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Sample GSM1925088 Query DataSets for GSM1925088
Status Public on May 25, 2016
Title AP2EREBP_tnt.ERF105_colamp_a
Sample type SRA
 
Source name young leaf
Organism Arabidopsis thaliana
Characteristics protein: ERF105
gene id: AT5G51190
protein family: AP2EREBP
protein source: Arabidopsis thaliana
protein affinity tag: Halo
expression system: tnt
dna source: colamp
replicate: a
subset: motif+TFBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA is extracted from Arabidopsis young leaves by phenol:chloroform:isoamyl alchohol (25:24:1) followed by a chloroform extraction, ethanol precipitation and resuspension in Tris/EDTA buffer. The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter. Separately, a construct containing an affinity-tagged transcription factor (GST or HALO) is translated by either heterologous (E. coli) or in vitro (wheat germ) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin. The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina HiSeq 2500.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.
Data processing library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Reads were aligned by bowtie2 version 2.0.0-beta7 against the Arabidopsis TAIR10 genome assembly or Zea mays genome assembly B73 with default parameters, and additionally filter for highest scoring MAPQ alignments only (score=254).
Peaks were called using GEM peak caller version 2.3 with the default version 2.3 read distribution, TAIR10 genome sequences and parameters " --k_min 6 --k_max 20 --k_seqs 250 --outNP --k_neg_dinu_shuffle".
Genome_build: Arabidopsis TAIR10 or maize B73
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.
 
Submission date Nov 04, 2015
Last update date May 15, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL17639
Series (2)
GSE60141 A Comprehensive Atlas of Arabidopsis Regulatory DNA [DAP-seq]
GSE60143 In vitro, genomic context identification of transcription factor binding sites
Relations
BioSample SAMN04236549
SRA SRX1412068

Supplementary file Size Download File type/resource
GSM1925088_DAPSeq-AP2EREBP_tnt-ERF105_colamp_a-chr1-5_GEM_events.narrowPeak.gz 182.7 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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