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| Status |
Public on Jul 18, 2016 |
| Title |
Ctrl_FRT19A |
| Sample type |
SRA |
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| Source name |
Eye discs
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: L3
strain: FRT19A
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq libraries were constructed with the TruSeq RNA sample preparation (Low throughput protocol) kit from Illumina
One microgram of total RNA was used for the construction of the libraries. The RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase and random hexamer primers. The Second strand cDNA is synthesized. These 20 cDNA fragments then go through an end repair process, the addition of a single 'A' base and the subsequent ligation of the adapter. The products are then purified and enriched with 15 cycles of PCR. The final cDNA libraries are validated with a DNA 1000 Labchip on a Bioanalyzer (Agilent) and quantified with a KAPA qPCR kit. For one sequencing lane of a flowcell V3, three libraries were pooled in equal proportions, denatured with NaOH and diluted to 7 pM in hybridization buffer. Cluster formation, primer hybridisation and single read 50 cycles sequencing were performed
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
rep1 and rep2
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Alignment using TopHat 2.0.8b and Bowtie 2.1.0.0 with standard parameters
Analysis using edgeR 2.6.2
Genome_build: DM3, Transcript annotation BDGP5.74
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| Submission date |
Oct 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Giacomo Cavalli |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Lab |
INSTITUTE of HUMAN GENETICS
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| Street address |
IGH - CNRS, 141, rue de la Cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 Cedex5 |
| Country |
France |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE74080 |
Massive redeployment of PRC1 proteins suppresses tumor formation during Drosophila development |
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| Relations |
| Reanalyzed by |
GSM3277255 |
| BioSample |
SAMN04168808 |
| SRA |
SRX1339394 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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