description:
Library name: day 2 hPSC-derived lateral mesoderm  bulkrnaseq, replicate 1
trim


title: RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x lane 4

status: Public on Apr 06 2026

type: SRA

city: New York

first: Wen-Wei

last: Liang

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

description:
Library name: CaRPoolSeq-MDA-MB-231-BCG-Lane4
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
mda.g1_g2_umi.csv.gz

library_source: transcriptomic

data_processing:
Sequencing reads from the cDNA library were mapped to a pre-built reference (refdata-gex-GRCh38-2024-A, downloaded from https://www.10xgenomics.com/support/software/cell-ranger/downloads) using 10x Genomics Cell Ranger (v.9.0.0)97count function with the following parameter: --expect-cells=13000 --nosecondary --chemistry=SC3Pv3. Reads from the barcode guide RNA (bcgRNA) library were parsed from FASTQ files using a custom Python script. Cell barcodes (bases 1–16) and unique molecular identifiers (UMIs) (bases 17–28) were extracted from Read 1, and guide barcodes (bases 1–15) were extracted from Read 2. Read pairs were retained only if they matched the expected library structure, including the presence of capture sequence 1 (CS1) and concordance between the Read 1 barcode/UMI and the corresponding reverse-complemented barcode/UMI segments in Read 2. To resolve a reproducible discrepancy between Feature Barcode and gene expression cell barcodes, positions 8 and 9 of the Feature Barcode cell barcode were complemented before matching to the Cell Ranger-filtered gene expression barcode whitelist. Unique cell barcode-guide barcode-UMI combinations were first collapsed to generate per-cell guide UMI counts. In a separate post-processing step, singleton non-reference guide barcodes were corrected only when they differed by one nucleotide from a unique reference-matching guide barcode (Table S4A) present in the same cell and supported by at least two UMIs (Hamming distance = 1). Guide assignments supported by fewer than two UMIs were excluded from downstream calling. The resulting per-cell guide assignment tables were used for downstream analyses in Seurat (v.4.1.1).
Sequencing reads from the cDNA library were mapped to a pre-built reference (refdata-gex-GRCh38-2024-A, downloaded from https://www.10xgenomics.com/support/software/cell-ranger/downloads) using 10x Genomics Cell Ranger (v.9.0.0) count function with the following parameter: --expect-cells=3000 --nosecondary --chemistry=SC3Pv3. Reads from the barcode guide RNA (bcgRNA) library were parsed from FASTQ files using a custom Python script as following: cell barcodes (bases 1–16) and unique molecular identifiers (UMIs) (bases 17–28) were extracted from Read 1, and guide barcodes (bases 1–15) were extracted from Read 2. Read pairs were retained only if they matched the expected library structure, including the presence of capture sequence 1 (CS1) and concordance between the Read 1 barcode/UMI and the corresponding reverse-complemented barcode/UMI segments in Read 2. To resolve a reproducible discrepancy between Feature Barcode and gene expression cell barcodes, positions 8 and 9 of the Feature Barcode cell barcode were complemented before matching to the Cell Ranger-filtered gene expression barcode whitelist. Unique cell barcode-guide barcode-UMI combinations were first collapsed to generate per-cell guide UMI counts. In a separate post-processing step, singleton non-reference guide barcodes were corrected only when they differed by one nucleotide from a unique reference-matching guide barcode (Table S4A) present in the same cell and supported by at least two UMIs (Hamming distance = 1). Guide assignments supported by fewer than two UMIs were excluded from downstream calling. The resulting per-cell guide assignment tables were used for downstream analyses in Seurat (v.4.1.1).
Assembly: GRCh38
Supplementary files format and content: Cell-level data including Feature Barcode Market Exchange Matrices (MEX) and sparse matrix for top guide and second-top guide UMI count.

molecule: total RNA

organism: Homo sapiens

source_name: breast

growth_protocol: MDA-MB-231 cells were cultured in D10 medium:  Dulbecco’s Modified Eagle Medium with high glucose and stabilized L-glutamine (Cytiva SH30022.01) supplemented with 10% Tet-system approved serum (Gibco A4736201) and 5 µg/ml blasticidin. HAP1 cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium with L-glutamine (Cytiva SH30228.FS) supplemented with 10% Tet-system approved serum (Gibco A4736201) and 5 µg/ml blasticidin. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Puromycin selected, perturbed cells were harvest and loaded into a Chromium Controller (10X Genomics).
Single-cell sequencing library preparation for bcgRNAs and cDNA followed the 10X Genomics manual (CG000205 Rev D) with following modifications to allow for capture of bcgRNAs in our Cas13 CRISPR array configuration type X as previously described48. After elution of GEM-RT in 34 µL (Step 2.1-s.), we added 1 µL ADT additive primer (0.4 µM) to increase bcgRNA yield during cDNA amplification. The cDNA and bcgRNAs were purified using SPRI cleanup as indicated in steps 2.3A (Pellet Cleanup, 3′ GEX) and 2.3B (Transferred Supernatant Cleanup, CRISPR screening library), respectively. 45 µL of the purified bcgRNAs was used to construct the bcgRNA library through PCR amplification that adds Illumina P5 and P7 handles and an i7 index to the bcgRNA amplicon. We performed 12 cycles of PCR amplification (PCR1) in 100 µl reactions using 50 µl of 2× KAPA Hifi PCR Mastermix (Roche 07958935001) and 45 µl of bcgRNA PCR template as follows: 95 °C for 3 min, 12× (95 °C for 20 s, 60 °C for 8 s, 72 °C for 8 s), 72 °C for 1 min). For the PCR 2.5 µl of the following primers (10 µM) were used:  5′-AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3′ 5′-CAAGCAGAAGACGGCATACGAGAT(BC)8GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3′  where BC is a barcode of 8 nucleotides. After PCR product purification using a 1.6× SPRI cleanup, we performed 4 more cycles of PCR amplification using P5 and P7 primers in 100 µl reactions using 50 µl of 2× KAPA Hifi PCR Mastermix (Roche 07958935001) and 45 µl of PCR1 product as follows: 95 °C for 3 min, 4× (95 °C for 20 s, 60 °C for 8 s, 72 °C for 8 s), 72 °C for 1 min). For the PCR 2.5 µl of the following primers (10 µM) were used:  5′- AATGATACGGCGACCACCGA-3′ 5′- CAAGCAGAAGACGGCATACGAGA-3′  After purification using a 1.6× SPRI cleanup, bcgRNA and cDNA libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Q32851). The average amplicon size of each library was quantified using a Bioanalyzer 2100 using the High Sensitivity DNA Kit (Agilent 5067-4626). Using the average amplicon size and concentration, we then diluted both libraries appropriately for sequencing with standard Illumina sequencing primers (>= 28 cycles Read1 and >=15 cycles Read 2).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines. Following puromycin selection, RfxCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were were harvested 3 days post-Cas13d induction.

tag: tissue

value: breast

tag: cell line

tag: cell type

value: cancer cells

tag: genotype

value: lncRNAs knockdown

tag: treatment

value: doxycycline induction


title: RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10x lane 1

description:
Library name: CaRPoolSeq-MDA-MB-231-GEX-Lane1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell

molecule: polyA RNA


title: CAS129_MN_2

city: Berkeley

first: Rachel

middle: B

last: Brem

state: CA

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

description: Mmd x Mmc F1 hybrid

data_processing:
Reads were mapped to either the GRCm38, CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Gene counts were generated using STAR's built in quantification (--quantMode GeneCounts)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

organism: Mus musculus domesticus x Mus musculus castaneus

source_name: motor neuron

extract_protocol:
motor neurons were processed using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); PSCs were processed using RNAeasy-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); for both cell types samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: motor neuron


title: H1 hPSC bulkrnaseq, replicate 1

city: Stanford

first: Lay Teng

last: Ang

address: Institute for Stem Cell Biology & Regenerative Medicine, Lokey Stem Cell Bldg, 265 Campus Drive

department: Urology

institute: Stanford University

description:
Library name: H1 hPSC bulkrnaseq, replicate 1
trim

data_processing:
Assembly: Human reference genome Hg38 (GRCh38)
Supplementary files format and content: Processed data files abundance files generated using Kallisto (https://github.com/pachterlab/kallisto)

source_name: H1 hPSC

growth_protocol: hPSCs were maintained in mTesR Plus media before differentiation.

extract_protocol:
For bulk RNA-seq, Zymo RNA extraction was performed on cell lysates as per manufacturer's protocol.
Poly(A) mRNAs were converted into cDNA libraries during library construction by Novogene

treatment_protocol: Differentiation of hPSCs into artery and vein ECs. All differentiation was conducted in defined, serum-free CDM2 basal media. Detailed instructions to how to prepare CDM2 are available.  Seeding hPSCs for differentiation (Step 0).   Step 1: Mid primitive streak induction, 24 hours.   Step 2: Lateral mesoderm induction, 24 hours.   Step 3A: Artery EC induction, 24 hours.   Step 3B: Primed EC induction, 24 hours.   Step 4B: Vein EC induction, 24 hours.

value: H1 hPSC

value: hPSC

value: XY, wild-type

value: Unsorted


title: H1 hPSC bulkrnaseq, replicate 2

description:
Library name: H1 hPSC bulkrnaseq, replicate 2
trim


title: RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10x lane 3

description:
Library name: CaRPoolSeq-MDA-MB-231-GEX-Lane3
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: 129CAS_MN_1

description: Mmd x Mmc F1 hybrid


title: RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x lane 8

description:
Library name: CaRPoolSeq-HAP1-GEX-Lane8
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

source_name: bone marrow

value: bone marrow


title: CAS129_PSC_2

description: Mmd x Mmc F1 hybrid

source_name: pluripotent stem cell

value: pluripotent stem cell


title: CAS129_PSC_1

description: Mmd x Mmc F1 hybrid


title: CAS129_MN_1

description: Mmd x Mmc F1 hybrid


title: RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10x lane 2

description:
Library name: CaRPoolSeq-MDA-MB-231-GEX-Lane2
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RfxCas13d expressing MDA-MB-231 cells, mRNA-derived cDNA 10x lane 4

description:
Library name: CaRPoolSeq-MDA-MB-231-GEX-Lane4
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x lane 3

description:
Library name: CaRPoolSeq-MDA-MB-231-BCG-Lane3
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
mda.g1_g2_umi.csv.gz


title: RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x lane 6

description:
Library name: CaRPoolSeq-HAP1-GEX-Lane6
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


description:
Library name: day 1 hPSC-derived primitive streak bulkrnaseq, replicate 2
trim

source_name: H1 hPSC-derived

value: H1 hPSC-derived

value: primitive streak


title: RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x lane 2

description:
Library name: CaRPoolSeq-MDA-MB-231-BCG-Lane2
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
mda.g1_g2_umi.csv.gz


title: RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x lane 5

description:
Library name: CaRPoolSeq-HAP1-GEX-Lane5
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CAS129_MN_3

description: Mmd x Mmc F1 hybrid


title: RfxCas13d expressing MDA-MB-231 cells, bcgRNA-derived cDNA 10x lane 1

description:
Library name: CaRPoolSeq-MDA-MB-231-BCG-Lane1
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
mda.g1_g2_umi.csv.gz


title: RfxCas13d expressing HAP1 cells, mRNA-derived cDNA 10x lane 7

description:
Library name: CaRPoolSeq-HAP1-GEX-Lane7
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Dual RNA-seq of Salmonella enterica RAW_qychJ_2

