title: T786 PDXC, Untreated, 3

description: Library name: Sample 3

value: Patient-derived xenograft cell

value: Untreated


title: MC38, "Near" cells, rep4

status: Public on Mar 27 2026

type: SRA

city: Beijing

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

country: China

institute: Peking University

description:
Library name: MC38_Near_rep4
Column name in MC38_migration_all_counts.xlsx:Near4
MC38_migration_all_counts.xlsx

library_source: transcriptomic

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20).
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: HEK293T and MC38 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cortical neurons were dissected from neonatal Sprague Dawley rats (within 24 hours post-birth), plated onto 10-cm dishes, and cultured with GPM for 3-6 h before switching to neural cell culture medium (Neurobasal medium with 2% (v/v) B-27 supplement, 1% (v/v) GlutaMAX supplement, penicillin and streptomycin). Petri dishes were pre-incubated overnight with 50-100 μg/mL PDL at 37°C. The day of rat dissection was designated as DIV 0 (0 days in vitro), and thereafter, half of the spent culture medium was replaced with fresh neural cell culture medium every 3 days.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base.

treatment_protocol: For general CAP-seq labeling experiments, HEK293T cells were cultured until the confluence reached 90%, incubated with 10 mM propargylamine (PA) in HBSS for 5 min, and irradiated with blue light for 1-120 seconds. For the induction of stress granules, HEK293T cells were incubated with 0.5 mM sodium arsenite for 5-60 minutes. Primary cultures of rat cortical neurons were transduced with a lentivirus expressing G3BP1-Lantern or Lantern-NES at 3 days in vitro (DIV3). At DIV8, neurons were stimulated with 0.25 mM sodium arsenite for 3 hours, and conducted with the CAP-seq labeling procedure. For the cancer cell migration assay, MC38 cells were seeded on coverslips with a culture-insert to create a 500-μm cell-free gap. 24 hours after removing the culture-insert, migrating cells near the gap and remaining cells far from the gap were selectively labeled with DMD-controlled 450-nm laser and 2 mM Bio-NH2 probe.

tag: cell line

tag: cell type

value: colorectal tumor cells

tag: genotype

value: Lantern-TM


title: MC38, "Far" cells, rep4

description:
Library name: MC38_Far_rep4
Column name in MC38_migration_all_counts.xlsx: Far4
MC38_migration_all_counts.xlsx


title: HEK293T Scramble ASO normoxia rep1

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

country: USA

institute: University of Illinois at Urbana-Champaign

description:
Library name: Sample_25
con_nor2

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
RNA-seq reads were aligned to human reference genome GRCh38 assembly using STAR.
Raw gene counts were first analyzed by HTSEQ-Count.
Assembly: GRCh38
Supplementary files format and content: HTSeq gene count information in tab-separated tables for each set of experiments.

organism: Homo sapiens

growth_protocol: Cells were cultured at 37 degrees Celsius with 5% carbon dioxide.

extract_protocol:
RNA was extracted using Trizol and cleaned up using Qiagen RNeasy column.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: Hypoxia treatment was done by incubating the cells in 0.2% oxygen, 5% carbon dioxide chamber for 24 hours. Transient knockdown of MALAT1 was done using ASO. Stable knockdown of SRSF1 was done using shRNA.

value: Epithelial-like cell derived from human fetal kidney

value: Scramble ASO

tag: treatment

value: Normoxia


title: ID8 cells, T3_N6, Day14

city: Seoul

first: Mahesh

middle: Chandra

last: Patra

state: 경기도

address: 241 Gangnam-daero

country: South Korea

institute: Arontier Co. Ltd

description:
Library name: Sample39
Column name in mRNA.count_data.txt: T3_N6

data_processing:
Cutadapt → STAR (2-pass alignment) → HTSeq → TPM normalization → t-test DEG analysis
Assembly: Mus musculus reference genome (GRCm38.p6)
Supplementary files format and content: Tab delimited text files include raw counts and TPM-UQ values for each sample

molecule: total RNA

source_name: Ovary Epithelium

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Samples with RNA integrity number (RIN) ≥ 6.0 were used for library preparation.
RNA-seq libraries were prepared using a poly(A) mRNA enrichment strategy. Polyadenylated mRNA was isolated from total RNA using oligo(dT) magnetic beads. Purified mRNA was fragmented and reverse transcribed using random hexamer primers to generate first-strand cDNA, followed by second-strand synthesis. The resulting cDNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Libraries were amplified by PCR and purified prior to sequencing.

tag: tissue

value: Ovary Epithelium

value: Surface epithelial cells

value: WT

value: No Treatment

tag: time


title: MC38, "Far" cells, rep3

description:
Library name: MC38_Far_rep3
Column name in MC38_migration_all_counts.xlsx: Far3
MC38_migration_all_counts.xlsx


title: HEK293T Scramble ASO normoxia rep2

description:
Library name: Sample_26
con_nor3


title: MCF7 SRSF1 shRNA hypoxia rep2

description:
Library name: Sample_24
SRSF1sh4_Hyp_rep2

value: Breast epithelial cell

value: SRSF1 shRNA

value: Hypoxia


title: ID8 cells, T3_N5, Day14

description:
Library name: Sample38
Column name in mRNA.count_data.txt: T3_N5


title: T786 PDXC, Untreated, 2

city: Montreal

first: Mark

last: Basik

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute

description: Library name: Sample 2

data_processing:
Raw RNA-seq reads (FASTQ) were aligned to the human genome hg19 (UCSC) using STAR aligner v2.7.10a with default parameters.
Resulting BAM files were sorted and indexed using samtools v1.17 to prepare for counting.
Assembly: hg19 (UCSC)
Supplementary files format and content: Gene-level counts were generated from sorted BAMs using htseq-count v0.13.5 with hg19 GTF annotation, mode=strict, and stranded=yes.
Supplementary files format and content: Raw counts were used for submission.

source_name: Triple-negative breast cancer tumor

extract_protocol:
RNA extraction was done by using the RNeasy Mini Kit (QIAGEN cat#74104) with RNase A (QIAGEN Cat # 19101 ) and DNase (Qiagen Cat # 79254) according to  the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the KAPA mRNA HyperPrep kit following manufacture's protocol

value: Triple-negative breast cancer tumor


title: T786 PDXC, Untreated, 1

description: Library name: Sample 1


title: MCF7 SRSF1 shRNA hypoxia rep1

description:
Library name: Sample_23
SRSF1sh4_Hyp_rep1


title: ID8 cells, T3_N4, Day14

description:
Library name: Sample37
Column name in mRNA.count_data.txt: T3_N4


title: MC38, "Far" cells, rep2

description:
Library name: MC38_Far_rep2
Column name in MC38_migration_all_counts.xlsx: Far2
MC38_migration_all_counts.xlsx


title: MDA ETV4 KO (replicate 3)

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Library name: MDA-3D_c39_n3

data_processing:
Read quality was assessed using FastQC (version 0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk (version 38.92) and reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were then aligned using STAR (version 2.7.9a) to the human reference genome (hg38).
Raw gene counts were generated in R 4.1.1 using the featureCounts function from the Rsubread package (version 2.8.1) with gene annotation provided by GENCODE v44 for hg38 human genome.
Assembly: hg38
Supplementary files format and content: Raw gene counts

growth_protocol: Cells were cultured in DMEM/F12 with 10%FBS, 2% PS and 1% L-glutamine.

extract_protocol:
For harvesting of the 3D cultures, collagen 1 gels were washed once with HBSS and digested with 1ml collagenase I at 300U/ml for 10 minutes at 37°C. After 10 minutes, mechanical disruption of the gels was performed by pipetting. Additional 5 minutes incubation at 37°C was performed. The suspension was then washed with HBSS by centrifugation and cell pellet was frozen at -80°C. RNA extraction was performed using RNeasy Mini Kit (Qiagen); DNA was removed by DNase treatment.
RNA-seq libraries for deep-sequencing were prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: Nucleofection was carried out  with the SE-kit (Lonza) using Nucleofector (Lonza) following manufacturer’s instructions. For 3D cell cultures, cells  were resuspended at 100,000 cells/ml in collagen1 at 1.2 or 2.4 mg/ml. 80 ul droplets were let to jellify for 30 minutes at 37°C in 24 well Ultra Low Attachment plates. Complete media was then added to the wells.

value: Breast cancer cells

value: Knockout of  ETV1, ETV4, and ETV5 afeter nucleofection with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: MC38, "Far" cells, rep1

description:
Library name: MC38_Far_rep1
Column name in MC38_migration_all_counts.xlsx: Far1
MC38_migration_all_counts.xlsx


title: MDA ETV4 KO (replicate 2)

description: Library name: MDA-3D_c39_n2


title: Frontal cortex, CORT+DFP+LPS, 12 h, CT_12h4

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

description:
Library name: CT_12h4
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_12h_percent_methylation.tsv

library_source: genomic

data_processing:
Raw RRBS FASTQ files were processed as single-end reads. Adapters and low-quality bases were trimmed with Trim Galore! using RRBS mode (--rrbs), Phred quality cutoff 30, and FastQC was run on trimmed libraries.
After initial trimming, RRBS diversity adapters were removed using trimRRBSdiversityAdaptCustomers.py.
Trimmed single-end reads were aligned to the mouse reference genome GRCm38 (mm10) using Bismark with Bowtie2, and aligned BAM files were sorted with SAMtools.
Methylation levels for each CpG site were estimated in methylKit from the ratio of methylated to total reads at each locus; processed files are tissue-specific CpG-level percent methylation matrices for CORT+DFP+Saline, 6 h baseline controls versus CORT+DFP+LPS comparisons at 6 h, 12 h, and 24 h.
Differential methylation in the study was assessed using methylKit logistic regression with minimum 10x coverage in every sample, at least 5% methylation difference, and FDR-adjusted p < 0.05.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files are unfiltered TSV tables containing genomic coordinates (chr, start, end, strand) followed by sample-specific percent methylation values. These files are not restricted to statistically significant differentially methylated CpGs.
Supplementary files format and content: Nine processed files are included: Blood_Con_6h_percent_methylation.tsv, Blood_Con_12h_percent_methylation.tsv, Blood_Con_24h_percent_methylation.tsv, HPC_Con_6h_percent_methylation.tsv, HPC_Con_12h_percent_methylation.tsv, HPC_Con_24h_percent_methylation.tsv, CTX_Con_6h_percent_methylation.tsv, CTX_Con_12h_percent_methylation.tsv, and CTX_Con_24h_percent_methylation.tsv.

molecule: genomic DNA

source_name: Frontal cortex

growth_protocol: Adult male C57BL/6J mice (8-12 weeks old, approximately 30 g) were obtained from Jackson Laboratory and housed individually under controlled temperature and humidity on a 12 h light/12 h dark cycle with ad libitum access to food and water.

extract_protocol:
Genomic DNA was extracted from whole blood and dissected brain tissues using standard column-based purification methods; only high-quality DNA was used for RRBS library preparation.
RRBS libraries were prepared from 100 ng high-quality genomic DNA using the Ovation RRBS Methyl-Seq System (Tecan Genomics/NuGEN) according to the manufacturer's protocol, followed by bisulfite conversion and library amplification.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT; 200 mg/L in 0.6% ethanol) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP; 4 mg/kg). Mice then received periodic CORT administration for 7 days every other week to a total of 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS; 0.5 mg/kg, subcutaneous). Whole blood, hippocampus, and frontal cortex were collected 6 h, 12 h, or 24 h after challenge, depending on group.

