title: Tumor p53 deficient 6

description:
Library name: PDAC-SP3
10x_v2

extract_protocol:
Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) or immune cells (marked as mKate2-negative, CD45-positive and DAPI-negative) were sorted using Aria3 or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS). Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).
Cells were resuspended in 1X PBS and BSA (0.04%) and checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II). All sequencing experiments were performed on samples with a minimum of 80% viable cells. Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2 or v3). For pre-tumor p53 deficient samples, we spiked-in CD45+ cells to the cell suspension to allow visualization of cell pellets during sample preparation prior to encapsulation. Each sample loaded onto the cartridge contained approximately 5,000 cells (non-hashed samples) or 15,000 cells (hashed samples) at a final dilution of ~500 cells μl-1. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina sequencer (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads per cell) at MSK’s Integrated Genomics Operation Core Facility.

value: Epithelial

value: mKate2+/GFP- (p53 deficient)

value: Dox


title: CRISPRi B cell sgRNA2_rep2

status: Public on Mar 18 2026

type: SRA

city: Wuhan

first: Zhang

last: Tianzhe

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

country: China

institute: Wuhan University

description:
Library name: sample10
fin_B2_rep2

library_source: transcriptomic

data_processing:
For RNA-seq analysis, the reads were aligned to the human genome (hg38) and mouse genome (mm39) using hisat2 with default parameters. We used featureCounts to generate raw counts for other genes
Assembly: mm39
Supplementary files format and content: raw_counts.txt

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Total RNA was extracted from selected cells using the RNAprep Pure Cell/Bacteria Kit according to the manufacturer’s instructions.
PolyA RNA-seq standard protocol

tag: tissue

value: Spleen

tag: cell line

value: B cell

tag: cell type

value: primary

tag: genotype


title: ALI ccRCC organoid TAM treated by control_3

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University

description: Library name: Control TAM_3

data_processing:
Good quality of reads were generated by removing reads containing adapters, ploy-N, and low-quality reads using fastp software
Trimmed reads were mapped on human reference genome (hg) using Hisat2 v2.0.5
Read count matrices were generated using featureCounts v1.5.0-p3 and FPKM of each gene was calculated based on the length of the gene and read count
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: clear cell renal carcinoma

growth_protocol: ALI organoids from ccRCC were generated and culture for 8 days.

extract_protocol:
Cell population were extracted by FACS sorting by gating CD45+ CD11b+ HLA-DR+ CD68+ cells. TAM cells were sorted into PBS+10%FBS, followed by RNA isolation using PicoPure RNA isolation kit (Applied Biosystems, KIT0204).
Isolated RNA sample quality and quantity was assessed by BioAnalyzer RNA Pico Assay. Library construction was performed following to manufaturer's protocol for SMART-seq v4 Ultra Low Input RNA kit. Llibraries were sequenced on an Illumina NovaSeq X Plus.

treatment_protocol: IFN-γ or IL-4 were added into the cultre.

value: clear cell renal carcinoma

value: macrophages

tag: treatment

value: Control


title: CRISPRi B cell sgRNA1_rep2

description:
Library name: sample8
fin_B1_rep2


title: BLEO-IPF Nintedanib Sample 4016712501

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 4016712501

data_processing:
All downstream analyses were performed using R version 3.6.0.
Assembly: Reads were aligned to the GRCm38 release 96 Ensembl Mus musculus genome using STAR version 2.7.0f.
Supplementary files format and content: comma-delimited text file contains raw counts for each Sample.

source_name: Lung

extract_protocol:
The inferior lobe samples were homogenised in lysis buffer, and RNA was purified using NucleoSpin® RNA binding strips (cat. no. 740698.5, Macherey-Nagel, Dueren, Germany). RNA purity and concentration were measured using a NanoDrop 2000.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA library prep Kit for Illumina® (cat. no. E7760L, New England Biolabs, Ipswich, MA). cDNA libraries were sequenced to a depth of approximately 15 million reads per sample (single-end, 75 bp reads) on a NextSeq 500 System (Illumina, San Diego, CA) using the NextSeq 500/550 High Output Kit version 2.5 (cat. no. 20024906, Illumina).

value: Lung

value: BLEO-IPF Nintedanib


title: ALI ccRCC organoid TAM treated by control_2

description: Library name: Control TAM_2


title: Organoid_NSCLC_Paetient_1_IgG1

description: Library name: NSCLC1_Control

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggragation were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: non small cell lung cancer

growth_protocol: ALI organoids from ccRCC or NSCLC were generated and culture for 8 days cultures.

extract_protocol:
Cell population were extracted by FACS sorting by gating CD45+ cells or CD45+ CD11b+ HLA-DR+ CD68+ cells.
Purified cells were counted and subjected to 10X Genomics Chromium single cell 5' platform following to manufacurer's protocol using the Chromium NextGEM Single Cell 5' Kit v2 (PN-1000263).

treatment_protocol: IgG1 isotype control or anti-CD47 were added to the media.

value: non small cell lung cancer

value: immune cells


title: Tumor p53 deficient 8

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: 9268_PHLH_PDAC_SP
10x_v2

data_processing:
All scRNA-seq datasets were demultiplexed, barcode-corrected, aligned and UMI-corrected with SEQC using mouse genome mm10 and default parameters.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with our custom pipeline SEQC (v0.2.8) are deposited in the Matrix Market format for sparse matrix representation. Cell barcodes in processed data files are encoded using the DNA3Bit class of the SEQC package.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our KPLOH model (GFP, rtTA3-IRES-mKate2, shRen) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

source_name: Pancreas

growth_protocol: Mice were generated by 8-cell injection of KPLOH (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; p53flox/wt; TRE-GFP-shRen.713) ESCs.

treatment_protocol: GFP was induced by treatment of the resulting mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age.

value: Pancreas

tag: batch


title: Organoid_ccRCC_Paetient_1_IgG1

description: Library name: ccRCC1_Control


title: CRISPRi B cell Mock_rep2

description:
Library name: sample6
fin_BM_rep2

value: Mock


title: CRISPRi B cell sgRNA2_rep1

description:
Library name: sample9
fin_B2_rep1


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 9

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description: Library name: GC-840

data_processing:
Sequences were mapped to GRCm38.94 using STAR v2.6.0a.
Reads were quantified using htseq-count v0.11.1
Assembly: GRCm38.94
Supplementary files format and content: csv file includes raw counts for each sample

source_name: colonocyte

extract_protocol:
Total RNA of the colon was extracted using the Qiagen RNeasy Micro Kit (Qiagen, Germantown, MD).
Libraries were made from 200 ng of total RNA using Illumina Stranded mRNA prep kits (San Diego, CA) following manufacturers instructions.

treatment_protocol: C57BL/6 mice were fed a diet of either corn oil and cellulose or fish oil and pectin for 3 weeks.

value: colonocyte

value: corn oil cellulose fiber


title: K3_shp53_batch3

description:
Library name: p489c_shp53_caer_3weeks
10x_v3

data_processing:
All scRNA-seq datasets were demultiplexed, barcode-corrected, aligned and UMI-corrected with SEQC using mouse genome mm10 and default parameters.
Assembly: mm10
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with our custom pipeline SEQC (v0.2.8) are deposited in the Matrix Market format for sparse matrix representation. Cell barcodes in processed data files are encoded using the DNA3Bit class of the SEQC package.
Supplementary files format and content: Merged fastq files, encoding the cell and molecule barcode information in fastq record headers, were obtained using SEQC (v0.2.8). Merged fastq files were aligned to transgenes in our mouse models (GFP, rtTA3-IRES-mKate2, shRen, shp53) using BWA (0.7.17-r1188). Columns in _transgene_count.tsv.gz files are: (1) record_index, (2) numeric cell barcode resulting from encoding of sequence cell barcode using the DNA3Bit class of the SEQC package, (3) arbitrary gene identifier for each transgene, (4) UMI count (5) transgene_symbol.

growth_protocol: Mice were generated by 8-cell injection of KCshRen or KCshp53 (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shRen.713 or TRE-GFP-shp53.1224) ESCs.

extract_protocol:
Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. For every sample that would be subjected to cell hashing, we used DNAse-free buffers following digestion. Samples were resuspended in 1 mL ACK-lysis buffer and incubated for 5 min at room temperature to deplete red blood cells, and washed the ACK lysis buffer with 20 mL HBSS. We blocked samples with TruStain Fc block Plus (Biolegend, 156603; clone S17011E, 1:100) for 7 min at 4°C, followed by incubation with a sample-specific TotalSeq cell hashing antibody (Biolegend, 155832, 155833, 155835, 155837, 155839, 155841; clones M1/42; 30-F11). We incubated cell hashing antibodies at a 1:50 dilution for 30 min. We washed samples 3 times with DNAse-free FACS buffer + STI, followed by filtering through a 40-μm strainer and FACS-based isolation of mKate2+/GFP+ cells (KrasG12D+ pancreatic epithelial cells expressing shp53 or shCtrl). To prepare cells for scRNA-seq, we pooled samples from the same experimental conditions into the same tube, and resuspended cells at a 1000 cells μL-1.
Cells were resuspended in 1X PBS and BSA (0.04%) and checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II). All sequencing experiments were performed on samples with a minimum of 80% viable cells. Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v3). Each sample loaded onto the cartridge contained approximately 15,000 cells at a final dilution of ~500 cells μl-1. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina sequencer (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads per cell) at MSK’s Integrated Genomics Operation Core Facility.

value: Epithelial


title: K3_FLEX

description:
Library name: K3_shp53_ctrl_FLEX
10x GEMX FLEX

data_processing:
Raw BCL files were processed with Cell Ranger (9.0.0), and the resulting FASTQ files were quantified using a custom probe set reference for the mouse genome (GRCm39) within the Cell Ranger pipeline.
Assembly: GRCm39
Supplementary files format and content: Unfiltered count matrices resulting from alignment and demultiplexing with Cell Ranger (9.0.0) are deposited in the Matrix Market format for sparse matrix representation.
Supplementary files format and content: FLEX_cells_per_tag.json contains results from cell hashing assignment to individual biological repllicates.

growth_protocol: Mice were generated by 8-cell injection of KCshp53 (Ptf1a-Cre; LSL-KrasG12D; Rosa26-CAGS-LSL-rtTA3-IRES-mKate2; TRE-GFP-shp53.1224) ESCs.

extract_protocol:
Collected tissue was fixed in 10% neutral buffered formalin (Richard-Allan Scientific), and embedded in paraffin. Single cells were extracted from FFPE blocks. GEM encapsulation was performed following the 10x Genomics Flex GEM-X (PN-1000782) protocol, using their guidelines for cell and reagent volumes per well based on the desired cell recovery. After loading the Chip FX and running it on the Chromium X, GEMs were recovered and processed according to the manufacturer’s instructions.
Following GEM processing, the resulting product was pre-amplified and indexed to generate the sequencing library. All libraries were sequenced on an Illumina NovaSeq X+ (R1 – 28 cycles, i5 – 10 cycles, i7 – 10 cycles, R2 – 90 cycles) using standard dual indexing and demultiplexing.

