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| Status |
Public on Dec 31, 2021 |
| Title |
Top3D30R1 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Photoreceptor neuron
treatment: siRNA against Top3beta
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| Growth protocol |
Flies (genotype: P{w[+mC]=UAS-Dcr-2.D}1, w[1118];P{y[+t7.7] v[+t1.8]=TRiP.JF01282}attP2;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) or P{w[+mC]=UAS-Dcr-2.D}1, w[1118];P{w[v+]=[UAS-mCherry-RNAi]}attP2;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 30 days with transfer to new food every other day. Flies were collected at ZT 6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted with Direct-Zol microprep kit (ZymoResearch) and quantified with Qubit HS RNA (ThermoFisher)
Rnaseq libraries were constructed with Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen-Tecan) using 10 ng of RNA as starting material
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sanger/Illumina 1.9 used for base calling.
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: HEADCROP:8 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:30 MINLEN:75. Cleaned reads were mapped to Drosophila melanogaster genome version dm6 using STAR producing BAM files that are sorted by coordinate and gene counts
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Differential gene expression analysis was performed with DESeq2 using STAR-produced counts as input.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: Processed file is a text file that has STAR-produced raw counts for each sample
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| Submission date |
May 14, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Hana Hall |
| E-mail(s) |
hallh@purdue.edu
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| Phone |
7654940745
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| Organization name |
Purdue University
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| Department |
Biochemistry
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| Lab |
Hall Lab
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| Street address |
175 S University St, Biochemistry Builiding, room 320
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| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE174491 |
Nuclear RNA-seq of Drosophila Top3beta-deficient photoreceptor neurons |
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| Relations |
| BioSample |
SAMN19195503 |
| SRA |
SRX10895174 |
| 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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