|
| Status |
Public on Mar 19, 2024 |
| Title |
Week-10 Katnal2 knock-out replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: whole brain
age: 10 week
Sex: male
genotype: Katnal2 Knock-out
|
| Growth protocol |
ES cells containing the Katnal2-targeted allele were received from EUCOMM (MAE-4330; Katnal2tm1a(EUCOMM)Wtsi) and used to generate transgenic mice. The first-generation mice were backcrossed with mice in the C57BL/6J background for more than 5 generations before conducting experiments. Mating with Protamine-Flp mice was used to generate Katnal2fl/+ mice. Fertilized eggs (from the breeding with C57BL/6J WT mice) at the two-cell embryo stage were treated with purified HTNC, a cell-permeable Cre recombinase, at a final concentration of 0.3 μM for 30–40 min. All mice were housed and bred at the mouse facility of Korea Advanced Institute of Science and Technology (KAIST) and maintained according to the Animal Research Requirements of KAIST. All animals were fed ad libitum and housed under 12 h light/dark cycle (light phase during 1 am to 1 pm). Mice were weaned at around the age of postnatal day 21, and mixed-genotype littermate mice with same gender were housed together until experiments. All procedures were approved by the Committee of Animal Research at KAIST (KAIST; KA2020-80).
|
| 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 |
| |
|
| 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.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Mar 19, 2024 |
| Contact name |
Eunjoon Kim |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE219228 |
Transcriptome analysis of Katnal2 knock-out mutant and wild-type mice |
|
| Relations |
| BioSample |
SAMN31994681 |
| SRA |
SRX18465792 |
