|
| Status |
Public on Jun 22, 2021 |
| Title |
Transcriptome_E13.5_Brain Explant_Control-rep2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
E13.5 forebrain
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E13.5
tissue: forebrain
strain: ICR
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Forebrain were dissocated with trizol to obtain total RNA.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 |
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v. 2.3.5.1) with default parameters. MACS (v. 2.2.5) was used to call peaks (-q 0.05) relative to the IgG sample.High-quality reads of RNA-seq were quantified using Salmon (v.1.0.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).
Genome_build: GRCm38
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Dai Shang Kun |
| E-mail(s) |
daisk@sdut.edu.cn
|
| Organization name |
Shandong University of Technology
|
| Department |
School of Life Sciences and Medicine
|
| Lab |
Laboratory of Developmental and Evolutionary Biology
|
| Street address |
266 Xincun West Road
|
| City |
Zibo |
| State/province |
Shandong |
| ZIP/Postal code |
255000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE124540 |
ChIP-seq and RNA-seq analysis of histone Kcr in the embryonic forebrain and neural stem/progenitor cells. |
|
| Relations |
| BioSample |
SAMN16584107 |
| SRA |
SRX9391050 |
