title: k602_2_bm_m_4d: Bone marrow 4-day old W326R/+

data_processing:
Raw idat files were processed to beta and detection p-values using the Bioconducter package minfi (v1.50.0) using single-sample normal exponential out of band (ss noob) background correction and dye bias normalization annotations (IlluminaMouseMethylationanno.12.v1.mm10). Probes overlapping known SNPs (MAF>1% and within 5 bp of the probe’s CpG target, based on https://github.com/zhou-lab/InfiniumManifestAnnotator), located on sex chromosomes, or with detection p-value > 0.01 were excluded.
Normalized mean Beta and detection p-value.


status: Public on Apr 27 2026

type: SRA

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

country: USA

institute: National Cancer Institute

description:
Library name: Sample 8
mRNA-Seq of HAP1 cells with PladB 8h DMSO Replicate 2

library_source: transcriptomic

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using rMATS tool. Differential expression analysis was performed with DESeq2 tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with multiple sheets containing log2FoldChange (L2FC), pvalue, and adjusted pvalues (padj) from differential expression analysis with DESeq2 tool for all the significant genes identified with different spliceosomal inhibitions. An additional sheet contains FPKM values for all the expressed genes in all the samples.
Supplementary files format and content: Tab delimited excel file with multiple sheets containing PSI, ΔPSI, Pvalue, and FDR values from differential splicing analysis with rMATS tool for all the significant exon skipping splicing events identified with different spliceosomal inhibitions along with Tunicamycin treatments.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HAP1 cells were maintained in Dulbecco’s Modified Eagle’s Medium (supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads.
Library construction was carried out following the TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HAP1 cells were treated with Indisulam (10µM) and Pladienolide B (10nM) for 8h and 24h followed by treatment with either 10µg/mL of Tunicamycin or DMSO for 4h, before harvesting for total RNA extraction.

tag: cell line

tag: cell type

value: Near-haploid cell line derived from KBM-7 human CML cell line

tag: treatment

value: PladB_8h, DMSO


title: WT1

city: NEW YORK

first: LEVI

last: MANGARIN

state: NY

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

description: Library name: WT1

data_processing:
STAR v2.6.0
subread featureCounts v1.5.1
Assembly: GRCm38-2020-A
Supplementary files format and content: Tsv and matrix files

molecule: total RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, QIACube). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA LT Kit following manufacturer's protocols.

tag: tissue

value: tumor

value: Pmel

tag: genotype

value: Sirpa-wild type (WT)


description:
Library name: Sample 6
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in RPE1 cells, Untreated

data_processing:
(1) The sequencing reads (R1) from FASTQ files were analyzed with a custom bioinformatics pipeline, which involves STAR aligner tool for mapping to annotate CRISPR guides. Cell Barcode (CBC) and Unique Molecular Identifier (UMI) sequences were retrieved based on the adjacent plasmid vector regions and used to remove PCR duplicates from the samples. Splicing outcomes were assessed from the R2 reads to link the phenotype to gene knockout perturbation to determine regulatory influence.
(2) PIR (Percent Intron Retention) and ΔPIR values were calculated and analyzed across a XBP1 CRASP-Seq library to identify gene hits in a specific sample with a 10% FDR intergenic control threshold for positive and negative regulations. We also considered guide proportion of more than 0.5 for a gene to be a hit beside gene level qualifications for this threshold, ensuring greater reproducibility of the splicing regulations.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with two separate sheets containing (1) HIT gene ΔPIR values for XBP1 splicing reporter screens and (2) Whole library guide ΔPIR values for XBP1 splicing reporter screens.
Library strategy: CRISPR Screen

growth_protocol: HAP1, and RPE1 cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. HepG2 cells were cultured in Eagle's Minimum Essential Medium with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads
cDNA synthesis was performed using primers with Unique Molecular Identifier (UMI) sequences.  cDNAs were PCR amplified using illumina sequencing indexes such as i7,P7,i5, and P5 for paired-end sequencing. Next-generation sequencing was performed on an Illumina NovaSeq 6000 platform (300 cycles kit).

treatment_protocol: For the XBP1 CRASP-Seq screens, cells were treated with 10µg/mL Tunicamycin for 4h before cells were harvested for RNA extraction.

value: Human retinal pigment epithelial-1 cell line

value: Untreated


description:
Library name: Sample 7
mRNA-Seq of HAP1 cells with PladB 8h DMSO Replicate 1


title: TIL_WT

description:
Library name: TIL_WT
10X Chromium v3 scRNAseq FASTQ

library_source: transcriptomic single cell

data_processing:
Cellranger v3.1.0
Assembly: GRCm38-2020-A
Supplementary files format and content: Tsv and matrix files

extract_protocol: 10X Chromium v3 library preparation


title: TDLN_WT

description:
Library name: TDLN_WT
10X Chromium v3 scRNAseq FASTQ

source_name: LN

value: LN


title: MDA-MB-231 cells, TRIM27-WT, rep1

city: Zhengzhou City

first: Leixi

last: Cao

address: Zhengzhou University People's Hospital, Fengchan Road Subdistrict, Jinshui District, Zhengzhou City, Henan Province

country: China

institute: Zhengzhou University People's Hospital, Translational Medicine Research Center

description:
Library name: 1-1
Column name in raw_counts _All _Samples.txt:T27_WT_1

data_processing:
Base-calling：Raw sequencing data were generated using the Illumina sequencing platform with standard base-calling procedures to produce raw reads in FASTQ format. Filtering (Quality control)：Raw reads were filtered using fastp (v0.23.2) to remove adapter sequences, reads without insert fragments caused by adapter self-ligation, low-quality bases with quality score < 20 at the 3′ end; reads containing any bases with quality score < 10 after trimming were discarded. Reads with > 10% ambiguous N bases and reads shorter than 20 bp after trimming were also removed to generate high-quality clean reads. Alignment：Clean reads were mapped to the corresponding reference genome using HISAT2 (v2.2.1) with optimized default parameters for eukaryotic transcriptome sequencing, and unqualified mapped reads were discarded. Generation of normalized abundance measurements：FeatureCounts (v2.0.3) was employed to calculate raw read counts for each gene, and gene expression levels were normalized to FPKM using StringTie (v2.2.1) to construct the gene expression matrix. Sample repeatability and data reliability were further evaluated via sample correlation analysis and principal component analysis (PCA). Differential expression analysis：Differential expression analysis was performed using DESeq2 (v1.38.3) with thresholds of |log2FC| > 1 and padj < 0.05. All data processing steps were performed by Frasergen Bioinformatics Co., Ltd. (Wuhan, China) following standard routine protocols for eukaryotic mRNA sequencing
Assembly: Homo sapiens GRCh38
Supplementary files format and content: gene_fpkm_all_samples.txt: Gene-level FPKM expression values across all samples.
Supplementary files format and content: transcript_fpkm_all_samples.txt: Transcript-level FPKM expression values across all samples.
Supplementary files format and content: total_gene_information.xls: Integrated gene-level file containing sample FPKM values, differential expression results (padj, log2FC, regulation status) for all pairwise comparisons, and comprehensive functional annotations (Nr, Swiss-Prot, KEGG, GO, eggNOG, Pfam, CAZy, SignalP, TMHMM) alongside gene identifiers.

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 wild-type and TRIM27 knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained in a humidified atmosphere of 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent. RNA purity and concentration were routinely verified prior to subsequent library construction. Subsequently, 1 μg of high-quality total RNA was utilized to prepare mRNA sequencing libraries. Library sequencing and the following downstream bioinformatics analyses were performed by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).
mRNA was enriched from total RNA via oligo(dT) magnetic beads, followed by fragmentation and cDNA synthesis. The sequencing library was constructed through end repair, A-tailing, adapter ligation, and PCR amplification.

treatment_protocol: For Olaparib treatment, cells were seeded at a density of 2×10⁵ cells per well in 6-well plates and allowed to adhere overnight. The next day, medium was replaced with fresh medium containing 2 μM Olaparib (or an equivalent volume of vehicle control, DMSO), and cells were incubated for 24 hours prior to RNA extraction. For PARP1 knockdown, cells were transfected with 100 pM PARP1-specific siRNA (or non-targeting control siRNA) using Lipofectamine RNAiMAX reagent, following the manufacturer's instructions. After 48 hours of incubation, cells were harvested for RNA isolation.

value: Breast; Mammary gland

value: epithelial cell

value: TRIM27 Wild-type (TRIM27-WT)

tag: batch


title: k546_4_bm_w_4d: Bone marrow 4-day old +/+

type: genomic

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Infinium® Mouse Methylation BeadChip performed according to manufacturer instructions by Edinburgh ECRF

scan_protocol: Prepared arrays were scanned on Illumina iScan

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Bisulphite conversion was done using EZ-96 DNA Methylation kit from Zymo using the protocol adjustments recommended for preparing samples for Illumina Methylation  - protocol appendix points 1 and 6

extract_protocol: Genomic DNA was extracted using Dneasy Blood and Tissue Kit (QIAGEN).

value: Dnmt3a +/+

value: bone marrow


title: TDLN_KO

description:
Library name: TDLN_KO
10X Chromium v3 scRNAseq FASTQ


description:
Library name: Sample 6
mRNA-Seq of HAP1 cells with Indisulam 24h DMSO Replicate 2

value: Indisulam_24h, DMSO


description:
Library name: Sample 5
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in RPE1 cells, Tunicamycin

value: Tunicamycin


title: k546_3_bm_m_4d: Bone marrow 4-day old W326R/+

value: Dnmt3a W326R/+


description:
Library name: Sample 3
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in HepG2 cells, Tunicamycin

value: Human liver cancer cell line


description:
Library name: Sample 5
mRNA-Seq of HAP1 cells with Indisulam 24h DMSO Replicate 1

value: Near-haploid cell line derived from KBM-7 human CML cell line


description:
Library name: Sample 4
mRNA-Seq of HAP1 cells with Indisulam 8h DMSO Replicate 2

value: Indisulam_8h, DMSO


description:
Library name: Sample 4
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in HepG2 cells, Untreated


title: k602_1_bm_w_4d: Bone marrow 4-day old +/+


description:
Library name: Sample 2
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in HAP1 cells, Untreated


title: k546_1_bm_m_4d: Bone marrow 4-day old W326R/+


title: Male, Cav1-KO, Hypoxia rep 3

city: Chicago

first: Richard

middle: D.

last: Minshall

state: IL

address: 835 S Wolcott Ave - E709C MSB (M/C 868)

department: Anesthesiology & Pharmacology and Regenerative Medicine

institute: University of Illinois Chicago

description:
Library name: A413
A413 column name in gene_fpkm.xls

data_processing:
Novogene processed raw data with perl scripts to remove reads containing the adapter, ploy-N, and low-qualiy reads.
featureCounts v1.5.0-p3 calculated read numbers and FPKM for each gene with default parameters.
Due to uncertainty over sample ID, A402 is excluded from our final analysis but still included in raw data.
Assembly: Hisat2 v2.0.5 was used to align genome to reference genome mm10 (mus_musculus_Ensemble_94) with default parameters.
Supplementary files format and content: gene_fpkm.xls is an Excel file containing FPKM values.  Each column header indicates the library/sample name, each row represents a different gene.
Supplementary files format and content: gene_count.xls is an Excel file containing raw gene count values.  Each column header indicates the library/sample name, each row represents a different gene.

