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| Status |
Public on Jan 17, 2013 |
| Title |
HeLa_BAC_STARRseq |
| Sample type |
SRA |
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| Source name |
HeLa Kyoto cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa Kyoto
experimental procedure: STARR-Seq
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Genomic DNA (source: RPCI 11 human BAC library) 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 (pGL4-Promotor backbone (Promega; cat. no. E6651) with the sequence between BgIlI and FseI replaced with the following sequence, containing a Super Core Promoter 1 (SCP1) (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 HiSeq 2000 |
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| Description |
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 hg19 genome using bowtie (bowtie -p 12 -f -v 3 -m 1 --best --strata --quiet INDEX reads.fa) and an index on chr1 - chr22, chrX, and chrY. For all subsequently analysis we subsampled data overlapping the BAC regions. 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: hg19
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 |
Dec 19, 2012 |
| 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 |
GPL11154 |
| Series (1) |
| GSE40739 |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
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| Relations |
| SRA |
SRX212123 |
| BioSample |
SAMN01832251 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1055604_HeLa_BAC_STARRseq.peaks.txt.gz |
187 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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