|
| Status |
Public on Jun 30, 2018 |
| Title |
RNA E16.5 midbrain r1 |
| Sample type |
SRA |
| |
|
| Source name |
fetal midbrain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: midbrain
developmental stage: E16.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We first extracted total RNA using RNeasy Lipid tissue mini kit from Qiagen (cat no.#74804).
We used Truseq Stranded mRNA LT kit (Illumina, RS-122-2101 and RS-122-2102) to constructed stranded RNA-seq libraries on 4ug of the extracted total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MB_1_E16_5
|
| Data processing |
RNA-seq data was processed using the ENCODE RNA-seq uniform processing pipeline.
Briefly, RNA-seq reads were mapped to the mm10 mouse reference using STAR aligner (version 2.4.0k) with Gencode M4 annotation.
We quantified gene expression levels using RSEM (version 1.2.23), expressed as transcripts per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: A matrix of TPM values of each gene in each sample
|
| |
|
| Submission date |
Jun 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE100685 |
Dynamic methylome remodeling throughout mammalian fetal development |
|
| Relations |
| BioSample |
SAMN07304093 |
| SRA |
SRX2973673 |
