|
| Status |
Public on Jun 20, 2022 |
| Title |
snATAC-seq female e-cigarette |
| Sample type |
SRA |
| |
|
| Source name |
P7 rat brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
treatment: dam exposed to e-cigarette vapor
tissue: cortex and hippocampus
age: P7
Sex: male
|
| Treatment protocol |
E-cigarette aerosol was delivered with a puff duration of 4 sec, 3 puffs in an inter-puff interval of 30 sec per vaping episode, and one episode per 1 hour in the dark phase of 12 hrs each day, which generates similar nicotine blood pharmacokinetics in the pregnant rats to those observed in human e-cigarette users. The dams were exposed to e-cigarettes for a total of 17 days from gestational day 4 (E4) to E20.
|
| Growth protocol |
Pregnant Sprague-Dawley rats were purchased from Charles River Laboratories (Portage, MI) and were housed under controlled temperature (22 ºC) and photoperiod (12-h light and 12-h dark cycle) with food and water ad libitum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10X Genomics protocol CG000124 (Isolation of nuclei for single cell RNA sequencing) and protocol CG000122 (Nuclei isolation from mouse brain tissue for single cell ATAC sequencing).
Chromium Next GEM Single Cell 3ʹ v3.1 and Chromium Next GEM Single Cell ATAC v1.1.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
snATAC_FEcig
10X single-cell chromatin accessibility
Droplet single nucleus-ATAC-seq
Single nuclei isolation and capture
|
| Data processing |
HiSeq 4000 onboard basecalling by RTA 2.7.7.
snRNA-seq fastq files were generated using 10X Genomics cellranger (v3.1.0) mkfastq. Reads alignment, filtering, barcode and UMI counting were performed by cellrange count.
snATAC-seq fastq files were generated using 10X Genomics cellranger-atac (v1.0.0) mkfastq. Single-cell chromatin accessibility counts were generated by cellrange-atac count.
Genome_build: NCBI Rnor_6.0
Supplementary_files_format_and_content: For snRNA-seq, cell barcodes and genes are in tsv format; gene expression is in mtx format.
Supplementary_files_format_and_content: For snATAC-seq, barcoded and aligned fragment files are in tsv format, called peak locations are in BED format, and filtered peak barcode is in hdf5 format.
|
| |
|
| Submission date |
Oct 07, 2021 |
| Last update date |
Jun 22, 2022 |
| Contact name |
Charles Wang |
| E-mail(s) |
chwang@llu.edu
|
| Phone |
(909) 558-4325
|
| Organization name |
Loma Linda University
|
| Department |
Department of Basic Sciences
|
| Lab |
Center for Genomics
|
| Street address |
11021 Campus Street
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE185538 |
Single-nucleus chromatin accessibility and RNA-seq reveal impaired brain development in prenatal e-cigarette exposed neonatal rats |
|
| Relations |
| BioSample |
SAMN22136704 |
| SRA |
SRX12522640 |
