title: hEMO-hTOr Co-culture

description:
Library name: CoCulture_ET
snRNA-seq of hEMO and hTOr co-culture

data_processing:
Raw reads were processed using Cell Ranger v8.0.1 (10x Genomics) with the human reference genome GRCh38-2020-A.
Assembly: GRCh38-2020-A (10x Genomics)
Supplementary files format and content: filtered_feature_bc_matrix.h5 (HDF5 format containing sparse gene expression matrix), as generated by Cell Ranger.

molecule: nuclear RNA

source_name: human endometrium and trophoblast

growth_protocol: Human endometrial organoids (hEMO) were generated from human endometrial tissue as previously described. hTSCs were dissociated and seeded onto AggreWell 400 24 well-plates (Stem Cell Technologies) at 6 × 10⁵ cells/well in ECSY medium. After 24 hours, spheroids were transferred to rotational culture using a ClinoStar bioreactor (CelVivo) at 37°C with 5% CO₂ and continuous rotation, with medium supplemented with 50 ng/ml FGF2 and 20 ng/ml BMP4 to generate hTOr.

extract_protocol:
Nuclei were isolated from organoids using the Chromium Nuclei Isolation Kit (10x Genomics, CG000505) according to the manufacturer’s instructions.
Single-nucleus RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3' v3.1 Dual Index kit. Libraries were sequenced (150 bp paired-end) on Illumina NovaSeq X Plus.

treatment_protocol: For co-culture assays, day 11 hTOr were co-embedded with hEMO in Matrigel and maintained for eight days in ECSY medium to model the embryo-endometrial interface. Mono-culture controls were maintained in parallel.

value: human endometrium and trophoblast

value: hEMO + hTOr

value: epithelial and trophoblast cells

value: co-culture, day 8


title: 4T1 Tumor, anti-PD1 + anti-CTLA4, CP-5243

status: Public on Mar 09 2026

type: SRA

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

country: USA

institute: University of North Carolina at Chapel Hill

description:
Library name: 4T1_CP-5243
Column name in raw_counts_All_Samples.txt: 4T1_CP-5243

library_source: transcriptomic

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts.
The raw counts were upper quartile-normalized.
Assembly: mm10
Supplementary files format and content: Salmon-quantified, upper quartile-normalized read-counts. First column is the gene name, subsequent columns are individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: mammary tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to isolate the RNA according to the manufacturer's protocol.
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit.

tag: tissue

value: mammary tumor

tag: tumor model

tag: treatment

value: anti-PD1 + anti-CTLA4


city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

description: Library name: HSV1 A3A overexpressed HEK293 DRIP-seq IP

library_source: genomic

data_processing:
ChIP-seq and DRIP-seq reads were aligned to the HSV-1 KOS1 reference genome using two parallel strategies. (1) Bowtie2 with default parameters was used to generate the processed bigWig files. (2) BWA-MEM with the parameter -B 0 (all other settings left as default) was used for the analysis of APOBEC-associated mutations.
Alignments were filtered using samtools v1.10 keeping only primary alignments of properly paired reads that had >30 mapping quality score. PCR duplicates were also filtered out.
RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage (.bedgraph and .bigwig) files have been generated with 20 bp resolution using Deeptools bamCoverage v3.5.140.
deepTools were used to the input correction (bigwigCompare)
FreeBayes was used for mutation calling.
Assembly: HSV-1 KOS1 reference sequence
Supplementary files format and content: bigwig files
Supplementary files format and content: vcf files of the mutations

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Jurkat human T lymphoblast cells (ATCC-J.RT3-T3), HEK293-AD pCMVA3A-tGFP and pCMVA3G-tGFP cells, and human retinal pigment epithelium (RPE-1) pdoxA3A-HA cells were clutured according to standard protocols. The KOS1 strain of HSV-1 (ATCC-VR-1493; LOT: 59681562) was cultured in Vero cells.

extract_protocol:
Twenty million HSV-1 infected or mock control cells were grown to near-confluence, followed by crosslinking them with 1% formaldehyde for 10 minutes and quenching with glycine. After washing and lysing, the cells were stored until the chromatin could be prepared. Chromatin was then sheared by sonication to achieve the desired fragment size of 200–500 bp, with 2% of the fragmented material set aside as input DNA. Chromatin Immunoprecipitation (ChIP) was performed using 8 µg of specific polyclonal antibodies: anti-APOBEC3A and anti-APOBEC3G for Jurkat cells, anti-HA for RPE-1 cells, or anti-tGFP for HEK293-AD cells. Concurrently, DNA:RNA Hybrid Immunoprecipitation (DRIP) was conducted on the same samples using the S9.6 monoclonal antibody. For DRIP, 6 µg of genomic DNA was first isolated (omitting RNase A), fragmented by sonication, and then incubated overnight with S9.6 antibody-coated Protein G magnetic beads; a separate sample was treated with RNase H as a control. Following washing steps, the immunoprecipitated material was eluted using proteinase K, and the final DNA was purified using Ampure XP beads and quantified.
Illumina TruSeq ChIP Sample Preparation protocol were used to DRIP-seq. DRIP DNA were end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced (at the EMBL Genomics Core Facility, Heidelberg) using an Illumina HiSeq 2500 instrument in the 2x125 paired-end sequencing mode, and Illumina NovaSeq X Plus PE150 (at Novogene Ltd.).

treatment_protocol: HSV-1 KOS1 virus was employed to infect the above cell lines at a multiplicity of infection (MOI) of 5. HSV-1 infection of RPE-1 pdoxA3A-HA cells was performed 2 hours after the addition of doxycycline (dox) to induce A3A-HA expression, and dox was maintained throughout the experiment (12 hours post-infection). Following incubation of the cells with the virus for 2 hours, excess HSV-1 was removed, and the cells were cultivated for downstream analysis. We fixed cells in 1% formaldehyde (Thermo Fisher Scientific, Pierce™ 16% Formaldehyde (w/v), Methanol-free,) at various time points post-infection.

tag: cell line

tag: agent


title: cortical human organoids, P2, medium heteroplasmy

city: Cambridge

first: Denisa

last: Hathazi

address: Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description:
Library name: SITTE12
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

data_processing:
Raw read alignment ot the human reference genome (GRCh38) was performed with CellRanger software version 7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes).
Dataset integration, normaization and further procesing has been perfomred in R version 4.2.2, using Seurat package (version 4.0 and 5.0.0).
Assembly: Homo Sapiens, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: brain organoid

extract_protocol:
Single-cell suspensions were generated from human iPSC-derived cortical organoids. Organoids were dissociated into single cells using enzymatic digestion followed by mechanical trituration. Cells were filtered through a 40 µm strainer, counted, and viability assessed prior to library preparation.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1 platform according to the manufacturer's protocol. Single cells were encapsulated in droplets with barcoded gel beads using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library preparation. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: brain organoid

value: iPSC derived

tag: cell type

value: mixed neuronal populations

tag: genotype

value: m.3243A>G, 49% heteroplasmy

tag: batch


title: hTSC B31 Shaking culture

city: Sendai

first: Shun

last: Shibata

address: 2-1 Seiryo-chou

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: B31_shaking
Bulk RNA-seq of B31 hTSC-derived organoids cultured under horizontal shaking conditions for 11 days

data_processing:
Raw reads were quality-trimmed using TrimGalore (v0.6.7) with 10-bp 5' clipping and adapter removal.
Trimmed reads were aligned to GRCh38/hg38 using STAR (v2.7.11b) with RefSeq annotation and transcript quantification mode.
Transcript abundance was quantified using RSEM (v1.3.3) with strand-specific parameters, generating TPM and raw read counts.
Differential expression analysis was performed using DESeq2. Genes with adjusted P < 0.05 (Benjamini-Hochberg correction) and |log2FC| > 1.0 were considered significantly differentially expressed.
GRCh38/hg38
processed_data_all8.tsv: Tab-delimited text file containing RSEM-derived TPM (Transcripts Per Million) values for all 8 samples. Columns: gene_id (Ensembl gene ID), B31_10cm, B31_rot, B31_matrigel, B31_shake, CT27_10cm, CT27_rot, CT27_matrigel, CT27_shake.
Assembly: GRCh38-2020-A (10x Genomics)
Supplementary files format and content: *processed data files format and content barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene annotation), matrix.mtx.gz (UMI count matrix in Matrix Market format), as generated by Cell Ranger filtered_feature_bc_matrix output. Files are provided separately for CT27 (EVT_CT27_) and CT29 (EVT_CT29_) samples.

source_name: Trophoblast organoids

growth_protocol: hTSCs were dissociated and seeded onto AggreWell 400 24-well plates (Stem Cell Technologies) at 6 × 10⁵ cells/well in ECSY medium (DMEM/F-12, 1% ITS-X, 0.15% BSA, 1% KSR, 200 μM L-ascorbic acid, 1 μg/ml heparin, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, 10 μM Y27632). After 24 hours, spheroids were collected and transferred to four culture conditions: (1) Rotational culture using a ClinoStar bioreactor (CelVivo) at 37°C with 5% CO₂ and continuous rotation (9-20 rpm); (2) Floating culture in non-treated 100 mm dishes without agitation; (3) Shaking culture in non-treated 100 mm dishes with horizontal agitation; (4) Matrigel-embedded culture. All conditions used ECSY medium supplemented with 50 ng/ml FGF2 and 20 ng/ml BMP4, with Y27632 reduced to 2.5 μM. Organoids were cultured for 11 days.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) with genomic DNA removal by ribonuclease-free deoxyribonuclease I.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) with NEBNext Poly(A) mRNA Magnetic Isolation Module for poly(A) selection. Libraries were sequenced on Illumina NovaSeq X Plus (150 bp paired-end reads, 3 Gb per sample).

treatment_protocol: Four culture conditions were compared: rotation (simulated microgravity), floating (static suspension), shaking (horizontal agitation), and Matrigel embedding. Two independent hTSC lines (B31 and CT27) were used as biological replicates.