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description:
Library name: Sal_qychJ_2
Column name in gene_count_sal.xls: Sal_qychJ_2

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: txt file includes gene counts for all Sample

organism: Salmonella enterica

source_name: Salmonella enterica

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Salmonella enterica


title: RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x lane 6

description:
Library name: CaRPoolSeq-HAP1-BCG-Lane6
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
hap.g1_g2_umi.csv.gz


title: Dual RNA-seq of Salmonella enterica RAW_qychJ_3

description:
Library name: Sal_qychJ_3
Column name in gene_count_sal.xls: Sal_qychJ_3


title: Blank-2

city: Guangzhou

first: xin

last: nie

address: Room 1101-03, Building 22, CAS Changchun Institute of Applied Chemistry Huangpu Advanced Materials Research Institute Park, No. 388 Lianyun Road, Huangpu District

institute: Guangzhou Qingnang Biotechnology Co., Ltd.

description:
Library name: Blank-2
WT

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM value for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell using TRIzol reagent. Briefly, cell were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: HaCaT

value: Human Immortalized Epidermal Cells

value: WT


title: RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x lane 5

description:
Library name: CaRPoolSeq-HAP1-BCG-Lane5
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
hap.g1_g2_umi.csv.gz

value: cancer cells


title: Dual RNA-seq of Salmonella enterica RAW_WT_2

description:
Library name: Sal_WT_2
Column name in gene_count_sal.xls: Sal_WT_2


title: short-read RNAseq from 7310-donor2-7859 cells

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

description:
Library name: short-read_7310-donor2-7859
HOSEpiC-donor2

data_processing:
Raw long-read RNAseq slow5 files were base-called using Guppy v.6.4.6+ae70e8f and MinKNOW v.22.12.5. Raw FASTQ RNAseq files were processed using the HyDRA pipeline up to correction and trimming of both short and long reads. Briefly, data were checked for quality (FastQC v0.12.1, MultiQC v1.14, NanoPlot/NanoComp v1.41.6 and Fasta_splitter.py v1.0.6); short-reads were trimmed of adapters (Trimmomatics v0.36) and corrected using Rcorrector v1 and FilterUncorrectablePEfastq.py v2016; long-read were first corrected using RopeBWT2 vr187 and FMLRC2 v0.1.7 and then trimmed of adapters (Porechop v0.2.4, Chopper v0.5.0 and Cutadapt v3.9.13). TPM counts from short-reads were obtained by aligning them to GENCODEv36 + HyDRA ovarian metatranscriptome lncRNAs (STAR v2.7.1a, SAMtools v1.3, NovoSort v3.05.01) and quantifying the reads (RSEM v1.2.30). TPM counts from long-reads were obtained from aligning them to GENCODEv36 + HyDRA ovarian metatranscriptome lncRNAs (Minimap2 v2.26) and quantifying the reads (Salmon v1.3.0). All TPM counts were merged into the same file.
Assembly: GRCh38 v36
Supplementary files format and content: tpm_counts.tsv

source_name: Ovary

growth_protocol: Thaw and culture of primary and immortalized FTSECs and OSECs was conducted in specific growth media to each cell line. Cell lines were maintained under standard conditions (37C, 5% CO2)

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Mini kit
Short-read library: One microgram of total RNA was rRNA depleted with the Ribo-Zero™ Plus kit according to the manufacturers’ instructions (Illumina). Short-read RNAseq libraries were prepared using the Truseq Stranded mRNA Library Prep Kit (Illumina). Long-read library: cDNA libraries were generated with polyadenylation enrichment and SQK-NBD114.24 native barcoding kit.

value: Ovary

value: Primary ovarian surface epithelial cells

value: ribodepleted with Ribo-Zero™ Plus kit according to manufacturer's intructions (Illumina)

tag: batch

value: Illumina NovaSeq 6000


title: Glabridin-3

description:
Library name: Glabridin-3
Melanosome glabridin treatment

value: Melanosome glabridin treatment


title: RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x lane 8

description:
Library name: CaRPoolSeq-HAP1-BCG-Lane8
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
hap.g1_g2_umi.csv.gz

value: lncRNAs knockdown

value: doxycycline induction


title: CosMx Heart Slide 2

type: RNA

first: Carly

last: Tymm

state: New York

institute: Columbia University Medical Center

description:
CosMxHeartAtomxExportSlide2.RDS is seurat directly from AtoMx platform.
SeuratHeartICICosMx.rds is the Seurat object following FastReseg and combining the ICI-only treated mice across Slide 1 and 2 for a total of 4 ICI-treated mice.

scan_protocol: Slides were imaged on the CosMx SMI instrument following the manufacturer’s recommended scanning parameters for RNA detection.

data_processing: Raw spatial imaging data generated by the CosMx Spatial Molecular Imager were processed and downloaded using the AtoMx Spatial Informatics Platform (also referred to as ATOMX), a cloud‑based informatics suite that handles image registration, target decoding, cell segmentation, and generation of count and metadata matrices. Cell segmentation was performed in AtoMx using refined parameters, including nucleus detection thresholds, cell boundary expansion, and minimum/maximum cell size filters, to optimize single-cell identification and minimize over- or under-segmentation.

organism: Mus musculus

source_name: Heart

label_protocol: RNA from FFPE tissue sections was profiled using the CosMx SMI Mouse Universal Panel according to manufacturer protocols.

growth_protocol: 8–12-week-old AJ mice were housed under IACUC-approved standard conditions with ad libitum access to food and water

extract_protocol: Tissue sections were formalin-fixed and paraffin-embedded (FFPE). RNA was extracted using the CosMx SMI FFPE protocol, which includes deparaffinization, target retrieval, and tissue permeabilization steps to enable probe hybridization for spatial transcriptomic analysis.

treatment_protocol: Three treatment regimens with FOVs specified as above.                                                                                1. Isoproterenol (ISO)-treated A/J mouse (160 mg/kg, twice for 2 weeks, endpoint one week after last injection)   2. ISO + ICI (ISO 160 mg/kg twice for 2 weeks, then biweekly 400 µg aPD1 + 400 µg aCTLA4 for 2 weeks, endpoint 3 days after last injection)   3. ICI-only (biweekly 400 µg aPD1 + 400 µg aCTLA4 for 2 weeks, endpoint 3 days after last injection).  Heart tissue for CosMx spatial transcriptomics was fixed in 10% formalin for 24 hours and FFPE embedded. The tissue was analyzed on the CosMx Spatial Molecular Imager.

tag: strain

value: A/J


title: Testis, Low sperm motility,3

city: Daqing

first: Hechuan

last: Wang

state: Heilongjiang

address: No.5 Xinfeng Road

institute: Heilongjiang Bayi Agricultural University

description: Library name: L3

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format using bcl2fastq (version 5.0.1). Sample demultiplexing, barcode processing, and single-cell 3’ gene counting were performed using Cell Ranger (version 9.0.1)
Assembly: Taihu_goose_T2T_genome
Supplementary files format and content: Tab-separated barcodes files, features files, and matrix files

organism: Anser cygnoides

source_name: Testis

extract_protocol:
Preserved testicular tissue was transferred to a culture dish and washed with precooled 1 × PBS (Biosharp, Beijing, China) to remove residual blood and lipids. The tissue was cut into 0.5 mm² pieces and incubated in a dissociation solution containing 0.35% collagenase IV, 2 mg/mL papain, and 120 U/mL DNase I for 20 min in a 37°C water bath shaker (100 rpm). Digestion was terminated by the addition of 1 × PBS containing 10% fetal bovine serum (Thermo Fisher Scientific, MA, USA). The cell suspension was filtered through a 40-μm cell strainer and centrifuged at 4°C (300 × g, 5 min). Following centrifugation, the pellet was resuspended in red blood cell lysis solution (Miltenyi Biotec, North Rhine-Westphalia, Germany) and centrifuged at 4°C (300 × g, 5 min). Dead cells were removed using a Dead Cell Removal Kit (Miltenyi Biotec, North Rhine-Westphalia, Germany) and passed through MS columns (Miltenyi Biotec, North Rhine-Westphalia, Germany) to eliminate dead cells and residual reagents. The collected cells were centrifuged at 4°C (300 × g, 5 min) and resuspended in 1 × PBS supplemented with 0.04% bovine serum albumin (BSA) (Thermo Fisher Scientific, MA, USA), and then washed twice (each at 4°C, 300 × g, 5 min). The final cell suspension was resuspended in 100 μL of 1 × PBS containing 0.04% BSA to generate a single-cell suspension. Cell viability was assessed using the trypan blue exclusion method, with a threshold of > 85%. Cell counting was performed using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific, MA, USA), and the concentration was adjusted to 700–1200 cells/μL.
Single-cell suspensions were loaded onto a Chromium chip (10x Genomics, CA, USA) using a Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics, CA, USA), targeting the capture of –8,000 cells, according to the manufacturer’s protocol. cDNA amplification and library construction were performed following the standard protocol. The libraries were sequenced with 150-bp paired-end reads on a NovaSeq 6000 platform (Illumina, CA, USA).

