of an Illumina Read 1 primer binding site and a 12 nt random sequence to enable deduplication. The cDNA was re-purified with a MinElute column and amplified with Phusion High Fidelity DNA Polymerase (Thermo Fisher) and 200 nM of Illumina multiplex and Illumina Barcode Primers. Amplification was performed with an initial denaturation at 98°C for 5 sec followed by 15 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The products were purified with Agencourt AMPure XP beads (Beckman Coulter) with a 1.6x bead ratio to remove primers and adapter dimers.

treatment_protocol: EV purification from THP1 cells. shNS- and shDIS3L2-expressing cells were grown in suspension and treated with 1 μg/mL doxycycline for 4 days. Cells were then seeded at 1 x 107 cells per T75 flask x 15 flasks (15 mL/flask) in RPMI + 10% FBS supplemented with 1 μg/mL doxycycline and 100 nM PMA to induce macrophage differentiation. After 24 h, cells were attached to the bottoms of the flasks and were 70% confluent. Media was replaced with EV-depleted RPMI + 10% FBS supplemented with 1 μg/mL doxycycline. Media was harvested 24 h later, and cells were collected in Trizol for RNA extraction. Harvested media underwent sequential centrifugation at low and medium speeds (200 x g for 10 min x 2, 500 x g for 10 min x 2, 10,000 x g for 30 min). The supernatant was collected and sedimented in an SW 32 Ti rotor at 100,000 x g for 90 minutes. The pellet was resuspended in 100 μL PBS (Gibco 10010023) containing 0.2% BSA, diluted in 1.5 mL of 2.5 M sucrose, and transferred to a SW 40 Ti rotor tube. A discontinuous sucrose gradient of 15 0.7 mL fractions from 2 M (bottom) to 0.4 M (top) sucrose in PBS was layered over the vesicles. After sedimenting the gradients at 192,000 x g for 18 hours at 4°C, 1 mL fractions were collected. Fractions with densities between 0.12 and 0.18 g/mL (corresponding to 1.0 to 1.4 M sucrose) were pooled, diluted with 9.5 mL PBS + 0.2% ultracentrifuged BSA, and sedimented at 192,000 x g for 90 minutes. After removing the supernatant, pellets were resuspended in 130 μL PBS. 100 μL of the concentrated vesicles were treated with 20 U micrococcal nuclease for 30 min at 37°C. Digestion was quenched with EDTA (10 mM final concentration), and 345 μL TRIzol LS (Invitrogen) was immediately added.

tag: cell line

tag: cell type

value: macrophage

tag: genotype

tag: treatment

value: Doxycycline


title: THP1 EV, shNS

description:
Library name: EV_shNS
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)

value: shNS


title: Leukocytes_Lysis_P44

city: Liege

first: Gregory

last: Ehx

address: Avenue de l'Hopital, 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description:
Library name: P44Lysis
P44Lysis

data_processing:
Raw reads were counted with kallisto 0.51.1 (reverse-forward mode) using a transcriptome index built on human genome GRCh38 and Ensembl 113 annotations.
Assembly: GRCh38
Supplementary files format and content: The expression file is tab delimited with column 1 being Ensembl transcript identifiers and subsequent columns being the estimated counts of indicated samples in the first row.

molecule: polyA RNA

source_name: Blood

growth_protocol: None of the samples were expanded

extract_protocol:
RNA was extracted using the RNeasy mini kit of Qiagen.
RNA libraries were prepared with the TruSeq mRNA stranded kit of Illumina

treatment_protocol: No treatment applied

tag: tissue

value: Blood

value: Total leukocytes

value: WT

tag: isolation method

value: Red blood cell lysis


title: C2C12, FlncKO, day6, rep5

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

description:
Library name: Sample 39
FLNCKO_day6_5

data_processing:
Read quality was checked for each sample using FastQC v0.11.9.
Reads quality was evaluated using the FastQC tool (v0.11.9). Reads were aligned to the mouse GRCm38 genome using STAR v2.7.9 with GENCODE annotation. The FeatureCounts program (v2.0.3) was used to count mapped reads to the genome.
Aligned reads were count with featureCounts program v2.0.3.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each sample.

organism: Mus musculus

source_name: C2C12 cell line

growth_protocol: WT-C2C12 (wild type)and FlncKO-C2C12 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, 4.5 g/L d-Glucose, Gibco) supplemented with 10 % fetal bovine serum (FBS, Gibco), 2 mM l-glutamine, and 100 μg/ml penicillin-streptomycin (Pen-Strep, Gibco). Cells were re-plated every 48 h at a density of 100,000 cells per 100 mm dish.

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen)
RNA-libraries were constructed using TruSeq Stranded mRNA library prep kit.

treatment_protocol: Myogenic differentiation (1, 2, 4 and 6 days) was induced by culturing cells in low serum medium (DMEM, 2 mM l-glutamine, 100 μg/ml Pen-Strep) supplemented with 2 % horse serum (Gibco). During differentiation, the medium was refreshed daily.

value: C2C12 cell line

value: FlncKO

value: day 6 of myogenic differentiation


title: THP1 whole cell, shDIS3L2

description:
Library name: WC_shDIS3L2
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)


title: Patient 60, healthy, female, 38 years old

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Library name: 31179-125

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.2.4. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples in either plasma or serum were kept. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

source_name: Serum

extract_protocol:
Total RNA was extracted from serum or plasma.
Libraries were prepared with QIAseq miRNA Library Kit (QIAGEN).

value: Serum

value: BRCA mutated


title: THP1 whole cell, shNS

description:
Library name: WC_shNS
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)


title: C2C12, FlncKO, day6, rep4

description:
Library name: Sample 38
FLNCKO_day6_4


title: C2C12, FlncKO, day6, rep1

description:
Library name: Sample 37
FLNCKO_day6_1


title: C2C12, FlncKO, day4, rep5

description:
Library name: Sample 35
FLNCKO_day4_5

value: day 4 of myogenic differentiation


title: scTCR-seq of in vitro expanded HIV-1 latent clone B207 - Resting - rep1

description:
Library name: B207_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone B207

value: peripheral blood

value: HIV-1 infected

tag: batch


title: C2C12, FlncKO, day6, rep3

description:
Library name: Sample 36
FLNCKO_day6_3


title: C2C12, FlncKO, day4, rep1

description:
Library name: Sample 33
FLNCKO_day4_1


title: Patient 63, healthy, female, 47 years old

description: Library name: 31179-128


title: scTCR-seq of in vitro expanded HIV-1 latent clone 9247 - Resting - rep1

description:
Library name: 9247_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 9247 (files from 9206_R_rep01 directory), resting condition, replicate 1.

value: CD4+CD45RA- T cells


title: Patient 57, healthy, female, 48 years old

description: Library name: 31179-116


title: Patient 59, healthy, female, 67 years old

description: Library name: 31179-119

value: BRCA wild-type


title: C2C12, FlncKO, day4, rep4

description:
Library name: Sample 34
FLNCKO_day4_4


title: Patient 58, healthy, female, 48 years old

description: Library name: 31179-117


title: C2C12, FlncKO, day4, rep3

description:
Library name: Sample 32
FLNCKO_day4_3


title: C2C12, FlncKO, day2, rep5

description:
Library name: Sample 31
FLNCKO_day2_5

value: day 2 of myogenic differentiation


title: scTCR-seq of in vitro expanded HIV-1 latent clone 9247 - Activated - rep1

description:
Library name: 9247_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 9247 (files from 9206_A_rep01 directory), activated condition, replicate 1.

value: Activated (anti-CD3/CD28 + IL-2)


title: C2C12, FlncKO, day2, rep1

description:
Library name: Sample 30
FLNCKO_day2_1


title: scTCR-seq of in vitro expanded HIV-1 latent clone P301d - Activated - rep1

description:
Library name: P301_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone P301d

value: HIV-1 infected (defective provirus)


title: Patient 56, healthy, female, 50 years old

description: Library name: 31179-115


title: Patient 62, healthy, female, 55 years old

description: Library name: 31179-127


title: C2C12, FlncKO, day1, rep5

description:
Library name: Sample 28
FLNCKO_day1_5

value: day 1 of myogenic differentiation


title: Patient 55, healthy, female, 45 years old

description: Library name: 31179-114

value: Untested


title: scTCR-seq of in vitro expanded HIV-1 latent clone 603 - Resting - rep1

description:
Library name: 603_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 603

value: Resting


title: C2C12, FlncKO, day1, rep4

description:
Library name: Sample 27
FLNCKO_day1_4


title: scTCR-seq of in vitro expanded HIV-1 latent clone B207 - Activated - rep1

description:
Library name: B207_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone B207


title: Patient 54, healthy, female, 62 years old

description: Library name: 31179-110


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5203 - Activated - rep1

description:
Library name: 5203_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5203


title: C2C12, FlncKO, day1, rep1

description:
Library name: Sample 26
FLNCKO_day1_1


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5203 - Resting - rep1

description:
Library name: 5203_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5203


title: scTCR-seq of in vitro expanded HIV-1 latent clone 603 - Activated - rep1

description:
Library name: 603_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 603


title: C2C12, FlncKO, day1, rep3

description:
Library name: Sample 25
FLNCKO_day1_3


title: Patient 53, healthy, female, 57 years old

description: Library name: 31179-106


title: C2C12, FlncKO, day2, rep3

description:
Library name: Sample 29
FLNCKO_day2_3


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5125 - Resting - rep2

description:
Library name: 5125_R_rep02_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5125


title: C2C12, FlncKO, day0, rep5

description:
Library name: Sample 24
FLNCKO_day0_5

value: non-differentiated


title: C2C12, FlncKO, day0, rep4

description:
Library name: Sample 23
FLNCKO_day0_4

value: C2C12 cell line


title: C2C12, FlncKO, day0, rep1

description:
Library name: Sample 22
FLNCKO_day0_1

value: FlncKO


title: C2C12, FlncKO, day0, rep3

description:
Library name: Sample 21
FLNCKO_day0_3


title: C2C12, WT, day6, rep5

description:
Library name: Sample 20
WT_day6_5

value: Wild type

value: day 6 of myogenic differentiation


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5125 - Activated - rep2

description:
Library name: 5125_A_rep02_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5125


