title: O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep3

city: Madison

first: Lavanya

last: Babujee

state: WI

address: 425 Henry Mall

department: Genetics

institute: UW-Madison

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the presence of oxygen. It is the 3rd of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), without background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Yersinia intermedia ATCC 29909

source_name: Yersinia intermedia ATCC29909

label_protocol: Labeling was performed following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Yersinia intermedia ATCC29909 was grown to mid log phase at 28 °C in minimal medium with glucose in the presence or in the absence of oxygen

extract_protocol: Total RNA was extracted using the hot-phenol method (Bernstein et al 2004) followed by two DNAse digestion steps. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA).

value: Wild Type

tag: treatment

value: aerobic


title: no_O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep3

status: Public on Aug 21 2013

type: RNA

country: USA

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the absence of oxygen. It is the 3rd of three biological replicates used in this experiment, each from separate cultures.

molecule: total RNA

treatment_protocol: Yersinia intermedia ATCC29909 was grown to mid log phase at 28 °C in minimal medium with glucose in the presence or in the absence of oxygen

tag: genotype

value: anaerobic


title: O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep2

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the presence of oxygen. It is the 2nd of three biological replicates used in this experiment, each from separate cultures.


title: Carotid body paraganglioma case 5

city: Chieti Scalo

first: Renato

last: Mariani-Costantini

state: CH

address: Via Colle dell'Ara

department: Ageing Research Center (CeSI)

country: Italy

institute: "G. d'Annunzio" University Foundation

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <700 in more than 1 group were excluded. Data were analyzed with Genome Studio Software (Differential Expression Analysis with Mann-Whitney error model plus False Discovery Rate, FDR). *SH-SY5Y cells replicates were used as quality controls and excluded from the main analysis after normalization and quality check.

label: biotin

organism: Homo sapiens

source_name: Tumor specimen (5PC) from multiple paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the Qiagen miRNeay Kit, following manufacturer's instructions. Quality control was performed with Biorad Experion.

tag: disease state

value: Carotid body paraganglioma

tag: age

tag: tissue

value: Paraganglioma Tumor Specimen


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 5 Cy5 0

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-3

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: Continuous anaerobically grown cultures in Evans medium, prior to CORM-3 addition

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: Wild type strain MG1655

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min


title: O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep1

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the presence of oxygen. It is the 1st of three biological replicates used in this experiment, each from separate cultures.


title: Tympano-jugular paraganglioma case 21

description: replicate 1

source_name: Tumor specimen (21PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Tympano-jugular paraganglioma


title: Tympano-jugular paraganglioma case 1

type: genomic

description: replicate 1

data_processing: Genotyping data were generated using Genome Studio v2010.3 with Genotyping module v1.8.4 and GenCall v6.3.0 with score Cutoff 0.15. *replicates were used as quality controls and exluded from the main analysis after normalization and quality check. The unique lymph node metastasis was also excluded from the main analysis, being this limited to primary tumors.

molecule: genomic DNA

source_name: Tumor specimen (1PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

extract_protocol: Total DNA was extracted using Qiagen Dneasy Blood e Tissue Kit, following manufacturer's instructions. DNA purity was checked by spectrophotometer, and DNA integrity by examination on agarose gel electrophoresis. DNA concentration was measured with the Quant-IT dsDNA BR assay kits with the Qubit fluorometer (Invitrogen) following manufacturer’s instructions.

value: Head and Neck paraganglioma


title: Aviandiv_101_85M

city: Wageningen

first: richard

last: crooijmans

address: de Elst 1

department: Animal Breeding and Genomics Centre

country: Netherlands

institute: Wageningen University

scan_protocol: Agilent CHG protocols (for FFPE samples) version 1.02007 were stricktly followed for scanning . The arrays were scanned with 100% PMT laser power.

data_processing: the feature extraction software version 9.5, protocvol CGH-v4_95_feb07 from Agilent was used to generate te feature extraction data.

organism: Gallus gallus

source_name: Aviandiv

label_protocol: for each DNA sample 2.5 μg  ws used for the labeling experiments using the Agilent Genomic DNA Labeling kit PLUS. Afterwards the concentration and fluorescent dye incorporation of the labeled fragments were measured using the nanodrop. For each array equal amounts of fluorescent DNA is used for hybridization

extract_protocol: Genomic DNA was isolated with the oPuregene blood kit of the Qiagen Qiamap DNA blood kit.

tag: gender

value: male

tag: line

value: Aviandiv

source_name: UCD001 reference


title: no_O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep2

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the absence of oxygen. It is the 2nd of three biological replicates used in this experiment, each from separate cultures.


title: Tympano-jugular paraganglioma case 4

description: replicate 1

source_name: Tumor specimen (4PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympanic paraganglioma case 3

description: replicate 1

source_name: Blood sample (3B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: tympanic paraganglioma

value: blood


title: SH-SY5Y cell line Replicate 2

description: Technical replicate 2*

source_name: SH-SY5Ycell line Replicate 2

tag: cell line

value: Not Applicable


title: Tympano-jugular paraganglioma case 37

description: replicate 1

source_name: Tumor specimen (37PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympano-jugular paraganglioma case 1

description: replicate 1


title: Tympano-jugular paraganglioma case 2

description: replicate 1

source_name: Tumor specimen (2PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympano-jugular paraganglioma case 6

description: replicate 1

source_name: Tumor specimen (6PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympano-jugular paraganglioma case 4

description: replicate 1


title: Carotid body paraganglioma case 7

description: replicate 1

source_name: Tumor specimen (7PC) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Vagal paraganglioma case 5

description: replicate 1

source_name: Tumor specimen (5PV) from multiple paragangliomas patient of Gruppo Otologico clinic, Piacenza, Italy

value: Vagal paraganglioma


title: Tympanic paraganglioma case 3

description: replicate 1

source_name: Tumor specimen (3PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Tympanic paraganglioma


title: Jacobson's Nerve JN23

description: replicate 1

source_name: Jacobson's Nerve case 23

value: control

value: Jacobson's Nerve


title: SH-SY5Y cell line Replicate 1

description: Technical replicate 1*

source_name: SH-SY5Y cell line Replicate 1


title: Jacobson's Nerves JN25, JN26, JN27, JN50 and JN51 (Pool 21)

description: replicate 1

source_name: Pool of five Jacobson's Nerves (Pool 21)

value: Not applicable


title: Tympanic paraganglioma case 14

description: replicate 1

source_name: Tumor specimen (14PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 40

source_name: Continuous anaerobically grown cultures in Evans medium, prior to CORM-3 addition

