|
| Status |
Public on Feb 26, 2024 |
| Title |
E10.5 otocyst Sox2CreER/+ replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
E10.5 otocyst
|
| Organism |
Mus musculus |
| Characteristics |
tissue: E10.5 otocyst
genotype: Sox2CreER/+
|
| Treatment protocol |
N/A
|
| Growth protocol |
Timed pregnancies were established to generate litters of embryos, with the morning of seminal plug detection marking E0.5. The day of birth was defined as Postnatal day 0 (P0).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Otocysts were collected from E10.5 embryos in ice-cold PBS and RNALater (Ambion AM7021). RNA was isolated from pairs of otocysts from three embryos of each genotype (WT, Chd7Gt/+, Sox2CreER/+ and Chd7Gt/+;Sox2CreER/+) using the RNAqueous Micro Scale RNA Isolation kit according to the manufacturer’s instructions (Ambion AM1931, Austin, TX).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions (NEB E7760, Ipswich, MA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Libraries were subjected to 151-bp paired-end sequencing on an Illumina NovaSeq machine following the manufacturer’s protocol (Illumina, San Diego, CA).
Bcl2fastq2 Conversion software was used to create de-multiplexed FastQ files (Illumina).
Sequencing reads were trimmed with Cutadapt v2.3 (2) and read quality was assessed using FastQC v0.11.8 (3).
Reads were aligned to the mouse reference genome GRCm38 (ENSEMBL) with STAR v2.7.8a (4) and RSEM v1.3.3 was used to assign count estimates to aligned genes (5).
Quality control metrics from this pipeline were integrated and evaluated using multiQC v1.7 (6)
Assembly: mm9
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
|
| |
|
| Submission date |
Jul 26, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Donna Martin |
| E-mail(s) |
donnamm@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
1150 Medical Center Dr
|
| City |
Ann Arbor |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE239361 |
CHD7 and SOX2 Act in a Common Gene Regulatory Network During Mammalian Semicircular Canal and Cochlear Development (RNA-Seq) |
| GSE239363 |
CHD7 and SOX2 Act in a Common Gene Regulatory Network During Mammalian Semicircular Canal and Cochlear Development |
|
| Relations |
| BioSample |
SAMN36718185 |
| SRA |
SRX21166580 |
