title: deltahetP, ChIP, biol rep 3

city: Wuhan

first: Yali

last: Wang

address: NO.152 Luoyu Road

department: School of Life Sciences

institute: Central China Normal University

description: Library name: deltahetP_3_IP

data_processing:
Low-quality ChIP-seq reads were filtered out using Trimmomatic (version 0.38).
Clean reads were mapped to the Nostoc sp. PCC 7120 genome by Bwa (version 0.7.15).
Potential PCR duplicates were removed using Samtools (version 1.3.1).
Peaks  were called using MACS2 software version 2.1.1 by default parameters [bandwidth, 300 bp; model fold, 5, 50; q-value (false discovery rate adjusted p-value) < 0.05, fold enrichment > 1].
bigWig files were generated using bamCoverage with default parameters.
Assembly: Nostoc sp. PCC 7120
Supplementary files format and content: bigWig

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: cell culture

growth_protocol: Nostoc sp. PCC 7120 strains were cultured in BG11 at 30 oC in the light of 30 mE m-2 s-1, on a rotary shaker.

extract_protocol:
After 8 h of nitrogen stepdown, 200 mL of Nostoc cells were cross-linked with 1% formaldehyde under vacuum conditions (-0.085 Mpa) at room temperature for 15 min, and the reaction was terminated by addition of 2 M glycine stock solution to 125 mM and incubation for 5 min. Cells were collected by centrifugation, washed twice with cold D-PBS solution (136.89 mM NaCl, 2.67 mM KCl, 8.10 mM Na2HPO4, 1.47 mM KH2PO4, pH 7.4) and re-suspended in 10 mL of cold D-PBS buffer with protease inhibitors. Cells were broken by passing through a French press at 15 Mpa. The disrupted cell suspension was supplemented with 400 mL of lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, 0.12 mg mL-1 tablet of protease inhibitors, pH 7.2) and incubated on ice for 40 min. The cell lysates were then subjected to sonication to shear the DNA into 200-500 bp fragments (12 cycles of 30s ON/30s OFF intervals, Diagenode Bioruptor). One hundred microliters of the sheared DNA were diluted with 900 μL of ChIP dilution buffer (16.7 mM Tris-HCl, 167 mM NaCl, 1.2 mM EDTA, 1% Triton X-100, pH 7.2), mixed with 30 μL of Dynabeads™ Protein G (Invitrogen) preloaded with antibody and incubated at 4 oC for 12 h. The beads were collected and incubated with 1 mL of diluted sheared DNA again. Beads with antibody-protein-DNA complexes were washed once with washing buffer 1 (20 mM Tris-HCl, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, pH 7.5), twice with washing buffer 2 (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid, pH 7.5), and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). Bound material was then eluted from the beads with 300 μL of elution buffer (100 mM NaHCO3, 1% SDS), treated with 8 mg mL-1 RNase A at 65 oC for 6 h and with 345 mg mL-1 proteinase K at 45 oC overnight.
Immunoprecipitated DNA was used to construct sequencing libraries using the NEXTFLEX® ChIP-Seq Library Prep Kit (Bioo Scientific, Austin, USA) for Illumina sequencing.

treatment_protocol: For nitrogen stepdown, mid-logarithmic phase cells were collected by centrifugation, washed 3 times with BG110 (BG11 without nitrate) and re-suspended in the same medium in the light for 8 h to induce heterocyst differentiation.

value: cell culture

tag: strain

value: deltahetP mutant

value: nitrogen stepdown for 8 h

value: Rabbit anti-HetZ IgG (Self-prepared, 1:1000 dilution)


title: Patient2 A

status: Public on Nov 20 2025

type: SRA

city: Houston

first: Yu

middle: Leo

last: Lei

state: TX

address: 1901 East Rd

department: Head and Neck Surgery

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

description: Library name: Samples 3

library_source: transcriptomic

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7 (Ewels et al., 2016)
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt was provided for all samples
Supplementary files format and content: gene_FPKM.annot.txt was provided for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Oral Cancer

growth_protocol: Fresh samples

extract_protocol:
Total RNA was extracted by RNeasy Plus Mini Kit (74136, Qiagen). The RNA concentration was determined using a Nanodrop Spectrophotometer from Thermo Fisher Scientific.
RNA libraries for RNA-seq were prapered by NGS core of University of Michigan .

treatment_protocol: Wash with cold PBS

tag: tissue

value: Oral Cancer

tag: treatment

value: no


title: Right cervical lymph nodes from four replicate mice pooled, control, depleted, control, replicate 2

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description:
Library name: b6.ctl.rcln.dep.2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, transcript counting, and aggregation was performed using CellRanger v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest). Only genes detected in at least 3 cells in across the entire dataset were retained. Cells with less than 200 or more than 4000 genes detected genes were discarded as were cells in which more than 5% of reads mapped to mitochondrial transcripts. Cell type annotations were assigned by comparing the transcriptome of each cell with the Immgen database.
Assembly: mm10
Supplementary files format and content: cln.rds: Seurat object containing the counts for each transcript detected in each single cell

molecule: total RNA

organism: Mus musculus

source_name: cervical lymph node

extract_protocol:
Lymph nodes were removed by dissection, minced into small pieces, and digested to a single cell suspension in RPMI containing 100 ug/mL DNase, 200 ug/mL Collagenase P, and 64 ug/mL Dispase II at 37 C, pipetting gently every 5 minutes. After 25 minutes, the digestion was stopped by adding EDTA to a final concentration of 10 mM. The suspension was passed through a 70 uM filter to remove undigested tissue and brought to a volume of 5 mL in MACS buffer. Cells were then counted and pelleted at 500g for 5 minutes and resuspended in 100 uL of MACS buffer per 1e7 total cells. T and B cells were then removed by negative magnetic selection using CD3ε-Biotin followed by Anti-Biotin MicroBeads and CD19-MicroBeads (all from Miltenyi) following the manufacturers instructions.
Libraries were prepared according to the manufacturers instructions (10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1). Briefly, CD3/CD19-depleted single-cell suspensions of lymph nodes were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate gel bead-in-emulsions (GEMs). Poly-A RNA from the cell lysate contained in each GEM was retrotranscribed to cDNA containing the Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and 10X Barcode. The pooled, barcoded cDNA was then processed with Silane DynaBeads, amplified by PCR, and size-selected with SPRIselect reagent for library construction. During library construction, the Illumina R2 primer sequence and sample indices were added.

treatment_protocol: CMTB was established by intradermal inoculation of the right ear with 10,000 CFU Mtb (strain H37Rv) in 10 uL of PBS.

value: cervical lymph node

tag: genotype


title: deltahetP, Input, biol rep 3

country: China

description: Library name: deltahetP_3_IN

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: HEK293 eGFP-YAP control replicate 2 Hi-C

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HEK293_eGFP_YAP_control_rep2
Hi-C of HEK293 cells at 0h

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Hi-C contact matrices in .hic format (hg38 reference genome). Files include both individual biological replicates and merged replicates (megaMap) for each condition. Datasets include HCT116 wild-type cells (control and 1h sorbitol treatment), HEK293 wild-type cells from the Phanstiel lab (control and sorbitol treatment), HEK293 eGFP-YAP cells from the Cai lab (control and sorbitol treatment), HEK293 wild-type sorbitol timecourse (10m, 30m, 1h, 3h, 6h, 12h, 24h), and HEK293 eGFP-YAPdTAD cells from the Cai lab (control and sorbitol treatment). MegaMap files represent merged replicates for increased sequencing depth. Spike-in normalized loop calls at 5kb resolution are provided for eGFP-YAP and WT Phanstiel conditions. Differential loop analysis (diffLoops_WT_noDroso_10kb.rds) comparing control vs sorbitol treatment is provided for WT Phanstiel samples.

growth_protocol: HEK293T and HCT116 cells were cultured at 37 °C in a humidified incubator with 5% CO₂. HEK293T cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin. HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and penicillin/streptomycin. Cells were routinely monitored for mycoplasma contamination and maintained at ~70–80% confluence to ensure log-phase growth. Cells were harvested for experiments only when healthy and within 5–15 passages from thaw.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
In situ Hi-C libraries were prepared using MboI restriction digestion, fill-in with biotinylated nucleotides, proximity ligation, reverse crosslinking, and DNA purification. Libraries were size-selected and PCR-amplified prior to sequencing.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

tag: cell line

value: eGFP-YAP

value: untreated


title: Right cervical lymph nodes from four replicate mice pooled, control, depleted, control, replicate 1

description:
Library name: b6.ctl.rcln.dep.1
10X Genomics


title: HEK293 eGFP-YAP control replicate 1 Hi-C

description:
Library name: HEK293_eGFP_YAP_control_rep1
Hi-C of HEK293 cells at 0h


title: deltahetP, ChIP, biol rep 2

description: Library name: deltahetP_2_IP


title: Patient1 A

description: Library name: Samples 1


title: Isolated Human Hepatocytes, HH003, PNPLA3-I148M

city: Pittsburgh

first: Soto

middle: Gutierrez

last: Alejandro

state: PA

address: 200 Lothrop St.

