Table 3

Biopsy specimen processing

SpecimenRecipient fluidProcessingPurpose
Biopsy #1RNAlaterNucleic acid extractionTranscriptomics
Biopsy #2HBSSFACSCell isolation
Biopsy #3NoneFlash frozenCulture-independent and culture-based assays of mucosa-associated microbial community
Biopsy #4NoneFlash frozenArchiving for validation of drug targets
Biopsies #5 and #6*FormalinParaffin embeddedHistochemistry (H&E) and immunohistochemistry;
Morphometric analyses and EED scoring
Duodenal AspirateMicrobiota: glycerol/cysteine solution
Other: Nil
Precharged N2 dry shipper to −80 freezerCulture-independent and culture-based assays
  • *Biopsy site: biopsy #6 from duodenal bulb, all others distal to the ampulla of Vater.

  • EED, environmental enteric dysfunction; FACS, fluorescence-activated cell sorting; HBSS, Hank’s balanced salt solution.