|
| Status |
Public on Jan 27, 2017 |
| Title |
Whole astrocyte translatome [Astrocyte1] |
| Sample type |
SRA |
| |
|
| Source name |
Whole astrocyte translatome
|
| Organism |
Mus musculus |
| Characteristics |
strain: Aldh1L1 JD130
genotype/variation: tg: Aldh1L1-L10aGFP
age: 2 months
tissue: Brain
molecule subtype: polysome mRNAs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BAC array purification; mRNAs were purified following the bacTRAP immnuoprecipitation protocol using GFP antibodies and further purified using the RNAeasy protocol (Qiagen).
Ovation RNA-Seq system NuGEN
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha5. Before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 75) using the Bowtie mapper (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from from Ensembl version mm10-ens75 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 75
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample
|
| |
|
| Submission date |
Sep 11, 2015 |
| Last update date |
May 15, 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 |
GPL18480 |
| Series (1) |
| GSE72937 |
The endfeetome, a astroglial translatome of the neurovascular unit |
|
| Relations |
| BioSample |
SAMN04047481 |
| SRA |
SRX1224645 |
