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Sample GSM938345 Query DataSets for GSM938345
Status Public on Aug 07, 2012
Title atxr56_seedling_RNAseq_setC
Sample type SRA
 
Source name atxr56_seedling_RNAseq
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: atxr56
tissue: 10 day seedlings
Extracted molecule polyA RNA
Extraction protocol DNA-seq libraries: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei. For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions. Libraries were generated and sequenced following manufacturer instructions (Illumina).

RNA-seq libraries: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol (Invitrogen). Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).

Bisufite-Seq libraries: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 16
Data processing DNA-Seq reads were were first trimmed to 36mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Reads mapping to identical coordinates were collapsed into one read.
Genome_build: TAIR8
Supplementary_files_format_and_content: DNA-seq data: Column 1 is chromosome. Column 2 is strand read mapped to (+/-). Column 3 is the genomic coordinate.

mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Each RNA-seq processed file gives 20- or 25-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads. Column 1 is chromosome. Column 2 is the genomic coordinate. Column 3 is the normalized counts.

BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR8
Supplementary_files_format_and_content: BS-seq data: Column 1 is chromosome (1..5). Column 2 is the coordinate of the genomic cytosine. Column 2 is genomic strand (+/-) of the cytosine. Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).
 
Submission date May 29, 2012
Last update date May 15, 2019
Contact name Hume Stroud
Organization name UT Southwestern
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL13222
Series (1)
GSE38286 DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis.
Relations
SRA SRX150073
BioSample SAMN00998789

Supplementary file Size Download File type/resource
GSM938345_atxr56_seedling_RNAseq_setC_processed.txt.gz 17.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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