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| Status |
Public on Jun 01, 2015 |
| Title |
N2_GVN0EHB01 |
| Sample type |
SRA |
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| Source name |
Whole worm RNA extraction
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were maintained, propagated and collected at RT. Tens of L4 worms were seeded on each large (15cm) agar plate with E.coli OP50 as the food. 5 days later, the gravid hermaphrodites were collected and lysed with bleach. Eggs were transferred to large agar plates with E.coli OP50 and larvae were harvested 1 day (L1-L2 stage) or 2 days (L3-L4 stage) later.
We generated 3’UTR libraries from wild type and sydn-1 mutant by oligo (dT) priming (Mangone et al., 2010), which were later subjected to 454 sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX Titanium |
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| Description |
clusters_positions.txt
clusters_isoforms.txt
clusters_pas.txt
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| Data processing |
Reads were aligned to C. elegans genome (WS190) using Bowtie2version 2.0.0-beta6 with the parameters --local --very-sensitive-local -X 750.
Aligned reads were converted to PSL format for clustering and poly A site analysis by custom scripts (Mangone et al., 2010).
Custom scripts (Mangone et al., 2010) were used to identify recurrent polyA signal sequences in the clustered reads and perform additional analyses.
Genome_build: WS190
Supplementary_files_format_and_content: clusters_positions.txt: Tab-delimited text file with gene, chromosome, strand, and 3'UTR start position(s). Used to compile polyA signal statistics in clusters_pas.txt.
Supplementary_files_format_and_content: clusters_isoforms.txt: Tab-delimited text file with gene, # of isoforms and # of 3'UTR start positions. Used to compile polyA signal statistics in clusters_pas.txt.
Supplementary_files_format_and_content: clusters_pas.txt: Tab-delimited text file with genep=gene, chr=chromosome, utr_start=3'UTR start position, utr_end=3'UTR end position, utr_length=3'UTR length, variable number of sample names, tot=# of mapped reads in the cluster, src=one or both samples has a PAS site, class=annotated genic feature (CDS, 5UTR, 3UTR, intron), pas=polyA signal sequence, pas_pos=position of PAS in 3'UTR, pas1=annotation as canonical AATAAA signal or alternative PAS signal, isocnt=# of UTR isoforms, isolen=which of the isoforms is represented by the mapped read clusters, neuron=annotation as present in neuronal (sydn-1) mutant sample, abun_pass=Y/N if passed abundance filter, abun_count=# of samples with PAS present, iso_pass=Y/B if passed isoform filter.
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| Submission date |
Apr 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Mills |
| E-mail(s) |
remills@med.umich.edu
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| Phone |
734-647-9628
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| Organization name |
University of Michigan
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| Department |
Computational Medicine and Bioinformatics
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| Lab |
Ryan E. Mills, Ph.D.
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| Street address |
100 Washtenaw Ave
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL14832 |
| Series (1) |
| GSE67649 |
The RNA polymerase II CTD phosphatase SSUP-72 regulates alternative polyadenylation in C. elegans neurons. |
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| Relations |
| BioSample |
SAMN03464335 |
| SRA |
SRX982054 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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