title: scRNA-seq of Homo sapiens: 397-06 d181 FNA 2

description: Library name: ELAB-WU397-006-d181_FNA_2-GEX


title: scRNA-seq of Homo sapiens: 397-06 d57 FNA 1

status: Public on Apr 18 2026

type: SRA

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

country: USA

institute: Washington University in St. Louis

description: Library name: ELAB-WU397-006-d57_FNA_1-GEX

library_source: transcriptomic single cell

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v6.0.1
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.
Supplementary files format and content: aggregation.csv.gz contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

molecule: polyA RNA

organism: Homo sapiens

source_name: lymph node

extract_protocol:
Fine-needle aspiration was performed on draining ipsilateral axillary lymph nodes. PBMCs were isolated from blood and further sorted for either plasmablasts or IgDlo B cells.
Libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' gene expression workflow.

tag: tissue

value: lymph node

tag: cell type

value: various

tag: isolate

tag: timepoint

tag: biological replicate


title: scRNA-seq of Homo sapiens: 397-06 d15 FNA 1

description: Library name: ELAB-WU397-006-d15_FNA_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d181 FNA 1

description: Library name: ELAB-WU397-006-d181_FNA_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d0 FNA 1

description: Library name: ELAB-WU397-006-d0_FNA_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d0 FNA 2

description: Library name: ELAB-WU397-006-d0_FNA_2-GEX


title: scRNA-seq of Homo sapiens: 397-06 d121 FNA 1

description: Library name: ELAB-WU397-006-d121_FNA_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d181 MBC 2

description: Library name: ELAB-WU397-006-d181_MBC_2-GEX

source_name: blood

value: blood

value: IgDlo B cell


title: scRNA-seq of Homo sapiens: 397-06 d181 MBC 1

description: Library name: ELAB-WU397-006-d181_MBC_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d8 PB 2

description: Library name: ELAB-WU397-006-d8_PB_2-GEX

value: plasmablast


title: experiment 1: RpA70-EGFP NC1-10 ChIP for H3K27me3, replicate 2

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description: Library name: rpa70_NC10_K27me3_Rep2

library_source: genomic

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates. Duplicate-filtered mapped reads with mapquality >20 were used in downstream steps. Coverage plots (bigwigs) for experiment 1 were calculated using deeptools for 100 bp bins using Counts-per-million normalized data, and scaled to chromosome M reads as an internal spike in control.
single nucleotide polymorphisms between oreR and RpA70-EGFP were identified using bcftools. Mapped reads from experiment two carrying maternal or paternal SNPs identified from whole-genome resequencing experiments were split into separate files and coverage was computed using deeptools using 25 kbp bins and are presented as counts-per-million normalized data.
Assembly: Drosophila dm6
Supplementary files format and content: bigwig files for samples (merged replicates) are provided showing counts-per-million and internal spike-in normalized average reads over 100 bp bins for experiment 1. For experiment 2, samples were split based on maternal and paternal SNP content and these were merged by biological replicate. Bigwigs are provided showing counts-per-million normalized average reads over 25 kilobase bins.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
Following ChIP fixation (15 minutes Formaldehyde + PBS-triton-X-100 + Heptane) embryos were sorted by stage using RpA70-EGFP fluorescence observed under a stereomicroscope. Interphase embryos with NC10 or earlier nuclear density were collected for the NC1-10 sample, and late NC14 embryos including those with cephalic furrows, but not ventral furrows, were collected for the NC14 sample.
ChIP was performed by initially sonicating chromatin and incubating overnight with a primary antibody. Antibody-DNA complexes were pulled down using protein G dynabeads. Before washing, antibody-DNA complexes were subjected to tagmentation with Illumina Tn5 transposase for 40 minutes at 37°C. Transposed samples were then washed in low and high salt solutions (2x 5' each) followed by one wash in TE buffer. Crosslinks were reversed for 4 hours at 65°C with moderate shaking in the presence of 5 µg/ml ProteinaseK. DNA was cleaned up using a Zymo ChIP Clean and Concentrator kit, and PCR was performed using sets of unique-dual-indexed Nextera PCR primers. Libraries were amplified within the linear range of PCR prior to Ampure clean up. Libraries were pooled as necessary and sent to Admera Health for sequencing on a NovaSeq X platform (paired-end 150 bp reads). Admera returned barcode-split, compressed fastq files for reads 1 and 2.

value: embryo

tag: genotype

value: y w; RpA70-EGFP


title: scRNA-seq of Homo sapiens: 397-06 d8 PB 1

description: Library name: ELAB-WU397-006-d8_PB_1-GEX


title: scRNA-seq of Homo sapiens: 397-06 d0 MBC 1

description: Library name: ELAB-WU397-006-d0_MBC_1-GEX


title: scRNA-seq of Homo sapiens: 397-09 d8 PB 2

description: Library name: ELAB-WU397-009-d8_PB_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d8 PB 1

description: Library name: ELAB-WU397-009-d8_PB_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d57 FNA 1

description: Library name: ELAB-WU397-009-d57_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d15 FNA 2

description: Library name: ELAB-WU397-009-d15_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d121 MBC 1

description: Library name: ELAB-WU397-009-d121_MBC_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d57 FNA 2

description: Library name: ELAB-WU397-009-d57_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d121 FNA 1

description: Library name: ELAB-WU397-009-d121_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d121 FNA 2

description: Library name: ELAB-WU397-009-d121_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d121 MBC 2

description: Library name: ELAB-WU397-009-d121_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d15 FNA 1

description: Library name: ELAB-WU397-009-d15_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d0 FNA 1

description: Library name: ELAB-WU397-009-d0_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-09 d0 MBC 2

description: Library name: ELAB-WU397-009-d0_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d8 PB 1

description: Library name: ELAB-WU397-022-d8_PB_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d57 FNA 2

description: Library name: ELAB-WU397-022-d57_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-09 d0 FNA 2

description: Library name: ELAB-WU397-009-d0_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-06 d0 MBC 2

description: Library name: ELAB-WU397-006-d0_MBC_2-GEX


title: scRNA-seq of Homo sapiens: 397-09 d0 MBC 1

description: Library name: ELAB-WU397-009-d0_MBC_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d8 PB 2

description: Library name: ELAB-WU397-022-d8_PB_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d57 FNA 1

description: Library name: ELAB-WU397-022-d57_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d181 MBC 2

description: Library name: ELAB-WU397-022-d181_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d181 FNA 2

description: Library name: ELAB-WU397-022-d181_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d181 FNA 1

description: Library name: ELAB-WU397-022-d181_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d121 FNA 2

description: Library name: ELAB-WU397-022-d121_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d15 FNA 1

description: Library name: ELAB-WU397-022-d15_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d15 FNA 2

description: Library name: ELAB-WU397-022-d15_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d121 FNA 1

description: Library name: ELAB-WU397-022-d121_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d0 MBC 1

description: Library name: ELAB-WU397-022-d0_MBC_1-lib1


title: scRNA-seq of Homo sapiens: 397-22 d0 MBC 2

description: Library name: ELAB-WU397-022-d0_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d0 FNA 2

description: Library name: ELAB-WU397-022-d0_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-22 d0 FNA 1

description: Library name: ELAB-WU397-022-d0_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d8 PB 1

description: Library name: ELAB-WU397-005-d8_PB_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d57 FNA 2

description: Library name: ELAB-WU397-005-d57_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d57 FNA 1

description: Library name: ELAB-WU397-005-d57_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d8 PB 2

description: Library name: ELAB-WU397-005-d8_PB_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d181 MBC 1

description: Library name: ELAB-WU397-005-d181_MBC_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d181 MBC 2

description: Library name: ELAB-WU397-005-d181_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d181 FNA 1

description: Library name: ELAB-WU397-005-d181_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d181 FNA 2

description: Library name: ELAB-WU397-005-d181_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d121 FNA 1

description: Library name: ELAB-WU397-005-d121_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d15 FNA 2

description: Library name: ELAB-WU397-005-d15_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d15 FNA 1

description: Library name: ELAB-WU397-005-d15_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-05 d121 FNA 2

description: Library name: ELAB-WU397-005-d121_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-05 d0 FNA 1

description: Library name: ELAB-WU397-005-d0_FNA_1-lib1


title: scRNA-seq of Homo sapiens: 397-29 d8 PB

description: Library name: WU397-029_d8_PB_GEX


title: scRNA-seq of Homo sapiens: 397-29 d8 PB 2

description: Library name: WU397-029_d8_PB_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d181 MBC 2

description: Library name: WU397-029_d181_MBC_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d181 MBC

description: Library name: WU397-029_d181_MBC_GEX


title: scRNA-seq of Homo sapiens: 397-29 d181 FNA 2

description: Library name: WU397-029_d181_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d57 FNA 2

description: Library name: WU397-029_d57_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-05 d0 MBC 2

description: Library name: ELAB-WU397-005-d0_MBC_2-lib1


title: scRNA-seq of Homo sapiens: 397-29 d181 FNA

description: Library name: WU397-029_d181_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-29 d121 FNA

description: Library name: WU397-029_d121_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-29 d0 FNA

description: Library name: WU397-029_d0_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-05 d0 MBC 1

description: Library name: ELAB-WU397-005-d0_MBC_1-lib1


title: scRNA-seq of Homo sapiens: 397-29 d15 FNA

description: Library name: WU397-029_d15_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-05 d0 FNA 2

