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Sample GSM8189463 Query DataSets for GSM8189463
Status Public on May 13, 2024
Title leaf_WT_AtH2AZ_2
Sample type SRA
 
Source name third or fourth pair of rosette leaves
Organism Arabidopsis thaliana
Characteristics tissue: third or fourth pair of rosette leaves
genotype: WT
treatment: anti-AtH2AZ
Treatment protocol NA
Growth protocol Plants were grown in soil in growth chambers at +20°C under a 16 hour-light/8-hour dark cycle.
Extracted molecule genomic DNA
Extraction protocol Chromatin of immunoprecipitated as described previously [ Zhao L, et al. 2020], with following modifications: 1) For each sample, 0.5 grams of leaf tissue was used, 2) ground samples were lysed in 600 μl of buffer S, 3) around 400 μl of the slurry were transferred to 0.6 ml tubes and sonicated in the Bioruptor (Diagenode) at + 4°C for 1 hour on the “high” setting with sonication intervals set to 45 seconds on/15 seconds off, 4) The sonicated lysates were centrifuged at 20,000xg for 10 min at + 4°C and 300 μl of the supernatants were transferred to a fresh 5 ml tube where 2.7 ml of buffer F was added and mixed well, 5) 50 μl of this mixture was saved as the input sample while 1.5 ml was used for immunoprecipitation with specific antibodies, 6) Arabidopsis-specific H2A.Z antibody [Deal R, et al. 2007] and human-specific H2A.Z antibody (Abcam, ab188314) were added to the diluted lysates at a final concentration of ~2 μg/ml and incubated overnight at + 4°C with rocking, 7) 25 μl of washed Protein A dynabeads were added to each sample and incubated at + 4°C for 2 hours with rocking, 8) immunoprecipitated DNA fragments were purified using Qiagen Minelute kit and eluted in 14 μl of elution buffer. Eluted DNA samples were quantified using Picogreen reagents.
ChIP-seq libraries were prepared starting with ~1000 picograms of ChIP or input DNA samples using the ThruPlex DNA-seq kit (Takara) according to the manufacturer’s instructions. Libraries were pooled together and sequenced using paired-end 150 nt reads on an Illumina NovaSeq 6000 instrument.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were trimmed of adapter content using and mapped to the Arabidopsis thaliana Col-PEK genome assembly using Bowtie2 with the following parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were converted to the BAM file format and quality filtered using Samtools. Duplicate reads were removed using Picard markDuplicates. For visualization, deduplicated BAM files of each genotype were converted to bedgraph files using bedtools bamtobed followed by genomecov. Samples were then normalized to the lowest read depth and converted to BigWig using bedGraphToBigWig. Finally, the signal from each sample was expressed as the log2 ratio relative to the corresponding input using bigWigCompare with –psuedocount = 1 to avoid 0/x.
Assembly: Col-PEK
Supplementary files format and content: bigWig
 
Submission date Apr 05, 2024
Last update date May 13, 2024
Contact name Roger B Deal
E-mail(s) roger.deal@emory.edu
Phone 404-727-8087
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL26208
Series (2)
GSE263312 Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (ChIP-Seq)
GSE263313 Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development
Relations
BioSample SAMN40760727
SRA SRX24165253

Supplementary file Size Download File type/resource
GSM8189463_WT_2_GeneBody_counts.txt.gz 108.4 Kb (ftp)(http) TXT
GSM8189463_WT_2_v_WT_input_coverageScaled_plusOne.bw 21.2 Mb (ftp)(http) BW
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Raw data are available in SRA

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