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| Status |
Public on Jul 13, 2016 |
| Title |
Layer B2 |
| Sample type |
SRA |
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| Source name |
Brain-Piriform Cortex
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks
genotype: wild type
tissue: piriform cortex
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| Treatment protocol |
Fresh-frozen brain section were used to collect the piriform layers by laser capture.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the collected tissue using the RNeasy Micro Kit (Qiagen)
Ovation RNA-Seq system NuGEN
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
layerB replica 2
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| Data processing |
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.2.2. Before mapping, poly N read tails were trimmed, 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 UCSC) 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 UCSC (mm10) 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
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample
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| Submission date |
Jul 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
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| Department |
Genomic Core Facility
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| Street address |
46 rue Ulm
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| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE70800 |
Molecular signatures of neural connectivity in the olfactory cortex |
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| Relations |
| BioSample |
SAMN03855813 |
| SRA |
SRX1091999 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1819204_expression_5.tsv.gz |
374.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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