11479.00077E8B87; Genome-wide mapping of gene-microbiome interaction: implication in behavior and effect on microbiome and metabolome
rat gut metagenome
cecum; Heterogeneous Stock rat; University of Michigan
ENA first public
2025-10-30
INSDC center name
UCSDMI
INSDC status
public
anonymized_name
not applicable
bad_rat
FALSE
barcode_16s
GGTCCTTCCCGA
batch
Batch17
batchnumber
not applicable
cage
B17-17
cage_density
2
ccc_box
box10
cecum_box
MI-B17-CC3
center_name
UCSDMI
center_name_16s
UCSDMI
center_project_name
Heterogeneous Stock rats
center_project_name_16s
Heterogeneous Stock rats
clean_ids_16s
00077E8B87
collection date
2017-06-08
collection_date
2017-06-08
collection_timestamp
2017-06-08
color
albino
compound_name_16s
11479_prep_6462_20191016-101040_11479.00077E8B87
country
USA
crf_mi_box
crf_MI_box13
crf_ny_box
not provided
dam
HSF02442
datetime_dissected
2017-06-08 14:42:00
datetime_fasting_started
2017-06-07 18:00:00
datetime_glucose_measured_at_dissection
2017-06-08 14:36:00
deblur_biom_id
175553
deblur_rooname
175553.11479.00077E8B87
delay_discounting_box
not provided
dna_extracted
not provided
dob
2017-03-06
dow
2017-03-27
duplicated_16s
NA
earpunchlcn
LB
elevation
840
empo_1
Host-associated
empo_2
Animal (non-saline)
empo_3
Animal proximal gut (non-saline)
empo_4
Animal proximal gut (non-saline)
env_biome
urban biome
env_feature
animal-associated habitat
env_material
cecum
env_package
host-associated
extraction_robot_16s
Carmen_KF3
extractionkit_lot_16s
160033450
full_ids_16s
70124.11479.00077E8B87
generation
80
genotyped
TRUE
geo_loc_name
USA:MI:Ann Arbor
geographic location (country and/or sea)
USA
glucose_at_dissection
83
glucose_at_weaning
120
glucose_units
mg_dl
has_dupl_16s
no
host_age
94.8625
host_age_units
days
host_body_habitat
UBERON:gastro-intestinal system
host_body_product
UBERON:lumen of gut
host_body_site
UBERON:cecum
host_common_name
rat
host_height
not collected
host_height_units
not applicable
host_life_stage
not provided
host_scientific_name
Rattus norvegicus
host_subject_id
00077E8B87
host_taxid
10116
host_weight
172
host_weight_units
g
in_16s_prep
YES
instrument_model
Illumina MiSeq
instrument_model_16s
Illumina MiSeq
latitude
42.28
length_units
cm
length_w_tail
35
length_wo_tail
19
library_construction_protocol
Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4
library_construction_protocol_16s
Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4
linker_16s
GT
litternumber
1
littersize
12
locomotor_testing_box
not provided
longitude
-83.74
losttransp
not applicable
mastermix_lot_16s
453873
metabolomicsed
NO
nb_seqs_16s
15442
notes_cecum
not_thawed
novelty_seeking_box
box10
orig_name_16s
00077E8B87
otu_biom_id_16s
70124
pavca_mi_box
box13
pavca_ny_box
not provided
pcr_primers
FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT
pcr_primers_16s
FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT
phenotyping_center
MI
physical_specimen_location
Baud lab, Centre for Genomic Regulation, Barcelona, Spain
physical_specimen_remaining
not provided
platform
Illumina
platform_16s
Illumina
plating_16s
GT
prep_name_16s
11479_prep_6462_20191016-101040
primer_16s
GTGTGYCAGCMGCCGCGGTAA
primer_date
101918
primer_date_16s
101918
primer_plate
7
primer_plate_16s
7
processing_robot_16s
ROBE
project_name_16s
Palmer Rats Winter2018
qiita_prep_id_16s
6462
reaction_time_box
not provided
run_center
UCSDMI
run_center_16s
UCSDMI
run_date
3/28/19
run_date_16s
3/28/19
run_prefix_16s
Palmer_Rats_Winter_2018_7-8_Perez_Lopez_1_AGP_259-261_S1_L001
runid_16s
190328_M05314_0162_000000000-BLGCP
sample name
ERS27120022
sample_name_16s
11479.00077E8B87
sample_name_in_metadata_16s
00077E8B87
sample_name_metabo
not applicable
sample_name_mg
not applicable
sample_plate_16s
Palmer_Rats_Winter2018_Plate_7
sample_type
cecum content
scientific_name
rat gut metagenome
sequenced_16s
YES
sequenced_mg
NO
sequencing_meth_16s
Sequencing by synthesis
sequencing_method
Sequencing by synthesis
sex
female
shipment_to_phenotyping_center_date
2017-04-18
sire
HSM02413
social_reinforcement_box
not provided
study
MI
target_gene
16S rRNA
target_gene_16s
16S rRNA
target_subfragment
V4
target_subfragment_16s
V4
time_elapsed_removefood_dissection
20.7
time_elapsed_removefood_measure
20.6
tm1000_8_tool_16s
216152F
tm300_8_tool_16s
208484Z
tm50_8_tool_16s
108364Z
tn_cage
not provided
tn_track
not provided
tube_id
00077E8B87
unknown_rat
FALSE
water_lot_16s
2003606
weaning_cagecard
16-149-382
weaning_cagelocation
3-A4
weaning_roomnumber
630
weaning_shippingbox
MI-B17-6
weaning_suite
F
weight_at_weaning
42
well_description_16s
Palmer_Rats_Winter2018_Plate_7_00077E8B87_D2
well_id_16s
D2