title: Expt 2 - D1 (IL3@10 ng/ml)

description: DM-48: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: OV202SH1_1

status: Public on Mar 20 2015

type: RNA

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

country: USA

institute: Mayo Clinic

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary OV202 cell line

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: cell type

value: ovarian carcinoma

tag: group


title: Expt 11 - D0

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

state: MD

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

description: DM-8: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

data_processing: Illumina Bead Studio was used for generating the data. Due to the way data was processed in the published description of these results (no global normalization), the matrix of results that is normally entered as normalized is not normalized but instead a replicate of the non-normalized data.

source_name: peripheral blood

growth_protocol: purified basophils were cultured in RPMI-1640 medium supplemented with 20 µg/ml gentamycin, 0.03% human serum albumin and glutamine

extract_protocol: mRNA was isolated by miRNEasy kit extractions and contained both mRNA and miRNA, RIN values > 6 (lower allowed because of presence of miRNA)

treatment_protocol: the title of each sample identifies the treatment; D0 = day 0, D1 = day 1, D3 = day 3; IL-3 = interleukin-3, anti-IgE Ab = a monoclonal 6061P (Hybridoma Labs, Baltimore, MD) anti-IgE antibody (where 0.5 µg/ml is considered optimal)

value: basophils (purified to average of 99%)

tag: treatment


title: OV202NTC_3

description: replicate 3

value: NTC


title: Expt 5 - D0

description: DM-49: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 2 - D1 (no IL3)

description: DM-47: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (no IL3)


title: OV202NTC_2

description: replicate 2


title: d6 PGCLC, rep1

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744101

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

organism: Mus musculus

source_name: primordial germ cell-like cells (PGCLCs) at day 6 after induction of EpiLCs by BMP4, BMP8a, SCF, EGF, and LIF

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: ES cells were maintained with 2i+LIF, feeder free condition.

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

treatment_protocol: EpiLCs were induced from the ES cells with activin and bFGF.  PGCLCs were induced from day 2 EpiLCs with BMP4, BMP8a, SCF, EGF, and LIF.  For detail,  please see Hayashi et al., Cell 2011.

tag: strain

tag: transgene

value: Blimp1-mVenus, stella-CFP

tag: Sex

value: male


title: d6 PGCLC, rep2

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744102


title: OV202NTC_1

description: replicate 1


title: Expt 1 - D1 (IL3@10 ng/ml)

description: DM-45: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: EpiLC, rep2

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744096

source_name: epiblast-like cells (EpiLCs) at day 2 after induction of ESCs by activin and bFGF


title: OV202SH2_3

description: replicate 3


title: Expt 5 - D3 (IL3@10 ng/ml)

description: DM-50: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: wt_4glu_3_wt_2ac_5csw

status: Public on Mar 19 2015

city: Bielefeld

first: Hironori

last: Taniguchi

department: Biology

country: Germany

institute: Bielefeld University

description: Phospahte starvation was induced in the exponential growth phase.

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with applified PCR fragments, hybridisation and stringent washing of the microarrays were performed as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 6000 laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing:
Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.
Described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

organism: Corynebacterium glutamicum ATCC 13032

source_name: 4% glucose as carbon sourse

label_protocol: Synthesis of fluorescently labelled cDNA was carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

extract_protocol: Preparation of total RNA was carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

treatment_protocol: C. glutamicum wild-type strain ATCC 13032 (WT)  was  inoculated from 5 ml LB medium overnight culture to an optical density at 600 nm (OD600) of 0.6 in 60 ml CGXII-medium with 0.03 g/l protocatechuic acid as iron chelator and 40 g/l glucose or 20 g/l sodium acetate as carbon and energy source. Cells were grown aerobically at 30°C on a rotary shaker (120 rpm) in 500 ml baffled shake flasks and harvested 14-18 hours after inoculation by centrifugation at 4°C, washed with CGXII without Pi and carbon sources, and inoculated in 60 ml CGXII medium with sufficient Pi (13 mM) to an optical density at 600 nm (OD600) of 0.6. These main cultures were cultivated until OD600 of around 4. The cells were harvested and washed with CGXII without Pi and carbon source, and resuspended in an equal volume of fresh CGXII medium that contained a limiting Pi concentration (0.065 mM). After incubation at 30°C for 90 in the Pi low or Pi free medium, cells were harvested and stored for RNA extraction.

tag: protocol

value: 90 min after phosphate starvation

source_name: 2% acetate as carbon sourse


title: Expt 1 - D1 (no IL3)

description: DM-44: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: wt_4glu_5_wt_2ac_3


title: OV202SH2_2

description: replicate 2


title: Expt 2 - D0

description: DM-46: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: EpiLC, rep1

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744095


title: Immature dendritic cell

city: Hangzhou City, Zhejiang Province

first: Liangjing

last: Zhou

address: no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province

department: Department of General Surgery

country: China

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

description:
iDC
comparison of iDC vs exo-DC

hyb_protocol: Prepare the hybridization solution with labeled microRNA target .Denature the hybridization solution at 95°C for 3 minutes,and then cool for 20 seconds on ice.Remove the hybridization solution from ice and keep it at room temperature.Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting.A small air bubble wil form,and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue,and cover the solution portals with adhesive tape.Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation.

scan_protocol: Remove the microarray from the clamp and place it horizontally. Cover the semiconductor microarray surface with the imaging solution.Using a fresh lifterslip cover it,taking care not to introduce air bubbles.Load the microarray into the scanner to scan.

data_processing: After normalizing with subtract background correction and quantile normalization method using R version 2.14.0, normalized spot intensities were transformed to gene expression log2 ratios.

source_name: dendritic cell

label_protocol: Total RNA was amplified and transcribed into fluorescent cRNA by Amino Allyl messageAmp II(Ambion, Life Technologies, Carlsbad, California, USA) according to the manufacturers’ recommended procedure.

growth_protocol: The CD14 positive monocyte fraction was cultured for up to 7 days in RPMI 1640 medium, containing 100 U/mL penicillin, 100 ug/ml streptomycin, interleukin-4 (40 ng/mL) and granulocyte–macrophage colony stimulating factor (100 ng/mL).

extract_protocol: Total RNA of cells was isolated and purified by miRNeasy Mini Kit (Qiagen, Maryland, USA), following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were quantified using a NanoDrop spectrophotometer (ND-1000 V3.5.2 software, USA).RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.

treatment_protocol: At 7th day, dendritic cells were stimulated by exosome  for 24 h (exo-iDC), and PBS was used as negative control (Immature dendritic cell,iDC)

tag: stimulation

value: treated with PBS at 7th day


title: Expt 1 - D0

description: DM-43:the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: 125AA-EL35_control-2010_30

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

hyb_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).

data_processing: Data were RMA normalized using R/Bioconductor.

organism: Vitis vinifera

source_name: berry

growth_protocol: Grape berries from Pinot noir (Vitis vinifera) grafted on rootstocks Richter 110 (V. rupestris x V. berlandieri) and Kober 125AA (V. riparia x V. berlandieri), were sampled from field-grown vines at two different developmental stages (E-L 35 and E-L 36) according to the modified Eichhorn and Lorenz developmental scale24, during two growing seasons (2009 and 2010). Vines were trained using a vertical shoot positioning system. The experimental vineyard belongs to the University of Geisenheim (49°59’N, 7°57’W, Germany). Twenty rows of Pinot noir were selected, with an average of 17 plants per row.

extract_protocol: Total RNA from berries of Pinot noir grafted onto 110R and 125AA was extracted as described by Reid et al., 2006 (Reid KE, Olsson N, Schlosser J, Peng F, Lund ST. An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biology 2006; 6: 27.). Seeds of each berry were removed before grinding in liquid nitrogen. Total RNA was subjected to DNA digestion with 5 units of RNase-free DNase I (Promega) for 1 h at 37°C. RNA integrity was measured at 260 nm with a micro-spectrophotometer (NanoDrop 200C, NanoDrop products, Wilmington, USA) and visualized by electrophoresis on 1.2% agarose gels. RNA quality was also confirmed using a lab-on-chip (2100 Bioanalyzer, Agilent Technologies, Santa Clara, USA).

treatment_protocol: Two water conditions were established for the vines grafted on the two rootstocks: control (C) and water stress treatment (S). To impose water stress, half the rows of the vineyard chosen were covered with a removable plastic film from flowering onwards, covering completely the width of the inter-row on both sides of the plants during rainy days. Water stress was applied to the upper part of the vineyard (slope with 6-7% of inclination) and the control was situated at the lower part.

tag: tissue

value: berry

tag: scion cultivar

value: pinot noir

tag: rootstock

tag: developmental stage

value: control

tag: year


title: OV202SH2_1

description: replicate 1


title: exosome-treated dendritic cell

description:
exo-DC
comparison of iDC vs exo-DC

value: treated with pancreatic cancer derived exosome at 7th day


title: ESC, rep1

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744093

source_name: embryonic stem cells (ESCs) cultured in 2iLIF condition


title: 110R-EL36_water_stress-2010_45

scan_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).

value: water stress


title: ESC, rep2

description:
cDNA, amplified with 22-cycle PCR from 5ng total RNA (equivalent to 500 cells)
obtained from GSM744094


title: 110R-EL36_control-2010_37

label_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).