description: Library name: ELAB-WU397-005-d0_FNA_2-lib1


title: scRNA-seq of Homo sapiens: 397-29 d57 FNA

description: Library name: WU397-029_d57_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-28 d8 PB

description: Library name: WU397-028-d8_PB_GEX


title: scRNA-seq of Homo sapiens: 397-28 d8 PB 2

description: Library name: WU397-028-d8_PB_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d121 FNA 2

description: Library name: WU397-029_d121_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d57 FNA

description: Library name: WU397-028-d57_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-29 d15 FNA 2

description: Library name: WU397-029_d15_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d181 FNA

description: Library name: WU397-028-d181_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-29 d0 MBC

description: Library name: WU397-029_d0_MBC_GEX


title: ko_mi_200_opn5_remote

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

country: China

institute: Xiamen University

description: Library name: RNA 33

library_source: transcriptomic

data_processing:
For RNA-seq, Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1) 23. Gene-level counts were obtained using featureCounts (v2.0.1); For scRNA-seq, Gene expression count matrices were produced using MobiVision v3.2 software.
Assembly: mm10
Supplementary files format and content: table-delimitted txt files containing raw counts; and Tab-separted values files and matix files

organism: Mus musculus

source_name: Heart

growth_protocol: Male mice (C57BL/6J) at 8 weeks old were used to minimize variability associated with hormonal cycles in females. Cd163-/- mice on a C57BL/6 genetic background were used alongside their wild-type littermates as experimental controls following our previous reports 17,18. Given that CD163 is highly and exclusively expressed by cells of the monocytic–macrophage lineage 19, its genetic deletion primarily disrupts macrophage function. All animals were maintained under specific pathogen-free conditions with a 12-hour light/dark cycle and ambient temperature controlled at 22–23 °C at the animal facility of Xiamen University. For tissue collection, mice were deeply anesthetized using 5% isoflurane delivered via inhalation, followed by euthanasia through exsanguination and heart excision. Hearts were perfused through the left ventricle with phosphate-buffered saline and 10% potassium chloride (KCl) before collection. All procedures were approved by the Xiamen University Animal Ethics Committee (Protocol No. XMULAC20200150) and adhered to the standards set by Directive 2010/63/EU of the European Parliament and the U.S. National Institutes of Health guidelines on animal welfare.

extract_protocol:
Left ventricular tissues were dissected from the infarct zone (anterior wall) and remote zone (posterior wall) of each heart. One sample contains 2 to 3 mice. Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol; For scRNA-seq, Whole hearts were enzymatically digested as previously described, and CD45+ immune cells were isolated by fluorescence-activated cell sorting (FACS) using a BD FACSAria III.
Approximately 30,000 sorted cells were processed for single-cell suspension preparation and library construction using a 5′ transcriptome library kit according to the manufacturer’s protocol. Polyadenylated RNA was enriched and converted into cDNA libraries using a commercial library preparation kit. Libraries were multiplexed and sequenced to produce 150-base pair paired-end reads.

treatment_protocol: MI was induced in male mice by permanent ligation of the left anterior descending (LAD) coronary artery as reports . One day prior to surgery, chest hair was removed with depilatory cream. Mice were anesthetized with 2% isoflurane and placed on a heating pad to maintain body temperature. After disinfecting the skin with povidone-iodine, a 1.2 cm left thoracic incision was made to expose the fourth intercostal space. The pleura and pericardium were opened, and the heart was gently exteriorized. The left coronary artery (LCA) was ligated approximately 3 mm from its origin using a 6-0 silk suture, and successful ligation was confirmed by pallor of the anterior left ventricular wall. The heart was then returned to the thoracic cavity, residual air was evacuated, and the chest was closed. Mice typically recovered within 3–5 minutes under observation. Sham-operated mice underwent the same procedure without LCA ligation. Recombinant osteopontin (OPN) was dissolved in sterile phosphate-buffered saline (PBS) at 5 ng/μL. A total of 200 ng OPN (40 μL) or an equal volume of PBS was injected at three sites along the infarct border zone immediately after LAD ligation using a Hamilton syringe with a 30-gauge, 4 mm needle.

value: Heart

value: remote

tag: treatment


title: scRNA-seq of Homo sapiens: 397-28 d57 FNA 2

description: Library name: WU397-028-d57_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d181 MBC 2

description: Library name: WU397-028-d181_MBC_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d181 FNA 2

description: Library name: WU397-028-d181_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d0 MBC 2

description: Library name: WU397-029_d0_MBC_2_GEX


title: scRNA-seq of Homo sapiens: 397-29 d0 FNA 2

description: Library name: WU397-029_d0_FNA_2_GEX


title: ko_mi_200_opn2_infarct

description: Library name: RNA 31

value: infarct


title: scRNA-seq of Homo sapiens: 397-28 d121 FNA 2

description: Library name: WU397-028-d121_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d15 FNA

description: Library name: WU397-028-d15_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-28 d15 FNA 2

description: Library name: WU397-028-d15_FNA_2_GEX


title: ko_mi_pbs6_remote

description: Library name: RNA 29

value: MI+PBS


title: ko_mi_pbs1_infarct

description: Library name: RNA 25


title: ko_mi_200_opn4_remote

description: Library name: RNA 32


title: scRNA-seq of Homo sapiens: 397-28 d121 FNA

description: Library name: WU397-028-d121_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-28 d0 MBC 2

description: Library name: WU397-028-d0_MBC_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d0 FNA

description: Library name: WU397-028-d0_FNA_GEX


title: ko_sham6_remote

description: Library name: RNA 24

value: Sham


title: scRNA-seq of Homo sapiens: 397-28 d0 FNA 2

description: Library name: WU397-028-d0_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-17 d181 FNA

description: Library name: WU397-017_d181_FNA_GEX


title: ko_mi_pbs2_infarct

description: Library name: RNA 26


title: ko_mi_pbs5_remote

description: Library name: RNA 28


title: ko_sham5_remote

description: Library name: RNA 23


title: scRNA-seq of Homo sapiens: 397-17 d121 FNA 2

description: Library name: WU397-017_d121_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-28 d0 MBC

description: Library name: WU397-028-d0_MBC_GEX


title: ko_sham4_remote

description: Library name: RNA 22


title: scRNA-seq of Homo sapiens: 397-17 d181 FNA 2

description: Library name: WU397-017_d181_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-17 d57 FNA 2

description: Library name: WU397-017_d57_FNA_2_GEX


title: ko_mi_pbs4_remote

description: Library name: RNA 27


title: ko_sham3_infarct

description: Library name: RNA 21


title: wt_mi_200_opn6_remote

description: Library name: RNA 18

value: WT


title: scRNA-seq of Homo sapiens: 397-17 d121 FNA

description: Library name: WU397-017_d121_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-17 d15 FNA 2

description: Library name: WU397-017_d15_FNA_2_GEX


title: ko_sham2_infarct

description: Library name: RNA 20


title: scRNA-seq of Homo sapiens: 397-17 d15 FNA

description: Library name: WU397-017_d15_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-17 d121 MBC 2

description: Library name: WU397-017_d121_MBC_2_GEX


title: wt_mi_200_opn1_infarct

description: Library name: RNA 13


title: wt_mi_200_opn5_remote

description: Library name: RNA 17


title: ko_sham1_infarct

description: Library name: RNA 19


title: wt_mi_200_opn4_remote

description: Library name: RNA 16


title: wt_mi_pbs6_remote

description: Library name: RNA 12


title: wt_mi_200_opn3_infarct

description: Library name: RNA 15


title: wt_mi_200_opn2_infarct

description: Library name: RNA 14


title: scRNA-seq of Homo sapiens: 397-17 d0 FNA 2

description: Library name: WU397-017_d0_FNA_2_GEX


title: scRNA-seq of Homo sapiens: 397-17 d0 FNA

description: Library name: WU397-017_d0_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-17 d121 MBC

description: Library name: WU397-017_d121_MBC_GEX


title: scRNA-seq of Homo sapiens: 397-17 d57 FNA

description: Library name: WU397-017_d57_FNA_GEX


title: scRNA-seq of Homo sapiens: 397-17 d8 PB 2

description: Library name: WU397-017_d8_PB_2_GEX


title: wt_mi_pbs5_remote

description: Library name: RNA 11


title: scRNA-seq of Homo sapiens: 397-17 d8 PB

description: Library name: WU397-017_d8_PB_GEX


title: wt_mi_pbs4_remote

description: Library name: RNA 10


title: wt_mi_pbs3_infarct

description: Library name: RNA 9


title: scRNA-seq of Homo sapiens: 397-17 d0 MBC 2

description: Library name: WU397-017_d0_MBC_2_GEX


title: S04, PEComa tumor sample, snRNA-seq, AdiPEC

city: Illkirch

first: Gabriel

last: Malouf

state: Grand Est

address: 1 rue Laurent Fries

country: France

institute: INSTITUT/GENETIQUE/BIOLOGIE MOLEC/CELL

description:
Library name: S04
Singleron GEXSCOPE®

data_processing:
Raw base call files were demultiplexed and converted to FASTQ files using the manufacturer’s software.
Sequencing reads were aligned to the human reference genome using a standard single-cell RNA-seq alignment pipeline.
Unique molecular identifier (UMI) counts were generated to produce a gene-by-nucleus expression matrix.
Low-quality nuclei were removed based on quality-control metrics, including low transcript counts and high mitochondrial RNA proportion.
Potential doublets and nuclei with poor-quality transcriptomes were excluded from downstream analyses.
Expression data were normalized and integrated across samples for downstream clustering and annotation.
Cell clusters were identified by unsupervised analysis and annotated using canonical marker genes.
Assembly: GRCh38 / hg38
Supplementary files format and content: HDF5 file (.h5) containing the gene-by-nucleus count matrix. Rows correspond to genes and columns correspond to nuclei. Values represent UMI-based expression counts.
Supplementary files format and content: Compressed CSV file (.csv.gz) containing nucleus-level metadata, including sample identity, quality-control metrics, cluster assignment, and cell type annotation.

