 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 21, 2024 |
| Title |
W22_ZmNAC128_ChIP1 |
| Sample type |
SRA |
| |
|
| Source name |
Kernel
|
| Organism |
Zea mays |
| Characteristics |
tissue: Kernel
background: W22
gene id: Zm00001d040189
genotype: W22
age: 15 DAP
|
| Growth protocol |
W22 inbried line and zmnac128 mutant cultivated in the field of Shangzhuang Experimental Station of China Agricultural University (Beijing, China)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 2 g of kernel powder was resuspended in pre-cold M1 buffer (10 mM sodium phosphate[pH 7], 0.1 M NaCl, 1 M 2-methyl 2,4-pentanediol, 10 mM β-mercaptoethanol and complete protease inhibitor cocktail). Cell nuclei were extracted using pre-cold M2 buffer (like M1 buffer with 10 mM MgCl2 and 0.5% Triton X-100), and M3 buffer (like M1 buffer without 2-methyl 2,4-pentanediol), then washed 5 times separately.
Cell nuclei were incubated with ZmNAC128, ZmNAC130 and IgG antibodies (final concentration, 20 μg/mL) for 12 h at 4℃. Then supernatant were incubated with dynabeads Protein A (Invitrogen) for 2 h at 4℃. After washing the samples four times, they were incubated with Tn5 transposome and tagmentation buffer (10 mM TAPS-NaOH (pH 8.5), 10 mM MgCl2, 10% (v/v) DMF, 0.5 mM spermidine, 0.05% (v/v) digitonin, and 1% (v/v) plant cocktail) at 37℃ for 5 min. The reactions were stopped and then the protein-DNA complexes were eluted from the beads. Finally, after proteinase k (Invitrogen) treatment, ChIP-DNA libraries were constructed and sequenced using an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) by BerryGenomics (China).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina software used for base calling
Trimmomatic (version 0.39) was used to trim the fastq files as follows: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, HEADCROP:0, MINLEN:75 and bowtie2 (version: 2.4.1) was used to align them to the B73 v4 reference genome with the following parameters: -p 40 -I 75 -X 1000 --no-discordant --no-mixed.
Peak calling was performed separately for each biological replicate using MACS2 (v2.0.10) with specific parameters: -m 10 30 -g 2.106e9.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak
|
| |
|
| Submission date |
Mar 24, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Teng Song |
| E-mail(s) |
huoqiang@cau.edu.cn
|
| Organization name |
China agricultural university
|
| Street address |
Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE262335 |
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN40594231 |
| SRA |
SRX24035284 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8163416_chip-W22-1_L1_U14602.sorted.bw |
115.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
