description:
Library name: BOOST014_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST014_Hu_2_CD4_9D


status: Public on Jul 29 2025

type: SRA

city: La Jolla

first: Alessandro

last: Sette

state: CA

address: 9420 Athena Cir

department: Center for Infectious Disease and Vaccine Research

country: USA

institute: La Jolla Institute for Immunology

description:
Library name: BOOST014_Hu_3_CD8_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST014_Hu_3_CD8_9D

library_source: transcriptomic single cell

data_processing:
Processing of scRNA-seq libraries: Data from scRNA-seq libraries were preprocessed by employing the 10x’s cellranger suite (v7.1.0) and the pre-built GRCh38 human genome reference (2020-A) as previously described (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020). Gene expression data from individual libraries were merged into one aggregated set for CD4+ T cells and another for CD8+ T cells. Metric reports for all single-cell transcriptome libraries and aggregated datasets indicate good-quality data. As detailed before (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020), the Seurat toolkit (v3.2.3) (Stuart et al., Cell, 2019) was employed in R to perform quality control (QC), unbiased clustering, dimensionality reduction and cluster annotation on each aggregated dataset. The following QC criteria were enforced to minimize doublets and eliminate low-quality transcriptomes: 1,500 unique molecular identifier (UMI) count 20,000; 800 gene count 4,400; and mitochondrial UMI percentage 10%. For dimensionality reduction and unbiased clustering, only the most variable genes accounting for 30% of the total standardized variance and the 30 principal components (PCs) were considered as arguments in the workflow described previously (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020). The final set of clusters identified at resolutions 0.4 and 0.2, respectively, for CD4+ and CD8+ T cells, were considered for in-depth annotation on the basis of their markers and gene set enrichment analysis (GSEA), as well as for downstream analyses. For comparisons involving early and late time points, samples collected at 1, 3, 6 and 9 months following the second vaccine dose were altogether considered as early time points, whereas samples collected at 3, 6, 9 and 12 months following the fourth vaccine dose were grouped and designated as late time points.
Processing of hashtag oligonucleotide (HTO)-seq libraries: Hashtag oligonucleotide (HTO) data were leveraged to perform sample deconvolution and further identify and remove multiplets, with the HTO data processed with the cellranger suite (v7.1.0) and deconvolution performed with the function MULTIseqDemux function from Seurat (v3.2.3) as detailed before (Kusnadi et al., Science Immunol, 2021; Meckiff et al., Cell, 2020).
Assembly: GRCh38 (2020-A reference prebuilt and provided by 10x cellranger).
Supplementary files format and content: BOOST-1-CD4_processed_data_umi_counts.RDS: RDS file storing a numeric dgcMatrix object with raw UMI counts (seurat object slot "counts") for the aggregated dataset of CD4+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD4_processed_data_normalized_counts.RDS: RDS file storing a numeric dgcMatrix object with non-scaled normalized UMI counts (seurat object slot "data") for the aggregated dataset of CD4+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD4_processed_data_annotations.txt: The metadata including custom annotations made for the aggregated dataset of CD4+ T cells. Data are provided as tab-separated values; each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant Hashtag Oligo (HTO) data-related annotations have been provided in this file as well, including sample- and donor-related annotations.
Supplementary files format and content: BOOST-1-CD8_processed_data_umi_counts.RDS: RDS file storing a numeric dgcMatrix object with raw UMI counts (seurat object slot "counts") for the aggregated dataset of CD8+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD8_processed_data_normalized_counts.RDS: RDS file storing a numeric dgcMatrix object with non-scaled normalized UMI counts (seurat object slot "data") for the aggregated dataset of CD8+ T cells (gene expression data). In matrix, each column represents a cell (column names are 10x cell barcodes) and each row represents a gene (row names are gene symbols as in reference).
Supplementary files format and content: BOOST-1-CD8_processed_data_annotations.txt: The metadata including custom annotations made for the aggregated dataset of CD8+ T cells. Data are provided as tab-separated values; each column represents a metadata annotation (column names are mostly self-explanatory, but any questions about them may be addressed to our GitHub repository; see manuscript) and each row represents a cell barcode. Relevant Hashtag Oligo (HTO) data-related annotations have been provided in this file as well, including sample- and donor-related annotations.
Supplementary files format and content: feature_README.txt: File alike the feature_reference.csv file used as input for cellranger feature count. However, 1) it is in tsv format and 2) it lists the information for all HTO/ADT libraries included in this project, which are specified under column "sample_id".

molecule: total RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: The blood samples from multiple visits (time-points) from 54 donors were collected in heparin-coated blood bags. Peripheral blood mononuclear cells (PBMCs) were isolated using the same methodology as in previous studies (Dan et al., Science, 2021; Grifoni et al., Cell, 2020; Zhang et al., Cell, 2022), employing Ficoll-Paque (Lymphoprep, Nycomed Pharma, Oslo, Norway). In brief, whole blood was centrifuged for 15 minutes at 400g to separate the cellular fraction and plasma. Plasma was collected and stored at -20°C. PBMCs were separated by density-gradient sedimentation with Ficoll-Paque® PLUS. Isolated PBMCs were washed twice with RPMI 1640 to remove any residual Ficoll-Paque® PLUS. Subsequently, the PBMCs were resuspended in freezing media containing 90% fetal bovine serum (FBS; Hyclone Laboratories, Logan, UT) and 10% dimethyl sulfoxide (DMSO; Gibco, Waltham, MA) before time and temperature-controlled cryopreservation in liquid nitrogen until used for experiments.

extract_protocol:
To detect T cell-specific responses to SARS-CoV-2 Spike (S) antigens, we employed an activation-induced marker (AIM) assay methodology in combination with peptide megapool (MP) stimulation using the dual activation marker expression of OX40+4-1BB+ or CD69+4-1BB+ to detected antigen-specific CD4+ and CD8+ T cells, respectively (da Silva Antunes et al., Curr Protoc, 2023; Dan et al., J Immunol, 2016). Briefly, PBMC vials were thawed with subsequent determination of cell number. PBMCs were then plated in 96-well U-bottom plates at a concentration of 1-2×10^6 cells per well and immediately cultured together with peptide MPs (1 µg/mL), or phytohemagglutinin-L (PHA) (10 µg /mL; Roche, San Diego, CA) and DMSO as positive and negative controls, respectively, in 5% human serum (Gemini Bio-Products) for 18-24 h. After culture, cells were collected, washed and stained with the following antibody cocktail: CD8 BUV496 (1:50; BioLegend, clone RPA-T8, Cat# 612942), CD3 BUV805 (1:50; BioLegend, clone UCHT1, Cat# 612895), CD14 V500 (1:50; BioLegend, clone M5E2, Cat# 561391), CD19 V500 (1:50; BioLegend, clone HIB19, Cat# 561121), CD4 BV605 (1:100; BioLegend, clone RPA-T4, Cat# 562658), CD69 PE (1:50; BioLegend, clone FN50, Cat# 555531), OX40 PE-Cy7 (1:50; BioLegend, clone Ber-ACT35, Cat# 350012), 4-1BB APC (1:25; BioLegend, clone 4B4-1, Cat# 309810), Live/Dead Viability dye eFLuor506 (0.1:100; Invitrogen, Cat# 65-0866-14), brilliant staining buffer and PBS before being refrigerated for 30 minutes at 4°C, protected from light. TotalSeqTM-C oligonucleotide-conjugated antibodies (BioLegend) were also added at this step at 0.01mg/mL final concentration (one distinct antibody per sample). After two washes in PBS, cells were resuspended into 500 μl of MACS buffer (PBS containing 2mM EDTA (pH 8.0) and 0.5% BSA) and stored at 4ºC until flow cytometry acquisition. Activated CD4+ (OX40+4-1BB+) and CD8+ (4-1BB+CD69+) AIM+ cells were subsequently sorted using a BD FACSAria Fusion cell sorter (Becton Dickinson), and by employing the gating strategy represented in Fig S5 of the manuscript associated to these data. After sorting, ice-cold PBS was added, cells spun down, and single-cell libraries prepared.
For single-cell RNA-seq assays (10x Genomics, Pleasantown), in average 20,000- 50,000 AIM+ T cells per subject were sorted directly into low-retention, sterile 1.5 mL collection tubes (Thermo-fisher) pre-chilled on ice and containing 500 µl of PBS:FBS solution (1:1, vol:vol) supplemented with RNAse inhibitor (1:100, Takara Bio). 5 to 6 different samples were multiplexed using the TotalSeq-C DNA-oligo barcoded cell-surface housekeeping molecule antibodies (Biolegend) totaling approximately 60,000 cells per 10x lane (equivalent to one well of the 10x chip). Multiplexed samples were centrifuged at 600 ×g for 10 minutes at 4°C, and the supernatant was carefully removed, leaving behind 10-12 µL of residual volume. Cell pellets were resuspended in 25 µL of 10x Genomics-compatible resuspension buffer (0.22 µm filtered PBS containing 0.04 % ultrapure bovine serum albumin, Sigma-Aldrich). A 33 µL aliquot of the resuspended cells was transferred to an 8-strip PCR tube for downstream processing as per the 10x Genomics protocol. Left-over was used as cell-counting quality control check. Following the manufacturer's recommendations, single-cell RNA libraries were generated using the 10x Genomics standard 5’TAG v2 chemistry. Both cDNA amplification and library preparation were carried out using 13 PCR cycles. Barcoded cDNA products were collected, quantified, and pooled at equimolar concentrations. The libraries were sequenced on the Illumina Novaseq6000 (NIH, S10) platform with paired-end sequencing (S4 100x100cycle, Illumina) configured as follows: read length: read 1, 100 cycles; read 2, 100 cycles; i7 index, 10 cycles and i5 index 10 cycles. Size and quantity quality controls were performed throughout the procedure by capillary DNA high sensitivity electrophoresis (HS NGS Fragment Kit ,1-6000bp, Fragment Analyzer, Agilent) and Picogreen assay (Quant-iT™ PicoGreen™ dsDNA Assay Kits and dsDNA Reagents). Sequencing depth was aimed to reach 30,000 reads per cell for gene expressions, 8,000 reads/ cell for TCR, and antibody-feature sequencing (multiplexing analysis).