value: Frontal cortex

value: wild type

value: CORT+DFP+LPS, 12 h


title: MCF7 SRSF1 shRNA normoxia rep2

description:
Library name: Sample_22
SRSF1sh4_Nor_rep2


title: ID8 cells, T2_AW4, Day7

description:
Library name: Sample31
Column name in mRNA.count_data.txt: T2_AW4

value: Anaesthesia + Wounding

value: Day 7


title: MDA ETV4 KO (replicate 1)

description: Library name: MDA-3D_c39_n1


title: MDA control (control, replicate 1)

description: Library name: MDA-3D_sgCTRL_n1

value: Nucleofected with Cas9 and Control sgRNA sequences, 3D Collagen I cultures


title: SAHA3

city: Houston

first: Chaitra

last: Rai

state: TX

address: ABBR 631C, 1 BAYLOR PLAZA

institute: Baylor College of Medicine

description: Library name: Sample6

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: Excel file consists of FPKM value for each sample

source_name: Tumor

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer  (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: Tumor


title: ID8 cells, T3_N3, Day14

description:
Library name: Sample36
Column name in mRNA.count_data.txt: T3_N3

value: Ovary Epithelium


title: BBM17_anti-H3K4-Me1

data_processing:
Sequencing read quality control was performed with FastQC v0.11.9 and MultiQC v1.9
Reads were aligned to the human genome using BWA- mem v0.7.17, sorted with SAMtools v1.10 and converted into binary files (BAM)
PCR duplicates, multi-mapped, and low quality reads were marked and removed using Picard v2.23.1 and Samtools v1.10
bedGraph tracks were generated using the GenomeCoverageBed function from bedtools v2.29.2 and converted into bigwig using bedGraphToBigWig v357
Assembly: hg38
Supplementary files format and content: bigWig

source_name: brain metastasis

growth_protocol: Organoid coltures were established and handled according to Dekkers, J.F., van Vliet, E.J., Sachs, N. et al. Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids. Nat Protoc 16, 1936–1965 (2021). https://doi.org/10.1038/s41596-020-00474-1

extract_protocol:
Chomatin isolation and ChIP were performed as described in Della Chiara G, Gervasoni F, Fakiola M, Godano C, D'Oria C, Azzolin L, Bonnal RJP, Moreni G, Drufuca L, Rossetti G, Ranzani V, Bason R, De Simone M, Panariello F, Ferrari I, Fabbris T, Zanconato F, Forcato M, Romano O, Caroli J, Gruarin P, Sarnicola ML, Cordenonsi M, Bardelli A, Zucchini N, Ceretti AP, Mariani NM, Cassingena A, Sartore-Bianchi A, Testa G, Gianotti L, Opocher E, Pisati F, Tripodo C, Macino G, Siena S, Bicciato S, Piccolo S, Pagani M. Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ. Nat Commun. 2021 Apr 20;12(1):2340. doi: 10.1038/s41467-021-22544-y. PMID: 33879786; PMCID: PMC8058065 with minor modification. Sonication was performed on a Covaris Evolution with settings: Peak Incidence Power 105W, Duty Factor 10%, Cycles per Burst 200, 7 min)
Watchmaker DNA Library Prep Kit for double-stranded DNA (Watchmaker Genomics) according to manufacturer instructions

tag: chip antibody

value: anti-H3K4-Me1 (DIAGENODE C15410194)


title: ID8 cells, T3_N1, Day14

description:
Library name: Sample35
Column name in mRNA.count_data.txt: T3_N1

value: Surface epithelial cells

value: WT


title: SAHA2

description: Library name: Sample5


title: MCF7 pLKO vector normoxia rep2

description:
Library name: Sample_18
pLK0_Nor_rep2

value: Breast epithelial cell

value: Empty shRNA lentivirus

value: Normoxia


title: SAA2

description: Library name: Sample8


title: MDA control (control, replicate 2)

description: Library name: MDA-3D_sgCTRL_n2


title: MCF7 pLKO vector normoxia rep1

description:
Library name: Sample_17
pLK0_Nor_rep1


title: BBM17_anti-H3K4-Me3

value: anti-H3K4-Me3 (Millipore 07-473)


title: ID8 cells, T2_AW8, Day7

description:
Library name: Sample33
Column name in mRNA.count_data.txt: T2_AW8


title: BBM17_inputDNA


title: MCF7 SRSF1 shRNA normoxia rep1

description:
Library name: Sample_21
SRSF1sh4_Nor_rep1

value: SRSF1 shRNA


title: MCF7 pLKO vector hypoxia rep1

description:
Library name: Sample_19
pLK0_Hyp_rep1

value: Hypoxia


title: ID8 cells, T2_AW9, Day7

description:
Library name: Sample34
Column name in mRNA.count_data.txt: T2_AW9


title: MCF7 pLKO vector hypoxia rep2

description:
Library name: Sample_20
pLK0_Hyp_rep2


title: SAA1

description: Library name: Sample7


title: SAA3

description: Library name: Sample9


title: MCF7 MALAT1KO hypoxia rep2

description:
Library name: Sample_16
8_KO_hyp2

value: MALAT1 KO


title: MDA control (control, replicate 3)

description: Library name: MDA-3D_sgCTRL_n3

value: Breast cancer cells


title: ID8 cells, T2_AW6, Day7

description:
Library name: Sample32
Column name in mRNA.count_data.txt: T2_AW6


title: ID8 cells, T2_AW3, Day7

description:
Library name: Sample30
Column name in mRNA.count_data.txt: T2_AW3


title: CNT3

description: Library name: Sample3


title: SAHA1

description: Library name: Sample4


title: BBM17_anti-H3K36-Me3

value: anti-H3K36-Me3 (DIAGENODE C15410192)


title: MCF7 MALAT1KO hypoxia rep1

description:
Library name: Sample_15
7_KO_Hyp1


title: ID8 cells, T2_A7, Day7

description:
Library name: Sample27
Column name in mRNA.count_data.txt: T2_A7

value: Anaesthesia


title: CNT2

description: Library name: Sample2


title: MCF7 MALAT1KO normoxia rep2

description:
Library name: Sample_14
6_KO_nor2


title: BBM2_inputDNA


title: BBM17_anti-H3K27-Ac

value: anti-H3K27-Ac (abcam 4729)


title: ID8 cells, T2_A8, Day7

description:
Library name: Sample28
Column name in mRNA.count_data.txt: T2_A8

value: Day 7


title: CNT1

description: Library name: Sample1

value: Tumor


title: ID8 cells, T2_A6, Day7

description:
Library name: Sample26
Column name in mRNA.count_data.txt: T2_A6

value: Ovary Epithelium


title: BBM2_anti-H3K4-Me3


title: Bone marrow, IL18m-day3, 10x

city: Hangzhou

first: Ting

last: Zhou

state: Zhejiang

address: No. 600 Dunyu Road, Xihu District

department: Immunology and Microbiology

institute: Westlake University

description:
Library name: Sample 5
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.2.0 for scRNA-seq. The demultiplexing, barcoded processing, gene counting and aggregation were made using the spaceranger software v3.0.0 for spatial transcriptomics.
Assembly: GRCm39
Supplementary files format and content: cells-genes matrix

source_name: bone marrow

extract_protocol:
Microfluidic chips(10x Genomics) and magnetic bead methods (BD Rhapsody)
The erythroid sequencing was processed using the 10x Genomics protocol, whereas the myeloid component was conducted according to the BD Rhapsody Single-Cell Whole Transcriptome (WTA) and Sample Multiplexing Kit (SMK) Library Construction Guide.

value: bone marrow

tag: library type

value: mRNA


title: MCF7 Control hypoxia rep2

description:
Library name: Sample_12
4_WT_hyp2

value: WT


title: Bone marrow, PBS, 10x

description:
Library name: Sample 4
10x Genomics


title: Spleen, IL18m-day5, ST

description:
Library name: Sample 8
Fresh Frozen Spatial Transcriptome Sequencing

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.2.0 for scRNA-seq. The demultiplexing, barcoded processing, gene counting and aggregation were made using the spaceranger software v3.0.0 for spatial transcriptomics.
Assembly: GRCm39
Supplementary files format and content: cells-genes matrix
Library strategy: Spatial Transcriptomics

source_name: spleen

value: spleen


title: MCF7 Control hypoxia rep1

description:
Library name: Sample_11
3_WT_Hyp1

value: Breast epithelial cell


title: BBM2_anti-H3K36-Me3


title: MCF7 Control normoxia rep1

description:
Library name: Sample_9
1_WT_nor1

value: Normoxia


title: ID8 cells, T2_A4, Day7

description:
Library name: Sample24
Column name in mRNA.count_data.txt: T2_A4

value: Surface epithelial cells


title: Spleen, IL18m-day5, 10x

description:
Library name: Sample 3
10x Genomics


title: ID8 cells, T2_A3, Day7

description:
Library name: Sample23
Column name in mRNA.count_data.txt: T2_A3


title: Bone marrow, IL18m-day5, 10x

description:
Library name: Sample 6
10x Genomics


title: ID8 cells, T2_A5, Day7

description:
Library name: Sample25
Column name in mRNA.count_data.txt: T2_A5


title: ID8 cells, T2_AW2, Day7

description:
Library name: Sample29
Column name in mRNA.count_data.txt: T2_AW2

value: Anaesthesia + Wounding


title: BBM2_anti-H3K4-Me1

value: anti-H3K4-Me1 (DIAGENODE C15410194)


title: MCF7 MALAT1KO normoxia rep1

description:
Library name: Sample_13
5_KO_nor1

value: MALAT1 KO


title: ID8 cells, T2_A2, Day7

description:
Library name: Sample22
Column name in mRNA.count_data.txt: T2_A2


title: MCF7 MALAT1 ASO hypoxia rep2

description:
Library name: Sample_8
MALAT1kd_Hyp_rep2

value: MALAT1 ASO

value: Hypoxia


title: BBM2_anti-H3K27-Ac


title: MCF7 Control normoxia rep2

description:
Library name: Sample_10
2_WT_nor2


title: BBM2_anti-H3K27-Me3

value: anti-H3K27-Me3 (Millipore 07449)


title: ID8 cells, T2_A10, Day7

description:
Library name: Sample21
Column name in mRNA.count_data.txt: T2_A10

value: Anaesthesia


title: Spleen, IL18m-day3, 10x

description:
Library name: Sample 2
10x Genomics


title: BBM7_inputDNA


title: MCF7 MALAT1 ASO hypoxia rep1

description:
Library name: Sample_7
MALAT1kd_Hyp_rep1


title: Spleen, PBS, 10x

description:
Library name: Sample 1
10x Genomics


title: ID8 cells, T2_A1, Day7

description:
Library name: Sample20
Column name in mRNA.count_data.txt: T2_A1

value: Day 7


title: m_astrocyte, H202_D1, 2 [ATAC-seq]

city: Daejeon

first: C. Justin

last: Lee

address: 55 Expo-ro

institute: Institute for Basic Science

data_processing:
Basecalls was performed using bcl2fastq v2.19.0.316. for NovaSeq output.
Quality evaluation is performed using FASTQC (v.0.12.1).
Adaptor trimming is performed using Cutadapt (v.2.6), (-q 10 -m 15 -e 0.10).
Trimmed reads are mapped to the mouse genome (GRCm38/mm10) using Bowtie2 (v.2.2.5).
Visualizing peak is conducted using BamCoverage v.3.5.4.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

source_name: Primary cortical astrocyte

growth_protocol: Astrocytes were dissected from cerebral cortices of P4 mice and plated on 6 or 24 well plates coated with 0.1 mg/ml of poly-D-lysine (Sigma). Cultured astrocytes were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Corning) supplemented with 4.5 g/L glucose, L-glutamine, sodium pyruvate, 10% heat-inactivated horse serum, 10% heat-inactivated FBS, and 1000 units/ml of penicillin-streptomycin at 37℃ with 5% CO2.