title: Patient 52, healthy, female, 47 years old

description: Library name: 31179-103

value: Serum


title: C2C12, WT, day6, rep1

description:
Library name: Sample 18
WT_day6_1


title: Patient 50, healthy, female, 63 years old

description: Library name: 31179-100


title: C2C12, WT, day6, rep3

description:
Library name: Sample 17
WT_day6_3


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5104 - Resting - rep1

description:
Library name: 5104_R_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5104


title: C2C12, WT, day4, rep5

description:
Library name: Sample 16
WT_day4_5

value: day 4 of myogenic differentiation


title: scTCR-seq of in vitro expanded HIV-1 latent clone 5104 - Activated - rep1

description:
Library name: 5104_A_rep01_VDJ
Single-cell V(D)J T-cell receptor (10X Genomics) sequencing of in vitro expanded HIV-1 latent clone 5104

value: peripheral blood


title: C2C12, WT, day4, rep4

description:
Library name: Sample 15
WT_day4_4


title: Patient 49, healthy, female, 50 years old

description: Library name: 31179-099

value: BRCA mutated


title: C2C12, WT, day4, rep3

description:
Library name: Sample 13
WT_day4_3


title: scRNA-seq of in vitro expanded HIV-1 latent clone P301d - Resting - rep1

description:
Library name: P301_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone P301d

library_source: transcriptomic single cell

data_processing:
Binary base call (BCL) files from the NovaSeq 6000 sequencer were demultiplexed and converted to FASTQ format using Illumina's BCLtoFastq software.
FASTQ files were processed using Cellranger multi (v8.0.1). Reads were aligned to a modified version of the human genome hg38 that included HIV specific sequences from each HIV-1 provirus clone.
TCR sequences were assembled and annotated using Cellranger multi with the 10x VDJ human reference (GRCh38-alts-ensembl-7.1.0).
Downstream analysis was performed using Seurat (v5.3.0) in Rstudio (2024.12.0). Cells were filtered (200-2500 features, <10% mitochondrial content). Data was merged, normalized, and scaled using SCTransform.
Latent clones were identified based on identical combined TRA CDR3 and TRB CDR3 nucleotide sequences.
Assembly: hg38 (modified with HIV-1 provirus sequences)
Supplementary files format and content: Filtered feature-barcode matrices and V(D)J annotation files (CSV format) and airr_rearrangement.tsv (TSV format) generated by CellRanger.

value: CD4+CD45RA- T cells


title: C2C12, WT, day2, rep5

description:
Library name: Sample 12
WT_day2_5


title: C2C12, WT, day4, rep1

description:
Library name: Sample 14
WT_day4_1


title: scRNA-seq of in vitro expanded HIV-1 latent clone P301d - Activated - rep1

description:
Library name: P301_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone P301d


title: Patient 47, healthy, female, 70 years old

description: Library name: 31179-096


title: Patient 48, healthy, female, 38 years old

description: Library name: 31179-098


title: Patient 46, healthy, female, 38 years old

description: Library name: 31179-095

value: BRCA wild-type


title: scRNA-seq of in vitro expanded HIV-1 latent clone B207 - Resting - rep1

description:
Library name: B207_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone B207

value: HIV-1 infected


title: C2C12, WT, day2, rep1

description:
Library name: Sample 10
WT_day2_1

value: day 2 of myogenic differentiation


title: Patient 51, healthy, female, 41 years old

description: Library name: 31179-101


title: C2C12, WT, day1, rep5

description:
Library name: Sample 8
WT_day1_5


title: Patient 45, healthy, female, 52 years old

description: Library name: 31179-094


title: C2C12, WT, day1, rep1

description:
Library name: Sample 6
WT_day1_1


title: C2C12, WT, day6, rep4

description:
Library name: Sample 19
WT_day6_4


title: scRNA-seq of in vitro expanded HIV-1 latent clone B207 - Activated - rep1

description:
Library name: B207_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone B207

value: Activated (anti-CD3/CD28 + IL-2)


title: scRNA-seq of in vitro expanded HIV-1 latent clone 9247 - Resting - rep1

description:
Library name: 9247_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 9247 (files from 9206_R_rep01 directory), resting condition, replicate 1.


title: C2C12, WT, day1, rep4

description:
Library name: Sample 7
WT_day1_4

value: day 1 of myogenic differentiation


title: C2C12, WT, day1, rep3

description:
Library name: Sample 5
WT_day1_3


title: Patient 44, healthy, female, 39 years old

description: Library name: 31179-093

value: RAD51 mutated


title: scRNA-seq of in vitro expanded HIV-1 latent clone 9247 - Activated - rep1

description:
Library name: 9247_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 9247 (files from 9206_A_rep01 directory), activated condition, replicate 1.


title: Patient 43, healthy, female, 55 years old

description: Library name: 31179-090


title: C2C12, WT, day0, rep1

description:
Library name: Sample 2
WT_day0_1


title: C2C12, WT, day0, rep4

description:
Library name: Sample 3
WT_day0_4


title: Patient 42, healthy, female, 38 years old

description: Library name: 31179-085


title: scRNA-seq of in vitro expanded HIV-1 latent clone 603 - Resting - rep1

description:
Library name: 603_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 603

value: Resting


title: C2C12, WT, day2, rep4

description:
Library name: Sample 11
WT_day2_4


title: scRNA-seq of in vitro expanded HIV-1 latent clone 603 - Activated - rep1

description:
Library name: 603_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 603


title: C2C12, WT, day0, rep3

description:
Library name: Sample 1
WT_day0_3

value: non-differentiated


title: Patient 41, healthy, female, 40 years old

description: Library name: 31179-083


title: Patient 40, healthy, female, 42 years old

description: Library name: 31179-081


title: Mouse ENS 63

city: New York

first: Robert

last: Lovelett

address: 430 E 29th Street, 10th Floor

institute: Kallyope

description:
Library name: K_10X_mENS063
10X Genomics

data_processing:
Demultiplexed and counted using CellRanger 6.1 with the --include_introns flag set to True
Assembly: A modified mm10 where each gene was extended in the 3' direction up to 5000 bp, unless it conflicted with another gene on either strand
Supplementary files format and content: Raw and filtered count matrices output from CellRanger Count as h5 files

source_name: Myenteric layer of Antrum

extract_protocol:
Snap frozen myenteric tissue was pulverized and then dounce homogenized with in CST buffer, filtered through a 40µm filter, spun down at 800g for 8 minutes at 4°C, and blocked in ST-SB buffer for 10 minutes. Nuclei were inubated in directly conjugated HuC/D antibody (1:200) for 30 minutes at 4°C in the dark. Homogenates were then washed with additional ST buffer, spun at 800g for 8 min at 4°C, supernatant was removed, and nuclei were resuspended in ST-SB and filtered through a 40µm Flowmi filter. Single nuclei were sorted on a Sony SH800 as AF488+ directly into a tube with 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 reverse transcription master mix without RT Enzyme C. RT Enzyme C was added when sorting was complete and the nuclei in master mix was then loaded into a 10X Chip G for barcoding and droplet generation. The sample protocol was done for submucosal tissue but some buffers were changed. TSP was used in the dounce homogenization step, blocking and staining was performed in SP-SB buffer, and washes were done in SPMB buffer.
Used 10x Genomics 3' v3.1 kit. Enzyme C was added to the RT reaction after sorting and before GEM generation. Manufacturer instructions were followed for reverse transcription, cDNA amplification, fragmentation, ligation and sample single indexing PCR.

value: Myenteric layer of Antrum


title: C2C12, WT, day2, rep3

description:
Library name: Sample 9
WT_day2_3

value: C2C12 cell line


title: Mouse ENS 61

description:
Library name: K_10X_mENS061
10X Genomics


title: Mouse ENS 60

description:
Library name: K_10X_mENS060
10X Genomics

source_name: Submucosal layer of Whole Small Intestine


title: Patient 39, healthy, female, 37 years old

description: Library name: 31179-078


title: Mouse ENS 59

description:
Library name: K_10X_mENS059
10X Genomics

value: Submucosal layer of Whole Small Intestine


title: C2C12, WT, day0, rep5

description:
Library name: Sample 4
WT_day0_5

value: Wild type


title: Patient 38, healthy, female, 43 years old

description: Library name: 31179-074

value: Serum


title: Mouse ENS 58

description:
Library name: K_10X_mENS058
10X Genomics

source_name: Myenteric layer of Corpus

value: Myenteric layer of Corpus


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5125 - Resting - rep2

description:
Library name: 5125_R_rep02_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5125

value: peripheral blood


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5125 - Activated - rep2

description:
Library name: 5125_A_rep02_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5125


title: Patient 37, healthy, female, 38 years old

description: Library name: 31179-072

value: BRCA mutated


title: RAW264.7 EV, shDis3l2, miRNA-seq

description: Library name: EV_shDis3l2

data_processing:
Adapter sequences were trimmed with CutAdapt. After trimming, reads < 15 nt were discarded.
Transcript reads were quantified by Salmon utilizing sequences from GENCODE vM25 and high confidence tRNA sequences (GtRNAdb).
Reads were mapped to the mouse genome (GRCm38) using NovoAlign (Novocraft). Parameters included: gap opening penalty of 20 (-g), gap penalty of 4 (-x), and soft-clip penalty of 0. Reads were multi-mapped, allowing up to 100 mapping events, and separately mapped to a single best mapping site.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were cultured at 37°C with 5% CO2 and maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin-streptomycin, and 2 mM L-glutamine.

extract_protocol:
EV RNA was extracted with a Direct-Zol RNA Miniprep Kit and eluted into 25 μL water. Whole cell RNA was extracted from Trizol.
miRNA libraries were prepared from total cell and EV RNA by the NCI Center for Cancer Research (CCR) sequencing facility using the QIAseq miRNA library kit (Qiagen 331502), according to the manufacturer’s instructions. Samples were sequenced on an Illumina NextSeq 2000 P1 cell, obtaining 50 nt sequencing reads.

