|
| Status |
Public on Jan 17, 2013 |
| Title |
OSC STARR-seq biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
OSC cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: OSC cells
sample type: PCR amplified cDNA (STARR-seq transcript)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) was isolated, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PCR amplified cDNA (STARR-seq transcript)
|
| Data processing |
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
daniel.gerlach@boehringer-ingelheim.com
|
| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
|
| Department |
Global Computational Biology and Digital Sciences
|
| Street address |
Dr.-Boehringer-Gasse 5-11
|
| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE40739 |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
|
| Relations |
| Reanalyzed by |
GSM1397688 |
| SRA |
SRX187076 |
| BioSample |
SAMN01176861 |