extract_protocol:
The total genomic DNA was isolated using ATAC-seq kit (Activemotif, 53150).
The transposase accessible peaks were isolated using ATAC-seq kit (Activemotif, 53150) following the manufacturer's protocol.

treatment_protocol: 200 µm of H2O2 (Sigma, 88597) was treated for 3 hours and washed with maintaining media. After 24 hours of washing, cells were harvested.

tag: age

value: Primary cortical astrocyte

value: H2O2 3hr

tag: time point


title: ID8 cells, T2_N8, Day7

description:
Library name: Sample19
Column name in mRNA.count_data.txt: T2_N8

value: Ovary Epithelium

value: No Treatment


title: MCF7 Scramble ASO hypoxia rep2

description:
Library name: Sample_4
Scr631_Hyp_rep2

value: Scramble ASO


title: m_astrocyte, H202_D1, 1 [ATAC-seq]


title: MCF7 MALAT1 ASO normoxia rep1

description:
Library name: Sample_5
MALAT1kd_Nor_rep1


title: m_astrocyte, H202_D3, 3

data_processing:
Basecalls was performed using bsc2fastq v2.19.0.316 for NovaSeq output.
Quality evaluation is performed using FASTQC (v.0.12.1).
Adaptor trimming is performed using Cutadapt (v.2.6), (-q 10 -m 15 -e 0.10).
Trimmed reads are mapped to the mouse genome (GRCm38/mm10) using STAR (v.2.7.3a).
Differential expression analysis is conducted using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes values for each Sample.

extract_protocol:
The total RNA was isolated using Qiagen RNeasy mini kit.
The RNA sequencing library was generated using NEBNext Ultra RNA Library prep kit following the manufacturer's instruction.

treatment_protocol: 200 µm of H2O2 (Sigma, 88597) was treated for 3 hours and washed with maintaining media. After 24 or 72 hours of washing, cells were harvested.


title: MCF7 Scramble ASO hypoxia rep1

description:
Library name: Sample_3
Scr631_Hyp_rep1


title: MCF7 Scramble ASO normoxia rep2

description:
Library name: Sample_2
Scr631_Nor_rep2


title: BBM7_anti-H3K4-Me1


title: BBM7_anti-H3K4-Me3

value: anti-H3K4-Me3 (Millipore 07-473)


title: MCF7 Scramble ASO normoxia rep1

description:
Library name: Sample_1
Scr631_Nor_rep1

value: Breast epithelial cell


title: ID8 cells, T2_N4, Day7

description:
Library name: Sample17
Column name in mRNA.count_data.txt: T2_N4

value: WT


title: MDA-MB-231 ETV KO 3D rep2

extract_protocol:
2D cell cultures were collected using the RNeasy Mini Kit (Qiagen) for total RNA extraction. For harvesting of the 3D cultures, collagen 1 gels were washed once with HBSS and digested with 1ml collagenase I at 300U/ml for 10 minutes at 37°C. After 10 minutes, mechanical disruption of the gels was performed by pipetting. Additional 5 minutes incubation at 37°C was performed. The suspension was then washed with HBSS by centrifugation and cell pellet was frozen at -80°C. RNA extraction was performed using RNeasy Mini Kit (Qiagen); DNA was removed by DNase treatment.
RNA-seq libraries for deep-sequencing were prepared with TruSeq Stranded mRNA (Illumina).

treatment_protocol: Nucleofection was carried out  with the SE-kit (Lonza) using Nucleofector (Lonza) following manufacturer’s instructions.  2D cell cultures were carried out on cell-culture plastic wells. For 3D cell cultures, cells  were resuspended at 100,000 cells/ml in collagen1 at 1.2 or 2.4 mg/ml. 80 ul droplets were let to jellify for 30 minutes at 37°C in 24 well Ultra Low Attachment plates. Complete media was then added to the wells.

value: Breast cancer cells

value: Knockout of ETV1, ETV4 and ETV5 by nucleofected with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: ID8 cells, T2_N5, Day7

description:
Library name: Sample18
Column name in mRNA.count_data.txt: T2_N5

value: Surface epithelial cells


title: ID8 cells, T2_N1, Day7

description:
Library name: Sample15
Column name in mRNA.count_data.txt: T2_N1


title: BBM7_anti-H3K36-Me3

value: anti-H3K36-Me3 (DIAGENODE C15410192)


title: BC4

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
The UMI count matrix was used for downstream analysis with Seurat v3.1.5 R package and popsicleR v0.2.1 R package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix file

source_name: breast cancer

extract_protocol:
After surgery, human samples were preserved in RPMI supplemented with antibiotics. Tissues were trimmed into smaller pieces (3-5mm of size) and digested in a gentleMACS C tube with 5ml of RPMI supplemented with antibiotics and enzymes A, H and R from Tumor Dissociation kit (Miltenyi). h_tumor_01 and 37C_NTDK_1 digestion programs from gentleMACS Octo Dissociator were used for primary BCs and brain metastases, respectively. Cell suspensions were filtered with a 100 µm cell strainer to remove undigested material and then pelleted at 300g for 10 min. When necessary, cells were incubated with BD Pharm Lyse Lysing Buffer (BD Biosciences) for 3 minutes on ice to lysate red blood cells. After dissociation, cells were counted and viability assessed by Trypan Blue exclusion. Only suspensions being at least 70% viable cells were used for this study.
Single-cell collection was performed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chip G in a Chromium Controller (10X Genomics) targeting 10,000 cells, following manufacturer’s instructions. Sequencing of single-indexed libraries was performed on Illumina HiSeq or NovaSeq platforms (2x150bp; 40 to 50 thousand reads per cell).

value: breast cancer

tag: type

value: primary tumor


title: ID8 cells, T2_N3, Day7

description:
Library name: Sample16
Column name in mRNA.count_data.txt: T2_N3


title: m_astrocyte, Control, 1 [ATAC-seq]

value: Control


title: BBM7_anti-H3K27-Me3

value: anti-H3K27-Me3 (Millipore 07449)


title: m_astrocyte, H202_D3, 1


title: ID8 cells, T1_AW6, Day1

description:
Library name: Sample14
Column name in mRNA.count_data.txt: T1_AW6

value: Anaesthesia + Wounding

value: Day 1


title: m_astrocyte, H202_D3, 2

value: Primary cortical astrocyte


title: MDA-MB-231 ETV KO 3D rep1


title: BC16

description: 10x Genomics


title: m_astrocyte, Control, 2 [ATAC-seq]


title: MCF7 MALAT1 ASO normoxia rep2

description:
Library name: Sample_6
MALAT1kd_Nor_rep2

value: MALAT1 ASO

value: Normoxia


title: BC3

description: 10x Genomics


title: BBM7_anti-H3K27-Ac

value: anti-H3K27-Ac (abcam 4729)


title: MDA-MB-231 CTRL 3D rep2

value: Nucleofected with Cas9 and Control sgRNA sequences, 3D Collagen I cultures


title: MDA-MB-231 CTRL 3D rep1


title: ID8 cells, T1_AW5, Day1

description:
Library name: Sample13
Column name in mRNA.count_data.txt: T1_AW5

value: Ovary Epithelium


title: m_astrocyte, H202_D1, 3


title: m_astrocyte, H202_D1, 2


title: ID8 cells, T1_AW3, Day1

description:
Library name: Sample12
Column name in mRNA.count_data.txt: T1_AW3

value: WT


title: ID8 cells, T1_AW1, Day1

description:
Library name: Sample11
Column name in mRNA.count_data.txt: T1_AW1


title: ID8 cells, T1_A3, Day1

description:
Library name: Sample10
Column name in mRNA.count_data.txt: T1_A3

value: Anaesthesia


title: BBM13

description: 10x Genomics

value: brain metastasis


title: m_astrocyte, H202_D1, 1


title: MDA-MB-231 ETV KO 2D rep2

value: Breast cancer cells

value: Knockout of ETV1, ETV4 and ETV5 by nucleofected with Cas9 and gene-specific sgRNA sequences, 2D cultures in plastics


title: MDA-MB-231 CTRL 2D rep2

value: Nucleofected with Control sgRNA sequences, 2D cultures in plastics


title: BBM9

description: 10x Genomics

value: breast cancer


title: MDA-MB-231 CTRL 2D rep1


title: BBM10

description: 10x Genomics


title: BBM8

description: 10x Genomics


title: m_astrocyte, Control, 1

value: Control


title: m_astrocyte, Control, 2


title: Jurkat, BCL11BdTAG, dTAGV-1, rep2, RNA

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Library name: BRUseq_Jurkat_BCL11BdTAG_dTAGV-1_rep2

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: BRU-Seq

molecule: nuclear RNA

source_name: Jurkat

growth_protocol: CD34+ HSPCs were expanded in Stemspan media supplemented with 1X penicillin-streptomycin-glutamine, 100ng/mL SCF, TPO, IL-6 and FLT3-L, and 1 µM stemregenin-1. Jurkat cells were cultured in RPMI-1640 supplemented with 1X penicillin-streptomycin-glutamine and 10% FBS.

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

treatment_protocol: Cells were treated with 500nM dTAGV-1 or an equivalent volume of DMSO(1ul/mL media) for 6 hours and then immediately harvested for downstream processing.

value: Jurkat

value: T cell acute lymphoblastic leukemia

tag: genetic modifiction

value: BCL11B-dTAG (CRISPR knockin)


title: ID8 cells, T1_N4, Day1

description:
Library name: Sample7
Column name in mRNA.count_data.txt: T1_N4

value: Surface epithelial cells

value: No Treatment

value: Day 1


title: BBM7

description: 10x Genomics


title: ID8 cells, T1_N5, Day1

description:
Library name: Sample8
Column name in mRNA.count_data.txt: T1_N5


title: Visium_P12_Brain_WT

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

data_processing:
Generated libraries were sequenced on Illumina NovaSeq 6000
Sequenced reads were de-multiplexed and mapped to the mouse genome (mm10-3.0.0) SpaceRanger (v3.1.0, 10x Genomics)
Outputs SpaceRanger were analyzed using Seurat
Assembly: mm10
Supplementary files format and content: tsv files contain cell barcodes or gene names for the corresponding mtx file
Supplementary files format and content: mtx files are gene by cell count matrices
Supplementary files format and content: tif files are images of brain slices for Visium
Supplementary files format and content: rds files are analyzed seurat objects
Library strategy: Visium Spatial

source_name: Brain

extract_protocol:
Brains were simultaneously frozen and embedded in OCT for cryo-sectioning at 10uM thickness
Visium libraries were prepared with the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Rea-gent Kits according to the manufacturer’s protocol with recommended reagents (10X Genomics, 1000193 and 1000187).

