|
| Status |
Public on Aug 02, 2019 |
| Title |
globular-seed-input replicate 1 (YAB1 study) |
| Sample type |
SRA |
| |
|
| Source name |
Soybean seeds containing globular stage embryos
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 82
developmental stage: globular stage
tissue: whole seeds
chip antibody: none
|
| Treatment protocol |
Whole seeds were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10mM 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.
|
| Growth protocol |
Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).
|
| 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 10ug of polyclonal antibody raised against GmYAB1-like peptide STSFSPDQQHLSPSD in rabbit. 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 DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Whole seeds 1.0 - 1.5 mm in length were collected
|
| 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 were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2
|
| |
|
| Submission date |
Aug 01, 2019 |
| Last update date |
Aug 02, 2019 |
| Contact name |
Bob Goldberg |
| E-mail(s) |
bobglab@mcdb.ucla.edu
|
| Phone |
310-825-3270
|
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Street address |
610 Charles E Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL19246 |
| Series (1) |
| GSE135268 |
Identification of soybean YAB1-like binding sites in soybean seeds during seed development |
|
| Relations |
| BioSample |
SAMN12425756 |
| SRA |
SRX6638416 |