value: Trophoblast organoids

value: human trophoblast stem cells (hTSCs) B31

value: trophoblast

value: wild-type

value: Shaking culture (horizontal agitation, 11 days)


title: cortical human organoids, P1, high heteroplasmy

description:
Library name: SITTF8
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: m.3243A>G, 72% heteroplasmy


title: HSV1 A3A induced RPE-1 IP RNaseH

description: Library name: HSV1 A3A induced RPE-1 IP RNaseH


title: hEMO Mono-culture

description:
Library name: hEMO_Mono
snRNA-seq of hEMO mono-culture

library_source: transcriptomic single cell

source_name: human endometrium

value: human endometrium

value: human endometrial organoids (hEMO)

value: epithelial cells

value: mono-culture, day 8


title: hTSC B31 Floating culture

description:
Library name: B31_floating
Bulk RNA-seq of B31 hTSC-derived organoids cultured under static floating conditions for 11 days

value: Floating culture (static suspension in 10cm dish, 11 days)


title: HSV1 A3A overexpressed HEK293 input

description: Library name: HSV1 A3A overexpressed HEK293 input


title: cortical human organoids, P1, medium heteroplasmy

description:
Library name: SITTE8
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: m.3243A>G, 42% heteroplasmy


title: cortical human organoids, P2, low heteroplasmy 1

description:
Library name: SITTH3
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: m.3243A>G, 30% heteroplasmy


title: 4T1 Tumor, anti-PD1 + anti-CTLA4, CP-5242

description:
Library name: 4T1_CP-5242
Column name in raw_counts_All_Samples.txt: 4T1_CP-5242

value: mammary tumor

value: anti-PD1 + anti-CTLA4


title: HSV1 A3A induced RPE-1 DRIP-seq IP REP2

description: Library name: HSV1 A3A induced RPE-1 DRIP-seq IP REP2


title: 4T1 Tumor, anti-PD1 + anti-CTLA4, CP-5241

description:
Library name: 4T1_CP-5241
Column name in raw_counts_All_Samples.txt: 4T1_CP-5241


title: cortical human organoids, P2, low heteroplasmy 2

description:
Library name: SITTD12
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: brain organoid

value: iPSC derived

value: mixed neuronal populations

value: m.3243A>G, 0% heteroplasmy


title: cortical human organoids, P1, low heteroplasmy

description:
Library name: SITTD11
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: m.3243A>G, 12% heteroplasmy


title: hTOr Mono-culture

description:
Library name: hTOr_Mono
snRNA-seq of hTOr mono-culture

source_name: human trophoblast

value: human trophoblast

value: human trophoblast organoids (hTOr)

value: trophoblast cells

value: wild-type

value: mono-culture, day 11


title: 25444FL-02-01-05_S28_L001.counts [Day 14]

city: Bronx

first: Russell

last: Scharf

state: New York

address: 1945 Eastchester Rd

institute: Albert Einstein College of Medicine

description: Library name: Day 14

data_processing:
Reads trimmed with cutadapt
Aligned to hg38 with Bowtie2
Peaks called with MACS2
Read counts per peak quantified with BEDTools
Assembly: hg38
Supplementary files format and content: tab-delimited files with raw counts per each peak per sample

source_name: Peripheral blood leukocytes

growth_protocol: HL60 cells were cultured and maintained in RPMI + 10% FBS + 1% PenStrap

extract_protocol:
Chromatin was extracted using Active Motif ATAC-Seq Express Kit (Cat # 53157) and protocol was followed using manufacturer's instruction
Library preparation was done following manufacturer's instruction (Active Motif #53157)

treatment_protocol: HL60 cells were treated with 250nM AraC for 1 day (Day 1 sample) or 3 days followed by cuture in non-drug media for another 9 days (Day 14 sample). Controls were treated with the AraC solvent DMSO. Cells were stained for Pyronin Y and Hoechst and G0/G1 cells were sorted using flow cytometry for ATAC analysis

value: Peripheral blood leukocytes

value: Promyeloblast

value: AraC


title: HSV1 A3A induced RPE-1 DRIP-seq IP REP1

description: Library name: HSV1 A3A induced RPE-1 DRIP-seq IP REP1


title: KPB1-A Tumor, anti-PD1 + anti-CTLA4, CP-5239

description:
Library name: KPB1-A_CP-5239
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-5239


title: KPB1-A Tumor, anti-PD1 + anti-CTLA4, CP-5240

description:
Library name: KPB1-A_CP-5240
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-5240


title: 25444FL-02-01-03_S76_L003.counts [Day 1]

description: Library name: Day 1


title: cortical human organoids, P2, high heteroplasmy

description:
Library name: SITTC12
Single-cell RNA sequencing of human iPSC-derived cortical organoids carrying the mitochondrial DNA mutation m.3243A>G with varying heteroplasmy levels.

value: m.3243A>G, 70% heteroplasmy


title: 25444FL-02-01-02_S75_L003.counts [control]

description: Library name: Control

value: Control


title: HSV1 A3A induced RPE-1 ChIP-seq IP REP1

description: Library name: HSV1 A3A induced RPE-1 ChIP-seq IP REP1


title: KPB1-A Tumor, anti-PD1 + anti-CTLA4, CP-5238

description:
Library name: KPB1-A_CP-5238
Column name in raw_counts_All_Samples.txt: KPB1-A_CP-5238

value: mammary tumor


title: Untreated biol rep 3

description: Library name: C3U

data_processing:
Reads trimmed with cutadapt
Reads aligned to the hg38 with STAR
Gene by count matrix generated with featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited file that contains raw counts for each sample

extract_protocol:
RNA was extracted from cells using a RNeasy Mini Kit (Qiagen). 400 ng of total RNA from control and AraC-treated cells or Pyronin-Y high and low cells were enriched using poly-T oligo-attached magnetic beads, fragmented, and reverse transcribed into cDNA.
The cDNA libraries were constructed and sequenced on an Illumina NovaSeq platform, generating paired-end reads

treatment_protocol: HL60 cells were treated with 250nM AraC for 1 day. Controls were treated with the AraC solvent DMSO. Cells were stained for Pyronin Y and Hoechst and G0/G1 cells were sorted using flow cytometry for RNA seq analysis


title: Distal tumor tissue-2

city: Hangzhou

first: Yongjie

last: Wang

address: 2318 Yuhangtang Rd

country: China

institute: Hangzhou Normal University

description: Library name: Sample 5

data_processing:
Raw BCL files were converted into fastq files using bcl2fastq.
Trimmomatic (v0.39) was used to remove adapters and low-quality bases from raw FASTQ reads. The resulting high-quality reads were then mapped to the GRCh38 reference genome with STAR (v2.7.3a)
Gene-level read quantification was performed with featureCounts (v2.0.1), applying the "-s 2" parameter for reverse-stranded library orientation.
DESeq2 was employed to identify differentially expressed genes. Significance thresholds were set at p-value < 0.05 and |log2FC| > 1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen, Grand Island, NY) and subsequently purified using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). The integrity of each RNA sample was verified on an Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA); only those with an RNA Integrity Number (RIN) exceeding 7.0 were carried forward for library preparation.
Library preparation was conducted using the TruSeq RNA Sample Preparation Kit (Illumina), which facilitated mRNA purification, fragmentation, and subsequent double-stranded cDNA synthesis. The completed libraries were quantified with a Qubit fluorometer (Invitrogen, CA, USA), pooled at equimolar concentrations, and finally sequenced on an Illumina NovaSeq X Plus platform.

value: tumor

value: Small cell lung cancer cell

value: Distal tumor tissue


title: MMTV-Neu Tumor, Carboplatin + Paclitaxel, CP-5161

description:
Library name: MMTV-Neu_CP-5161
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-5161

value: MMTV-Neu

value: Carboplatin + Paclitaxel


title: MMTV-Neu Tumor, Carboplatin + Paclitaxel, CP-5163

description:
Library name: MMTV-Neu_CP-5163
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-5163


title: Distal tumor tissue-1

description: Library name: Sample 4


title: Treated biol rep 3

description: Library name: C3T


title: Neurons drug treated. Replicate 1

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts (.count.txt)

source_name: iPSC-derived neurons

growth_protocol: iPSC-derived neurons and glia were independently differentiated and kept in their final maturation medium

extract_protocol:
Cells were dissociated using accutase, and RNA was generated using RNeasy Mini Kit (Cat. number: 74106, Qiagen, Germany) according to the manufacturer’s instructions.
High-quality RNA samples were subjected to bulk RNA sequencing (RNA-seq) at GENEWIZ GmbH (Leipzig, Germany)
Strand-specific RNA sequencing with polyA selection

treatment_protocol: iPSC-derived microglia and astrocyes were treated for 6h with 1uM of CDDO-Me or left untreated for the control experiment.iPSC-derived neurons were treated for 24h with 1uM of CDDO-Me or left untreated for the control experiment

value: iPSC-derived neurons

value: 1uM CDDO-Me

tag: time point


title: Untreated biol rep 2

description: Library name: C2U


title: Treated biol rep 2

description: Library name: C2T


title: Neurons drug treated. Replicate 2

description: Strand-specific RNA sequencing with polyA selection


title: C3-TAG Tumor, Carboplatin + Paclitaxel, CP-5147

description:
Library name: C3-TAG_CP-5147
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-5147


title: Proximal tumor tissue-3

description: Library name: Sample 3

value: Proximal tumor tissue


title: Untreated biol rep 1

description: Library name: C1U


title: Neurons control. Replicate 2

value: Vehicle treated


title: Proximal tumor tissue-2

description: Library name: Sample 2


title: HSV1 A3A induced RPE-1 ChIP-seq IP REP2

description: Library name: HSV1 A3A induced RPE-1 ChIP-seq IP REP2


title: Neurons control. Replicate 1


title: C3-TAG Tumor, Carboplatin + Paclitaxel, CP-5149

description:
Library name: C3-TAG_CP-5149
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-5149


title: MMTV-Neu Tumor, Carboplatin + Paclitaxel, CP-5154

description:
Library name: MMTV-Neu_CP-5154
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-5154


title: Treated biol rep 1

description: Library name: C1T


title: Distal tumor tissue-3

description: Library name: Sample 6


title: T11-APOBEC Tumor, Carboplatin + Paclitaxel, CP-5114

description:
Library name: T11-APOBEC_CP-5114
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-5114


title: Proximal tumor tissue-1

description: Library name: Sample 1


title: Neurons drug treated. Replicate 3


title: Human Brain Metastasis Patient-derived Cancer Associated Fibroblast Cell Line, CM03, GEX

city: Los Angeles

first: Bodour

last: Salhia

state: CA

address: 1450 Biggy Street

department: Department of Cancer Biology

institute: University of Southern California

description:
Library name: CM03_PDC_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence

data_processing:
RNA: De-multiplexing, alignment, filtering and Unique Molecular Identifier (UMI) counting was performed using the Cell Ranger ARC Single Cell Software Suite version 2.0.2. Quality check and subsequent filtering was performed before analysis.
ATAC: Cell by gene (scRNA-seq) and cell by peak (scATAC-seq) count matrices were generated using the Cell Ranger ARC pipeline as described above for the scRNA-seq analysis. Gene expression and ATAC peak data were processed using the R packages Seurat and Signac.
Assembly: hg38
Supplementary files format and content: counts.csv.gz = count files (GEX)
Supplementary files format and content: atac.fragments.tsv.gz = list of unique fragments generated by transposition (ATAC)
Supplementary files format and content: barcodes.tsv.gz = list of unique barcode sequences identifying individual nuclei (ATAC)
Supplementary files format and content: features.tsv.gz = list of genomic features (ATAC)
Supplementary files format and content: matrix.mtx.gz = chromatin accessibility counts (ATAC)

growth_protocol: CM01, CM02, CM03 and CM08 Cancer Associated Fibroblast Cell Lines were cultured in advanced DMEM/F12 media (Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), 1% Glutamax (Gibco), 10ng/mL epidermal growth factor, 5U/mL penicillin, 5g/mL streptomycin (Gibco), 2.5% Nu-Serum™ IV (Corning) and 10ng/mL cholera toxin (Millipore Sigma). Cells were incubated at 37C in a humidified atmosphere at 5% CO2. Media was changed twice a week. Cells were dissociated at confluence using trypsin/EDTA (Gibco). All cells were tested negative for mycoplasma at the beginning of the study.

extract_protocol:
Fresh Brain Metastasis tissue samples were collected, transferred to a tube containing MACS© tissue storage solution (Miltenyi) and placed on ice before being processed for tissue snap freezing, OCT cryopreservation or cell dissociation within 24h. The proportion of each tissue sample designated for scMultiome-seq was snap frozen in liquid nitrogen and stored at -80C until nuclei isolation.
Nuclei isolation from frozen BM patient tissue samples was performed according to the 10x Genomics ‘Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing’ protocol. Nuclei isolation from CAF cell lines was performed according to the 10x Genomics ‘Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing’. Nuclei quality check and concentration measurement was performed at the end of the isolation process using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and ApoTome.2 microscope (ZEISS).
Nuclei suspensions were loaded onto a 10x Genomics Chromium Next gel beads in emulsion (GEM) Chip for transposed nuclei capture using 10x Genomics Chromium Controller. ScMultiome-seq libraries were performed using Chromium Next GEM Single Cell Multiome Reagent Kits according to the ‘Chromium Next GEM Single Cell Multiome ATAC + Gene Expression’ user guide provided by 10x Genomics.