source_name: Whole Lung

growth_protocol: Mice were kept and bred in standard conditions and fed standard feed in accordance with Institutional Animal Care and Use Committee of the University of Illinois Chicago. All mice used in final experiment are adults, at least 3 months of age.

extract_protocol:
Mice were humanely euthanized and whole lung RNA was isolated through TRIzol chloroform extraction.
Messenger RNA was purified with poly A enrichment, first strand cDNA generated with random hexamer primers, and second-strand cDNA was generated with dUTP for directional-library construction.

treatment_protocol: Mice were transferred to new cages for experiment.  Standard cages for normoxia, or specialized ventilated chamber cages using Nitrogen to displace oxygen to 10% for hypoxia.  Mice remained in their respective cages and oxygen levels for 6 weeks before sacrificing and tissue collection.

value: Whole Lung

value: Male

value: Chronix Hypoxia (6 weeks 10% Oxygen)


description:
Library name: Sample 1
mRNA-Seq for XBP1 splicing reporter CRASP-Seq assay in HAP1 cells, Tunicamycin


title: Male, Cav1-RC, Normoxia rep 3

description:
Library name: A329_1
A329_1 column name in gene_fpkm.xls

value: Normoxia


description:
Library name: Sample 2
mRNA-Seq of HAP1 cells with CTL DMSO Replicate 2

value: CTL, DMSO


description:
Library name: Sample 3
mRNA-Seq of HAP1 cells with Indisulam 8h DMSO Replicate 1


title: Male, Cav1-KO, Normoxia rep 3

description:
Library name: A422_2
A422_2 column name in gene_fpkm.xls


title: k546_2_bm_w_4d: Bone marrow 4-day old +/+


description:
Library name: Sample 1
mRNA-Seq of HAP1 cells with CTL DMSO Replicate 1


title: Single cells from PKT tumors treated with isotype control

city: Miami

first: Jashodeep

last: Datta

state: FL

address: 1425 NW 10th Ave

department: Surgery

institute: University of Miami Miller School of Medicine

description: Library name: Vehicle

data_processing:
Raw sequencing data were processed using the nf-core/scrnaseq pipeline (v4.1.0). Base calling and demultiplexing were performed with Illumina bcl2fastq (v2.20) to generate FASTQ files for each sample (Vehicle and CAN04). Reads subsequently aligned to the Mus musculus (mm10) reference genome using STARsolo (STAR v2.7) which executed cell barcode correction, UMI collapsing, and gene-level quantification to produce raw count matrices. Cells with high mitochondrial content,  low UMI and feature counts, or genes expressed in fewer than three cells were excluded from analysis. The resulting matrices were imported into Seurat (v4.3) for normalization, dimensional reduction, and clustering.
Assembly: Mus musculus (mm10) reference genome
Supplementary files format and content: Processed data are provided as 3 files per sample (Vehicle and CAN04) in the standard 10X Genomics format: matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz. The matrix file contains gene-by-cell count matrix of UMI counts and the barcodes file lists the unique cell barcodes which correspond to each column in the matrix. The features file lists the gene identifiers corresponding to each row.

molecule: cytoplasmic RNA

source_name: PDAC tumor

growth_protocol: Mice were housed and fed in accordance with IACUUC-approved protocol (21-076) at the University of Miami for two weeks prior to sacrifice

extract_protocol:
Whole tumors were harvested and live cells were collected by passing cells through L/D column.  Samples were sent to the Onco-Genomics shared resource for library prep and processing
RNA-seq

treatment_protocol: PKT mice received intraperitoneal injections of mNadunolimab (Cantargia AB; anti-mouse surrogate of human IgG1 IL1RAP inhibitor; 10 mg/kg7) or isotype control, twice on the first day of treatment (at 4-4.5 weeks of age), followed by 3x weekly dosing for two weeks, after which mice were sacrificed

value: PDAC tumor

value: Whole PDAC tumors from Ptf1aCre/+;LSL-KrasG12D/+;Tgfbr2flox/flox mice (PKT) mice on a C57Bl/6 background

value: isotype control


title: Single cells from PKT tumors treated with mNadunolimab (CAN04)

description: Library name: CAN04

value: mNadunolimab (CAN04)


title: Female, Cav1-KO, Normoxia rep 1

description:
Library name: A424_2
A424_2 column name in gene_fpkm.xls

value: Female


description:
Library name: Sample 16
mRNA-Seq of HAP1 cells with siSF3B3 Tunicamycin Replicate 2

data_processing:
Raw FASTQ file reads were trimmed with Cutadapt tool and mapped with STAR aligner. Differential splicing analysis was performed using rMATS tool. Differential expression analysis was performed with DESeq2 tool.
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab delimited excel file with multiple sheets containing log2FoldChange (L2FC), pvalues, and adjusted pvalues (padj) from differential expression analysis with DESeq2 tool for all the significant genes identified with different spliceosomal gene knockdowns. An additional sheet contains FPKM values for all the expressed genes in all the samples.
Supplementary files format and content: Tab delimited excel file with multiple sheets containing PSI, ΔPSI, Pvalue, and FDR values from differential splicing analysis with rMATS tool for all the significant exon skipping splicing events that were detected in different spliceosomal knockdown samples.

extract_protocol:
Total RNA was extracted using RNeasy plus miniprep RNA isolation kit and polyA mRNAs were enriched using oligo-dT magentic beads
Library construction was carried out following the TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HAP1 cells were transfected with siRNAs targeting spliceosomal components or a non-targeting control. Forty-eight hours after transfection, the cells were treated with 10µg/mL Tunicamycin or DMSO for 4h before harvesting for total RNA extraction.

value: siSF3B3, Tunicamycin


title: SW620 cells, sh-control,  bio rep 3

city: Changchun

first: Sui

last: Yujie

address: 265 Ziqiang Street

institute: The Second Hospital of Jilin University

description:
Library name: Sample 6
Column name in gene_fpkm.txt:  Ctrl_S3R

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: colon cancer

extract_protocol:
RNA was harvested using Total RNA was extracted from the cells using TriZol (Invitrogen). 1.3 µg of total RNA was used for the construction of sequencing libraries.
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction

value: colon cancer

value: colon cancer cells

value: WT


title: SW620 cells, sh-control,  bio rep 1

description:
Library name: Sample 4
Column name in gene_fpkm.txt: Ctrl_S1R


title: Female, Cav1-KO, Normoxia rep 2

description:
Library name: A425_2
A425_2 column name in gene_fpkm.xls


title: C. albicans single biofilm 48h in urine 3

city: South Bend

first: Ellsa

last: Wongso

address: 809 Lindenwood Dr S

institute: University of Notre Dame

description: Library name: CA3

data_processing:
Sequence reads were trimmed for adapter sequence/low quality sequence using Trimmomatic on UseGalaxy (E. faecalis and E. coli) and by GeneWiz for C. albicans
HISAT2 and htseq-count were used to mapped reads to reference genome. Deseq2 was used to normalized and analyzed counts
Assembly: GCF_000013265.1 (E. coli UTI89), GCF_000172575.2 (E. faecalis OG1RF), GCF_000182965.3 (C. albicans SC5314)
Supplementary files format and content: tab delimited text files includes raw counts for each file provided by GeneWiz

organism: Candida albicans

source_name: fungi

growth_protocol: Bacteria and/or fungi were grown in human sterilized urine in a fibrinogen-coated flasks for 48 hours at 37℃

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep kit from Zymo Research. 500 ng of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by GeneWiz

tag: strain

value: fungi

value: urine 48h


title: SW620 cells, sh-control,  bio rep 2

description:
Library name: Sample 5
Column name in gene_fpkm.txt: Ctrl_S2R


description:
Library name: Sample 15
mRNA-Seq of HAP1 cells with siSF3B3 Tunicamycin Replicate 1

value: Near-haploid cell line derived from KBM-7 human CML cell line


description:
Library name: Sample 14
mRNA-Seq of HAP1 cells with siSF3B1 Tunicamycin Replicate 2

value: siSF3B1, Tunicamycin


title: SW620 cells, shANO1, bio rep 2

description:
Library name: Sample 2
Column name in gene_fpkm.txt: ANsh_S2R

value: ANO1 knockdown


title: SW620 cells, shANO1, bio rep 1

description:
Library name: Sample 1
Column name in gene_fpkm.txt: ANsh_S1R


description:
Library name: Sample 13
mRNA-Seq of HAP1 cells with siSF3B1 Tunicamycin Replicate 1


title: Male, Cav1-KO, Normoxia rep 2

description:
Library name: A423
A423 column name in gene_fpkm.xls

value: Whole Lung

value: Male


title: C. albicans single biofilm 48h in urine 2

description: Library name: CA2


title: Male, Cav1-KO, Normoxia rep 1

description:
Library name: A421
A421 column name in gene_fpkm.xls

value: Normoxia


title: SC5314 wor2△/△bcr1△/△, bio rep 3

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

description: Library name: WOR2BCR1_YPD_3

data_processing:
Original data file from high-throughput sequencing platform (Illumina) is transformed to sequenced reads by CASAVA base recognition.
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Removed reads with adapter contamination. Removed reads when uncertain nucleotides constitute more than 10% of either read. Removed reads when low quality nucleotides constitute more than 50% of the read.
Assembly: HISAT2 was used to align reads to provided reference genome (assembly 22)
Supplementary files format and content: xls files include FPKM values for each sample based on condition

source_name: Yeast and hyphae

growth_protocol: C. albicans cells were grown in YPD for 4hrs at 37C shaking.

extract_protocol:
RNA extraction was performed by disrupting cells with Zirconia beads and isolating RNA using 25:24:1 phenol:chloroform:isoamylalcohol in combination with a Qiagen Rneasy Mini Kit
Sequencing libraries were generated by purifying messenger RNA from total RNA using poly-T oligo–attached magnetic beads. The first cDNA was synthesized using random hexamer primers, followed by sequencing of both ends of cDNA fragments using the Illumina platform

value: Yeast and hyphae

value: YPD, 4hrs


title: Apulla of Vatter 2

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

description:
Library name: AV2
10X Genomics

data_processing:
bcl2 files conversion to FASTQ format using cellranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC for discarding cell doublets and dying cells were performed using the R package Seurat
The integrated (cell x gene) matrices of all single cells are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample

source_name: Apulla of Vatter

growth_protocol: After recovering the samples, samples were diggested and dissociated to obtain single-cell suspensions, them theses were frozen for longterm storage until thawed before sequenicing without growth protocol

extract_protocol:
After thawing, cell suspensions were filtered (40 µM), followed by two sequential washing steps (RPMI-1640 medium + 10% FBS), and resuspended in cold PBS 1X. Cell suspensions of approximately 20,000 cells were obtained, and cell viability was manually evaluated using trypan blue staining. Only samples with more than 50% cell viability were further used for a droplet-based single-cell capture protocol.
Samples were prepared following the user guide “Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (Dual Index)” and loaded into the Chromium X (10x Genomics).

