Proteomic dataset: Profiling of cultivated Echerichia coli isolates from Crohn's disease patients and healthy individuals

Daria Rakitina; Julia Baikova; Olga Pobeguts; Olga Bukato; Ivan Butenko; Irina Garanina; Mark Levites; Alexander Manolov; Alexandra Kanygina; Elena Kostryukova; Tatiana Semashko; Irina Karpova; Vladislav Babenko; Petr Scherbakov; Igor Khalif; Marina Shapina; Asfold Parfenov; Irina Ruchkina; Oleg Knyazev; Nina Fadeeva; Alexandr Subbotin; Sergey Chamkin; Alexandr Pyrkh; Marina Ivantsova; Vadim Govorun

doi:10.1016/j.dib.2019.103734

Proteomic dataset: Profiling of cultivated Echerichia coli isolates from Crohn's disease patients and healthy individuals

Data Brief. 2019 Mar 7:23:103734. doi: 10.1016/j.dib.2019.103734. eCollection 2019 Apr.

Authors

Daria Rakitina¹, Julia Baikova¹, Olga Pobeguts¹, Olga Bukato¹, Ivan Butenko¹, Irina Garanina¹, Mark Levites¹, Alexander Manolov¹, Alexandra Kanygina², Elena Kostryukova¹, Tatiana Semashko¹, Irina Karpova¹, Vladislav Babenko¹, Petr Scherbakov^{1

3}, Igor Khalif⁴, Marina Shapina⁴, Asfold Parfenov³, Irina Ruchkina³, Oleg Knyazev³, Nina Fadeeva³, Alexandr Subbotin⁵, Sergey Chamkin⁶, Alexandr Pyrkh⁷, Marina Ivantsova⁸, Vadim Govorun¹

Affiliations

¹ Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
² Moscow Institute for Physics and Technology, Moscow, Russia.
³ Moscow Clinical Research Centre, Moscow, Russia.
⁴ State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia.
⁵ City Clinic #13 of Nigjny Novgorod, Russia.
⁶ Poliklinika of Railways of Syktyvkar, Russia.
⁷ Clinic "Vivea" Khabarovsk, Russia.
⁸ S.V. Nudelman Medical Center of Plastic Surgery, Ekaterinburg, Russia.

Abstract

One of the dysbioses often observed in Crohn's disease (CD) patients is an increased abundance of Escherichia coli (10-100 fold compared to healthy individuals) (Gevers et al., 2014). The data reported is a large-scale proteome profile for E. coli isolates collected from CD patients and healthy individuals. 43 isolates were achieved from 30 CD patients (17 male, 12 female, median age 30) and 19 isolates from 7 healthy individuals (7 male, median age 19). Isolates were cultivated on LB medium at aerobic conditions up to medium log phase. Protein extraction was performed with sodium deoxycholate (DCNa) and urea, alcylation with tris(2-carboxyethyl)phosphine and iodacetamide. Protein trypsinolysis was performed as described in (Matyushkina et al., 2016). Total cell proteomes were analysed by shotgun proteomics with HPLC-MS/MS on a maXis qTOF mass-spectrometer. The data including HPLC-MS/MS raw files and exported Mascot search results was deposited to the PRIDE repository project accession: PXD010920, project https://doi.org/10.6019/PXD010920.

Keywords: Crohn's disease; E. coli; HPLC-MS/MS; Proteome.