value: Cancer Associated Fibroblast

tag: library type

value: mRNA


title: Control-3

description: Library name: Sample 6

data_processing:
Raw BCL files were converted into fastq files using bcl2fastq.
Trimmomatic (v0.39) was used to remove adapters and low-quality bases from raw FASTQ reads. The resulting high-quality reads were then mapped to the GRCh38 reference genome with STAR (v2.7.3a)
Gene-level read quantification was performed with featureCounts (v2.0.1), applying the "-s 2" parameter for reverse-stranded library orientation.
DESeq2 was employed to identify differentially expressed genes. Significance thresholds were set at an adjusted p-value < 0.05 and |log2FC| > 1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw count values for each sample


title: Human Brain Metastasis Patient-derived Cancer Associated Fibroblast Cell Line, CM02, GEX

description:
Library name: CM02_PDC_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: Neurons control. Replicate 3


title: T11-APOBEC Tumor, Carboplatin + Paclitaxel, CP-5113

description:
Library name: T11-APOBEC_CP-5113
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-5113


title: Human Brain Metastasis Tissue, LBM-USC-3, Multiome, ATAC

description:
Library name: LBM_USC_3_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence

library_source: genomic single cell

source_name: Brain metastasis

value: Brain metastasis

value: ATAC


title: T11-APOBEC Tumor, Carboplatin + Paclitaxel, CP-5112

description:
Library name: T11-APOBEC_CP-5112
Column name in raw_counts_All_Samples.txt: T11-APOBEC_CP-5112


title: Control-2

description: Library name: Sample 5


title: β-alanine-2

description: Library name: Sample 2

value: β-alanine


title: T12 Tumor, anti-PD1 + anti-CTLA4, CP-5111

description:
Library name: T12_CP-5111
Column name in raw_counts_All_Samples.txt: T12_CP-5111

value: anti-PD1 + anti-CTLA4


title: T12 Tumor, anti-PD1 + anti-CTLA4, CP-5110

description:
Library name: T12_CP-5110
Column name in raw_counts_All_Samples.txt: T12_CP-5110


title: β-alanine-3

description: Library name: Sample 3


title: Microglia drug treated. Replicate 2

source_name: iPSC-derived microglia

value: iPSC-derived microglia


title: Human Brain Metastasis Tissue, LBM-USC-3, Multiome, GEX

description:
Library name: LBM_USC_3_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: Microglia control. Replicate 3


title: Human Brain Metastasis Patient-derived Cancer Associated Fibroblast Cell Line, CM08, GEX

description:
Library name: CM08_PDC_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: Human Brain Metastasis Patient-derived Cancer Associated Fibroblast Cell Line, CM01, GEX

description:
Library name: CM01_PDC_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: β-alanine-1

description: Library name: Sample 1


title: Control-1

description: Library name: Sample 4

value: Control


title: p53RB-624 Tumor, anti-PD1 + anti-CTLA4, CP-5108

description:
Library name: p53RB-624_CP-5108
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-5108

value: mammary tumor


title: T12 Tumor, anti-PD1 + anti-CTLA4, CP-5109

description:
Library name: T12_CP-5109
Column name in raw_counts_All_Samples.txt: T12_CP-5109


title: Human Brain Metastasis Tissue, LBM-USC-2-2, Multiome, ATAC

description:
Library name: LBM_USC_2_2_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence


title: CT29 hTSC-derived EVT-differentiated trophoblast organoids, snRNA-seq

description:
Library name: EVT_CT29_snRNA
Single-nucleus RNA-seq of CT29 hTSC-derived organoids cultured under simulated microgravity for 11 days, then differentiated toward EVT lineage for 14 days in Matrigel

data_processing:
Raw reads were processed using Cell Ranger v8.0.1 (10x Genomics) with the human reference genome GRCh38-2020-A-2.0.0.
Assembly: GRCh38-2020-A (10x Genomics)
Supplementary files format and content: *processed data files format and content barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene annotation), matrix.mtx.gz (UMI count matrix in Matrix Market format), as generated by Cell Ranger filtered_feature_bc_matrix output. Files are provided separately for CT27 (EVT_CT27_) and CT29 (EVT_CT29_) samples.

growth_protocol: hTSCs were dissociated and seeded onto AggreWell 400 24-well plates (Stem Cell Technologies) at 6 × 10⁵ cells/well in ECSY medium (DMEM/F-12, 1% ITS-X, 0.15% BSA, 1% KSR, 200 μM L-ascorbic acid, 1 μg/ml heparin, 50 ng/ml EGF, 2 μM CHIR99021, 2 μM SB202190, 10 μM Y27632). After 24 hours, spheroids were collected, filtered through a 200 μm cell strainer to eliminate aggregates, and transferred to rotational culture under simulated microgravity using a ClinoStar bioreactor (CelVivo) at 37°C with 5% CO₂ and continuous rotation at optimized RPM to maintain organoids in central suspension. The culture medium was ECSY supplemented with 50 ng/ml FGF2 (Heat Stable, Thermo Fisher Scientific) and 20 ng/ml BMP4 (R&D Systems), with Y27632 concentration reduced to 2.5 μM. Organoids were cultured for 11 days under these rotational conditions.th medium supplemented with 50 ng/ml FGF2 (Heat Stable, Thermo Fisher Scientific) and 20 ng/ml BMP4 (R&D Systems).

extract_protocol:
For extravillous trophoblast (EVT) differentiation, day 11 rotation-cultured hTOr were embedded in Matrigel and cultured in EVT differentiation medium for 14 days according to established protocols.
Single-nucleus RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3′ v3.1 Dual Index kit. Approximately 10,000 nuclei per sample were used to generate libraries. Libraries were sequenced (150 bp paired-end) on Illumina NovaSeq X Plus.

value: Trophoblast organoids

value: human trophoblast stem cells (hTSCs) CT29

value: extravillous trophoblast (EVT)

value: wild-type

value: Rotational culture (simulated microgravity, 11 days) followed by Matrigel embedding and EVT differentiation medium (14 days)


title: Microglia control. Replicate 1

description: Strand-specific RNA sequencing with polyA selection


title: p53RB-624 Tumor, anti-PD1 + anti-CTLA4, CP-5107

description:
Library name: p53RB-624_CP-5107
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-5107


title: p53RB-624 Tumor, anti-PD1 + anti-CTLA4, CP-5106

description:
Library name: p53RB-624_CP-5106
Column name in raw_counts_All_Samples.txt: p53RB-624_CP-5106


title: Astrocyte drug treated. Replicate 2

source_name: iPSC-derived astrocyte

value: iPSC-derived astrocyte

value: 1uM CDDO-Me


title: CT27 hTSC-derived EVT-differentiated trophoblast organoids, snRNA-seq

description:
Library name: EVT_CT27_snRNA
Single-nucleus RNA-seq of CT27 hTSC-derived organoids cultured under simulated microgravity for 11 days, then differentiated toward EVT lineage for 14 days in Matrigel

treatment_protocol: For extravillous trophoblast (EVT) differentiation, day 11 rotation-cultured hTOr were embedded in Matrigel and cultured in EVT differentiation medium for 14 days according to established protocols.

value: human trophoblast stem cells (hTSCs) CT27


title: Astrocyte drug treated. Replicate 3


title: Microglia control. Replicate 2

value: Vehicle treated


title: Astrocyte drug treated. Replicate 1


title: Trophoblast-mesoderm assembloids day 23, snRNA-seq

description: Library name: TSOr_ExM_TS_Day23_snRNA

data_processing:
Raw reads were processed using Cell Ranger v8.0.1 (10x Genomics) with the human reference genome GRCh38-2020-A-2.0.0.
Assembly: GRCh38-2020-A-2.0.0 (10x Genomics
Supplementary files format and content: barcodes.tsv (cell barcodes), features.tsv (gene annotation), matrix.mtx.gz (UMI count matrix in Matrix Market format), as generated by Cell Ranger.

source_name: trophoblast-mesoderm assembloids (hTSCs + hESCs)

growth_protocol: ExM-primed cells (day 8) were dissociated using TrypLE Express for 3 minutes at 37°C, followed by differential adhesion on 0.1% gelatin-coated plates for 30 minutes to remove MEF feeders. Non-adherent cells were collected, filtered through a 70 μm cell strainer, counted, and resuspended in RCL medium with 10 μM Y27632 at 1.6 × 10⁵ cells/mL. hTSCs were prepared by centrifugation (380 × g, 1 minute) and resuspended in ECSY medium at 6.0 × 10⁵ cells/mL. ExM cells and hTSCs were mixed to achieve final concentrations of 1.6 × 10⁵ and 6.0 × 10⁵ cells/mL, respectively (total 7.6 × 10⁵ cells/mL), and seeded in AggreWell 400 24-well plates (2 mL per well). Plates were centrifuged at 100 × g for 3 minutes and incubated overnight at 37°C under 5% CO₂ and 5% O₂ conditions. The following day, formed spheroids were collected by gentle pipetting, filtered through a 200 μm cell strainer, and transferred to a ClinoStar bioreactor containing pre-warmed ECSYFB medium. Rotational culture was initiated at 9.6 rpm, with medium changes performed three times weekly. Rotation speed was gradually increased as assembloids enlarged to prevent contact with the vessel wall during extended culture periods.

extract_protocol:
Single nuclei were isolated using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer's instructions. Approximately 10,000 nuclei per sample were used for library generation.
Single-nucleus RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 with dual indexing. Libraries were sequenced (150 bp paired-end) on Illumina NovaSeq X Plus.

treatment_protocol: Rotational culture under simulated microgravity conditions in ClinoStar bioreactor, day 23

value: co-culture assembloids, rotational culture, day 23


title: 2250 Tumor, Carboplatin + Paclitaxel, CP-5105

description:
Library name: 2250_CP-5105
Column name in raw_counts_All_Samples.txt: 2250_CP-5105

value: Carboplatin + Paclitaxel


title: 2250 Tumor, Carboplatin + Paclitaxel, CP-5104

description:
Library name: 2250_CP-5104
Column name in raw_counts_All_Samples.txt: 2250_CP-5104


title: MORC3 ChIP-Seq, replicate 2, lane 5

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: Library name: sgAAVS1_DMSO_R2_L2

data_processing:
ChIP-Seq: nf-core/chipseq v1.1.0 was run with default parameters to quality check and align the data, create coverage tracks (bigWig) and call peaks.
Cut-and-Run: nf-core/cutandrun: 3.2.2 was run  with default parameters to quality check and align the data, create coverage tracks (bigWig) and call peaks.
Assembly: GRCh38
Supplementary files format and content: .bigWig: genome-wide read coverage track

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640 supplemented with L-glutamine, sodium pyruvate, 100U/ml penicillin-streptomycin (Thermo Fisher) and 10% (v/v) FCS (Omega Scientific).

