title: 32Dcl3_cells_MSCV-CD8+CEBPalpha-puro_day3_exp1

source_name: 32Dcl.3 cells, empty MSCV-CD8 and MSCV-C/EBPalpha-puro transduced, day 3, experiment 1


title: Gammadelta_HiIncidence_Stim_rep3

status: Public on Aug 26 2014

type: RNA

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

country: USA

institute: University of California, San Francisco

description: Gene expression in Vdelta2+ gammadelta T cells after Pf iRBC stimulation

hyb_protocol: 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent 8x60k mouse gene expression microarrays as per manufacturer instructions.

scan_protocol: Arrays were scanned on an Agilent scanner at 3 um resolution as 20-bit TIFF images.

data_processing: Features were extracted using Agilent Feature Extraction software. Non-background subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.

molecule: total RNA

organism: Homo sapiens

source_name: Gammadelta T cells, high incidence, iRBCs, replicate 3

label_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

growth_protocol: PBMCs were isolated from Ugandan children over Ficoll-Histopaque and cryopreserved in liquid nitrogen.

extract_protocol: RNA was isolated with the RNAqueous Micro kit (Life Technologies).  Isolated RNA was amplified using the Aminoallyl MessageAmp II kit (Life Technologies).

treatment_protocol: PBMCs were thawed, rested overnight, and co-incubated with P. falciparum-infected red blood cells for 6 hours, followed by FACS isolation of the Vdelta2+ subset of gammadelta T cells.

tag: cells

value: Vdelta2+ gammadelta T cells

tag: treatment

value: P. falciparum-infected red blood cells

tag: incidence

value: high


title: Gammadelta_HiIncidence_Stim_rep2

source_name: Gammadelta T cells, high incidence, iRBCs, replicate 2


title: 32Dcl3_cells_MSCV-CD8+MSCV-puro_day3_exp2

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and normalized.

organism: Mus musculus

source_name: 32Dcl.3 cells, empty MSCV-CD8 and MSCV-puro transduced, day 3, experiment 2

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

growth_protocol: 32D.cl3 cells were cultured with WEHI3B conditioned medium.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturers' instructions.

treatment_protocol: 32Dcl.3 cells were transduced with retroviral vectors by spinoculation.

tag: cell type

value: 32Dcl.3 cells

value: 3 days after transduction

tag: plasmids used for transduction

value: Empty MSCV-IRES-hCD8t + Empty MSCV-IRES-puro


title: Gammadelta_LoIncidence_Unstim_rep1

description: Gene expression in Vdelta2+ gammadelta T cells after incubation without stimulation

source_name: Gammadelta T cells, low incidence, unstimulated, replicate 1

value: Unstimulated

value: low


title: colon cancer 10

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

country: China

institute: Sun Yat-sen University

description: Gene expression data from colon cancer 10 of sensitive

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with NexusExp3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: colon cancer patient 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: snap-frozen tissue samples were obtained from 20 colorectal cancer (CRC) patients during the surgery

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

treatment_protocol: colon cancer samples were harvested and treated with Trizol

tag: group

value: RFS>3 years


title: 32Dcl3_cells_MSCV-CD8+MSCV-puro_day3_exp1

source_name: 32Dcl.3 cells, empty MSCV-CD8 and MSCV-puro transduced, day 3, experiment 1


title: colon cancer 9

description: Gene expression data from colon cancer 9 of sensitive

source_name: colon cancer patient 9


title: Gammadelta_LoIncidence_Stim_rep3

source_name: Gammadelta T cells, low incidence, iRBCs, replicate 3


title: Gammadelta_LoIncidence_Stim_rep2

source_name: Gammadelta T cells, low incidence, iRBCs, replicate 2


title: f-MDSC, before contact, replicate 7

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data of CD33+IL4Ra+ sorted cell before contact with autologus PHA activated CD3+ T cells

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit - Following labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST arrays. GeneChips were washed and stained (streptavidin,R-phycoerythrin conjugate and biotinylated anti-streptavidin) in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GeneChip® Scanner 3000 7G . Affymetrix GeneChip® Command Console® Software (AGCC)- used to view CEL file images.