value: Brain

tag: genetic modification


title: ID8 cells, T1_N2, Day1

description:
Library name: Sample6
Column name in mRNA.count_data.txt: T1_N2


title: Jurkat, BCL11BdTAG, dTAGV-1, rep1, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_dTAGV-1_rep1


title: Jurkat, BCL11BdTAG, DMSO, rep2, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_DMSO_rep2

value: DMSO


title: m_astrocyte, Control, 3

value: Primary cortical astrocyte


title: hMG3

description: 10x Genomics

source_name: mammary gland

extract_protocol:
After surgery, human samples were preserved in RPMI supplemented with antibiotics. Tissues were minced into small pieces, discarding necrotic areas; the tissue was then incubated in haemolytic solution for 2 min at 4°C to remove red blood cells. After washing, tissue was digested in a solution containing Collagenase I, Hyaluronidase and DNAse for 30 min for tumor tissues and overnight for mammary gland tissues. After washing, digested tissue was further incubated in haemolytic solution for 5 min at 4°C to complete red blood cell lysis. Dissociation of tumor clumps to single cells was performed with Tryple at 37°C, whereas dissociation of clumps of MG cells was performed using 0.25%Tripsin/EDTA in HBSS for 5 min, followed with addition of 10 U/ml dispase/1 mg/ml DNAse. Digestion was stop when, by visual inspection, most cells appeared as single cells. Cells were washed and then filtered through a 40µm cell strainer. After dissociation, cells were counted and viability assessed by Trypan Blue exclusion. Only suspensions being at least 70% viable cells were used for this study.
Single-cell collection was performed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chip G in a Chromium Controller (10X Genomics) targeting 10,000 cells, following manufacturer’s instructions. Sequencing of single-indexed libraries was performed on Illumina HiSeq or NovaSeq platforms (2x150bp; 40 to 50 thousand reads per cell).

value: mammary gland

value: normal


title: ID8 cells, Base5, Day0

description:
Library name: Sample4
Column name in mRNA.count_data.txt: Base5

value: Ovary Epithelium

value: WT

value: Day 0


title: ID8 cells, Base9, Day0

description:
Library name: Sample5
Column name in mRNA.count_data.txt: Base9


title: scRNAseq_P12_Brain_Alk5iEKO_KL

description: CD31/CD140b sorted

data_processing:
Generated libraries were sequenced on Illumina NovaSeq 6000
Sequenced reads were de-multiplexed and mapped to the mouse genome (mm10-3.0.0) using CellRanger (v3.1.0, 10x Genomics)
Outputs from CellRanger were analyzed using Seurat
Assembly: mm10
Supplementary files format and content: tsv files contain cell barcodes or gene names for the corresponding mtx file
Supplementary files format and content: mtx files are gene by cell count matrices
Supplementary files format and content: rds files are analyzed seurat objects

extract_protocol:
Brains were enzymatically digested using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628) for 30 min at 37°C
scRNAseq libraries were prepared using the Chromium Single Cell Reagent Kits v3.1

value: Mix background, #028701, Jackson Laboratory


title: Visium_P6_Brain_WT


title: Jurkat, BCL11BdTAG, DMSO, rep1, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_DMSO_rep1


title: ID8 cells, Base3, Day0

description:
Library name: Sample3
Column name in mRNA.count_data.txt: Base3


title: hMG1

description: 10x Genomics


title: ID8 cells, T1_A2, Day1

description:
Library name: Sample9
Column name in mRNA.count_data.txt: T1_A2

value: Anaesthesia


title: MDA-MB-231 ETV KO 2D rep1

value: Breast cancer cells

value: Knockout of ETV1, ETV4 and ETV5 by nucleofected with Cas9 and gene-specific sgRNA sequences, 2D cultures in plastics


title: ID8 cells, Base10, Day0

description:
Library name: Sample2
Column name in mRNA.count_data.txt: Base10


title: BSM1

description: 10x Genomics

value: breast cancer

value: skin metastasis


title: scRNAseq_P12_Brain_Alk5iEKO_EF

description: CD31/CD140b sorted


title: hMG2

description: 10x Genomics


title: SUM159_CCR5+

city: los angeles

first: XUELIAN

last: CHEN

state: CA

address: 1450 BIGGY ST, NRT 3509

institute: UNIVERSITY OF SOUTHERN CALIFORNIA

description:
Library name: SUM159_CCR5+
Bulk sequencing

data_processing:
Partek Flow version 4
Sequencing was used the STAR which optimized for mapping transcriptomic data to a reference genome
Assembly: hg38
Supplementary files format and content: Normalized_counts

source_name: brest

extract_protocol:
TRIzol RNA extration
Illumina Stranded mRNA Prep kit

value: brest

value: breast stem cell

value: FACS sorting

tag: batch


title: BBM5

description: 10x Genomics

value: brain metastasis


title: SUM159-CCR5-

description:
Library name: SUM159-CCR5-
Bulk sequencing


title: ID8 cells, Base1, Day0

description:
Library name: Sample1
Column name in mRNA.count_data.txt: Base1

value: Surface epithelial cells

value: No Treatment


title: E21DCD36B0 (Nacc)

status: Public on Mar 26 2026

city: La Jolla

first: Daniel

last: Munro

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description:
Library name: E21DCD36B0
Original label before genotype mismatch fix: unknown-NAcc3-8

data_processing:
Expression levels were quantified directly from FASTQ files using kallisto v0.48. Transcript sequences from GRCr8 RefSeq were used as reference. Isoform-level counts were summed per gene to get gene expression counts.
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

organism: Rattus norvegicus

source_name: Nucleus accumbens core

growth_protocol: Outbred laboratory rats

extract_protocol:
Unknown
Unknown

value: Nucleus accumbens core


title: scRNAseq_P12_Brain_WT_AB

description: CD31/CD140b sorted

value: Brain

value: Tgfβr1 I/I


title: scRNAseq_P12_Brain_WT_IJ

description: CD31/CD140b sorted


title: unknown-NAcc3-7 (Nacc)

description:
Library name: unknown-NAcc3-7
removed_no_matching_genotype_sample


title: unknown-NAcc3-9 (Nacc)

description:
Library name: unknown-NAcc3-9
removed_no_matching_genotype_sample


title: unknown-NAcc3-6 (Nacc)

description:
Library name: unknown-NAcc3-6
removed_no_matching_genotype_sample


title: E21DCD363A (Nacc)

description:
Library name: E21DCD363A
Original label before genotype mismatch fix: unknown-NAcc3-44


title: E21DCD377D (Nacc)

description:
Library name: E21DCD377D
Original label before genotype mismatch fix: unknown-NAcc3-40


title: E21DCD37A1 (Nacc)

description:
Library name: E21DCD37A1
Original label before genotype mismatch fix: unknown-NAcc3-45


title: E21DCD37D8 (Nacc)

description:
Library name: E21DCD37D8
Original label before genotype mismatch fix: unknown-NAcc3-43


title: E21DCD3610 (Nacc)

description:
Library name: E21DCD3610
Original label before genotype mismatch fix: unknown-NAcc3-37


title: unknown-NAcc3-36 (Nacc)

description:
Library name: unknown-NAcc3-36
removed_no_matching_genotype_sample


title: E21DCD37BB (Nacc)

description:
Library name: E21DCD37BB
Original label before genotype mismatch fix: unknown-NAcc3-41


title: E21DCD3780 (Nacc)

description:
Library name: E21DCD3780
Original label before genotype mismatch fix: unknown-NAcc3-39


title: E21DCD37E1 (Nacc)

description:
Library name: E21DCD37E1
Original label before genotype mismatch fix: unknown-NAcc3-42


title: unknown-NAcc3-35 (Nacc)

description:
Library name: unknown-NAcc3-35
removed_no_matching_genotype_sample


title: E21DCD37CD (Nacc)

description:
Library name: E21DCD37CD
Original label before genotype mismatch fix: unknown-NAcc3-38


title: BBM0

description: 10x Genomics


title: unknown-NAcc3-34 (Nacc)

description:
Library name: unknown-NAcc3-34
removed_no_matching_genotype_sample


title: unknown-NAcc3-33 (Nacc)

description:
Library name: unknown-NAcc3-33
removed_no_matching_genotype_sample


title: unknown-NAcc3-29 (Nacc)

description:
Library name: unknown-NAcc3-29
removed_no_matching_genotype_sample


title: unknown-NAcc3-28 (Nacc)

description:
Library name: unknown-NAcc3-28
removed_no_matching_genotype_sample


title: unknown-NAcc3-32 (Nacc)

description:
Library name: unknown-NAcc3-32
removed_no_matching_genotype_sample


title: unknown-NAcc3-31 (Nacc)

description:
Library name: unknown-NAcc3-31
removed_no_matching_genotype_sample


title: unknown-NAcc3-30 (Nacc)

description:
Library name: unknown-NAcc3-30
removed_no_matching_genotype_sample


title: unknown-NAcc3-5 (Nacc)

description:
Library name: unknown-NAcc3-5
removed_no_matching_genotype_sample


title: E21DCD3708 (Nacc)

description:
Library name: E21DCD3708
Original label before genotype mismatch fix: unknown-NAcc3-3


title: unknown-NAcc3-4 (Nacc)

description:
Library name: unknown-NAcc3-4
removed_no_matching_genotype_sample


title: 77493_3 (Nacc)

description:
Library name: 77493_3
Original label before genotype mismatch fix: unknown-NAcc3-27


title: unknown-NAcc3-25 (Nacc)

description:
Library name: unknown-NAcc3-25
removed_no_matching_genotype_sample


title: unknown-NAcc3-22 (Nacc)

description:
Library name: unknown-NAcc3-22
removed_no_matching_genotype_sample


title: unknown-NAcc3-15 (Nacc)

description:
Library name: unknown-NAcc3-15
removed_no_matching_genotype_sample


title: E21DCD36AE (Nacc)

description:
Library name: E21DCD36AE
Original label before genotype mismatch fix: unknown-NAcc3-2


title: unknown-NAcc3-19 (Nacc)

description:
Library name: unknown-NAcc3-19
removed_no_matching_genotype_sample


title: unknown-NAcc3-23 (Nacc)

description:
Library name: unknown-NAcc3-23
removed_no_matching_genotype_sample


title: unknown-NAcc3-21 (Nacc)

description:
Library name: unknown-NAcc3-21
removed_no_matching_genotype_sample


title: unknown-NAcc3-20 (Nacc)

description:
Library name: unknown-NAcc3-20
removed_no_matching_genotype_sample


title: unknown-NAcc3-24 (Nacc)

description:
Library name: unknown-NAcc3-24
removed_no_matching_genotype_sample


title: unknown-NAcc3-26 (Nacc)

description:
Library name: unknown-NAcc3-26
removed_no_matching_genotype_sample


title: unknown-NAcc3-18 (Nacc)

description:
Library name: unknown-NAcc3-18
removed_no_matching_genotype_sample


title: unknown-NAcc3-14 (Nacc)

description:
Library name: unknown-NAcc3-14
removed_no_matching_genotype_sample


title: unknown-NAcc3-17 (Nacc)

description:
Library name: unknown-NAcc3-17
removed_no_matching_genotype_sample


title: unknown-NAcc3-13 (Nacc)

description:
Library name: unknown-NAcc3-13
removed_no_matching_genotype_sample


title: unknown-NAcc3-16 (Nacc)

description:
Library name: unknown-NAcc3-16
removed_no_matching_genotype_sample


title: Yeast, Control plasmid, biol rep 3

city: San Diego

first: Helge

last: Zieler

address: 10790 Roselle St

institute: Primrose Bio

description: Library name: RESUB-C02-PP2061

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based deduplication was performed using fastp v.0.23.1 simultaneously.
Trimmed and deduplicated reads were then mapped to the S. cerevisiae S288C reference genome (GCF_000146045.2_R64, downloaded from ncbi.nlm.nih.gov) using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GCF_000146045.2_R64
Supplementary files format and content: tab-delimited text file output from featureCounts, which includes raw counts for the specified sample

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: BY4742 transformants were grown in SDCGal-Ura to mid-logarithmic phases of growth, cells harvested and pelleted, then frozen at -80°C until RNA extraction.

