|
| Status |
Public on Jun 14, 2018 |
| Title |
SPR_CO_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mature sperm cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
tissue: mature sperm cells
|
| Treatment protocol |
Males were fed etiher a control or low-protein (LP) diet from 3 to 10 weeks of age.Mature sperm was collected from fathers and Mammary tissue from their female offspring.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary gland and sperm samples were removed. Frozen crushed tissue were used for RNA extraction according with the manufacturer's instructions. The total RNA was performed using miRNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Small RNA
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.3.4.1 with parameters --sensitive-local -p 4 -q
Exon, piRNA, miRNA, precursor, GtRNA and ncRNA GTF files were acquired from UCSC genome browser. Raw reads were generated from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw reads for each Sample
|
| |
|
| Submission date |
May 14, 2018 |
| Last update date |
Jun 14, 2018 |
| Contact name |
Lu Jin |
| E-mail(s) |
lj74@georgetown.edu
|
| Organization name |
Georgetown University
|
| Department |
Oncology
|
| Lab |
NRB Room W405B
|
| Street address |
3970 Reservoir Rd NW
|
| City |
Washington |
| State/province |
D.C. |
| ZIP/Postal code |
20057 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE114421 |
Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model (small RNA-seq) |
| GSE114423 |
Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model |
|
| Relations |
| BioSample |
SAMN09206636 |
| SRA |
SRX4081195 |
