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| Status |
Public on Sep 16, 2023 |
| Title |
GmCOT_GLYMA.06G314400-ChIP-br2 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Glycine max |
| Characteristics |
tissue: embryos
genotype: Williams 82
cell type: cotyledon stage
chip antibody: anti-peptide GLYMA.06G314400
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| Treatment protocol |
Cotyledon stage embryos were dissected from 3.5 to 4.5 mm seeds. Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.
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| Growth protocol |
Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide SRSQPQPQPLHPQYHH (corresponding to the amino acids 117-132 of GLYMA.04G093300), or 3 ug of antibody raised against the peptide CPEPRYQIRRTSSASF (corresponding to the amino acids 302-316 of GLYMA.06G314400). Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles. Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS3, using default parameters and a q value threshold of 0.01.
Assembly: Wm82.a2.v1
Supplementary files format and content: NarrowPeak files generated by MACS3.
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| Submission date |
Sep 07, 2023 |
| Last update date |
Sep 16, 2023 |
| Contact name |
John Harada |
| E-mail(s) |
[email protected]
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| Organization name |
University of California
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| Department |
Plant Biology
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| Lab |
Harada lab
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL28801 |
| Series (1) |
| GSE242528 |
Identification of GLYMA.04G093300 and GLYMA.06G314400 binding sites in soybean cotyledon stage embryos. |
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| Relations |
| BioSample |
SAMN37313197 |
| SRA |
SRX21658402 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7765150_COT-GLYMA.06G314400-P2-BR2_q0.01_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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