|
| Status |
Public on Jun 09, 2014 |
| Title |
prg-1_L2_small RNA |
| Sample type |
SRA |
| |
|
| Source name |
prg-1 L2, whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
genotype: prg-1 mutant
strain: wm161
|
| Growth protocol |
Animals were grown at 20˚C with feeding on OP50
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each of the six different developmental stages using the Trizol protocol. Small RNAs were size-selected by gel electrophoresis, and used poly(A) to extract L1-L4 mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Removed the low quality sequence and adaptor using the independent development of software by BGI
Removed the sequence smaller than 18nt
Removed the sequence containing polyA
Achieved clean datasets from BGI, length-reads-sequence
Clean small RNAs aligned to the ce10 genome with no mismatach by using Bowtie-0.12.8
genome build: ce10
|
| |
|
| Submission date |
Mar 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiajia Wang |
| E-mail(s) |
wangjiajia_816@126.com
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Lab |
Key Laboratory of the Zoological Systematics and Evolution
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE56272 |
The expression of small RNAs after prg-1 mutation |
| GSE56274 |
The expression of mRNAs and small RNAs after prg-1 mutation |
|
| Relations |
| BioSample |
SAMN02709112 |
| SRA |
SRX501870 |
