 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 21, 2024 |
| Title |
CPP2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Zea mays |
| Characteristics |
tissue: leaf
background: B73
gene id: Zm00001d031008
genotype: B73
age: 14 DAG
|
| Growth protocol |
B73 inbried line cultivated in the greenhouse of China Agricultural University (Beijing, China)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from maize B73 14 DAG leaf. gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (TIANGEN) according to the manufacturer’s instructions.
gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (TIANGEN) according to the manufacturer’s instructions. Full length maize transcription factors’ coding sequences were cloned from maize 14 DAG leaf cDNA into the NotI and AscI sites of pUC57-Halo using MultlF Seamless Assembly Mix (ABclonal). Protein expression was using TNT SP6 High-YIELD Wheat Germ Master Protein Expression System (Promega) according to the manufacturer’s instructions. Halo-fusion protein was bound to Magne HaloTag Beads (Promega) and washed three times using TBSN buffer( 100 mM Tris buffer, pH 7.5, 50 mM NaCl, 0.005 % NP40). Then, 500 ng gDNA libraries was added and incubated at room temperature for 1.5 h. After incubation the beads was washed four times. Resuspended the beads in 30µl of EB buffer to recover DNA. The recovered DNA was were cleaned up with Silane magnetic beads, and amplified via PCR. The PCR products were cleaned up with Silane magnetic beads and sequenced using an NovaSeq platform (Illumina) by BerryGnomics (China).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| 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: -I 75 -X 1000 --no-discordant --no-mixed.
Peaks were called using GEM v3.4 with the following parameters: --d Read_Distribution_default.txt --k_min 4 --k_max 12 --outNP --q 3 --nrf --outNP --outHOMER –outMEME. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak
Library strategy: ampDAP-seq
|
| |
|
| 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) |
| GSE262337 |
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [DAP-Seq] |
|
| Relations |
| BioSample |
SAMN40594246 |
| SRA |
SRX24035318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8163437_CP-01_FKDL202601306.bw |
29.1 Mb |
(ftp)(http) |
BW |
| GSM8163437_CP-01_FKDL202601306.rmblacklist.bed.gz |
2.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