value: Testis


title: Melanosome-2

description:
Library name: Melanosome-2
Melanosom treatment

value: Melanosom treatment


title: Melanosome-3

description:
Library name: Melanosome-3
Melanosom treatment


title: RfxCas13d expressing HAP1 cells, bcgRNA-derived cDNA 10x lane 7

description:
Library name: CaRPoolSeq-HAP1-BCG-Lane7
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains bcgRNA-derived reads
hap.g1_g2_umi.csv.gz

value: bone marrow


title: Glabridin-2

description:
Library name: Glabridin-2
Melanosome glabridin treatment


title: Blank-1

description:
Library name: Blank-1
WT


title: short-read RNAseq from ABC-TC5521 cells

description:
Library name: short-read_ABC-TC5521
ABC-TC5521

source_name: Fallopian tube

value: Fallopian tube

value: Primary fallopian tube secretory epithelial cells


title: Glabridin-1

description:
Library name: Glabridin-1
Melanosome glabridin treatment

value: cell culture

value: HaCaT


title: Blank-3

description:
Library name: Blank-3
WT

value: Human Immortalized Epidermal Cells

value: WT


title: Dual RNA-seq of Salmonella enterica RAW_WT_3

description:
Library name: Sal_WT_3
Column name in gene_count_sal.xls: Sal_WT_3

value: Salmonella enterica


title: Melanosome-1

description:
Library name: Melanosome-1
Melanosom treatment


title: Testis, High sperm motility,1

description: Library name: H1


title: Dual RNA-seq of Salmonella enterica RAW_qychJ_1

description:
Library name: Sal_qychJ_1
Column name in gene_count_sal.xls: Sal_qychJ_1


title: Dual RNA-seq of Salmonella enterica RAW_WT_1

description:
Library name: Sal_WT_1
Column name in gene_count_sal.xls: Sal_WT_1


title: RPE1_MRE11pPASKO_Day6_rep3

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end RNA-seq reads were aligned to a Bowtie2 indexed human genome (hg38 sourced from UCSC) using STAR with default settings. For better alignment, the first aligned splicing junctions detected by STAR (SJ.out.tab) were used for STAR alignment again with parameters “--sjdbFileChrStartEnd SJ.out.tab --readFilesIn $R1 $R2 --quantMode TranscriptoomeSAM GeneCounts --sjdbGTFfile $GTF_file --outSAMtype BAM Unsorted SortedByCoordinate”. Then the aligned to transcriptome bam files (AlignedtoTranscriptome.out.bam) were used to quantify gene expression levels by rsem-calculate-expression function from RSEM. Tag per million reads (TPM) from gene expression results files (.genes.results) were extracted and assembled for subsequent differential gene expression analysis by DESeq2.
Assembly: hg38
Supplementary files format and content: genes.results.gz
Supplementary files format and content: raw_counts.txt.gz

source_name: cell line

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomyicin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (QIAGEN, #74136)
After the QC procedures, mRNA is enriched using oligo(dT) beads. Then, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: cell line

value: Epithelial cell

value: MRE11pPAS knockout


title: short-read RNAseq from 7310-donor1-24593 cells

description:
Library name: short-read_7310-donor1-24593
HOSEpiC-donor1

value: Ovary

value: Primary ovarian surface epithelial cells

value: ribodepleted with Ribo-Zero™ Plus kit according to manufacturer's intructions (Illumina)

value: Illumina NovaSeq 6000


title: RPE1_eCas9_Day6_rep2

value: Control


title: CosMx Heart Slide 1

description:
CosMxHeartAtomxExportSlide1.RDS is seurat directly from AtoMx platform.
SeuratHeartICICosMx.rds is the Seurat object following FastReseg and combining the ICI-only treated mice across Slide 1 and 2 for a total of 4 ICI-treated mice.

hyb_protocol: RNA from FFPE tissue sections was profiled using the CosMx SMI Mouse Universal Panel according to manufacturer protocols

value: A/J


title: short-read RNAseq from FC-0081-2839 cells

description:
Library name: short-read_FC-0081-2839
FC-0081-2839


title: short-read RNAseq from IOSE7576 cells

description:
Library name: short-read_IOSE7576
IOSE7576

value: Immortalized ovarian surface epithelial cells


title: short-read RNAseq from IOSE397 cells

description:
Library name: short-read_IOSE397
IOSE397


title: short-read RNAseq from FT194 cells

description:
Library name: short-read_FT194
FT194

value: Fallopian tube

value: Immortalized fallopian tube secretory epithelial cells


title: RPE1_MRE11pPASKO_Day6_rep1


title: Testis, Low sperm motility,2

description: Library name: L2

value: Testis


title: short-read RNAseq from ABC-TC3743 cells

description:
Library name: short-read_ABC-TC3743
HOSEpiC-ABC-TC3743


title: Testis, High sperm motility,2

description: Library name: H2


title: short-read RNAseq from FC-0081-4583 cells

description:
Library name: short-read_FC-0081-4583
FC-0081-4583

value: Primary fallopian tube secretory epithelial cells


title: RPE1_eCas9_Day6_rep1


title: short-read RNAseq from FT282 cells

description:
Library name: short-read_FT282
FT282


title: Testis, Low sperm motility,1

description: Library name: L1


title: EV-F3 (Small)

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

description:
Library name: Sample 12 (Small)
Processed DATA-Small.xls

data_processing:
FastQC was used to check quality of reads
Hisat2 and featureCounts was used to align and count reads.
(1)Discard the read pair if either one read contains adapter contamination;
(2)Discard the read pair if more than 10% of bases are uncertain in either one read;
(3)Discard the read pair if the proportion of low quality bases is over 50% in either one read.
DeSeq2 was used for differential expression analysis.
Assembly: hg18
Supplementary files format and content: Processed DATA-*.xls

source_name: Leiomyoma

extract_protocol:
TRIzol
Performed by Novogene Corporation Inc.
Total RNA was used for library preparation using the QIAseq Large and Small RNA Library Kit (QIAGEN) according to the manufacturer’s protocol. Briefly, RNA was subjected to adapter ligation for both small and long RNA species, followed by reverse transcription and PCR amplification with unique sample indices. Libraries were purified and size-selected according to kit instructions and assessed for quality and concentration prior to sequencing.

value: Leiomyoma

tag: sample group

value: EV-F (Small)


title: Testis, High sperm motility,3

description: Library name: H3


title: EV-M3 (Small)

description:
Library name: Sample 11 (Small)
Processed DATA-Small.xls

source_name: Myometrium

value: Myometrium

value: EV-M (Small)


title: RPE1_MRE11pPASKO_Day3_rep2

value: cell line

value: Epithelial cell


title: EV-F2 (Small)

description:
Library name: Sample 10 (Small)
Processed DATA-Small.xls


title: RPE1_MRE11pPASKO_Day6_rep2

value: MRE11pPAS knockout


title: EV-M3 (Large)

description:
Library name: Sample 5 (Large)
Processed DATA-Large.xls

value: EV-M (Large)


title: RPE1_MRE11pPASKO_Day3_rep3


title: EV-M2 (Small)

description:
Library name: Sample 9 (Small)
Processed DATA-Small.xls


title: EV-F1 (Small)

description:
Library name: Sample 8 (Small)
Processed DATA-Small.xls


title: EV-F3 (Large)

description:
Library name: Sample 6 (Large)
Processed DATA-Large.xls

value: EV-F (Large)


title: RPE1_MRE11pPASKO_Day3_rep1


title: RPE1_eCas9_Day6_rep3


title: RPE1_eCas9_Day3_rep3


title: EV-F2 (Large)

description:
Library name: Sample 4 (Large)
Processed DATA-Large.xls


title: EV-M2 (Large)

description:
Library name: Sample 3 (Large)
Processed DATA-Large.xls


title: EV-M1 (Small)

description:
Library name: Sample 7 (Small)
Processed DATA-Small.xls


title: RPE1_eCas9_Day3_rep1


title: RPE1_eCas9_Day3_rep2


title: control_RNAi_3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291, Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: Sample 3

data_processing:
Sequencing reads were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 104) by using Spliced Transcripts Alignment to a Reference (STAR, v2.7.0e). Quantification of the aligned reads to genes and transcripts was performed by using the RNA-Seq by Expectation-Maximization (RSEM, v.1.3.1).
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Synchronized L4-prefertile wild-type worms under control or fars-1 RNAi conditions were maintained on HT115 at 20°C.

extract_protocol:
Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions.
Synchronized L4-prefertile wild-type worms under control or fars-1 RNAi conditons were maintained on OP50 at 20°C, and harvested after washing three times independently using M9 buffer. Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions. A sequencing library was constructed and paired-end RNA sequencing using Illumina NovaSeq 6000 platform was performed (Macrogen, South Korea).

value: whole body

tag: Sex

value: hermaphrodite

tag: developmental stage

value: L4-Prefertile adults


title: EV-F1 (Large)

description:
Library name: Sample 2 (Large)
Processed DATA-Large.xls


title: fars1_RNAi_3

description: Library name: Sample 6


title: eat2dis3_2

description: Library name: Sample 11

data_processing:
Sequencing reads were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 107) by using Spliced Transcripts Alignment to a Reference (STAR, v2.7.0e). Quantification of the aligned reads to genes and transcripts was performed by using the RNA-Seq by Expectation-Maximization (RSEM, v.1.3.1).
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

growth_protocol: Synchronized prefertile wild-type worms, dis-3(L75Q), eat-2(ad1116), and eat-2(ad1116); dis-3(L75Q) mutants were maintained on OP50 at 20°C.

extract_protocol:
Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions.
Synchronized prefertile wild-type worms, dis-3(L75Q), eat-2(ad1116), and eat-2(ad1116); dis-3(L75Q) mutants maintained on OP50 at 20°C, were harvested three times independently using M9 buffer containing 0.01% polyethylene glycol (PEG). Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions. A sequencing library was constructed and paired-end RNA sequencing using Illumina NovaSeq 6000 platform was performed (Macrogen, South Korea).

value: Prefertile adults


title: fars1_RNAi_1

description: Library name: Sample 4


title: RPE1_MRE11pPAS-/-_Clone46_EdU-seq_rep2

description: Library name: RPE1_MRE11pPAS-/-_Clone46_EdU_rep2

library_source: genomic

data_processing:
Raw reads were trimmed by Trimmomatic (V0.39). Then, clean reads were aligned to a bowtie2 (V2.2.6) indexed human genome (hg19 sourced from UCSC) with default parameters. Proper paired and high-quality mapped reads (MAPQ >30) were selected with samtools (v1.9). PCR duplicates are marked and removed using picard tools (v2.22.3-0), and blacklist regions are removed before subjecting to peak calling using MACS2 (v2.1.1). Bigwig files were generated using the bedGraphToBigWig command. ChIP-seq heatmap and profiles were drawn with deeptools (3.4.3). Peak annotation was performed using annotatePeaks function from HOMER. Differential peaks were called by MACS2 bdgdiff function with default parameters and log10LR cutoff set to 1.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
ChIP libraries were prepared using using NEBNext® Ultra™ II DNA Library Prep Kit complemented with NEB DNA Barcodes.1 ng of DNA was used as starting material for input and ChIP samples. Libraries were amplified using 15 cycles on the thermocycler.Post amplification libraries were size selected at 200-400bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the High sensitivity DNA Kit.
ChIP-seq

treatment_protocol: cells were fixed with 1% formaldehyde for 5 minutes, After quenching and cell lysis, chromatin was sonicated using a E220 covaris

value: human retinal pigment epithelium cells

tag: chip antibody

value: Streptavidin (Invitrogen, #65001)


