title: PTEN-deletion 6W induced prostate

description: FACS isolated 10k YFP+ epithelial cells pooled from at least three K5CreER/Ptenfl/fl/Rosa-YFP mice 6 weeks following TAM administration

data_processing:
Sequencing reads were aligned and annotated with the mm10-2020-A reference dataset as provided by 10X Genomics and demultiplexed using CellRanger (v.6.0.0) with default parameters.
Quality control and downstream analysis were performed using the Seurat R package (v.4.2.0).
For each sample, cells were filtered using the following criteria: showed expression of more than 2500 and less than 7500 unique genes and had less than 15% UMI counts belonging to mitochondrial sequences.
Read counts were normalized using the NormalizeData() function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’.
A PCA for each sample was calculated using the scaled expression data of the 2000 most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes().
UMAP calculation and graph-based clustering were performed for each sample using Seurat (default parameters) with the first 30 respective PCA components as input.
The clusters which expressed high levels of stromal markers (Vim, Zeb2, Fscn), fibroblast (Pdgfra, Fn1, Col1a1, Fbn1) and macrophage markers (Ptprc, Cd86, Cd68, Ccr1) were excluded and dimensionality reductions were recalculated after the exclusion of these cells.
The final clustering resolution for each sample was chosen based on the reflected biological heterogeneity that emerged from the different cell types.
Assembly: mm10-2020-A
Supplementary files format and content: tsv.gz / cell barcode and list of features
Supplementary files format and content: mtx.gz / count matrix

extract_protocol:
Single cells were dissociated and loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics).
RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics).


title: Patient 20847 (Lymphoepithelioma) Paired Normal2

status: Public on Apr 24 2025

type: SRA

city: San Francisco

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave, HSE

department: Department of Medicine

country: USA

institute: UCSF

description: Library name: HY_20847_N2_S16

library_source: transcriptomic single cell

data_processing:
Demultiplexed pair-end FASTQ files were aligned to hg19 whole genome using dropseq_workflow pipeline on Terra
Assembly: hg19
Supplementary files format and content: txt format matrix table with raw gene counts for every gene and every cell barcode

molecule: total RNA

organism: Homo sapiens

source_name: Bladder

extract_protocol:
Tumor and adjacent normal liver tissues were dissociated by mincing tissue in 1-2mm squares, followed by incubation in Liver Perfusion Medium (ThermoFisher Scientific) for 15 min at 37°C in a rotating oven. After being washed in PBS (ThermoFisher Scientific), tissues were incubated with Liver Digest Medium (ThermoFisher Scientific) supplemented with HEPES and collagenase type IV (Worthington Biochemical, Lakewood, NJ) (600 to 800 U/ml) for 30 min at 37°C with rotation. Further dissociation was achieved by pipetting 10 times through a 25 mL serological pipette. Single cells were then separated from clumps using a 70 µm strainer (Fisher Scientific, Hampton, NH). After lysis of red blood cells with ACK RBC Lysis Buffer (Fisher Scientific), single cells were counted using a LUNA™ Automated Cell Counter (Logos biosystems, South Korea) and processed for scRNA-seq analysis. Patient derived spheroids embedded in Matrigel were washed with PBS, then digested in TrypLE 1X (ThermoFisher Scientific) for 30 to 45 min at 37°C with rotation to obtain a single cell suspension. Cells were washed, then, filtered through a 70-µm strainer, counted using a LUNA™ Automated Cell Counter, and processed for scRNA-seq analysis.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared. These dilutions were pooled for sequencing on a NovaSeq S4 flow cell.

tag: tissue

value: Bladder


title: Patient 20847 (Lymphoepithelioma) Tumor1 Replica1

description: Library name: HY_20847_T1-1_S19


title: Prdm16NSC_Input_1

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

library_source: genomic

data_processing:
Three replicates of ChIP-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The ChIP-seq coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
The CUT&TAG samples of Prdm16_E and Prdm16 mutant NSCs in four replicates, and of Prdm16 from CH and ChP area at stage 12.5 embryos in three replicates, were mapped to mm10 genome assembly using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700). The CUT&TAG coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: Primary NSCs

growth_protocol: NSCs proliferation medium for primary NSCs with or without BMP4

extract_protocol:
stardard for ChIPseq or Cut&Tag
NEB ultra II DNA libary kit for ChIP-seq libararies, standard protocol for cut&tag

tag: cell type

value: Primary NSCs

tag: genotype

tag: antibody

value: Normalization control


title: C57BL6 mice, rAAV8-Scramble, Bio2

city: Storrs

first: Beshoy

last: Armanios

state: CT

address: 69 N Eagleville Road

institute: University of Connecticut

description:
Library name: 1S
column name: 1HS

library_source: transcriptomic

data_processing:
00_fastq: raw data raw data in fastq format: sample_R1_001.fastq.gz sample_R2_001.fastq.gz bam: aligned data alignment file in bam format: sample.bam hit-counts: hit count for all the genes unique hit counts for each sample: sample.counts.txt DEG: differential gene expression analysis results raw gene hit counts of all samples used in the comparison: counts/raw_counts.csv normalized gene hit counts of all samples used in the comparison: counts/normalized_counts.csv rlog transformed gene hit counts of all samples used in the comparison: counts/rlog_trasnformed_counts.csv log2 fold change and (adjusted) p-value table: Differential_expression_analysis_table.csv log2 fold change and (adjusted) p-value table for significantly DE genes: Significant-DEGs.csv GO: GO enrichment analysis results GO enrichment analsysis table: comparison_GO_analysis.csv differential_splice_variant_expression: differential splicing anlysis results Results generated by DEXSeq: DEXSeqReport in zipped format
Assembly: GRCm39
Supplementary files format and content: tab-delimited tex files include raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each samples

source_name: liver

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer's protocol.
The first step involves ribosomal RNA (rRNA) depletion, where rRNA is removed to enrich for non-rRNA molecules such as mRNA, ensuring that the library focuses on the RNA of interest. Next, the RNA is subjected to fragmentation and random priming, breaking the RNA into smaller pieces to facilitate even sequencing coverage and initiating complementary DNA (cDNA) synthesis with random primers. Subsequently, the fragmented RNA is converted into double-stranded cDNA through first and second-strand cDNA synthesis. To prepare the cDNA for adapter ligation, the ends of the cDNA fragments undergo end repair, phosphorylation, and dA-tailing. This step ensures that the cDNA fragments have uniform and compatible ends for ligation with sequencing adapters. Finally, adapter ligation is performed, attaching specific adapters to the cDNA fragments for their identification and amplification. The library is then enriched through a PCR step to increase the quantity of adapter-ligated fragments. The final library is ready for high-throughput sequencing, enabling comprehensive RNA analysis.

value: liver


title: C57BL6 mice, rAAV8-Scramble. Bio1

description:
Library name: 0S
column name: 0HS


title: PTEN-deletion 10M induced prostate

city: Bruxelles

first: Yura

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: FACS isolated 10k YFP+ epithelial cells pooled from at least three K5CreER/Ptenfl/fl/Rosa-YFP mice 10 months following TAM administration

source_name: mouse prostate

value: mouse prostate


title: Prdm16NSC_pSMAD_2

value: pSMAD1/5/8 antibody


title: CD1 mouse prostate basal, replicate 2

data_processing:
Quality of each raw dataset was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by Trimmomatic.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v. 2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalized gene expression

molecule: polyA RNA

source_name: mouse prostate basal

extract_protocol:
RNA extraction from FACS-isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations.
Indexed complementary DNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: mouse prostate basal

tag: treatment

value: Etoh treated


title: YTK376YP-1-Input

status: Public on Apr 23 2025

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
FastQC-0.11.5 checked the quality of raw sequences. Cutadapt-1.8 was used to trim adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the combined reference (R64-1-1 and ASM294v2).
Picard-tools-2.18.1 removed duplicates with parameters "VALIDATION_STRINGENCY=SILENT AS=TRUE".
Assembly: R64-1-1/sacCer3
Supplementary files format and content: bigWig files were generated using deepTools-3.1.3 bamCoverage.
Supplementary files format and content: narrowPeak files were generated using macs2-2.1.1 with corresponding controls and a parameter "-q 0.01".

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD media at 30℃ until O.D600nm was 0.5~0.6 and half of the cells were harvested.

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.

treatment_protocol: Half of the cells were subsequently shifted from YPD to 0.15x YP media for 4 hours at 30℃.

tag: strain

tag: chip antibody

value: Wild type (Hda1-myc)

value: 0.15x YP (Starvation, -N)


title: YTK376YP-2-IP

value: Purified anti-c-Myc (BioLegend, 626802)


title: YTK376YP-1-IP


title: YTK376YP-2-Input


title: YTK524YP-2-Input

value: Wild type (Rpc40-myc)


title: YTK524YP-2-Rpb3

value: Purified anti-RNA Polymerase II RPB3 (BioLegend, 665004)


title: YTK524YP-1-Rpb3


title: YTK524-2-Input

value: YPD (Nutrient-rich, +N)


title: YTK524YP-1-Input


title: YTK524-2-Rpc40-myc


title: YTK524YP-1-Rpc40-myc


title: YTK524-1-Rpc40-myc


title: CD1 mouse prostate

description: FACS isolated 10k epithelial cells pooled from at least three CD1 mice


title: YTK524-1-Rpb3


title: YTK524-1-Input


title: YTK524-2-Rpb3


title: YTK109YP-2-H4ac

value: Anti-acetyl-Histone H4 (Millipore, 06-598)


title: YTK109YP-1-H4ac


title: YTK109YP-1-H3ac

value: Anti-acetyl-Histone H3 (Millipore, 06-599)


title: YTK109YP-2-H3ac


title: YTK109-2-H3

value: Anti-Histone H3 (Abcam, ab1791)


title: YTK109-1-H3


title: YTK109-2-H4ac


title: YTK109-2-H3ac


title: YTK109-1-H4ac


title: YTK109-1-H3ac


title: YF336YP-1-H3

value: Wild type


title: YF336YP-1-H4ac


title: YF336YP-2-H3ac


title: YTK524YP-2-Rpc40-myc


title: YF336YP-2-H4ac


title: YTK109YP-1-H3


title: YTK109YP-2-H3


title: YF336YP-1-H3ac


title: YF336YP-2-H3


title: YF336-2-H4ac


title: YF336-1-H3ac


title: YF336-1-H4ac


title: YF336-2-H3ac


title: Brain organoids, Agmatine 100 µM, Day 3_3

city: CLEVELAND

first: Feixiong

last: Cheng

state: OH

address: 9620 Carnegie Ave.