treatment_protocol: EV purification from RAW 264.7 cells. Cells were seeded at 1.5 x 106 cells/T75 flask x 15 flasks in DMEM supplemented with 1 μg/mL doxycycline, which was replenished daily. After 3 days, media was replaced with DMEM supplemented with doxycycline and 10% EV-depleted FBS (made by spinning 30% FBS at 100,00xg overnight to pellet vesicles).Media was harvested after 24h, and cells were collected in Trizol for RNA extraction. Harvested media underwent sequential centrifugation at low and medium speeds (200 x g for 10 min x 2, 500 x g for 10 min x 2, 10,000 x g for 30 min). The supernatant was collected and sedimented in an SW 32 Ti rotor at 100,000 x g for 90 minutes. The pellet was resuspended in 100 μL PBS (Gibco 10010023) containing 0.2% BSA, diluted in 1.5 mL of 2.5 M sucrose, and transferred to a SW 40 Ti rotor tube. A discontinuous sucrose gradient of 15 0.7 mL fractions from 2 M (bottom) to 0.4 M (top) sucrose in PBS was layered over the vesicles. After sedimenting the gradients at 192,000 x g for 18 hours at 4°C, 1 mL fractions were collected. Fractions with densities between 0.12 and 0.18 g/mL (corresponding to 1.0 to 1.4 M sucrose) were pooled, diluted with 9.5 mL PBS + 0.2% ultracentrifuged BSA, and sedimented at 192,000 x g for 90 minutes. After removing the supernatant, pellets were resuspended in 130 μL PBS. 100 μL of the concentrated vesicles were treated with 20 U micrococcal nuclease for 30 min at 37°C. Digestion was quenched with EDTA (10 mM final concentration), and 345 μL TRIzol LS (Invitrogen) was immediately added.

value: macrophage

value: Doxycycline


title: RAW264.7 EV, shNS, miRNA-seq

description: Library name: EV_shNS

value: shNS


title: RAW264.7 whole cell, shNS, miRNA-seq

description: Library name: WC_shNS


title: RAW264.7 EV, shDis3l2 + Dis3l2 D389N

description:
Library name: EV shDis3l2 + Dis3l2 D389N
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
EV_shDis3l2+D389N

data_processing:
Illumina adapter sequences were trimmed with CutAdapt. After trimming, reads < 15 nt were discarded.
Transcript reads were quantified by Salmon utilizing sequences from GENCODE vM25 and high confidence tRNA sequences (GtRNAdb). For coding RNAs, separate sequences for each region of a transcript (exons, introns, and UTRs) were utilized to be able to analyze the differential enrichment of these elements.
UMI sequences were extracted from Read 1 using UMI-tools.
Reads were mapped to the mouse genome (GRCm38) using NovoAlign (Novocraft). Parameters included: gap opening penalty of 20 (-g), gap penalty of 4 (-x), and soft-clip penalty of 0. Reads were mapped to a single best mapping site and separateliy multi-mapped.
Reads were deduplicated using UMI-tools
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

treatment_protocol: EV purification from RAW 264.7 cells. Cells were seeded at 1.5 x 106 cells/T75 flask x 15 flasks in DMEM supplemented with 1 μg/mL doxycycline, which was replenished daily. After 3 days, media was replaced with DMEM supplemented with doxycycline and 10% EV-depleted FBS (made by spinning 30% FBS at 100,00xg overnight to pellet vesicles).Media was harvested after 24h, and cells were collected in Trizol for RNA extraction. Harvested media underwent sequential centrifugation at low and medium speeds (200 x g for 10 min x 2, 500 x g for 10 min x 2, 10,000 x g for 30 min). The supernatant was collected and sedimented in an SW 32 Ti rotor at 100,000 x g for 90 minutes. The pellet was resuspended in 100 μL PBS (Gibco 10010023) containing 0.2% BSA, diluted in 1.5 mL of 2.5 M sucrose, and transferred to a SW 40 Ti rotor tube. A discontinuous sucrose gradient of 15 0.7 mL fractions from 2 M (bottom) to 0.4 M (top) sucrose in PBS was layered over the vesicles. After sedimenting the gradients at 192,000 x g for 18 hours at 4°C, 1 mL fractions were collected. Fractions with densities between 0.12 and 0.18 g/mL (corresponding to 1.0 to 1.4 M sucrose) were pooled, diluted with 9.5 mL PBS + 0.2% ultracentrifuged BSA, and sedimented at 192,000 x g for 90 minutes. After removing the supernatant, pellets were resuspended in 130 μL PBS. 100uL of the concentrated vesicles were treated with 20 U micrococcal nuclease for 30 min at 37°C. Digestion was quenched with EDTA (10 mM final concentration), and 345 μL TRIzol LS (Invitrogen) was immediately added.

value: shDis3l2 + Dis3l2r D389N


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5104 - Activated - rep1

description:
Library name: 5104_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5104

value: CD4+CD45RA- T cells

value: HIV-1 infected

value: Activated (anti-CD3/CD28 + IL-2)


title: Patient 35, healthy, female, 44 years old

description: Library name: 31179-070

value: BRCA wild-type


title: RAW264.7 whole cell, shDis3l2, miRNA-seq

description: Library name: WC_shDis3l2


title: RAW264.7 EV, shDis3l2 + Vector

description:
Library name: EV shDis3l2 + Vector
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
EV_shDis3l2+Vector

value: shDis3l2 + Vector


title: Patient 34, healthy, female, 60 years old

description: Library name: 31179-069


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5203 - Resting - rep1

description:
Library name: 5203_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5203

value: Resting


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5203 - Activated - rep1

description:
Library name: 5203_A_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5203


title: Patient 36, healthy, female, 49 years old

description: Library name: 31179-071


title: RAW264.7 EV, shDis3l2 + Dis3l2r

description:
Library name: EV shDis3l2 + Dis3l2r
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
EV_shDis3l2+Dis3l2r

value: shDis3l2 + Dis3l2r


title: RAW264.7 EV, shDis3l2

description:
Library name: EV shDis3l2
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
EV_shDis3l2


title: Patient 33, healthy, female, 53 years old

description: Library name: 31179-067


title: AsPC1, KDM4C KO1, H3K36me3, rep3

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description:
Library name: 6-2aI-3_K36me3
S2-100 Xp (50nt PE)

library_source: genomic

data_processing:
Raw FASTQ files were processed using the ENCODE ChIP-seq pipeline2, and peaks were identified with MACS2 based on the aligned data.
Assembly: hg38
Supplementary files format and content: Gzipped BED

molecule: genomic DNA

growth_protocol: AsPC1 cells were maintained in RPMI 1640 (Gibco/ThermoFisher), supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL) under standard cell culture conditions.The cell lines were routinely tested and confirmed to be Mycoplasma free using MycoAlert® Mycoplasma Detection Kit (Lonza).

extract_protocol:
AsPC1 parental and KDM4C knockout cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 5 minutes.  Chromatin was prepared by sonication to generate DNA fragments ranging from 200-600bp. ChIP was performed overnight using DiaMag Protein A-conjugated antibodies against H3K27ac (ab4729, Abcam), and H3K36me3 (ab9050, Abcam).   Immunocomplexes were collected the following day using DynaMag, then washed, and reverse crosslinked overnight, followed by DNA extraction.
Libraries were prepared using NEB Ultra II DNA library prep kit (New England Biolabs), according to the manufacturer's protocol.

treatment_protocol: For KDM4C knockout: the genomic sequence for the KDM4C gene was downloaded from the UCSC genome browser, and sgRNA cassettes targeting exon2 of human KDM4C were designed using the CRISPR design tool (http://crispr.mit.edu), and cloned into pspCas9 plasmid vector (5'-TAGTGAATCGAACTTCTGG-3'). AsPC1 cells were transfected with sgRNA Cas9 plasmid and selected under 2 μg/ml puromycin for 5 days before the cells were serially diluted into 96 well plates to form single colony clones. Knock-out clones were then expanded, and successful gene editing was confirmed using T7-endonuclease assay. Biallelic deletion of KDM4C was validated using in vitro transcription (Guide-it™ Genotype Confirmation Kit, Takara), and frameshift mutation was confirmed by sequencing.

value: Human pancreatic ductal adenocarcinoma

value: KDM4C knockout


title: AsPC1, KDM4C KO1, H3K27Ac, rep3

description:
Library name: 6-2aI-3_K27ac
S2-100 Xp (50nt PE)


title: Bleo_2W_WholeLung_1 (biological replicate 1)

city: New Orleans

first: Yong

last: Zhou

state: LA

address: 333 S Liberty St

department: Medicine - Pulmonary Diseases

institute: Tulane University

description:
Library name: Lung_AAVGFP_S1
Single-cell RNA sequencing of mouse lung 2 weeks after bleomycin injury (biological replicate 1). EpCAM+ and stromal populations combined (WholeLung).

data_processing:
Raw sequencing data were processed using Cell Ranger v9.0.0 (10x Genomics).
Reads were aligned to the mouse reference genome GRCm39-2020-A using the Chromium Mouse Transcriptome Probe Set v1.1.1.
Filtered gene-by-cell matrices were generated using Cell Ranger “count” and used for downstream analysis.
Downstream analyses were performed with Scanpy v1.9.0, including quality filtering (low-gene and high-mitochondrial transcript removal), normalization to 10,000 counts per cell, log-transformation, PCA, neighborhood graph construction, Leiden clustering (resolution 0.8), and UMAP visualization.
Differential expression was assessed using the Wilcoxon rank-sum test (Scanpy rank-genes-groups), with Benjamini–Hochberg FDR correction. Plots were generated using Seaborn v0.12 and Matplotlib v3.7.
Assembly: GRCm39 (Ensembl 2020-A, 10x Chromium Mouse Transcriptome Probe Set v1.1.1)
Supplementary files format and content: Processed data include the 10x Cell Ranger output file filtered_feature_bc_matrix.h5, which contains gene-by-cell UMI count matrices in HDF5 format, and filtered_feature_bc_matrix.tar.gz, a plain-text archive of the same data (matrix.mtx, features.tsv, barcodes.tsv).
Supplementary files format and content: These files provide the complete quantitative expression values for all detected genes across all cells in the Bleo_2W_WholeLung_1 sample.

