|
| Status |
Public on Oct 25, 2022 |
| Title |
E9.5 single cell ATAC WT |
| Sample type |
SRA |
| |
|
| Source name |
Cranial Region
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cranial Region
age: E9.5
strain: C57BL/6J background
genotype: miR-302+/+
developmental stage: TS15 28s
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
E7.5 TS11d 0s whole embryo, E8.25 TS12a 3s cranial region, E8.5 TS13 8-12s cranial region, and E9.5 TS15 26-28s cranial region were harvested for single cell mRNA and single cell ATAC sequencing using a 10X Genomics platform. Embryos were dissected in PBS, the corresponding tissue (whole embryo for E7.5 and cranial region for E8.25-E9.5) was dissociated with papain, neutralized with FBS, and cells were pelleted and resuspended for partitioning on a 10X chromum controller
10x scRNA - Single Cell 3' v3; 10x scATAC v1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or v1.1 (E8.25 ATAC)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
filtered peak bc matrix files
E9.5_KOvWT_ATAC-2022-Signacv1.7.0.rds
|
| Data processing |
Cell Ranger mkfastq version 3.0.2 (mRNA); cellranger-atac mkfastq version 1.1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or version 2.0.0 (E8.25 ATAC)
Cell Ranger count version 3.0.2 (mRNA); cellranger-atac count version 1.1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or version 2.0.0 (E8.25 ATAC)
Seurat 3.1.5 (mRNA); Seurat 4.1.1 and Signac version 1.7.0 (ATAC)
Assembly: mm10
Supplementary files format and content: filtered matrix files for both mRNA and atac
Supplementary files format and content: RDS objects for both mRNA and atac
|
| |
|
| Submission date |
Oct 19, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Rachel Keuls |
| E-mail(s) |
Rachel.Keuls@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
One baylor plaza, Alkek N1020
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE216136 |
Post-transcriptional regulation in cranial neural crest cells expands developmental potential [II] |
| GSE216138 |
Post-transcriptional regulation in cranial neural crest cells expands developmental potential |
|
| Relations |
| BioSample |
SAMN31370021 |
| SRA |
SRX17959310 |
