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| Status |
Public on Jun 30, 2020 |
| Title |
Myc RNAi rep2 |
| Sample type |
SRA |
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| Source name |
imaginal wing disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: tsGAL80;tubG4/Myc RNAi
stock number: BL7019, BL5138, V2947
developmental stage: mid-third instar larvae
tissue: wing imaginal disc
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| Treatment protocol |
RNAi using tubulin-GAL4 driver in the background of temperature-sensitive GAL80
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| Growth protocol |
Drosophila melanogaster wandering third instar larvae were grown at 18 degrees C for 4 days following 25 degrees C for 3 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Promega ReliaPrep RNA Cell miniprep system (Z6012) following the manufacturer’s protocol and eluted in 50 μL nuclease-free water. RNA purity and integrity were assessed using an automated electrophoresis system (2200 TapeStation, Agilent Technologies)
RNA was prepared using the standard TruSeq Illumina protocol preserving strandedness information, with Oligo-dT beads used to enrich for mRNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Myc RNAi
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| Data processing |
Sequence quality was verified using FastQC v0.11.6
Alignment was performed using Tophat2 2.1.1
Gene counts were performed using HTSeq 0.6.1
Significant differential expression was analysed using DESeq2 1.12.0
Significant differential splicing was analysed using rMATS 4.0.2
Genome_build: dmel-r6.10 (Flybase)
Supplementary_files_format_and_content: Plain text (.txt) file containing raw gene-level counts for each sample
Supplementary_files_format_and_content: Comma separated values (.csv) files containing output of DESeq2 (differential gene expression). Each column contains: FlybaseID, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, geneSymbol, EntrezID, normalised counts for each sample
Supplementary_files_format_and_content: Microsoft Excel workbook (.xls) file containing combined output of rMATS (differential splicing), arranged into tabs according to splice events: alternative 3’splice site (A3SS.MATS.JCEC), alternative 5’ splice site (A5SS.MATS.JCEC), mutually exclusive exons (MXE.MATS.JCEC), retained intron (RI.MATS.JCEC), skipped exon (SE.MATS.JCEC),
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| Submission date |
May 01, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Olga Zaytseva |
| E-mail(s) |
olga.zaytseva@anu.edu.au
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| Organization name |
John Curtin School of Medical Research
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| Street address |
131 Garran Road
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| Platform ID |
GPL17275 |
| Series (2) |
| GSE149719 |
RNA-sequencing following Psi or Myc knockdown in Drosophila larval wing tissue |
| GSE149721 |
Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue |
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| Relations |
| BioSample |
SAMN14791479 |
| SRA |
SRX8241434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4509604_counts_sorted_MYCRNAi_rep2_rvStrand.txt.gz |
67.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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