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Example output: extracted_object:
study_title: Root Exudates Alter the Expression of Diverse Metabolic, Transport,
Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas
authors:
- Olga V. Mavrodi
- Janiece R. McWilliams
- Jacob O. Peter
- Anna Berim
- Karl A. Hassan
- Liam D. H. Elbourne
- Melissa K. LeTourneau
- David R. Gang
- Ian T. Paulsen
- David M. Weller
- Linda S. Thomashow
- Alex S. Flynt
- Dmitri V. Mavrodi
doi: 10.3389/fmicb.2021.651282
date: 14 April 2021
experiments:
- label: The study involved the collection and analysis of root exudates of Brachypodium
distachyon.
experiment_motivation: Not provided
experiment_design: The experiment involved growing Brachypodium distachyon in
a controlled environment with surface-sterilized seeds and hydroponic conditions.
environment: Environmental controlled growth chamber
host:
- AUTO:Brachypodium%20distachyon
host_type: Plant
target_microbes:
- AUTO:Not%20provided
biological_system: Root system
conditions:
- Not provided
experimental_factors:
- AUTO:Not%20provided
is_biolog_experiment: no
type_of_biolog_experiment: Not provided
plates:
- Not provided
replicates: Not provided
protocol_steps:
- surface-sterilization of seeds
- pregermination
- placement in sterile 1 L widemouth glass jars
- covering with vented caps
- growing hydroponically
plate_reader_types_of_data_collected:
- Not provided
od_protocol: Not provided
respiration_protocol: Not provided
instrument_used:
- Not provided
analysis_software:
- Not provided
incubation_temperature: Not provided
incubation_duration: Not provided
- label: This experiment involves the metabolomic profiling of root exudates using
liquid chromatography mass spectrometry analysis.
experiment_motivation: Not provided
experiment_design: Not provided
environment: Not provided
host:
- AUTO:Not%20provided
host_type: plant
target_microbes:
- AUTO:Not%20provided
biological_system: root exudates
conditions:
- 50% aqueous acetonitrile
experimental_factors:
- AUTO:Not%20provided
is_biolog_experiment: no
type_of_biolog_experiment: Not provided
plates:
- Not provided
replicates: Not provided
protocol_steps:
- freeze-drying residues
- suspending in 500 ml 50% aqueous acetonitrile
- clarifying by centrifugation
- separating exudate metabolites on a SeQuant ZIC-pHILIC HPLC column
plate_reader_types_of_data_collected:
- Not provided
od_protocol: Not provided
respiration_protocol: Not provided
instrument_used:
- liquid chromatography mass spectrometry
- SeQuant ZIC-pHILIC HPLC column
analysis_software:
- Not provided
incubation_temperature: Not provided
incubation_duration: Not provided
- label: The experiment analyzed the utilization of carbon sources by eight Pseudomonas
strains using Phenotype MicroArrays.
experiment_motivation: Not provided
experiment_design: The bacteria were cultured overnight, then inoculated into
PM01 and PM02A plates to analyze carbon source utilization.
environment: Laboratory
host:
- AUTO:None
host_type: Not applicable
target_microbes:
- AUTO:Pseudomonas%20strains
biological_system: Not specified
conditions:
- Not provided
experimental_factors:
- AUTO:Carbon%20source%20utilization
is_biolog_experiment: yes
type_of_biolog_experiment: Phenotype MicroArray
plates:
- PM01
- PM02A
replicates: Not provided
protocol_steps:
- overnight culture on Luria-Bertani agar
- harvesting and suspension in inoculating fluid
- inoculation of 100 microliter aliquots into PM01 and PM02A plates
plate_reader_types_of_data_collected:
- Not provided
od_protocol: Not provided
respiration_protocol: Not provided
instrument_used:
- Not provided
analysis_software:
- Not provided
incubation_temperature: Not provided
incubation_duration: overnight
- label: This experiment involves the isolation of RNA from bacteria cultured
in root exudates and subsequent RNA-Seq analysis.
experiment_motivation: Not provided
experiment_design: The bacteria were pregrown overnight, subcultured into 96-well
microplates with liquid 21C-glucose medium amended with Brachypodium exudates.
environment: Not provided
host:
- AUTO:Brachypodium
host_type: Plant
target_microbes:
- AUTO:Not%20provided
biological_system: Rhizosphere
conditions:
- 21C-glucose medium
- Brachypodium exudates
experimental_factors:
- AUTO:Brachypodium%20exudates
is_biolog_experiment: no
type_of_biolog_experiment: Not provided
plates:
- Not provided
replicates: Not provided
protocol_steps:
- Pregrown overnight
- subcultured into 96-well microplates
- liquid medium prepared by dissolving lyophilized root exudate material in
21C-glucose medium
- RNA isolation
- RNA-Seq analysis
plate_reader_types_of_data_collected:
- Not provided
od_protocol: Not provided
respiration_protocol: Not provided
instrument_used:
- Not provided
analysis_software:
- Not provided
incubation_temperature: Not provided
incubation_duration: Overnight
- label: The experiment involves the bioinformatic analysis of RNA-Seq data to
determine differential expression.
experiment_motivation: Not provided
experiment_design: Not provided
environment: Not provided
host:
- AUTO:Not%20provided
host_type: Not provided
target_microbes:
- AUTO:Not%20provided
biological_system: Not provided
conditions:
- Not provided
experimental_factors:
- AUTO:Not%20provided
is_biolog_experiment: no
type_of_biolog_experiment: Not provided
plates:
- Not provided
replicates: Not provided
protocol_steps:
- count tables were generated using the JGI RNA-Seq pipeline
- data were analyzed using DESeq2 to determine differential expression
plate_reader_types_of_data_collected:
- Not provided
od_protocol: Not provided
respiration_protocol: Not provided
instrument_used:
- Not provided
analysis_software:
- JGI RNA-Seq pipeline
- DESeq2
incubation_temperature: Not provided
incubation_duration: Not provided
named_entities:
- id: AUTO:Brachypodium%20distachyon
label: Brachypodium distachyon
original_spans:
- 2671:2693
- 7905:7927
- 75924:75946
- 82382:82404
- 84035:84057
- 92737:92759
- 94848:94870
- id: AUTO:Not%20provided
label: Not provided
- id: AUTO:None
label: None
original_spans:
- 38725:38728
- 73446:73449
- id: AUTO:Pseudomonas%20strains
label: Pseudomonas strains
original_spans:
- 3099:3117
- 11282:11300
- 20973:20991
- 25301:25319
- 26061:26079
- 27214:27232
- 27931:27949
- 28219:28237
- 28312:28330
- 29742:29760
- 31193:31211
- 32095:32113
- 32974:32992
- 38450:38468
- 41680:41698
- 42911:42929
- 50286:50304
- 60794:60812
- 64441:64459
- id: AUTO:Carbon%20source%20utilization
label: Carbon source utilization
original_spans:
- 22549:22573
- id: AUTO:Brachypodium
label: Brachypodium
original_spans:
- 2671:2682
- 3839:3850
- 7905:7916
- 8017:8028
- 9681:9692
- 10041:10052
- 12426:12437
- 17660:17671
- 60264:60275
- 62908:62919
- 63969:63980
- 65756:65767
- 67572:67583
- 67792:67803
- 71304:71315
- 75924:75935
- 76637:76648
- 82382:82393
- 84035:84046
- 92737:92748
- 94848:94859
- id: AUTO:Brachypodium%20exudates
label: Brachypodium exudates
original_spans:
- 17660:17680
- 60264:60284 |
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