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: UCB derided CD33+IL4Rα+ sorted and incubated for 4 days with GM-CSF and G-CSF

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit - sense-strand cDNA is fragmented with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 and its yield is further labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Human Umbilical cord blood (UCB) samples underwent Ficoll-Paque gradient separation and ACK red cell lysis, and then were cultured for 4 days in the presence of GM-CSF and G-CSF (40ng/ml).  CD33 and IL-4Rα positive cells were sterilely sorted, part of the cells stored for RNA extraction, and part co-cultured for 3 days with autologous PHA activated CFSE labeled CD3+ T cells either in cell to cell contact (CONTACT) or using a transwell device to avoid cell contact (TRANSWELL). HEK-293 cells were maintained in complete RPMI-140 10% FBS.

extract_protocol: RNA was purified using the miRNA easy kit from Qiagen and following the manufacture instruction.

treatment_protocol: Sterilely sorted CD33 and IL-4Rα positive cells before and after been co-culture with autologous CD3+ T cells were lysed with TRIZOL and stored at -80◦C till RNA extraction was performed. TRIZOL samples preservation was also used for the control cells line HEK-293.

value: Before contact

tag: cell state

value: Preactivated cells


title: f-MDSC, before contact, replicate 5

value: UCB derided CD33+IL4Rα+ sorted and incubated for 4 days with GM-CSF and G-CSF


title: Irf8KO_MDPs_exp2

source_name: Irf8KO MDPs, isolated from bone marrow cells, experiment 2

value: Bone marrow derived MDPs

value: Primary isolated cells


title: f-MDSC, contact, replicate 1

description: Gene expression data of CD33+IL4Rα+ sorted cell after contact with autologus PHA activated CFSE labeled CD3+ T cells

source_name: UCB derived CD33+IL4Rα+ after 3 days in contact with autologus PHA activated CD3+T cells

value: After co-culture in contact

value: Activated by T cells contact


title: f-MDSC, before contact, replicate 6


title: Gammadelta_LoIncidence_Stim_rep1

source_name: Gammadelta T cells, low incidence, iRBCs, replicate 1


title: colon cancer 5

description: Gene expression data from colon cancer 5 of sensitive

source_name: colon cancer patient 5


title: colon cancer 8

description: Gene expression data from colon cancer 8 of sensitive

source_name: colon cancer patient 8


title: colon cancer 6

description: Gene expression data from colon cancer 6 of sensitive

source_name: colon cancer patient 6


title: Preadipocytes treated with DMIOA+20S, biological replicate 3

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

country: Canada

institute: University of Manitoba

description: Gene expression data from preadipocytes isolated from laying hen, treated with DMIOA+20S oxysterol

hyb_protocol: Following fragmentation, 12.5 µg of biotinylated total RNA were hybridized for 16 hours at 45C on Affymetrix Chicken Genome Array. Genechips were washed and stained using Fluidics station 450 (Affymetrix).

scan_protocol: The stained chips were scanned using Scanner 3000 (Affynetrix)

data_processing: Data were background corrected and normalised using GC-RMA

organism: Gallus gallus

source_name: Adipose tissue

label_protocol: 15 µg of biotinylated aRNA were prepared according to the standard Affymetrix protocol (3' IVT Express Kit user manual, Affymetrix)

growth_protocol: The isolated preadipoctes were incubated in FBS containing 10% DMEM in an incubator with 5% CO2

treatment_protocol: Confluent preadipocytes were treated with adipogeneic cocktail (DMIOA) and DMIOA+20S oxysterol