extract_protocol:
BLaER1 cells were washed with PBS and fixed with 1% formaldehyde for 10 min at RT before quenching the reaction with 0.6 M glycine. Fixed cells were washed with cold PBS and lysed in 50mM TRIS pH 8, 10mM EDTA and 1% SDS. Lysates were sonicated using the Bioruptor (Diagenode) with cycles of 30s ON / 30s OFF in the high-power mode until a fragment length of 200-500bp was achieved. Lysates were mixed with dilution buffer to a final concentration of 20 mM TRIS pH 8, 150 mM NaCl, 2 mM EDTA ,1% Triton-X100 and 0.1% SDS. 2.5% drosophila melanogaster S2 cell derived chromatin (prepared similarly) was spiked into the samples. Lysates were pre-incubated at 4°C for 2 h with ProteinA-coated magnetic beads (G&E) previously blocked in TE with 1% BSA. After removal of the beads, target and spike-in antibodies were added to the lysates and incubated at 4°C overnight. Fresh blocked beads were added and incubated with the lysates for 2h at 4°C. Beads were washed with RIPA buffer (150 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 0.5% Na-deoxycholate, 1% Igepal), high salt buffer (500 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 1% Igepal), LiCl buffer (250 mM LiCl, 50 mM TRIS pH 8, 0.5% Na-deoxycholate, 1% Igepal) and TE wash buffer (10 mM TRIS-HCl, 1 mM EDTA, 50 mM NaCl) and protein DNA complexes were eluted with 100mM NaHCO3 + 1% SDS. ChIP and input samples were incubated overnight at 55°C with 200mM NaCl, 10mM EDTA, 20mM Tris-HCl pH 6.5 and 300 µg/ml Proteinase K (Thermo Fisher). DNA was isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research).
NEBNext Ultra II liabrary prep was performed accoring to manufacturer's instructions

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-estradiol (Sigma-Aldrich)

value: monocytes

value: IFNAR1-/- IFNAR2-/- Cas9 MORC3.AID.V5 + sgAAVS1

value: DMSO

tag: chip antibody

value: anti-V5 antibody; SV-Pk5, Thermo Fisher


title: Human Brain Metastasis Tissue, LBM-USC-2-1, Multiome, ATAC

description:
Library name: LBM_USC_2_1_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence

value: Brain metastasis

value: ATAC


title: Human Brain Metastasis Tissue, LBM-RIH-5, Multiome, ATAC

description:
Library name: LBM_RIH_5_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence


title: Control trophoblast organoids day 15, snRNA-seq

description:
Library name: TSOr_Control_Day15_snRNA
Single-nucleus RNA-seq of CT27 hTSC-derived organoids cultured under simulated microgravity for 15 days without doxycycline treatment

data_processing:
Raw reads were processed using Cell Ranger v8.0.1 (10x Genomics) via Docker (litd/docker-cellranger) with the human reference genome GRCh38-2020-A.
Assembly: GRCh38-2020-A (10x Genomics)
Supplementary files format and content: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene annotation), matrix.mtx.gz (UMI count matrix in Matrix Market format), as generated by Cell Ranger filtered_feature_bc_matrix output. Files are provided separately for control (TSOr_) and YAP5SA-treated (TSOr_YAP_) samples.

growth_protocol: hTSCs were dissociated and seeded onto AggreWell 400 24 well-plates (Stem Cell Technologies) at 6 × 10⁵ cells/well in ECSY medium (DMEM/F-12, 1% ITS-X, 0.15% BSA, 1% KSR, 200 M L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 2 µM SB202190, 10 µM Y-27632). After 24 hours, spheroids were collected, filtered through a 200 µm cell strainer to eliminate aggregates, and transferred to different 3D culture conditions for comparative studies. Rotational culture under simulated microgravity was performed using a ClinoStar bioreactor (CelVivo) at 37°C with 5% CO₂ and continuous rotation at optimized RPM to maintain organoids in central suspension, with medium supplemented with 50 ng/ml FGF2 (Heat Stable, Thermo Fisher Scientific) and 20 ng/ml BMP4 (R&D Systems). Organoids were cultured for 15 days total.

extract_protocol:
Nuclei were isolated from organoids using the Chromium Nuclei Isolation Kit (10x Genomics, CG000505) according to the manufacturer’s instructions.
Single-nucleus RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3' v3.1 Dual Index kit. Libraries were sequenced (150 bp paired-end) on Illumina NovaSeq X Plus

treatment_protocol: For YAP gain-of-function studies, hTSCs were transduced with TRE-YAP5SA and rtTA lentiviral constructs to generate doxycycline-inducible YAP5SA expression system. During rotational culture, YAP5SA expression was induced by adding 100 ng/ml doxycycline to the medium and maintained throughout the 15-day culture period. Control organoids were cultured under identical conditions without doxycycline treatment (vehicle control).

value: Trophoblast organoids

value: hTSC

value: control (no doxycycline), simulated microgravity culture, day 15


title: Human Brain Metastasis Tissue, LBM-RIH-5, Multiome, GEX

description:
Library name: LBM_RIH_5_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence

value: mRNA


title: Astrocyte control. Replicate 1


title: 2250 Tumor, anti-PD1 + anti-CTLA4, CP-5102

description:
Library name: 2250_CP-5102
Column name in raw_counts_All_Samples.txt: 2250_CP-5102

value: mammary tumor

value: anti-PD1 + anti-CTLA4


title: Microglia drug treated. Replicate 3

value: iPSC-derived microglia

value: 1uM CDDO-Me


title: Astrocyte control. Replicate 2

value: iPSC-derived astrocyte

value: Vehicle treated


title: Human Brain Metastasis Tissue, LBM-USC-2-2, Multiome, GEX

description:
Library name: LBM_USC_2_2_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: MORC3 ChIP-Seq, replicate 2, lane 7

description: Library name: sgAAVS1_DMSO_R2_L1


title: YAP5SA-induced trophoblast organoids day 15, snRNA-seq

description:
Library name: TSOr_YAP_Day15_snRNA
Single-nucleus RNA-seq of CT27 hTSC-derived organoids cultured under simulated microgravity for 15 days with doxycycline treatment for YAP5SA induction

value: human trophoblast stem cells (hTSCs) CT27

value: doxycycline (100 ng/ml) for YAP5SA induction, simulated microgravity culture, day 15


title: 2250 Tumor, Carboplatin + Paclitaxel, CP-5103

description:
Library name: 2250_CP-5103
Column name in raw_counts_All_Samples.txt: 2250_CP-5103

value: Carboplatin + Paclitaxel


title: Astrocyte control. Replicate 3


title: Human Brain Metastasis Tissue, LBM-USC-2-1, Multiome, GEX

description:
Library name: LBM_USC_2_1_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: 2250 Tumor, anti-PD1 + anti-CTLA4, CP-5101

description:
Library name: 2250_CP-5101
Column name in raw_counts_All_Samples.txt: 2250_CP-5101


title: RNA-seq of EPG5KO, Rep3

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

description: biological replicate 3

data_processing:
Trimmometrix 0.38
Trimmomatic performs trimming with various parameters for illumina paired-end or single-end.
Iluminaclip : Cut adapter or specific sequence from read
Sliding Window: Perform sliding window trimming. The average quality within the window is the threshold.
LEADING: If it is below the threshold, the base of the start part of the read is cut off. TRAILING: If it is below the threshold, the base at the end of the read is truncated. Truncate if less than, and CROP: truncate reads to a specific length.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file included RFPKM each sample

source_name: NPC

growth_protocol: The dual-SMAD inhibition protocol from previous study was used to initiate midbrain dopamine neuron (DA) differentiation derived from hESC. Accutase® (Gibco Grand Island, NY) was used to dissociate the cells, which were then seeded as single cells and allowed to grow onto Matrigel (Corning, Corning, NY)-coated culture dish at density 5 x 105 per 24-well plate until confluence.KSR was supplemented with 200 nM LDN193189 (STEMCELL Technologies, Vancouver, BC, Canada) and 10 μM SB431542 (Tocris; “day 0”), 2µM Purmophamine, and 3uM CHIR 99021 were added to KSR medium at specific time exposures. Starting on day 5 of differentiation, 25% of the N2 medium was gradually added, and the proportion of N2 was raised by 50% and 75% every two days.

extract_protocol:
Total RNA was isolated using TRIZOL (Life Technology), and RNA quality was checked by OD 260/280 ratio and analyzed by Agilent 2100 Bioanalyzer
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: CRISPR-Cas9 based Knockout of EPG5 gene

value: NPC

value: Knock-Out


title: Human Brain Metastasis Tissue, LBM-RIH-3, Multiome, ATAC

description:
Library name: LBM_RIH_3_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence

value: Brain metastasis


title: Human Brain Metastasis Tissue, LBM-RIH-3, Multiome, GEX

description:
Library name: LBM_RIH_3_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: MORC3 ChIP-Seq, replicate 1, lane 5

description: Library name: sgAAVS1_DMSO_R1_L2

value: monocytes

value: IFNAR1-/- IFNAR2-/- Cas9 MORC3.AID.V5 + sgAAVS1

value: DMSO

value: anti-V5 antibody; SV-Pk5, Thermo Fisher


title: 2250 Tumor, anti-PD1 + anti-CTLA4, CP-5100

description:
Library name: 2250_CP-5100
Column name in raw_counts_All_Samples.txt: 2250_CP-5100


title: RNA-seq of EPG5KO, Rep2

description: biological replicate 2


title: RNA-seq of EPG5KO, Rep1

description: biological replicate 1


title: Microglia drug treated. Replicate 1

description: Strand-specific RNA sequencing with polyA selection


title: RNA-seq of WT, Rep3

description: biological replicate 3

value: No-treatment


title: Human Brain Metastasis Tissue, LBM-RIH-2, Multiome, ATAC

description:
Library name: LBM_RIH_2_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence

value: ATAC


title: KPB25L-UV Tumor, Carboplatin + Paclitaxel, CP-5097

description:
Library name: KPB25L_CP-5097
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5097

value: mammary tumor


title: MORC3 ChIP-Seq input, replicate 2, lane 5

description: Library name: Input_sgAAVS1_DMSO_R2_L2


title: Human Brain Metastasis Tissue, LBM-RIH-2, Multiome, GEX

description:
Library name: LBM_RIH_2_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence

value: mRNA


title: MORC3 ChIP-Seq, replicate 1, lane 7

description: Library name: sgAAVS1_DMSO_R1_L1


title: MORC3 ChIP-Seq input, replicate 2, lane 7

description: Library name: Input_sgAAVS1_DMSO_R2_L1


title: Human Brain Metastasis Tissue, LBM-RIH-1, Multiome, ATAC

description:
Library name: LBM_RIH_1_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence


title: KPB25L-UV Tumor, Carboplatin + Paclitaxel, CP-5099

description:
Library name: KPB25L_CP-5099
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5099


title: RNA-seq of WT, Rep1

description: biological replicate 1


title: MORC3 ChIP-Seq input, replicate 1, lane 7

description: Library name: Input_sgAAVS1_DMSO_R1_L1


title: MORC3 ChIP-Seq input, replicate 1, lane 5

description: Library name: Input_sgAAVS1_DMSO_R1_L2


title: KPB25L-UV Tumor, Carboplatin + Paclitaxel, CP-5098

description:
Library name: KPB25L_CP-5098
Column name in raw_counts_All_Samples.txt: KPB25L_CP-5098


title: Human Brain Metastasis Tissue, BBM-USC-5-2, Multiome, ATAC

description:
Library name: BBM_USC_5_2_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence


title: Human Brain Metastasis Tissue, LBM-RIH-1, Multiome, GEX

description:
Library name: LBM_RIH_1_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: 9263 Tumor, Carboplatin + Paclitaxel, CP-5096

description:
Library name: 9263_CP-5096
Column name in raw_counts_All_Samples.txt: 9263_CP-5096


title: RNA-seq of WT, Rep2

description: biological replicate 2


title: Nrvm, Vehicle, replicate 4

city: Philadelphia

first: Jeanette

middle: Marie

last: Einspahr

state: Pa

address: 3500 N Broad Street

department: Aging & Cardiovascular Discovery Center

institute: Temple University School of Medicine

description: Library name: Veh4

data_processing:
Sequence reads (fastq) were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: Significant-DEGs_extended_info.csv includes all DEGs

organism: Rattus norvegicus

source_name: Heart

growth_protocol: NRVMs were isolated as previously described and maintained in Supplemented Hams F10 containing 5% FBS and 1% P/S in a humdified atmosphere of 5% CO2 at 37C.

