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Sample GSM6265579 Query DataSets for GSM6265579
Status Public on Jun 24, 2022
Title III_Col-0 IgG_ChIP-seq
Sample type SRA
 
Source name etiolated seedling
Organism Arabidopsis thaliana
Characteristics t-dna mutant: Col-0
antibodies: mouse IgG (Jackson ImmunoResearch, 015-000-003)
Treatment protocol no treatment
Growth protocol Seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose, sample 12 is derived from flowers of soil-grown plants
Extracted molecule genomic DNA
Extraction protocol Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description control
Data processing base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600), FDR (0.01)
Genome_build: TAIR10
 
Submission date Jun 23, 2022
Last update date Nov 29, 2022
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 (1)
GSE108401 The Complex Architecture of Transgene Insertions
Relations
BioSample SAMN29271703
SRA SRX15855515

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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