 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 03, 2019 |
| Title |
Mut_Krox20 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Sciatic Nerve
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Sciatic Nerve
age: post natal day 14
genotype: Krox20 mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sciatics nerves were dissected at 14 days post natal, and total RNA was harvested using Rneasy Fibrous Tissus ( Qiagen).
Illumina TruSeq RNA Sample Prep Kit was used with 250 ng of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version
Data were filtered before mapping. The reads following these criteria are kept : Illumina quality filter passed, global quality threshold above 30, polyN at the end of reads trimmed, read length above 30
RNAseq reads were aligned to the mm10 genome from Ensembl genome assembly using STAR. Reads were aligned as paired-end reads.
Data were filtered after mapping. Unmapped reads and multimapped reads were discarded.
Reads ailgned in the genes were counted using htseq-count
Normalisation and differential analysis were performed using DESeq1.83
Genome_build: mm10
Supplementary_files_format_and_content: Count text files
|
| |
|
| Submission date |
Nov 27, 2017 |
| Last update date |
Sep 03, 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 |
GPL19057 |
| Series (1) |
| GSE107401 |
Transcriptome analysis of sciatic nerve in mutant krox20 mice at 14 day post natal compared to wild-type mice |
|
| Relations |
| BioSample |
SAMN08102739 |
| SRA |
SRX3425304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2866307_expression_output_expression_20130268.tsv.gz |
181.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