tag: tissue

value: Blood

tag: cell type

value: SARS-CoV-2 Spike (S) AIM+ CD8 T cells:CD3+ CD8+ CD69+ 4-1BB+

tag: treatment

value: Activation-induced marker (AIM) assay


description:
Library name: BOOST014_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST014_Hu_1_CD4_9D

value: SARS-CoV-2 Spike (S) AIM+ CD4 T cells:CD3+ CD4+ OX40+ 4-1BB+


title: ADARhet_MDA5het_Tdt_1

city: Stanford

first: Chad

middle: S

last: Weldy

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

description: 10X Genomics, tdT positive cells only

data_processing:
Demultiplexed Fastq files and matrix files were generated with Cellranger.
Assembly: mm10 genome used for reference
Supplementary files format and content: filtered sequence read with matrix.h5 files are reported and ultimately used in Seurat for data analysis.

organism: Mus musculus

source_name: aortic root, ascending aorta to brachiocephalic artery take off

extract_protocol:
readme_extract_protocol.txt
scRNA libraries were prepared following 10X protocol.
cDNA libraries were then sequenced to at least 50K reads per cell.

value: tdT positive cells only

tag: genotype

value: Adar1 fl/WT, Ifih1-/+, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 24 weeks of age with atherosclerosis


title: ADAR_MDA5_Tdt_3

description: 10X Genomics, tdT positive cells only

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Adar1 fl/fl, Ifih1-/-, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 10 weeks of age


description:
Library name: BOOST017_Hu_1_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST017_Hu_1_CD4_9D


description:
Library name: BOOST017_Hu_2_CD4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST017_Hu_2_CD4_9D


description:
Library name: BOOST013_Hu_3_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST013_Hu_3_9D


description:
Library name: BOOST013_Hu_4_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST013_Hu_4_9D


description:
Library name: BOOST013_Hu_2_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST013_Hu_2_9D


description:
Library name: BOOST013_Hu_1_9D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST013_Hu_1_9D


title: ADARhet_MDA5het_nTdt_3

description: 10X Genomics, tdT negative cells only

value: tdT negative cells only


title: ADAR_MDA5_nTdt_2

description: 10X Genomics, tdT negative cells only


title: ADAR_MDA5_Tdt_1

description: 10X Genomics, tdT positive cells only


title: ADAR_MDA5_nTdt_1

description: 10X Genomics, tdT negative cells only


description:
Library name: BOOST012_Hu_3_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_3_CD4_13D


title: E16.5

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

country: China

institute: the First Affiliated Hospital of China Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: knee joint tissue

extract_protocol:
Knee regions were dissected out from E16.5 C57BL/6 mouse embryos by microsurgical procedures with the aid of a Leica dissecting microscope, regions that included the developing joint itself and neighboring tissues. Samples were finely minced and dissociated into single cell suspensions by treatment with dispase (50 U/ml in HBSS) for 2 hrs at 37C. Cells were then suspended in 5% FBS/DMEM at a concentration of 700-1200 cells/l. Cell suspensions were immediately delivered to the Center for Applied Genomics (Children’s Hospital of Philadelphia) for determination of cell viability and sample processing. Viability of  > 95% in all samples.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: knee joint tissue

value: joint tissue cell

value: wt


description:
Library name: BOOST012_Hu_3_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_3_CD8_13D


description:
Library name: BOOST012_Hu_2_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_2_CD8_13D


title: E3

city: Jilin Province

first: He

middle: Yu

last: hang

address: 5451 Xi'an Road

department: College of Veterinary Medicine

institute: Jilin University

description: E3:Administer PBS orally daily for seven consecutive days.

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
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.
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10

source_name: Uterine samples

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.

value: uterus

value: Administer PBS orally daily for seven consecutive days, and then collect uterine tissue for RNA seq detection


title: E2

description: E2:Administer PBS orally daily for seven consecutive days.


description:
Library name: BOOST012_Hu_1_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_1_CD8_13D


title: ADAR_MDA5_Tdt_2

description: 10X Genomics, tdT positive cells only


description:
Library name: BOOST011_Hu_6_12
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_6_12


title: ADAR_MDA5_nTdt_3

description: 10X Genomics, tdT negative cells only


title: DE2

description: DE2:Administer 400mg/kg DI (Dimethyl itaconate) orally daily for seven consecutive days.

value: Administer 400mg/kg DI (Dimethyl itaconate) orally daily for seven consecutive days, and then collect uterine tissue for RNA seq detection


description:
Library name: BOOST011_Hu_5_12
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_5_12

value: Blood


title: DE1

description: DE1:Administer 400mg/kg DI (Dimethyl itaconate) orally daily for seven consecutive days.


description:
Library name: BOOST011_Hu_4_12
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_4_12

value: SARS-CoV-2 Spike (S) AIM+ CD8 T cells:CD3+ CD8+ CD69+ 4-1BB+


description:
Library name: BOOST011_Hu_1_12
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST011_Hu_1_12

value: Activation-induced marker (AIM) assay


title: TA_IL-7_H2A.Z-CUTandTag_rep2

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

library_source: genomic

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to quantify the H2A.Z CUT&Tag signal throughout the genome.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: spleen

growth_protocol: T cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 10mM HEPES, 1% NEAA, 1% P/S, 50uM β-Mercaptoethanol in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z antibody (abcam, #ab4174) in Tcells and Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904).
CUT&Tag assay was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904) following the manufacturer’s instructions.

treatment_protocol: OT-I naive CD8+ T cells (CD62L+CD44-) were stimulated by 1 µg/ml coated anti-CD3/CD28 Abs for 24 h (Activated T cells, TA), and then stimulated with 50 ng/ml IL-7 or IL-15 for another 24 h, respectively. Collected all subsets and then detected the deposition of H2A.Z via CUT&Tag-seq.

value: spleen

tag: cell line

value: naive CD8+ T cell

value: WT

value: anti-CD3/CD28 Abs for 24 h, and then stimulated with IL-7 for another 24 h


title: TA_IL-7_H2A.Z-CUTandTag_rep1


description:
Library name: BOOST010_1_CD8
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_1_CD8


description:
Library name: BOOST010_2_CD4
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_2_CD4

value: SARS-CoV-2 Spike (S) AIM+ CD4 T cells:CD3+ CD4+ OX40+ 4-1BB+


description:
Library name: BOOST012_Hu_2_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_2_CD4_13D


title: TA_H2A.Z-CUTandTag_rep1

value: anti-CD3/CD28 Abs for 24 h


title: TA_H2A.Z-CUTandTag_rep2


title: Naive_H2A.Z-CUTandTag_rep2

value: unstimulated


description:
Library name: BOOST009_Hu_CD8_13D_4
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD8_13D_4


title: Naive_H2A.Z-CUTandTag_rep1


description:
Library name: BOOST009_Hu_CD8_13D_2
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD8_13D_2


description:
Library name: BOOST012_Hu_1_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST012_Hu_1_CD4_13D


description:
Library name: BOOST008_Hu_2_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_2_CD4_13D


title: WT-TM_H3K27ac-ChIP-seq_rep2

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Splenocytes were isolated and specific CD8 T cell subsets were sorted by FACS. ATAC-seq was performed with TruePrep® DNA Library Prep Kit V2 for Illumina® (Vazyme, #TD501-01).  DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z antibody (abcam, #ab4174), Pol II phospho S5 (abcam, #ab5131), H3K4me3 (abcam, #ab8580), H3K27me3 (Millipore, #07-449) in Tcells and Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904). The ChIP experiment was conducted using the ULI-NChIP protocol to detect the enrichment of H3K27ac (abcam, #ab4729).
ATAC-seq library was constructed by TruePrep® DNA Library Prep Kit V2 for Illumina® (Vazyme, #TD501-01),  following the manufacturer’s instructions. CUT&Tag libraries was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904), following the manufacturer’s instructions.   ChIP libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, #E7645L), following the manufacturer's instructions.

value: memory CD8+ T cell


title: RB6935_51

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

description: APOE4, 15 months, Irregular menstrual cycles

data_processing:
Salmon v 0.15.0 was used to map the reads to Mouse cDNA library to get the quants
Tximport was used to get the unnormalized gene counts
DESeq2 was used to get the normalized gene counts for each sample
Assembly: Mus musculus Emsembl Release 95
Supplementary files format and content: Each processed file (.sf) contains the counts of each mapped transcript
Supplementary files format and content: unormalized counts,deseq2_p3apoe_unNormalizedCounts.csv
Supplementary files format and content: normalized counts,deseq2_p3apoe_NormalizedCounts.csv

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

tag: age

value: 15 months

tag: menstrual cycle

value: Irregular menstrual cycles


title: cKO-TM_H3K27ac-ChIP-seq_rep2

value: cKO


description:
Library name: BOOST008_Hu_2_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_2_CD8_13D


title: DE3

description: DE3:Administer 400mg/kg DI (Dimethyl itaconate) orally daily for seven consecutive days.

value: uterus


description:
Library name: BOOST008_Hu_1_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_1_CD8_13D


title: WT-TM_H3K27ac-ChIP-seq_rep1


title: cKO-TM_H3K27ac-ChIP-seq_rep1


description:
Library name: BOOST010_1_CD4
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_1_CD4


title: cKO-TM_Input-ChIP-seq_rep2


description:
Library name: BOOST007_Hu_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST007_Hu_CD4_13D


description:
Library name: BOOST010_3_CD8
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST010_3_CD8


description:
Library name: BOOST009_Hu_CD4_13D_3
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD4_13D_3


title: cKO-TM_Input-ChIP-seq_rep1


title: WT-TM_Input-ChIP-seq_rep2


title: WT-TM_Input-ChIP-seq_rep1


title: cKO-TM_PolIIS5P-CUTandTag_rep2

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag


description:
Library name: BOOST006_Hu_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST006_Hu_CD8_13D


description:
Library name: BOOST008_Hu_1_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST008_Hu_1_CD4_13D


description:
Library name: BOOST006_Hu_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST006_Hu_CD4_13D


description:
Library name: BOOST009_Hu_CD4_13D_1
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST009_Hu_CD4_13D_1


description:
Library name: BOOST005_Hu_2_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_2_CD8_13D


title: cKO-TM_PolIIS5P-CUTandTag_rep1


description:
Library name: BOOST005_Hu_1_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_1_CD8_13D


title: WT-TM_PolIIS5P-CUTandTag_rep2


title: WT-TM_PolIIS5P-CUTandTag_rep1


title: E1

description: E1:Administer PBS orally daily for seven consecutive days.