value: Preadipocytes


title: f-MDSC, before contact, replicate 4


title: WT_MDPs_exp2

source_name: WT MDPs, isolated from bone marrow cells, experiment 2


title: Irf8KO_MDPs_exp1

source_name: Irf8KO MDPs, isolated from bone marrow cells, experiment 1


title: colon cancer 7

description: Gene expression data from colon cancer 7 of sensitive

source_name: colon cancer patient 7


title: WT_MDPs_exp1

source_name: WT MDPs, isolated from bone marrow cells, experiment 1


title: f-MDSC, before contact, replicate 3


title: colon cancer 3

description: Gene expression data from colon cancer 3 of sensitive

source_name: colon cancer patient 3


title: colon cancer 4

description: Gene expression data from colon cancer 4 of sensitive

source_name: colon cancer patient 4


title: Preadipocytes treated with DMIOA, biological replicate 3

description: Gene expression data from preadipocytes isolated from laying hen, treated with DMIOA


title: sak1-891_F376_36C_2Hr/WT_972_F108_LogPhase

status: Public on Aug 25 2014

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Microarray Labelling and Hybridization were performed using Quick Amp Labelling Kit (two color) or Low Input Quick Amp Labelling Kit (two color) (Agilent Technologies). Agilent Gene Expression Array 8X15K custom design 020613 (Carter-O’Connell et al., 2012) was used for all experiments. All experiments were labelled with Cy3 and hybridized against a common (F108) WT log phase control Cy5 labelled sample.

scan_protocol: Slide was scanned using Agilent G2505 B Microarray Scanner using parameteres as described in  Quick Amp Labelling Kit (two color) protocol. Fluorescence values were extracted using Agilent Feature Extraction (v9.5.3) software.

data_processing:
Log2 values from all synchronous spore germination experiments, sak1-891-ts strain, and upstream ChIP-Seq peaks from the study (If present Log2 value = 4) were clustered along with the top 750 genes from Oliva et al. (PMID 15966770) using the hierarchical clustering method (Complete Linkage) (Eisen et al., 1998) and visualized using Java Treeview (Saldanha, 2004). The control for the fkh2Δ S.G. (Spore germination), sak1Δ S.G. and sep1Δ S.G. was the WT S.G. experiment at each of the time points respectively. The control for sak1-891-ts strain was a WT (F14) strain kept at that temperature for an equal duration of time. Cross-referencing was possible as labelled control sample was the same for all experiments. Each experiment from this study was given a weight of 1 and each of the experiment from Oliva et al. was given a weight of 0.058 for clustering. Only experiments from this study are shown after clustering.
normalized data are Log2 ratio (green;test/red;reference) and raw data are Log10 ratio (red/green) values. Values are normalized using default parameters of the Agilent feature extraction software.  NA/Ignore array features were excluded from the analysis.

organism: Schizosaccharomyces pombe

extract_protocol: Samples were harvested by adding ice directly to the culture and washing once with cold water. Harvested cells were snap frozen in liquid nitrogen and saved for RNA preparation. Total RNA was isolated using the RiboPureTM-Yeast kit (Ambion).

tag: strain

tag: genotype/variation

tag: growth conditions

tag: time (harvest time, post-spore inoculation)

tag: growth medium

value: YES medium

source_name: [CONTROL] WT_972_(Strain_F108)

value: WT


title: sak1-891_F376_36C_4Hr/WT_972_F108_LogPhase

label_protocol: Microarray Labelling and Hybridization were performed using Quick Amp Labelling Kit (two color) or Low Input Quick Amp Labelling Kit (two color) (Agilent Technologies). Agilent Gene Expression Array 8X15K custom design 020613 (Carter-O’Connell et al., 2012) was used for all experiments. All experiments were labelled with Cy3 and hybridized against a common (F108) WT log phase control Cy5 labelled sample.