source_name: Lung

extract_protocol:
Viable lung cells were enzymatically dissociated into single-cell suspensions, treated with the 10x Genomics proprietary crosslinking reagent to preserve RNA integrity, and stored at –80 °C until all experimental groups were collected.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Fixed RNA Profiling (scRNA-seq Flex) chemistry following the manufacturer’s protocol. Target transcript capture and sample barcoding were performed using the Chromium Mouse Transcriptome Probe Set v1.0.1 with an additional custom probe targeting EGFP. Barcoded cells were encapsulated into Gel Bead-in-Emulsions (GEMs) using the Chromium Chip Q. Inside each GEM, probe pairs were ligated, and unique molecular identifiers (UMIs), GEM barcodes, and partial Read 1 sequences were incorporated through polymerase extension. Libraries were PCR-amplified and indexed to generate sequencing-ready libraries containing Illumina P5/P7 adapters. Library quality was assessed by Agilent Bioanalyzer and Qubit fluorometer prior to sequencing.

value: Lung

value: Whole lung single-cell suspension

value: Wild type

value: Bleomycin for 2 weeks, AAV-Sprr1a-sesR-EGFP infection


title: Mouse ENS 57

description:
Library name: K_10X_mENS057
10X Genomics

source_name: Myenteric layer of Ileum

value: Myenteric layer of Ileum


title: AsPC1, KDM4C KO1, H3K36me3, rep2

description:
Library name: 5-2aI-2_K36me3
S2-100 Xp (50nt PE)


title: Mouse ENS 62

description:
Library name: K_10X_mENS062
10X Genomics

source_name: Myenteric layer of Fundus

value: Myenteric layer of Fundus


title: RAW264.7 whole cell, shDis3l2

description:
Library name: WC shDis3l2
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
WC_shDis3l2

value: macrophage

value: Doxycycline


title: Patient 32, healthy, female, 39 years old

description: Library name: 31179-066

value: Serum

value: Untested


title: PCa16 organoids, inactive compound, 72h, scRNA

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: Library name: PCa16-A858_scRNA

data_processing:
RNA-seq: Sequencing reads were aligned against the human genome hg38 with STAR v.2.7.3a. Gene counts were generated with RSEM v.1.3.2, whose index was generated using the GENCODE v33 primary assembly annotation.
ChIP-seq: Fastq files were aligned on the hg38 human genome reference using Bowtie2  (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s MarkDuplicates  (v1.126) function, followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.26.0), followed by the generation of bigwig  (wigToBigWig v377) files. Peaks were called with macs2 (v2.2.4) for each treatment sample using a pooled input alignment (.bam file) as control. Downstream analyses were performed with DiffBind v3.11.1 with default parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
ATAC-seq: ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline (version 1). Reads were trimmed of adapters using cutadapt (version 1.9.1) and mapped to hg38 using Bowtie 2 (version 2.2.6). Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strands and −5 bp for negative strands. TagAlign files were used to call peaks using MACS2 (version 2.1.0), and those peaks with P < 1 × 10−6 were retained for differential analysis with DiffBind (version 3.0.13) or the bamCount function of the R package bamsignals (version 1.24.0). Differential accessibility analysis was performed using either the R package DiffBind (version 3.0.13) or DESeq2 (version 1.32.0). The genomic distribution of differential peaks was annotated with ChIPpeakAnno (version 3.24.1). Bigwigs corresponding to a fold change against the background control were generated by MACS2 and used to generate heatmaps with the heatmap function of deepTools (version 3.5.0).
scRNA: Harvested cells were stained with 100ng/ml DAPI to stain dead cells. Using a cell sorter (conducted by Flow Cytometry Core, DBMR, Bern) and the recommended settings (Single Cell Discoveries B.V.), DAPI-negative cells were sorted as single cells in 376 wells of four 384-well plates containing immersion oil per condition. Resulting in a theoretical cell number of 1504 cells per condition. All post-harvesting steps were performed at 4°C. Plates were snap-frozen on dry ice for 15 minutes and sent out for sequencing at Single Cell Discoveries B.V. Data were analyzed using the Seurat package v.4.3.0. Cell QC filtering was done using the following thresholds: nCount > 4000, nFeature > 1000, percent.mito < 25, log10GenesPerUMI > 0.85. Cell phase was regressed out using the Seurat function ScaleData(seur.filt, vars.to.regress = c("S.Score", "G2M.Score")).
PRO-cap: Sequencing data was trimmed with fastp version 0.22.0 and then aligned to the human genome (hg38) concatenated with EBV and human rDNA sequences (GenBank U13369.1) using STAR V2.7.10b. Raw alignments were filtered with samtools version 1.18 and deduplicated using umi_tools version 1.1.2. Alignments were converted to bigwig files using bedtools version 2.30.0 and kentUtils bedGraphToBigWig V2.8. Peaks were called using PINTS version 1.1.6. Divergent peaks not overlapping with TSS +/-500 bp (GENCODE V37) were regarded as candidate enhancer RNAs.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tables of gene counts. Tab-delimited text files.
Supplementary files format and content: ChIP-seq: BigWig files. Peak regions text files. Sample metadata text file.
Supplementary files format and content: ATAC-seq: BigWig files. Peak regions text files. Sample metadata text file.
Supplementary files format and content: scRNA: Raw cell counts and filtered cell counts as RDS files containing Seurat objects.
Supplementary files format and content: PRO-cap: BigWig files. Peak bed files.

source_name: organoid

growth_protocol: Metastatic prostate cancer biopsy pieces were minced and digested in 5 ml of 5 mg/ml collagenase type II (Invitrogen) in Advanced DMEM/F12 (ADMEM/F12) and digested for 0.5–2 hr at 37°C with gently shaking. Dissociated cells were washed and seeded in growth factor reduced Matrigel (BD biosciences).

extract_protocol:
RNA-seq: RNA was extracted using the RNeasy Kit (Qiagen)
Standard Illumina library
scRNA: 1x10e6 cells were harvested in PBS. SORT-seq was performed using Single Cell Discoveries (SCD) service.
ATAC-seq: Performed from 50’000 cryo-preserved cells per condition.
PRO-cap: Approximately 30 million cells were processed per sample. Library preparations for two biological replicates were performed separately. Cells were permeabilized, and run-on reactions were performed. After RNA isolation, two adaptor ligations and reverse transcription were performed with custom adaptors. Between adaptor ligations, cap state selection reactions were carried out using a series of enzymatic steps. RNA washes, phenol:chloroform extractions and ethanol precipitations were conducted between reactions. All steps were performed under RNase-free conditions.

treatment_protocol: organoids were treated with A858 or A947 (1µM)

value: organoid

value: prostate tumor

value: inactive compound


title: AsPC1, KDM4C KO1, H3K27Ac, rep2

description:
Library name: 5-2aI-2_K27ac
S2-100 Xp (50nt PE)


title: PCa16 organoids, active compound, 72h, scRNA

description: Library name: PCa16-A947_scRNA

value: SMARCA2/SMARCA4 targeting PROTAC


title: Patient 30, healthy, female, 58 years old

description: Library name: 31179-063

value: BRCA wild-type


title: Patient 31, healthy, female, 37 years old

description: Library name: 31179-064

value: BRCA mutated


title: scRNA-seq of in vitro expanded HIV-1 latent clone 5104 - Resting - rep1

description:
Library name: 5104_R_rep01_RNA
5' Single-cell gene expression (10X Genomics) of in vitro expanded HIV-1 latent clone 5104

value: peripheral blood

value: CD4+CD45RA- T cells

value: HIV-1 infected

value: Resting


title: WCM1078 organoids, inactive compound, 72h, scRNA

description: Library name: WCM1078-A858_scRNA


title: WCM1078 organoids, active compound, 72h, scRNA

description: Library name: WCM1078-A947_scRNA


title: Patient 45, female, 57 years old, breast cancer, serum

description: Library name: 30223-100

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.3.0. Contamination filtration was switched on with minor modification added to allow for detailed quantification of contaminants. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples in either plasma or serum were kept. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

source_name: serum

value: serum

tag: Sex

value: female

tag: age

value: 57 years old

tag: disease

value: breast cancer


title: RAW264.7 whole cell, shNS

description:
Library name: WC shNS
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
WC_shNS

value: macrophage

value: shNS

value: Doxycycline


title: RAW264.7 EV, shNS

description:
Library name: EV shNS
RNA-seq protocol using Thermostable Group II Intron Reverse Transcriptases (TGIRTs)
EV_shNS


title: Patient 1, female, 69 years old, healthy, serum

description: Library name: 30223-091

value: 69 years old

value: healthy


title: AsPC1, KDM4C KO1, H3K27Ac, rep1

description:
Library name: 4-2aI-1_K27ac
S2-100 Xp (50nt PE)

value: Human pancreatic ductal adenocarcinoma

value: KDM4C knockout


title: Patient 40, female, 37 years old, ovarian cancer, serum

description: Library name: 30223-099

value: 37 years old

value: ovarian cancer


title: Patient 28, healthy, female, 37 years old

description: Library name: 31179-061

value: Serum

value: BRCA mutated


title: AsPC1, KDM4C KO1, H3K36me3, rep1

description:
Library name: 4-2aI-1_K36me3
S2-100 Xp (50nt PE)


title: Patient 49, female, 60 years old, healthy, serum

description: Library name: 30223-080

value: 60 years old


title: Patient 29, healthy, female, 41 years old

description: Library name: 31179-062

value: BRCA wild-type


title: Patient 27, healthy, female, 70 years old

description: Library name: 31179-059


title: AsPC1, KDM4C KO1

description:
Library name: 4-2aI-1_Input
S2-100 Xp (50nt PE)


title: Patient 26, healthy, female, 44 years old

description: Library name: 31179-058


title: AsPC1, KDM4C WT, H3K36me3, rep2

description:
Library name: 2-AspcI-Flag-2_K36me3
S2-100 Xp (50nt PE)

value: WT


title: Patient 77, female, 43 years old, healthy, serum

description: Library name: 30223-052

value: serum

value: female

value: 43 years old


title: Patient 41, female, 63 years old, ovarian cancer, serum

description: Library name: 30223-051

value: 63 years old


title: Patient 31, female, 73 years old, healthy, serum

description: Library name: 30223-049

value: 73 years old


title: AsPC1, KDM4C WT, H3K36me3, rep1

description:
Library name: 1-AspcI-Flag-1_K36me3
S2-100 Xp (50nt PE)


title: AsPC1, KDM4C WT, H3K27Ac, rep2

description:
Library name: 2-AspcI-Flag-2_K27ac
S2-100 Xp (50nt PE)


title: Patient 75, female, 60 years old, healthy, serum

description: Library name: 30223-095

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.3.0. Contamination filtration was switched on with minor modification added to allow for detailed quantification of contaminants. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples kept for further analysis. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

extract_protocol:
Total RNA was extracted from serum.
Libraries were prepared according to the manufacturer’s instructions.