department: Genome center

institute: The Cleveland Clinic Lerner Research Institute

description: Library name: 18_P1

data_processing:
Raw RNA-seq paired-end data was quality checked and filtered implementing standard FastQC (v0.11.9) and fastp (v0.23.2) multithreaded tools applying default parameters with deduplication, quality filtering (Phred score ≥ 20), allowed unqualified bases (=30%), N-base (>5) removal.
Quality filtered reads were aligned and summarized with ignoring duplicated reads utilizing align and featureCounts function from Rsubread (v2.16.1), where human genome reference GRCh38 and inbuilt NCBI refseq annotation.
Further, org.Hs.eg.db (v3.16.0) package is used for assigning gene symbols to ENTREZIDs from summarized count table.
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts for each sample.

source_name: Brain

growth_protocol: Cerebral organoids were generated according to manufacturer’s instructions of the commercial STEMdiff™ Cerebral Organoid Kit (STEMCELL Technologies) with minor modification. We differentiated P1 iPSCs into cerebral organoids within a close time frame and used cerebral organoids with normal size range (typically 1.5–3mm of diameter) for our experiments. Briefly, on day 0, iPSCs were subcultured using ReLeSR™ (STEMCELL Technologies) to ensure collection of undifferentiated  iPSC colonies. After cell counting, 9,000 cells were plated into each well of a U-bottom ultra-low-attachment 96-well plate in EB formation media (medium A) supplemented with 10 μM Y27632. The wells were topped with extra 100 μl EB formation medium on day 2 and day 4, respectively. On day 5, EBs were moved to 24-well low attachment plates containing neural induction medium (medium B) for next 2 days. EBs were further embedded into 20 μl of matrigel and cultured in neural expansion medium (medium C + D) for 3 days in 6-well low attachment plates for organoid formation. In the last stage, the organoids were shifted to  maturation medium (medium E) and moved to an orbital shaker for further culture. Organoid were cultured at least till day 40 to ensure 50 - 60% success rate for obtaining organoids with dense cores as per manufacturer.

extract_protocol:
RNA was extracted using RNeasy mini kit, in combination with RNAase-free DNAase to remove the potential genomic DNA contamination (Qiagen).
Libraries were constructed using the lllumina Stranded kits following the recommended protocol.

treatment_protocol: At day 40, cerebral organoids were treated with Agmatine for 1 and 3 days and collected for RNA-seq.

value: Brain

tag: cell line

value: iPSC

value: Brain organoids derived from AD patient iPSC (HVRDi001-A-1)

value: APPV717l mutation

value: Agmatine

tag: batch


title: Brain organoids, Agmatine 100 µM, Day 3_2

description: Library name: 15_P1


title: YF336-2-H3


title: Brain organoids, DMSO, Day 3_3

description: Library name: 16_P1

value: DMSO


title: Brain organoids, Agmatine 100 µM, Day 3_1

description: Library name: 12_P1


title: Brain organoids, DMSO, Day 3_1

description: Library name: 10_P1


title: Brain organoids, DMSO, Day 1_3

description: Library name: 7_P1


title: Brain organoids, Agmatine 100 µM, Day 1_3

description: Library name: 9_P1


title: Brain organoids, Agmatine 100 µM, Day 1_2

description: Library name: 6_P1


title: Brain organoids, Agmatine 100 µM, Day 1_1

description: Library name: 3_P1


title: Brain organoids, DMSO, Day 3_2

description: Library name: 13_P1


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells Arginine-Glycine-Aspartic Acid, biol repl3

city: Nanjing

first: Taige

last: Chen

address: 321 Zhongshan Road

country: China

institute: Affiliated Drum Tower Hospital, Medical School of Nanjing University

description: Library name: RGD_Alg_MSCs_3

data_processing:
Raw sequencing data were quality-filtered using fastp (default parameters) to remove adapters, low-quality reads, and undetermined bases. Clean reads were aligned to the Homo sapiens GRCh38 reference genome using HISAT2. Transcripts were assembled and merged across samples using StringTie and gffcompare, respectively. Gene expression levels were quantified as FPKM (fragments per kilobase of transcript per million mapped reads) using StringTie.
Assembly: hg38
Supplementary files format and content: Excel reads count values of genes for each sample

source_name: experiment

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. RNA quantity and purity were assessed with a NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and integrity was confirmed using a Bioanalyzer 2100 (Agilent, CA, USA; RIN > 7.0) and denaturing agarose gel electrophoresis.
Poly(A) mRNA was isolated from 1 μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) with two purification rounds, fragmented at 94°C for 5–7 minutes using the Magnesium RNA Fragmentation Module (NEB, cat. E6150, USA), and reverse-transcribed into cDNA with SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA). Second-strand DNA was synthesized using E. coli DNA polymerase I (NEB, cat. M0209, USA), RNase H (NEB, cat. M0297, USA), and dUTP Solution (Thermo Fisher, cat. R0133, USA). After adding A-bases to the blunt ends, indexed adapters were ligated, and size selection was performed using AMPureXP beads. The U-labeled second-strand DNA was treated with UDG enzyme (NEB, cat. M0280, USA), followed by PCR amplification (initial denaturation at 95°C for 3 min; 8 cycles of 98°C for 15 s, 60°C for 15 s, 72°C for 30 s; final extension at 72°C for 5 min). The resulting cDNA libraries (average insert size: 300 ± 50 bp) were sequenced on an Illumina NovaSeq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) using 2×150 bp paired-end sequencing (PE150).

value: mesenchymal stem/stromal cells


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells Arginine-Glycine-Aspartic Acid, biol repl1

description: Library name: RGD_Alg_MSCs_1


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells, biol repl3

description: Library name: MSCs3


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells Arginine-Glycine-Aspartic Acid, biol repl2

description: Library name: RGD_Alg_MSCs_2


title: Brain organoids, DMSO, Day 1_1

description: Library name: 1_P1


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells, biol repl2

description: Library name: MSCs2


title: Homo sapiens, mesenchymal stem/stromal cells, control, biol repl3

description: Library name: Control3

source_name: Control blank


title: Homo sapiens, mesenchymal stem/stromal cells, Human corneal epithelial cells, biol repl1

description: Library name: MSCs1


title: Homo sapiens, mesenchymal stem/stromal cells, control, biol repl2

description: Library name: Control2


title: Homo sapiens, mesenchymal stem/stromal cells, control, biol repl1

description: Library name: Control1


title: YF336-1-H3


title: Corrected_NPC_KDM5C70, H3K4me3, rep3

city: Dallas

first: Wen

last: Gu

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Library name: Corrected_NPC_KDM5C70_H3K4me3_rep3
H3K4me3 ChIP-seq from Corrected_NPC_KDM5C70, rep3

data_processing:
Reads were quality-checked using FastQC.
Reads were aligned to the hg38 genome using Bowtie2.
Signal tracks were generated with deepTools bamCoverage and normalized to reads per kilobase per million (RPKM).
Assembly: hg38
Supplementary files format and content: Files include normalized coverage BigWigs.

source_name: Patient1 iPSC-derived NPCs

growth_protocol: Cells were cultured in NPC medium on Matrigel-coated plates and maintained under standard feeder-free conditions at 37°C with 5% CO₂. Cells were routinely tested for mycoplasma.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Nuclei were isolated, and chromatin was sheared using a sonicator to 200–500 bp fragments. Chromatin was incubated overnight with antibodies against H3K4me2, H3K4me3, or with no antibody for input controls, and immunoprecipitated using Protein A/G beads.
ChIP and input DNA were processed using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer’s protocol. Library size distribution was confirmed by Bioanalyzer and quantified using Qubit.

treatment_protocol: For inhibitor-treated samples, neural progenitor cells (NPCs) were treated with 25 μM KDM5 inhibitor (C70) or vehicle (DMSO) for 14 days prior to chromatin extraction. Untreated control and unedited NPCs were maintained under the same differentiation conditions without additional compounds.

value: neural progenitor cells

value: NPC

value: L2HGDH WT


title: Corrected_NPC_KDM5C70, H3K4me3, rep1

description:
Library name: Corrected_NPC_KDM5C70_H3K4me3_rep1
H3K4me3 ChIP-seq from Corrected_NPC_KDM5C70, rep1


title: Corrected_NPC_KDM5C70, H3K4me3, rep2

description:
Library name: Corrected_NPC_KDM5C70_H3K4me3_rep2
H3K4me3 ChIP-seq from Corrected_NPC_KDM5C70, rep2


title: Corrected_NPC_KDM5C70, H3K4me2, rep1

description:
Library name: Corrected_NPC_KDM5C70_H3K4me2_rep1
H3K4me2 ChIP-seq from Corrected_NPC_KDM5C70, rep1


title: Corrected_NPC_KDM5C70, Input, rep2

description:
Library name: Corrected_NPC_KDM5C70_Input_rep2
Input ChIP-seq from Corrected_NPC_KDM5C70, rep2


title: Corrected_NPC_KDM5C70, Input, rep3

description:
Library name: Corrected_NPC_KDM5C70_Input_rep3
Input ChIP-seq from Corrected_NPC_KDM5C70, rep3


title: Corrected_NPC_DMSO, H3K4me3, rep3

description:
Library name: Corrected_NPC_DMSO_H3K4me3_rep3
H3K4me3 ChIP-seq from Corrected_NPC_DMSO, rep3


title: Corrected_NPC_KDM5C70, H3K4me2, rep3

description:
Library name: Corrected_NPC_KDM5C70_H3K4me2_rep3
H3K4me2 ChIP-seq from Corrected_NPC_KDM5C70, rep3


title: Corrected_NPC_KDM5C70, H3K4me2, rep2

description:
Library name: Corrected_NPC_KDM5C70_H3K4me2_rep2
H3K4me2 ChIP-seq from Corrected_NPC_KDM5C70, rep2


title: Corrected_NPC_DMSO, H3K4me3, rep2

description:
Library name: Corrected_NPC_DMSO_H3K4me3_rep2
H3K4me3 ChIP-seq from Corrected_NPC_DMSO, rep2


title: Corrected_NPC_DMSO, H3K4me2, rep3

description:
Library name: Corrected_NPC_DMSO_H3K4me2_rep3
H3K4me2 ChIP-seq from Corrected_NPC_DMSO, rep3


title: Corrected_NPC_DMSO, H3K4me2, rep2

description:
Library name: Corrected_NPC_DMSO_H3K4me2_rep2
H3K4me2 ChIP-seq from Corrected_NPC_DMSO, rep2


title: Corrected_NPC_DMSO, Input, rep3

description:
Library name: Corrected_NPC_DMSO_Input_rep3
Input ChIP-seq from Corrected_NPC_DMSO, rep3


title: Corrected_NPC_DMSO, H3K4me3, rep1

description:
Library name: Corrected_NPC_DMSO_H3K4me3_rep1
H3K4me3 ChIP-seq from Corrected_NPC_DMSO, rep1


