|
| Status |
Public on Apr 04, 2022 |
| Title |
FAH3F |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: fluctuating
Sex: female
timepoint: high2
lifestage: adult
|
| Treatment protocol |
Experimental animals subjected to constant temperature at 19 degree centigrade or a fluctuating temperature with a mean of 19 and an amplitude of plus or minus 8 degree centigrade. The treatment was continued for 7 days during larval development and for 13 days during adult stage, during which animals were taken for RNA sequencing at different timepoints
|
| Growth protocol |
Experimental animals were kept in vials with 7ml standard Drosophila food medium. Adult flies were tipped to fresh food containing vials every second day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extrraction and Library construction performed by Novogene using standard protocols.
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
sampled at high temperature point after 6 fluctuation cycles during adult stage
|
| Data processing |
The raw reads were checked for quality using FastQC (Andrews, 2010) and trimmed using trimmomatic based on a minimum length of 80 bp. Alignment of the trimmed reads was done using HISAT2 with default settings (Kim et al., 2015). StringTie (Pertea et al., 2015) was used to assemble the transcripts based on Drosophila melanogaster reference genome. All the transcripts were further merged using StringTie merge. The StringTie was run again with the B option on the merged transcripts to produce Ballgown input table files.
hisat2 -p 19 --dta -t -q -x
stringtie align_1/${sample}.bam -o align_1/${sample}.gtf -p 19 -G drosGTF/Dros_mel.BDGP6.92.chr.gtf
stringtie --merge -p 19 -o align_1/stringtie_merged.gtf -G drosGTF/Dros_mel.BDGP6.92.chr.gtf align_1/mergelist.txt
stringtie -e -B align_1/${sample}.bam -o align_1/ballgown/${sample}/${sample}.gtf -p 19 -G align_1/stringtie_merged.gtf
Genome_build: BDGP6
Supplementary_files_format_and_content: .csv file containing count data for all samples, generated using a python script provided by the developers of StringTie
|
| |
|
| Submission date |
May 13, 2020 |
| Last update date |
Apr 04, 2022 |
| Contact name |
Paul Vinu Salachan |
| Organization name |
Aarhus University
|
| Street address |
Brendstrupgårdsvej 21A
|
| City |
Aarhus N |
| State/province |
Aarhus |
| ZIP/Postal code |
8200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23702 |
| Series (1) |
| GSE150450 |
Molecular mechanisms underlying plasticity in a thermally varying environment |
|
| Relations |
| BioSample |
SAMN14910478 |
| SRA |
SRX8335279 |
