title: D5

city: Shanghai

first: Peizhan

last: Chen

institute: Ruijin Hospital North

hyb_protocol: Following manufacture's protocol

scan_protocol: Iscan

data_processing: SWAN normalization method with the minfi Bioconductor package. Processed data with probe annotation is available on the series record in the file Matrix_processed.xlsx.

source_name: Whole Blood DNA

label_protocol: Following manufacture's protocol

extract_protocol: Qiagen DNA extract kit

value: whole blood

tag: Sex

value: Male

value: 23 years old

value: hypopituitarism


title: FOL-005 (3uM) 6 hours 2

status: Public on Dec 05 2017

type: RNA

city: Münster

first: Majid

last: Alam

state: NRW

address: Mendelstraße 17

country: Germany

institute: Monasterium Laboratory

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix  GeneArray Scanner 3000

data_processing: The data were analyzed with Transcriptome Analysis Console 3.0 (Affymetrix) and gene expression profiling was performed using human transcriptome arrays 2.0 (HTA-2_0) from Affymetrix with RMA.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HFs 3uM FOL 6hr 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5ug total RNA

growth_protocol: Hair follicles (HFs) were microdissected from human occipital scalp skin and inbated in supplemented Williams E media overnight

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

treatment_protocol: After overnight incubation HFs were treated with corresponding groups of vehicle, FOL-005 (300nM) and FOL-005 (3uM) for 6 and 24 hours

tag: tissue

value: Hair Follicle


title: FOL-005 (300nM) 6 hours 2

source_name: HFs 300nM FOL 6hr 2


title: D4

status: Public on Dec 06 2017

type: genomic

country: China

label: Cy5 and Cy3

molecule: genomic DNA

tag: age

value: 21 years old

tag: diagnosis


title: C16

value: 26 years old

value: Normal


title: D11

value: 24 years old


title: FOL-005 (3uM) 24 hours 1

source_name: HFs 3uM FOL 24hr 1


title: C10

value: 28 years old


title: FOL-005 (300nM) 6 hours 1

source_name: HFs 300nM FOL 6hr 1


title: C11


title: Vehicle 6 hours 1

source_name: HFs Vehicle 6hr 1


title: FOL-005 (300nM) 24 hours 1

source_name: HFs 300nM FOL 24hr 1


title: Vehicle 24 hours 1

source_name: HFs Vehicle 24hr 1


title: C7


title: D12

value: 22 years old


title: D3

value: 20 years old


title: C6

value: 29 years old


title: FOL-005 (3uM) 6 hours 1

source_name: HFs 3uM FOL 6hr 1


title: D8

value: 25 years old


title: D6

value: 18 years old


title: C17

value: 27 years old


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from Neutrophils from Donor 6 infected with RPMI time point 18 hour

hyb_protocol: Labeled samples were hybridized to GeneChip® Human Gene 2.0 ST Arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7Gplus scanner

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

label: biotin

label_protocol: RNA amplification and labeling was carried out by GeneChip® WT PLUS Reagent Kit (Affymetrix/ThermoFisher, Santa Clara, CA) in accordance with the manufacturer’s protocol.

growth_protocol: Human neutrophils were isolated from fresh heparinized venous blood using standard dextran sedimentation coupled with Hypaque-Ficoll gradient centrifugation

extract_protocol: Total RNA was purified using a Direct-zol RNA MiniPrep kit according to the manufacturer’s protocol (Zymo Research Corp., Irvine, CA)

treatment_protocol: Infected and RPMI samples were incubated to designated time point of 1,3,6 and up to 18 h at 37 °C with 5% CO2.

tag: cell type

value: Neutrophils

tag: infection

value: infection with RPMI medium

tag: time

value: infection for 18 hour


title: C2

value: whole blood

value: Male


description: Gene expression data from Neutrophils from Donor 8 infected with RPMI time point 18 hour


description: Gene expression data from Neutrophils from Donor 6 infected with RPMI time point 3 hour

value: infection for 3 hour


description: Gene expression data from Neutrophils from Donor 8 infected with RPMI time point 1 hour

value: infection for 1 hour


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Mex09 time point 18 hour

value: infection with influenza A virus strain Mex09


title: D2

value: 19 years old

value: hypopituitarism


title: C5

value: 23 years old

value: Normal


description: Gene expression data from Neutrophils from Donor 9 infected with RPMI time point 18 hour


title: D1


title: C1

value: 20 years old


title: D14


description: Gene expression data from Neutrophils from Donor 8 infected with RPMI time point 6 hour

value: infection for 6 hour


description: Gene expression data from Neutrophils from Donor 8 infected with RPMI time point 3 hour


description: Gene expression data from Neutrophils from Donor 9 infected with RPMI time point 6 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Mex09 time point 6 hour


title: C3

value: 21 years old


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Mex09 time point 3 hour


title: C9

value: 24 years old


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Mex09 time point 3 hour


title: D7


description: Gene expression data from Neutrophils from Donor 6 infected with RPMI time point 6 hour


description: Gene expression data from Neutrophils from Donor 9 infected with RPMI time point 1 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Mex09 time point 1 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Mex09 time point 1 hour


title: C4


title: D13


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Kawasaki time point 18 hour

value: infection with influenza A virus strain Kawasaki


description: Gene expression data from Neutrophils from Donor 6 infected with RPMI time point 1 hour

value: Neutrophils


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Kawasaki time point 18 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Kawasaki time point 6 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Kawasaki time point 6 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Mex09 time point 18 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Mex09 time point 18 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Mex09 time point 3 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Kawasaki time point 3 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Kawasaki time point 3 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Mex09 time point 6 hour


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Kawasaki time point 18 hour


title: Subject 3 - BDNF-treated

city: Rochester

first: Zvonimir

middle: S

last: Katusic

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: B3; miRNA expression

hyb_protocol: Labeled samples were subsequently processed according to manufacturer’s instructions for the Affymetrix miRNA Array 3.0 (Carlsbad, CA).  After hybridization for 16 h at 45oC, the arrays were washed and stained in an Affymetrix Fluidics station 450.

scan_protocol: Samples were then scanned in an Affymetrix 3000 7G scanner.

data_processing: Raw data was extracted without normalization by using the Expression Console software (Affymetrix, Carlsbad, CA). Unless otherwise, stated, the default detection criteria was used.

source_name: early EPCs treated with BDNF

label_protocol: Samples were labeled using the FlashTag™ Biotin HSR RNA Labeling kit (Carlsbad, CA).  Briefly, 500ng of total RNA was incubated with ATP and Poly A polymerase to add a 3’ polyA tail.  A ligation reaction was then performed to covalently attach to the miRNA population a multiple-biotin molecule containing a 3DNA dendrimer.

growth_protocol: Early EPCs were cultured in EBM2 for 7 hours

extract_protocol: miRNeasy mini kit (Qiangen) was used to extract total RNA

treatment_protocol: Early EPCs were treated with BDNF (100 ng/ml) for 7 hours, or EBM2 alone (control) for 7 hours.

tag: subject id

value: Subject 3

tag: subject gener

value: male

tag: subject age

value: 55 yrs

value: human early endothelial progenitor cells (EPCs)

tag: treated with

value: brain-derived neurotrophic factor (BDNF) for 7hrs


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Mex09 time point 6 hour


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Mex09 time point 1 hour

value: infection for 1 hour


title: Subject 4 - BDNF-treated

description: B4; miRNA expression

value: Subject 4

value: 50 yrs


title: Subject 1 - BDNF-treated

description: B1; miRNA expression

value: Subject 1

value: 52 yrs


title: Subject 1 - Control

description: C1; miRNA expression

source_name: early EPCs in control culture condition

value: EBM2 alone (control) for 7hrs


title: Subject 3 - Control

description: C3; miRNA expression


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Kawasaki time point 6 hour


title: Subject 2 - Control

description: C2; miRNA expression

value: Subject 2


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Kawasaki time point 3 hour

value: infection for 3 hour


title: Subject 4 - Control

description: C4; miRNA expression


description: Gene expression data from Neutrophils from Donor 8 infected MOI 5 with IVA strain Kawasaki time point 1 hour


description: Gene expression data from Neutrophils from Donor 6 infected MOI 5 with IVA strain Kawasaki time point 1 hour


title: Mn11_supp_2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: Mn11 cells grown in media supplemented with manganese

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Neo and Mn11 cell lines were cultivated in RPMI 1640 high glucose (2 g/L) with glutamine (300 mg/L) from Gibco® (Thermo Scientific, Grand Island, NY), and added streptomycin (100 mg/L)/penicillin (100 U/L), 1 mM pyruvate, 0.4 mM uridine, 50 μg/mL Geneticin® (Invitrogen™, Thermo Scientific, Grand Island, NY) and 10% FBS (ATCC, Manassas, VA).

extract_protocol: Total RNA was isolated from three independent triplicates using the QIAshredder and RNeasy Midi® Kit (QIAGEN, Valencia, CA) with in-column DNAse treatment (QIAGEN, Valencia, CA).

treatment_protocol: When indicated, cells were cultivated for at least 21 days with manganese-supplemented medium (regular medium with 25 μM MnCl2). Cultures cultivated with regular medium or manganese-supplemented medium were age-matched. Confluent cells were collected for RNA isolation by trypsinization, washed with PBS and stored at -80°C.