molecule: total RNA

source_name: PEComa

growth_protocol: Not applicable (clinical human tumor samples; no in vitro cell culture).

extract_protocol:
Nuclei were isolated from frozen PEComa tumor tissue and used for single-nucleus RNA sequencing according to the manufacturer’s protocol.
Single-nucleus RNA-seq libraries were generated from isolated nuclei using a droplet-based single-cell gene expression workflow according to the manufacturer’s instructions. Libraries were prepared for 3′ gene expression profiling and sequenced on an Illumina platform.

treatment_protocol: Not applicable.

value: PEComa


title: wt_mi_pbs1_infarct

description: Library name: RNA 7


title: wt_mi_pbs2_infarct

description: Library name: RNA 8


title: S05, PEComa tumor sample, snRNA-seq, StemPEC

description:
Library name: S05
Singleron GEXSCOPE®


title: scRNA-seq of Homo sapiens: 397-17 d0 MBC

description: Library name: WU397-017_d0_MBC_GEX


title: S02, PEComa tumor sample, snRNA-seq, MesPEC

description:
Library name: S02
Singleron GEXSCOPE®


title: S01, PEComa tumor sample, snRNA-seq, MesPEC

description:
Library name: S01
Singleron GEXSCOPE®


title: wt_sham6_remote

description: Library name: RNA 6


title: wt_sham5_remote

description: Library name: RNA 5


title: wt_sham1_infarct

description: Library name: RNA 1


title: wt_sham2_infarct

description: Library name: RNA 2


title: S03, PEComa tumor sample, snRNA-seq, AdiPEC

description:
Library name: S03
Singleron GEXSCOPE®


title: Hypoxia-OE-1

city: Wenzhou

first: Zhaohang

last: Wu

address: Chashan

institute: Wenzhou Medical University

description: Library name: Hypoxia-OE-1

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HUVECs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HUVECs

value: primary culture cell


title: Hypoxia-OE-3

description: Library name: Hypoxia-OE-3


title: wt_sham4_remote

description: Library name: RNA 4


title: wt_sham3_infarct

description: Library name: RNA 3


title: Hypoxia-OE-2

description: Library name: Hypoxia-OE-2


title: RNA-seq_rep_sgKlf2_sgRunx3_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

first: Zifeng

last: Li

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_Runx3_rep_3
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt

data_processing:
For RNA-seq analyses, sequencing reads were aligned to the GRCm38.p6 mouse reference genome using STAR (v.2.7.10b). Gene-level read counts (raw counts) were summarized using featureCounts (v.2.0.6)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen

extract_protocol:
A total of 1 × 10⁵ donor-derived P14 cells were sorted and lysed in lysis buffer (100 mM Tris-HCl, pH 7.5; 500 mM LiCl; 10 mM EDTA, pH 8; 1.5% SDS) containing oligo-dT magnetic beads conjugated with Oligo-dT25. The mixture was incubated for five minutes to facilitate mRNA binding. Subsequently, the sample was placed on a magnetic rack to separate the beads, and the supernatant was discarded. The beads were washed twice with Wash Buffer A (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8; 0.1% SDS) and once with Wash Buffer B (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8) to remove non-specific contaminants. The supernatant was carefully removed after each wash. Elution of mRNA was achieved by adding 5 μL of Elution Buffer (10 mM Tris-HCl) and incubating the beads at 80°C for two minutes. The mixture was then subjected to magnetic separation, and the supernatant containing the extracted mRNA was collected.
The isolated RNA was reverse transcribed into cDNA using a reaction mixture containing dNTPs (Transgen, AD101), oligodT mix, Maxima H Minus Reverse Transcriptase (Thermo Fisher, EP0753), and RNase inhibitor (Thermo Fisher, EO0382). A template switch primer was added for synthesizing the second strand of cDNA, followed by 11 cycles of amplification. The DNA fragments were then fragmented, and the library was constructed according to the manufacturer’s procedure using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). The library was purified and subjected to paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq platform.

value: Spleen

value: T cell

value: Klf2 KO + Runx3 KO

value: virus infection


title: Hypoxia-3

description: Library name: Hypoxia-3

value: Hypoxia


title: RNA-seq_rep_sgKlf2_sgRunx3_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_Runx3_rep_2
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: Hypoxia-2

description: Library name: Hypoxia-2


title: RNA-seq_rep_sgRunx3_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgRunx3_rep_3
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt

value: Runx3 KO


title: RNA-seq_rep_sgRunx3_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgRunx3_rep_2
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: RNA-seq_rep_sgKlf2_sgRunx3_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_Runx3_rep_1
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: RNA-seq_rep_sgRunx3_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgRunx3_rep_1
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: skin_Placebo_T2_14

city: Ecublens

first: Davide

last: D'Amico

address: EPFL Innovation Park, Building C

country: Switzerland

institute: Amazentis SA

data_processing:
Quality Control (QC) and preprocessing of raw reads was performed by an in-house QC pipeline. The pipeline utilizes fastP version 0.23.2 [Chen, 2018], for quality control, quality trimming, and adapter clipping procedures. Reads with a minimum PHRED score of 15, a minimum length of 15 bp, and a minimum unqualified percent limit of 40 (40%) were retained for downstream analysis. QC reports were summarized by MultiQC version 1.12 [Ewels et al., 2016]. Quality-processed read pairs were mapped against the Ensembl human reference genome GRCh38.99, using a transcriptome annotation GTF file (version GRCh38.105). In particular, an in-house RNA-sequencing alignment pipeline that utilizes the STAR algorithm version 2.6.1c [Dobin et al., 2013] was applied. Read counting was performed on the gene-level, using htseq-count [Putri, 2022].
Assembly: hg38
Supplementary files format and content: Text files include raw counts for each sample

source_name: Skin

extract_protocol:
Skin tissue samples were disrupted in a TissueLyser and RNA extraction performed using an automated QiaSymphony extraction robot and the QIAsymphony RNA Kit
Strand-specific cDNA library preparation was performed by purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis (strand-specific), adapter ligation and adapter specific PCR amplification.
RNA-seq run was performed using the NovaSeq6000 using S4 flowcells with 2x150bp

value: Skin

value: Placebo

tag: time


title: Hypoxia-1

description: Library name: Hypoxia-1


title: skin_Mitopure_T2_14

value: Mitopure


title: RNA-seq_rep_sgKlf2_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_rep_1
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt

value: Klf2 KO


title: RNA-seq_rep_sgNTC_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_rep_3
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: skin_Mitopure_T1_14


title: skin_Mitopure_T2_13


title: skin_Mitopure_T2_12


title: RNA-seq_rep_sgKlf2_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_rep_3
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: skin_Placebo_T1_15


title: RNA-seq_sgKlf2_P14_Cl13_D5.5_4

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_4
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: skin_Placebo_T1_14


title: skin_Mitopure_T1_13


title: RNA-seq_rep_sgKlf2_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_rep_2
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: skin_Placebo_T1_13


title: skin_Placebo_T2_12


title: RNA-seq_rep_sgNTC_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_rep_2
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: RNA-seq_rep_sgNTC_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_rep_1
RNAseq_sgKlf2_sgRunx3_day5.5_counts.txt


title: RNA-seq_sgKlf2_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_3
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: RNA-seq_sgKlf2_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_1
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: skin_Placebo_T2_13


title: skin_Mitopure_T1_12


title: skin_Placebo_T2_11


title: RNA-seq_sgNTC_P14_Cl13_D5.5_4

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_4
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: skin_Mitopure_T2_11


title: skin_Placebo_T1_12


title: skin_Mitopure_T2_10


title: RNA-seq_sgNTC_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_1
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: skin_Mitopure_T1_11


title: RNA-seq_Texterm-es_P14_Cl13_D7.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texterm-es_2
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt

value: PD-1+Ly108-Tim-3+CX3CR1loCXCR6hi T cell


title: RNA-seq_Texterm-es_P14_Cl13_D7.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texterm-es_3
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt


title: skin_Placebo_T2_10


title: skin_Placebo_T1_11


title: RNA-seq_Texeff-es-like_P14_Cl13_D7.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texeff-like-es_2
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt

value: PD-1+Ly108-Tim-3+CX3CR1hiCXCR6lo T cell


title: RNA-seq_Texeff-es-like_P14_Cl13_D7.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texeff-like-es_3
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt


title: scRNA-seq of Homo sapiens: 397-28 d181 MBC

description: Library name: WU397-028-d181_MBC_GEX

value: blood

value: IgDlo B cell


title: skin_Placebo_T2_9


title: RNA-seq_Texterm-es_P14_Cl13_D7.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texterm-es_1
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt

