|
| Status |
Public on Sep 10, 2014 |
| Title |
PL_drug_18hr_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
young adult hermaphrodites
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: puf-8; lip-1
treatment type: 100 uM U0126
treatment length (hrs): 18
developmental stage: young adult hermaphrodites
|
| Treatment protocol |
For DMSO or U0126 treatments, young adults were transferred to 1 mL of S media supplemented with OP50 bacteria and either DMSO vehicle alone or 100 uM U0126 (Sigma).
|
| Growth protocol |
Synchronized L1 worms were grown to young adulthood on seeded NGM plates.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were washed and pelleted, flash frozen with liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA Illumina software 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ce10 whole genome and WS220 poly(A)+ transcriptome using tophat with options -m 2 -G 1 -g 1
Normalized gene and isoform counts per million were obtained from SAM files using scripts with the DESeq vignette (Anders and Huber, Genome Biology, 2010).
Genome_build: ce10
Supplementary_files_format_and_content: tab-delimited text files including CPM (counts per million) for each sample
|
| |
|
| Submission date |
Jan 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Elena Sorokin |
| E-mail(s) |
sorokin@wisc.edu
|
| Organization name |
UW-Madison
|
| Department |
Biochemistry
|
| Lab |
Kimble
|
| Street address |
433 Babcock Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53703 |
| Country |
USA |
| |
|
| Platform ID |
GPL13776 |
| Series (1) |
| GSE54030 |
Competence for reprogramming sex |
|
| Relations |
| BioSample |
SAMN02582741 |
| SRA |
SRX426040 |