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit
A. mRNA enrichment, mRNA fragmentation and Random Priming. B. First and second strand cDNA synthesis. C. End repair, 5' phosphorylation, and dA-Tailing. D. Adaptor ligation, PCR enrichment, and sequencing.

treatment_protocol: Cells were infected with adenoviruses encoding ADGRF5 or uninfected.

value: Heart

value: Neonatal Rat Ventricular Myocytes

value: Control

value: Veh


title: DonorF_irr3pt5_day7

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: Library name: DonorF_irr3pt5_day7

data_processing:
Quality control was done with FastQC (v0.12.1)
Reads were trimmed with TrimGalore (v0.6.10)
Trimmed reads were aligned to hg38 with STAR (v2.7.10a) with GTF file gencode.v44.basic.annotation.gtf file.
RNA seq metrics were collected using GATK CollectRnaSeqMetrics (v4.3.0.0) with hg38 refFlat.
MuliQC (v1.21) visualized all previous steps.
Assembly: GRCh 38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Abdominal skin

growth_protocol: Human tissue specimens had fat removed via trimming with forceps and dissecting scissors. Specimens were then cleaned with 70% ethanol 5 times and 1x PBS 3 times. Specimens were then placed in DMEM+GlutaMAX and maintained at an air-liquid interface, at interface, at 37°C/% CO2  for up to 7 days.

extract_protocol:
RNAlater-preserved samples were maintained on ice while being dissected and weighed (< 30mg). The samples were then finely chopped with a scalpel prior to being placed in tubes with RLT-βME and 3.0mm zirconium beads (Benchmark D10320-30). Samples then underwent 4 rounds of homogenization at 400 speed for 30 seconds with 1 minute rest between rounds in a BEADBug6 (Benchmark) homogenizer. Lysates were centrifuged at 16000 x g for 3 minutes, and the supernatant was thoroughly mixed with an equal volume of 70% ethanol. Total RNA was then isolated using QIAGEN's RNeasy Mini Kit (QIAGEN Inc, Valencia, CA, USA) following the manufacturer's protocol.
RNA libraries had ribosomal RNA (rRNA) removed with the resuling mRNA used for library prep with the Illumina Stranded mRNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol: Human skin specimens were irradiated with single doses of 3.5Gy by an Xstrahl cabinet irradiator, model RS225 with the following parameters: 190kV and 10mA with 0.5mm Cu filter for 3 minutes and 42 seconds for a total dose of 3.5Gy.

value: Abdominal skin

tag: Sex

value: Female

tag: time

value: Day 7


title: Nrvm, Vehicle, replicate 3

description: Library name: Veh3


title: 9263 Tumor, Carboplatin + Paclitaxel, CP-5095

description:
Library name: 9263_CP-5095
Column name in raw_counts_All_Samples.txt: 9263_CP-5095

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts.
The raw counts were upper quartile-normalized.
Assembly: mm10
Supplementary files format and content: Salmon-quantified, upper quartile-normalized read-counts. First column is the gene name, subsequent columns are individual samples.

value: Carboplatin + Paclitaxel


title: DonorF_irr3pt5_day5

description: Library name: DonorF_irr3pt5_day5

value: Day 5


title: 9263 Tumor, Carboplatin + Paclitaxel, CP-5094

description:
Library name: 9263_CP-5094
Column name in raw_counts_All_Samples.txt: 9263_CP-5094


title: Human Brain Metastasis Tissue, BBM-USC-5-2, Multiome, GEX

description:
Library name: BBM_USC_5_2_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence

value: Brain metastasis


title: 9263 Tumor, anti-PD1 + anti-CTLA4, CP-5093

description:
Library name: 9263_CP-5093
Column name in raw_counts_All_Samples.txt: 9263_CP-5093

value: anti-PD1 + anti-CTLA4


title: Human Brain Metastasis Tissue, BBM-USC-5-1, Multiome ATAC

description:
Library name: BBM_USC_5_1_HPT_ATAC
ATAC = read 1 contains cell barcode and UMI; read 2 contains ATAC sequence


title: Nrvm, Vehicle, replicate 2

description: Library name: Veh2


title: Human Brain Metastasis Tissue, BBM-USC-5-1, Multiome GEX

description:
Library name: BBM_USC_5_1_HPT_GEX
mRNA= read 1 contains cell barcode and UMI; read 2 contains transcript sequence


title: 9263 Tumor, anti-PD1 + anti-CTLA4, CP-5092

description:
Library name: 9263_CP-5092
Column name in raw_counts_All_Samples.txt: 9263_CP-5092


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 48h induction, Rep 3

city: Liverpool

first: Claire

last: Wilson

address: Ashton Street

institute: University of Liverpool

description: Library name: K48C

data_processing:
Quality assessed using FastQC(v0.11.9).
Sequence reads were trimmed for adapters and low-quality reads using TrimGalore (v0.6.6).
Genome mapping was performed with STAR (v2.7.10b) against the human reference genome (hg38 assembly).
Reads were counted using FeatureCounts (subread v2.0.3).
Differential analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: Foreskin

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin at 37°C in 5% CO2 in a humidified incubator. All cell lines were authenticated using 17-locus short tandem repeat (STR) analysis (ATCC) and frequently tested for Mycoplasma infection

extract_protocol:
All RNA extraction was performed using the Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions. Briefly, cell or nuclei pellets were extracted in TRI Reagent® (Zymo Research) and stored at -80°C until required. RNA extraction was performed by adding equal volume of ethanol to TRI Reagent® before binding to bind directly to the Zymo-Spin™ Column. The column was washed according to the manufacturer’s instructions and incubated with DNase I to remove any DNA contamination. Purified RNA was eluted from the column using DNase/RNase-Free Water. RNA quality and concentration was determined using 4200 TapeStation (Agilent).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

treatment_protocol: Cells were treated with 500 nM 4-hydroxytamoxifen (4-OHT) for 24 or 48 h to induce HRASG12V or KRASG12V. Non-induced cells (0h) were used as controls.

value: Foreskin

value: BJ-hTert

value: Human fibroblast cells

value: 48h induction


title: DonorF_irr3pt5_day1

description: Library name: DonorF_irr3pt5_day1

value: Day 1


title: 2336 Tumor, Carboplatin + Paclitaxel, CP-5090

description:
Library name: 2336_CP-5090
Column name in raw_counts_All_Samples.txt: 2336_CP-5090

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to isolate the RNA according to the manufacturer's protocol.
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit.

value: mammary tumor


title: DonorF_ctrl_day7

description: Library name: DonorF_ctrl_day7


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 48h induction, Rep 2

description: Library name: K48B


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 48h induction, Rep 1

description: Library name: K48A


title: Nrvm, Vehicle, replicate 1

description: Library name: Veh1

value: Heart


title: Nrvm overexpression of ADGRF5, replicate 3

description: Library name: adF5 3

value: Neonatal Rat Ventricular Myocytes

value: Overexpression of F5


title: 2336 Tumor, Carboplatin + Paclitaxel, CP-5089

description:
Library name: 2336_CP-5089
Column name in raw_counts_All_Samples.txt: 2336_CP-5089


title: 9263 Tumor, anti-PD1 + anti-CTLA4, CP-5091

description:
Library name: 9263_CP-5091
Column name in raw_counts_All_Samples.txt: 9263_CP-5091


title: DonorF_ctrl_day5

description: Library name: DonorF_ctrl_day5


title: 2336 Tumor, Carboplatin + Paclitaxel, CP-5088

description:
Library name: 2336_CP-5088
Column name in raw_counts_All_Samples.txt: 2336_CP-5088


title: Nrvm overexpression of ADGRF5, replicate 2

description: Library name: adF5 2


title: DonorF_ctrl_day2

description: Library name: DonorF_ctrl_day2

value: Day 2


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 24h induction, Rep 3

description: Library name: K24C

value: 24h induction


title: DonorF_ctrl_day1

description: Library name: DonorF_ctrl_day1

value: Abdominal skin

value: Female


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 24h induction, Rep 2

description: Library name: K24B


title: Nrvm overexpression of ADGRF5, replicate 1

description: Library name: adF5 1


title: XHLT2-HS9-BLE1

city: San Francisco

first: Ravi

last: Patel

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

description:
Library name: XHLT2-HS9-BLE1
Baseline PBMC: donor HS9

data_processing:
Sequencing reads were aligned to the human reference genome and Ensembl annotation (GRCh38 genome build, version 95) using STAR (v2.7.5c) with the following parameters: --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 -outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 -alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000. Duplicate reads were removed using Picard Tools (v2.23.3).
The raw read counts per gene from *ReadsPerGene.out.tab output of STAR are provided here.
Nucleotide variants were identified from the resulting bam files using the Genome Analysis Tool Kit (v4.0.11.0) following the best practices for RNA-seq variant calling. This included splitting spliced reads, calling variants with HaplotypeCaller (added parameters: --dont-use-soft-clipped-bases -standcall-conf 20.0), and filtering variants with VariantFiltration (added parameters: -window 35 cluster 3 --filter-name FS -filter FS >30.0 --filter-name QD -filter QD <2.0). Variants were further filtered to include a list of high quality SNP for identification of the subject of origin of individual cells by removing all novel variants, maintaining only biallelic variants with MAF greater than 5%, a max missing of one individual with a missing variant call at a specific site and requiring a minimum depth of two (parameters: --max-missing 1.0 --min-alleles 2 --max-alleles 2 --removeindels --snps snp.list.txt --min-meanDP 2 --maf 0.05 --recode --recode-INFO-all –out). The filtered VCF files are provided here.
Assembly: hg38
Supplementary files format and content: .vcf files are variant call format files derived from bulk RNA-seq of PBMC
Supplementary files format and content: .ReadsPerGene.out.tab files are output of STAR, containing four columns: (1) gene ID, (2) counts for unstranded RNA-seq, (3) counts for the 1st read strand aligned with RNA (htseq-count option -s yes), (4) counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

source_name: PBMC

extract_protocol:
Blood was collected in EDTA tubes within a 90 min window for all participants of the study. Peripheral blood mononuclear cells (PBMC) were obtained by density gradient centrifugation of whole blood at 800g for 30 min at room temperature without brake, using Ficoll-Paque (Cytiva). Isolated cells were cryopreserved in a solution containing fetal Bovine Serum and 10% DMSO (Sigma). Cell counts and viability of thawed PBMCs were determined using CellacaMX and 0.5 million cells were used for each sample. RNA was extracted using the Quick-RNA MagBead kit (Zymo Research) on the KingFisher automated extraction and purification system (ThermoFisher) according to manufacturer’s instructions. Quality and quantification of extracted RNA was assessed on the 5300 Fragment Analyzer System (Agilent).
The cDNA libraries were generated using the Universal Plus mRNA-Seq with NuQuant kit according to manufacturer’s instructions (Tecan). The libraries were subsequently sequenced on a HiSeq 4000 platform (Illumina).