value: Administer PBS orally daily for seven consecutive days, and then collect uterine tissue for RNA seq detection


description:
Library name: BOOST005_Hu_1_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_1_CD4_13D

value: Blood


title: WT-TM_H3K27me3-CUTandTag_rep1


title: cKO-TM_H3K27me3-CUTandTag_rep2


title: cKO-TM_H3K27me3-CUTandTag_rep1


description:
Library name: BOOST004_Hu_3_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_3_CD8_13D

value: SARS-CoV-2 Spike (S) AIM+ CD8 T cells:CD3+ CD8+ CD69+ 4-1BB+


description:
Library name: BOOST004_Hu_2_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_2_CD4_13D

value: Activation-induced marker (AIM) assay


title: cKO-TM_H3K4me3-CUTandTag_rep2

value: spleen


description:
Library name: BOOST003_Hu_2_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_2_CD4_13D


title: cKO-TM_H3K4me3-CUTandTag_rep1


description:
Library name: BOOST003_Hu_1_CD8_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_1_CD8_13D


title: WT-TM_H3K4me3-CUTandTag_rep2


title: WT-TM_H3K4me3-CUTandTag_rep1


title: cKO-TM_ATAC-seq_rep2


title: cKO-TM_ATAC-seq_rep1


description:
Library name: BOOST005_Hu_2_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST005_Hu_2_CD4_13D


description:
Library name: BOOST001_Hu_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST001_Hu_CD4_13D


title: WT-TM_H3K27me3-CUTandTag_rep2


description:
Library name: BOOST003_Hu_1_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST003_Hu_1_CD4_13D


description:
Library name: BOOST002_Hu_2_CD8_12D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_2_CD8_12D


title: WT-TM_ATAC-seq_rep1


title: WT-TM_ATAC-seq_rep2


description:
Library name: BOOST002_Hu_1_CD4_12D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_1_CD4_12D


description:
Library name: BOOST002_Hu_1_CD8_12D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_1_CD8_12D


title: cKO-TM_H2A.Z-CUTandTag_rep2


title: cKO-TM_H2A.Z-CUTandTag_rep1


title: Lot LA82 from 3D culture at day 4

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description:
Library name: 823DD4
Lot LA82 from 3D culture at day 4

data_processing:
RNA sequencing (RNA-seq) libraries were prepared by Azenta Life Sciences and sequenced on an Illumina NextSeq 500 platform, generating paired-end reads. Raw FASTQ files were trimmed using Trim Galore to remove adaptor sequences and low-quality bases. Alignment to the Homo sapiens reference genome (GRCh38/hg38) was performed using the align() function from the Rsubread package (v2.12.3; Liao Y, Smyth GK, Shi W (2019)), generating sorted BAM files. The mapping efficiency was assessed using the propmapped() function. Gene-level quantification was conducted using the featureCounts() function in Rsubread, with annotation from the inbuilt hg38 gene model. Only uniquely mapped, properly paired reads were counted.
Downstream analysis was performed in R using the edgeR and limma packages (edgeR;Robinson MD, McCarthy DJ, Smyth GK (2010), limma; Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015)). Raw counts were converted into a DGEList object and annotated using the org.Hs.eg.db database from Bioconductor. Lowly expressed genes were filtered out using a threshold of ≥0.5 counts-per-million (CPM) in at least six libraries. Normalization for library size and composition bias was performed using the trimmed mean of M-values (TMM) method.
Differential expression analysis was carried out using the limma-voom pipeline. The voom() function was used to model the mean-variance relationship and generate precision weights, which were then used in linear modeling via the lmFit() function. Contrast matrices were defined for each comparison, and empirical Bayes moderation of variance estimates was applied using the eBayes() function. Adjusted p-values were calculated using the Benjamini–Hochberg procedure to control the false discovery rate. Genes with an adjusted p-value < 0.05 were considered significantly differentially expressed.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel file with normalized raw counts for all samples.

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: All cultures were grown in complete endothelial cell growth medium for the indicated time points.

extract_protocol:
Cultures were washed with cyclohexamide diluted in PBS and flash frozen on dry ice prior to homogenization in 400uL of polysome lysis buffer. Homogenized lysates are incubated with anti-HA beads for 18 hours at 4 degrees celsius. RNA was isolated from the magnetic beads with the Qiagen RNeasy Plus Micro Kit (Ref # 74034), the concentration determined using the Qubit RNA High Sensitivity Kit) Ref# Q32853 C), and the RIN score calculated using the Agilent Technologies RNA Pico Chips for use with the Agilent 2100 Bioanalyzer system (#5057-1513). Only RIN scores greater than 7 were used for library preparation at Genewiz/Azenta.
Library preparation by Azenta Life Sciences; https://www.genewiz.com/public/services/next-generation-sequencing/rna-seq

value: Human Umbilical Vein Endothelial Cells

value: Rpl22- 3X HA

tag: batch

value: 3D Day 4


title: Lot LA82 input from 3D culture at day 8

description:
Library name: 823DD8i
Lot LA82 input from 3D culture at day 8

value: 3D Day 8 Input


title: WT-TM_H2A.Z-CUTandTag_rep2

value: WT


description:
Library name: BOOST004_Hu_1_CD4_13D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST004_Hu_1_CD4_13D

value: SARS-CoV-2 Spike (S) AIM+ CD4 T cells:CD3+ CD4+ OX40+ 4-1BB+


title: Lot LA82 from 2D culture at day 1

description:
Library name: 822DD1
Lot LA82 from 2D culture at day 1

value: 2D Day 1


title: Lot LA42 from 3D culture at day 4

description:
Library name: 423DD4
Lot LA42 from 3D culture at day 4


title: WT-TM_H2A.Z-CUTandTag_rep1

value: memory CD8+ T cell

value: unstimulated


title: TN_H2A.Z-CUTandTag_rep2

value: naive CD8+ T cell


title: Lot LA42 from 3D culture at day 1

description:
Library name: 423DD1
Lot LA42 from 3D culture at day 1

value: 3D Day 1


title: Lot LA42 from 2D culture at day 1

description:
Library name: 422DD1
Lot LA42 from 2D culture at day 1


title: TN_H2A.Z-CUTandTag_rep1


title: Lot PT19 input from 3D culture at day 8

description:
Library name: 193DD8i
Lot PT19 input from 3D culture at day 8


title: TM_PolIIS5P-CUTandTag_rep2


title: Lot PT19 from 3D culture at day 8

description:
Library name: 193DD8
Lot PT19 from 3D culture at day 8

value: 3D Day 8


title: TN_PolIIS5P-CUTandTag_rep2


title: Lot PT19 from 3D culture at day 4

description:
Library name: 193DD4
Lot PT19 from 3D culture at day 4


title: TM_PolIIS5P-CUTandTag_rep1


title: Lot PT19 from 2D culture at day 1

description:
Library name: 192DD1
Lot PT19 from 2D culture at day 1


title: Lot PT19 from 3D culture at day 1

description:
Library name: 193DD1
Lot PT19 from 3D culture at day 1


title: 24h_TM_stimulated_rep2

data_processing:
Trim Galore (v0.6.7) and Trimmomatic (v0.39) was used to remove the low quality reads (parametrs- --quality 20 --stringency 3)
STAR (v2.7.9a) was used to align reads to the mouse genome
RSEM (version 1.3.1) with the command rsem-calculate-expression was used to calculate the FPKM values for gene expression in each sample
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

growth_protocol: T cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
0h, 6h and 24h after treatment, RNA was isolated from the T cells using EasyPure® RNA Kit (TransGen Biotech, Cat# ER101-01).
RNA libraries for RNA-seq was prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme, Cat# TR502-02) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with or without 2 µg/ml coated anti-CD3 antibody and 1 µg/ml soluble anti-CD28 antibody.


title: 24h_TM_stimulated_rep1


title: TN_PolIIS5P-CUTandTag_rep1


title: Lot PT25 from 2D culture at day 1

description:
Library name: 25-2D-D1
Lot PT25 from 2D culture at day 1


title: Lot PT25 from 3D culture at day 4

description:
Library name: 253DD4
Lot PT25 from 3D culture at day 4


title: 0h_TM_resting_rep2


title: 6h_TM_stimulated_rep2


title: Lot PT25 from 3D culture at day 1

description:
Library name: 253DD1
Lot PT25 from 3D culture at day 1


title: 6h_TM_stimulated_rep1


title: Lot PT25 input from 3D culture at day 8

description:
Library name: 253DD8i
Lot PT25 input from 3D culture at day 8


title: Lot PT25 from 3D culture at day 8

description:
Library name: 253DD8
Lot PT25 from 3D culture at day 8


title: 24h_TN_stimulated_rep2


title: 0h_TM_resting_rep1


title: 24h_TN_stimulated_rep1


title: AsPC-1-HNF1A-siRNA-3

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: Library name: RS-04164779

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE r38
Supplementary files format and content: Comma-separated file with raw counts

source_name: pancreas

extract_protocol:
Total rRNA is depleted then fragmented and primed for cDNA synthesis. Fragmented RNA was reverse transcribed into first strand cDNA using random primers. The RNA template was removed and replaced with a complementary strand incorporating dUTP (instead of dTTP), resulting in double-stranded cDNA (ds cDNA).
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) with 100ng RNA

value: pancreas

value: Epithelial/adenocarcinoma


title: 6h_TN_stimulated_rep2


title: AsPC-1-HNF1A-siRNA-1

description: Library name: RS-04164777


title: 6h_TN_stimulated_rep1


title: 0h_TN_resting_rep2


title: AsPC-1-Control-siRNA-2

description: Library name: RS-04164775

value: Control


title: AsPC-1-Control-siRNA-3

description: Library name: RS-04164776


title: 0h_TN_resting_rep1


title: ASD Het Stroma 3 (MEH291)

