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Sample GSM1875000 Query DataSets for GSM1875000
Status Public on Jan 27, 2017
Title Perivascular endfeet translatome [Endfeet4]
Sample type SRA
 
Source name Perivascular endfeet translatome
Organism Mus musculus
Characteristics strain: Aldh1L1 JD130
genotype/variation: tg: Aldh1L1-L10aGFP
age: 2 months
tissue: Purified brain vessels
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 SAMN04047487
SRA SRX1224651

Supplementary file Size Download File type/resource
GSM1875000_countgene_output_expression_20150038.tsv.gz 305.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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