value: WT


title: RNA-seq_sgNTC_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_3
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: RNA-seq_sgNTC_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgNTC_2
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt


title: RNA-seq_Texeff-es-like_P14_Cl13_D7.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Texeff-like-es_1
RNA-seq_Texeff-like_Texterm_P14_Cl13_D7.5_1_counts.txt


title: skin_Mitopure_T1_10


title: skin_Mitopure_T2_9


title: RNA-seq_pMIG-Klf2_in_vitro_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: OE_Cx3cr1_hi_3
RNAseq_pMIG-Klf2_in_vitro_counts.txt

value: Klf2 OE


title: skin_Placebo_T1_10


title: skin_Placebo_T2_8


title: RNA-seq_pMIG-Klf2_in_vitro_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: OE_Cx3cr1_hi_2
RNAseq_pMIG-Klf2_in_vitro_counts.txt


title: RNA-seq_pMIG-Klf2_in_vitro_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: OE_Cx3cr1_hi_1
RNAseq_pMIG-Klf2_in_vitro_counts.txt


title: skin_Placebo_T1_9


title: skin_Mitopure_T2_8


title: RNA-seq_pMIG_in_vitro_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Vec_total_3
RNAseq_pMIG-Klf2_in_vitro_counts.txt


title: skin_Mitopure_T1_9


title: RNA-seq_pMIG_in_vitro_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Vec_total_2
RNAseq_pMIG-Klf2_in_vitro_counts.txt


title: RNA-seq_pMIG_in_vitro_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: Vec_total_1
RNAseq_pMIG-Klf2_in_vitro_counts.txt


title: TCRb_gp33_WT3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_WT3

data_processing:
data were aligned using the RNA-seq pipeline in MIXCR v4.6.0(with parameter -Xmx16g analyze rna-seq)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes mapping result
Library strategy: TCR-Seq

extract_protocol:
A total of 1 × 10⁵ donor-derived P14 cells were sorted and lysed in lysis buffer (100 mM Tris-HCl, pH 7.5; 500 mM LiCl; 10 mM EDTA, pH 8; 1.5% SDS) containing oligo-dT magnetic beads conjugated with Oligo-dT25. The mixture was incubated for five minutes to facilitate mRNA binding. Subsequently, the sample was placed on a magnetic rack to separate the beads, and the supernatant was discarded. The beads were washed twice with Wash Buffer A (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8; 0.1% SDS) and once with Wash Buffer B (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8) to remove non-specific contaminants. The supernatant was carefully removed after each wash. Elution of mRNA was achieved by adding 5 μL of Elution Buffer (10 mM Tris-HCl) and incubating the beads at 80°C for two minutes. The mixture was then subjected to magnetic separation, and the supernatant containing the extracted mRNA was collected.
The RNA was reverse transcribed into cDNA using the Smart-Seq2 protocol,, followed by amplification for 13 cycles. A two-round nested PCR was performed with primers specific to TCRα and TCRβ.

value: Tetramer+ T cell


title: skin_Placebo_T2_7


title: skin_Placebo_T1_8


title: skin_Mitopure_T2_7


title: skin_Mitopure_T1_8


title: TCRb_gp33_WT1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_WT1

value: Spleen


title: TCRb_gp33_KO2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_KO2


title: skin_Mitopure_T1_7


title: TCRb_gp33_KO3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_KO3


title: skin_Mitopure_T2_5


title: skin_Placebo_T1_7


title: TCRb_gp33_WT2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_WT2


title: TCRb_gp33_KO1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_gp33_KO1


title: skin_Mitopure_T1_6


title: skin_Mitopure_T2_6


title: TCRb_PD1_WT2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_WT2

value: PD1+ T cell


title: skin_Placebo_T2_6


title: TCRb_PD1_WT1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_WT1


title: skin_Placebo_T2_5


title: TCRb_PD1_WT3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_WT3


title: TCRb_PD1_KO3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_KO3


title: TCRb_PD1_KO2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_KO2


title: TCRb_PD1_KO1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRb_PD1_KO1


title: skin_Mitopure_T2_4


title: TCRa_gp33_WT3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_WT3


title: ko_mi_200_opn1_infarct

description: Library name: RNA 30

value: Heart

value: infarct


title: skin_Placebo_T1_6


title: TCRa_gp33_WT2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_WT2

value: virus infection


title: skin_Placebo_T2_4


title: skin_Mitopure_T1_5


title: TCRa_PD1_WT2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_WT2


title: skin_Mitopure_T1_4


title: TCRa_gp33_KO1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_KO1


title: skin_Placebo_T1_4


title: skin_Placebo_T2_3


title: TCRa_gp33_KO2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_KO2


title: skin_Mitopure_T2_2


title: TCRa_PD1_KO2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_KO2


title: TCRa_PD1_KO1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_KO1


title: TCRa_PD1_KO3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_KO3


title: TCRa_gp33_WT1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_WT1


title: skin_Mitopure_T1_2


title: RNA-seq_sgKlf2_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description:
Library name: sgKlf2_2
RNAseq_sgKlf2_P14_Cl13_D5.5_counts.txt

value: T cell


title: skin_Mitopure_T2_1

value: Skin


title: skin_Mitopure_T2_3


title: ATAC_sgKlf2_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgKlf2_P14_Cl13_D5.5_2

data_processing:
In brief, 2×150-bp paired-end reads obtained from NovaSeq were trimmed for Nextera adaptors using cutadapt (v4.8, with parameters -m 36 -n 3 -q 10) and aligned to the mouse genome (GRCm38.p6) using Bowtie2 (v2.5.1, with parameters --very-sensitive -X 2000 --no-mixed --no-discordant)
Duplicate reads were marked using Picard (v2.9.5), and only non-duplicated, properly paired reads were retained using samtools (v1.18, with parameters --F 1804 -f 2 --q 20).
Reads were adjusted for Tn5 transposase shifts (+4 bp for the sense strand and −5 bp for the antisense strand) using deeptools, pooled by sample type, and peaks were called using MACS2 (v2.2.7.1, with parameters -q 0.05 --nolambda --keep-dup all --call-summits -f BAMPE). Peaks were finalized by retaining those with higher cut-offs (MACS2 -q 0.05)
Assembly: GRCm38.p6
Supplementary files format and content: bigWig

extract_protocol:
For ATAC-seq, 50,000 cells were pelleted at 500 g for 5 minutes and lysed on ice for 10 minutes in pre-chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20, 0.01% Digitonin and 0.1% IGEPAL CA-630). Nuclei were harvested and subjected to a transposition reaction. For RNA-seq, 50,000 donor-derived P14 cells were sorted and lysed in lysis buffer (100 mM Tris-HCl, pH 7.5; 500 mM LiCl; 10 mM EDTA, pH 8; 1.5% SDS) containing oligo-dT magnetic beads conjugated with Oligo-dT25. The mixture was incubated for five minutes to facilitate mRNA binding. Subsequently, the sample was placed on a magnetic rack to separate the beads, and the supernatant was discarded. The beads were washed twice with Wash Buffer A (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8; 0.1% SDS) and once with Wash Buffer B (10 mM Tris-HCl, pH 7.5; 0.15 M LiCl; 1 mM EDTA, pH 8) to remove non-specific contaminants. The supernatant was carefully removed after each wash. Elution of mRNA was achieved by adding 5 μL of Elution Buffer (10 mM Tris-HCl) and incubating the beads at 80°C for two minutes. The mixture was then subjected to magnetic separation, and the supernatant containing the extracted mRNA was collected.
ATAC-seq was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) with minor modifications.Nuclei were harvested to perform transposition reaction using TD501. The tagmented DNA was purified using the MinElute kit (Qiagen, 28004). Nextera indexing was performed on the tagmented DNA, which was amplified for 11 cycles as described, using a BIO-GENER GE4851T PCR machine. Amplified products were purified with VAHTS DNA Clean Beads, washed twice with 80% ethanol, and eluted in DEPC-treated Water. Libraries were sequenced on an Illumina NovaSeq platform, generating 150 bp paired-end reads.

treatment_protocol: Naïve Cas9-expressing P14 or OT-I cells were isolated from the spleen and peripheral lymph nodes (pLN) of Cas9-P14 or Cas9-OT-1 mice using a naïve CD8α+ T cell isolation kit and magnetic bead purification, following the manufacturer’s instructions (BioLegend). The purified cells were activated in vitro for 18 hours with plate-bound anti-CD3 (10 μg/ml; Bio-X-Cell) and anti-CD28 (5 μg/ml; Bio-X-Cell) antibodies. Viral transduction was performed using spin-infection at 900 g for 3 hours at 25 °C in the presence of 10 μg/ml polybrene (Sigma-Aldrich), followed by a 3-hour rest at 37°C and 5% CO₂. After washing, the cells were cultured with mouse IL-7 (2.5 ng/ml; PeproTech) and IL-15 (5 ng/ml; PeproTech) for 3 days.