title: 125AA-EL36_control-2010_40


title: 110R-EL35_control-2010_26


title: 110R-EL36_control-2010_38


title: 110R-EL35_water_stress-2010_32


title: 110R-EL36_water_stress-2010_43


title: 110R-EL35_water_stress-2010_33


title: 125AA-EL36_water_stress-2010_46


title: 125AA-EL36_control-2010_42


title: 125AA-EL35_water_stress-2010_36


title: 125AA-EL35_water_stress-2010_34


title: 110R-EL36_control-2010_39


title: 125AA-EL36_control-2010_41


title: 110R-EL35_control-2010_27


title: 125AA-EL36_water_stress-2010_47


title: 125AA-EL35_control-2010_28


title: 110R-EL35_control-2010_25


title: 125AA-EL35_water_stress-2009_35


title: 110R-EL35_control-2009_27


title: 125AA-EL35_water_stress-2010_35


title: 125AA-EL35_water_stress-2009_53


title: 125AA-EL35_control-2010_29


title: 110R-EL35_water_stress-2010_31


title: 125AA-EL36_water_stress-2010_48


title: 125AA-EL36_control-2009_17


title: 110R-EL35_water_stress-2009_33


title: 125AA-EL36_water_stress-2009_52


title: 125AA-EL36_water_stress-2009_23


title: 110R-EL36_water_stress-2009_20


title: 110R-EL36_control-2009_13ter


title: 110R-EL35_water_stress-2009_32


title: 110R-EL35_control-2009_26


title: 125AA-EL35_water_stress-2009_34


title: 110R-EL35_control-2009_25


title: 110R-EL35_water_stress-2009_31


title: 125AA-EL35_control-2009_30ter


title: 110R-EL36_control-2009_14


title: 110R-EL36_water_stress-2009_21


title: 110R-EL36_water_stress-2010_44


title: 125AA-EL35_control-2009_28


title: 125AA-EL36_water_stress-2009_22


title: 110R-EL36_water_stress-2009_19


title: 125AA-EL36_control-2009_18


title: 125AA-EL36_control-2009_16


title: KO3

city: Cambridge

first: Yohei

last: Kobayashi

state: MA

address: 52 Oxford Street

institute: Harvard University

description:
replicate 3
SAMPLE 5

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio.

source_name: Sorted PV-cells from cerebral cortex

label_protocol: RNA was amplified with the NuGEN Ovation PicoSL WTA System V2 kit, and biotinylated cRNA were prepared with the NuGEN Encore BiotinIL Module.

tag: genotype/variation

value: PV-GFP; Clock-/-

tag: age


title: KO1

description:
replicate 1
SAMPLE 4


title: WT3

description:
replicate 3
SAMPLE 3

value: PV-GFP; Clock+/+


title: HomoBapx1 Spleen Cells-Rep2

first: Thomas

last: Lufkin

state: NY

address: 8 Clarkson Avenue

institute: Clarkson University

hyb_protocol: Standard Illumina Hyb

scan_protocol: Standard Illumina Scan

data_processing: Illumina output was imported to Genome Studio and no normalization was done. Genespring(Gx 11.0) was used to do normalize the data using the following parameters- Normalization Algorithm-Scale. Scale to median of all samples. Threshold raw signal to 1.

source_name: HomoBapx1 Spleen Cells-Rep2

label_protocol: Biotinylated cRNA samples were prepared using the TargetAmp-Nano labelling kit for Illumina Arrays

extract_protocol: Total RNA was extracted from the sorted cells by Trizol followed by DNAse treatment and QIAGEN RNeasy kit  as per manufacturer's instruction

treatment_protocol: Spleen was dissected out of WT embryos where was Bapx1 gene was tagged with EGFP at the 3' UTR vis IRES and Homozygous embryos where Bapx1 was knocked out by EGFP and subjected to Fluoroscent activated cell sorting

value: spleen

value: Bapx1 HOMO


title: WT1

description:
replicate 1
SAMPLE 1


title: HomoBapx1 Spleen Cells-Rep4

source_name: HomoBapx1 Spleen Cells-Rep4


title: HomoBapx1 Vertebral Column Cells-Rep2

source_name: HomoBapx1 Vertebral Column Cells-Rep2

treatment_protocol: Vertebral column was dissected out of WT embryos where was Bapx1 gene was tagged with EGFP at the 3' UTR vis IRES and homozygous embryos where Bapx1 was knocked out by EGFP nadsubjected to Fluoroscent activated cell sorting

value: Verebral Column


title: HomoBapx1 Vertebral Column Cells-Rep4

source_name: HomoBapx1 Vertebral Column Cells-Rep4


title: WTBapx1 Vertebral Column Cells-Rep3

source_name: WTBapx1 Vertebral Column Cells-Rep3

value: Bapx1 WT


title: 125AA-EL35_control-2009_29


title: HomoBapx1 SpleenCells-Rep1

source_name: HomoBapx1 SpleenCells-Rep1


title: WTBapx1 Vertebral Column Cells-Rep2

source_name: WTBapx1 Vertebral Column Cells-Rep2


title: HomoBapx1 Spleen Cells-Rep3

source_name: HomoBapx1 Spleen Cells-Rep3


title: WTBapx1 SpleenCells-Rep3

source_name: WTBapx1 SpleenCells-Rep3


title: WTBapx1 Spleen Cells-Rep4

source_name: WTBapx1 Spleen Cells-Rep4


title: HomoBapx1 Vertebral Column Cells-Rep1

source_name: HomoBapx1 Vertebral Column Cells-Rep1


title: HomoBapx1 HL Cells-Rep1

source_name: HomoBapx1 HL Cells-Rep1

treatment_protocol: Hindlimb was dissected out of WT embryos where was Bapx1 gene was tagged with EGFP at the 3' UTR vis IRES and Homozygous embryos where Bapx1 was knocked out by EGFP and subjected to Fluoroscent activated cell sorting

value: hindlimb


title: HomoBapx1 HL Cells-Rep3

source_name: HomoBapx1 HL Cells-Rep3


title: WTBapx1 SpleenCells-Rep2

source_name: WTBapx1 SpleenCells-Rep2


title: HomoBapx1 HL Cells-Rep2

source_name: HomoBapx1 HL Cells-Rep2


title: WTBapx1 HL Cells-Rep4

source_name: WTBapx1 HL Cells-Rep4


title: WTBapx1 HL Cells-Rep2

source_name: WTBapx1 HL Cells-Rep2


title: HomoBapx1 HL Cells-Rep4

source_name: HomoBapx1 HL Cells-Rep4


title: WTBapx1 Vertebral Column Cells-Rep1

source_name: WTBapx1 Vertebral Column Cells-Rep1


title: WTBapx1 Vertebral Column Cells-Rep4

source_name: WTBapx1 Vertebral Column Cells-Rep4


title: WT2

description:
replicate 2
SAMPLE 2

source_name: Sorted PV-cells from cerebral cortex


title: HomoBapx1 Vertebral Column Cells-Rep3

source_name: HomoBapx1 Vertebral Column Cells-Rep3


title: WTBapx1 HL Cells-Rep1

source_name: WTBapx1 HL Cells-Rep1


title: HomoBapx1 gut Cells-Rep2

source_name: HomoBapx1 gut Cells-Rep2

treatment_protocol: Gut was dissected out of WT embryos where was Bapx1 gene was tagged with EGFP at the 3' UTR vis IRES and Homozygous embryos where Bapx1 was knocked out by EGFP and subjected to Fluoroscent activated cell sorting

value: gut


title: WTBapx1 gut Cells-Rep3

source_name: WTBapx1 gut Cells-Rep3


title: HomoBapx1 gut Cells-Rep3

source_name: HomoBapx1 gut Cells-Rep3


title: WTBapx1 gut Cells-Rep2

source_name: WTBapx1 gut Cells-Rep2


title: WTBapx1 Spleen Cells-Rep1

source_name: WTBapx1 Spleen Cells-Rep1


title: WTBapx1 HL Cells-Rep3

source_name: WTBapx1 HL Cells-Rep3


title: WTBapx1 gut Cells-Rep4

source_name: WTBapx1 gut Cells-Rep4


title: HomoBapx1 gut Cells-Rep4

source_name: HomoBapx1 gut Cells-Rep4


title: HomoBapx1 gut Cells-Rep1

source_name: HomoBapx1 gut Cells-Rep1


title: WTBapx1 gut Cells-Rep1

source_name: WTBapx1 gut Cells-Rep1


title: HomoBapx1 FL Cells-Rep1

source_name: HomoBapx1 FL Cells-Rep1

treatment_protocol: forelimb was dissected out of WT embryos where was Bapx1 gene was tagged with EGFP at the 3' UTR vis IRES and Homozygous embryos where Bapx1 was knocked out by EGFP and subjected to Fluoroscent activated cell sorting

value: forelimb


title: HomoBapx1 FL Cells-Rep4

source_name: HomoBapx1 FL Cells-Rep4


title: WTBapx1 FL Cells-Rep2

source_name: WTBapx1 FL Cells-Rep2


title: HomoBapx1 FL Cells-Rep3

source_name: HomoBapx1 FL Cells-Rep3


title: WTBapx1 FL Cells-Rep1

source_name: WTBapx1 FL Cells-Rep1


title: 110R-EL36_control-2009_15

source_name: berry


title: HomoBapx1 FL Cells-Rep2

source_name: HomoBapx1 FL Cells-Rep2


title: WTBapx1 FL Cells-Rep3

source_name: WTBapx1 FL Cells-Rep3


title: WTBapx1 FL Cells-Rep4

source_name: WTBapx1 FL Cells-Rep4


title: MEF_Rep1.

city: Seoul

first: Hyun Woo

last: Choi

country: South Korea

institute: Konkuk University

description: Mouse embryonic fibroblast

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref-8 expression v.2 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using fold-change and LPE (Local Pooled Error) test. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: MEF

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: The established ESCs in conventional ESC medium were transferred in conventional ESC medium supplemented with LIF or serum free N2B27 medium supplemented with LIF and 2i inhibitors. The serum free N2B27 prepared as described (Ying and smith, 2003)

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: 2i inhibitor - CHIR99021(3 μM) and PD0325901 (1 μM)

value: MEF


title: EpiSCs_Rep2.

description: EpiSCs were generated from E6.6 epiblasts

source_name: EpiSCs

value: EpiSCs


title: O4-DE-GFP_ESCs_serum+LIF_Rep2.

description: Embryonic stem cells from O5-DE-GFP blastocyst

value: ESCs


title: MEF_Rep2.

description: Mouse embryonic fibroblast


title: O4-DE-GFP/O4-PE-RFP_ESCs_N2B27+LIF+2i_GFP+RFP-_Rep1.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct8 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.


title: O4-DE-GFP_ESCs_serum+LIF_Rep1.