title: RPE1_MRE11pPAS-/-_clone46_MRE11_ChIP_rep2

description: Library name: RPE1_MRE11pPAS-/-_Clone46_MRE11,Novus_rep2

value: MRE11 (Novus Biogogicals, #NB100-142)


title: EV-M1 (Large)

description:
Library name: Sample 1 (Large)
Processed DATA-Large.xls


title: RPE1_WT_MRE11_ChIP_rep2

description: Library name: RPE1_WT_MRE11,Novus_rep2

value: WT


title: RPE1_WT_MRE11_ChIP_rep1

description: Library name: RPE1_WT_MRE11,Novus_rep1


title: RPE1_MRE11pPAS-/-_clone46_MRE11_ChIP_rep1

description: Library name: RPE1_MRE11pPAS-/-_Clone46_MRE11,Novus_rep1


title: fars1_RNAi_2

description: Library name: Sample 5


title: RPE1_MRE11pPAS-/-_clone58_MRE11_ChIP_rep1

description: Library name: RPE1_MRE11pPAS-/-_Clone58_MRE11_Novus_rep1


title: control_RNAi_2

description: Library name: Sample 2


title: control_RNAi_1

description: Library name: Sample 1


title: eat2dis3_3

description: Library name: Sample 12


title: RPE1_MRE11pPAS-/-_Clone58_EdU-seq_rep2

description: Library name: RPE1_MRE11pPAS-/-_Clone58_EdU_rep2


title: RPE1_MRE11pPAS-/-_Clone46_EdU-seq_rep1

description: Library name: RPE1_MRE11pPAS-/-_Clone46_EdU_rep1


title: eat2_2

description: Library name: Sample 8


title: RPE1_MRE11pPAS-/-_clone58_MRE11_ChIP_rep2

description: Library name: RPE1_MRE11pPAS-/-_Clone58_MRE11_Novus_rep2


title: RPE1_WT_EdU-seq_rep2

description: Library name: RPE1_WT_EdU_rep2


title: RPE1_WT_EdU-seq_rep1

description: Library name: RPE1_WT_EdU_rep1


title: dis3_2

description: Library name: Sample 5


title: RPE1_MRE11pPAS-/-_Clone58_EdU-seq_rep1

description: Library name: RPE1_MRE11pPAS-/-_Clone58_EdU_rep1


title: eat2_3

description: Library name: Sample 9


title: eat2_1

description: Library name: Sample 7


title: dis3_1

description: Library name: Sample 4


title: dis3_3

description: Library name: Sample 6


title: CTCF ChIP in RIVA ARID1A WT 2

city: New York City

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: 22_RIVA_Standard_ChIP_Arid1aWt_CTCF

data_processing:
Processed through nfcore ChIPseq analysis pipeline.
Trimmed by TrimGalore, aligned with BWA, sequences filtered and duplicates marked.
Peak calling by macs2
Assembly: hg38
Supplementary files format and content: macs2 narrowPeak bed file

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min in 37 C. The reaction was quenched with glycine. Nuclei were isolated with a Triton-X-100-containing buffer, and chromatin was subject to sonication with BioRuptor Pico (Diagenode). After immunoprecipitation and reversal of crosslinking, the DNA was isolated with the phenol-chloroform method, and subject to library preparation.
Ultra II DNA Library Prep Kit for Illumina, with dual indexes. Size distribution of the libarries was assessed by Agilent Bioanalyzer.

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: Arid1a WT


title: WT_1

description: Library name: Sample 1


title: CTCF ChIP in RIVA ARID1A HET 1

description: Library name: 14_RIVA_Standard_ChIP_Arid1aHet_CTCF

value: Arid1a HET


title: RPE1_MRE11pPAS-/-_clone58_Input

description: Library name: RPE1_MRE11pPAS-/-_Clone58_Input_for_EdU_seq

value: cell line


title: RPE1_MRE11pPAS-/-_clone46_Input

description: Library name: RPE1_MRE11pPAS-/-_Clone46_Input_for_edu_seq


title: Input to SMC3 and CTCF ChIP in hES ARID1A WT clone 2

description: Library name: 23_Input_DMSO_2_11_10_hES

value: hES

value: Human embryonic stem cells


city: Palo Alto

first: Basak

last: Eraslan

address: 2360 Saint Francis Drive

institute: Genentech

description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch9_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad

library_source: other

data_processing:
scRNA files were demultiplexed using Cellranger mkfastq
Assembly: mm10
Supplementary files format and content: H5AD file containing raw counts matrix

molecule: other

source_name: Blood cells

extract_protocol:
BMDCs derived from mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a Chromium Single Cell 3' GEM Library and Gel Bead kit.
Hashtag (HTO) and guide dial out (GDO) libraries were generated as described (Geiger-Schuller and Eraslan et al., 2020)

value: Blood cells

value: BMDCs

tag: library type

value: GDO


title: eat2dis3_1

description: Library name: Sample 10

value: whole body

value: hermaphrodite


title: RPE1_WT_Input

description: Library name: RPE1_WT_Input_for_EdU_seq


title: WT_3

description: Library name: Sample 3

value: Prefertile adults


title: CTCF ChIP in hES ARID1A HET clone 2

description: Library name: 20_CTCF_VNT_FHD_2_hES


title: WT_2

description: Library name: Sample 2


title: Input to SMC3 and CTCF ChIP in hES ARID1A HET clone 2

description: Library name: 24_Input_FHD_2_11_10_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch8_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch8_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad

value: mRNA


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch6_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch7_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


title: CTCF ChIP in RIVA ARID1A HET 2

description: Library name: 30_RIVA_Standard_ChIP_Arid1aHet_CTCF


title: CTCF ChIP in RIVA ARID1A WT 1

description: Library name: 06_RIVA_Standard_ChIP_Arid1aWt_CTCF


title: SMC3 ChIP in hES ARID1A HET clone 2

description: Library name: 08_SMC3_VNT_FHD_2_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch5_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch7_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


title: CTCF ChIP in hES ARID1A WT clone 2

description: Library name: 19_CTCF_VNT_DMSO_2_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch9_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


title: Input to SMC3 and CTCF ChIP in hES ARID1A WT clone 1

description: Library name: 21_Input_DMSO_1_11_10_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch4_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


title: SMC3 ChIP in hES ARID1A WT clone 2

description: Library name: 07_SMC3_VNT_DMSO_2_hES


title: Input to SMC3 and CTCF ChIP in hES ARID1A HET clone 1

description: Library name: 22_Input_FHD_1_11_10_hES


title: CTCF ChIP in hES ARID1A WT clone 1

description: Library name: 17_CTCF_VNT_DMSO_1_hES


title: CTCF ChIP in hES ARID1A HET clone 1

description: Library name: 18_CTCF_VNT_FHD_1_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch4_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch6_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch5_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


title: SMC3 ChIP in hES ARID1A HET clone 1

description: Library name: 06_SMC3_VNT_FHD_1_hES


title: SMC3 ChIP in hES ARID1A WT clone 1

description: Library name: 05_SMC3_VNT_DMSO_1_hES


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch3_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch3_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


title: Input to SMC3 and CTCF ChIP in RIVA ARID1A HET clone 2

description: Library name: 32_TQ2_Arid1aHET_input


title: Input to SMC3 and CTCF ChIP in RIVA ARID1A WT clone 1

description: Library name: 29_DQ1_Arid1aWT_input


title: Untr_7_C_rep2

city: Oklahoma City

first: Aneta

last: Pankow

state: Oklahoma

address: 825 NE 13th St

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

description: Library name: 10_10p__S33

data_processing:
Data were normalized using DESEq2
Assembly: GRCm39.112
Supplementary files format and content: Count matrix table with raw gene counts for each population

source_name: Lung

extract_protocol:
Whole lungs were chopped and homogenized in cold homogenization buffer (10 mM Tris, 5mM EDTA, 1% NP-40). An aliquot of the homogenate was mixed with 10 times the volume of Trizol. RNA extraction was done according to the ImmGen Protocol (https://www.immgen.org) “RNA extraction with Trizol”.
Watchmaker Genomics mRNA kit

value: Lung

value: RORaf/f

tag: agent

tag: time point


title: Untr_7_C_rep1

description: Library name: 7_7p__S30


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch1_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


title: Untr_7_KO_rep3

description: Library name: 8_8p__S31


title: Tr_7_C_rep2

description: Library name: 6_6p__S29

value: naphthalene


title: Input to SMC3 and CTCF ChIP in RIVA ARID1A WT clone 2

description: Library name: 31_DQ2_Arid1aWT_input

value: RIVA


title: Input to BRD7 ChIP in RIVA ARID1A HET clone 2 batch 1 rep2

description: Library name: 16_RIVA_ChIP_Arid1aHet_TQ2_inputBRD7_R2

value: B-cell lymphoma ABC-DLBCL


title: CTCF ChIP in RIVA ARID1A HET clone 1

description: Library name: 22_TQ1_Arid1aHET_CTCF


title: SMC3 ChIP in RIVA ARID1A WT clone 1

description: Library name: 17_DQ1_Arid1aWT_SMC3

value: Arid1a WT


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch1_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


title: Input to SMC3 and CTCF ChIP in RIVA ARID1A HET clone 1

description: Library name: 30_TQ1_Arid1aHET_input

value: Arid1a HET


title: Tr_2_KO_rep3

description: Library name: 6_6a__S6


title: Input to BRD7 ChIP in RIVA ARID1A HET clone 2 batch 1 rep1

description: Library name: 15_RIVA_ChIP_Arid1aHet_TQ2_inputBRD7_R1

value: cell line


title: Input to BRD7 ChIP in RIVA ARID1A WT clone 2 batch 1 rep2

description: Library name: 14_RIVA_ChIP_Arid1aWt _DQ2_inputBRD7_R1


title: CTCF ChIP in RIVA ARID1A WT clone 1

description: Library name: 21_DQ1_Arid1aWT_CTCF


title: Input to BRD7 ChIP in RIVA ARID1A WT clone 2 batch 1 rep1

description: Library name: 13_RIVA_ChIP_Arid1aWt _DQ2_inputBRD7_R1


title: CTCF ChIP in RIVA ARID1A WT clone 2

description: Library name: 23_DQ2_Arid1aWT_CTCF


title: Tr_7_KO_rep2

description: Library name: 14_14p__S35


title: SMC3 ChIP in RIVA ARID1A HET clone 2

description: Library name: 20_TQ2_Arid1aHET_SMC3


title: CTCF ChIP in RIVA ARID1A HET clone 2

description: Library name: 24_TQ2_Arid1aHET_CTCF


title: Untr_7_C_rep3

description: Library name: 11_11p__S34


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch2_FB
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_combo_val_R2_raw.h5ad


