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| Status |
Public on Mar 17, 2014 |
| Title |
pid-1(xf14)_TAP |
| Sample type |
SRA |
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| Source name |
pid-1(xf14) TAP
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: RFK180 (mjls144 [Pmex-5::egfp::his-58::21UR-1_as::tbb-2(3’UTR)] II, pid-1 (xf14) II)
treatment: TAP
library prep: NEBNext small RNA
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| Growth protocol |
C. elegans was cultured on NGM plates with E. coli OP50 as food source
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from a synchronized adult population using Trizol (Sigma- Aldrich)
Samples were enriched for small RNAs using the Mirvana kit from Life Technologies. For CIP treated samples 5 ug of small RNAs were treated with 50 U of calf intestine phosphatase (CIP, NEB) at 37C for 1 hour (Gu et al. 2012), followed by Trizol extraction and TAP treatment. One µg of enriched small RNA was size-selected between 15- to 30-nt on 15% TBE-urea gel after treating with 10 U of tobacco acid phosphatase (Epicenter) at 37°C for 2 h to digest 5’ tri- and di-phosphates to mono-phosphates. NebNext small RNA: Small RNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) according to the manufacture’s instruction. In brief, small RNA was first ligated to the 3’ adapter and then the 5’ adapter, both for 1 h at 25°C. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 15 cycles using NEBNext index primers #13-24. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit. Only the fraction containing 135-161 bp was pooled in equal molar ratio. Kamminga2012: Library preparation as described in Kamminga et al., PloS Genetics 8(7):e1002702, 2013.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
Adapter trimming performed using Flexbar version 2.4
Small RNA reads aligned to C. elegans Wbcel215 including additional sequence for GFP_HIS_66 construct.
Read counts for known miRNA and 21U RNA loci obtained using girafe 1.0 Bioconductor package.
Genome_build: WBcel215, additional sequence for GFP_HIS_66 construct.
Supplementary_files_format_and_content: Read assignments to known 21U loci in csv (tab separated). Column names: strand, read ref, chromosome, vread start, read length, corresponding 21U name, corresponding 21U sequence, read start position relative to 21U locus, read end position relative to 21U locus.
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| Submission date |
Feb 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Holger Klein |
| Organization name |
Boehringer Ingelheim Pharma GmbH & Co KG
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| Department |
global Computational Biology and Digital Sciences
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| Street address |
Birkendorfer Str. 65
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| City |
Biberach an der Riß |
| State/province |
Rhineland Palatinate |
| ZIP/Postal code |
88397 |
| Country |
Germany |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE55309 |
PID-1 is a novel factor that operates during 21U RNA biogenesis in Caenorhabditis elegans |
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| Relations |
| BioSample |
SAMN02650954 |
| SRA |
SRX475456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1333908_pid-1_xf14_TAP.csv.gz |
199.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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