title: NPCs, T/I-EVTPD, 2

city: Wuhan

first: Bide

last: Tong

state: Hubei

address: Jiefang Avenve 1277, Jianghan District, wuhan

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: LIB-Deg2

data_processing:
Libraries were sequenced using PE150 (150 bp paired-end) on an Illumina NovaSeq 6000 sequencing platform.
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values for each Sample

molecule: polyA RNA

source_name: Intervertebral disc

growth_protocol: Nucleus pulposus samples were obtained from patients who were about to undergo scoliosis correction surgery with informed consent and no harm to the patient's interests. Tissues were digested using 0.4% collagenase type II (Sigma, USA) for 6 h under 37 ℃.

extract_protocol:
RNA was extracted from the samples using a TRIzol kit (Thermo Fisher Scientific, USA), and mRNA was isolated from total RNA using magnetic beads containing oligo-dT.
The captured mRNA was fragmented and reverse transcribed to synthesize cDNA, which was subsequently subjected to end repair via the addition of an A base at the 3' end. Subsequently, the cDNA fragments were ligated to the sequencing adaptor, and incomplete ligation products and adaptor self-ligation products were removed. A sequencing library was obtained using PCR amplification with primers that were complementary to the adaptor sequence, followed by purification with magnetic beads. A Qubit was used to determine library concentration, whereas an Agilent fragment analyzer was used to determine library fragment length to ensure library quality.

treatment_protocol: Non-targeting EVTPD and T/I-EVTPD were coincubated with NPCs for 24 h

value: Intervertebral disc

value: Nucleus pulpsus cells

tag: genotype

value: wild type

value: T/I-EVTPD


title: NPCs, T/I-EVTPD, 1

status: Public on Dec 10 2025

type: SRA

country: China

description: Library name: LIB-Deg1

library_source: transcriptomic

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment


title: MR157

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Library name: Sample 110

data_processing:
De-multiplexing and generation of FASTQ files were performed using Illumina CASAVA v1.8.2.
FastQC v0.11.7 (RRID: SCR_014583) was used to examine the quality of raw reads and cutadapt v1.18 was used for trimming the sequencing adaptors (5’- AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’, -trim-n). Reads unlikely to be properly sequenced mature miRNA transcripts were discarded (reads shorter than 16 nt or longer than 25 nt with –m 16 –M 25 in cutadapt).
Alignment and quantification of mature miRNAs based on miRBase v22 (RRID: SCR_003152) were performed with miRDeep2 v0.1.0 with mapper.pl parameters –e –h –m –i –j and quantifier.pl parameter –k –j –d -P. For mature miRNAs associated with multiple precursor miRNAs, the max counts were used.
We performed miRNA-seq sample quality assessments and miRNA filtering separately for each sample type (endobronchial biopsies and bronchial brushes). We limited the analysis to the miRNA samples with previously analyzed (GSE109743, dbGaP:phs003185.v1.p1) matched mRNA expression profiles (n=160 biopsies, n=89 brushes). The raw counts were converted into log2 counts per million of miRNA reads mapped (logCPM) and quantile normalized with voom. miRNAs with logCPM less than 1 in more than half of the samples were removed. We excluded samples (n=4 biopsies, n=2 brushes) if sequencing quality metrics were outside 2 standard deviations from the mean. The quality metrics we used included the first and the second principal components from the PCA using filtered miRNA expression, the mean Pearson expression correlation with all other samples across the filtered miRNAs, and the transcript integrity number (TIN) of the matched mRNA sequencing sample (calculated using RSeQC v3.0.0, RRID: SCR_005275). Finally, 156 biopsies and 87 brush samples from 30 patients were retained.
The gene filter and normalization described above were performed on the final high-quality samples with matching mRNA data (n=525 miRNAs in biopsies and n=489 miRNAs in brushes). The residual miRNA expressions adjusting for sequencing batch were computed with limma (RRID: SCR_010943) for downstream analysis.
Assembly: hg38
Supplementary files format and content: PCGA_miRNA_raw_count_table_BX.csv: Comma-separated value (CSV) table of raw counts, 2656 miRNAs x 156 samples
Supplementary files format and content: PCGA_miRNA_residual_table_BX.csv: Comma-separated value (CSV) table of residuals, 525 rows x 156 columns

molecule: total RNA

source_name: bronchial biopsy

extract_protocol:
miRNA was extracted from biopsies or brushing samples using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
miRNA sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEBioLabs). Sequencing adapters that target the 3’ hydroxyl group of small RNAs were ligated and the transcripts were reverse transcribed and PCR-amplified into single-stranded cDNA libraries. The libraries were pooled, and size selected for small RNA fragments on PAGE gel in groups of 6-10.

value: bronchial biopsy

tag: pcga id

tag: patient id

tag: flowcell

tag: dysplasia grade

value: metaplasia

tag: molecular subtype

value: Normal

tag: progression status

value: normal/stable

tag: median tin


title: NPCs, EVTPD, 3

description: Library name: LIB-LT-3

value: EVTPD


title: MR250

description: Library name: Sample 107

value: moderate dysplasia

value: Secretory

value: unknown


title: MR_252

description: Library name: Sample 106

value: mild dysplasia

value: Proliferative


title: NPCs, EVTPD, 1

description: Library name: LIB-LT-1


title: non-tumor bearing GS-KO (Cre)

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 2
GS-KO (Cre)

library_source: transcriptomic single cell

data_processing:
10X Cell ranger for read alignment and quantification
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix file

organism: Mus musculus

source_name: liver

extract_protocol:
Livers were subjected to a two-step collagenase digestion 2 weeks post-viral infection. Briefly, after anesthetizing the mice, a 27.5” gauge catheter was placed into the inferior vena cava and 0.3 mg/mL of collagenase II (Worthington) was perfused through the liver to promote digestion. Livers were then placed in DMEM/F12 medium (Corning) supplemented with 5% FBS (Biowest). This was then passed through a 100 μm filter followed by a 70 μm filter and centrifuged at low speed (400 rpm for 3 minutes) and the pellet was washed twice. Hepatocyte viability, determined by trypan blue staining, was typically >80%. Isolated hepatocytes and purified non-parenchymal cells were used for sc-RNA-Seq. Cells isolated from 1 individual control and 1 individual Glul-KO mouse were sequenced in separate wells on the flow cell. At minimum, 10,000 cells were sequenced at 20,000 reads per cell. Single cell sequencing was performed on NextSeq 2000 and 5PrimeV3 library prep was conducted according to standard methods.
10X snRNA-seq 5PrimeV3 library preparation

value: liver

value: GS-KO (Cre)


title: non-tumor bearing GFP control

description:
Library name: Sample 1
GFP control

value: GFP control


title: NPCs, EVTPD, 2

description: Library name: LIB-LT-2

value: Intervertebral disc


title: tumor bearing GS-KO (Cre)

description:
Library name: Sample 2
GS-KO (Cre)

extract_protocol:
After liver digestion via collagenase perfusion as described, the supernatant from the first centrifugation was used to enrich for F4/80 expressing cells using magnetic anti-F4/80 microbeads according to manufacturer’s instructions (Miltenyi Cat. No. 130-110-443). Live cells were enriched using a dead cell removal kit (Miltenyi Cat. No. 130-090-101) and used for sc-RNA-Seq. Cells isolated from 1 individual tumor bearing control and 1 individual tumor bearing Glul-KO mouse were sequenced in separate wells on the flow cell. At minimum, 7,500 cells were sequenced at 20,000 reads per cell. Single cell sequencing was performed on NextSeq 2000 and 3PrimeV2 library prep was conducted according to standard methods.
10X snRNA-seq 3PrimV2 library preparation


title: MR_253

description: Library name: Sample 105

value: severe dysplasia


title: tumor bearing GFP control

description:
Library name: Sample 1
GFP control


title: 640T

city: Tokyo

first: Yu-Yu

address: 5-1-1 Tsukiji, Chūō district

country: Japan

institute: National Cancer Center Research Institute

description:
Library name: 640T
Column name in GEOrsem_expected_count.csv: 640T

data_processing:
The sequencing data were subjected to quality control filtering, trimming, and adapter removal using fastp (v0.24.0) with default parameters.
The filtered paired-end reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b), and gene-level read counts were quantified using RNA-Seq by Expectation-Maximization (v1.3.1).
Genes with FDR < 0.05 and log Fold-change > 1 or < -1 were considered as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: csv file includes rsem expected count for each sample
Supplementary files format and content: Tab delimited files including rsem results for each sample

source_name: Papillary renal cell carcinoma

extract_protocol:
For samples processed at Macrogen, total RNA was extracted using QIAzol Lysis reagent (QIAGEN). For samples processed at BGI, total RNA was extracted using TRIzol Reagent (Invitrogen).
For samples processed at Macrogen, libraries were constructed from the total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For samples processed at BGI, libraries were prepared using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

value: Papillary renal cell carcinoma


title: 53T

description:
Library name: 53T
Column name in GEOrsem_expected_count.csv: 53T


title: 624T

description:
Library name: 624T
Column name in GEOrsem_expected_count.csv: 624T


title: 492T

description:
Library name: 492T
Column name in GEOrsem_expected_count.csv: 492T


title: MR_254

description: Library name: Sample 103


title: 470T

description:
Library name: 470T
Column name in GEOrsem_expected_count.csv: 470T


title: 414T

description:
Library name: 414T
Column name in GEOrsem_expected_count.csv: 414T


title: 4T

description:
Library name: 4T
Column name in GEOrsem_expected_count.csv: 4T


title: D28 rep 1

city: Muenster

first: Marcos

middle: J

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the mouse reference genome GRCm38 using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts with HTSeq.
Variance stabilization performed using log2 scaling.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include log2 counts values for each sample

source_name: Murine mesenchymal progenitors

growth_protocol: C57/BL6 mice were purchased from Charles River Laboratories. Murine mesenchymal progenitors were isolated from 5 or 6 days-old pups. Briefly, heads and condyles from femurs and tibiae were separated using a scalpel, incubated with digestion solution (MEM alpha containing 1% penicillin-streptomycin and Collagenase D 3 mg/ml) for 45 min at 37C, retrieved and incubated overnight with diluted digestion solution (MEM alpha, nucleoside containing 1% penicillin-streptomycin and 0,5 mg/ml of Collagenase D). Cell aggregates were retrieved the following day, and cells were filtered through a cell strainer (70 microm) to remove undigested tissue or debris. Cells were incubated in adhesion in standard conditions (5% CO2 atmosphere and 37C) during 24 h with complete culture medium (MEM alpha containing 1% penicillin-streptomycin and 10% Fetal Bovine Serum (FBS)), then detached using trypsin/EDTA and characterized by flow cytometry.

