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| Status |
Public on Aug 22, 2019 |
| Title |
mdt-15(tm2182) 15oC rep3 |
| Sample type |
SRA |
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| Source name |
Caenorhabditis elegans mdt-15 mutant at 15oC
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole body
developmental stage: Day 1 adult
genotype/variation: mdt-15(tm2182)
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| Growth protocol |
Caenorhabditis elegans strains were grown on OP50-seeded NGM plates at 25oC or 15oC
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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)
Three independent biological repeats were used for analysis. cDNA library was prepared and cDNA sequencing was performed by using a HiSeq 4000 platform (MACROGEN, South Korea). Paired-end reads were aligned to the C. elegans genome ce11, and analyzed by using HISAT2 (v.2.0.5), StringTie (v.1.3.3), and Ballgown (v.2.0.0) methods (56). R packages limma (v.3.24.15) (57) and edgeR (v.3.10.5) (58) were used for analyzing differentially expressed genes (DEG), and genes whose expression was not detected (counts per million (cpm) < 1) were excluded
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v2.17.1.14).
Sequenced reads were trimmed for adaptor sequence, then mapped to C. elegans genome (ce11) using HISAT2 (v.2.0.5), StringTie (v.1.3.3), and Ballgown (v.2.0.0) methods.
R packages limma (v.3.24.15) and edgeR (v.3.10.5) were used for analyzing differentially expressed genes (DEG).
Genome_build: ce11
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| Submission date |
Mar 25, 2019 |
| Last update date |
Aug 22, 2019 |
| Contact name |
Seung-Jae V Lee |
| E-mail(s) |
seungjaevlee@kaist.ac.kr
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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 |
GPL22765 |
| Series (1) |
| GSE128815 |
Analysis of mRNA expression changes caused by mdt-15(tm2182) mutation at 15oC and 25 oC |
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| Relations |
| BioSample |
SAMN11250168 |
| SRA |
SRX5572769 |
| 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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