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description:
10x Genomics
ASD 135 Stroma - 2122759

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38(mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FACS purified PECAM1-;Tomato- stroma cells

extract_protocol:
Tissues were manually dissociated and then digested for 1 hour at 37°C in 2U/mLCollagenaseB (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50mM HEPES/KOH pH 7.4; 150mM NaCl. Cells were then spun down and resuspended in 2X volume 10%fetal bovine serum(FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70μm (#22363548, Fisher) and 40μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPIused as a live/dead cell marker.
RNA extraction and library preparation was performed according to manufacturer's instructions (single cell 3' v3.1 protocol, 10x Genomics)

value: aP2-Cre;Dicer1+/-;R26 tdTom/SmoM2


title: AsPC-1-Control-siRNA-1

description: Library name: RS-04164774


title: ASD WT Stroma 2 (MEH290)

description:
10x Genomics
ASD 136 Stroma - 2122758

value: FACS purified PECAM1-;Tomato- stroma cells

value: aP2-Cre;Dicer1+/+;R26 tdTom/SmoM2


title: ASD Het Stroma 2 (MEH289)

description:
10x Genomics
ASD 132 Stroma - 2122757


title: 53BP1koBRCA1ko Untreated

city: Amsterdam

first: Judith

last: Haarhuis

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample 3

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 and v3.0 (Servant et al., 2015).
Assembly: hg19
Supplementary files format and content: .hic file (contains contact matrices at various resolutions).

growth_protocol: HAP1 cells were grown in Iscove’s modified Dulbecco’s medium (IMDM, Gibco) supplemented with 10% heat-inactivated fetal calf serum (FCS, Sigma-Aldrich), 1% penicillin-streptomycin (PS) (Gibco) and 1% L-glutamine (Gibco).

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: Cells were untreated or exposed to 1μM olaparib for 24 hours.

value: 53BP1ko BRCA1ko

value: Untreated


title: Wild Type Untreated

description: Library name: Sample 1

value: Wild Type


title: ASD WT Stroma 1 (MEH279)

description:
10x Genomics
ASD 78 Stroma - 2081354


title: 53BP1koBRCA1ko Olaparib

description: Library name: Sample 4

value: Olaparib 24 hours


title: ASD Het Tumor 1 (MEH288)

description:
10x Genomics
ASD 135 Tumor - 2122756

source_name: FACS purified PECAM1-;Tomato+ tumor cells


title: ASD Het Stroma 1 (MEH281)

description:
10x Genomics
ASD 80 Stroma - 2081356


title: Wild Type Olaparib

description: Library name: Sample 2


title: siSF1-1, NPC line 2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Library name: cell2_siSF1_1
100M reads / replicate

data_processing:
Analysis of sequencing data quality, reads repartition (e.g., for potential ribosomal contamination), inner distance size estimation, genebody coverage, strand-specificity of library were performed using FastQC v0.11.2, Picard-Tools v1.119, Samtools v1.0, and RSeQC v2.3.9.
Reads were mapped using STAR v2.7.5a on the human hg38 genome assembly and read count was performed using featureCount from SubRead v1.5.0. Gene expression was estimated as described previously using Human FAST DB v2022_1 annotations. Only genes expressed in at least one of the two compared conditions were analyzed further. Genes were considered as expressed if their FPKM value was greater than FPKM of 98% of the intergenic regions (background).
Assembly: hg38
Supplementary files format and content: FPKM_with_gene_annotations.txt: Tab-delimited text file includes FPKM normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2022_1 were also provided.

source_name: Human cortical NPCs

growth_protocol: NPCs were seeded on dishes that were coated with Poly-L-ornithine and Laminin solutiuons and culture in Neurobasal™-A medium containing B-27 without vitamin A supplement, GlutaMAX™, 2-mercaptoethanol, and Antibiotic-Antimycotic. EGF (20ng/mL) and FGF (20ng/mL) were added to the medium. NPCs were cultured at 37°C in an atmosphere of 5% CO₂.

extract_protocol:
Total RNA was isolated using the NucleoSpin® RNA isolation kit (Macherey-Nagel). RNA integrity numbers (RINs) were consistently above 9.5.
Library preparation including end repair, tailing, ligation, and purification, was performed using 500 ng of RNA in a 50 µL reaction volume.

treatment_protocol: Gene knockdown in human NPCs was performed using a set of 4 siRNA against human SF1 gene (Dharmacon, ON-TARGETplus siRNA). A negative (non-targeting siRNA) and positive fluorescent siRNA were used as controls.

value: Human cortical NPCs

value: WTSli008-A-derived NPC

value: Cortical Neural Progenitor Cells

value: WT

tag: transfection duration


title: ASD WT Tumor 1 (MEH278sc)

description:
10x Genomics
ASD 78 Tumor - 2081353

value: FACS purified PECAM1-;Tomato+ tumor cells


title: siSF1-3, NPC line 2

description:
Library name: cell2_siSF1_3
100M reads / replicate


title: siSF1-2, NPC line 2

description:
Library name: cell2_siSF1_2
100M reads / replicate


title: Adar1Het_16wk_3_nontdT

description: 10X Genomics, tdT negative cells only

extract_protocol:
Aortic tissue was dissected from the aortic root to the brachiocephalic artery. Protocol follows as such:1) Prepare the Enzyme Solution (on ice):
Final (working) concentration of Liberase is 2 units/mL
Final (working) concentration of Elastase is 2 units/mL
For 1mL of enzyme solution:
Liberase TM (26 units/mL)77  uL
Elastase (125 units/mL)16  uL
HBSS907 uL
Total1   mL
2) Place enzyme mixture on ice while aorta is being harvested
3) Perfuse mouse with ~10mL PBS via LV puncture
4) Harvest aortic root and open longitudinally. Wash with PBS x3 in 12-well dish. Keep on ice while collecting from multiple mice.
5) Move root to 12-well dish with 1mL of enzyme mixture.
6) Incubate in 37C incubator for ~30-45 minutes (adjust time based on age and extent of calcification e.g. if Apoe w/ 16wk HFD incubate for 45 minutes). At the end of the incubation, mince thoroughly with scissors for a few minutes (<5min) until tissue is mostly dissolved.
7) Pipet up and down ~20-30 times to thoroughly disrupt tissue. Confirm full digestion under the microscope (single cells w/o clumps). If the tissue is not fully digested after pipetting incubate at 37C for an additional 10-15 minutes (may lead to increased cell lysis).
8) Transfer cell suspension into 1.5mL Eppendorf and centrifuge at 500xg for 5 minutes.
9) Carefully remove supernatant (confirm that the cell pellet is still present).
10) Resuspend the cells in 200uL HBSS (adjust volume as needed). Cell solution was then sorted for live cells on FACS and then proceeded to 10X capture following 10X protocol.
11) Immediately prior to FACS and/or staining, pass cells through a 35um strainer. Note: Coating collection tubes in BSA solution may improve cell survival.
scRNA libraries were prepared following 10X protocol.
cDNA libraries were then sequenced to at least 50K reads per cell.

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Adar1 fl/WT, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 24 weeks of age


title: siCTRL-3, NPC line 2

description:
Library name: cell2_siCtrl_3
100M reads / replicate


title: siCTRL-2, NPC line 2

description:
Library name: cell2_siCtrl_2
100M reads / replicate


title: Adar1Het_16wk_2_nontdT

description: 10X Genomics, tdT negative cells only


title: siCTRL-1, NPC line 2

description:
Library name: cell2_siCtrl_1
100M reads / replicate


title: siSF1-3, NPC line 1

description:
Library name: cell1_siSF1_3
100M reads / replicate

value: WTSli21-B-derived NPC


title: Adar1Het_16wk_1_nontdT

description: 10X Genomics, tdT negative cells only


title: Adar1Het_16wk_2_tdT

description: 10X Genomics, tdT positive cells only


title: Adar1Het_16wk_1_tdT

description: 10X Genomics, tdT positive cells only


title: siCTRL-3, NPC line 1

description:
Library name: cell1_siCtrl_3
100M reads / replicate


title: TA_IL-15_H2A.Z-CUTandTag_rep1

value: spleen

value: naive CD8+ T cell

value: anti-CD3/CD28 Abs for 24 h, and then stimulated with IL-15 for another 24 h


title: Control_16wk_3_tdT

description: 10X Genomics, tdT positive cells only

value: Adar1 WT/WT, Myh11 CreERT2, ApoE-/-, ROSA tdTomato


title: Control_16wk_3_nontdT

description: 10X Genomics, tdT negative cells only


title: AsPC-1-HNF1A-siRNA-2

description: Library name: RS-04164778

value: pancreas

value: Epithelial/adenocarcinoma


title: siCTRL-2, NPC line 1

description:
Library name: cell1_siCtrl_2
100M reads / replicate


title: siCTRL-1, NPC line 1

description:
Library name: cell1_siCtrl_1
100M reads / replicate


title: Adar1Het_16wk_3_tdT

description: 10X Genomics, tdT positive cells only


title: Control_16wk_2_tdT

description: 10X Genomics, tdT positive cells only


title: Control_16wk_2_nontdT

description: 10X Genomics, tdT negative cells only


title: XLAS Severe Organoid d22

first: Hassan

last: Saei

address: 24 boulevard de Montparnasse

department: Imagine Institute of Genetic Diseases

institute: Universite Paris Cite

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v7.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: iPSC-derived kidney organoid

