|
| Status |
Public on Sep 01, 2016 |
| Title |
Sample5 |
| Sample type |
SRA |
| |
|
| Source name |
Emx1-Cre 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: E10.5
tissue: neocortex
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
neocortices were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent followed by Rneasy Plug Micro Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The library was generated with Kapa stranded mRNA-seq Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadpat to trim low quality bases and Illumina sequencing adapters from the 3'end of the reds.
Only paris where both reads were 20nt or longer were kept for further analysis.
Reads were mapped to the NCBIM38r73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool
Gene counts were compiled using the HTSeq tool.
Normalization and differential expression was carried out using the EdgeR Bioconductor package with the R statistical programming environment
Genome_build: mm10
|
| |
|
| Submission date |
Aug 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Debra Silver |
| E-mail(s) |
[email protected]
|
| Phone |
919-668-7909
|
| Organization name |
Duke University School of Medicine
|
| Department |
Molecular Genetics and Microbiology
|
| Street address |
224 CARL Building
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE85576 |
Transcriptome analyses of EJC haploinsufficient neocortices |
|
| Relations |
| BioSample |
SAMN05571457 |
| SRA |
SRX2019476 |