description: Embryonic stem cells from O4-DE-GFP blastocyst


title: EpiSCs_Rep1.

description: EpiSCs were generated from E6.5 epiblasts


title: serum sample

type: other

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description: molecule: Viral DNA/RNA

hyb_protocol: Hybridization was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 8 µg of labelled DNA was used for hybridization. Hybridization was performed in a NimbleGen Hybridization system using the NimbleGen Hybridization kit (Roche NimbleGen).

scan_protocol: Microarrays were scanned in-house at SSI, Denmark using a MS 200 Scanner (Roche, Nimblegen)

data_processing:
Data was analyzed using the NimbleScan software and the in-house SSI data analysis method described in Rosenstierne et al., 2014 and Erlandsson et al., 2011. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Virus were classified as detected if the mean intensity exceeded a threshold equal to the 95th percentile of intensities for negative control probes.
Nimblegen Software was used to calculate the avarage signal intensities for each classified virus. Data is not normalised since the SSI data analysis method (Rosenstierne et al., 2014) uses the avarage signal intensity above the 95% percentile of negative control probes to define a positive signal.

molecule: other

source_name: Human Pegivirus (Hepatitis_GB_virus_C)

label_protocol: Labelling was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 1 µg of heat-denatured WTA-amplified sample was labelled using nick translation with Cy3- labeled random nonamer primers and Klenow fragment (exo-) (NEB) at 37 ºC for 2 hours. Labelled DNA was iso-propanol precipitated and the pellet washed, dried, reconstituted and quantitated.

extract_protocol: Two-hundred and thirty microliters of sample was centrifuged at 17,000 g for 10 minutes. The supernatant was filtered through a 0.22 µm Ultrafree MC spin filter (Costar) at 2000 g for 2 minutes and DNase treated (5 U DNaseI (Invitrogen or New England Biolabs) for 1½ hours at room temperature (CSF sample was considered free of genomic DNA and hence not DNAse treated). The viral nucleic acid (NA) was extracted using the PureLink Viral RNA/DNA kit (Invitrogen), without the addition of carrier RNA. The extracted viral NA was eluted with 30 µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. To be able to amplify both DNA virus and RNA virus samples with the same protocol, we used the described Whole Transcriptome Amplification (WTA) method (Berthet et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Molecular Biology 2008, 9:77) by using the QuantiTect WTA kit (Qiagen) according to manufacturer’s protocol, except for the reverse transcription step that was replaced by the Superscript III Reverse Transcription kit (Invitrogen) combined with 5´-phosphorylated random hexamers (P-N6)(Eurofines MWG Operon)(Rosenstierne et al., 2014). The WTA protocol includes 3 sequential reactions: firstly a reverse transcription reaction to generate cDNA, secondly a ligation of generated cDNA into larger transcriptomes and thirdly a Repli-g amplification of the generated transcriptomes. Neither of the two first reactions (cDNA synthesis and ligation) had any adverse effects when performed on a DNA-virus. Briefly, 11 µl of extracted viral NA was put into a 20 µl RT reaction and incubated at 42 ºC for 1 hour. The Superscript enzyme was inactivated at 95 ºC for 5 minutes, 10 µl of the cDNA reaction was added to 10 µl of ligation mix and incubated at 22 ºC for 2 hours. Thirty microliters of amplification mix containing Phi29 polymerase and random primers was then added and amplification performed at 30 ºC for 2-8 hours. The reaction was terminated by incubation at 95 ºC for 5 minutes. Amplified material was purified using QIAamp DNA mini kit (Qiagen) using a modified protocol (www.qiagen.com), and checked for purity and concentration using a NanoDrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis. The DNA was then stored at -80 ºC or immediately used for microarray analysis.

tag: isolation source

value: serum


title: O4-DE-GFP/O4-PE-RFP_ESCs_serum+LIF_GFP+RFP-_Rep2.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct7 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.


title: O4-DE-GFP/O4-PE-RFP_EpiLC_GFP-RFP+_Rep1.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oc10 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.

value: EpiLCs


title: O4-DE-GFP/O4-PE-RFP_ESCs_N2B27+LIF+2i_GFP+RFP-_Rep2.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct9 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.


title: spinal_sample

description: molecule: Viral DNA/RNA

value: cerebrospinal fluid


title: O4-DE-GFP/O4-PE-RFP_EpiLC_GFP-RFP+_Rep2.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oc11 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.


title: O4-DE-GFP/O4-PE-RFP_ESCs_serum+LIF_GFP+RFP+_Rep2.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct5 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.


title: HCC827 8day Erlotinib replicate 3

first: Joshua

middle: M

last: Korn

address: 250 Mass Ave

institute: Novartis

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: HCC827 cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: PC9 and HCC827 cells were cultured in RPMI media supplemented with 10% FBS.

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: For DMSO treatment 1.5 million cells were plated in 10cm dishes. DMSO was added the next day and cells were retreated with fresh media and DMSO after 4 days. For erlotinib treatment 8 million cells were plated into two 150cm-flasks. 2uM erlotinib was added the next day and cells were retreated with fresh media and 2uM erlotinib after 4 days. Cells were harvested after 8 days of treatment with DMSO or erlotinib.

value: lung

tag: cell line

tag: agent

value: Erlotinib


title: HCC827 8day Erlotinib replicate 1


title: HCC827 8day Erlotinib replicate 2


title: PC-9 8day Erlotinib replicate 3

source_name: PC9 cells


title: O4-DE-GFP/O4-PE-RFP_ESCs_serum+LIF_GFP+RFP-_Rep1.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct6 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.

tag: cell type


title: Mut, PEI Treated, biological rep2 Mut.PEI.2_2

city: Charlotte

first: Qi Long

last: Lu

state: North Carolina

address: 1000 Blythe Blvd

department: Neurology

institute: Carolinas HealthCare System

hyb_protocol: Hybridization, washing, staining and scanning was performed using Affymetrix GeneAtlas® personal microarray system instruments.

scan_protocol: GeneChips were scanned using Affymetrix GeneAtlas® personal microarray system instruments.

data_processing: .CEL files containing raw, probe-level signal intensities were analyzed using Partek Genomics Suite version 6.6.12.0713 (Partek, St. Louis, MO, USA). Robust multichip averaging (RMA) was used for background correction, quantile normalization and probeset summarization with median polish (Bolstad et al., 2003). Statistical difference was calculated by two-way ANOVA analysis with false discovery rate (FDR).

source_name: tibialis anterior muscle

label_protocol: RNA samples were reverse transcribed, amplified and labeled using 3’ IVT Express Kit (Affymetrix Inc.), and the resultant labeled cRNA was purified and fragmented as per vendor’s instructions.

extract_protocol: Trizol extracted total RNA from TA muscles, RNA integrity assessed using Agilent 2100 Bioanalyzer, RNA integrity number (RIN) >7 were considered acceptable for use.

treatment_protocol: Notexin (NTX; 40μl at 5μg/ml; Latoxan, Valence, France) and polyethyleminine (PEI; 25k; 40ul at 0.5ug/μl; Sigma, St. Louis,MO, USA) were injected into the tibialis anterior (TA) muscle of treated mice.

value: tibialis anterior

tag: treatment

value: PEI

tag: time

value: 2 d


title: Mut, NTX Treated, biological rep3 Mut.NTX.14_3

tag: strain

value: NTX


title: Mut, PEI Treated, biological rep3 Mut.PEI.2_3


title: Mut, NTX Treated, biological rep4 Mut.NTX.2_4


title: HCC827 8day DMSO replicate 1

value: DMSO


title: PC-9 8day Erlotinib replicate 1


title: Mut, PEI Treated, biological rep1 Mut.PEI.2_1


title: PC-9 8day DMSO replicate 2


title: Mut, PEI Treated, biological rep4 Mut.PEI.2_4


title: PC-9 8day DMSO replicate 1


title: HCC827 8day DMSO replicate 3


title: Mut, NTX Treated, biological rep2 Mut.NTX.14_2


title: HCC827 8day DMSO replicate 2


title: PC-9 8day DMSO replicate 3


title: Mut, NTX Treated, biological rep1 Mut.NTX.14_1


title: U2OS cell line 2.5 Gy irradiated post 4hr

city: Neuherberg

first: Valerie

middle: B.

last: O'Leary

state: Bavaria

address: Ingolstädter Landstrasse 1

department: Institute of Radiation Biology

institute: Helmholtz Zentrum Munich

description: lncRNA expression after 4hr in 2.5Gy irradiated tissue culture cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C 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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cultured cells, 4hr, 2.5Gy, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: U2OS (American Type Culture Collection (ATCC)) were grown in Dulbecco modified eagle medium (DMEM; 4.5g/L D-glucose, L-glutamine and sodium pyruvate additive), fetal bovine serum (FBS) (10%; Life Technologies), penicillin and streptomycin (1%; Sigma). T47D (ATCC) were cultured as previously described (Falkenberg et al., 2013). HUVEC were propagated in Medium 200 (Cascade Biologics, cat. # M-200-500) supplemented with 1x LSGS (Cascade Biologics, cat. # S-000-10).

extract_protocol: Total RNA was isolated from cell lines using a mirVanaTM miRNA isolation kit (Ambion RNA Life Technologies, cat. # AM1560).

treatment_protocol: Cell lines were grown to 80% confluence and exposed to  2.5 Gy irradiation using a closed HWM-D 2000 Cesium137 source (Wälischmiller Engineering GmbH, Markdorf, DE; 10cm height, 33cm diameter) at a dose rate of 0.0082Gy/sec. Sham irradiation of controls involved only transport to the irradiation facility.