tag: cell line

tag: genotype

value: SOD2-overexpressing cell line

tag: medium

value: Manganese supplemented


title: neo_supp_2

source_name: Neo cells grown in media supplemented with manganese

value: neo

value: Parental cell line


title: Mn11_2

source_name: Mn11 cells grown in regular media (RPMI and 10% FBS)

value: Regular


title: neo_supp_3


title: Mn11_1


description: Gene expression data from Neutrophils from Donor 9 infected MOI 5 with IVA strain Kawasaki time point 1 hour

value: Neutrophils

value: infection with influenza A virus strain Kawasaki


title: neo_1

source_name: Neo cells grown in regular media (RPMI and 10% FBS)


title: neo_2


title: Mn11_3


title: MM_E11.5_96h induced_rep2

city: Oulu

first: Anatoliy

last: Samoylenko

address: Aapistie 5A

department: FBMM

country: Finland

institute: Oulu University

hyb_protocol: Eukaryotic Target Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual, we used GeneChip®Hybridisation Oven 640 and GeneChip® Fluidics Station 450 (Protocol EukGe_WS2v5_450, User Prep'd Buffers).

scan_protocol: GeneChip® Scanner 7G and Affymetrix GeneChip Command Console v. 3.1 were used

data_processing: RMA was used as backgrouynd correction method, the data were then quantile normalized, and only perfect match data were used for median polish

organism: Mus musculus

source_name: Kidney MM, E11.5, 96h induced

label_protocol: cRNA was labelled with biotin

growth_protocol: Mouse embryonic kidney mesenchymes (MM) were extracted at E11.5 and then cultured for 0h or 96h with embryonic spinal cord (transfilter set-up, two 1,0µm pore size polycarbonate membranes separating the MM and the eSC ). The mesenchymes were collected without eSC and pooled (referring the time points) to obtain enough RNA. Freshly extracted, uncultured MM was set as time point 0h for the future analysis.

extract_protocol: The RNA was isolated from the pooled mesenchymes at different time points using Qiagen RNeasy Plus –kit and concentrated by LiCl/EtOH precipitation

treatment_protocol: Embryonic kidneys were dissected from CD1 embryos at E11.5 and incubated in 1.125%  pancreatin- 2.25% trypsin for 30-40 sec, and the ureteric bud (UB) was separated from the 15 nephron progenitor/stem cell containing metanephric mesenchyme (MM) in media supplemented with 10% FBS and antibiotics (Lauri Saxen, 1987). The MM was treated with 40 μl of 2 mg/ml collagenase III in 280 μl of physiological buffer at 37 °C for 10 min to obtain single cells suspension. The MM cells were washed twice with cell culture medium, placed on Nuclepore polycarbonate membrane (Whatman, pore size 1.0 μm) and a piece of embryonic dorsal spinal cord (E11.5) was glued on the other filer side serving as a robust tubulogenesis inducer. The conjugate was cultured in 37 °C, at 5% CO2 for 96hr, a time sufficient to induce and advance nephrogenesis (Lauri Saxen, 1987), snap frozen in liquid nitrogen and stored at -80°C until used for RNA purification. Collectively 40 freshly prepared control and induced MM were processed for the oligonucleotide gene chip analysis. These analyses were conducted in triplicates.

tag: strain

value: Mouse embryonic kidney mesenchymes (MM)

tag: developmental stage


title: Mn11_supp_3


title: MM_E11.5_uninduced_rep3

source_name: Kidney MM, E11.5, uninduced


title: Subject 2 - BDNF-treated

description: B2; miRNA expression

value: male

value: 55 yrs

value: human early endothelial progenitor cells (EPCs)

value: brain-derived neurotrophic factor (BDNF) for 7hrs


title: neo_supp_1


title: MM_E11.5_96h induced_rep3


title: MM_E11.5_uninduced_rep2


title: neo_3


title: MM_E11.5_96h induced_rep1


title: ENS cells at E15.5 replicate 3

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: FACS sorted ENS cells from E15.5 mouse bowel

hyb_protocol: Samples were hybridised according to the Affymetrix specifications. Hybridisation to Affymetrix Mouse Gene Arrays 1.0ST was performed for 16 hours at 45C with constant rotation.

scan_protocol: Washing and scanning of the arrays was performed on an Affymetrix GeneChip Fluidics station 450 and GCS3000 Affymetrix scanner respectively according to the manufacturer’s recommendations

data_processing: Data was analysed using the Partek software and normalised using the rma algorithm

label: YFP

source_name: ENS cells at E15.5

label_protocol: Up to 5ug cDNA was fragmented and labelled using the Encore Biotin module (Nugen) as outlined in the manufacturer's instructions.

extract_protocol: Total RNA was extracted using RNAeasy Micro kit (Qiagen)

value: Wnt1Cre x R26ReYFP

value: whole bowel

value: mixed (contained inbred C57BL/6 and outbred Parkes)

value: ENS


title: non-ENS bowel cells at E15.5 replicate 1

description: FACS sorted non-ENS cells from E15.5 mouse bowel

label: non-YFP

source_name: non-ENS bowel cells at E15.5

value: non-ENS bowel cells


title: ENS cells at E15.5 replicate 1


title: non-ENS bowel cells at E15.5 replicate 2


title: Mn11_supp_1

value: SOD2-overexpressing cell line


title: non-ENS bowel cells at E15.5 replicate 3


title: Lpcat3 tamoxifen inducible intestinal specific knockout crypts

city: Los Angeles

first: Bo

last: Wang

state: CALIFORNIA

address: 675 Charles E Young Dr. S

department: Pathology and Laboratory Medicine

institute: UCLA

description: Gene expression data from Lpcat3 F/F, Villin-CreERT2 crypts

hyb_protocol: Standard Affymetrix microarray protocol

scan_protocol: Standard Affymetrix microarray protocol

source_name: crypts isolated from Lpcat3 F/F, Villin-CreERT2 mice

label_protocol: Standard Affymetrix microarray protocol

value: small intestine

value: Lpcat3F/F, Villin-CreERT2


title: WT crypts

description: Gene expression data from Lpcat3 F/F crypts

source_name: crypts isolated from Lpcat3 F/F mice

value: Lpcat3 F/F


title: non-ENS bowel cells at E11.5 replicate 2

description: FACS sorted non-ENS cells from E11.5 mouse bowel

source_name: non-ENS bowel cells at E11.5


title: ENS cells at E15.5 replicate 2


title: MM_E11.5_uninduced_rep1


title: Sox10+ ENS cells at E15.5 replicate 4

description: FACS sorted Sox10+ cells from E15.5 mouse bowel

source_name: Sox10+ ENS cells at E15.5, YFP-reporter induction by 4-OHT injection at E14.5

value: Sox10CreERT2 x R26ReYFP


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [325_MA__1400252108810058__Cy3_33_cDNA_1_4]

city: Barcelona

first: Ben

last: Lehner

address: Carrer Doctor Aiguader, 88

department: systems biology

country: Spain

institute: CRG

hyb_protocol: 1650ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples

organism: Caenorhabditis elegans

source_name: individual C. elegans

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the SureTag complete DNA labeling kit (Agilent 5190-04240) according to manufacturer’s instructions. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer.

extract_protocol: Total RNA was extracted from the snap frozen single worms with RNAClean XP kit (Agentcourt A63987) following the manufacturer’s instructions and immediately amplified using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma WTA2) to generate the cDNA

tag: protocol

tag: batch


title: ENS cells at E11.5 replicate 1

description: FACS sorted ENS cells from E11.5 mouse bowel

source_name: ENS cells at E11.5

tag: tissue


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [322_MA__1100252108810058__Cy3_25_cDNA_1_1]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [324_MA__1300252108810058__Cy3_31_cDNA_1_3]


title: ENS cells at E11.5 replicate 2

tag: age


title: ENS cells at E11.5 replicate 3


title: Sox10+ ENS cells at E15.5 replicate 2


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [323_MA__1200252108810058__Cy3_30_cDNA_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [319_MA__1200252108810059__Cy3_16_cDNA_1_2]


title: Sox10+ ENS cells at E11.5 replicate 4

description: FACS sorted Sox10+ cells from E11.5 mouse bowel

source_name: Sox10+ ENS cells at E11.5, YFP-reporter induction by 4-OHT injection at E10.5


title: Sox10+ ENS cells at E11.5 replicate 3


title: Sox10+ ENS cells at E15.5 replicate 3


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [320_MA__1300252108810059__Cy3_19_cDNA_1_3]


title: Sox10+ ENS cells at E15.5 replicate 1


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [299_MA__1200252108810060__Cy3_10_cDNA_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [321_MA__1400252108810059__Cy3_23_cDNA_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [316_MA__1300252108810060__Cy3_13_cDNA_1_3]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [297_MA__1400252108810061__Cy3_8_cDNA_1_4]


title: Sox10+ ENS cells at E11.5 replicate 1

value: mixed (contained inbred C57BL/6 and outbred Parkes)\n!Sample_characteristics_ch1 = strain:mixed (contained inbred C57BL/6 and outbred Parkes)


title: non-ENS bowel cells at E11.5 replicate 3


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [296_MA__1300252108810061__Cy3_7_cDNA_1_3]


title: Sox10+ ENS cells at E11.5 replicate 2


title: PAZr3

city: Mexico City

first: Marco

last: Checa

address: Calada de Tlalpan 4502, Colonia XVI Delegación Tlalpan

department: Pulmonary Fibrosis

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

description:
Fibroblasts from normal lung, biological rep 3
Gene expression data from human lung fibroblasts after MET-like process

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: The statistical analyses were performed with R 2.11.0. All samples were normalized and summarized by Robust Multiarray Average (RMA). Times series analysis was carried out using bioconductor timecourse package. Differential expression analysis between NK cells non stimulated and LPG-stimulated was performed using LIMMA. The Benjamini and Hochberg multiple hypothesis testing correction procedure was applied to control the false discovery rate (FDR). Data were filtered to include only genes that had a 2-fold-change difference between the groups and an adjusted p value of 0.05

source_name: Human lung fibroblasts derived from normal subjects after brain death

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: Fibroblasts  cultured in 25-cm2 tissue culture flasks using Ham's F-12 nutrient mixture (F-12) supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin and 2.5 μg/ml amphotericin B. All cultures were maintained at 37°C in a humidified atmosphere of 5% humidified atmosphere of CO2.