value: PBMC


title: E0771 Tumor, anti-PD1 + anti-CTLA4, CP-5086

description:
Library name: E0771_CP-5086
Column name in raw_counts_All_Samples.txt: E0771_CP-5086

source_name: mammary tumor


title: E0771 Tumor, anti-PD1 + anti-CTLA4, CP-5087

description:
Library name: E0771_CP-5087
Column name in raw_counts_All_Samples.txt: E0771_CP-5087


title: XHLT2-HS98-BLE1

description:
Library name: XHLT2-HS98-BLE1
Baseline PBMC: donor HS98


title: DonorE_irr3pt5_day7

description: Library name: DonorE_irr3pt5_day7

value: Day 7


title: DonorF_irr3pt5_day2

description: Library name: DonorF_irr3pt5_day2


title: DonorE_irr3pt5_day5

description: Library name: DonorE_irr3pt5_day5

value: Day 5


title: E0771 Tumor, anti-PD1 + anti-CTLA4, CP-5085

description:
Library name: E0771_CP-5085
Column name in raw_counts_All_Samples.txt: E0771_CP-5085

value: anti-PD1 + anti-CTLA4


title: Nrvm overexpression of ADGRF5, replicate 4

description: Library name: adF5 4


title: XHLT2-HS97-BLE1

description:
Library name: XHLT2-HS97-BLE1
Baseline PBMC: donor HS97


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 24h induction, Rep 1

description: Library name: K24A

value: Foreskin


title: DonorE_irr3pt5_day2

description: Library name: DonorE_irr3pt5_day2


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 0h induction, Rep 2

description: Library name: K0B

value: BJ-hTert

value: 0h inducion


title: KPB1-B Tumor, anti-PD1 + anti-CTLA4, CP-5083

description:
Library name: KPB1-B_CP-5083
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-5083


title: DonorE_irr3pt5_day1

description: Library name: DonorE_irr3pt5_day1


title: 2224 Tumor, Carboplatin + Paclitaxel, CP-5081

description:
Library name: 2224_CP-5081
Column name in raw_counts_All_Samples.txt: 2224_CP-5081

value: Carboplatin + Paclitaxel


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 48h induction, Rep 2

description: Library name: H48B

value: Human fibroblast cells

value: 48h induction


title: KPB1-B Tumor, anti-PD1 + anti-CTLA4, CP-5082

description:
Library name: KPB1-B_CP-5082
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-5082

value: mammary tumor


title: DonorE_ctrl_day7

description: Library name: DonorE_ctrl_day7


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 48h induction, Rep 1

description: Library name: H48A


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 0h induction, Rep 3

description: Library name: K0C

value: 0h induction


title: RNA-Seq, BJ-hTert cells, KRASG12V expression, 0h induction, Rep 1

description: Library name: K0A


title: XHLT2-HS95-BLE1

description:
Library name: XHLT2-HS95-BLE1
Baseline PBMC: donor HS95


title: DonorE_ctrl_day5

description: Library name: DonorE_ctrl_day5


title: 2224 Tumor, Carboplatin + Paclitaxel, CP-5080

description:
Library name: 2224_CP-5080
Column name in raw_counts_All_Samples.txt: 2224_CP-5080


title: DonorE_ctrl_day1

description: Library name: DonorE_ctrl_day1

value: Day 1


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 24h induction, Rep 3

description: Library name: H24C


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 48h induction, Rep 3

description: Library name: H48C


title: XHLT2-HS91-BLE1

description:
Library name: XHLT2-HS91-BLE1
Baseline PBMC: donor HS91


title: DonorE_ctrl_day2

description: Library name: DonorE_ctrl_day2

value: Day 2


title: KPB1-B Tumor, anti-PD1 + anti-CTLA4, CP-5084

description:
Library name: KPB1-B_CP-5084
Column name in raw_counts_All_Samples.txt: KPB1-B_CP-5084


title: XHLT2-HS96-BLE1

description:
Library name: XHLT2-HS96-BLE1
Baseline PBMC: donor HS96


title: XHLT2-HS93-BLE1

description:
Library name: XHLT2-HS93-BLE1
Baseline PBMC: donor HS93


title: 2224 Tumor, Carboplatin + Paclitaxel, CP-5079

description:
Library name: 2224_CP-5079
Column name in raw_counts_All_Samples.txt: 2224_CP-5079


title: DonorD_irr3pt5_day7

description: Library name: DonorD_irr3pt5_day7


title: XHLT2-HS92-BLE1

description:
Library name: XHLT2-HS92-BLE1
Baseline PBMC: donor HS92


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 24h induction, Rep 2

description: Library name: H24B

value: 24h induction


title: 2224 Tumor, anti-PD1 + anti-CTLA4, CP-5078

description:
Library name: 2224_CP-5078
Column name in raw_counts_All_Samples.txt: 2224_CP-5078


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 24h induction, Rep 1

description: Library name: H24A


title: DonorD_irr3pt5_day5

description: Library name: DonorD_irr3pt5_day5

value: Abdominal skin


title: XHLT2-HS90-BLE1

description:
Library name: XHLT2-HS90-BLE1
Baseline PBMC: donor HS90


title: XHLT2-HS94-BLE1

description:
Library name: XHLT2-HS94-BLE1
Baseline PBMC: donor HS94


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 0h induction, Rep 3

description: Library name: H0C


title: 2224 Tumor, anti-PD1 + anti-CTLA4, CP-5077

description:
Library name: 2224_CP-5077
Column name in raw_counts_All_Samples.txt: 2224_CP-5077


title: DonorD_irr3pt5_day2

description: Library name: DonorD_irr3pt5_day2

value: Female


title: 2224 Tumor, anti-PD1 + anti-CTLA4, CP-5076

description:
Library name: 2224_CP-5076
Column name in raw_counts_All_Samples.txt: 2224_CP-5076


title: DonorD_irr3pt5_day1

description: Library name: DonorD_irr3pt5_day1


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 0h induction, Rep 2

description: Library name: H0B


title: XHLT2-HS88-BLE1

description:
Library name: XHLT2-HS88-BLE1
Baseline PBMC: donor HS88

value: PBMC


title: XHLT2-HS8-BLE1

description:
Library name: XHLT2-HS8-BLE1
Baseline PBMC: donor HS8


title: XHLT2-HS89-BLE1

description:
Library name: XHLT2-HS89-BLE1
Baseline PBMC: donor HS89


title: DonorD_irr3pt5_day0

description: Library name: DonorD_irr3pt5_day0

value: Day 0


title: DonorD_ctrl_day5

description: Library name: DonorD_ctrl_day5

value: Day 5


title: p53RB-426 Tumor, anti-PD1 + anti-CTLA4, CP-5075

description:
Library name: p53RB-426_CP-5075
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-5075

value: anti-PD1 + anti-CTLA4


title: p53RB-426 Tumor, anti-PD1 + anti-CTLA4, CP-5074

description:
Library name: p53RB-426_CP-5074
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-5074


title: MMTV-PyMT Tumor, Carboplatin + Paclitaxel, CP-5072

description:
Library name: MMTV-PyMT_CP-5072
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-5072

value: MMTV-PyMT


title: XHLT2-HS86-BLE1

description:
Library name: XHLT2-HS86-BLE1
Baseline PBMC: donor HS86


title: BJ-hTert cells, KRASG12V expression, 48h induction, Rep 3

description: Library name: K48C

library_source: other

data_processing:
Quality assessed using FastQC(v0.11.9).
Sequence reads were trimmed for adapters and low-quality reads using TrimGalore (v0.6.6).
Genome mapping was performed with STAR (v2.7.10b) against the human reference genome (hg38 assembly).
Read coverage performed to calculate raw counts using samtools/1.13.
RPKM calculated and differential analysis was performed using R Studio.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

molecule: other

extract_protocol:
Cell fractionation was performed as previously described in (PMID: 25910208) with modifications described below. All steps were conducted on ice or at 4°C and in the presence of 20 μM α-amanitin (Sigma, A2263), 25 μM RNA polymerase I inhibitor CX-5461 (Merck, 5.09265), 25 μM RNA polymerase III inhibitor ML-60218 (Merck, 557403), 50 Units SUPERaseIN (Life Technologies, AM2696) and Protease inhibitors cOmplete (Roche, 11873580001). Briefly, 5 × 106 cells for each condition were resuspended and incubated in 0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl for 5min, then layered onto a sucrose buffer (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose) and centrifuged at 16,000 g for 10 min. The supernatant carefully removed, and the nuclei pellet was gently resuspended in nuclei wash buffer (0.1% Triton X-100, 1 mM EDTA, in 1x PBS) and centrifuged at 1500 g for 1 min. The supernatant was removed, and the pellet was gently resuspended in glycerol buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT) before an equal volume of nuclei lysis buffer (1% NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1M Urea, 0.2 mM EDTA, 1 mM DTT) was added. Samples were vortexed, incubated on ice for 2 min and centrifuged at 18,500 g for 2 min. The supernatant was removed, and the chromatin pellet was immediately incubated with TRI Reagent® (Zymo Research) and stored at -80°C for RNA extraction with Direct-zol RNA Miniprep Kit. Approximately, 200-300 ng of input RNA in each repeat were depleted of ribosomal RNA with NEBNext® rRNA Depletion Kit v2 according to manufacturer’s guidelines. Chromatin RNA-Seq was performed on chromatin fractions.
NEBNext Ultra II 8482 Directional RNA Library Prep kit for Illumina

treatment_protocol: Cells were treated with 500 nM 4-hydroxytamoxifen (4-OHT) to induce HRASG12V or KRASG12V. Non-induced cells (0h) were used as controls.

value: Foreskin

value: BJ-hTert


title: BJ-hTert cells, KRASG12V expression, 48h induction, Rep 2

description: Library name: K48B


title: BJ-hTert cells, KRASG12V expression, 48h induction, Rep 1

description: Library name: K48A


title: DonorD_ctrl_day2

description: Library name: DonorD_ctrl_day2


title: XHLT2-HS85-BLE1

description:
Library name: XHLT2-HS85-BLE1
Baseline PBMC: donor HS85


title: MMTV-PyMT Tumor, Carboplatin + Paclitaxel, CP-5071

description:
Library name: MMTV-PyMT_CP-5071
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-5071

value: Carboplatin + Paclitaxel


title: BJ-hTert cells, KRASG12V expression, 0h induction, Rep 3

description: Library name: K0C

value: Human fibroblast cells


title: XHLT2-HS84-BLE1

description:
Library name: XHLT2-HS84-BLE1
Baseline PBMC: donor HS84


title: BJ-hTert cells, KRASG12V expression, 0h induction, Rep 2

description: Library name: K0B

value: 0h inducion


title: MMTV-PyMT Tumor, Carboplatin + Paclitaxel, CP-5070

description:
Library name: MMTV-PyMT_CP-5070
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-5070

value: mammary tumor


title: DonorD_ctrl_day7

description: Library name: DonorD_ctrl_day7

value: Day 7


title: RNA-Seq, BJ-hTert cells, HRASG12V expression, 0h induction, Rep 1

description: Library name: H0A

value: 0h induction


title: XHLT2-HS83-BLE1

description:
Library name: XHLT2-HS83-BLE1
Baseline PBMC: donor HS83


title: XHLT2-HS82-BLE1

description:
Library name: XHLT2-HS82-BLE1
Baseline PBMC: donor HS82


title: p53RB-426 Tumor, anti-PD1 + anti-CTLA4, CP-5073

description:
Library name: p53RB-426_CP-5073
Column name in raw_counts_All_Samples.txt: p53RB-426_CP-5073


title: DonorD_ctrl_day0

description: Library name: DonorD_ctrl_day0


title: C3-TAG Tumor, Carboplatin + Paclitaxel, CP-5050

description:
Library name: C3-TAG_CP-5050
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-5050


title: DonorC_irr3pt5_day7

description: Library name: DonorC_irr3pt5_day7


title: BJ-hTert cells, HRASG12V expression, 48h induction, Rep 3

description: Library name: H48C

value: 48h induction


title: K14-TRT Tumor, Untreated, CP-4973

description:
Library name: K14-TRT_CP-4973
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4973