title: SMC3 ChIP in RIVA ARID1A HET clone 1

description: Library name: 18_TQ1_Arid1aHET_SMC3


title: SMC3 ChIP in RIVA ARID1A WT clone 2

description: Library name: 19_DQ2_Arid1aWT_SMC3


title: Tr_7_C_rep3

description: Library name: 9_9p__S32


description:
Library name: BMDC E3 screen, Combo Validation Round 2, ch2_RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_combo_val_R2_raw.h5ad


title: Tr_7_C_rep1

description: Library name: 5_5p__S28


title: Tr_5_KO_rep3

description: Library name: 5_5b__S11


title: Tr_2_C_rep3

description: Library name: 5_5a__S5


title: Input to BRD7 ChIP in RIVA ARID1A WT clone 1 batch 1 rep2

description: Library name: 10_RIVA_ChIP_Arid1aWt _DQ1_inputBRD7_R2


title: Input to BRD7 ChIP in RIVA ARID1A HET clone 1 batch 1 rep2

description: Library name: 12_RIVA_ChIP_Arid1aHet_TQ1_inputBRD7_R2


title: Input to BRD7 ChIP in RIVA ARID1A HET clone 1 batch 1 rep1

description: Library name: 11_RIVA_ChIP_Arid1aHet_TQ1_inputBRD7_R1


title: Tr_2_C_rep2

description: Library name: 4_4a__S4


title: Tr_7_KO_rep1

description: Library name: 2_2p__S25


title: BRD7 ChIP in RIVA ARID1A WT clone 2 batch 1 rep1

description: Library name: 05_RIVA_ChIP_Arid1aWt _DQ2_BRD7_R1


title: Untr_5_C_rep3

description: Library name: 4_4f__S22


title: BRD7 ChIP in RIVA ARID1A HET clone 2 batch 1 rep2

description: Library name: 08_RIVA_ChIP_Arid1aHet _TQ2_BRD7_R2


title: Tr_2_KO_rep2

description: Library name: 3_3a__S3


title: Tr_5_C_rep2

description: Library name: 3_3b__S9


title: Untr_2_C_rep3

description: Library name: 2_2n__S18


title: Input to BRD7 ChIP in RIVA ARID1A WT clone 1 batch 1 rep1

description: Library name: 09_RIVA_ChIP_Arid1aWt _DQ1_inputBRD7_R1


title: Tr_5_C_rep3

description: Library name: 4_4b__S10


title: Untr_5_KO_rep2

description: Library name: 2_2o__S24


title: BRD7 ChIP in RIVA ARID1A WT clone 1 batch 1 rep2

description: Library name: 02_RIVA_ChIP_Arid1aWt _DQ1_BRD7_R2


title: Untr_2_KO_rep2

description: Library name: 3_3k__S15


title: BRD7 ChIP in RIVA ARID1A HET clone 1 batch 1  rep1

description: Library name: 03_RIVA_ChIP_Arid1aHet _TQ1_BRD7_R1


title: Untr_5_KO_rep3

description: Library name: 3_3f__S21


title: BRD7 ChIP in RIVA ARID1A WT clone 1 batch 1 rep1

description: Library name: 01_RIVA_ChIP_Arid1aWt _DQ1_BRD7_R1


title: Untr_2_KO_rep3

description: Library name: 4_4k__S16


title: RIVA-ARID1AHET treated with DMSO rep3

description: Library name: 30_RIVA_ATAC_Arid1aHet _TQ_DMSO_5uM_R3

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

treatment_protocol: Inhibitor or DMSO treatment for 24h.

value: ARID1A HET

value: DMSO


title: BRD7 ChIP in RIVA ARID1A WT clone 2 batch 1 rep2

description: Library name: 06_RIVA_ChIP_Arid1aWt _DQ2_BRD7_R2


title: Untr_2_C_rep2

description: Library name: 2_2k__S14


title: RIVA-ARID1AHET treated with DMSO rep2

description: Library name: 29_RIVA_ATAC_Arid1aHet _TQ_DMSO_5uM_R2


title: BRD7 ChIP in RIVA ARID1A HET clone 1 batch 1 rep2

description: Library name: 04_RIVA_ChIP_Arid1aHet_TQ1_BRD7_R2


title: Untr_7_KO_rep1

description: Library name: 3_3p__S26


title: Untr_7_KO_rep2

description: Library name: 4_4p__S27


title: Untr_5_C_rep2

description: Library name: 2_2f__S20


title: RIVA-ARID1AWT treated with DMSO rep2

description: Library name: 26_RIVA_ATAC_Arid1aWt _DQ_DMSO_5uM_R2

value: ARID1A WT


title: Tr_5_C_rep1

description: Library name: 2_2b__S8


title: RIVA-ARID1AHET treated with BRD-K98645985 rep3

description: Library name: 18_RIVA_ATAC_Arid1aHet _TQ_ARID1Ai_5uM_R3


title: RIVA-ARID1AHET treated with BRD-K98645985 rep2

description: Library name: 17_RIVA_ATAC_Arid1aHet _TQ_ARID1Ai_5uM_R2


title: RIVA-ARID1AWT treated with DMSO rep1

description: Library name: 25_RIVA_ATAC_Arid1aWt _DQ_DMSO_5uM_R1


title: Untr_2_C_rep1

description: Library name: 1_1k__S13


title: RIVA-ARID1AHET treated with DMSO rep1

description: Library name: 28_RIVA_ATAC_Arid1aHet _TQ_DMSO_5uM_R1


title: RIVA-ARID1AHET treated with PBRM1-BD2-IN-8 rep2

description: Library name: 23_RIVA_ATAC_Arid1aHet _TQ_PBRM1i_5uM_R2


title: Untr_5_C_rep1

description: Library name: 1_1o__S23


title: RIVA-ARID1AHET treated with PBRM1-BD2-IN-8 rep3

description: Library name: 24_RIVA_ATAC_Arid1aHet _TQ_PBRM1i_5uM_R3


title: Untr_2_KO_rep1

description: Library name: 1_1n__S17


title: Tr_2_KO_rep1

description: Library name: 1_1a__S1


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO AngII, biol rep 3

city: Lexington

first: Shayan

last: Mohammadmoradi

state: KY

address: 741 South Limestone, Saha CVRC BBSRB B364B

department: Saha Cardiovascular Research Center

institute: University of Kentucky

description:
Library name: V8KO_AngII_3
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_AngII_3

data_processing:
Raw reads trimmed for adapter and low-quality sequences using Novogene in-house pipeline
Trimmed reads aligned to mm39 (GRCm39) reference genome using HISAT2 v2.0.5 (default parameters)
Gene-level read counts quantified using featureCounts v1.5.0-p3 (default parameters)
Differential expression analysis using DESeq2 v1.20.0; threshold: |log2FoldChange| >= 1 and padj <= 0.05
Assembly: mm39 (GRCm39)
Supplementary files format and content: Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: tab-delimited text file with raw read counts per gene (rows=genes with Ensembl ID and gene name, columns=16 samples: WT_Saline 1-4, WT_AngII 1-4, V8KO_Saline 1-4, V8KO_AngII 1-4)

source_name: suprarenal aorta

growth_protocol: Male Vamp8-/- knockout and C57BL/6 wild-type mice were used. Alzet osmotic minipump (Model 2004) implanted subcutaneously into the interscapular space.

extract_protocol:
Suprarenal aortae were perfused with saline and periaortic tissues removed. Samples incubated in RNAlater (AM7020, Invitrogen) for 1 hr. mRNA extracted using RNeasy Fibrous Tissue Mini Kit (74704, Qiagen).
mRNA libraries constructed following poly-A enrichment with poly-T oligo-attached magnetic beads. First-strand cDNA synthesized using random hexamer primers, followed by second-strand synthesis. Libraries prepared after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Quality assessed by Qubit and bioanalyzer.

treatment_protocol: AngII (1,000 ng/kg/min; H-1705, Bachem) or saline delivered via continuous subcutaneous infusion for 5 days. Aortae with intramural hemorrhage or overt pathology were excluded.

value: suprarenal aorta

value: aortic tissue

value: Vamp8-/- knockout

value: AngII 1000 ng/kg/min via osmotic minipump, 5 days


title: RIVA-WT treated with PBRM1-BD2-IN-8 rep1

description: Library name: 19_RIVA_ATAC_Arid1aWt _DQ_PBRM1i_5uM_R1


title: RIVA-WT treated with PBRM1-BD2-IN-8 rep2

description: Library name: 20_RIVA_ATAC_Arid1aWt _DQ_PBRM1i_5uM_R2


title: RIVA-ARID1AHET treated with BRD-K98645985 rep1

description: Library name: 16_RIVA_ATAC_Arid1aHet _TQ_ARID1Ai_5uM_R1


title: RIVA-ARID1AWT treated with DMSO rep3

description: Library name: 27_RIVA_ATAC_Arid1aWt _DQ_DMSO_5uM_R3


title: RIVA-ARID1AHET treated with PBRM1-BD2-IN-8 rep1

description: Library name: 22_RIVA_ATAC_Arid1aHet _TQ_PBRM1i_5uM_R1


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO AngII, biol rep 4

description:
Library name: V8KO_AngII_4
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_AngII_4


title: Untr_5_KO_rep1

description: Library name: 1_1f__S19


title: Tr_2_C_rep1

description: Library name: 2_2a__S2


title: RIVA-WT treated with PBRM1-BD2-IN-8 rep3

description: Library name: 21_RIVA_ATAC_Arid1aWt _DQ_PBRM1i_5uM_R3


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO AngII, biol rep 2

description:
Library name: V8KO_AngII_2
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_AngII_2


title: Tr_5_KO_rep2

description: Library name: 1_1i__S12


title: Tr_5_KO_rep1

description: Library name: 1_1b__S7


title: RIVA-WT treated with BRD-K98645985 rep3

description: Library name: 15_RIVA_ATAC_Arid1aWt _DQ_ARID1Ai_5uM_R3


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO AngII, biol rep 1

description:
Library name: V8KO_AngII_1
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_AngII_1


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO Saline, biol rep 4

description:
Library name: V8KO_Saline_4
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_Saline_4

value: Saline infusion via osmotic minipump, 5 days


title: RIVA-WT treated with BRD-K98645985 rep2

description: Library name: 14_RIVA_ATAC_Arid1aWt _DQ_ARID1Ai_5uM_R2


title: RIVA-WT treated with BRD-K98645985 rep1

description: Library name: 13_RIVA_ATAC_Arid1aWt _DQ_ARID1Ai_5uM_R1


title: BRD7 ChIP in RIVA ARID1A HET clone 2 batch 1 rep1

description: Library name: 07_RIVA_ChIP_Arid1aHet _TQ2_BRD7_R1


title: RIVA-ARID1AHET treated with FHT006710 rep3

description: Library name: 12_RIVA_ATAC_Arid1aHet _TQ_FHT006710_5nM_R3


title: RIVA-ARID1AHET treated with FHT006710 rep1

description: Library name: 10_RIVA_ATAC_Arid1aHet _TQ_FHT006710_5nM_R1


title: RIVA-ARID1AHET treated with FHT006710 rep2

description: Library name: 11_RIVA_ATAC_Arid1aHet _TQ_FHT006710_5nM_R2


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO Saline, biol rep 1

description:
Library name: V8KO_Saline_1
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_Saline_1


