|
| Status |
Public on Mar 06, 2019 |
| Title |
RNA-seq_dLGN_Math5KO_P23 |
| Sample type |
SRA |
| |
|
| Source name |
dLGN from P23 Math5-KO mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6J.129-Atoh7tm1Gla/Mmucd
developmental stage: P23
tissue/cell type: brain (dLGN)
genotype: Math5-KO
gender: male
|
| Growth protocol |
Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mouse dLGN tissues using Aurum Total RNA Fatty and Fibrous Kit (BioRad) according to the manufacturer’s instructions. RNA-Seq libraries were generated from total RNA with polyA+ selection using the TruSeq Stranded mRNA Library Preparation Kit (Cat# RS-122-2101, Illumina, San Diego, CA).
RNA-seq 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 |
Sequencing adapters in raw sequencing reads were removed by Cutadapt (v.11.2). Moreover, the bad quality of bases in either ends of reads were trimmed by a customized Perl script. After trimming, reads were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH (.bdg)
|
| |
|
| Submission date |
Jan 22, 2019 |
| Last update date |
Mar 06, 2019 |
| Contact name |
Xiguang Xu |
| E-mail(s) |
xiguang@vt.edu
|
| Organization name |
Virginia Tech
|
| Department |
Department of Biomedical Sciences and Pathobiology
|
| Lab |
Epigenomics and Computational Biology Laboratory
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE125479 |
RNA-seq of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 3, postnatal day 7, postnatal day 14 and postnatal day 23 |
| GSE125482 |
Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day time points |
|
| Relations |
| BioSample |
SAMN10789602 |
| SRA |
SRX5279611 |