treatment_protocol: Experiments were performed when cells reached 75% confluence or when they spontaneously exhibited an epithelial-like cell phenotype at 10 to 100 % of predominance in relation to original fibroblasts

value: Fibroblasts from normal lung


title: 6PAZr

description:
Fibroblasts from normal lung, biological rep 1
Gene expression data from human lung fibroblasts after MET-like process


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [318_MA__1100252108810059__Cy3_15_cDNA_1_1]


title: NOVAC3

description:
Epithelial-like cell from normal lung, biological rep3
Gene expression data from fibroblasts where  a MET-like process was observed

value: Fibroblasts from normal lung transformed into ephithelial like cells


title: PAZC1

description:
Epithelial-like cell from normal lung, biological rep1
Gene expression data from fibroblasts where  a MET-like process was observed


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [298_MA__1100252108810060__Cy3_9_cDNA_1_1]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [295_MA__1200252108810061__Cy3_6_cDNA_1_2]


title: PAZC2

description:
Epithelial-like cell from normal lung, biological rep2
Gene expression data from fibroblasts where  a MET-like process was observed


title: non-ENS bowel cells at E11.5 replicate 1


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [292_MA__1300252108810062__Cy3_3_cDNA_1_3]


title: NOVAr1


title: PAZr2

description:
Fibroblasts from normal lung, biological rep 2
Gene expression data from human lung fibroblasts after MET-like process


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [290_MA__1100252108810062__Cy3_1_cDNA_1_1]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [317_MA__1400252108810060__Cy3_14_cDNA_1_4]


title: NOVAr3


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [291_MA__1200252108810062__Cy3_2_cDNA_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [16_MA__1400252108810021__Cy3_29_S_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [14_MA__1200252108810021__Cy3_27_S_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [293_MA__1400252108810062__Cy3_4_cDNA_1_4]


title: PAZC3


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [13_MA__1300252108810050__Cy3_26_S_1_3]


title: NOVAC2


title: 241C3

description:
Epithelial-like cell from interstitial lung disease, biological rep3
Gene expression data from fibroblasts where  a MET-like process was observed

source_name: Human lung fibroblasts derived from biopsies from patients with IPF

value: Fibroblasts from interstitial lung disease transformed into ephithelial like cells


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [09_MA__1200252108810051__Cy3_20_S_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [11_MA__1300252108810046__Cy3_23_SW_1_3]


title: 241r1

description:
Fibroblasts from interstitial lung disease, biological rep 1
Gene expression data from human lung fibroblasts after MET-like process


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [11_MA__1100252108810050__Cy3_22_S_1_1]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [07_MA__1100252108810049__Cy3_18_S_1_1]


title: 1241c

description:
Epithelial-like cell from interstitial lung disease, biological rep1
Gene expression data from fibroblasts where  a MET-like process was observed


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [07_MA__1300252108810045__Cy3_3_SW_1_3]


title: 3NOVAc


title: 241r3

description:
Fibroblasts from interstitial lung disease, biological rep 3
Gene expression data from human lung fibroblasts after MET-like process


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [05_MA__1100252108810045__Cy3_11_SW_1_1]


title: 241r2

description:
Fibroblasts from interstitial lung disease, biological rep 2
Gene expression data from human lung fibroblasts after MET-like process


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [10_MA__1400252108810051__Cy3_21_S_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [15_MA__1300252108810021__Cy3_28_S_1_3]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [08_MA__1300252108810049__Cy3_19_S_1_3]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [04_MA__1400252108810044__Cy3_10_SW_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [12_MA__1200252108810050__Cy3_24_S_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [08_MA__1400252108810045__Cy3_8_SW_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [05_MA__1200252108810007__Cy3_14_S_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [10_MA__1200252108810046__Cy3_9_SW_1_2]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [06_MA__1400252108810007__Cy3_17_S_1_4]


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [02_MA__1200252108810044__Cy3_2_SW_1_2]


title: 241C2

description:
Epithelial-like cell from interstitial lung disease, biological rep2
Gene expression data from fibroblasts where  a MET-like process was observed


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [03_MA__1300252108810044__Cy3_6_SW_1_3]


title: Healthy control 6

status: Public on Dec 03 2017

city: Santiago de Compostela

first: Cintia

middle: Micaela

last: Chamorro

address: Entrerríos s/n

department: Oral Medicin

institute: Santiago de Compostela University

hyb_protocol: We have used Affymetrix®miRNA 4.1 Array Plate

scan_protocol: we have used GeneTitan®Instrument

data_processing: we have used Affymetrix®GeneChip® Command Console® (AGCC) and finally the trancriptome analysis console (TAC)

source_name: oral cavity

label_protocol: We have used the Affymetrix® FlashTagTM Biotin HSR RNA Labeling Kit following the manufacturer instructions

extract_protocol: We have extracted totalRNA from frozen tissue samples using the miRVana Isolation kit following the manufacturers instructions except the first part where we have disgregated the samples using diamond drill and hand piece. We have measured the concentration with the NanoDrop and the integrity of RNAtotal with the NanoChip and Bioanalyzer 2100, where all the samples had at least a RIN of 7

value: Oral mucosa

tag: gender

value: male

tag: smoker

value: no

tag: cigarettes (number/day)

tag: localization

value: oral mucosa


title: Healthy control 7

value: female


title: Healthy control 4


title: Healthy control 2


title: Healthy control 8

value: yes


title: OSCC CASE C

value: Oral Squamous cell carcinoma

tag: tumor

value: II

value: NO


title: Healthy control 5


title: healthy control 1


title: RORac_LKO_ZT22_Liver_Microarray 3

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: Gene expression data from RORac KO ZT22 mouse liver

hyb_protocol: Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Array images were captured on a GCS3000 laser scanner (Affymetrix) and analyzed by the Penn Microarray Core using Partek Genomics Suite.

data_processing: Data analysis was done using BioConductor packages  (Oligo)

label_protocol: GeneChIP WT terminal labeling

growth_protocol: C57BL/6 mice were grown on normal chow on normal light/dark schedule

treatment_protocol: no specific treatment was performed

value: 12 weeks old

tag: genotype/variation

value: RORac KO

value: liver


title: RORac_LKO_ZT22_Liver_Microarray 2


title: OSCC CASE B

value: IV

value: trigono zone


title: RORac_Control_ZT22_Liver_Microarray 1

description: Gene expression data from RORac control ZT22 mouse liver

value: RORac control


title: RORac_LKO_ZT22_Liver_Microarray 1


title: RORac_Control_ZT22_Liver_Microarray 4


title: RORac_Control_ZT22_Liver_Microarray 2


title: RORc_LKO_ZT22_Liver_Microarray 4

description: Gene expression data from RORc KO ZT22 mouse liver

value: RORc KO


title: RORac_Control_ZT22_Liver_Microarray 3


title: OSCC CASE E

value: tongue


title: OSCC CASE F

value: YES


title: RORc_LKO_ZT22_Liver_Microarray 2

value: male


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [294_MA__1100252108810061__Cy3_5_cDNA_1_1]


title: RORc_LKO_ZT22_Liver_Microarray 3


title: OSCC CASE A


title: OSCC CASE H

value: floor mouth


title: OSCC CASE G


title: RORac_LKO_ZT22_Liver_Microarray 4


title: OSCC CASE D

value: oral mucosa


title: RORc_LKO_ZT22_Liver_Microarray 1


title: Healthy control 3

value: Oral mucosa

value: no


title: NOVAr2

value: Fibroblasts from normal lung


title: RORc_Control_ZT22_Liver_Microarray 3

description: Gene expression data from RORc control ZT22 mouse liver

value: RORc control


title: RORc_Control_ZT22_Liver_Microarray 1


title: RORa_Control_ZT22_Liver_Microarray 4

description: Gene expression data from RORa control ZT22 mouse liver

value: RORa control


title: RORc_Control_ZT22_Liver_Microarray 2

value: 12 weeks old


title: RORa_LKO_ZT22_Liver_Microarray 2

description: Gene expression data from RORa KO ZT22 mouse liver

value: RORa KO


title: Primary tumor from ME59

status: Public on Dec 01 2017

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

hyb_protocol: Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

scan_protocol: Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

data_processing: Data were normalized by RMA using the Affy R package and batch effects were corrected using ComBat using the sva R package.

source_name: Primary tumor

label_protocol: Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen.

tag: disease state

value: CRC

tag: patient

tag: origin

value: Primary tumor

value: tumor


title: Primary tumor from RC511


title: Primary tumor from DA13


title: Ctrl 4

status: Public on Dec 02 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotinylated single stranded sense  cDNA is then hybridized to GeneChip® Mousegene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, Chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file from Brain Array for entrezgene id  V17 was used for annotation.

organism: Mus

source_name: Ctrl

label_protocol: 50 of total RNA is reverse transcribed  following the Ovation PicoSLV2 kit (Nugen). Briefly, the resulting double stranded cDNA is used to produce sens target cDNA using SPIA. This cDNA is fragmented and biotin labelled using EncoreBiotin module (Nugen)

extract_protocol: Total RNA of liver samples were extracted using TRizol protocol.

value: Liver

value: Ctrl


title: Ctrl 3


title: KO_LKB1 3

value: LKB1 KO


title: KO_LKB1 2


title: RORa_Control_ZT22_Liver_Microarray 2

value: liver


title: RORa_Control_ZT22_Liver_Microarray 1

value: male


title: KO_LKB1 1


title: Ctrl 1


title: RORc_Control_ZT22_Liver_Microarray 4


title: RORa_LKO_ZT22_Liver_Microarray 3


title: KO_LKB1 4


title: Ctrl 2


title: RORa_LKO_ZT22_Liver_Microarray 1


title: LM23

hyb_protocol: Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

scan_protocol: Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

data_processing: Data were normalized by RMA using the Affy R package and batch effects were corrected using ComBat using the sva R package

source_name: CRC spheroid cultures

label_protocol: Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

growth_protocol: The cell lines were cultured as spheroids under ultralow-adherent condition (Corning, Amsterdam, the Netherlands)  in cancer stem cell medium.

