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| Status |
Public on Jul 10, 2018 |
| Title |
F3 testis chlordecone 1mg 2 |
| Sample type |
SRA |
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| Source name |
testes
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: testes
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| Growth protocol |
We treated adult female mice with chlordecone with doses 0 (control), 100 Xg/kg/day and 1 mg/kg/day during gestation period E6- E15. Male born from Chlordecone- treated mice were crossed for a three generations. The testes from F3 generations were taken for mRNA extraction. For mRNA extraction we used columb. Three biological replicates used for each condition . We hypothesize that chlordecone cause changes in mRNA due to transgenerational effect of pesticides (Skinner et al, Science 2005).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA-seq 10 mkg of total RNA was used. Total RNA was extracted using Trizol reagent
A strand-specific library preparation protocol for RNA sequencing was performed using the sequencing technological platform at IGBMC, Strasbourg, France. Paired end, 50-bp sequencing stranded RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The reads in FASTQ format were processed for quality control using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For the analysis of differentially expressed genes, the quality-checked reads for each condition were processed using the TopHat version 2.0.12 package (Kim et al. 2013). The reads were mapped to the reference genome [Mus musculus Ensembl mm10 sequence], and the alignment files were generated as BAM files. These files were used as the input for Cufflinks, a complement method used to generate assembled transcripts for each condition; the abundance was evaluated using read data. The assembled transcripts were compared and annotated using Cuffmerge against the Ensembl (mm10) gene annotations (Trapnell et al. 2012). These assemblies are used in Cuffquant and Cuffnorm from the Cufflinks 2.2.1 package to calculate the expression levels. To identify transcripts differentially expressed between chlordecone- and control-derived samples, we first selected the cases for which we obtained values greater than the 50th quantile of all values in at least one condition, and then we filtered transcripts which are more than a 2-fold different between chlordecone and control -derived samples. Finally, we employed a statistical test implemented in the R package, Limma, with the false-discovery rate set at less than 5% (Ritchie et al. 2015). RNA-Seq data were visualized using the Integrated Genomics Viewer (version 2.3.36) (Thorvaldsdottir et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph
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| Submission date |
Sep 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxiang HAO |
| E-mail(s) |
chunxianghao@outlook.com
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| Organization name |
Université de Rennes 1
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| Street address |
263, ave du Général Leclerc
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| City |
rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE86438 |
Transgenerational effect of Chlordecone [RNA-seq] |
| GSE86440 |
Transgenerational effect of Chlordecone |
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| Relations |
| BioSample |
SAMN05730088 |
| SRA |
SRX2138780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2302777_accepted_hits_Chlor_1mg_2_run12_sorted.bedgraph.gz |
291.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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