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Sample GSM732109 Query DataSets for GSM732109
Status Public on Jan 26, 2012
Title Cel mixed N2 dsRNA Hiseq
Sample type SRA
Source name mixed stage N2 worms, dsRNA
Organism Caenorhabditis elegans
Characteristics target molecules: double-stranded RNA (dsRNA)
strain: N2
cell line: whole organism
rnase treatment: ssRNase (RNase One)
Extracted molecule total RNA
Extraction protocol Total RNA was subjected to two rounds of rRNA depletion (Ribominus, Invitrogen (Carlsbad, CA)), and then treated with a single-strand specific ribonuclease (RNase One, Promega (Madison, WI)) for dsRNA-seq or with a double-strand specific ribonuclease (RNase V1, ABI (Foster City, CA)) for ssRNA-seq, all per manufacturer's instructions. The RNA samples are then used as the substrate for sequencing library construction using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer's instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description 3' adapter sequence: ATCTCGTATGCCGTCTTCTGCTTG
Data processing Abundance info of NR-seqs (*info.txt file): All reads are reduced to non-redundant (NR) sequences at first to minimize the computational requirement for subsequent analysis steps. Only NR-seqs that can map to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes are shown (either trimmed or untrimmed).
NR-seq after trimming of 3'-adapters (*seq.fasta file): In order to detect 3'-adapter sequences, all NR-sequences are aligned to the Illumina 3'-adapter version 1.5 sequence using the "cross-match" program. The alignment parameters for cross-match are carefully tuned to maintain all alignments with less than 6% mis-matches. The cross-match alignment results are parsed using in-house Perl scripts. All NR-sequences that align to ≥ 6 bp of the 3'-adapter sequence at their 3' end are defined as short and are subsequently trimmed at the adapter-sequence boundary. The remaining NR-sequences (without detectable 3'-adapters) remain "untrimmed". Only NR-seqs that can map to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes are shown (either trimmed or untrimmed).
Alignment (*loc.txt file): All trimmed and untrimmed NR-sequences are aligned to the D. melanogaster (UCSC, dm3) or C. elegans (UCSC, ce6) genomes using cross-match, with the program parameters set to guarantee all sequences that align with 6% mis-matches to the respective genome. Alignment results for trimmed or untrimmed inputs are then parsed independently using in-house Perl scripts. More specifically, alignments for trimmed sequences are required to extend to the ends of the query sequences, whereas alignments for untrimmed sequences are only required to extend to the imaginary positions of undetectable 3'-adapters (< 6 bp from the 3' end of the sequence). The true lengths of the untrimmed sequences are also determined in this step by the most-frequent aligned length of all possible alignments to the respective genome. At last, trimmed and untrimmed NR-sequences, as well as their genome loci information, are combined to form the final dataset using in-house Perl scripts. The smRNA libraries are pre-processed by this balanced pipeline as well.
Submission date May 26, 2011
Last update date Jun 11, 2013
Contact name Fan Li
Organization name University of California Los Angeles
Department Pediatrics
Street address 675 Charles E Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90024
Country USA
Platform ID GPL13657
Series (1)
GSE29571 Global analysis of RNA secondary structure conservation between two metazoans
BioSample SAMN02198291

Supplementary file Size Download File type/resource
GSM732109_cel_dsrna_hiseq_NR_ce6_loc.txt.gz 144.7 Mb (ftp)(http) TXT
GSM732109_cel_dsrna_hiseq_mapped_NR_info.txt.gz 18.9 Mb (ftp)(http) TXT
GSM732109_cel_dsrna_hiseq_mapped_NR_seq.fa.gz 39.4 Mb (ftp)(http) FA
Processed data provided as supplementary file

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