tag: cell line

value: colon tumor

value: AMC


title: DA13

value: Palermo


title: CO152


title: CO115


title: LR14


title: individual C. elegans grown at 20˚C and collected 46 hours after hatching [09_MA__1100252108810046__Cy3_5_SW_1_1]


title: CC09


title: CO133


title: ME59


title: CO123


title: Liver Metastasis from LM23

source_name: Liver Metastasis

value: Liver Metastasis


title: CO108


title: Primary tumor from CO108


title: Primary tumor from CO115


title: CO147


title: LR13


title: RC511


title: RORa_Control_ZT22_Liver_Microarray 3


title: Primary tumor from CO164


title: Primary tumor from CO152


title: Primary tumor from CO149


title: Primary tumor from CO153


title: Primary tumor from CO150


title: CO01


title: Liver Metastasis from LM39


title: Liver Metastasis from LM37


title: Xenograft P2 established from LM39

source_name: Xenograft P2

tag: passage

value: xenograft


title: Xenograft P2 established from LM40


title: Xenograft P1 established from LM40

source_name: Xenograft P1


title: Xenograft P3 established from LM39

source_name: Xenograft P3


title: Primary tumor from CO128


title: Liver Metastasis from LM40


title: Primary tumor from CO123


title: Liver Metastasis from LM38


title: Xenograft P1 established from LM38


title: AG2


title: Liver Metastasis from LM28


title: Xenograft P3 established from LM27


title: Xenograft P2 established from LM38


title: Liver Metastasis from LM27


title: Xenograft P2 established from LM28


title: Xenograft P1 established from LM27


title: Xenograft P2 established from LM27


title: Xenograft P2 established from CO164


title: Xenograft P1 established from CO164


title: Xenograft P3 established from CO153


title: Xenograft P3 established from CO164


title: Xenograft P1 established from LM28


title: Xenograft P3 established from LM28


title: Liver Metastasis from LM29


title: Xenograft P3 established from LM37


title: Xenograft P1 established from LM29


title: Primary tumor from CO144


title: Xenograft P2 established from CO153


title: Xenograft P1 established from CO152


title: Xenograft P1 established from CO144


title: Xenograft P3 established from CO149


title: Xenograft P3 established from CO123


title: Xenograft P1 established from CO149


title: Xenograft P2 established from CO123


title: Xenograft P3 established from CO152


title: Xenograft P3 established from CO150


title: Xenograft P2 established from CO149


title: Xenograft P1 established from CO153


title: RORa_LKO_ZT22_Liver_Microarray 4

tag: strain


title: Xenograft P1 established from CO150


title: Xenograft P1 established from CO128


title: P20T

data_processing: Data were normalized by RMA using the Affy R package

source_name: CRC organoids

growth_protocol: The cell lins were cultured as organoids in Matrigel

value: colon tumor organoid

tag: individual

value: patient 20


title: P25T

value: patient 25


title: P26T

value: patient 26


title: P19Tb

value: CRC

value: patient 19


title: P17T

value: patient 17


title: P24Ta

value: patient 24


title: Xenograft P1 established from CO123

value: Primary tumor


title: P18T

value: patient 18


title: P16T

value: patient 16


title: P24Tb


title: P31T

value: patient 31


title: P28T

value: patient 28


title: P23T

value: patient 23


title: Xenograft P2 established from CO152


title: Xenograft P2 established from CO150


title: P14T

value: patient 14


title: P8T

value: patient 8


title: HUTU80

source_name: CRC cell line

growth_protocol: Cell lines RKO, SW48, HT55, SW948, SW1463, CL40, LS180, CAR1, HUTU80 and OUMS23 were cultured in Dulbecco's modified Eagle's medium (DMEM)/F-12 medium with Ll-glutamine, 15 mM HEPES (Thermo-Fisher Scientific, Bleiswijk, The Netherlands) with added fetal bovine serum (Lonza, Breda, The Netherlands) and penicillin and streptomycin. HCT-116, KM12, RCM-1, SNU-C1, LS-513, COLO-320-HSR, MDST8 and NCI-H716 were cultured in RPMI 1640 with Ll-glutamine, 25 mM HEPES (Thermo-Fisher Scientific) added fetal bovine serum, penicillin and streptomycin, 1% Dd-glucose solution plus (Sigma-Aldrich, Zwijndrecht, The Netherlands) and 100 μM sodium pyruvate (Life Technologies, Bleiswijk, The Netherlands). All cultures were maintained in humidified 37°C 5% CO2 incubators and cells were regularly tested for mycoplasma infection.


title: OUMS23


title: COLO320HSR


title: P6T

value: patient 6


title: P9T

value: colon tumor organoid

value: patient 9


title: NCIH716


title: MDST8


title: SW1463


title: LS513


title: CAR1


title: P11T

value: patient 11


title: CL40


title: Plasma_HIV_old_infected_case_rep9

city: Nanning

first: Jiegang

last: Huang

state: Guangxi

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

description: This sample is of HIV old infected case. It is the ninth of ten HIV old infected cases used in this experiment, each from separate individual.

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.    a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first          denatured for 2 min at 95°C, incubated on ice for 2 min    b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization          System - Nimblegen Systems, Inc., Madison, WI, USA)      c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: plasma, HIV old infected case

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:    a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture          was incubated for 30 min at 37°C.      b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of          fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling          reaction was incubated for 1 h at 16°C    c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: EDTA-blood samples were obtained by venipuncture and plasma was separated by one centrifugation step at 800 * g for 8 minutes at room temperature (RT).

value: male

tag: estimated duration of infection (day)


title: HT55

value: CRC


title: Plasma_HIV_old_infected_case_rep7

description: This sample is of HIV old infected case. It is the seventh of ten HIV old infected cases used in this experiment, each from separate individual.

value: female


title: HCT116


title: Plasma_HIV_new_infected_case_rep10

description: This sample is of HIV new infected case. It is the tenth of ten HIV new infected cases used in this experiment, each from separate individual.

source_name: plasma, HIV new infected case


title: KM12


title: Plasma_HIV_old_infected_case_rep6

description: This sample is of HIV old infected case. It is the sixth of ten HIV old infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_old_infected_case_rep1

description: This sample is of HIV old infected case. It is the first of ten HIV old infected cases used in this experiment, each from separate individual.


title: SW948


title: SNUC1


title: 22-2

city: Tokyo

first: Rulan

last: Bai

address: 1-1-1 Yayoi, Bunkyouku

country: Japan

institute: The University of Tokyo

description: Gene expression data from concpus of day 22 in pregnant cows

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

organism: Bos taurus

source_name: Bovine conceptus at day 22

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Thirty embryos derived from the superovulation were transferred non-surgically into the uterine horn of fifteen Holstein heifers (two blastocysts/recipient), ipsilateral to the corpus luteum on day 7 (day 0 = day of estrus) of the synchronized estrous cycle.

extract_protocol: Isogen extraction of total RNA according to the manufactuture's instractions

treatment_protocol: For RNA analyses, elongated conceptuses were collected non-surgically by uterine flushing on day 20, or 22 (n=3 each day) with 500 ml sterile phosphate-buffered saline (PBS, pH 7.2).  Conceptuses in the uterine flushing media were obtained by centrifugation at 1,000 x g for 5 min and snap-frozen in liquid nitrogen.

value: Bovine conceptus

tag: cell type

value: trophoblast


title: 20-3

description: Gene expression data from concpus of day 20 in pregnant cows

source_name: Bovine conceptus at day 20

tag: tissue


title: Plasma_HIV_new_infected_case_rep9

description: This sample is of HIV new infected case. It is the ninth of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_old_infected_case_rep8

description: This sample is of HIV old infected case. It is the eighth of ten HIV old infected cases used in this experiment, each from separate individual.


title: SW48


title: Plasma_HIV_old_infected_case_rep5

description: This sample is of HIV old infected case. It is the fifth of ten HIV old infected cases used in this experiment, each from separate individual.


title: RKO

value: RKO


title: Plasma_HIV_old_infected_case_rep4

description: This sample is of HIV old infected case. It is the fourth of ten HIV old infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_old_infected_case_rep10

description: This sample is of HIV old infected case. It is the tenth of ten HIV old infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_old_infected_case_rep3

description: This sample is of HIV old infected case. It is the third of ten HIV old infected cases used in this experiment, each from separate individual.


title: 22-1


title: 22-3


title: RCM1


title: 20-2


title: 20-1


title: Plasma_HIV_old_infected_case_rep2

description: This sample is of HIV old infected case. It is the second of ten HIV old infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep8

description: This sample is of HIV new infected case. It is the eighth of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep5

description: This sample is of HIV new infected case. It is the fifth of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep6

description: This sample is of healthy control. It is the sixth of ten healthy controls used in this experiment, each from separate individual.

source_name: plasma, healthy control


title: Plasma_HIV_new_infected_case_rep4

description: This sample is of HIV new infected case. It is the fourth of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep8

description: This sample is of healthy control. It is the eighth of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep2

description: This sample is of healthy control. It is the second of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep7

description: This sample is of healthy control. It is the seventh of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep7

description: This sample is of HIV new infected case. It is the seventh of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep6

description: This sample is of HIV new infected case. It is the sixth of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep4

description: This sample is of healthy control. It is the fourth of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep3

description: This sample is of healthy control. It is the third of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep2

description: This sample is of HIV new infected case. It is the second of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep3

description: This sample is of HIV new infected case. It is the third of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep10

description: This sample is of healthy control. It is the tenth of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_HIV_new_infected_case_rep1

description: This sample is of HIV new infected case. It is the first of ten HIV new infected cases used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep5

description: This sample is of healthy control. It is the fifth of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep9

description: This sample is of healthy control. It is the ninth of ten healthy controls used in this experiment, each from separate individual.