title: colon cancer 2

description: Gene expression data from colon cancer 2 of sensitive

source_name: colon cancer patient 2


title: WT_F14_26C/WT_972_F108_LogPhase


title: WT_F14_36C_4Hr/WT_972_F108_LogPhase


title: WT_F14_36C_2Hr/WT_972_F108_LogPhase


title: sep1::ura4+_spore_germ_12Hr/WT_972_F108_LogPhase

value: selective germination

value: EMM+LAH medium


title: f-MDSC, transwell replicate 4

description: Gene expression data of CD33+IL4Ra+ sorted cell after in vitro co-culture with autologus PHA activated CD3+ T cells in transwell condition

source_name: UCB derived CD33+IL4Rα+ after 3 days with autologus PHA activated CD3+T cells in transwell condition

value: After co-culture in transwell

value: No activated by T cells contact


title: f-MDSC, before contact, replicate 2

source_name: UCB derided CD33+IL4Rα+ sorted and incubated for 4 days with GM-CSF and G-CSF


title: WT_cMoPs_exp1

source_name: WT cMoPs, isolated from bone marrow cells, experiment 1

value: Bone marrow derived cMoPs


title: sak1::ura4+_spore_germ_12Hr/WT_972_F108_LogPhase


title: f-MDSC, before contact, replicate 1


title: sak1-891_F376_26C/WT_972_F108_LogPhase


title: sep1::ura4+_spore_germ_8Hr/WT_972_F108_LogPhase


title: sak1::ura4+_spore_germ_10Hr/WT_972_F108_LogPhase


title: sak1::ura4+_spore_germ_HU(10Hr)/WT_972_F108_LogPhase

value: EMM+LAH medium, with HU (Hydroxyurea)


title: sak1::ura4+_spore_germ_8Hr/WT_972_F108_LogPhase


title: sep1::ura4+_spore_germ_10Hr/WT_972_F108_LogPhase


title: sep1::ura4+_spore_germ_HU(10Hr)/WT_972_F108_LogPhase


title: RB cell line Y79 SNP

type: genomic

first: Xiaoliang Leon

last: Xu

state: NY

institute: MSKCC

description:
Hybridized to CytoScan HD 750K
20130903_162457_001_Cell line 1-Y79

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Reagent Kit  Bundle, catalog no. 901835). The DNA was hybridized to the microarray, washed on the GeneChip Fluidics Station 450 (Affymetrix), stained with Affymetrix GeneChip Stain Reagents.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G System (Affymetrix, 00-0213).

data_processing:
The array image was acquired using Affymetrix® GeneChip® Command Console® (AGCC) Software and CEL files were created for signal intensity data. Copy number values for individual SNPs were extracted and converted from CEL files using Chromosome Analysis Suite 2.0 (Affymetrix CHAS 2.0) software. Genomic Smoothing analysis was performed by combination of segments of gains or losses if they are separated by small spans of normal copy number segments. The default value defining “small spans” in ChAS is 50 markers and 200 kbp. Inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in Chromosome Analysis Suite 2.0. Standard named setting was used as segments filters setting in CHAS 2.0. UCSC Genomic Version hg19 was used as reference.
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.1
program-name = apt-copynumber-cyto.exe
program-version = 1.15.1
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: RB cell line Y79

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions. Cells were cultured in RB culture medium (Iscove’s Modified Dulbecco’s Medium (IMDM), 10% fetal bovine serum (FBS), 55 micro-Molar beta-mercaptoethanol, with glutamine, penicillin, streptomycin, fungizone, and 10μg/ml Plasmocin (Invivogen)

extract_protocol: Genomic DNA was extracted from RB cell lines or xenografted mouse eye samples using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Concentrated LKO-shRB1 and shp130 virus was used to infect total retinal cells or sorted retinal cone precursor cell population in filtered conditioned RB culture medium in the presence of 4 μg/ml polybrene (Sigma-Aldrich) followed by gentle pipetting 25 times and shaking for 10 minutes in the hood. Cells were cultured for 3-4 months in vitro or xenografted in mouse eyes within 7 days after infection. Xenografts were performed on 6-week-old male athymic (Foxn1-/-) mice (Taconic, Hudson, NY) or 6-week-old male Nod/Scid/Il2r-gamma-/- mice (Jackson Laboratories).