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO Saline, biol rep 2

description:
Library name: V8KO_Saline_2
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_Saline_2


title: Mouse suprarenal aorta RNA-seq, VAMP8-KO Saline, biol rep 3

description:
Library name: V8KO_Saline_3
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: V8KO_Saline_3


title: RIVA-WT treated with FHT006710 rep2

description: Library name: 08_RIVA_ATAC_Arid1aWt _DQ_FHT006710_5nM_R2


title: Mouse suprarenal aorta RNA-seq, WT AngII, biol rep 4

description:
Library name: WT_AngII_4
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_AngII_4

value: C57BL/6 wildtype


title: Mouse suprarenal aorta RNA-seq, WT Saline, biol rep 4

description:
Library name: WT_Saline_4
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_Saline_4


title: RIVA-WT treated with FHT006710 rep1

description: Library name: 07_RIVA_ATAC_Arid1aWt _DQ_FHT006710_5nM_R1


title: Mouse suprarenal aorta RNA-seq, WT Saline, biol rep 1

description:
Library name: WT_Saline_1
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_Saline_1


title: RIVA-WT treated with FHT006710 rep3

description: Library name: 09_RIVA_ATAC_Arid1aWt _DQ_FHT006710_5nM_R3


title: RIVA-WT treated with FHD609 rep3

description: Library name: 03_RIVA_ATAC_Arid1aWt _DQ_FHD609_5nM_R3


title: Mouse suprarenal aorta RNA-seq, WT AngII, biol rep 3

description:
Library name: WT_AngII_3
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_AngII_3


title: RIVA-ARID1HET treated with FHD609 rep3

description: Library name: 06_RIVA_ATAC_Arid1aHet _TQ_FHD609_5nM_R3


title: RIVA-ARID1HET treated with FHD609 rep1

description: Library name: 04_RIVA_ATAC_Arid1aHet _TQ_FHD609_5nM_R1


title: RIVA-WT treated with FHD609 rep2

description: Library name: 02_RIVA_ATAC_Arid1aWt _DQ_FHD609_5nM_R2


title: Mouse suprarenal aorta RNA-seq, WT AngII, biol rep 2

description:
Library name: WT_AngII_2
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_AngII_2


title: Mouse suprarenal aorta RNA-seq, WT Saline, biol rep 3

description:
Library name: WT_Saline_3
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_Saline_3


title: p53/Runx1/Rb1-null mammary tumor #3

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Library name: PRR-3

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file include normalized TPM matrices for each sample.

source_name: mammary tumor

extract_protocol:
Total RNA was extracted by Zymo RNA extraction kit with Dnase I treatment to remove the genomic DNA
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance.

value: mammary tumor

value: total tumor cells

value: Trp53 L/L;Runx1 L/L;Rb1 L/L;Rosa26-LSL-YFP

value: Tumorigenesis induced by intraductal injection of Ad-K8-Cre


title: Mouse suprarenal aorta RNA-seq, WT Saline, biol rep 2

description:
Library name: WT_Saline_2
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_Saline_2


title: RIVA-ARID1HET treated with FHD609 rep2

description: Library name: 05_RIVA_ATAC_Arid1aHet _TQ_FHD609_5nM_R2

value: RIVA

value: B-cell lymphoma ABC-DLBCL


title: p53/Runx1/Rb1-null mammary tumor #5

description: Library name: PRR-5


title: RIVA-WT treated with FHD609 rep1

description: Library name: 01_RIVA_ATAC_Arid1aWt _DQ_FHD609_5nM_R1


title: SKMEL-239 treated with DMSO rep2

description: Library name: 26_SK-MEL_DMSO_R2

value: Skin

value: WT


title: p53/Runx1/Rb1-null mammary tumor #2

description: Library name: PRR-2


title: SKMEL-239 treated with DMSO rep3

description: Library name: 27_SK-MEL_DMSO_R3

value: cell line


title: Rb1/p53-null mammary tumor #8

description: Library name: PRb-8

value: Rb1 L/L;Trp53L/L;Rosa26-LSL-YFP


title: Rb1/p53-null mammary tumor #7

description: Library name: PRb-7


title: SKMEL-239 treated with DMSO rep1

description: Library name: 25_SK-MEL_DMSO_R1

value: DMSO


title: SKMEL-239 treated with FHD-286 rep3

description: Library name: 30_SK-MEL_FHD_R3


title: Rb1/p53-null mammary tumor #3

description: Library name: PRb-3


title: WI treated with DMSO rep1

description: Library name: 37_WI_DMSO_R1

value: WI

value: Lung


title: WI treated with DMSO rep2

description: Library name: 38_WI_DMSO_R2


title: WI treated with FHD-286 rep3

description: Library name: 42_WI_FHD_R3


title: Rb1/p53-null mammary tumor #6

description: Library name: PRb-6


title: Rb1/p53-null mammary tumor #4

description: Library name: PRb-4


title: Rb1/p53-null mammary tumor #2

description: Library name: PRb-2


title: Rb1/p53-null mammary tumor #1

description: Library name: PRb-1


title: p53/Runx1/Rb1-null mammary tumor #1

description: Library name: PRR-1


title: Mouse suprarenal aorta RNA-seq, WT AngII, biol rep 1

description:
Library name: WT_AngII_1
Column name in Ao_VAMP8_WT_AngII_vs_Saline_raw_counts.txt: WT_AngII_1

value: suprarenal aorta

value: aortic tissue


title: WI treated with FHD-286 rep2

description: Library name: 41_WI_FHD_R2


title: SKMEL-239 treated with FHD-286 rep1

description: Library name: 28_SK-MEL_FHD_R1


title: WI treated with DMSO rep3

description: Library name: 39_WI_DMSO_R3


title: SV-HUC treated with DMSO rep3

description: Library name: 21_SV-HUC_DMSO_R3

value: SVHUC

value: Epithelial


title: Runx1/p53-null mammary tumor #2

description: Library name: PRunx-2

value: mammary tumor

value: Runx1 L/L;Trp53L/L;Rosa26-LSL-YFP


title: Runx1/p53-null mammary tumor #1

description: Library name: PRunx-1

value: total tumor cells


title: SV-HUC treated with DMSO rep2

description: Library name: 20_SV-HUC_DMSO_R2


title: SV-HUC treated with DMSO rep1

description: Library name: 19_SV-HUC_DMSO_R1


title: F-HF-KO-4

city: Chicago

first: Jose

last: Cordoba-Chacon

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

description: Library name: HFCKO_f1573

data_processing:
Sequencing Ilumina HiSeq PE150 Platform 6G/sample Q3>95%
Mapping with hisat2 v 2.0.5
Analsyis of gene expression Htseq v0.6.1
Differential expression analysis DESeq2 R package v2_1.20.0
Enrichment analysis clusterProfiler R package v3.8.1
Assembly: Mouse reference genome sequence (GRCm38/mm10)
Supplementary files format and content: HFC_mvsLF_m_deg.txt. This file shows the differential expression induced by HFC+Fr diet in male mice. The file is in excel format. The columns are: Gene ID; Values of each liver; log2FoldChange; p-value; p adjusted; Gene Name; Chromosome; Strand; Start; End; Gene Length; Gene Description; Values of each mouse (reads counts); Values of each  mouse (FPKM)
Supplementary files format and content: HFC_fvsLF_f_deg.txt. This file shows the differential expression induced by HFC+Fr diet in female mice. The file is in excel format. The columns are: Gene ID; Values of each liver; log2FoldChange; p-value; p adjusted; Gene Name; Chromosome; Strand; Start; End; Gene Length; Gene Description; Values of each mouse (reads counts); Values of each  mouse (FPKM)
Supplementary files format and content: HFCKO_mvsHFC_m_deg.txt. This file shows the differential expression induced by the knockout of hepatocyte PPARg in HFC+Fr-fed male mice. The file is in excel format. The columns are: Gene ID; Values of each liver; log2FoldChange; p-value; p adjusted; Gene Name; Chromosome; Strand; Start; End; Gene Length; Gene Description; Values of each mouse (reads counts); Values of each  mouse (FPKM)
Supplementary files format and content: HFCKO_fvsHFC_f_deg.txt. This file shows the differential expression induced by the knockout of hepatocyte PPARg in HFC+Fr-fed female mice. The file is in excel format. The columns are: Gene ID; Values of each liver; log2FoldChange; p-value; p adjusted; Gene Name; Chromosome; Strand; Start; End; Gene Length; Gene Description; Values of each mouse (reads counts); Values of each  mouse (FPKM)

source_name: Liver

growth_protocol: Adult mice were fed a LF diet (LF, D12450J, Research Diets) or a HFC diet (HFC, D12120101, Research Diets) and the drinking water was supplemented with 10% fructose for 24 weeks.

extract_protocol:
Whole liver RNA was extracted using Trizol reagent
250-300bp insert cDNA libraries non strand specific.

treatment_protocol: Half of the PPARg floxed mice fed the HFC+Fr diet  were given AAV8-TBG-Cre to generate  hepatocyte-specific PPARgamma knockout mice. The remaining mice were given AAV8-TBG-null to generate control mice.

