|
| Status |
Public on Oct 12, 2016 |
| Title |
RNA-seq of L2 larvae at 34°C, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
L2 larvae
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L2 larvae
tissue: whole animal
strain: N2
genotype: wild type
|
| Treatment protocol |
Worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.
|
| Growth protocol |
Age synchronization was achieved by treatment of alkaline hypochlorite solution and eggs were hatched in M9. L1 larvae were transferred to 10 cm NGM plates seeded with OP50 and grown at 20°C to mid-L2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Trizol and QIAGEN RNeasy RNA extraction kit with on-column DNaseI digestion as per manufacturer’s instructions.
polyA selection and library construction were done following the Illumina Truseq RNA sample preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using TopHat2 (Kim et al. 2013) with default settings except that the proper intron size for C. elegans genes (10 to 22000 bp) was used.
Expression analyses were done using Cuffdiff (Trapnell et al. 2010) with quartile normalization. The exon model used in the analyses was based on the gtf file queried from Wormbase (WS220).
Genome_build: ce10/WS220
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed genes upon heat shock (FDR 0.05).
|
| |
|
| Submission date |
May 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University
|
| Department |
Molecular Biosciences
|
| Lab |
Morimoto
|
| Street address |
2205 Tech Drive, Hogan 2-100
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE81520 |
RNA-seq analysis in C. elegans larval development and heat shock |
| GSE81523 |
E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response |
|
| Relations |
| BioSample |
SAMN05004781 |
| SRA |
SRX1769981 |