title: Corrected_NPC_DMSO, Input, rep1

description:
Library name: Corrected_NPC_DMSO_Input_rep1
Input ChIP-seq from Corrected_NPC_DMSO, rep1


title: Corrected_NPC_DMSO, Input, rep2

description:
Library name: Corrected_NPC_DMSO_Input_rep2
Input ChIP-seq from Corrected_NPC_DMSO, rep2


title: Corrected_NPC_DMSO, H3K4me2, rep1

description:
Library name: Corrected_NPC_DMSO_H3K4me2_rep1
H3K4me2 ChIP-seq from Corrected_NPC_DMSO, rep1


title: Unedited_NPC, H3K4me2, rep1

description:
Library name: Unedited_NPC_H3K4me2_rep1
H3K4me2 ChIP-seq from Unedited_NPC, rep1

value: L2HGDH mutant


title: Unedited_NPC, H3K4me3, rep3

description:
Library name: Unedited_NPC_H3K4me3_rep3
H3K4me3 ChIP-seq from Unedited_NPC, rep3


title: Unedited_NPC, H3K4me2, rep2

description:
Library name: Unedited_NPC_H3K4me2_rep2
H3K4me2 ChIP-seq from Unedited_NPC, rep2


title: Unedited_NPC, H3K4me3, rep1

description:
Library name: Unedited_NPC_H3K4me3_rep1
H3K4me3 ChIP-seq from Unedited_NPC, rep1


title: Unedited_NPC, H3K4me2, rep3

description:
Library name: Unedited_NPC_H3K4me2_rep3
H3K4me2 ChIP-seq from Unedited_NPC, rep3


title: Unedited_NPC, Input, rep1

description:
Library name: Unedited_NPC_Input_rep1
Input ChIP-seq from Unedited_NPC, rep1


title: Corrected_NPC, H3K4me3, rep3

description:
Library name: Corrected_NPC_H3K4me3_rep3
H3K4me3 ChIP-seq from Corrected_NPC, rep3


title: Unedited_NPC, Input, rep2

description:
Library name: Unedited_NPC_Input_rep2
Input ChIP-seq from Unedited_NPC, rep2


title: Unedited_NPC, H3K4me3, rep2

description:
Library name: Unedited_NPC_H3K4me3_rep2
H3K4me3 ChIP-seq from Unedited_NPC, rep2


title: Corrected_NPC_KDM5C70, Input, rep1

description:
Library name: Corrected_NPC_KDM5C70_Input_rep1
Input ChIP-seq from Corrected_NPC_KDM5C70, rep1


title: Corrected_NPC, H3K4me3, rep1

description:
Library name: Corrected_NPC_H3K4me3_rep1
H3K4me3 ChIP-seq from Corrected_NPC, rep1


title: Corrected_NPC, H3K4me2, rep1

description:
Library name: Corrected_NPC_H3K4me2_rep1
H3K4me2 ChIP-seq from Corrected_NPC, rep1


title: Corrected_NPC, Input, rep2

description:
Library name: Corrected_NPC_Input_rep2
Input ChIP-seq from Corrected_NPC, rep2


title: Corrected_NPC, H3K4me2, rep2

description:
Library name: Corrected_NPC_H3K4me2_rep2
H3K4me2 ChIP-seq from Corrected_NPC, rep2


title: Corrected_NPC, Input, rep1

description:
Library name: Corrected_NPC_Input_rep1
Input ChIP-seq from Corrected_NPC, rep1


title: Corrected_NPC, H3K4me2, rep3

description:
Library name: Corrected_NPC_H3K4me2_rep3
H3K4me2 ChIP-seq from Corrected_NPC, rep3


title: Corrected_NPC, Input, rep3

description:
Library name: Corrected_NPC_Input_rep3
Input ChIP-seq from Corrected_NPC, rep3


title: Patient1_Unedited_Neuron biological replicate 3

description:
Library name: Patient1_Unedited_Neuron_rep3
Bulk RNA-seq of Patient1_Unedited_Neuron, replicate 3

data_processing:
Reads were quality checked using FastQC.
Reads were aligned to the GRCh38 (hg38) reference genome.
TPM values were computed.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data includes gene-level TPM tables for each sample.
Supplementary files format and content: Each row corresponds to a gene and each column to a sample; values represent TPMs.

source_name: Patient 1 iPSC-derived

growth_protocol: iPSCs were cultured on Matrigel-coated plates in mTeSR1 medium and differentiated into neural progenitor cells (NPCs) using a dual SMAD inhibition protocol. Neurons were generated via directed differentiation from NPCs.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions, including on-column DNase digestion.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) following poly(A) enrichment. Libraries were quantified, pooled, and sequenced on an Illumina platform.

value: induced pluripotent stem cell-derived culture

value: Neuron

value: unedited


title: Patient1_Unedited_Neuron biological replicate 2

description:
Library name: Patient1_Unedited_Neuron_rep2
Bulk RNA-seq of Patient1_Unedited_Neuron, replicate 2


title: Patient1_Corrected_Neuron biological replicate 3

description:
Library name: Patient1_Corrected_Neuron_rep3
Bulk RNA-seq of Patient1_Corrected_Neuron, replicate 3

value: corrected


title: Patient1_Unedited_Neuron biological replicate 1

description:
Library name: Patient1_Unedited_Neuron_rep1
Bulk RNA-seq of Patient1_Unedited_Neuron, replicate 1


title: Patient1_Unedited_NPC biological replicate 3

description:
Library name: Patient1_Unedited_NPC_rep3
Bulk RNA-seq of Patient1_Unedited_NPC, replicate 3


title: Patient1_Corrected_Neuron biological replicate 1

description:
Library name: Patient1_Corrected_Neuron_rep1
Bulk RNA-seq of Patient1_Corrected_Neuron, replicate 1


title: Patient1_Corrected_Neuron biological replicate 2

description:
Library name: Patient1_Corrected_Neuron_rep2
Bulk RNA-seq of Patient1_Corrected_Neuron, replicate 2


title: Patient1_Unedited_NPC biological replicate 1

description:
Library name: Patient1_Unedited_NPC_rep1
Bulk RNA-seq of Patient1_Unedited_NPC, replicate 1


title: Patient1_Unedited_NPC biological replicate 2

description:
Library name: Patient1_Unedited_NPC_rep2
Bulk RNA-seq of Patient1_Unedited_NPC, replicate 2


title: Corrected_NPC, H3K4me3, rep2

description:
Library name: Corrected_NPC_H3K4me3_rep2
H3K4me3 ChIP-seq from Corrected_NPC, rep2


title: Unedited_NPC, Input, rep3

description:
Library name: Unedited_NPC_Input_rep3
Input ChIP-seq from Unedited_NPC, rep3


title: Patient1_Corrected_NPC biological replicate 3

description:
Library name: Patient1_Corrected_NPC_rep3
Bulk RNA-seq of Patient1_Corrected_NPC, replicate 3


title: Patient1_Corrected_NPC biological replicate 1

description:
Library name: Patient1_Corrected_NPC_rep1
Bulk RNA-seq of Patient1_Corrected_NPC, replicate 1


title: iPSC from donor 81280 derived cells grown in AM and AGS media

city: Montreal

first: Thomas

last: Durcan

state: Quebec

address: 3801 University Street

department: The Neuro

country: Canada

institute: McGill University

description:
Library name: 81280_AM_AGS
ParseBio WT

data_processing:
Generated Fastq files are read into the Parse Bioscience analysis pipeline (version 1.0.5p) on the high-performance Digital Research Alliance of Canada computing cluster Béluga to assign samples to barcodes, combine sublibraries, and undergo initial quality control. Analysis (Seurat, Slingshot, tradeSeq) The Parse pipeline output was read into R v4.3.3 using Seurat v5.1.0 to further quality control and process the data. Filters were set to nFeature_RNA < 12000 &  nFeature_RNA >300, nCount_RNA < 50000, and percent.mt < 25. Slingshot v2.10.0 (16) was used for the pseudotime analysis, and tradeSeq v1.16.0 (18) for evaluation of DEGs associated with lineage divergence. GO Enrichment Analysis was performed with clusterProfiler v4.10.1 (20).
Assembly: GRCh38
Supplementary files format and content: comma separated values files, matrix files, and h5ad array files

source_name: Glial Progenitor

growth_protocol: Glial progenitors were generated from human iPSCs according to our previous publication (14).  At day 75 of the protocol, we have a mixed-glial culture consisting of committed glial progenitors, astrocytes and OPCs (Figure 1B). Passaging our mixed-progenitor culture allows for expansion and use for differentiation as needed. For differentiation, a commercially available basal medium is supplemented with growth serum (Astrocyte Medium with Astrocyte Growth Supplements, ScienCell) for 10 days (Day 85), followed by 10ng/mL IGF-1 (Peprotech) and 60ng/mL T3 (Sigma Aldrich) for the following 11 days to reach a majority of OL-lineage cells at a total of 21 days (Day 95).

extract_protocol:
Cells generated from both 3450 and 81280 (one cell prep per condition), were collected using TrypLE (Gibco), resuspended in PBS (Gibco) with 1% BSA Fraction V (Gibco). Cells were counted and then fixed using the Parse fixation workflow that allows samples to be stored at -80°C until the barcoding and library steps are carried out.
On the day of library preparation, 2770 cells from each sample are combinatorically barcoded, with each cell receiving three unique barcodes over three consecutive splitting and pooling steps. Barcoded cells are then split into sublibraries, lysed, reverse transcribed, and barcoded once more in a sub library-specific manner. Sublibraries were sequenced at a depth of 50k reads/cell through the McGill Genome Centre Platform using an Illumina NovaSeq 6000

value: Glial Progenitor

value: Healthy control


title: iPSC from donor 81280 derived cells grown in AM, AGS, IGF, and T3 media

description:
Library name: 81280_AM_AGS_IGF_T3
ParseBio WT


title: iPSC from donor 3450 derived cells grown in PDGF media

description:
Library name: 3450_PDGF
ParseBio WT


title: iPSC from donor 3450 derived cells grown in AM and AGS media

description:
Library name: 3450_AM_AGS
ParseBio WT


title: iPSC from donor 3450 derived cells grown in AM, AGS, IGF, and T3 media

description:
Library name: 3450_AM_AGS_IGF_T3
ParseBio WT


title: iPSC from donor 81280 derived cells grown in PDGF media

description:
Library name: 81280_PDGF
ParseBio WT


title: Patient1_Corrected_NPC biological replicate 2

description:
Library name: Patient1_Corrected_NPC_rep2
Bulk RNA-seq of Patient1_Corrected_NPC, replicate 2


title: Gastric cancer with peritoneal metastasis, ZR

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

institute: The Fourth Hospital of Hebei Medical University

description: Library name: Sample 16

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Homo sapiens Ensembl V107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.