growth_protocol: Induced pluripotent stem cells were differentiated into kidney organoids using a modified version of the Morizane et al. protocol and cultured in Advanced RPMI 1640 medium in a humidified atmosphere with 5% CO₂ at 37°C

extract_protocol:
Two separate batches of sample collection were performed for this project. In the first batch, 16 organoids were collected on day 22 of differentiation, including one isogenic control organoids, one severe XLAS organoid, and one moderate XLAS organoid, resulting in three libraries. An additional isogenic control was harvested on day 22 (Control_d22_2) and kept in culture for 38 days (Control_d38) and harvested at this later time point (two library, 5 libraries in total). Organoids were dissociated in two rounds of 10 minutes at 37°C with 500 µL of TrypLE. During each round, the tubes were gently flicked every five minutes for homogenization. At the beginning of each round, mechanical dissociation was performed by pipetting up and down five times. After a quick centrifugation, the supernatant was aspirated and inactivated in PBS with 10% SVF on ice. For the second round, 200 µL of TrypLE was added to the remaining organoids. The final suspension was filtered through a 40 µm cell strainer before pelleting the dissociated cells at 300g for 3 minutes. Cells were then resuspended in 1 mL of PBS containing 1% BSA and 1 mM EDTA and kept on ice. Cell viability, as assessed by cell counting, ranged between 70% and 85%. Libraries obtained from these two batches were sequenced together.
Libraries were generated using Chromium Next GEM Single Cell 3’ and Next GEM Chip G Single Cell Kits (10x Genomics) at the genomics platform at the Institute du Cerveau. The quality of the libraries was assessed using the High Sensitivity D5000 ScreenTape Assay for TapeStation Systems (Agilent), and the libraries were sequenced on NovaSeq X using the NovaSeq X plus 10B Reagent Kit (100 cycles). The minimum requested coverage was 50,000 reads per cell.

value: iPSC-derived kidney organoid

value: iPSC line 004

value: Kidney Organoid

tag: culture day

value: day 22


title: XLAS Moderate Organoid d22

description: 10x Genomics


title: Adar1KD_3_nontdT

description: 10X Genomics, tdT negative cells only

value: Adar1 fl/fl, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 10 weeks of age


title: siSF1-2, NPC line 1

description:
Library name: cell1_siSF1_2
100M reads / replicate

value: Human cortical NPCs

value: Cortical Neural Progenitor Cells

value: WT


title: Control_16wk_1_nontdT

description: 10X Genomics, tdT negative cells only

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 24 weeks of age


title: Adar1KD_2_nontdT

description: 10X Genomics, tdT negative cells only


title: siSF1-1, NPC line 1

description:
Library name: cell1_siSF1_1
100M reads / replicate

value: WTSli21-B-derived NPC


title: Control Organoid d22 R2

description: 10x Genomics

value: Isogenic Control


title: Healthy Organoids, iPSC-derived, Day 42, Replicate 3

data_processing:
Imagine Institutes in-house data processing protocol at bioinformatic platform - illumina Dragen IT for read aligmant and FeatureCounts for generating count matrix
Sequence reads were quality checked, trimed and aligned to the human genome GRCh38 using illumina Dragen IT pipeline
Read counts extrcation was performed by FeatureCounts and normalization was perfomed by DESeq2 package in R
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample

source_name: iPSC-derived kidney Organoid

extract_protocol:
Total RNA was extracted using Rnasey mini plus Kit (Qiagen, 74136) from a pool of nine organoids, and 200ng of total RNA was used for library preparation.
RNA libraries for RNA-seq was prepared using TECAN Universal Plus mRNA-seq library preparation kit, Tecan.

treatment_protocol: No treatment.

value: iPSC-derived kidney Organoid

value: Male - Line 004

value: Induced pluripotent stem cells

value: Healthy

tag: harvest time

value: Day 42


title: Adar1KD_2_tdT

description: 10X Genomics, tdT positive cells only


title: Control Organoid d22 R1

description: 10x Genomics

value: iPSC-derived kidney organoid

value: iPSC line 004


title: Adar1KD_1_tdT

description: 10X Genomics, tdT positive cells only


title: Healthy Organoids, iPSC-derived, Day 42, Replicate 1


title: Healthy Organoids, iPSC-derived, Day 32, Replicate 3

value: Day 32


title: TA_IL-15_H2A.Z-CUTandTag_rep2

value: spleen

value: naive CD8+ T cell

value: anti-CD3/CD28 Abs for 24 h, and then stimulated with IL-15 for another 24 h


title: Control Organoid d38

description: 10x Genomics

value: Kidney Organoid

value: day 38


description:
Library name: BOOST002_Hu_2_CD4_12D
Pooled scRNA-seq library from multiple donors (HTO-labeled), S-specific T cells, sample BOOST002_Hu_2_CD4_12D

value: Blood

value: SARS-CoV-2 Spike (S) AIM+ CD4 T cells:CD3+ CD4+ OX40+ 4-1BB+

value: Activation-induced marker (AIM) assay


title: Control_16wk_1_tdT

description: 10X Genomics, tdT positive cells only

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Adar1 WT/WT, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 24 weeks of age


title: Control_3_nontdT

description: 10X Genomics, tdT negative cells only

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 10 weeks of age


title: Healthy Organoids, iPSC-derived, Day 32, Replicate 2

value: iPSC-derived kidney Organoid

value: Male - Line 004

value: Induced pluripotent stem cells

value: Healthy


title: Adar1KD_3_tdT

description: 10X Genomics, tdT positive cells only

value: Adar1 fl/fl, Myh11 CreERT2, ApoE-/-, ROSA tdTomato


title: Healthy Organoids, iPSC-derived, Day 22, Replicate 2

value: Day 22


title: Healthy Organoids, iPSC-derived, Day 32, Replicate 1

value: Day 32


title: Healthy Organoids, iPSC-derived, Day 22, Replicate 3


title: Healthy Organoids, iPSC-derived, Day 42, Replicate 2

value: Day 42


title: Healthy Organoids, iPSC-derived, Day 22, Replicate 1


title: Control_2_tdT_nontdT_combined

description: 10X Genomics, combined tdTomato positive and negative cells


title: Control_3_tdT

description: 10X Genomics, tdT positive cells only


title: SCC35R2

city: Sheffield

first: Hannah

last: Crane

address: Western Bank

country: United Kingdom

institute: University of Sheffield

data_processing:
Samples were aligned and quantified using Salmon on high-performance computer (HPC) cluster at the University of Sheffield
Assembly: Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary files format and content: For each sample, a salmon (.sf) file is provided which contains the effective length and transcripts per million (TPM)

source_name: cell line

growth_protocol: Cells were routinely cultured in low-glucose Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin and 1% L-glutamine.

extract_protocol:
RNA was extracted using Monarch Total RNA miniprep kit (New England Biotechnologies (NEB) #T2010)
PolyA library prep

value: cell line

value: Squamous cell carcinoma

value: HPV+, resistant


title: O0505mM

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

description: with MSC co-culture

data_processing:
Raw reads from both RNA-seq were checked by FastQC (v0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed by Trim Galore (v0.4.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
For RNA-seq data, trimmed reads were mapped to the mouse reference genome (mm10) by TopHat (v2.1.1) [68] with default parameters and Cufflinks was employed to quantify gene expression level with gene annotation obtained from Ensembl GRCm38.p5 [69].
Gene expression level was calculated in the form of fragments per kilobase million (FPKM). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: mm10
Supplementary_files_format_and_content: text files include expected_count, TPM, FPKM.

extract_protocol:
7 µl of soft lysis buffer containing 500 mM KCl (Sigma), 100mM pH 8.0 Tris-HCl (Sigma), 1.35 mM MgCl2 (Sigma), 4.5 mM DTT (Thermo Fisher Scientific), 0.45% Nonidet P-40 (Sigma), 0.18U SUPERase-In (Thermo Fisher) and 0.36U recombination RNase-inhibitor (Thermo Fisher) were added into each PCR tube containing a single oocyte and were incubated at 4˚C for 30 min. Then, the lysate was vortexed at room temperature for 1 min and centrifuged at 1000g for 5 min to allow the nucleus to sink to the bottom of the tube. 6.5 µl of supernatant containing RNA was carefully transferred to a new PCR tube for generating scRNA-seq library.
TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was used for library construction.

value: in vitro-matured metaphase II (IVM-MII) oocyte

tag: strain

value: 12 months

value: wild type

tag: co-culture

value: with MSC co-culture


title: O0504mM

description: with MSC co-culture


title: O0502M

description: without MSC co-culture

value: without MSC co-culture


title: Control_1_tdT_nontdT_combined

data_processing:
Demultiplexed Fastq files and matrix files were generated with Cellranger.
Assembly: mm10 genome used for reference
Supplementary files format and content: filtered sequence read with matrix.h5 files are reported and ultimately used in Seurat for data analysis.

