|
| Status |
Public on May 25, 2016 |
| Title |
AP2EREBP_tnt.ERF4_col_a |
| Sample type |
SRA |
| |
|
| Source name |
young leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
protein: ERF4
gene id: AT3G15210
protein family: AP2EREBP
protein source: Arabidopsis thaliana
protein affinity tag: Halo
expression system: tnt
dna source: col
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
|
| 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 |
SAMN04236563 |
| SRA |
SRX1412082 |