title: AsPC1, KDM4C WT, H3K27Ac, rep3

description:
Library name: 3-AspcI-Flag-3_K27ac
S2-100 Xp (50nt PE)


title: AsPC1, KDM4C WT, H3K27Ac, rep1

description:
Library name: 1-AspcI-Flag-1_K27ac
S2-100 Xp (50nt PE)


title: AsPC1, KDM4C WT

description:
Library name: 1-AspcI-Flag-1_Input
S2-100 Xp (50nt PE)


title: Patient 78, female, 56 years old, healthy, serum

description: Library name: 30223-038

value: 56 years old


title: Patient 22, healthy, female, 58 years old

description: Library name: 31179-049


title: Patient 28, female, 81 years old, healthy, serum

description: Library name: 30223-037

value: 81 years old


title: Patient 74, female, 50 years old, healthy, serum

description: Library name: 30223-092

value: 50 years old


title: Patient 27, female, 73 years old, healthy, serum

description: Library name: 30223-034

value: healthy


title: Patient 25, healthy, female, 42 years old

description: Library name: 31179-057


title: Patient 42, female, 66 years old, ovarian cancer, serum

description: Library name: 30223-033

value: 66 years old


title: Patient 56, female, 33 years old, healthy, serum

description: Library name: 30223-090

value: 33 years old


title: Patient 21, healthy, female, 38 years old

description: Library name: 31179-048


title: Patient 20, healthy, female, 40 years old

description: Library name: 31179-047


title: Patient 17, female, 68 years old, healthy, serum

description: Library name: 30223-098

value: 68 years old


title: Patient 24, healthy, female, 35 years old

description: Library name: 31179-055

value: Serum


title: Patient 23, healthy, female, 65 years old

description: Library name: 31179-053

value: BRCA mutated


title: AsPC1, shKDM4C-1, Day 90, rep2

description:
Library name: AsPC1_sh1_late_2
PE150 (12 G raw data per sample)

data_processing:
Sequencing reads were mapped using STAR against the Homo sapiens genome (UCSC hg38), and gene level quantification was performed with featureCounts
Assembly: hg38
Supplementary files format and content: CSV file with featureCounts for all the samples combined

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy Mini Kit (Qiagen), following the manufacturer's protocol
Libraries were prepared using Illumina TruSeq® Stranded Total RNA kit, according to the manufacturer's protocol.

treatment_protocol: For KDM4C knockout: the genomic sequence for the KDM4C gene was downloaded from the UCSC genome browser, and sgRNA cassettes targeting exon2 of human KDM4C were designed using the CRISPR design tool (http://crispr.mit.edu), and cloned into pspCas9 plasmid vector (5'-TAGTGAATCGAACTTCTGG-3'). AsPC1 cells were transfected with sgRNA Cas9 plasmid and selected under 2 μg/ml puromycin for 5 days before the cells were serially diluted into 96 well plates to form single colony clones. Knock-out clones were then expanded, and successful gene editing was confirmed using T7-endonuclease assay. Biallelic deletion of KDM4C was validated using in vitro transcription (Guide-it™ Genotype Confirmation Kit, Takara), and frameshift mutation was confirmed by sequencing. For lentiviral shRNA knockdown of KDM4C: shRNAs targeting human KDM4C were obtained from Horizon Discovery and cloned into pLKO.1 vector (5'-TAGTGAATCGAACTTCTGG-3'). Lentivirus was produced in HEK293 cells by transfecting the vectors with psPAX2 and PMD2.G packaging system. Virus particles were collected after 48 and 72 hours and concentrated using a Lenti-X concentrator (Takara). Cells were transduced with the lentivirus carrying shRNA or empty vector as a control using polybrene, then selected under 2 μg/ml puromycin for five days.

value: Human pancreatic ductal adenocarcinoma

value: KDM4C knockdown


title: Patient 39, female, 43 years old, healthy, serum

description: Library name: 30223-097


title: Patient 33, female, 66 years old, healthy, serum

description: Library name: 30223-096


title: Patient 58, female, 31 years old, healthy, serum

description: Library name: 30223-094

value: 31 years old


title: AsPC1, KDM4C WT, H3K36me3, rep3

description:
Library name: 3-AspcI-Flag-3_K36me3
S2-100 Xp (50nt PE)

value: WT


title: Patient 3, female, 61 years old, healthy, serum

description: Library name: 30223-089

value: serum

value: female

value: 61 years old


title: Patient 76, female, 57 years old, healthy, serum

description: Library name: 30223-076

value: 57 years old


title: AsPC1, shKDM4C-1, Day 90, rep1

description:
Library name: AsPC1_sh1_late_1
PE150 (12 G raw data per sample)


title: Patient 21, female, 39 years old, healthy, serum

description: Library name: 30223-093

value: 39 years old


title: Patient 51, female, 32 years old, healthy, serum

description: Library name: 30223-087

value: 32 years old


title: AsPC1, shKDM4C-1, Day 90, rep3

description:
Library name: AsPC1_sh1_late_3
PE150 (12 G raw data per sample)


title: Patient 14, female, 60 years old, healthy, serum

description: Library name: 30223-075

value: 60 years old


title: Patient 34, female, 55 years old, healthy, serum

description: Library name: 30223-073

value: 55 years old


title: AsPC1, shNT, Day 90, rep3

description:
Library name: AsPC1_shNT_late_3
PE150 (12 G raw data per sample)

value: non-targeting hairpin control


title: Patient 32, female, 50 years old, healthy, serum

description: Library name: 30223-072

value: 50 years old


title: Patient 19, healthy, female, 43 years old

description: Library name: 31179-046

value: BRCA wild-type


title: Patient 16, healthy, female, 55 years old

description: Library name: 31179-039

value: Serum


title: Patient 25, female, 43 years old, healthy, serum

description: Library name: 30223-082

value: 43 years old


title: Patient 18, healthy, female, 46 years old

description: Library name: 31179-043

value: BRCA mutated


title: AsPC1, shNT, Day 90, rep2

description:
Library name: AsPC1_shNT_late_2
PE150 (12 G raw data per sample)

value: Human pancreatic ductal adenocarcinoma


title: Patient 16, female, 49 years old, healthy, serum

description: Library name: 30223-070

value: 49 years old


title: Patient 5, female, 42 years old, healthy, serum

description: Library name: 30223-071

value: 42 years old


title: AsPC1, shNT, Day 90, rep1

description:
Library name: AsPC1_shNT_late_1
PE150 (12 G raw data per sample)


title: Patient 71, female, 30 years old, healthy, serum

description: Library name: 30223-068

value: serum

value: 30 years old


title: SNU1 cells ; I6 60 microM ;Replicate 2

city: Madrid

first: Luis

last: del Peso

email: luis.peso@uam.es, lpeso@iib.uam.es

state: Madrid

address: Arturo Duperier 4

department: Biochemistry

country: Spain

institute: Universidad Autonoma de Madrid

description: Library name: GC-SNU1-I6-2

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the raw reads.
Adapters were removed from reads with cutadapt version 3.5 and aligned to the human genome (GRCh38, version 40; GENCODE, April 11, 2022) using HISAT2 (version 2.2.1). Gene-level counts were obtained from the resulting BAM files using htseq-count (version 2.0.4), with annotations from the same genome version and using the “reverse” option for strandedness.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file contain read counts per gene and sample.

growth_protocol: The human gastric adenocarcinoma cell lines MKN45 (poorly differentiated; DSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) and SNU1 (ATCC) were cultured in RPMI 1640 (Sigma); AGS GC cells (primary tumor; ATCC/LGC Standards, Spain) were cultured in HAM’s F-12 + AA’s (Gibco), according to the specifications of the manufacturer’s datasheet. Pancreatic cell line PANC1 (ATCC) was cultured in RPMI 1640 (Sigma). PDAC patient-derived xenografts (PDAC PDX) PDAC PDXs were obtained from Dr. Manuel Hidalgo under a Material Transfer Agreement with the Spanish National Cancer Centre (CNIO), Madrid, Spain (Reference no. I409181220BSMH). To establish low-passage primary PDX-derived in vitro cultures, PDX tumors were minced, enzymatically digested with collagenase (Stem Cell Technologies) for 60 min at 37°C, clarified via multiple rounds of filter purification with 100μm and 40μm Fisherbrand™ Sterile Cell Strainers (FisherScientific, Cat no. 11517532 and 11587522), and after centrifugation for 5 min at 1800 rpm, the cell pellets were resuspended and cultured in RPMI. PDAC PDX-derived cultures are referred to by a random number designation (e.g., Panc185 or Panc354). All the culture media were supplemented with 10% FBS (v/v), 2 mM L-Glutamine, Fungizone (2.5 μg/mL) and Gentamicin (0.035 mg/mL). Cultures were kept at 37°C, 5% CO2, and 95% humidity. Mycoplasma contamination tests are frequently run in our laboratory. Experiments were performed between passage two to eight.

extract_protocol:
Total RNA was isolated by using Tri-Reagent (Life Technologies), according to the manufacturer’s instructions. (RNA Integrity Number > 8.0).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer’s protocolos.

