|
| Status |
Public on Feb 26, 2024 |
| Title |
dpi14_scATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Heart
genotype: wild type
|
| Treatment protocol |
Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. After apex resection, fish were returned to a recovery tank with fresh system water.
|
| Growth protocol |
Zebrafish were raised and maintained under standard laboratory conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated noncardiomyocytes were used as input for nuclei preparation following the 10X Genomics Chromium single-cell ATAC-seq solution protocol
scATAC-seq libraries were prepared for sequencing as outlined in the 10X Genomics single-cell ATAC-seq solution protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the danRer11 reference genome using Cell Ranger ATAC.
Assembly: danRer11 genome
Supplementary files format and content: one csv file containing raw count values for scATAC-seq peaks of all the samples
|
| |
|
| Submission date |
Oct 18, 2022 |
| Last update date |
Feb 26, 2024 |
| Contact name |
LI QIAN |
| E-mail(s) |
li_qian@med.unc.edu
|
| Phone |
919 9624982
|
| Organization name |
UNC
|
| Department |
Department of pathology
|
| Lab |
Qian Lab
|
| Street address |
111 Mason Farm Road, MBRB
|
| City |
Chapel Hill |
| ZIP/Postal code |
27517 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (2) |
| GSE215986 |
Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [scATAC-seq] |
| GSE215988 |
Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration |
|
| Relations |
| BioSample |
SAMN31340355 |
| SRA |
SRX17928655 |
