GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6265581 Query DataSets for GSM6265581
Status Public on Jun 24, 2022
Title III_Col-0 H2A.Z_ChIP-seq
Sample type SRA
Source name etiolated seedling
Organism Arabidopsis thaliana
Characteristics t-dna mutant: Col-0
antibodies: H2A.Z (Active Motif, 39647)
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 Histone variant
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
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
BioSample SAMN29271705
SRA SRX15855517

Supplementary file Size Download File type/resource 30.3 Mb (ftp)(http) BW
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