treatment_protocol: shp53 was induced by treatment of two mice mice with doxycycline (200 mg/kg; Envigo) in the chow starting at 5-6 weeks of age. Another set of two mice were left in normal chow as negative controls.

value: on or off dox


title: K3_shp53_batch5

description:
Library name: shp53_caer_3weeks_repeat
10x_v3

value: Dox


title: DLGG181

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw sequencing reads were processed using the CellRanger v7.0.1 pipeline (10x Genomics) with ARC-V1 chemistry. This involved alignment to the GRCh38 human reference genome (Ensembl 98) and generation of a cell-gene count matrix.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gv, features.tsv.gv, matrix.mtx.gz

source_name: brain tumor resection specimen

extract_protocol:
Snap frozen tissue samples from brain tumor resection specimens (5-15 mg) were thawed in 1 ml of HB buffer (0.25 m sucrose, 25 mm KCl, 5 mm MgCl2, 20 mm Tricine-KOH pH 7.8, 0.15 mm spermine tetrahydrochloride, 0.5 mm spermidine trihydrochloride, 1 mm DTT).  The tissue was then transferred to a 7-ml dounce homogenizer.  To this, 340 μl of 5% IGEPAL CA-630 (Sigma-Aldrich) and 4 ml of HB buffer were added. Tissue homogenization was performed using a tight pestle with 10-15 strokes. The homogenate was transferred to a 15-ml tube and the total volume was adjusted to 10 ml with 50% iodixanol solution.  A discontinuous iodixanol density gradient was prepared in a separate Corex tube (ThermoFisher) by layering 1 ml of 30% iodixanol solution over 1 ml of 40% iodixanol solution. The 9 ml tissue homogenate was carefully layered on top of the iodixanol cushion. Nuclei were isolated by centrifugation at 10,000 x g for 18 minutes.  The nuclei-enriched fraction at the 30-40% iodixanol interface (approximately 1 ml) was carefully collected.
The concentration of nuclei in the isolated fraction was determined using a hemocytometer. The sample was then diluted to a final concentration of 100,000 nuclei/ml using 30% iodixanol solution supplemented with Protector RNase Inhibitor (Sigma-Aldrich). Single-nucleus encapsulation was performed using the 10x Genomics Chromium platform according to the manufacturer's instructions.  Libraries were generated using the 10x Genomics multiomics kit (version 2) and sequenced on the Illumina NovaSeq 6000 S4 platform at the SickKids Center for Applied Genomics (TCAG). Please note that while both gene expression (GEX) and assay for transposase accessible chromatin (ATAC) libraries were constructed, in the related manuscript only GEX data was used and therefore only that is submitted here.

value: brain tumor resection specimen

tag: tissue processing

value: snap frozen tissue

value: KIAA1549-BRAF, 1p del, 1q gain

tag: pathology

value: DLGNT with malignant transformation


title: BLEO-IPF Nintedanib Vehicle Sample 4016712351

description: Library name: 4016712351

value: BLEO-IPF Nintedanib Vehicle


title: CTRL Vehicle Sample 4016712981

description: Library name: 4016712981

value: CTRL Vehicle


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 7

description: Library name: GC-819


title: DLGG038

description:
Library name: Sample 1
10x Genomics

value: KIAA1549-BRAF, FGFR1 K6565E

value: DLGNT


title: CRISPRi B cell sgRNA1_rep1

description:
Library name: sample7
fin_B1_rep1

value: Spleen

value: B cell

value: primary


title: CRISPRi T cell Mock_rep2

description:
Library name: sample2
fin_TM_rep2

value: T cell

value: Mock


title: CRISPRi B cell Mock_rep1

description:
Library name: sample5
fin_BM_rep1


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 6

description: Library name: GC-743

value: colonocyte

value: fish oil pectin fiber


title: SN-MM5 cell line, IFN-γ Treated, 4h, biol rep 1

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

description: Library name: SN-MM5_IFN_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38 with STAR
Read count extraction was performed using RSEM
Differential expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: mucosal melanoma

growth_protocol: Mucosal Melanoma cells were maintained in RPMI 1640 medium supplemented with 10% FBS, 2 mM Glutammine, 0.5% Penicillin/Streptomycin in humidified atmposhere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using RNeasy Plus Micro Kit (cat.n. 74034 Qiagen)
TruSeq RNA Sample Prep Kit v2 (Illumina) after polyA-capture, from 400ng total RNA

treatment_protocol: 2x105 mucosal melanoma cells were seeded in 6-well plates in 2 mL of complete RPMI medium overnight. Then, medium was replaced with fresh medium with or without IFN-γ (100 ng/mL) for 4 hours.

value: mucosal melanoma

value: mucosal melanoma cells


title: Pre-tumor p53 deficient 5

description:
Library name: pre_sp_2
10x_v3

value: Pancreas

value: Epithelial

value: mKate2+/GFP- (p53 deficient)

value: Dox


title: CRISPRi T cell Mock_rep1

description:
Library name: sample1
fin_TM_rep1


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 5

description: Library name: GC-730


title: SN-MM5 cell line, Untreated Control, 4h, biol rep 2

description: Library name: SN-MM5_CTRL_2


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 7

description: Library name: GC-782


title: SN-MM5 cell line, IFN-γ Treated, 4h, biol rep 3

description: Library name: SN-MM5_IFN_3


title: Tumor p53 proficient 7

description:
Library name: 53_LHRH_PDACreg_GFPh
10x_v2

value: mKate2+/GFP+ (p53 proficient)


title: SN-MM5 cell line, IFN-γ Treated, 4h, biol rep 2

description: Library name: SN-MM5_IFN_2


title: Tumor p53 proficient 12

description:
Library name: 53_LHRH_PanINreg_GFPh
10x_v2


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 4

description: Library name: GC-720


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 8

description: Library name: GC-835

value: corn oil cellulose fiber


title: Tumor p53 deficient 7

description:
Library name: 53_LHRH_PDACreg_KATE
10x_v2


title: CRISPRi T cell sgRNA1_rep2

description:
Library name: sample4
fin_T1_rep2


title: SN-MM5 cell line, Untreated Control, 4h, biol rep 3

description: Library name: SN-MM5_CTRL_3


title: CRISPRi T cell sgRNA1_rep1

description:
Library name: sample3
fin_T1_rep1


title: Pre-tumor p53 deficient 2

description:
Library name: 254_RH_PanINPM_Kate_CD45_1_4
10x_v2


title: Pre-tumor p53 deficient 1

description:
Library name: 254_2RH_PanINPM_Kate_CD45_1_31
10x_v2


title: Pre-tumor p53 deficient 4

description:
Library name: Preclinical_SP_batch1
10x_v3


title: Tumor p53 proficient 8

description:
Library name: 9268_PHLH_PDAC_DP
10x_v2


title: Tumor p53 proficient 6

description:
Library name: PDAC-DP
10x_v2


title: SN-MM4 cell line, IFN-γ Treated, 4h, biol rep 2

description: Library name: SN-MM4_IFN_2


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 6

description: Library name: GC-708


title: Pre-tumor p53 proficient 4

description:
Library name: Preclinical_DP_batch1
10x_v3


title: Pre-tumor p53 proficient 3

description:
Library name: 9268_RH_PanINPM_DP
10x_v2


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 4

description: Library name: 841Q


title: SN-MM4 cell line, Untreated Control, 4h, biol rep 3

description: Library name: SN-MM4_CTRL_3


title: BMDM ST IL4/IL13 biol rep1

type: RNA

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

hyb_protocol: For fragmentation and labeling 5.5µg single-stranded cDNA was used, hybridized to Mouse Clariom S array and washed according to manufacturer´s instructions.

scan_protocol: The arrays were scanned on a Affynetrix Gene Chip Scanner 3000 and CEL intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing: For probe set extraction and normalization (SST-RMA), expression raw data were transferred to Transcriptome Analysis Console (TAC, 4.0.2.15, Thermo Fisher Scientific, Waltham, MA, USA).  Statistical analysis of the case control study on 3 biological replicates for each group was performed using Anova with ebayes correction. Statistically significant differentially expressed genes were assumed with a fold change of > |2| and FDR <0.05.

label: biotin

source_name: STAT6-/- IL4/IL13 stimulated

label_protocol: After purification and quality assessment of the total RNA preparations (average RIN = 10, concentration 263 ± 50 ng/µl), transcriptional profiling of stimulated and unstimulated macrophages derived from wild type and STAT6-/- mice was performed with 200 ng total RNA using the WT Plus Kit and ClariomTM S mouse arrays (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer´s instructions.

growth_protocol: Bone marrow derived macrophages (BMDM) were isolated from wild type and STAT6(-/-) mice (each N = 3) and stimulated with IL4/IL13 for 24 hours and compared to unstimulated incubated BMDM.

extract_protocol: All incubated cells were lysed in 1mL TRIzol® and snap frozen before RNA extraction. Total RNA was isolated following the manufacturer’s instructions for total RNA isolation from TRIzol® (Thermo Fisher Scientific, Waltham, MA, USA). The aqueous RNA containing solution was further processed according to the protocol RNA Clean-up and Concentration from Phenol/Guanidine-based RNA isolation methods (RNA_Clean-Up and Concentration Kit, NorgenBiotek, Thorold, Canada).

treatment_protocol: IL4/IL13 stimulated cells of both mice groups  were compared to untreated cells.

value: bone marrow derived macrophages

value: stimulation using IL4/IL13 (10ng/mL)


title: SN-MM4 cell line, IFN-γ Treated, 4h, biol rep 1

description: Library name: SN-MM4_IFN_1


title: SN-MM4 cell line, Untreated Control, 4h, biol rep 1

description: Library name: SN-MM4_CTRL_1


title: BMDM ST  IL4/IL13 biol rep2


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 3

description: Library name: GC-714


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 1

description: Library name: 712Q


title: SN-MM4 cell line, IFN-γ Treated, 4h, biol rep 3

description: Library name: SN-MM4_IFN_3


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 5

description: Library name: GC-703


title: Pre-tumor p53 proficient 5

description:
Library name: pre_dp_2
10x_v3


title: BMDM ST control biol rep3

source_name: STAT6-/- control


title: BMDM WT IL4/IL13 biol rep3

source_name: WT IL4/IL13 stimulated

value: wild type


title: cKO_cerebellum

city: SAN FRANCISCO

first: Xiaoxin

last: Chen

state: California

address: 555 mission bay blvd. south, RM382A

department: Cardiovascular Research Institute

institute: University of California, San Francisco

description:
Library name: P1_Cerebellum_Nestin-cre;Tox3f/f
10x Genomics

data_processing:
The sequences were de-multiplexed using bcl2fastq. Reads were aligned to a Gencode Reference vM23/Ensembl 98 genome provided by 10X using CellRanger version 7.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

molecule: nuclear RNA

source_name: Cerebellum

growth_protocol: The mice were maintained according to the University of California, San Francisco institutional guidelines with free access to water and fed ad libitum with regular chow.