title: ATAC_sgKlf2_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgKlf2_P14_Cl13_D5.5_3


title: skin_Mitopure_T1_3


title: skin_Placebo_T1_2

value: Placebo


title: skin_Mitopure_T1_1

value: Mitopure


title: JNGR180, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR180

data_processing:
Base calling and demultiplexing were performed using RTA (v2.7.7) and either bcl2fastq (v2.20.0.422) or BCL Convert (v3.8.4).
For QuantSeq libraries, UMI sequences were extracted using UMI-tools (v1.1.2), and adapter trimming and quality filtering were performed using cutadapt (v1.10). Reads shorter than 40 bp were discarded.
Reads were aligned to rRNA sequences using Bowtie2 (v2.2.8), and rRNA-mapped reads were removed.
Filtered reads were aligned to the human reference genome (GRCh38/hg38) using STAR (v2.5.3a).
PCR duplicates (for QuantSeq data) were removed using UMI-tools dedup.
Gene-level read counts were generated using htseq-count (v0.6.1p1) with Ensembl annotation (v107) in “union” mode.
Expression values were normalized TPM for downstream analyses.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file containing gene expression matrix. Rows correspond to genes and columns correspond to samples. Expression values are normalized as TPM (transcripts per million).
Supplementary files format and content: The file “TPMs_all_Samples.txt” contains TPM-normalized gene expression values for all samples across genes.

extract_protocol:
Total RNA was extracted from tissue samples using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA using either (i) the Illumina TruSeq RNA Exome kit (capture-based library preparation) or (ii) the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) following the manufacturers’ protocols. For TruSeq RNA Exome libraries, cDNA was generated by random priming, followed by adapter ligation, PCR amplification, and exome capture using sequence-specific probes. For QuantSeq libraries, first-strand synthesis was performed using oligo(dT) priming, followed by second-strand synthesis with UMI-containing primers, PCR amplification, and bead purification.

value: PEComa


title: ATAC_sgKlf2_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgKlf2_P14_Cl13_D5.5_1

value: Klf2 KO


title: JNGR157, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR157


title: ATAC_sgNTC_P14_Cl13_D5.5_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgNTC_P14_Cl13_D5.5_2


title: iALI-Control+_scRNA

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

institute: IRMB, Hôpital Saint Eloi

description: 10x Genomics

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using cellranger mkfastq v6.1.2. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
cellranger count v6.1.2 was used to align reads to the reference genome (refdata-gex-GRCh38-2020-A) and generate the raw and filtered gene-barcodes matrices.
cellranger aggr v6.1.2 was used to combine the results of the two samples.
Assembly: GRCh38
Supplementary files format and content: MEX file format: the matrix.mtx file contains the filtered gene-barcode matrix (total UMI count per cell and gene combination); the .tsv files contain all annotated genes and cell barcodes represented in the mtx file.

source_name: Lung

growth_protocol: Bronchial epithelial cells were generated from induced pluripotent stem cell as previously described (Ahmed et al 2022). Cells were maintained in air liquid interface in PneumaCult™-ALI Medium, changed dialy , and collected at day 48 of cell culture.

extract_protocol:
Trypsin was used during 15 minutes at 37°C, to dissociate iALI cells from Transwells. Dissociated cells were then filtered through a 40 μm porosity (Corning) on PneumaCult™-ALI Medium and then centrifuged (1200 rpm for 5 min). Cells were resuspended in 1,5 mL of PneumaCult™-ALI Medium and labeled with isotype-PE or CD326 antibody  during 30 min at 4°C. Cells were washed with media complemented with BSA (0,01%) and then sorted on BD FACSAria™, with MRI platform. 112 700 alive epithelial cells were collected and 10 000 cells were captured for single cell RNA sequencing.
Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.

value: Lung

value: iPS-derived airway epithelium


title: skin_Placebo_T1_1


title: JNGR150, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR150


title: skin_Placebo_T2_1


title: ATAC_sgNTC_P14_Cl13_D5.5_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgNTC_P14_Cl13_D5.5_1


title: EHP 5

city: Guangzhou

first: Cankun

last: Zheng

address: Guangzhou Avenue

institute: Nanfang Hospital

description:
Library name: sample 10
E5

data_processing:
A total amount of 3 μg total RNA per sample was used to prepare the RNA library. The RNA-seq used PE150 (paired-end 150nt) illumine sequencing. Raw data of FASTQ format were firstly processed through in-house python scripts. Clean reads for each sample were first mapped to the mouse genome with annotation GTF file (GRCm38) by the software HISAT2 with-rna-strandness RF parameter.
Reads alignment results were transferred to the program StringTie for transcript assembly. Quantification of the transcripts and genes was performed using StringTie and featureCounts software, thus Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and reads count matrix was obtained for downstream analysis.
DEseq2 was used for differential expression analysis. The adjusted P value (P.adj) was calculated using the Benjamini-Hochberg method to control the false discovery rate. Genes with | log2 (Fold Change) | ≥ 0.5 & P.adj < 0.05 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample

source_name: heart

extract_protocol:
The heart sample from mice in sedentary group and EHP group were collected at the one week after the termination of swimming. For each sample, the whole cardiac tissue was isolated and treated with RNAlater (Qiagen, CA) RNA stabilization reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: heart

value: swimming 3w + sedentary 1w


title: skin_Placebo_T1_5


title: TCRa_gp33_KO3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_gp33_KO3


title: JNGR134, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR134


title: JNGR114, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR114


title: JNGR98, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR98


title: TCRa_PD1_WT3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_WT3

value: WT


title: JNGR179, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR179


title: TCRa_PD1_WT1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: TCRa_PD1_WT1


title: ATAC_pMIG-Klf2_in_vitro_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG-Klf2_in_vitro_2

value: Klf2 OE


title: EHP 3

description:
Library name: sample 8
E3


title: ATAC_pMIG-Klf2_in_vitro_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG-Klf2_in_vitro_3

value: Spleen


title: EHP 4

description:
Library name: sample 9
E4


title: ATAC_pMIG-Klf2_in_vitro_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG-Klf2_in_vitro_1


title: JNGR178, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR178


title: EHP 2

description:
Library name: sample 7
E2


title: JNGR158, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR158


title: JNGR177, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR177


title: JNGR176, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR176


title: JNGR174, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR174


title: skin_Placebo_T1_3


title: JNGR175, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR175


title: ATAC_pMIG_in_vitro_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG_in_vitro_3


title: skin_Placebo_T2_2


title: JNGR171, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR171


title: JNGR172, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR172


title: JNGR169, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR169


title: JNGR170, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR170


title: JNGR166, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR166


title: Sedentary 5

description:
Library name: sample 5
S5

value: sedentary 4w


title: ATAC_pMIG_in_vitro_1

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG_in_vitro_1


title: Sedentary 3

description:
Library name: sample 3
S3


title: Sedentary 4

description:
Library name: sample 4
S4


title: JNGR162, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR162


title: JNGR163, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR163


title: Sedentary 1

description:
Library name: sample 1
S1


title: shMed4 #4 H3K79me2 biol rep 2

city: New York

first: Seongyeon

last: Bae

state: NY

institute: Columbia University

data_processing:
ChIP-seq reads were aligned to  GrCm39 (mm39) using Bwa-mem.
RPKM-normalized bigwigs were generated by deepTools.
peaks were called using MACS2 (ref. 38) (false discovery rate < 0.01; broad peak mode for H3K4me1, H3K9me3, and H3K79me2 default for H3K27ac and H3K4me3).
Assembly: Genome_build: mm39 (GRCm39)
Supplementary files format and content: bigwig

source_name: Breast

growth_protocol: D2A1-d breast cancer cell lines were maintained in DMED supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37°C with shaking. After quenching with 150 mM glycine for 10 min at 37°C with shaking, cells were washed twice with ice-cold PBS and frozen at -80°C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 √ó PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200‚Äì500 bp) and centrifuged at 15,000 √ó g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 Œºg/3 √ó 106 cells) were coupled with 30 Œºl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 ¬∞C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 ¬∞C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris‚ÄìHCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris‚ÄìHCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris‚ÄìHCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200 - 500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol: D2A1-d cells were transduced either non targeting control (NTC) or shRNAs targeting Med4.

value: Breast

value: Murine breast carcinoma

value: Med4 Knockdown

tag: chip antibody

value: H3K79me2 (Abcam, ab3594)


title: JNGR161, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR161


title: Sedentary 2

description:
Library name: sample 2
S2


title: shMed4 #4 Input biol rep 1


title: shMed4 #4 Input biol rep 2


title: JNGR159, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR159


title: ATAC_sgNTC_P14_Cl13_D5.5_3

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_sgNTC_P14_Cl13_D5.5_3

value: T cell

value: virus infection


title: PerturbPair Validation lane 2 ADT

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

institute: New York University

description: Library name: LIB6297172_SAM24539795_lane2

data_processing:
Raw reads were processed using Cell Ranger v7.0.0 with default parameters.
Reads were aligned to the mm10 reference genome.
Perturbation assignment was performed by demultiplexing gRNA barcodes with kallisto/bustools/kite.
Assembly: Mus musculus mm10 reference genome.
Supplementary files format and content: Processed data files are provided in Matrix Market (.mtx) format with accompanying feature and barcode annotation files (.tsv) for single-cell counts. In addition, perturbation assignment tables and processed gene expression matrices are provided as .csv and .h5ad (AnnData) formats for downstream analysis.
Library strategy: CITE-seq

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from tibias and femurs of 6–12 week old Cas9 transgenic mice. Cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum, GlutaMAX, penicillin/streptomycin, and 100 ng/ml recombinant mouse M-CSF to differentiate into bone marrow–derived macrophages (BMDMs).