value: osteosarcoma


title: Mut, Untreated, biological rep4 Mut.Untr_1

value: untreated


title: U2OS cell line non irradiated (sham irradiated) post 4hr

description: lncRNA expression after 4hr in 0Gy irradiated tissue culture cells

source_name: cultured cells, 4hr, 0Gy, replicate 1


title: T47D cell line non irradiated (sham irradiated) post 4hr

value: ductal breast epithelial tumor


title: HUVEC cell line 2.5 Gy irradiated post 4hr

value: HUVEC (umbilical vein endothelial)


title: Mut, NTX Treated, biological rep1 Mut.NTX.2_1


title: T47D cell line 2.5 Gy irradiated post 4hr


title: HUVEC non irradiated (sham irradiated) post 4hr


title: Mut, NTX Treated, biological rep2 Mut.NTX.2_2


title: Mut, NTX Treated, biological rep1 Mut.NTX.4_1

value: 4 d


title: Mut, NTX Treated, biological rep3 Mut.NTX.4_3


title: WT, NTX Treated, biological rep3 C57.NTX_3


title: WT, NTX Treated, biological rep1 C57.NTX_1


title: Mut, Untreated, biological rep3 Mut.Untr_3


title: Mut, Untreated, biological rep1 Mut.Untr_1


title: Mut, NTX Treated, biological rep2 Mut.NTX.4_2


title: Homo Sox9 Vertebral Column Cells-Rep2

data_processing: Illumina output was imported to Genome Studio and no normalization was done. Genespring was used to do normalize the data using the following parameters- Normalization Algorithm-Scale. Scale to median of all samples. Threshold raw signal to 1.

source_name: E12.5 Verebral Column

treatment_protocol: Vertebral column was dissected out of WT embryos where Sox9 gene was tagged with EGFP at the 3' UTR vis IRES and homozygous embryos where Sox9 was knocked out by EGFP and subjected to Fluoroscent activated cell sorting

value: Skeletal

value: Sox9 HOMO


title: O4-DE-GFP/O4-PE-RFP_ESCs_serum+LIF_GFP+RFP+_Rep1.

description: To generate Oct4-ΔDE-RFP transgene, tdTomato (red fluorescent protein, RFP) gene was inserted into Genomic Oct4 Fragments of 6 kb in length, which lack DE. Oct4-ΔDE-RFP transgene express tdTomato transgene under the control of Oct4 PE and proximal promoter.  Oct4-ΔDE-RFP (O4-PE-RFP) founder transgenic mice were generated and was crossed with O4-DE-GFP mouse. ESCs were established from O4-DE-GFP/O4-PE-RFP blastocyst.

value: ESCs


title: WT, Untreated, biological rep3 C57.Untr_3


title: Mut, Untreated, biological rep2 Mut.Untr_2


title: WT, Untreated, biological rep2 C57.Untr_2


title: WT, NTX Treated, biological rep2 C57.NTX_2


title: Homo Sox9 Vertebral Column Cells-Rep1


title: Homo Sox9 Vertebral Column Cells-Rep4


title: WT Sox9 Vertebral Column Cells-Rep4

value: Sox9 WT


title: WT Sox9 Vertebral Column Cells-Rep3


title: WT Sox9 Vertebral Column Cells-Rep2


title: WT Sox9 Vertebral Column Cells-Rep1


title: WT, Untreated, biological rep1 C57.Untr_1


title: Homo Sox9 Vertebral Column Cells-Rep3


title: TMD8_ITF-A_exp1

status: Public on Mar 18 2015

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan Illumina HiScan

data_processing:
The data were normalised using quantile method
The data were normalised using quantile method

source_name: TMD8 cell lines treated with  ITF-A

label_protocol:
Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays
Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol:
in vitro
in vitro

extract_protocol:
RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).
RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol:
treatment with ITF-A or ITF-B, a HDAC inhibitor.
treatment with OTX015, a BET Bromodomain inhibitor.

value: ITF-A


title: DOHH2_NT-ITF-B_exp2

source_name: DOHH2 cell lines treated with DMSO


title: ERA022_F_Eosinophilic

type: genomic

city: Callaghan

first: Katherine

last: Baines

state: NSW

address: University drive

country: Australia

institute: The University of Newcastle

description: Asthma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 (for data extraction) Bioconductor packages in the R software platform (www.r-project.org) were used for data analysis. The non_normalized.txt contains unmethylated and methylated signal intensities.

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from samples using the All Prep DNA/RNA/Protein kit, following the manufacturer’s protocol (Qiagen, cat# 8004)

tag: gender

value: female

tag: subject group

value: asthma patient

tag: inflammatory phenotypes of asthma

value: Eosinophilic

value: Blood monocytes


title: DOHH2_ITF-A_exp2

source_name: DOHH2 cell lines treated with ITF-A


title: DOHH2_ITF-B_exp1

source_name: DOHH2 cell lines treated with ITF-B

value: ITF-B


title: Mut, NTX Treated, biological rep3 Mut.NTX.2_3

tag: tissue

value: tibialis anterior

value: NTX

value: 2 d


title: ERA016_F_Eosinophilic

description: Asthma


title: TMD8_NT-ITF-A_exp1

source_name: TMD8 cell lines treated with DMSO

value: DMSO


title: ERA034_F_Eosinophilic

description: Asthma


title: TNT064_F_Eosinophilic

description: Asthma


title: ERA033_M_Paucigranulocytic

description: Asthma

value: male

value: Paucigranulocytic


title: TNT054_M_Eosinophilic

description: Asthma


title: DOHH2_NT-ITF-B_exp1


title: TMD8_ITF-B_exp1

source_name: TMD8 cell lines treated with ITF-B


title: ERA009_F_Neutrophilic

description: Asthma

value: Neutrophilic


title: ERA103_F_Healthy

description: Control

value: healthy control


title: DOHH2_NT-ITF-A_exp2


title: ERA025_F_Paucigranulocytic

description: Asthma


title: ERA008_F_Paucigranulocytic

description: Asthma


title: TMD8_NT-ITF-B_exp1


title: DOHH2_NT-ITF-A_exp1


title: ERA038_M_Paucigranulocytic

description: Asthma


title: ERA003_F_Eosinophilic

description: Asthma


title: DOHH2_ITF-A_exp3


title: TNT055_F_Paucigranulocytic

description: Asthma


title: ERA109_M_Healthy

description: Control


title: DOHH2_ITF-A_exp1


title: DOHH2_ITF-B_exp2


title: TMD8_NT-ITF-B_exp3


title: TNT061_F_Paucigranulocytic

description: Asthma


title: DOHH2_NT-ITF-A_exp3


title: ERA107_M_Healthy

description: Control


title: TMD8_ITF-B_exp2


title: TNT059_M_Eosinophilic

description: Asthma


title: PC-9 8day Erlotinib replicate 2

value: lung

value: Erlotinib


title: TMD8_ITF-A_exp3

source_name: TMD8 cell lines treated with ITF-A


title: TMD8_ITF-B_exp3

source_name: TMD8 cell lines treated with  ITF-B


title: TNT056_F_Eosinophilic

description: Asthma


title: TMD8_NT-ITF-A_exp3


title: DOHH2_ITF-B_exp3


title: ERA030_F_Neutrophilic

description: Asthma


title: WSUDLCL2

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method

source_name: WSUDLCL2 cell line not treated

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with OTX015, a BET Bromodomain inhibitor.