extract_protocol:
Qiagen RNeasy Mini Kit
New England Biolabs NEBNext Ultra™ II RNA Library Prep Kit for Illumina with the Twist Bioscience UMI Adapter System

value: whole organism

tag: strain

value: Control plasmid


title: unknown-NAcc3-10 (Nacc)

description:
Library name: unknown-NAcc3-10
removed_no_matching_genotype_sample


title: E21DCD37F1 (Nacc)

description: Library name: E21DCD37F1


title: unknown-NAcc3-12 (Nacc)

description:
Library name: unknown-NAcc3-12
removed_no_matching_genotype_sample


title: unknown-NAcc3-1 (Nacc)

description:
Library name: unknown-NAcc3-1
removed_no_matching_genotype_sample


title: Yeast, Control plasmid, biol rep 2

description: Library name: E4-p416-GAL1


title: Yeast, M492-E01 fusion gene, biol rep 1

description: Library name: D1-M585-B08

value: M492-E01 fusion gene


title: Yeast, Control plasmid, biol rep 1

description: Library name: E3-p416-GAL1


title: E21DCD37ED (Nacc)

description: Library name: E21DCD37ED


title: Yeast, M492-E01 fusion gene, biol rep 2

description: Library name: D2-M585-B08


title: E21DCD37DE (Nacc)

description: Library name: E21DCD37DE


title: unknown-NAcc3-11 (Nacc)

description:
Library name: unknown-NAcc3-11
removed_no_matching_genotype_sample


title: Yeast, M492-E01 fusion gene, biol rep 3

description: Library name: RESUB-B07-M492-E01


title: E21DCD37DA (Nacc)

description: Library name: E21DCD37DA


title: E21DCD37E3 (Nacc)

description: Library name: E21DCD37E3


title: Yeast, M497-F10 fusion gene, biol rep 2

description: Library name: E2-M497-F10

value: M497-F10 fusion gene


title: Yeast, M495-F02 fusion gene, biol rep 1

description: Library name: D11-M495-F02

value: M495-F02 fusion gene


title: E21DCD37E6 (Nacc)

description: Library name: E21DCD37E6


title: Yeast, M495-F02 fusion gene, biol rep 3

description: Library name: RESUB-B12-M495-F02


title: E21DCD37D4 (Nacc)

description: Library name: E21DCD37D4


title: Yeast, M497-F10 fusion gene, biol rep 3

description: Library name: RESUB-C01-M497-F10


title: Yeast, M497-F10 fusion gene, biol rep 1

description: Library name: E1-M497-F10


title: E21DCD37BF (Nacc)

description: Library name: E21DCD37BF


title: Yeast, M495-D09 fusion gene, biol rep 3

description: Library name: RESUB-B11-M495-D09

value: M495-D09 fusion gene


title: E21DCD37BE (Nacc)

description: Library name: E21DCD37BE


title: Yeast, M495-F02 fusion gene, biol rep 2

description: Library name: D12-M495-F02


title: E21DCD37B9 (Nacc)

description: Library name: E21DCD37B9


title: E21DCD37BD (Nacc)

description: Library name: E21DCD37BD


title: Yeast, M495-D09 fusion gene, biol rep 1

description: Library name: D10-M495-D09


title: Yeast, M495-C02 fusion gene, biol rep 2

description: Library name: D8-M495-C02

value: M495-C02 fusion gene


title: Yeast, M495-C02 fusion gene, biol rep 3

description: Library name: RESUB-B10-M495-C02


title: E21DCD37B2 (Nacc)

description: Library name: E21DCD37B2


title: E21DCD37CF (Nacc)

description: Library name: E21DCD37CF


title: E21DCD3791 (Nacc)

description: Library name: E21DCD3791


title: Yeast, M495-C02 fusion gene, biol rep 1

description: Library name: D7-M495-C02


title: E21DCD3790 (Nacc)

description: Library name: E21DCD3790


title: Yeast, M495-D09 fusion gene, biol rep 2

description: Library name: D9-M495-D09


title: E21DCD37B0 (Nacc)

description: Library name: E21DCD37B0


title: E21DCD37A6 (Nacc)

description: Library name: E21DCD37A6


title: E21DCD3788 (Nacc)

description: Library name: E21DCD3788


title: Yeast, M493-C02 fusion gene, biol rep 2

description: Library name: D6-M493-C02

value: M493-C02 fusion gene


title: Yeast, M493-C02 fusion gene, biol rep 1

description: Library name: D5-M493-C02


title: E21DCD3766 (Nacc)

description: Library name: E21DCD3766


title: Yeast, M492-E11 fusion gene, biol rep 2

description: Library name: D4-M492-E11

value: M492-E11 fusion gene


title: E21DCD377B (Nacc)

description: Library name: E21DCD377B


title: Yeast, M492-D07 fusion gene, biol rep 3

description: Library name: RESUB-B06-M492-D07

value: M492-D07 fusion gene


title: Yeast, M492-E11 fusion gene, biol rep 1

description: Library name: D3-M492-E11


title: E21DCD3757 (Nacc)

description: Library name: E21DCD3757


title: Yeast, M492-E11 fusion gene, biol rep 3

description: Library name: RESUB-B08-M492-E11


title: E21DCD375C (Nacc)

description: Library name: E21DCD375C


title: E21DCD376B (Nacc)

description: Library name: E21DCD376B


title: Yeast, M492-D07 fusion gene, biol rep 1

description: Library name: C11-M492-D07


title: Yeast, M492-D07 fusion gene, biol rep 2

description: Library name: C12-M492-D07


title: Yeast, M493-C02 fusion gene, biol rep 3

description: Library name: RESUB-B09-M493-C02


title: Yeast, M492-C11 fusion gene, biol rep 2

description: Library name: C9-M492-C11

value: M492-C11 fusion gene


title: E21DCD375A (Nacc)

description: Library name: E21DCD375A


title: E21DCD3745 (Nacc)

description: Library name: E21DCD3745


title: E21DCD3754 (Nacc)

description: Library name: E21DCD3754


title: E21DCD3781 (Nacc)

description: Library name: E21DCD3781


title: E21DCD3739 (Nacc)

description: Library name: E21DCD3739


title: Yeast, M492-C04 fusion gene, biol rep 2

description: Library name: C8-M492-C04

value: M492-C04 fusion gene


title: E21DCD3753 (Nacc)

description: Library name: E21DCD3753


title: Yeast, M492-C04 fusion gene, biol rep 3

description: Library name: RESUB-B04-M492-C04


title: Yeast, M492-C11 fusion gene, biol rep 1

description: Library name: C10-M492-C11


title: Yeast, M492-C04 fusion gene, biol rep 1

description: Library name: C7-M492-C04


title: E21DCD375F (Nacc)

description: Library name: E21DCD375F


title: E21DCD3737 (Nacc)

description: Library name: E21DCD3737


title: Yeast, M491-F10 fusion gene, biol rep 2

description: Library name: C6-M491-F10

value: M491-F10 fusion gene


title: E21DCD3735 (Nacc)

description: Library name: E21DCD3735


title: Yeast, M492-C11 fusion gene, biol rep 3

description: Library name: RESUB-B05-M492-C11


title: Yeast, M491-F10 fusion gene, biol rep 3

description: Library name: RESUB-B03-M491-F10


title: E21DCD372A (Nacc)

description: Library name: E21DCD372A


title: E21DCD3728 (Nacc)

description: Library name: E21DCD3728


title: Yeast, M491-F10 fusion gene, biol rep 1

description: Library name: C5-M491-F10


title: Yeast, M491-F02 fusion gene, biol rep 3

description: Library name: RESUB-B02-M491-F02

value: M491-F02 fusion gene


title: E21DCD3725 (Nacc)

description: Library name: E21DCD3725

value: Nucleus accumbens core


title: E21DCD371E (Nacc)

description: Library name: E21DCD371E


title: Yeast, M491-F02 fusion gene, biol rep 1

description: Library name: C3-M491-F02


title: Yeast, M491-E09 fusion gene, biol rep 3

description: Library name: RESUB-B01-M491-E09

value: M491-E09 fusion gene


title: E21DCD3713 (Nacc)

description: Library name: E21DCD3713


title: Yeast, M491-E09 fusion gene, biol rep 1

description: Library name: C1-M491-E09


title: Yeast, M491-E04 fusion gene, biol rep 3

description: Library name: RESUB-A12-M491-E04

value: M491-E04 fusion gene


title: E21DCD3706 (Nacc)

description: Library name: E21DCD3706


title: E21DCD370D (Nacc)

description: Library name: E21DCD370D


title: E21DCD3703 (Nacc)

description: Library name: E21DCD3703


title: Yeast, M491-E04 fusion gene, biol rep 2

description: Library name: B12-M491-E04

value: whole organism


title: Yeast, M491-F02 fusion gene, biol rep 2

description: Library name: C4-M491-F02


title: Yeast, M491-D09 fusion gene, biol rep 2

description: Library name: B9-M491-D09

value: M491-D09 fusion gene


title: Yeast, M491-E04 fusion gene, biol rep 1

description: Library name: B11-M491-E04


title: Yeast, M491-D07 fusion gene, biol rep 3

description: Library name: RESUB-A10-M491-D07

value: M491-D07 fusion gene


title: Yeast, M491-D09 fusion gene, biol rep 3

description: Library name: RESUB-A11-M491-D09


title: E21DCD36DF (Nacc)

description: Library name: E21DCD36DF


title: Yeast, M491-D09 fusion gene, biol rep 1

description: Library name: B10-M491-D09


title: E21DCD36DB (Nacc)

description: Library name: E21DCD36DB


title: E21DCD370F (Nacc)

description: Library name: E21DCD370F


title: Yeast, M491-E09 fusion gene, biol rep 2

description: Library name: C2-M491-E09


title: E21DCD36D7 (Nacc)

description: Library name: E21DCD36D7


title: E21DCD36E0 (Nacc)

description: Library name: E21DCD36E0


title: E21DCD36EF (Nacc)

description: Library name: E21DCD36EF


title: E21DCD36E6 (Nacc)

description: Library name: E21DCD36E6


title: Yeast, M491-D01 fusion gene, biol rep 3

description: Library name: RESUB-A09-M491-D01

value: M491-D01 fusion gene


title: E21DCD3704 (Nacc)

description: Library name: E21DCD3704


title: Yeast, M491-D07 fusion gene, biol rep 2

description: Library name: B8-M491-D07


title: Yeast, M491-D07 fusion gene, biol rep 1

description: Library name: B7-M491-D07


title: E21DCD36BA (Nacc)

description: Library name: E21DCD36BA


title: Yeast, M491-D01 fusion gene, biol rep 2

description: Library name: B6-M491-D01


title: Yeast, M491-C12 fusion gene, biol rep 3

description: Library name: RESUB-A08-M491-C12

value: M491-C12 fusion gene


title: E21DCD368C (Nacc)

description: Library name: E21DCD368C


title: E21DCD36AD (Nacc)

description: Library name: E21DCD36AD


title: Yeast, M491-D01 fusion gene, biol rep 1

description: Library name: B5-M491-D01


title: E21DCD3694 (Nacc)

description: Library name: E21DCD3694


title: Yeast, M491-C09 fusion gene, biol rep 2

description: Library name: B2-M491-C09

value: M491-C09 fusion gene


title: E21DCD3681 (Nacc)

description: Library name: E21DCD3681


title: E21DCD367A (Nacc)

description: Library name: E21DCD367A


title: Yeast, M491-C12 fusion gene, biol rep 1

description: Library name: B3-M491-C12


title: Yeast, M491-C09 fusion gene, biol rep 3

description: Library name: RESUB-A07-M491-C09


title: Yeast, M491-C07 fusion gene, biol rep 3

description: Library name: RESUB-A06-M491-C07

value: M491-C07 fusion gene


title: E21DCD367E (Nacc)

description: Library name: E21DCD367E


title: E21DCD3671 (Nacc)

description: Library name: E21DCD3671


title: E21DCD366B (Nacc)

