|
| Status |
Public on Jun 03, 2021 |
| Title |
Stomach-scATAC-Sample1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary human stomach body biopsy sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fresh frozen endoscopic biopsy
antibody: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from fresh frozen clinical biopsy specimens by douncing in nuclear lysis buffer. Nuclei were purified by sorting using DAPI as a nuclear stain.
Once nuclei were purified bulk transposition was carried out using Tn5 (10x Genomics) followed by formation of gel emulsion beads to encapsulate individual nuclei separately and initial library amplification was carried out.
Libraries were prepared using the 10x Genomics scATAC library preparation reagents and 50bp paired end sequencing was performed on the Novaseq SP flowcell (Illumina)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment: ChIP-seq, ATAC-seq:bowtie2; RNA-seq: STAR; scATAC: CellRanger
CHIP-seq peak calling, ATAC-seq peak calling: MACS, version 2.0
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ATAC-seq, ChIP-seq, CUT&RUN: bigwig file for visualizing aligned sequence tags; RNA-seq: unprocessed gene counts; scATAC-seq: unfiltered peak-cell counts
|
| |
|
| Submission date |
Dec 19, 2019 |
| Last update date |
Jun 04, 2021 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE97178 |
Hybrid stomach-intestinal chromatin states underlie human Barrett’s metaplasia |
|
| Relations |
| BioSample |
SAMN13638746 |
| SRA |
SRX7417678 |