extract_protocol: RNA was extracted at different time points using the Monarch Total RNA Miniprep Kit (including gDNA removal) and following the manufacturer’s instructions. Roughly 150 ng of high quality total RNA (RIN >8) was used for the transcriptomic assays using Illumina’s Stranded mRNA Prep ligation according to the manufacturer’s instructions. Briefly, oligo(dT) magnetic beads were used to capture and purify poly-adenylated mRNA molecules from total RNA. The purified mRNA was then fragmented and reverse-transcribed to cDNA using random primers. A second strand cDNA synthesis step removed the RNA template while incorporating dUTP in place of dTTP in order to preserve strand specificity. Next, double-stranded cDNA was A-tailed, then ligated to Illumina anchors bearing T-overhangs. PCR-amplification of the library allowed the barcoding of the samples with 10bp dual indexes and the completion of Illumina sequences for cluster generation. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay. RNA Sequencing and data processing : The quantity and quality of the RNAs were evaluated using Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855) and Agilent RNA 6000 Nano Chips (Agilent Technologies, Cat.# 5067-1511), respectively. Sequencing libraries were prepared following “TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E)” using the “TruSeq Stranded mRNA Library Prep” kit (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792). Starting from 700 ng of total RNA, mRNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat. # 18064-014) for 10 min at 25C, 15 min at 42C, 15 min at 70C and pause at 4C. cDNA second strand was synthesized with Illumina reagents at 16C for 1 hour. Then, A-tailing and adaptor ligation were performed. Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626 ) and quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854). Sequencing was carried out in an Illumina NextSeq2000 using paired-end, dual-index sequencing (Rd1: 59 cycles, i7: 10 cycles, i5: 10 cycles, Rd2: 59 cycles) at a depth of 30 million reads per sample.

treatment_protocol: At this step, cells were divided in aliquots of 5x105 cells, centrifuged at 200 G to form pellets, and incubated during 7 days with chondrogenic differentiation media (Stem Cell Tech, UK) (Media replaced every 4 days). After that, media was replaced with osteogenic differentiation media and cultured during additional 21 days (Media replaced every 4 days).

tag: time point

tag: strain


title: NPCs, T/I-EVTPD, 3

description: Library name: LIB-Deg3

value: Nucleus pulpsus cells

value: wild type

value: T/I-EVTPD


title: 346T

description:
Library name: 346T
Column name in GEOrsem_expected_count.csv: 346T


title: 344T

description:
Library name: 344T
Column name in GEOrsem_expected_count.csv: 344T


title: MR278

description: Library name: Sample 101

value: bronchial biopsy

value: metaplasia

value: progressive/persistent


title: 479T

description:
Library name: 479T
Column name in GEOrsem_expected_count.csv: 479T


title: D28 rep 3

description: replicate 3


title: 332T

description:
Library name: 332T
Column name in GEOrsem_expected_count.csv: 332T


title: MR2R-44

description: Library name: Sample 100


title: D10 rep 3

description: replicate 3


title: SLCC469

description: Library name: Sample 99

value: normal/stable


title: 250T

description:
Library name: 250T
Column name in GEOrsem_expected_count.csv: 250T


title: 261T

description:
Library name: 261T
Column name in GEOrsem_expected_count.csv: 261T


title: 827-MR251

description: Library name: Sample 104

value: Secretory


title: D10 rep 2

description: replicate 2


title: 234T

description:
Library name: 234T
Column name in GEOrsem_expected_count.csv: 234T


title: 169T

description:
Library name: 169T
Column name in GEOrsem_expected_count.csv: 169T


title: MR2R-43

description: Library name: Sample 98

value: normal

value: unknown


title: 490T

description:
Library name: 490T
Column name in GEOrsem_expected_count.csv: 490T


title: D28 rep 2

description: replicate 2


title: MR2R-45

description: Library name: Sample 102

value: mild dysplasia

value: Proliferative


title: 166T

description:
Library name: 166T
Column name in GEOrsem_expected_count.csv: 166T


title: 876-MR276

description: Library name: Sample 97

value: Inflammatory


title: D8 rep 2

description: replicate 2


title: SLCC_468

description: Library name: Sample 96

value: moderate dysplasia

value: regressive


title: MR2R-66

description: Library name: Sample 95

value: Normal


title: Endometrium_01-15_Epithelium_AS-Post

city: Paterna

first: Carlos

last: Simon

state: Valencia

address: Rda Narcis Monturial, parc. 118 Parque Tecnologico

country: Spain

institute: Carlos Simon Foundation

description:
Library name: Endometrium_01-15_Epithelium_AS-Post
10x Genomics

data_processing:
Processing of scRNA-seq data was conducted with the CellRanger software suite (version 3.1.0). Raw reads were demultiplexed using the mkfastq wrapper command of bcl2fastq (Illumina). The libraries were mapped using GRCh38-3.0.0 as a reference provided by 10x Genomics. The count gene expression matrices per cell were computed per sample using the counts pipeline with default parameters. This pipeline includes read alignment using the STAR aligner, UMI counting, barcode calling, and filtering of empty droplets. The filtering step relies on a Good-Turing smoothing model of background gene expression to distinguish low-RNA-content cells from ambient RNA.
Filtered count matrix files generated by Cell Ranger count pipeline: 1) matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices; 2) features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz; 3) barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz.
Low-quality cells (cells with a low number of detected genes or a high proportion of mitochondrial reads) were filtered out. Doublet detection was performed with two methods: DoubletFinder (v2.0.3) and scds (v1.6.0) packages. Individual samples were aggregated, processed, and integrated with functions from the Seurat (v4.0.1) package. Processed samples were merged and saved into RDS files (SeuratObject v5.0.2).
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: Filtered count matrices for each sample generated by Cell Ranger (matrix.mtx, features.tsv, and barcodes.tsv files)
Supplementary files format and content: A single Seurat RDS object containing aggregated and processed count matrices for all cells and samples, along with associated metadata

source_name: Endometrium

extract_protocol:
A two-stage dissociation protocol separated endometrial biopsies into stromal fibroblasts and epithelial-enriched single-cell suspensions. Before dissociation, tissue was rinsed with PBS in a petri dish to remove blood and mucus, and excess PBS was removed after rinsing. The tissue was then minced into small pieces and dissociated with 3 mL collagenase mix (Collagenase V, Sigma, USA), RPMI+10% fetal bovine serum, and DNaseI (Sigma, USA) at 37ºC under continuous shaking at 175 rpm for 25 min in a 15 mL Falcon tube in a horizontal position. This primary enzymatic step mostly dissociates stromal fibroblasts into single cells while leaving epithelial glands and lumen mostly undigested. The contents were transferred to a 50 mL tube in RPMI media and filtered with a 100 mm cell strainer. The tissue remaining on the filter was used for the epithelial enrichment cell isolation by resuspending and incubating in 10 mL Trypsin mix (Trypsin -EDTA (0.25%) phenol and DNaseI) for 10 min. The resulting two contents were transferred to 50 mL tubes with 20 mL RPMI, filtered with a 100 mm cell strainer, centrifuged, and then resuspended in 1 mL RPMI. Dead cells were removed using the MACS dead cell removal kit (Miltenyi Biotec, Germany).
Live-cell suspensions were loaded into a Chromium Next GEM Chip G (10X Genomics, USA) to obtain cDNA from individual cells. Cell suspension was loaded into a Chromium Next GEM Chip G (10x Genomics) and run in a Chromium Controller (10x Genomics). cDNA synthesis and amplification were performed using the Single Cell 3' Reagent Kit v3.1 (10x Genomics). 25% of the resulting cDNA was used for enzymatic fragmentation, end repair, A-tailing, adapter ligation, and amplification (with an expected yield of 0.1 ng/μl and a peak size between 200 and 9000 bp as determined in a TapeStation using HSD1000 assay reagents), serving as a quality control. Libraries were then quantified in a TapeStation using HSD1000 assay reagents. 10x-Genomics v3 libraries were prepared as per the manufacturer's instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell, on an Illumina NovaSeq 6000 S2v1.5 300 cycles at a mean 40x coverage (paired-end; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles)

treatment_protocol: Isolated CD133+ BMDSCs were delivered into the spiral arterioles of the patient using a minimal invasive radiology intervention through the left brachial artery, using the Seldinger technique.

value: Endometrium

tag: biopsy origin

value: Epithelium

tag: individual

value: Patient 15

tag: treatment stage

value: Post-AS therapy


title: Endometrium_01-15_Epithelium_AS-Pre

description:
Library name: Endometrium_01-15_Epithelium_AS-Pre
10x Genomics

value: Pre-AS therapy


title: Endometrium_01-15_Stroma_AS-Pre

description:
Library name: Endometrium_01-15_Stroma_AS-Pre
10x Genomics

value: Stroma


title: Endometrium_01-14_Stroma_AS-Pre

description:
Library name: Endometrium_01-14_Stroma_AS-Pre
10x Genomics

value: Patient 14


title: Endometrium_01-14_Stroma_AS-Post

description:
Library name: Endometrium_01-14_Stroma_AS-Post
10x Genomics


title: Endometrium_01-15_Stroma_AS-Post

description:
Library name: Endometrium_01-15_Stroma_AS-Post
10x Genomics


title: D8 rep 1

description: replicate 1


title: D7 rep 3

description: replicate 3


title: D10 rep 1

description: replicate 1


title: D7 rep 1

description: replicate 1


title: 582-MR171

description: Library name: Sample 93

value: bronchial biopsy

value: severe dysplasia

value: progressive/persistent


title: Endometrium_01-13_Epithelium_AS-Post

description:
Library name: Endometrium_01-13_Epithelium_AS-Post
10x Genomics

value: Patient 13


title: MR209

description: Library name: Sample 92

value: hyperplasia

value: normal/stable


title: 14T

description:
Library name: 14T
Column name in GEOrsem_expected_count.csv: 14T

value: Papillary renal cell carcinoma


title: D8 rep 3

description: replicate 3


title: Endometrium_01-12_Stroma_AS-Post

description:
Library name: Endometrium_01-12_Stroma_AS-Post
10x Genomics

value: Patient 12


title: Endometrium_01-13_Epithelium_AS-Pre

description:
Library name: Endometrium_01-13_Epithelium_AS-Pre
10x Genomics


title: MR2R-22

description: Library name: Sample 91

value: moderate dysplasia

value: Proliferative


title: No template control

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

description:
Library name: No template control
raw_counts.txt

data_processing:
Nanostring quality control process
Assembly: FASTQ files processed into DCC files by geomxngspipeline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC and rawcount
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: No template control

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

value: MLH1 deficient

tag: rpl22 status

value: control

tag: immune status

value: No template control


title: Endometrium_01-12_Stroma_AS-Pre

description:
Library name: Endometrium_01-12_Stroma_AS-Pre
10x Genomics

tag: tissue

value: Pre-AS therapy


title: MR_208

description: Library name: Sample 90


title: Endometrium_01-14_Epithelium_AS-Post

description:
Library name: Endometrium_01-14_Epithelium_AS-Post
10x Genomics

value: Epithelium

value: Post-AS therapy


title: Endometrium_01-12_Epithelium_AS-Post

description:
Library name: Endometrium_01-12_Epithelium_AS-Post
10x Genomics


title: MR210

description: Library name: Sample 94

value: bronchial biopsy

value: normal


title: Endometrium_01-14_Epithelium_AS-Pre

description:
Library name: Endometrium_01-14_Epithelium_AS-Pre
10x Genomics

value: Patient 14


title: D7 rep 2

description: replicate 2


title: INTRUST_31, timepoint: C3D1

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

description: Library name: MB30337

data_processing:
Trimming of adapter sequences with Trimmomatic
Alignment to hg38 GENCODE 39 with STAR v2.7.11b
Quantification by featureCounts v2.0.6
Assembly: hg38 GENCODE 39
Supplementary files format and content: rawcounts.txt – txt file containing the raw counts matrix
Supplementary files format and content: metadata.xlsx – xlsx file containing additional metadata for use in analysis

source_name: primary tumor

growth_protocol: Frozen tissue biopsies (20-30 mg) were placed into tubes (Sarstedt ref. 72.694.005)containing 300 µl of chilled homogenization solution (2% thioglycerol, Promega Simply RNATissue kit) and a 6.5 mm stainless steel bead (Marteau & Lemarie, AISI 316).