department: Department of Pathology

institute: University of Pittsburgh

description:
Library name: Sample 7
Column name in Normalized_Counts_All_Samples.csv: HH003

data_processing:
The quality of the raw fastq files were checked using FASTQC (version 0.11.9). In summary, the FastQC reports shows that the guanine-cytosine content of the samples ranges from 47% to 54%. As reference, a guanine-cytosine content between 30-40% is considered as too low as the DNA will be unstable, while a guanine-cytosine content between 70 -80% is considered to be too high because it makes PCR amplification more difficult. So, a guanine-cytosine content of about 50 to 60% is desirable10. Another important metric is the mean quality scores. All the samples have a score that falls within the acceptable threshold of 30. The QC-passed raw reads were then aligned to genome with STAR (version 2.7.5a)11. The quality of the aligned reads were assessed using QoRTs (version 1.3.6)12. The quality of the aligned reads was assessed based on the percentage of novel splice events. For all the samples, the percentage of novel splice events is about 1%.
We are not expecting too many novel splicing events in this set of samples, therefore, this value is within acceptable limits. Also, the sample pass the strandedness test. For all the samples, about 97% of the reads are mapped to the first strand. This attests to the quality of the sequenced RNA fragments. Downstream analysis were performed using DESeq2 in R (CRAN 4.04), BEAVR (a Browser-based tool for the Exploration And Visualization of RNAseq data)13, GSEA14, 15 and GraphPad prism version 8. The p value was computed based on Wald test statistics. Genes with fold change greater than 1.5 and p-value less than 0.05 are considered significant.
Assembly: hg38
Supplementary files format and content: csv file contains Normalized count output from DESEq2

source_name: Liver

extract_protocol:
total RNA was extracted from isolated primary human hepatocytes using RNeasy Plus Micro Kit (Qiagen). RNA integrity was assessed using the High Sensitivity RNA ScreenTape system on an Agilent 2200 TapeStation (Agilent). The SMART-Seq HT Kit (Takara Bio) was used to generate cDNA from 10 ng of total RNA, and the cDNA product was checked by an Agilent Fragment Analyzer system (Agilent) for quality control.
The sequencing library was constructed by following the Illumina Nextera XT Sample Preparation Guide. One nanogram of input cDNA was tagmented and amplified using the Illumina Nextera XT kit. Equimolar amounts of each sample were finally pooled and sequenced on an Illumina Nextseq 500 system, using a paired-end 75-bp strategy

value: Liver


title: Isolated Human Hepatocytes, HH1072, PNPLA3-I148M

description:
Library name: Sample 8
Column name in Normalized_Counts_All_Samples.csv: HH1072


title: flp-7+ neurons (rep1), L1 stage hermaphrodite Caenorhabditis elegans, 11239

city: Nashville

first: David

middle: M

last: Miller III

state: Tennessee

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
Library name: Sample 15
10X Genomics

data_processing:
Real-Time Analysis software (RTA,version 2.4.11; Illumina) was used for base calling.
Analysis was completed using 10X Genomics Cell Ranger software (v6.0.0).
Data analysis downstream of CellRanger was performed in R using DropUtils (v1.6.1), SoupX (v1.6.1), scater (v1.24), and monocle3 (v1.2.9) packages.
UMAP clusters were created by the monocle3 package and were assigned cell type identities based on the expression of known cell-type specific genes.
Assembly: Custom WS273 reference genome with extended 3’ UTR sequences.
Supplementary files format and content: all_cells_cell_annotations.csv [comma separated values file featuring cell annotations for each cell]
Supplementary files format and content: all_cells_gene_annotations.csv [comma separated values file featuring gene annotations for all genes]
Supplementary files format and content: all_cells_gene_by_barcode_matrix.mtx [matrix file containing raw gene counts for each cell]

organism: Caenorhabditis elegans

source_name: Subgroups of neurons (SAA)

extract_protocol:
Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™III Cell Sorter equipped with 70-micron diameter nozzles. DAPI was added to the sample (final concentration of 1 μg/mL) to label dead and dying cells. We used a variety of fluorescent reporter strains to label subsets of neuronal cells. N2 worms lacking fluorescence and single-color controls (for intersectional labeling strategies and dual-color sorts) were used to set gates to exclude auto-fluorescent cells and to compensate for spillover between fluorescent channels. In three experiments, single-cell suspensions from separate strains were combined prior to FACS: (1) NC3583, NC2957; (2) OH16003, EG1285, ZM5488 and uIs152; (3) CZ631, NC3523, PS3504. Cells were sorted under the “4-way purity” mask. Cells expressing the desired fluorescent proteins were collected into 400 μL of chilled (4o C) L-15 media containing 33% FBS (L-15-33) and stored on ice. We concentrated the collected cells by centrifuging at 500 rcf for 5 minutes at 4o C. We removed all but ~30-50 μL of the supernatant, resuspended the cells and counted fluorescent cells on a hemocytometer. Cell suspensions loaded into the 10X Chromium Controller ranged in concentration from 350-1000 cells/uL.
Libraries were prepared using P/N 1000121 following the manufacturer’s protocol. The libraries were sequenced using the Illumina NovaSeq 6000 with 150 bp paired end reads.

value: Subgroups of neurons (SAA)

value: NY2066 ynIs66 [flp-7p::GFP]

value: wt

tag: age

tag: cell status

value: Live


title: deltahetP, ChIP, biol rep 1

description: Library name: deltahetP_1_IP


title: deltahetP, Input, biol rep 2

description: Library name: deltahetP_2_IN


title: Isotype treated_Donor3

city: Chicago

first: Shalini

last: Singh

state: IL

address: 300 E. Superior Street

department: Department of Medicine (Infectious Diseases)

institute: Northwestern University

description: Library name: 116358_S130_L008_R1_001

data_processing:
Fatsq files were aligned to GRCh38 using salmon (v 1.10.1) software in conjunction with STAR aligner (v 2.7.10a) to obtain estimated raw counts. Those counts were used to get the differential expression using DESeq2 in R.
Assembly: GRCh38
Supplementary files format and content: csv file with log2 normailsed counts

source_name: Primary monocytes and CD4 T cells

extract_protocol:
Qiagen RNAeasy micro kit
Stranded mRNA Library Prep Kit (Illumina)

tag: cell type

value: Primary monocytes and CD4 T cells


title: flp-7+ neurons (rep2), L1 stage hermaphrodite Caenorhabditis elegans, 11314

description:
Library name: Sample 16
10X Genomics


title: 10-1074 Sia treated_Donor3

description: Library name: 116357_S129_L008_R1_001


title: Isolated Human Hepatocytes, HH002, PNPLA3-I148M

description:
Library name: Sample 6
Column name in Normalized_Counts_All_Samples.csv: HH002


title: Isolated Human Hepatocytes, 1, PNPLA3-I148M

description:
Library name: Sample 5
Column name in Normalized_Counts_All_Samples.csv: One


title: P-lineage progenitors and neurons, 21-24 hph (rep2), L1 stage hermaphrodite Caenorhabditis elegans, 10906

description:
Library name: Sample 14
10X Genomics

source_name: P-lineage progenitors and neurons

value: P-lineage progenitors and neurons

value: UD381 [phlh-3::vab-10abd::venus, phlh-3::nls::tdTomato, odr-1::gfp]


title: 10-1074 treated_Donor3

description: Library name: 116356_S128_L008_R1_001


title: hetZ4-201, ChIP, biol rep 3

description: Library name: hetZ4-201_3_IP

value: cell culture

value: hetZ4-201 mutant


title: P-lineage progenitors and neurons, 11-14 hph, L1 stage hermaphrodite Caenorhabditis elegans, 10866

description:
Library name: Sample 13
10X Genomics


title: Isotype treated_Donor2

description: Library name: 116355_S127_L008_R1_001


title: P-lineage progenitors and neurons, 15.5-18.5 hph, L1 stage hermaphrodite Caenorhabditis elegans, 10712

description:
Library name: Sample 11
10X Genomics

value: UD381 ycIs11[phlh-3::vab-10abd::venus, phlh-3::nls::tdTomato, odr-1::gfp]


title: Isolated Human Hepatocytes, HH80, PNPLA3-WT

description:
Library name: Sample 4
Column name in Normalized_Counts_All_Samples.csv:: HH80

value: WT


title: hetZ4-201, Input, biol rep 3

description: Library name: hetZ4-201_3_IN

value: nitrogen stepdown for 8 h


title: 10-1074 Sia treated_Donor2

description: Library name: 116354_S126_L008_R1_001


title: Isolated Human Hepatocytes, HH68, PNPLA3-WT

description:
Library name: Sample 3
Column name in Normalized_Counts_All_Samples.csv: HH68


title: unc-4c+ neurons, ceh-2+ neurons, acr-2+ neurons, L1 stage hermaphrodite Caenorhabditis elegans, 8672

description:
Library name: Sample 10
10X Genomics

source_name: Subgroups of neurons (DA, DB, SAB, I3, M3, NSM)


title: P-lineage progenitors and neurons, 21-24 hph (rep1), L1 stage hermaphrodite Caenorhabditis elegans, 10795

description:
Library name: Sample 12
10X Genomics


title: Patient1 B

description: Library name: Samples 2

value: Oral Cancer

value: no


title: ceh-34+ neurons, unc-4+ neurons (methanol-fixed cells), L1 stage hermaphrodite Caenorhabditis elegans, 8482

description:
Library name: Sample 9
10X Genomics

source_name: Subgroups of neurons (pharyngeal neurons, SAB, DA)

value: Methanol-fixed after sorting


title: hetZ4-201, Input, biol rep 2

description: Library name: hetZ4-201_2_IN


title: deltahetP, Input, biol rep 1

description: Library name: deltahetP_1_IN

value: deltahetP mutant


title: hetZ4-201, ChIP, biol rep 1

description: Library name: hetZ4-201_1_IP

value: Rabbit anti-HetZ IgG (Self-prepared, 1:1000 dilution)


title: Isotype treated_Donor1

description: Library name: 116352_S124_L008_R1_001


title: Isolated Human Hepatocytes, HH1148, PNPLA3-WT

description:
Library name: Sample 1
Column name in Normalized_Counts_All_Samples.csv: HH1148

value: Liver


title: 10-1074 Sia treated_Donor1

description: Library name: 116351_S123_L008_R1_001


title: GEO_120DIV_ARX_1

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: One UTSA Circle

department: Department of Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

description:
10X Genomics
GEO_120DIV_ARX_1

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) . All further analysis was done by Suerat v.3.2 or v.4.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values, files and matrix files