title: Plasma_healthy_control_rep1

description: This sample is of healthy control. It is the first of ten healthy controls used in this experiment, each from separate individual.


title: 121T

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description: Gene expression of Head & Neck (HNSCC) tissue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on human GeneChip® Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: data were background adjusted and quantile normalized. The gene expression values were calculated by using Robust    Multiple-array Average (RMA) procedure. Average value was considered for any duplicate. Gene expression profiles with variance lower than 10% were removed. Data processed by MATLAB.

source_name: tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fresh frozen tissues samples were obtained immediately after surgical resection and stored in RNA later (Ambion)

extract_protocol: total RNA was extracted using miRNeasy Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Tissues were disrupted and homogenized using QIAzol Lysis Reagent  (Qiagen, Chatsworth, CA)

value: HN tumor tissue

tag: site

value: Oral Cavity

value: Male

tag: g

tag: t

tag: n

value: N+

tag: mut p53

value: WT

value: HNSCC


title: 113T

value: Larynx

tag: gender


title: 71N

source_name: normal

value: HN normal tissue

value: Female


title: 133T


title: 121N


title: 133N


title: 113N


title: 71T


title: 122N


title: 122T


title: 86T

value: Pharynx


title: 86N


title: 88N


title: 105N


title: 105T


title: 69T


title: 85T


title: 104T


title: 104N


title: 84T


title: 88T


title: 82N


title: 82T


title: 91N


title: 81N


title: 76T


title: 69N


title: 80N


title: 91T


title: LS180


title: 80T


title: P7T

value: colon tumor organoid

value: patient 7


title: 67T


title: 85N


title: 76N


title: 65T


title: 68T


title: 67N


title: 65N


title: 84N


title: 55T


title: 81T


title: 62N


title: 73N


title: 62T


title: 74N


title: 68N


title: siCYP27B1 25D3

city: Itabashi-ku

first: Takao

last: Susa

state: Tokyo

department: Department of Biochemistry

institute: Teikyo University School of Medicine

description: Gene expression after 25D3 treatment for 24hr in siCYP27B1 LNCaP

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: LNCaP, siCYP27B1, 25D3, replicate 1

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell

value: LNCaP cells


title: siCYP27B1+siVDR 25D3

description: Gene expression after 25D3 treatment for 24hr in siCYP27B1+siVDR LNCaP

source_name: LNCaP, siCYP27B1+siVDR, 25D3, replicate 1


title: 73T

tag: disease state


title: siCYP27B1+siVDR V

description: Gene expression after vehicle treatment for 24hr in siCYP27B1+siVDR LNCaP

source_name: LNCaP, siCYP27B1+siVDR, vehicle, replicate 1


title: siCT 25D3

description: Gene expression after 25D3 treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, 25D3, replicate 1


title: Fg IAAld vs Fg NT BR3

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

hyb_protocol: F. graminearum custom-designed 4x44K microarrays (Agilent Technologies, AMADID 020717) (NCBI, GEO record# GPL11046) were hybridized overnight at 65°C in the dark with 825 ng each cy3 and cy5 labelled probes in a Robbins Scientific Model 400 incubator and an Agilent Scientific G2530-60020 rotator. Hybridization was carried out as per manufacturer's protocol. Slides were washed as per protocol except omitting the 3rd wash (Stabilization and Drying Solution).

scan_protocol: Slides were scanned using a Genepix 4200a scanner (Molecular Devices) at 5µm resolution. Feature-finding analysis was performed in Genepix Pro 6.0 and then manually correct any misaligned features. Raw data was saved as .gpr files and imported in Acuity 4.0 (Molecular Devices) for analysis.

data_processing: Genepix Pro 6.0 .gpr files for each array were imported in Acuity 4.0. The data was normalized with the Normalization Wizard using Lowess M log ratio. A dataset was created and spike-in and other controls were removed. Features within the dataset that had Lowess A values above 7.5 in at least 2 of the 6 arrays were kept. Reverse-dye replicates were combined after cy3 test columns were swapped to cy5. The normalized data was analysed in Acuity 4.0 to identify candidate genes that were significantly differentially expressed, using the following cut-off parameters: t-test p-value < 0.05 and fold changes ≥ 4 in expression ratios (i.e. log2 ratio ≥ 2.0 or -2.0; L-TRP vs control).

organism: Fusarium graminearum

label_protocol: 500 ng total RNA was labelled using the Two-Color Quick-Amp Labelling Kit (Agilent Technologies) using the manufacturer's instructions except using half the reagent volumes in Step 2 of the protocol.

growth_protocol: Mycelia from F. graminearum strain DAOM180378 was grown as follows: 1x106 macroconidia were inoculated into 50 mL of 1st stage medium (Taylor et al 2008. Proteomics. 8: 2256-2265) in 250 mL Erlenmeyer flasks, 200 rpm, 28 ºC, in the dark for 72 h. The mycelia were homogenized in their medium, filtered through Miracloth (Calbiochem, Canada), rinsed with sterile 0.9% saline solution then resuspended in 50 mL of 2nd stage medium (Taylor et al 2008) to induce mycotoxin production containing either 2 mM L-TRP, 0.2 mM TAM, 0.2 mM IAAld or no treatment (NT) and shaken at 200 rpm, at 28ºC in the dark. In control samples (no treatment), mycelia was transferred to 2nd stage medium without the addition of any intermediate.

extract_protocol: The frozen mycelia were ground using a mortar and pestle and stored at -80 ºC. RNA from the ground mycelia was extracted using TRIZOL reagent (Invitrogen, Life Technologies Co., Canada), following the manufacturer’s protocol, and then purified further using the RNeasy Mini Kit (Qiagen Science, Canada) and the RNA cleanup protocol which included a RNase-free DNase I treatment. The RNA quality and quantity were determined using the 2100 Bioanalyzer (Agilent Technologies Inc., Canada).

treatment_protocol: The mycelia were homogenized in their medium, filtered through Miracloth (Calbiochem, Canada), rinsed with sterile 0.9% saline solution then resuspended in 50 mL of 2nd stage medium to induce mycotoxin production containing either 2 mM L-TRP, 0.2 mM TAM, 0.2 mM IAAld or no treatment (NT) and shaken at 200 rpm, at 28ºC in the dark. In control samples (no treatment), mycelia was transferred to 2nd stage medium without the addition of any intermediate.. Three biological replicates were grown for each treatment; mycelia were collected for 6 h after treatment, filtered and immediately submerged into liquid nitrogen.

tag: treatment

value: 0.2 mM indole-3-acetaldehyde

value: Untreated


title: siCT V1

description: Gene expression after vehicle treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, vehicle1, replicate 1


title: siCYP27B1 V

description: Gene expression after vehicle treatment for 24hr in siCYP27B1 LNCaP

source_name: LNCaP, siCYP27B1, vehicle, replicate 1


title: Fg IAAld vs Fg NT BR2


title: Fg NT vs Fg IAAld BR1


title: ISL-treated (Cy5)/Control (Cy3)-LNCaP

city: Shanghai

first: Biyan

last: Zhang

state: Shanghai

address: 1200 Cai Lun Road, Pudong District

department: School of Basic Medicine

institute: Shanghai University of Traditional Chinese Medicine

description: single sample, using qRT-PCR to validate the microarray result

hyb_protocol: Labeled DNA was hybridized in 2X GEx Hyb Buffer (HI-RPM) containing 25% formamide at  45°C overnight. After hybridization, microarrays were washed sequentially.

scan_protocol: Microarrays were scanned on an Agilent G2565CA Microarray Scanner.

data_processing: Agilent Feature Extraction Software was used for image quantification, background subtraction and LOWESS mormalization.

source_name: ISL-treated LNCaP cells

label_protocol: The labeling process was performed by using Jingxin cRNA Amplification and Labeling Kit according to the manufacture's instructions.

growth_protocol: LNCaP cells or PC-3 cells were maintained in RPMI-1640 (Hyclone, USA) supplemented with 10% FBS (Hyclone, USA), 1% penicillin and streptomycin at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: After treatment, cells were harvested and washed with cold PBS. Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer's instrctions and stored at -80°C waiting for quality test and microarray analysis. The quality test and microarray experiment were performed by CapitlBio Corporation (Beijing, China). Total RNA was purified using NucleoSpin RNA clean-up kit (MACHEREY-NAGEL, Germany) and quantified by a spectrophotometer. The quality of samples were tested through electrophoresis on gel containing formaldehyde. Samples passing the qualifty test were allowed to step into the next stage of the experiment.

treatment_protocol: LNCaP cells and PC-3 cells were seeded into 25 cm2 flask at a density of 5×104 cells per flask. After 24h of incubation, cells were treated with 25 μM ISL or 0.025% DMSO as control for 48h.