value: Apulla of Vatter


title: SC5314 wor2△/△bcr1△/△, bio rep 2

description: Library name: WOR2BCR1_YPD_2


title: SC5314 wor2△/△bcr1△/△, bio rep 1

description: Library name: WOR2BCR1_YPD_1


title: SC5314 bcr1△/△, bio rep 3

description: Library name: BCR1_YPD_3


description:
Library name: Sample 10
mRNA-Seq of HAP1 cells with siCTL Tunicamycin Replicate 2

value: siCTL, Tunicamycin


description:
Library name: Sample 9
mRNA-Seq of HAP1 cells with siCTL Tunicamycin Replicate 1


title: Male, Cav1-KO, Hypoxia rep 1

description:
Library name: A417
A417 column name in gene_fpkm.xls

value: Chronix Hypoxia (6 weeks 10% Oxygen)


title: C. albicans single biofilm 48h in urine 1

description: Library name: CA1


title: Female, Cav1-KO, Hypoxia rep 3

description:
Library name: A419
A419 column name in gene_fpkm.xls

value: Female


description:
Library name: Sample 12
mRNA-Seq of HAP1 cells with siRBM39 Tunicamycin Replicate 2

value: siRBM39, Tunicamycin


title: SC5314 bcr1△/△, bio rep 2

description: Library name: BCR1_YPD_2


title: Female, Cav1-KO, Hypoxia rep 2

description:
Library name: A415
A415 column name in gene_fpkm.xls


title: SW620 cells, shANO1, bio rep 3

description:
Library name: Sample 3
Column name in gene_fpkm.txt: ANsh_S3R

value: colon cancer

value: colon cancer cells


title: Male, Cav1-KO, Hypoxia rep 2

description:
Library name: A418
A418 column name in gene_fpkm.xls


title: Uncertain ID; Possibly Female, Cav1-KO, Normoxia

description:
Library name: A402
Uncertainty over sample ID, excluded from final analysis; A402 column name in gene_fpkm.xls

value: Female (unceratin)

value: Cav1(tm1Mls/)J (Uncertain)

value: Normoxia (Uncertain)


title: Ampullary carcinoma patient 3

description:
Library name: AC3
10X Genomics

source_name: Ampullary carcinoma

value: Ampullary carcinoma


title: Apulla of Vatter 1

description:
Library name: AV1
10X Genomics


title: Female, Cav1-KO, Hypoxia rep 1

description:
Library name: A412
A412 column name in gene_fpkm.xls


title: Ampullary carcinoma patient 2

description:
Library name: AC2
10X Genomics


description:
Library name: Sample 11
mRNA-Seq of HAP1 cells with siRBM39 Tunicamycin Replicate 1

value: Near-haploid cell line derived from KBM-7 human CML cell line


title: Ampullary carcinoma patient 1

description:
Library name: AC1
10X Genomics


title: Female, Cav1-RC, Hypoxia rep 3

description:
Library name: A334
A334 column name in gene_fpkm.xls

value: Whole Lung


title: SC5314 bcr1△/△, bio rep 1

description: Library name: BCR1_YPD_1


title: SC5314 wor2△/△, bio rep 3

description: Library name: WOR2_YPD_3


description:
Library name: Sample 7
mRNA-Seq of HAP1 cells with siSF3B3 DMSO Replicate 1

value: siSF3B3, DMSO


description:
Library name: Sample 8
mRNA-Seq of HAP1 cells with siSF3B3 DMSO Replicate 2


description:
Library name: Sample 6
mRNA-Seq of HAP1 cells with siSF3B1 DMSO Replicate 2

value: siSF3B1, DMSO


title: MD08R_Chromium_gene_expression

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

description: Library name: MD08R

data_processing:
Chromium scRNA-seq
Assembly: GRCh38 for Homo sapiens
Supplementary files format and content: RDS

molecule: nuclear RNA

extract_protocol:
Nuclei from frozen tumor tissue were isolated as previously described. Tissue was thawed and mechanically dissociated in ST buffer (10mM Tris-HCL pH7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2) with 0.49% CHAPS (Millipore). Single-nuclei suspensions were filtered using a 40 μm strainer, centrifuged at 500g for 5min, and resuspended in ST buffer supplemented with 0.01% BSA (Sigma). Nuclear suspensions were inspected by microscope, counted using a hemocytometer, and used for 10x Genomics workflow.
10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) was used according to manufacturer's protocol. In brief, nuclei were loaded on the Chromium Chip (10x Genomics) with a target cell recovery of 6,000-8,000 nuclei and processed in the Chromium Controller. Single-nuclei were partitioned into Gel Beads-in-emulsion (GEMs), followed by RNA reverse transcription with barcoding. Libraries were created by breaking GEMs and pooling barcoded fractions, cDNA amplification, fragmentation and attachment of sample index and adapter, and sequenced on  Nextseq200 or Novaseq (Illumina).

tag: Sex

tag: histology

value: Astrocytoma

tag: grade


title: Male, Cav1-RC, Normoxia rep 2

description:
Library name: A331
A331 column name in gene_fpkm.xls

value: Male

value: Normoxia


title: Female, Cav1-RC, Normoxia rep 2

description:
Library name: A333
A333 column name in gene_fpkm.xls


title: SC5314 wor2△/△, bio rep 2

description: Library name: WOR2_YPD_2

value: Yeast and hyphae

value: YPD, 4hrs


title: MD08P_Chromium_gene_expression

description: Library name: MD08P

value: Female


description:
Library name: Sample 5
mRNA-Seq of HAP1 cells with siSF3B1 DMSO Replicate 1


title: MD07R_Chromium_gene_expression

description: Library name: MD07R


description:
Library name: Sample 4
mRNA-Seq of HAP1 cells with siRBM39 DMSO Replicate 2

value: siRBM39, DMSO


title: SC5314 wor2△/△, bio rep 1

description: Library name: WOR2_YPD_1


title: Male, Cav1-RC, Normoxia rep 1

description:
Library name: A330
A330 column name in gene_fpkm.xls


description:
Library name: Sample 3
mRNA-Seq of HAP1 cells with siRBM39 DMSO Replicate 1


title: SC5314 WT, bio rep 3

description: Library name: WT_YPD_3

value: WT


title: MD07P_Chromium_gene_expression

description: Library name: MD07P


title: Female, Cav1-RC, Hypoxia rep 1

description:
Library name: A326
A326 column name in gene_fpkm.xls

value: Chronix Hypoxia (6 weeks 10% Oxygen)


title: Female, Cav1-RC, Hypoxia rep 2

description:
Library name: A327
A327 column name in gene_fpkm.xls


title: MD06R_Chromium_gene_expression

description: Library name: MD06R


title: SC5314 WT, bio rep 2

description: Library name: WT_YPD_2


description:
Library name: Sample 2
mRNA-Seq of HAP1 cells with siCTL DMSO Replicate 2

value: siCTL, DMSO


title: Teratoma_CD45+Lin-

city: Shanghai

first: Cui

last: Xinyu

address: Siping Road

institute: Tongji University

description: Library name: Teratoma_CD45+Lin-

data_processing:
Single-cell RNA sequencing data were processed using Cell Ranger (v.7.2.0). The raw reads were mapped to the hg38/GRCm38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix. After the preprocessing of data, R package Seurat(v.5.0.2) was used to perform the scRNAseq analysis. Cells with less than 800 unique molecular identifiers (UMIs) or greater than 10% mitochondrial expression were removed from further analysis. To exclude cells that might possibly include multiple cells or doublets, each sample was filtered for potential doublets by simulating synthetic doublets using R package DoubletFinder(v.2.0.3). The Seurat function NormalizeData was used to normalize the raw counts. Variable genes were identified using the FindVariableGenes function. The ScaleData function was used to scale and centre expression values in the dataset. UMAP was used to reduce the dimensions of the data, and the first two dimensions were used in the plots. The FindClusters function was used to cluster the cells. Cell types were annotated based on their match to canonical markers. Dot and violin plots were generated using the original normalized count data (Seurat). For PCA analysis in CD8+T cell samples, we generated pseudo-bulk expression profiles for each cluster using AverageExpression (Seurat), log-transformed the data, and generated PCA using the prcomp function. GSEA was performed using R package clusterProfiler(v.4.10.1) comparing the gene sets against all expressed genes ranked by their PC loading values.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: teratoma

extract_protocol:
For 10× genomics, cells were counted and then loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
For 10× genomics, sequencing libraries were constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Novaseq xplus according to the manufacturer’s instructions (Illumina).

value: teratoma

value: ES H1


title: Male, Cav1-RC, Hypoxia rep 3

description:
Library name: A324
A324 column name in gene_fpkm.xls


title: MD06P_Chromium_gene_expression

description: Library name: MD06P


title: SC5314 WT, bio rep 1

description: Library name: WT_YPD_1


title: rad53-H3K4A cells, H3_normalization for Pho23-Myc-ChIP, repeat-2

city: Yilan City

first: Shin Yen

last: Chong

state: Yilan County

address: No.1, Shennong Rd.,

department: Department of Food Science

country: Taiwan

institute: National Ilan University

description: Library name: rad53-H3K4A_Pho23Myc_H3_input_rep2, ChIP

library_source: genomic

data_processing:
Bowtie2 (2.3.5.1)
bamCoverage (deeepTools ver. 3.5.1), RPGC, bin size = 25 bp
Assembly: sacCer3
Supplementary files format and content: bigwig file, RPGC-normalized

organism: Saccharomyces cerevisiae

growth_protocol: Grow in typical YPD media, 30°C.

extract_protocol:
Cells were fixed with formaldehyde fixation solution (5 mM HEPES, pH 7.6; 0.1 mM EDTA; 10 mM NaCl; and 1.1% formaldehyde) for 20 minutes at room temperature and subsequently quenched with 125 mM glycine for 5 minutes. Cell pellets were washed and resuspended in 10 mL of ice-cold TBS (20 mM Tris, pH 7.6, and 150 mM NaCl). Cells were disrupted using a homogenizer (FastPrep®-24 5G) with the built-in program optimized for Saccharomyces cerevisiae. Chromatin was sheared by sonication using a Diagenode Bioruptor® Pico sonicator to generate DNA fragments with an average size of approximately 200–500 bp in 700 μL of FA buffer (50 mM HEPES-KOH, pH 7.6; 150 mM NaCl; 1 mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; and 1× protease inhibitor cocktail). Equal volumes of chromatin were subjected to immunoprecipitation. For H3K9/14ac ChIP, 4 μL of anti-H3K9/14ac antibody (Merck Millipore, 06-599) was conjugated to 20 μL of Protein G magnetic beads (Cytiva Protein G Mag Sepharose™). For H3K18ac ChIP, 5 μL of anti-H3K18ac antibody (Abcam, ab1191) was conjugated to 20 μL of Protein G magnetic beads. For total H3 ChIP, 4 μL of anti-H3 antibody (Abcam, ab1791) was conjugated to 20 μL of Protein G magnetic beads. For Myc-tagged protein ChIP, 4 μL of anti-Myc antibody (Merck Millipore, 05-419) was conjugated to 20 μL of Protein A magnetic beads (Cytiva Protein A Mag Sepharose™). Antibody-conjugated beads were resuspended in 30 μL of PBS-T for immunoprecipitation assays. For each immunoprecipitation, 200 μL of sonicated chromatin was incubated with antibody-conjugated beads at 4 °C overnight. Chromatin-bound beads were washed three times with FA buffer, twice with FA-HS buffer (FA buffer containing 500 mM NaCl), and once with RIPA buffer (10 mM Tris, pH 8.0; 250 mM LiCl; 0.5% NP-40; 0.5% sodium deoxycholate; 1 mM EDTA; and 1× protease inhibitor cocktail). Bound chromatin was eluted using stop buffer (20 mM Tris, pH 8.0; 100 mM NaCl; 20 mM EDTA; and 1% SDS) at 75 °C for 15 minutes. Eluates were incubated at 75 °C overnight to reverse cross-links, followed by treatment with proteinase K (2 μL of 10 mg/mL) at 50 °C for 6 hours and RNase A (2 μL of 10 mg/mL) at 42 °C for 2 hours. DNA was purified using the MinElute PCR Purification Kit (Qiagen, 28004) according to the manufacturer’s instructions and eluted in 12 μL of elution buffer. Purified ChIP DNA was quantified using Qubit fluorometric quantification prior to library preparation.
Sequencing libraries were prepared using the KAPA HyperPrep Kit (Roche, KK8504). Paired-end sequencing was performed on an Illumina platform at Taiwan Genomic Industry Alliance Inc.

