|
| Status |
Public on Aug 06, 2024 |
| Title |
scRNA_cMN6_Hb9_E11-5 |
| Sample type |
SRA |
| |
|
| Source name |
CN6 e11.5 GFP-positive and negative
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CN6 e11.5 GFP-positive and negative
genotype: WILDTYPE
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
10x Genomics Chromium Next GEM Single Cell 3' GEM-Library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
HiSeq 4000 software (Illumina) used for basecalling
bcl outputs from HiSeq 4000 were processed using 10x Cell Ranger RNA mkfastq pipeline (https://www.10xgenomics.com/support/software/cell-ranger/) for demultiplexing and fastq file generation
Transcript counts were tabulated using the Cell Ranger count function using default parameters
Tab separated values files and matrix files were processed and analysed using Seurat v4 (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files
|
| |
|
| Submission date |
Jan 24, 2024 |
| Last update date |
Aug 06, 2024 |
| Contact name |
Elizabeth C Engle |
| E-mail(s) |
elizabeth.engle@childrens.harvard.edu
|
| Phone |
6179194030
|
| Organization name |
Boston Childrens Hospital
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE254089 |
Noncoding Mendelian epigenomics - single cell RNAseq mouse cMN data |
| GSE254090 |
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders |
|
| Relations |
| BioSample |
SAMN39597233 |
| SRA |
SRX23381777 |
