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| Status |
Public on Nov 28, 2023 |
| Title |
EREB209 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Zea mays |
| Characteristics |
cultivar: B73
gene id: Zm00001d049364
age: 14 DAG
tissue: leaf
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| Growth protocol |
B73 inbred line cultivated in the greenhouse of China Agricultural University (Beijing, China)
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| 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) (cat. no. NG101, TIANGEN) according to the manufacturer’s instructions.
gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (cat. no. NG101, 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 (cat. no. RM20523, ABclonal). Protein expression was using TNT SP6 High-YIELD Wheat Germ Master Protein Expression System (cat. no. L3260; Promega) according to the manufacturer’s instructions. Halo-fusion protein was bound to Magne HaloTag Beads (cat. no. G7281; 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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.
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: DAP-seq
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| Submission date |
Apr 27, 2022 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Qiang Huo |
| E-mail(s) |
huoqiang@cau.edu.cn
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| Organization name |
China Agricultural University
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| Street address |
Yuanmingyuan West Road
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| City |
Beijing |
| ZIP/Postal code |
100091 |
| Country |
China |
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| Platform ID |
GPL25410 |
| Series (2) |
| GSE201700 |
Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq] |
| GSE201701 |
Decoding the gene regulatory network of endosperm differentiation in maize |
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| Relations |
| BioSample |
SAMN27917353 |
| SRA |
SRX15016950 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6069708_AP-44_FKDL192550970.bw |
24.1 Mb |
(ftp)(http) |
BW |
| GSM6069708_AP-44_FKDL192550970.narrowPeak.gz |
3.5 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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