extract_protocol:
Following stimulation, cells were dissociated with Accutase and AccuMAX, washed, and prepared for single-cell encapsulation. Cellular RNA was extracted in droplet format using the 10x Genomics Chromium GEM-X chemistry according to manufacturer’s instructions.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell 3’ GEM-X kit. Libraries were indexed and sequenced on an Illumina NextSeq 2000 platform with 100 bp paired-end reads.

treatment_protocol: On day 10 of differentiation, cells were stimulated with lipopolysaccharide (LPS, 100 ng/ml) for 9 hours prior to collection for scRNA-seq.

value: bone marrow

value: BMDMs


title: JNGR156, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR156

value: PEComa


title: JNGR173, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR173


title: shMed4 #4 H3K79me2 biol rep 1


title: shMed4 #4 H3K27Ac biol rep 2

value: H3K27ac (Abcam, ab4729)


title: JNGR155, PEComa tumor, bulk RNA-seq, pair-end

description: Library name: JNGR155


title: JNGR153, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR153


title: MCF-7_RNA-seq_100nM-E2_2H_rep3

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: MCF7_E2dosage_100nM_2H_set4_S7_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 nM E2

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

source_name: ER+ breast adenocarcinoma

growth_protocol: MCF-7 human epithelia cells from breast adenocarsinoma cells from American Type Cell Culture (ATCC) were maintained in MEM supplemented with 5% calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin. MCF-7 cells were maintained in phenol red-free MEM supplimented with 5% charcoal-dextrantreated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin for at least 3 days prior to experimentation.

extract_protocol:
MCF-7 cells were seeded at at density of 0.5x10^6 cells per well in a 6-well plate and treated as described above. Total RNA was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol.
RNA-seq libraries were generated as previously described with the following modifications [24]. Total RNA from MCF-7 cells treated as indicated was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol. Total RNA was then enriched for mRNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002). Further fragmentation, first-strand cDNA synthesis, and subsequent procedures have been done as described [25].The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Illumina TruSeq RNA Prep kit, multiplexed, and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded at a density of 0.5 x 10^6 cells per well in a 6-well dish one day prior to experimentation. At least biological replicates were used for each experimental condition. For E2 continuous treatment, 100 nM E2 was applied to the cells for the indicated times prior to collection. For E2 washout treatments, cells were treated with 100 nM of E2 for 40 mins., washed onced in stripped medium, then inclubated in stripped medium for the remainder of the experiment.

value: ER+ breast adenocarcinoma

value: epithelial cells

value: 100 nM E2 for 2 hours


title: PerturbPair Validation lane 2 gRNA pelllet

description: Library name: LIB6297170_SAM24539795_lane2


title: MCF-7_RNA-seq_100nM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_100nM_2H_set1_S8_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 nM E2


title: PerturbPair Validation lane 1 gRNA pellet

description: Library name: LIB6297169_SAM24539795_lane1


title: PerturbPair Validation lane 1 ADT

description: Library name: LIB6297171_SAM24539795_lane1


title: shMed4 #4 H3K27Ac biol rep 1


title: MCF-7_RNA-seq_10nM-E2_2H_rep3

description:
Library name: MCF7_E2dosage_10nM_2H_set4_S6_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 nM E2

value: 10 nM E2 for 2 hours


title: MCF-7_RNA-seq_100nM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_100nM_2H_set3_S24_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 nM E2


title: shMed4 #4 H3K4me3 biol rep 2

value: H3K4me3 (Abcam, ab8580)


title: JNGR152, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR152


title: JNGR151, PEComa tumor, bulk RNA-seq, single-end

description: Library name: JNGR151


title: EHP 1

description:
Library name: sample 6
E1

value: heart

value: WT

value: swimming 3w + sedentary 1w


title: MCF-7_RNA-seq_10nM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_10nM_2H_set3_S23_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 nM E2


title: PerturbPair Validation lane 2 gRNA supernatant

description: Library name: LIB6297168_SAM24539795_lane2


title: shMed4 #4 H3K9me3 biol rep 1

value: Breast

value: Murine breast carcinoma

value: H3K9me3 (Abcam, ab8898)


title: MCF-7_RNA-seq_1nM-E2_2H_rep3

description:
Library name: MCF7_E2dosage_1nM_2H_set4_S5_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 nM E2

value: 1 nM E2 for 2 hours


title: MCF-7_RNA-seq_10nM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_10nM_2H_set1_S7_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 nM E2


title: shMed4 #4 H3K9me3 biol rep 2

value: Med4 Knockdown


title: MCF-7_RNA-seq_1nM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_1nM_2H_set1_S6_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 nM E2


title: PerturbPair Validation lane 2 GEX

description: Library name: LIB6297166_SAM24539795_lane2

value: bone marrow


title: MCF-7_RNA-seq_500pM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_500pM_2H_set3_S21_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 500 pM E2

value: 500 pM E2 for 2 hours


title: ATAC_pMIG_in_vitro_2

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

description: Library name: ATAC_pMIG_in_vitro_2

value: Spleen

value: T cell

value: virus infection


title: MCF-7_RNA-seq_1nM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_1nM_2H_set3_S22_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 nM E2

value: ER+ breast adenocarcinoma

value: epithelial cells


title: shMed4 #4 H3K4me3 biol rep 1


title: shMed4 #4 H3K4me1 biol rep 2

value: H3K4me1 (Abcam, ab8895)


title: PerturbPair Validation lane 1 gRNA supernatant

description: Library name: LIB6297167_SAM24539795_lane1

value: BMDMs


title: MCF-7_RNA-seq_100pM-E2_2H_rep3

description:
Library name: MCF7_E2dosage_100pM_2H_set4_S4_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 pM E2

value: 100 pM E2 for 2 hours


title: MCF-7_RNA-seq_500pM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_500pM_2H_set1_S5_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 500 pM E2


title: MCF-7_RNA-seq_100pM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_100pM_2H_set3_S20_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 pM E2


title: PerturbPair Validation lane 1 HTO

description: Library name: LIB6297163_SAM24539795_lane1


title: PerturbPair Validation lane 2 HTO

description: Library name: LIB6297164_SAM24539795_lane2


title: MCF-7_RNA-seq_10pM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_10pM_2H_set3_S19_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 pM E2

value: 10 pM E2 for 2 hours


title: PerturbPair lane15 ADT

description: Library name: LIB6253126_SAM24474587_lane15


title: shMed4 #1 Input biol rep 1


title: shMed4 #4 H3K4me1 biol rep 1


title: shMed4 #1 Input biol rep 2


title: MCF-7_RNA-seq_100pM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_100pM_2H_set1_S4_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 100 pM E2


title: MCF-7_RNA-seq_10pM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_10pM_2H_set1_S3_R1_001_final.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 pM E2


title: MCF-7_RNA-seq_1pM-E2_2H_rep3

description:
Library name: MCF7_E2dosage_1pM_2H_set4_S2_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 pM E2

value: 1 pM E2 for 2 hours


title: PerturbPair Validation lane 1 GEX

description: Library name: LIB6297165_SAM24539795_lane1


title: MCF-7_RNA-seq_1pM-E2_2H_rep1

description:
Library name: MCF7_E2dosage_1pM_2H_set1_S2_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 pM E2


title: MCF-7_RNA-seq_10pM-E2_2H_rep3

description:
Library name: MCF7_E2dosage_10pM_2H_set4_S3_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 10 pM E2


title: MCF-7_RNA-seq_1pM-E2_2H_rep2

description:
Library name: MCF7_E2dosage_1pM_2H_set3_S18_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 1 pM E2


title: MCF-7_RNA-seq_DMSO_2H_rep2

description:
Library name: MCF7_E2dosage_Veh_2H_set3_S17_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with DMSO

value: DMSO for 2 hours


title: shMed4 #1 H3K79me2 biol rep 2

value: Breast

value: Murine breast carcinoma

value: H3K79me2 (Abcam, ab3594)


title: shMed4 #1 H3K79me2 biol rep 1

value: Med4 Knockdown


title: PerturbPair lane14 ADT

description: Library name: LIB6253125_SAM24474586_lane14

value: bone marrow


title: shMed4 #1 H3K27Ac biol rep 2

value: H3K27ac (Abcam, ab4729)


title: MCF-7_PRO-seq_10 nM E2 30min_rep3

description:
Library name: E2_10nm_mergeruns_set3_S15_R1_001.fastq.gz
cDNA library derived from nascent RNA, labeled with biotin then purifed after treatment for 30 min. with 10 nM E2

data_processing:
The PRO-seq reads were aligned to the hg38 human reference genome using bwa.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using deeptools
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser
Library strategy: PRO-Seq

molecule: nuclear RNA

extract_protocol:
Nuclei were purified, run-on assay performed, and biontin-labeled RNA extracted by Trizol LS reagent followed by binding to streptavidin-conjugated dynabeads as described.
PRO-seq libraries were generated as previously described (Judd J, et al., BioRxiv 2020). Total RNA was then enriched for biotin-labeled nascent transcripts by streptavidin-conjugated dynabead. Further fragmentation, barcoding of RNA fragments, and first strand synthesis was performed as described. The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, adapter cleanup by SPRI-bead purification, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described using RPI-n indexed barcodes and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded such that cells will bet at 70 to 80% confluency at the time of experimentation. Cells were treated with the indicated concentrations of E2 for 30 min., after which nuclei were extracted and stored at -80C before PRO-seq library preparation. At least three biological replicates were used for each experimental condition.