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min


title: Jacobson's Nerves JN8, JN9 and JN12 (Pool 8)

description: replicate 1

source_name: Pool of three Jacobson's Nerves (Pool 8)


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 20

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min


title: Blood of tympano-jugular paraganglioma case 2

description: replicate 1

source_name: Blood sample (2B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: tympano-jugular paraganglioma


title: Jacobson's Nerves JN10 and JN14 (Pool 10)

description: replicate 1

source_name: Pool of two Jacobson's Nerves (Pool 10)


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 5

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min


title: Blood of tympano-jugular paraganglioma case 1

description: replicate 1

source_name: Blood sample (1B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 80

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min


title: Broiler2_39152428

hyb_protocol: Agilent CHG protocols (for FFPE samples) version 1.02007

source_name: UCD001 reference


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 10

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 2.5

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min


title: Jacobson's Nerves JN5 and JN6 (Pool 6)

description: replicate 1

source_name: Pool of two Jacobson's Nerves (Pool 6)


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 2.5 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 5


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 2.5


title: no_O2_Y_intermedia_ATCC29909_Oxygenstudy_28C_rep1

description: This sample is of Y. intermedia ATCC 29909 grown in minimal medium with glucose at 28 C in the absence of oxygen. It is the 1st of three biological replicates used in this experiment, each from separate cultures.

source_name: Yersinia intermedia ATCC29909

value: Wild Type

value: anaerobic


title: ko_replica3

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: mouse tissue, neonatal tail tip fibroblasts, Hotair knockout, replicate3

hyb_protocol: 10ug Fragmented and Labeled aRNA in 200ulHybridization Cocktail use affymetrix Hybridization Oven 640 for 16 hours at 45C

scan_protocol: GeneChip® Scanner 3000 (or higher) Affymetrix

data_processing: RMA normalization using justRMA package in R 2.11.1

label: Biotin

organism: Mus musculus

label_protocol: biotin-labbeled aRNA  following the manual of GeneChip®3’ IVT Express Kit

extract_protocol: Qiagen RNeasy kit following the manual

value: backcross to C57BL6 with over 97% similarity

tag: cell type

value: neonatal tail tip fibroblasts

tag: genotype/variation

value: Hotair knockout


title: ko_replica2

description: mouse tissue, neonatal tail tip fibroblasts, Hotair knockout, replicate2


title: ko_replica1

description: mouse tissue, neonatal tail tip fibroblasts, Hotair knockout, replicate1


title: Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0

value: Wild type strain MG1655


title: wt_replica3

description: mouse tissue, neonatal tail tip fibroblasts, wildtype, replicate3

source_name: neonatal tail tip fibroblasts, wildtype

value: Hotair wildtype


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 80 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 2.5 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 5 Cy5 0


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0


title: wt_replica2

description: mouse tissue, neonatal tail tip fibroblasts, wildtype, replicate2


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 10 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 40

source_name: Continuous anaerobically grown cultures in Evans medium, prior to CORM-3 addition

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 40 Cy5 0


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 20

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 2.5 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min


title: Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 80


title: Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 2.5


title: Untreated-Distal 89

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

institute: University of Aberdeen

description: Caesarean-delivered preterm pigs were fed 3 d of parenteral nutrition followed by 2 d of enteral formula feeding. Antibiotics (n=11) or control saline (n=13) were given twice daily from birth to tissue collection at d 5. NEC-lesions and intestinal structure, function, microbiology and immunity markers were recorded.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.01, FC>2.

organism: Sus scrofa

source_name: Distal intestine, untreated

label_protocol: Fragmented and biotin-labelled aRNA was synthesized from total RNA using the 3' IVT Express Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: Twenty-four preterm piglets (Landrace x Large white x Duroc) were delivered by caesarean section on day 105 of gestation from two healthy sows. Piglets were housed in incubators with regulated temperature and oxygen supply. All piglets were initially provided with parenteral nutrition via a vascular catheter, combined with small amounts of minimal enteral nutrition. On day three, all parenteral nutrition was stopped and total enteral nutrition was given through an oro-gastric feeding tube until sacrifice and tissue collection on day five.

extract_protocol: Tissue was lyzed in Trizol (Invitrogen). RNA was isolated using standard chloroform/isopropanol steps. Total RNA was further purified with the RNeasy Kit (Qiagen), including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: Piglets from each litter were stratified according to birth weight and sex, and allocated into controls (CON, n=13) and an intervention group receiving oral and systemic broad-spectrum antibiotics (Ampicillin, Gentamycin, Metronidazol, ANTI, n=11). To assure high systemic and intra luminal MIC values antibiotics were given both orally and intramuscularly. All antibiotics were given directly after feeding with an oral bolus and control pigs were given corresponding amounts of saline. On day five, all piglets were euthanized, and small intestinal tissue collected.

value: distal intestine

value: control saline were given twice daily from birth to tissue collection at d 5


title: Slide 11_Anaerobic culture_CORM-3_biol rep 1_Cy3 5 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min


title: Antibiotics-Distal 87

source_name: Distal intestine, antibiotics

value: Antibiotics were given twice daily from birth to tissue collection at d 5.