extract_protocol:
Cerebella were collected from P1 Nestin-cre;Tox3f/f and Cre-negative control mice, snap-frozen in dry ice, and stored at –80°C for single-nuclei extraction. Single nuclei were generated from 12 snap-frozen cerebella from each condition using the SingulatorTM 100 system (S2Genomics, Livermore, CA), following the regular nuclei isolation protocol.
We pooled 12 control cerebella and 12 mutant cerebella from P1 animals to generate one control library and one mutant library. Single-nucleus RNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ v.3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 nuclei per sample.

value: Cerebellum

value: conditional knockout


title: Ctrl_cerebellum

description:
Library name: P1_Cerebellum_Tox3f/f_or_Tox3f/+
10x Genomics

value: control littermate


title: SN-MM5 cell line, Untreated Control, 4h, biol rep 1

description: Library name: SN-MM5_CTRL_1


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 3

description: Library name: 839Q


title: SN-MM3 cell line, IFN-γ Treated, 4h, biol rep 1

description: Library name: SN-MM3_IFN_1


title: Pre-tumor p53 proficient 2

description:
Library name: 254_RH_PanINPM_GFPh
10x_v2


title: BMDM WT IL4/IL13 biol rep1


title: mouse,colonocytes, fish oil pectin fiber diet biol rep 2

description: Library name: 713A


title: SN-MM3 cell line, Untreated Control, 4h, biol rep 3

description: Library name: SN-MM3_CTRL_3


title: Cerebellum_cKO_3

description:
Library name: Tox3_P1_Cerebellum_cKO_3
cKO3

data_processing:
RNA-seq analysis was performed by Novogene Inc.
Sequencing generated 150 bp paired-end reads, which were processed by removing reads containing adapters, ploy-N, and low-quality reads. The clean reads were aligned to the mm10 reference genome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each sample
Supplementary files format and content: txt files include raw count values for each sample

extract_protocol:
Total RNA was extracted from P1 cerebella of the indicated genotypes using TRIzolTM reagent (Invitrogen, #15596026) following the manufacturer’s instructions.
RNA-seq was performed by Novogene Inc. The procedure involved mRNA purification using poly-T oligo-attached magnetic beads, fragmentation, first and second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification to generate the library.


title: BMDM ST  IL4/IL13 biol rep3


title: SN-MM4 cell line, Untreated Control, 4h, biol rep 2

description: Library name: SN-MM4_CTRL_2


title: Pre-tumor p53 proficient 1

description:
Library name: 254_2RH_PanINPM_GFPh
10x_v2


title: SN-MM3 cell line, Untreated Control, 4h, biol rep 2

description: Library name: SN-MM3_CTRL_2


title: SN-MM3 cell line, IFN-γ Treated, 4h, biol rep 3

description: Library name: SN-MM3_IFN_3


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 1

description: Library name: 704A


title: Drosophila S2 cells, ZSWIM8-knockout clonal line 3

city: Cambridge

first: Lianne

middle: Wang

last: Blodgett

address: 455 Main St

institute: Whitehead Institute/MIT

description: Library name: S2_KO3

library_source: other

data_processing:
Using cutadapt (v4.8; Martin 2011), the first 4 bases of raw reads were trimmed to remove 4N random ends from the 5p adapter, the 3p adapter was trimmed, and trimmed reads shorter than 12 nucleotides were discarded.
Reads were filtered based on a quality score of 30 or above for 100% of bases using fastq_quality_filter (v0.0.14; FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/).
The first 13 bases of trimmed and filtered reads were string-matched (100% match) to a dictionary of miRNA sequences. The length of the read was also recorded, resulting in a table of read counts for each length of each miRNA.
Assembly: TargetScanFly release 7.2 or TargetScanMouse release 8.0, supplemented with sequences in MiRGeneDB 3.0
Supplementary files format and content: Raw, unscaled read counts matching each length of each miRNA are compiled for all 12 samples (6 S2 and 6 MEF libraries).

molecule: other

organism: Drosophila melanogaster

growth_protocol: MEFs were grown in DMEM supplemented with 10% FBS in a humidified incubator at 37C and 5% CO2. S2 cells were grown in Schneider's growth medium supplemented with 10% heat-inactivated FBS at 26C.

extract_protocol:
Flash-frozen cell pellets were lysed and clarified with centrifugation. AGO-bound small RNAs were isolated from clarified lysates using FLAG-tagged T6B peptide, which binds AGO protein. After washes, small RNAs were eluted from T6B-coupled beads with TRI reagent, extracted, and preciptiated with isopropanol.
Small-RNA sequencing libraries were prepared as described: http://bartellab.wi.mit.edu/protocols.html, with the following changes: a 12-nt size marker was used in all RNA size-selection steps, and subtractive hybridization with a biotinylated antisense oligo was used to deplete 2S rRNA from S2 cell samples.

treatment_protocol: MEFs were contact-inhibited for 5 days prior to harvesting. S2 cells were harvested at confluence.

value: derived from late embryo; hemocyte-like

value: ZSWIM8 KO


title: Drosophila S2 cells, ZSWIM8-knockout clonal line 2

description: Library name: S2_KO2


title: 0042536_Region_2

description:
Spatial Transcriptomics
Xenium Analyzer
FFPE spatial transcriptomic

data_processing:
Data were processed using the Xenium analysis pipeline (version xenium-1.7.1.0), which included signal segmentation, transcript decoding, quality score assignment, and spatial mapping of transcripts to x/y coordinates.
mm10
Gene expression matrix (HDF5), Transcript table (CSV), Metadata files (CSV)

extract_protocol:
No RNA extraction was performed. FFPE tissue sections from human pancreas were cut at 5 µm thickness and mounted onto Xenium slides. After deparaffinization and decrosslinking, we performed probe hybridization, ligation, and amplification according to the 10x Genomics Xenium FFPE Tissue Preparation Guide
No sequencing library was constructed. A custom Xenium probe panel targeting 480 genes was hybridized to RNA in situ, followed by fluorescent labeling, imaging, and decoding using the Xenium Analyzer (v1.7.6.0).

tag: condition


title: SN-MM3 cell line, IFN-γ Treated, 4h, biol rep 2

description: Library name: SN-MM3_IFN_2


title: Pre-tumor p53 proficient 0

description:
Library name: 53_NH_PanINPM_GFPh
10x_v2


title: mouse,colonocytes, corn oil cellulose fiber diet biol rep 2

description: Library name: 705Q

value: colonocyte


title: Drosophila S2 cells, ZSWIM8-knockout clonal line 1

description: Library name: S2_KO1


title: 0042724_Region_1


title: SN-MM2 cell line, IFN-γ Treated, 4h, biol rep 3

description: Library name: SN-MM2_IFN_3

value: mucosal melanoma


title: 0042724_Region_3


title: Cerebellum_cKO_2

description:
Library name: Tox3_P1_Cerebellum_cKO_2
cKO2


title: Cerebellum_cKO_1

description:
Library name: Tox3_P1_Cerebellum_cKO_1
cKO1


title: SN-MM3 cell line, Untreated Control, 4h, biol rep 1

description: Library name: SN-MM3_CTRL_1

value: mucosal melanoma cells


title: 0042569_Region_3

value: Pancreas


title: 0042724_Region_2


title: Cerebellum_Ctrl_3

description:
Library name: Tox3_P1_Cerebellum_Ctrl_3
Ctrl3


title: Cerebellum_Ctrl_2

description:
Library name: Tox3_P1_Cerebellum_Ctrl_2
Ctrl2


title: Cerebellum_Ctrl_1

description:
Library name: Tox3_P1_Cerebellum_Ctrl_1
Ctrl1


title: BMDM ST control biol rep2


title: BMDM WT control biol rep3

source_name: WT control


title: Drosophila S2 cells, WT clonal line 3

description: Library name: S2_WT3

value: WT


title: SN-MM2 cell line, IFN-γ Treated, 4h, biol rep 1

description: Library name: SN-MM2_IFN_1


title: 0028094_Region_2


title: VG_Saline 1.5hr-4

city: San Diego

first: Ziai

last: Zhu

address: 9500 Gilman Dr

institute: UCSD

description:
Library name: Saline5
column name:Saline5

data_processing:
FASTQ files were aligned to the GRCm38 mouse reference genome using STAR70.
FeatureCounts was used for read counting.
Assembly: mm10
Supplementary files format and content: txt file with raw count for each sample

source_name: Vagal ganlia

extract_protocol:
Samples were homogenized using a tissuelyser (Qiagen) and RNA was RNA was purified using the RNAeasy micro Kit (Qiagen).
cDNA Libraries were constructed using the Illumina mRNA Stranded Prep (Illumina) and sequenced on the Illumina NovaSeq 6000 instrument, with 50 bp paired end reads.

value: Vagal ganlia

value: Saline


title: BMDM WT control biol rep1


title: 0042536_Region_1


title: 0028094_Region_1


title: Mouse_Abcb5_negative_S3

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Mouse sample 6

data_processing:
(1) For mouse samples: RNA-seq counts were generated by bcbio and bcbioRNASeq using salmon. Counts were imported into R using tximport and DESeq2.(2) For human samples: The reads were adaptor trimmed and aligned using the STAR program (version 2.6.1d). Transcript counts were inferred from alignment files and all transcripts with either 0 or 1 counts were removed. Gene expression was measured using EdgeR. Differential expression analyses were performed by the DESeq2.
Assembly: mm10, hg38
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: Corneal epithelium

extract_protocol:
(1) Dissociated mouse corneal epithelial cells were resuspended with2% fetal bovine serum (FBS) supplemented phosphate-buffered saline (PBS). The cells were incubated with 40μg/ml human anti-Abcb5 mAb (clone 3B9) at 37°C for 30min and subsequently incubated with Donkey Anti-Human IgG H+L (DyLight 650) on ice for 30min. To remove the hematopoietic cells, the cells were incubated with 0.1μg/ml PE-conjugated anti-CD45 mAb and 3µg/ml PE-conjugated anti-CD11b mAb on ice for 30min. To exclude the dead cells, the cells were incubated with 30nM SYTOX Green Dead Cell Stain on ice for 20min. RNA was extracted from the FACS sorted Abcb5-positive cells and Abcb5-negative cells. (2) Human donor corneas were obtained from eye banks. The central cornea was removed by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, CD63 knockdown#1 and CD63 knockdown#2).  On day 5, the cells were harvested for RNA extraction after siRNA transfection.
After the removal of rRNA, approximately 500 ng of total RNA underwent library preparation with the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research). Sequencing was carried out by an Illumina NovaSeq to a sequencing depth of ~50-75 million read pairs (150 bp paired-end sequencing) per sample. (1) For mouse samples: SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, Mountain View, CA) was used to generate mRNA libraries. (2) For human samples: Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research) was used to generate mRNA libraries.

