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Sample GSM632213 Query DataSets for GSM632213
Status Public on Dec 02, 2010
Title L1_arrest
Sample type SRA
Source name wild-type L1 arrest
Organism Caenorhabditis elegans
Characteristics strain: wild-type N2_hermaphrodites
developmental stage: developmentally arrested L1
growth condition: 20 °C
stress conditions: L1s without food for 48 hrs
Treatment protocol Wild-type N2 young adults were exposed to each stress during Day 0 stage (day X represents days post-L4 molt), 6 hrs at 32 °C for heat shock treatment and 12 hrs for PA14 exposure. RNAs were purified from Day 1 stage animals just after stress treatment together with the untreated control. As for L1 arrest sample, prepared embryos were incubated without a food source in M9 buffer for 48 hrs, and then used for RNAs preparation.
Growth protocol Wild-type N2 hermaphrodites were maintained for a few generations without starvation at 20 °C to collect embryos. After embryos were harvested, they were incubated at 20 °C without a food source in M9 buffer for 24 hrs with rotation to arrest their growth at the L1 stage. Synchronized animals were exposed to each stress when they were Day 0 young adult (day X represents days post-L4 molt). As for L1 arrest sample, embryos were prepared in a similar manner but incubated without food for 48 hrs.
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared using the mirVana miRNA Isolation kit (Ambion), and 10 μg of total RNAs were used for cDNA library preparation for small RNAs using the DGE-Small RNA Sample Prep Kit ver. 1.0 (Illumina) according to the manufacturers' instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing The raw data were aligned to the C. elegans genome (genome build WormBase WS190) using the SOAP program (ver. 1.10 Li, R. et al., Bioinformatics 24: 713-714. 2008) with the following command options: –w 5 –S 3 –A TCGTATGCCGTCTTCTGCTTGT (maximum 2 base pair mismatches were allowed as a default option). Then, the number of times of each read sequenced was examined.
Submission date Dec 01, 2010
Last update date May 15, 2019
Contact name Frank J Slack
Organization name Yale University
Department MCDB
Street address 266 Whitney Ave
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
Platform ID GPL9269
Series (1)
GSE25739 Changes in expression of small non-coding RNAs, including microRNAs, in response to stress in C. elegans
SRA SRX033026
BioSample SAMN00139638

Supplementary file Size Download File type/resource
GSM632213.txt.gz 4.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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