description: Library name: E21DCD366B


title: Yeast, M491-C07 fusion gene, biol rep 2

description: Library name: A12-M491-C07


title: E21DCD36D2 (Nacc)

description: Library name: E21DCD36D2


title: Yeast, M491-C09 fusion gene, biol rep 1

description: Library name: B1-M491-C09


title: E21DCD3678 (Nacc)

description: Library name: E21DCD3678


title: E21DCD3672 (Nacc)

description: Library name: E21DCD3672


title: Yeast, M491-C07 fusion gene, biol rep 1

description: Library name: A11-M491-C07


title: E21DCD3664 (Nacc)

description: Library name: E21DCD3664


title: Yeast, M491-C12 fusion gene, biol rep 2

description: Library name: B4-M491-C12


title: Yeast, M491-C06 fusion gene, biol rep 3

description: Library name: RESUB-A05-M491-C06

value: M491-C06 fusion gene


title: E21DCD365F (Nacc)

description: Library name: E21DCD365F


title: E21DCD365B (Nacc)

description: Library name: E21DCD365B


title: Yeast, M491-C06 fusion gene, biol rep 2

description: Library name: A9-M491-C06


title: E21DCD3656 (Nacc)

description: Library name: E21DCD3656


title: E21DCD3655 (Nacc)

description: Library name: E21DCD3655


title: Yeast, M491-C06 fusion gene, biol rep 1

description: Library name: A10-M491-C06


title: Yeast, M491-C04 fusion gene, biol rep 3

description: Library name: RESUB-A04-M491-C04

value: M491-C04 fusion gene


title: Yeast, M491-C04 fusion gene, biol rep 2

description: Library name: A8-M491-C04


title: E21DCD364A (Nacc)

description: Library name: E21DCD364A


title: Yeast, M491-C04 fusion gene, biol rep 1

description: Library name: A7-M491-C04


title: Yeast, M491-C03 fusion gene, biol rep 3

description: Library name: RESUB-A03-M491-C03

value: M491-C03 fusion gene


title: E21DCD3644 (Nacc)

description: Library name: E21DCD3644


title: E21DCD3640 (Nacc)

description: Library name: E21DCD3640


title: E21DCD3639 (Nacc)

description: Library name: E21DCD3639


title: Yeast, M490-F09 fusion gene, biol rep 3

description: Library name: RESUB-A02-M490-F09

value: M490-F09 fusion gene


title: Yeast, M491-C03 fusion gene, biol rep 1

description: Library name: A5-M491-C03


title: E21DCD3635 (Nacc)

description: Library name: E21DCD3635


title: E21DCD3616 (Nacc)

description: Library name: E21DCD3616


title: Yeast, M491-C03 fusion gene, biol rep 2

description: Library name: A6-M491-C03


title: Yeast, M490-A12 fusion gene, biol rep 3

description: Library name: RESUB-A01-M490-A12

value: M490-A12 fusion gene


title: E21DCD362F (Nacc)

description: Library name: E21DCD362F


title: Yeast, M490-F09 fusion gene, biol rep 2

description: Library name: A4-M490-F09


title: E21DCD3603 (Nacc)

description: Library name: E21DCD3603


title: Yeast, M490-F09 fusion gene, biol rep 1

description: Library name: A3-M490-F09


title: Yeast, M490-A12 fusion gene, biol rep 1

description: Library name: A1-M490-A12


title: E21DCD3600 (Nacc)

description: Library name: E21DCD3600


title: E21DCD360D (Nacc)

description: Library name: E21DCD360D


title: Yeast, M490-A12 fusion gene, biol rep 2

description: Library name: A2-M490-A12


title: E21DCD362D (Nacc)

description: Library name: E21DCD362D


title: CUT&Tag of CTD in OE-BRIP1 Early_S cells treated with siNEFLA rep1

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: BRIP1_siNELFA_CTD_1

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: liver

value: tumor cells

value: BRIP1_OE + siNELFA


title: CUT&Tag of CTD in OE-BRIP1 Early_S cells treated with siNEFLA rep2

description: Library name: BRIP1_siNELFA_CTD_2


title: E21DCD364D (Nacc)

description: Library name: E21DCD364D

value: Nucleus accumbens core


title: CUT&Tag of CTD in OE-BRIP1 Early_S cells rep2

description: Library name: BRIP1_CTD_2


title: AA1DCD6806 (Nacc)

description: Library name: AA1DCD6806


title: AA1DCD67CE (Nacc)

description: Library name: AA1DCD67CE


title: CUT&Tag of CTD in OE-BRIP1 Early_S cells rep1

description: Library name: BRIP1_CTD_1


title: CUT&Tag of CTD in OE-DHX36 Early_S cells treated with siNEFLA rep2

description: Library name: DHX_NELFA_CTD_2

value: DHX36_OE + siNELFA


title: 933000320187873 (Nacc)

description: Library name: 933000320187873


title: 933000320187872 (Nacc)

description: Library name: 933000320187872


title: 933000320187870 (Nacc)

description: Library name: 933000320187870


title: CUT&Tag of CTD in OE-DHX36 Early_S cells rep2

description: Library name: DHX_CTD_2


title: CUT&Tag of CTD in OE-DHX36 Early_S cells treated with siNEFLA rep1

description: Library name: DHX_NELFA_CTD_1


title: 933000320187869 (Nacc)

description:
Library name: 933000320187869
removed


title: 933000320187858 (Nacc)

description: Library name: 933000320187858


title: 933000320187471 (Nacc)

description: Library name: 933000320187471


title: CUT&Tag of CTD in Early_S cells treated with siNEFLA rep1

description: Library name: ctrl_siNELFA_CTD_1

value: siNELFA


title: CUT&Tag of CTD in Early_S cells treated with siNEFLA rep2

description: Library name: ctrl_siNELFA_CTD_2


title: 933000320049149 (Nacc)

description: Library name: 933000320049149


title: CUT&Tag of CTD in Early_S cells rep1

description: Library name: ctrl_CTD_1

value: ctrl


title: CUT&Tag of CTD in Early_S cells rep2

description: Library name: ctrl_CTD_2


title: 933000320187462 (Nacc)

description: Library name: 933000320187462


title: 933000320187463 (Nacc)

description: Library name: 933000320187463


title: 933000320049126 (Nacc)

description: Library name: 933000320049126


title: CUT&Tag of NELFE in Late_S cells rep1

description: Library name: Late_S_NELFE_1


title: 933000320049096 (Nacc)

description: Library name: 933000320049096


title: CUT&Tag of NELFE in Late_S cells rep2

description: Library name: Late_S_NELFE_2


title: CUT&Tag of NELFCD in Late_S cells rep1

description: Library name: Late_S_NELFC-D_1


title: CUT&Tag of CTD in OE-DHX36 Early_S cells rep1

description: Library name: DHX_CTD_1


title: CUT&Tag of NELFE in G1_S cells rep2

description: Library name: G1_S_NELFE_2


title: 933000320049086 (Nacc)

description: Library name: 933000320049086


title: 933000320049084 (Nacc)

description: Library name: 933000320049084


title: 933000320049093 (Nacc)

description: Library name: 933000320049093


title: 933000320049082 (Nacc)

description: Library name: 933000320049082


title: 933000320049079 (Nacc)

description: Library name: 933000320049079


title: CUT&Tag of NELFCD in G1_S cells rep2

description: Library name: G1_S_NELFC-D_2


title: CUT&Tag of NELFCD in Late_S cells rep2

description: Library name: Late_S_NELFC-D_2


title: 933000320049074 (Nacc)

description: Library name: 933000320049074


title: 933000320049075 (Nacc)

description: Library name: 933000320049075


title: 933000320049070 (Nacc)

description: Library name: 933000320049070


title: CUT&Tag of NELFCD in Early_S cells rep2

description: Library name: Early_S_NELFC-D_2


title: CUT&Tag of NELFE in Early_S cells rep2

description: Library name: Early_S_NELFE_2


title: 933000320049068 (Nacc)

description: Library name: 933000320049068


title: CUT&Tag of NELFCD in Early_S cells rep1

description: Library name: Early_S_NELFC-D_1


title: CUT&Tag of NELFE in Early_S cells rep1

description: Library name: Early_S_NELFE_1


title: CUT&Tag of NELFE in Early_S DHX36-OE cells rep2

description: Library name: DHX36_NELFE_2


title: 933000320049056 (Nacc)

description: Library name: 933000320049056


title: CUT&Tag of NELFE in Early_S DHX36-OE cells rep1

description: Library name: DHX36_NELFE_1


title: 933000320049066 (Nacc)

description: Library name: 933000320049066


title: 933000320049038 (Nacc)

description: Library name: 933000320049038


title: CUT&Tag of NELFE in Early_S BRIP1-OE cells rep1

description: Library name: BRIP1_NELFE_1


title: CUT&Tag of NELFCD in G1_S cells rep1

description: Library name: G1_S_NELFC-D_1


title: 933000320049036 (Nacc)

description: Library name: 933000320049036


title: CUT&Tag of NELFCD in Early_S BRIP1-OE cells rep2

description: Library name: BRIP1_NELFC-D_2


title: CUT&Tag of NELFCD in Early_S DHX36-OE cells rep2

description: Library name: DHX36_NELFC-D_2


title: 933000320049063 (Nacc)

description: Library name: 933000320049063


title: CUT&Tag of NELFE in G1_S cells rep1

description: Library name: G1_S_NELFE_1


title: CUT&Tag of NELFCD in Early_S BRIP1-OE cells rep1

description: Library name: BRIP1_NELFC-D_1


title: CUT&Tag of NELFE in Early_S BRIP1-OE cells rep2

description: Library name: BRIP1_NELFE_2


title: 933000320049037 (Nacc)

description: Library name: 933000320049037


title: 933000320049047 (Nacc)

description: Library name: 933000320049047


title: 933000320049067 (Nacc)

description: Library name: 933000320049067


title: CUT&Tag of NELFE in Early_S Ctrl cells rep1

description: Library name: OE_ctrl_NELFE_1


title: 933000320048896 (Nacc)

description: Library name: 933000320048896


title: CUT&Tag of NELFCD in Early_S Ctrl cells rep1

description: Library name: OE_ctrl_NELFC-D_1


title: 933000320048893 (Nacc)

description: Library name: 933000320048893


title: CUT&Tag of NELFCD in Early_S DHX36-OE cells rep1

description: Library name: DHX36_NELFC-D_1


title: 933000320048883 (Nacc)

description: Library name: 933000320048883


title: CUT&Tag of G4-DNA in Early_S cells treated with Piperlongumine rep2

description: Library name: M3_piperlongumine_BG4_2

value: piperlongumine


title: 933000320049029 (Nacc)

description: Library name: 933000320049029


title: 933000320048867 (Nacc)

description: Library name: 933000320048867


title: CUT&Tag of G4-DNA in Early_S cells rep1

description: Library name: M3_ctrl_BG4_1


title: CUT&Tag of G4-DNA in Early_S cells treated with Piperlongumine rep1

description: Library name: M3_piperlongumine_BG4_1


title: CUT&Tag of NELFCD in Early_S Ctrl cells rep2

description: Library name: OE_ctrl_NELFC-D_2


title: 933000320048860 (Nacc)

description: Library name: 933000320048860


title: 933000320048856 (Nacc)

description: Library name: 933000320048856


title: CUT&Tag of G4-DNA in Early_S cells rep2

description: Library name: M3_ctrl_BG4_2


title: 933000320048862 (Nacc)

description: Library name: 933000320048862


title: 933000320048840 (Nacc)

description: Library name: 933000320048840


title: 933000320048835 (Nacc)

description: Library name: 933000320048835


title: 933000320048826 (Nacc)

