ChIP-Seq Information For KN1


General Information


TF Name: ZmHB1
Species: Maize
TF Family: HOMEOBOX
Gene Name (Synonym): KN1
Gene ID: GRMZM2G017087


Summary


Title: Unraveling the KNOTTED1 regulatory network in maize
Overall Design: ChIP-seq was performed using two biological replicates of ear primordia and two of tassel primordia. Input DNA from each sample was used as a normalization control.
Library Construction Protocol: Inflorescences primordia were dissected, fixed for 10 minutes in 1% formaldehyde and nuclei isolated. Fragmented (sonicated) chromatin was incubated with anti-KN1 antibodies to pull down KN1-bound regions. ChIP-seq libraries were prepared according to the standard Illumina protocol using Illumina adapters and oligos (ear libraries), or custom made adapters containing a barcode for pooling multiple samples per sequencing lane (tassel libraries), while other reagents were obtained from major manufacturers (Promega, NEB). Prior to ChIP, chromatin from ear and tassel primordia was sonicated to obtain an average size of about 100 and 400 bp, respectively. One notable modification to the standard Illumina protocol was that the gel selection of fragments 150-350 bp was performed after the PCR amplification step (18 cycles) for the ear libraries, and was omitted for the tassel libraries.
Data Processing: ChIP-Seq reads were aligned to the maize genome assembly version 2 using Bowtie. MACS ver. 1.4.0beta was used for calling peaks by using uniquely aligned reads.
Authors: Nathalie Bolduc, Alper Yilmaz, Maria Katherine Mejia-Guerra, Kengo Morohashi, Devin O'Connor, Erich Grotewold, and Sarah Hake
Reference: Genes Dev. 2012; 26(15):1685-90 PubMed link: 22855831


Figures and Tables


Zea mays ear primordia in the stage used for ChIP experiments. Picture provided by Dr Nathalie Bolduc.
Zea mays immature leaves from from left to right: +/+, Kn1-N/+, Kn1-N/Kn1-N (WT to gain-of-function KN1) in the stage used for RNA-Seq experiments. Picture provided by Dr Nathalie Bolduc.


Download ChIP-Seq Files


Description File Type Name
Biological Replicate 1, Tassel, Input DNA Illumina read *.txt BioRep1_wtinput_Tassels.txt.gz
Biological Replicate 1, Tassel, anti-KN1 Illumina reads *.txt BioRep1_wtknotted_Tassels.txt.gz
Biological Replicate 2, Technical Replicate 1, Tassel, Input DNA Illumina reads *.txt BioRep2.1_wtinput_Tassels.txt.gz
Biological Replicate 2, Technical Replicate 2, Tassel, Input DNA Illumina reads *.txt BioRep2.2_wtinput_Tassels.txt.gz
Biological Replicate 2, Technical Replicate 1, Tassel, anti-KN1 Illumina reads *.txt BioRep2.1_wtknotted_Tassels.txt.gz
Biological Replicate 2, Technical Replicate 2, Tassel, anti-KN1 Illumina reads *.txt BioRep2.2_wtknotted_Tassels.txt.gz
Biological Replicate 1, Technical Replicate 1, Ear, Input DNA Illumina reads *.txt BioRep1.1_wtinput_Ear.txt.gz
Biological Replicate 1, Technical Replicate 1, Ear, anti-KN1 Illumina reads *.txt BioRep1.1_wtknotted_Ear.txt.gz
All BioRep1, Tassel, Input DNA Alignment *bam *bai Tassel_BioRep1_wtinput.tar
All BioRep1, Tassel, anti-KN1 Alignment *bam *bai Tassel_BioRep1_wtknotted.tar
All BioRep2, Tassel, Input DNA Alignment *bam *bai Tassel_BioRep2_wtinput.tar
All BioRep2, Tassel, anti-KN1 Alignment *bam *bai Tassel_BioRep2_wtknotted.tar
All BioRep1, Ear, Input DNA Alignment *bam *bai Ear_BioRep1_wtinput.tar
All BioRep1, Ear, anti-KN1 Alignment *bam *bai Ear_BioRep1_wtknotted.tar
All BioRep2, Ear, Input DNA Alignment *bam *bai Ear_BioRep2_wtinput.tar
All BioRep2, Ear, anti-KN1 Alignment *bam *bai Ear_BioRep2_wtknotted.tar
All BioRep1, Tassel, Peaks Location Peaks position *.bed KN1_Tassel1_peaks.bed
All BioRep2, Tassel, Peaks Location Peaks position *.bed KN1_Tassel2_peaks.bed
All BioRep1, Ear, Peaks Location Peaks position *.bed KN1_Ear1_peaks.bed
All BioRep2, Ear, Peaks Location Peaks position *.bed KN1_Ear2_peaks.bed


GEO Accession Numbers


ChIP-Seq: GSE39161
RNA-Seq: GSE38487


Others


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