|
| Status |
Public on Jun 25, 2024 |
| Title |
siControl_2 |
| Sample type |
SRA |
| |
|
| Source name |
HCN
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: HCN
cell type: Rat hippocampus-derived neural stem cells
genotype: Control knockdown
treatment: Induction to quiescence state
|
| Treatment protocol |
Derlin-1 was knocked down by reverse transfection using Thermo's Stealth RNAi™ siRNA.Thermo's Stealth RNAi™ siRNA Control Duplex was used as a control knockdown.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent RNAScreenTape. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (version 0.39) (parameter- adapters:NexteraPE-PE, LEADING:20 TRAILING:20, SLIDINGWINDOW:4:15, MINLEN:50)
Trimmed sequence reads were mapped to rn6 using STAR (version 2.7.3a) (parameters- quantMode: TranscriptomeSAM)
The mapped sequences were converted to TPM (transcripts per million) using RSEM (version 1.3.2) (parameter- --paired-end --estimate-rspd)
Differential gene expression analysis was performed using edgeR (version 3.28.1) (used function- calcNormFactors(), estimateCommonDisp(), estimateTagwiseDisp(), exactTest())
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 08, 2023 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Naoya Murao |
| E-mail(s) |
naoya_murao@med.miyazaki-u.ac.jp
|
| Organization name |
University of Miyazaki
|
| Department |
Medical Sciences
|
| Lab |
Biochemistry and Molecular Biology
|
| Street address |
Kihara5200
|
| City |
Miyazaki |
| ZIP/Postal code |
889-1692 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE229251 |
Transcriptome analysis of Derlin-1 knockdown neural stem cells |
|
| Relations |
| SRA |
SRX19910861 |
| BioSample |
SAMN34121436 |
