|
| Status |
Public on Feb 14, 2013 |
| Title |
WT + NO rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: WT
age: L4
agent: NO
|
| Treatment protocol |
Synchronized stage L4 C.elegans were treated with 1mM MAHMA NONOate, let recover for 4 hours at 20oC and then total RNA isolated.
|
| Growth protocol |
C.elegans were grown on NGM plates seeded with E.coli OP50 at 20oC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C.elegans mixed with Trizol reagents were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) 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 II |
| |
|
| 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 run through the tophat (version 2.0.2) / cufflinks (version 2.0.5) pipeline against Ensembl WS220 C.elegans genome assembly with the default parameters.
CummeRbund package version 2.0.0 with R version 2.15.2 were used for the analysis and visualization of the differential gene expression results.
Genome_build: WS220 (Ensembl release 66)
Supplementary_files_format_and_content: tab-delimited text file that includes FPKM values for each Sample and differential expression test statistics.
|
| |
|
| Submission date |
Jan 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ivan Gusarov |
| E-mail(s) |
gusari01@nyumc.org
|
| Organization name |
NYU School of Medicine
|
| Department |
Biochemistry
|
| Street address |
450E 29th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE43614 |
NO-mediated transcriptional response in C. elegans |
|
| Relations |
| SRA |
SRX218383 |
| BioSample |
SAMN01889435 |
