DOI: 10.5061/dryad.vq83bk40q
title: Commensal bacteria maintain a Qa-1b-restricted unconventional CD8+ T population in gut epithelium

description: Intestinal intraepithelial lymphocytes (IELs) are characterized by an
 unusual phenotype and developmental pathway, yet their specific ligands
 and functions remain largely unknown. Here by analysis of QFL T cells, a
 population of CD8+ T cells critical for monitoring the MHC I antigen
 processing pathway, we established that unconventional Qa-1b-restricted
 CD8+ T cells are abundant in intestinal epithelium. We found that QFL T
 cells showed a Qa-1b-dependent unconventional phenotype in the spleen and
 small intestine of naïve wild-type mice. The splenic QFL T cells showed
 innate-like functionality exemplified by rapid response to cytokines or
 antigens, while the gut population was refractory to stimuli. Microbiota
 was required for the maintenance, but not the initial gut homing of QFL T
 cells. Interestingly, monocolonization with Pediococcus pentosaceus, which
 expresses a peptide that cross-activated QFL T cells, was sufficient to
 maintain QFL T cells in the intestine. Thus, microbiota is critical for
 shaping the Qa-1b-restricted IEL landscape.
description: The raw data were collected from flow cytometry analysis. The
 numbers were calculated in Excel.
description: # Commensal Bacteria Maintain a Qa-1b-restricted Unconventional CD8+ T
 Population in Gut Epithelium
 ## 1. Author Information
 ``` A. Corresponding Author Contact Information Name: Jian Guan
 Institution: Department of Pathology and the Institute of Cell
 Engineering, Johns Hopkins University School of Medicine Address:
 Baltimore, MD 21287 USA Email: jian.guan.cc@outlook.com B.
 Co-corresponding Author Contact Information Name: Scheherazade
 Sadegh-Nasseri Institution: Department of Pathology and the Institute of
 Cell Engineering, Johns Hopkins University School of Medicine Address:
 Baltimore, MD 21287 USA Email: ssadegh@jhmi.edu ``` 2\. Information about
 funding sources that supported the collection of the data: This work was
 supported by grants R01AI130210, R37AI060040 and R01AI149341 from the
 National Institutes of Health to NS. 3\. DATA & FILE OVERVIEW File
 name: RawData_Figure_SPF vs GF QFL-T The file contains data acquired
 through flow cytometry for analysis of various populations of immune cells
 in SPF/GF WT and SPF ERAP1-KO, Qa-1b-KO, TAP-KO mice. These data were used
 for analysis presented in Figure 1,2,3, 5 and 7. Mice information is
 indicated by the sheet names. Sample information is indicated in the
 'Sample' column. Population information is indicated in the
 first row of each sheet. The absolute QFL T numbers per tissue were
 calculated using counting beads (absolute_QFL_T_number =
 sample_QFL_T_number/number_animal_pool; sample_QFL_T_number =
 QFL_T_count/fraction_acquired; fraction_acquired =
 beads_count/beads_added). 4\. SHEET-SPECIFIC INFORMATION 1\) Sheet name:
 ’SPF Sp QFL-T’, ‘GF Sp QFL-T’ ``` Data List: \* Sample: sample ID (date of
 collection_strain_.fcs) \* QFL/organ/animal: number
 of QFL T cells per organ per tissue \* Age: age of mouse (weeks) \* %QFL-T
 Va3.2: percentage of Va3.2+ in QFL T \* %Total Va3.2: percentage of Va3.2+
 in total CD8 \* % QFL-T CD44: percentage of CD44hi in QFL T \* %Total
 CD44: percentage of CD44hi in total CD8 \* no. CD4 QFL-T: number of CD4+
 QFL T ``` 2\) Sheet Name: ‘SPF IEL’, ‘GF IEL’ ``` Data List: \* Sample:
 sample ID (date of collection_strain_.fcs) \*
 QFL/organ/animal: number of QFL T cells per organ per tissue \* Age: age
 of mouse (weeks) \* %QFL-T Va3.2: percentage of Va3.2+ in QFL T \* %CD8aa
 in Va3.2+QFL: percentage of CD8aa+ in Va3.2+ QFL T \* %CD8ab in Va3.2+QFL:
 percentage of CD8ab+ in Va3.2+ QFL T \* No.Va3.2+QFL: number of Va3.2+ QFL
 T \* No.CD8aa Va3.2+QFL: number of CD8aa+ Va3.2+ QFL T \* No. CD8ab
 Va3.2+QFL: number of CD8ab+ Va3.2+ QFL T \* No.Va3.2-QFL: number of Va3.2-
 QFL T \* %CD8aa in Va3.2-QFL: percentage of CD8aa+ in Va3.2- QFL T \*
 %CD8ab in Va3.2-QFL: percentage of CD8ab+ in Va3.2- QFL T \* No.CD8aa
 Va3.2-QFL: number of CD8aa+ Va3.2- QFL T \* No. CD8ab Va3.2-QFL: number of
 CD8ab+ Va3.2- QFL T ``` 3\) Sheet name: ‘SPF strains IEL QFL T number’,
 ‘SPF strains Sp QFL T number’ ``` Data List: \* Sample: sample ID (date of
 collection_strain_.fcs) \* Beads| Count: number of
 beads in aquired \* No. Of Beads Added: number of Beads Added \* Fraction
 Aquired: ‘Beads| Count’ divided by ‘No. Of Beads Added’ \*
 Lymphocytes/Single Cells/CD45+CD19-/TCRb+CD4-/QFL-T | Count: number of QFL
 T in gate \* No. of animals pooled: number of animals pooled \* Panel :
 antibody panel used for analysis \* QFL/organ/animal: number of QFL T
 cells per organ per tissue ``` 4\) Sheet name: ‘Total spleen Va3.2 CD44’
 ``` Data List: \* Sample: sample ID (date of
 collection_strain_.fcs) \* Beads| Count: number of
 beads in aquired \* No. Of Beads Added: number of Beads Added \* Fraction
 Aquired: ‘Beads| Count’ divided by ‘No. Of Beads Added’ \*
 Lymphocytes/Single Cells/CD45+CD19-/TCRb+CD4-/Va3.2+/CD8ab/CD44hi | Count:
 number of total Va3.2+CD8+CD44hi in gate \* Lymphocytes/Single
 Cells/CD45+CD19-/TCRb+CD4-/Va3.2-/CD8ab/CD44hi | Count: number of total
 Va3.2-CD8+CD44hi in gate \* Va3.2+ CD44hi No.: number of Va3.2+CD8+CD44hi
 per animal per tissue \* Va3.2- CD44hi No. : number of Va3.2-CD8+CD44hi
 per animal per tissue ``` 5\. Missing data codes: None 6\. Specialized
 formats or other abbreviations used: Qa-1b-ko(Qko/Q-ko), ERAAP-KO (EKO),
 Tap-KO(TKO), Before enrichment (Bf), Enriched(Er), Germ-free(GF)