 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 07, 2022 |
| Title |
GBC_TNF, scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
GBC_TNF
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GBC
treatment: TNF-a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
This is achieved by transposing nuclei in a bulk solution; then using a microfluidic chip, the nuclei are partitioned into nanoliter-scale Gel Beadsin-emulsion (GEMs).
A pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus. Libraries are generated and sequenced, and 10x Barcodes are used to associate individual reads back to the individual partitions, and thereby, to each individual nucleus.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GBC cell line with stimulation of TNF-a for 8h
|
| Data processing |
The Cell Ranger ATAC software pipeline (version 1.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the BWA-MEM aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.5)
Library size normalization was performed with NormalizeData function in Seurat.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with peaks for every peak and every cell
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Jan 08, 2022 |
| Contact name |
Wenbin Liu |
| E-mail(s) |
wenbinl_lxb@sina.com
|
| Phone |
+86-13127696716
|
| Organization name |
Second Military Medical University
|
| Street address |
800 Xiangyin Rd..
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE166372 |
Transcriptional repression and apoptosis influence the effect of APOBEC3A/3B functional polymorphisms on biliary tract cancer risk |
|
| Relations |
| BioSample |
SAMN17834443 |
| SRA |
SRX10049149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5069298_GBC_TNF_barcodes.tsv.gz |
35.0 Kb |
(ftp)(http) |
TSV |
| GSM5069298_GBC_TNF_matrix.mtx.gz |
177.1 Mb |
(ftp)(http) |
MTX |
| GSM5069298_GBC_TNF_peaks.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
