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| Status |
Public on Mar 17, 2017 |
| Title |
Wild-type rep1 |
| Sample type |
SRA |
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| Source name |
Caenorhabditis elegans wild-type
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole body
developmental stage: Day 1 adult
strain: Bristol N2
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| Growth protocol |
All strains were grown on OP50-seeded NGM plates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from synchronized day 1 adult worms was extracted by using RNA Isoplus (Takara, Shiga, Japan).
We used TruSeq RNA library preparation kit (illumina, San Diego, USA). RNA is first purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Next, the second strand is generated to create double-stranded cDNA that is ready for the TruSeq library construction. The short ds-cDNA fragments were then connected with sequencing adapters, and suitable fragments were separated by agarose gel electrophoresis. Finally, truseq RNA libraries were built by PCR amplification and quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer. (Agilent technologies,Palo Alto CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The BCL (base calls) binary is converted to FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Sequenced reads were trimmed for adaptor sequence, then mapped to C. elegans genome (WS220/ce10) with transcriptome (Ensembl 65) using Tophat-2.0.14 (bowtie2-2.2.5) with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using Cufflinks with default parameters.
Genome_build: ce10
Supplementary_files_format_and_content: Tab-delimited text files with BigWig format that read counts are normalized to 107.
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| Submission date |
Jan 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Seung-Jae V Lee |
| E-mail(s) |
[email protected]
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| Organization name |
KAIST
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| Department |
Life Sciences
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| Lab |
Room 4203
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| Street address |
291 Daehak-ro
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE94077 |
Analysis of nonsense-mediated mRNA decay in daf-2 mutants |
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| Relations |
| BioSample |
SAMN06270736 |
| SRA |
SRX2516749 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2468323_wt_1_norm.bw |
59.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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