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Sample GSM415888 Query DataSets for GSM415888
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

Supplementary file Size Download File type/resource
GSM415888_Yale_N2_RNA_StarvedL1_eland_results_rep2_FC30P2UHM_20081217_s_7.txt.gz 331.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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