extract_protocol:
Samples werethen homogenized using a Retsch MM400 bead mill (4 min, 30 Hz). Tissue homogenateswere centrifuged at 4°C for 5 min at 6000 rpm, and 200 µL of the supernatant wassubsequently used for RNA extraction with the Maxwell RSC 16 (Promega). Finally, RNAwas subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo FisherScientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (AgilentTechnologies).
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit(Illumina) following the manufacturer’s protocol. All sequencing libraries were constructedfrom 100 ng of total RNA according to the manufacturer's instructions. Briefly, the protocolselects and purifies poly(A) containing RNA molecules using magnetic beads coated withpoly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into the first cDNAstrand using random primers. The second cDNA strand is synthesized in the presence ofdUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XPbeads (Beckman Coulter), adenylated at 3′ ends, and then ligated with uniquely indexedsequencing adapters. Ligated fragments are purified and PCR amplified to obtain the finallibraries. The quality and quantity of the libraries were verified using the Qubit dsDNA HSAssay Kit (Thermo Fisher Scientific) and a 4200 TapeStation with High Sensitivity D1000ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000sequencer (Illumina). 50 million pair-end reads (100 bp; Rd1:51; Rd2:51) were sequencedfor each sample and demultiplexed using bcl2fastq. RNA-seq sequencing was carried out atthe Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad deNavarra).

treatment_protocol: Intratumoral injections of Urelumab 8 mg / dose & systemic nivolumab 240 mg / dose

value: primary tumor

tag: tumor

value: Melanoma

tag: cohort

value: PD-1/PD-L1 treatment refractory

value: Nivolumab

tag: batch


title: Endometrium_01-10_Stroma_AS-Pre

description:
Library name: Endometrium_01-10_Stroma_AS-Pre
10x Genomics

value: Stroma

value: Patient 10


title: MR_170

description: Library name: Sample 89

tag: pcga id

tag: patient id

value: severe dysplasia

value: Normal

value: progressive/persistent


title: INTRUST_31, timepoint: C1D1

description: Library name: MB30335

tag: treatment

value: Baseline


title: INTRUST_31, timepoint: C2D1

description: Library name: MB30336

value: Urelumab


title: Endometrium_01-10_Epithelium_AS-Pre

description:
Library name: Endometrium_01-10_Epithelium_AS-Pre
10x Genomics

value: Endometrium

value: Pre-AS therapy


title: Endometrium_01-13_Stroma_AS-Post

description:
Library name: Endometrium_01-13_Stroma_AS-Post
10x Genomics

value: Patient 13

value: Post-AS therapy


title: Endometrium_01-12_Epithelium_AS-Pre

description:
Library name: Endometrium_01-12_Epithelium_AS-Pre
10x Genomics

value: Epithelium

value: Patient 12


title: Endometrium_01-10_Stroma_AS-Post

description:
Library name: Endometrium_01-10_Stroma_AS-Post
10x Genomics


title: MR2R-68

description: Library name: Sample 87

value: bronchial biopsy

tag: flowcell

tag: dysplasia grade

value: normal

tag: molecular subtype

value: Proliferative

value: normal/stable


title: Endometrium_01-13_Stroma_AS-Pre

description:
Library name: Endometrium_01-13_Stroma_AS-Pre
10x Genomics

value: Stroma


title: Endometrium_01-10_Epithelium_AS-Post

description:
Library name: Endometrium_01-10_Epithelium_AS-Post
10x Genomics

value: Patient 10


title: MR_100

description: Library name: Sample 88

value: unknown

tag: progression status

tag: median tin


title: INTRUST_30, timepoint: C1D1

description: Library name: MB30324

value: primary tumor

value: Renal carcinoma

value: PD-1/PD-L1 treatment naive


title: MR2R-25

description: Library name: Sample 86

value: mild dysplasia

value: Secretory

value: regressive


title: Endometrium_01-09_Epithelium_AS-Post

description:
Library name: Endometrium_01-09_Epithelium_AS-Post
10x Genomics

value: Endometrium

tag: biopsy origin

value: Patient 09


title: Endometrium_01-09_Epithelium_AS-Pre

description:
Library name: Endometrium_01-09_Epithelium_AS-Pre
10x Genomics

value: Epithelium

tag: individual

value: Pre-AS therapy


title: INTRUST_30, timepoint: C2D1

description: Library name: MB30328

value: Urelumab


title: Endometrium_01-09_Stroma_AS-Pre

description:
Library name: Endometrium_01-09_Stroma_AS-Pre
10x Genomics

tag: treatment stage


title: INTRUST_31, timepoint: C4D1

description: Library name: MB30338

value: Melanoma

value: PD-1/PD-L1 treatment refractory

value: Repeat Ure+Nivo


title: MR_212

description: Library name: Sample 85

value: bronchial biopsy

value: hyperplasia

value: Normal

value: progressive/persistent


title: Endometrium_01-08_Stroma_AS-Post

description:
Library name: Endometrium_01-08_Stroma_AS-Post
10x Genomics

value: Stroma

value: Patient 08

value: Post-AS therapy


title: INTRUST_29, timepoint: C1D1

description: Library name: MB30323

value: primary tumor

value: Neuroendocrine tumors

value: Baseline


title: Endometrium_01-08_Stroma_AS-Pre

description:
Library name: Endometrium_01-08_Stroma_AS-Pre
10x Genomics

value: Endometrium


title: Endometrium_01-08_Epithelium_AS-Post

description:
Library name: Endometrium_01-08_Epithelium_AS-Post
10x Genomics

value: Epithelium


title: INTRUST_28, timepoint: C4D1

description: Library name: MB30334

value: Thyroid carcinoma

value: PD-1/PD-L1 treatment naive


title: Endometrium_01-08_Epithelium_AS-Pre

description:
Library name: Endometrium_01-08_Epithelium_AS-Pre
10x Genomics

value: Pre-AS therapy


title: MR_141

description: Library name: Sample 84

value: metaplasia


title: Endometrium_01-07_Stroma_AS-Post

description:
Library name: Endometrium_01-07_Stroma_AS-Post
10x Genomics

value: Patient 07


title: INTRUST_28, timepoint: C3D1

description: Library name: MB30331

value: Nivolumab


title: Endometrium_01-07_Epithelium_AS-Pre

description:
Library name: Endometrium_01-07_Epithelium_AS-Pre
10x Genomics


title: Endometrium_01-09_Stroma_AS-Post

description:
Library name: Endometrium_01-09_Stroma_AS-Post
10x Genomics

value: Patient 09


title: MR2R-24

description: Library name: Sample 82

value: bronchial biopsy

value: severe dysplasia

value: Inflammatory


title: MR2R-7

description: Library name: Sample 81

value: moderate dysplasia

value: Secretory

value: progressive/persistent


title: INTRUST_28, timepoint: C2D1

description: Library name: MB30326

value: primary tumor

value: Urelumab


title: Endometrium_01-05_Stroma_AS-Pre

description:
Library name: Endometrium_01-05_Stroma_AS-Pre
10x Genomics

value: Endometrium

value: Stroma

value: Patient 05


title: INTRUST_28, timepoint: C1D1

description: Library name: MB30322

value: Thyroid carcinoma

value: PD-1/PD-L1 treatment naive

value: Baseline


title: Endometrium_01-05_Stroma_AS-Post

description:
Library name: Endometrium_01-05_Stroma_AS-Post
10x Genomics

value: Post-AS therapy


title: Endometrium_01-07_Stroma_AS-Pre

description:
Library name: Endometrium_01-07_Stroma_AS-Pre
10x Genomics

value: Patient 07

value: Pre-AS therapy


title: MR103

description: Library name: Sample 80

value: bronchial biopsy

value: Proliferative


title: Organoids_CO-9_Control

description:
Library name: Organoids_CO-9_Control
10x Genomics

data_processing:
Processing of scRNA-seq data was conducted with the CellRanger software suite (version 3.1.0). Raw reads were demultiplexed using the mkfastq wrapper command of bcl2fastq (Illumina). The libraries were mapped using GRCh38-3.0.0 as a reference provided by 10x Genomics. The count gene expression matrices per cell were computed per sample using the counts pipeline with default parameters. This pipeline includes read alignment using the STAR aligner, UMI counting, barcode calling. Finally, CellBender was used to filter out the ambient RNA.
Filtered count matrix generated with the CellBender pipeline, saved as an H5 file, with ambient/background RNA removed and containing only droplets classified as cells, including corresponding feature and cell barcode information.
Low-quality cells (cells with a low number of detected genes or a high proportion of mitochondrial reads) were filtered out. Doublet detection was performed with two methods: DoubletFinder (v2.0.3) and scds (v1.6.0) packages. Individual samples were aggregated, processed, and integrated with functions from the Seurat (v4.0.1) package. Processed samples were merged and saved into RDS files (SeuratObject v5.0.2).
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: h5 files with filtered count matrix data from CellBender output
Supplementary files format and content: A single Seurat RDS object containing aggregated and processed count matrices for all cells and samples, along with associated metadata

growth_protocol: Organoids were generated from AS patients’ endometrium pre- and post-treatment and from healthy control endometrium. After enzymatic dissociation of the endometrial biopsies, epithelial and stromal cells were obtained and total cell numbers were counted. After centrifugation at 300 g, the pellet was resuspended in 70% Matrigel (Corning, 356231) and 30% DMEM/F12 (Thermo Fisher Scientific, 11330032) and supplemented with the ROCK inhibitor Y-27632 (1/500). The suspension was cultured in 20-µL droplets containing 25,000 cells, deposited in prewarmed 48-well plates, and allowed to form a gel at 37ºC and 5% CO2 before adding culture medium. Organoid culture medium was prepared as previously described21,22. Matrigel droplets were cultured for 14-16 days in the first passage (P0) with medium changes every two days. Organoids were then grown for seven days before the following passage, with media changes every two days.   Organoids were recovered for passaging by liquifying the Matrigel droplets with ice-cold DMEM/F12 (without any growth factors, serum, or enzymes), followed by repeated pipetting to ensure maximum recovery. Organoids were then dissociated by incubation with TrypLE supplemented with Y-27632 (1/1000) and mechanically triturated. The resulting cell suspension was centrifuged at 300 g, and the pellets were resuspended in 70% Matrigel and 30% DMEM/F12 supplemented with Y-27632 and placed as droplets in 48-well plates. Two passages were performed to remove the contaminating stromal cells from the epithelial organoids.

