|
| Status |
Public on Jun 30, 2016 |
| Title |
B_ChIP_ZT15_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Aerial tissues
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73
antibody: ZmCCA1b
age: 5 days after planting
time-point (zt): 15
|
| Growth protocol |
All maize plants were grown at 600 µmol/m2/sec under 16L:8D cycle with temperature 28 °C (light) and 23 °C (dark) except for photosynthesis, starch and sucrose measurements for which natural sunlight was supplemented. The plants were placed in a randomized design by rotating around the growth room on a daily basis to minimize positional effects.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ZmCCA1b-DNA complexes were isolated with antibody.
ChIP-seq libraries for ChIP and input samples from two biological replicates were constructed using the standard NEB protocol (New England BioLabs) using custom made adapters containing barcodes for pooling multiple samples per each sequencing lane. Adapter and barcode sequences are listed in Supplementary Table 3. ChIPed DNA was subjective to end repair, dA-tailing, ligation with the adapters, and amplification by 18 cycles of PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs). 100-bp pair-end sequencing was performed on an Illumina Hi-Seq 2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B73.txt
|
| Data processing |
Raw reads were subjective to quality trimming and adaptor clipping using FASTX-Toolkit (hannonlab.cshl.edu/fastx_toolkit) followed by removing orphan reads.
For B73 or Mo17, the filtered pair-end reads were mapped to the maize B73 reference genome (release 5b.60), or the Mo17 reference genome (reference-guided assembly based on the B73 genome), respectively. For hybrids, the filtered pair-end reads were mapped to both B73 and Mo17 reference genomes and the best alignment was selected for each read.
The latest version of MACS (version 2.0.1) algorithm was used to identify enriched peaks on each ChIP-seq file against the corresponding input file using a mappable genome size of –g 2.07e+09 and cut off p-value of 1e-3. Peaks were defined if they overlapped in both biological replicates.
To make a master-peak list from the three time-points, the peaks obtained from each time-point were merged for each genotype.
Genome_build: B73 RefGen_v2, Mo17
Supplementary_files_format_and_content: tab-delimited text files include peak coordinates for each genotype ...
|
| |
|
| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dae Kwan Ko |
| E-mail(s) |
dkko@msu.edu
|
| Phone |
512-300-7521
|
| Organization name |
Michigan State University
|
| Department |
Plant Research Laboratories
|
| Lab |
The Brandizzi Lab
|
| Street address |
612 Wilson Rd. Plant Biology RM 122
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE67655 |
Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids |
|
| Relations |
| BioSample |
SAMN03465254 |
| SRA |
SRX982342 |
