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Sample GSM1354669 Query DataSets for GSM1354669
Status Public on Dec 01, 2015
Title PJ34-10um rep1
Sample type SRA
 
Source name late embryonic stage cells
Organism Drosophila melanogaster
Characteristics cell type: late embryonic stage cells
passages: 10-15
cell line: S2
treatment: PARylation inhibited 10um
Growth protocol D. Melanogaster S2-DRSC cells (obtained from the Drosophila Genomics Resource Center) were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone).
Extracted molecule total RNA
Extraction protocol RNA was extracted using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description PARylation inhibited 10um
Data processing Illumina Casava software used for basecalling.
Reads were mapped to the D. melanogaster genome version dm3 using Tophat2 v2.0.10 with the multithreading option -p 5 and the remaining parameters as the default allowing for two mismatches. Tophat2 was using bowtie2 v2.1.0.0 as the underlying mapper
Mapped reads were assembled into transcripts with cufflinks v2.1.1 using the multithreading option -p 5 and the remaining options as the defaults. The gtf used for transcript construction was the flyBase
Aligned reads were used as inputs for cuffdiff2 to determine gene expression levels (FPKM) and differential expression between conditions using the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7). All other parameters were set to the defaults.
Differential expression was tested for dose independent PARylation inhibition results by comparing the combined alignments of samples 2 and 3 (PARylation) to the combined alignments of samples 1 and 4 (control) using cuffdiff2.
Differential expression was tested for dose-independent PARP knockdown results by comparing the combined alignments of samples 5 and 6 (PARP-1 Knockdown) to the combined alignments of samples 1 and 4 (control) using cuffdiff2.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Genes_FPKMValues.txt is a tab-delimited text file containing the gene ID, locus, and FPKM values for each gene assembled using cufflinks. PARP-1-KD_tss_group_exp.dff and PARylation_tss_group_exp.diff are the resulting combined dose-independent differential expression results for PARP-1 knockdown and PARylation inhibition, respectively. These files are output by cuffdiff. A p-value cutoff of 0.05 was used to determine differentially expressed genes.
 
Submission date Mar 20, 2014
Last update date May 15, 2019
Contact name Eric Christian Rouchka
E-mail(s) eric.rouchka@louisville.edu
Organization name University of Louisville
Department Biochemistry and Molecular Genetics
Lab KY INBRE Bioinformatics Core
Street address 522 East Gray Street
City Louisville
State/province Kentucky
ZIP/Postal code 40292
Country USA
 
Platform ID GPL17275
Series (1)
GSE56073 PARP-1 regulation of alternative splicing
Relations
Reanalyzed by GSM3285526
BioSample SAMN02693106
SRA SRX497457

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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