source_name: Ganglionic Eminence Organoid

extract_protocol:
For single cell dissociation and RNA seq, cortical and ganglionic eminence organoid were dissociated using Worthington papain dissociation kit (Cat. No. LK003150) as per instruction manual. Each developmental timepoint (30 DIV and 120 DIV) and each subtype of spheroid (cortical and ganglionic eminence) was processed separately. A total of 3 lines, and one clone per line, were used for each condition. Briefly, 3-4 organoids for each timepoint and subtype were collected in a small petri dish with 5 ml of prewarmed Worthington papain solution and 250 µl of Worthington DNase solution. The spheroids were chopped into small pieces using sterile blades and the dishes were placed on a digital rocker in a cell culture incubator for 60 minutes at 37 °C. Digested tissue was collected in a 15-ml tube and 5 ml of room temperature (RT) Earle's Balanced Salt Solution (EBSS) was added. The mixture was then triturated by gently pipetting up and down 10 times with 10-ml plastic pipette followed by 1-ml and 200-µl pipettes. Any undissociated tissue was allowed to settle at the bottom of the tube and the cloudy suspension was carefully aspirated in a clean 15-ml tube. Next, 3.15 ml of inhibitor solution (2.7 ml of EBSS, 300 µl of reconstituted Worthington albumin-ovomucoid solution and 150 µl of DNase solution) was carefully layered over the cloudy suspension and tubes were centrifuged at 300 g for 5 minutes at RT. The supernatant was carefully discarded, and cell pellet was gently suspended in 500 µl of cold neurobasal A media. Cell viability was determined using trypan blue.
10x Genomics single cell libraries were generated by the University of Texas at San Antonio (UTSA) Genomics Core. Cell suspensions were loaded into 10x Genomics microfluidics chips from Chip B Single Cell kit (Cat. No. 1000153) and onto the 10x Chromium controller to capture single cells in Gel Beads-in-emulsion (GEMs). 7,000 cells/sample were targeted for capture in GEMs preceding library prep following manufacturer’s recommendations for 10x Genomics 3’ Gene Expression Reagent kit (Cat. No. 1000269) with v3 chemistry. Sequencing was performed on either NextSeq 500 at University of Texas Health Science Center (UTHSC) at San Antonio or NovaSeq 6000 at North Texas Genome Center (NTGC) to generate 50,000 reads/cell in each sample.

value: Ganglionic Eminence Organoid


title: ceh-34+ neurons, unc-4+ neurons (live cells), L1 stage hermaphrodite Caenorhabditis elegans, 8304

description:
Library name: Sample 7
10X Genomics

value: Subgroups of neurons (pharyngeal neurons, SAB, DA)

value: wt


title: hetZ4-201, Input, biol rep 1

description: Library name: hetZ4-201_1_IN


title: 10-1074 treated_Donor1

description: Library name: 116350_S122_L008_R1_001

value: Primary monocytes and CD4 T cells


title: mec-3+, unc-47+, nlp-13+, ceh-10+ neurons, L1 stage hermaphrodite Caenorhabditis elegans, 8305

description:
Library name: Sample 8
10X Genomics

source_name: Subgroups of neurons(NSM, RIB, RID, CAN, PLM, ALM, FLP, PVT)

value: Live


title: WT_HetZ, Input, biol rep 3

description: Library name: WT_HetZ_3_IN

value: wild type


title: FK866 & NAD liposome-treated cell

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
The integrity of the sequencing data was assessed using FastQC v0.11.9. Alignment of FASTQ files to the mouse reference genome (GRCh38, release 109, December 2022) was performed utilizing the Spliced Transcripts Alignment to a Reference (STAR) software v2.7.10a. Gene abundance was quantified employing the RNA-Seq by Expectation-Maximization (RSEM) tool v1.3.1.
Assembly: GRCh38
Supplementary files format and content: comma-separated values (CSV) files include TPM values for each Sample

source_name: Skin

extract_protocol:
Total RNAs were extracted using AccuPrep® Universal RNA Extraction Kit according to the manufacture's instruction.
transcriptome library was generated using the TruSeq stranded mRNA library protocol

value: Skin

value: Fibroblast


title: GEO_120DIV_Control_1

description:
10X Genomics
GEO_120DIV_Control_1


title: WT_HetZ, ChIP, biol rep 3

description: Library name: WT_HetZ_3_IP

value: cell culture


title: unc-86+ neurons, L1 stage hermaphrodite Caenorhabditis elegans, 8029

description:
Library name: Sample 5
10X Genomics

source_name: Subgroups of neurons (RIR, RIH, RIP, etc.)

value: kyIs262 [unc-86::myr-GFP + odr-1::RFP]


title: GEO_30DIV_ARX_1

description:
10X Genomics
GEO_30DIV_ARX_1


title: hetZ4-201, ChIP, biol rep 2

description: Library name: hetZ4-201_2_IP

value: hetZ4-201 mutant

value: nitrogen stepdown for 8 h


title: WT_HetZ, ChIP, biol rep 2

description: Library name: WT_HetZ_2_IP


title: Isolated Human Hepatocytes, HH36, PNPLA3-WT

description:
Library name: Sample 2
Column name in Normalized_Counts_All_Samples.csv: HH36

value: WT


title: 10-1074 treated_Donor2

description: Library name: 116353_S125_L008_R1_001


title: FK866-treated cell_2


title: GEO_30DIV_Control_1

description:
10X Genomics
GEO_30DIV_Control_1


title: FK866-treated cell_1


title: CO_120DIV_ARX_1

description:
10X Genomics
CO_120DIV_ARX_1

source_name: Cortical Organoid

value: Cortical Organoid


title: Neurons, L1 stage hermaphrodite Caenorhabditis elegans, 7226, Rep2

description:
Library name: Sample 4
10X Genomics

source_name: All neurons

value: All neurons


title: WT_HetZ, Input, biol rep 2

description: Library name: WT_HetZ_2_IN


title: Neurons, L1 stage hermaphrodite Caenorhabditis elegans, 7226, Rep1

description:
Library name: Sample 3
10X Genomics


title: CO_120DIV_Control_1

description:
10X Genomics
CO_120DIV_Control_1


title: Non-treated cell 2


title: WT_HetZ, ChIP, biol rep 1

description: Library name: WT_HetZ_1_IP

value: Rabbit anti-HetZ IgG (Self-prepared, 1:1000 dilution)


title: Sensory neurons, L1 stage hermaphrodite Caenorhabditis elegans, 6065

description:
Library name: Sample 2
10X Genomics

source_name: Sensory neurons

value: Sensory neurons


title: WT_HetZ, Input, biol rep 1

description: Library name: WT_HetZ_1_IN


title: eat-4+ neurons, L1 stage hermaphrodite Caenorhabditis elegans, 8029, bio rep 2

description:
Library name: Sample 6
10X Genomics

source_name: Glutametergic neurons

value: Glutametergic neurons


title: CO_30DIV_Control_1

description:
10X Genomics
CO_30DIV_Control_1


title: CO_30DIV_ARX_1

description:
10X Genomics
CO_30DIV_ARX_1


title: Non-treated cell 1


title: freshwater sponge w/algae, light, S5_Emu10

status: Public on Nov 19 2025

city: Lewiston

first: April

middle: L

last: Horton

email: ahorton@bates.edu, ahill5@bates.edu

state: Maine

address: 44 Campus Avenue, Carnegie Science Hall

department: Biology

institute: Bates College

description: Library name: Sample 12

data_processing:
Performed by LC Sciences: Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
HISAT2 to map reads to the genome of https://spaces.facsci.ualberta.ca/ephybase/. The mapped reads of each sample were assembled using StringTie
all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Assembly: JABACO000000000.1
Supplementary files format and content: csv files include FPKM values for samples

organism: Ephydatia muelleri

source_name: whole sponge

growth_protocol: Sponge gemmules were hatched at room temperature in 1X Strekal’s solution [19] in Petri dishes or in 35 mm glass bottom dishes if used for confocal microscopy. All sponges used in this study were either hatched and cultured in the dark or under a 12 hour light:dark cycle where media was refreshed every 48 hours.

extract_protocol:
Total RNA extracted from flash frozen cultured sponge tissue using Norgen Biotek Animal tissue kit
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification.

value: whole sponge

value: grown in 12:12 light dark

tag: developmental time

value: stage 5


title: Command interneurons, L1 stage hermaphrodite Caenorhabditis elegans, 5929

description:
Library name: Sample 1
10X Genomics

source_name: Command interneurons

value: Command interneurons

value: NC3581 otIs708 [sra-11p::Scarlet + inx-6p18::tagRFP]; rhIs2 [glr-1::GFP]

value: wt

value: Live


title: freshwater sponge w/algae, light, S5_Emu5

description: Library name: Sample 11


title: freshwater sponge w/algae, light, S3_Emu5

description: Library name: Sample 8

value: stage 3


title: freshwater sponge w/algae, light, S5_Emu1

description: Library name: Sample 10


title: freshwater sponge w/algae, light, S3_Emu1

description: Library name: Sample 7


title: freshwater sponge w/algae, light, S2_Emu1

description: Library name: Sample 4

value: stage 2


title: freshwater sponge w/algae, light, S1_Emu5

description: Library name: Sample 2

value: stage 1


title: freshwater sponge w/algae, light, S2_Emu10

description: Library name: Sample 6


title: freshwater sponge w/algae, light, S1_Emu1

description: Library name: Sample 1


title: freshwater sponge w/algae, light, S3_Emu10

description: Library name: Sample 9


title: 6.9.3_High_freq, BulkTCR

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

description:
Library name: BulkTCR10
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz

data_processing:
Cellranger-7.0.1, Kallisto (v0.46.2), MIXCR(v4.7.0)
Assembly: GRCh38
Supplementary files format and content: Cellranger output file: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger output file: airr_rearrangement.tsv
Supplementary files format and content: Kallisto output files: abundance.h5, abundance.tsv
Supplementary files format and content: MIXCR output files: clones_TRA.tsv, clones_TRB.tsv
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
Following the recommendation of 10x genomics :: single cell Using RNeasy Plus Mini Kit from Qiagen
Following the recommendation of 10x genomics :: single cell Following NEBNext Ultra II RNA Library Prep Kit protocol :: BulkRNAseq Following SMART-Seq Human TCR (with UMIs) protocol from Takara Bio :: BulkTCR

value: Blood

value: NLV-specific T cells


title: freshwater sponge w/algae, light, S2_Emu5

description: Library name: Sample 5


title: freshwater sponge w/algae, light, S1_Emu10

description: Library name: Sample 3


title: 6.9.2_Low_freq, BulkTCR

description:
Library name: BulkTCR9
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: 10.2_High_freq, BulkTCR

description:
Library name: BulkTCR8
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: I_Low_freq, BulkTCR

description:
Library name: BulkTCR6
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: H_High_freq, BulkTCR

description:
Library name: BulkTCR4
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: J_High_freq, BulkTCR

description:
Library name: BulkTCR7
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: 6.10.1_Low_freq, BulkTCR

description:
Library name: BulkTCR11
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: G_Low_freq, BulkTCR

description:
Library name: BulkTCR5
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: D_High_freq, BulkTCR

description:
Library name: BulkTCR3
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: A_Low_freq, BulkTCR

description:
Library name: BulkTCR1
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: pooledCells_scADT3

