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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 26, 2016 |
| Title |
zfh1_genome-wide_rep1 |
| Sample type |
SRA |
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| Source name |
STAP-seq screen using zfh1 enhancer, with library derived from genome-wide Drosophila melanogaster fragments
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
experimental procedure: STAP-Seq
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| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) or BAC DNA was isolated, sheared and size selected (~100-250bp). Following the instructions of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB; cat. no. E7645L) ,Illumina NEBnext Multiplexing Adaptors (NEB; cat. no. E7335 or E7500) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STAP-seq vectors. To construct the STAP-seq vector, the sequence between BglII and FseI from the pGL3-Promoter backbone (Promega; cat. no. E1751) was replaceda ccdB suicide gene flanked by homology arms (used for cloning the promoter candidates during library generation), an intron (mhc16), an ORF (truncated sgGFP, Qbiogene, Inc), followed by the pGL3’s SV40 late polyA-signal. The enhancers were cloned between the KpnI and BglII sites. The control screens were performed with a vector not harboring an enhancer. 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 HiSeq 2000 |
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| Description |
PCR amplified cDNA (STAP-seq transcript)
polyA+ RNA
zfh1_genome-wide_eTSS.txt
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| Data processing |
Library strategy: STAP-seq
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STAP-Seq
Paired-end STAP-seq reads were trimmed to 44bp, with the first 8bp as the unique molecular barcode identifier. The reads were mapped using the remaining 36bp to dm3 and dp3 (for spike-in controls) genome assemblies using Bowtie 0.12.9 (bowtie -p 4 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For paired-end reads that are mapped to the same positions, we collapsed those that have the exact barcodes as well as those with 1bp mismatch, and removed all mapped reads containing N’s in their barcodes. For focused STAP-seq screens, we subsampled all reads at 700,000 reads before mapping and removed fragments outside of the focused regions from analysis.
Genome_build: dm3
Supplementary_files_format_and_content: Processed data file is in plain text. We report for each eTSS the chromosome, the +1 position, the core promoter strength, and p-value.
Analyses on Samples sgl, ham, ncm and ssp3_BAC were based on zfh1_BAC_eTSS.txt in the manuscript, and hence no corresponding files are generated.
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| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Stark |
| Organization name |
Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC
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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 |
GPL13304 |
| Series (1) |
| GSE78886 |
Genome-wide quantitative core promoter activity maps reveal a wide range of sequence-intrinsic transcription initiation strengths |
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| Relations |
| BioSample |
SAMN04531885 |
| SRA |
SRX1613198 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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