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| Status |
Public on Feb 20, 2018 |
| Title |
FV1 |
| Sample type |
SRA |
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| Source name |
Drosophila eye antenna imaginal disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Eye antenna imaginal disc
developmental stage: third larval instar
genotype: FRT82B atf3[wt]
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| Growth protocol |
Fly crosses were carried out at 25°C on standard media in large bottles
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from FRT82B atf3 mosaic EAD 7 days AEL as described (Mundorf & Uhlirova, 2016)
Libraries were prepared according to Illumina's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
experimental sample
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| Data processing |
Data were processed using a high-throughput Next-Generation Sequencing analysis pipeline (Wagle et al, 2015)
Basic read quality check was performed with FastQC (v0.10.1)
Read statistics were acquired with SAMtools v0.1.19 (Li et al, 2009).
Reads were mapped to the Drosophila reference assembly (version BDGP R5/dm3, April 2006) using Tophat v2.0.10 (Trapnell et al, 2009),
Gene quantification was carried out using a combination of Cufflinks v2.1.1 (Trapnell et al, 2010), and the DESeq2 package v1.10.1 (Anders & Huber, 2010), with genomic annotation from the Ensembl database, version 84.
The results were uploaded into an in-house MySQL database and joined with BiomaRt v2.26.1 (Durinck et al, 2005) annotations from Ensembl, version 84. Lists of differentially expressed genes were defined by a final database export using 5 and 0.01 as cutoffs for DESeq2-based FCs and p-values, respectively.
Genome_build: version BDGP R5/dm3, April 2006
Supplementary_files_format_and_content: tab-delimited text file contains FPKM values for each FRT82B control (GSM1591021, GSM1591022, GSM1591023, GSM1591024) and FRT82B atf3 samples (FV1, FV2, FV3, FV4)
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| Submission date |
Nov 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mirka Uhlirova |
| E-mail(s) |
[email protected]
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| Organization name |
CECAD Research Center Cologne
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| Department |
Institute for Genetics
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| Lab |
Uhlirova Lab
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| Street address |
Joseph-Stelzmann Str. 26
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| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE89845 |
Transcriptional response to Activating transcription factor 3 (Atf3) activity in the Drosophila eye antenna imaginal disc (EAD) epithelium. |
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| Relations |
| Reanalyzed by |
GSM3282510 |
| BioSample |
SAMN06017295 |
| SRA |
SRX2348480 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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