|
Status |
Public on Mar 27, 2014 |
Title |
sel-1_N2_1 |
Sample type |
SRA |
|
|
Source name |
whole animal
|
Organism |
Caenorhabditis elegans |
Characteristics |
strain/genotype: N2 developmental stage: young adult bacteria: HT115(sel-1 RNAi)
|
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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2000 |
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|
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.
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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 |
|
Relations |
BioSample |
SAMN02569751 |
SRA |
SRX415105 |