|
| Status |
Public on Aug 26, 2024 |
| Title |
B6N-OFL-1 |
| Sample type |
SRA |
| |
|
| Source name |
anterior cingulate cortex (ACC) tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: anterior cingulate cortex
strain: C57BL/6NJ mice
condition: OFL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were obtained from anterior cingulate cortex (ACC) tissues using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). TruSeq RNA Sample Prep Kit v2 for Illumina kit was used for the construction of sequencing libraries, 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 NovaSeq 6000 |
| |
|
| Data processing |
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 18, 2023 |
| Last update date |
Aug 26, 2024 |
| Contact name |
Sehyun Chae |
| E-mail(s) |
shchae@kbri.re.kr
|
| Organization name |
Korea Brain Research Institute
|
| Department |
Neurovascular Unit Research Group
|
| Street address |
61, Cheomdan-ro, Dong-gu
|
| City |
Daegu |
| ZIP/Postal code |
41062 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE248193 |
ARNT2 Controls Prefrontal Somatostatin Interneurons Mediating Affective Empathy |
|
| Relations |
| BioSample |
SAMN38314179 |
| SRA |
SRX22567662 |