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Universitätsklinikum Erlangen

description:
Library name: Run3_ADT
10x Genomics

data_processing:
The sequencing sample was processed via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics), the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics), and custom feature barcodes (barcodes.csv).
Assembly: GRCh38 (version 2020A, 10x Genomics), vdj-GRCh38 (version 5.0.0, 10x Genomics), barcodes.csv
Supplementary files format and content: comma-separated value files and matrix files
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
PBMCs were thawed from cryopreserved stocks and rested overnight at 1x10^6 cells/mL in cRPMI medium (RPMI 1640 Medium + 10% heat-inactivated FCS, 0.05 mM β-mercaptoethanol, 0.05 mg/mL gentamicin, 1.1915 g/L HEPES, 0.2 g/L L-glutamine, 100 U/mL Penicillin-Streptomycin). For each donor, 2x10^6 PBMCs were stimulated with stimulated with 11aa overlapping 15-mer PepMixTM SARS-CoV-2 spike glycoprotein peptide pool (JPT, PM-WCPV-S-2) at a concentration of 1 µg/mL for 4 h at 37°C. For the unstimulated condition, PBMCs were cultured in cRPMI medium and respective dilution of solvent DMSO. After stimulation, cells were washed with cold FACS buffer and stained with surface antibodies (anti-CD19-PE/CF594, anti-CD56-FITC, anti-CD8-APC, anti-CD4-PE, anti-CD62L-PacificBlue, anti-CD45RA-PerCP-Cy5.5). Additionally, individual hashtag antibodies (2.5 µL per 5x106 PBMCs of TotalSeq-C anti-human hashtag antibodies 1–8, BioLegend, 394661, 394663, 394665, 394667, 394669, 394671, 394673, 394675) were included for sample multiplexing. All samples were incubated for 30 minutes on ice, followed by two washes with cold FACS buffer. Live/dead discrimination was performed using PI (1:200) immediately before sorting. Single, live, CD19- and CD56-negative, CD4- or CD8-positive, non-naïve (defined as CD45RA-positive and CD62L-negative, CD45RA-negative and CD62L-negative, or CD45RA-negative and CD62L-positive) lymphocytes were sorted in previously FCS-coated 96-well U-bottom plates filled with FACS buffer. Eight different samples were pooled prior to sequencing and later distinguished using the unique TotalSeq-C hashtags during scRNAseq analysis. Cells were sorted on a FACS Aria II cell sorter (BD). Immediately after sorting, cells were loaded to a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX, VDJ and CITEseq libraries according to the manufacturer’s instructions (10X Genomics, 1000263, 1000256, 1000252, 1000286, 1000250, 1000215, 1000190). Libraries were sent to Novogene (Cambridge, UK) and sequenced on an Illumina NovaSeq platform with PE150 strategy.
Library construction was performed according to manufacturer's instructions (10x Genomics) for 5' GEX, VDJ and CITEseq, V2 chemistry dual index

value: PBMC

value: T cells


title: pooledCells_scADT2

description:
Library name: Run2_ADT
10x Genomics


title: pooledCells_scADT1

description:
Library name: Run1_ADT
10x Genomics


title: pooledCells_scVDJ3

description:
Library name: Run3_VDJ
10x Genomics

data_processing:
The sequencing sample was processed via the cellranger (version 6.0.2, 10x Genomics) `multi`-command using the gene expression reference GRCh38 (version 2020A, 10x Genomics), the VDJ reference vdj-GRCh38 (version 5.0.0, 10x Genomics), and custom feature barcodes (barcodes.csv).
Assembly: GRCh38 (version 2020A, 10x Genomics), vdj-GRCh38 (version 5.0.0, 10x Genomics), barcodes.csv
Supplementary files format and content: comma-separated value files and matrix files


title: pooledCells_scVDJ2

description:
Library name: Run2_VDJ
10x Genomics


title: pooledCells_scGEX2

description:
Library name: Run2_GEX
10x Genomics


title: pooledCells_scGEX1

description:
Library name: Run1_GEX
10x Genomics


title: pooledCells_scGEX3

description:
Library name: Run3_GEX
10x Genomics


title: T1_DonorA5_stimulated_VDJ4

description:
Library name: Run4_T1_VDJ
10x Genomics

extract_protocol:
PBMCs were thawed from cryopreserved stocks and rested overnight at 1x10^6 cells/mL in cRPMI medium (RPMI 1640 Medium + 10% heat-inactivated FCS, 0.05 mM β-mercaptoethanol, 0.05 mg/mL gentamicin, 1.1915 g/L HEPES, 0.2 g/L L-glutamine, 100 U/mL Penicillin-Streptomycin). For each donor, 2x10^6 PBMCs were stimulated with stimulated with 11aa overlapping 15-mer PepMixTM SARS-CoV-2 spike glycoprotein peptide pool (JPT, PM-WCPV-S-2) at a concentration of 1 µg/mL for 4 h at 37°C. For the unstimulated condition, PBMCs were cultured in cRPMI medium and respective dilution of solvent DMSO. After stimulation, cells were washed with cold FACS buffer and stained with surface antibodies (anti-CD19-PE/CF594, anti-CD56-FITC, anti-CD8-APC, anti-CD4-PE, anti-CD62L-PacificBlue, anti-CD45RA-PerCP-Cy5.5). All samples were incubated for 30 minutes on ice, followed by two washes with cold FACS buffer. Live/dead discrimination was performed using PI (1:200) immediately before sorting. Single, live, CD19- and CD56-negative, CD4- or CD8-positive, non-naïve (defined as CD45RA-positive and CD62L-negative, CD45RA-negative and CD62L-negative, or CD45RA-negative and CD62L-positive) lymphocytes were sorted in previously FCS-coated 96-well U-bottom plates filled with FACS buffer. Cells were sorted on a FACS Aria II cell sorter (BD). Immediately after sorting, cells were loaded to a Chromium Next GEM Chip K (10X Genomics) and Chromium Next GEM Single-Cell 5′ kits v.2 were used to generate GEX and VDJ libraries according to the manufacturer’s instructions (10X Genomics). Libraries were sent to Novogene (Cambridge, UK) and sequenced on an Illumina NovaSeq platform with PE150 strategy.
Library construction was performed according to manufacturer's instructions (10x Genomics) for 5' GEX and VDJ, V2 chemistry dual index

value: stimulated


title: T1_DonorA4_stimulated_VDJ3

description:
Library name: Run3_T1_VDJ
10x Genomics


title: S1_DonorA5_stimulated_VDJ4

description:
Library name: Run4_S1_VDJ
10x Genomics


title: S1_DonorA4_stimulated_VDJ3

description:
Library name: Run3_S1_VDJ
10x Genomics


title: S1_DonorA5_unstimulated_VDJ2

description:
Library name: Run2_S1_VDJ
10x Genomics

value: unstimulated


title: S1_DonorA4_unstimulated_VDJ1

description:
Library name: Run1_S1_VDJ
10x Genomics


title: T1_DonorA5_stimulated_GEX4

description:
Library name: Run4_T1_GEX
10x Genomics


title: B_Low_freq. BulkTCR

description:
Library name: BulkTCR2
BulkTCR.tar.gz
BulkTCR_immunarch.tar.gz


title: T1_DonorA4_stimulated_GEX3

description:
Library name: Run3_T1_GEX
10x Genomics


title: T1_DonorA5_unstimulated_VDJ2

description:
Library name: Run2_T1_VDJ
10x Genomics


title: S1_DonorA4_stimulated_GEX3

description:
Library name: Run3_S1_GEX
10x Genomics


title: S1_DonorA5_stimulated_GEX4

description:
Library name: Run4_S1_GEX
10x Genomics


title: S1_DonorA4_unstimulated_GEX1

description:
Library name: Run1_S1_GEX
10x Genomics


title: T1_DonorA4_unstimulated_GEX1

description:
Library name: Run1_T1_GEX
10x Genomics


title: pooledCells_scVDJ1

description:
Library name: Run1_VDJ
10x Genomics


title: RE080

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

description: Library name: RE080

data_processing:
NovaSeq 6000 System
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
RNA was isolated from brain (10mg) with miRNeasy Purification of Total RNA (Qiagen), using Qiazol with handheld pestle-equipped device, 22-gauge needle. RNA quality and concentration was determined by Agilent Bioanalyzer.
Libraries were created by NYU GTC with Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Cat.20040529)

