|
| Status |
Public on Oct 14, 2023 |
| Title |
Adult male 24hr+midL4, Wild Type, piRNA, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole Animal
genotype: Wild Type
|
| Treatment protocol |
N/A
|
| Growth protocol |
20-30 male, mid-L4 stage animals were collected of each genotype from C. elegans stocks cultured at 25°C. These male animals were seperately cultured at 25°C until adulthood (24 hours past mid-L4 stage) at which point animals were collected for small RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were extracted using a mirVana miRNA isolation kit (Ambion) following manufacturers protocol. Purified small RNA samples were treated with Acid Pyrophosphotase to allow for cloning of small RNAs bearing a 5' triphosphate.
Libraries were contructured using a TruSeq Small RNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Small RNA sample
|
| Data processing |
Raw data were first analyzed for quality using FastQC (Version 0.12.0).
Adapter sequences were trimmed using CutAdapt (Version 3.7).
Reads were aligned to C. elegans piRNAs (piRNAdb.cel.v1_7_6.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Aligned piRNA reads for each sample were normalized to total number of reads mapping to the C. elegans genome (per million).
Assembly: piRNAdb.cel.v1_7_6
Assembly: ce11genome
Supplementary files format and content: tab-delimited text file includes raw counts of piRNA reads
Supplementary files format and content: tab-delimited text file includes raw counts of reads aligning to C. elegans genome
Supplementary files format and content: xlsx file includes normalization of piRNA reads to the total number of reads aligning to the C. elegans genome per million
|
| |
|
| Submission date |
Oct 10, 2023 |
| Last update date |
Oct 14, 2023 |
| Contact name |
Jacob Manuel Ortega |
| E-mail(s) |
[email protected]
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Genetics
|
| Lab |
Swathi Arur
|
| Street address |
6550 Bertner Ave
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15716 |
| Series (2) |
| GSE245023 |
Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression (piRNA) |
| GSE245025 |
Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression |
|
| Relations |
| BioSample |
SAMN37753970 |
| SRA |
SRX22047814 |
