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| Status |
Public on Oct 01, 2020 |
| Title |
cel4SDHB1DELTR |
| Sample type |
SRA |
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| Source name |
whole worm mRNA extract
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
condition: sdhb-1 deletional mutant
age: L2 larvae
genotype: sdhb-1(gk165)
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| Growth protocol |
C. elegans strains were maintained under standard conditions, on NGM plates seeded with OP50 bacteria at 20°C degrees.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total nucleic acid extraction of wild-type and mutant animals was conducted by TRI Reagent® (Molecular Research Center, Inc, Cincinnati, Ohio USA) as recommended by the manufacturer. The crude extract was further purified with RNeasy Mini Kit (Qiagen, Hilden, Germany) using the manufacturer’s protocol. To remove DNA contamination which might interfere with downstream applications, Column DNase treatment with Qiagen RNase free DNase kit was applied. To purify pure mature polyA-tailed mRNA, we performed a magnetic bead based separation on the purified total RNA with NEB NEXT Poly(A) mRNA magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). 100 ng of mature polyA-tailed mRNA per sample was used to construct RNA-SEQ libraries.
NEB NEXT ULTRA II Directional RNA Library Preparation Kit (Illumina,San Diego, CA, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
cel4SDHB1DELTR
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| Data processing |
FASTQ Generation | Version: 1.0.0 on Illumina BaseSpaceFS version: 2.0.1018 system
Sequenced reads were trimmed for adaptor and low-quality sequence with trim_galore version 0.4.1 and cutadapt version 1.14
The trimmed sequence sets were aligned to the WBcel235 genome with TopHat v2.1.0 (bowtie2-align-s version 2.3.4.3), using default parameters
Performed union-exon based count with R Rsubread package version 1.34.7 , and count processing and rpkm calculation with R edgeR package version 3.26.8
Genome_build: C. elegans WBcel235 genome Ensembl release 94
Supplementary_files_format_and_content: tab-delimited text files include union-exon based RPKM values and annotation information for each Sample
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| Submission date |
Sep 30, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
István Likó |
| E-mail(s) |
[email protected]
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| Organization name |
Semmelweis University
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| Lab |
HAS-SE Momentum Hereditary Endocrine Tumour Syndromes Research Group, Hungarian Academy of Sciences and Semmelweis University
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| Street address |
Üllői út 26.
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| City |
Budapest |
| ZIP/Postal code |
H - 1085 |
| Country |
Hungary |
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| Platform ID |
GPL15716 |
| Series (1) |
| GSE158836 |
The SDHB Arg230His mutation causing familial paraganglioma alters glycolysis in a new Caenorhabditis elegans model |
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| Relations |
| BioSample |
SAMN16319859 |
| SRA |
SRX9221108 |
| 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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