Effect of Micro-patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress
Cite this dataset:
Parmar, Dharmeshkumar; Jia, Jin; Shrout, Joshua; Sweedler, Jonathan; Bohn, Paul (2022): Effect of Micro-patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0382919_V1
Use this persistent URL to link to this dataset:
Dataset Description

#### Details of Pseudomonas aeruginosa biofilm dataset ####

----------------*Folder Structure*-------------------------------------

This dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in "MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip", each folder contains 3 sub-folders as listed below.

1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]:

(1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h

2. StaticBiofilms [Static biofilms grown on mucin surface]:

(1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones

----------------*File name*----------------------------------------------

Sample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below.

*Example file name "Rep1-Stat-FRD1-mPat-48-FS"*

~ Each unit of information is separated by "-"
~Unit 1 - "Rep1" - Biological replicate ( Rep1, Rep2, and Rep3)
~Unit 2 - "Stat" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant)
~Unit 3 - "FRD1" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain)
~Unit 4 - "mPat" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface)
~Unit 5 - "48" - Sample time point (hours = 48, 72, 96)
~Unit 6 - "FS" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288))

----------------*File structure*------------------------------------------

All MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix.

----------------*End of Information*--------------------------------------
Subject Life Sciences
Keywords mass spectrometry imaging (MSI); biofilm; antibiotic resistance; Pseudomonas aeruginosa; quorum sensing; rhamnolipids
License CC BY
Funder U.S. National Institutes of Health (NIH)-Grant:R01AI113219-06
Corresponding Creator Jonathan Sweedler
Downloaded 119 times
Version DOI Comment Publication Date
1 10.13012/B2IDB-0382919_V1 2022-07-19
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update: {"nested_updated_at"=>[nil, Mon, 09 Jan 2023 17:53:08.741967000 UTC +00:00]} 2024-01-03T18:24:02Z
update: {"description"=>["#### Details of Pseudomonas aeruginosa biofilm dataset ####\r\n\r\n----------------*Folder Structure*-------------------------------------\r\n\r\nThis dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in \"MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip\", each folder contains 3 sub-folders as listed below. \r\n\r\n\r\n1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]:\r\n\r\n\t\t(1)Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h\r\n\r\n2. StaticBiofilms [Static biofilms grown on mucin surface]:\r\n\r\n\t\t(1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones\r\n\r\n\r\n----------------*File name*----------------------------------------------\r\n\r\nSample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below.\r\n\r\n*Example file name \"Rep1-Stat-FRD1-mPat-48-FS\"*\r\n\r\n~ Each unit of information is separated by \"-\"\r\n~Unit 1 - \"Rep1\" - Biological replicate ( Rep1, Rep2, and Rep3)\r\n~Unit 2 - \"Stat\" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant)\r\n~Unit 3 - \"FRD1\" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain)\r\n~Unit 4 - \"mPat\" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface)\r\n~Unit 5 - \"48\" - Sample time point (hours = 48, 72, 96)\r\n~Unit 6 - \"FS\" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288))\r\n\r\n\r\n----------------*File structure*------------------------------------------\r\n\r\nAll MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix.\r\n\r\n----------------*End of Information*--------------------------------------", "#### Details of Pseudomonas aeruginosa biofilm dataset ####\r\n\r\n----------------*Folder Structure*-------------------------------------\r\n\r\nThis dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in \"MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip\", each folder contains 3 sub-folders as listed below. \r\n\r\n\r\n1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]:\r\n\r\n\t\t(1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h\r\n\r\n2. StaticBiofilms [Static biofilms grown on mucin surface]:\r\n\r\n\t\t(1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones\r\n\r\n\r\n----------------*File name*----------------------------------------------\r\n\r\nSample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below.\r\n\r\n*Example file name \"Rep1-Stat-FRD1-mPat-48-FS\"*\r\n\r\n~ Each unit of information is separated by \"-\"\r\n~Unit 1 - \"Rep1\" - Biological replicate ( Rep1, Rep2, and Rep3)\r\n~Unit 2 - \"Stat\" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant)\r\n~Unit 3 - \"FRD1\" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain)\r\n~Unit 4 - \"mPat\" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface)\r\n~Unit 5 - \"48\" - Sample time point (hours = 48, 72, 96)\r\n~Unit 6 - \"FS\" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288))\r\n\r\n\r\n----------------*File structure*------------------------------------------\r\n\r\nAll MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix.\r\n\r\n----------------*End of Information*--------------------------------------"]} 2022-07-19T19:56:15Z