value: retinoblastoma

tag: cell line


title: RB cell line RB176 SNP

description:
Hybridized to CytoScan HD 750K
20130903_162457_002_Cell line 2-176

source_name: RB cell line RB176


title: RB cell line WERI SNP

description:
Hybridized to CytoScan HD 750K
20130903_162458_003_Cell line 3-WERI

source_name: RB cell line WERI

value: WERI


title: fkh2::ura4+_spore_germ_12Hr/WT_972_F108_LogPhase


title: fkh2::ura4+_spore_germ_10Hr/WT_972_F108_LogPhase


title: fkh2::ura4+_spore_germ_8Hr/WT_972_F108_LogPhase


title: fkh2::ura4+_spore_germ_6Hr/WT_972_F108_LogPhase


title: fkh2::ura4+_spore_germ_HU(10Hr)/WT_972_F108_LogPhase


title: ura4+_spore_germ_6Hr/WT_972_F108_LogPhase


title: ura4+_spore_germ_HU(10Hr)/WT_972_F108_LogPhase


title: ura4+_spore_germ_8Hr/WT_972_F108_LogPhase


title: ura4+_spore_germ_12Hr/WT_972_F108_LogPhase


title: Rb depleted cone-RB tumor mouse xenograft 2 SNP

description:
Hybridized to CytoScan HD 750K
20130417_102554_001-mouse

tag: tissue

value: Rb depleted


title: Rb/p130 depleted cone-RB cell line cone 2 SNP

description:
Hybridized to CytoScan HD 750K
20130306_182755_003-cone 2

value: Rb/p130 depleted


title: Rb/p130 depleted cone-RB cell line all 4 SNP

description:
Hybridized to CytoScan HD 750K
20130306_182756_004-all 4


title: Rb/p130 depleted cone-RB tumor mouse xenograft 1 SNP

description:
Hybridized to CytoScan HD 750K
20130304_182744_003-Mouse-4


title: ura4+_spore_germ_10Hr/WT_972_F108_LogPhase


title: LungADC68

city: Beijing

first: Lin

last: Feng

address: Panjiayuan nanli 17#

institute: Peiking union medical school

description: lung adenocarcinoma tissue sample 68

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (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 brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lung adenocarcinoma tissue

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).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: All samples were snap-frozen in liquid nitrogen and stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied.

value: lung adenocarcinoma


title: LungADC52

description: lung adenocarcinoma tissue sample 52


title: LungADC58

description: lung adenocarcinoma tissue sample 58


title: LungADC65

description: lung adenocarcinoma tissue sample 65


title: LungADC56

description: lung adenocarcinoma tissue sample 56


title: LungADC64

description: lung adenocarcinoma tissue sample 64


title: LungADC49

description: lung adenocarcinoma tissue sample 49


title: LungADC55

description: lung adenocarcinoma tissue sample 55


title: LungADC63

description: lung adenocarcinoma tissue sample 63


title: LungADC61

description: lung adenocarcinoma tissue sample 61


title: LungADC54

description: lung adenocarcinoma tissue sample 54


title: LungADC67

description: lung adenocarcinoma tissue sample 67


title: LungADC57

description: lung adenocarcinoma tissue sample 57


title: LungADC66

description: lung adenocarcinoma tissue sample 66


title: LungADC51

description: lung adenocarcinoma tissue sample 51


title: LungADC60

description: lung adenocarcinoma tissue sample 60


title: LungADC53

description: lung adenocarcinoma tissue sample 53


title: LungADC62

description: lung adenocarcinoma tissue sample 62


title: LungADC69

description: lung adenocarcinoma tissue sample 69


title: LungADC48

description: lung adenocarcinoma tissue sample 48


title: LungADC59

description: lung adenocarcinoma tissue sample 59


title: LungADC47

description: lung adenocarcinoma tissue sample 47


title: LungADC50

description: lung adenocarcinoma tissue sample 50


title: LungADC46

description: lung adenocarcinoma tissue sample 46


title: LungADC44

description: lung adenocarcinoma tissue sample 44


title: Non-treated control preadipocytes, biological replicate 3

description: Gene expression data from preadipocytes isolated from laying hen, control


