NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4551729 Query DataSets for GSM4551729
Status Public on Sep 07, 2020
Title SEP3_rep3
Sample type SRA
 
Source name 3-Sep
Organism Arabidopsis thaliana
Characteristics tissue: 2-weeks old seedlings
primary protein epitope tags: SEP3-3FLAG
molecule subtype: PCR amplified genomic DNA
Growth protocol 2-weeks old seedlings of Arabidopsis thaliana
Extracted molecule genomic DNA
Extraction protocol Recombiant proteins were produced by TnT in vitro transcription translation system from Promega
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Data processing library strategy: sequential DNA affinity purification sequencing [DAP-seq]
Image data generated by Miseq is transferred into raw reads through base calling software (BCL2FASTQ v2.17)
Alignement to genome is done by Bowtie2 with parameters:
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters
Peaks called where Control read coverage is too high are removed from analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: NarrowPeaks representing peaks positions and p-values
Supplementary_files_format_and_content: Bedgraphs are whole genome profile of reads
 
Submission date May 13, 2020
Last update date Sep 08, 2020
Contact name Jérémy LUCAS
E-mail(s) jeremy.lucas@cea.fr
Organization name CNRS
Street address 17 avenue des Martyrs
City Grenoble
ZIP/Postal code 38000
Country France
 
Platform ID GPL17970
Series (1)
GSE150528 Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing
Relations
BioSample SAMN14916583
SRA SRX8339616

Supplementary file Size Download File type/resource
GSM4551729_SEP3_rep3.bedGraph.gz 144.9 Mb (ftp)(http) BEDGRAPH
GSM4551729_SEP3_rep3.narrowPeak.gz 47.4 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap