 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 05, 2018 |
| Title |
WT_HC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
dorsal hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: dorsal hippocampus
strain: C57BL6
age: 8 months
genotype: WT
Sex: male
|
| Treatment protocol |
Total RNA was extracted from the dorsal hippocampal tissues using TRizol reagent (Invitrogen). Freshly dissected tissues were chopped with a razor blade and 400μl of TRizol reagent were added on half hippocampus. The tissues were homogenized and frozen (20min at -80°C), followed by 3min centrifugation at 14000g to remove cellular debris before chloroform/isoamyl extraction. DNA precipitation was performed on the supernatant using isopropanol and RNAse free glycogen (10min at RT). The pellet was washed once with 70% ethanol and resuspended in milliQ water for DNAse treatment (30min at 37°C). RNA samples were further purified using a phenol/chloroform extraction, followed by a new precipitation (overnight at -20°C, with 100% ethanol, 3M NaOAC and Glycogen RNAse free). The next day two last 70% ethanol washes were done before air drying the resulting RNA pellet. The pellets were resuspended in 30μl nuclease-free milliQ water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq libraries were generated from 300 ng of total RNA Illumina® TruSeq® RNA Sample Preparation Kit v2 (Part Number RS-122-2001). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis followed, using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Sequencing was performed on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Home_Cage (no training)_S
processed data file: S15010_genesdiff_HS179_HS190.txt
|
| Data processing |
Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped onto the mm9 assembly of mouse genome using Tophat v2.0.10 (Kim et al., 2013) and the bowtie v2.1.0 aligner.
Quantification : Gene expression was quantified from uniquely aligned reads using HTSeq v0.5.4p3 (Anders et al., 2013) and gene annotations from Ensembl release 67.
Normalization : Read counts were normalized across libraries with the method proposed by Anders and Huber (2010). Statistical analysis was performed with the method proposed by Love et al. (2014) implemented in the DESeq2 Bioconductor library (v1.0.19).
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing raw read counts, and normalized read counts.
|
| |
|
| Submission date |
Aug 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anne-Laurence Boutillier |
| E-mail(s) |
laurette@unistra.fr
|
| Organization name |
UMR7364
|
| Department |
LNCA
|
| Street address |
12 rue Goethe
|
| City |
Strasbourg |
| ZIP/Postal code |
67000 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE103359 |
Epigenetic correction of defective plasticity in a tauopathy mouse model with an acetyltransferase activator [RNA-Seq] |
| GSE103360 |
Epigenetic correction of defective plasticity in a tauopathy mouse model with an acetyltransferase activator |
|
| Relations |
| BioSample |
SAMN07585821 |
| SRA |
SRX3152296 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
