|
| Status |
Public on Jun 24, 2024 |
| Title |
Hi-C of E.coli: MG1655 + DPAG 50 uM (15 min) WT |
| Sample type |
SRA |
| |
|
| Source name |
MG1655
|
| Organism |
Escherichia coli |
| Characteristics |
cell line: MG1655
cell type: bacteria
genotype: MG1655 pFR66 (sfGFP) + pFD245 (PhlF sfGFP)
treatment: DAPG 15 min
|
| Treatment protocol |
DAPG 50 μM was then added, followed by incubation for 15 and 30min. To compare the effect of PARIS activation with that of treatment with chloramphenicol,E. coliMG1655 harboring pFR66 were diluted 1:100 from an overnight culture in LB + kanamycin 50 μg/ml until OD600= 0.3, followed by addition of chloramphenicol 20 μg/ml and incubation for 15 and 30min
|
| Growth protocol |
E. coliMG1655 carrying plasmids pFR85 (PtetariAB) and pFD250 (PPhlFocr), or the pFR66 (sfGFP) + pFD245 (PhlF sfGFP) control plasmids were diluted 1:100 from an overnight culture in LB + kanamycin 50 μg/ml + chloramphenicol 20 μg/ml and grown until OD600 = 0.3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell fixation was performed with 4% formaldehyde (Sigma-Aldrich, Cat. F8775) as described in Cockram et al. (2021)41. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with the Arima kit. Samples were sonicated using Covaris (DNA 300bp).
Preparation of the samples for paired-end sequencing was performed using Invitrogen TM Colibri TM PS DNA Library Prep Kit for Illumina according to manufacturer instructions. The detailed protocol is available in Cockram et al. (2021)
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AT640
|
| Data processing |
Reads were aligned with bowtie2 v2.4.4 and Hi-C contact maps were generated using hicstuff v3.0.3 (https://github.com/koszullab/hicstuff) with default parameters and using HpaII enzyme to digest. Contacts were filtered as described in42, and PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded.
Matrices were binned 4kb. Balanced normalizations were performed using ICE algorithm43. For all comparative analyses, matrices were downsampled to the same number of contacts. The Hi-C signal was computed as the contacts between adjacent 5kb bins as described in Lioyet al. (2018)44. In order to compare this signal with other genomics tracks, we binned it at the desired resolution
Assembly: hicstuff v3.0.3
Supplementary files format and content: raw files and cool files
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Justine Rozenn Groseille |
| E-mail(s) |
justine.groseille@pasteur.fr
|
| Organization name |
Institut Pasteur
|
| Street address |
28 rue du Dr Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE270519 |
Activation of the PARIS immune complex by viral proteins results in host tRNA cleavage and can be overcome by viruses encoding non-cleavable tRNAs |
|
| Relations |
| BioSample |
SAMN42002032 |
| SRA |
SRX25016823 |
