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| Status |
Public on Mar 03, 2015 |
| Title |
C57BL6_control WT |
| Sample type |
SRA |
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| Source name |
Brain vessel
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL6
age: 3 months
genotype/variation: WT
tissue: brain vessel
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Lipid tissue kit (Qiagen). PolyA+ RNAs were purified from 1 µg of total RNA using oligo(dT).
Libraries were prepared using the bi-directional RNA-Seq library preparation TruSeq RNA Sample Prep Kits v2 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
Sample 3
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| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.1.6. Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using the Bowtie mapper (version 0.12.7). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from UCSC (mm10) was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample.
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| Submission date |
Jul 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Laurent Jourdren |
| Organization name |
École Normale Supérieure
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| Department |
Biologie
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| Lab |
Genomic platform
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| Street address |
46 rue d'Ulm
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| City |
Paris |
| ZIP/Postal code |
75230 |
| Country |
France |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE59148 |
The Sarcoglycan complex is expressed in the cerebrovascular system and is specifically regulated by astroglial Cx30 channels |
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| Relations |
| BioSample |
SAMN02904320 |
| SRA |
SRX647328 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1429423_expression_3.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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