|
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 |