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Sample GSM2647711 Query DataSets for GSM2647711
Status Public on Sep 23, 2019
Title 10-1day-Kainate-technical-replicate-b
Sample type SRA
 
Source name Hippocampus CA1 area
Organism Mus musculus
Characteristics genetic background: C57BL6
time: 1 day
treatment: Kainate
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel). For each sample 10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards an average of 180 ng of amplified cDNA was used to prepare libraries.
Libraries were prepared using the Nextera XT DNA kit (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina Bcl2fastq 2.17.1.14 software was used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.0-beta3, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome from Ensembl version 81 using STAR (version 2.4.0k). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced genes were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq2 1.8.1 [5]. Statistical treatments and differential analyses were also performed using DESeq2 1.8.1.
Genome_build: mm10 (Ensembl 81)
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample
 
Submission date Jun 01, 2017
Last update date Sep 23, 2019
Contact name Stephane Le Crom
Organization name IBENS
Department Genomic Core Facility
Street address 46 rue Ulm
City PARIS
ZIP/Postal code 75230
Country France
 
Platform ID GPL19057
Series (1)
GSE99577 Lipid signaling during neuronal degeneration in KA-treated mice
Relations
BioSample SAMN07189242
SRA SRX2879060

Supplementary file Size Download File type/resource
GSM2647711_expression_output_expression_2015559b.tsv.gz 167.1 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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