value: Liver

value: Hepatocyte PPARg knockout

value: High fat and cholesterol diet supplemented with 10% fructose in water

value: Female


title: F-HF-KO-3

description: Library name: HFCKO_f1567


title: F-HF-KO-5

description: Library name: HFCKO_f1575


title: SV-HUC treated with FHD-286 rep2

description: Library name: 23_SV-HUC_FHD_R2

value: WT


title: SV-HUC treated with FHD-286 rep1

description: Library name: 22_SV-HUC_FHD_R1

value: cell line


title: F-HF-KO-2

description: Library name: HFCKO_f1565


title: M-HF-KO-5

description: Library name: HFCKO_m1536

value: Male


title: hES treated with DMSO batch 2 rep3

description: Library name: 63_hES_DMSO_B2_R3

value: hES

value: human embryonic stem cells

value: DMSO


title: WI treated with FHD-286 rep1

description: Library name: 40_WI_FHD_R1

value: WI

value: Lung


title: M-HF-KO-4

description: Library name: HFCKO_m1530


title: F-HF-C-5

description: Library name: HFC_f1574

value: Control


title: F-HF-KO-1

description: Library name: HFCKO_f1556


title: hES treated with DMSO batch 2 rep2

description: Library name: 62_hES_DMSO_B2_R2


title: hES treated with DMSO batch 2 rep1

description: Library name: 61_hES_DMSO_B2_R1


title: hES treated with DMSO batch 1 rep3

description: Library name: 45_hES_DMSO_B1_R3


title: hES treated with FHD-286 batch 2 rep3

description: Library name: 66_hES_FHD_B2_R3


title: M-HF-KO-2

description: Library name: HFCKO_m1508


title: hES treated with FHD-286 batch 2 rep1

description: Library name: 64_hES_FHD_B2_R1


title: M-HF-KO-1

description: Library name: HFCKO_m1497


title: hES treated with DMSO batch 1 rep2

description: Library name: 44_hES_DMSO_B1_R2


title: M-HF-KO-3

description: Library name: HFCKO_m1527


title: hES treated with FHD-286 batch 2 rep2

description: Library name: 65_hES_FHD_B2_R2


title: F-HF-C-4

description: Library name: HFC_f1572


title: hES treated with DMSO batch 1 rep1

description: Library name: 43_hES_DMSO_B1_R1


title: P1_opc_Abeta

city: shanghai

first: Wenxiu

last: Dai

address: No. 746, Zhongshan Middle Road, Songjiang District, Shanghai

institute: Shanghai Jiao Tong University

description: Library name: Sample 1

data_processing:
The Raw data obtained from sequencing was filtered using SOAPnuke.
The clean data was aligned to the reference gene set using Bowtie2.
Assembly: GCF_000001895.5 Rnor_6.0
Supplementary files format and content: tmp, FPKM, read_counts value of each sample

organism: Rattus norvegicus

source_name: brain

growth_protocol: OPC grows in OGM culture medium with a humidity of 5% CO2 and a temperature of 37℃.

extract_protocol:
The RNA of adult OPCs was prepared using the Illumina RNA-Seq preparation kit,1 ug of total RNA was used to construct the sequencing library.
Library preparation using the BGI Optimal series dual-module mRNA library construction kit (BGI-Shenzhen, China), RNA-seq libraries were prepared in accordance with the manufacturer's protocol.

treatment_protocol: The OPC was treated with 1uM Abeta for 2 days before sample collection.

value: brain

value: OPC

value: Aβ


title: F-HF-C-3

description: Library name: HFC_f1555


title: P1_opc_ctrl

description: Library name: Sample 2


title: hES treated with FHD-286 batch 1 rep3

description: Library name: 48_hES_FHD_B1_R3


title: F-HF-C-2

description: Library name: HFC_f1553


title: HUES64, Nocodazole

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: HUES64, Nocodazole

data_processing:
For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.1.1 was used to detect the nucleoside analog within individual reads. CpG methylation and hydroxymethylation were called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as the number of reads, read length N50, mean and median read length, and mean and median read quality.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Processed data are available in bedMethyl files (.bed) and read-level calls (.tsv).

growth_protocol: HUES64 and HUES8 TKO hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies). H9 hESCs (WiCell) were cultured on tissue culture plates coated with Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems, 343301001) in StemFlex medium (Thermo Fisher Scientific, A3349401). Cells were maintained at 37°C with 5% CO2. Medium was changed daily or every other day, and cells were passaged at ~80% confluency using Accutase (Innovative Cell Technologies, AT104). Following passaging, 2µM Thiazovivin (Selleck Chemicals LLC, S1049) was added for 24 h only. MDA-MB-231 breast cancer cells were maintained in DMEM (Gibco) media supplemented with 10% Fetal Bovine Serum (FBS, Seradigm). Cells were incubated at 37°C with 5% CO2. Media was changed every other day and cells were passaged upon reaching 80% confluency using  TrypLE (Gibco).

extract_protocol:
Genomic DNA was isolated using the Puregene Cell Kit (Qiagen, 158043) according to the manufacturer’s instructions.
For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions. Libraries generated from labeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and sequenced using a MinION Mk1b device. Libraries for samples labeled with BrdU and samples not labeled with BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device (Oxford Nanopore Technologies) for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were arrested with 1 µg/ml nocodazole for 16h, stained with the Live/Dead Fixable Violet Dead Cell Stain Kit (Invitrogen, L34964), fixed in  75% ethanol, counterstained with Propidium Iodide (Invitrogen, P3566), and live G2/M cells were isolated by FACS before genomic DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following a 16h incubation.

value: 1 µg/ml nocodazole


title: hES treated with FHD-286 batch 1 rep2

description: Library name: 47_hES_FHD_B1_R2


title: MDA-MB-231, Mock 500uM, 0h chase

description: Library name: MDA-MB-231, Mock 500uM 0h chase

value: human breast cancer cells

value: Mock 500 µM, 10m pulse, 0h chase


title: HUES64, Noc_Untreated_Control

description: Library name: HUES64, Noc_Untreated_Control

value: DMSO vehicle control


title: M-HF-C-6

description: Library name: HFC_m1539M

value: Liver

value: High fat and cholesterol diet supplemented with 10% fructose in water


title: MDA-MB-231, Mock 500uM, 16h chase

description: Library name: MDA-MB-231, Mock 500uM 16h chase

value: WT


title: MDA-MB-231, BrdU 500 uM, 0h chase

description: Library name: MDA-MB-231, BrdU 500 uM 0h chase

value: 500 µM BrdU, 10m pulse, 0h chase


title: F-HF-C-1

description: Library name: HFC_f1547

value: Female


title: MDA-MB-231, BrdU 500 uM, 16h chase

description: Library name: MDA-MB-231, BrdU 500 uM 16h chase

value: 500 µM BrdU, 10m pulse, 16h chase


title: KG1 treated with DMSO rep3

description: Library name: 33_KG1_DMSO_R3

value: cell line

value: Myeloblastic

value: DMSO


title: M-HF-C-5

description: Library name: HFC_m1537

value: Control

value: Male


title: HUES8 TKO, Mock 500uM, 0h chase

description: Library name: HUES8 TKO, Mock 500uM 0h chase

value: human embryonic stem cells

value: TET1/2/3 triple-knockout


title: HUES8 TKO, BrdU 500 uM, 16h chase

description: Library name: HUES8 TKO, BrdU 500 uM 16h chase


title: M-HF-C-4

description: Library name: HFC_m1535


title: KG1 treated with DMSO rep2

description: Library name: 32_KG1_DMSO_R2


title: HUES8 TKO, BrdU 500 uM, 0h chase

description: Library name: HUES8 TKO, BrdU 500 uM 0h chase


title: hES treated with FHD-286 batch 1 rep1

description: Library name: 46_hES_FHD_B1_R1

value: hES


title: M-HF-C-2

description: Library name: HFC_m1522


title: HUES8 TKO, Mock 500uM, 16h chase

description: Library name: HUES8 TKO, Mock 500uM 16h chase


title: M-HF-C-3

description: Library name: HFC_m1528


title: H9, Mock 0h

description: Library name: H9, Mock 0h

value: Mock 50 µM, 10m pulse, 0h chase


title: CAST_MN_8

first: Rachel

last: Brem

address: 321 Koshland Hall

institute: UC Berkeley

description:
Library name: CAST_MN_8
MF_read_matrix_2.txt

data_processing:
Reads were mapped to either the CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

organism: Mus musculus castaneus

source_name: CAST/EiJ

extract_protocol:
motor neurons were processed using Rneasy Micro Kit (Qiagen); samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: CAST/EiJ

value: motor neuron


title: CAST_MN_7

description:
Library name: CAST_MN_7
MF_read_matrix_2.txt


title: H9, Mock 16h

description: Library name: H9, Mock 16h

value: Mock 50 µM, 10m pulse, 16h chase


title: KG1 treated with DMSO rep1

description: Library name: 31_KG1_DMSO_R1


title: H9, BrdU 50uM, 10m pulse 16h chase

description: Library name: H9, BrdU 10m pulse 16h chase

value: 50 µM BrdU, 10m pulse, 16h chase


title: KG1 treated with FHD-286 rep3

description: Library name: 36_KG1_FHD_R3

value: WT


title: KG1 treated with FHD-286 rep1

description: Library name: 34_KG1_FHD_R1


title: M-HF-C-1

description: Library name: HFC_m1496

value: Liver

value: High fat and cholesterol diet supplemented with 10% fructose in water


title: H9, BrdU 50uM, 30m pulse 0h chase

description: Library name: H9, BrdU 30m pulse 0h chase

value: 50 µM BrdU, 30m pulse, 0h chase


title: F-LF-C-5

description: Library name: LF_f1582

value: Low fat diet

value: Female


title: H9, BrdU 50uM, 1h pulse 0h chase

description: Library name: H9, BrdU 1h pulse 0h chase

value: 50 µM BrdU, 1h pulse, 0h chase


title: H9, BrdU 50uM, 10m pulse 0h chase

description: Library name: H9, BrdU 10m pulse 0h chase

value: 50 µM BrdU, 10m pulse, 0h chase


title: CAST_MN_3

description: Library name: CAST_MN_3


title: KG1 treated with FHD-286 rep2

description: Library name: 35_KG1_FHD_R2

value: cell line

value: Myeloblastic


title: F-LF-C-4

description: Library name: LF_f1581

value: Control


title: CAST_MN_2

description: Library name: CAST_MN_2


title: HEPG2 treated with DMSO rep3

description: Library name: 15_HEPG2_DMSO_R3

value: DMSO


title: CAST_PSC_1

data_processing:
Reads were mapped to either the GRCm38, CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Gene counts were generated using STAR's built in quantification (--quantMode GeneCounts)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

source_name: pluripotent stem cell

extract_protocol:
motor neurons were processed using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); PSCs were processed using RNAeasy-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); for both cell types samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: pluripotent stem cell


title: F-LF-C-2

description: Library name: LF_f1579


title: F-LF-C-3

description: Library name: LF_f1580


title: CAST_neuron_rep1

data_processing:
Reads were re-mapped to either the GRCm38 or CAST_EiJ genome using TopHat v 2.1.1 (parameters: -N 0 --library-type fr-unstranded)
Aligned reads were sorted with Samtools sort (parameters: -o)
Gene counts were generated using the htseq-count Python script (parameters: -s no -r pos)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

source_name: motor neuron

value: CAST/EiJ

tag: batch info


title: CAST_MN_1

description: Library name: CAST_MN_1

value: motor neuron


title: CAST_PSC_2


title: MG_rep3_WGBS

city: Beijing

first: Zejia

address: Yanyuan Street

institute: Peking University

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to reference genome(2019 gigascience) using BSseeker2  under default. Reads with more than three consecutive methylated CHH were removed as described previously. CGmaptools is used for downstream analysis and visualization
Assembly: V_corymbosum_v1.0
Supplementary files format and content: The processed data is generated  by BSseeker2 and Cgmaptools.