treatment_protocol: Cells were synchronized in G1 phase at the onset of log phase by treatment with α-factor (100 ng/mL) for 2.5 hours. G1-arrested RAD53 cells were treated with 200 mM hydroxyurea (HU) for 1 hour, whereas rad53 cells were treated with 25 mM HU for 1 hour, prior to harvesting and cross-linking for chromatin immunoprecipitation.

value: yeast cell

tag: chip antibody

value: ChIP antobody (Abcam, ab1791)

value: G1 release in 25 mM HU, 1h


description:
Library name: Sample 1
mRNA-Seq of HAP1 cells with siCTL DMSO Replicate 1

value: Near-haploid cell line derived from KBM-7 human CML cell line


title: rad53-H3K4A cells, H3_normalization for Pho23-Myc-ChIP, repeat-1

description: Library name: rad53-H3K4A_Pho23Myc_H3_input_rep1, ChIP


title: Male, Cav1-RC, Hypoxia rep 2

description:
Library name: A323
A323 column name in gene_fpkm.xls

value: Whole Lung


title: MD05R2_Chromium_gene_expression

description: Library name: MD05R2

value: Astrocytoma


title: rad53-H3 cells, H3_normalization for Pho23-Myc-ChIP, repeat-2

description: Library name: rad53-H3_Pho23Myc_H3_input_rep2, ChIP


title: MD04R_Chromium_gene_expression

description: Library name: MD04R

value: Male


title: Male, Cav1-RC, Hypoxia rep 1

description:
Library name: A322
A322 column name in gene_fpkm.xls


title: KS3

city: La Jolla

first: Gabriel

last: Haddad

department: Pediatrics

institute: University of California, San Diego

description: Library name: sample 6

data_processing:
Rigorous quality controls of the 150-nucleotide paired-end reads were assessed using FastQC tools, and the adapter sequences and low-quality bases were removed using Trimmomatic. The trimmed reads were mapped to the human hg38 reference genome using the STAR aligner. Differential expression was calculated using DESeq2 with default settings, and differentially expressed genes (DEGs) were identified with a threshold of |Fold-Change| > 1.5 and adjusted p-value < 0.05.
Assembly: human hg38
Supplementary files format and content: xlsx file includes TPM and NumReads for each sample

extract_protocol:
The quality of total RNA was examined using TapeStation (Agilent, CA) and Samples with an RNA Integrity Number (RIN) greater than 7 were used for library preparation and sequencing.
PolyA+ selected libraries were prepared using the Illumina TruSeq mRNA Stranded Library Prep Kit with TruSeq UDI96 indexed adaptors

treatment_protocol: Total RNA was extracted using the Zymo Quick-RNA™ Miniprep Kit (Zymo, CA) according to the manufacturer’s instructions.

value: Neurons/Cortical organoids

value: XXY

tag: disease

value: Klinefelter syndrome


title: Female, Cav1-RC, Normoxia rep 1

description:
Library name: A302
A302 column name in gene_fpkm.xls

value: Female

value: Normoxia


title: KS1

description: Library name: sample 4


title: KS2

description: Library name: sample 5


title: Female, WT Control, Hypoxia rep 3

description:
Library name: A230
A230 column name in gene_fpkm.xls


title: Con3

description: Library name: sample 3

value: XY

value: Healthy control


title: Con2

description: Library name: sample 2


title: rad53-H3 cells, H3_normalization for Pho23-Myc-ChIP, repeat-1

description: Library name: rad53-H3_Pho23Myc_H3_input_rep1, ChIP


title: Female, WT Control, Hypoxia rep 2

description:
Library name: A229
A229 column name in gene_fpkm.xls

value: Chronix Hypoxia (6 weeks 10% Oxygen)


title: Con1

description: Library name: sample 1


title: H3K4A cells, H3_normalization for Pho23-Myc-ChIP, repeat-1

description: Library name: H3K4A_Pho23Myc_H3_input_rep1, ChIP

value: G1 release in 200 mM HU, 1h


title: MD05P_Chromium_gene_expression

description: Library name: MD05P


title: PDX-C15, VK1727 treatment 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: PDX-C15_VK1727-3

data_processing:
Quality of RNA-seq raw datasets was determined using FastQC (version, 1.0.0) coupled with MultiQC. Adaptor sequences from each read was removed using Trim Galore (version 0.6.10) program with pair-end trimming algorithm. RNA reads were mapped to integrated human (Hg19, also known as GRCh37) and EBV (NC007605) reference genomes using STAR aligner (version 2.7.11b). The count table of reads per gene was generated using featureCounts program and utilized for subsequential analysis (e.g. Differential Gene expression and functional analysis). DESeq2 package (version, 1.50.0), embodied in R (version, 4.5.2) program, was used for differential gene expression analysis.
Assembly: Human(GRCh37) and EBV (NC007605)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
RNeasy Kit mini (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: EBV+, nasopharyngeal carcinoma

value: EBNA1 inhibitor treatment


title: Female, WT Control, Normoxia rep 2

description:
Library name: A227
A227 column name in gene_fpkm.xls


title: H3 cells, H3_normalization for Pho23-Myc-ChIP, repeat-2

description: Library name: H3_Pho23Myc_H3_input_rep2, ChIP

value: yeast cell

value: ChIP antobody (Abcam, ab1791)


title: H3K4A cells, H3_normalization for Pho23-Myc-ChIP, repeat-2

description: Library name: H3K4A_Pho23Myc_H3_input_rep2, ChIP


title: Female, WT Control, Normoxia rep 3

description:
Library name: A228
A228 column name in gene_fpkm.xls


title: MD04P_Chromium_gene_expression

description: Library name: MD04P


title: MD03R_Chromium_gene_expression

description: Library name: MD03R


title: H3 cells, H3_normalization for Pho23-Myc-ChIP, repeat-1

description: Library name: H3_Pho23Myc_H3_input_rep1, ChIP


title: rad53-H3K4A cells, Pho23-Myc-ChIP, repeat-2

description: Library name: rad53-H3K4A_Pho23Myc_rep2, ChIP

value: ChIP antobody (Merck Millipore, 05-419)

value: G1 release in 25 mM HU, 1h


title: MD03R2_Chromium_gene_expression

description: Library name: MD03R2

value: Astrocytoma


title: PDX-C15, VK1727 treatment 2

description: Library name: PDX-C15_VK1727-2


title: Teratoma_CD45_Rep1

description: Library name: Teratoma_CD45_Rep1

data_processing:
Single-cell RNA sequencing data were processed using Cell Ranger (v.7.2.0), while CD8+T cell samples were provided by the MobiDrop platform following the manufacturer's protocol (Shanghai Baimu Biotechnology Co., Ltd.). The MobiVision Single-Cell Software (v.3.0) was used to perform T cell samples demultiplexing, barcode processing and single-cell 3′ gene counting. The raw reads were mapped to the hg38/GRCm38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix. After the preprocessing of data, R package Seurat(v.5.0.2) was used to perform the scRNAseq analysis. Cells with less than 800 unique molecular identifiers (UMIs) or greater than 10% mitochondrial expression were removed from further analysis. To exclude cells that might possibly include multiple cells or doublets, each sample was filtered for potential doublets by simulating synthetic doublets using R package DoubletFinder(v.2.0.3). The Seurat function NormalizeData was used to normalize the raw counts. Variable genes were identified using the FindVariableGenes function. The ScaleData function was used to scale and centre expression values in the dataset. UMAP was used to reduce the dimensions of the data, and the first two dimensions were used in the plots. The FindClusters function was used to cluster the cells. Cell types were annotated based on their match to canonical markers. Dot and violin plots were generated using the original normalized count data (Seurat). For PCA analysis in CD8+T cell samples, we generated pseudo-bulk expression profiles for each cluster using AverageExpression (Seurat), log-transformed the data, and generated PCA using the prcomp function. GSEA was performed using R package clusterProfiler(v.4.10.1) comparing the gene sets against all expressed genes ranked by their PC loading values.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For 10× genomics, cells were counted and then loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
For MobiNova-100, CD8+ T cells were collected and extracted following the manufacturer's instructions (MobiDrop, Shanghai Baimu Biotechnology Co., Ltd.). After quality control assessment, samples were loaded to a pre-prepared chip containing reverse transcription reagents, cell-phase reagents, and droplet generation oil. The chip holder was then carefully transferred to the MobiNova®-100 instrument for droplet generation and single-cell barcoding. A droplet pre-processor was employed to pre-treat the generated droplets, before reverse-transcription to cDNA. The resultant cDNA after reverse transcription underwent GEM breaking and pre-amplification. Subsequently, SPRIselect beads were used for cDNA purification, and the cDNA quality was assessed using Qubit and Agilent 2100 HS DNA.
For 10× genomics, sequencing libraries were constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Novaseq xplus according to the manufacturer’s instructions (Illumina).
For MobiNova-100, library construction included the following steps: cDNA fragmentation, adapter ligation to the fragmented products, size selection of the ligated products, amplification of the library with tags, and size selection of the amplified library fragments.

