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| Status |
Public on May 16, 2024 |
| Title |
ZM4, RM, rep1 |
| Sample type |
SRA |
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| Source name |
ZM4
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| Organism |
Zymomonas mobilis |
| Characteristics |
strain: ZM4
treatment: RM
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| Growth protocol |
Z. mobilis strains were cultured to exponential phase and 10^6 cells were collected by centrifugation at 2,000 g and washed with TE.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were then crosslinked with 3% fresh formaldehyde for 30 min at room temperature, followed by 30 min at 4 °C. Formaldehyde was finally quenched with 0.375 M glycine for 20 minutes at 4 °C. Fixed cells were collected, frozen in liquid nitrogen, and stored at -80 °C until use. 1 × 10^9 cells were suspended in 100 μl TE with 2 μl of Ready-Lyse lysozyme (Epicentre), and incubated at room temperature for 20 min before being treated with 0.5% SDS treatment for 10 min at 65 °C. SDS was quenched by adding 50 μl 10% Triton X-100 and incubating it for 15 min at 37 °C. The chromosomal DNA in the cell lysate was then digested for 1 h at 37 °C by adding 50 μl 10x NEB buffer 2.1(NEB), 300μl water, and 100U of Sau3AI. Biotin-14-dCTP (TriLINK) was used to label the restriction fragment ends with biotinylated cytosine nucleotides. Labeled DNA was diluted in a 10.0 ml ligation mix containing 100 Weiss units of T4 DNA ligase (Thermo) and ligated overnight at 16 °C. The crosslinking was reversed overnight at 65°C with 200 μg ml-1 proteinase K (Thermo), and DNA was purified using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. Purified DNA was sheared to a length of ~400 bp.
Biotinylated DNA fragments were pulled down by Dynabeads MyOne Streptavidin C1 beads (Thermo fisher) and prepared for Illumina sequencing by NEBNext Ultra II DNA Library Prep Kit (NEB) as per manufacturer’s instructions. The DNA fragments between 400 and 600 bp were purified and paired-end sequenced on the Illumina HiSeq X Ten platform with 150PE mode.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
Hi-C_ZM4_RM_10k.heatmap_ICed.matrix
Hi-C_ZM4_RM_5kb_heatmap.mcool
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| Data processing |
The Hi-C raw data generated from the Hi-C library were quality filtered using Trimmomatic v0.3882 and the clean data from two replicates were iteratively mapped to the reference genome Z. mobilis ZM4 (https://www.ncbi.nlm.nih.gov/nuccore/NC_006526.2) using the ICE software package.
Dangling ends and other unusable data were filtered, the valid pairs were used to analyze the correlation efficiency of the two biological replicates for each sample using GenomeDISCO. The valid pairs after pooling were binned into 10 kb, 5 kb, or 2 kb nonoverlapping genomic intervals to generate contact maps.
An insulation score algorithm was used to identify the CID boundaries of each sample, as well as the location and numbers of CIDs.
The bacterial chromosome was binned at 5 kb, and the intra-chromosome contacts of each sample were transferred to Fit-Hi-C software. Significant interactions were identified when both the both the p-value and q-value (false discovery rate, FDR) were less than 0.01 and contact count was greater than 2.
Assembly: NC_006526.2
Supplementary files format and content: Contact matrix
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| Submission date |
Dec 21, 2022 |
| Last update date |
May 16, 2024 |
| Contact name |
Mao Chen |
| E-mail(s) |
chenmao92@hotmail.com
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| Organization name |
Biogas Institute of Ministry of Agriculture and Rural Affairs
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| Street address |
Section 4-13, Renmin Rd. South
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| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL32966 |
| Series (2) |
| GSE221497 |
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C] |
| GSE221499 |
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation |
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| Relations |
| BioSample |
SAMN32348344 |
| SRA |
SRX18804820 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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