title: TMD8_ITF-A_exp2


title: VAL

source_name: VAL cell line not treated

value: VAL


title: ERA028_M_Paucigranulocytic

description: Asthma


title: DOHH2_NT-ITF-B_exp3


title: ERA108_M_Healthy

description: Control


title: TNT050_F_Paucigranulocytic

description: Asthma


title: TMD8_NT-ITF-A_exp2


title: TNT049_M_Eosinophilic

description: Asthma


title: OCI-Ly8

source_name: OCI-Ly8 cell line not treated


title: ERA005_F_Paucigranulocytic

description: Asthma


title: OCI-Ly1

source_name: OCI-Ly1 cell line not treated


title: HBL-1

source_name: HBL-1 cell line not treated


title: RIVA

source_name: RIVA cell line not treated

value: RIVA


title: ERA032_M_Neutrophilic

description: Asthma


title: RCK8

source_name: RCK8 cell line not treated


title: OCI-Ly7

source_name: OCI-Ly7 cell line not treated


title: ERA036_F_Paucigranulocytic

description: Asthma

value: female


title: U-2932

source_name: U-2932 cell line not treated


title: ERA026_M_Paucigranulocytic

description: Asthma

value: asthma patient


title: SU-DHL-7

source_name: SU-DHL-7 cell line not treated


title: ERA012_F_Eosinophilic

description: Asthma

value: Eosinophilic


title: SU-DHL-6

source_name: SU-DHL-6 cell line not treated


title: ERA031_F_Paucigranulocytic

description: Asthma

value: Blood monocytes


title: ERA102_F_Healthy

description: Control


title: TMD8

source_name: TMD8 cell line not treated


title: TNT058_M_Eosinophilic

description: Asthma


title: TMD8 _NT-ITF-B_exp2


title: ERA043_F_Neutrophilic

description: Asthma


title: SU-DHL-2

source_name: SU-DHL-2 cell line not treated


title: SU-DHL-4

source_name: SU-DHL-4 cell line not treated


title: SU-DHL-5

source_name: SU-DHL-5 cell line not treated


title: ERA037_M_Neutrophilic

description: Asthma


title: OCI-Ly3

source_name: OCI-Ly3 cell line not treated


title: OCI-Ly2

source_name: OCI-Ly2 cell line not treated


title: ERA100_M_Healthy

description: Control


title: ERA027_F_Eosinophilic

description: Asthma


title: OCI-Ly19

source_name: OCI-Ly19 cell line not treated


title: OCI-Ly10

source_name: OCI-Ly10 cell line not treated


title: ERA040_F_Eosinophilic

description: Asthma


title: SU-DHL-10

source_name: SU-DHL-10 cell line not treated


title: DoHH2

source_name: DoHH2 cell line not treated


title: SUDHL6-OTX015-12h-exp3

source_name: SUDHL6 cell lines treated with OTX015


title: ERA017_M_Paucigranulocytic

description: Asthma


title: SUDHL6-NT-exp3

source_name: SUDHL6 cell line not treated


title: SUDHL6-OTX015-1h-exp3


title: TNT067_M_Eosinophilic

description: Asthma


title: ERA101_F_Healthy

description: Control


title: SUDHL6-DMSO-12h-exp3

source_name: SUDHL6 cell lines treated with DMSO


title: SUDHL6-DMSO-2h-exp3


title: SUDHL6-OTX015-2h-exp3


title: SUDHL6-DMSO-1h-exp2


title: ERA039_M_Neutrophilic

description: Asthma


title: Karpas-422

source_name: Karpas-422 cell line not treated


title: ERA105_F_Healthy

description: Control


title: SUDHL6-DMSO-1h-exp3


title: SUDHL6-DMSO-2h-exp1


title: TNT046_F_Paucigranulocytic

description: Asthma


title: SUDHL6-DMSO-12h-exp2


title: TNT065_F_Paucigranulocytic

description: Asthma


title: SUDHL6-OTX015-12h-exp2


title: ERA035_F_Eosinophilic

description: Asthma


title: SUDHL6-OTX015-1h-exp1


title: SUDHL6-OTX015-2h-exp2


title: TNT066_F_Paucigranulocytic

description: Asthma


title: SUDHL6-OTX015-1h-exp2


title: SUDHL6-DMSO-1h-exp1


title: SUDHL6-NT-exp2


title: SUDHL6-OTX015-12h-exp1


title: SUDHL6-OTX015-2h-exp1


title: ERA014_F_Paucigranulocytic

description: Asthma


title: TNT045_M_Eosinophilic

description: Asthma


title: SUDHL2-DMSO-1h-exp3

source_name: SUDHL2 cell lines treated with DMSO


title: SUDHL2-DMSO-12h-exp3


title: ERA106_F_Healthy

description: Control


title: SUDHL6-DMSO-12h-exp1


title: SUDHL6-NT-exp1


title: SUDHL2-OTX015-1h-exp3

source_name: SUDHL2 cell lines treated with OTX015


title: ERA041_F_Eosinophilic

description: Asthma


title: SUDHL2-DMSO-2h-exp2


title: TNT048_M_Paucigranulocytic

description: Asthma


title: SUDHL2-OTX015-2h-exp3


title: SUDHL2-DMSO-2h-exp3


title: TNT051_M_Paucigranulocytic

description: Asthma


title: SUDHL2-NT-exp2

source_name: SUDHL2 cell line not treated


title: ERA044_F_Neutrophilic

description: Asthma


title: ERA019_F_Paucigranulocytic

description: Asthma


title: ERA042_M_Neutrophilic

description: Asthma


title: ERA024_F_Paucigranulocytic

description: Asthma


title: ERA029_M_Eosinophilic

description: Asthma


title: SUDHL2-DMSO-1h-exp2


title: SUDHL2-DMSO-12h-exp2


title: SUDHL2-OTX015-12h-exp3


title: SUDHL2-DMS- 2h-exp1


title: SUDHL2-OTX015-1h-exp2


title: SUDHL2-NT-exp3


title: SUDHL2-OTX015-12h-exp2


title: SUDHL2-DMSO-12h-exp1


title: SUDHL2-OTX015-12h-exp1


title: SUDHL2-NT-exp1


title: TNT062_F_Paucigranulocytic

description: Asthma


title: SUDHL2-OTX015-2h-exp2


title: ERA020_M_Neutrophilic

description: Asthma


title: ERA004_F_Eosinophilic

description: Asthma


title: SUDHL2-OTX015-1h-exp1


title: DOHH2-ST-7612-2

data_processing:
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)
The data were normalised using quantile method

source_name: DOHH2 cell lines treated with ST7612AA1

treatment_protocol: treatment with pan-histone deacetylase inhibitor (HDACi), a thioacetate-ω (γ-lactam amide) derivative.

value: lymphoma cell line

tag: treated with


title: DOHH2-ST-7612-1


title: DOHH2-ST-7612-3


title: ERA002_M_Eosinophilic

description: Asthma


title: ERA001_M_Eosinophilic

description: Asthma


title: DOHH2-DMSO-1

source_name: DOHH2 cell lines treated with DMSO


title: Replicate 2 - timepoint 3 (9h)

city: Newark

first: Stefan

middle: Marcus

last: Gaida

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description:
1 ml cell pellet
R2-3

hyb_protocol: 250 ng of each labeled cDNA (cy3 & cy5) were mixed with 10X Blocking Agent and 2X Hybridization Buffer HI-RPM (Gene Expression Hybridization Kit, Agilent) and loaded in a clean Agilent Gasket Slide before the microarray was added. The assembled chambers were incubated at 65°C for 17 hours in a rotator equipped oven. After hybridization, slides were washed sequential in Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2, Acetonitrile and finally with Stabilization and Drying Solution.

scan_protocol: Scanned on an Agilent G2505B scanner.Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing: Background subtractions and normalization of extracted data were performed through R using the Bioconductor package as described (Yang, Y.H. et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucleic Acid Res 30, e15, 2002; Smyth, G.K. in Bioinformatics and Computational Biology Solutions using R and Bioconductor. 397-420, Springer, New York, 2005).

organism: Escherichia coli

source_name: pControl_stationary growth phase_1 ml cell pellet

label_protocol: 25ug of total RNA were primed with 3 µl of random hexamer primers [p(dN)6; 5 mg/ml] (Roche Molecular Biochemicals, Indianapolis, IN) at 70°C for 10min, then reversed transcribed at 50°C overnight in the presence of 200U SuperScript III RTase (Invitrogen), and 360 µM aminoallyl labeling mix (dATP, dCTP, dGTP, dTTP, aa-dUTP) containing a 2:3 aa-dUTP:dTTP ratio. Leftover RNA was hydrolyzed with NaOH and unused dNTP’s removed through washing using Microcon column (Millipore, Billerica, MA). The cleaned-up cDNA was than labeled using Cy3 and Cy5 dyes (Amersham CyDye Mono-Reactive Dye, GE Healthcare, Pittsburgh, PA) following the manufactures recommendations and leftover dye removed by using a QIAquick PCR purification kit (Qiagen).

growth_protocol: Cultures of both strains were started with a 2% overnight inoculum in LB media containing 35ug/ml chloramphenicol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufactures recommendations.

treatment_protocol: The optical density was measured every 30 min and expression of the heterologous sigma factor was induced with 1mM IPTG at an optical density of 0.1. Samples for RNA extractions (1ml) were taken after 4.5, 6 and 9 hours after induction. Cell pellets were stored at -80°C until total RNA extraction was performed.

tag: plasmid

value: pControl

tag: time point

value: 9 hrs after induction

tag: growth phase

value: stationary growth phase

source_name: pLPLσ_stationary growth phase_1 ml cell pellet

value: pLPLσ


title: 48h_miR mimic-transfected LNCaP versus control LNCaP 3

city: Lyon Cedex 07

first: Nathalie

last: ALLIOLI

address: 46 Allée d'Italie

department: Institut de Génomique Fonctionnelle de Lyon (IGFL)

country: France

institute: Ecole Normale Supérieure de Lyon (ENS)

description:
US45103047_252665217420_S01_GE2_107_Sep09_1_3
Dual swap 48h-1

hyb_protocol: 1 µg of Cy3/Cy5 dye-labelled aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µL containing 2x Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µL of 2x Agilent hybridization buffer was added to the final mixture. Combinated Cy3/Cy5 dye-labelled aRNA were hybridized competitively to Agilent Whole Human Genome 4x44k V2 oligonucleotides microarray slides for 18 h at 62 °C in hybridization buffer (5185-5973, Agilent) and under an Agilent Gasket slide coverslip (Agilent hybridization chamber, G2534A, Agilent) in a rotative Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using two color scan setting (for both Cy3 and Cy5 channels) for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters. Data files (txt format) were generated. Data were normalized using R and limma library. Briefly, background was subtracted using the correction Half with an offset=100. Then Loess normalization and between array normalization with quantile were performed.

source_name: 48h miR mimic-transfected LNCaP

label_protocol: 1 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine Cy3 or Cy5 dyes. Fluorescent probes were purified using the RNeasy mini kit (Qiagen). Dye incorporation and aRNA yield were checked with the Nanodrop ND-1000 spectrophotometer.

growth_protocol: 6x10^5 LNCaP cells were plated onto 25cm2 flasks in antibiotic-free RPMI-1640 medium containing 10% fetal calf serum for 72 h.

extract_protocol: Total RNA were extracted using TriPure reagent (ROCHE) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: LNCaP cells were transfected using Lipofectamine2000 (LifeTech) with 50 nM miR mimic or negative control for 24h and 48h.

value: LNCaP

value: prostate cancer cells

tag: transfection

value: 50nM hsa-miR-135a mimic

source_name: 48h control LNCaP

value: 50nM negative control


title: 48h_miR mimic-transfected LNCaP versus control LNCaP 4

description:
US45103047_252665217420_S01_GE2_107_Sep09_1_4
Dual swap 48h-2


title: DOHH2-DMSO-3

value: DMSO


title: DOHH2-DMSO-2


title: SUDHL2-OTX015-2h-exp1


title: TMD8-ST-7612-2

source_name: TMD8 cell lines treated with ST7612AA1


title: TMD8-ST-7612-3


title: Replicate 2 - timepoint 3 (9h) - dye swap

description:
1 ml cell pellet
R2-3-DS


title: SUDHL6-DMSO-2h-exp2


title: 24h_miR mimic-transfected LNCaP versus control LNCaP 1

description:
US45103047_252665217420_S01_GE2_107_Sep09_1_1
Dual swap 24h-1

source_name: 24h miR mimic-transfected LNCaP

source_name: 24h control LNCaP


title: Replicate 1 - timepoint 3 (9h) - dye swap

description:
1 ml cell pellet
R1-3-DS


title: Replicate 1 - timepoint 3 (9h)

description:
1 ml cell pellet
R1-3


title: Replicate 2 - timepoint 2 (6h) - dye swap

description:
1 ml cell pellet
R2-2-DS

source_name: pControl_transition growth phase_1 ml cell pellet

value: 6 hrs after induction

value: transition growth phase

source_name: pLPLσ_transition growth phase_1 ml cell pellet


title: 24h_miR mimic-transfected LNCaP versus control LNCaP 2

description:
US45103047_252665217420_S01_GE2_107_Sep09_1_2
Dual swap 24h-2


title: 48h_miR mimic-transfected HeLa versus control HeLa 3

description:
25148504041_48hmiRCy3
Dual swap 48h-1.