title: Untreated-Distal 83


title: wt_replica1

description: mouse tissue, neonatal tail tip fibroblasts, wildtype, replicate1


title: Antibiotics-Distal 95


title: Untreated-Distal 92


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 80 Cy5 0


title: Untreated-Distal 88


title: Slide 11_Anaerobic culture_CORM-3_biol rep 1_Cy3 20 Cy5 0


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 20 Cy5 0


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 40 Cy5 0


title: AA_v8_6

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

data_processing: quantile normalized and variance transformed using LUMI package in R

source_name: PBMCs

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: population

value: African-American

value: 1,25-dihydroxyvitamin D

tag: in vitro lymphocyte vitd sensitivity (lgs - %inhibition by vitd)

tag: duration of treatment (hours)

value: male

tag: age (years)


title: AA_v24_5


title: EA_v8_6

value: European-American


title: Antibiotics-proximal 87

source_name: Proximal intestine, antibiotics

value: proximal intestine


title: Untreated-Proximal 83

source_name: Proximal intestine, untreated


title: AA_v8_5


title: Antibiotics-Distal 86


title: Antibiotics-Distal 85


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 10 Cy5 0


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 5 Cy5 0


title: AA_v24_6


title: EA_v24_5

value: female


title: EA_v8_4


title: EA_v24_6


title: Antibiotics-proximal 98


title: EA_v8_5


title: Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 2.5 Cy5 0


title: Slide 10_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 10


title: Slide 10_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 5


title: EA_v24_4


title: EA_v24_3


title: EA_v8_3


title: Antibiotics-proximal 95


title: AA_v24_3


title: Untreated-Proximal 92


title: AA_v24_4


title: AA_v8_3


title: AA_v8_4


title: Untreated-Proximal 89


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 80


title: Untreated-Proximal 88


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 10


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 5


title: AA_v8_2


title: Antibiotics-proximal 86


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 2.5


title: EA_v8_1


title: HepG2_Control

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

hyb_protocol: The amplified RNA was fragmented using 4.8μL of 5X fragmentation buffer (GeneChip® WT Terminal labeling kit; Affymetrix;P/N 900671) and hybridized to the gene containing over 33,290 transcripts, as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix). After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.

data_processing: Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console1.1 . To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out.

source_name: mRNA isolated from HepG2 cell

label_protocol: About 300ng of total RNA from each sample was converted to cDNA, after amplification the double strands of cDNA was labelled with biotin-labeling (Ambion® WT Expression kit)

growth_protocol: Cells were maintained in culture flasks with MEM media at 37oC with 5% CO2

extract_protocol: Total RNA from control and GO/rGO treated samples (EC20 doses for 24 h) were extracted by using RNA extraction kit (NucleoSpin, Macherey-Nagel)

treatment_protocol: The cells were exposed to respective EC20 (prepared in MEM media from stock) dose for 24h. The EC20 doses were calculated from % viability bioassays with a range of concentartions of GO and rGO


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 20


title: EA_v8_2


title: HepG2_rGO

value: reduced graphene oxide (rGO) for 24h


title: EA_v24_1


title: Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 40


title: AA_v24_1


title: EA_v24_2


title: HepG2_GO

value: Grpahene oxide for 24h


title: T3_HypM

city: Fukuoka

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

country: Japan

institute: Kyushu University

description:
SAMPLE 12
replicate 3

hyb_protocol: The biotinylated-cRNA (total amount, 1,500 ng) prepared from each sample was overlaid onto an individual array spot of the rat microarray chip (RatRef12-v1 BeadChip; Illumina), according to the hybridization protocol. The chip was hybridized at 58°C for 19 hours.

data_processing: The data were normalized by quantile normalization using lumi and preprocess package in R. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.

organism: Rattus norvegicus

source_name: maternal exposure to dioxin, HypM

label_protocol: The total RNA (250 ng) was converted to its biotinylated-cRNA according to the manufacturer’s procedures (Illumina TotalPrep RNA Amplification Kit). Briefly, reverse transcription to synthesize the first-strand cDNA was performed for 2 hours at 42°C, using an oligo (dT) primer bearing a T7 promoter and reverse transcriptase (ArrayScript; Ambion). The second strand cDNA was synthesized by incubating the first strand for 2 hours at 16°C in the presence of DNA polymerase I and ribonuclease H. After cDNA purification by a short column, the eluted cDNA was used for in vitro transcription with T7 RNA polymerase. In vitro transcription was performed at 37°C for 14 hours, yielding the multiple copies of the biotinylated antisense RNA originated from respective mRNAs in the sample.

extract_protocol: The total RNA was extracted from the pituitary and hypothalamus of PND70 male pups according to the manufacturer's protocol (RNeasy Mini Kits).

treatment_protocol: Pregnant Wistar rats were orally treated with TCDD (1 mg/kg in corn oil) at GD15.

value: Wistar

tag: agent (mother exposed to)

value: TCDD

tag: gender (pup)

tag: age (pup)

tag: tissue (pup)

value: hypothalamus


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 80 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, prior to CORM-3 addition

