|
| Status |
Public on Jan 01, 2024 |
| Title |
DKO-B-3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
genotype: PS1/PS2 DKO
treatment: water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCm38.p6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 24, 2022 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Bo Meng |
| E-mail(s) |
bmeng2019@gmail.com
|
| Organization name |
East China Normal Univeristy
|
| Street address |
3663 Zhongshan Rd(N.)
|
| City |
Shanghai |
| ZIP/Postal code |
200062 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE211983 |
Chronic oral administration of nicotine affects transcriptomic profiling in conditional Presenilin 1/2 knockout mice and wild type mice |
|
| Relations |
| BioSample |
SAMN30480401 |
| SRA |
SRX17198939 |