extract_protocol:
After seven days of P2 culture, organoids were dissociated for single-cell transcriptomic analysis following the same protocol described for passaging but with an additional cell counting step for the single-cell transcriptomics protocol as per manufacturer’s instructions (10x Genomics).
Live-cell suspensions were loaded into a Chromium Next GEM Chip G (10X Genomics, USA) to obtain cDNA from individual cells. Cell suspension was loaded into a Chromium Next GEM Chip G (10x Genomics) and run in a Chromium Controller (10x Genomics). cDNA synthesis and amplification were performed using the Single Cell 3' Reagent Kit v3.1 (10x Genomics). 25% of the resulting cDNA was used for enzymatic fragmentation, end repair, A-tailing, adapter ligation, and amplification (with an expected yield of 0.1 ng/μl and a peak size between 200 and 9000 bp as determined in a TapeStation using HSD1000 assay reagents), serving as a quality control. Libraries were then quantified in a TapeStation using HSD1000 assay reagents. 10x-Genomics v3 libraries were prepared as per the manufacturer's instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell, on an Illumina NovaSeq 6000 S2v1.5 300 cycles at a mean 40x coverage (paired-end; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles)

value: Patient-derived endometrial epithelial organoids

value: Control 9

value: Control


title: Endometrium_01-05_Epithelium_AS-Post

description:
Library name: Endometrium_01-05_Epithelium_AS-Post
10x Genomics

value: Epithelium


title: MR_211

description: Library name: Sample 79

value: normal

value: Normal

value: normal/stable


title: Organoids_CO-8_Control

description:
Library name: Organoids_CO-8_Control
10x Genomics

value: Endometrium

value: Control 8


title: INTRUST_27, timepoint: C4D1

description: Library name: MB30333

value: primary tumor

value: Neuroendocrine tumors

value: Repeat Ure+Nivo


title: INTRUST_27, timepoint: C3D1

description: Library name: MB30329

value: PD-1/PD-L1 treatment naive

value: Nivolumab


title: 464-MR140

description: Library name: Sample 78

value: Secretory

value: progressive/persistent


title: Organoids_1-15_AS-Post

description:
Library name: Organoids_1-15_AS-Post
10x Genomics

value: Patient 15

value: Post-AS therapy


title: Organoids_1-15_AS-Pre

description:
Library name: Organoids_1-15_AS-Pre
10x Genomics

value: Patient-derived endometrial epithelial organoids

value: Pre-AS therapy


title: MR234

description: Library name: Sample 77

value: bronchial biopsy

value: unknown


title: Endometrium_01-07_Epithelium_AS-Post

description:
Library name: Endometrium_01-07_Epithelium_AS-Post
10x Genomics

value: Epithelium

value: Patient 07


title: Organoids_1-14_AS-Pre

description:
Library name: Organoids_1-14_AS-Pre
10x Genomics

value: Endometrium

value: Patient 14


title: INTRUST_27, timepoint: C1D1

description: Library name: MB30318

value: primary tumor

value: Baseline


title: Organoids_1-13_AS-Pre

description:
Library name: Organoids_1-13_AS-Pre
10x Genomics

value: Patient 13


title: INTRUST_26, timepoint: C1D1

description: Library name: MB30315

value: Pleural mesothelioma

value: PD-1/PD-L1 treatment naive


title: Organoids_1-13_AS-Post

description:
Library name: Organoids_1-13_AS-Post
10x Genomics


title: INTRUST_26, timepoint: C2D1

description: Library name: MB30320

value: Urelumab


title: MR_235

description: Library name: Sample 75

value: normal

value: Normal


title: MR2R-67

description: Library name: Sample 83

value: severe dysplasia

value: Proliferative

value: progressive/persistent


title: MR_111

description: Library name: Sample 74

value: bronchial biopsy

value: metaplasia

value: normal/stable


title: MR197

description: Library name: Sample 73


title: U2OS cells ZNF354A siRNA_2

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

description: Library name: ZNF354A-2_S6

data_processing:
Adapters were trimmed using bclconvert v3.9.3.
Read quality was assessed with FastQC v0.11.9 and screened for contaminants using FastQ Screen v0.14.0.
Trimmed reads were aligned to the human hg19 genome using HISAT2 with parameters –k 5 –-seed 42 –-rna-strandness RF.
Gene-level read counts were obtained with featureCounts, including only uniquely mapped reads.
Normalization and differential expression analysis were performed using the TMM and voom methods in the limma R package; genes with fold change > 2 and adjusted p < 0.05 were considered differentially expressed.
Assembly: Human genome hg19.
Supplementary files format and content: Gene-level read count tables in tab-delimited text format; one file per sample.
Supplementary files format and content: Differential expression results (log₂ fold change, p-value, adjusted p-value) in tab-delimited text format.

source_name: osteosarcoma cells

growth_protocol: U2OS human osteosarcoma cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was confirmed with a TapeStation 4200 (Agilent).
Poly(A)+ mRNA libraries were prepared from 800 ng total RNA using the Illumina Stranded mRNA Ligation kit. Libraries were indexed and sequenced on an Illumina NovaSeq 6000 platform to generate 2 × 60 bp paired-end reads (~70 million read pairs per sample).

treatment_protocol: Cells were transfected with 50 nM control siRNA (siCtrl) or siRNA targeting ZNF354A (siZNF354A) using TRANSIT-X2 reagent (Mirus) and harvested 72 h after transfection.

value: osteosarcoma cells

tag: cell line

tag: cell type

tag: genotype

value: ZNF354A Knock down

value: siRNA ZNF354A


title: U2OS cells ZNF354A siRNA_1

description: Library name: ZNF354A-1_S5

tag: tissue


title: INTRUST_27, timepoint: C2D1

description: Library name: MB30325

value: primary tumor

tag: tumor

value: Neuroendocrine tumors

tag: cohort


title: 367-MR108

description: Library name: Sample 76

tag: pcga id

value: Inflammatory


title: MR149

description: Library name: Sample 72

tag: patient id

value: mild dysplasia

value: Secretory

value: regressive


title: U2OS cells Control siRNA_3

description: Library name: CTle4_S4

value: Control

tag: treatment

value: siRNA Control


title: U2OS cells Control siRNA_2

description: Library name: CTle2_S2


title: Organoids_CO-14_Control

description:
Library name: Organoids_CO-14_Control
10x Genomics

value: Endometrium

value: Patient-derived endometrial epithelial organoids

value: Control 14


title: INTRUST_25, timepoint: C2D1

description: Library name: MB30316

value: Gastric carcinoma

value: PD-1/PD-L1 treatment naive

value: Urelumab

tag: batch


title: U2OS cells Control siRNA_1

description: Library name: CTle1_S1

value: osteosarcoma cells


title: MR2R-41

description: Library name: Sample 71

value: bronchial biopsy

tag: flowcell

tag: dysplasia grade

value: metaplasia

value: Normal

value: unknown


title: Organoids_1-14_AS-Post

description:
Library name: Organoids_1-14_AS-Post
10x Genomics

value: Patient 14

value: Post-AS therapy


title: BA combined with TNF-α and IFN-γ treated group, #3

city: Kyoto

first: Kazuyuki

last: Takata

state: Kyoto

address: 5 Nakauchi-cho, Misasagi, Yamashina-ku

institute: Kyoto Pharmaceutical University

description: Library name: ASC-TNIF-3

data_processing:
Quality check: FastQC ver. 0.11.7
Trimming: Trimmomatic ver. 0.38, Low quality bases and adaptor sequences were trimmed.
Mapping: HISAT2 ver.2.1.0
Assembling and quantifying transcripts representing multiple splice variants: StringTie version 2.1.3b
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Human ASC were maintained in POWEREDBY10 medium in humodified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was harvested using Nucleospin RNA kit (Macherey-Nagel).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols (TruSeq Stranded mRNA Reference Guide # 1000000040498 v00).

treatment_protocol: Cells were treated with or without 1.0 mM BA in the presence of 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ for 72 h.

value: Adipose-derived stem cells

value: wild type


title: U2OS cells Control siRNA_4

description: Library name: CTlel3_S3

value: Control


title: U2OS cells ZNF354A siRNA_3

description: Library name: ZNF354A-3_S7

value: ZNF354A Knock down

value: siRNA ZNF354A


title: BA combined with TNF-α and IFN-γ treated group, #2

description: Library name: ASC-TNIF-2

value: 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ for 72 h


title: BA combined with TNF-α and IFN-γ treated group, #1

description: Library name: ASC-TNIF-1


title: INTRUST_24, timepoint: C4D1

description: Library name: MB30330

value: primary tumor

value: Neuroendocrine tumors

value: Repeat Ure+Nivo


title: 651-MR198

description: Library name: Sample 70

value: hyperplasia

tag: molecular subtype

tag: progression status

value: normal/stable


title: INTRUST_26, timepoint: C3D1

description: Library name: MB30332

value: Pleural mesothelioma

value: PD-1/PD-L1 treatment naive

value: Nivolumab


title: MR_151

description: Library name: Sample 69

value: bronchial biopsy

value: metaplasia

value: Normal

tag: median tin


title: The TNF-α and IFN-γ treated group, #1

description: Library name: ASC-BA-TNIF-1

value: Adipose-derived stem cells

value: 1.0 mM BA, 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ for 72 h


title: INTRUST_24, timepoint: C3D1

description: Library name: MB30319


title: The TNF-α and IFN-γ treated group, #2

description: Library name: ASC-BA-TNIF-2

value: wild type


title: INTRUST_25, timepoint: C3D1

description: Library name: MB30321

value: Gastric carcinoma


title: The BA treated group, #3

description: Library name: ASC-BA-3

value: 1.0 mM BA for 72 h


title: MR_263

description: Library name: Sample 68

value: normal

value: unknown


title: INTRUST_24, timepoint: C2D1

description: Library name: MB30313

value: primary tumor

value: Neuroendocrine tumors

value: Urelumab


title: MR215

description: Library name: Sample 67

value: hyperplasia

value: Inflammatory

value: normal/stable


title: The BA treated group, #1

description: Library name: ASC-BA-1


title: INTRUST_24, timepoint: C1D1

description: Library name: MB30308

value: PD-1/PD-L1 treatment naive

value: Baseline


title: The vehicle control group, #3

description: Library name: ASC-3

value: Vehicle control


title: 472-MR142

description: Library name: Sample 66

value: bronchial biopsy

value: Normal


title: The vehicle control group, #2

description: Library name: ASC-2

value: Adipose-derived stem cells


title: The vehicle control group, #1

description: Library name: ASC-1

value: wild type


title: INTRUST_23, timepoint: C2D1

description: Library name: MB30311

value: Gastric carcinoma


title: U2OS cells ZNF354A siRNA_4

description: Library name: ZNF354A-4_S8

value: osteosarcoma cells

value: ZNF354A Knock down

value: siRNA ZNF354A


title: INTRUST_25, timepoint: C1D1

description: Library name: MB30309

value: primary tumor


title: 3D-DCIScom-PCSK5-WT-noGDF11-rep4

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description: Library name: 3D-DCIScom-PCSK5-WT-noGDF11-rep4

data_processing:
RNA-seq data was aligned to the human assembly GRCh38.114 with HISAT2 and assembled with stringtie v2.2.1.
Assembly: GRCh38.114
Supplementary files format and content: Marohl_MCF10DCIScomPCSK5addback3D_counts.csv = counts data, where each column is a sample and each row is a gene

source_name: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (WT)

growth_protocol: MCF10DCIS.com cells were transduced with a destabilizing domain (DD)-containing Cas9-P2A-Venus and a single-guide RNA targeting Exon 4 of PCSK5 (sgPCSK5). Transduced cells were treated with 200 nM Shield-1 to stabilize Cas9-P2A-Venus and 2% matrigel to promote PCSK5 expression before sorting single Venus-positive cells into 10 ng/ml GDF11 (to aid recovery upon PCSK5 loss) and screening genomic DNA (gDNA) of expanded clones for knockout. One confirmed PCSK5–/– clone was then transduced with sgPCSK5-resistant, tetracycline (tet)-regulated, V5-tagged alleles (wildtype, M452I, or T288P) of PCSK5 and selected polyclonally for hygromycin resistance to produce three stable addback lines. PCSK5 addback (wildtype, M452I, or T288P) lines were seeded at a density of 5000 cells per well in 400 μl MCF10A assay medium supplemented with 5 ng/ml EGF and 2% growth factor-reduced matrigel (Corning, 356253) in eight-well chamber slides coated with 40 μl matrigel. Medium was replaced at day 4 and samples (n=4 wells per condition) were harvested at day 8.

