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Sample GSM2417733 Query DataSets for GSM2417733
Status Public on Aug 17, 2017
Title 1stOrderSpared_L4_1
Sample type SRA
 
Source name Barrel Cortex B/D Columns Layer 4
Organism Mus musculus
Characteristics group: Spared, first order
age: Postnatal day 23-24
strain: C57BL/6
Extracted molecule total RNA
Extraction protocol Tissue samples originating from the same animal, columns and layer were pooled. Tissue was quickly dissolved in Qiazol (Qiagen #79306) and RNA was isolated using the miRNeasy Mini kit (Qiagen #217004). The extracted RNA was DNAse treated (Thermo Scientific, #EN0521) and finally cleaned up using RNeasy MinElute kit (Qiagen #74204).
The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (New England Biolabs, catalogue #E7530). For the library enrichment, 13-14 PCR cycles were performed
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description B221
Data processing Basecalls were performed using Illumina RTA version 2.4.6.
Reads were trimmed to 75 bp using Trimmomatic version 0.36, with the configurations: PE (Paired End) and CROP:75
Reads were mapped to the mm10 genome using STAR version 2.5.2a; output for all samples can be found in Genecounts_Colourcoded.xlsx
Genome_build: mm10
Supplementary_files_format_and_content: Genecounts_Colourcoded.xlsx contains read counts for all samples after STAR mapping; colours indicate experimental groups (n=4 for all)
 
Submission date Dec 06, 2016
Last update date May 15, 2019
Contact name Koen Kole
E-mail(s) k.kole@neurophysiology.nl
Organization name Donders Institute for Brain Cognition and Behaviour
Department Neurophysiology
Street address Heyendaalsweg 135
City Nijmegen
ZIP/Postal code 6525 EN
Country Netherlands
 
Platform ID GPL19057
Series (1)
GSE90929 Transcriptional changes in the primary somatosensory cortex upon sensory deprivation
Relations
BioSample SAMN06112898
SRA SRX2398402

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

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