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Sample GSM1499355 Query DataSets for GSM1499355
Status Public on Feb 01, 2015
Title Bisulfite_seq-nrpe1
Sample type SRA
 
Source name Bisulfite_seq-nrpe1
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype/variation: nrpe1-12
tissue: 3 week leaf tissue
molecule subtype: Bisulfite-treated genomic DNA
Growth protocol All plants were grown at 22 degrees celsius in constant light.
Extracted molecule genomic DNA
Extraction protocol phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
This is duplicated sample record of GSM981040 for the convenient retrieval of the complete raw data from SRA.
Data processing ChIP-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Samples 5 and 6 are biological replicates of samples 7 and 8 respectively.
miRNA-seq - Reads were demultiplexed (perfect matches to each index were required). Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained. Reads with no identifiable adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch. Both unique and non-uniquely mapping reads were retained for normalization purposes but only uniquely mapping reads were used for downstream analysis. For downstream analyses up to 100 identical mapping reads were allowed to be counted at any given region, locations with more than 100 siblings were flattened to 100 mapping reads.
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. The drm2, drm3, and nrpe1 mutant libraries used in this study were previously published (GSE39901), as were the 2 other Col replicates used (Series:GSE36129-Sample:GSM881756, Series:GSE49090-Sample:GSM1193638).
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP-seq: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins /total unique mapping reads)
Supplementary_files_format_and_content: miRNA-seq: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome for 24nt class of small RNAs with each bin given a value corresponding to the relative 24 nt read density at that location (24nt reads in 25bp bins / total mapping small RNA reads of all size classes - unique and non-uniquely mapping)
Supplementary_files_format_and_content: BS-seq: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
 
Submission date Sep 08, 2014
Last update date May 15, 2019
Contact name Christopher Joel Hale
E-mail(s) chris.joel.hale@gmail.com
Organization name University of Washington
Department Pathology
Lab Center for Precision Diagnostics
Street address 1959 NE Pacific St., HSC H-458
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL13222
Series (1)
GSE61192 The catalytically inactive Domains Rearranged Methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis
Relations
BioSample SAMN03023742
SRA SRX695826
Named Annotation GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CG.wig.gz
Named Annotation GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CHG.wig.gz
Named Annotation GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CHH.wig.gz

Supplementary file Size Download File type/resource
GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CG.wig.gz 15.3 Mb (ftp)(http) WIG
GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CHG.wig.gz 15.7 Mb (ftp)(http) WIG
GSM1499355_cytosine2wig--wiggle_track--nrpe1_bin_size_1_context_CHH.wig.gz 63.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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