extract_protocol:
Samples (n=4 wells per condition) were harvested at day 8 with 500 μl RNA Stat-60 followed by phenol cholorophorm extraction and cleanup.
RNA-seq on 386–500 ng total RNA was performed after Poly(A) selection by Azenta Life Sciences with 2x150bp sequencing on an Illumina NovaSeq instrument.

treatment_protocol: Four conditions were cultured: WT addback cells, M452I addback cells, T288P addback cells, and T288P addback cells cultured with recombinant GDF11. In all conditions, assay medium was supplemented with 1 μg/ml doxycycline from Day 4 onward to induce PCSK5 expression. The fourth condition (T288P addback cells) was also supplemented with 250 ng/ml recombinant mature GDF11 protein (Peprotech, 120-11) throughout the experiment.

value: 1 μg/ml doxycycline beginning at day 4.


title: MR_264

description: Library name: Sample 65

value: metaplasia

value: unknown


title: INTRUST_23, timepoint: C1D1

description: Library name: MB30305


title: 3D-DCIScom-PCSK5-WT-noGDF11-rep3

description: Library name: 3D-DCIScom-PCSK5-WT-noGDF11-rep3

value: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (WT)


title: 3D-DCIScom-PCSK5-WT-noGDF11-rep1

description: Library name: 3D-DCIScom-PCSK5-WT-noGDF11-rep1


title: MR_143

description: Library name: Sample 63

value: Inflammatory

value: normal/stable


title: 3D-DCIScom-PCSK5-WT-noGDF11-rep2

description: Library name: 3D-DCIScom-PCSK5-WT-noGDF11-rep2


title: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep4

description: Library name: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep4

source_name: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (T288P)

value: 1 μg/ml doxycycline beginning at day 4, 250 ng/ml recombinant mature GDF11 protein (Peprotech, 120-11) for entire experiment.


title: The TNF-α and IFN-γ treated group, #3

description: Library name: ASC-BA-TNIF-3

value: 1.0 mM BA, 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ for 72 h


title: The BA treated group, #2

description: Library name: ASC-BA-2

value: 1.0 mM BA for 72 h


title: 3D-DCIScom-PCSK5-T288P-noGDF11-rep4

description: Library name: 3D-DCIScom-PCSK5-T288P-noGDF11-rep4

value: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (T288P)


title: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep1

description: Library name: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep1


title: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep3

description: Library name: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep3


title: INTRUST_22, timepoint: C3D1

description: Library name: MB30327

value: Adrenal carcinoma

value: PD-1/PD-L1 treatment naive

value: Nivolumab


title: 509-MR156

description: Library name: Sample 61

value: bronchial biopsy

value: moderate dysplasia

value: regressive


title: MR196

description: Library name: Sample 62

value: Proliferative


title: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep2

description: Library name: 3D-DCIScom-PCSK5-T288P-plusGDF11-rep2


title: INTRUST_22, timepoint: C1D1

description: Library name: MB30304

value: primary tumor

value: Baseline


title: 864-MR272

description: Library name: Sample 60

value: metaplasia

value: progressive/persistent


title: INTRUST_21, timepoint: C2D1

description: Library name: MB30312

value: Esophagic carcinoma

value: Urelumab


title: 3D-DCIScom-PCSK5-T288P-noGDF11-rep1

description: Library name: 3D-DCIScom-PCSK5-T288P-noGDF11-rep1

value: 1 μg/ml doxycycline beginning at day 4.


title: MR_168

description: Library name: Sample 59

value: mild dysplasia


title: 3D-DCIScom-PCSK5-T288P-noGDF11-rep3

description: Library name: 3D-DCIScom-PCSK5-T288P-noGDF11-rep3


title: 3D-DCIScom-PCSK5-T288P-noGDF11-rep2

description: Library name: 3D-DCIScom-PCSK5-T288P-noGDF11-rep2


title: INTRUST_21, timepoint: C1D1

description: Library name: MB30303


title: 3D-DCIScom-PCSK5-M452I-noGDF11-rep3

description: Library name: 3D-DCIScom-PCSK5-M452I-noGDF11-rep3

source_name: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (M452I)


title: 732-MR216

description: Library name: Sample 64

value: Inflammatory

value: unknown


title: MR2R-78

description: Library name: Sample 58

value: severe dysplasia


title: 3D-DCIScom-PCSK5-M452I-noGDF11-rep2

description: Library name: 3D-DCIScom-PCSK5-M452I-noGDF11-rep2

value: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (M452I)


title: 3D-DCIScom-PCSK5-M452I-noGDF11-rep1

description: Library name: 3D-DCIScom-PCSK5-M452I-noGDF11-rep1


title: INTRUST_20, timepoint: C1D1

description: Library name: MB30302

value: Melanoma

value: PD-1/PD-L1 treatment refractory


title: INTRUST_22, timepoint: C2D1

description: Library name: MB30310

value: Adrenal carcinoma

value: PD-1/PD-L1 treatment naive


title: MR169

description: Library name: Sample 57

value: bronchial biopsy

value: moderate dysplasia

value: Secretory


title: RNA-Seq, PDX-2, PBS

city: Suita

first: Sikun

last: Meng

state: Osaka

address: Yamadaoka 2-2

institute: the Universiy of Osaka

description:
Library name: Sample 5
PDX-2, PBS

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed with Trimmomatic.
Reads were aligned to the human reference genome (hg19) using HISAT2.
SAM files were converted to BAM format with SAMtools.
Gene-level read counts were quantified using featureCounts.
Assembly: hg19
Supplementary files format and content: A tab-delimited text file containing raw read counts for all genes across all samples, generated by featureCounts. Rows represent gene IDs and columns represent sample IDs.

source_name: colorectal tumor tissue (PDX)

extract_protocol:
A moderate amount of tumor tissue was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted with the Ribo-Zero Plus rRNA Depletion Kit (Illumina). Stranded libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the manufacturer’s protocol, omitting the mRNA purification step.

value: colorectal tumor tissue (PDX)

value: PBS

tag: host

value: NOG mouse


title: RNA-Seq, PDX-2, 7SL1+LNP

description:
Library name: Sample 4
PDX-2, 7SL1+LNP

value: Splenocytes (7SL1 knock-in) with FAP-CAR mRNA-LNPs


title: INTRUST_19, timepoint: C3D1

description: Library name: MB30300

value: primary tumor

value: Breast carcinoma

value: Nivolumab


title: RNA-Seq, PDX-2, WT+LNP

description:
Library name: Sample 3
PDX-2, WT+LNP

value: Splenocytes (wild-type) with FAP-CAR mRNA-LNPs


title: 402-MR123

description: Library name: Sample 56

value: Proliferative

value: progressive/persistent


title: INTRUST_19, timepoint: C4D1

description: Library name: MB30317

value: Repeat Ure+Nivo


title: RNA-Seq, PDX-1, PBS

description:
Library name: Sample 1
PDX-1, PBS


title: PDX-2, 7SL1+LNP

description: Library name: Sample 3

library_source: genomic

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter trimming and low-quality base removal were performed with Trim Galore.
Reads were aligned to the human reference genome (hg19) using Bowtie2.
PCR duplicates were removed with Picard MarkDuplicates.
Peaks of accessible chromatin regions were identified using MACS2 (q-value < 0.01).
Assembly: hg19
Supplementary files format and content: Processed data include peak files generated by MACS2, provided in tab-delimited text format. Each file contains genomic coordinates of accessible chromatin regions with associated enrichment statistics, including peak length, summit position, pileup, and fold enrichment. Rows represent individual peaks and columns represent peak features.

molecule: genomic DNA

extract_protocol:
Nuclei were isolated from tumor tissue fragments according to the Active Motif ATAC-Seq Kit protocol.
ATAC-seq libraries were prepared using the Active Motif ATAC-Seq Kit following the manufacturer’s instructions. Briefly, isolated nuclei were subjected to transposition with Tn5 transposase, followed by PCR amplification and purification.


title: 744-MR220

description: Library name: Sample 55

value: normal

value: Normal

value: unknown


title: INTRUST_19, timepoint: C1D1

description: Library name: MB30294

value: PD-1/PD-L1 treatment naive

value: Baseline


title: 3D-DCIScom-PCSK5-M452I-noGDF11-rep4

description: Library name: 3D-DCIScom-PCSK5-M452I-noGDF11-rep4

value: MCF10DCIS.com PCSK5-/- clone with pSLIK PCSK5-V5 (M452I)

value: 1 μg/ml doxycycline beginning at day 4.


title: RNA-Seq, PDX-1, 7SL1+LNP

description:
Library name: Sample 2
PDX-1, 7SL1+LNP

value: colorectal tumor tissue (PDX)


title: INTRUST_19, timepoint: C2D1

description: Library name: MB30297

value: Urelumab


title: INTRUST_23, timepoint: C3D1

description: Library name: MB30314

value: Gastric carcinoma


title: PDX-1, 7SL1+LNP

description: Library name: Sample 2

value: Splenocytes (7SL1 knock-in) with FAP-CAR mRNA-LNPs

value: NOG mouse


title: MR121

description: Library name: Sample 53

value: bronchial biopsy

value: moderate dysplasia


title: 748-MR224

description: Library name: Sample 52

value: severe dysplasia

value: Proliferative


title: PDX-1, PBS

description: Library name: Sample 1

value: PBS


title: INTRUST_18, timepoint: C4D1

description: Library name: MB30306

value: primary tumor

value: Pleural mesothelioma

value: Repeat Ure+Nivo


title: INTRUST_18, timepoint: C3D1

description: Library name: MB30299

value: PD-1/PD-L1 treatment naive

value: Nivolumab


title: H1299-NC-3

city: Shanghai

first: Feng

last: Li

address: 2901 Caolang Highway

institute: Shanghai Public Health Clinical Center

description:
Library name: Sample 9
H1299_raw_gene_count.txt

data_processing:
BCL files were converted into fastq files using bcl2fastq (v2.17)
Raw sequencing data in FASTQ format were quality-controlled and adapter-trimmed using Trimmomatic (v0.39). The filtered reads were aligned to the reference genome (GRCh38) using STAR (v2.7.3a).
Read counts for each gene were generated using featureCounts (v2.0.1) with the parameter “-s 2” to specify strand-specific reverse transcription.
Differential gene expression analysis was performed using DESeq2. Significantly differentially expressed genes were defined as those with pvalue < 0.05 and an absolute log2foldchange  > 1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of A549
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of H1299

growth_protocol: The human lung cancer cell lines (A549 and H1299) were sourced from the Chinese Academy of Sciences Cell Resource Center. These cells were cultured in DMEM or RPMI-1640 medium (Gibco, USA), supplemented with 10% fetal bovine serum (Gibco, USA), and maintained under standard conditions (37℃, 5% CO2).