hyb_protocol: 1 µg of Cy3/Cy5 dye-labelled aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µL containing 2x Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µL of 2x Agilent hybridization buffer was added to the final mixture. Combinated Cy3/Cy5 dye-labelled aRNA were hybridized competitively to Agilent Whole Human Genome 4x44k V2 oligonucleotides microarray slides for 18 h at 62 °C in hybridization buffer (5185-5973, Agilent) and under Agilent Gasket slide coverslip (Agilent hybridization chamber, G2534A, Agilent) in a rotative Agilent hybridization oven.

scan_protocol: Fluorescent microarray TIFF images were collected for both Cy3 and Cy5 by scanning washed dried glass slides with a GenePix 4000B microarray scanner (Axon Instruments). Image intensity data were extracted and analysed with GenePix Pro6.0 microarray analysis software. After visual inspection, spots of insufficient quality were flagged and GenePix data files (gpr format) were finally generated.

data_processing: Signal intensities were log2-transformed and normalization was performed by the intensity-dependent Lowess method. Data were imported and analyzed into the R Bioconductor software in order to identify genes with significant change in expression in response to miR mimic transfection.

source_name: 48h miR mimic-transfected HeLa

label_protocol: 1 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer's instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine Cy3 or Cy5 dyes. Fluorescent probes were purified using the RNeasy mini kit (Qiagen). Dye incorporation and aRNA yield were checked with the Nanodrop ND-1000 spectrophotometer.

growth_protocol: 3x10^5 HeLa cells were plated onto 6-well plates in antibiotic-free DMEM medium containing 10% fetal calf serum for 24 h.

extract_protocol: Total RNA were extracted using TriPure reagent (ROCHE) following manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HeLa cells were then transfected using Lipofectamine2000 (LifeTech) with 50 nM miR mimic or negative control for 24h and 48h.

value: HeLa

value: hsa-miR-135a mimic

source_name: 48h control HeLa


title: Replicate 2 - timepoint 2 (6h)

description:
1 ml cell pellet
R2-2


title: TMD8-ST-7612-1


title: Replicate 1 - timepoint 2 (6h)

description:
1 ml cell pellet
R1-2


title: Replicate 2 - timepoint 1 (4.5h) - dye swap

description:
1 ml cell pellet
R2-1-DS

source_name: pControl_exponential growth phase_1 ml cell pellet

value: 4.5 hrs after induction

value: exponential growth phase

source_name: pLPLσ_exponential growth phase_1 ml cell pellet


title: TMD8-DMSO-1

source_name: TMD8 cell lines treated with DMSO


title: Replicate 1 - timepoint 2 (6h) - dye swap

description:
1 ml cell pellet
R1-2-DS


title: TMD8-DMSO-2


title: Replicate 2 - timepoint 1 (4.5h)

description:
1 ml cell pellet
R2-1


title: BAT_cold_DT_16

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: brown adipose tissue from FoxP3 DTR B6 mouse with diphteria toxin injection

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with JMP Genomics 6 from SAS. Gene expression profiling was performed using arrays of mogene_2_0-type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

label_protocol: Fifteen μl (corresponding to 5-10 μg total RNA) of each biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: FoxP3 DTR B6 female mice were housed in a single cages at 22°C in a control environment for 1 week. Animals were i.p. injected  in two consecutive days. After first injection, temperature was decreased to 4°C. Animals were sacrificed after 2 days of cold challenge.

extract_protocol: Brown adipose tissue was powderized and lysed with Qiazol. RNA was prepared using Rneasy Mini kit (Qiagen) according to the manufacturer instructions. Dnase digestion was included.

treatment_protocol: Mice were intraoeritoneally injected with PBS or diphtheria toxin (DT) in two consecutive days.

value: DT


title: TMD8-DMSO-3

value: lymphoma cell line


title: Replicate 1 - timepoint 1 (4.5h) - dye swap

description:
1 ml cell pellet
R1-1-DS

value: pControl


title: BAT_cold_PBS_18

description: brown adipose tissue from FoxP3 DTR B6 mouse with PBS injection

value: PBS


title: Replicate 1 - timepoint 1 (4.5h)

description:
1 ml cell pellet
R1-1


title: BAT_cold_PBS_12

source_name: brown adipose tissue from FoxP3 DTR B6 mouse with PBS injection


title: BAT_cold_PBS_20


title: TIG107

city: Tsukua

first: Osamu

last: Hashizume

state: Ibaraki

address: Ten-noudai 1-1-1

institute: University of Tsukuba

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C 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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for SurePrint G3 Human Gene Expression 8x60k v2 Microarray slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human fibroblast TIG107

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fibroblasts were grown in Minimum Essential Medium (MEM; Gibco, USA) containing 10% fetal bovine serum (SIGMA, USA) and 1% penicillin/streptomycin (Gibco)

extract_protocol: RNA was prepared using the Isogen (Nippon gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: age

value: fibroblasts


title: TIG3S

source_name: Human fibroblast TIG3S

value: Fetus


title: BAT_cold_DT_5

source_name: brown adipose tissue from FoxP3 DTR B6 mouse with diphteria toxin injection


title: 24h_miR mimic-transfected HeLa versus control HeLa 2

description:
25148504041_24hctrlCy3
Dual swap 24h-2.

source_name: 24h control HeLa

source_name: 24h miR mimic-transfected HeLa


title: TIG102

source_name: Human fibroblast TIG102


title: BAT_cold_DT_9


title: TIG121

source_name: Human fibroblast TIG121


title: 29 dph High ARA high VA Tank 8

status: Public on Mar 17 2015

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

description:
Sample name: 2010-370/23
Whole animal

hyb_protocol: Hybridization was performed by Roche NimbleGen (Roche NimbleGen , Madison, WI), following their standard operating protocol (Nimblegen Arrays User’s Guide: Gene Expression Arrays v5.0, 2010

scan_protocol: Scanning was performed by Roche NimbleGen (Roche NimbleGen , Madison, WI), following their standard operating protocol (Nimblegen Arrays User’s Guide: Gene Expression Arrays v5.0, 2010

data_processing:
signal intensities extraction and global quantile normalization were done according to Nimblegen Arrays User’s Guide: Gene Expression Arrays v5.0, 2010 Roche Nimblegen. The analysis of the Nimblegen microarray data was performed in the R environment for statistical computing and graphics (R Development Core Team, 2009; version 3.0.2) as implemented in RStudio (Integrated development environment for R, 2013; version 0.98.507) using software from the Bioconductor project [42].
Following an approach previously described, the pdInfoBuilder package protocol version 1.26.0 (http://www.bioconductor.org/packages/release/bioc/html/pdInfoBuilder.html) was used to create an annotation package for the Nimblegen custom design file “100610_GM_FY_EXP.ndf”. Raw expression values of the XYS files were read into R using the oligo package protocol version 1.26.6. (http://bioconductor.org/packages/release/bioc/vignettes/oligo/inst/doc/V2NExpression.pdf) Prior to statistical analysis, the microarray data was further processed applying RMA background subtraction and normalization. (gene calls) were estimated from triplicate probes using  multichip average (RMA) as previously described (Irizarry et al., 2003. Nucleic Acids Res. 31 and Irizarry et al., 2003 Biostatistics, 4: 249-264) Gene calls with large variation (SE > 0.8) between triplicate probes were omitted from the dataset.

organism: Gadus morhua

source_name: 29 dph, whole animal, High ARA high VA

label_protocol: Labeling was performed by Roche NimbleGen (Roche NimbleGen , Madison, WI), following their standard operating protocol (Nimblegen Arrays User’s Guide: Gene Expression Arrays v5.0, 2010 Roche Nimblegen)

growth_protocol: The rotifer cultures (5 to 7-days batch cultures) were kept in 2 m3 conical tanks at 24°C with rotifer densities ranging between 800 and 2000 rotifers•ml-1, and fed four times•hour-1 on a daily basis. The diet consisted of dry baker’s yeast (0.11-0.18 g•million rotifers-1) and Rotifer Diet® (Reed Mariculture Inc., CA, USA, 0.3-1.5 g•million rotifers-1). The Atlantic cod larvae were kept in 16 50L cylindrical, flat bottomed tanks with center tubes covered with 250 µm filter, at the Institute of Marine Research, Austevoll Research Station (Storebø, Norway). Water of the same quality and salinity as above was used, with an initial temperature of 9.4 °C. Temperature was increased to 12 °C at 13 dph over a three day period to avoid temperature stress. Modest oxygen bubbling around the center tube was used to ensure even distribution of live prey in the tanks. A steady flow of daily fresh made algal “soup” was added to create green water and optimal turbidity (1 formazine turbidity units) in the tanks. Larvae were hatched according to protocols used at Austevoll marine station (van der Meeren T and Ivannikov VP. 2006, Aquac Res. 37: 898-913).

