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| Status |
Public on Jan 11, 2022 |
| Title |
ZI197,stress,non-deletion,replicate 1 [ZI197s_I1] |
| Sample type |
SRA |
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| Source name |
ZI197_stress_non-deletion_whole head
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| Organism |
Drosophila melanogaster |
| Characteristics |
population: Siavonga, Zambia
treatment: stress
genotype: non-deletion
tissue: whole head
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Poly-A mRNA purification, reverse transcription, and high-throughput sequencing were performed by Novogene (Cambridge, UK) using a Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
From RNA-sequencing we obtained from 29.3 – 67.6 million reads per library, and an average of 97% of these reads were successfully mapped to the D. melanogaster transcriptome (FlyBase, release 6.31) using NextGenMap (version 0.5.5) .
Differentially expressed genes were called with DESeq2 (version 1.28.1) as implemented in R (version 4.0.0) .
Genome_build: dmel-all-transcript-r6.31
Supplementary_files_format_and_content: text file with sample- and gene-wise expression table
Supplementary_files_format_and_content: text file with sample information
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| Submission date |
May 21, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Sonja Grath |
| E-mail(s) |
grath@bio.lmu.de
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| Organization name |
Ludwig-Maximilians University Munich
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| Department |
Department Biology II
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| Lab |
Evolutionary Biology
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| Street address |
Grosshaderner Str. 2
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| City |
Planegg-Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL25244 |
| Series (1) |
| GSE174813 |
Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress |
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| Relations |
| BioSample |
SAMN19296104 |
| SRA |
SRX10954746 |
| 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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