value: Corneal epithelium

value: In vivo mouse corneal epithelial cells

value: Purified Abcb5-negative cells


title: VG_Saline 1.5hr-2

description:
Library name: Saline3
column name:Saline3


title: Drosophila S2 cells, WT clonal line 1

description: Library name: S2_WT1


title: SN-MM2 cell line, Untreated Control, 4h, biol rep 2

description: Library name: SN-MM2_CTRL_2


title: SN-MM2 cell line, Untreated Control, 4h, biol rep 3

description: Library name: SN-MM2_CTRL_3


title: BMDM ST control biol rep1

value: bone marrow derived macrophages


title: BMDM WT control biol rep2

value: wild type


title: VG_Saline 1.5hr-3

description:
Library name: Saline4
column name:Saline4


title: BMDM WT  IL4/IL13 biol rep2

value: stimulation using IL4/IL13 (10ng/mL)


title: Drosophila S2 cells, WT clonal line 2

description: Library name: S2_WT2


title: SN-MM1 cell line, IFN-γ Treated, 4h, biol rep 2

description: Library name: SN-MM1_IFN_2


title: SN-MM2 cell line, IFN-γ Treated, 4h, biol rep 2

description: Library name: SN-MM2_IFN_2


title: VG_Saline 1.5hr-1

description:
Library name: Saline2
column name:Saline2


title: SN-MM2 cell line, Untreated Control, 4h, biol rep 1

description: Library name: SN-MM2_CTRL_1


title: VG_HDM 1.5hr-4

description:
Library name: HDM5
column name:HDM5

value: HDM


title: Mouse_Abcb5_positive_S3

description: Library name: Mouse sample 5

value: Purified Abcb5-positive cells


title: 0011181_Region_2


title: Mouse_Abcb5_negative_S1

description: Library name: Mouse sample 2


title: 0011178_Region_2


title: SN-MM1 cell line, IFN-γ Treated, 4h, biol rep 1

description: Library name: SN-MM1_IFN_1


title: Mouse_Abcb5_negative_S2

description: Library name: Mouse sample 4


title: SN-MM1 cell line, IFN-γ Treated, 4h, biol rep 3

description: Library name: SN-MM1_IFN_3


title: Mouse_Abcb5_positive_S1

description: Library name: Mouse sample 1


title: Mouse_Abcb5_positive_S2

description: Library name: Mouse sample 3


title: VG_HDM 1.5hr-3

description:
Library name: HDM4
column name:HDM4


title: PyMT tumor total immune cells with 6-OHDA treatment_2

city: Beijing

first: Jialin

last: Yu

address: Chinese Institute for Brain Research, Beijing(CIBR), Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District, Beijing, China

institute: CIBR

description: Library name: Sample_4

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrices using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline (Singleron Biotechnologies). UMI counts and gene counts of each cell were acquired with featureCounts (v2.0.) software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCm38/mm10
Supplementary files format and content: matrix files

source_name: breast tumor

extract_protocol:
Tumor tissues were prepared by mechanical disruption followed by 1-hour treatment with Collagenase Type 3 (280 U/ml, Worthington Biochemical,Cat. #LS004183) and DNase I (4 μg/ml,Merck#DN25) at 37 °C. After the digestion steps, the cell suspension was filtered through a 70 μM cell strainer. Cell surface staining was performed by incubating cells with specific antibodies for 30 mins on ice in the presence of CD16/CD32 mAb to block Fc binding. Live CD45+ immune cells were gated as DAPI-CD45+E-Cadherin-   by using BD FACS Aria III.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPER® Single-Cell RNA Library Kit (Singleron 4180011). Briefly, single cell suspension loaded onto the GEXSCOPE microchip which integrates single cell capture, cell lysis, capture of the cellular mRNA and molecular labeling. The barcoded cDNA was then amplified and used for the construction of single cell NGS libraries. The loading of the GEXSCOPE microchip was performed using the Singeron Matrix instrument. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina NovaSeq 6000 with 150 bp paired end reads.

value: breast tumor

tag: gender

value: Female

value: immune cells

value: PyMT


title: Old mice 2 months after MAC infection 3

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

institute: Tsukuba university

description: Library name: SAMPLE12

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: excel files include expression values of total counts, RPKM, TPM, and CPM for each sample

source_name: Lung tissue

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 500 ng total RNA was used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420). Illumina NextSeq500 was used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung tissue

value: Balb/c WT

value: M. avium infection


title: Old mice 2 months after MAC infection 2

description: Library name: SAMPLE11


title: VG_HDM 1.5hr-1

description:
Library name: HDM2
column name:HDM2

value: Vagal ganlia

value: WT


title: VG_HDM 1.5hr-2

description:
Library name: HDM3
column name:HDM3


title: SN-MM1 cell line, Untreated Control, 4h, biol rep 3

description: Library name: SN-MM1_CTRL_3

value: mucosal melanoma

value: mucosal melanoma cells


title: Young mice 2 months after MAC infection 3

description: Library name: SAMPLE9


title: 0027845_Region_1

value: Pancreas


title: 0011181_Region_1


title: Healthy_Donor_cfDNA_H6

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

library_source: genomic

data_processing:
Raw reads were filtered to retain only those with a mean base quality score above 20. Adapter sequences were removed with Cutadapt, and reads were then aligned to the hg19 genome using Bowtie v1.2.2. Duplicate reads were removed using the MarkDuplicates tool from Picard-tools v2.26.4. Paired-end reads were converted into single fragments for metaplot analysis and visualization on the UCSC Genome Browser. After dataset-specific normalization, bigWig files were generated to display genomic coverage.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: healthy donor

extract_protocol:
NEXFLEX Rapid DNA-Seq Kit 2.0 was used to prepare cfDNA libraries. Approximately 650 µL of blood plasma from either cancer patients or healthy donors was processed for cfDNA extraction using the SubX™ Exo-DNA Kit (Capital Biosciences). The isolated cfDNA was quantified with the Qubit dsDNA High Sensitivity (HS) Assay Kit.
Libraries were prepared using the NEXTFLEX Rapid DNA-Seq Kit 2.0 (Revvity). Half the volume of purified cfDNAs, ranging from approximately 1 ng to 10 ng, was utilized. After adapter ligation, a total of 11 PCR cycles were performed.

tag: ID

tag: figure id

value: healthy donor

tag: sample type

value: cfDNA

tag: data ids


title: 0027846_Region_3


title: 0027846_Region_1


title: 0011178_Region_1


title: SN-MM1 cell line, Untreated Control, 4h, biol rep 2

description: Library name: SN-MM1_CTRL_2


title: SN-MM1 cell line, Untreated Control, 4h, biol rep 1

description: Library name: SN-MM1_CTRL_1


title: 0027845_Region_2


title: 0015410_Region_4


title: WT_P28_831

city: Los Angeles

first: Jennifer

last: Zieba

state: CA

address: 615 Charles E. Young Dr.

institute: University of California, Los Angeles

description: Library name: WT_P28_831

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (htts://support. 10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole Lung Tissue

extract_protocol:
Lungs from postnatal day 5 and 28 mouse pups were collected and digested with Collagenase I tissue removal solution (Collagenase/Dispase (2.5 mg/ml), and DNase (30 μg/ml) in PBS) at 37ºC for 60 minutes with brief vortexing every 10-15 minutes. Single cells were passed through a 40um cell strainer in PBS containing 0.04% BSA.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loade together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRiselect reagent for subsequent library construction.During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole Lung Tissue

tag: strain

value: Wild type

tag: age


title: 0027846_Region_2


title: PyMT tumor total immune cells with vehicle treatment_2

description: Library name: Sample_3

value: vehicle


title: Old mice 2 months after MAC infection 1

description: Library name: SAMPLE10


title: Young mice 2 months after MAC infection 1

description: Library name: SAMPLE7


title: PyMT tumor total immune cells with vehicle treatment_1

description: Library name: Sample_1

value: breast tumor


title: Healthy_Donor_cfDNA_H4


title: 0015410_Region_3


title: Healthy_Donor_cfDNA_H8


title: PyMT tumor total immune cells with 6-OHDA treatment_1

description: Library name: Sample_2

value: Female


title: Healthy_Donor_cfDNA_H5


title: Healthy_Donor_cfDNA_H7


title: 0027845_Region_3


title: Young mice 2 months after MAC infection 2

description: Library name: SAMPLE8


title: Aga_P28_101-1

description: Library name: Aga_P28_101-1

value: Mutant


title: WT_P28_808

description: Library name: WT_P28_808


title: WT_P28_809

description: Library name: WT_P28_809


title: Old mice control 2

description: Library name: SAMPLE5

value: control


title: Aga_P28_810

description: Library name: Aga_P28_810


title: Young mice control 3

description: Library name: SAMPLE3

value: Lung tissue


title: Young mice control 2

description: Library name: SAMPLE2

value: Balb/c WT


title: Healthy_Donor_cfDNA_H2


title: Old mice control 3

description: Library name: SAMPLE6


title: 0015409_Region_4


title: 0015409_Region_2


title: Healthy_Donor_cfDNA_H3


title: BC_cfDNA_AfterTreatment_47

source_name: breast cancer

value: breast cancer

tag: subtype

value: luminal


title: 0015409_Region_5

tag: tissue


title: 0015410_Region_2


title: Y384G D21.3_biol rep_3

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

description: Library name: Sample 25

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided.

source_name: Primary B-cells

growth_protocol: Cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (#74106, Qiagen) as per manufacturer's protocol. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 1ug total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7765, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using Lymphoprep Density Gradient Medium (Stem Cell Technologies), followed by negative selection of primary B cells using RosetteSep and EasySep Human B Cell Enrichment Kits (Stem Cell Technologies), in accordance with the manufacturers’ instructions.

