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| Status |
Public on Oct 09, 2023 |
| Title |
Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions |
| Organism |
Zea mays |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). Among 16 sequenced samples, 20,478 to 49,640 (mean: 34,766) peaks were called, and these peaks represent potential chromatin accessible regions. Distribution of the peaks on chromatins varies among samples: 54.35% - 66.73% peaks are located at distal intergenic region (>3kb upstream and >300 bp downstream of a gene) and 6.7% - 12.1% are located at promoter region (within 3 kb flanking transcription starting site), and 4.62% - 8.88% peaks are located within 1kb flanking transcription starting site. Also, in WT background, nkd1 and nkd2 single mutants have overall greater number of opening regions (upregulated peaks) than closing regions (downregulated peaks), whereas nkd1,2 double mutant has similar number of opening and closing regions. In contrast, in o2-background, all nkd1, nkd2 and nkd1,2 mutants have greater number of closing than opening regions. This indicates that o2 may alter differential accessibility of nkd1, nkd2 single or nkd1,2 double mutants.
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| Overall design |
Frozen 16 DAP endosperms of nkd1, 2 and o2 single, double and triple mutants, as well as the wild type counterpart (two biological replicates each) were collected and the crude nuclei were extracted. The crude nuclei were stained with 4,6-Diamidino-2-phenylindole (DAPI) for nuclear sorting using a flow cytometer. At least 50,000 triploid nuclei (3C) were sorted for ATAC-Seq library construction. The library was constructed using the Active Motif ATAC-Seq Kit. The library was sequenced using NovaSeq 6000 SP flow cell sequencing platform at 2X50 bp paired-end in 50 million bp depth.
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| Contributor(s) |
Wu H, Becraft PW |
| Citation(s) |
37795691 |
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| Submission date |
Sep 28, 2022 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Hao Wu |
| E-mail(s) |
hw388@cornell.edu
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| Organization name |
Cornell University
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| Street address |
236 Tower Rd, Plant Science Building Room #236
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platforms (1) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
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| Samples (16)
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| GSM6605456 |
Endosperm, nkd1nkd2, rep2 |
| GSM6605457 |
Endosperm, nkd1nkd2o2, rep1 |
| GSM6605458 |
Endosperm, nkd1nkd2o2, rep2 |
| GSM6605459 |
Endosperm, nkd1o2, rep1 |
| GSM6605460 |
Endosperm, nkd1o2, rep2 |
| GSM6605461 |
Endosperm, nkd2, rep1 |
| GSM6605462 |
Endosperm, nkd2, rep2 |
| GSM6605463 |
Endosperm, nkd2o2, rep1 |
| GSM6605464 |
Endosperm, nkd2o2, rep2 |
| GSM6605465 |
Endosperm, o2, rep1 |
| GSM6605466 |
Endosperm, o2, rep2 |
| GSM6605467 |
Endosperm, WT, rep1 |
| GSM6605468 |
Endosperm, WT, rep2 |
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| Relations |
| BioProject |
PRJNA885167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214415_RAW.tar |
1006.5 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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