GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5093687 Query DataSets for GSM5093687
Status Public on Apr 29, 2021
Title clf_Input_S4
Sample type SRA
Source name seedlings
Organism Arabidopsis thaliana
Characteristics genotype: clf mutant
antibody: input
Growth protocol ChIPseq assays were performed on shoot or root of 14‐day‐old seedlings
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were then generated using 10ng of DNA and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Trimmomatic-0.38: Minimum length of 36 bp; Mean Phred quality > 30; Leading and trailing bases removal with base quality <5. The reads were mapped onto the TAIR10 assembly using Bowtie2 with mismatch permission of 1 bp. MACS2 for peaks detection were set as follows: Number of duplicate reads at a location:1; mfold of 5:50; q-value cutoff: 0.05; extsize 200; broad peak
Genome_build: TAIR10
Supplementary_files_format_and_content: BIGWIG
Submission date Feb 19, 2021
Last update date Apr 29, 2021
Contact name Sanchari Sircar
Organization name IPS2
Lab Chromosome Dynamics
Street address Batiment 630 Rue Noetzlin
City Orsay
ZIP/Postal code 75015
Country France
Platform ID GPL19580
Series (1)
GSE155502 Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis
BioSample SAMN17998768
SRA SRX10133722

Supplementary file Size Download File type/resource 56.4 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