extract_protocol: RNA was extracted from pooled larvae samples using BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen). DNAse treatment step was implemented according to the protocol (Qiagen). Total RNA quantity and quality were determined using the NanoDrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), while RNA integrity (RIN) was analyzed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip® kit (Agilent Technologies, Palo Alto, CA, USA). All samples had 260/230 and 260/280 ratios of > 2.0 and RIN of > 8, respectively

treatment_protocol: Experimental diets consisted of four different enriched rotifer cultures. Two oil mixtures were made, named Control and High ARA. Control contained 90% EPAX4510 and 10% EPAX5010, while High ARA contained 65% Cargill ARA oil, 5% EPAX4510 and 30%EPAX5010. The mixtures were then divided in two fractions. VA in the form of retinylpalmitate (Sigma-Aldrich, Oslo, Norway) was added to one fraction from each oil mixture (5 g retinylpalmitate L-1 oil). This gave four different mixtures Control, Control+VA, High ARA and High ARA+VA. Four enriceh The rotifer cultures (5 to 7-days batch cultures) were kept in 2 m3 conical tanks at 24°C with rotifer densities ranging between 800 and 2000 rotifers•ml-1, and fed four times•hour-1 on a daily basis. The diet consisted of dry baker’s yeast (0.11-0.18 g•million rotifers-1) and Rotifer Diet® (Reed Mariculture Inc., CA, USA, 0.3-1.5 g•million rotifers-1). Approximately 1.2 mill rotifers were fed to each tank at the start of the feeding trial and this was increased according to Austevoll standard feeding protocol (van der Meeren T, Mangor-Jensen A, Pickova J. 2007 Aquaculture. 265: 206-217)

tag: tank

tag: protocol

value: High ARA, high VA

value: 29 dph

value: Whole larvae


title: 29 dph High ARA high VA Tank 4

description:
Sample name: 2010-370/10
Whole animal


title: 29 dph High ARA high VA Tank 10

description:
Sample name: 2010-370/30
Whole animal


title: 29 dph High ARA low VA Tank 12

description:
Sample name: 2010-370/36
Whole animal

source_name: 29 dph, whole animal, High ARA low VA

value: High ARA, low VA


title: 29 dph Low ARA high VA Tank 14

description:
Sample name: 2010-370/40
Whole animal

source_name: 29 dph, whole animal, Low ARA high VA

value: Low ARA, high VA


title: 29 dph High ARA high VA Tank 5

description:
Sample name: 2010-370/14
Whole animal


title: 17 dph High ARA low VA Tank 11

description:
Sample name: 2010-369/106
Whole animal

source_name: 17 dph, whole animal, High ARA low VA

value: 17 dph


title: 29 dph High ARA low VA Tank 6

description:
Sample name: 2010-370/16
Whole animal


title: 17 dph High ARA high VA Tank 10

description:
Sample name: 2010-369/103
Whole animal

source_name: 17 dph, whole animal, High ARA high VA


title: 29 dph Low ARA high VA Tank 16

description:
Sample name: 2010-370/47
Whole animal


title: 29 dph Low ARA low VA Tank 15

description:
Sample name: 2010-370/44
Whole animal

source_name: 29 dph, whole animal, Low ARA low VA

value: Low ARA, low VA


title: 17 dph High ARA high VA Tank 4

description:
Sample name: 2010-369/91
Whole animal


title: 29 dph Low ARA low VA Tank 3

description:
Sample name: 2010-370/8
Whole animal


title: 29 dph Low ARA low VA Tank 9

description:
Sample name: 2010-370/26
Whole animal


title: 29 dph High ARA low VA Tank 13

description:
Sample name: 2010-370/37
Whole animal


title: 17 dph High ARA low VA Tank 13

description:
Sample name: 2010-369/109
Whole animal


title: 29 dph Low ARA high VA Tank 2

description:
Sample name: 2010-370/6
Whole animal


title: 17 dph High ARA low VA Tank 12

description:
Sample name: 2010-369/108
Whole animal


title: 17 dph High ARA high VA Tank 8

description:
Sample name: 2010-369/99
Whole animal


title: 17 dph High ARA high VA Tank 5

description:
Sample name: 2010-369/93
Whole animal


title: 29 dph High ARA low VA Tank 11

description:
Sample name: 2010-370/31
Whole animal


title: 29 dph Low ARA low VA Tank 1

description:
Sample name: 2010-370/2
Whole animal


title: 17 dph Low ARA high VA Tank 14

description:
Sample name: 2010-369/112
Whole animal

source_name: 17 dph, whole animal, Low ARA high VA


title: 17 dph High ARA low VA Tank 6

description:
Sample name: 2010-369/95
Whole animal


title: 17 dph Low ARA low VA Tank 9

description:
Sample name: 2010-369/101
Whole animal

source_name: 17 dph, whole animal, Low ARA low VA


title: 17 dph Low ARA low VA Tank 15

description:
Sample name: 2010-369/113
Whole animal


title: 3_primary human bone marrow CD45-CD271+ cells

city: Lund

first: Hongzhe

last: Li

address: Klinikgatan 26

department: Lund Stem Cell Center

country: Sweden

institute: Lund University

hyb_protocol: Illumina hybridization protocol (Manuel 11322187 Revision A)

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation using the GenomeStudio software V2011.1.

source_name: bone marrow_CD45-CD271+

label_protocol: RNA was converted to cDNA and amplified. Biotinylated aRNA were prepared with TargetAmp 2-round biotin-aRNA amplification kit 3.0 for Illumina arrays

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

tag: age (yrs)

value: primary human bone marrow

value: CD45-CD271+ cells


title: 17 dph Low ARA high VA Tank 7

description:
Sample name: 2010-369/97
Whole animal


title: 2_primary human bone marrow CD45-CD271+ cells

tag: cell type


title: 1_primary human bone marrow CD45-CD271+ cells


title: 17 dph Low ARA high VA Tank 2

description:
Sample name: 2010-369/88
Whole animal


title: 10_primary human bone marrow CD45-CD271- cells

source_name: bone marrow_CD45-CD271-

value: CD45-CD271- cells


title: 4_primary human bone marrow CD45-CD271+ cells


title: 17 dph Low ARA low VA Tank 1

description:
Sample name: 2010-369/86
Whole animal


title: 5_primary human bone marrow CD45-CD271+ cells


title: 17 dph Low ARA low VA Tank 3

description:
Sample name: 2010-369/89
Whole animal


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 3 Tech 1

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

description: Biological Replicate 3 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Optimize intensities manually. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Campylobacter jejuni

source_name: strain 81-176ΔCjj1484

label_protocol: 2 µg of genomic DNA were Cy5-dUTP labeled during random primed synthesis with Klenow fragment.  20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy3-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C on blood agar base II medium.

extract_protocol: Campylobacter genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit. Total RNA was extracted from  stationary phase cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications.

growth_protocol: Precultures of Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C in Heart Infusion broth (HI) , diluted to an A550 of 0.02 in 5 ml of HI, and incubated on a gyratory shaker (150 rpm) under microaerobic conditions at 42°C to stationary phase (A550 of 1.0-1.4) .

value: strain 81-176ΔCjj1484


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 3 Tech 2

description: Biological Replicate 3 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.


title: 6_primary human bone marrow CD45-CD271- cells


title: 7_primary human bone marrow CD45-CD271- cells


title: SUDHL2-DMSO-1h-exp1

source_name: SUDHL2 cell lines treated with DMSO

tag: cell line

tag: treatment

value: DMSO


title: ERA104_M_Healthy

description: Control

value: male

value: healthy control

value: Blood monocytes


title: M2_adh_3

city: Seattle

first: Anne

last: Grosse-Wilde

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C 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), then dried immediately by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the AgilentHD-GX-1-color scan setting for 4x44k arrays.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115).
Normalized signal intensity: The normalization of the gene expression arrays was generated using the program 'GeneData', and was first a Central Tendency normalization, followed by relative normalization towards the average expression of adherent E and M clones.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 to 100 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: _adh cells were grown in normal tissue culture plates in a mixture of 1:1 DMEM:MEGM medium, and lysed directly in the dish by adding Trizol; _sus cells were grown in ultra-low adhesion plates for 21 days in DMEM:MEGM with 1% methylcellulose and B27, and lyzed by gentle dissociation with trypsin, followed by Trizol lysis.

extract_protocol: RNA was extracted using Trizol (Life Technologies) using the manufacturer's instructions. Ethanol-precipitated RNA was additionally purified using the RNeasy micro kit (Qiagen).

treatment_protocol: Cells were either grown in adhesion (_adh) or grown in suspension (_sus) as mammospheres.

tag: source cell line

value: HMLER

tag: condition

value: adhesion culture

tag: clonality

value: single cell-derived clone


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 2 Tech 2

description: Biological Replicate 2 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.

tag: strain


title: M2_adh_2


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 2 Tech 1

description: Biological Replicate 2 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.


title: 17 dph Low ARA high VA Tank 16

description:
Sample name: 2010-369/116
Whole animal

tag: time

tag: tissue


title: 9_primary human bone marrow CD45-CD271- cells


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 3 Tech 2

description: Biological Replicate 3 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.

source_name: strain 81-176ΔCjj1483

value: strain 81-176ΔCjj1483


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 3 Tech 1

description: Biological Replicate 3 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.


title: 8_primary human bone marrow CD45-CD271- cells


title: 24h_miR mimic-transfected HeLa versus control HeLa 1

description:
25148504041_24hmiRCy3
Dual swap 24h-1.

value: HeLa

value: hsa-miR-135a mimic

source_name: 24h control HeLa

value: 50nM negative control


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 1 Tech 1

description: Biological Replicate 1 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.


title: C. jejuni strain 81-176ΔCjj1484 Bio Replicate 1 Tech 2

description: Biological Replicate 1 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1484  grown to log phase.


title: M5_adh_1


title: 48h_miR mimic-transfected HeLa versus control HeLa 4

description:
25148504041_48hctrlCy3
Dual swap 48h-2.

source_name: 48h control HeLa

source_name: 48h miR mimic-transfected HeLa


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 2 Tech 2

description: Biological Replicate 2 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.


title: C. jejuni strain 81-176 wildtype Bio Replicate 2 Tech 2

description: Biological Replicate 2 Technical replicate 2 of 2. C. jejuni strain WT81-176  grown to log phase.

source_name: strain WT81-176

value: strain WT81-176


title: C. jejuni strain 81-176 wildtype Bio Replicate 2 Tech 1

description: Biological Replicate 2 Technical replicate 1 of 2. C. jejuni strain WT81-176  grown to log phase.


title: C. jejuni strain 81-176 wildtype Bio Replicate 1 Tech 2

description: Biological Replicate 1 Technical replicate 2 of 2. C. jejuni strain WT81-176  grown to log phase.


title: M2_adh_1


title: C. jejuni strain 81-176 wildtype Bio Replicate 3 Tech 1

description: Biological Replicate 3 Technical replicate 1 of 2. C. jejuni strain WT81-176  grown to log phase.


title: C. jejuni strain 81-176 wildtype Bio Replicate 3 Tech 2

description: Biological Replicate 3 Technical replicate 2 of 2. C. jejuni strain WT81-176  grown to log phase.


