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Sample GSM2237835 Query DataSets for GSM2237835
Status Public on Jul 31, 2017
Title Input chromatin from Col - bioRep 3
Sample type SRA
 
Source name 30 hrs old plants
Organism Arabidopsis thaliana
Characteristics ecotype: Col
transgene: gAZF1-Myc in Col
ip antibody: N/A
antibody source: N/A
antibody lot: N/A
Treatment protocol No treatment
Growth protocol Plants were grown in long day (16 hr light/ 8 hr dark, light intensity: ~110 ╬╝Mol/m2s1) on standard growth plates (1/2 Murashige and Skoog (MS) medium)
Extracted molecule genomic DNA
Extraction protocol ChIP assay is performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA was end repaired, A-tailed, and ligated to universal PE adapters using reagents from enzymatics. Libraries were amplified using custom-designed dual-indexed oligos.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Col.input.merge.bw
Data processing reads were aligned to the genome using bowtie2
reads were extended to 200 bp using bedtools
coverage was calculated using bedtools
coverage was normalized to 10 million reads mapped per million reads sequenced (10RPM) using a custom script
mean coverage from replicates was calculated using wiggleTools
in some tracks (input-corrected) mean input noise was subtracted from the mean ChIP signal using wiggleTool (diff command)
Genome_build: TAIR10 release 31 (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/arabidopsis_thaliana/dna/)
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for single replicates
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample
Supplementary_files_format_and_content: bigwig normalized to 10RPKM for the mean of three replicates for each sample after subtracting the relevant background sample
Supplementary_files_format_and_content: peaks were called using MACS version 2.1.1.20160309 using default parameters for AZF, BPC, and FIE, and the broad peaks option for H3K27me3; peak lists were filtered for Q-value < 1e-10
 
Submission date Jul 17, 2016
Last update date Feb 04, 2022
Contact name Roberto Bonasio
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Bonasio
Street address 3400 Civic Center Blvd - SCTR 9-111
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL19580
Series (1)
GSE84483 ChIP-seq for Polycomb and associated transcription factors in Arabidopsis
Relations
BioSample SAMN05412828
SRA SRX1957725

Supplementary file Size Download File type/resource
GSM2237835_Col.input.b3.bw 114.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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