|
| Status |
Public on Sep 16, 2013 |
| Title |
RNAseq L3 KLE2 het Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: VC768
developmental stage: L2-L3
|
| Treatment protocol |
~500 heterozygote and homozygote early L3 worms were hand picked and resuspended in 1 ml of Trizol and frozen at -80C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by freeze cracking embryos by freezein gin liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from ~0.5-1 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations.
supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.
Genome_build: WS220
|
| |
|
| Submission date |
Aug 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sevinc Ercan |
| Organization name |
New York University
|
| Department |
Biology
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE45678 |
Genome-wide distribution of the three condensin complexes in C. elegans |
|
| Relations |
| BioSample |
SAMN02299583 |
| SRA |
SRX330991 |