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen, Grand Island, NY) and further purified with the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). RNA integrity was assessed using an Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA), and samples with an RNA Integrity Number (RIN) greater than 7.0 were used for subsequent library preparation.
The TruSeq RNA Sample Preparation Kit (Illumina) was employed for mRNA purification, fragmentation, first-strand cDNA synthesis and second-strand cDNA synthesis.The resulting libraries were quantified using a Qubit fluorometer (Invitrogen, CA, USA), pooled in equimolar amounts, and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: For circFUT8 silencing experiments, A549 and H1299 cells were transduced with lentiviral vectors encoding either shRNA targeting circFUT8 (sh-circFUT8) or non-targeting control shRNA (sh-NC).

value: lung cancer

value: WT


title: H1299-sh-circFUT8-1

description:
Library name: Sample 10
H1299_raw_gene_count.txt

value: circFUT8 knockdown


title: H1299-sh-circFUT8-2

description:
Library name: Sample 11
H1299_raw_gene_count.txt


title: INTRUST_18, timepoint: C1D1

description: Library name: MB30290

value: Baseline


title: H1299-NC-2

description:
Library name: Sample 8
H1299_raw_gene_count.txt


title: H1299-sh-circFUT8-3

description:
Library name: Sample 12
H1299_raw_gene_count.txt


title: MR122

description: Library name: Sample 51

value: unknown

value: Secretory


title: H1299-NC-1

description:
Library name: Sample 7
H1299_raw_gene_count.txt


title: 432-SLCC432

description: Library name: Sample 50

value: metaplasia

value: Normal

value: normal/stable


title: A549-sh-circFUT8-2

description:
Library name: Sample 5
A549_raw_gene_count.txt


title: A549-sh-circFUT8-3

description:
Library name: Sample 6
A549_raw_gene_count.txt


title: INTRUST_18, timepoint: C2D1

description: Library name: MB30295

value: Urelumab


title: A549-sh-circFUT8-1

description:
Library name: Sample 4
A549_raw_gene_count.txt


title: 340-SLCC340

description: Library name: Sample 49

value: bronchial biopsy

value: severe dysplasia

value: Proliferative

value: regressive


title: 745-MR221

description: Library name: Sample 54

value: hyperplasia


title: A549-NC-3

description:
Library name: Sample 3
A549_raw_gene_count.txt


title: INTRUST_17, timepoint: C1D1

description: Library name: MB30285

value: primary tumor

value: Vulvar carcinoma

value: PD-1/PD-L1 treatment refractory


title: MR_167

description: Library name: Sample 48


title: A549-NC-2

description:
Library name: Sample 2
A549_raw_gene_count.txt

value: lung cancer

value: WT


title: INTRUST_17, timepoint: C2D1

description: Library name: MB30291


title: INTRUST_17, timepoint: C3D1

description: Library name: MB30296

value: Nivolumab


title: SLCC_433

description: Library name: Sample 47

value: moderate dysplasia


title: A549-NC-1

description:
Library name: Sample 1
A549_raw_gene_count.txt


title: MR205

description: Library name: Sample 46

value: unknown


title: MR_153

description: Library name: Sample 45

value: metaplasia

value: Inflammatory


title: TGFb1, TGFb1+AI drug Repeat 8

city: PALO ALTO

first: YUAN

last: GUAN

state: CA

address: 1701 Page Mill Road

institute: Stanford University

description:
Library name: L8
Evercode WT_V3

library_source: other

data_processing:
scRNA-seq demultiplexing, barcoded processing, gene counting and aggregation were made using the split-pipe software (1.0.3p) (ParseBiosciences-Pipeline.1.0.3p, https://support.parsebiosciences.com/hc/en-us)
For scRNA-seq data further analysis and sample demultiplexing, both 18 sublibs and 8 sublibs from 'Mega' and 'WT' experiments were concatenated and demultiplexing using sample barcode information provided in supplemental file ('scRNA-seq_Mega_libs_sample_barcode.csv', 'scRNA-seq_WT_libs_sample_barcode.csv') respectively according to ParseBiosciences pipeline.
For snATAC-seq, raw sequencing data were demultiplexed, and FASTQ files were generated using the the ScaleTagToolkit from the Scale Bio seq Suite Suite (https://github.com/ScaleBio/ScaleTagToolkit). This suite processes the data from demultiplex samples, and the 150 bp paired-end (PE) snATAC-seq reads were aligned to the GRCh38 (hg38) reference genome.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: C3 COL1A1::Clover iPSC

growth_protocol: The human iPSC line (C3 COL1A1-P2A-Clover) was used in this study. To produce microHOs, 50~60% confluent iPSC cultures were cultured in a series of differentiation media as previously described 2.  First, a definitive endoderm differentiation media that consisted of Advanced DMEM/F-12 (Gibco, 12634010) + ITS (Gibco, 41400045) supplemented with 0.1 mM nonessential amino acids, 1 mM pyruvate and 2 mM L-alanyl-L-glutamine dipeptide (GlutaMAX). On days 1 to 2, 100 ng/ml Activin-A (Peprotech, Rocky Hill, NJ), 10 ng/ml BMP4 (Peprotech), 100 ng/ml bFGF (Peprotech), 3 mM CHIR99021 (Sellechchem, Houston, TX) and 10 uM LY294002 (Sellechchem) were added the culture. On day 3, 100 ng/ml Activin-A and 100 ng/ml bFGF were added the definitive endoderm differentiation medium. From days 4 to 9, 20 ng/ml FGF10 (Peprotech) and 20 ng/ml BMP4 were added to the hepatoblast medium, which consisted of which consisted of Advanced RPMI 1640 Medium (Gibco) that was supplemented with GlutaMAX and ITS.

extract_protocol:
Control, TGFb1 and TGFb1+drug-treated  microHOs (n>30 per group) were harvested from multiple independently prepared sets of cultures, and single cell suspensions were prepared by protease digestion..  Single cell suspensions were visually inspected under a microscope, cells were counted using a Scepter™ 2.0 Handheld Automated Cell Counter (EMD Millipore, Burlington, MA), and then resuspended in PBS with 0.01% BSA.
scRNA-seq libraries were prepared by using the spit-pool based scRNA-Seq method (Evercode™ WT mini/WT/Mega from Parse biosciences) according to the manufacturer’s instructions. snATAC-seq used the same single cell samples as those prepared for scRNA-seq. For the snATAC-seq analyses, 3 batches of microHO samples were prepared. Single nuclei were isolated from those samples using the nuclei Isolation kit (Nuclei EZ Prep, Sigma Aldrich, NUC101-1KT) according to the manufacturer’s instructions and the samples were pre-indexed using the scATAC Pre-Indexing Kit (ScaleBio) according to the manufacturer’s instructions. The pooled single nuclei were loaded onto the 10xChromium Next GEM Single Cell v2 workflow.

treatment_protocol: After day 9, the hepatoblasts were dissociated to single cells in Accutase (Invitrogen) medium with 10 uM Y-27632 (Santa Cruz Biotechnology, Dallas, Texas). Then, 10,000 cells/well were re-aggregated in low-cell-adhesion Nunclon™ Sphera™ 96 well Microplates (ThermoFisher) that contained serum-free HO growth and differentiation medium, which consisted of William's E medium supplemented with 0.1% Polyvinyl alcohol (Sigma-Aldrich), 0.1 mM nonessential amino acids, 1 mM pyruvate, 2 mM L-alanyl-L-glutamine dipeptide (GlutaMAX), 10 mM Y-27632, 100 ng/ml EGF, 10 ng/ml HGF, 10 mM Dexamethasone and 10 mM Hydrocortisone (Sigma, St. Louis MO). On day 13, 50 ng/ml of TGF1 (Peprotech, 100-21; or Sinobiological, 10804-HNAC) and drugs at the indicated concentration were added to each microwell.  The microHO cultures were allowed to differentiate over 21 to 31 days.

value: C3 COL1A1::Clover iPSC

value: Hepatic organoid

value: TGFb1, TGFb1+AI drug


title: INTRUST_16, timepoint: C2D1

description: Library name: MB30287

value: Breast carcinoma

value: PD-1/PD-L1 treatment naive

value: Urelumab


title: INTRUST_16, timepoint: C1D1

description: Library name: MB30279

value: Baseline


title: TGFb1, TGFb1+AI drug Repeat 6

description:
Library name: L6
Evercode WT_V3


title: INTRUST_15, timepoint: C4D1

description: Library name: MB30298

value: primary tumor

value: Repeat Ure+Nivo


title: TGFb1, TGFb1+AI drug snATAC-seq

description:
Library name: snATAC-L2
barcode file ('samples.csv') to demuxlet snATAC-seq data
Scalebio pre-indexing + 10X genomics snATAC-seq v2; pooled sample raw file demultiplexed into 24 processed data files


