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Sample GSM1301735 Query DataSets for GSM1301735
Status Public on Mar 27, 2014
Title OP50_hj41_1
Sample type SRA
Source name whole animal
Organism Caenorhabditis elegans
Characteristics strain/genotype: rde-12(hj41)
developmental stage: young adult
bacteria: OP50
Growth protocol Synchronized L1 worms were grown on RNAi plates seeded with HT115 E. coli expressing a sel-1 RNAi trigger as previously described (Pak and Fire 2007) or OP50. After 50 hrs at 20oC, ~50000 worms were washed 5 times with 10ml M9, and then homogenized in Tri-reagent. Samples were kept at -80oC.
Extracted molecule total RNA
Extraction protocol Purified total RNA were processed with MirVana kit (Invitrogen) for small RNA enrichment. Equal amount of small RNAs (30~40ug) were resolved on 15% TBE-Urea Acrylamide gels. Gels containing small RNAs of 20-26nt were cut out and purified with a small-RNA PAGE Recovery Kit (Zymo Research, R1070).
Each small RNA sample was treated with TAP and processed with the ScriptMiner Small RNA-Seq Library Preparation Kit (Epicentre, SMMP1012). Libraries from different samples were indexed with RNA-Seq Barcode Primers (Epicentre, RSBC10948). Two biological samples of each condition (wild type +sel-1 RNAi, rde-12+sel-1 RNAi, wild type+OP50 and rde-12+OP50) were used for library preparation
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
Data processing Sequencing reads were clipped with Fastx_clipper (v0.0.13) to remove adaptor sequence
Alignment was performed using TopHat (1.4.1) using the ce6 reference genome. Alignment was performed on each replicate separately and then the resulting alignments were merged using samtools. These merged alignments were used for the rest of the downstream analysis
Bedtools was used to determine the number of reads aligned to the different types of small RNA.
Genome_build: ce6
Supplementary_files_format_and_content: tab-delimited text files include counts of small RNA for each sample in listed genes or regions. File (small RNA expression.txt) shows the abundance of small RNA that we quantified, OP50_N2_sample_1_counts represents small RNA counts in sample 1 of N2 animals fed with OP50; OP50_N2_sample_2_counts represents small RNA counts in sample 2 of N2 animals fed with OP50; OP50_hj41_sample_1_counts represents small RNA counts in sample 1 of hj41 animals fed with OP50; OP50_hj41_sample_2_counts represents small RNA counts in sample 2 of hj41 animals fed with OP50. File(sel-1 siRNA expression.txt) shows the small RNA abundance in gene sel-1 locus; region represents the region where small RNAs were mapped to; counts represents the number of small RNA that were mapped to that region.
Submission date Jan 06, 2014
Last update date May 15, 2019
Contact name Huan Yang
Organization name Stowers Institute for Medical Research
Lab Mak Lab
Street address 1000 East 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
Platform ID GPL13657
Series (1)
GSE53830 The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans
BioSample SAMN02569748
SRA SRX415103

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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