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| Status |
Public on Sep 04, 2018 |
| Title |
Spinal cord 1 |
| Sample type |
SRA |
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| Source name |
Spinal cord
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
tissue: Spinal cord
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| Extracted molecule |
total RNA |
| Extraction protocol |
From each rat, 5 structures of the central nervous system were dissected : the olfactory bulb, a part of the cortex, the hippocampus, the striatum and the dorsal spinal cord, and immediately placed into a 1,5 mL tube containing 700 uL of TriZol reagent (Qiagen), on ice. Samples were crushed with the Fast Prep 24 instrument (MP Biomedicals). Total RNA was extracted following the manufacturer’s instructions, allowing an isolation of all RNAs including the small RNAs (miRNeasy Micro Kit, Qiagen).
Libraries were synthesized from 1 ug of RNA for each sample, following the manufacturer’s instructions (NEXTflex Illumina Rapid directional mRNA-Seq, BiooScientific).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence then mapped to rat genome (Rnor6.0 ) using STAR in default parametres with quantifification mode --quantMode GeneCounts
Genome_build: Rn6.0
Supplementary_files_format_and_content: tab-delimited text files include number of reads per gene for each sample
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| Submission date |
Aug 31, 2018 |
| Last update date |
Sep 04, 2018 |
| Contact name |
Alexandre FAVEREAUX |
| E-mail(s) |
alexandre.favereaux@u-bordeaux.fr
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| Phone |
+33533514763
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| Organization name |
CNRS UMR 5297
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| Street address |
146 rue leo saignat
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| City |
Bordeaux |
| ZIP/Postal code |
33000 |
| Country |
France |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE119349 |
Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures |
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| Relations |
| BioSample |
SAMN09943342 |
| SRA |
SRX4630585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3371629_M1_ReadsPerGene_final.txt.gz |
144.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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