value: teratoma

value: ES H1


title: Male, WT Control, Normoxia rep 3

description:
Library name: A226
A226 column name in gene_fpkm.xls

value: Whole Lung

value: Male


title: Male, WT Control, Normoxia rep 2

description:
Library name: A224
A224 column name in gene_fpkm.xls


title: Teratoma_CD45_Rep2

description: Library name: Teratoma_CD45_Rep2


title: PDX-C15, DMSO treatment 3

description: Library name: PDX-C15_DMSO-3

value: Control


title: PDX-C15, VK1727 treatment 1

description: Library name: PDX-C15_VK1727-1


title: rad53-H3 cells, Pho23-Myc-ChIP, repeat-2

description: Library name: rad53-H3_Pho23Myc_rep2, ChIP


title: Male, WT Control, Normoxia rep 1

description:
Library name: A223
A223 column name in gene_fpkm.xls

value: Normoxia


title: Male, WT Control, Hypoxia rep 3

description:
Library name: A222
A222 column name in gene_fpkm.xls


title: Day3_SP140LSL

description: Library name: Day3_SP140LSL

source_name: Embryoid body

value: Embryoid body


title: Male, WT Control, Hypoxia rep 2

description:
Library name: A221
A221 column name in gene_fpkm.xls


title: rad53-H3 cells, Pho23-Myc-ChIP, repeat-1

description: Library name: rad53-H3_Pho23Myc_rep1, ChIP


title: rad53-H3K4A cells, Pho23-Myc-ChIP, repeat-1

description: Library name: rad53-H3K4A_Pho23Myc_rep1, ChIP


title: Day1_SP140LSL

description: Library name: Day1_SP140LSL


title: Day2_SP140LSL

description: Library name: Day2_SP140LSL


title: PDX-C15, DMSO treatment 2

description: Library name: PDX-C15_DMSO-2


title: H3 cells, Pho23-Myc-ChIP, repeat-2

description: Library name: H3_Pho23Myc_rep2, ChIP


title: PDX-C15, DMSO treatment 1

description: Library name: PDX-C15_DMSO-1


title: Male, WT Control, Hypoxia rep 1

description:
Library name: A218
A218 column name in gene_fpkm.xls


title: H3K4A cells, Pho23-Myc-ChIP, repeat-2

description: Library name: H3K4A_Pho23Myc_rep2, ChIP


title: Day1_WT

description: Library name: Day1_WT


title: H3K4A cells, Pho23-Myc-ChIP, repeat-1

description: Library name: H3K4A_Pho23Myc_rep1, ChIP


title: Day3_WT

description: Library name: Day3_WT


title: H3 cells, Pho23-Myc-ChIP, repeat-1

description: Library name: H3_Pho23Myc_rep1, ChIP


title: SNU719, VK1727 treatment 3

description: Library name: SNU719_VK1727-3

value: EBV+ gastric cancer


title: Day2_WT

description: Library name: Day2_WT


title: SNU719, VK1727 treatment 2

description: Library name: SNU719_VK1727-2


title: Female, WT Control, Hypoxia rep 1

description:
Library name: A212
A212 column name in gene_fpkm.xls

value: Female

value: Chronix Hypoxia (6 weeks 10% Oxygen)


title: Female, WT Control, Normoxia rep 1

description:
Library name: C206
C206 column name in gene_fpkm.xls


title: rad53-rpd3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: rad53-rpd3_H3_Input_rep1, ChIP


title: SNU719, VK1727 treatment 1

description: Library name: SNU719_VK1727-1


title: SNU719, DMSO treatment 1

description: Library name: SNU719_DMSO-1


title: CD34_SP140iTOP1i_Rep3

description: Library name: CD34_SP140iTOP1i_Rep3

data_processing:
RNA-seq reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (hg38) using Hisat2 (v.2.1.0) with the parameters `--no-unal --no-mixed --no-discord¬ant`. Expression level of genes were calculated using Stringtie (v2.2.1). Read counts were calculated using featureCounts(v.2.0.1). Differential gene expression analysis was performed using Bioconductor package DESeq2 (v.1.26.0). Significantly genes were defined as having a fold change > 2 and P.adj < 0.05. Principal component analysis (PCA) was performed using the prcomp function of R software (v.4.3.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files including TPM values for each Sample

extract_protocol:
RNA was harvested in trizol (Invitrogen), and extracted by NovoGene.
RNA integrity was assessed using the RNANano 6000 Assay Kit of the Bioanalyzer2100 system (Agilent Technologies, CA, USA). Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand SynthesisReaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNAsynthesis was subsequently performed usingDNA PolymeraseI and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: hemogenic endothelium


title: rad53-rpd3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: rad53-rpd3_H3_Input_rep2, ChIP


title: Mouse 1-3, spleen, thymus, lung (hashtag)

city: Saint Louis

first: Shitong

last: Wu

state: MO

address: 660 S Euclid Avenue

institute: Washington University in St. Louis

description:
Library name: Sample 3
spleen, thymus, lung extracted as described in manuscript

library_source: other

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Paired scRNAseq data produced from Chromium Single Cell Multiome ATAC + Gene Expression was processed using the cellranger-arc count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz.

molecule: protein

source_name: spleen, thymus, lung

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v2 or v3 User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: spleen, thymus, lung

value: DCs and pDCs

tag: library type

value: HTO


title: CD34_SP140i_Rep2

description: Library name: CD34_SP140i_Rep2


title: CD34_SP140iTOP1i_Rep2

description: Library name: CD34_SP140iTOP1i_Rep2


title: CD34_SP140iTOP1i_Rep1

description: Library name: CD34_SP140iTOP1i_Rep1


title: SNU719, DMSO treatment 3

description: Library name: SNU719_DMSO-3


title: Mouse 1-3, spleen, thymus, lung (RNA)

description:
Library name: Sample 4
spleen, thymus, lung extracted as described in manuscript

value: RNA


title: SNU719, DMSO treatment 2

description: Library name: SNU719_DMSO-2


title: C666-1, VK1727 treatment 3

description: Library name: C666-1_VK1727-3

value: EBV+, nasopharyngeal carcinoma

value: EBNA1 inhibitor treatment


title: CD34_SP140i_Rep3

description: Library name: CD34_SP140i_Rep3


title: Mouse 1-3, skin, sLN, mLN (hashtag)

description:
Library name: Sample 1
skin, sLN, mLN extracted as described in manuscript

source_name: skin, sLN, mLN

value: skin, sLN, mLN


title: C666-1, VK1727 treatment 1

description: Library name: C666-1_VK1727-1


title: rad53-H3K4A cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: rad53-H3K4A_H3_Input_rep2, ChIP

value: yeast cell

value: ChIP antobody (Abcam, ab1791)

value: G1 release in 25 mM HU, 1h


title: Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 3

city: Rochester

first: John

middle: D

last: Lueck

address: 601 Elmwood Ave

department: Pharmacology and Physiology

institute: University of Rochester

description: Library name: 46c

data_processing:
Data Formatting, bcltofastq-2.19.1
Data Cleaning, fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Data alignment, STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read count, subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Splicing, MAJIQ
Assembly: GRCm39 + Gencode-M31 Annotation
Supplementary files format and content: Counts.txt, tab delimited text file of read counts per gene
Supplementary files format and content: Splicing.xlsx, excel spreadsheet of MAJIQ output for splicing analysis

source_name: Quadriceps

growth_protocol: Mice of the above genotypes were housed in accordance with UCAR policy at University of Rochester Medical Center. Mice were sacrificed at 4-6 months postnatal with UCAR approved methods, with quadriceps tissue immediately dissected and stored at -80˚C.

extract_protocol:
Total RNA was isolated from murine quadriceps tissue with Rneasy kit (Qiagen).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

value: Quadriceps

value: Clcn1 delta E7a


title: rad53-pho23 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: rad53-pho23_H3_Input_rep1, ChIP


title: C666-1, DMSO treatment 3

description: Library name: C666-1_DMSO-3

value: Control


title: Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 4

description: Library name: 47c


title: rad53-H3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: rad53-H3_H3_Input_rep2, ChIP


title: C666-1, VK1727 treatment 2

description: Library name: C666-1_VK1727-2


title: Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 1

description: Library name: 44c


title: Mouse 1-3, skin, sLN, mLN (RNA)

description:
Library name: Sample 2
skin, sLN, mLN extracted as described in manuscript


title: rad53-pho23 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: rad53-pho23_H3_Input_rep2, ChIP


title: CD34_SP140i_Rep1

description: Library name: CD34_SP140i_Rep1

value: Embryoid body


title: C666-1, DMSO treatment 2

description: Library name: C666-1_DMSO-2


title: Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 2

description: Library name: 45c


title: rad53-H3K4A cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: rad53-H3K4A_H3_Input_rep1, ChIP


title: CD34_DMSO_Rep3

description: Library name: CD34_DMSO_Rep3


title: rad53-H3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: rad53-H3_H3_Input_rep1, ChIP


title: Mbnl1 knockout; Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 3

description: Library name: 50c

value: Mbnl1 knockout; Clcn1 delta E7a


title: CD34_DMSO_Rep2

description: Library name: CD34_DMSO_Rep2


title: rpd3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: rpd3_H3_Input_rep1, ChIP

value: G1 release in 200 mM HU, 1h


title: TK20R_Chromium_gene_expression

description: Library name: TK20R

value: Male

value: Oligodendroglioma


title: C666-1, DMSO treatment 1

description: Library name: C666-1_DMSO-1


title: CD34_DMSO_Rep1

description: Library name: CD34_DMSO_Rep1

value: hemogenic endothelium


title: pho23 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: pho23_H3_Input_rep2, ChIP


title: CD31_SP140i_Rep2

description: Library name: CD31_SP140i_Rep2

value: mesoderm


title: CD31_SP140i_Rep1

description: Library name: CD31_SP140i_Rep1


title: Mbnl1 knockout; Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 2

description: Library name: 41c


title: rpd3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: rpd3_H3_Input_rep2, ChIP


title: CD31_SP140i_Rep3

description: Library name: CD31_SP140i_Rep3


title: Mbnl1 knockout murine quadrieps muscle, 4-6 mth old, rep 4

description: Library name: 39c

value: Mbnl1 knockout


title: Mbnl1 knockout; Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 1

description: Library name: 40c


title: TK19R2_Chromium_gene_expression

description: Library name: TK19R2

value: Female


title: H3K4A cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: H3K4A_H3_Input_rep2, ChIP


title: CD31_DMSO_Rep3

description: Library name: CD31_DMSO_Rep3


title: CD31_DMSO_Rep1

description: Library name: CD31_DMSO_Rep1


title: TK19R_Chromium_gene_expression

description: Library name: TK19R


title: pho23 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: pho23_H3_Input_rep1, ChIP


title: H3K4A cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: H3K4A_H3_Input_rep1, ChIP


title: TK17R2_Chromium_gene_expression

description: Library name: TK17R2


title: CD31_DMSO_Rep2

description: Library name: CD31_DMSO_Rep2


title: TK20P_Chromium_gene_expression

description: Library name: TK20P


title: TK18R_Chromium_gene_expression

description: Library name: TK18R


title: Mbnl1 knockout; Clcn1 delta E7a murine quadriceps muscle, 4-6 mth old, rep 4

description: Library name: 43c


title: TK17R_Chromium_gene_expression

description: Library name: TK17R


title: 2577-CSF-11-3mo

first: Mahesh Chandra

last: Kodali

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

description: 10x Genomics

data_processing:
Reads were aligned to reference 2020-A (Ensembl 98) transcriptome 156 and quantified using Cell Ranger v6.0.2 multipipeline.
Assembly: reference 2020-A (Ensembl 98) transcriptome
Supplementary files format and content: 10X Cell Ranger Outputs