value: LNCaP Prostate Cancer Cell Line

value: ISL

source_name: Control LNCaP cells

value: Control (untreated)


title: ISL-treated (Cy5)/Control (Cy3)-PC-3

source_name: ISL-treated PC-3 cells

value: PC-3 Prostate Cancer Cell Line

source_name: Control PC-3 cells


title: siCT V2

source_name: LNCaP, siCT, vehicle2, replicate 1


title: Fg IAAld vs Fg NT BR1


title: Fg TAM vs Fg NT BR1

value: 0.2 mM Tryptamine


title: Fg NT vs Fg TAM BR1


title: siCT 1,25D3

description: Gene expression after 1,25D3 treatment for 24hr in siCT LNCaP

source_name: LNCaP, siCT, 1,25D3, replicate 1


title: Fg NT vs Fg TAM BR3


title: Fg TAM vs Fg NT BR3


title: 74T

value: HN tumor tissue

value: Male


title: Fg NT vs Fg IAAld BR3


title: Fg NT vs Fg TAM BR2


title: Fg TAM vs Fg NT BR2


title: Fg TRP vs Fg NT BR1

value: 2 mM L-Tryptophan


title: Fg NT vs Fg TRP BR3


title: Fg NT vs Fg TRP BR1


title: Fg TRP vs Fg NT BR2


title: Fg TRP vs Fg NT BR3


title: GF re-conventionalised (CONV), biological rep 1

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

country: Ireland

institute: UCC

hyb_protocol: controls BioB, BioC, BioD and Cre and PolyA (Lys, Phe, Thr and Dap) . (ALMAC)

scan_protocol: ALMAC

data_processing:
Expression console v1.1, RMA- sketch,  HCA and PCA using Partek Genomics Suite (ALMAC)
probe group file: MoEx-1_0-st-v1.r2.pgf (ALMAC generated)
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.full (ALMAC generated)
Almac Diagnostics applies hierarchical clustering analysis and principal components analysis (PCA) using Partek Genomics Suite to assess the integrity of expression data prior to any downstream analysis.     The data was pre-processed using Robust Multichip Algorithm (RMA) based on standard RMA background correction, quantile normalisation and median polish summarisation (Bolstad et al. 2003) on the gene core probes. The pre-processed data matrix of all samples with Log2 expressions for each sample and each gene probeset is provided for ileum and liver datasets. Furthermore, the data matrix of exon data is also provided. Clustering was performed using Euclidean as the distance metric and Ward’s method for linkage. (ALMAC)
Further data analysis and interpretation was applied using Subio Platform, (JMS UCC)

source_name: GF Conv

label_protocol: biotin (ALMAC)

extract_protocol: The colon was removed and the RNA extracted (RNAeasy plus universal kit (Qiagen)) and quantified (Nanodrop).

treatment_protocol: Germ free Swiss Webster mice were monocolonised with Bifidobacterium with or without mutant of the bacterial gene,  TadA. The treatment groups and relevant controls were; 1.  Germ Free(GF) Bif UCC 2003  n=4 , 2.  GF and Bif TadA (mutant) n=4, 3. GF 1 n=4, 4.   GF re-conventionalised (CONV) n= 5.  The colons were removed and the RNA extracted (RNAeasy plus universal  kit (Qiagen), quantified and Microarrays were carried out using mouse Exon ST1.0 arrays (Affymetrix) by Almac Group, Craigavon, Northern Ireland. Analysis and pathway mapping was carried out by ALMAC and using Subio Platform software (Subio Inc) and Genesis Software.

value: Swiss Webster

value: GF re-conventionalised (CONV)

value: colon


title: GF re-conventionalised (CONV), biological rep 4


title: GF+ Bif Tad A, biological rep 2

source_name: GF + TadA

value: GF and Bif TadA


title: GF re-conventionalised (CONV), biological rep 2


title: GF+ Bif Tad A, biological rep 4


title: Fg NT vs Fg TRP BR2


title: GF control biological rep 3

source_name: GF control

value: GF control


title: GF+ Bif Tad A, biological rep 3


title: GF control biological rep 2


title: GF re-conventionalised (CONV), biological rep 3


title: GF+ Bif Tad A, biological rep 1


title: GF+ Bif UCC2003, biological rep 3

source_name: GF UCC2003

value: Germ Free(GF) Bif UCC 2003


title: GF+ Bif UCC2003, biological rep 4


title: GF control biological rep 4


title: GF control biological rep 1


title: Fg NT vs Fg IAAld BR2


title: GF+ Bif UCC2003, biological rep 2


title: GF+ Bif UCC2003, biological rep 1


title: Day 2 CD4 Tmem cells_rep1

hyb_protocol: Following fragmentation, 3.6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 Scanner.

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file ENTREZG V20 was used for annotation.

source_name: Resident memory CD4 T cells

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation PicoV2 protocol from 900 pg total RNA.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (QIAGEN) according to manufacturer's manual.

treatment_protocol: CD4 T cells from peripheral and mesenteric lymph nodes of C57BL/6 Foxp3-GFP mice were purified by using Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen). Then, CD4 Treg and Tmem cells were flow-cytometry sorted as CD4+ CD8α- TCRβ+ GFP+ for Treg and CD4+ CD8α- TCRβ+ GFP- CD44hi for Tmem using a FACS-ARIA3 flow cytometer.

tag: strain/background

value: C57BL/6 Foxp3-GFP

tag: age

value: 6-8 weeks

value: Resident memory CD4 T cells


title: Control CD4 Treg cells_rep3

source_name: Regulatory CD4 T cells

value: Regulatory CD4 T cells


title: Day 2 CD4 Treg cells_rep3

source_name: Resident Regulatory CD4 T cells

value: Resident Regulatory CD4 T cells


title: Day 2 CD4 Treg cells_rep1


title: Control CD4 Tmem cells_rep3

source_name: Memory CD4 T cells

value: Memory CD4 T cells


title: Control CD4 Treg cells_rep2


title: Day 2 CD4 Tmem cells_rep3


title: Day 2 CD4 Tmem cells_rep2


title: Day 2 CD4 Treg cells_rep2


title: Control CD4 Treg cells_rep1


title: Control CD4 Tmem cells_rep1


title: macrophages_control_rep2

city: WenZhou

first: Bozhi

last: Ye

state: ZheJiang

address: 2 Fuxue Road

department: Department of Cardiology

institute: the First Affiliated Hospital of WenZhou Medical University

description: Gene expression  in control macrophages

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, circRNA that have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed circRNA with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed circRNA between the two samples were identified through Fold Change filtering.

source_name: macrophages, control, replicate 2

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The THP-1 were maintained in RPMI 1640 medium containing 4,500 mg/L glucose and supplemented with 10% (v/v) FBS, 10 mM HEPES  and 1% pen/strep solution at 37 °C in a humidified 5% CO2 incubator.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: The THP-1 were pretreated with 100 nM PMA for 48 h ,which allowed them to differentiate into adherent macrophages, stimulated with oxLDL (50 mg/ml) for 24h. Total RNAs were extracted from the each group using TRIzol reagent.

tag: cell line

tag: agent


title: macrophages_ox-LD_rep3

description: Gene expression after ox-LDL treated in macrophages-derived faom cells

source_name: macrophages, ox-LDL, replicate 3

value: oxLDL (50 mg/ml)


title: IFNg-IL13_C16-18_4

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

hyb_protocol: hybridized 17h using the standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Command Console used to generate CEL files

data_processing:
Imported into Partek Genomics Suite 6.6.RMA was generated using RMA background correction, quantile normalization and summarization by Median Polis
Clariom_S_Mouse_HT.r1.pgf
Clariom_S_Mouse_HT.r1.mps

label_protocol: Affymetrix WT Plus using 100ng of total RNA

growth_protocol: 12-7, 12-7, 13-11, 13-7, 16-8 maintained by weekly antigen restimulation with immune B cell APC; 3-10 weekly restimulation with immune splenocyte APC;  all T cell clones in RPMI media with 3 ng/ml IL-7 for 48h prior to extraction

extract_protocol: RNEasy with G-eliminator (Qiagen)

tag: phenotype

value: IFN-g/ IL-13


title: Treated_Bio_Replicate 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent designed Rice Gene expression Microarray 4x44K (AMADID No: G2514F_064815) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift method .Gene based analysis was performed.

organism: Oryza sativa

source_name: Rice roots

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Seedlings germinated in half strength MS media

extract_protocol: The RNA extraction from the samples was performed by Isol-RNA Lysis method (Cat.No. 2302700) with DNAse treatment as per manufacturer’s protocol.

treatment_protocol: Plantlets treated with P. putida in a hydroponics set up (using Hoagland's solution)

value: root

value: PGPR after 48 hrs


title: macrophages_control_rep1

description: Gene expression  in control macrophages

source_name: macrophages, control, replicate 1


title: macrophages_control_rep3

description: Gene expression  in control macrophages

source_name: macrophages, control, replicate 3


title: IFNg_C3-10_2

value: IFN-g


title: IFNg_C3-10_1


title: macrophages_ox-LDL_rep1

source_name: macrophages, ox-LDL, replicate 1


title: macrophages_ox-LD_rep2

source_name: macrophages, ox-LDL, replicate 2


title: IFNg_C3-10_4


title: IFNg-IL13_C16-18_3


title: Treated_Bio_Replicate 1


title: Control CD4 Tmem cells_rep2


title: IFNg_C3-10_3


title: IFNg-IL13_C16-18_1


title: Control_Bio_Replicate 1

value: control


title: IFNg_C13-11_4


title: Treated_Bio_Replicate 3


title: Control_Bio_Replicate 2


title: IFNg+IL13_C13-7_4


title: F_succingenes_Wheat_Straw

city: Saint-Genès-Champanelle

first: Sophie

last: Comtet-Marre

address: Centre Auvergne-Rhône-Alpes

institute: Université Clermont Auvergne, INRA

description: mRNA enriched RNA

hyb_protocol: RNA hybridization (1 μg for each condition)was performed at 65°C during 17 h following the Agilent protocol ‘ Two-Color Microarray-Based Gene Expression’ with few modifications for the use of a supplementary blocking agent (Kreablock, Kreatech Diagnostics, Amsterdam, Netherlands). Briefly, RNA fragmentation was performed at 60°C during 30 min in a mix composed of 12,5 μL of Kreablock buffer (Kreatech Diagnostics, Amsterdam, Netherlands), 6.5 μL of aRNA, 5μL of 10X Gene Expression Blocking Agent (Agilent, Santa Clara, CA, USA) and 1 μL of 25X fragmentation buffer (Agilent, Santa Clara, CA, USA). Next steps of hybridization and slide washing were according to Agilent protocol.

scan_protocol: Immediately after washing steps, microarray slides were scanned using an Agilent G2505B microarray scanner (Agilent Technologies) with a resolution of 5 μm and the XDR mode (Extended Dynamic Range) set up at 10% and 100% PMT gain.

