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| Status |
Public on Apr 28, 2014 |
| Title |
cDNA_Dwil_rep1 |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila willistoni |
| Characteristics |
cell type: S2 cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Genomic DNA (source: https://stockcenter.ucsd.edu) was isolated for all Drosophila species listed above, 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. See also Arnold et al. Science 2013.
STARR-Seq (Arnold et al. Science 2013)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
STARR-Seq
PCR amplified cDNA (STARR-seq transcript)
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| 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 respective genomes ( droYak2, droAna3, dp4, droWil1) using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Fragments mapped in the respective genomes were translated to dm3 coordinates using the liftover tool. 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 at the summit, and the p-value.
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| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
daniel.gerlach@boehringer-ingelheim.com
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| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
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| Department |
Global Computational Biology and Digital Sciences
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| Street address |
Dr.-Boehringer-Gasse 5-11
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| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
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| Platform ID |
GPL14359 |
| Series (1) |
| GSE48251 |
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution |
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| Relations |
| BioSample |
SAMN02212574 |
| SRA |
SRX314729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1173350_cDNA_Dwil_rep1.peaks.txt.gz |
110.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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