|
| Status |
Public on Jun 22, 2016 |
| Title |
N2 (wild type) 25ºC |
| Sample type |
SRA |
| |
|
| Source name |
N2 (wild type)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4; preadults
genotype/variation: N2 (wild type)
condition: shifed to 25ºC (restrictive temperature)
tissue: whole nematode
|
| Treatment protocol |
Nematodes were shifted to 25ºC at the L3/L4 stage for 22 hr or kept at 15ºC.
|
| Growth protocol |
Nematodes were grown as semi-synchronized populations at 15ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from approximately 3,000 worms using an RNeasy Kit (Qiagen) with in-column DNase digestion. The RNA quality was verified to have an RNA integrity number (RIN) greater than 8.0 through using a Bioanalyzer (Agilent).
Stranded mRNA-seq (mRNA sequencing) libraries were prepared from poly(A) RNA after oligo(dT) selection.
Paired-end mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ADTH04
N2 25ºC (FPKM)
|
| Data processing |
The paired-end reads were aligned to C elegans genome WS220/ce10 by using STAR aligner (https://github.com/alexdobin/STAR).
The expression of C elegans genes was quantified by using HOMER (http://homer.salk.edu).
The differential gene expression analysis was performed by using edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: WS220/ce10
Supplementary_files_format_and_content: FPKM expression values of C elegans WS220/ce10 genes, as computed by HOMER (http://homer.salk.edu)
|
| |
|
| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Heimbucher |
| E-mail(s) |
thomas.heimbucher@biologie.uni-freiburg.de
|
| Organization name |
Thomas Heimbucher
|
| Department |
Biologie III
|
| Lab |
Ralf Baumeister
|
| Street address |
Schaenzlestrasse 1
|
| City |
Freiburg |
| State/province |
Baden Württemberg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE70117 |
RNA sequencing analysis of DAF-16 target gene expression when math-33 function is genetically inactivated |
|
| Relations |
| BioSample |
SAMN03785129 |
| SRA |
SRX1067758 |