treatment_protocol: Cells were treated with the compounds at the indicated doses or vehicle (DMSO) for 24h.

value: gastric carcinoma

value: I6 60 microM


title: Patient 53, female, 56 years old, healthy, serum

description: Library name: 30223-066

value: female

value: 56 years old


title: Patient 15, healthy, female, 54 years old

description: Library name: 31179-037


title: Patient 46, female, 49 years old, healthy, serum

description: Library name: 30223-064


title: Patient 14, healthy, female, 52 years old

description: Library name: 31179-034


title: Patient 50, female, 53 years old, healthy, serum

description: Library name: 30223-067

value: 53 years old


title: Patient 2, female, 64 years old, healthy, serum

description: Library name: 30223-063

value: 64 years old


title: SNU1 cells ; I6 60 microM ;Replicate 1

description: Library name: GC-SNU1-I6-1


title: Patient 9, female, 27 years old, healthy, serum

description: Library name: 30223-062

value: 27 years old


title: Patient 13, healthy, female, 45 years old

description: Library name: 31179-033


title: Patient 12, healthy, female, 42 years old

description: Library name: 31179-032


title: Patient 13, female, 52 years old, healthy, serum

description: Library name: 30223-059

value: 52 years old


title: Patient 10, female, 42 years old, healthy, serum

description: Library name: 30223-057


title: Patient 11, healthy, female, 46 years old

description: Library name: 31179-030


title: Patient 29, female, 35 years old, healthy, serum

description: Library name: 30223-058

value: 35 years old


title: SNU1 cells ; I5 15 microM ;Replicate 1

description: Library name: GC-SNU1-I5-1

value: I5 15 microM


title: Patient 19, female, 28 years old, healthy, serum

description: Library name: 30223-055

value: 28 years old


title: SNU1 cells ; Vehicle  ;Replicate 2

description: Library name: GC-SNU1-CNT-2

value: Vehicle


title: Patient 70, female, 45 years old, healthy, serum

description: Library name: 30223-069

value: 45 years old


title: Patient 10, healthy, female, 39 years old

description: Library name: 31179-026

value: Serum

value: PALB2 mutated


title: Patient 55, female, 44 years old, healthy, serum

description: Library name: 30223-054

value: serum

value: 44 years old


title: Patient 60, female, 72 years old, healthy, serum

description: Library name: 30223-056

value: 72 years old


title: SNU1 cells ; Vehicle  ;Replicate 1

description: Library name: GC-SNU1-CNT-1

value: gastric carcinoma


title: Patient 35, female, 62 years old, healthy, serum

description: Library name: 30223-050

value: female

value: 62 years old


title: Patient 67, female, 60 years old, healthy, serum

description: Library name: 30223-048

value: 60 years old


title: Patient 9, healthy, female, 50 years old

description: Library name: 31179-024

value: BRCA mutated


title: Patient 17, healthy, female, 43 years old

description: Library name: 31179-042


title: Patient 8, healthy, female, 62 years old

description: Library name: 31179-023


title: Patient 37, female, 52 years old, healthy, serum

description: Library name: 30223-044


title: AGS cells ; I6 50 microM ;Replicate 1

description: Library name: GC-AGS-I6-1

source_name: AGS

value: AGS

value: I6 50 microM


title: Patient 7, healthy, female, 58 years old

description: Library name: 31179-018

value: BRCA wild-type


title: Patient 59, female, 56 years old, healthy, serum

description: Library name: 30223-042

value: 56 years old


title: Patient 22, female, 66 years old, healthy, serum

description: Library name: 30223-043

value: 66 years old


title: Patient 64, female, 43 years old, healthy, serum

description: Library name: 30223-046

value: 43 years old


title: SNU1 cells ; I5 15 microM ;Replicate 2

description: Library name: GC-SNU1-I5-2

value: I5 15 microM


title: Patient 52, female, 50 years old, healthy, serum

description: Library name: 30223-041

value: 50 years old


title: Patient 6, healthy, female, 40 years old

description: Library name: 31179-016

value: Serum


title: Patient 44, female, 76 years old, healthy, serum

description: Library name: 30223-040

value: serum

value: 76 years old


title: AGS cells ; I5 40 microM ;Replicate 2

description: Library name: GC-AGS-I5-2

value: I5 40 microM


title: AGS cells ; I5 40 microM ;Replicate 1

description: Library name: GC-AGS-I5-1

value: gastric carcinoma


title: Patient 15, female, 52 years old, healthy, serum

description: Library name: 30223-039

value: female

value: 52 years old


title: Patient 5, healthy, female, 47 years old

description: Library name: 31179-014


title: AGS cells ; Vehicle  ;Replicate 2

description: Library name: GC-AGS-CNT-2

value: Vehicle


title: Patient 63, female, 61 years old, healthy, serum

description: Library name: 30223-036

value: 61 years old


title: Patient 4, healthy, female, 45 years old

description: Library name: 31179-011

value: BRCA mutated


title: Patient 7, female, 42 years old, healthy, serum

description: Library name: 30223-032

value: 42 years old


title: Patient 69, female, 32 years old, healthy, serum

description: Library name: 30223-035

value: 32 years old


title: Patient 3, healthy, female, 42 years old

description: Library name: 31179-004


title: AGS cells ; I6 50 microM ;Replicate 2

description: Library name: GC-AGS-I6-2

value: AGS

value: I6 50 microM


title: AGS cells ; Vehicle  ;Replicate 1

description: Library name: GC-AGS-CNT-1


title: Patient 61, female, 52 years old, healthy, serum

description: Library name: 30223-030


title: Patient 2, healthy, female, 75 years old

description: Library name: 31179-002

value: BRCA wild-type


title: Patient 65, female, 28 years old, healthy, serum

description: Library name: 30223-029

value: 28 years old


title: Patient 38, female, 36 years old, healthy, serum

description: Library name: 30223-031

value: 36 years old


title: MKN45 cells ; I6 50 microM ;Replicate 2

description: Library name: GC-MKN45-I6-2


title: Patient 23, female, 79 years old, healthy, serum

description: Library name: 30223-027

value: 79 years old


title: Patient 12, female, 60 years old, healthy, serum

description: Library name: 30223-026

value: serum

value: 60 years old


title: Patient 11, female, 53 years old, healthy, serum

description: Library name: 30223-022

value: 53 years old


title: MKN45 cells ; I5 30 microM ;Replicate 2

description: Library name: GC-MKN45-I5-2

value: gastric carcinoma

value: I5 30 microM


title: Patient 30, serum, healthy, female

description: Library name: 31274-051

value: Serum


title: Patient 36, female, 76 years old, healthy, serum

description: Library name: 30223-020

value: female

value: 76 years old


title: Patient 47, female, 56 years old, healthy, serum

description: Library name: 30223-019

value: 56 years old


title: MKN45 cells ; I5 30 microM ;Replicate 1

description: Library name: GC-MKN45-I5-1


title: Patient 66, female, 58 years old, healthy, serum

description: Library name: 30223-018

value: 58 years old


title: Patient 29, serum, healthy, female

description: Library name: 31274-059


title: MKN45 cells ; Vehicle  ;Replicate 2

description: Library name: GC-MKN45-CNT-2

value: Vehicle


title: Patient 62, female, 62 years old, healthy, serum

description: Library name: 30223-017

value: 62 years old


title: Patient 6, female, 63 years old, healthy, serum

description: Library name: 30223-016

value: 63 years old


title: Patient 28, serum, healthy, female

description: Library name: 31274-060

value: BRCA wild-type


title: Patient 18, female, 53 years old, healthy, serum

description: Library name: 30223-013


title: Patient 48, female, 32 years old, healthy, serum

description: Library name: 30223-015

value: 32 years old


title: MKN45 cells ; Vehicle  ;Replicate 1

description: Library name: GC-MKN45-CNT-1


title: Patient 8, female, 65 years old, healthy, serum

description: Library name: 30223-012

value: 65 years old


title: Patient 27, serum, healthy, female

description: Library name: 31274-058


title: PANC1 cells ; I6 20 microM ;Replicate 2

description: Library name: PC-PANC1-I6-2

value: pancreatic carcinoma

value: I6 20 microM


title: Patient 26, serum, healthy, female

description: Library name: 31274-057


title: PANC1 cells ; I6 20 microM ;Replicate 1

description: Library name: PC-PANC1-I6-1


title: Patient 68, female, 54 years old, healthy, serum

description: Library name: 30223-009

value: serum

value: 54 years old


title: Patient 1, healthy, female, 57 years old

description: Library name: 31179-001

value: Untested


title: Patient 30, female, 63 years old, healthy, serum

description: Library name: 30223-010


title: PANC1 cells ; I5 20 microM ;Replicate 2

description: Library name: PC-PANC1-I5-2

value: I5 20 microM


title: Patient 72, female, 50 years old, healthy, serum

description: Library name: 30223-007

value: 50 years old


title: Patient 24, serum, healthy, female

description: Library name: 31274-055

value: Serum


title: MKN45 cells ; I6 50 microM ;Replicate 1

description: Library name: GC-MKN45-I6-1

value: gastric carcinoma

value: I6 50 microM


title: PANC1 cells ; I5 20 microM ;Replicate 1

description: Library name: PC-PANC1-I5-1


title: Patient 24, female, 42 years old, healthy, serum

description: Library name: 30223-005

value: female

value: 42 years old


title: Patient 57, female, 54 years old, healthy, serum

description: Library name: 30223-004


title: PANC1 cells ; Vehicle  ;Replicate 2

description: Library name: PC-PANC1-CNT-2

value: Vehicle


title: Patient 22, serum, healthy, female

description: Library name: 31274-053


title: Patient 20, female, 55 years old, healthy, serum

description: Library name: 30223-002

value: 55 years old


title: Patient 26, female, 50 years old, healthy, serum

description: Library name: 30223-003


title: PANC1 cells ; Vehicle  ;Replicate 1

description: Library name: PC-PANC1-CNT-1


title: Patient 43, female, 62 years old, healthy, serum

description: Library name: 30223-001

value: 62 years old


title: Patient 4, female, 57 years old, healthy, serum

description: Library name: 30223-011

