|
Status |
Public on Jun 21, 2018 |
Title |
WT PAX6+ cells, replicate 4 |
Sample type |
SRA |
|
|
Source name |
Embryonic cerebral cortex
|
Organism |
Mus musculus |
Characteristics |
tissue: Embryonic cerebral cortex cell type: radial glia genotype: Prdm16 flox/flox developmental stage: E15.5
|
Extracted molecule |
total RNA |
Extraction protocol |
Sorted cells were resuspended in the lysis solution of RecoverAll total nucleic acid isolation kit (Ambion) and incubated for 3 hrs at 50oC. RNA was then purified according to manufacturer’s instructions. The concentration and quality of purified RNA was determined using BioAnalyzer (Agilent) RNA was reverse-transcribed into cDNA and amplified by RNA-based single primer isothermal amplification (SPIA) using the Ovation RNA-seq system V2 (NuGEN). Synthesized cDNA was sonicated using a Covaris S2 ultrasonicator to reduce fragment size range to 100-600 bp. For library preparation, 100 ng of sheared cDNA was end repaired, ligated with barcoded adaptors, amplified for 9 PCR cycles and purified using the Ovation Ultralow System V2 (NuGEN).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
LIB018752_GEN00046955_S7_L001 LIB018752_GEN00046955_S7_L002
|
Data processing |
Raw reads were examined for quality issues using FastQC Sequenced reads were trimmed for adaptor sequence (if required) using Cutadapt Trimmed reads were aligned to the UCSC genome mm10 using STAR Counts of reads aligning to known genes were generated by featureCounts. Raw counts were normalized and differentially expressed genes were identified using the R Bioconductor package DESeq2 Genome_build: mm10 Supplementary_files_format_and_content: Tab-delimited text files for raw counts and normalized counts
|
|
|
Submission date |
Mar 11, 2018 |
Last update date |
Jun 21, 2018 |
Contact name |
Corey Harwell |
E-mail(s) |
[email protected]
|
Phone |
617-432-5529
|
Organization name |
Harvard Medical School
|
Department |
Neurobiology
|
Street address |
200 Longwood Avenue
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE111660 |
Transcriptome profiling of WT and Prdm16 mutant cells in embryonic mouse cerebral cortex. |
|
Relations |
BioSample |
SAMN08683797 |
SRA |
SRX3780255 |