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| Status |
Public on Apr 28, 2009 |
| Title |
H3K36me3_ChIPSeq_root |
| Sample type |
SRA |
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| Source name |
seedling roots
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| Organism |
Zea mays |
| Characteristics |
strain: B73 Strain
age: 14 day-old
tissue type: seedling roots
antibody: H3K36me3
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
n/a
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| 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
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| Submission date |
Mar 18, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiangfeng Wang |
| E-mail(s) |
bryan4587@hotmail.com
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| Phone |
2035084833
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| Organization name |
Yale University
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| Department |
MCDB
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| Lab |
Xing Wang Deng
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| Street address |
352 OML, 165 Prospect st
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520-8104 |
| Country |
USA |
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| Platform ID |
GPL9141 |
| Series (1) |
| GSE15286 |
Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize |
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| Relations |
| SRA |
SRX012390 |
| BioSample |
SAMN00004717 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM381723_H3K36me3_MQ00_50_peaks.bed.gz |
230.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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