value: 57 years old


title: Patient 25, serum, healthy, female

description: Library name: 31274-056

value: BRCA wild-type


title: Patient 20, serum, healthy, female

description: Library name: 31274-040

value: BRCA mutation


title: 354 cells ; I6 25 microM ;Replicate 1

description: Library name: PC-354-I6-1

value: pancreatic carcinoma

value: I6 25 microM


title: Patient 19, serum, healthy, female

description: Library name: 31274-038


title: 354 cells ; I6 25 microM ;Replicate 2

description: Library name: PC-354-I6-2


title: Patient 54, female, 37 years old, healthy, serum

description: Library name: 30223-008

value: serum

value: 37 years old


title: 354 cells ; I5 25 microM ;Replicate 2

description: Library name: PC-354-I5-2

value: I5 25 microM


title: PC3 cocultivated 5

city: Toulouse

first: Camille

last: Attane

address: 205 route de Narbonne

country: France

institute: CNRS/IPBS

description: Library name: Sample 10

data_processing:
The dual-indexed sequencing parameters were 74, 10, 10, 74 cycles (read 1, index i7, index i5, read 2).
Sequencer output files have been demultiplexed with the Illumina’s software bcl2fastq.
Reads were mapped to the annotated Homo sapiens genome (GRCh38v97) using bowtie2 aligner (v2.4.4)46.
RSEM software (v1.3.3)47 was used to quantify the gene expression.
Assembly: Reads were mapped to the annotated Homo sapiens genome (GRCh38v97) using bowtie2 aligner (v2.4.4)46.
Supplementary files format and content: Each processed data files is an excel file
Supplementary files format and content: Each file contain the following columns: gene_id; transcript_id; length; effective_length; expected_count; TPM;FPKM

source_name: prostate

extract_protocol:
RNA extraction was performed using the RNeasy® Mini kit columns (Qiagen) following the manufacturer’s instructions. RNA was quantified by Qubit RNA kit (Thermofischer Scientific) and qualified with the HS RNA kit for the Fragment Analyzer (Agilent Technologies).
The mRNAseq librairies were prepared with the Illumina Stranded mRNA Prep Ligation kit using an input of 500ng of highquality RNA (RQN =10) following manufacturer’s instructions. The librairies were profiled with the HS NGS kit for the Fragment Analyzer and quantified by qPCR using the KAPA library quantification kit (Roche Diagnostics), pooled and sequenced on the Illumina NextSeq550 High Output flow cell 150 cycles.

value: prostate

value: Prostate cancer cell

value: WT

value: Cocultivated


title: PC3 non cocultivated 3

description: Library name: Sample 5

value: Non cocultivated


title: PC3 cocultivated 4

description: Library name: Sample 8


title: Patient 73, female, 39 years old, healthy, serum

description: Library name: 30223-006

value: female

value: 39 years old


title: Patient 18, serum, healthy, female

description: Library name: 31274-036

value: Serum


title: PC3 non cocultivated 5

description: Library name: Sample 9


title: PC3 cocultivated 2

description: Library name: Sample 4


title: Patient 17, serum, healthy, female

description: Library name: 31274-034


title: PC3 non cocultivated 4

description: Library name: Sample 7


title: PC3 non cocultivated 2

description: Library name: Sample 3


title: Patient 23, serum, healthy, female

description: Library name: 31274-054


title: PC3 cocultivated 1

description: Library name: Sample 2


title: PC3 non cocultivated 1

description: Library name: Sample 1


title: 354 cells ; I5 25 microM ;Replicate 1

description: Library name: PC-354-I5-1


title: 354 cells ; Vehicle  ;Replicate 2

description: Library name: PC-354-CNT-2

value: Vehicle


title: Patient 21, serum, healthy, female

description: Library name: 31274-052


title: Patient 16, serum, healthy, female

description: Library name: 31274-032


title: AsPC1, KDM4C KO1, rep3

description:
Library name: 6.2a1.C
High 150 (75 nt PE)

value: Human pancreatic ductal adenocarcinoma

value: KDM4C knockout


title: Patient 15, serum, healthy, female

description: Library name: 31274-030

value: BRCA mutation


title: 12-week old male KPC, replicate 1

city: NAGOYA

first: XINGXING

last: WANG

state: 愛知県

address: 65 Tsurumai-cho, Showa-ku

department: cancer biology

country: Japan

institute: Nagoya University

library_source: genomic single cell

data_processing:
ArchR v1.0.2 was used for single-cell ATAC sequencing analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include chromosomal locations for each fragment with cell barcode ID.

source_name: pancreas

extract_protocol:
pancreatic tissue were dissociated into single cells using a MACS Tumor Dissociation Kit
Single-cell ATAC-seq libraries were prepared utilizing a SureCell ATAC-Seq Library Prep Kit and SureCell ddSEQ Index Kit following the manufacturer's

value: pancreas

value: 12-week old

value: male

value: Unfractionated live cell mixtures

value: KPC (Pdx1cre/+; LSL-KrasG12D/+; LSL-Trp53+/R172H)


title: PC3 cocultivated 3

description: Library name: Sample 6

value: prostate


title: 185 cells ; I6 25 microM ;Replicate 2

description: Library name: PC-185-I6-2

value: pancreatic carcinoma

value: I6 25 microM


title: AsPC1, KDM4C KO1, rep2

description:
Library name: 5.2a1.B
High 150 (75 nt PE)


title: Patient 14, serum, healthy, female

description: Library name: 31274-028


title: 185 cells ; I6 25 microM ;Replicate 1

description: Library name: PC-185-I6-1


title: 185 cells ; I5 25 microM ;Replicate 2

description: Library name: PC-185-I5-2

value: I5 25 microM


title: Patient 13, serum, healthy, female

description: Library name: 31274-026


title: 185 cells ; I5 25 microM ;Replicate 1

description: Library name: PC-185-I5-1


title: AsPC1, KDM4C WT, rep3

description:
Library name: 3.AsPc.Flag.Ctl.C
High 150 (75 nt PE)

value: WT


title: AsPC1, KDM4C KO1, rep1

description:
Library name: 4.2a1.A
High 150 (75 nt PE)


title: Patient 12, serum, healthy, female

description: Library name: 31274-024


title: 185 cells ; Vehicle  ;Replicate 2

description: Library name: PC-185-CNT-2


title: AsPC1, KDM4C WT, rep2

description:
Library name: 2.AsPc.Flag.Ctl.B
High 150 (75 nt PE)


title: 12-week old male KPC, replicate 2


title: 354 cells ; Vehicle  ;Replicate 1

description: Library name: PC-354-CNT-1


title: MM1S_shN2_2_rep3

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

description:
MM1S_TPM_count_table
MM1S_DESeq2_comparison_shN2_2_vs_shNTC

data_processing:
Following sequencing, base calling was done with Illumina’s FASTQ Generation software and high quality PF-clusters (according to the CASAVA filter) were selected for further analyses.
For RNA-seq, reads were mapped to the human genome using the STAR aligner (version 2.7.2b) with default parameters. The subsequent bioinformatics analysis of the aligned reads was done with the featureCounts tool (v1.6.4) followed by the DESeq2 package form Bioconductor.
Assembly: GRCh38.p13
Supplementary files format and content: For RNA-seq, a count-matrix with rawcounts, normalized to 1 million tags, and a count table with vst (variance stabilizing transformation) transformed counts are provided in text-format (*.csv). Furthermore, the DESeq2 calculated differential expressions for all analyzed genes for the relevant comparisons are provided for both cell-lines in text-format (*.csv).

growth_protocol: MM.1S and RPMI-8226 cells were grown and cultured in RPMI 1640 medium with GlutaMAX (Thermo Fisher Scientific, Darmstadt, Germany), supplemented with 10 % fetal calf serum (FCS) (Anprotec, Bruckberg, Germany), 1 % penicillin/streptomycin (10.000 U/ml, Thermo Fisher Scientific, Darmstadt, Germany), and 1 % sodium pyruvate (100 mM, Thermo Fisher Scientific, Darmstadt, Germany).

extract_protocol:
For RNA-seq, cells were harvested and total RNA was extracted from 1x10^7 cells using the Qiagen RNAeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. To isolate protein coding messenger RNAs from the total RNA, the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Frankfurt, Germany) was used.
Library preparation was performed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Frankfurt, Germany) according to the manufacturer’s protocol. Libraries were size-selected using AMPure XP beads (Beckman Coulter, Beverly, USA). Samples were amplified and sample-specific indexes were introduced for the sequencing step using NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set 1, Illumina, New England Biolabs, Frankfurt, Germany) in a 8-cycle PCR reaction. Determination of library size and concentration was performed with a 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with a NextSeq 500 System (Illumina, San Diego, CA, USA) in a dual-index, single-read format.
RNA-sequencing (Illumina NextSeq 500)

treatment_protocol: For the RNA-seq experiment, MM.1S cells and RPMI-8226 cells were either transduced with a lentiviral shRNA vector that constitutively expresses a shRNA targeting Notch1 or Notch2 or a non-targeting shRNA. Transduced cells were then puromycin-selected by adding 0.75 µg per ml puromycin (Thermo Fisher Scientific)

tag: induction of shrna

value: constitutively expressed shRNA


title: Patient 9, serum, healthy, female

description: Library name: 31274-018


title: sulfatide_2

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

country: China

institute: Renmin Hospital of Wuhan University

description: Library name: sample 5

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 DM 1-3 516 R44 (v6.1)  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: mm10
Supplementary files format and content: tab-delimited text file includes fpkm for each sample

source_name: bronchoalveolar lavage fluid

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: bronchoalveolar lavage fluid

value: the sulfatide-treated group, where mice received 20μg of sulfatide via intraperitoneal injection,


title: sulfatide_3

description: Library name: sample 6


title: sulfatide_1

description: Library name: sample 4


title: Patient 10, serum, healthy, female

description: Library name: 31274-020

value: Serum


title: vehicle_3

description: Library name: sample 2

value: the vehicle-treated group, where mice were treated with vehicle as a control


