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| Status |
Public on Jan 16, 2014 |
| Title |
M1W (experimental) |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
developmental stage: adult
tissue: Testis
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| Growth protocol |
Male mice (C57Bl/6) were continuously reared on diet with a high content of lipids (HFD, see Methods) starting at the age of 4 weeks. When 4-month old, they were mated to females grown on control diet. Males were removed after 1 day and control diet was exclusively provided during gestation, lactation, weaning and growth of the progeny.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol procedure (Invitrogen)
SOLiD Total RNA-seq kit (STAR-cDNA-PCR)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Data processing |
Reads has been first filtered against pre-formated fasta file including, SOLiD P1 and P2 adaptors, SOLiD barcodes, polynucleotides (polyA,polyT,polyC and polyG), ribosomal RNAs.
Genome alignment was performs against mm9 release using Bowtie aligner allowing 2 mismatchs after discarding SOLiD adaptor.
Read count was performs using custom Java class based on the parsing of .bam alignment file and sequential annotation using .gff annotation files gathering genomic positions of microRNAs (mirbase release 18), UCSC tRNAs tracks table, Ensembl ncRNAs (release 69) and fRNAdb.
Differential expression analysis has been performed with the DESeq R (bionconductor) package. DESeq size factor normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Not normalized table counts of features identified within all samples.
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| Submission date |
Jan 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL15907 |
| Series (1) |
| GSE43555 |
RNA-mediated paternal heredity of diet induced type II diabetes and obesity. |
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| Relations |
| SRA |
SRX217800 |
| BioSample |
SAMN01888255 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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