Work Description

Title: Preterm Birth Open Access Deposited

http://creativecommons.org/licenses/by-nc/3.0/us/
Attribute Value
Methodology
  • DNA was extracted from previous stored vaginal slides; and DNA was pre-amplified using universal bacterial primers based on 16s rDNA; total bacterial and species specific bacterial copy numbers were identified using total bacteria primers and primers specific to each bacteria taxa; samples with copy numbers fewer than 100 were under the limit of detection and were considered to be negative
Description
  • This is the bacterial DNA data extracted from the gram stain slides. The targeted bacteria genera and species include: Atopobium spp., bacterial vaginosis-associated bacterium (BVAB) types 1, 2 and 3 in the order Clostridiales, Escherichia coli, Gardnerella vaginalis, Group B Streptococcus, Lactobacillus spp., Mobiluncus spp., Mycoplasma spp., and Ureaplasma spp. We also used a primer set for Lactic Acid Bacteria (LAB) that includes lactic acid producing bacteria of the genera Lactobacillus, Pediococcus, Leuconostoc, and Weissella. We calculated the relative proportion of each bacterial taxon using the bacterial copies measured by each specific bacteria primer divided by the total bacterial copies. The limit of detection was 100 copies and readings lower than the limit were considered negative
Creator
Depositor
  • weaverd@umich.edu
Contact information
Discipline
Citations to related material
  • Wen A, Srinivasan U, Goldberg D, Owen J, Marrs CF, Misra D, Wing DA, Ponnaluri S, Miles-Jay A, Bucholz B, Abbas K, Foxman B. Selected vaginal bacteria and risk of preterm birth: an ecological perspective. J Infect Dis. 2014 Apr 1;209(7):1087-94. https://doi.org/10.1093/infdis/jit632. Epub 2013 Nov 22. PMID: 24273044; PMCID: PMC3952673.
  • Foxman B, Wen A, Srinivasan U, Goldberg D, Marrs CF, Owen J, Wing DA, Misra D. Mycoplasma, bacterial vaginosis-associated bacteria BVAB3, race, and risk of preterm birth in a high-risk cohort. Am J Obstet Gynecol. 2014 Mar;210(3):226.e1-7. https://doi.org/10.1016/j.ajog.2013.10.003. Epub 2013 Oct 4. PMID: 24096128; PMCID: PMC3943817.
Resource type
Curation notes
  • Each of these files was originally published in separate works in Deep Blue Data. They were brought together into this work on Sept 28, 2020.
Last modified
  • 09/28/2020
Published
  • 06/29/2016
Language
DOI
  • https://doi.org/10.7302/vkyk-tf90
License
To Cite this Work:
Wen, A., Foxman. Betsy, Srinivasan, U., Goldberg, D., Marrs, C., Owen, J., Wing, D., Misra, D., Cronenwett, A., Ponnaluri, S., Miles-Jay, A., Bucholz, B., Abbas, K. (2016). Preterm Birth [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/vkyk-tf90

Relationships

In Collection:

Files (Count: 6; Size: 3.41 MB)

The Preterm Birth (PTB) Work contains files related to the two papers:
Wen A, Srinivasan U, Goldberg D, Owen J, Marrs CF, Misra D, Wing DA, Ponnaluri S, Miles-Jay A, Bucholz B, Abbas K, Foxman B. Selected vaginal bacteria and risk of preterm birth: an ecological perspective. J Infect Dis. 2014 Apr 1;209(7):1087-94. doi: 10.1093/infdis/jit632. Epub 2013 Nov 22. PMID: 24273044; PMCID: PMC3952673.

Foxman B, Wen A, Srinivasan U, Goldberg D, Marrs CF, Owen J, Wing DA, Misra D. Mycoplasma, bacterial vaginosis-associated bacteria BVAB3, race, and risk of preterm birth in a high-risk cohort. Am J Obstet Gynecol. 2014 Mar;210(3):226.e1-7. doi: 10.1016/j.ajog.2013.10.003. Epub 2013 Oct 4. PMID: 24096128; PMCID: PMC3943817.

Data for these samples were originally analyzed using SAS. The dataset otuput is "visit1_0417.sas7bdat"
The output is also exported in Excel and uploaded here "visit1_0417.xls

CONTENTS
1. PTB microbial data (data_0417_rename.xls)
Authored by Usha Srinivasan at the University of Michigan
Description: This is the bacterial DNA data extracted from the gram stain slides. The targeted bacteria genera and species include: Atopobium spp., bacterial vaginosis-associated bacterium (BVAB) types 1, 2 and 3 in the order Clostridiales, Escherichia coli, Gardnerella vaginalis, Group B Streptococcus, Lactobacillus spp., Mobiluncus spp., Mycoplasma spp., and Ureaplasma spp. We also used a primer set for Lactic Acid Bacteria (LAB) that includes lactic acid producing bacteria of the genera Lactobacillus, Pediococcus, Leuconostoc, and Weissella. We calculated the relative proportion of each bacterial taxon using the bacterial copies measured by each specific bacteria primer divided by the total bacterial copies. The limit of detection was 100 copies and readings lower than the limit were considered negative,
Methodology: DNA was extracted from previous stored vaginal slides; and DNA was pre-amplified using universal bacterial primers based on 16s rDNA; total bacterial and species specific bacterial copy numbers were identified using total bacteria primers and primers specific to each bacteria taxa; samples with copy numbers fewer than 100 were under the limit of detection and were considered to be negative

2. PTB demographic and visit data (cl_info_sep.xls)
Authored by Ai Wen at the University of Michigan
Description: This is the clinical data and vaginal measurement data U of Alabama provided. The column names are fairly self-explanatory. There was not an original data codebook associated with it.
Methodology: Cervical and clinical information were collected by University of Alabama at Birmingham and provided to U Michigan; data were then combined with file that includes information on the shortest post-cerclage cervical measurement using a SAS code

3. PTB post-randomization shorteest cerclage measurement (pr_shortest_cl_0125.xls)
Authored by John Owens at the University of Alabama - Birmingham
Description: This is the post-randomization shortest cerclage measurement of each participant who entered the randomization (which means their cerclage measurement was less than 25mm at one of the visits). No codebook was associated with it.
Methodology: Participants were continuously monitored during the study and their shorted cervical length measured after randomization was reported in this file; this file was created and provided by University of Alabama.

4. Excel file after combine (visit1_0417.XLS)
Authored by Ai Wen at the University of Michigan
Description: This is the excel output from the SAS code used to analyze the data (not included in this data set).

5. SAS data file after combine (visit1_0417.sas7bdat)
Authored by Ai Wen at the University of Michigan
Description: This is the SAS data output using the SAS code used to analyze the data (not included in this data set).

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