value: brain

tag: group

value: RE


title: RE081

description: Library name: RE081


title: RE078

description: Library name: RE078


title: RE079

description: Library name: RE079


title: RE076

description: Library name: RE076


title: RE077

description: Library name: RE077


title: RE072

description: Library name: RE072


title: RE071

description: Library name: RE071


title: RE074

description: Library name: RE074


title: T1_DonorA4_unstimulated_VDJ1

description:
Library name: Run1_T1_VDJ
10x Genomics


title: RE065

description: Library name: RE065


title: RE063

description: Library name: RE063


title: RE062

description: Library name: RE062


title: RE064

description: Library name: Sample_88


title: RE061

description: Library name: Sample_87


title: RE060

description: Library name: RE060


title: S1_DonorA5_unstimulated_GEX2

description:
Library name: Run2_S1_GEX
10x Genomics


title: T1_DonorA5_unstimulated_GEX2

description:
Library name: Run2_T1_GEX
10x Genomics


title: RE058

description: Library name: RE058


title: RE055

description: Library name: RE055


title: RE056

description: Library name: RE056


title: RE053

description: Library name: RE053


title: RE057

description: Library name: RE057


title: RE052

description: Library name: RE052


title: RE048

description: Library name: RE048

value: PWE


title: RE047

description: Library name: RE047


title: RE045

description: Library name: RE045


title: RE042

description: Library name: RE042


title: RE039

description: Library name: RE039


title: RE046

description: Library name: RE046


title: RE066

description: Library name: RE066


title: RE038

description: Library name: RE038


title: RE069

description: Library name: RE069


title: RE044

description: Library name: Sample_86


title: RE068

description: Library name: RE068


title: RE033

description: Library name: RE033

value: Control


title: RE041

description: Library name: RE041


title: RE024

description: Library name: RE024


title: RE009

description: Library name: RE009


title: RE005

description: Library name: RE005


title: RE029

description: Library name: RE029


title: RE059

description: Library name: RE059


title: RE026

description: Library name: RE026


title: RE049

description: Library name: RE049


title: RE006

description: Library name: RE006


title: RE007

description: Library name: RE007


title: RE003

description: Library name: RE003


title: RE002

description: Library name: RE002


title: RE001

description: Library name: RE001


title: RE004

description: Library name: RE004


title: PBMC_M1_7

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

institute: Yonsei University

description:
Library name: PBMC_7
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient with PSA > 5000 ng/mL (sample PBMC_M1_7_PSA5000) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.

data_processing:
Raw BCL files were demultiplexed and converted to FASTQ using Cell Ranger mkfastq.
FASTQ files were aligned to the GRCh38 human reference genome and gene-barcode matrices were generated using Cell Ranger count.
Gene expression matrices were loaded into Seurat. Cells with <500 or >7500 detected genes or >15% mitochondrial content were filtered out.
Gene expression data were log-normalized, and dimensionality reduction (PCA, UMAP), clustering, and batch correction were performed using Seurat v5.
Cell type annotation was performed using canonical marker genes and SingleR referencing HumanPrimaryCellAtlasData and DICE.
Assembly: GRCh38
Supplementary files format and content: expression_matrix_data1.csv: log-normalized gene expression matrix (rows = genes, columns = cells).
Supplementary files format and content: cell_metadata.csv: cell-level metadata including sample ID, cluster, cell type, QC metrics.

source_name: Peripheral blood mononuclear cells (PBMCs)

growth_protocol: Not applicable. Biopsy samples were processed immediately after collection without in vitro culturing.

extract_protocol:
Fresh metastatic prostate cancer biopsy tissues were enzymatically dissociated into single-cell suspensions using a tissue dissociation kit (e.g., Miltenyi). Cells were filtered, counted, and loaded onto the 10x Genomics Chromium controller.
Single-cell RNA libraries were generated using the 10x Genomics Chromium Single Cell 3’ v3 kit according to the manufacturer’s protocol. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 2×101 bp paired-end reads.

treatment_protocol: None. Patients did not receive treatment prior to metastatic lesion biopsy.

value: multiple


title: PBMC_M1_6

description:
Library name: PBMC_6
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_6) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.

value: Peripheral blood mononuclear cells (PBMCs)


title: Negative control (neutral medium)

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description:
Library name: ControlMetabo
Negative control in neutral medium

data_processing:
Cell Ranger version 6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 (Hierarchical Data Format 5) count matrices. Genes as rows, cells as columns.

source_name: breast

growth_protocol: Neutral medium (control): 1.44mL insulin; 250µL hydrocortisone; 5.3mL pyruvate (1mM); 5.7mL glucose (6mM); 2.65mL glutamine (1mM).

extract_protocol:
10X Genomics Single Cell 3' v3
10X Genomics Single Cell 3' v3 kit (UMI-based)

treatment_protocol: Glucose-rich medium (glycolysis induction): 19.1 mL glucose; 2.65 mL glutamine; no hydrocortisone; no pyruvate; no insulin. Glucose-deprived medium (oxidative phosphorylation induction): 250µL hydrocortisone; 5.3 mL pyruvate (1mM); 2.6 mL glucose (0.5mM); 2.6mM glutamine (1mM); 4.5 mL galactose (5mM); no insulin.

value: breast

value: hMEC

value: cell line

value: wild type

value: untreated


title: PBMC_M1_4

description:
Library name: PBMC_4
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_4) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.


title: Glycolysis

description:
Library name: Glyco
Cells post-glycolysis induction

value: glycolysis-inducing medium


title: PBMC_M1_5

description:
Library name: PBMC_5
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_5) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.


title: Interferon alpha response

description:
Library name: IFNa
Response to interferon alpha

data_processing:
Cell Ranger version 6.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 (Hierarchical Data Format 5) count matrices. Genes as rows, cells as columns.

extract_protocol:
10X Genomics Single Cell 3' v3
10x Genomics 3' v3 kit (UMI-based)

treatment_protocol: MDA-MB-468 were exposed to IFNα and gamma IFNγ for respectively 4 and 18 hours before single-cell analyses. Control MDA-MB-468 cells were not exposed to any interferon.


title: Oxidative phosphorylation

description:
Library name: OxPhos
Cells post-oxphos induction

value: oxphos-inducing medium


title: PBMC_M1_3

description:
Library name: PBMC_3
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_3) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.


title: RE022

description: Library name: RE022


title: PBMC_M1_2

description:
Library name: PBMC_2
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_2) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.


title: Negative control (no IFN stimulation)

description:
Library name: controlIFN
Negative control without exposure to any IFN


title: Interferonn gamma response

description:
Library name: IFNg
Response to interferon gamma


title: RE008

description: Library name: Sample_85


title: PBMC_M1_1

description:
Library name: PBMC_1
Single-cell RNA-seq from peripheral blood mononuclear cells (PBMCs) of a metastatic prostate cancer patient (sample PBMC_M1_1) using 10x Genomics Chromium Single Cell 3′ Gene Expression v3 kit.


title: Day 1

description:
Library name: D1
Day 1 post EMT induction

data_processing:
Cell Ranger version 7.1.0
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 (Hierarchical Data Format 5) count matrices. Genes as rows, cells as columns.

treatment_protocol: The epithelial-to-mesenchymal transition was induced in MCF10A cells, via the addition of TGF-β in the medium.

value: 1 day post TGFb-mediated EMT


title: Day 3

description:
Library name: D3
Day 3 post EMT induction

value: 3 days post TGFb-mediated EMT


title: Day 4

description:
Library name: D4
Day 4 post EMT induction

value: 4 days post TGFb-mediated EMT


title: Day 5

description:
Library name: D5
Day 5 post EMT induction

value: 5 days post TGFb-mediated EMT


title: EMT

description:
Library name: EMT
Post EMT induction positive control

data_processing:
Cell Ranger version 3.1.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 (Hierarchical Data Format 5) count matrices. Genes as rows, cells as columns.

treatment_protocol: The epithelial-to-mesenchymal transition was induced in MCF10A cells, via the addition of TGF-β in the medium. MCF10A cells were irradiated at 4Gy using the Centre Léon Bérard radiology facility. Cells were analysed 4 hours post-irradiation.

tag: batch


title: Control

description:
Library name: Control_MCF10A
Negative control for both EMT and DNArepair induction


title: TCR, Subject 5, vehicle, challenge 3

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

description:
Library name: TCRS5P3
10x Genomics

data_processing:
Demultiplexing and data preprocessing including quality control, read alignment (hg38), and gene quantification was conducted using the 10x Cell Ranger software (v6.0.2).
Assembly: hg38
Supplementary files format and content: Comma separated values files

source_name: Epidermis

extract_protocol:
Skin samples were incubated overnight in 2.4 mg/ml Dispase (Roche) in phosphate buffered saline (PBS) solution at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.5 mg/ml Collagenase D (Roche) with deoxyribonuclease (0.1%, Sigma-Aldrich) in PBS for a total of 1 hour at 37°C, quenched with 2% bovine serum albumin (BSA) (Sigma Aldrich) in PBS, and strained through a 70-μm mesh strainer. The strainer was washed through with 2% BSA in PBS to collect any remaining cells. The single cell suspension was always kept on ice.
We used 10X Genomics Chromium Next GEM Single Cell 5’ kit, v2 with 5’ Feature Barcode kit alongside Chromium Single Cell Human TCR Amplification kit for TCRαβ and Dual Index Kit TT and TN Set A. The kit was used to the manufacturer’s instructions. The samples were multiplexed, using TotalSeq-C hashtag antibodies (Biolegend). The sequencing was carried out on an Illumina NovaSeq 6000 using a S4 flow cell, 200 cycles, to the manufacturer’s instructions.