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 20 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 40 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min


title: C3_HypM

description:
SAMPLE 8
replicate 2

source_name: maternal exposure to vehicle, HypM

value: vehicle


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 10 Cy5 0

value: Wild type strain MG1655

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min


title: AA_v8_1

tag: treatment


title: T2_HypM

description:
SAMPLE 11
replicate 2


title: AA_v24_2


title: C2_HypM

description:
SAMPLE 7
replicate 1


title: T5_pitM

description:
SAMPLE 6
replicate 3

source_name: maternal exposure to dioxin, pitM

value: pituitary


title: C4_HypM

description:
SAMPLE 9
replicate 3


title: T1_HypM

description:
SAMPLE 10
replicate 1


title: RS056

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

description: SAMPLE 40

hyb_protocol: RT-PCR protocol: TaqMan Low Density Array (TLDA, Applied Biosystems, Foster City, CA), including array A and B, were used to measure genome-wide miRNAs expression profiles. A three-step process was performed involving a reverse transcription (RT) reaction followed by preamplification reactions and a quantitative real-time PCR (qRT-PCR). The RT reaction was carried out according to the manufacturer's instructions including 1mM dNTPs (including TTP), 50U MultiScribe Reverse Transcriptase, 3.8U RNase inhibitor, and 1×Reverse Transcription buffer. Input RNA of 10-100ng was used for each RT reaction. TaqMan stem-loop primers for 746 unique human miRNAs, 2 endogenous controls (MammU6 and U6 snRNA) and 1 negative control (ath-miR-159a) were used in the RT reaction. Conditions for the RT reaction were as follows: 16°C for 30 min, 42°C for 30 min, 85°C for 5 min, then hold at 4°C. The preamplification reaction can preamplify specific cDNA targets to increase the quantity of desired miRNA expression. Within a total volume of 25μl preamplification reaction, it included 2.5μl RT product, 12.5μl TaqMan® OreAmp Master Mix (2x), 2.5μl MagaplexTM PreAmp Primers (10x) and 7.5μl nuclease-free water. Conditions for preamplification included 95°C for 3 min, 55°C for 2 min, 72°C for 2 min, followed by 12 cycles of 95°C for 15 sec, 60°C for 4 min, then hold at 99°C for 10 min. The preamplification products were then diluted (10x) by 0.1xTE (pH 8.0) prior to adding TaqMan 2× Universal PCR Master Mix (No AmpErase UNG). The entire mixture was added to individual ports of the TaqMan Human MicroRNA Array v3. The array were centrifuged at 1,200 rpm for 1 min, and then run on 7900HT Fast Real-Time PCR system for 95°C, 10 min followed by 40 cycles of 95°C for 15 s, 60°C for 1 min. Cycle threshold (Ct) values were calculated using the SDS2.2.2. Normalized expression was reported as 2−ΔΔCt, where Ct was the threshold cycle to detect fluorescence. Ct value greater than 40 was considered as below the detection threshold of the array.

data_processing:
Please note that many microRNA data are undetectable in circulation (defined as detected in at least two samples for each group -HCC case or control  group), resulting in a subset of detectable microRNAs data (258 data rows out of possible 762).
For the normalization it uses the average of two endogenous controls: MammU6 and U6 snRNA
Target miRNA signals normalized to the average of two endogenous controls; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_Controls)]
ABI DataAssist TM software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The 'fold_change.txt' contains HCC case/control ratios.

label: FAM

extract_protocol: Total RNA, including miRNAs was isolated from 250μl plasma using miRNeasy® Mini Kit (Qiagen, Frederick, MA) according to the manufacturer’s protocol.

tag: age

value: Male

tag: sample group

value: control group

value: Plasma


title: C5_pitM

description:
SAMPLE 3
replicate 3

source_name: maternal exposure to vehicle, pitM

tag: strain


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min


title: AS1081

description: SAMPLE 39

tag: gender

value: hepatocellular carcinoma (HCC) patients

tag: tissue


title: T4_pitM

description:
SAMPLE 5
replicate 2


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 40


title: T2_pitM

description:
SAMPLE 4
replicate 1


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 80


title: Mouse Embryonice Stem Cells, pCIP siRNA 2, Rep2

city: London

last: Torchia

state: Ontario

address: 800 Commissioners Rd E

country: Canada

institute: LRCP

hyb_protocol: Conducted at the London Regional Genomic centre.

scan_protocol: Scanned using ArrayVision v6.0.

data_processing:
The Data was analyzed using Partek Genomic Suit Version 6.6
The data was normalized to baseline and no filtering was applied.

source_name: ESCs_pCIP siRNA 2

growth_protocol: Mouse Embryonic Stem cells were grown on adherant plates in vitro at 37C and 5% CO2.

extract_protocol: RNA was isolated using Qiagen, Rneasy Mini Kit (74104) according to manufacturer's instuctions.

treatment_protocol: Mouse Embryonic Stem cells were treated with either control siRNA containing random oligo pool or siRNA targetting the pCIP proteins. Two different siRNAs (siRNA1 and siRNA1) were used to silence pCIP.

value: embryonic stem cells [E14]

tag: transfected with

value: siRNA targeting the pCIP proteins


title: Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 20


title: C1_pitM

description:
SAMPLE 1
replicate 1

value: male


title: Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 2.5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min


title: Mouse Embryonice Stem Cells, control si RNA, Rep1

source_name: ESCs_control siRNA

label_protocol: Conducted at the London Regional Genomic centre.

tag: cell type

value: pooled non-specific siRNAs (control)


title: C4_pitM

description:
SAMPLE 2
replicate 2


title: Mouse Embryonice Stem Cells, pCIP siRNA 1, Rep1

source_name: ESCs_pCIP siRNA 1


title: Mouse Embryonice Stem Cells, control si RNA, Rep2


title: Mouse Embryonice Stem Cells, pCIP siRNA 1, Rep2


title: RS032

description: SAMPLE 38

value: Female


title: AS1074

description: SAMPLE 37


title: Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 10


title: Mouse Embryonice Stem Cells, pCIP siRNA 2, Rep1


title: Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 5


title: RS038

description: SAMPLE 36


title: AS1069

description: SAMPLE 35


title: RS060

description: SAMPLE 34


title: AS1068

description: SAMPLE 33


title: RS054

description: SAMPLE 32


title: AS1066

description: SAMPLE 31


title: RS037

description: SAMPLE 30


title: RS059

description: SAMPLE 28


title: Rice_WT_rep2

city: Beijing,

first: Xiaoqiang

last: Liu

address: No.1 West Beichen Road,Chaoyang District

department: Chinese academy of sciences

country: China

institute: the institute of genetics and developmental biology

description: Leaf blades from rice (Oryza sativa L.) wild-type Nipponbare plant at two months after sowing.