data_processing: Fluorescence intensities of oligonucleotide spots were extracted from the scanned images using the Feature Extraction software (V11.0, Agilent Technologies). Then data were processed with dedicated scripts based on C++ and Delphi languages. For each probe, median intensity value of the 3 replicates was conserved and used as the probe signal value. The SNR (Signal-to-Noise Ratio), similar to the detection threshold response (positive hybridization) and corresponding to the probe signal value divided by the local background intensity value, was calculated for each probe. The SNR thresholds were set to 3 for 25-mer probes and 6 for 54-mer probes. Such SNR threshold values ensured a very specific response of the FibroChip, except for genes belonging to very close strains from the same species. Results for 25- and 54-mer probes were treated independently and for each probe type, a gene was considered as detected when 65% of probes were positive. The SNR value of a detected gene was then calculated by the mean of the SNR of all 25- or 54-mer probes targeting this gene, meeting or not the defined SNR threshold.

organism: Fibrobacter succinogenes subsp. succinogenes S85

source_name: Bacteria cultured in wheat straw

label_protocol: Fraction of mRNA-enriched RNA (200 ng) were amplified with the MessageAmp II-Bacteria RNA Amplification kit (Ambion) according to the modified protocol of Dugat-Bony et al. (2012) to incorporate aminoallyl UTP during a 14 h-in vitro transcription (Ambion). For each sample, 10 μg of amplified RNA (aRNA) were labelled with Cy3 or Cy5 cyanines (Pack Amersham CyDye Post-Labeling Reactive Dye, GE Healthcare), following the manufacturer’s recommendations. Labelled aRNA were finally purified with NucleoSpin RNA Clean-Up kit (Macherey-Nagel). Labelling density was acceptable when values were between 30 and 60.

growth_protocol: The strain F. succinogenes S85 was grown with 0.2 g of cellobiose (Sigma-Aldrich, Saint-Louis, MO, USA) under static conditions or 0.5 g of wheat straw under shaking conditions. The strain was subcultured 3 times on the same medium. Cultures were harvested at the end of the exponential growth after 6 h and 50 h respectively (Béra-Maillet et al., 2000; Nouaille et al., 2009).

extract_protocol: Total RNA from F. succinogenes S85 was extracted in duplicate from 10 ml of culture for both substrate conditions (cellobiose and wheat straw). RNA isolation was performed using Trizol reagent (Invitrogen) with slight modifications of the manufacturer’s instructions. Cultures were centrifuged 15 min at 12,000 g at +4°C. Then, 10 mL of Trizol were added to the pellets and the mix was vigorously vortexed. Cells were disrupted with ~100 mg of 0.1 mm zirconia beads (BioSpec Products) in a 2 ml-microtube using the FastPrep instrument (MP Biomedicals), set to 6.5 m/s, during 4 cycles of 30 sec intersecting with 5 min of incubation on ice. Following steps were those recommended by the Trizol protocol. Total RNA were submitted to mRNA enrichment using an in house-procedure based on rRNA subtractive hybridization principle as previously described (Comtet-Marre et al., 2017).

treatment_protocol: No treatment

tag: gut origin

value: Rumen


title: IFNg-IL13_C16-18_2


title: F_succingenes_Cellobiose

description: mRNA enriched RNA

source_name: Bacteria cultured in cellobiose


title: RNA_rumen_content

description: mRNA enriched RNA

hyb_protocol: RNA hybridization (5 μg) was performed at 65°C during 17 h following the Agilent protocol ‘ Two-Color Microarray-Based Gene Expression’ with few modifications for the use of a supplementary blocking agent (Kreablock, Kreatech Diagnostics, Amsterdam, Netherlands). Briefly, RNA fragmentation was performed at 60°C during 30 min in a mix composed of 12,5 μL of Kreablock buffer (Kreatech Diagnostics, Amsterdam, Netherlands), 6.5 μL of aRNA, 5μL of 10X Gene Expression Blocking Agent (Agilent, Santa Clara, CA, USA) and 1 μL of 25X fragmentation buffer (Agilent, Santa Clara, CA, USA). Next steps of hybridization and slide washing were according to Agilent protocol.

data_processing: Fluorescence intensities of oligonucleotide spots were extracted from the scanned images using the Feature Extraction software (V11.0, Agilent Technologies). Then data were processed with dedicated scripts based on C++ and Delphi languages. For each probe, median intensity value of the 3 replicates was conserved and used as the probe signal value. The SNR (Signal-to-Noise Ratio), similar to the detection threshold response (positive hybridization) and corresponding to the probe signal value divided by the local background intensity value, was calculated for each probe. For complex ecosystems the SNR threshold is usually set at lower values than for pure cultures (Dugat-Bony et al., 2012). For rumen RNA hybridizations the SNR threshold was set to 2 such that a positive response was considered when the signal intensity of a probe was 2 times superior to the signal of background and negative control probes (He and Zhou, 2008). Results for 25- and 54-mer probes were treated independently and for each probe type, a gene was considered as detected when 65% of probes were positive.  The SNR value of a detected gene was then calculated by the mean of the SNR of all 25- or 54-mer probes targeting this gene, meeting or not the defined SNR threshold.

organism: bovine gut metagenome

source_name: Cow Rumen content

growth_protocol: The rumen sample was obtained from a lactating dairy cow fed with a total mixed ration (forage:concentrate ratio 50:50, on a dry matter content) based on grass silage. In brief, the total mixed ration contained (g/kg dry matter) neutral detergent fiber (401), acid detergent fiber (228), and starch (120). Samples were taken before the morning feeding from five different sites in the rumen, composited, and mixed thoroughly to obtain a representative sample of rumen contents. For molecular analysis, rumen content was subsampled (50 g) and mixed with 100 mL of RNAlater (Thermo Fisher Scientific) to prevent RNA degradation. The mixture was maintained overnight at +4°C and then stored at -80°C until nucleic acid extraction. RNAseq data from this rumen sample have been deposited in the NCBI Sequence Read Archive under accession number SRP070140 (Comtet-Marre, 2017).

extract_protocol: Total RNA from rumen content was extracted in duplicate from 400 mg of centrifuged rumen content using Trizol as previously described  (Comtet-Marre et al., 2017). The integrity of RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chip (Agilent Technologies, Santa Clara, CA, USA) and quantity was assessed with the Nanodrop 1000 spectrophotometer (Thermo Fischer Scientific, Illkirch, France). Duplicates of total RNA were pooled and the resulting RNA solutions were stored at -80°C until further processing. Total RNA were submitted to mRNA enrichment using an in house-procedure based on rRNA subtractive hybridization principle as previously described (Comtet-Marre et al., 2017).


title: Control_Bio_Replicate 3


title: IFNg_C13-11_1


title: gDNA_Ralbus_20

description: gDNA

hyb_protocol: DNA hybridization (1 μg for each DNA) was performed at 65°C during 24 h following the Agilent protocol ‘Oligonucleotide Array-Based CGH for Genomic DNA Analysis’.

organism: Ruminococcus albus

source_name: Bacteria

label_protocol: Genomic DNAs from each bacterial strain (2 µg) were sheared in a 200 μL milliQ water volume by 10 sec of sonication (Vibra Cell VC300, Sonics & Materials). The length of sheared gDNA (range between 500 bp and 1500 bp) was checked by 1% agarose gel electrophoresis. Fragmented gDNA was labelled using the Bioprime Total Genomic Labelling kit (Invitrogen) and Alexa Fluor 3 or 5 dyes following the supplier’s instructions. A degree of labelling higher than 0.7 for the Alexa fluor 3 and 1.2 for the Alexa fluor 5 was considered as acceptable.

growth_protocol: Genomic DNA was extracted from 4 bacteria strains. Strains Fibrobacter succinogenes S85 (ATCC 19169), Ruminococcus albus 20 (ATCC 27211) and Bacteroides xylanisolvens XB1A (DSM 18836T) were grown 15 h under strictly anaerobic conditions (Hungate, 1950) in a complex medium containing 20% of clarified rumen fluid (Béra-Maillet et al., 2000) and 0.2 g of cellobiose (Sigma-Aldrich) as carbon source, at 39°C for the two first ones and 37°C for the third one. The strain Escherichia coli K12 (ATCC 10798) was cultivated 15 h at 37°C in Luria-Bertani medium under shaking and aerobic conditions. (

extract_protocol: Culture of bacterial strains (10 mL) were centrifuged 20 min at 10,000 g and bacterial pellets were washed 3 times with 2 mL of phosphate buffered saline (PBS). DNA extraction was performed using the EasyDNA kit (Invitrogen) following the manufacturer instructions slightly modified. Briefly, the bacterial pellet was incubated 5 min in 200 μL of PBS and 1 μL of protéinase K (20 mg/mL, Invitrogen). Then, bacteria were grinded 3 min with ~100 mg of 0.1 mm zirconia beads (BioSpec Products) using the model MM2000 BeadBeater instrument (Retsch). Concentration and quality of isolated gDNA were checked with the spectrophotometer Nanodrop 1000 (Thermo Fisher Scientific). Their integrity was verified by 1% agarose gel electrophoresis. gDNA were kept at -20°C.

tag: strain

value: Ruminococcus albus 20


title: IFNg_C13-11_2


title: IFNg_C13-11_3


title: gDNA_Bxylanisolvens_XB1A

description: gDNA

organism: Bacteroides xylanisolvens XB1A

value: Human colon


title: gDNA_Fsuccinogenes_S85

description: gDNA


title: PCR_product_GH5_Fsuccinogenes_S85

description: PCR product

hyb_protocol: DNA hybridization (50 ng for each PCR product) was performed at 65°C during 24 h following the Agilent protocol ‘Oligonucleotide Array-Based CGH for Genomic DNA Analysis’.