value: Epidermis

tag: disease

value: Allergic contact dermatitis

value: Petrolatum


title: TCR, Subject 5, vehicle, challenge 2

description:
Library name: TCRS5P2
10x Genomics


title: TCR, Subject 5, vehicle, challenge 1

description:
Library name: TCRS5P1
10x Genomics


title: TCR, Subject 5, nickel, challenge 3

description:
Library name: TCRS5N3
10x Genomics

value: Nickel


title: Day 2

description:
Library name: D2
Day 2 post EMT induction

value: 2 days post TGFb-mediated EMT


title: DNArepair

description:
Library name: DNArepair
Post DNArepair induction positive control

value: 4h post irradiation (4Gy)


title: TCR, Subject 5, nickel, challenge 1

description:
Library name: TCRS5N1
10x Genomics


title: TCR, Subject 4, vehicle, challenge 3

description:
Library name: TCRS4P3
10x Genomics


title: TCR, Subject 5, nickel, challenge 2

description:
Library name: TCRS5N2
10x Genomics


title: Not induced

description:
Library name: NI
Untreated negative control

value: breast


title: TCR, Subject 4, vehicle, challenge 2

description:
Library name: TCRS4P2
10x Genomics


title: TCR, Subject 4, vehicle, challenge 1

description:
Library name: TCRS4P1
10x Genomics


title: TCR, Subject 4, nickel, challenge 3

description:
Library name: TCRS4N3
10x Genomics


title: TCR, Subject 4, nickel, challenge 1

description:
Library name: TCRS4N1
10x Genomics


title: TCR, Subject 4, nickel, challenge 2

description:
Library name: TCRS4N2
10x Genomics


title: TCR, Subject 3, vehicle, challenge 2

description:
Library name: TCRS3P2
10x Genomics


title: TCR, Subject 3, vehicle, challenge 3

description:
Library name: TCRS3P3
10x Genomics


title: TCR, Subject 3, vehicle, challenge 1

description:
Library name: TCRS3P1
10x Genomics


title: TCR, Subject 3, nickel, challenge 3

description:
Library name: TCRS3N3
10x Genomics


title: TCR, Subject 3, nickel, challenge 2

description:
Library name: TCRS3N2
10x Genomics


title: TCR, Subject 3, nickel, challenge 1

description:
Library name: TCRS3N1
10x Genomics


title: TCR, Subject 2, vehicle, challenge 3

description:
Library name: TCRS2P3
10x Genomics


title: TCR, Subject 2, vehicle, challenge 2

description:
Library name: TCRS2P2
10x Genomics


title: TCR, Subject 2, vehicle, challenge 1

description:
Library name: TCRS2P1
10x Genomics


title: TCR, Subject 1, vehicle, challenge 3

description:
Library name: TCRS1P3
10x Genomics


title: TCR, Subject 1, nickel, challenge 2

description:
Library name: TCRS1N2
10x Genomics


title: TCR, Subject 1, vehicle, challenge 1

description:
Library name: TCRS1P1
10x Genomics


title: TCR, Subject 2, nickel, challenge 3

description:
Library name: TCRS2N3
10x Genomics


title: TCR, Subject 1, nickel, challenge 1

description:
Library name: TCRS1N1
10x Genomics


title: TCR, Subject 2, nickel, challenge 2

description:
Library name: TCRS2N2
10x Genomics


title: LCL_WT_H4K16ac_rep2

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Library name: Sample 4

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

source_name: lymphoblastoid cell lines

growth_protocol: Lymphoblastoid cell lines (LCLs) from EBV-transformed patient lymphocytes were maintained in RPMI-1640 (Biological Industries Beit Haemek, Israel) supplemented with appropriate serum, 1% L-glutamine and 1% penicillin-streptomycin antibiotics (Biological Industries Beit Haemek, Israel).

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

value: lymphoblastoid cell lines

value: lymphocytes

value: WT


title: TCR, Subject 1, vehicle, challenge 2

description:
Library name: TCRS1P2
10x Genomics


title: TCR, Subject 1, nickel, challenge 3

description:
Library name: TCRS1N3
10x Genomics


title: LCL_input

description: Library name: Sample 5


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_2

first: Jesper

middle: Q

last: Svejstrup

department: ICMM

institute: University of Copenhagen

description: Library name: UBC_500nM_2

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.20.0.422) and resultant FASTQ files were quality checked using MultiQC (v1.11).
Paired-end reads were aligned separately to the GRCh38 and sacCer3 genomes using hisat2 (v2.2.1) with options --no-mixed --no-discordant -p 16 --rna-strandness RF, followed by identification of PCR duplicates using picard Markduplicates.
For external reference normalization using yeast spike-in material, reads mapping to genes in the GRCh38 and sacCer3 genome were counted using FeatureCounts from the subread package (v2.0.6; featureCounts -O -M -T 4 -s 2 --fraction -t gene). Afterwards, a dds object was generated with DESeq2, using the yeast sizeFactors for normalization to account for global changes in transcription. Differential gene expression was then determined using the results() function with alpha=0.01 and for visualization as MA-plots, the fold-change was shrunken using the apeglm method.
Additionally, BAM files were converted to strand-specific bigWig files using the bamCoverage function from the deeptools package (v3.5.5, options: --samFlagInclude 64 --normalizeUsing None --scaleFactor ${scalefactor} -p 16 --binSize 1 --filterRNAstrand=forward/reverse).
Assembly: GRCh38
Supplementary files format and content: bigwig, scaled according to yeast spike-in material

growth_protocol: RPB1 degron cells were cultured in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 100U/mL penicillin, and 100µg/mL streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Following a 15 minute pulse with 1mM 4sU, media was aspirated and cells were harvested by the addition of 1mL Trizol to stop the reaction. To isolate total RNA, one-fifth of chloroform was added to lysates and shaken well, followed by centrifugation (12000g, 5 minutes at 4C). The upper aqueous phase was transferred to MaXtract high-density phase-lock tubes, that were previously prepared according to manufacturer’s instructions, and an equal volume of chloroform/isoamyl alcohol (24:1) was added. Lysates were then centrifuged again (12000g, 5 minutes at 4C) and the upper aqueous phase was transferred to a new tube. The RNA was then precipitated through the addition of 1.1X volumes of 100% isopropanol, incubation at room temperature for 20 minutes and centrifugation (12000g, 20 minutes at 4C). RNA pellets were washed once with 85% (v/v) ethanol, and air dried at room temperature before resuspension in Ultrapure DNase/RNase-free distilled water. As an external reference control, 500ng S.cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) nascent RNA was spiked-in to 100µg of H.sapiens total RNA. The RNA was then fragmented by the addition of 20µL 1M NaOH and incubation on ice for 20 minutes. Fragmentation was stopped by the addition of 80µL 1M Tris HCl pH 6.8 and material was purified twice using the Micro Bio-Spin P-30 Gel Columns according to manufacturer’s instructions. Thiol-specific biotinylation of RNA was performed using 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 mg MTSEA biotin-XX linker in a final volume of 250µL and incubation at room temperature for 30 minutes in the dark. Biotinylated RNA was then purified by addition of 250μL of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol)), followed by shaking and addition to MaXtract high-density phase-lock tubes that were previously prepared according to manufacturers instructions. Following centrifugation (12000g, 5minutes at 4C), the upper aqueous phase was transferred to a new tube and biotinylated RNA was precipitated using one-tenth the volume 5M NaCl and 1.1X volume 100% isopropanol, followed by incubation at room temperature for 10 minutes and centrifugation (20000g, 20 minutes at 4C). RNA pellets were washed once in 85% (v/v) ethanol, air dried at room temperature, and resuspended in 50µL Ultrapure DNase/RNase-free distilled water. The RNA was then denatured by incubating for 10 minutes at 65°C in the dark. Biotinylated RNA was separated from the total RNA pool by addition of 100 μL μMACS Streptavidin MicroBeads and incubation for 15 minutes at room temperature with constant rotation. Beads were then applied to a μColumn pre-equilibrated with 100 µL nucleic acid equilibration buffer and immobilised on a magnetic stand, washed twice with pre-warmed (55°C) wash buffer (100 mM Tris HCl pH 7.4 10mM EDTA, 1M NaCl and 0.1% (v/v) Tween 20) and biotinylated RNA was eluted by two additions of 100μL 100 mM DTT, 5 minutes apart. Purification of biotinylated RNA was performed using the RNeasy MinElute kit according to manufacturer’s instructions, where 1050 μL 100% ethanol and 750 μL RLT buffer was added per 200μL reaction to precipitate RNA < 200 nt.
Sequencing libraries were then constructed from biotinylated RNA using a KAPA RNA HyperPrep kit (Roche) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol: RPB1 degron cells were seeded at a density of 4 million cells in a 10cm plate and were either treated with DMSO or different concentrations of dTAGv-1 for 16 hours before harvest. Prior to harvest, cells were pulsed for 15 minutes with 1mM 4-thiouridine, to metabolically label nascently transcribed RNA.

