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Sample GSM4097639 Query DataSets for GSM4097639
Status Public on Mar 13, 2020
Title H3 ddm1rdr6 Rep 1
Sample type SRA
 
Source name 10 day-old seedlings
Organism Arabidopsis thaliana
Characteristics genotype: ddm1-2 rdr6-15
genetic background: Col-0
Growth protocol Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium and seedlings were transplanted to soil 7 day after germination.
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation was performed using H3 antibody (Abcam; ab1791). After washing, DNA was eluted and reverse-crosslinked and purified with ChIP DNA clean and concentrator kit (Zymo Research).
NEBNext Ultra II DNA Library Prep Kit
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Supplementary_files_format_and_content: Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Supplementary_files_format_and_content: ChIP-seq: Adapter trimming was performed using Trimmomatic, and read quality was assessed with FastQC. Reads were aligned to the TAIR10 reference genome using BWA-MEM with default parameters. Only primary alignments were retained, and optical and PCR duplicates were removed using Samtools. Bedgraph files were generated using Bedtools (genomeCoverageBed –bg).
 
Submission date Sep 26, 2019
Last update date Mar 13, 2020
Contact name Robert A Martienssen
E-mail(s) martiens@cshl.edu
Organization name Cold Spring Harbor Laboratory
Department Delbruck Bldg.
Lab Martienssen
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL19580
Series (1)
GSE128932 Arabidopsis retrotransposon virus-like-particles and their regulation by epigenetically activated small RNA
Relations
BioSample SAMN12856816
SRA SRX6911465

Supplementary file Size Download File type/resource
GSM4097639_h3_ddm1rdr6_rep1.bedgraph.gz 287.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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