description: Library name: 933000320048826


title: CUT&Tag of NELFA in Early_S cells treated with dmso rep2

description: Library name: LLPS_ctrl_NELFA_2


title: 933000320048831 (Nacc)

description: Library name: 933000320048831


title: 933000320048876 (Nacc)

description: Library name: 933000320048876


title: CUT&Tag of NELFA in Early_S cells treated with 1_6_hexa rep2

description: Library name: 1_6_hexa_NELFA_2


title: CUT&Tag of NELFA in Early_S cells treated with 1_6_hexa rep1

description: Library name: 1_6_hexa_NELFA_1


title: CUT&Tag of NELFA in Early_S cells treated with dmso rep1

description: Library name: LLPS_ctrl_NELFA_1


title: CUT&Tag of NELFE in Early_S Ctrl cells rep2

description: Library name: OE_ctrl_NELFE_2


title: 933000320048829 (Nacc)

description: Library name: 933000320048829


title: CUT&Tag of NELFE in cells treated with piperlongumine rep2

description: Library name: piperlongumine_NELFE_2


title: 933000320048823 (Nacc)

description: Library name: 933000320048823


title: CUT&Tag of NELFE in cells treated with spermine rep1

description: Library name: spermine_NELFE_1

value: spermine


title: CUT&Tag of NELFE in cells treated with L-thyroxine rep2

description: Library name: L-thyroxine_NELFE_2

value: L-thyroxine


title: CUT&Tag of NELFE in cells treated with L-thyroxine rep1

description: Library name: L-thyroxine_NELFE_1


title: 933000320048639 (Nacc)

description: Library name: 933000320048639


title: 933000320048725 (Nacc)

description: Library name: 933000320048725


title: CUT&Tag of NELFE in cells treated with delta_tocopherol rep2

description: Library name: delta_tocopherol_NELFE_2

value: deltatocopherol


title: CUT&Tag of NELFE in cells treated with spermine rep2

description: Library name: spermine_NELFE_2


title: 933000320048635 (Nacc)

description: Library name: 933000320048635


title: CUT&Tag of NELFE in cells rep1

description: Library name: ctrl_NELFE_1


title: CUT&Tag of NELFE in cells rep2

description: Library name: ctrl_NELFE_2


title: 933000320048572 (Nacc)

description: Library name: 933000320048572


title: CUT&Tag of NELFE in cells treated with delta_tocopherol rep1

description: Library name: delta_tocopherol_NELFE_1


title: CUT&Tag of NELFCD in cells treated with spermine rep2

description: Library name: spermine_NELFCD_2


title: 933000320048575 (Nacc)

description: Library name: 933000320048575


title: 933000320048574 (Nacc)

description: Library name: 933000320048574


title: CUT&Tag of NELFE in cells treated with piperlongumine rep1

description: Library name: piperlongumine_NELFE_1


title: 933000320048573 (Nacc)

description: Library name: 933000320048573


title: 933000320048570 (Nacc)

description: Library name: 933000320048570


title: CUT&Tag of NELFCD in cells treated with spermine rep1

description: Library name: spermine_NELFCD_1


title: 933000320048571 (Nacc)

description: Library name: 933000320048571


title: CUT&Tag of NELFCD in cells treated with piperlongumine rep2

description: Library name: piperlongumine_NELFCD_2


title: CUT&Tag of NELFCD in cells treated with piperlongumine rep1

description: Library name: piperlongumine_NELFCD_1


title: 933000320048557 (Nacc)

description: Library name: 933000320048557


title: 933000320048563 (Nacc)

description: Library name: 933000320048563


title: 933000320048567 (Nacc)

description: Library name: 933000320048567


title: CUT&Tag of NELFCD in cells treated with L-thyroxine rep2

description: Library name: L-thyroxine_NELFCD_2


title: CUT&Tag of NELFCD in cells rep2

description: Library name: ctrl_NELFCD_2


title: 933000320048711 (Nacc)

description: Library name: 933000320048711


title: CUT&Tag of NELFCD in cells treated with delta_tocopherol rep2

description: Library name: delta_tocopherol_NELFCD_2


title: 933000320048565 (Nacc)

description: Library name: 933000320048565


title: CUT&Tag of NELFCD in cells treated with L-thyroxine rep1

description: Library name: L-thyroxine_NELFCD_1


title: CUT&Tag of NELFCD in cells treated with delta_tocopherol rep1

description: Library name: delta_tocopherol_NELFCD_1


title: 933000320048556 (Nacc)

description: Library name: 933000320048556


title: 933000320048559 (Nacc)

description: Library name: 933000320048559


title: CUT&Tag of NELFCD in cells rep1

description: Library name: ctrl_NELFCD_1


title: 933000320048551 (Nacc)

description: Library name: 933000320048551


title: 933000320048554 (Nacc)

description: Library name: 933000320048554


title: 933000320048512 (Nacc)

description: Library name: 933000320048512


title: 933000320048552 (Nacc)

description: Library name: 933000320048552


title: CUT&Tag of NELFB in cells treated with L-thyroxine rep2

description: Library name: L-thyroxine_NELFB_2


title: CUT&Tag of NELFB in cells treated with piperlongumine rep2

description: Library name: piperlongumine_NELFB_2


title: 933000320048422 (Nacc)

description: Library name: 933000320048422


title: 933000320048404 (Nacc)

description: Library name: 933000320048404


title: CUT&Tag of NELFB in cells treated with spermine rep2

description: Library name: spermine_NELFB_2


title: CUT&Tag of NELFB in cells treated with piperlongumine rep1

description: Library name: piperlongumine_NELFB_1


title: 933000320048555 (Nacc)

description: Library name: 933000320048555


title: CUT&Tag of NELFB in cells treated with L-thyroxine rep1

description: Library name: L-thyroxine_NELFB_1


title: 933000320048356 (Nacc)

description: Library name: 933000320048356


title: 933000320048351 (Nacc)

description: Library name: 933000320048351


title: unknown-pVTA1-7, pVTA

description:
Library name: unknown-pVTA1-7
removed_no_matching_genotype_sample

source_name: Posterior ventral tegmental area

value: Posterior ventral tegmental area


title: CUT&Tag of NELFB in cells treated with delta_tocopherol rep1

description: Library name: delta_tocopherol_NELFB_1


title: unknown-pVTA1-9, pVTA

description:
Library name: unknown-pVTA1-9
removed_no_matching_genotype_sample


title: CUT&Tag of NELFB in cells rep2

description: Library name: ctrl_NELFB_2


title: E21DCD36AE, pVTA

description:
Library name: E21DCD36AE
Original label before genotype mismatch fix: unknown-pVTA1-8


title: unknown-pVTA1-6, pVTA

description:
Library name: unknown-pVTA1-6
removed_no_matching_genotype_sample


title: CUT&Tag of NELFA in cells treated with spermine rep2

description: Library name: spermine_NELFA_2


title: CUT&Tag of NELFA in cells treated with spermine rep1

description: Library name: spermine_NELFA_1


title: CUT&Tag of NELFA in cells treated with piperlongumine rep1

description: Library name: piperlongumine_NELFA_1


title: unknown-pVTA1-5, pVTA

description:
Library name: unknown-pVTA1-5
removed_no_matching_genotype_sample


title: CUT&Tag of NELFB in cells treated with delta_tocopherol rep2

description: Library name: delta_tocopherol_NELFB_2


title: CUT&Tag of NELFA in cells treated with piperlongumine rep2

description: Library name: piperlongumine_NELFA_2


title: CUT&Tag of NELFA in cells treated with L-thyroxine rep2

description: Library name: L-thyroxine_NELFA_2


title: CUT&Tag of NELFA in cells treated with L-thyroxine rep1

description: Library name: L-thyroxine_NELFA_1


title: unknown-pVTA1-4, pVTA

description:
Library name: unknown-pVTA1-4
removed_no_matching_genotype_sample


title: E21DCD37A1, pVTA

description:
Library name: E21DCD37A1
Original label before genotype mismatch fix: unknown-pVTA1-40


title: CUT&Tag of NELFA in cells treated with delta_tocopherol rep2

description: Library name: delta_tocopherol_NELFA_2


title: CUT&Tag of NELFB in cells rep1

description: Library name: ctrl_NELFB_1


title: E21DCD37CD, pVTA

description:
Library name: E21DCD37CD
Original label before genotype mismatch fix: unknown-pVTA1-37


title: CUT&Tag of NELFA in cells rep1

description: Library name: ctrl_NELFA_1


title: CS20_E1S7, run6

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description:
Library name: V2.5R2305180074
single nucleus RNA sequencing

data_processing:
Gene count matrices were generated from FASTQ files by an in-house pipeline (BGI-Research, China).
The downstream analyses were performed using Scanpy package (V1.8.2).
Briefly, in the quality control step, cells with less than 1k genes, less than 2k counts, more than 10% mitochondrial genes, or more than 90 quantiles of total counts per library were filtered out from raw counts by scanpy.pp.filter_cells.
Genes that were captured in less than 3 cells were filtered out as well by scanpy.pp.filter_genes.
Assembly: GRCh38.p12
Supplementary files format and content: h5ad: raw counts, normalized counts and cell type annotation

source_name: embryo

extract_protocol:
Fresh frozen tissue were OCT embedded, and sagittal sections next to Stereo-seq section in five embryos (CS19E1, CS19E2, CS20E1, CS20E2 and CS23E1) were obtained for snRNA-seq.
Single-nucleus sequencing libraries were prepared with DNBelab C4 kits.

value: embryo

tag: developmental stage

tag: Sex

value: Female


title: E21DCD37BB, pVTA

description:
Library name: E21DCD37BB
Original label before genotype mismatch fix: unknown-pVTA1-42


title: E21DCD37E1, pVTA

description:
Library name: E21DCD37E1
Original label before genotype mismatch fix: unknown-pVTA1-38


title: E21DCD3610, pVTA

description:
Library name: E21DCD3610
Original label before genotype mismatch fix: unknown-pVTA1-35


title: E21DCD3780, pVTA

description:
Library name: E21DCD3780
Original label before genotype mismatch fix: unknown-pVTA1-36


title: CUT&Tag of NELFA in cells rep2

description: Library name: ctrl_NELFA_2

tag: cell line


title: CUT&Tag of NELFB in cells treated with spermine rep1

description: Library name: spermine_NELFB_1

tag: cell type


title: E21DCD363A, pVTA

description:
Library name: E21DCD363A
Original label before genotype mismatch fix: unknown-pVTA1-41


title: unknown-pVTA1-32, pVTA

description:
Library name: unknown-pVTA1-32
removed_no_matching_genotype_sample


title: unknown-pVTA1-33, pVTA

description:
Library name: unknown-pVTA1-33
removed_no_matching_genotype_sample


title: CS20_E1S7, run3

description:
Library name: V2.5R2305180071
single nucleus RNA sequencing


title: unknown-pVTA1-34, pVTA

description:
Library name: unknown-pVTA1-34
removed_no_matching_genotype_sample


title: CS20_E1S7, run1

description:
Library name: V2.5R2305180069
single nucleus RNA sequencing


title: CS20_E1S7, run2

description:
Library name: V2.5R2305180070
single nucleus RNA sequencing


title: CS20_E1S6, run6

description:
Library name: V2.5R2305180068
single nucleus RNA sequencing


title: CS20_E1S6, run5

description:
Library name: V2.5R2305180067
single nucleus RNA sequencing


title: CUT&Tag of NELFA in cells treated with delta_tocopherol rep1

description: Library name: delta_tocopherol_NELFA_1


title: CS20_E1S6, run4

description:
Library name: V2.5R2305180066
single nucleus RNA sequencing


title: E21DCD377D, pVTA

description:
Library name: E21DCD377D
Original label before genotype mismatch fix: unknown-pVTA1-39