source_name: CSF Cells

extract_protocol: Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

value: Primary

tag: subject

tag: months after_bcg_vaccine

value: CSF Cells


title: Mbnl1 knockout murine quadrieps muscle, 4-6 mth old, rep 3

description: Library name: 38c


title: TK19P_Chromium_gene_expression

description: Library name: TK19P


title: Mbnl1 knockout murine quadrieps muscle, 4-6 mth old, rep 2

description: Library name: 37c


title: TK16R2_Chromium_gene_expression

description: Library name: TK16R2

value: Astrocytoma


title: H3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-2

description: Library name: H3_H3_Input_rep2, ChIP

value: yeast cell

value: ChIP antobody (Abcam, ab1191)


title: 2577-CSF-11-12mo

description: 10x Genomics


title: Mbnl1 knockout murine quadrieps muscle, 4-6 mth old, rep 1

description: Library name: 36c

value: Quadriceps


title: SM16P_Chromium_gene_expression

description: Library name: SM16P


title: WT murine quadriceps muscle, 4-6 mth old, rep 4

description: Library name: 35c

value: WT


title: 2577-CSF-9-0mo

description: 10x Genomics


title: 2577-CSF-11-0mo

description: 10x Genomics


title: rad53-pho23 cells, H3K18, repeat-2

description: Library name: rad53-pho23_H3K18ac_rep2, ChIP

value: G1 release in 25 mM HU, 1h


title: H3 cells, H3_normalization for H3K9/14ac and K18ac ChIP, repeat-1

description: Library name: H3_H3_Input_rep1, ChIP


title: 2577-CSF-6-3mo

description: 10x Genomics


title: rad53-rpd3 cells, H3K18, repeat-2

description: Library name: rad53-rpd3_H3K18ac_rep2, ChIP


title: rad53-rpd3 cells, H3K18, repeat-1

description: Library name: rad53-rpd3_H3K18ac_rep1, ChIP


title: WT murine quadriceps muscle, 4-6 mth old, rep 1

description: Library name: 32c


title: WT murine quadriceps muscle, 4-6 mth old, rep 2

description: Library name: 33c


title: WT murine quadriceps muscle, 4-6 mth old, rep 3

description: Library name: 34c


title: 2577-CSF-9-3mo

description: 10x Genomics


title: LAPC9 mouse fibroblasts, p2, Experiment  63_22, m3, #2

city: Bern

first: Panagiotis

last: Chouvardas

address: Murtenstrasse 24

country: Switzerland

institute: University of Bern

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m3 techn.repl. #2
BRB-seq

data_processing:
library strategy: Bulk RNA Barcoding and sequencing (BRB-seq)
Read trimming, alignment, and quantification steps were performed by Alithea Genomics using STARsolo v2.7.9a
Deduplicated unique molecular identifiers (umi) count matrices were used to create the initial DESeq2 (v1.46.0). Genes with fewer than 3 counts in fewer than 3 samples were removed.
Differential expression analysis was performed using DESeq2 with the Wald method. Shrinkage of fold changes was applied using the "normal" method as specified in the DESeq package. Genes were considered differentially expressed if they had an adjusted p-value below 0.05 and an absolute shrunken fold change greater than 2
Assembly: GRCm38, Ensembl 102
Supplementary files format and content: text file/UMI count matrix

source_name: mouse fibroblasts passage 2 (p2)

extract_protocol:
RNA was extracted from PDX tissue-derived stromal (mouse) fraction cells and PDX-fibroblasts lysed in TriPure Isolation Reagent (Sigma-Aldrich). RNA extraction was performed using the Direct-zol RNA Microprep kit (Zymo research). RNA concentration was measured with NanoDrop™ 2000/2000c Spectrophotometer and with QubitTM RNA Broad Range (BR) Assay Kit (ThermoFisher). RNA quality was assessed through the Agilent Total RNA 6000 Nano Kit (Bioanalyzer) or with the Qubit™ RNA IQ Assay Kits (Thermo Fisher)
RNA samples with an amount > 200ng and RNA integrity number >6 were sent for sequencing. Samples were sent to Alithea Genomics (Lausanne, Switzerland) for sequencing using the BRB-seq method

value: mouse fibroblasts passage 2 (p2)


title: SM15R2_Chromium_gene_expression

description: Library name: SM15R2


title: SM15R_Chromium_gene_expression

description: Library name: SM15R


title: SM15P_Chromium_gene_expression

description: Library name: SM15P


title: rad53-pho23 cells, H3K18, repeat-1

description: Library name: rad53-pho23_H3K18ac_rep1, ChIP


title: 2577-CSF-6-0mo

description: 10x Genomics


title: SM14R_Chromium_gene_expression

description: Library name: SM14R


title: LAPC9 mouse fraction, p0, Experiment 63_22, m3, #2

description:
Library name: LAPC9 ms fract p0 63_22 m3 techn.repl. #2
BRB-seq

source_name: single cells (p0) from prostate PCa PDX tissue


title: rad53-H3K4A cells, H3K18, repeat-2

description: Library name: rad53-H3K4A_H3K18ac_rep2, ChIP


title: 2577-CSF-5-3mo

description: 10x Genomics


title: PNPCa mouse fibroblasts, p2, Experiment 48_22, #2

description:
Library name: PNPCa ms fibr p2 Exp 48_22 techn.repl. #2
BRB-seq

value: single cells (p0) from prostate PCa PDX tissue

value: PNPCa


title: rad53-H3K4A cells, H3K18, repeat-1

description: Library name: rad53-H3K4A_H3K18ac_rep1, ChIP


title: BM18 mouse fibroblasts, p2, Experiment 3_22, m4, #2

description:
Library name: BM18 ms fibr p2 Exp 3_22 m4 techn.repl. #2
BRB-seq


title: PNPCa mouse fraction, p0, Experiment 48_22, #2

description:
Library name: PNPCa ms fract p0 48_22  techn.repl. #2
BRB-seq


title: SM14P_Chromium_gene_expression

description: Library name: SM14P

value: Male


title: 2577-CSF-5-0mo

description: 10x Genomics


title: 2577-CSF-2-12mo

description: 10x Genomics


title: 2577-CSF-2-3mo

description: 10x Genomics


title: SM12R_Chromium_gene_expression

description: Library name: SM12R


title: LAPC9 mouse fibroblasts, p2, Experiment 63_22, m3,  #1

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m3  techn.repl. #1
BRB-seq


title: SM12P_Chromium_gene_expression

description: Library name: SM12P


title: rad53-H3 cells, H3K18, repeat-1

description: Library name: rad53-H3_H3K18ac_rep1, ChIP


title: rpd3 cells, H3K18, repeat-1

description: Library name: rpd3_H3K18ac_rep1, ChIP

value: G1 release in 200 mM HU, 1h


title: SM10R2_Chromium_gene_expression

description: Library name: SM10R2


title: rad53-H3 cells, H3K18, repeat-2

description: Library name: rad53-H3_H3K18ac_rep2, ChIP


title: 242-CSF-19-0mo

description: 10x Genomics


title: PNPCa mouse fibroblasts, p2, Experiment 48_22, #1

description:
Library name: PNPCa ms fibr p2 Exp 48_22 techn.repl. #1
BRB-seq


title: SM10R_Chromium_gene_expression

description: Library name: SM10R


title: BM18 mouse fibroblasts, p2, Experiment 3_22, m4, #1

description:
Library name: BM18 ms fibr p2 Exp 3_22 m4 techn.repl. #1
BRB-seq


title: rpd3 cells, H3K18, repeat-2

description: Library name: rpd3_H3K18ac_rep2, ChIP


title: 242-CSF-16-12mo

description: 10x Genomics


title: pho23 cells, H3K18, repeat-1

description: Library name: pho23_H3K18ac_rep1, ChIP


title: pho23 cells, H3K18, repeat-2

description: Library name: pho23_H3K18ac_rep2, ChIP


title: 242-CSF-16-3mo

description: 10x Genomics


title: PNPCa mouse fraction, p0, Experiment 48_22,  #1

description:
Library name: PNPCa ms fract p0 48_22  techn.repl. #1
BRB-seq


title: H3K4A cells, H3K18, repeat-2

description: Library name: H3K4A_H3K18ac_rep2, ChIP


title: 242-CSF-15-3mo

description: 10x Genomics


title: LAPC9 mouse fraction, p0, Experiment 63_22, m3, #1

description:
Library name: LAPC9 ms fract p0 63_22 m3 techn.repl. #1
BRB-seq


title: IDH-G_single-nucleus_TK16R2

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021.
Assembly: GRCh38 for Homo sapiens

extract_protocol:
Nuclear suspension was stained by Vybrant DyeCycle Ruby Stain (Thermo Fisher Scientific) immediately before FACS-sorting. Single-nucleus sorting was performed on a FACS Aria Fusion sorter (Becton Dickinson) using 640nm laser (Ruby, 670/14 filter). After doublet discrimination, intact nuclei were selected with ruby positive and were sorted into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80℃ prior to joint XRBS and Smart-seq2  experiment.
Genomic DNA (gDNA) and mRNA in 96 well plats were separated by oligo-dT primer conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies). The mRNA was then collected to the side of the well using a magne, and the supernatant, containing the gDNA, was transferred to a fresh plate for XRBS protocol. XRBS (Shareef et al Nat Biotchnol 2021) was done by modifying RRBS protocol used in a previous paper (Chaligne et al Nat Genet 2021). The gDNA was restricted by enzyme Msp. Digested DNA was filled-in and A-tailed at the 3′ sticky ends with  Klenow supplemented with dNTP. Custom barcoded methylated adaptors were then ligated with T4 DNA ligase. Pooled genomic DNA was cleaned-up and was then sodium bisulfite-converted. Next, bisulfite-converted DNA was eluted in TE, then Hexamer extension were performed as reported by Shareef et al, with a slight modification. Bisulfite-converted single-stranded DNA was mixed with random hexamer primer. Then, 1.3 μl of Klenow enzyme was added to each reaction. Hexamer base pairing is mediated through a gradual increase in temperature. The product was washed by AMPure XP beads , and was then amplified using primers containing Illumina i7 and i5 index. Library enrichment was by PCR using KAPA HiFi Uracil+ master mix. Enriched libraries were cleaned-up and concentrated using AMPure XP beads. The library was pooled sequenced by a Nextseq2000.