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Adar1 WT/WT, Myh11 CreERT2, ApoE-/-, ROSA tdTomato

value: Tamoxifen at 8 weeks of age, sacrifice for tissue collection at 10 weeks of age


title: Adar1KD_1_nontdT

description: 10X Genomics, tdT negative cells only


title: SCC35R1


title: O0404M

description: without MSC co-culture


title: SCC2R2

value: HPV+, parental


title: SCC2R1


title: O0407mM

description: with MSC co-culture


title: O0403M

description: without MSC co-culture


title: SCC411R2

value: HPV-, resistant


title: SCC89R1

value: HPV-, parental


title: SCC89R2


title: SCC411R1


title: O0402

description: without MSC co-culture

value: germinal vesicle (GV) oocyte


title: O0501

description: without MSC co-culture


title: O0101

description: without MSC co-culture


title: HTR8/Svneo SRC-2 siRNA-3

city: HOUSTON

first: Vineet

middle: Kumar

last: Maurya

state: TX

address: ONE BAYLOR PLAZA

department: Molecular & Cell Biology

institute: BAYLOR COLLEGE OF MEDICINE

data_processing:
Raw sequenced reads in Ilumina fastq file format were aligned to the Human genome (The reference genome(GRCh38) is from GENCODE(https://www.gencodegenes.org/human/) through the use of the hierarchical indexing for spliced alignment of transcripts (HISAT2). The number of reads aligned to known genes was determined by the Python-based software package HTSeq  (http://www-huber.embl,de/users/anders/HTSeq).
The Bioconductor package DESeq was applied to the gene expression data to detect differentially expressed genes between the two groups.
Fragments per kilobase of transcript per million (FPKM) values of transcripts were used for hierarchical clustering; the pheatmap package in R was used to draw the clustered heatmap.
Assembly: The reference genome(GRCh38) is from GENCODE(https://www.gencodegenes.org/human/).
Supplementary files format and content: tab-delimited text file include FPKM values for each samples

extract_protocol:
HTR8 SVneo were lysed in RNeasy Plus RNA lysis buffer and total RNA was isolated using the Qiagen RNeasy Plus Mini kit.
Sequencing libraries were prepared from 250ng of RNA using the TruSeq Stranded mRNA kit (Illumina Inc, # 20020594).

value: Extravillous Trophoblast

value: SRC-2 siRNA


title: HTR8/Svneo SRC-2 siRNA-1


title: HTR8/Svneo NT siRNA-3

value: NT siRNA


title: Proximal small intestine

first: Bernett

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: Library name: SIP

data_processing:
10x Genomics single-cell RNA-Seq data was obtained as FASTQ files which were processed by Cell Ranger 7.1.0 using the mouse mm10 annotations for each individual tissue.
Assembly: mm10
Supplementary files format and content: 10X HDF5 files

source_name: Small intestine

extract_protocol:
Crypts from individual regions of the colon and small intestine were isolated and dissociated into single cells.
Single cell library was build incorporating single cells into Chromium beads (10X genomics).

value: Small intestine

value: Intestinal


title: Jejunum; Day 0, Day 2, Day 2, Day 4, Day 4, Day 6 post-IR; 6 mice; rep 4

city: Piscataway

first: Verzi

last: Michael

state: New Jersey

address: 145 bevier road

department: Genetics

institute: Rutgers University

description: Library name: Rep4_day0,2,4,6_postIR

data_processing:
Space Ranger (v3.1.3 and v4.0) was used to process and quantify Visium HD libraries, outputting FASTQ files with data binned at 2μm and 8μm resolution
Gene expression was quantified using Space Ranger (v3.1.3 and v4.0) with default parameters and a RefSeq based transcriptome.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes (square_008um/filtered_feature_bc_matrix)
Supplementary files format and content: features.tsv.gz: list of gene IDs  (square_008um/filtered_feature_bc_matrix)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format  (square_008um/filtered_feature_bc_matrix)
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: square_008um_cloupe.cloupe: Space Ranger output file designed to be opened using Loupe Browser
Supplementary files format and content: segmented_outputs_cloupe.cloupe: Space Ranger output using Cell Segmentation feature, opened using Loupe Browser
Library strategy: Spatial Transcriptomics

source_name: Jejunum of small intestine

extract_protocol:
Freshly harvested tissues were formalin-fixed paraffin-embedded (FFPE) into tissue blocks. 5μm sections were cut for spatial transcriptomics assay using Visium HD 10x Genomics, and as per manufacturor's protcol
Spatial transcriptomic sequencing libraries were prepared using 10x Genomics Visium HD FFPE Spatial Gene Expression Slides & Reagents Kit. Sequencing was performed using Illumina NovaSeq X Plus platform

treatment_protocol: 12 Gy whole-body irradiation was performed at the indicated timepoint. Jejunum harvest took place on the same day for all mice, and processed together for spatial transcriptomics

value: Jejunum of small intestine

value: Day 0, Day 2, Day 4, Day 6 post-IR


title: Jejunum; Day 0, Day 0, Day 1, Day 3, Day 5 post-IR; 5 mice; rep 1

description: Library name: Rep1_day0,1,3,5_postIR


title: Jejunum; Day 0, Day 1, Day 2, Day 3, Day 4, Day 5 post-IR; 6 mice; rep 2

description: Library name: Rep2_day0,1,2,3,4,5_postIR


title: HTR8/Svneo NT siRNA-2


title: Jejunum; Day 0, Day 1, Day 2, Day 3, Day 4, Day 5 post-IR; 6 mice; rep 3

description: Library name: Rep3_day0,1,2,3,4,5_postIR


title: HTR8/Svneo SRC-2 siRNA-2


title: HTR8/Svneo NT siRNA-1


title: Middle colon

description: Library name: CM

source_name: Colon

value: Colon


title: Allo15MCAR-NKT (week 6) spleen

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The raw sequencing data were processed and mapped to the human reference (GRCh38) dataset using the Cell Ranger. The processed data were filtered for further downstream analysis.
Assembly: hg38
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells. barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell. features.tsv.gz: Tab-separated values, where each row represents a gene.

extract_protocol:
Peritoneal cavity cells (the tumor site) harvested from experimental animals at week 4 were subjected to FACS sorting for isolating therapeutic cells including MCAR-T and Allo15MCAR-NKT cells. Cells isolated from 10 experimental mice were combined for each group.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: spleen

value: T cells


title: Distal small intestine

description: Library name: SID


title: Distal colon

description: Library name: CD


title: Allo15MCAR-NKT (Post)

description: 10x Genomics

source_name: In vitro

value: In vitro


title: Allo15MCAR-NKT (week 8) peritoneal cavity

description: 10x Genomics

source_name: peritoneal cavity

value: peritoneal cavity


title: Proximal colon

description: Library name: CP


title: Middle small intestine

description: Library name: SIM


title: TM-cKO-Day7_rep2

description:
Library name: TM-cKO-Day7_2
TM-cKO-D7_2

growth_protocol: T cells were maintained in RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (BI), 10mM Hepes (Gibco), 1% NEAA (Gibco), 1% penicillin/streptomycin (Gibco), 50uM β-Mercaptoethanol (Gibco) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
6h after treatment, RNA was isolated from the T cells using HiPure Total RNA Nano Kit (Magen, Cat# R4125-02).
RNA libraries for RNA-seq was prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme, Cat# TR502-02) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with  2ug/ml coated anti-CD3 Ab and 1ug/ml soluble anti-CD28 Ab.

value: antigen-specific CD8+ T cell

value: cKO

value: Day7 post-reinfection


title: TM-cKO-Day7_rep1

description:
Library name: TM-cKO-Day7_1
TM-cKO-D7_1


title: Allo15MCAR-NKT (week 6) liver

description: 10x Genomics

source_name: liver

value: liver


title: TM-WT-Day7_rep2

description:
Library name: TM-WT-Day7_2
TM-WT-D7_2

value: WT


title: Allo15MCAR-NKT (week 6) blood

description: 10x Genomics

source_name: blood

value: blood


title: TM-WT-Day7_rep1

description:
Library name: TM-WT-Day7_1
TM-WT-D7_1

source_name: spleen


title: Allo15MCAR-NKT (week 4) liver

description: 10x Genomics


title: TM-WT-0h_rep2

description:
Library name: TM-WT-0h_2
TM-WT-0h_2

value: memory CD8+ T cell

value: unstimulated


title: Allo15MCAR-NKT (week 4) spleen

description: 10x Genomics


title: Lot LA82 from 3D culture at day 8

description:
Library name: 823DD8
Lot LA82 from 3D culture at day 8

value: Human Umbilical Vein Endothelial Cells

value: Rpl22- 3X HA

value: 3D Day 8


title: TM-WT-0h_rep1

description:
Library name: TM-WT-0h_1
TM-WT-0h_1


title: Allo15MCAR-NKT (week 4) blood

description: 10x Genomics


title: Allo15MCAR-NKT (week 6) peritoneal cavity

description: 10x Genomics


title: Allo15MCAR-NKT (week 4) peritoneal cavity

description: 10x Genomics


title: TEM-6h-rep1

description:
Library name: TEM-6h-1
TEM-6h-1

value: effector memory CD8+ T cell


title: TEM-6h-rep2

description:
Library name: TEM-6h-2
TEM-6h-2


title: TCM-6h-rep2

description:
Library name: TCM-6h-2
TCM-6h-2

value: central memory CD8+ T cell


title: Allo15MCAR-NKT (week 2) liver

description: 10x Genomics


title: Allo15MCAR-NKT (week 2) blood

description: 10x Genomics


title: Allo15MCAR-NKT (week 2) peritoneal cavity

description: 10x Genomics


title: TCM-6h-rep1

description:
Library name: TCM-6h-1
TCM-6h-1

value: spleen


title: TN-6h-rep1

description:
Library name: TN-6h-1
TN-6h-1

value: naive CD8+ T cell


title: MCAR-T (week8) peritoneal cavity

description: 10x Genomics

value: T cells


title: TEM-0h-rep2

description:
Library name: TEM-0h-2
TEM-0h-2


title: MCAR-T (week6) liver

description: 10x Genomics


title: MCAR-T (Post)

description: 10x Genomics

value: In vitro


title: MCAR-T (week6) spleen

description: 10x Genomics


title: TEM-0h-rep1

description:
Library name: TEM-0h-1
TEM-0h-1


title: TCM-0h-rep1

description:
Library name: TCM-0h-1
TCM-0h-1


title: TN-6h-rep2

description:
Library name: TN-6h-2
TN-6h-2


title: MCAR-T (week6) peritoneal cavity

description: 10x Genomics

value: peritoneal cavity


title: MCAR-T (week6) blood

description: 10x Genomics


title: Allo15MCAR-NKT (week 2) spleen

description: 10x Genomics


title: 24h_TM-cKO_stimulated_rep2

growth_protocol: T cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
24h after treatment, RNA was isolated from the T cells using HiPure Total RNA Nano Kit (Magen, Cat# R4125-02).
RNA libraries for RNA-seq was prepared using TruePrep RNA Library Prep Kit for Illumina (Vazyme, Cat# TR502-02) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with 200 nM OVA257-264.

