|
| Status |
Public on Oct 20, 2021 |
| Title |
Snubar-CoAssay_cell_line_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Snubar-CoAssay
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell lines: A20+K562
|
| Treatment protocol |
28 mice were treated under 7 different conditions (4 mice in each group): 1) Control; 2) Chemotherapy + 2 Gy Radiotherapy; 3) 4 Gy Radiotherapy; 4) Chemotherapy + 2 Gy Radiotherapy + Talazoparib; 5) Chemotherapy + 2 Gy Radiotherapy + PD-L1 Blockade; 6) 4Gy Radiotherapy + PD-L1 Blockade; 7) 4Gy Radiotherapy + Talazoparib + PD-L1 Blockade.
|
| Growth protocol |
The A20 and K562 cell lines were purchased from the American Type Culture Collection and cultured based on ATCC guidelines. The MDA-MB-231 and MDA-MB-436 cell lines were obtained from the MD Anderson Characterized Cell Line Core Facility and were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose medium supplemented with 10% FBS and 1X penicillin-streptomycin. Mice were purchased from the Jackson Laboratory and housed in the Research Animal Support Facility at MD Anderson Cancer Center.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits, CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)
single cell ATAC-seq, single cell RNA&ATAC co-assay, and barcode libraries
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Snubar-CoAssay_ATAC
SnubarATAC&RNA-Coassay-2cell line mixture (A20-K562)-scATAC
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2
SnubarARC single cell ATAC-seq library
|
| Data processing |
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Anil K Sood |
| Organization name |
MDACC
|
| Department |
genetics
|
| Lab |
Navin Lab
|
| Street address |
6767 Bertner Ave
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE162798 |
Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility |
|
| Relations |
| BioSample |
SAMN17016341 |
| SRA |
SRX9642085 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4960042_Snubar-CoAssay.scATAC.cell_metainfo.csv.gz |
9.1 Mb |
(ftp)(http) |
CSV |
| GSM4960042_Snubar-CoAssay.scATAC.coassay_matched_cell_names.csv.gz |
5.9 Mb |
(ftp)(http) |
CSV |
| GSM4960042_Snubar-CoAssay.scATAC.filtered_peak_bc_matrix.barcodes.tsv.gz |
39.1 Kb |
(ftp)(http) |
TSV |
| GSM4960042_Snubar-CoAssay.scATAC.filtered_peak_bc_matrix.count_matrix.mtx.gz |
279.6 Mb |
(ftp)(http) |
MTX |
| GSM4960042_Snubar-CoAssay.scATAC.filtered_peak_bc_matrix.peaks.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
| GSM4960042_Snubar-CoAssay.scATAC.fragments.tsv.gz |
2.4 Gb |
(ftp)(http) |
TSV |
| GSM4960042_Snubar-CoAssay.scATAC.fragments.tsv.gz.tbi.gz |
1.6 Mb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
