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| Status |
Public on Feb 01, 2010 |
| Title |
rde-4_P-independent |
| Sample type |
SRA |
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| Source name |
whole L4 hermaphrodite
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| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: rde-4(ne299)
strain: WM48
growth temperature (°c): 20
small rna capture method: 5'-monophosphate-independent
final rna type: small RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Intact small RNA or fragmented polyA RNA was first ligated to an adenylated 3' adapter (IDT linker 1). In the case of polyA RNA and 5'-P-dependent small RNA, the samples were then ligated to a barcoded 5' adapter. In the case of 5'-P-independent small RNA, the sample were first treated with Antarctic phosphatase then T4 Polynucleotide Kinase before ligating to a barcoded 5' adapter. Subsequently, all samples were reverse transcribed using a primer complementary to the 3' adapter, then PCR amplified with primers carrying extrensions to add the the Illumina primer sites.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
The processed data files in fasta format contain the parsed small RNA reads for each sample (without 5' barcode sequence or 3' adapter sequences). The raw files each correspond to a single lane of sequence sequences; however, multiple samples were present in each lane. Each sample was barcoded with a 3 or 4 nt sequence at the 5’ end, such that the first letter of each read is the first letter of the barcode. Since the small RNAs were ~22 nt in length and 36 nucleotides were sequenced, most of the reads also contain a short stretch of the 3’ adapter sequence at the 3’ end. Custom-built Java scripts were used to sort the reads according to their barcodes and to trim off both the barcodes and 3’ adapter to produce the small RNA processed data files. The start of the 3’ adapter was recognized by the 3’-most instance of it’s first four nucleotides, “CTGT”. The polyA RNA processed data files are slightly different in that the RNA fragments were > 100 nt in length such that the 3’ adapter was not included in the 36 nt reads. Hence, only the 5’ barcode was trimmed off for these samples.
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| Submission date |
Feb 01, 2010 |
| Last update date |
May 30, 2014 |
| Contact name |
Ayelet Lamm |
| E-mail(s) |
ayeletla@stanford.edu
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| Phone |
650-725-1609
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| Organization name |
Stanford University School of Medicine
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| Department |
Pathology
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| Lab |
Fire Lab
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| Street address |
300 Pasteur Drive, Lane Bldg Room L302
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5324 |
| Country |
USA |
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| Platform ID |
GPL9269 |
| Series (1) |
| GSE19414 |
Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma |
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| Relations |
| BioSample |
SAMN02196503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM503826_Gent_rde-4_P-independent.fa.gz |
3.3 Mb |
(ftp)(http) |
FA |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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