value: cKO


title: TN-0h-rep1

description:
Library name: TN-0h-1
TN-0h-1


title: MCAR-T (week4) spleen

description: 10x Genomics


title: MCAR-T (week4) liver

description: 10x Genomics


title: 24h_TM-cKO_stimulated_rep1


title: MCAR-T (week4) blood

description: 10x Genomics


title: 24h_TM-WT_stimulated_rep2


title: MCAR-T (week4) peritoneal cavity

description: 10x Genomics


title: MCAR-T (week2) spleen

description: 10x Genomics


title: TCM-0h-rep2

description:
Library name: TCM-0h-2
TCM-0h-2


title: MCAR-T (week2) blood

description: 10x Genomics


title: Cmm+IAA H3K4me3 Rep3 6.5hpf

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

description: Library name: 16

data_processing:
Sequencing reads were aligned to the Xenopus laevis genome (v10.1) and a spike-in genome (Escherichia coli, GCA_001606525) using Bowtie2 (v2.4). The alignment process excluded discordant and mixed reads, with paired-end reads mapped to the reference genome. Aligned reads were converted to BAM format and filtered to retain only properly paired alignments. Normalization scaling factors were computed using deepTools (v3.5.3) based on the read distribution across genomic regions. HOMER (v4.11) was used for peak identification. Narrow peaks were called using histone-style parameters and converted to BED format for downstream analysis.  Differential peak analysis for H3K4me3 signal was performed on a consensus peak set defined based on narrow H3K4me3 peaks called in at least two out of three independent biological replicates from wildtype embryos, using the findOverlaps function from GenomicRanges (v1.58.0) with maxgap=150 bp.
Assembly: Xenopus laevis (v10.1)
Supplementary files format and content: Coverage files (.bigwig)
Supplementary files format and content: Narrow peak calling files (.bed)
Library strategy: CUT&Run

organism: Xenopus laevis

source_name: Whole embryos 6.5hpf

extract_protocol:
Independent experiments were performed on three different frogs, serving as three biological replicates. Within each biological replicate, 45 embryos each were collected per condition, corresponding to three replicates within each independent experiment. Embryos were collected at 6.5hpf. Nuclei were isolated from whole embryos, bound to concanavalin A beads, followed by antibody incubation with H3K4me3 or IgG as a control. Targeted digestion with pAG-MNase was performed, and soluble chromatin fragments for DNA purification were extracted using a modified CUT&RUN method.
Sequencing libraries were generated using the NEB Ultra II DNA library prep kit (NEB, #E7645) as per the manufacturer’s instructions using 12 PCR amplification cycles.

treatment_protocol: For the “treated” condition, embryos were co-injected at the 1-cell stage with 11ng Kdm5bwt, 345pg H3.3K4M and 5ng TIR1 mRNA. “Control” condition embryos were co-injected at the 1-cell stage with 4ng Kdm5bci, 345pg H3.3wt and 5ng TIR1 mRNA. For “+IAA” depletion treatment, embryos were grown until the pre-ZGA stage (4.5hpf/256-cell stage) and transferred to an auxin solution (500μM auxin in 0.1 × MMR) to develop further. “-IAA” depletion treatment embryos were grown in 0.1x MMR throughout development.

value: Whole embryos 6.5hpf

value: Whole embryos

value: Control window


title: Wt H3K4me3 Rep3 6.5hpf

description: Library name: 17

value: WT


title: MCAR-T (week2) peritoneal cavity

description: 10x Genomics


title: Wt IgG Rep3 6.5hpf

description: Library name: 18


title: TN-0h-rep2

description:
Library name: TN-0h-2
TN-0h-2


title: Cmm-IAA H3K4me3 Rep3 6.5hpf

description: Library name: 15

value: Control persistent


title: Tmm+IAA H3K4me3 Rep3 6.5hpf

description: Library name: 14

value: Treated window


title: D WT E2

description: Sample E2 (Same patient as E1 and same block number)

data_processing:
Raw reads were trimmed using Trim-Galore (version 0.60)
Trimmed sequence reads were mapped to GRCm38 using STAR (version 2.7), and then the gene level values were quantified (RSEM version 1.31) based on GENCODE annotation (M22).
Assembly: GRCm38
Supplementary files format and content: tab delimited text files include RSEM gene counts for each sample

source_name: ERMS

extract_protocol:
RNA was extracted from FFPE tissue by Novogene
Libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase
total stranded RNA-seq

treatment_protocol:
Human FN-RMS samples were fixed in 10% neutral buffered formalin for 8-12 hours at room temperature
Four 10 µm scrolls per sample were submitted for RNA-sequencing

value: ERMS

value: DICER1 +/+


title: D WT F1

description: Sample F


title: MCAR-T (Pre)

description: 10x Genomics


title: Tmm-IAA H3K4me3 Rep3 6.5hpf

description: Library name: 13

value: Treated persistent


title: D HET D1

description: Sample D

source_name: cervical ERMS

value: cervical ERMS

value: DICER1 +/-


title: Wt H3K4me3 Rep2 6.5hpf

description: Library name: 11


title: D WT E1

description: Sample E1


title: Wt IgG Rep2 6.5hpf

description: Library name: 12


title: D HET C2

description: Sample C2 (Same patient as C1 but different tissue block)


title: Cmm+IAA H3K4me3 Rep2 6.5hpf

description: Library name: 10


title: 24h_TM-WT_stimulated_rep1

value: spleen

value: memory CD8+ T cell


title: Cmm-IAA H3K4me3 Rep2 6.5hpf

description: Library name: 9


title: D HET B1

description: Sample B


title: D HET A1

description: Sample A


title: MCAR-T (week2) liver

description: 10x Genomics

value: liver

value: T cells


title: D HET C1

description: Sample C1


title: Allo15MCAR-NKT (Pre)

description: 10x Genomics

value: In vitro


title: S35_RHI

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

description: 10x Genomics

data_processing:
CellRanger v6.0.1 was used to align reads to the GRCH38 reference and generate filtered count matrices provided in the processed data files
Assembly: GRCH38
Supplementary files format and content: Tab-separated and matrix files with counts, feature (gene), and barcode data.
Supplementary files format and content: Tab-separated and matrix files with unfiltered counts, feature (gene), and barcode data.

molecule: nuclear RNA

source_name: Dorsolateral Frontal Cortex - Brain

extract_protocol:
Nuclei isolation and sorting were performed on two donor samples per day, randomizing for diagnosis and age. Tissue was kept on ice throughout nuclei isolation. Tissue was homogenized and lysed in NST Buffer with DAPI (146mM NaCl, 10mM Tris, 1mM CaCl2, 21mM MGCl2, 0.1%BSA, 0.1% NP-40, 40U/ml Protector RNase Inhibitor, DAPI) and snipped with scissors on ice for 10 minutes. Debris was removed using a 70μm filter. Cells were spun down and resuspended in nuclei storage buffer (2% BSA, 400U/mL Protector RNase Inhibitor) to reach a concentration of 500-1000 nuclei/μL. Nuclei were purified for DAPI positive cells with a FACS-Aria flow cytometer to remove debris
Library was performed according to the manufacturer's instructions (single cell 3' V2 protocol, 10xGenomics). Briefly, nuclei were combined with the master mix at the correct dilution and loaded with partitioning oil and gell beads into the chip to generate the gel bead emulsion or GEMs. Retrotranscription was performed to create cDNA from the RNA in the beads, with primer sequences and unique molecular identifier (UMI) barcodes, and the 10x genomics barcode included. Pooled barcoded cDNA was put through the 10x library prep protocol which includes amplification with PCR, SPRI bead cleanups for size selections and addition of paired end constructs and sample indices.
single nucleus RNA sequencing

value: Dorsolateral Frontal Cortex - Brain

value: RHI


title: S34_CTE

description: 10x Genomics

value: CTE


title: Wt H3K4me3 Rep1 6.5hpf

description: Library name: 5

value: Whole embryos 6.5hpf

value: Whole embryos


title: S32_RHI

description: 10x Genomics


title: S31_Control

description: 10x Genomics

value: Control


title: S30_CTE

description: 10x Genomics


title: Cmm-IAA H3K4me3 Rep1 6.5hpf

description: Library name: 3

value: Control persistent


title: Tmm+IAA H3K4me3 Rep1 6.5hpf

description: Library name: 2

value: Treated window


title: HCT116, si3_3

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

description:
Library name: si3_3
HRS1606145
HRX1798919
HRR2222527
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz

data_processing:
The electronic raw signals (FAST5 data) were translated into bases (FASTQ data) using Guppy. Nanoplexer was performed on the FASTQ data to generate individual cell data of SCAN-seq based on the 24 bp barcode information. Reads with barcode mapping score below 31 were discarded. Low-quality reads (read quality score < 7) and short reads (read length < 100) were then filtered using NanoFilt. In order to obtain full-length reads, PCR anchor sequence and cell barcode sequence were identified and trimmed using Pychopper, and polyA tail was trimmed using trim_isoseq_polyA command. The full-length reads were aligned to the human reference genome (GRCh38, Ensembl, release-108) using minimap2 (v2.17) (-ax splice -uf -k14 --secondary=no --junc-bed). All bam files were consolidated into a single bam file, followed by transcriptome assembly conducted by StringTie. Transcript isoforms with coverage below 3 were subsequently eliminated.
Assembly: GRCh38
Supplementary files format and content: CRC_NewRef_LongRead_assembled_Sorted.gtf.gz includes gene/transcript annotations that have beed assembled from the long-read scRNA-seq data.
Supplementary files format and content: CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz includes the categorizaation of isoforms from SQANTI3.
Supplementary files format and content: Counts.csv.gz files include gene/isoform-level expression counts in human colorectal cancer or human colorectal cancer cell lines.
Supplementary files format and content: CRC_Metadata_Cell_Info.csv.gz includes the detailed information about each cell.