value: RPB1 degron D4; UBC-RPB1-His

value: 500nM dTAGv1


title: LCL_PHF20KO_H4K16ac_rep2

description: Library name: Sample 2


title: LCL_PHF20KO_H4K16ac_rep1

description: Library name: Sample 1


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_3

description: Library name: UBC_500nM_3


title: LCL_WT_H4K16ac_rep1

description: Library name: Sample 3


title: RPB1degron_UBC-RPB1_500nM_dTAGv1_DMSO_1

description: Library name: UBC_500nM_1


title: RPB1degron_UBC-RPB1_DMSO_1

description: Library name: UBC_DMSO_1

value: DMSO


title: RPB1degron_500nM_dTAGv1_2

description: Library name: 500nM_2

value: RPB1 degron D4


title: RPB1degron_UBC-RPB1_DMSO_2

description: Library name: UBC_DMSO_2


title: RPB1degron_250nM_dTAGv1_3

description: Library name: 250nM_3

value: 250nM dTAGv1


title: RPB1degron_500nM_dTAGv1_3

description: Library name: 500nM_3


title: RPB1degron_250nM_dTAGv1_2

description: Library name: 250nM_2


title: RPB1degron_167nM_dTAGv1_3

description: Library name: 167nM_3

value: 167nM dTAGv1


title: TCR, Subject 2, nickel, challenge 1

description:
Library name: TCRS2N1
10x Genomics


title: RPB1degron_167nM_dTAGv1_1

description: Library name: 167nM_1


title: RPB1degron_167nM_dTAGv1_2

description: Library name: 167nM_2


title: RPB1degron_125nM_dTAGv1_2

description: Library name: 125nM_2

value: 125nM dTAGv1


title: RPB1degron_125nM_dTAGv1_1

description: Library name: 125nM_1


title: RPB1degron_83nM_dTAGv1_1

description: Library name: 83nM_1

value: 83nM dTAGv1


title: RPB1degron_83nM_dTAGv1_3

description: Library name: 83nM_3


title: RPB1degron_62nM_dTAGv1_2

description: Library name: 62nM_2

value: 62nM dTAGv1


title: RPB1degron_83nM_dTAGv1_2

description: Library name: 83nM_2


title: RPB1degron_32nM_dTAGv1_3

description: Library name: 32nM_3

value: 32nM dTAGv1


title: RPB1degron_62nM_dTAGv1_3

description: Library name: 62nM_3


title: RPB1degron_32nM_dTAGv1_2

description: Library name: 32nM_2


title: RPB1degron_500nM_dTAGv1_1

description: Library name: 500nM_1


title: RPB1degron_UBC-RPB1_DMSO_3

description: Library name: UBC_DMSO_3


title: RPB1degron_16nM_dTAGv1_2

description: Library name: 16nM_2

value: 16nM dTAGv1


title: RPB1degron_8nM_dTAGv1_3

description: Library name: 8nM_3

value: 8nM dTAGv1


title: RPB1degron_16nM_dTAGv1_3

description: Library name: 16nM_3


title: RPB1degron_32nM_dTAGv1_1

description: Library name: 32nM_1


title: RPB1degron_16nM_dTAGv1_1

description: Library name: 16nM_1


title: RPB1degron_250nM_dTAGv1_1

description: Library name: 250nM_1


title: RPB1degron_4nM_dTAGv1_1

description: Library name: 4nM_1

value: 4nM dTAGv1


title: RPB1degron_8nM_dTAGv1_1

description: Library name: 8nM_1


title: RPB1degron_4nM_dTAGv1_3

description: Library name: 4nM_3


title: RPB1degron_2nM_dTAGv1_3

description: Library name: 2nM_3

value: 2nM dTAGv1


title: RPB1degron_2nM_dTAGv1_1

description: Library name: 2nM_1


title: RPB1degron_DMSO_3

description: Library name: DMSO_3


title: RPB1degron_DMSO_2

description: Library name: DMSO_2


title: RPB1degron_2nM_dTAGv1_2

description: Library name: 2nM_2


title: RPB1degron_DMSO_1

description: Library name: DMSO_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040318

description: Library name: OP23YS040156

data_processing:
Raw sequencing reads were quality-checked using FastQC. Adapter trimming was performed using Trimmomatic.
Trimmed reads were aligned to the human reference genome (GRCh38) using STAR aligner with default parameters.
Gene-level quantification was performed using featureCounts based on GENCODE annotations.
Expression values were normalized to TPM, log2-transformed, and compiled into a processed expression matrix.
All processed data are provided in a matrix format where rows represent genes and columns represent samples.
Assembly: GRCh38 (GENCODE v38 annotation)
Supplementary files format and content: Processed data files are in CSV format and contain TPM-log2 normalized expression values. Each row represents a gene, and each column represents a sample. File name: YUHS_TPM_EXPR_Biopsy_processed.csv
Supplementary files format and content: Gene symbols are used as row names; expression values are log2(TPM + 1) transformed.

source_name: prostate

extract_protocol:
Total RNA was extracted from frozen biopsy tissues using the Qiagen RNeasy Mini Kit, following the manufacturer's protocol. On-column DNase I treatment was included to remove genomic DNA contamination.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly-A selection was used to enrich for mRNA. Libraries were quantified using Qubit and Bioanalyzer.

treatment_protocol: Fresh prostate adenocarcinoma biopsy samples were collected from patients at Yonsei University Health System. Samples were immediately stabilized in RNAlater and stored at −80°C until RNA extraction.

value: prostate


title: RPB1degron_8nM_dTAGv1_2

description: Library name: 8nM_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040317

description: Library name: OP23YS040087


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040316

description: Library name: OP24YS040141


title: RPB1degron_125nM_dTAGv1_3

description: Library name: 125nM_3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040315

description: Library name: OP24YS040134


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040314

description: Library name: OP24YS040089


title: RPB1degron_62nM_dTAGv1_1

description: Library name: 62nM_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040313

description: Library name: OP23YS040123


title: RPB1degron_4nM_dTAGv1_2

description: Library name: 4nM_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040312

description: Library name: OP24YS040143


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040309

description: Library name: OP23YS040302


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040307

description: Library name: OP23YS040160


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040305

description: Library name: OP23YS040132


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040308

description: Library name: OP23YS040299


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040303

description: Library name: OP23YS040073


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040306

description: Library name: OP23YS040133


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040302

description: Library name: OP23YS040051


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040304

description: Library name: OP23YS040097


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040299

description: Library name: OP23YS040305


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040300

description: Library name: OP23YS040040


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040297

description: Library name: OP23YS040124


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040301

description: Library name: OP23YS040045


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040296

description: Library name: OP23YS040096


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040298

description: Library name: OP23YS040157


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040295

description: Library name: OP23YS040080


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040294

description: Library name: OP23YS040075


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040293

description: Library name: OP23YS040043


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040291

description: Library name: OP24YS040131


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040292

description: Library name: OP23YS040022


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040311

description: Library name: OP24YS040142


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040288

description: Library name: OP24YS040095


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040290

description: Library name: OP24YS040115


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040310

description: Library name: OP24YS040118


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040287

description: Library name: OP23YS040309


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040285

description: Library name: OP23YS040158


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040284

description: Library name: OP23YS040155


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040283

description: Library name: OP23YS040154


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040282

description: Library name: OP23YS040142


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040281

description: Library name: OP23YS040092


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040280

description: Library name: OP23YS040091


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040279

description: Library name: OP23YS040089


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040276

description: Library name: OP23YS040072


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040275

description: Library name: OP23YS040058


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040278

description: Library name: OP23YS040085


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040273

description: Library name: OP23YS040041


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040272

description: Library name: OP23YS040039


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040271

description: Library name: OP23YS040027


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040274

description: Library name: OP23YS040044


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040269

description: Library name: OP23YS040005


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040268

description: Library name: OP24YS040139


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040267

description: Library name: OP24YS040138


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040270

description: Library name: OP23YS040011


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040266

description: Library name: OP24YS040126


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040286

description: Library name: OP23YS040308


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040265

description: Library name: OP24YS040119


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040264

description: Library name: OP24YS040117


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040263

description: Library name: OP24YS040116


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040289

description: Library name: OP24YS040106


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040259

description: Library name: OP23YS040306


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040261

description: Library name: OP24YS040097


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040262

description: Library name: OP24YS040101


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040277

description: Library name: OP23YS040083


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040260

description: Library name: OP23YS040393


title: TCam-2, DMSO, biol rep 3

city: Bonn

first: Aylin

last: Hansen

address: Venusberg-Campus 1

department: Pathology, Developmental Pathology

institute: University Hospital Bonn

data_processing:
The nf-core rnaseq pipeline (version 3.17) was applied for the preprocessing and the quantification of the reads using default parameters
Here the first step is quality and adapter trimming with TrimGalore
This will be followed by aligning the trimmed reads against human genome (GRCh38) with STAR (version 2.7.11b)
The aligned data are then used as input for Salmon (version 1.9.0), which employs pseudoalignment to estimate transcript abundances
The transcript-level quantifications will then be aggregated to obtain gene-level expression estimates.
The statistical analysis was executed in the R environment (version 4.2.0)
. To ensure the robustness of the results, only genes with a minimum count of 5 in at least three samples were utilized for the inference analysis
The Bioconductor package DESeq2 was employed for the differential gene expression analysis
Subsequently, the Benjamini-Hochberg method was applied to calculate multiple testing adjusted p-values (false discovery rate, FDR) for each contrast.
Assembly: human genome (GRCh38)
Supplementary files format and content: tab limited text file includes raw gene counts for each sample

growth_protocol: 2102 EP cell were cultured in DMEM supplemented with 10 % FBS, 1 % Penicillin/Streptomycin and 1 % L-Glutamine. TCam-2 cells were cultivated in RPMI supplemented with 10 % FBS, 1 % Penicillin/Streptomycin and 1 % L-Glutamine. All cells were cultivated in an incubator at 37 °C and 7.5 % CO2

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Quiagen).
RNA libraries for RNA-seq were preapared using the Lexogen QuantSeq 30-mRNA Library Prep Kit.

treatment_protocol: Cell were treated with I-BRD9 (15 µM) or solvent control DMSO.

value: seminoma

tag: time

value: 24 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040256

description: Library name: OP23YS040140


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040258

description: Library name: OP23YS040148


title: TCam-2, DMSO, biol rep 1

value: WT


title: TCam-2, DMSO, biol rep 2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040255

description: Library name: OP23YS040139


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040257

description: Library name: OP23YS040144


title: TCam-2, I-BRD9, biol rep 3


title: TCam-2, I-BRD9, biol rep 1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040253

description: Library name: OP23YS040134


title: TCam-2, I-BRD9, biol rep 2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040254

description: Library name: OP23YS040138


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040252

description: Library name: OP23YS040127


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040251

description: Library name: OP23YS040076


title: 2102 EP, DMSO, biol rep 3

value: embryonal carcinoma


title: 2102 EP, DMSO, biol rep 2

value: DMSO


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040250

description: Library name: OP23YS040074


title: 2102 EP, DMSO, biol rep 1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040249

description: Library name: OP23YS040065


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040248

description: Library name: OP23YS040064


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040247

description: Library name: OP23YS040059


title: 2102 EP, I-BRD9, biol rep 2


title: D6_Dax_PRP

city: Naples

first: Logan

last: Piening

state: FL

address: 1370 Creekside Blvd

department: Orthobiologics

institute: Arthrex Inc.

description: Extracellular Vesicle miRNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.0
Supplementary files format and content: excel,expression profiles
Supplementary files format and content: GZ files, expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA).

