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Sample GSM381717 Query DataSets for GSM381717
Status Public on Apr 28, 2009
Title H3K4me3_ChIPSeq_root
Sample type SRA
 
Source name seedling roots
Organism Zea mays
Characteristics strain: B73 Strain
age: 14 day-old
tissue type: seedling roots
antibody: H3K4me3
Growth protocol Maize inbred line B73 was obtained from the USDA-ARS North Central Regional Plant Introduction Station in Ames, IA. Seeds were planted in individual pots containing a mixture of three parts soil (Premier Pro-Mix Bx Professional, Premier Horticulture, Quakertown, PA) and two parts vermiculite (D3 Fine Graded Horticultural Vermiculite, Whittemore Co., Lawrence, MA). Plants were grown under controlled environmental conditions (15 hours light/25 ºC, 9 hours dark/20 ºC) in a growth chamber, and the soil mixture was kept moist by watering the pots with 0.7mM Ca(NO3)2. Seedlings were harvested after 14 days, separated into shoots and roots, frozen in liquid nitrogen and stored at –80 ºC or processed directly after harvesting for ChIP.
Extracted molecule genomic DNA
Extraction protocol Maize tissue from 10 different seedlings was ground in liquid nitrogen, and genomic DNA was extracted from 1 g pooled tissue using a Qiagen DNeasy plant maxi kit. To enrich for methylated genomic DNA, 20 mg genomic DNA were digested with 200 units McrBC (New England Biolabs) overnight, and fragments 500 nucleotides and smaller were gel purified and used for library construction following the manufacturer's instructions, but adding a final gel purification step. To enrich for histonemodified regions, ChIP was conducted using 5 g fresh maize tissue from 10 seedlings following a previously described procedure (Lee et al., 2007). The following antibodies were used: H3K9ac (Upstate; 07-352), H3K27me3 (Upstate; 07-449), H3K4me3 (Abcam; ab8580), and H3K36me3 (Abcam; ab9050). For each 1-mL ChIP reaction, 5 mL antibody were added. The ChIPed DNA from three reactions was pooled to construct Solexa libraries essentially following the manufacturer's standard protocol but running 18 PCR cycles before gel purification of the samples. Total RNA was isolated using TRIzol reagent (Invitrogen) following the manufacturer's instructions. mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. After elution from the beads, first- and secondstrand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen), and the standard Solexa protocol was followed thereafter to create mRNA libraries. smRNA was extracted by running total RNA on a 15% PAGE gel and cutting out bands in the ;19- to 24-nucleotide size range. Libraries for smRNAs were constructed following previously published procedures (Mi et al., 2008; see Supplemental Methods online for details). All samples were prepared for sequencing following the manufacturer's standard protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description n/a
Data processing Sequencing reads were mapped to genome using MAQ software. ChIP-enriched regions were detected by MACS software. Further details found at http://www.plantcell.org/cgi/content/abstract/tpc.109.065714v1?papetoc
 
Submission date Mar 18, 2009
Last update date May 15, 2019
Contact name Xiangfeng Wang
E-mail(s) bryan4587@hotmail.com
Phone 2035084833
Organization name Yale University
Department MCDB
Lab Xing Wang Deng
Street address 352 OML, 165 Prospect st
City New Haven
State/province CT
ZIP/Postal code 06520-8104
Country USA
 
Platform ID GPL9141
Series (1)
GSE15286 Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize
Relations
SRA SRX012387
BioSample SAMN00004714

Supplementary file Size Download File type/resource
GSM381717_H3K4me3_MQ00_50_peaks.bed.gz 330.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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