tag: cell line

value: Primary B-cells

value: Lymphoblastoid

value: TESm LMP1 with functional domain point mutation YYD->GYD


title: WT_P5_74-5

description: Library name: WT_P5_74-5


title: BC_cfDNA_AfterTreatment_43


title: BC_cfDNA_AfterTreatment_46


title: 0015409_Region_3

source_name: Pancreas

value: Pancreas


title: Aga_P28_69-3

description: Library name: Aga_P28_69-3


title: Aga_P28_70-1

description: Library name: Aga_P28_70-1


title: Young mice control 1

description: Library name: SAMPLE1


title: BC_cfDNA_AfterTreatment_44


title: Old mice control 1

description: Library name: SAMPLE4


title: 0004329_Region_3


title: TES2m D21.3_biol rep_3

description: Library name: Sample 23

tag: cell type

value: TES2 LMP1 with functional domain point mutation YYD->ID


title: TES2m D21.2_biol rep_2

description: Library name: Sample 22

tag: genotype


title: Healthy_Donor_cfDNA_H1

value: healthy donor

value: cfDNA


title: Y384G D21.2_biol rep_2

description: Library name: Sample 24

value: TES2 LMP1 with functional domain point mutation YYD->GYD


title: WT_P5_59-3

description: Library name: WT_P5_59-3

value: Whole Lung Tissue

value: Wild type


title: WT_P5_59-2

description: Library name: WT_P5_59-2


title: 0004279_Region_3


title: TES2m D21.1_biol rep_1

description: Library name: Sample 21


title: BC_cfDNA_AfterTreatment_37


title: BC_cfDNA_AfterTreatment_34


title: BC_cfDNA_AfterTreatment_31


title: WT_P5_24-2

description: Library name: WT_P5_24-2


title: 0015409_Region_1


title: Aga_P5_74-2

description: Library name: Aga_P5_74-2


title: BC_cfDNA_AfterTreatment_41


title: Aga_P5_74-3

description: Library name: Aga_P5_74-3


title: 0004329_Region_1


title: 0004329_Region_2


title: BC_cfDNA_AfterTreatment_33


title: WT D21.3_biol rep_3

description: Library name: Sample 20

value: Wildtype LMP1


title: 0004279_Region_2


title: 0004279_Region_1


title: Aga_P5_59-5

description: Library name: Aga_P5_59-5

value: Mutant


title: BC_cfDNA_AfterTreatment_30


title: DM D7.3_biol rep_3

description: Library name: Sample 17

value: TES1 and TES LMP1 with functional domain point mutations PXQXT->AXAXA and YYD-> ID


title: 0015410_Region_1


title: WT D21.1_biol rep_1

description: Library name: Sample 18


title: WT_P28_794

description: Library name: WT_P28_794


title: Aga_P5_59-1

description: Library name: Aga_P5_59-1


title: MEFs, ZSWIM8-knockout clonal line 3

description: Library name: MEF_KO3

source_name: MEF

value: MEF

value: immortalized embryonic fibroblast

value: ZSWIM8 KO


title: WT D21.2_biol rep_2

description: Library name: Sample 19


title: BC_cfDNA_AfterTreatment_28

value: breast cancer

value: luminal


title: DM D7.2_biol rep_2

description: Library name: Sample 16

value: Primary B-cells

value: Burkitt-Like


title: MEFs, ZSWIM8-knockout clonal line 2

description: Library name: MEF_KO2


title: A224_miR625-3p_rep2

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression data from A224 cell line transfected with mature miR-625-3p oligo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Ovarian cancer cell A224 transfected with mature miR-625-3p oligo

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: All cell lines were cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNAs were isolated using TRI reagent (Molecular Research Center) according to the manufacturer's instructions.

treatment_protocol: A224 cells were transfected with either negative miR control oligo or mature miR-625-3p oligo for 24 hours before RNA extraction.

tag: cell

value: High grade serous ovarian cancer cells


title: BC_cfDNA_AfterTreatment_25


title: BC_cfDNA_AfterTreatment_24


title: A224_miR625-3p_rep3


title: BC_cfDNA_AfterTreatment_27


title: DM D7.1_biol rep_1

description: Library name: Sample 15


title: BC_cfDNA_AfterTreatment_23


title: TES2m D7.2_biol rep_2

description: Library name: Sample 13

value: TES2 LMP1 with functional domain point mutation YYD->ID


title: BC_cfDNA_AfterTreatment_21


title: 6-10B circMLLT1

city: Guangzhou

first: Fei

last: Li

state: Guangdong

address: 135 Xingang West Road, Haizhu District

institute: Sun Yat-sen University

description:
Library name: B6CM1
ref_trans_full_table1.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: human NCBI genome build 36
Supplementary files format and content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

growth_protocol: NPC cells were cultured in 10%FBS RPMI medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: NPC cells were transfected with control or circRBM6/circMLLT1-expressing vectors for 48h

value: Nasopharyngeal carcinoma cell line

value: circMLLT1 overexpression

tag: treatment


title: MEFs, ZSWIM8-knockout clonal line 1

description: Library name: MEF_KO1


title: MEFs, WT clonal line 3

description: Library name: MEF_WT3

value: WT


title: 5-8F Vector1

description:
Library name: F5VEC1
ref_trans_full_table1.txt

value: Normal control

value: Vector overexpression


title: 5-8F circMLLT1

description:
Library name: F5CM1
ref_trans_full_table1.txt


title: AML12-TBOEP2

city: Changzhou

first: Shuai

state: Jiangsu

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

description:
Library name: sample5
AML12-TBOEP2

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: GRCm39.110
Supplementary files format and content: processed data.xlsx

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: Mouse hepatocytes

value: TBOEP


title: TES2m D7.1_biol rep_1

description: Library name: Sample 12


title: MEFs, WT clonal line 1

description: Library name: MEF_WT1


title: TES2m D7.3_biol rep_3

description: Library name: Sample 14


title: BC_cfDNA_AfterTreatment_14

value: cfDNA


title: BC_cfDNA_AfterTreatment_13


title: MEFs, WT clonal line 2

description: Library name: MEF_WT2

value: MEF


title: TES1m D7.3_biol rep_3

description: Library name: Sample 11

value: TES1 LMP1 with functional domain point mutation PXQXT->AXAXA


title: AML12-TBOEP3

description:
Library name: sample6
AML12-TBOEP3


title: A224_mock_rep2

description: Gene expression data from A224 cell line transfected with negative control miR oligo

source_name: Ovarian cancer cell A224 transfected with negative miR control oligo


title: A224_miR625-3p_rep1


title: BC_cfDNA_AfterTreatment_12


title: A224_mock_rep1


title: Y384G D7.3_biol rep_3

description: Library name: Sample 8

value: TES2 LMP1 with functional domain point mutation YYD->GYD


title: 6-10B Vector1

description:
Library name: B6VEC1
ref_trans_full_table1.txt


title: 5-8F circRBM6

description:
Library name: F5CR6
ref_trans_full_table.txt

value: circRBM6 overexpression


title: AML12-TBOEP1

description:
Library name: sample4
AML12-TBOEP1


title: TES1m D7.1_biol rep_1

description: Library name: Sample 9


title: A224_mock_rep3


title: 5-8F Vector

description:
Library name: F5VEC
ref_trans_full_table.txt


title: BC_cfDNA_AfterTreatment_10

value: breast cancer

value: luminal


title: M_Chronic_sham+ vehicle_Rep5

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

description:
Library name: 22131R-04-34
Count

data_processing:
Quality control was performed using an Agilent Bioanalyzer to ensure all RNA samples had an RNA Integrity Number (RIN) greater than 7. Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation and Ultra II Directional RNA Library Prep Kits and sequenced on the Illumina NovaSeq 6000 platform to a depth of approximately 30–40 million paired-end reads per sample. Reads from four technical replicate lanes were merged per sample. Sequencing reads were aligned to the Mus musculus genome assembly GRCm39 (mm39) using STAR aligner. Gene-level quantification was performed using featureCounts. Genes with fewer than 200 raw counts in more than 5% of total samples were excluded. Non-coding genes were also filtered out. Data were normalized using the DESeq2 R package, avaliable on Bioconductor.
Assembly: Transcripts were aligned to the Mus musculus genome assembly GRCm39 (mm39).
Supplementary files format and content: Raw count values in csv format.

source_name: Brain Somatosensory Cortex

growth_protocol: Mice were maintained in standard housing conditions with ad libitum access to food and water.  All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and performed in accordance with institutional guidelines.

extract_protocol:
RNA was isolated from mouse brain tissue  tissues using Qiagen RNeasy kit (217804; Qiagen; Hilden, Germany) according to the manufacturer’s protocols.
A NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S; New England Biolab; Ipswich, MA, USA) and NEBNext Ultra II Directional RNA Library Prep Kit (E7760; New England Biolab) were used to generate libraries for sequencing.

value: Brain Somatosensory Cortex

tag: Sex

value: M

tag: timepoint

value: Chronic

tag: cohort

tag: conditions

value: sham + vehicle

tag: injury

value: sham

value: vehicle


title: BC_cfDNA_AfterTreatment_3

tag: ID


title: M_Chronic_sham+ vehicle_Rep4

description:
Library name: 22131R-04-05
Count


title: WT D7.3_biol rep_3

description: Library name: Sample 3

value: Primary B-cells

value: Burkitt-Like

value: Wildtype LMP1


title: AML12-NC3

description:
Library name: sample3
AML12-NC3

value: Mouse hepatocytes

value: DMSO


title: BC_cfDNA_AfterTreatment_11

tag: sample type

value: cfDNA


title: 6-10B circRBM6

description:
Library name: B6CR6
ref_trans_full_table.txt

value: Nasopharyngeal carcinoma cell line


title: M_Chronic_sham+ vehicle_Rep3

description:
Library name: 22131R-04-11
Count


title: Y384G D7.2_biol rep_2

description: Library name: Sample 7

value: TES2 LMP1 with functional domain point mutation YYD->GYD


title: BC_cfDNA_AfterTreatment_5

tag: data ids


title: MiaPaCa_cas9_R1

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

description: Replicate 1

data_processing:
Sequenced files were demultiplexed from illumina
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: amplicon sequencing

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral library (lentiCRISPRv2_A) containing 65,000 sgRNAs to yield a library coverage of 300x.  Infected cells were selected for with puromycin.  T0 replicates (x2) of 2.5x10^7 cells were collected and triplicate replicates for culture in hypoxia were plated at 2x10^7 per replicate.

