All important metadata related to the project and files in 00_Files.md and Files directory

FS19C_metadata.xlsx

Sample nomenclature key:

(NovaSeqSequenceID#)-(Animal#)(RAMS or Fecal sample)(Time aka day negative #)(Isolate A/B/C/D)

NovaSeqSequenceID

Number 1-96

Animal'#'

See FS19C_metadata.xlsx for animal # metadata

RAMS or Fecal sample

R = RAMS (collected from RAMS plates)
F = fecal (collected from fecal plates)
RE = RAMS-enriched (collected from RAMS-enriched plates)
FE = fecal-enriched (collected from Fecal-enriched plates)

Time aka day negative '#'

N# = Day negative 1, 2, 3, 5 or 7 (see FS19 study for timeline)
- N1
- N2
- N3
- N5
- N7
Any sample names that don't have an N# were collected on day of necropsy

Isolate A/B/C/D

Isolate A/B/C/D: collected up to four separate colonies from one plate of (Animal#)(R/F/RE/FE)(Time aka day negative #)

Examples of sample nomenclature and explanation:

1-428RN3A
- NovaSeq sample #1, animal 428, collected from RAMS plate (R), RAMS sample collected from animal on day -3 (N3), colony A
2-437RN1A
- NovaSeq sample #2, animal 437, collected from RAMS plate (R), RAMS sample collected from animal on day -1 (N1), colony A
6-437REN3B
- NovaSeq sample #6, animal 437, collected from RAMS-enriched plate (RE), RAMS sample collected from animal on day -3 (N3), colony B
9-429FN2A
- NovaSeq sample #9, animal 429, collected from Fecal plate (F), fecal sample collected from animal on day -2 (N2), colony A
59-437REC
- NovaSeq sample #59, animal 437, collected from RAMS-enriched (RE) plate, RAMS sample collected from animal on necropsy day, colony C
89-436FED
- NovaSeq sample #89, animal 436, collected from Fecal-enriched (FE) plate, fecal sample collected from animal on necropsy day, colony D