mouse gut metagenome
Antibiotics + Lung carcinoma  mouse 2 Exp 1
collection_date
2019-04-11
env_broad_scale
gut(UBERON:0001007)
env_local_scale
colon(UBERON:0001155)
env_medium
feces(UBERON:0001988)
geo_loc_name
USA:Arkansas,Little Rock (GAZ,00165676)
host
Mus musculus (C57BL/6J)
lat_lon
34.7504 N 92.3227 W
chem_administration
ad libitum availability to drinking water containing ampicillin (250 mg/L) & vancomycin (125 mg/L) & neomycin (250 mg/L) & metronidazole (250 mg/L)
host_body_habitat
Gastrointestinal
host_body_product
feces
host_diet
ad libitum availability to drinking water containing ampicillin (250 mg/L) & vancomycin (125 mg/L) & neomycin (250 mg/L) & metronidazole (250 mg/L) with ad libitum availability standard chow
host_infra_specific_rank
C57BL/6J mouse from Jackson Laboratory, USA (Mus musculus)
host_last_meal
standard chow
host_life_stage
adult
host_sex
female
host_taxid
10090
perturbation
ampicillin (250 mg/L) & vancomycin (125 mg/L) & neomycin (250 mg/L) & metronidazole (250 mg/L)
samp_mat_process
Fecal samples less than 6 hr old were collected from individual mice and stored at -80C (doi:10.1186/s12866-018-1359-5). DNA extraction was performed using ZymoBiomics DNA Miniprep kit (#D4300; Zymo Research, Irvine, CA) according to the manufacturer's instruction. Briefly, samples were suspended in lysis buffer and heated to 60 °C for 20 min prior to 20 min of horizontal vortexing with beads to homogenize the samples. Samples were centrifuged and the supernatant collected. From this several processing steps were performed to remove residual protein and the final DNA sample was eluted in 100 μL of nuclease-free H2O. The concentration and purity was determined by the A260/A280 value (Cytation 5; BioTek, Winooski VT, USA). The extracted sample DNA was sent to the ZymoBIOMICS® Targeted Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA) and sequenced using the Qucik-16S™ Primer set V3-V4 (Zymo Research, Irvine, CA) via the Illumina MiSeq v3 reagent kit using a 10% PhiX spike-in. Summary of the sequencing service: PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The pooled library was cleaned using the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation Santa Clara, CA) (Agilent Technologies, (Thermo Fisher Scientific, Waltham, WA).
samp_store_temp
-80 C
source_material_id
feces
tumor_cell_incoculum_type
Lewis-lung Carcinoma
tumor_cell_inoculum_volume
100 microliters
tumor_incoculum_cell_count
1x10^6
zymobiomics_id_label
zr2551_22
sequencing_run
1
amplicon_region
V3V4
sequencing_kit
Qucik-16S Primer set V3-V4 (Zymo Research - Irvine CA)
R1_forward_primer_5prime_trim_length_bp
16
R2_reverse_primer_5prime_trim_length_bp
24
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.host-associated