value: Untreated


title: XHLT2-HS81-BLE1

description:
Library name: XHLT2-HS81-BLE1
Baseline PBMC: donor HS81


title: BJ-hTert cells, KRASG12V expression, 0h induction, Rep 1

description: Library name: K0A


title: DonorC_irr3pt5_day5

description: Library name: DonorC_irr3pt5_day5

value: Abdominal skin


title: BJ-hTert cells, HRASG12V expression, 48h induction, Rep 2

description: Library name: H48B


title: DonorC_irr3pt5_day2

description: Library name: DonorC_irr3pt5_day2

value: Female

value: Day 2


title: DonorD_ctrl_day1

description: Library name: DonorD_ctrl_day1

value: Day 1


title: DonorC_irr3pt5_day1

description: Library name: DonorC_irr3pt5_day1


title: XHLT2-HS79-BLE1

description:
Library name: XHLT2-HS79-BLE1
Baseline PBMC: donor HS79

value: PBMC


title: K14-TRT Tumor, Untreated, CP-4911

description:
Library name: K14-TRT_CP-4911
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4911


title: BJ-hTert cells, HRASG12V expression, 48h induction, Rep 1

description: Library name: H48A


title: XHLT2-HS7-BLE1

description:
Library name: XHLT2-HS7-BLE1
Baseline PBMC: donor HS7


title: DonorC_irr3pt5_day0

description: Library name: DonorC_irr3pt5_day0

value: Day 0


title: K14-TRT Tumor, Untreated, CP-4910

description:
Library name: K14-TRT_CP-4910
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4910


title: BJ-hTert cells, HRASG12V expression, 0h induction, Rep 3

description: Library name: H0C


title: XHLT2-HS78-BLE1

description:
Library name: XHLT2-HS78-BLE1
Baseline PBMC: donor HS78


title: XHLT2-HS87-BLE1

description:
Library name: XHLT2-HS87-BLE1
Baseline PBMC: donor HS87


title: C3-TAG Tumor, anti-PD1 + anti-CTLA4, CP-4740

description:
Library name: C3-TAG_CP-4740
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4740

value: anti-PD1 + anti-CTLA4


title: DonorC_ctrl_day2

description: Library name: DonorC_ctrl_day2


title: DonorC_ctrl_day5

description: Library name: DonorC_ctrl_day5

value: Day 5


title: XHLT2-HS77-BLE1

description:
Library name: XHLT2-HS77-BLE1
Baseline PBMC: donor HS77


title: BJ-hTert cells, HRASG12V expression, 0h induction, Rep 2

description: Library name: H0B

value: Foreskin

value: BJ-hTert


title: K14-TRT Tumor, Untreated, CP-4912

description:
Library name: K14-TRT_CP-4912
Column name in raw_counts_All_Samples.txt: K14-TRT_CP-4912


title: C3-TAG Tumor, Untreated, CP-4738

description:
Library name: C3-TAG_CP-4738
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4738


title: BJ-hTert cells, HRASG12V expression, 0h induction, Rep 1

description: Library name: H0A

value: Human fibroblast cells


title: XHLT2-HS76-BLE1

description:
Library name: XHLT2-HS76-BLE1
Baseline PBMC: donor HS76


title: WT15, Differentiation Week 7, repeat 3

first: Thomas

last: De Raedt

state: PA

address: 3501 Civic Center boulevard CTRB 4028

institute: CHOP

description: Library name: WT15.W12.3

data_processing:
Performed by genewiz, QC follwed by trimming of ends, mapping to hg38 genome
Assembly: hg38
Supplementary files format and content: Gene counts quantified with TPM normalization

extract_protocol:
Trizol followed by RNAeasy column cleanup
Libraries prepared and sequenced by GeneWiz: mRNA enrichment, mRNA fragmentation, Random priming followed by first and second strand cDNA synthesis, pair end phosphorylation and dA-tailing, adaptor ligation PCR enrichment and sequencing

value: migratory interneuron precursors

value: MIP differentiation


title: MMTV-PyMT Tumor, anti-PD1 + anti-CTLA4, CP-4735

description:
Library name: MMTV-PyMT_CP-4735
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4735

value: mammary tumor

value: MMTV-PyMT


title: XHLT2-HS75-BLE1

description:
Library name: XHLT2-HS75-BLE1
Baseline PBMC: donor HS75


title: DonorB_irr3pt5_day5

description: Library name: DonorB_irr3pt5_day5


title: DonorB_irr3pt5_day7

description: Library name: DonorB_irr3pt5_day7

value: Day 7


title: MMTV-PyMT Tumor, anti-PD1 + anti-CTLA4, CP-4734

description:
Library name: MMTV-PyMT_CP-4734
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4734


title: DonorC_ctrl_day0

description: Library name: DonorC_ctrl_day0


title: C3-TAG Tumor, Untreated, CP-4739

description:
Library name: C3-TAG_CP-4739
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4739

value: Untreated


title: DonorC_ctrl_day1

description: Library name: DonorC_ctrl_day1

value: Abdominal skin


title: XHLT2-HS80-BLE1

description:
Library name: XHLT2-HS80-BLE1
Baseline PBMC: donor HS80


title: NKX, Differentiation Week 7, repeat 2

description: Library name: NKX.W7.2


title: WT15, Differentiation Week 7, repeat 1

description: Library name: WT15.W12.1


title: XHLT2-HS74-BLE1

description:
Library name: XHLT2-HS74-BLE1
Baseline PBMC: donor HS74


title: WT15, Differentiation Week 7, repeat 2

description: Library name: WT15.W12.2


title: NKX, Differentiation Week 7, repeat 3

description: Library name: NKX.W7.3


title: XHLT2-HS73-BLE1

description:
Library name: XHLT2-HS73-BLE1
Baseline PBMC: donor HS73


title: MMTV-PyMT Tumor, Untreated, CP-4729

description:
Library name: MMTV-PyMT_CP-4729
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4729


title: MMTV-PyMT Tumor, anti-PD1 + anti-CTLA4, CP-4733

description:
Library name: MMTV-PyMT_CP-4733
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4733


title: XHLT2-HS72-BLE1

description:
Library name: XHLT2-HS72-BLE1
Baseline PBMC: donor HS72


title: MMTV-PyMT Tumor, Untreated, CP-4728

description:
Library name: MMTV-PyMT_CP-4728
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4728


title: DonorB_irr3pt5_day1

description: Library name: DonorB_irr3pt5_day1

value: Female


title: DonorB_irr3pt5_day2

description: Library name: DonorB_irr3pt5_day2

value: Day 2


title: XHLT2-HS70-BLE1

description:
Library name: XHLT2-HS70-BLE1
Baseline PBMC: donor HS70


title: NKX, Differentiation Week 7, repeat 1

description: Library name: NKX.W7.1


title: MMTV-PyMT Tumor, Untreated, CP-4727

description:
Library name: MMTV-PyMT_CP-4727
Column name in raw_counts_All_Samples.txt: MMTV-PyMT_CP-4727


title: LHX6, Differentiation Week 8, repeat 3

description: Library name: LHX6.W8.3


title: MMTV-Neu Tumor, anti-PD1 + anti-CTLA4, CP-4721

description:
Library name: MMTV-Neu_CP-4721
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4721

value: MMTV-Neu


title: DonorB_irr3pt5_day0

description: Library name: DonorB_irr3pt5_day0


title: XHLT2-HS6-BLE1

description:
Library name: XHLT2-HS6-BLE1
Baseline PBMC: donor HS6

value: PBMC


title: LHX6, Differentiation Week 8, repeat 1

description: Library name: LHX6.W8.1


title: MMTV-Neu Tumor, anti-PD1 + anti-CTLA4, CP-4719

description:
Library name: MMTV-Neu_CP-4719
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4719


title: DonorB_ctrl_day7

description: Library name: DonorB_ctrl_day7


title: LHX6, Differentiation Week 7, repeat 2

description: Library name: LHX6.W7.2


title: DonorB_ctrl_day2

description: Library name: DonorB_ctrl_day2


title: MMTV-Neu Tumor, Untreated, CP-4717

description:
Library name: MMTV-Neu_CP-4717
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4717


title: MMTV-Neu Tumor, anti-PD1 + anti-CTLA4, CP-4720

description:
Library name: MMTV-Neu_CP-4720
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4720


title: XHLT2-HS71-BLE1

description:
Library name: XHLT2-HS71-BLE1
Baseline PBMC: donor HS71


title: XHLT2-HS67-BLE1

description:
Library name: XHLT2-HS67-BLE1
Baseline PBMC: donor HS67


title: DonorA_irr3pt5_day5

description: Library name: DonorA_irr3pt5_day5


title: MMTV-Neu Tumor, Untreated, CP-4718

description:
Library name: MMTV-Neu_CP-4718
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4718


title: DonorB_ctrl_day1

description: Library name: DonorB_ctrl_day1

value: Day 1


title: LHX6, Differentiation Week 6, repeat 3

description: Library name: LHX6.W6.3


title: XHLT2-HS68-BLE1

description:
Library name: XHLT2-HS68-BLE1
Baseline PBMC: donor HS68


title: XHLT2-HS65-BLE1

description:
Library name: XHLT2-HS65-BLE1
Baseline PBMC: donor HS65


title: LHX6, Differentiation Week 7, repeat 1

description: Library name: LHX6.W7.1


title: LHX6, Differentiation Week 8, repeat 2

description: Library name: LHX6.W8.2


title: XHLT2-HS64-BLE1

description:
Library name: XHLT2-HS64-BLE1
Baseline PBMC: donor HS64


title: LHX6, Differentiation Week 7, repeat 3

description: Library name: LHX6.W7.3


title: XHLT2-HS69-BLE1

description:
Library name: XHLT2-HS69-BLE1
Baseline PBMC: donor HS69


title: XHLT2-HS66-BLE1

description:
Library name: XHLT2-HS66-BLE1
Baseline PBMC: donor HS66


title: C3-TAG Tumor, anti-PD1 + anti-CTLA4, CP-4714

description:
Library name: C3-TAG_CP-4714
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4714

value: anti-PD1 + anti-CTLA4


title: XHLT2-HS63-BLE1

description:
Library name: XHLT2-HS63-BLE1
Baseline PBMC: donor HS63


title: C3-TAG Tumor, anti-PD1 + anti-CTLA4, CP-4715

description:
Library name: C3-TAG_CP-4715
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4715


title: DonorB_ctrl_day0

description: Library name: DonorB_ctrl_day0

value: Day 0


title: LHX6, Differentiation Week 6, repeat 2

description: Library name: LHX6.W6.2


title: MMTV-Neu Tumor, Untreated, CP-4716

description:
Library name: MMTV-Neu_CP-4716
Column name in raw_counts_All_Samples.txt: MMTV-Neu_CP-4716


title: DonorA_irr3pt5_day7

description: Library name: DonorA_irr3pt5_day7


title: LHX6, Differentiation Week 6, repeat 1

description: Library name: LHX6.W6.1


title: DonorB_ctrl_day5

description: Library name: DonorB_ctrl_day5

value: Day 5


title: DonorA_irr3pt5_day2

description: Library name: DonorA_irr3pt5_day2


title: C3-TAG Tumor, Untreated, CP-4695

description:
Library name: C3-TAG_CP-4695
Column name in raw_counts_All_Samples.txt: C3-TAG_CP-4695


title: LHX6, Differentiation Week 4, repeat 3

description: Library name: LHX6.W4.3


title: XHLT2-HS62-BLE1

description:
Library name: XHLT2-HS62-BLE1
Baseline PBMC: donor HS62


title: p53RB-626 Tumor, anti-PD1 + anti-CTLA4, CP-4693

description:
Library name: p53RB-626_CP-4693
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4693