title: Gastric cancer with peritoneal metastasis, WJW

description: Library name: Sample 15


title: Gastric cancer with peritoneal metastasis, JZZ

description: Library name: Sample 13


title: Gastric cancer without peritoneal metastasis, ZRS

description: Library name: Sample 12


title: Gastric cancer without peritoneal metastasis, WSJ

description: Library name: Sample 10


title: Gastric cancer without peritoneal metastasis, LYH

description: Library name: Sample 8


title: Gastric cancer with peritoneal metastasis, LLZ

description: Library name: Sample 14


title: Gastric cancer without peritoneal metastasis, WDZ

description: Library name: Sample 9


title: Gastric cancer without peritoneal metastasis, ZB

description: Library name: Sample 11


title: Gastric cancer without peritoneal metastasis, LLJ

description: Library name: Sample 6


title: Gastric cancer without peritoneal metastasis, LXH

description: Library name: Sample 7


title: Gastric cancer without peritoneal metastasis, HYZ

description: Library name: Sample 3


title: Gastric cancer without peritoneal metastasis, HXX

description: Library name: Sample 2


title: Gastric cancer without peritoneal metastasis, GFY

description: Library name: Sample 1


title: K562, MK, siRHOB, 3

city: beijing

first: Xin

last: Yuan

address: haidian

institute: Beijing Institute of Radiation Medicine

data_processing:
The samples were subjected for PE150 (paired-end 150nt) sequencing using the Illumina NovaSeq 6000.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2 software(V2.2.1). Featurecount software (V2.0.2) was used to count the reads numbers mapped to each gene.
EdgeR software was used for differential expression analysis.
Assembly: GRCh37.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen) and the quality of RNA was assessed using NanoDrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). 1ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: bone marrow

value: human leukemia cells

value: RHOB knockdown

value: megakaryocyte differentiation


title: Gastric cancer without peritoneal metastasis, LHJ

description: Library name: Sample 5


title: K562, MK, siRHOB, 2


title: K562, MK, siRHOB, 1


title: K562, MK, siNC, 3

value: WT


title: K562, MK, siNC, 2


title: Gastric cancer with peritoneal metastasis, ZYQ

description: Library name: Sample 17


title: K562, Ctl, siRHOB, 2

value: normal culture


title: K562, Ctl, siRHOB, 3


title: K562, Ctl, siRHOB, 1


title: K215M_Tex2

city: Shanghai

first: Wei

last: Lu

state: Shanghai

address: 320 YueYang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
Library name: K215M_Tex2
K215M_Tex2

data_processing:
The trimmed reads were mapped to the mouse reference genome (GRCm38.p6).
Assembly: GRCm38.p6
Supplementary files format and content: The rawcount file and metadata were provided for each sample

source_name: tumor

extract_protocol:
Tumors were collected and incubated in serum-free RPMI medium containing 1mg/ml Collagenase D Type 4 (Gibco) and 0.02 mg/ml of DNase I (Sigma) for one hour at 37℃ under agitation. The cell suspension was filtered through a 70µm cell strainer and treated with RBC lysis buffer (eBioscience). Tumor-infiltrating CD8+ T cells were sorted
The scRNA-Seq libraries and V(D)J libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 5' library & gel bead kit, along with the V(D)J enrichment kit (10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to approximately 1000 cells/uL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken, and barcoded cDNA was purified and amplified. The amplified barcoded cDNA was used to construct 5' gene expression and TCR-enriched libraries. For 5' library construction, the amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and index PCR amplified. For the V(D)J library, mouse T cell V(D)J sequences were enriched from the amplified cDNA followed by fragmentation, A-tailing, adaptor ligation, and index PCR amplification.

value: tumor

value: Card11 K215M

value: I.H. B16-OVA


title: K562, Ctl, siNC, 3


title: K215M_Tex1

description:
Library name: K215M_Tex1
K215M_Tex1


title: K562, Ctl, siNC, 2


title: K562, Ctl, siNC, 1


title: WT_Tex1

description:
Library name: WT_Tex1
WT_Tex1


title: WT_Tex2

description:
Library name: WT_Tex2
WT_Tex2


title: Gastric cancer without peritoneal metastasis, LFJ

description: Library name: Sample 4


title: P120N, TCR

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem.63 Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated peripheral blood mononuclear cells.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json
Library strategy: scTCR-seq

source_name: Cancer lymph node

extract_protocol:
Bulk RNAseq: Total RNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol. RNA concentration and quality were assessed using NanoDrop.  Whole exome sequencing: Genomic DNA was extracted from tumor tissue, PBMCs, or cell lines using the Qiagen DNeasy Blood & Tissue Kit following the manufacturer’s instructions. DNA concentration and purity were assessed with NanoDrop. Extracted DNA was used for exome library preparation. Single-cell sequecing: Single-cell suspensions were prepared from tumor or PBMCs, and viable cells were loaded into the 10x Genomics Chromium platform for partitioning. RNA from individual cells was reverse-transcribed, and libraries were prepared according to the 10x Genomics protocol. Spatial: Slides were processed through the 10x Genomics Gene Expression workflow with pre-sequencing H&E imaging completed on the Keyence Microscope per 10x Genomics workflows. Next, transcripts were de-crosslinked, hybridized to a probe panel, ligation completed, and probes released for capture on the gridded, barcoded surface of the Visium slide (CytAssist, 10x Genomics, RRID:SCR_024570). After barcoding, the samples underwent library preparation, amplification, and clean-up with quality assessment ensuring that fragments were ~240bp.
Bulk RNAseq: RNA was extracted and used for mRNA library preparation with poly(A) enrichment, following Novogene's standard protocol. Library construction and sequencing were performed on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Whole exome sequencing: Genomic DNA was extracted and used for library preparation with the Agilent V6 kit, according to Novogene's standard workflow. Library quality was assessed, and sequencing was conducted on the NovaSeq X Plus Series platform with paired-end 150 bp (PE150) reads. Single-cell sequencing: Library preparation was completed at the MCW Mellowes Center (RRID:SCR_022926) with 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits (10X Genomics, sample dual indexes with cellular and molecular barcodes with VDJ amplification). Target capture of 10,000 cells per sample was used. Prior to sequencing, libraries were quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems). Spatial: Libraries were sequenced at the Mellowes Center Facility on the Illumina NovaSeq6000 with paired end reads per the 10x Genomics protocol and generating 25 million read pairs per spot covered by tissue. The quality control of raw reads was processed by FastQC.

value: Cancer lymph node

value: Pre-Treatment


title: P120PBMC, TCR

source_name: PBMC

value: PBMC


title: P120N, GEX

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem.63 Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated peripheral blood mononuclear cells.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json


title: KM2

description:
Library name: KM2
K215M2


title: EG1

description:
Library name: EG1
E134G1

value: Card11 E134G


title: EG2

description:
Library name: EG2
E134G2


title: P120T, TCR

source_name: Oral cancer

value: Oral cancer


title: P120T, GEX


title: WT2

description:
Library name: WT2
WT2


title: HyPR-HN 04_3, TCR

value: 6 Weeks Post-Radiation


title: WT1

description:
Library name: WT1
WT1


title: K562, MK, siNC, 1


title: HyPR-HN 04_3, GEX


title: HyPR-HN 04_2, TCR

value: Last Day of Radiation


title: qyHD3

city: Ji an

first: huimin

last: sun

state: Jiangxi

address: No. 28 Xueyuan Road, Qingyuan District

department: College of Life Sciences

institute: Jinggangshan University

description: Library name: sample_12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GCA_047301065.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GCA_047301065.1
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

organism: Citrus maxima

source_name: Taoxi, Disease, replicate biosample3

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Fruit

tag: cultivar

value: Taoxi

value: Disease


title: qyHD2

description: Library name: sample_11

source_name: Taoxi, Disease, replicate biosample2


title: J2.2-HKU1.IP.KO.5

city: Newark

first: Adriana

last: Messyasz

address: 185 South Orange Avenue

institute: Rutgers-New Jersey Medical School

description: Library name: MHV_HKU1_IPKO_5

data_processing:
nf-core RNAseq workflow
Raw transcriptome reads were assessed for quality control (FASTQC v0.11.9) and trimmed for quality and adapter contaminant (cutadapt v 3.4)
Trimmed reads were aligned to the Mus musculus genome using STAR (v2.7.10a)
Transcript abundance calculation and hit count extraction with StringTie (v2.2.1) and featureCounts (v2.0.1) respectively
Hit count normalization and differential gene expression group cross-comparisons were performed using DESeq2 (v1.28.0)
Assembly: GRCm38
Supplementary files format and content: Plain-text, tab-separated file with a single header line (which names all of the columns), includes Salmon quantification values for each Sample

growth_protocol: Standard housing condition for mice

extract_protocol:
RNA in the brain was isolated with TRIZOL following manufacturer's protocol
polyA selection

