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Sample GSM4699047 Query DataSets for GSM4699047
Status Public on Dec 01, 2020
Title DAP-bHLH115
Sample type SRA
 
Source name 10 days-old seedlings
Organism Arabidopsis thaliana
Characteristics protein: bHLH115
gene id: AT1G51070
protein expression: E.coli expressed
Growth protocol 10 days-old seedlings grown in MS medium
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description Sample 12
Protein-DNA interaction
Data processing Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4
 
Submission date Jul 28, 2020
Last update date Dec 04, 2020
Contact name Jose M. Franco-Zorrilla
Organization name Centro Nacinal de Biotecnologia-CSIC
Department Plant Molecular Genetics
Street address Darwin, 3
City Madrid
State/province Madrid
ZIP/Postal code 28049
Country Spain
 
Platform ID GPL23157
Series (2)
GSE155317 DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq]
GSE155321 DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs
Relations
BioSample SAMN15662444
SRA SRX8840843

Supplementary file Size Download File type/resource
GSM4699047_bHLH115.GEM_events.narrowPeak.gz 12.7 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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