|
| Status |
Public on Feb 13, 2023 |
| Title |
EV3, 37C |
| Sample type |
SRA |
| |
|
| Source name |
C. elegans N2 ; control RNAi
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
temperature: 37C
strain: N2
treatment: control RNAi
|
| Treatment protocol |
C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50. Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C. The adults were then subjected to heat shock at 37C for hours and collected for RNA isolation and library prep
|
| Growth protocol |
C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50. Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Young adult C. elegans were lysed in 0.5% SDS, 5% b-ME, 10 mM EDTA, 10 mM Tris-HCl pH 7.4, 0.5 mg/ml Proteinase K, then RNA was purified with Tri-Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA for deep sequencing was purified by Qiagen RNAeasy. Duplicate samples were sent for library construction and sequencing at BGI (China)
Raw sequencing reads were processed using an in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School
The raw read pairs were first aligned to C. elegans reference genome with ws245 annotation. The RSEM method was used to quantify the expression levels of genes
Deseq was used to produce differentially expressed gene sets with more than a 2-fold difference in gene expression, with replicates being within 0.05 in a Students T test and a False Discovery Rate (FDR) under 0.01.
Statistics were calculated with DeBrowser
Assembly: ce11 with ws254 notations
Supplementary files format and content: abundance measurements
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Feb 13, 2023 |
| Contact name |
Amy K Walker |
| E-mail(s) |
[email protected]
|
| Organization name |
UMass Chan Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Amy Walker
|
| Street address |
Suite 137, Biotech 2, 373 Plantation St
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE223596 |
S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress [RNA-seq: sams-4 RNAi, Heat shock] |
| GSE223597 |
S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress |
|
| Relations |
| BioSample |
SAMN32886865 |
| SRA |
SRX19148256 |
