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Sample GSM2898313 Query DataSets for GSM2898313
Status Public on Jan 05, 2018
Title WT Mnase-seq - rep2
Sample type SRA
 
Source name 4-5 leaf developmentally-staged shoot tissue
Organism Arabidopsis thaliana
Characteristics genotype/variation: WT
tissue: 4-5 leaf developmentally-staged shoot
Treatment protocol N/A
Growth protocol Arabidopsis seedlings were grown on soil in 16 hours light/ 8 hours dark conditions.
Extracted molecule genomic DNA
Extraction protocol Native chromatin from purified nuclei was digested with MNase. After lysing nuclei with 1% SDS, nucleosome associated DNA was purified using the MinElute kit (Qiagen), after RNase A and Proteinase K treatments. Fragments were size selected for those >400 bp using SeraPure magnetic beads.
Libraries were prepared with the ThruPLEX DNA-Seq kit (Rubicon Genomics) using 25 ng of MNase-digested DNA. Libraries were sequenced on a an Illumina NextSeq500 with 76 bp paired-end reads.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina NextSeq 500
 
Description Nucleosomal DNA
processed data: WT_30M.nucleosomes.bw
processed data: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls
processed data: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls
Data processing ChIP-seq workflow:
Reads were mapped to the TAIR10 A. thaliana reference genome with Bowtie2, using default parameters.
Reads were processed and quality filtered with the –q 2 option using SAMtools software.
H2A.Z peaks were called with Homer findpeaks software, using options “style histone” and “–region”.
RNA-seq workflow:
Sequencing reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Tophat2 (using the second strand option) and the accepted hits file was name-sorted and indexed using SAMtools.
Read counts were quantified for each exon using htseq-counts with name order and strict intersection options.
Differential expression was calculated using edgeR software.
MNase-seq workflow:
Sequence reads were mapped to the TAIR10 Arabidopsis thaliana reference genome using Bowtie2 and were then further sorted and indexed using SAMtools.
We filtered using the SAMtools view command with the –q 2 option to filter for quality and option –f 0x02 to filter for properly paired reads.
Libraries were subsampled using SAMtools –s parameter to normalize all to the same number of reads (30.46 M reads).
Mapped reads from both biological replicates for each of the four genotypes were analyzed using the DANPOS2 dpos program to generate nucleosome peak files and nucleosome occupancy wiq files.
DANPOS2 generated wig files were converted to the bigwigwig format with wig2bigwig command (UCSC).
arp6 deletion mapping workflow:
Sequenced reads were mapped using BWA mem software, indexed and quality sorted (-s option) using SAMtools, and randomly subsetted using a python script, leaving 61.5 M mapped reads.
Deletions were called in the arp6 mutant using CNVnator (v0.3.3) software using bin sizes of 100 bp.
Genome_build: TAIR10
Supplementary_files_format_and_content: WT1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 1 sample.
Supplementary_files_format_and_content: WT2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the WT replicate 2 sample.
Supplementary_files_format_and_content: A1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 1 sample.
Supplementary_files_format_and_content: A2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the arp6 replicate 2 sample.
Supplementary_files_format_and_content: B1_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 1 sample.
Supplementary_files_format_and_content: B2_Z_histone.bed: Bed file of H2A.Z ChIP-seq peak coordinates called with the Homer software (as described in the data processing section) for the brm replicate 2 sample.
Supplementary_files_format_and_content: WT_vs_arp6.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6 mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_vs_arp6brm.edgeR.txt: Text file of RNA-seq Log2 Fold Change values and statistical measures for transcript levels from two arp6;brm mutant replicates compared to two WT plant replicates generated by edgeR software.
Supplementary_files_format_and_content: WT_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from WT plants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6 mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6brm_30M.nucleosomes.bw: Bigwig files consisting of nucleosome signals generated from two MNase-seq libraries from arp6;brm mutants. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6 mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: data_arp6brm_bam_30M-data_WT_bam_30M.positions.integrative.xls: Excel spreadsheet containing nucleosome coordinates and occupancy signals, comparisons between arp6;brm mutant nucleosomes and WT nucleosomes, and corresponding statistical measures, generated by the DANPOS2 program. Nucleosome data was generated from two MNase-seq libraries from each genotype. Libraries were first normalized to 30M reads.
Supplementary_files_format_and_content: arp6_CNVnator_deletions.bed: Bed file containing the coordinates for large (>200bp) deletions in arp6 genotype relative to the TAIR10 reference genome generated by the CNVnator software.
 
Submission date Dec 22, 2017
Last update date Jan 05, 2018
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 GPL19580
Series (1)
GSE108450 The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis
Relations
BioSample SAMN08226336
SRA SRX3505361

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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