value: Brain

value: C57BL/6 mice

value: infected with J2.2 expressing control sequence


title: J2.2-HKU1.IP.KO.3

description: Library name: MHV_HKU1_IPKO_3


title: HyPR-HN 04_2, GEX


title: qyCK3

description: Library name: sample_9

source_name: Taoxi, control, replicate biosample3

value: control


title: J2.2-HKU1.IP.KO.4

description: Library name: MHV_HKU1_IPKO_4


title: qyHD1

description: Library name: sample_10

source_name: Taoxi, Disease, replicate biosample1


title: WT scRNA+TCRseq

description:
Library name: WT_RNA_TCR
WT_RNA_TCRseq

value: tumor

value: WT


title: qyCK2

description: Library name: sample_8

source_name: Taoxi, control, replicate biosample2


title: KM1

description:
Library name: KM1
K215M1

value: Card11 K215M


title: HyPR-HN 04_1, TCR


title: qyCK1

description: Library name: sample_7

source_name: Taoxi, control, replicate biosample1


title: HyPR-HN 04_1, GEX


title: P120PBMC, GEX


title: J2.2-HKU1.IP.KO.2

description: Library name: MHV_HKU1_IPKO_2

source_name: Brain


title: jshHD2

description: Library name: sample_5

source_name: Jinsha, Disease, replicate biosample2

value: Jinsha


title: HyPR-HN 04_1_PBMC, TCR

value: Pre-Treatment


title: jshHD3

description: Library name: sample_6

source_name: Jinsha, Disease, replicate biosample3


title: afHD3

description: Library name: sample_3

source_name: Jinlan, disease, replicate biosample3

value: Jinlan

value: disease


title: jshHD1

description: Library name: sample_4

source_name: Jinsha, Disease, replicate biosample1


title: afHD2

description: Library name: sample_2

source_name: Jinlan, disease, replicate biosample2


title: afHD1

description: Library name: sample_1

source_name: Jinlan, disease, replicate biosample1


title: J2.2-HKU1.IP.4

description: Library name: MHV_HKU1_IP_4

value: infected with J2.2 expressing HKU1 I protein


title: J2.2-HKU1.IP.5

description: Library name: MHV_HKU1_IP_5


title: HyPR-HN 04_1_PBMC, GEX

value: PBMC


title: afhHB2

description: Library name: sample_11

source_name: Jinlan, Disease, replicate biosample2


title: afhHB1

description: Library name: sample_10

source_name: Jinlan, Disease, replicate biosample1


title: HyPR-HN 03_2, GEX

value: Oral cancer

value: Last Day of Radiation


title: J2.2-HKU1.IP.1

description: Library name: MHV_HKU1_IP_1


title: HyPR-HN 03_2, TCR


title: afhHB3

description: Library name: sample_12

source_name: Jinlan, Disease, replicate biosample3

value: Fruit


title: J2.2-HKU1.IP.3

description: Library name: MHV_HKU1_IP_3


title: J2.2-HKU1.IP.KO.1

description: Library name: MHV_HKU1_IPKO_1


title: J2.2-HKU1.IP.2

description: Library name: MHV_HKU1_IP_2


title: afCK1

description: Library name: sample_7

source_name: Jinlan, control, replicate biosample1


title: afCK3

description: Library name: sample_9

source_name: Jinlan, control, replicate biosample3


title: HyPR-HN 03_1, GEX

source_name: Oral cancer


title: jshHB3

description: Library name: sample_6

value: Disease


title: afCK2

description: Library name: sample_8

source_name: Jinlan, control, replicate biosample2


title: HyPR-HN 02_3_PBMC, TCR

source_name: PBMC

value: 6 Weeks Post-Radiation


title: jshHB1

description: Library name: sample_4


title: jshCK3

description: Library name: sample_3

source_name: Jinsha, control, replicate biosample3


title: jshCK2

description: Library name: sample_2

source_name: Jinsha, control, replicate biosample2


title: HyPR-HN 02_3_PBMC, GEX


title: P14 CD8+ T cells sgZc3h12a, Day14 post infection

city: Beijing

first: Min

last: Peng

address: Haidian

institute: Tsinghua university

description: Library name: Zc3h12a

data_processing:
For scATAC-seq data analysis, raw fastq data were aligned to mm10 by cellranger-atac count. Data clustering and dimensionality reduction were performed using the R package Siganc following its recommended procedure. A unified set of peaks from cellranger–atac results was created to quantify each dataset. Cells with less ATAC counts than 500, more ATAC counts than 50000, less in-peak reads ratio than 50%, more in-blacklist reads ratio than 5%, more nucleosome signal than 2, or less TSS enrichment fold than 2.5 were excluded from downstream analysis, yielding a matrix of 24514 cells by 104107 features (sgControl: 5721, sgBcor: 6163, sgZc3h12a: 6699, sgBcor/Zc3h12a: 5931). Term frequency-inverse document frequency (TF-IDF) normalization was performed by function RunTFIDF of Signac. Most frequently observed features were identified by function FindTopFeatures of Signac. Singular value decomposition (SVD) was run on the TD-IDF matrix by function RunSVD of Signac. The first 7 LSI components will be used for subsequent data analysis, except for the first and third LSI components, as they are highly correlated with sequencing depth. UMAP dimension reduction and clustering were performed by signac function RunUMAP, FindNeighbors and FindClusters. To analyze motif activity of different TFs, we ran signac function AddMotifs to add the DNA sequence motif information from JASPAR 2016 dataset. Motif activity was calculated by signac function RunChromVAR.
Assembly: mm10
Supplementary files format and content: tsv file include fragments for each sample; bed file include peaks for each sample;

source_name: spleen

extract_protocol:
Control, BCOR-deficient, ZC3H12A-deficient and BCOR/ZC3H12A-deficient P14 cells were transferred into Cas9+ B6 mice that were infected with LCMV Clone 13 one day before cell transfer. Fourteen days after transfer, Thy1.1+ P14 cells from spleen were sorted by a S3e cell sorter with purity > 98% and sent to Novogene for scATAC-seq.
scATAC-seq libraries were generated using the 10x Genomics Chromium Cell ATAC Reagent Kit (v1). In brief, sorted CD8+ P14 T cells were washed with 0.04% BSA PBS, then approximately 40,000 cells were subjected to the nuclei preparation protocol according to the manufacturer’s instructions. Then, 16,000 nuclei were loaded into a 10x Chromium controller. All downstream library preparation steps were performed according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq.

value: spleen

value: P14 CD8+ T cell

value: T cell


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14 post infection

description: Library name: DKO


title: HyPR-HN 02_3, Spatial

data_processing:
Bulk sequencing: DNA reads were cleaned using TrimGalore. Illumina short reads were mapped to the current reference genome, GRCh38, using BWA-mem.63 Somatic mutations including single nucleotide variants and indels were evaluated by Mutect2, SomaticSniper, and Varscan2 with comparison to patient-matched germline WES obtained from isolated peripheral blood mononuclear cells.  Single-cell sequencing: Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction. Spatial: Raw reads were mapped to the human GRCh38 reference genome with Visium Probe_Set_v2.0 by Space Ranger. Fiducial detection, barcode/UMI counting, zero-count spot filtering, and normalization were also performed by Space Ranger. Visualization was performed with 10x Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix: .mtx.gz Barcodes and features: .tsv.gz Metadata and annotations: .csv Aligned reads: .bam Index files: .bam.bai Spatial images: .png, .jpg Spatial scaling factors: .json
Library strategy: Spatial Transcriptomics


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14, Replicate2

description: Library name: S42

data_processing:
Raw reads were trimmed by cutadapt (version 1.18) with parameter -j 3 -m 20 -e 0.1 -O 3 -q 20 --quality-base=33 to remove low-quality bases and adaptor sequences. The ribosomal RNA (rRNA) reads were detected as those aligned to ribosomal genes using bowtie2 (version 2.3.3.1). The alignment ratio of rRNA was determined as ratio of the number of uniquely mapped reads to rRNA of all reads. For integrative genome browser visualization (IGV), sequencing reads were aligned to mm10 using STAR with parameter --outSAMtype BAM SortedByCoordinate --twopassMode Basic --limitBAMsortRAM 30000000000. The sequencing reads were trimmed by cutadapt (version 1.18) with parameter -m 20 -e 0.1 -O 3 -q 20 --quality-base=33 to remove low-quality bases and adaptor sequences. The trimmed reads were aligned to mouse reference genome (mm10) using STAR (version 2.5.3a) with parameters --runThreadN 8 --readFilesIn --readFilesCommand gunzip -c –outSAMtype BAM SortedByCoordinate --twopassMode Basic --limitBAMsortRAM 30000000000 --outSAMstrandField intronMotif --quantMode TranscriptomeSAM. Expression matrix was generated by RSEM (version 1.3.0). Deferential expression analysis was executed by DEseq2 (version 1.34.0). Log-transformed RNA expression change were calculated by DEseq2 and used to process GSEA enrichment analysis with performed by ClusterProfiler (version 4.2.2)
Assembly: mm10
Supplementary files format and content: txt files include raw counts and FPKM for each sample

extract_protocol:
1000 P14 cells were sorted in Buffer TCL (Qiagen, 1031576) and RNA was purified by 2.2 × VAHTS RNA Clean Beads.
The cDNA libraries were generated following a modified SMART-seq2 protocol.


title: U118_resistant_miRNA-seq_1

city: Chongqing

first: liao

last: bin

address: 118 Xingguang Avenue

institute: Chongqing General Hospital, Chongqing University

data_processing:
The first step in our data analysis is removing adapters with software cutadapter (1.14), then low quality (20) bases from both 3' end and 5' end were trimmed with Trimmomatic (v0.36).
The known mature miRNA and precursor miRNA of the species were archived from mirBase (v21). We used mirDeep2 (v2.0.0.8) to discover novel miRNAs, predicate hairpin structure of precursor-miRNA and quantify miRNA.
Assembly: human miRBase build 22
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample.

extract_protocol:
Total RNA was extracted using the Total RNA Extractor（Trizol）kit (B511311, Sangon, China) according to the manufacturer’s protocol.A total of 2μg total RNA per sample was used as input material for small RNA library preparations.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations.

tag: phenotype

value: resistant


title: U118_resistant_miRNA-seq_3


title: HyPR-HN 02_3, TCR


title: HyPR-HN 03_1, TCR


title: U118_sensitive_miRNA-seq_3

value: sensitive


title: U118_sensitive_miRNA-seq_1


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14, Replicate1

description: Library name: S41


title: P14 CD8+ T cells sgBcor, Day14, Replicate2

description: Library name: S32


title: U118_sensitive_miRNA-seq_2


title: jshHB2

description: Library name: sample_5

source_name: Jinsha, Disease, replicate biosample2


title: HyPR-HN 02_3, GEX


title: HyPR-HN 02_2, TCR

value: Last Day of Radition


title: U87_resistant_miRNA-seq_2

source_name: U-87 MG

value: U-87 MG


title: U87_sensitive_miRNA-seq_3


title: jshCK1

description: Library name: sample_1

source_name: Jinsha, control, replicate biosample1

value: Jinsha

value: control


title: P14 CD8+ T cells sgBcor, Day14 post infection

description: Library name: Bcor


title: U87_sensitive_miRNA-seq_1


title: HyPR-HN 02_1, Spatial

value: Pre-Treatment


title: U118_resistant_miRNA-seq_2


title: U87_resistant_miRNA-seq_1


title: HyPR-HN 02_2, GEX


title: U87_sensitive_miRNA-seq_2


title: P14 CD8+ T cells sgZc3h12a, Day14, Replicate2

description: Library name: S22


title: HyPR-HN 02_1, TCR


title: P14 CD8+ T cells sgControl, Day14 post infection

description: Library name: Control


title: P14 CD8+ T cells sgZc3h12a, Day14, Replicate1

description: Library name: S21


title: HyPR-HN 02_1, GEX


title: P14 CD8+ T cells sgControl, Day14, Replicate2

description: Library name: S12


title: SVBN206, CONTROL

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Quality score trimming and filtering were performed with TrimGalore.
Trimmed reads were aligned to the Hg38 annotated  genome ( using Hisat2 (v2.1.0)
Per gene read counts were calculated using htseq-count (v0.5.4p5)
Differential expression was obtained using R-package DeSeq2 (1.42.1)
Assembly: Hg38
Supplementary files format and content: tab-delimited text file include IDs, gene names and RPKM values for each sample

source_name: cumulus cells

extract_protocol:
RNA extraction will be performed using the Arcturus PicoPure RNA isolation Kit from AppliedBiosystems
P3004, P3012 : RNA-Seq libraries were generated from 100 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

