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Sample GSM3498711 Query DataSets for GSM3498711
Status Public on Jun 21, 2019
Title ATAC-Seq_mbd9-3_R2
Sample type SRA
 
Source name flowers
Organism Arabidopsis thaliana
Characteristics developmental stage: 4 weeks
genotype/variation: mbd9-3
background ecotype: Columbia-0
Growth protocol Plants were grown in soil in a greenhouse under long day conditions for 4 weeks. Flowers were collected for nuclei extraction. Two replicates for each genotype were collected.
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated as described in Liu, W et al, 2018. ATAC-seq was performed as described in Buenrostro, J.D., et al, 2013.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing ATAC seq read adaptors were been removed with trim_galore
Reads were mapped using Bowtie2 (-X 2000 -m 1).
Chloroplast and mitochondrial DNA aligned reads were filtered out and duplicate reads were removed using Samtools
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig, narrowPeak
 
Submission date Dec 03, 2018
Last update date Jun 21, 2019
Contact name magdalena ewelina potok
Organization name UCLA
Department MCDB
Lab Jacobsen lab
Street address 4045 Terasaki Life Sciences Building
City Los Angeles
State/province CA
ZIP/Postal code 90095-7239
Country USA
 
Platform ID GPL13222
Series (2)
GSE123257 Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ATAC-Seq]
GSE123263 Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.
Relations
BioSample SAMN10517051
SRA SRX5088433

Supplementary file Size Download File type/resource
GSM3498711_mbd9_rep2.bw 34.4 Mb (ftp)(http) BW
GSM3498711_mbd9_rep2_peaks_no_control_peaks.narrowPeak.gz 867.3 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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