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| Status |
Public on Aug 14, 2024 |
| Title |
Female, smoker, ATAC, subject3 |
| Sample type |
SRA |
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| Source name |
Tumor-distant normal lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor-distant normal lung
Sex: Female
subject status: smoker
subject id: subject3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The tissues were collected at a ~2 cm3 size and put in MACS Tissue Storage Solution (Miltenyl biotec cat.130-100-008) within 30 mins of surgical dissection. Samples were kept at 4°C and processed within 3 hours of dissection. Tissues were chopped into 2 mm diameter pieces within a dissociation tube to reduce the cell loss. Multi Tissue Dissociation Kit 1 and gentleMACS Octo Dissociator (Miltenyi Biotec) were used for dissociation of the tissue into single-cell suspension with a reduced amount of enzyme R (25% of the regular amount). Red blood cells were removed using Red Blood Cell Lysis Solution (Miltenyl biotec cat.130-094-183). Single-cell suspension of samples was frozen using 90% FBS and 10% DMSO and stored in liquid nitrogen until further processing except for the time of transfer in dry ice. The dissociated single-cell suspensions were thawed and filtered using a 70 μm cell strainer (Miltenyi Biotec) to remove debris. The filtered cells were labelled with cell viability marker (DAPI) and antibody markers of EPCAM, CD31, and CD45. Live single-cells (DAPI-negative) were sorted into lysis plates based on three gates: EPCAM+CD45- (designated “epithelial”), EPCAM-CD45+ (designated “immune”), and EPCAM-CD45- (designed “endothelial or stromal”). To enrich epithelial cells, which are considered to have key roles in lung cancer etiology, we collected all “epithelial” cells from EPCAM+CD45- gates and balanced the ratios to 6:3:1 (“epithelial”: “immune”: “endothelial or stromal”). Nuclei isolation was performed based on “Low Cell Input Nuclei Isolation” protocol (CG000365-Rev C, 10X Genomics) with a modification of the 1X lysis buffer treatmenet time (3-second duration).
Isolated nuclei were used for single-cell capture and sequencing library preparation using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits following the manufacturer’s guidelines (CG000338- Rev E, 10X Genomics, USA).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics
FS3_raw_feature_bc_matrix.h5
FS3_ATAC
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| Data processing |
The demultiplexing, barcode processing, and alignment to human genome reference sequences (GRCh38) were performed using Cell Range ARC software (10x Genomics, v.2.0.1 or 2.0.0)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: .rds: Seurat object
Supplementary files format and content: ATAC-seq fragments and index files
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| Submission date |
Aug 22, 2023 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Jiyeon Choi |
| Organization name |
NCI
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| Street address |
9615 Medical Center Drive, Rm 3116
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| City |
Rockville |
| State/province |
Maryland |
| ZIP/Postal code |
20850 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE241468 |
Context-aware single-cell multiomics approach identifies cell-type specific lung cancer susceptibility genes |
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| Relations |
| BioSample |
SAMN37117516 |
| SRA |
SRX21460109 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7729472_FS3_atac_fragments.tsv.gz |
4.2 Gb |
(ftp)(http) |
TSV |
| GSM7729472_FS3_atac_fragments.tsv.gz.tbi.gz |
1.5 Mb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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