title: unknown-pVTA1-29, pVTA

description:
Library name: unknown-pVTA1-29
removed_no_matching_genotype_sample


title: unknown-pVTA1-3, pVTA

description:
Library name: unknown-pVTA1-3
removed_no_matching_genotype_sample


title: unknown-pVTA1-31, pVTA

description:
Library name: unknown-pVTA1-31
removed_no_matching_genotype_sample


title: CS20_E1S7, run4

description:
Library name: V2.5R2305180072
single nucleus RNA sequencing


title: unknown-pVTA1-30, pVTA

description:
Library name: unknown-pVTA1-30
removed_no_matching_genotype_sample


title: CS20_E1S6, run3

description:
Library name: V2.5R2305180065
single nucleus RNA sequencing


title: CS20_E1S6, run2

description:
Library name: V2.5R2305180064
single nucleus RNA sequencing


title: unknown-pVTA1-27, pVTA

description:
Library name: unknown-pVTA1-27
removed_no_matching_genotype_sample


title: CS19_E2S3, run6

description:
Library name: V2.5R2306010031
single nucleus RNA sequencing

value: Male


title: CS20_E1S6, run1

description:
Library name: V2.5R2305180063
single nucleus RNA sequencing


title: 77493_3, pVTA

description:
Library name: 77493_3
Original label before genotype mismatch fix: unknown-pVTA1-24


title: CS19_E2S3, run5

description:
Library name: V2.5R2306010030
single nucleus RNA sequencing


title: unknown-pVTA1-28, pVTA

description:
Library name: unknown-pVTA1-28
removed_no_matching_genotype_sample


title: unknown-pVTA1-26, pVTA

description:
Library name: unknown-pVTA1-26
removed_no_matching_genotype_sample


title: unknown-pVTA1-23, pVTA

description:
Library name: unknown-pVTA1-23
removed_no_matching_genotype_sample


title: unknown-pVTA1-25, pVTA

description:
Library name: unknown-pVTA1-25
removed_no_matching_genotype_sample


title: CS19_E2S3, run4

description:
Library name: V2.5R2306010029
single nucleus RNA sequencing


title: unknown-pVTA1-22, pVTA

description:
Library name: unknown-pVTA1-22
removed_no_matching_genotype_sample


title: CS19_E2S3, run3

description:
Library name: V2.5R2306010028
single nucleus RNA sequencing


title: unknown-pVTA1-21, pVTA

description:
Library name: unknown-pVTA1-21
removed_no_matching_genotype_sample


title: CS19_E2S2, run6

description:
Library name: V2.5R2306010012
single nucleus RNA sequencing


title: CS19_E2S3, run1

description:
Library name: V2.5R2306010026
single nucleus RNA sequencing


title: E21DCD3708, pVTA

description:
Library name: E21DCD3708
Original label before genotype mismatch fix: unknown-pVTA1-2


title: CS19_E2S3, run2

description:
Library name: V2.5R2306010027
single nucleus RNA sequencing


title: unknown-pVTA1-20, pVTA

description:
Library name: unknown-pVTA1-20
removed_no_matching_genotype_sample


title: unknown-pVTA1-19, pVTA

description:
Library name: unknown-pVTA1-19
removed_no_matching_genotype_sample


title: unknown-pVTA1-17, pVTA

description:
Library name: unknown-pVTA1-17
removed_no_matching_genotype_sample


title: CS19_E2S2, run3

description:
Library name: V2.5R2306010009
single nucleus RNA sequencing


title: CS19_E2S2, run2

description:
Library name: V2.5R2306010008
single nucleus RNA sequencing


title: CS19_E2S1, run6

description:
Library name: V2.5R2306010006
single nucleus RNA sequencing


title: CS19_E2S2, run1

description:
Library name: V2.5R2306010007
single nucleus RNA sequencing


title: CS19_E2S2, run4

description:
Library name: V2.5R2306010010
single nucleus RNA sequencing


title: unknown-pVTA1-13, pVTA

description:
Library name: unknown-pVTA1-13
removed_no_matching_genotype_sample


title: CS19_E2S2, run5

description:
Library name: V2.5R2306010011
single nucleus RNA sequencing


title: CS19_E2S1, run5

description:
Library name: V2.5R2306010005
single nucleus RNA sequencing


title: unknown-pVTA1-16, pVTA

description:
Library name: unknown-pVTA1-16
removed_no_matching_genotype_sample


title: CS19_E2S1, run4

description:
Library name: V2.5R2306010004
single nucleus RNA sequencing


title: unknown-pVTA1-15, pVTA

description:
Library name: unknown-pVTA1-15
removed_no_matching_genotype_sample


title: unknown-pVTA1-12, pVTA

description:
Library name: unknown-pVTA1-12
removed_no_matching_genotype_sample


title: CS19_E2S1, run3

description:
Library name: V2.5R2306010003
single nucleus RNA sequencing


title: E21DCD36B0, pVTA

description:
Library name: E21DCD36B0
Original label before genotype mismatch fix: unknown-pVTA1-10


title: unknown-pVTA1-11, pVTA

description:
Library name: unknown-pVTA1-11
removed_no_matching_genotype_sample


title: CS19_E2S1, run1

description:
Library name: V2.5R2306010001
single nucleus RNA sequencing


title: E21DCD37F1, pVTA

description: Library name: E21DCD37F1


title: unknown-pVTA1-18, pVTA

description:
Library name: unknown-pVTA1-18
removed_no_matching_genotype_sample


title: CS23_E1S3, run9

description:
Library name: V2.5R2306010050
single nucleus RNA sequencing


title: E21DCD37ED, pVTA

description: Library name: E21DCD37ED


title: unknown-pVTA1-14, pVTA

description:
Library name: unknown-pVTA1-14
removed_no_matching_genotype_sample


title: CS23_E1S3, run10

description:
Library name: V2.5R2306010051
single nucleus RNA sequencing


title: CS23_E1S3, run8

description:
Library name: V2.5R2306010049
single nucleus RNA sequencing


title: CS23_E1S3, run7

description:
Library name: V2.5R2306010048
single nucleus RNA sequencing


title: CS19_E2S1, run2

description:
Library name: V2.5R2306010002
single nucleus RNA sequencing


title: E21DCD37E6, pVTA

description: Library name: E21DCD37E6


title: unknown-pVTA1-1, pVTA

description:
Library name: unknown-pVTA1-1
removed_no_matching_genotype_sample


title: CS23_E1S3, run5

description:
Library name: V2.5R2306010046
single nucleus RNA sequencing


title: CS23_E1S3, run6

description:
Library name: V2.5R2306010047
single nucleus RNA sequencing


title: E21DCD37DE, pVTA

description: Library name: E21DCD37DE


title: E21DCD37D4, pVTA

description: Library name: E21DCD37D4


title: E21DCD37DA, pVTA

description: Library name: E21DCD37DA


title: CS23_E1S3, run4

description:
Library name: V2.5R2306010045
single nucleus RNA sequencing


title: E21DCD37BF, pVTA

description: Library name: E21DCD37BF


title: CS23_E1S3, run3

description:
Library name: V2.5R2306010044
single nucleus RNA sequencing


title: CS23_E1S3, run2

description:
Library name: V2.5R2306010043
single nucleus RNA sequencing


title: CS23_E1S2, run9

description:
Library name: V2.5R2306010040
single nucleus RNA sequencing


title: E21DCD37B9, pVTA

description: Library name: E21DCD37B9


title: CS23_E1S2, run10

description:
Library name: V2.5R2306010041
single nucleus RNA sequencing


title: CS23_E1S3, run1

description:
Library name: V2.5R2306010042
single nucleus RNA sequencing


title: CS23_E1S2, run8

description:
Library name: V2.5R2306010039
single nucleus RNA sequencing


title: E21DCD37B2, pVTA

description: Library name: E21DCD37B2


title: CS23_E1S2, run7

description:
Library name: V2.5R2306010038
single nucleus RNA sequencing


title: E21DCD37B0, pVTA

description: Library name: E21DCD37B0


title: CS23_E1S2, run6

description:
Library name: V2.5R2306010037
single nucleus RNA sequencing


title: E21DCD37CF, pVTA

description: Library name: E21DCD37CF


title: CS23_E1S2, run5

description:
Library name: V2.5R2306010036
single nucleus RNA sequencing


title: E21DCD37E3, pVTA

description: Library name: E21DCD37E3


title: E21DCD37A6, pVTA

description: Library name: E21DCD37A6


title: CS23_E1S2, run4

description:
Library name: V2.5R2306010035
single nucleus RNA sequencing


title: E21DCD3791, pVTA

description: Library name: E21DCD3791


title: CS23_E1S2, run2

description:
Library name: V2.5R2306010033
single nucleus RNA sequencing


title: CS23_E1S2, run3

description:
Library name: V2.5R2306010034
single nucleus RNA sequencing


title: E21DCD37BD, pVTA

description: Library name: E21DCD37BD


title: E21DCD3781, pVTA

description: Library name: E21DCD3781


title: E21DCD376B, pVTA

description: Library name: E21DCD376B


title: E21DCD377B, pVTA

description: Library name: E21DCD377B


title: CS23_E1S1, run30

description:
Library name: V2.5R2306010025
single nucleus RNA sequencing


title: E21DCD37BE, pVTA

description: Library name: E21DCD37BE


title: CS23_E1S2, run1

description:
Library name: V2.5R2306010032
single nucleus RNA sequencing


title: E21DCD3788, pVTA

description: Library name: E21DCD3788


title: CS23_E1S1, run28

description:
Library name: V2.5R2306010023
single nucleus RNA sequencing


title: E21DCD3766, pVTA

description: Library name: E21DCD3766


title: CS23_E1S1, run29

description:
Library name: V2.5R2306010024
single nucleus RNA sequencing


title: E21DCD3790, pVTA

description: Library name: E21DCD3790


title: E21DCD375F, pVTA

description: Library name: E21DCD375F


title: CS23_E1S1, run26

description:
Library name: V2.5R2306010021
single nucleus RNA sequencing


title: E21DCD375A, pVTA

description: Library name: E21DCD375A


title: CS23_E1S1, run24

description:
Library name: V2.5R2306010019
single nucleus RNA sequencing


title: E21DCD3754, pVTA

description: Library name: E21DCD3754


title: E21DCD3757, pVTA

description: Library name: E21DCD3757


title: E21DCD3753, pVTA

description: Library name: E21DCD3753


title: CS23_E1S1, run23

description:
Library name: V2.5R2306010018
single nucleus RNA sequencing


title: CS23_E1S1, run27

description:
Library name: V2.5R2306010022
single nucleus RNA sequencing


title: CS23_E1S1, run25

description:
Library name: V2.5R2306010020
single nucleus RNA sequencing


title: E21DCD375C, pVTA

description: Library name: E21DCD375C


title: CS23_E1S1, run22

description:
Library name: V2.5R2306010017
single nucleus RNA sequencing


title: CS23_E1S1, run20

description:
Library name: V2.5R2305180095
single nucleus RNA sequencing


title: E21DCD3739, pVTA

description: Library name: E21DCD3739


title: CS23_E1S1, run21

description:
Library name: V2.5R2306010016
single nucleus RNA sequencing


title: E21DCD3737, pVTA

description: Library name: E21DCD3737


title: E21DCD3745, pVTA

description: Library name: E21DCD3745


title: CS23_E1S1, run19

description:
Library name: V2.5R2305180094
single nucleus RNA sequencing


title: E21DCD3735, pVTA

description: Library name: E21DCD3735