title: TGFb1, TGFb1+AI drug Repeat 3

description:
Library name: L3
Evercode WT_V3


title: MR_152

description: Library name: Sample 43

value: bronchial biopsy

value: Normal

value: normal/stable


title: TGFb1, TGFb1+AI drug Repeat 5

description:
Library name: L5
Evercode WT_V3


title: TGFb1, TGFb1+AI drug Repeat 1

description:
Library name: L1
Evercode WT_V3


title: TGFb1, TGFb1+AI drug Repeat 2

description:
Library name: L2
Evercode WT_V3


title: TGFb1, TGFb1+Expert drug Repeat 18

description:
Library name: Mega_L18
Evercode WT_V2

value: TGFb1, TGFb1+Expert drug


title: MR262

description: Library name: Sample 42

value: Secretory


title: INTRUST_15, timepoint: C2D1

description: Library name: MB30286

value: Vulvar carcinoma


title: INTRUST_15, timepoint: C3D1

description: Library name: MB30293

value: Nivolumab


title: TGFb1, TGFb1+Expert drug Repeat 16

description:
Library name: Mega_L16
Evercode WT_V2


title: INTRUST_14, timepoint: C2D1

description: Library name: MB30283

value: Urothelial carcinoma

value: PD-1/PD-L1 treatment refractory


title: TGFb1, TGFb1+Expert drug Repeat 17

description:
Library name: Mega_L17
Evercode WT_V2

value: C3 COL1A1::Clover iPSC

value: Hepatic organoid


title: MR_165

description: Library name: Sample 40

value: moderate dysplasia

value: Proliferative

value: regressive


title: TGFb1, TGFb1+Expert drug Repeat 15

description:
Library name: Mega_L15
Evercode WT_V2


title: MR261

description: Library name: Sample 41

value: metaplasia

value: progressive/persistent


title: TGFb1, TGFb1+Expert drug Repeat 14

description:
Library name: Mega_L14
Evercode WT_V2


title: TGFb1, TGFb1+AI drug Repeat 7

description:
Library name: L7
Evercode WT_V3

value: TGFb1, TGFb1+AI drug


title: TGFb1, TGFb1+Expert drug Repeat 13

description:
Library name: Mega_L13
Evercode WT_V2


title: TGFb1, TGFb1+Expert drug Repeat 12

description:
Library name: Mega_L12
Evercode WT_V2


title: INTRUST_14, timepoint: C1D1

description: Library name: MB30277

value: primary tumor

value: Baseline


title: 700-MR204

description: Library name: Sample 44

value: bronchial biopsy

value: normal

value: unknown


title: TGFb1, TGFb1+Expert drug Repeat 11

description:
Library name: Mega_L11
Evercode WT_V2

value: TGFb1, TGFb1+Expert drug


title: MR2R-14

description: Library name: Sample 39

value: Secretory


title: INTRUST_13, timepoint: C3D1

description: Library name: MB30288

value: Urothelial carcinoma

value: Nivolumab


title: TGFb1, TGFb1+Expert drug Repeat 10

description:
Library name: Mega_L10
Evercode WT_V2

value: C3 COL1A1::Clover iPSC


title: 844-MR260

description: Library name: Sample 38


title: TGFb1, TGFb1+Expert drug Repeat 9

description:
Library name: Mega_L9
Evercode WT_V2

value: Hepatic organoid


title: MR164

description: Library name: Sample 37


title: TGFb1, TGFb1+Expert drug Repeat 8

description:
Library name: Mega_L8
Evercode WT_V2


title: TGFb1, TGFb1+Expert drug Repeat 7

description:
Library name: Mega_L7
Evercode WT_V2


title: INTRUST_13, timepoint: C1D1

description: Library name: MB30274

value: PD-1/PD-L1 treatment refractory


title: TGFb1, TGFb1+AI drug Repeat 4

description:
Library name: L4
Evercode WT_V3


title: INTRUST_13, timepoint: C2D1

description: Library name: MB30280

value: Urelumab


title: 835-MR256

description: Library name: Sample 36

value: mild dysplasia

value: Proliferative


title: INTRUST_12, timepoint: C2D1

description: Library name: MB30278

value: Hepatocarcinoma

value: PD-1/PD-L1 treatment naive


title: TGFb1, TGFb1+Expert drug Repeat 5

description:
Library name: Mega_L5
Evercode WT_V2


title: TGFb1, TGFb1+Expert drug Repeat 4

description:
Library name: Mega_L4
Evercode WT_V2


title: MR127

description: Library name: Sample 35

value: moderate dysplasia

value: progressive/persistent


title: TGFb1, TGFb1+Expert drug Repeat 6

description:
Library name: Mega_L6
Evercode WT_V2


title: TGFb1, TGFb1+Expert drug Repeat 3

description:
Library name: Mega_L3
Evercode WT_V2


title: INTRUST_12, timepoint: C3D1

description: Library name: MB30282

value: primary tumor


title: MR2R-47

description: Library name: Sample 34

value: bronchial biopsy


title: TGFb1, TGFb1+Expert drug Repeat 2

description:
Library name: Mega_L2
Evercode WT_V2


title: INTRUST_11, timepoint: C2D1

description: Library name: MB30273

value: Ovarian carcinoma


title: TGFb1, TGFb1+Expert drug Repeat 1

description:
Library name: Mega_L1
Evercode WT_V2

value: TGFb1, TGFb1+Expert drug


title: MR258

description: Library name: Sample 33

value: hyperplasia

value: Secretory

value: unknown


title: INTRUST_11, timepoint: C3D1

description: Library name: MB30281

value: Nivolumab


title: Donor3_HIVseq

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

description: Library name: JFSTNR09_GEX6

data_processing:
Alignment of scRNAseq reads, collapsing of reads to unique molecular identifier (UMI) counts, and cell calling was performed using CellRanger 7.1.0 (10X Genomics).
Assembly: hg38  + consensus subtype B genome for HIV
Supplementary files format and content: CellRanger output files : features.tsv.gz, matrix.mtx.gz, barcodes.tsv.gz

source_name: blood

extract_protocol:
CD4+ T cells were purified by negative selection using the EasySep Human CD4 T cell enrichment kit (StemCell)
libraries construction according to 10X protocol "Chromium Single Cell 5’ Reagent Kits v2 (Dual Index) User Guide (10x Genomics CG000330, Rev A)".

value: blood

value: PBMC_T cells


title: Donor3_regular10X

description: Library name: JFSTNR09_GEX5


title: Donor2_HIVseq

description: Library name: JFSTNR11_GEX4


title: 839-MR257

description: Library name: Sample 32

extract_protocol:
miRNA was extracted from biopsies or brushing samples using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
miRNA sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEBioLabs). Sequencing adapters that target the 3’ hydroxyl group of small RNAs were ligated and the transcripts were reverse transcribed and PCR-amplified into single-stranded cDNA libraries. The libraries were pooled, and size selected for small RNA fragments on PAGE gel in groups of 6-10.

value: normal/stable


title: Donor2_regular10X

description: Library name: JFSTNR11_GEX3


title: INTRUST_11, timepoint: C1D1

description: Library name: MB30268

value: Baseline


title: SLCC527

description: Library name: Sample 31

value: Inflammatory


title: INTRUST_10, timepoint: C3D1

description: Library name: MB30276

value: Melanoma

value: PD-1/PD-L1 treatment refractory


title: Donor1_regular10X

description: Library name: JFSTNR11_GEX1


title: P30_rep2

city: dongguan

first: Lushuang

last: Mao

state: guangdong

address: No.1 Xincheng Avenue, Songshan Lake Science and Technology Industrial Park

department: 2.Dongguan Key Laboratory of Aging and Anti-Aging

institute: Guangdong Medical University

description:
Library name: sample 11
P30 group, replicate biosample 2

data_processing:
For CUT&Tag-seq data, reads were mapped to the human reference genome (hg19) using Bowtie2 (version 2.4.5). The aligned BAM files were subjected to quality control using SAMtools, and only uniquely mapped reads were retained for further analysis. Significant peaks were called using MACS2, with the exception of the -q 0.01 parameter, all other parameters were set to default values. BigWig files were generated from the BAM files using bamCoverage from deepTools, with the following parameters: -binSize 10 -effective GenomeSize 2864785220 and normalized using RPKM. CUT&Tag signal of H3K27ac was used to define super-enhancers, ROSE was employed for enhancer and super-enhancer identification, along with the annotation of relevant genes. Spearman correlation coefficient analysis based on the read coverages for genomic regions for Bigwig files was performed using deepTools multiBigwigSummary. Peak distributions were analyzed by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: tab-delimited text fie includes the peak for each sample
Library strategy: CUT&Tag

source_name: cell culture

growth_protocol: We collected 1.5 × 10⁵ HUVECs at different stages using 0.05% trypsin digestion and performed subsequent library construction with the Hyperactive Universal CUT&Tag Assay Kit. Briefly, cells were washed with 500 μL of wash buffer and centrifuged at 600 × g for 5 min at room temperature. The cell pellet was resuspended in 100 μL of wash buffer. A total of 10 μL of ConA beads was washed twice with 100 μL of binding buffer, and then added to the cells, followed by incubation at room temperature for 10 min. After removal of the supernatant, the cells bound to the magnetic beads were resuspended in 50 μL of antibody buffer containing 1 μg of antibodies (H3K27ac, H3K4me1, H3K4me3) and incubated overnight at 4 ℃. Subsequently, 1 μL of goat anti-rabbit IgG diluted in 50 μL of Dig-wash buffer was added to the cells and incubated with rotation for 1 h at room temperature. The cells were gently washed three times with 200 μL of Dig-wash buffer, and then 2 μL of pA/G-Tnp and 98 μL of Dig-300 buffer were added to each sample. After incubating at room temperature for 1 h, the samples were gently washed three times with 200 μL of Dig-300 buffer. Next, 10 μL of 5 × Tagmentation DNA Buffer (TTBL) mixed with 40 μL of Dig-300 buffer was added to each sample, and the samples were incubated at 37 ℃ for 1 h.

extract_protocol:
DNA extraction was performed by adding 5 μL of proteinase K, 100 μL of buffer L/B, and 20 μL of DNA extraction beads, followed by incubation at 55 ℃ for 10 min.
For library amplification, 15 μL of extracted DNA was mixed with 25 μL of 2 × CAM, P5 Primer, and P7 Primer. The H3K27ac library was amplified for 13 cycles, while the H3K4me1 and H3K4me3 libraries were amplified for 11 cycles. To purify the PCR products, 2 × VAHTS DNA Clean Beads was added, followed by incubation at room temperature for 5 min. After purification, paired-end sequencing was performed on the NovaSeq 6000 platform with three biological replicates at Novogene Biotech Co., Ltd.

value: cell culture

value: HUVEC


title: P30_rep3

description:
Library name: sample 12
P30 group, replicate biosample 3


title: P30_rep1

description:
Library name: sample 10
P30 group, replicate biosample 1


title: INTRUST_10, timepoint: C2D1

description: Library name: MB30271

value: primary tumor

value: Urelumab


title: SLCC526

description: Library name: Sample 29

data_processing:
De-multiplexing and generation of FASTQ files were performed using Illumina CASAVA v1.8.2.
FastQC v0.11.7 (RRID: SCR_014583) was used to examine the quality of raw reads and cutadapt v1.18 was used for trimming the sequencing adaptors (5’- AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’, -trim-n). Reads unlikely to be properly sequenced mature miRNA transcripts were discarded (reads shorter than 16 nt or longer than 25 nt with –m 16 –M 25 in cutadapt).
Alignment and quantification of mature miRNAs based on miRBase v22 (RRID: SCR_003152) were performed with miRDeep2 v0.1.0 with mapper.pl parameters –e –h –m –i –j and quantifier.pl parameter –k –j –d -P. For mature miRNAs associated with multiple precursor miRNAs, the max counts were used.
We performed miRNA-seq sample quality assessments and miRNA filtering separately for each sample type (endobronchial biopsies and bronchial brushes). We limited the analysis to the miRNA samples with previously analyzed (GSE109743, dbGaP:phs003185.v1.p1) matched mRNA expression profiles (n=160 biopsies, n=89 brushes). The raw counts were converted into log2 counts per million of miRNA reads mapped (logCPM) and quantile normalized with voom. miRNAs with logCPM less than 1 in more than half of the samples were removed. We excluded samples (n=4 biopsies, n=2 brushes) if sequencing quality metrics were outside 2 standard deviations from the mean. The quality metrics we used included the first and the second principal components from the PCA using filtered miRNA expression, the mean Pearson expression correlation with all other samples across the filtered miRNAs, and the transcript integrity number (TIN) of the matched mRNA sequencing sample (calculated using RSeQC v3.0.0, RRID: SCR_005275). Finally, 156 biopsies and 87 brush samples from 30 patients were retained.
The gene filter and normalization described above were performed on the final high-quality samples with matching mRNA data (n=525 miRNAs in biopsies and n=489 miRNAs in brushes). The residual miRNA expressions adjusting for sequencing batch were computed with limma (RRID: SCR_010943) for downstream analysis.
Assembly: hg38
Supplementary files format and content: PCGA_miRNA_raw_count_table_BX.csv: Comma-separated value (CSV) table of raw counts, 2656 miRNAs x 156 samples
Supplementary files format and content: PCGA_miRNA_residual_table_BX.csv: Comma-separated value (CSV) table of residuals, 525 rows x 156 columns