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 1 Tech 1

description: Biological Replicate 1 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.


title: C. jejuni strain 81-176 wildtype Bio Replicate 1 Tech 1

description: Biological Replicate 1 Technical replicate 1 of 2. C. jejuni strain WT81-176  grown to log phase.


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 1 Tech 2

description: Biological Replicate 1 Technical replicate 2 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.


title: C. jejuni strain 81-176ΔCjj1483 Bio Replicate 2 Tech 1

description: Biological Replicate 2 Technical replicate 1 of 2. C. jejuni strain 81-176ΔCjj1483  grown to log phase.


title: spleen

city: Osaka

first: Kosuke

last: Endo

address: 5-7-1 Fujishirodai, Suita

department: Dept. of Genomic Medicine

institute: National Cerebral and Cardiovascular Center

description: SAMPLE 12

scan_protocol: The ABI Prism 7900 HT Sequence Detection System (Applied Biosystems) was used for amplification and detection.

data_processing: Ct values were obtained from the amplification plot using the SDS software (Applied Biosystems). U6 was used as endogenous control and deltaCt defined by the formula (Ct of the specific miRNAs - average Ct of the endogenous control U6 in the sample).

label: FAM

source_name: tissue

label_protocol: ABI TaqMan Human MicroRNA Array kit (Card A; Applied Biosystems, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Total RNA isolated by a modified guanidinium thiocyanate method

tag: race

value: caucasian

tag: gender

value: female

tag: tissue/cell type

value: spleen


title: colon

description: SAMPLE 10

value: colon


title: skeletal muscle

description: SAMPLE 11

value: 2 male/female

value: skeletal muscle


title: mesangial cell

description: SAMPLE 14

source_name: cells

value: mesangial cell


title: prostate

description: SAMPLE 9

value: 32 males

value: prostate


title: proximal tubule

description: SAMPLE 13

value: proximal tubule


title: trachea

description: SAMPLE 5

value: pooled from 22 male/female

value: trachea


title: liver

description: SAMPLE 7

value: male

value: liver


title: brain

description: SAMPLE 6

value: brain


title: pancreas

description: SAMPLE 4

value: pancreas


title: salivary gland

description: SAMPLE 3

value: pooled from 24 male/female

value: salivary gland


title: 29 dph Low ARA high VA Tank 7

description:
Sample name: 2010-370/20
Whole animal

source_name: 29 dph, whole animal, Low ARA high VA

value: Low ARA, high VA

value: 29 dph

value: Whole larvae


title: C57BL/6

city: tukuba

first: Yuki

last: Tanaka

state: ibaraki

address: 1-1-1 tennodai

institute: University of tsukuba

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting . Data of test sample was normalized to data of control sample by MAS5.0.

source_name: tissue, immunization,day7

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit（Affymetrix) and TaKaRa cDNA Synthesis Kit （TaKaRa Bio） from 3ug total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit(Affymetrix)

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


title: E6_adh_1

value: HMLER

value: adhesion culture

value: single cell-derived clone


title: heart

description: SAMPLE 8

value: caucasian

value: pooled from 3 male/female

value: heart


title: lung

description: SAMPLE 2

value: lung


title: kidney

description: SAMPLE 1

value: female

value: kidney


title: DBA/1


title: P intermediate 4

city: Bethesda

first: Baoying

last: Liu

address: 9000 Rockville Pike

institute: NEI

description: Sample 16

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip human genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000 operated by Affymetrix GeneChip Operating Software, version 1.4 (GCOS 1.4).

data_processing:
GeneSpring software GX 7.3.1 (Agilent Technologies) or R package limma (version 3.23.6)
data processing was performed in two groups; [1] HD intermediate, classical and non-classical samples (total 12 samples) [2] HD intermediate and P intermediate samples (total 9 samples).
For group [1], values (raw intensity) were determined by using GeneSpring software GX 7.3.1 (Agilent Technologies) and the normalization algorithm is RMA.
For group [2], RMA function in Limma (version 3.23.6) was used to do the following:
1. Probe specific correction of the PM probes using a model based on observed intensity being the sum of signal and noise 2. Normalization of corrected PM probes using quantile normalization (Bolstad et al., 2003) 3. Calculation of Expression measure using median polish.
Reference of Limma:
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3.

source_name: human intermediate monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (MessageAmp™ II-Biotin Enhanced Kit).

growth_protocol: PBMCs were purified and then flow cytometry was used to sort 3 monocyte subsets

extract_protocol: RNeasy (QIAGEN) was used to purify total RNA according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: subject status

value: autoimmune uveitis patient

tag: subject id

value: patient 4

value: human peripheral monocytes

tag: tissue subtype

value: intermediate monocyte subset


title: HD intermediate 3 [re-analysis]

description: Sample 7 [re-analysis]

value: healthy donor


title: P intermediate 5

description: Sample 17

value: patient 5


title: HD intermediate 2 [re-analysis]

description: Sample 4 [re-analysis]


title: HD intermediate 4

description: Sample 10


title: E2_adh_2


title: P intermediate 1

description: Sample 13

value: patient 1


title: P intermediate 3

description: Sample 15

value: patient 3


title: HD classical 4

description: Sample 11

source_name: human classical monocytes

value: classical monocyte subset


title: HD intermediate 3

description: Sample 7


title: HD non-classical 4

description: Sample 12

source_name: human non-classical monocytes

value: non-classical monocyte subset


title: HD non-classical 3

description: Sample 9


title: E2_adh_1

value: HMLER

value: adhesion culture

value: single cell-derived clone


title: P intermediate 2

description: Sample 14

value: patient 2


title: E1_adh_1


title: HD classical 3

description: Sample 8


title: HD non-classical 2

description: Sample 6


title: E1_adh_2


title: E2_adh_3


title: skeletal muscle (B)

description:
SAMPLE 10
replicate 1

data_processing: Ct values were obtained from the amplification plot using the SDS software (Applied Biosystems). U6 was used as endogenous control and DCt defined by the formula (Ct of the specific miRNAs - average Ct of the endogenous control U6 in the sample).

organism: Rattus norvegicus

source_name: Tissue

label_protocol: ABI TaqMan Human MicroRNA Array kit (Card B; Applied Biosystems, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Total RNA isolated by TRIzol reagent for tissue samples and mirVana PARIS Kit for LMD samples.

value: Sprague-Dawley

tag: age

value: 4 weeks

value: skeletal muscle

tag: pre-amp

value: no


title: spleen (B)

description:
SAMPLE 11
replicate 1

value: spleen


title: HD classical 2

description: Sample 5

value: human peripheral monocytes


title: heart (B)

description:
SAMPLE 9
replicate 1

value: heart


title: HD intermediate 2

description: Sample 4

value: healthy donor

value: intermediate monocyte subset


title: liver (B)

description:
SAMPLE 8
replicate 1

value: liver


title: Stim1Cd4 mouse 3

city: New York City

last: Feske

address: 550 First Avenue

department: Pathology

institute: New York University

description: RMA expression value derived from Expression Console software

hyb_protocol: Biotin-labeled amplified aRNA was prepared and hybridized to 1.0 Eon expression chips  (Affymetrix) according to the manufacturer’s protocols

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The values in the CHP sample data tables were derived from the Expression Console Software (Affymetrix) by performing a gene-level normalization and signal summarization on the raw CEL files (gene-level analysis).
Data were further analyzed and visualized using TCA software (Affymetrix) and IPA pathway analysis software (Qiagen). Probesets were defined using a treshold with  p<0.05 and FC >1.5 or  <-1.5.

label: Biotin

source_name: Stim1 deficient mouse (Stim1CD4)

growth_protocol: CD4+ T cells were isolated from the spleens of WT mice using a negative selection kit (STEMCELL Technologies) and stimulated with 0.5 µg/ml plate-bound anti-CD3 and 1 µg/ml anti-CD28 antibodies (BioXCess) and cultured in the presence  or absence of 2.5 ng/ml TGF-β (Peprotech)

extract_protocol: Total RNA was isolated using the RNeasy micro RNA isolation kit (Quiagen)

treatment_protocol: For the generation of  Thn cells (non-polarizing conditions), CD4+ T cells were stimulated  for 48h with 0.5 µg/ml anti-CD3 and 1µg/ml anti-CD28. For the generation of inducible T regulatory cells (iTreg), CD4+ T cells were stimulated for 48h with 0.5 µg/ml anti-CD3 and 1.0 µg/ml anti-CD28 in the presence of 2.5 ng/ml TGF-β.

tag: genotype/variation

value: STIM1 deficient CD4+ T cells

value: stimulation with aCD3/aCD28+TGFbeta (48)


title: Stim1Cd4 mouse 2

label_protocol: Biotin-labeled amplified aRNA was prepared and hybridized to 1.0 Eon expression chips  (Affymetrix) according to the manufacturer’s protocols


title: glomerulus (A)

description:
SAMPLE 17
replicate 1

source_name: cell

value: glomerulus

value: 12 cycles


title: intestinal villus (A)

description:
SAMPLE 15
replicate 1

value: intestinal villus


title: proximal tubule (A)

description:
SAMPLE 16
replicate 1

value: proximal tubule


title: kidney (B)

description:
SAMPLE 1
replicate 1

value: kidney


title: Wt iTreg mouse 2

source_name: Wt mouse

value: WT CD4+ T cells


title: Wt iTreg mouse 3


title: lung (B)

description:
SAMPLE 6
replicate 1

value: Sprague-Dawley

value: 4 weeks

value: lung


title: Wt iTreg mouse 1

value: stimulation with aCD3/aCD28+TGFbeta (48h)


title: mammary gland (A)

description:
SAMPLE 14
replicate 1

value: mammary gland