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Sample GSM3036760 Query DataSets for GSM3036760
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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