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| Status |
Public on Apr 02, 2014 |
| Title |
BG3_STARRseq_rep1 |
| Sample type |
SRA |
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| Source name |
BG3 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: BG3 cells
experimental procedure: STARR-Seq
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| Extracted molecule |
total RNA |
| Extraction protocol |
STARR-Seq: 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 pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
polyA+ RNA
PCR amplified cDNA (STARR-seq transcript)
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| Data processing |
STARR-Seq:
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.
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| Submission date |
Aug 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
J. Omar Yanez-Cuna |
| E-mail(s) |
jorge.yanez@imp.ac.at
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| Organization name |
Research Institute of Molecular Pathology
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| Lab |
Stark
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| Street address |
Dr. Bohr-Gasse 7
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL11203 |
| Series (1) |
| GSE49809 |
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features |
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| Relations |
| BioSample |
SAMN02315686 |
| SRA |
SRX333714 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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