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| Status |
Public on Jul 18, 2018 |
| Title |
Hand>Bru3-rep1 |
| Sample type |
SRA |
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| Source name |
adult fly
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| Organism |
Drosophila melanogaster |
| Characteristics |
age: 1 week
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from about 10, 1-week or 5-weeks old, entire or dissected (head, legs, wings and ovaries removed) adult flies, using TRIzol reagent (Invitrogen) following manufacturer’s instructions. The following genotypes dedicated for TU-tagging cell - specific transcript isolation were used: Hand>LacZ;HA-UPRT, Hand>MblRNAi;HA-UPRT, Hand>Bru3;HA-UPRT and Hand>960CTG;HA-UPRT
Library preparation was performed on about 50 ng of cardiac specific RNA from the previously described conditions, using the Ovation RNA-Seq Systems 1-16 for Model Organisms adapted to Drosophila (NuGEN, #0350-32) following manufacturer’s instructions with few modifications. First-strand synthesis was performed with the integrated DNAse treatment (HL-dsDNAse, ArcticZymes) and cDNA was fragmented using Bioruptor sonication system (Diagenode) with 30 cycles of 30 seconds ON/OFF on low power. 15 PCR cycles for library amplification were performed for 50 ng of starting RNA and a size-selection bead purification step was done using RNAClean XP beads (Agencourt AMPure, Beckman Coulter).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
FastQC was used to test Quality control
Paired-end reads were aligned using bowtie 2 to the dm5 genome assembly
Differential expression studies were performed between several genotypes using a specific pipeline using Deseq2
Genome_build: Dm5.49
Supplementary_files_format_and_content: excel files were generated containing expression and differential expression with statistics and scores
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| Submission date |
Jan 18, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
yoan renaud |
| E-mail(s) |
yoan.renaud@uca.fr
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| Organization name |
igred
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| Street address |
place henri dunand
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| City |
clermont ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE109370 |
Deregulation associated with cardiac conduction defects in Myotonic Dystrophy Type 1 using TU-Tagging |
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| Relations |
| BioSample |
SAMN08376839 |
| SRA |
SRX3586117 |
| 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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