title: IDH-G_single-nucleus_TK18R


title: 242-CSF-15-12mo

description: 10x Genomics


title: LAPC9 mouse fibroblasts, p2, Experiment 65_22, m20, #2

description:
Library name: LAPC9 ms fibr p2 Exp 65_22 m20 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_TK16R


title: H3K4A cells, H3K18, repeat-1

description: Library name: H3K4A_H3K18ac_rep1, ChIP


title: IDH-G_single-nucleus_TK19R2


title: 242-CSF-13-12mo

description: 10x Genomics


title: 242-CSF-13-3mo

description: 10x Genomics


title: 242-CSF-15-0mo

description: 10x Genomics


title: IDH-G_single-nucleus_TK17R2


title: LAPC9 mouse fibroblasts, p2, Experiment 26_22, #2

description:
Library name: LAPC9 ms fibr p2 Exp 26_22 techn.repl. #2
BRB-seq


title: PNPCa mouse fibroblasts, p2, Experiment 63_22, m9, #2

description:
Library name: PNPCa ms fibr p2 Exp 63_22 m9 techn.repl. #2
BRB-seq


title: LAPC9 mouse fraction, p0, Experiment 26_22, #2

description:
Library name: LAPC9 ms fract p0 26_22 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_TK19R


title: rad53-rpd3 cells, H3K9/14, repeat-1

description: Library name: rad53-rpd3_H3K9/14ac_rep1, ChIP

value: ChIP antobody (Merck Millipore, 06-599)


title: IDH-G_single-nucleus_TK17R


title: BM18 mouse fraction, p0, Experiment 65_22, #2

description:
Library name: BM18 ms fract p0 65/22 techn.repl. #2
BRB-seq


title: H3 cells, H3K18, repeat-1

description: Library name: H3_H3K18ac_rep1, ChIP


title: IDH-G_single-nucleus_TK19P


title: rad53-rpd3 cells, H3K9/14, repeat-2

description: Library name: rad53-rpd3_H3K9/14ac_rep2, ChIP


title: 242-CSF-13-0mo

description: 10x Genomics


title: H3 cells, H3K18, repeat-2

description: Library name: H3_H3K18ac_rep2, ChIP


title: rad53-pho23 cells, H3K9/14, repeat-2

description: Library name: rad53-pho23_H3K9/14ac_rep2, ChIP


title: 242-CSF-11-12mo

description: 10x Genomics


title: IDH-G_single-nucleus_TK20P


title: PNPCa mouse fraction, p0, Experiment 63_22, m9, #2

description:
Library name: PNPCa ms fract p0 63_22 m9 techn.repl. #2
BRB-seq


title: rad53-H3K4A cells, H3K9/14, repeat-2

description: Library name: rad53-H3K4A_H3K9/14ac_rep2, ChIP


title: IDH-G_single-nucleus_TK15R


title: LAPC9 mouse fibroblasts, p2, Experiment 26_22, #1

description:
Library name: LAPC9 ms fibr p2 Exp 26_22 techn.repl. #1
BRB-seq


title: rad53-pho23 cells, H3K9/14, repeat-1

description: Library name: rad53-pho23_H3K9/14ac_rep1, ChIP


title: 242-CSF-11-3mo

description: 10x Genomics


title: IDH-G_single-nucleus_SM16P


title: IDH-G_single-nucleus_TKU3197


title: PNPCa mouse fibroblasts, p2, Experiment  63_22, m9, #1

description:
Library name: PNPCa ms fibr p2 Exp 63_22 m9 techn.repl. #1
BRB-seq


title: 242-CSF-5-3mo

description: 10x Genomics


title: PNPCa mouse fraction, p0, Experiment 63_22, m9, #1

description:
Library name: PNPCa ms fract p0 63_22 m9 techn.repl. #1
BRB-seq


title: BM18 mouse fraction, p0, Experiment 65_22, #1

description:
Library name: BM18 ms fract p0 65/22 techn.repl. #1
BRB-seq


title: LAPC9 mouse fibroblasts, p2, Experiment 65_22, m20, #1

description:
Library name: LAPC9 ms fibr p2 Exp 65_22 m20 techn.repl. #1
BRB-seq


title: 242-CSF-11-0mo

description: 10x Genomics


title: rad53-H3 cells, H3K9/14, repeat-2

description: Library name: rad53-H3_H3K9/14ac_rep2, ChIP


title: 242-CSF-7-3mo

description: 10x Genomics


title: LAPC9 mouse fraction, p0, Experiment 26_22, #1

description:
Library name: LAPC9 ms fract p0 26_22 techn.repl. #1
BRB-seq


title: rad53-H3K4A cells, H3K9/14, repeat-1

description: Library name: rad53-H3K4A_H3K9/14ac_rep1, ChIP


title: IDH-G_single-nucleus_TK20R


title: 242-CSF-7-0mo

description: 10x Genomics


title: rad53-H3 cells, H3K9/14, repeat-1

description: Library name: rad53-H3_H3K9/14ac_rep1, ChIP


title: IDH-G_single-nucleus_TK15P


title: 242-CSF-5-12mo

description: 10x Genomics


title: LAPC9 mouse fibroblasts, p2, Experiment 63_22, m4, #2

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m4 techn.repl. #2
BRB-seq


title: rpd3 cells, H3K9/14, repeat-2

description: Library name: rpd3_H3K9/14ac_rep2, ChIP


title: 242-CSF-5-0mo

description: 10x Genomics


title: rpd3 cells, H3K9/14, repeat-1

description: Library name: rpd3_H3K9/14ac_rep1, ChIP


title: BM18 mouse fraction, p0, Experiment 45_22, #2

description:
Library name: BM18 ms fract p0 45/22 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_SM15P


title: pho23 cells, H3K9/14, repeat-1

description: Library name: pho23_H3K9/14ac_rep1, ChIP


title: BM18 mouse fibroblasts, p2, Experiment 65_22, #2

description:
Library name: BM18 ms fract p2 65/22 techn.repl. #2
BRB-seq


title: H3 cells, H3K9/14, repeat-2

description: Library name: H3_H3K9/14ac_rep2, ChIP


title: IDH-G_single-nucleus_SM14R


title: 242-CSF-4-0mo

description: 10x Genomics


title: 242-CSF-4-12mo

description: 10x Genomics


title: H3 cells, H3K9/14, repeat-1

description: Library name: H3_H3K9/14ac_rep1, ChIP


title: IDH-G_single-nucleus_SM15R2


title: 2577-CSF-10-12mo-LPS

description: 10x Genomics

source_name: CSF

extract_protocol:
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

value: CSF

tag: have paired_pbmc_and_csf

tag: tissue-(cell)type

tag: stimulation treatment

value: LPS


title: IDH-G_single-nucleus_SM12P


title: E. faecalis single biofilm 48h in urine 3

description: Library name: EF3

organism: Enterococcus faecalis

source_name: bacteria

tag: cell type

value: bacteria

value: urine 48h


title: pho23 cells, H3K9/14, repeat-2

description: Library name: pho23_H3K9/14ac_rep2, ChIP

tag: cell line

tag: treatment


title: H3K4A cells, H3K9/14, repeat-1

description: Library name: H3K4A_H3K9/14ac_rep1, ChIP


title: LAPC9 mouse fraction, p0, Experiment 65_22, m20, #1

description:
Library name: LAPC9 ms fract p0 Exp 65_22 m20 techn.repl. #1
BRB-seq

tag: tissue

tag: genotype


title: LAPC9 mouse fraction, p0, Experiment 65_22, m20, #2

description:
Library name: LAPC9 ms fract p0 Exp 65_22 m20 techn.repl. #2
BRB-seq


title: 242-CSF-1-12mo

description: 10x Genomics

value: Primary

value: CSF Cells


title: 242-CSF-1-3mo

description: 10x Genomics


title: 242-CSF-4-3mo

description: 10x Genomics


title: IDH-G_single-nucleus_SM15R


title: PNPCa mouse fraction, p0, Experiment 63_22, m8, #2

description:
Library name: PNPCa ms fract p0 63_22 m8 techn.repl. #2
BRB-seq


title: H3K4A cells, H3K9/14, repeat-2

description: Library name: H3K4A_H3K9/14ac_rep2, ChIP

value: yeast cell


title: IDH-G_single-nucleus_SM12R


title: 242-CSF-1-0mo

description: 10x Genomics


title: 2577-CSF-10-12mo-Ctrl

description: 10x Genomics

value: Ctrl


title: LAPC9 mouse fibroblasts, p2, Experiment 63_22, m4, #1

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m4 techn.repl. #1
BRB-seq


title: E. faecalis single biofilm 48h in urine 1

description: Library name: EF1

tag: strain


title: PNPCa mouse fibroblasts, p2, Experiment 63_22, m8, #1

description:
Library name: PNPCa ms fibr p2 Exp 63_22 m8 techn.repl. #1
BRB-seq


title: E. faecalis and E. coli  co-biofilm 48h in urine 3

description: Library name: EF-EC3

organism:
Escherichia coli
Enterococcus faecalis

value: OG1RF, UTI89


title: IDH-G_single-nucleus_SM14P


title: 2577-CSF-10-12mo-BCG

description: 10x Genomics

value: HKBCG


title: PNPCa mouse fibroblasts, p2, Experiment 63_22, m8, #2

description:
Library name: PNPCa ms fibr p2 Exp 63_22 m8 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_MD06R


title: 2577-CSF-10-3mo-Ctrl

description: 10x Genomics


title: IDH-G_single-nucleus_SM10R2


title: E. faecalis single biofilm 48h in urine 2

description: Library name: EF2

value: WT


title: PNPCa mouse fraction, p0, Experiment 63_22, m8, #1

description:
Library name: PNPCa ms fract p0 63_22 m8 techn.repl. #1
BRB-seq


title: IDH-G_single-nucleus_SM10R


title: E. faecalis and E. coli  co-biofilm 48h in urine 1

description: Library name: EF-EC1


title: 2577-CSF-10-3mo-LPS

description: 10x Genomics


title: BM18 mouse fibroblasts, p2, Experiment 65_22, #1

description:
Library name: BM18 ms fract p2 65/22 techn.repl. #1
BRB-seq

value: mouse fibroblasts passage 2 (p2)


title: E. faecalis and E. coli  co-biofilm 48h in urine 2

description: Library name: EF-EC2


title: IDH-G_single-nucleus_MD04P


title: BM18 mouse fraction, p0, Experiment 45/22, #1

description:
Library name: BM18 ms fract p0 45/22 techn.repl. #1
BRB-seq

value: single cells (p0) from prostate PCa PDX tissue


title: 2577-CSF-10-0mo-LPS

description: 10x Genomics


title: IDH-G_single-nucleus_MD07R


title: 2577-CSF-10-3mo-BCG

description: 10x Genomics


title: 2577-CSF-10-0mo-BCG

description: 10x Genomics


title: PNPCa mouse fibroblasts, p2, Experiment 26_22, #2

description:
Library name: PNPCa ms fibr p2 Exp 26_22 techn.repl. #2
BRB-seq

value: PNPCa


title: IDH-G_single-nucleus_MD05P


title: 242-PBMC-3-3mo-LPS

description: 10x Genomics

source_name: PBMC

value: PBMC

value: PBMCs


title: LAPC9 mouse fraction, p0, Experiment 63_22, m4.2, #2

description:
Library name: LAPC9 ms fract p0 63_22 m4.2 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_MD04R


title: IDH-G_single-nucleus_MD05R2


title: PNPCa mouse fraction p0, Experiment 26_22, #2

description:
Library name: PNPCa ms fract p0 26_22 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_MD08P


title: Transcriptome of Complemented_luxR_2

city: Auburn

first: Mark

last: Liles

state: AL

address: Room 101 Rouse Life Sciences Building

department: Biological Sciences

institute: Auburn University

description: Library name: Complemented_luxR_2

data_processing:
bioinformatic analyses performed in house using the OmicsBox v3.3.2 platform
Assembly: no genome assembly was conducted
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: counts.txt

organism: Flavobacterium covae

growth_protocol: Cultures were grown in FCGM medium to late log phase

extract_protocol:
Total RNA from each of the three strains was extracted in triplicate using an E.Z.N.A bacterial RNA isolation kit (Omega Bio-tek Inc, GA, USA) following the manufacturer’s protocol. RNA samples were quantified by spectrophotometry
a service provider (Novogene, Beijing, China) conducted RNA sequencing using a 2 x 150 bp paired-end configuration on an Illumina (San Diego, CA, USA) sequencer.