hyb_protocol: Incubate the probe array filled with Pre-Hybridization Mix at 45 °C for 10 minutes with rotation. Transfer the hybridization cocktail that has been heated at 99 °C to a 45 °C heat block for 5 minutes. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. Place the probe array into the hybridization oven, set to 45 °C. Rotate at 60 rpm. Hybridize for 16 hours. Using the GeneChip Fluidics Station 450: Loaded 600μL stain1, 600μL stain2, 800μL Array Holding Buffer, and washed and scanned.

scan_protocol: Slides were scanned by the GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by the MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

organism: Oryza sativa Japonica Group

source_name: leaf blades, wild type, two months after sowing

label_protocol: GeneChip® 3' IVT Express Protocol.

growth_protocol: In the experimental field of the Institute of Genetics and Developmental Biology (IGDB) in Beijing, China.

extract_protocol: TRIzol was used to isolate total RNA. The RNA was purified using the QIAGEN RNeasy Kit.

tag: background

value: Nipponbare

tag: genotype/variation

value: wild type

value: leaf blades

value: 2 months after sowing


title: Rice_mutant_rep3

description: Leaf blades of the rice (Oryza sativa L.) cea62 mutant in the Nipponbare (ssp japonica) background that displayed lesion mimic (LM) phenotype at two months after sowing.

source_name: leaf blades, cea62 mutant, two months after sowing

value: cea62 mutant

tag: phenotype

value: lesion mimic (LM)


title: Rice_WT_rep3


title: Rice_mutant_rep2


title: AS1030

description: SAMPLE 27


title: Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 2.5

value: Wild type strain MG1655


title: Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0


title: Rice_mutant_rep1


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 10


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 5


title: Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0


title: AS1043

description: SAMPLE 29


title: RS057

description: SAMPLE 26


title: Rice_WT_rep1


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 20


title: AS1029

description: SAMPLE 25


title: Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 5 Cy5 0


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 40


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 2.5 Cy5 0


title: Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 80


title: RS047

description: SAMPLE 22


title: AS1024

description: SAMPLE 21


title: RS015

description: SAMPLE 20


title: Heterozygous HHR lactation day1

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

description: Gene expression data from rat in lactation.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mammary gland of Heterozygous HHR lactation day1

label_protocol: Approximately 3 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

value: Heterozygous Hirosaki hairless

value: mammary gland

tag: time

value: lactation day1


title: AS1022

description: SAMPLE 19

value: Male

value: Plasma


title: RS030

description: SAMPLE 18

value: control group


title: Homozygous HHR lactation day1

source_name: Mammary gland of Homozygous HHR lactation day1

value: Homozygous Hirosaki hairless


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 80 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, prior to CORM-3 addition

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min


title: Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 2.5


title: SDR Involution day1

source_name: Mammary gland of SDR Involution day1

value: Sprague-Dawley

value: involution day1


title: [KO IP0] heart_ischemic preconditioning 4x5 min_ rep 3

city: Denver

first: Tobias

last: Eckle

state: CO

address: 12700 E 19th Avenue

department: Anesthesiology

institute: UC Denver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.1 ST Array Plate. GeneChips were washed and stained in the GeneTitan® Multi-Channel (MC) Instrument

scan_protocol: GeneChips were scanned using the GeneTitan® Multi-Channel (MC) Instrument

data_processing: For each array CEL files were imported into Partek Genomic Suite software (Partek), and data were normalized using the RMA (Robust Multichip Averaging) algorithm

source_name: left ventricel treated with 4 x (5 min ischemia and 5 min reperfusion)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All mice were anesthetized, catheterized and hearts stitched + flushed with ice cold saline before harvest.

value: heart left ventricle

value: male

tag: genotype

value: Per2 KO


title: [wt IP0] heart_ischemic preconditioning 4x5 min_ rep 2

value: wildtype


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 80


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 40 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min


title: [KO IP0] heart_ischemic preconditioning 4x5 min_ rep 1


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 20 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min


title: [KO IP0] heart_ischemic preconditioning 4x5 min_ rep 2


title: [wt IP0] heart_ischemic preconditioning 4x5 min_ rep 1


title: AS1020

description: SAMPLE 17

value: hepatocellular carcinoma (HCC) patients


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 10 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min


title: [wt I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 3

source_name: ischemic left ventricle_ 30 min ischemia with 60 min reperfusion


title: SDR lactation day1

source_name: Mammary gland of SDR lactation day1


title: [wt I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 2


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 2.5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min


title: Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 40


title: [wt IP0] heart_ischemic preconditioning 4x5 min_ rep 3


title: RS050

description: SAMPLE 16


title: [ko I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 3


title: Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 10


title: AS1008

description: SAMPLE 15


title: [ko I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 2


title: AS1007

description: SAMPLE 13


title: RS031

description: SAMPLE 14


title: AS1002

description: SAMPLE 11


title: RS007

description: SAMPLE 12


title: [wt I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 1


title: Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 2.5


title: AS1044

description: SAMPLE 9


title: [C wt] heart_untreated control_rep 3

source_name: left ventricle, untreated, sham operated


title: RA-treated RXRα-KO, biological rep2

city: Sacramento

first: Yuqi

last: He

state: California

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

description: Microarray-based gene expression data of livers from hepatic RXRα-knockout mouse feed with RA-containing diet

hyb_protocol: Twenty μg purified cRNA was fragmented and 15 μg fragmented cRNA was hybridized to Affymetrix Mouse  Genome 430A 2.0  Array GeneChips (Affymetrix, Santa Clara, CA) according to the Expression  Analysis Technical  Manual.