value: 10 nM E2 for 30 min.


title: PerturbPair lane12 ADT

description: Library name: LIB6253123_SAM24474584_lane12


title: PerturbPair lane13 ADT

description: Library name: LIB6253124_SAM24474585_lane13


title: MCF-7_RNA-seq_DMSO_2H_rep3

description:
Library name: MCF7_E2dosage_Veh_2H_set4_S1_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with DMSO


title: shMed4 #1 H3K27Ac biol rep 1


title: MCF-7_PRO-seq_1 nM E2 30min_rep2

description:
Library name: E2_1nm_mergeruns_set2_S9_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 1 nM E2

value: 1 nM E2 for 30 min.


title: MCF-7_PRO-seq_100 pM E2 30min_rep3

description:
Library name: E2_100pm_mergeruns_set3_S13_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 100 pM E2

value: 100 pM E2 for 30 min.


title: MCF-7_PRO-seq_1 nM E2 30min_rep1

description:
Library name: E2_1nm_mergeruns_set1_S4_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 1 nM E2

value: ER+ breast adenocarcinoma


title: shMed4 #1 H3K4me3 biol rep 2

value: H3K4me3 (Abcam, ab8580)


title: MCF-7_PRO-seq_1 nM E2 30min_rep3

description:
Library name: E2_1nm_mergeruns_set3_S14_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 1 nM E2

value: epithelial cells


title: MCF-7_PRO-seq_10 pM E2 30min_rep2

description:
Library name: E2_10pm_mergeruns_set2_S7_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 10 pM E2

value: 10 pM E2 for 30 min.


title: MCF-7_PRO-seq_10 pM E2 30min_rep3

description:
Library name: E2_10pm_mergeruns_set3_S12_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 10 pM E2


title: PerturbPair lane9 ADT

description: Library name: LIB6253120_SAM24474581_lane9

value: BMDMs


title: shMed4 #1 H3K9me3 biol rep 1

value: H3K9me3 (Abcam, ab8898)


title: PerturbPair lane8 ADT

description: Library name: LIB6253119_SAM24474580_lane8


title: PerturbPair lane11 ADT

description: Library name: LIB6253122_SAM24474583_lane11


title: MCF-7_PRO-seq_DMSO 30min_rep3

description:
Library name: Veh_mergeruns_set3_S11_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with DMSO

value: DMSO for 30 min.


title: MCF-7_RNA-seq_DMSO_2H_rep1

description:
Library name: MCF7_E2dosage_Veh_2H_set1_S1_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with DMSO

value: DMSO for 2 hours


title: MCF-7_PRO-seq_100 pM E2 30min_rep2

description:
Library name: E2_100pm_mergeruns_set2_S8_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 100 pM E2


title: MCF-7_PRO-seq_DMSO 30min_rep2

description:
Library name: Veh_mergeruns_set2_S6_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with DMSO


title: MCF-7_PRO-seq_10 nM E2 30min_rep2

description:
Library name: E2_10nm_mergeruns_set2_S10_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 10 nM E2


title: PerturbPair lane10 ADT

description: Library name: LIB6253121_SAM24474582_lane10


title: shMed4 #1 H3K4me1 biol rep 2

value: Breast

value: H3K4me1 (Abcam, ab8895)


title: shMed4 #1 H3K9me3 biol rep 2

value: Murine breast carcinoma


title: MCF-7_PRO-seq_10 nM E2 30min_rep1

description:
Library name: E2_10nm_mergeruns_set1_S5_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 10 nM E2


title: shMed4 #1 H3K4me3 biol rep 1

value: Med4 Knockdown


title: MCF-7_PRO-seq_10 pM E2 30min_rep1

description:
Library name: E2_10pm_mergeruns_set1_S2_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 10 pM E2


title: PerturbPair lane7 ADT

description: Library name: LIB6253118_SAM24474579_lane7

value: bone marrow


title: MCF-7_PRO-seq_100 pM E2 30min_rep1

description:
Library name: E2_100pm_mergeruns_set1_S3_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with 100 pM E2


title: shMed4 #1 H3K4me1 biol rep 1


title: PerturbPair lane6 ADT

description: Library name: LIB6253117_SAM24474578_lane6


title: PerturbPair lane5 ADT

description: Library name: LIB6253116_SAM24474577_lane5


title: MCF-7_PRO-seq_DMSO 30min_rep1

description:
Library name: Veh_mergeruns_set1_S1_R1_001.fastq.gz
cDNA library derived from nascent RNA_labeled with biotin then purifed after treatment for 30 min. with DMSO


title: PerturbPair lane4 ADT

description: Library name: LIB6253115_SAM24474576_lane4


title: MCF-7 cells treated with 1nM for 30 min, Rep3

description:
Library name: MCF7_E2dosage_1nM_30min_set3
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

data_processing:
The ATAC-seq reads were aligned to the hg38 human reference genome using bwa.
Mapped reads were sorted and captured in bam files for further downstream analysis of peak calling and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

extract_protocol:
ATAC-seq libraries were generated as previously described with a few modifications. Cells were collected by trypsinization counted at experimental endpoint, and 50,000 live cells were used for each experimental condition. Nuclei were purified by resuspending cell pellets in hypotonic lysis buffer and incubating on ice for 3 minutes. Nuclei were then washed once with hypotonic lysis buffer without NP-40 or digitonin. Nuclei were then resuspended in transposition mix containing 100 mM Tn5 transposase and incubated at 37°C for 30 minutes shaking at 1000 rpm. Resulting tagmented DNA fragments were purified by column purification using the Qiagen PCR purification kit (cat. 28104).
Final amplification of libraries was performed using the NEBNext High-Fidelity Master Mix, and Nextera i5 and i7 primers for a total of 7 cycles. Final samples were purified of excess adapters by using 1.3X volume of AMPure beads.  The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Nextera i5/i7 indexed barcodes, multiplexed, and sequenced using Illumina NextSeq 2000 by 100 bp paired-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded such that cells will bet at 70 to 80% confluency at the time of experimentation. Cells were treated with the indicated concentrations of E2 for 30 min., after which nuclei were extracted and stored at -80C before ATAC-seq library preparation. At least three biological replicates were used for each experimental condition.


title: MCF-7 cells treated with 10nM for 30 min, Rep3

description:
Library name: MCF7_E2dosage_10nM_30min_set3
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with 100 nM E2 then washed out for the indicated time.


title: MCF-7 cells treated with 10nM for 30 min, Rep2

description:
Library name: MCF7_E2dosage_10nM_30min_set2
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with DMSO then washed out for the indicated time.


title: NTC Input biol rep 2

value: WT


title: MCF-7 cells treated with 100pM for 30 min, Rep3

description:
Library name: MCF7_E2dosage_100pM_30min_set3
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: MCF-7 cells treated with 1nM for 30 min, Rep2

description:
Library name: MCF7_E2dosage_1nM_30min_set2
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: PerturbPair lane3 ADT

description: Library name: LIB6253114_SAM24474575_lane3


title: NTC. H3K79me2 biol rep 2

value: H3K79me2 (Abcam, ab3594)


title: NTC H3K27Ac biol rep 2

value: H3K27ac (Abcam, ab4729)


title: NTC. H3K79me2 biol rep 1


title: MCF-7 cells treated with 100pM for 30 min, Rep1

description:
Library name: MCF7_E2dosage_100pM_30min_set1
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: 100 pM E2 for 30 min.


title: PerturbPair lane2 ADT

description: Library name: LIB6253113_SAM24474574_lane2


title: PerturbPair lane15 gRNA

description: Library name: LIB6253111_SAM24474587_lane15


title: MCF-7 cells treated with 1nM for 30 min, Rep1

description:
Library name: MCF7_E2dosage_1nM_30min_set1
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: ER+ breast adenocarcinoma

value: 1 nM E2 for 30 min.


title: NTC H3K27Ac biol rep 1


title: MCF-7 cells treated with 100pM for 30 min, Rep2

description:
Library name: MCF7_E2dosage_100pM_30min_set2
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: epithelial cells


title: PerturbPair lane1 ADT

description: Library name: LIB6253112_SAM24474573_lane1


title: NTC Input biol rep 1


title: MCF-7 cells treated with 10pM E2 for 30 min, Rep2

description:
Library name: MCF7_E2dosage_10pM_30min_set2
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.

value: 10 pM E2 for 30 min.


title: MCF-7 cells treated with DMSO for 30 min, Rep3

description:
Library name: MCF7_E2dosage_Veh_30min_set3
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: MCF-7 cells treated with 10pM E2 for 30 min, Rep3

description:
Library name: MCF7_E2dosage_10pM_30min_set3
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: MCF-7 cells treated with 10nM for 30 min, Rep1

description:
Library name: MCF7_E2dosage_10nM_30min_set1
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated actuely for 40mins with DMSO then washed out for the indicated time.

value: 10 nM E2 for 30 min.


title: PerturbPair lane14 gRNA

description: Library name: LIB6253110_SAM24474586_lane14

value: BMDMs


title: NTC H3K9me3 biol rep 2

value: H3K9me3 (Abcam, ab8898)


title: MCF-7 cells treated with 10pM E2 for 30 min, Rep1

description:
Library name: MCF7_E2dosage_10pM_30min_set1
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with 100 nM for indicated time.


