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| Status |
Public on Sep 23, 2019 |
| Title |
1-6h-NACl-technical-replicate-d |
| Sample type |
SRA |
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| Source name |
Hippocampus CA1 area
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| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL6
time: 6 hours
treatment: NaCl
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Jun 01, 2017 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
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| Department |
Genomic Core Facility
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| Street address |
46 rue Ulm
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| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE99577 |
Lipid signaling during neuronal degeneration in KA-treated mice |
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| Relations |
| BioSample |
SAMN07189266 |
| SRA |
SRX2878978 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2647629_expression_output_expression_2015550d.tsv.gz |
166.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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