title: DonorA_irr3pt5_day0

description: Library name: DonorA_irr3pt5_day0


title: LHX6, Differentiation Week 4, repeat 2

description: Library name: LHX6.W4.2


title: DonorA_irr3pt5_day1

description: Library name: DonorA_irr3pt5_day1


title: XHLT2-HS61-BLE1

description:
Library name: XHLT2-HS61-BLE1
Baseline PBMC: donor HS61


title: p53RB-626 Tumor, anti-PD1 + anti-CTLA4, CP-4692

description:
Library name: p53RB-626_CP-4692
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4692


title: p53RB-626 Tumor, anti-PD1 + anti-CTLA4, CP-4691

description:
Library name: p53RB-626_CP-4691
Column name in raw_counts_All_Samples.txt: p53RB-626_CP-4691


title: DonorA_ctrl_day2

description: Library name: DonorA_ctrl_day2


title: LHX6, Differentiation Week 4, repeat 1

description: Library name: LHX6.W4.1


title: LHX6, Stem Cells, repeat 1

description: Library name: LHX6.ES.1

value: Embryonic stem cells

value: undifferentiated


title: 2208 Tumor, Carboplatin + Paclitaxel, CP-4687

description:
Library name: 2208_CP-4687
Column name in raw_counts_All_Samples.txt: 2208_CP-4687

value: Carboplatin + Paclitaxel


title: DonorA_ctrl_day1

description: Library name: DonorA_ctrl_day1


title: LHX6, Stem Cells, repeat 3

description: Library name: LHX6.ES.3


title: DonorA_ctrl_day7

description: Library name: DonorA_ctrl_day7


title: XHLT2-HS60-BLE1

description:
Library name: XHLT2-HS60-BLE1
Baseline PBMC: donor HS60


title: 2208 Tumor, Carboplatin + Paclitaxel, CP-4685

description:
Library name: 2208_CP-4685
Column name in raw_counts_All_Samples.txt: 2208_CP-4685


title: XHLT2-HS58-BLE1

description:
Library name: XHLT2-HS58-BLE1
Baseline PBMC: donor HS58


title: XHLT2-HS57-BLE1

description:
Library name: XHLT2-HS57-BLE1
Baseline PBMC: donor HS57


title: pool-7, well-4, ADT

description:
Library name: XHLT2-POOL-DB7-SCG4_ADT
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2 (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Gencode v32-primary assembly) and the raw fastqs of surface protein expression to a TotalSeq-C antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of individual participants from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3) was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-800 and >6,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <400-2,000 and >40,000), mitochondrial content (>15%), and ribosomal content (<8-15% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
For processing of follow-up timepoint, the baseline samples were reanalyzed along with the the follow-up timepoint (separated by ~19 months). After generating single-cell count data from sequencing reads and performing quality control, the identification of cell subsets in the follow-up data was performed using Azimuth. The Seurat object from original baseline data was converted to Azimuth reference, and the follow-up dataset was mapped onto it using Azimuth, which provided predicted cell subset labels for single cells.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format for the high-quality single-cells
Supplementary files format and content: cell_metadata_baseline.rds and cell_metadata_followup.rds are R object files containing metadata for single-cells in baseline and follow-up datasets, respectively. The metadata include sample id (donor id + timepoint id), library id, cell annotations, and timepoint.
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Blood was collected in EDTA tubes within a 90 min window for all participants of the study. Peripheral blood mononuclear cells (PBMC) were obtained by density gradient centrifugation of whole blood at 800g for 30 min at room temperature without brake, using Ficoll-Paque (Cytiva). Isolated cells were cryopreserved in a solution containing fetal Bovine Serum and 10% DMSO (Sigma). Thawed PBMC suspensions from 14-16 individuals were pooled together with equivalent numbers to a total of 1 million live cells. Pools were resuspended in Cell Staining Buffer (Biolegend) and incubated with Fc Receptor Blocking Solution (Biolegend) at 20mg/mL for 10 minutes on ice. Cells were then stained with a cocktail of 140 TotalSeq-C oligo-tagged antibodies (Biolegend) for 30 minutes at 4°C. Stained cells were washed in PBS containing 1% BSA, filtered through a 70uM filter, and re-suspended in a final solution of PBS containing 0.04% BSA.
Stained cells (n=60,000) were loaded on the Chromium Controller (10X Genomics) for GEM generation. The cDNA libraries were generated using the Chromium Next GEM Single Cell 5’ v1.1 Library Kit for gene expression (GEX) and the Chromium Single Cell 5’ Feature Barcode Library kit for antibody derived tag (ADT) according to manufacturer’s instructions (10X Genomics). Each batch of 14-16 samples was sampled four times to prepare four independent cDNA libraries per batch to obtain a sufficient number of cells per sample. The libraries were subsequently sequenced on a NovaSeq 6000 S4 platform (Illumina).

value: ADT


title: LHX6, Stem Cells, repeat 2

description: Library name: LHX6.ES.2


title: XHLT2-HS59-BLE1

description:
Library name: XHLT2-HS59-BLE1
Baseline PBMC: donor HS59


title: DonorA_ctrl_day0

description: Library name: DonorA_ctrl_day0


title: DonorA_ctrl_day5

description: Library name: DonorA_ctrl_day5


title: XHLT2-HS56-BLE1

description:
Library name: XHLT2-HS56-BLE1
Baseline PBMC: donor HS56


title: 2208 Tumor, Carboplatin + Paclitaxel, CP-4686

description:
Library name: 2208_CP-4686
Column name in raw_counts_All_Samples.txt: 2208_CP-4686

value: mammary tumor


title: 2208 Tumor, anti-PD1 + anti-CTLA4, CP-4683

description:
Library name: 2208_CP-4683
Column name in raw_counts_All_Samples.txt: 2208_CP-4683


title: XHLT2-HS55-BLE1

description:
Library name: XHLT2-HS55-BLE1
Baseline PBMC: donor HS55


title: 2208 Tumor, anti-PD1 + anti-CTLA4, CP-4684

description:
Library name: 2208_CP-4684
Column name in raw_counts_All_Samples.txt: 2208_CP-4684


title: pool-7, well-4, GEX

description:
Library name: XHLT2-POOL-DB7-SCG4_GEX
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1

value: mRNA


title: pool-7, well-3, ADT

description:
Library name: XHLT2-POOL-DB7-SCG3_ADT
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1


title: XHLT2-HS54-BLE1

description:
Library name: XHLT2-HS54-BLE1
Baseline PBMC: donor HS54


title: MDA5_HCT116_TGFP_MT_NT_rep1

city: Oxford

first: Yucheng

state: Oxfordshire

address: Roosevelt Drive, Headington

institute: University of Oxford

description: Library name: MDA5_HCT116_TGFP_MT_NT_rep1

data_processing:
All sequencing FASTQ files were trimmed using the Trim_Galore program. The trimmed FASTQ files were then aligned to the human genome (hg38) using the STAR aligner program (v2.7.9a). MDA5-protected regions were identified as sequencing signal peaks from RNaseA-treated samples against total cytoplasmic RNA samples. For each sample, total BAM files were split into forward strand aligned and reverse strand aligned bam files, and then peaks were called from strand-specific BAM files using MACS2 (v2.2.6) with the following parameters: -q 0.01 –keep-dup all –nomodel. Peaks identified from the forward and reverse strands were combined for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Colorectal cancer

growth_protocol: HT29 and HCT116 human colorectal cancer cell lines were cultured in McCoy’s 5A medium supplemented with penicillin-streptomycin (1%), and Fetal-Bovine-serum (10%).

extract_protocol:
We used the RNase A protection assay followed by RNA sequencing as previously described [9]. In brief, the RNA from cytosolic fraction was isolated using a QIAGEN RNeasy mini kit from colorectal cancer cell lines. Isolated cytosolic RNA was pre-incubated with MDA5-Δ2CARD protein (150 nM)room temperature for 10 min in 20 mM HEPES pH 7.5, 50 mM NaCl, 2 mM MgCl2 and 2 mM DTT, followed by addition of RNase A (final concentration 2 n/ul) and incubation for another 5 min at room temperature. The RNase A digestion was inactivated by adding TRIzol reagent and the RNA was purified with a Directzol RNA miniprep kit, using the manufacturer’s protocol. To remove small fragments resulting from RNase A digestion (less than 100 bp), the extracted RNA was further cleaned up using the QIAGEN RNeasy mini kit. The final RNA was used for the cDNA library preparation.
One hundred nanograms of RNA was used by WIMM single cell Genomics for the cDNA library construction using KAPA RNA Hyper-Prep with RiboErase Library Preparation Kit (Roche) according to the manufacturer's instruction, with the following modifications. For the fragmentation step, total CytoRNA was heated at 94 °C for 8 min. MDA5-protected RNA was heated at 65 °C for 1 min. 1.5µM KAPA Unique Dual-Indexed Adapters were used for adapter ligation. Libraries were incubated in C1000 Touch Thermal Cycler (Bio-rad) for 45s at 98°C and 11 PCR cycles were used  (for total CytoRNA) and 16 PCR cycles were used (for MDA5-protected samples), for 15s at 98°C, 30s at 60°C, and 30s at 72°C. The libraries were then incubated at 72°C for 1min for final extension. Following a 1x Kapa Pure Bead clean-up, post-PCR enriched libraries were eluted in 20uL of 10mM Tris-HCl (pH8.0) and validated using Agilent D5000 ScreenTape and Reagents on the 2200 TapeStation System  The cDNA libraries for total CytoRNA and MDA5-protected were pooled and 6 pM of cDNA libraries were sequenced using paired-ended 150-bp reads on  NovaSeq X Plus by Novogene.

value: Colorectal cancer

value: human colorectal cancer cell line

value: wild type

value: Mock treated


title: XHLT2-HS53-BLE1

description:
Library name: XHLT2-HS53-BLE1
Baseline PBMC: donor HS53


title: 2208 Tumor, anti-PD1 + anti-CTLA4, CP-4682

description:
Library name: 2208_CP-4682
Column name in raw_counts_All_Samples.txt: 2208_CP-4682


title: MDA5_HCT116_TGFP_MT_NT_rep2

description: Library name: MDA5_HCT116_TGFP_MT_NT_rep2


title: pool-7, well-3, GEX

description:
Library name: XHLT2-POOL-DB7-SCG3_GEX
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1


title: MDA5_HCT116_TGFP_MT_RNaseA_rep1

description: Library name: MDA5_HCT116_TGFP_MT_RNaseA_rep1


title: 2153 Tumor, Carboplatin + Paclitaxel, CP-4678

description:
Library name: 2153_CP-4678
Column name in raw_counts_All_Samples.txt: 2153_CP-4678


title: MDA5_HCT116_TGFP_MT_RNaseA_rep2

description: Library name: MDA5_HCT116_TGFP_MT_RNaseA_rep2


title: XHLT2-HS52-BLE1

description:
Library name: XHLT2-HS52-BLE1
Baseline PBMC: donor HS52


title: pool-7, well-2, ADT

description:
Library name: XHLT2-POOL-DB7-SCG2_ADT
Pool of XHLT2-HS102-BLE1, XHLT2-HS108-BLE1, XHLT2-HS20-BLE1, XHLT2-HS35-BLE1, XHLT2-HS41-BLE1, XHLT2-HS45-BLE1, XHLT2-HS53-BLE1, XHLT2-HS58-BLE1, XHLT2-HS61-BLE1, XHLT2-HS81-BLE1, XHLT2-HS86-BLE1, XHLT2-HS90-BLE1, XHLT2-HS92-BLE1, XHLT2-HS96-BLE1


title: 2153 Tumor, Carboplatin + Paclitaxel, CP-4676

description:
Library name: 2153_CP-4676
Column name in raw_counts_All_Samples.txt: 2153_CP-4676