label_protocol: Each PCR products (2 µg) were labelled independently using the ULS aRNA Labelling kit (Kreatech Diagnostics) and Cy3 or Cy5 cyanines following the manufacturer’s recommendations. A degree of labelling between 1.0 and 2.5% was considered as acceptable.

growth_protocol: The 7 target genes PCR-amplified were beforhand cloned in plasmid as previously described (Rakotoarivonina et al., 2009; Mirande et al., 2010; Devillard et al., 2003) or in this work using PCRII-TOPO vector (Invitrogen). Escherichia coli (One Shot TOP10 Chemically Competent E. coli, Invitrogen) were transformed with recombinant plasmids. Recombinant cells were cultivated in LB medium with ampicillin (100 μg/mL) or kanamycin (50 µg/mL).

extract_protocol: Plasmids were extracted with the QIAprep MiniPrep kit (Qiagen) from 5 mL of a 15 h culture of E. coli. Inserts were sequenced to ensure that cloned DNA fragments had the same sequence than genes used for probe design. Cloned genes were then PCR amplified with the Pfx50 DNA Polymerase (Invitrogen). PCR products were gel purified with the QIAquick PCR purification kit (Qiagen).


title: PCR_product_GH9_Ralbus_20

description: PCR product


title: IFNg+IL13_C13-7_3


title: IFNg_C12-7_2


title: PCR_product_GH11_Ralbus_7

description: PCR product

value: Ruminococcus albus 7


title: IFNg-IL13_C12-17_2

value: IFN-g/ lost IL-13


title: gDNA_Ecoli_K12

description: gDNA

organism: Escherichia coli K-12


title: PCR_product_GH48_Ralbus_20

description: PCR product


title: IFNg-IL13_C12-17_1


title: IFNg-IL13_C12-17_4


title: PCR_product_GH9_Piromyces_sp_M4

description: PCR product

organism: Piromyces sp.

source_name: Fungi

value: Piromyces sp. M4


title: WT25 DMM 6 WK_mRNA

status: Public on Nov 30 2017

city: Melbourne

last: Bateman

address: Flemington Road

department: Skeletal Biology

country: Australia

institute: Murdoch Childrens Research Institute

description: Bilateral surgeries performed. Knees taken from the same mouse for both histology and expression profiling.

hyb_protocol: mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.

scan_protocol: The arrays were scanned on a G2565CA microarray scanner and the features were extracted using Agilent Feature Extraction 12.0.07 software

data_processing: The raw microarray data was processed in statistical language R, using the limma package (limma_3.20.9) and background corrected with Normexp, normalized within arrays with cyclic loess. This SCB mRNA array data was normalised with mRNA array data from synovial tissue from the same cohort of mice as part of a separate study (GSE99731). Only probes with 10% greater signal than the negative controls in at least 5 samples were maintained for differential expression analysis. Probes were summarised and the data was adjusted for multiple testing using Benjamini-Hochberg method to control for false discovery rate.

label: Cyanine 3-pCp

source_name: Subchondral bone

growth_protocol: Mice with DMM and sham surgery were co-housed 2-5 animals/30×20×18cm individually-ventilated-cage with filter lids, provided with sterilised bedding and environmental enrichment, maintained at 21-22°C with a 12-hour light/dark cycle, and received water and complete pelleted food ad libitum. Mice received no post-arthritis-induction medication and were allowed unrestricted cage exercise. Animals were sacrificed at 1 and 6 weeks after surgery.

extract_protocol: Mice were randomly allocated to groups/harvest time point prior to study commencement using their individual ID numbers. Animals were sacrificed at 1 and 6 weeks after surgery. For each animal, one joint was processed for histology whilst the other was used for microarray expression profiling/qPCR. Microarray experiments on SCB samples were performed on n = 4/group/time point with qPCR validation performed on a different cohort of 4 mice/group/time point. Joint dissection, laser micro-dissection and RNA extraction from mouse cartilage and SCB was performed in a similar fashion to previously described. Briefly, mice were sacrificed 1 and 6 weeks after surgery and the tibial epiphyses were isolated and placed in RNA Later (Life Technologies) containing 10% EDTA for at least 72 hrs at 4°C. After decalcification the samples were washed in DEPC-treated PBS, embedded in OCT and stored at -80°C. Serial 10 µm sagittal cryo-sections were fixed in ethanol and air-dried. Sections of the cartilage and underlying SCB of the medial tibial plateau were laser micro-dissected (Arcturus Bioscience) and collected. Total RNA was extracted from pooled laser micro-dissected sections from each individual mouse joint using TRIzol according to the manufacturer’s instructions

treatment_protocol: Post-traumatic OA was surgically induced in 10-12 week old male wild type C57BL6 mice by bilateral destabilization of the medial meniscus (DMM), as described previously. Briefly, the medial menisco-tibial ligament was exposed (by medial parapatellar arthrotomy and intrapatellar fat pad elevation, without tissue resection) and transected with curved dissecting forceps by one surgeon (CBL). Bilateral sham-operations were also performed, where the medial menisco-tibial ligament was visualised but not transected. All joints were flushed with sterile saline to remove any blood prior to separate closure of the joint capsule (simple continuous 8/0 polyglactin 910), subcutaneous tissue (mattress suture 8/0 polyglactin 910) and skin (cyanoacrylate).

value: Male

tag: tissue

value: subchondral bone

tag: time post-surgery (weeks)


title: IFNg_C12-7_1


title: IFNg+IL13_C13-7_2


title: WT21 DMM 6 WK_mRNA

label_protocol: mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.


title: WT12 SHAM 6 WK_mRNA


title: IFNg-IL13_C12-17_3


title: WT86 SHAM 1 WK_mRNA


title: IFNg_C12-7_3


title: PCR_product_GH10_Pmultivesiculatum

description: PCR product

organism: Polyplastron multivesiculatum

source_name: Protozoa


title: WT26 SHAM 6 WK_mRNA


title: IFNg+IL13_C13-7_1


title: PCR_product_GH10_Bxylanisolvens_XB1A

description: PCR product


title: IFNg_C12-7_4


title: WT22 SHAM 6 WK_mRNA


title: WT6 DMM 6 WK_mRNA


title: WT93 DMM 1 WK_mRNA


title: WT96 SHAM 1 WK_mRNA


title: WT5 DMM 6 WK_mRNA


title: MS_F6789_1

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

description: Gene expression in sample from F6789 strain, biological rep 1, at 45 g/L released CO2 in synthetic medium

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using the R 3.1.3 software and the limma package. Normalization was done by the quantile method considering all arrays.

organism: Saccharomyces cerevisiae

source_name: Strain F6789_45gCO2_SyntheticMedium

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: Standard fermentation was conducted using the synthetic fermentation medium SM425 (glucose + fructose, 50 ⁄ 50), buffered to pH 3.3 at 24°C in laboratory-scale fermenters. The population inoculated in every flask was 1.5*106 cell/ml from fresh pre-adapted yeast cultures. Secondary fermentation experiments (sparkling wines) were conducted in a synthetic base wine according to Marti-Raga et al. (2015) with some modifications. It contained 24 g/l of sucrose, ethanol 8% v/v, tartaric acid 4 g/l, L-citric acid 0.5 g/l, malic acid 0.5 g/l, sodium acetate 0.134 g/l, YNB 1.7 g/l, glycerol 4.0 g/l, 0.1% v/v of lipid factors (LF), 0.46 g/l of ammonium chloride and 13.09 ml of aminoacid mix. The ﬁnal pH was adjusted to 3.3. Yeasts were inoculated into adaptation medium at 106 cells/ml and incubated for 4 to 5 days at 28 °C at 150 rpm.

extract_protocol: Total RNA extraction from synthetic medium fermentation were performed with Trizol reagent (Gibco BRL, Life Technologies). Total RNA extraction from sparking wine fermentation were performed using MOBIO RNA Power Soil kit (MO BIO Laboratories, Inc.) according to the manufacturer’s instructions. In both cases, total RNAs were purified by isopropanol precipitation then using RNeasy kit (Qiagen).

treatment_protocol: Cells were sampled during the alcoholic fermentation (45 g of CO2 released). 10^9 cells were pelleted (3000 rpm, 2 min), washed with DEPC-treated water and freezed in methanol at -80°C.

tag: medium

value: Synthetic medium


title: WT77 DMM 1 WK_mRNA


title: SW_F6789Dflo_1

description: Gene expression in sample from F6789deltaFLO5 strain, biological rep 1, at 45 g/L released CO2 in sparking wine medium

source_name: Strain F6789Dflo_45gCO2_SparkingWine

value: F6789 delta FLO5

value: Sparking wine


title: WT10 SHAM 6 WK_mRNA


title: WT85 DMM 1 WK_mRNA


title: WT67 DMM 1 WK_mRNA


title: WT68 SHAM 1 WK_mRNA


title: WT66 SHAM 1 WK_mRNA


title: SW_F6789Dflo_2

description: Gene expression in sample from F6789deltaFLO5 strain, biological rep 2, at 45 g/L released CO2 in sparking wine medium


title: MS_F6789Dflo_1

description: Gene expression in sample from F6789deltaFLO5 strain, biological rep 1, at 45 g/L released CO2 in synthetic medium

source_name: Strain F6789Dflo_45gCO2_SyntheticMedium


title: MS_F6789Dflo_2

description: Gene expression in sample from F6789deltaFLO5 strain, biological rep 2, at 45 g/L released CO2 in synthetic medium


title: SW_F6789_1

description: Gene expression in sample from F6789 strain, biological rep 1, at 45 g/L released CO2 in sparking wine medium

source_name: Strain F6789_45gCO2_SparkingWine


title: MS_F6789_2

description: Gene expression in sample from F6789 strain, biological rep 2, at 45 g/L released CO2 in synthetic medium

source_name: Strain F6789_45gCO2_Synthetic medium