source_name: colorectum

extract_protocol:
Dissected tumor samples and matched normal mucosa were digested into single-cell suspension via 1.5 mg/ml collagenase type II and 1.5 mg/ml collagenase type IV, All samples treated at 37°C for 30-60 min, depending on viscosity. We used CD45 antibody and EPCAM antibody in FACS to collect CD45-EPCAM+ epithelial cells. Cells were sorted into 96-well plates containing SCAN-seq lysis buffer and stored at -80°C.
Plates were thawed and thoroughly vortexed for 60 s, and incubated at 72˚C for 3 minutes to release the linearized RNA molecules and immediately transferred them on ice. Reverse transcription and PCR amplification were performed as described before. Then, we pooled the cDNAs of different cell barcodes together and purified twice with 0.4X Ampure XP beads and 0.8X Ampure XP beads separately. A total of 500 ng to 1 ug cDNA products were used for further library construction.

value: colorectum

value: epithelial cells

tag: crc patient_tissue_type


title: S27_Control

description: 10x Genomics


title: Tmm-IAA H3K4me3 Rep1 6.5hpf

description: Library name: 1

value: Treated persistent


title: Tmm+IAA H3K4me3 Rep2 6.5hpf

description: Library name: 8


title: HCT116, si3_2

description:
Library name: si3_2
HRS1606144
HRX1798918
HRR2222526
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: HCT116, si3_1

description:
Library name: si3_1
HRS1606143
HRX1798917
HRR2222525
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: S24_Control

description: 10x Genomics


title: Wt IgG Rep1 6.5hpf

description: Library name: 6

value: WT


title: S26_CTE

description: 10x Genomics


title: Tmm-IAA H3K4me3 Rep2 6.5hpf

description: Library name: 7


title: MEFs, NIL RISDD, rep A

city: Cambridge

first: Brittany

last: Lende-Dorn

state: MA

address: 25 Ames St

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description: Library name: NIL.RISDD_A

data_processing:
Raw sequencing reads were trimmed using Trim Galore (version 0.6.10) and then pseudoaligned and quantified using Salmon (version 1.10.3) against the GRCm39 reference transcriptome. Read counts from Salmon quantification were normalized with PyDESeq2 (version 0.5.1).
Assembly: GRCm39 with appended ERCC spike in sequences
Supplementary files format and content: CSV file containing normalized gene expression counts. The first column lists Ensembl gene IDs, the second column provides corresponding gene symbols, and the remaining columns contain normalized counts for each sample (one column per sample).

source_name: primary mouse embryonic fibroblasts

growth_protocol: Primary mouse embryonic fibroblasts (MEFs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C.

extract_protocol:
At 4 days post infection, conditions expressing SNAP-p53DD were stained using a fluorescent SNAP substrate (New England Biolabs, #S9105S), then all conditions were dissociated with trypsin. Cells were resuspended in N3 media and kept on ice for fluorescence-activated cell sorting (FACS). Cells were sorted on live, single-cells for conditions without SNAP, and SNAP positive for conditions with SNAP-p53DD. Total RNA was extracted from 50k sorted cells using the Monarch® Total RNA Purification Kit (New England Biolabs, #T2010S). ERCC RNA spike-in controls (Thermo Fisher Scientific, #4456740) were added to the lysis buffer prior to RNA isolation.
Libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Prep Kit.

treatment_protocol: Primary mouse embryonic fibroblasts were infected with retrovirus of NIL, NIL + SDD, NIL + SDDIR, NIL + RISDD (NIL is Ngn2-2A-Isl1-2A-Lhx3; SDD is SNAP-p53DD, SDDIR is SDD-IRES-HRAS(G12V); RISDD is HRAS(G12V)-IRES-SDD). At 3 days post infection (dpi), the media was switched to N3 media (DMEM / F-12 media supplemented with N2, B27, Glutamax, BDNF, GDNF, CNTF, FGF; all conditions except NIL also included RepSox beginning at 3 dpi).

value: primary mouse embryonic fibroblasts

value: NIL RISDD

tag: biorep

value: A


title: MEFs, NIL SDDIR, rep C

description: Library name: NIL.SDDIR_C

value: NIL SDDIR

value: C


title: MEFs, NIL RISDD, rep B

description: Library name: NIL.RISDD_B

value: B


title: HCT116, si2_1

description:
Library name: si2_1
HRS1606140
HRX1798914
HRR2222522
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: MEFs, NIL RISDD, rep C

description: Library name: NIL.RISDD_C


title: HCT116, si2_2

description:
Library name: si2_2
HRS1606141
HRX1798915
HRR2222523
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: S23_CTE

description: 10x Genomics

value: Dorsolateral Frontal Cortex - Brain


title: Cmm+IAA H3K4me3 Rep1 6.5hpf

description: Library name: 4

value: Control window


title: S22_RHI

description: 10x Genomics

value: RHI


title: MEFs, NIL SDDIR, rep B

description: Library name: NIL.SDDIR_B


title: HCT116, si1_3

description:
Library name: si1_3
HRS1606139
HRX1798913
HRR2222521
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: S28_RHI

description: 10x Genomics


title: HCT116, si1_2

description:
Library name: si1_2
HRS1606138
HRX1798912
HRR2222520
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: HCT116, si1_1

description:
Library name: si1_1
HRS1606137
HRX1798911
HRR2222519
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: HCT116, si2_3

description:
Library name: si2_3
HRS1606142
HRX1798916
HRR2222524
PPIG knockdown in HCT116
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: S20_CTE

description: 10x Genomics

value: CTE


title: HCT116, NC_3

description:
Library name: NC_3
HRS1606136
HRX1798910
HRR2222518
Negative control
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: MEFs, NIL SDD, rep C

description: Library name: NIL.SDD_C

value: NIL SDD


title: S19_RHI

description: 10x Genomics


title: HCT116, NC_1

description:
Library name: NC_1
HRS1606134
HRX1798908
HRR2222516
Negative control
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: HT29

description:
Library name: HT29
HRS1606132
HRX1798906
HRR2222514
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: SW480

description:
Library name: SW480
HRS1606133
HRX1798907
HRR2222515
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: MEFs, NIL SDD, rep B

description: Library name: NIL.SDD_B


title: MEFs, NIL SDD, rep A

description: Library name: NIL.SDD_A


title: LoVo

description:
Library name: LoVo
HRS1606131
HRX1798905
HRR2222513
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz

value: LoVo


title: S18_Control

description: 10x Genomics

value: Control


title: HTCRC05_PT2

description:
Library name: HTCRC05_PT2
HRS1582100
HRX1774761
HRR2198245
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: colorectum

value: PT


title: HTCRC05_PT1

description:
Library name: HTCRC05_PT1
HRS1582100
HRX1774760
HRR2198244
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: S17_CTE

description: 10x Genomics


title: MEFs, NIL, rep B

description: Library name: NIL_B


title: MEFs, NIL, rep C

description: Library name: NIL_C


title: MEFs, NIL SDDIR, rep A

description: Library name: NIL.SDDIR_A


title: S15_Control

description: 10x Genomics


title: S16_CTE

description: 10x Genomics


title: MEFs, NIL, rep A

description: Library name: NIL_A


title: HTCRC01_PT

description:
Library name: HTCRC01_PT
HRS1582098
HRX1774756
HRR2198240
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: HTCRC01_NT

description:
Library name: HTCRC01_NT
HRS1582098
HRX1774755
HRR2198239
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz

value: NT


title: S12_RHI

description: 10x Genomics


title: HCT116, NC_2

description:
Library name: NC_2
HRS1606135
HRX1798909
HRR2222517
Negative control
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz

value: epithelial cells


title: HTCRC05_NT

description:
Library name: HTCRC05_NT
HRS1582100
HRX1774759
HRR2198243
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC09_L3_CRC10_L1

description:
Library name: CRC09_L3_CRC10_L1
HRS995186
HRX1128578
HRR1451166
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC10_L3

description:
Library name: CRC10_L3
HRS995180
HRX1128580
HRR1451168
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: HCT116

description:
Library name: HCT116
HRS1606130
HRX1798904
HRR2222512
CellLine_Gene_Counts.csv.gz
CellLine_Isoform_Counts.csv.gz


title: S9_Control

description: 10x Genomics


title: HTCRC04_PT

description:
Library name: HTCRC04_PT
HRS1582099
HRX1774758
HRR2198242
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC09_L1

description:
Library name: CRC09_L1
HRS995179
HRX1128576
HRR1451164
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: HTCRC04_NT

description:
Library name: HTCRC04_NT
HRS1582099
HRX1774757
HRR2198241
SCAN-seq2
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC08_L5

description:
Library name: CRC08_L5
HRS995178
HRX1128575
HRR1451163
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: S7_CTE

description: 10x Genomics


title: CRC07_L7

description:
Library name: CRC07_L7
HRS995177
HRX1128573
HRR1451161
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0305

description: with MSC co-culture

value: in vitro-matured metaphase II (IVM-MII) oocyte

value: 6 weeks

value: wild type

value: with MSC co-culture


title: CRC07_L6

description:
Library name: CRC07_L6
HRS995177
HRX1128572
HRR1451160
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0306

description: with MSC co-culture


title: CRC05_L4_CRC08_L4

description:
Library name: CRC05_L4_CRC08_L4
HRS995185
HRX1128571
HRR1451159
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: S14_Control

description: 10x Genomics


title: CRC09_L4_CRC10_L2

description:
Library name: CRC09_L4_CRC10_L2
HRS995186
HRX1128579
HRR1451167
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: CRC05_L3_CRC08_L3

description:
Library name: CRC05_L3_CRC08_L3
HRS995185
HRX1128570
HRR1451158
SCAN-seq
CRC_Gene_Counts.csv.gz
CRC_Isoform_Counts.csv.gz
CRC_Metadata_Cell_Info.csv.gz
CRC_NewRef_Isoform_StructuralCategory_SQANTI3.txt.gz
CRC_NewRef_LongRead_assembled_Sorted.gtf.gz


title: Y0105

description: with MSC co-culture


title: S4_CTE

description: 10x Genomics