treatment_protocol: Comparison was conducted in the same growth medium no differences in environment for this experiment


title: 242-PBMC-3-3mo-Ctrl

description: 10x Genomics


title: Transcriptome of Complemented_luxR_3

description: Library name: Complemented_luxR_3


title: BM18 mouse fibroblasts, p2, Experiment 45_22, #2

description:
Library name: BM18 ms fibr p2 Exp 45_22 techn.repl. #2
BRB-seq


title: LAPC9 mouse fibroblasts, p2, Experiment 63_22, m4.2, #2

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m4.2 techn.repl. #2
BRB-seq


title: IDH-G_single-nucleus_MD08R


title: LAPC9 mouse fibroblasts, p2, Experiment 63_22, m4.2, #1

description:
Library name: LAPC9 ms fibr p2 Exp 63_22 m4.2 techn.repl. #1
BRB-seq


title: Transcriptome of WT_3

description: Library name: WT_3


title: IDH-G_single-nucleus_MD07P


title: BM18 mouse fraction, p0, Experiment 3_22, m5

description:
Library name: BM18 ms fract p0 3/22 m5
BRB-seq


title: Transcriptome of Complemented_luxR_1

description: Library name: Complemented_luxR_1


title: 242-PBMC-3-12mo-LPS

description: 10x Genomics


title: 2577-CSF-10-0mo-Ctrl

description: 10x Genomics


title: Transcriptome of Delta_luxR_3

description: Library name: Delta_luxR_3


title: Transcriptome of Delta_luxR_2

description: Library name: Delta_luxR_2


title: IDH-G_single-nucleus_MD03R


title: Transcriptome of Delta_luxR_1

description: Library name: Delta_luxR_1


title: 242-PBMC-3-3mo-BCG

description: 10x Genomics


title: IDH-G_single-nucleus_MD03R2


title: 242-PBMC-3-0mo-LPS

description: 10x Genomics


title: ILC2 Control 3

city: Los Angeles

first: Jafar

last: Cain

state: CA

address: 1450 Biggy St

department: MMI

institute: University of Southern California

description:
Library name: Sample6
21079R-09-34v1_S0

data_processing:
Image analysis andbase calling was carried out usingRTA 1.13.48.0. Final file formatting,demultiplexing andfastq generation were carried out usingCASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genomemm39 usingSTAR (v2.7.8) with default parameter settings
Gencode M33 annotation was used to quantify the aligned reads to genes/transcripts usingPartek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression usingPartek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Assembly: mm39
Supplementary files format and content: CSV file of normalised gene counts per sample

source_name: Lung

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: DMSO


title: WT-7

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description: Library name: 22466X9

data_processing:
A standard RNASeq alignment and differential expression analysis was performed to compare the five replicas of WT cj38637 cells and five replicase of deltaHSUR1 knockdown.  This entailed creating a STAR  (v2.7.9a) reference sequence index using a combine Callithrix jacchus (v3.2.1) and Saimiriine herpesvirus 2 (Genbank ID: X64346.1) fasta sequences. Likewise, gene annotations from Callithrix Jacchus Ensembl (v91) and X64346.1 were merged. The STAR ‘genomeGenerate’ command was used to create an index file using these reference and annotation files with ‘sjdbOverhang’ set to 149
The paired end, 150bp, NovaSeq6000 fastq datasets were processed using cutadapt (v3.4) to remove adapter sequence (R1= AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, R2= AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and aligned using STAR (--twopassMode Basic --outSAMtype BAM SortedByCoordinate --outBAMsortingBinsN 800 --quantMode TranscriptomeSAM --outWigType bedGraph --outWigStrand Unstranded --seedPerWindowNmax 30) to generate bam alignments and unique observation read depth big wig tracks for each replica.
Differential expression analysis was performed using the USeq DefinedRegionDifferentialSeq (v9.3.5, DRDS) application that maps unique alignments to transcripts (MQ>=13), wraps DESeq2((v1.14.1), estimates differential splicing events, hierarchically clusters samples, and exports a spreadsheet of differentially expressed genes and replica-gene normalized abundance estimates including the DESeq2 rLog values for principal component analysis (PCA).
Assembly: CalJac3
Supplementary files format and content: tab-delimited text file containing EnsemblID, Gene Name, Log2 Fold Change, Adjusted P-value, and DESeq2 normalized counts.
Supplementary files format and content: xxx.counts : SubBread featureCount ensembl transcript abundance estimates in the CalJac3.2 build
Supplementary files format and content: xxx.bw : Relative read depth tracks for unique paired end alignments in the CalJac3.2 build

organism: Callithrix jacchus

source_name: Cell line

growth_protocol: HVS-infected Marmoset T cells were grown at at density of 500,000-1 million cells/ml in RPMI 1640 medium supplemented with 20% FBS, 100 Units of penicllin, 100 µg/ml streptomycin, 1 mM of sodium pyruvate, 2 mM glutaMAX and 0.001% b-mercaptoethanol.

extract_protocol:
For iRICC experiment, total RNA was extracted with TRIzol following the manufacturer's protocol (Invitrogen).  Poly A+ RNA was selected with oligo-dT magnetic beads following the manufacturer's protocol (New England Biolabs). Ten percent of each sample was saved as input and stored in TRIzol.  Crosslinked HSUR1-mRNA complexes were captured with HSUR1 antisense oligonucleotide and magnetic streptavidin beads (Dynabeads).  Bound RNA was released from the beads with TRIzol.  HSUR1 and control pull down samples were purified and used directly to library preparation.
Libraries for iRICC experiments were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). For RNA-seq experiments, libraries were prepared with the  NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation.

treatment_protocol: For iRICC experiments, three independent samples of 200 million HVS-infected marmoset T cells each were crosslinked with psoralen at 365 nm for one hour at 4°C.  Samples were then lysed with 6 M guanidium hydrochloride, 0.8% SDS & proteinase K and incubated at 65°C for one hour.  One milliliter of TRIzol was added to each sample and stored at -80°C.

value: Cell line

value: T cell


title: IDH-G_single-nucleus_MD06P


title: LAPC9 mouse fraction, p0, Experiment 63_22, m4.2, #1

description:
Library name: LAPC9 ms fract p0 63_22 m4.2 techn.repl. #1
BRB-seq


title: Transcriptome of WT_1

description: Library name: WT_1


title: ILC2 Control 1

description:
Library name: Sample4
21079R-09-32v1_S0


title: 242-PBMC-3-12mo-Ctrl

description: 10x Genomics


title: PNPCa mouse fraction, p0, Experiment 26_22, #1

description:
Library name: PNPCa ms fract p0 26_22 techn.repl. #1
BRB-seq


title: BM18 mouse fraction, p0, Experiment 3_22, m4

description:
Library name: BM18 ms fract p0 3/22 m4
BRB-seq


title: IDH-G_single-nucleus_Smart-seq2

description: Library name: IDH-G_single-nucleus_Smart-seq2

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7).
Assembly: GRCh38 for Homo sapiens
Supplementary files format and content: tsv

extract_protocol:
Nuclear suspension was stained by Vybrant DyeCycle Ruby Stain (Thermo Fisher Scientific) immediately before FACS-sorting. Single-nucleus sorting was performed on a FACS Aria Fusion sorter (Becton Dickinson) using 640nm laser (Ruby, 670/14 filter). After doublet discrimination, intact nuclei were selected with ruby positive and were sorted into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80℃ prior to  Smart-seq2 and XRBS experiment
Genomic DNA (gDNA) and mRNA in 96 well plats were separated by oligo-dT primer conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies). The mRNA was then collected to the side of the well using a magnet. The mRNA plates were processed by Smart-seq2 protocol.  On 96-well plates, RNA derived from single-nuclei was first purified with Agencourt RNAClean XP beads (Beckman Coulter). Then, Oligo-dT primed reverse transcription was performed using Maxima H Minus reverse transcriptase (Thermo Fisher Scientific) and locked TSO oligonucleotide (Qiagen). This was followed by PCR amplification (22 cycles for snRNA-seq) using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters. Libraries from 768 cells with unique barcodes were pooled and sequenced on Illumina sequencer.


title: Transcriptome of WT_2

description: Library name: WT_2


title: 242-PBMC-3-12mo-BCG

description: 10x Genomics


title: Mus musculus, oocyte, Psma7 cKO, MII, biol repl 3

city: Hangzhou

first: Chen

last: Yingyan

address: No. 3 Qingchundong Road

institute: Zhejiang University

description:
Library name: Sample 15
Column name fpkm-RNAseq.xls: PM23

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mm10 mouse genome using TopHat 2.1.1, with the default parameters. Expression levels of each gene were quantified as normalized fragments per kilobase of exons per million mapped fragments (FPKM) using Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: xls file includes FPKM values for all Sample

source_name: oocyte (MII)

extract_protocol:
Five oocytes per sample were collected from the wildtype and Psma7 cKO female mice for RNA-seq. Each sample was immediately lysed with 4 µL lysis buffer (containing 0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 0.2 µL 1:1000 ERCC mRNA spike-in dilution for mouse oocyte samples).
RNA libraries for RNA-seq were prepared using the published Smart-seq2 method.

treatment_protocol: Female mice (3–4-week-old) were injected with 5 IU pregnant mare serum gonadotropin (PMSG) and humanely euthanized 44 h later. Oocytes at the germinal vesicle (GV) stage were harvested in M2 medium. To obtain oocytes at the metaphase II (MII) stage, female mice at 3–4 weeks of age were intraperitoneally injected with 5 IU PMSG, followed by human chorionic hormone (hCG) 44 h later. Oocytes (MII) were harvested from the oviducts using M2 medium 14-16 h after hCG injection, followed by digestion using 0.3% hyaluronidase.

value: oocyte (MII)

value: Zp3-Cre; Psma7 flox/flox


title: deltaH1-7

description: Library name: 22466X10


title: BM18 mouse fibroblasts, p2, Experiment 45_22, #1

description:
Library name: BM18 ms fibr p2 Exp 45_22 techn.repl. #1
BRB-seq


title: ILC2 Control 2

description:
Library name: Sample5
21079R-09-33v1_S0

value: Primary


title: 242-PBMC-3-0mo-Ctrl

description: 10x Genomics


title: PNPCa mouse fibroblasts, p2, Experiment 26_22, #1

description:
Library name: PNPCa ms fibr p2 Exp 26_22 techn.repl. #1
BRB-seq


title: 242-PBMC-3-0mo-BCG

description: 10x Genomics


title: deltaH1-6

description: Library name: 22466X8


title: Mus musculus, oocyte, Psma7 cKO, MII, biol repl 4

description:
Library name: Sample 16
Column name fpkm-RNAseq.xls: PM24


title: ILC2 Melatonin 3

description:
Library name: Sample3
21079R-09-22_S0

value: Melatonin


title: WT-6

description: Library name: 22466X7


title: deltaH1-5

description: Library name: 22466X6


title: 242-PBMC-14-3mo-Ctrl

description: 10x Genomics

value: Ctrl


title: 242-PBMC-14-3mo-LPS

description: 10x Genomics

value: LPS