treatment_protocol: Anticoagulated (13% v/v ACD-A) whole blood was processed using the Arthrex ACP Max and Arthrex Angel Systems for 60 mL. The resulting platelet-rich and platelet-poor plasma were collected. Extracellular vesicles were isolated from the fluids using the SystemBio ExoQuick Ultra kit according to manufacturer's instructions

value: Blood

value: Plasma Separation and Reuspension


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040245

description: Library name: OP23YS040008


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040246

description: Library name: OP23YS040009


title: D6_Max_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040243

description: Library name: OP23YS040311


title: D6_Angel_PRP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040241

description: Library name: OP24YS040128


title: D6_Angel_PPP

description: Extracellular Vesicle miRNA


title: D5_Dax_PRP

description: Extracellular Vesicle miRNA


title: D5_Max_PPP

description: Extracellular Vesicle miRNA


title: D5_Angel_PRP

description: Extracellular Vesicle miRNA


title: D5_Angel_PPP

description: Extracellular Vesicle miRNA


title: 2102 EP, I-BRD9, biol rep 3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040237

description: Library name: OP24YS040087


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040242

description: Library name: OP24YS040145


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040235

description: Library name: OP23YS040403


title: D4_Angel_PRP

description: Extracellular Vesicle miRNA


title: 2102 EP, I-BRD9, biol rep 1


title: D4_Dax_PRP

description: Extracellular Vesicle miRNA


title: D4_Max_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040234

description: Library name: OP23YS040387


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040238

description: Library name: OP24YS040111


title: D3_Dax_PRP

description: Extracellular Vesicle miRNA


title: D4_Angel_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040233

description: Library name: OP23YS040310


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040232

description: Library name: OP23YS040307


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040236

description: Library name: OP24YS040084


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040239

description: Library name: OP24YS040120


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040231

description: Library name: OP23YS040149


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040230

description: Library name: OP23YS040068


title: D3_Angel_PPP

description: Extracellular Vesicle miRNA


title: D3_Angel_PRP

description: Extracellular Vesicle miRNA


title: D2_Dax_PRP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040244

description: Library name: OP23YS040159


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040229

description: Library name: OP23YS040052


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040240

description: Library name: OP24YS040123


title: D2_Max_PPP

description: Extracellular Vesicle miRNA


title: 463-Texpand

city: Kgs. Lyngby

first: Kamilla Kjærgaard

last: Munk

address: Henrik Dams Allé, 204

department: Department of Health Technology

institute: Technical University of Denmark

description: Library name: 463-Texpand

data_processing:
RNA-Seq reads were trimmed and quantified with Kallisto.
Raw RNA-Seq reads were trimmed using Trim Galore v0.6.4 (parameters; quality: 20, length: 30).
Trimmed reads were pseudoaligned to the human genome (GRCh38), and transcript abundances were quantified using Kallisto v0.42.1 (parameters; 500 bootstrap samples).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with transcript abundances for each sample

source_name: Human T cells

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Micro kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: Human T cells

value: Human T cells engineered to express a chimeric antigen receptor

value: Texpand


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040227

description: Library name: OP23YS040391


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040228

description: Library name: OP22YS040032


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040226

description: Library name: OP23YS040143


title: D2_Angel_PRP

description: Extracellular Vesicle miRNA


title: 463-Dynabead

description: Library name: 463-Dynabead

value: Dynabead


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040225

description: Library name: OP23YS040086


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040224

description: Library name: OP23YS040069


title: D3_Max_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040223

description: Library name: OP23YS040063


title: D1_Dax_PRP

description: Extracellular Vesicle miRNA


title: 462-Texpand

description: Library name: 462-Texpand


title: 462-Dynabead

description: Library name: 462-Dynabead


title: D1_Max_PPP

description: Extracellular Vesicle miRNA


title: D2_Angel_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040221

description: Library name: OP23YS040035


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040222

description: Library name: OP23YS040047


title: 461-Texpand

description: Library name: 461-Texpand


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040220

description: Library name: OP24YS040137


title: D1_Angel_PRP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040219

description: Library name: OP24YS040133


title: 461-Dynabead

description: Library name: 461-Dynabead


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040217

description: Library name: OP24YS040129


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040218

description: Library name: OP24YS040130


title: D1_Angel_PPP

description: Extracellular Vesicle miRNA


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040216

description: Library name: OP24YS040127


title: 460-Texpand

description: Library name: 460-Texpand


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040215

description: Library name: OP24YS040102


title: XVE:EPFL4, 8h induction, rep 4

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Library name: EPFL4_8h_4

data_processing:
Paired-end reads were mapped to the Arabidopsis TAIR10 genome (EnsemblePlants, release 58) sequence with corresponding gtf file to obtain reads per gene using STAR aligner (v 2.7.11a )
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count per gene, one file per sample

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

growth_protocol: Seeds were surface-sterilized with absolute ethyl alcohol for 5 min and 75% ethanol for 15 min, then washed three-four times with sterilized distilled water under aseptic conditions. Surface-sterilized seeds were germinated on half-strength Murashige and Skoog (MS) medium in an incubator (22 °C on a 16 h/8 h light/dark cycle).

extract_protocol:
RNA was extracted from 7-day-old Arabidopsis seedlings using ReliaPrep™ RNA Miniprep.
RNA library for RNA-Seq were prepared using SMARTER mRNA-Seq library prep kit following manufacturers' protocol.

treatment_protocol: For estradiol induction, seeds of wild type, er mutant and XVE:ER transformed er mutant were first germinated on ½MS plates for seven days, and then the 7-day-old seedlings were transferred to mock-plates for 0h induction, or 5 mM 17-β estradiol plates for 3h or 8h induction.

value: 7-day-old seedlings

value: XVE:EPFL4 transformed wild type

value: Estradiol induction

tag: estradiol induction_time

value: 8 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040214

description: Library name: OP24YS040091


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040213

description: Library name: OP24YS040090


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040211

description: Library name: OP23YS040395


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040212

description: Library name: OP24YS040086


title: 6.9.3_High_freq, BulkRNA

description:
Library name: BulkRNA10
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz

data_processing:
Cellranger-7.0.1, Kallisto (v0.46.2), MIXCR(v4.7.0)
Assembly: GRCh38
Supplementary files format and content: Cellranger output file: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger output file: airr_rearrangement.tsv
Supplementary files format and content: Kallisto output files: abundance.h5, abundance.tsv
Supplementary files format and content: MIXCR output files: clones_TRA.tsv, clones_TRB.tsv

value: NLV-specific T cells


title: XVE:EPFL4, 8h induction, rep 3

description: Library name: EPFL4_8h_3


title: 6.10.1_Low_freq, BulkRNA

description:
Library name: BulkRNA11
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: XVE:EPFL4, 8h induction, rep 1

description: Library name: EPFL4_8h_1


title: XVE:EPFL4, 8h induction, rep 2

description: Library name: EPFL4_8h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040209

description: Library name: OP23YS040313

value: prostate


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040210

description: Library name: OP23YS040385


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040207

description: Library name: OP23YS040304


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040208

description: Library name: OP23YS040312


title: er XVE:ER, 8h induction, rep 4

description: Library name: ER_15_8h_4

value: XVE:ER transformed er mutant


title: 10.2_High_freq, BulkRNA

description:
Library name: BulkRNA8
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040206

description: Library name: OP23YS040303


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040204

description: Library name: OP23YS040145


title: er XVE:ER, 8h induction, rep 3

description: Library name: ER_15_8h_3


title: J_High_freq, BulkRNA

description:
Library name: BulkRNA7
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040205

description: Library name: OP23YS040293


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040203

description: Library name: OP23YS040141


title: er XVE:ER, 8h induction, rep 2

description: Library name: ER_15_8h_2


title: I_Low_freq, BulkRNA

description:
Library name: BulkRNA6
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: 460-Dynabead

description: Library name: 460-Dynabead


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040202

description: Library name: OP23YS040130


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040201

description: Library name: OP23YS040126


title: 6.9.2_Low_freq, BulkRNA

description:
Library name: BulkRNA9
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040200

description: Library name: OP23YS040125


title: er XVE:ER, 8h induction, rep 1

description: Library name: ER_15_8h_1


title: G_Low_freq, BulkRNA

description:
Library name: BulkRNA5
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: WT, 8h induction, rep 4

description: Library name: WT_8h_4

value: Wild type


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040197

description: Library name: OP23YS040082


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040198

description: Library name: OP23YS040084


title: WT, 8h induction, rep 3

description: Library name: WT_8h_3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040195

description: Library name: OP23YS040079


title: D_High_freq, BulkRNA

description:
Library name: BulkRNA3
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: B_Low_freq. BulkRNA

description:
Library name: BulkRNA2
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: WT, 8h induction, rep 2

description: Library name: WT_8h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040193

description: Library name: OP23YS040054


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040192

description: Library name: OP23YS040024


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040190

description: Library name: OP24YS040135


title: A_Low_freq, BulkRNA

description:
Library name: BulkRNA1
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: XVE:EPFL4, 3h induction, rep 4

description: Library name: EPFL4_3h_4

value: 3 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040191

description: Library name: OP23YS040012


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040189

description: Library name: OP24YS040124


title: NLV-specific T cells from HF donors , VDJ_GEM2

description:
Library name: VDJ_GEM2
GEX_HTO_ADT_VDJ_multiout_GEM2.tar.gz
single_cell_processed_seu_obj.tar.gz

library_source: other

molecule: other


title: XVE:EPFL4, 3h induction, rep 3

description: Library name: EPFL4_3h_3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040188

description: Library name: OP24YS040109


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040187

description: Library name: OP24YS040108


title: XVE:EPFL4, 3h induction, rep 2

description: Library name: EPFL4_3h_2


title: NLV-specific T cells from HF donors , VDJ_GEM1

description:
Library name: VDJ_GEM1
GEX_HTO_ADT_VDJ_multiout_GEM1.tar.gz
single_cell_processed_seu_obj.tar.gz


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040199

description: Library name: OP23YS040088


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040185

description: Library name: OP24YS040098


title: H_High_freq, BulkRNA

description:
Library name: BulkRNA4
BulkRNA.tar.gz
BulkRNA_Deseq_obj.tar.gz


title: XVE:EPFL4, 3h induction, rep 1

description: Library name: EPFL4_3h_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040196

description: Library name: OP23YS040081


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040194

description: Library name: OP23YS040078


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040184

description: Library name: OP23YS040392


title: NLV-specific T cells from HF donors , HTO_ADT_GEM3

description:
Library name: HTO_ADT_GEM3
GEX_HTO_ADT_VDJ_multiout_GEM3.tar.gz
single_cell_processed_seu_obj.tar.gz

molecule: protein


title: WT, 8h induction, rep 1

description: Library name: WT_8h_1