|
Status |
Public on Jun 11, 2009 |
Title |
N2_starved L1_rep 2 |
Sample type |
SRA |
|
|
Source name |
N2 starved L1 RNA
|
Organism |
Caenorhabditis elegans |
Characteristics |
strain: N2 stage: Starved L2
|
Growth protocol |
Worms were routinely grown on plates to obtain many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. For L1 stage samples, After collect adults from liquid culture and bleach to obtain embryos, The embryos were hatched overnight in M9 Buffer without any food to obtain L1s. The pellet can be stored at -80 oC.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted by TRIzol (Invitrogen) according to the manufacturer’s protocol (TRIzol: pellet= 2:1). PolyA RNA was purified using the Applied Biosystem (Ambion) MicroPoly(A) Purist kit. PolyA RNA was fragmented using Fragmentation Reagent (Ambion). First strand cDNA was synthesized from polyA RNA using a mixture of oligo dT and random primer (Invitrogen). Double stranded cDNA synthesis was performed using the SuperScript double stranded cDNA synthesis kit (Invitrogen).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
n/a
|
Data processing |
RNA-Seq libraries were prepared for sequencing using the Illumina protocol as described (Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-9 (2008)). RNA-seq scoring was performed as previously described (Hillier, L.W. et al. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19, 657-66 (2009)).
|
|
|
Submission date |
Jun 11, 2009 |
Last update date |
May 15, 2019 |
Contact name |
Flora Vaccarino |
Organization name |
Yale University
|
Department |
Child Study Center
|
Lab |
Vaccarino
|
Street address |
230 South Frontage Road
|
City |
New Haven |
State/province |
CT |
ZIP/Postal code |
06520 |
Country |
USA |
|
|
Platform ID |
GPL9309 |
Series (1) |
GSE16552 |
Transcriptome of wild type N2 worms at embronic stage and starved L1 stage |
|
Relations |
SRA |
SRX006988 |
BioSample |
SAMN02197708 |