value: cumulus cells

tag: group

value: CONTROL


title: SVBN208, CONTROL


title: SVBN209, CONTROL


title: U87_resistant_miRNA-seq_3


title: SVBN201, PCOS

value: PCOS


title: P14 CD8+ T cells sgControl, Day14, Replicate1

description: Library name: S11


title: P14 CD8+ T cells sgBcor, Day14, Replicate1

description: Library name: S31


title: SVBN204, CONTROL


title: HyPR-HN 02_1_PBMC, GEX

value: PBMC


title: Galctwi/twi Sting-/, 32days, 3

last: Yan

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

description: Library name: GALCDKO3

data_processing:
Data is processed with Astrocyte RNASeq Analysis Workflow on UTSW BioHPC
Assembly: GRCh38, GRCm38
Supplementary files format and content: txt files include FPKM for the samples

source_name: Cerebrum

extract_protocol:
The total RNA was first extracted using TRI Reagent, followed by a clean up with RNeasy plus mini. All steps were done according to manufacturer's protocol
For cerebrum samples, the RNA library was prepared non-stranded with polyA enrichment. For cell line samples, the RNA library was prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's instructions

value: Cerebrum

value: Galctwi/twiSting-/-


title: SVBN200, PCOS


title: SVBN198, PCOS


title: SVBN210, CONTROL


title: HyPR-HN 01_3 tumor, GEX

value: Oral cancer

value: 6 Weeks Post-Radiation


title: Galctwi/twi Sting-/, 32days, 2

description: Library name: GALCDKO2


title: SVBN195, PCOS


title: Galctwi/twi Sting-/-, 32days, 1

description: Library name: GALCDKO1


title: SVBN193, PCOS


title: SVBN192, CONTROL


title: HyPR-HN 01_2 tumor, GEX

value: Last Day of Radiation


title: SVBN190, CONTROL


title: Galctwi/twi, 32days, 3

description: Library name: GALCKO3

value: Galctwi/twi


title: HyPR-HN 01_1 tumor, GEX


title: SVBN187, CONTROL


title: Galctwi/twi, 32days, 2

description: Library name: GALCKO2


title: HyPR-HN 02_1_PBMC, TCR


title: pat. 4, SRA, fundus, repl.2

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v. 3.7.5
Fastq were preprocessed for QC by fastp.
Alignment was performed with STAR 2.6.
Quantification at gene level was determined using htseq-count 0.6.1p1.
Assembly: Illumina iGenome Homo sapiens UCSC hg38
Supplementary files format and content: Tab-delimited files including raw counts for each sample

source_name: Gastric

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) following manufacturer’ instructions.
10ng of total RNA were processed using the NEBNext Low Input RNA Library Prep Kit (New England Biolabs p/n E6420) according to manufacturer’s instructions.

value: Gastric

tag: subtissue

value: Fundus

tag: culture system

value: SRA


title: SVBN184, CONTROL


title: Tissue, antrum, repl. 3

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) following manufacturer’ instructions.
10ng of total RNA were processed using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580) according to manufacturer’s instructions.

value: Antrum

value: Tissue (mucosal biopsy)


title: Galctwi/twi, 32days, 1

description: Library name: GALCKO1


title: pat. 4, SRA, body, repl2

value: Body


title: SVBN205, CONTROL


title: Tissue, antrum, repl. 2


title: Tissue, antrum, repl. 1


title: pat. 4, SRA, antrum, repl.2


title: Tissue, body, repl. 2


title: Galc+/+, 32days, 3

description: Library name: GALCWT3

value: Galc+/+


title: pat. 4, SRA, fundus, repl.1


title: Tissue, body, repl. 3


title: pat. 4, SRA, body, repl.1


title: Tissue, body, repl. 1


title: Tissue, fundus, repl. 3


title: Galc+/+, 32days, 1

description: Library name: GALCWT1


title: Tissue, fundus, repl. 2


title: Tissue, fundus, repl. 1


title: SVBN185, CONTROL

value: cumulus cells


title: pat. 4, MRA, fundus, repl.2

value: MRA


title: Implanted MRA, antrum, repl. 3

value: Implanted multi-region assembloid


title: Implanted MRA, antrum, repl. 1


title: Galc+/+, 32days, 2

description: Library name: GALCWT2


title: Implanted MRA, antrum, repl. 2


title: LLC1 bulk tumor, Vehicle, rep1

city: Baltimore

first: Jina

last: Park

state: Maryland

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
Salmon was used for transcript level alignment with raw FASTQ files to gencodevM34 transcript annotation, and the gene-level count matrices were generated using the tximport R package.
Assembly: hg38
Supplementary files format and content: A text file includes VST-normalized expression values for each sample

source_name: LLC1 bulk tumor cells

extract_protocol:
RNA was extracted from the enriched tumor population using the RNeasy Mini Kit (Qiagen, #74104).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) according to the manufacturer's protocols.

value: LLC1 bulk tumor cells

value: Vehicle


title: LLC1 bulk tumor, MYCi975, rep1


title: pat. 4, SRA, antrum, repl.1


title: Implanted MRA, body, repl. 3


title: Implanted MRA, body, repl. 1


title: LLC1 bulk tumor, MYCi975, rep2


title: Implanted MRA, fundus, repl. 3


title: LLC1 bulk tumor, Combo, rep1

value: Combo


title: pat. 4, MRA, body, repl.12


title: pat. 4, organoid, fundus, repl.2

value: Organoid


title: MRA, antrum, repl. 3

value: Multi-region assembloid


title: pat. 4, organoid, body, repl.2


title: LLC1 bulk tumor, Vehicle, rep2


title: Implanted MRA, fundus, repl. 2


title: LLC1 bulk tumor, MYCi975, rep3


title: Implanted MRA, fundus, repl. 1


title: MRA, antrum, repl. 2


title: MRA, body, repl. 3


title: LLC1 bulk tumor, TMP195, rep1


title: pat. 4, organoid, antrum, repl.2


title: MRA, body, repl. 2


title: pat. 3, SRA, fundus, repl.2


title: MRA, fundus, repl. 3


title: pat. 3, SRA, body, repl.2


title: pat. 3, SRA, antrum, repl.2


title: MRA, fundus, repl. 2


title: Implanted MRA, body, repl. 2


title: LLC1 bulk tumor, Vehicle, rep3


title: SRA, antrum, repl. 3

value: Single-region assembloid


title: pat. 3, SRA, fundus, repl.1


title: MRA, fundus, repl. 1


title: MRA, body, repl. 1


title: SRA, antrum, repl. 2


title: SRA, antrum, repl. 1


title: LLC1 bulk tumor, Vehicle, rep4


title: pat. 3, SRA, body, repl.1


title: pat. 4, MRA, antrum, repl.2


title: LLC1 bulk tumor, TMP195, rep2


title: LLC1 bulk tumor, Combo, rep3


title: SRA, body, repl. 3


title: pat. 3, SRA, antrum, repl.1


title: MRA, antrum, repl. 1


title: SRA, body, repl. 2


title: LLC1 bulk tumor, Combo, rep2


title: SRA, body, repl. 1


title: SRA, fundus, repl. 3


title: LLC1 bulk tumor, TMP195, rep3


title: SRA, fundus, repl. 1


title: pat. 3, MRA, body, repl.2


title: SRA, fundus, repl. 2


title: pat. 3, MRA, fudnus, repl.2


title: Organoid, antrum, repl. 3


title: Organoid, antrum, repl. 2


title: Organoid, antrum, repl. 1


title: pat. 3, MRA, antrum, repl.2


title: LLC1 enriched tumor cells, Vehicle, rep4

source_name: LLC1 enriched tumor cells

value: LLC1 enriched tumor cells


title: Organoid, body, repl. 3

value: Gastric


title: pat. 3, organoid, fundus, repl.2

value: Fundus


title: LLC1 enriched tumor cells, MYCi975, rep4


title: Organoid, body, repl. 1


title: LLC1 enriched tumor cells, Combo, rep4


title: LLC1 bulk tumor, MYCi975, rep4


title: Organoid, body, repl. 2


title: Organoid, fundus, repl. 1


title: pat. 3, organoid, body, repl.2


title: LLC1 enriched tumor cells, MYCi975, rep3


title: pat. 2, SRA, fundus, repl.2

value: SRA


title: Organoid, fundus, repl. 2


title: SP2577, Replicate2

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

data_processing:
Proprietary perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: ensembl_93_felis_catus_felis_catus_9_0_toplevel
Supplementary files format and content: tab-delimited text file includes normalized count for each samples

organism: Felis catus

source_name: Tongue

extract_protocol:
RNA was isolated using TRIzol and purified with RNeasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
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.

value: Tongue


title: Organoid, fundus, repl. 3


title: LLC1 enriched tumor cells, MYCi975, rep2


title: SP2577 Replicate1


title: LLC1 enriched tumor cells, Vehicle, rep3


title: LLC1 enriched tumor cells, TMP195, rep4


title: Vehicle, Replicate2


title: Vehicle, Replicate1


title: pat. 2, SRA, body, repl.2


title: LLC1 enriched tumor cells, Combo, rep3


title: SP2577, Replicate3


title: pat. 2, SRA, fundus, repl.1


title: STING KO BJ1 diABZI treated 8h, 2

description: Library name: BJ1SKOD2

value: Fibroblasts

value: Sting-/-

value: diABZI


title: STING KO BJ1 diABZI treated 8h, 1

description: Library name: BJ1SKOD1


title: LLC1 enriched tumor cells, TMP195, rep3


title: STING KO BJ1 Vehicle treated 8h, 1

description: Library name: BJ1SKOV1

value: DMSO


title: pat. 2, SRA, body, repl.1

value: Body


title: pat. 2, SRA, antrum, repl.2

value: Antrum


title: LLC1 enriched tumor cells, Combo, rep2


title: pat. 2, SRA, antrum, repl.1


title: Vehicle, Replicate3


title: BJ1 diABZI treated 8h, 1

description: Library name: BJ1WTD1

value: WT


title: LLC1 enriched tumor cells, TMP195, rep2


title: pat. 2, MRA, fundus, repl.2

value: MRA


title: pat. 3, organoid, antrum, repl.2


title: BJ1 Vehicle treated 8h, 1

description: Library name: BJ1WTV1


title: pat. 2, MRA, body, repl.2


title: BJ1 Vehicle treated 8h, 2

description: Library name: BJ1WTV2


title: LCMVc13 infection, CD44+Ly108+ GFI1-low, D7, rep1

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

institute: The University of Queensland

description:
Library name: Slamf6Lo1
GFI1_rep_CM_TSCM_countdata.csv

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Reads were mapped to the mouse genome (mm10) using STAR v2.7.10
After mapping, reads were quantified with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: Read counts following mapping to mm10 using featurecount

extract_protocol:
RNA was extracted from CD8+ T cell isolated using RNeasy Plus Micro kit (Qiagen)
CM and TSCM GFI1-reporter cell libraries were prepared with NEBNext Single Cell/low Input Library prep kit (New England Biolabs).