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014

treatment_protocol: Cells were cultured in 1% oxygen and passaged every 72 hours for a period of 20 generations.  2x10^7 cells were collected from each replicate following each passage.  2x10^7 cells were maintained in culture for each replicate for the subsequent generation to maintain 300x library coverage

value: Pancreas


title: AML12-NC1

description:
Library name: sample1
AML12-NC1


title: delPXQXT D7.2_biol rep_2

description: Library name: Sample 5

value: TES1 LMP1 with functional domain deletion


title: BC_cfDNA_AfterTreatment_7

value: breast cancer

value: luminal


title: delPXQXT D7.3_biol rep_3

description: Library name: Sample 6


title: M_Chronic_sham+ vehicle_Rep2

description:
Library name: 22131R-04-33
Count

tag: strain

value: Brain Somatosensory Cortex

value: M


title: WT D7.1_biol rep_1

description: Library name: Sample 1


title: delPXQXT D7.1_biol rep_1

description: Library name: Sample 4


title: BC_cfDNA_AfterTreatment_42

tag: paired sample_id_-_same_patient


title: BC_cfDNA_AfterTreatment_40

tag: subtype


title: MiaPaCa_cas9_R2

description: Replicate 2

tag: tissue


title: BC_cfDNA_AfterTreatment_45


title: BC_cfDNA_AfterTreatment_48


title: AML12-NC2

description:
Library name: sample2
AML12-NC2

tag: cell line


title: MDAMB231_cas9_R2

description: Replicate 2

source_name: Breast

value: Breast

value: MDA MB 231

tag: cell type


title: articular chondrocytes, Peptide p[63-82] treatment4

city: maastricht

first: Marjolein

last: Caron

department: Orthopedic Surgery

country: Netherlands

institute: Maastricht University

description:
Library name: Sample8
peptl.L1-peptl5-24h

data_processing:
Pooled libraries consisting of equal molar samples were sequenced on a high-output 75-bp single read on the NextSeq500 (Illumina). For each sample, the number of reads covering one or more exons of a given transcript was extracted. Triplicates of samples that were treated with either p[62-83] peptide or nothing (control) were grouped separately and compared to one another. The fold-change difference and the p-value were calculated using the R package edgeR15, 16, after which the p-value was corrected for multiple testing [false discovery rate (FDR)-corrected].
For each sample, the number of reads covering one or more exons of a given transcript was extracted. Triplicates of samples that were treated with either p[62-83] peptide or nothing (control) were grouped separately and compared to one another. The fold-change difference and the p-value were calculated using the R package edgeR15, 16, after which the p-value was corrected for multiple testing [false discovery rate (FDR)-corrected].
Assembly: Hg19
Supplementary files format and content: tab-delimited txt file representing counts per gene

source_name: Cartilage

growth_protocol: Human articular chondrocytes (HACs) were isolated from the articular cartilage of patients with late-stage OA who underwent total knee arthroplasty. Ethical permission was received from the Local Ethical Committee (METC approval ID: 2017-0183). Cartilage was removed from the femoral bone, cut into small pieces, and digested in Collagenase II (300 units/ml in HEPES-buffered Dulbecco's Modified Eagle's Medium (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffered DMEM)/F-12 with 1% antibiotics). HACs were cultured until passage two in DMEM/F12 (Gibco Life Technologies), supplemented with 10% fetal calf serum (FCS; Sigma-Aldrich), 1% antibiotic/antimitotic (Gibco Life Technologies), and 1% non-essential amino acids (Gibco Life Technologies) in a humidified atmosphere at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy kit with gDNA eliminator (Qiagen) according to the manufacturer's protocol and subjected to rRNA depletion. Was checked for quality and integrity on the Agilent 2100 Bioanalyzer (Santa Clara, CA, United States) via 2100.
An Expert Eukaryotic Total RNA Nano chip was used according to the manufacturer’s protocol. The mRNA sequencing library was generated using the TruSeq mRNA Sample Preparation Kit (Illumina, Eindhoven, Netherlands). In short, mRNA was enriched using magnetic beads coated with poly(dT), then fragmented. The fragmented mRNA-enriched samples were subjected to cDNA synthesis by reverse transcriptase, followed by dA-tailing and ligation of specific double-stranded bar-coded adapters. Next, the library was amplified, followed by a cleanup. The library sizes were determined using an Agilent 2100 Bioanalyzer with a DNA 1000 chip, according to the manufacturer’s protocol. Pooled libraries consisting of equal molar samples were sequenced on a high-output 75-bp single read on the NextSeq500 (Illumina).

treatment_protocol: For the experiments, a pool of HACs from six donors was used; cells were plated in replicates at a seeding density of 30.000 cells/cm2 and stimulated for 24 hours with or without 100 nM p[63-82] peptide (H-AAYYSEGESAFPLNSYMNAT-OH; Biosynth)

value: Cartilage

value: Chondrocytes

value: Peptide p[63-82]


title: MiaPaCa_WT_R2

description: Replicate 2

value: Wild Type


title: WT D7.2_biol rep_2

description: Library name: Sample 2

value: Primary B-cells

value: Burkitt-Like

tag: genotype

value: Wildtype LMP1


title: 6-10B Vector

description:
Library name: B6VEC
ref_trans_full_table.txt

value: Nasopharyngeal carcinoma cell line

value: Normal control

value: Vector overexpression


title: M_Chronic_sham+ SB_Rep1

description:
Library name: 22131R-04-12
Count

value: Chronic

value: sham + SB

value: sham

value: SB


title: BC_cfDNA_AfterTreatment_8

value: breast cancer

value: luminal

value: cfDNA


title: M_Chronic_sham+ vehicle_Rep1

description:
Library name: 22131R-04-61
Count

value: Brain Somatosensory Cortex

value: M

value: sham + vehicle

value: vehicle


title: MiaPaCa_WT_R1

description: Replicate 1

value: Pancreas

value: Wild Type


title: MDAMB231_cas9_R1

description: Replicate 1

value: Breast

value: MDA MB 231


title: articular chondrocytes, Peptide p[63-82] treatment3

description:
Library name: Sample7
peptl.L1-peptl4-24h

value: Cartilage

value: Chondrocytes

value: Peptide p[63-82]


title: M_Chronic_sham+ SB_Rep2

description:
Library name: 22131R-04-06
Count

value: Chronic

value: sham + SB


title: articular chondrocytes, Peptide p[63-82] treatment2

description:
Library name: Sample6
peptl.L1-peptl3-24h


title: M_Chronic_5xCHI+ vehicle_Rep8

description:
Library name: 22131R-04-04
Count

value: 5xCHI + vehicle


title: BC_cfDNA_AfterTreatment_39

value: breast cancer


title: MDAMB231_WT_R1

description: Replicate 1


title: BC_cfDNA_AfterTreatment_36

value: luminal


title: articular chondrocytes, Peptide p[63-82] treatment1

description:
Library name: Sample5
peptl.L1-peptl2-24h


title: MDAMB231_WT_R2

description: Replicate 2


title: M_Chronic_5xCHI+ vehicle_Rep7

description:
Library name: 22131R-04-31
Count


title: articular chondrocytes, Control4

description:
Library name: Sample4
contrl.contrl8-24h

value: Vehicle


title: M_Chronic_5xCHI+ vehicle_Rep6

description:
Library name: 22131R-04-03
Count

value: Brain Somatosensory Cortex


title: BC_cfDNA_AfterTreatment_32

value: cfDNA


title: BC_cfDNA_AfterTreatment_38


title: BC_cfDNA_AfterTreatment_26


title: HCT15_cas9_R1

description: Replicate 1

source_name: Colon

value: Colon


title: HCT15_WT_R2

description: Replicate 2


title: articular chondrocytes, Control1

description:
Library name: Sample1
contrl.contrl1-24h


title: articular chondrocytes, Control2

description:
Library name: Sample2
contrl.contrl2-24h


title: M_Chronic_5xCHI+ vehicle_Rep5

description:
Library name: 22131R-04-10
Count

value: M

value: vehicle


title: articular chondrocytes, Control3

description:
Library name: Sample3
contrl.contrl4-24h


title: M_Chronic_5xCHI+ vehicle_Rep3

description:
Library name: 22131R-04-58
Count


title: HCT15_cas9_R2

description: Replicate 2


title: BC_cfDNA_AfterTreatment_20


title: M_Chronic_5xCHI+ vehicle_Rep4

description:
Library name: 22131R-04-32
Count


title: HC_54 blood plasma EV

city: Berlin

first: Oliver

last: Knight

address: Föhrer Strasse 15

department: Institut für Medizinische Immunologie

institute: Charité – Universitätsmedizin Berlin

description: Library name: HC_54

data_processing:
Sequences were produced using an Illumina NGS sequencer 500 with 1 x 75 base pairs. Deduplication based on unique molecular identifiers was carried out using in-house scripts.
Unprocessed sequencing reads underwent adapter and quality trimming using Cutadapt (version 4.3).
Processed sequencing reads were aligned to the human reference genome using Bowtie2 and alignments were analyzed by Samtools .
MultiQC (version 1.16) was used for aggregated quality assessment and differential expression analysis was performed using DE-Seq2.
Assembly: hg38
Supplementary files format and content: tsv file includes counts for all samples (patients and healthy controls)
Supplementary files format and content: tsv file listing the small RNAs found according to their differential expression between patients and controls;  log2FC value, p-values and fdr correction

source_name: Blood plasma

extract_protocol:
Total RNA was extracted using two phenol-chloroform extractions. miRNAs were isolated via the RNA Clean & Concentrator-5’ Kit (Zymo Research)
Library preparation was performed using the ultra-sensitive TrueQuant small RNA-Seq kit by the company GeneXPro (Frankfurt, D).

value: Blood plasma

value: Healthy control (HC)


title: BC_cfDNA_AfterTreatment_29


title: HC_36 blood plasma EV

description: Library name: HC_36


title: HC_30 blood plasma EV

description: Library name: HC_30


title: BC_cfDNA_AfterTreatment_17


title: ES2_cas9_R2

description: Replicate 2

source_name: Ovary

value: Ovary


title: BC_cfDNA_AfterTreatment_22


title: CFS_82 blood plasma EV

description: Library name: CFS_82

value: Chronic fatigue syndrome (CFS)


title: ES2_cas9_R1

description: Replicate 1


title: ES2_WT_R1

description: Replicate 1

value: Wild Type


title: HCT15_WT_R1

description: Replicate 1


title: M_Chronic_5xCHI+ SB_Rep8

description:
Library name: 22131R-04-30
Count

value: 5xCHI + SB

value: SB


title: M_Chronic_5xCHI+ vehicle_Rep1

description:
Library name: 22131R-04-09
Count

value: Chronic


title: BC_cfDNA_AfterTreatment_16


title: 22RV1_cas9_R1

description: Replicate 1

source_name: Prostate

value: Prostate


title: Doxy+_2

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

description: Library name: Doxy+_2

data_processing:
Sequencing reads were processed using Biopython to generate sgRNA count tables. Differential enrichment analysis between Dox(+) and Dox(−) populations was performed using the MAGeCK pipeline to identify candidate genes as described by Li et al.
Assembly: hg38
Supplementary files format and content: count
Library strategy: CRISPR Screen

source_name: Kidney

growth_protocol: Doxycycline-inducible HK-2 cells were maintained in Advanced DMEM/F-12, supplemented with 1.5% Tet-approved FBS, 1× GlutaMAX, puromycin (0.8 μg/mL), blasticidin S (2 μg/mL), and 1% penicillin–streptomycin.

