|
| Status |
Public on Jun 18, 2012 |
| Title |
wild-type (A) |
| Sample type |
SRA |
| |
|
| Source name |
whole animal_wild-type_young adult
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: young adult
genetic background: N2
transgene: NA
barcode: 5' barcode (CGGA)
|
| Treatment protocol |
Synchronized worms were collected as young adults by washes in M9 and worm pellets were snap-frozen in liquid Nitrogen.
|
| Growth protocol |
C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). We used bleaching followed by starvation-induced L1 arrest to generate synchronized cultures. The wild-type strain was Bristol N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA libraries were prepared by Vertis Biotechnologie AG (Martinsried). Briefly total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to ~18-30 nucleotides by denaturing polyacrylamide gel fractionation. cDNA libraries that did not depend on 5'-monophosphates were constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
wild-type (A)
|
| Data processing |
Fastq entries with missing bases or barcodes not matching any of the expected sequences were excluded. Reads were trimmed by removing 5' barcodes (if applicable) and any 3'As. Inserts with length outside the relevant size range (18-30 nucleotides) were excluded. To account for differences in read depth a between-sample normalization was performed within each set of libraries (A, B, C). Size factors based on miRNA read counts were obtained essentially as in Anders et al. 2010. The library with smallest size factor was chosen as a reference. Normalization of the remaining libraries was performed by sampling sequence reads without replacement, where the total number of draws was given by # reads x reference size factor / size factor. Reads were considered miRNA reads if they were identical to the sequence of a mature miRNA (miRBase 13) (3' As were trimmed off miRNA sequences before sequence matching). Read sequences were aligned to the C. elegans genome (WS190/ce6) downloaded from the UCSC Genome Browser website (http://genome.ucsc.edu/) and transgenic sequences (if applicable). Perfect alignments were obtained using bowtie 0.12.7 allowing for multiple matches (Langmead et al. 2009).
BED files including perfect alignments to the reference genome and transgene sequences (if applicable). Entries in the 'name' column have format sequence-#reads/#alignments. The 'score' column indicates the number of mismatches.
|
| |
|
| Submission date |
Apr 14, 2011 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Leonard Goldstein |
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9269 |
| Series (2) |
| GSE28617 |
Function, targets and evolution of Caenorhabditis elegans piRNAs (small RNA-Seq) |
| GSE37433 |
Function, targets and evolution of Caenorhabditis elegans piRNAs |
|
| Relations |
| SRA |
SRX057509 |
| BioSample |
SAMN00259624 |