title: LungADC45

description: lung adenocarcinoma tissue sample 45


title: LungADC42

description: lung adenocarcinoma tissue sample 42


title: LungADC43

description: lung adenocarcinoma tissue sample 43


title: T-cell acute lymphoblastic leukemia (patient 9)

city: Perugia

first: Cristina

last: Mecucci

address: Santa Maria della Misericordia University Hospital

institute: University of Perugia

description: acute leukemia

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Consolle  (AGCC) Software. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Chromosome Analysis Suite Software (ChAS) 2.0 software.

source_name: T-cell acute lymphoblastic leukemia

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Leukemic cells were not grown

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using classical Salting out method

tag: phenotype

value: T-cell acute lymphoblastic leukemia


title: colon cancer 1

description: Gene expression data from colon cancer 1 of sensitive

source_name: colon cancer patient 1

value: RFS>3 years


title: LungADC40

description: lung adenocarcinoma tissue sample 40


title: LungADC39

description: lung adenocarcinoma tissue sample 39


title: LungADC36

description: lung adenocarcinoma tissue sample 36


title: LungADC41

description: lung adenocarcinoma tissue sample 41


title: LungADC31

description: lung adenocarcinoma tissue sample 31


title: LungADC33

description: lung adenocarcinoma tissue sample 33


title: LungADC32

description: lung adenocarcinoma tissue sample 32


title: LungADC29

description: lung adenocarcinoma tissue sample 29


title: LungADC26

description: lung adenocarcinoma tissue sample 26


title: LungADC35

description: lung adenocarcinoma tissue sample 35


title: LungADC34

description: lung adenocarcinoma tissue sample 34


title: LungADC25

description: lung adenocarcinoma tissue sample 25


title: Refractory anemia with excess of blasts (patient 2)

description: acute leukemia

source_name: Refractory anemia with excess of blasts

value: Refractory anemia with excess of blasts

value: mononuclear cell preparations of leukemic blasts


title: T-cell acute lymphoblastic leukemia (patient 8)

description: acute leukemia


title: LungADC27

description: lung adenocarcinoma tissue sample 27


title: Acute myeloid leukemia (patient 3)

description: acute leukemia

source_name: Acute myeloid leukemia

value: Acute myeloid leukemia


title: LungADC30

description: lung adenocarcinoma tissue sample 30


title: LungADC28

description: lung adenocarcinoma tissue sample 28


title: LungADC24

description: lung adenocarcinoma tissue sample 24


title: Acute myeloid leukemia (patient 7)

