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| Status |
Public on Mar 06, 2024 |
| Title |
phoB-FLAG3_2 |
| Sample type |
SRA |
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| Source name |
phoB-FLAG3 strains
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| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
tissue: phoB-FLAG3 strains
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| Growth protocol |
The phoB-FLAG3 strains were grown in phosphate limited medium of YBG11
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The samples were cross-linked with formaldehyde at a final concentration of 1%, and the cross-linking reaction was terminated with glycine. Ultranic interruption of the DNA-protein complexes formed by cross-linking; The target protein antibody is added to form an antibody-target protein-DNA complex; This complex was precipitated using Protein G beads, specifically enriching DNA fragments bound to the protein of interest; Multiple washes to remove non-specifically bound chromatin and purify the complex; Unraveling cross-links and purifying DNA fragments; q-PCR or sequencing analysis.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The first part is data preprocessing. Delinker sequences, polluting sequences, and low-quality bases, clean data sequences were obtained, and relevant data statistics were performed.
In the second part, the clean data is mapped to the reference genome to obtain a BAM file, and the repetitive sequences are removed, and the uniquely aligned sequences are retained.
In the third part, the BAM file was tested for Peak to obtain information on the enrichment region, and the distribution of Peak in gene functional elements, recent gene search and motif prediction were performed.
In the fourth part, the distribution of Peak was counted, and the functional annotation and enrichment of GO and KEGG of the nearest Peak genes were carried out, and transcription factor prediction was carried out.
Assembly: ASM972v1
Supplementary files format and content: PhoB_Flag.peak_annotation.xls
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| Submission date |
Mar 04, 2024 |
| Last update date |
Mar 06, 2024 |
| Contact name |
wencan zheng |
| E-mail(s) |
z0425@mails.ccnu.edu.cn
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| Phone |
13971468058
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| Organization name |
Central China Normal University
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| Department |
School of Life Sciences
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| Street address |
NO.152 Luoyu Road
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430079 |
| Country |
China |
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| Platform ID |
GPL31267 |
| Series (1) |
| GSE260812 |
Phosphorus deficiency alleviates cyanobacterial iron-limitation through a direct PhoB_x0002_ mediated gene regulation |
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| Relations |
| BioSample |
SAMN40255166 |
| SRA |
SRX23831510 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8124896_IP_PhoB_Flag_2.tdf |
1.8 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
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