|
| Status |
Public on May 09, 2023 |
| Title |
WT-21_2-cell |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 2-cell
tissue: embryo
strain: C57BL6
age: 26 - 28 hours post fertilization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two-cell embryos were collected between 26 and 28 hours post fertilization. Each embryo was immediately placed into a single well of a plexWell Rapid Single Cell plate (SmartSeq Platform), which was then frozen until sample prep.
Libraries were generated from 2 cell embryos using Smart Seq2 platform.
Single-embryo RNA sequencing using NovaSeq 6000 Illumina platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Smart-seq2
Sample_5056-LM-20
|
| Data processing |
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression matrix
|
| |
|
| Submission date |
Feb 14, 2023 |
| Last update date |
May 09, 2023 |
| Contact name |
Qianyi Ma |
| E-mail(s) |
qzm100@gmail.com
|
| Organization name |
University of Michigan
|
| Department |
Human Genetics
|
| Street address |
1141 E Catherine St
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE225270 |
Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1 [scRNA-Seq] |
| GSE225271 |
Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1 |
|
| Relations |
| BioSample |
SAMN33285530 |
| SRA |
SRX19364285 |
