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| Status |
Public on May 21, 2021 |
| Title |
HPD group1 |
| Sample type |
SRA |
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| Source name |
spermatozoa
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
cell type: spermatozoa
age: 5-months old rat
genotype: wild type
diet: High Protein (HPD)
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| Growth protocol |
Male Wistar rats at the age of 10 weeks, weighing approximately 330 g, were housed (2 rats per cage) and divided into two groups. One group was fed with standard diet (SD group) . The other group was fed with a high-protein diet (HPD) for 2 to 3 months (HPD group)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sperm were collected from epididym, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
small RNA
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| Data processing |
Illumina Casava1.7 software used for basecalling.
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.
Annotation through the pipeline SPORTS1.0
Generation of normalized abundance measurements through DESeq2
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: excel files with number of read counts
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| Submission date |
Mar 18, 2021 |
| Last update date |
May 21, 2021 |
| Contact name |
Maria Stathopoulou |
| E-mail(s) |
maria.stathopoulou@inserm.fr
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| Organization name |
Inserm
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| Department |
U1065, C3M
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| Lab |
Team 10
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| Street address |
151 Route de Saint-Antoine de Ginestière
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| City |
Nice Cedex 3 |
| ZIP/Postal code |
06204 |
| Country |
France |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE169157 |
Small RNA-seq comparing transcriptome (small RNAs) of spermatozoa from rat fed either a standard-Diet (SD) or a High-Protein-Diet (HPD) |
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| Relations |
| BioSample |
SAMN18350145 |
| SRA |
SRX10375189 |
| 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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