value: spleen

value: CD8+ T cells

value: CD44+Ly108+ GFI1-low, D7

value: LCMVc13 infection


title: LLC1 enriched tumor cells, Vehicle, rep2

value: LLC1 enriched tumor cells

value: Vehicle


title: LCMVc13 infection, CD44+Ly108+ GFI1-low, D7, rep2

description:
Library name: Slamf6Lo2
GFI1_rep_CM_TSCM_countdata.csv


title: LLC1 enriched tumor cells, Vehicle, rep1


title: pat. 2, MRA, antrum, repl.2

value: Gastric


title: LCMVc13 infection, CD44+Ly108+ GFI1-high, D7, rep1

description:
Library name: Slamf6Hi1
GFI1_rep_CM_TSCM_countdata.csv

value: CD44+Ly108+ GFI1-high, D7


title: LCMVc13 infection, CD44+Ly108+ GFI1-high, D7, rep2

description:
Library name: Slamf6Hi2
GFI1_rep_CM_TSCM_countdata.csv


title: LLC1 enriched tumor cells, Combo, rep1

value: Combo


title: LCMVc13 infection, CD44+Ly108+ GFI1-high, D7, rep3

description:
Library name: Slamf6Hi3
GFI1_rep_CM_TSCM_countdata.csv


title: LCMVc13 infection, CD44+Ly108+ GFI1-low, D7, rep3

description:
Library name: Slamf6Lo3
GFI1_rep_CM_TSCM_countdata.csv


title: pat. 2, organoid, fundus, repl.2

value: Fundus

value: Organoid


title: LCMVc13 infection, CD44+CD62L+  GFI1-low, D7, rep3

description:
Library name: 62LLo3
GFI1_rep_CM_TSCM_countdata.csv

value: CD44+CD62L+  GFI1-low, D7


title: LLC1 enriched tumor cells, MYCi975, rep1


title: pat. 2, organoid, body, repl.2


title: LCMVc13 infection, CD44+CD62L+  GFI1-low, D7, rep1

description:
Library name: 62LLo1
GFI1_rep_CM_TSCM_countdata.csv


title: LCMVc13 infection, CD44+CD62L+ GFI1-high, D7, rep3

description:
Library name: 62LHi3
GFI1_rep_CM_TSCM_countdata.csv

value: CD44+CD62L+ GFI1-high, D7


title: BJ1 diABZI treated 8h, 2

description: Library name: BJ1WTD2

value: Fibroblasts

value: diABZI


title: pat. 2, organoid, antrum, repl.2

value: Antrum


title: LCMVc13 infection, CD44+CD62L+ GFI1-high, D7, rep2

description:
Library name: 62LHi2
GFI1_rep_CM_TSCM_countdata.csv


title: pat. 4, MRA, fundus, repl.1

value: MRA


title: EBs 144h SADEiGEN rep3

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 from 10xGenomics (executed with default parameters)
Used reference: refdata-gex-mm10-2020-A from 10x documentation
See methods section in published paper for detailed methods for downstream analysis (QC, dim reduction, clustering and automated cell type annotation) applied for obtaining the final Seurat object (RDS file).
Assembly: mm10
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix files - (Filtered output from CellRanger)
Supplementary files format and content: RDS file including Seurat object (v5.0.0) with processed data (QC, dimensionality reduction and cell type annotation)

source_name: Embryoid Bodies

growth_protocol: IMDM (Cytiva, Cat #16SH30259.01) supplemented with 15% FBS (ESC-qualified; Gibco Cat #26140079), 1X Glutamax (Gibco; Cat #35050061), 50 μg/mL ascorbic acid (Sigma; Cat #A-4544), 180 μg/mL Transferrin (Roche; Cat #10652202001) and 0.45 mM alpha-monothioglycerol (MTG) (Sigma; Cat #M6145)

extract_protocol:
144h EBs were dislodged by TrypLE, and alive cells were isolated by FACS. Cellular suspension was counted manually with a hemocytometer, and visualized under a ZEISS Primovert Microscope. Cells were resuspended in PBS + BSA 0.04% to a final concentration of 700-1200 cells/μl per sample.  Number of cells encapsulated varied from 10000 to 14000 depending on the sample, to achieve a final target cell recovery of 5000-7000 cells.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). Resulting libraries were quantified and quality checked by using the 2200 TapeStation® (Agilent).

value: Embryoid Bodies

tag: time

value: 144 hours

value: SADEiGEN


title: LCMVc13 infection, CD44+CD62L+ GFI1-high, D7, rep1

description:
Library name: 62LHi1
GFI1_rep_CM_TSCM_countdata.csv

value: spleen

value: CD8+ T cells

value: LCMVc13 infection


title: EBs 144h SADEiGEN rep2


title: MEPs, WT, Rep 3

first: Glen

last: Liszczak

address: 5641 Southwestern Medical Ave, Suite B200

institute: UT Southwestern Medical Center

description: Library name: MEP_WT_3_S14

data_processing:
Quality assessment performed with FastQC
Transcript-level quantification performed with Salmon with reference to the GRCm39 genome
Gene-level aggregation performed with tximport
Assembly: GRCm39
Supplementary files format and content: csv files include raw gene-level count summaries for each sample generated from tximport

source_name: Bone Marrow

extract_protocol:
RNA was extracted from sorted cells using NucleoSpin RNA XS (Macherey-Nagel)
RNA libraries were generated using SMART-Seq v4 Ultra Low Input kit (Takara) following manufacture's protocols

value: Bone Marrow

value: MEP

value: WT


title: MEPs, WT, Rep 1

description: Library name: MEP_WT_1_S12


title: pat. 4, MRA, body, repl.1

value: Gastric

value: Body


title: MEPs, Etv6 S211I, Rep 1

description: Library name: MEP_S211I_1_S15

value: Etv6 P211I Mut


title: MEPs, Etv6 S211I, Rep 2

description: Library name: MEP_S211I_2_S16


title: EBs 144h SADEiGEN rep1


title: MEPs, Etv6 P216L, Rep 2

description: Library name: MEP_P216L_2_S18

value: Etv6 P216L Mut


title: EBs 144h WT rep3


title: pat. 4, organoid, fundus, repl.1

value: Fundus

value: Organoid


title: LCMVc13 infection, CD44+CD62L+  GFI1-low, D7, rep2

description:
Library name: 62LLo2
GFI1_rep_CM_TSCM_countdata.csv

value: CD44+CD62L+  GFI1-low, D7


title: MEPs, Etv6 P216L, Rep 1

description: Library name: MEP_P216L_1_S17


title: MEPs, Etv6 S211I P216L, Rep 3

description: Library name: MEP_DUB_3_S22

value: Etv6 P216L + P211I Mut


title: pat. 4, MRA, antrum, repl.1

value: Antrum

value: MRA


title: pat. 4, organoid, body, repl.1


title: MEPs, Etv6 P216L, Rep 3

description: Library name: MEP_P216L_3_S19


title: LLC1 enriched tumor cells, TMP195, rep1

value: LLC1 enriched tumor cells


title: MEPs, Etv6 S211I P216L, Rep1

description: Library name: MEP_DUB_1_S20


title: HSCs, WT, Rep 3

description: Library name: HSC_WT_3_S3

value: HSC


title: pat. 4, organoid, antrum, repl.1


title: EBs 144h WT rep2

value: Embryoid Bodies

value: 144 hours


title: MEPs, Etv6 S211I P216L, Rep 2

description: Library name: MEP_DUB_2_S21

value: Bone Marrow


title: HSCs, WT, Rep 2

description: Library name: HSC_WT_2_S2


title: pat. 3, MRA, fudnus, repl.1


title: BM 4.5mo PostTransp CD45 BFP+

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 from 10xGenomics (executed with default parameters).
Used reference: refdata-gex-mm10-2020-A from 10x documentation
See methods section in published paper for detailed methods for downstream analysis (QC, dim reduction, clustering and automated cell type annotation) applied for obtaining the final Seurat object (RDS file).
Assembly: mm10
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix files - (Filtered output from CellRanger)
Supplementary files format and content: RDS file including Seurat object (v5.0.0) with processed data (QC, dimensionality reduction and cell type annotation)

extract_protocol:
Freshly CD45 bone marrow cells were isolated by flushing the inner cavity of the long bones from 4.5 months post-transplanted NSG mice. Cell flushing was performed with a typical 1mL syringe containing 1mL DPBS (Gibco). Bone marrow cells were erythrocyte-depleted by incubation with  ACK lysis buffer (Gibco, Cat #A1049201) for 10 minutes at room temperature. Bone marrow cells were stained with anti-mouse CD45-FITC antibody (BD Pharmingen, Cat #553079), and CD45+ BFP+ and CD45+ BFP- cells were isolated by FACS into DPBS suplemented with 0.04% BSA to to a final concentration of 700-1200 cells/μl per sample.  Number of cells encapsulated varied from 10000 to 14000 depending on the sample, to achieve a final target cell recovery of 5000-7000 cells.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). Resulting libraries were quantified and quality checked by using the 2200 TapeStation® (Agilent).

value: CD45 BFP+

value: 4.5 months post-transplantation


title: HSCs, WT, Rep 1

description: Library name: HSC_WT_1_S1

value: WT


title: BM 4.5mo PostTransp CD45 BFP-

value: CD45 BFP-


title: HSCs, Etv6 S211I, Rep 1

description: Library name: HSC_S211I_1_S4

value: Etv6 P211I Mut


title: HSCs, Etv6 S211I, Rep 2

description: Library name: HSC_S211I_2_S5


title: pat. 3, MRA, body, repl.1

value: Gastric

value: Body


title: HSCs, Etv6 P216L, Rep 3

description: Library name: HSC_P216L_3_S8

value: Etv6 P216L Mut


title: HSCs, Etv6 P216L, Rep 2

description: Library name: HSC_P216L_2_S7


title: ATAC Day_8_WT_Term-2

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

description:
Day_8_WT_Term_peaks.narrowPeak
Day_8_WT_Term_scaled.bw

data_processing:
The sequencing quality of Cut&Run libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Low-quality bases and adapters were removed through Trim Galore (v0.6.7)(MAPQ > 30)
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling ATAC-seq peaks, where stringent criteria of FDR < 1e-5, --fe-cutoff 4 and --llocal 7500.
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig

source_name: WT Tex-Term cells

extract_protocol:
Gzmb-Cre; Rosa26-lsl-GFP; Hdac1 wild-type or floxed mice were directly infected with LCMV Clone 13. On day 8 post-infection, Gp33 tetramer-positive cells were sorted into three populations based on surface markers Cx3cr1 and Slamf6 for ATAC-seq analysis.
Sort-purified cells  were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina Nova seq platform.