extract_protocol:
Cells were harvested on day 18, and genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit according to the manufacturer’s instructions. All screening experiments were performed in duplicate using independent biological replicates.
The sgRNA cassettes were PCR-amplified from genomic DNA using KOD Plus Neo polymerase  with primers containing Illumina-compatible adapters and unique barcodes. PCR products were purified via agarose gel electrophoresis and a gel extraction kit. Purified libraries were quantified by qPCR using the KAPA Library Quantification Kit, normalized to 1 nM, and sequenced on an Illumina NextSeq 500.

treatment_protocol: 1.0 × 10^8 Cas9-expressing, PRCC-TFE3 inducible HK-2 cells were transduced with the lentiviral sgRNA pool at a transduction efficiency of approximately 30%, achieving an average library coverage exceeding 500× on day 1. Twenty-four hours after transduction, cells were selected with puromycin (5 μg/mL) and maintained under selection for 7 days. At all times, at least 6 × 107 cells were cultured to preserve sgRNA representation. On day 8, cells were divided into two conditions: one cultured in medium supplemented with doxycycline to induce PRCC-TFE3 expression, and the other maintained in medium without doxycycline.

value: Kidney

value: human renal proximal tubular epithelial cell line

value: Doxycyclin


title: ES2_WT_R2

description: Replicate 2


title: BC_cfDNA_AfterTreatment_19

value: breast cancer

value: luminal


title: M_Chronic_5xCHI+ vehicle_Rep2

description:
Library name: 22131R-04-59
Count

value: Brain Somatosensory Cortex

value: 5xCHI + vehicle


title: TES1m D7.2_biol rep_2

description: Library name: Sample 10

value: Primary B-cells

value: Burkitt-Like

value: TES1 LMP1 with functional domain point mutation PXQXT->AXAXA


title: 22RV1_cas9_R2

description: Replicate 2


title: BC_cfDNA_AfterTreatment_1

value: cfDNA


title: CFS_63 blood plasma EV

description: Library name: CFS_63

value: Blood plasma

value: Chronic fatigue syndrome (CFS)


title: M_Chronic_5xCHI+ SB_Rep7

description:
Library name: 22131R-04-29
Count

value: M

value: 5xCHI + SB


title: Doxy+_1

description: Library name: Doxy+_1


title: Doxy-_2

description: Library name: Doxy-_2


title: 22RV1_WT_R1

description: Replicate 1

value: Wild Type


title: M_Chronic_5xCHI+ SB_Rep3

description:
Library name: 22131R-04-02
Count

value: Chronic

value: SB


title: M_Chronic_5xCHI+ SB_Rep4

description:
Library name: 22131R-04-01
Count


title: CFS_74 blood plasma EV

description: Library name: CFS_74


title: M_Chronic_5xCHI+ SB_Rep6

description:
Library name: 22131R-04-56
Count


title: BC_cfDNA_AfterTreatment_18


title: BC_cfDNA_AfterTreatment_35


title: BC_cfDNA_AfterTreatment_15


title: Doxy-_1

description: Library name: Doxy-_1

value: Kidney

value: human renal proximal tubular epithelial cell line


title: F_Chronic_sham+ vehicle_Rep9

description:
Library name: 22131R-04-21
Count

value: F

value: sham + vehicle

value: sham

value: vehicle


title: HT_TERT_cas9_R1

description: Replicate 1

source_name: Fibrosarcoma

value: Fibrosarcoma

value: Soft tissue and Bone


title: HT1080_cas9_R2

description: Replicate 2


title: BC_cfDNA_AfterTreatment_6

value: breast cancer

value: luminal


title: HT_TERT_WT_R2

description: Replicate 2


title: DoxyPos_MSCPos_R1

description: Library name: Sample10

data_processing:
Adapter sequences were trimmed from raw RNA-seq reads using Trim Galore (version 0.6.7) with default parameters.
Duplicate reads were removed using HTStream (version 1.3.0) with default settings.
Trimmed, non-duplicated reads were aligned to the human reference transcriptome (GENCODE v43, GRCh38.p13) and quantified using Salmon (version 1.9.0).
Assembly: hg38
Supplementary files format and content: tsv

extract_protocol:
Total RNA was extracted using TRIzol reagent, and its quality was assessed using a BioAnalyzer 2100.
Library preparation was performed using the TruSeq Stranded mRNA Library Prep kit, following the manufacturer's protocol.


title: DoxyNeg_MSCPos_R3

description: Library name: Sample9


title: HT1080_cas9_R1

description: Replicate 1


title: DoxyPos_MSCPos_R3

description: Library name: Sample12


title: M_Chronic_5xCHI+ SB_Rep1

description:
Library name: 22131R-04-08
Count

value: Brain Somatosensory Cortex


title: M_Chronic_5xCHI+ SB_Rep5

description:
Library name: 22131R-04-57
Count


title: F_Chronic_sham+ vehicle_Rep6

description:
Library name: 22131R-04-48
Count


title: HT1080_WT_R2

description: Replicate 2


title: F_Chronic_sham+ vehicle_Rep7

description:
Library name: 22131R-04-49
Count


title: M_Chronic_5xCHI+ SB_Rep2

description:
Library name: 22131R-04-07
Count


title: BC_cfDNA_BeforeTreatment_23

tag: figure id

tag: figure id_-_treatment_sensitivity

value: cfDNA


title: F_Chronic_sham+ vehicle_Rep4

description:
Library name: 22131R-04-46
Count

tag: Sex

tag: treatment


title: 22RV1_WT_R2

description: Replicate 2

value: Prostate


title: HT_TERT_WT_R1

description: Replicate 1


title: HT1080_WT_R1

description: Replicate 1


title: F_Chronic_sham+ vehicle_Rep3

description:
Library name: 22131R-04-55
Count

tag: timepoint

tag: cohort


title: HT_hTERT_T12_R2 [sequencing]

description:
Soft tissue and Bone
T12 Timepoint Replicate 2

data_processing:
Sequenced files were demultiplexed from Illumina.
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Supplementary files format and content: Raw_read_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Library strategy: Amplicon sequencing

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral library (lentiCRISPRv2_A) containing 65,000 sgRNAs to yield a library coverage of 300x. Infected cells were selected for with puromycin. T0 replicates (x2) of 2.5x10^7 cells were collected and triplicate replicates for culture in hypoxia were plated at 2x10^7 per replicate.

extract_protocol:
Genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194).
Libraries were constructed following the previously described method in Shalem O et al. Science 2014.

treatment_protocol: Cells were cultured in 1% oxygen and passaged every 72 hours for a period of 20 generations. 2x10^7 cells were collected from each replicate following each passage. 2x10^7 cells were maintained in culture for each replicate for the subsequent generation to maintain 300x library coverage.

value: Infection with viral library lentiCRISPRv2_A

tag: time point

tag: condition

value: TERT overexpressed


title: BC_cfDNA_BeforeTreatment_20

tag: ID

tag: sample type


title: DoxyPos_MSCNeg_R2

description: Library name: Sample5


title: HT_hTERT_T12_R1 [sequencing]

description:
Soft tissue and Bone
T12 Timepoint Replicate 1


title: BC_cfDNA_AfterTreatment_9

tag: data ids


title: BC_cfDNA_AfterTreatment_4

tag: paired sample_id_-_same_patient


title: DoxyPos_MSCPos_R2

description: Library name: Sample11


title: F_Chronic_sham+ vehicle_Rep8

description:
Library name: 22131R-04-54
Count

tag: strain

value: Chronic

tag: conditions

tag: injury


title: HT_TERT_cas9_R2

description: Replicate 2

tag: tissue

tag: cell line

tag: cell type


title: BC_cfDNA_AfterTreatment_2

tag: subtype


title: BC_cfDNA_BeforeTreatment_17

tag: figure id

tag: figure id_-_treatment_sensitivity


title: DoxyNeg_MSCNeg_R2

description: Library name: Sample2

tag: treatment

value: DMSO


title: BC_cfDNA_BeforeTreatment_22


title: DoxyNeg_MSCPos_R2

description: Library name: Sample8

value: Kidney


title: BC_cfDNA_BeforeTreatment_15


title: DoxyPos_MSCNeg_R3

description: Library name: Sample6

value: human renal proximal tubular epithelial cell line


title: F_Chronic_sham+ SB_Rep1

description:
Library name: 22131R-04-27
Count

tag: Sex

value: F

tag: timepoint

tag: cohort

value: sham + SB

value: SB


title: BC_cfDNA_BeforeTreatment_18

tag: ID


title: BC_cfDNA_BeforeTreatment_24

tag: sample type


title: Stage2, 5c4E, day9, RNASeq

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

country: Australia

institute: MCRI

description:
(3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
RNAseq_repeat.mtx

data_processing:
Cell Ranger (v1.3.1) was used to process and aggregate raw data from each of the samples returning a count matrix and associated barcode and gene information
Cite-seq-count (v1.4.3) was used to process HTO reads
RNA-seq: The raw reads were quality and adapter trimmed using trim-galore v0.6.5
RNA-seq: The trimmed reads were mapped to the human genome (hg38) using the STAR aligner v2.7.4a in the two pass mapping mode
Assembly: hg38
Supplementary files format and content: scRNAseq: gene expression matrix and sample related metadata as a csv
Supplementary files format and content: RNAseq: gene expression matrix

growth_protocol: The iPSC line used in this study was CRL2429-MAFBmTagBFP2/GATA3mCherry (32), maintained and expanded at 37oC in 5% CO2 in Essential 8 medium (Thermo Fisher) on MatrigelTM-coated (Thermo Fisher) plates with daily media changes and passaged every 3-4 days with EDTA in 1x PBS buffer as described previously49. An initial seeding density of 7 x 104 cells into 6-well culture plates was then cultured with variations based on the Takasato protocol3 modified to use TeSR-E6 medium31 (STEMCELL technologies). Organoids were cultured from D0 in 1.5ml of E6 and 7µM CHIR for 3 (3c), 4 (4c) or 5 (5c) days. Following this, organoids were cultured in one of the following conditions; 2 (2F), 3 (3F) or 4 (4F and 4FG) days of 100ng/mL FGF9, 4 days of 100ng/mL FGF9 with one of 2.5µM AGN193189 (4FA), 1µM CHIR (4FC), 0.1µM LDN193109 (4FL), or 4 days of 200ng/mL FGF9 (4F200) or base media alone (4E). All conditions were then aggregated onto transwells by dissociating to single cell and transferring 1 x 104 cells as a 1ul cell/media droplet, as 3 sets of 2 technical replicates per transwell. Organoids were cultured in 1.1ml E6 with 5µM CHIR for 1 hour before replacing media with 1.1ml E6, 200ng/mL FGF9 and 1ug/mL heparin for 5 days. An additional set of 4F organoids were generated, with these receiving 50ng/mL GDF11 during these 4 days (4FG). After 5 days culture, all organoids were maintained in E6 media alone until day 27. Media was changed every 2 days for all organoids at all times, except when a culture change occurred in between. Samples were collected at the end of the four stages of differentiation as defined by changes in media composition, with the final organoids collected at day 27 of culture.

