human reproductive system metagenome
collection_date
not provided
env_broad_scale
uterus(UBERON:0000995)
env_local_scale
uterine cervix(UBERON:0000002)
env_medium
Liquid Based Cytology(NCIT:C99177)
geo_loc_name
USA:Arkansas,Little Rock(GAZ,00165676)
host
Homo sapiens
lat_lon
not applicable
host_body_product
cervical mucus(UBERON:0000316)
host_sex
female
host_subject_id
2055
samp_collect_device
ThinPrep Holologic (Marlborough, MA)
samp_mat_process
The cervical cytology specimens in this current study were collected and reserved in the vial of the ThinPrep Pap Test (Hologic) as previously described (dois: 10.1371/journal.pone.0237556, 10.1177/1534735419893063). The specimens were frozen (-80⁰C) on the day of collection. DNA was extracted using QIAamp DNA Midi Kit (Qiagen). Extracted DNA was sent to Argonne National Laboratory (Argonne,IL) for amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq sequencing platform. The same volume of DNA was used for each reaction, and then normalized at the PCR pooling step. This ensures that equal amounts of each amplified sample are added to the sequencing pool. Paired-end reads from libraries with ~250-bp inserts were generated for the V4 region using the barcoded primer set: 515FB: 5'-GTGYCAGCMGCCGCGGTAA-3' and 806RB: 5'-GGACTACNVGGGTWTCTAAT-3'. MiSeq Reagent Kit v2 (2 × 150 cycles, MS-102-2002) was used. Initial sequence processing and analyses were performed using QIIME 2 (doi: 10.1038/s41587-019-0209-9).
forward_primer
GTGTGYCAGCMGCCGCGGTAA
reverse_primer
GGACTACNVGGGTWTCTAAT
sequencing_run
1
vaccine
PepCan
time
Screen
time_vaccine
Pre-vaccination
histlogical_response
Non_Responder_Screeen
original_sample_labels
Screen.15173.2055
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.human-associated