|
| Status |
Public on Mar 08, 2023 |
| Title |
P0-M-WT3: P0-male-wildtype replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: whole brain
age: P0
Sex: male
genotype: wildtype
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
P0-M-WT3
|
| Data processing |
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.
|
| |
|
| Submission date |
Feb 18, 2021 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Eunjoon Kim |
| E-mail(s) |
kime@kaist.ac.kr
|
| Phone |
82-42-350-2633
|
| Organization name |
IBS/KAIST
|
| Department |
Center for Synaptic Brain Dysfunctions/Department of Biological Sciences
|
| Street address |
Kuseong-dong
|
| City |
Daejeon |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE167053 |
Transcriptome analysis of Chd8 S62X heterozygote mutant and wild-type mice |
|
| Relations |
| BioSample |
SAMN17979730 |
| SRA |
SRX10125859 |