organism: Vaccinium corymbosum

source_name: fruit

extract_protocol: Sample collection and preparation DNA quantification and qualification genomic DNA degradation and contamination was validated by agarose gels. DNA purity was checked using NanoPhotometer spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit DNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). Library preparation and quantification. A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Kaitai MingJing Gene-Tech (Beijing). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: fruit

value: wild type

value: no

tag: time

value: 42 days after anthesis


title: SG_rep3_WGBS

value: 35 days after anthesis


title: HEPG2 treated with FHD-286 rep1

description: Library name: 16_HEPG2_FHD_R1

value: Liver

value: WT


title: HEPG2 treated with FHD-286 rep3

description: Library name: 18_HEPG2_FHD_R3


title: FP_rep2_WGBS

value: 63 days after anthesis


title: F-LF-C-1

description: Library name: LF_f1543

value: Low fat diet

value: Female


title: M-LF-C-2

description: Library name: LF_m1513

value: Male


title: PC3 treated with DMSO rep3

description: Library name: 03_PC3_DMSO_R3

value: cell line

value: Prostate


title: FP_rep3_WGBS


title: LG_rep3_WGBS

value: 49 days after anthesis


title: HEPG2 treated with FHD-286 rep2

description: Library name: 17_HEPG2_FHD_R2


title: CAST_MN_1

city: Berkeley


title: HEPG2 treated with DMSO rep1

description: Library name: 13_HEPG2_DMSO_R1

value: DMSO


title: PP_rep2_WGBS

value: 56 days after anthesis


title: PP_rep3_WGBS


title: M-LF-C-4

description: Library name: LF_m1515

value: Control


title: M-LF-C-3

description: Library name: LF_m1514


title: PC3 treated with DMSO rep2

description: Library name: 02_PC3_DMSO_R2


title: LG_rep2_WGBS

value: fruit


title: MG_rep2_WGBS

value: wild type


title: M-LF-C-1

description: Library name: LF_m1501


title: PC3 treated with DMSO rep1

description: Library name: 01_PC3_DMSO_R1


title: SG_rep2_WGBS

value: no


title: PC3 treated with FHD-286 rep3

description: Library name: 06_PC3_FHD_R3


title: 11_4_Liver_KO_NK

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

institute: Washington University School of Medicine

description: Library name: sample.11_4_Liv_KO_NK

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq X Plus.  Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Assembly: Ensembl release 101 primary assembly with STAR version 2.7.9a
Supplementary files format and content: The count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights and is supplied in a tsv file format.

source_name: liver

extract_protocol:
Qiagen RNA easy micro kit was used to extract RNA of cells directly sorted into Buffer RLT + β-mercaptoethanol, following manufacturer’s protocol.
Sequencing library was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) and sequenced on Illumina NovaSeq X Plus.

value: liver

value: NK


title: FP_rep1_WGBS


title: PC3 treated with FHD-286 rep2

description: Library name: 05_PC3_FHD_R2


title: PP_rep1_WGBS


title: 11_4_Liver_KO_ILC

description: Library name: sample.11_4_Liv_KO_ILC

value: ILC


title: SG_rep1_WGBS

value: 35 days after anthesis


title: MG_rep1_WGBS

value: 42 days after anthesis


title: H1_hPSC scrnaseq, replicate 2

city: Stanford

first: Lay Teng

last: Ang

address: Institute for Stem Cell Biology & Regenerative Medicine, Lokey Stem Cell Bldg, 265 Campus Drive

institute: Stanford University

description:
Library name: H1_hPSC scrnaseq, replicate 2
10x Genomics
H1_old_filtered_feature_bc_matrix.h5

data_processing:
For scRNA-seq, the demultiplexing, barcoded processing and gene counting were made using the CellRanger Count v9.0.1 Cloud Analysis software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human reference genome Hg38 (GRCh38)
Supplementary files format and content: Processed data files are Cell Ranger output files in HDF5 (.h5) format containing filtered gene-by-cell UMI count matrices for each sample.

source_name: H1 hPSC

extract_protocol:
Cells were collected in papain and centrifuged at 300rcf for 5 min in DNA LoBind tubes. Cell pellets were resuspended in PBS containing 0.01% BSA and passed through a 40 µm cell strainer prior to counting. Cell concentration was adjusted as needed to approximately 1,000 cells/µL, followed by a second centrifugation and repeat cell count/viability assessment. Cell suspensions were maintained on ice until loading onto the Chromium Controller.
Library was prepared according to the manufacturer’s instructions for the Chromium Single Cell 3'GEM Library and Gel Bead kit v3 (PN-1000075), Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, PN-1000121)) workflow (10x Genomics). Briefly, single cells were loaded with gel beads and partitioning oil to generate gel bead-in-emulsions (GEMs). Poly(A) RNA from lysed single cells in each GEM was reverse transcribed to barcoded cDNA containing a cell barcode and unique molecular identifier (UMI). After GEM-RT, GEMs were broken, barcoded cDNA was purified and amplified by PCR, and amplified cDNA was subjected to fragmentation, end repair and A-tailing, adaptor ligation, sample index PCR, and SPRI bead-based cleanup/size selection to generate dual-indexed gene expression libraries for paired-end Illumina sequencing. Libraries were indexed using the 10x Genomics Dual Index Plate TT Set A.

value: H1 hPSC

value: hPSC

value: XY, wild-type

value: Unsorted


title: 11_3_Liver_KO_NK

description: Library name: sample.11_3_Liv_KO_NK


title: 11_3_Liver_KO_ILC

description: Library name: sample.11_3_Liv_KO_ILC


description:
Library name: day 3 hPSC-derived artery endothelial cells (unsorted) scrnaseq
10x Genomics

source_name: H1 hPSC-derived

value: H1 hPSC-derived

value: artery EC


title: LG_rep1_WGBS

value: 49 days after anthesis


title: SHSY5Y treated with DMSO rep2

description: Library name: 32_SHSY5Y_DMSO_R2

source_name: cell line

value: cell line

value: Neuronal

value: WT

value: DMSO


title: PC3 treated with FHD-286 rep1

description: Library name: 04_PC3_FHD_R1

value: Prostate


description:
Library name: day 3 hPSC-derived artery endothelial cells (sorted CD144+) scrnaseq
10x Genomics

value: CD144+ FACS sorted


title: H1 CRISPRi SOXF KD vein EC

description:
Library name: AM_6
10x Genomics

data_processing:
For scRNA-seq, the demultiplexing, barcoded processing and gene counting were made using the CellRanger Count v9.0.1 Cloud Analysis software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly:Human reference genome Hg38 (GRCh38)
Supplementary files format and content: Processed data files are Cell Ranger output files in HDF5 (.h5) format containing filtered gene-by-cell UMI count matrices for each sample.

growth_protocol: hPSCs were maintained in mTesR Plus media before differentiation. For CRISRPRi, H1 human pluripotent stem cells (hPSCs) engineered to constitutively express CRISPR interference machinery consisting of nuclease-dead Cas9 fused to ZIM3-KRAB were maintained in StemFlex medium supplemented with 1% penicillin/streptomycin. Cells were dissociated with Accutase for passaging/transduction, and 1 µM thiazovivin was used after replating.

extract_protocol:
For CRISPRi experiments, cells were collected in papain and centrifuged at 300rcf for 5 min in DNA LoBind tubes. Cell pellets were resuspended in PBS containing 0.01% BSA and passed through a 40 µm cell strainer prior to counting. Cell concentration was adjusted as needed to approximately 1,000 cells/µL, followed by a second centrifugation and repeat cell count/viability assessment. Cell suspensions were maintained on ice until loading onto the Chromium Controller.
Library was prepared according to the manufacturer’s instructions for the Chromium Next GEM Single Cell 3? Reagent Kits v3.1 (Dual Index) workflow (10x Genomics). Briefly, single cells were loaded with gel beads and partitioning oil to generate gel bead-in-emulsions (GEMs). Poly(A) RNA from lysed single cells in each GEM was reverse transcribed to barcoded cDNA containing a cell barcode and unique molecular identifier (UMI). After GEM-RT, GEMs were broken, barcoded cDNA was purified and amplifised by PCR, and amplified cDNA was subjected to fragmentation, end repair and A-tailing, adaptor ligation, sample index PCR, and SPRI bead-based cleanup/size selection to generate dual-indexed gene expression libraries for paired-end Illumina sequencing. Libraries were indexed using the 10x Genomics Dual Index Plate TT Set A.

treatment_protocol: Differentiation of hPSCs into artery and vein ECs. All differentiation was conducted in defined, serum-free CDM2 basal media. Detailed instructions to how to prepare CDM2 are available.

value: Vein EC

value: dCas9-ZIM3-KRAB CRISPRi; SOX17, SOX7, SOX18 sgRNAs

value: SOXF KD


title: H1 CRISPRi SOXF KD artery EC

description:
Library name: AM_4
10x Genomics

value: Artery EC


title: 11_2_Liver_WT_NK

description: Library name: sample.11_2_Liv_WT_NK

value: liver

value: NK


title: H1 CRISPRi vein EC

description:
Library name: AM_3
10x Genomics

value: dCas9-ZIM3-KRAB CRISPRi

value: Control


title: SHSY5Y treated with DMSO rep3

description: Library name: 33_SHSY5Y_DMSO_R3


title: H1 CRISPRi artery EC

description:
Library name: AM_1
10x Genomics

value: H1 hPSC-derived


title: SHSY5Y treated with FHD-286 rep3

description: Library name: 36_SHSY5Y_FHD286_R3


title: H1 CRISPRi SOXF KD primed EC

description:
Library name: AM_5
10x Genomics

value: Primed EC


title: 11_2_Liver_WT_ILC

description: Library name: sample.11_2_Liv_WT_ILC

value: ILC


title: SHSY5Y treated with DMSO rep1

description: Library name: 31_SHSY5Y_DMSO_R1

value: cell line


title: H1 CRISPRi primed EC

description:
Library name: AM_2
10x Genomics


title: 11_1_Liver_WT_ILC

description: Library name: sample.11_1_Liv_WT_ILC


title: 11_1_Liver_WT_NK

description: Library name: sample.11_1_Liv_WT_NK


title: ASC_NC_3

first: wuhan

last: wei

address: No. 33, Badachu Road, Shijingshan District

department: Plastic Surgery Hospital

institute: Chinese Academy of Medical Sciences

description:
Library name: ASC_NC_3
N10 WT

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: TPM value for each Sample

source_name: adipose-derived stem cells (ADSCs)

extract_protocol:
RNA was extracted from cell using TRIzol reagent. Briefly, cell were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: adipose-derived stem cells (ADSCs)

value: N10 WT