title: MM1S_shN2_2_rep2


title: vehicle_4

description: Library name: sample 3


title: AsPC1, KDM4C WT, rep1

description:
Library name: 1.AsPc.Flag.Ctl.A
High 150 (75 nt PE)

value: Human pancreatic ductal adenocarcinoma


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE SLC6A4, rep#3

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description:
Library name: PC3-SLC6A4_OE-3_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt

data_processing:
For RNA-seq, raw reads were trimmed with fastqc, then aligned to human genome and transcriptome (GRCh38.release108) using HISAT (version 2.1.0). Differentially expressed genes between the two groups were calculated in R using the DESeq2.
For Chip-seq, Raw sequencing reads were processed using FastQC for quality control and aligned to the human reference genome (GRCh38.release108) using Bowtie2. PCR duplicates have been removed. Peak calling was performed using MACS2, and annotation of binding sites was conducted using HOMER and in-house scripts.
Assembly: GRCh38.release108
Supplementary files format and content: csv files included Deseq2 normalized reads
Supplementary files format and content: BigWig files for ChIP-seq signal tracks of all samples.
Supplementary files format and content: NarrowPeak files for: H3K4me3 peaks; H3K4me3Q5ser peaks; H3K4me3Q5ser peaks overlapping with H3K4me3 peaks
Supplementary files format and content: FeatureCounts output for quantification within H3K4me3Q5ser peak regions

growth_protocol: The human prostate cancer cell lines PC3 (SCSP-532) was purchased from the Cell Bank, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. Cells were cultured in RPMI-1640 (Gibco), supplemented with 10% fetal bovine serum (Invitrogen), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco). Cells were incubated at 37°C in a humidified incubator with 5% CO2 and were routinely tested for mycoplasma contamination. The identity of the cell lines was verified through high-resolution short tandem repeat (STR) profiling.

extract_protocol:
RNA sequencing (RNA-seq) was performed on PC3 cells transduced with control (Ctrl), DDC, or SLC6A4 constructs. Total RNA was extracted using TRIzol Reagent (Invitrogen) and treated with DNase I to remove genomic DNA contamination.
mRNA was enriched using Oligo(dT)-modified magnetic beads and subsequently used for cDNA synthesis (Invitrogen). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared and quantified before sequencing on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA) in high-output mode.
ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology) following the manufacturer’s protocol. Briefly, cells were crosslinked with 1% formaldehyde and sonicated to obtain chromatin fragments averaging 250–1000 bp. Immunoprecipitated chromatin was subsequently reverse crosslinked.
For ChIP-seq, the immunoprecipitated DNA and input DNA were subjected to library preparation using the NEBNext Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer’s protocol.

value: Prostate Cancer

value: SLC6A4 OE


title: Patient 8, serum, healthy, female

description: Library name: 31274-016

value: BRCA mutation


title: vehicle_2

description: Library name: sample 1


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE SLC6A4, rep#2

description:
Library name: PC3-SLC6A4_OE-2_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: 12-week old male WT, control

value: pancreas

value: 12-week old

value: male

value: Wild type


title: MM1S_shN2_2_rep1


title: MM1S_shN2_1_rep3

description:
MM1S_TPM_count_table
MM1S_DESeq2_comparison_shN2_1_vs_shNTC


title: Patient 11, serum, healthy, female

description: Library name: 31274-022


title: wound skin,wound model in diabetic mice,  rep5

city: Hangzhou

first: Zhengtai

last: Chen

state: zhejiang

address: 88 Jie Fang Road, Hangzhou

institute: The Second Affiliated Hospital, Medical School, Zhejiang University

description:
Library name: sample15
DB9

data_processing:
mRNA was isolated by Oligo(dT)-attached magnetic beads
mRNA was then randomly fragmented in fragmentation buffer.
First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.
Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.
cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.
Assembly: DEK, FDX1
Supplementary files format and content: xls file represent for gene expression level (FPKM) matrix file
Supplementary files format and content: gene-count file represent for comparison diagram of FPKM density distribution, the peak value of distribution curve represents the region with the highest concentration of gene expression in the whole sample.

organism: Mus

source_name: skin metagenome

growth_protocol: Briefly, the wound tissues of type I diabetic mice, healthy mice, and normal skin were harvested, immediately frozen with liquid nitrogen, and stored at -80 °C. Total RNA was used as input material for RNA sample preparation. mRNA was purified from the total RNA using poly T oligo-attached magnetic beads.

extract_protocol:
Wound skin tissue were obtained from normal skin of healthy mice, wound skin of healthy mice and wound skin of diabetes mice, and then the TRIzol reagent (Invitrogen, 15596018) was used to extract the total RNA
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: There are three groups of mice in total, namely, the healthy mouse group, the healthy mouse wound model group, and the diabetes mouse wound model group

value: Diabetic wound skin

value: wound surgery


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE DDC, rep#3

description:
Library name: PC3-DDC_OE-3_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt

value: DDC OE


title: 185 cells ; Vehicle  ;Replicate 1

description: Library name: PC-185-CNT-1

value: pancreatic carcinoma

value: Vehicle


title: Patient 6, serum, healthy, female

description: Library name: 31274-012


title: wound skin,wound model in diabetic mice,  rep4

description:
Library name: sample14
DB8


title: MM1S_shN2_1_rep2

value: constitutively expressed shRNA


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE SLC6A4, rep#1

description:
Library name: PC3-SLC6A4_OE-1_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: wound skin,wound model in diabetic mice,  rep3

description:
Library name: sample13
DB7


title: MM1S_shN2_1_rep1


title: MM1S_shN1_2_rep3

description:
MM1S_TPM_count_table
MM1S_DESeq2_comparison_shN1_2_vs_shNTC


title: Patient 3, serum, healthy, female

description: Library name: 31274-006


title: Patient 5, serum, healthy, female

description: Library name: 31274-010


title: wound skin,wound model in diabetic mice,  rep2

description:
Library name: sample12
DB6


title: Patient 4, serum, healthy, female

description: Library name: 31274-008


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE DDC, rep#2

description:
Library name: PC3-DDC_OE-2_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: wound skin,wound model in diabetic mice,  rep1

description:
Library name: sample11
DB5


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE C, rep#3

description:
Library name: PC3-C-3_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt

value: Empty Vector OE


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE DDC, rep#1

description:
Library name: PC3-DDC_OE-1_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: Patient 2, serum, healthy, female

description: Library name: 31274-004

value: Serum


title: MM1S_shN1_2_rep1


title: Patient 1, serum, healthy, female

description: Library name: 31274-002


title: MM1S_shN1_2_rep2


title: Patient 7, serum, healthy, female

description: Library name: 31274-014


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE C, rep#2

description:
Library name: PC3-C-2_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: wound skin,wound model in healthy mice,  rep5

description:
Library name: sample10
Health5

value: wound skin


title: wound skin,wound model in healthy mice,  rep4

description:
Library name: sample9
Health4


title: Chip-seq, H3K4Me3Q5Ser, PC3, OE C, rep#1

description:
Library name: PC3-C-1_H3K4Me3Q5Ser
combined.H3K4Q5.final.narrowPeak
combined.H3K4Q5.overlapped.narrowPeak
FeatureCounts.H3Q5region.txt


title: MM1S_shN1_1_rep3

description:
MM1S_TPM_count_table
MM1S_DESeq2_comparison_shN1_1_vs_shNTC


title: Patient 30, plasma, healthy, female

description: Library name: 31274-050

source_name: Plasma

value: Plasma

value: BRCA wild-type


title: wound skin,wound model in healthy mice,  rep3

description:
Library name: sample8
Health3


title: Chip-seq, H3K4Me3, PC3, OE SLC6A4, rep#3

description:
Library name: PC3-SLC6A4_OE-3_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt

value: Prostate Cancer

value: SLC6A4 OE


title: MM1S_shN1_1_rep2


title: Patient 29, plasma, healthy, female

description: Library name: 31274-049


title: Chip-seq, H3K4Me3, PC3, OE SLC6A4, rep#2

description:
Library name: PC3-SLC6A4_OE-2_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: Patient 28, plasma, healthy, female

description: Library name: 31274-048


title: MM1S_shN1_1_rep1


title: normal skin,uninjured healthy mice,  rep5

description:
Library name: sample5
Sham5

value: normal skin

value: sham


title: Chip-seq, H3K4Me3, PC3, OE DDC, rep#3

description:
Library name: PC3-DDC_OE-3_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: Chip-seq, H3K4Me3, PC3, OE SLC6A4, rep#1

description:
Library name: PC3-SLC6A4_OE-1_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: normal skin,uninjured healthy mice,  rep4

description:
Library name: sample4
Sham4


title: MM1S_shNTC_rep1


title: MM1S_shNTC_rep2


title: Patient 25, plasma, healthy, female

description: Library name: 31274-045


title: normal skin,uninjured healthy mice,  rep3

description:
Library name: sample3
Sham3


title: Chip-seq, H3K4Me3, PC3, OE DDC, rep#1

description:
Library name: PC3-DDC_OE-1_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: RPMI_8226_shN2_2_rep3

description:
RPMI_8226_TPM_count_table
RPMI_8226_DESeq2_comparison_shN2_2_vs_shNTC


title: Patient 26, plasma, healthy, female

description: Library name: 31274-046


title: MM1S_shNTC_rep3


title: Patient 24, plasma, healthy, female

description: Library name: 31274-044


title: Patient 27, plasma, healthy, female

description: Library name: 31274-047


title: Chip-seq, H3K4Me3, PC3, OE C, rep#3

description:
Library name: PC3-C-3_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: RPMI_8226_shN2_2_rep2


title: normal skin,uninjured healthy mice,  rep2

description:
Library name: sample2
Sham2


title: Chip-seq, H3K4Me3, PC3, OE DDC, rep#2

description:
Library name: PC3-DDC_OE-2_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: normal skin,uninjured healthy mice,  rep1

description:
Library name: sample1
Sham1


title: Chip-seq, H3K4Me3, PC3, OE C, rep#2

description:
Library name: PC3-C-2_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt


title: RPMI_8226_shN2_2_rep1


title: wound skin,wound model in healthy mice,  rep2

description:
Library name: sample7
Health2