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| Status |
Public on Oct 19, 2017 |
| Title |
WT rep2 (mTAIL-seq) |
| Sample type |
SRA |
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| Source name |
whole organism
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| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4
genotype: wildtype N2
tissue: whole organism
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| Treatment protocol |
No special treatment
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| Growth protocol |
WT Caenorhabditis elegans (N2 Bristol) animals were cultured on OP50 bacteria at 25°C, and collected at the last larval stage (mid-L4 – 29 h time point). Standard worm synchronization methods were used.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol and DNAse treated.
A splint oligo was used to favor poly(A)+ RNAs being ligated to a 3′ adapter. After partially digesting the RNA from the ligation reaction with RNAse T1, RNAs were pulled down using Streptavidin beads, then 5' phosphorylated by PNK reaction. RNA was eluted and size selected for 250-1000 nt fragments. This was done by gel extraction and purification from a 6% Urea-PAGE gel. Libraries were normalized, pooled and then sequenced in the Illumina MiSeq platform (51 x 251 bp paired end run) with PhiX control library and the spike-in controls mixture. The quantified fluorescent signals were saved and processed by tailseeker2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
mTAIL-seq Rep2
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| Data processing |
Base calling, trimming of adapter sequences, removal of duplicated reads and determination of poly(A) tail sizes were performed by tailseeker2.
Reads were analyzed by mapping to the WS247 assembly of the C. elegans genome using RNA-STAR.
Poly(A) lengths were then assigned to individual coding genes by intersecting the mapped sequences with WormBase.org WS247 gene annotations using BEDTools.
Genome_build: WS247
Supplementary_files_format_and_content: Csv; contains the number of hits per gene, and the mean, median, standard deviation, and range of poly(A) tail lengths for RNAs that had more than 10 reads, as well as each individual poly(A) tail length that was read for each gene.
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| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Pasquinelli |
| E-mail(s) |
apasquinelli@ucsd.edu
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| Organization name |
University of California, San Diego
|
| Department |
Biological Sciences
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| Lab |
Pasquinelli Lab
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL15716 |
| Series (2) |
| GSE104501 |
Poly(A) Tail Length of L4 C. elegans |
| GSE104502 |
Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes |
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| Relations |
| BioSample |
SAMN07730931 |
| SRA |
SRX3237808 |
| 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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