extract_protocol:
Kidney organoids were dissociated to single cell, incubated with Totalseq-A antibodies (Biolegend; Cat# 394601, 394603, 394605, 394607, 394609, 394611, 394613, 394615) for sample hashing each samples collection day, pooled and super-loaded onto the 10x Genomics Chromium Controller (10x Genomics) to capture single cells. Briefly, 3x technical replicates for each sample were dissociated using TrypLE for 3 minutes, pooled and diluted in TEsR-E6 and centrifuged at 300 × g for three minutes. The cell pellets were resuspended in 100 µL cold Fluorescence-Activated Cell Sorting (FACS) buffer (PBS with 2% fetal bovine serum). Then, 2 µL of Totalseq-A hashing antibody was added and the cells were gently pipetted to mix before incubating for 20 min on ice. Cells were then washed twice with FACS buffer by centrifuging at 300 × g for 5 min, discarding the supernatant and resuspending the cell pellet in 100 µL cold FACS buffer. Approximately 40,000 cells were loaded onto the Chromium Single Cell Chip B (10x Genomics; Catalog Number: PN-1000073) to capture 20,000 single cells with the Gel Bead Kit V3.0 (10x Genomics; Catalog Number: PN-1000075). GEM generation, barcoding, cDNA amplification, and library construction were performed according to the 10x Genomics Chromium User Guide (CG000183).
Libraries were prepared with the Single Cell 3’ V3.0 Library and Gel Bead Kit (10x Genomics; Catalog Number: PN-1000075). The samples collected from stages 1, 2 and 3 occurred across six days, each capture multiplexed up to eight unique conditions and all were sequenced on the same run. The final collection of stage four cells occurred separately, multiplexing either 3 or 4 conditions to allow for greater cell numbers per condition for the more complex “mature” organoids.

tag: library type

value: mRNA


title: HT_P_T12_R2 [sequencing]

tag: time point

tag: condition

value: Parental


title: HT_hTERT_T0_R1 [sequencing]

description:
Soft tissue and Bone
T0 Timepoint Replicate 1


title: Stage2, 4c4E, day8, RNASeq


title: F_Chronic_5xCHI+ vehicle_Rep12

description:
Library name: 22131R-04-17
Count

tag: strain

tag: conditions

value: 5xCHI + vehicle

value: vehicle


title: BC_cfDNA_BeforeTreatment_21

tag: paired sample_id_-_same_patient

tag: tissue

value: breast cancer

value: luminal

tag: data ids


title: DoxyPos_MSCNeg_R1

description: Library name: Sample4

tag: cell line

tag: cell type


title: BC_cfDNA_BeforeTreatment_19

tag: figure id

tag: subtype

value: cfDNA


title: F_Chronic_5xCHI+ vehicle_Rep11

description:
Library name: 22131R-04-16
Count

value: Brain Somatosensory Cortex

tag: Sex

tag: injury

tag: treatment


title: HT_hTERT_T0_R2 [sequencing]

description:
Soft tissue and Bone
T0 Timepoint Replicate 2

value: Infection with viral library lentiCRISPRv2_A


title: F_Chronic_sham+ vehicle_Rep5

description:
Library name: 22131R-04-47
Count

tag: timepoint

tag: cohort

value: sham + vehicle

value: sham


title: HT_P_T6_R1 [sequencing]

description:
Soft tissue and Bone
T6 Timepoint Replicate 1


title: F_Chronic_sham+ SB_Rep2

description:
Library name: 22131R-04-20
Count

value: Chronic


title: F_Chronic_5xCHI+ vehicle_Rep8

description:
Library name: 22131R-04-18
Count


title: BC_cfDNA_BeforeTreatment_16

tag: ID

tag: figure id_-_treatment_sensitivity

tag: sample type


title: F_Chronic_sham+ vehicle_Rep1

description:
Library name: 22131R-04-28
Count

tag: strain


title: BC_cfDNA_BeforeTreatment_10


title: F_Chronic_5xCHI+ vehicle_Rep7

description:
Library name: 22131R-04-45
Count

tag: conditions


title: BC_cfDNA_BeforeTreatment_9

tag: paired sample_id_-_same_patient


title: DoxyNeg_MSCPos_R1

description: Library name: Sample7

tag: tissue

value: Kidney


title: GM_hTERT_T15_R2 [sequencing]

description:
Skin
T15 Timepoint Replicate 2

source_name: Skin

tag: time point

tag: condition

value: TERT overexpressed


title: F_Chronic_5xCHI+ vehicle_Rep6

description:
Library name: 22131R-04-44
Count

value: F


title: DoxyNeg_MSCNeg_R1

description: Library name: Sample1

tag: cell line

tag: cell type

value: human renal proximal tubular epithelial cell line

value: DMSO


title: Stage2, 3c4F200, day7, RNASeq

tag: library type

value: mRNA


title: F_Chronic_5xCHI+ vehicle_Rep10

description:
Library name: 22131R-04-26
Count

tag: Sex


title: DoxyNeg_MSCNeg_R3

description: Library name: Sample3


title: HT_hTERT_T6_R1 [sequencing]


title: BC_cfDNA_BeforeTreatment_12

tag: figure id

tag: subtype

tag: data ids


title: F_Chronic_5xCHI+ vehicle_Rep5

description:
Library name: 22131R-04-53
Count

tag: timepoint

tag: cohort

tag: injury

tag: treatment


title: Stage2, 5c4FC, day9, RNASeq


title: BC_cfDNA_BeforeTreatment_14

tag: ID

tag: figure id_-_treatment_sensitivity

tag: sample type


title: HT_P_T12_R1 [sequencing]

value: Parental


title: Stage2, 3c4FL, day7, RNASeq


title: F_Chronic_sham+ SB_Rep3

description:
Library name: 22131R-04-19
Count

tag: strain

tag: tissue

tag: conditions

value: sham + SB

value: SB


title: GM_hTERT_T6_R2 [sequencing]

description:
Skin
T6 Timepoint Replicate 2

tag: cell line

tag: time point

tag: condition


title: HT_P_T6_R2 [sequencing]

description:
Soft tissue and Bone
T6 Timepoint Replicate 2


title: HT_hTERT_T6_R2 [sequencing]


title: BC_cfDNA_BeforeTreatment_4

tag: paired sample_id_-_same_patient

value: breast cancer


title: Stage2, 3c4E, day7, RNASeq

tag: library type


title: BC_cfDNA_BeforeTreatment_13

tag: figure id

tag: subtype

value: luminal


title: BC_cfDNA_BeforeTreatment_5

value: cfDNA

tag: data ids


title: Stage2, 5c4FA, day9, RNASeq


title: BC_cfDNA_BeforeTreatment_11


title: F_Chronic_sham+ vehicle_Rep2

description:
Library name: 22131R-04-22
Count

value: Brain Somatosensory Cortex

tag: Sex

tag: timepoint

tag: cohort

value: vehicle


title: GM_hTERT_T0_R1 [sequencing]

description:
Skin
T0 Timepoint Replicate 1

tag: treatment

value: Infection with viral library lentiCRISPRv2_A


title: HT_P_T0_R1 [sequencing]


title: Stage2, 5c4FL, day9, RNASeq


title: F_Chronic_5xCHI+ vehicle_Rep9

description:
Library name: 22131R-04-25
Count

value: 5xCHI + vehicle

tag: injury


title: HT_P_T0_R2 [sequencing]


title: Stage2, 4c4FL, day8, RNASeq


title: BC_cfDNA_BeforeTreatment_7

tag: ID

tag: sample type


title: BC_cfDNA_BeforeTreatment_8

tag: tissue


title: F_Chronic_5xCHI+ SB_Rep10

description:
Library name: 22131R-04-36
Count

tag: strain

value: Chronic

tag: conditions

value: 5xCHI + SB


title: Stage2, 4c4FC, day8, RNASeq

tag: cell line


title: BC_cfDNA_BeforeTreatment_6


title: Stage2, 4c4F200, day8, RNASeq


title: GM_hTERT_T15_R1 [sequencing]

description:
Skin
T15 Timepoint Replicate 1

tag: time point

tag: condition

value: TERT overexpressed


title: BC_cfDNA_BeforeTreatment_1

tag: paired sample_id_-_same_patient

tag: figure id_-_treatment_sensitivity


title: GM_hTERT_T6_R1 [sequencing]

description:
Skin
T6 Timepoint Replicate 1


title: Stage4, sample capture 13, day 27, scRNAseq GEX

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
Kidney_organoid_atlas_ge_matrix.mtx
Kidney_organoid_atlas_metadata.csv

tag: library type


title: BC_cfDNA_BeforeTreatment_2

tag: figure id

tag: subtype

tag: data ids


title: F_Chronic_5xCHI+ SB_Rep9

description:
Library name: 22131R-04-13
Count

tag: Sex

value: F

tag: timepoint

tag: cohort


title: F_Chronic_5xCHI+ vehicle_Rep4

description:
Library name: 22131R-04-40
Count

tag: injury

tag: treatment


title: Stage2, 5c4F, day9, RNASeq


title: Stage 2, 3c4F, day 7, RNASeq


title: GM_hTERT_T0_R2 [sequencing]

description:
Skin
T0 Timepoint Replicate 2


title: F_Chronic_5xCHI+ vehicle_Rep3

description:
Library name: 22131R-04-41
Count

tag: tissue


title: F_Chronic_5xCHI+ SB_Rep11

description:
Library name: 22131R-04-35
Count

tag: strain


title: F_Chronic_5xCHI+ vehicle_Rep2

description:
Library name: 22131R-04-43
Count

tag: conditions


title: GM_P_T15_R2 [sequencing]

description:
Skin
T15 Timepoint Replicate 2

tag: cell line


title: Stage2, 3c4FA, day7, RNASeq


title: F_Chronic_5xCHI+ vehicle_Rep1

description:
Library name: 22131R-04-52
Count


title: F_Chronic_5xCHI+ SB_Rep8

description:
Library name: 22131R-04-50
Count


title: Stage2, 4c4F, day8, RNASeq


title: BC_cfDNA_BeforeTreatment_3

tag: ID

tag: sample type


title: All samples, scRNAseq HTO

description:
HTO library: read1 file contains cell barcoode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Kidney_organoid_atlas_metadata.csv

molecule: protein

value: HTO

tag: hto


title: Stage4, sample capture 11, day 27, scRNAseq GEX


title: GM_P_T0_R2 [sequencing]

description:
Skin
T0 Timepoint Replicate 2

tag: time point

tag: condition


title: GM_P_T6_R2 [sequencing]

description:
Skin
T6 Timepoint Replicate 2


title: GM_P_T0_R1 [sequencing]

description:
Skin
T0 Timepoint Replicate 1