value: bronchial biopsy


title: Donor1_HIVseq

description: Library name: JFSTNR11_GEX2


title: P22-rep3

description:
Library name: sample 9
P22 group, replicate biosample 3


title: P22-rep1

description:
Library name: sample 7
P22 group, replicate biosample 1


title: INTRUST_10, timepoint: C4D1

description: Library name: MB30292

value: Repeat Ure+Nivo


title: INTRUST_10, timepoint: C1D1

description: Library name: MB30267


title: P22-rep2

description:
Library name: sample 8
P22 group, replicate biosample 2


title: SLCC528

description: Library name: Sample 27

value: hyperplasia

value: Normal


title: P15-rep3

description:
Library name: sample 6
P15 group, replicate biosample 3


title: 454-SLCC454

description: Library name: Sample 30

value: metaplasia


title: INTRUST_09, timepoint: C3D1

description: Library name: MB30275

value: PD-1/PD-L1 treatment naive

value: Nivolumab


title: P15-rep2

description:
Library name: sample 5
P15 group, replicate biosample 2


title: SLCC_453

description: Library name: Sample 28

value: normal


title: P5-rep3

description:
Library name: sample 3
P5 group, replicate biosample 3


title: INTRUST_09, timepoint: C4D1

description: Library name: MB30289


title: P15-rep1

description:
Library name: sample 4
P15 group, replicate biosample 1


title: MR231

description: Library name: Sample 25

value: Secretory

value: normal/stable


title: P5-rep2

description:
Library name: sample 2
P5 group, replicate biosample 2


title: INTRUST_09, timepoint: C2D1

description: Library name: MB30270


title: MR_214

description: Library name: Sample 24

value: Inflammatory

value: unknown


title: P30_rep3_ATAC

description:
Library name: sample 8
P30 group, replicate biosample 2

data_processing:
For ATAC-seq data, reads were aligned to the human reference genome (hg19) using Bowtie2 (version 2.4.5). The aligned BAM files underwent quality control using SAMtools, and only uniquely mapped reads were retained. PCR duplicates were removed using Picard (http://broadinstitute.github.io/picard/) for subsequent analysis. Significant peaks were called using MACS2, with the exception of the -q 0.01 parameter, all other parameters were set to default values. BigWig files were generated from the BAM files using bamCoverage from deepTools, with the following parameters: -binSize 10 -effectiveGenomeSize 2864785220 and normalized using RPKM. Peak distributions were analyzed by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: tab-delimited text fie includes the peak for each sample

growth_protocol: 5 × 104 HUVECs at different stages were collected by 0.05% trypsin digestion and resuspended the samples in 1 × phosphate-buffered saline (PBS).

extract_protocol:
The cells were centrifuged at 500 g, 4 ℃ for 5 min, and the cell pellet was then resuspended in 50 μl of ice-cold lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% (v/v) Igepal CA-630. The cell suspension was placed on ice for 2 min to allow cell lysis, followed by centrifugation at 500 × g for 5 min at 4°C to collect the nuclei.
The lysed cells were then transferred to sterile PCR tubes and subjected to transposition reaction and library construction using the TruePrep DNA Library Prep Kit V2. For the transposition reaction and library construction, the lysed cell samples were mixed with 5 × TTBL, TTE-Mix V50, and ddH2O according to the kit instructions. The mixture was heated at 37°C for 30 min to facilitate the fragmentation reaction. Afterward, 5 × TAB, PPM, P5 Primer, and P7 Primer were added to the enzymatically treated products purified using VAHTS DNA Clean Beads. The DNA library was obtained by performing 15 cycles of PCR amplification. Subsequently, the library was purified and subjected to paired-end sequencing on the NovaSeq 6000 platform with two biological replicates at Novogene Biotech Co., Ltd.


title: INTRUST_09, timepoint: C1D1

description: Library name: MB30266

value: Melanoma

value: Baseline


title: P22_rep2_ATAC

description:
Library name: sample 6
P22 group, replicate biosample 2

value: cell culture

value: HUVEC


title: P22_rep1_ATAC

description:
Library name: sample 5
P22 group, replicate biosample 1


title: INTRUST_08, timepoint: C3D1

description: Library name: MB30269

value: primary tumor

value: Esophagic carcinoma


title: P15_rep3_ATAC

description:
Library name: sample 4
P15 group, replicate biosample 2


title: MR104

description: Library name: Sample 23

value: bronchial biopsy


title: MR181

description: Library name: Sample 22

value: mild dysplasia


title: P15_rep1_ATAC

description:
Library name: sample 3
P15 group, replicate biosample 1


title: P5_rep3_ATAC


title: P5_rep2_ATAC

description:
Library name: sample 1
P5 group, replicate biosample 1


title: INTRUST_08, timepoint: C2D1

description: Library name: MB30265

value: Urelumab


title: MR2R-11

description: Library name: Sample 21

value: hyperplasia


title: 455-SLCC455

description: Library name: Sample 26

value: Normal

value: regressive


title: MR202

description: Library name: Sample 20

value: metaplasia

value: Proliferative


title: INTRUST_08, timepoint: C1D1

description: Library name: MB30263

value: PD-1/PD-L1 treatment naive


title: Mutant

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

description:
Library name: S8067Nr22
10xGenomics

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for 'filtered_feature_bc_matrix' (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: iPSC-derived microglia

extract_protocol:
Cells were disociated with accutase 5min at 37C and resuspended in 0,04%BSA-PBS 1x. RNA libraries were prepared using standard 10X Genomics 3' Single Cell v3.1 protocol.
Cells loaded to Chromium Chip (target cell recovery): 6,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq 6000, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp.

value: iPSC-derived microglia

tag: disease state

value: Mutant carrying the C9orf72 hexanucleotide repeat expansion (C9)


title: PC9OR si-GLMP repeat3

city: Nanjing

first: Renhua

last: Guo

state: Jiangsu

address: 101 longmian Avenue

institute: Nanjing Medical University

description: Library name: Sample6

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
lung cancer cells RNA was harvested using Trizol reagent. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: lung cancer cells

value: GLMP knockdown


title: 412-MR126

city: Boston

first: Adam

address: 72 East Concord Street, E632

institute: Boston University School of Medicine

description: Library name: Sample 19

value: severe dysplasia


title: P5-rep1

value: cell culture

tag: cell type

value: HUVEC


title: INTRUST_07, timepoint: C4D1

description: Library name: MB30264

value: primary tumor

value: Ovarian carcinoma

value: Repeat Ure+Nivo


title: PC9OR si-GLMP repeat2

description: Library name: Sample5

tag: genotype


title: MR_203

description: Library name: Sample 18

tag: tissue

value: bronchial biopsy

value: normal

value: Secretory

value: normal/stable


title: PC9OR NC repeat3

description: Library name: Sample3

value: Control


title: PC9OR si-GLMP repeat1

description: Library name: Sample4


title: P30_rep1_ATAC

description:
Library name: sample 7
P30 group, replicate biosample 1


title: PC9OR NC repeat2

description: Library name: Sample2


title: INTRUST_07, timepoint: C3D1

description: Library name: MB30262

tag: tumor

value: Nivolumab


title: 442-SLCC442

description: Library name: Sample 17

value: metaplasia

value: unknown


title: PC9OR NC repeat1

description: Library name: Sample1


title: INTRUST_07, timepoint: C2D1

description: Library name: MB30261

tag: cohort

value: PD-1/PD-L1 treatment naive

value: Urelumab


title: INTRUST_08, timepoint: C4D1

description: Library name: MB30284

value: Esophagic carcinoma


title: SLCC441

description: Library name: Sample 16

tag: pcga id

value: moderate dysplasia

value: Normal


title: Enza_3

city: Aurora

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description: Library name: Enza_3

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCh38
Supplementary files format and content: Txt file containg gene counts

source_name: MCF7 ER Y537S

growth_protocol: Cells were grown in phenol-red free MEM supplemented with 5% charcoal stripped FBS, 2 mM glutamine, non-essential amino acids, pen/strep, 1 nM insulin, and 1 nM DHT

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits. Samples were quantitated and quality assessed using Nanodrop 2000 before submission to RNA sequencing core.
Universal Plus mRNA-Seq library preparation kit with NuQuant was used with 200 ng RNA input to generate libraries.

treatment_protocol: Cells were treated with DMSO or 30 uM Enzalutamide for 96 hours before harvest

value: MCF7 ER Y537S

value: ER+ breast cancer

value: ER Y537S Knock-in

value: 30 uM Enzalutamide


title: INTRUST_07, timepoint: C1D1

description: Library name: MB30260

value: primary tumor

value: Ovarian carcinoma

value: Baseline


title: MR2R-35

last: Gower

description: Library name: Sample 15

source_name: bronchial biopsy

value: bronchial biopsy

tag: patient id

value: Proliferative

value: regressive


title: Enza_2

description: Library name: Enza_2

tag: treatment


title: Enza_1

description: Library name: Enza_1

tag: batch


title: Control

description:
Library name: S8067Nr21
10xGenomics

value: iPSC-derived microglia

value: Isogenic Control


title: DMSO_2

description: Library name: DMSO_2

value: DMSO


title: 006-Tumor-1808_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-1808
raw_counts.txt

data_processing:
Nanostring quality control process
Assembly: FASTQ files processed into DCC files by geomxngspipeline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC and rawcount
Library strategy: Spatial Transcriptomics

source_name: FFPE endometrial tumor

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

value: Endometrium

value: MLH1 deficient

tag: rpl22 status

value: positive

tag: immune status

value: immune high


title: MR175

description: Library name: Sample 14

tag: flowcell

tag: dysplasia grade

value: normal

tag: molecular subtype

value: Secretory

value: progressive/persistent


title: MR_145

description: Library name: Sample 13

value: moderate dysplasia

tag: progression status

tag: median tin


title: DMSO_1

description: Library name: DMSO_1

tag: cell line

value: MCF7 ER Y537S

value: ER+ breast cancer

value: ER Y537S Knock-in


title: 480-MR144

description: Library name: Sample 12

value: bronchial biopsy

value: unknown

value: Inflammatory


title: Donor 55 – SIRPG WT CD8+ T cells, Day 4

first: Flavien

last: Marguerie

address: 60 Fenwood Road

department: Rheumatology and Immunology

institute: Brigham and Women's Hospital

description:
Library name: 55CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted

data_processing:
Data processing tool: Sequence reads were processed using fastp for quality control and adapter trimming, and Salmon (v1.3.2) for transcript quantification in quasi-mapping mode.
Mapping: Trimmed sequence reads were mapped to the GRCh38.p14 transcriptome.
Differential expression analysis: DESeq2 (v1.46.0) was used for differential gene expression analysis.
Gene Ontology (GO): GO enrichment was performed using the clusterProfiler (v4.10.0) R package
Analysis tool for protein-protein interactions: Protein-protein interaction analysis was done using the STRING database (v12.0).
Assembly: GRCh38.p14 (Human genome assembly)
Supplementary files format and content: The processed data is in CSV format, including FPKM values for each sample

source_name: PBMCs

extract_protocol:
RNA was isolated from PBMCs using Qiagen's RNeasy Mini Plus Kit, and lysates were stored at -80°C until further processing.
RNA-seq libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit, following the manufacturer's protocols. This method was used for preparing RNA libraries for SmartSeq2 protocol.

value: PBMCs

tag: cell type

value: CD8+ T cells

value: SIRPG WT

value: Anti-CD3, IL-2

tag: time

value: Day 4


title: Donor 55 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 55CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted

tag: tissue

tag: genotype

value: Day 2


title: Donor 55 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 55CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+

value: SIRPG KO


title: 005-Tumor-1808_ROI_RPL22 positive_immune high

description:
Library name: 005-Tumor-1808
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: positive

value: immune high


title: 005-Tumor-2201_ROI_RPL22negative_immune low

description:
Library name: 005-Tumor-2201
raw_counts.txt

value: negative

value: immune low


title: 004-Tumor-2201_ROI_RPL22 negative_immune low

description:
Library name: 004-Tumor-2201
raw_counts.txt


title: MR2R-32

description: Library name: Sample 11

value: hyperplasia

value: Secretory


title: Donor 55 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 55CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted

value: CD4+ T cells


title: Donor 55 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 55CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+