scan_protocol: Washing and staining of the hybridized arrays were carried out using the Fluidics Station 400 and arrays were subsequently scanned with the Hewlett Packard GeneArray Scanner.

data_processing: RMA (Robust Multiarray Average) by PARTEK 6.11. 0701

source_name: Liver Tissue

label_protocol: Biotin-labeled cRNA was synthesized from the purified cDNA using the BioArray High Yield Transcript Labeling Kit according to the manufacturer's specifications (ENZO Life Sciences, Farmingdale, NY).

extract_protocol: Trizol extraction followed by chlorofrom putification of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Retinoic acid (Sigma-Aldrich, MO) was given to wild type and hepatic RXRα-deficient mice at a dosage of 150 mg/kg diet for 7 days. As controls, mice were fed with normal diet.

value: RA-treated

value: Hepatic RXRα-Knockout

value: liver


title: RA-treated RXRα-KO, biological rep1


title: Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 20

value: Wild type strain MG1655


title: Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 80 Cy5 0


title: Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 5


title: Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 40 Cy5 0


title: PRC2

description: SAMPLE 8


title: untreated RXRα-KO, biological rep3

description: Microarray-based gene expression data of livers from hepatic RXRα-knockout mouse feed with normal diet

value: untreated


title: RA-treated RXRα-KO, biological rep3


title: [C wt] heart_untreated control_rep 2


title: [ko I30R60] heart_ischemia 30 min reperfusion 60 min_ rep 1


title: [C wt] heart_untreated control_rep 1


title: Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 20 Cy5 0


title: [C ko] heart_untreated control_rep 3


title: [C ko] heart_untreated control_rep 2


title: Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 10 Cy5 0


title: PRC1

description: SAMPLE 10


title: AS1039

description: SAMPLE 7


title: untreated RXRα-KO, biological rep2


title: [C ko] heart_untreated control_rep 1


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 5 Cy5 0


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 2.5 Cy5 0


title: V003

description: SAMPLE 6

value: Female


title: [ko I30] heart_ischemia 30 min rep 2

source_name: ischemic left ventricle_ 30 min ischemia without reperfusion


title: AS1028

description: SAMPLE 5


title: [ko I30] heart_ischemia 30 min rep 3


title: untreated RXRα-KO, biological rep1


title: PRC3

description: SAMPLE 4

value: Male


title: AS1023

description: SAMPLE 3

value: Plasma


title: [ko I30] heart_ischemia 30 min rep 1


title: RS017

description: SAMPLE 2

value: control group


title: [wt I30] heart_ischemia 30 min rep 2


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 40


title: AS1012

description: SAMPLE 1


title: untreated wild type,biological rep1

description: Microarray-based gene expression data of livers from wild type mouse feed with normal diet

value: Wild type


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 80

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-3


title: untreated wild type,biological rep3


title: RA-treated wild type, biological rep1

description: Microarray-based gene expression data of livers from wild type mouse feed with RA-containing diet


title: [wt I30] heart_ischemia 30 min rep 1


title: RA-treated wild type, biological rep2


title: [wt I30] heart_ischemia 30 min rep 3


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 5


title: RA-treated wild type, biological rep3


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 20


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 10


title: untreated wild type,biological rep2


title: Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 2.5


title: Toxoplasma gondii GT1 1

status: Public on Aug 20 2013

city: Cambridge

first: Ninghan

last: Yang

state: Massachusetts

address: 77 Massachusetts Ave, 68-270

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm. Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data was analyzed with Robust Multi-array Average (RMA), together with Toxoplasma gondii arrays from two other studies (Khan et al, 2009 and  Bahl et al, 2010) using default Affymetrix settings in Expression Console version 1.1. The log2 transformed values obtained were then set to minimum of 6.5 or higher.

organism: Toxoplasma gondii

source_name: HFF + GT1, 24 hours

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: Human foreskin fibroblasts were grown in 6 well plates at 37C, 5% CO2 confluency. Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Parasite strains were syringe lysed, washed once with PBS, and added to HFF monolayers for 24 hours.

value: Human foreskin fibroblast

value: infected with GT1 for 24 hours


title: Toxoplasma gondii RH-JSR 1

source_name: HFF + RH-JSR, 24 hours

value: infected with RH-JSR for 24 hours


title: Huh7-control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Probes against comprehensive mature microRNAs were used. Negative controls were included.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: Hepatocellular carcinoma cell line, control

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark).

growth_protocol: Huh7 cells were cultured in DMEM with 10% FBS.

extract_protocol: Total RNA was extracted using Trizol Reagent.

treatment_protocol: Apigenin was treated at 10microM for 24 hrs.

tag: cell line

value: hepatocellular carcinoma cells

value: control


title: Huh7-apigenin

source_name: Hepatocellular carcinoma cell line, apigenin

value: apigenin


title: AS1026

description: SAMPLE 23

value: hepatocellular carcinoma (HCC) patients


title: RS035

description: SAMPLE 24


title: 50 mM Butyric acid stress 30 min (E) vs. Butyric acid stress control reference pool (C)

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: two biological replicates

hyb_protocol: Microarrays were hybridized and washed according to Agilent Technologies' recommended protocols.

scan_protocol: Microarrays were scanned according to Agilent Technologies' recommended protocols.

