|
| Status |
Public on Oct 16, 2023 |
| Title |
E105_STZ_03 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic mouse heart at E10.5
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Streptozotocin
specific heart region: Cardiogenic region
strain: C57BL/6
additional cell lineages present in dataset: Non-cardiac mesoderm, ectoderm and endoderm
|
| Treatment protocol |
Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes, and supernatatn were removed. Cell pellets were lysed with Lysis Buffer on ice for 5min and then wasded with Wash Buffer. Nuclei were centrifuged at 500 rcf for 5 min and resuspended in 10x Nuclei Buffer. For the latter Nuclei isolation steps were accoding to the manufacture's instruction from 10x Genomics.
|
| Growth protocol |
Timed matings were set up between normal glycemic male mice and either Veh-pretreated normal glycemic female mice or STZ-pretreated hyperglycemic female mice. Morning of plug detection was considered embryonic day (E) 0.5 and embryos were harvested at E10.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After doing transposition step using 5ul of single nucli suspensions, samples were loaded onto the Chromium controller (10X genomics) microfluidic chip for single nuclei droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (PN- 1000176) and Single Index Kit N Set A (PN-1000212).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single-cell sequencing assay for transposase-accessible chromatin from cardiogenic region from E10.5 mouse embryo from STZ treated that stimulated hyperglycemic female
|
| Data processing |
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger-atac Suite (v2.0) from 10X genomics
Additional filtering, quality control and doublet removal was done using ArchR (v1.0.1) according to specifications in the tutorials (https://www.archrproject.com/)
Assembly: mm10
|
| |
|
| Submission date |
Mar 17, 2022 |
| Last update date |
Oct 16, 2023 |
| Contact name |
Tomohiro Nishino |
| E-mail(s) |
tomo.nishino@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institutes (UCSF)
|
| Department |
Cardiovascular Disease Institute
|
| Lab |
Srivastava Lab
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE198866 |
Single-cell chromatin accessibility profiling of mouse cardio-pharyngeal development under maternal diabetes mellitus |
| GSE198905 |
Single-cell profiling of mouse cardio-pharyngeal development under maternal diabetes mellitus |
|
| Relations |
| BioSample |
SAMN26752587 |
| SRA |
SRX14495235 |
