|
Status |
Public on Jan 17, 2013 |
Title |
HeLa_BAC_STARRseq_input |
Sample type |
SRA |
|
|
Source name |
BAC library (in STARR-seq vector)
|
Organism |
Homo sapiens |
Characteristics |
sample type: RPCI human BAC library 11 (6 BACS) experimental procedure: STARR-Seq
|
Extracted molecule |
genomic DNA |
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.
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
PCR amplified Plasmid library, used for HeLa STARR-seq
|
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
|
|
|
Submission date |
Dec 19, 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 |
GPL11154 |
Series (1) |
GSE40739 |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
|
Relations |
SRA |
SRX212124 |
BioSample |
SAMN01832252 |