data_processing: Data was normalized using the LOESS method and implemented using the Bioconductor package in the statistical application R  [Dudoit S, et al. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. The Analysis of Gene Expression Data: Methods and Software. Springer, NY, 2002.][Yang YH, et al. Nucleic Acids Res. 2002;30(4):e15.]. Dye swaps and replicate spots were averaged together to give one expression value per gene. If the spot's intensity was not greater than 50, the spot was assigned a value of NA because it was not above background intensity [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

organism: Clostridium acetobutylicum ATCC 824

source_name: 50 mM Butyric acid stress 30 min

label_protocol: cDNA was generated and labeled as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

growth_protocol: WT colonies were grown on solid defined CGM plates at 37°C under anaerobic conditions. Individual colonies were picked and put in 10 ml of defined CGM.  Colonies more than 5 days old were heat-shocked for 10 min at 70-80°C.  Tubes were grown to an OD600 ~1.0 and then used to inoculate 400 ml of defined CGM (2.5% inoculum). Flasks were allowed to grow for 12 hrs before inoculating BioFlo 310 Benchtop Fermentors (10% inoculum). Fermentors were operated in a pH controlled (>5) with an initial glucose concentration of 40 g/L as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.]. Appropriate volume of butyric acid was added depending on the level of stress when the cells reached an OD600 ~1.0. Smaples were collected at 0, 15, 30, 45, 60 and 75 min post stress.

extract_protocol: Total RNA was extracted as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.].

tag: stress level

value: Butyric acid (50 mM - High)

tag: time point

value: 30 min

source_name: Butyric acid Stress - Common Reference pool

tag: control pool

value: Equal amount of labeled cDNA (Cy5/Cy3) (from all 48 samples)


title: Toxoplasma gondii RH-ERP 1

source_name: HFF + RH-ERP, 24 hours

tag: treatment

value: infected with RH-ERP for 24 hours


title: 50 mM Butyric acid stress 75 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 50 mM Butyric acid stress 75 min

value: 75 min


title: 50 mM Butyric acid stress 15 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 50 mM Butyric acid stress 15 min

value: 15 min


title: 50 mM Butyric acid stress 60 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 50 mM Butyric acid stress 60 min

value: 60 min


title: 40 mM Butyric acid stress 60 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 60 min

value: Butyric acid (40 mM - Medium)


title: 50 mM Butyric acid stress 0 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 50 mM Butyric acid stress 0 min

value: 0 min


title: 50 mM Butyric acid stress 45 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 50 mM Butyric acid stress 45 min

value: 45 min


title: 40 mM Butyric acid stress 45 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 45 min


title: 40 mM Butyric acid stress 75 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 75 min


title: 40 mM Butyric acid stress 30 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 30 min


title: 40 mM Butyric acid stress 15 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 15 min


title: 40 mM Butyric acid stress 0 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 40 mM Butyric acid stress 0 min


title: 0 mM Butyric acid stress 60 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 60 min

value: Butyric acid (0 mM - No stress)


title: 0 mM Butyric acid stress 0 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 0 min


title: 30 mM Butyric acid stress 15 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 15 min

value: Butyric acid (30 mM - Low)


title: 30 mM Butyric acid stress 45 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 45 min


title: 0 mM Butyric acid stress 15 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 15 min

source_name: Butyric acid Stress - Common Reference pool


title: 30 mM Butyric acid stress 0 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 0 min


title: 30 mM Butyric acid stress 75 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 75 min


title: 0 mM Butyric acid stress 45 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 45 min


title: 30 mM Butyric acid stress 60 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 60 min


title: 0 mM Butyric acid stress 30 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 30 min


title: 0 mM Butyric acid stress 75 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butyric acid stress 75 min


title: 30 mM Butyric acid stress 30 min (E) vs. Butyric acid stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butyric acid stress 30 min


title: 90 mM Butanol stress 75 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 75 min

growth_protocol: WT colonies were grown on solid defined CGM plates at 37°C under anaerobic conditions. Individual colonies were picked and put in 10 ml of defined CGM.  Colonies more than 5 days old were heat-shocked for 10 min at 70-80°C.  Tubes were grown to an OD600 ~1.0 and then used to inoculate 400 ml of defined CGM (2.5% inoculum). Flasks were allowed to grow for 12 hrs before inoculating BioFlo 310 Benchtop Fermentors (10% inoculum). Fermentors were operated in a pH controlled (>5) with an initial glucose concentration of 40 g/L as described in [Jones SW, et al. Genome Biol. 2008;9(7):R114.]. Appropriate volume of butanol was added depending on the level of stress when the cells reached an OD600 ~1.0. Smaples were collected at 0, 15, 30, 45, 60 and 75 min post stress.

value: Butanol (90 mM - High)

source_name: Butanol Stress - Common Reference pool


title: 90 mM Butanol stress 30 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 30 min


title: 60 mM Butanol stress 15 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 15 min

value: Butanol (60 mM - Medium)


title: 60 mM Butanol stress 30 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 30 min


title: 60 mM Butanol stress 0 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 0 min


title: 30 mM Butanol stress 60 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 60 min

value: Butanol (30 mM - Low)


title: 90 mM Butanol stress 15 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 15 min


title: 60 mM Butanol stress 45 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 45 min


title: 90 mM Butanol stress 60 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 60 min


title: 90 mM Butanol stress 45 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 45 min


title: 60 mM Butanol stress 75 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 75 min


title: 30 mM Butanol stress 45 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 45 min


title: 90 mM Butanol stress 0 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 90 mM Butanol stress 0 min


title: 60 mM Butanol stress 60 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 60 mM Butanol stress 60 min


title: 30 mM Butanol stress 75 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 75 min


title: 30 mM Butanol stress 30 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 30 min


title: 30 mM Butanol stress 15 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 15 min


title: 0 mM Butanol stress 60 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 60 min

value: Butanol (0 mM - No stress)

source_name: Butanol Stress - Common Reference pool


title: 0 mM Butanol stress 30 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 30 min


title: 0 mM Butanol stress 45 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 45 min


title: HF/HS_11_RUMOBE

city: Saint Louis

first: Nathan

middle: P

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

description:
17161.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

hyb_protocol: Following fragmentation and labeling, cDNA (0.9-5.1 ug) was hybridized for 16 h at 45 C on custom GeneChip SynComm1 (Synthetic Human Gut Community GeneChip, v1.0, GEO platform GPL9803). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

data_processing: A custom mask file was first created for each of the 12 species analyzed, after which species-specific Expression Console custom configuration files were prepared (MAS5 probe set summarization; scaling by all select sets specified by probe masking file) and used to execute an advanced analysis. Raw values were then exported as pivot tables, filtered for those probe sets corresponding to the species being analyzed, and passed as input data to the Cyber-T web server. In each treatment group, genes for which at least 5 of 7 samples resulted in a 'present' call for the probe set were scored as having reliably detectable gene expression.