value: splenocytes

tag: cell population

value: Tex-Term cells


title: pat. 3, organoid, fundus, repl.1

value: Fundus

value: Organoid


title: HSCs, Etv6 S211I P216L, Rep 3

city: Dallas

description: Library name: HSC_DUB_3_S11

value: Etv6 P216L + P211I Mut


title: ATAC Day_8_WT_Term-1


title: ATAC Day_8_WT_Stem-2

description:
Day_8_WT_Stem_peaks.narrowPeak
Day_8_WT_Stem_scaled.bw

source_name: WT Tex-Stem cells

value: Tex-Stem cells


title: EBs 144h WT rep1

value: Embryoid Bodies


title: pat. 3, organoid, body, repl.1


title: ATAC Day_8_WT_Stem-1


title: HSCs, Etv6 P216L, Rep 1

description: Library name: HSC_P216L_1_S6

value: HSC


title: HSCs, Etv6 S211I P216L, Rep 2

description: Library name: HSC_DUB_2_S10

value: Bone Marrow


title: ATAC Day_8_WT_Int-2

description:
Day_8_WT_Int_peaks.narrowPeak
Day_8_WT_Int_scaled.bw

source_name: WT Tex-Int cells

value: Tex-Int cells


title: pat. 2, MRA, fundus, repl.6

value: MRA


title: HSCs, Etv6 S211I P216L, Rep1

description: Library name: HSC_DUB_1_S9


title: pat. 3, organoid, antrum, repl.1

value: Antrum


title: ATAC Day_8_WT_Int-1

value: WT


title: pat. 2, MRA, body, repl.1


title: HA/S Protein-52-d28

type: other

city: Irvine

first: Li

last: Liang

address: MedSurge II

institute: University of California Irvine

description: Total IgG

hyb_protocol: The microarray slides were probed with mouse sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. Mouse IgG  secondary antibody conjugated to AF647, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.

molecule: other

source_name: Plasma

tag: days post prime immunization


title: HA/S Protein-54-d28

description: Total IgG


title: HA/S Protein-53-d28

description: Total IgG


title: HA/S Protein-55-d28

description: Total IgG


title: HA/S mRNA-45-d28

description: Total IgG


title: HA/S Protein-51-d28

description: Total IgG


title: ATAC Day_8_Hdac1-KO_Term-2

description:
Day_8_Hdac1-KO_Term_peaks.narrowPeak
Day_8_Hdac1-KO_Term_scaled.bw

source_name: Hdac1-deficient Tex-Term cells

tag: tissue


title: HA/S mRNA-43-d28

description: Total IgG


title: HA/S mRNA-44-d28

description: Total IgG


title: HA/S mRNA-42-d28

description: Total IgG


title: HA/S mRNA-41-d28

description: Total IgG


title: pat. 2, organoid, fundus, repl.1


title: pat. 3, MRA, antrum, repl.1


title: S mRNA-34-d28

description: Total IgG


title: S mRNA-33-d28

description: Total IgG


title: S mRNA-31-d28

description: Total IgG


title: ATAC Day_8_Hdac1-KO_Stem-2

description:
Day_8_Hdac1-KO_Stem_peaks.narrowPeak
Day_8_Hdac1-KO_Stem_scaled.bw

source_name: Hdac1-deficient Tex-Stem cells


title: pat. 2, organoid, antrum, repl.1


title: HA mRNA 25-d28

description: Total IgG


title: HA mRNA 24-d28

description: Total IgG


title: ATAC Day_8_Hdac1-KO_Stem-1


title: ATAC Day_8_Hdac1-KO_Int-2

description:
Day_8_Hdac1-KO_Int_peaks.narrowPeak
Day_8_Hdac1-KO_Int_scaled.bw

source_name: Hdac1-deficient Tex-Int cells


title: HA mRNA 22-d28

description: Total IgG


title: PBS-15-d28

description: Total IgG


title: NRVM_Nit_2_2

city: Dover

first: David

middle: C

last: Zebrowski

state: DE

address: 1151 Walker Rd

institute: GenKardia Inc.

data_processing:
Raw sequence reads were mapped to the RAT genome (RN6) and human genome (hg38) using Tophat2 with Bowtie2 option where adaptor sequences were removed using trim_galore before read mapping.
BAM files containing the alignment results were sorted according to the mapping position. Raw read counts for each gene were calculated using featureCounts from Subread package.
Differential expression analysis was performed using DEseq2, with raw counts as input. The differentially expressed genes were identified by adjusted p value for multiple testing using Benjamini-Hochberg correction with False Discovery Rate (FDR) values less than 0.1.
Assembly: rat genome (RN6) and human genome (hg38)
Supplementary files format and content: Excel file includes results from differential expression analysis and normalized counts per gene and sample

organism: Rattus norvegicus

source_name: primary cells

growth_protocol: Neonatal Rat Ventricular Cardiomyocyte Isolation and Culture: Ventricular cardiomyocytes were isolated from 6-day old neonatal Sprague-Dawley rats as described previously (18). Cardiomyocytes were seeded and cultured in DMEM/F-12, GlutamaxTM-I (ThermoFisher Scientific, catalogue number: 10565018) + Penicillin (100 U/ml)/Streptomycin (100 µg/ml) (Pen/Step) (ThermoFisher Scientific, catalogue number: 15140122) for 2 days prior to experimentation.Cells were plated in 24-well plates on glass coverslips (ThermoScientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Fibronectin for at least 2 hours at RT prior to seeding. Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Human iPSC-derived Cardiomyocytes and Culture: Human induced-PSC-derived cardiomyocytes (hiPSC-CMs) were acquired from Fujifilm Cellular Dynamics International, Inc. (CDI) (iCell Cardiomyocytes, catalogue number: CMC-100-010-001). hiPSC-CMs from CDI were seeded and cultured according to manufacture´s directions (https://cellulardynamics.com/assets/CDI_iCellCardiomyocytes_UG.pdf). CDI iCell Cardiomyocyte lot numbers used in this study: #1833511, #1099441, #1098841. In brief, hiPSC-CMs were thawed and cultured in plating medium (CDI, catalogue number: M1003) for 2 days and then cultured in maintenance medium (CDI, catalogue number: M1001) for 4 days. Afterwards, hiPSC-CMs were treated with compounds for 2 days prior to fixation or RNA isolation. hiPSC-CMs were plated in 24-well plates on glass coverslips (Thermo Fisher Scientific. Menzel-Gläser. 13mm #0, catalogue number: 17274914) coated with Matrigel (Corning, catalogue number: 356255) for at least 2 hours at RT.

extract_protocol:
P6-NRVMs and CDI-CMs were treated with Nitrendipine or 1-NA-PP1 for 2 days prior to RNA extraction. In addition, both P6-NRVMs and CDI-CMs during treatment with Nitrendipine or 1-NA-PP1 were cultured in the presence of araC. AraC was used to reduce overgrowth of contaminating cardiac fibroblasts (which generally amount to ~3% of cultured cells in primary cardiomyocyte isolation procedure). RNA was extracted from sub-confluent 10-cm plates using Qiagen RNeasy mini kit. RNA quality (RNA integrity number, RIN) and quantity was measured in a Bioanalyzer 2100 (Agilent) using the Agilent RNA 6000 Nano Kit (part number 5067-1511). The sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England Biolabs), starting with 200 ng of total RNA. In brief, mRNA was isolated and fragmented using the NEBNext poly(A) mRNA magnetic isolation module (E7490S, New England Biolabs), with the first and second strands of cDNA synthesized and purified using AmPure XP SPRI beads (A63880, Beckman Coulter). Then adaptor ligation and size selection wereperformed according to the manufacturer’s protocol. Next, the adaptor ligated cDNA was PCR enriched to incorporate an Illumina compatible index sequence (NEBNext Oligos for Illumina, Dual Index Primers Set1 (E7600S, New England Biolabs). All libraries were purified using AmPure XP SPRI beads, and the size distribution of the libraries was analyzed at the Bioanalyzer 2100 using the Agilent High Sensitivity DNA Kit (part number 5067-4626). Subsequently, the quantification of the libraries was performed with the Qubit® 2.0 Fluorometer (ThermoFisher Scientific) and QubitTMdsDNA HS Assay Kits (Q32851, Invitrogen). Finally, all 19 libraries were pooled and diluted to 3.5 nM for sequencing on one lane of a Hiseq 3000 sequencer (Illumina), using a single read 50 bp and dual indexed sequencing strategy.
The sequencing libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacture's protocols.

treatment_protocol: Treatment of NRVMs with Nitrendipine and 1-NA-PP1 was done in the presence of 5%HS and 10%FBS for 2 days prior to fixation or RNA-isolation. Treatment of CDI cardiomyocytes with Nitrendipine and 1-NA-PP1 was done in the presence of CDI culture medium for 2 days prior to fixation or RNA-isolation.

value: primary cells

tag: cell type

value: cardiomyocytes

tag: developmental stage

value: neonatal

value: Nitrendipine, 48 hours

value: day 7 (P7)


title: HA mRNA-21-d28

description: Total IgG


title: Donor 1 facial skin

type: RNA

city: Hamburg

first: Tolga

last: Düz

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

description: The gene panel of 278 genes for our MERFISH analyses includes driver genes identified in the scRNA-seq sebocyte differentiation analysis, as well as additional markers of interest relevant to sebaceous gland biology and general skin function.

hyb_protocol: The generation of the MERFISH data was performed following the standard methods outlined by Chen et al. (2015). except for the tissue clearing procedure. After gel embedding, tissue digestion was conducted at 37°C for 6 hours. Subsequently, clearing was performed at 47°C overnight, followed by autofluorescence quenching for 6 hours. Finally, the samples were cleared at 37°C for 36 to 48 hours. Single-stranded DNA (ssDNA) staining was performed.

scan_protocol: MERFISH images were scanned on MERSCOPE™ platform provided by Vizgen.

data_processing:
The files were assembled in a proprietary data file type (.vzg) and were uploaded into the MERSCOPE Visualizer software, allowing data exploration through a user interface.
Individual transcript count per cell are presented in cell-by-gene matrix. Values in cell-metadata matrix are defined in 'MERSCOPE Instrument User Guide' Rev H.

source_name: Facial skin tissue

extract_protocol: Fresh frozen tissue were OCT embedded.

tag: condition

value: Healthy

tag: region

value: temporal region

tag: Sex

value: Female

tag: age

tag: ethnicities

value: Caucasian