title: PerturbPair lane12 gRNA

description: Library name: LIB6253108_SAM24474584_lane12


title: NTC H3K4me3 biol rep 2

value: H3K4me3 (Abcam, ab8580)


title: MCF-7 cells treated with DMSO for 30 min, Rep2

description:
Library name: MCF7_E2dosage_Veh_30min_set2
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO

value: DMSO for 30 min.


title: PerturbPair lane13 gRNA

description: Library name: LIB6253109_SAM24474585_lane13


title: MCF-7 cells treated with DMSO for 30 min, Rep1

description:
Library name: MCF7_E2dosage_Veh_30min_set1
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO


title: MCF7_GATA3-ChIP-seq_10 nM E2 30 min_set 1

description:
Library name: GATA3_nM1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.

data_processing:
The Chip-seq reads were aligned to the hg38 human reference genome using bowtie2.
Mapped reads were sorted and captured in bam files for further downstream analysis of peak calling and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

extract_protocol:
Nuclei were first extracted by inclubation in Farmham lysis buffer followed by centrifugation. Nuclei were then lysed in lysis buffer containing SDS, and sonicated for 8 cycles (30on/off) in a Dyagenode pico sonication device. Shear chromatin was cleared by incubation in dynabeads, protein concnetration measured, and at least 0.5 mg of material used for ChIP assays using the indicated antibody as described. Final ChIP'ed DNA was purified by phenol chloroform extraction followed by ethanol precipitation.
ChIP-seq libraries were generated as previously described (Judd J, et al., BioRxiv 2020). Libraries were generated from ChIP'ed DNA or input as described, and subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, adapter cleanup by SPRI-bead purification, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described using Illumina indexed barcodes and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded such that cells will bet at 70 to 80% confluency at the time of experimentation. Cells were treated with the indicated concentrations of E2 for 30 min., after which they were fixed with 1% formaldahyde for 10 mins at 37C before quencing with glycine at a final concentration of 125 mM. Fixed cells were snap frozen and stored at -80C until use.


title: MCF7_GATA3-ChIP-seq_10 nM E2 30 min_set 3

description:
Library name: GATA3_nM3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_GATA3-ChIP-seq_10 pM E2 30 min_set 2

description:
Library name: GATA3_pM2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: PerturbPair lane10 gRNA

description: Library name: LIB6253106_SAM24474582_lane10


title: NTC H3K4me1 biol rep 1

value: Breast

value: H3K4me1 (Abcam, ab8895)


title: MCF7_GATA3-ChIP-seq_DMSO 30 min_set 3

description:
Library name: GATA3_veh3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: MCF7_GATA3-ChIP-seq_10 pM E2 30 min_set 3

description:
Library name: GATA3_pM3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: NTC H3K9me3 biol rep 1

value: Murine breast carcinoma


title: NTC H3K4me3 biol rep 1


title: PerturbPair lane9 gRNA

description: Library name: LIB6253105_SAM24474581_lane9

value: bone marrow


title: PerturbPair lane11 gRNA

description: Library name: LIB6253107_SAM24474583_lane11


title: NTC H3K4me1 biol rep 2

value: WT


title: MCF7_GATA3-ChIP-seq_10 pM E2 30 min_set 1

description:
Library name: GATA3_pM1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_GATA3-ChIP-seq_10 nM E2 30 min_set 2

description:
Library name: GATA3_nM2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_GATA3-ChIP-seq_DMSO 30 min_set 1

description:
Library name: GATA3_veh1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: MCF7_GATA3-ChIP-seq_DMSO 30 min_set 2

description:
Library name: GATA3_veh2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: PerturbPair lane8 gRNA

description: Library name: LIB6253104_SAM24474580_lane8


title: ATAC_shMed1 #4 biol rep 3

data_processing:
Reads were trimmed for both quality and Illumina adapter sequences using ‘trim_galore’ then aligned to mouse assembly mm10 with BWA using the default parameters.
Enriched regions were discovered using MACS2 and scored against matched input libraries (|fold change| > 2 and p-value < 0.005).
Raw read counts were tabulated over this peak atlas using featureCounts (http://subread.sourceforge.net).
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
5x10e4 D2A1-d cells were prepared and collected. Cells were then washed once with cold 1xPBS and spinned down at 500g for 5min at 4C. Cells were kept on ice and subsequently resuspended in 25ul 2xTD buffer (Illumina Nextera kit), 2.5ul Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5ul Nuclease-free water in total of 50ul reaction for 1hr at 37C. DNA was then purified using Qiangen MinElute PCR purification kit (28004) in a final volume of 10ul.
ATAC-seq Libraries were prepared following the Buenrostro protocol (http://www.ncbi.nlm.gov/pmc/articles/PMC4374986/)

treatment_protocol: D2A1-d cells were transduced either non targeting control (NTC) or shRNAs targeting Med1.

value: Med1 Knockdown

value: Untreated


title: MCF7_FOXA1-ChIP-seq_10 nM E2 30 min_set 3

description:
Library name: FOXA1_nM3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_FOXA1-ChIP-seq_10 nM E2 30 min_set 2

description:
Library name: FOXA1_nM2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: PerturbPair lane7 gRNA

description: Library name: LIB6253103_SAM24474579_lane7


title: ATAC_shMed1 #4 biol rep 2


title: MCF7_FOXA1-ChIP-seq_10 nM E2 30 min_set 1

description:
Library name: FOXA1_nM1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: ATAC_shMed1 #4 biol rep 1


title: PerturbPair lane6 gRNA

description: Library name: LIB6253102_SAM24474578_lane6


title: PerturbPair lane5 gRNA

description: Library name: LIB6253101_SAM24474577_lane5


title: MCF7_FOXA1-ChIP-seq_10 pM E2 30 min_set 2

description:
Library name: FOXA1_pM2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_FOXA1-ChIP-seq_10 pM E2 30 min_set 3

description:
Library name: FOXA1_pM3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_FOXA1-ChIP-seq_DMSO 30 min_set 3

description:
Library name: FOXA1_veh3_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: PerturbPair lane4 gRNA

description: Library name: LIB6253100_SAM24474576_lane4


title: ATAC_shMed1 #2 biol rep 3


title: MCF7_FOXA1-ChIP-seq_DMSO 30 min_set 1

description:
Library name: FOXA1_veh1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: ATAC_shMed1 #2 biol rep 2


title: ATAC_shMed1 #2 biol rep 1


title: PerturbPair lane3 gRNA

description: Library name: LIB6253099_SAM24474575_lane3


title: MCF7_FOXA1-ChIP-seq_DMSO 30 min_set 2

description:
Library name: FOXA1_veh2_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with DMSO for 30 min.


title: MCF7_H3K27ac-ChIP-seq_10 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10nM_H3K27ac_set2_S4_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_H3K27ac-ChIP-seq_10 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_10nM_H3K27ac_set1_S10_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: MCF7_FOXA1-ChIP-seq_10 pM E2 30 min_set 1

description:
Library name: FOXA1_pM1_R1_R2.fastq.gz
Genomic DNA library derived from FOXA1 enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: MCF7_H3K27ac-ChIP-seq_1 nM E2 30 min_set 3

description:
Library name: MCF7_E2dose_1nM_H3K27ac_set3_S14_R1_001.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.


title: MCF7_H3K27ac-ChIP-seq_1 nM E2 30 min_set 2

description:
Library name: MCF7_E2dose_1nM_H3K27ac_set2_S2_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.


title: MCF7_H3K27ac-ChIP-seq_10 nM E2 30 min_set 3

description:
Library name: MCF7_E2dose_10nM_H3K27ac_set3_S15_R1_001.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 nM E2 for 30 min.


title: PerturbPair lane2 gRNA

description: Library name: LIB6251826_SAM24472316_lane2


title: PerturbPair lane1 gRNA

description: Library name: LIB6251825_SAM24472315_lane1


title: ATAC_NTC_biol rep 2


title: PerturbPair lane14 GEX

description: Library name: LIB6253097_SAM24474586_lane14


title: MCF7_H3K27ac-ChIP-seq_1 nM E2 30 min_set 1

description:
Library name: MCF7_E2dose_1nM_H3K27ac_set1_S9_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 1 nM E2 for 30 min.


title: ATAC_NTC_biol rep 3


title: MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_10pM_H3K27ac_set2_S1_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 10 pM E2 for 30 min.


title: PerturbPair lane15 GEX

description: Library name: LIB6253098_SAM24474587_lane15


title: ATAC_NTC_biol rep 1


title: MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 3

description:
Library name: MCF7_E2dose_100pM_H3K27ac_set3_S13_R1_001.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.

value: 100 pM E2 for 30 min.


title: MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 2

description:
Library name: MCF7_E2dose_100pM_H3K27ac_set2_S5_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.

value: ER+ breast adenocarcinoma


title: MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 1

description:
Library name: MCF7_E2dose_100pM_H3K27ac_set1_S8_R1_001_NEW.noIllAdapt.fastq.gz
Genomic DNA library derived from H3K27ac enriched ChIP'ed DNA of cells treated with 100 pM E2 for 30 min.


title: ATAC_shMed4 #4 biol rep 3

value: Med4 Knockdown


title: ATAC_shMed4 #4 biol rep 2