organism: Blautia obeum ATCC 29174

source_name: Defined bacterial assemblage of 12 species from a gnotobiotic mouse

label_protocol: cDNA was prepared from gDNA-free RNA using random hexamer priming and Invitrogen's SuperScript II enzyme. RNA template was degraded by NaOH treatment, and cDNA was subsequently fragmented by DNase I digestion. Finally, fragmented cDNA was biotinylated using the BioArray Terminal Labeling Kit with biotin-ddUTP (Enzo, 42630). Successful biotinylation of targets was verified using a shift assay with NeutrAvidin (Pierce, 31000).

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community into 10-12 week-old male gnotobiotic C57BL/6J mice. Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol: Samples previously stored at -80 C were incubated in Qiagen RNAprotect Bacteria Reagent per the manufacturer's instructions, after which they were mechanically disrupted using acid-washed glass beads in a Mini-BeadBeater-8 in the presence of acid phenol:chloroform:IAA (125:24:1). Following ethanol precipitation, RNA was further purified using the Qiagen RNeasy Mini Kit and subjected to two rounds of DNase treatment. All samples were shown to be free of contaminating gDNA by PCR before RT and labeling were performed.

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and were stored at -80 C until total community RNA could be extracted.

tag: mouse

tag: diet group

value: HF/HS


title: HF/HS_10_RUMOBE

description:
17160.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: 0 mM Butanol stress 0 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 0 min


title: 30 mM Butanol stress 0 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 30 mM Butanol stress 0 min


title: 0 mM Butanol stress 75 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 75 min


title: HF/HS_14_RUMOBE

description:
17164.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_RUMOBE

description:
17162.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_RUMOBE

description:
17163.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_RUMOBE

description:
17159.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: 0 mM Butanol stress 15 min (E) vs. Butanol stress control reference pool (C)

description: two biological replicates

source_name: 0 mM Butanol stress 15 min


title: LF/HPP_7_RUMOBE

description:
17157.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

value: LF/HPP


title: LF/HPP_4_RUMOBE

description:
17154.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_PARDIS

description:
17163.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Parabacteroides distasonis ATCC 8503


title: LF/HPP_1_RUMOBE

description:
17151.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_RUMOBE

description:
17152.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_RUMOBE

description:
17155.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_RUMOBE

description:
17153.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_DORLON

description:
17162.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Dorea longicatena DSM 13814


title: LF/HPP_5_PARDIS

description:
17155.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_PARDIS

description:
17161.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_DORLON

description:
17161.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_PARDIS

description:
17153.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_PARDIS

description:
17151.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_RUMOBE

description:
17158.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_PARDIS

description:
17156.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_DORLON

description:
17164.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_PARDIS

description:
17157.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_PARDIS

description:
17152.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_PARDIS

description:
17154.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_DORLON

description:
17159.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_PARDIS

description:
17160.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_PARDIS

description:
17164.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_PARDIS

description:
17159.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_DORLON

description:
17158.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_PARDIS

description:
17162.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_RUMOBE

description:
17156.RUMOBE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_PARDIS

description:
17158.PARDIS
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_DORLON

description:
17163.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_DORLON

description:
17156.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_DORLON

description:
17157.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_DORLON

description:
17155.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_COLAER

description:
17164.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Collinsella aerofaciens ATCC 25986


title: HF/HS_12_COLAER

description:
17162.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_COLAER

description:
17160.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_COLAER

description:
17159.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_CLOSPI

description:
17162.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Thomasclavelia spiroformis DSM 1552


title: LF/HPP_2_DORLON

description:
17152.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_COLAER

description:
17163.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_COLAER

description:
17161.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_COLAER

description:
17154.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_DORLON

description:
17151.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_COLAER

description:
17153.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_COLAER

description:
17156.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_COLAER

description:
17158.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_COLAER

description:
17155.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_CLOSPI

description:
17163.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_CLOSPI

description:
17161.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_COLAER

description:
17157.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_COLAER

description:
17151.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_DORLON

description:
17153.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_CLOSPI

description:
17164.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_DORLON

description:
17154.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_CLOSPI

description:
17160.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_COLAER

description:
17152.COLAER
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_CLOSPI

description:
17159.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_CLOSPI

description:
17151.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_CLOSPI

description:
17154.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_CLOSPI

description:
17153.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_CLOSPI

description:
17152.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_CLOSPI

description:
17155.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_CLOSPI

description:
17156.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_CLOSCI

description:
17163.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: [Clostridium] scindens ATCC 35704


title: HF/HS_11_CLOSCI

description:
17161.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_CLOSCI

description:
17159.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_CLOSCI

description:
17155.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_CLOSCI

description:
17157.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_CLOSCI

description:
17156.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_CLOSCI

description:
17158.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_CLOSCI

description:
17162.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_CLOSPI

description:
17157.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_CLOSCI

description:
17152.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_CLOSCI

description:
17164.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_CLOSCI

description:
17153.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_BACWH2

description:
17163.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides sp. WH2


title: LF/HPP_1_CLOSCI

description:
17151.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.