|
| Status |
Public on Apr 07, 2023 |
| Title |
ALK09_2_E775_con_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole embryo
strain: C57BL/6J
developmental stage: Late (lateE7.5-E7.75)
genotype: Control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dissociate whole mouse embryos in 0.25% TrypLE and quench with PBS+1%FBS to single cell suspension, perform nuclear lysis. Treat 10000 singularized nuclei with transposition enzyme. Load nuclei in 10X Chromium chip.
10X Genomics Chromium scATAC Library & Gel Bead Kit v1 used for library preparation according to manufacturer's protocol.
single cell ATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
Libraries pooled and sequenced on Illumina NovaSeq.
Reads were demultiplexed, aligned, read normalized, and quantified using 10X Genomics cellranger-atac-1.2.0 software suite.
Assembly: mm10
Supplementary files format and content: aligned fragments tab-separated values files
|
| |
|
| Submission date |
Aug 05, 2022 |
| Last update date |
Apr 08, 2023 |
| Contact name |
Alexis Leigh Krup |
| Organization name |
Gladstone Institutes
|
| Department |
Gladstone Institutes of Cardiovascular Disease
|
| Lab |
Bruneau Lab
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE210638 |
Chromatin accessibility profiles of early cardiac precursor cells at single cell resolution |
| GSE210639 |
A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors |
|
| Relations |
| BioSample |
SAMN30168091 |
| SRA |
SRX16888584 |