description: acute leukemia


title: LungADC38

description: lung adenocarcinoma tissue sample 38


title: LungADC18

description: lung adenocarcinoma tissue sample 18


title: LungADC21

description: lung adenocarcinoma tissue sample 21


title: LungADC20

description: lung adenocarcinoma tissue sample 20


title: LungADC14

description: lung adenocarcinoma tissue sample 14


title: LungADC23

description: lung adenocarcinoma tissue sample 23


title: LungADC15

description: lung adenocarcinoma tissue sample 15


title: LungADC19

description: lung adenocarcinoma tissue sample 19


title: LungADC09

description: lung adenocarcinoma tissue sample 9


title: LungADC12

description: lung adenocarcinoma tissue sample 12


title: LungADC06

description: lung adenocarcinoma tissue sample 6


title: LungADC37

description: lung adenocarcinoma tissue sample 37


title: LungADC16

description: lung adenocarcinoma tissue sample 16


title: LungADC01

description: lung adenocarcinoma tissue sample 1


title: LungADC04

description: lung adenocarcinoma tissue sample 4


title: LungADC13

description: lung adenocarcinoma tissue sample 13


title: LungADC17

description: lung adenocarcinoma tissue sample 17


title: LungADC22

description: lung adenocarcinoma tissue sample 22


title: LungADC10

description: lung adenocarcinoma tissue sample 10


title: LungADC05

description: lung adenocarcinoma tissue sample 5


title: LungADC11

description: lung adenocarcinoma tissue sample 11


title: WholeE07

description: whole embryo aged 3 to 5 weeks post ovulation,sample 7


title: LungADC07

description: lung adenocarcinoma tissue sample 7


title: LungADC08

description: lung adenocarcinoma tissue sample 8


title: WholeE09

description: whole embryo aged 3 to 5 weeks post ovulation,sample 9


title: LungADC02

description: lung adenocarcinoma tissue sample 2


title: WholeE10

description: whole embryo aged 3 to 5 weeks post ovulation,sample 10


title: WholeE05

description: whole embryo aged 3 to 5 weeks post ovulation,sample 5


title: WholeE06

description: whole embryo aged 3 to 5 weeks post ovulation,sample 6


title: WholeE04

description: whole embryo aged 3 to 5 weeks post ovulation,sample 4


title: LungADC03

description: lung adenocarcinoma tissue sample 3


title: WholeE08

description: whole embryo aged 3 to 5 weeks post ovulation,sample 8


title: WholeE01

description: whole embryo aged 3 to 5 weeks post ovulation,sample 1


title: WholeE03

description: whole embryo aged 3 to 5 weeks post ovulation,sample 3


title: WholeE02

description: whole embryo aged 3 to 5 weeks post ovulation,sample 2


title: MatureL14

description: lung from adult operated on for benign lung diseases, sample 14


title: MatureL12

description: lung from adult operated on for benign lung diseases, sample 12


title: MatureL13

description: lung from adult operated on for benign lung diseases, sample 13


title: MatureL10

description: lung from adult operated on for benign lung diseases, sample 10


title: MatureL11

description: lung from adult operated on for benign lung diseases, sample 11


title: MatureL15

description: lung from adult operated on for benign lung diseases, sample 15


title: MatureL07

description: lung from adult operated on for benign lung diseases, sample 7


title: MatureL04

description: lung from adult operated on for benign lung diseases, sample 4


title: MatureL08

description: lung from adult operated on for benign lung diseases, sample 8


title: 83-2vs82-65

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Human renal clear-cell carcinoma cells : control vs MUC1 overexpressing cells

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.5).

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction and LOWESS normalization.

source_name: control unexpressing MUC1 cells 82-65

label_protocol: manufacturer's instructions

extract_protocol: Total RNA extracted using kit Total RNA Purification, Nucleospin®RNA II (MACHERY-NAGEL) following manufacturer's instructions

treatment_protocol: Human kidney cell lines were invalidated for the MUC1 gene.

tag: tissue source

value: kidney

value: renal clear-cell carcinoma

source_name: MUC1 overexpressing cells 83-2


title: 82-F7vs83-5

source_name: MUC1 overexpressing cells 83-5

source_name: control unexpressing MUC1 cells 82-F7


title: 83-5vs82F7


title: MatureL06

description: lung from adult operated on for benign lung diseases, sample 6


title: MatureL09

description: lung from adult operated on for benign lung diseases, sample 9


title: MiddleL09

description: lung at 16 to 24 postovulatory weeks,sample 9

source_name: lung at 16 to 24 postovulatory weeks

value: lung at 16 to 24 postovulatory weeks


title: MatureL01

description: lung from adult operated on for benign lung diseases, sample 1


title: MiddleL07

description: lung at 16 to 24 postovulatory weeks,sample 7


title: MatureL05

description: lung from adult operated on for benign lung diseases, sample 5


title: MiddleL08

description: lung at 16 to 24 postovulatory weeks,sample 8


title: MatureL03

description: lung from adult operated on for benign lung diseases, sample 3


title: MiddleL06

description: lung at 16 to 24 postovulatory weeks,sample 6


title: MatureL02

description: lung from adult operated on for benign lung diseases, sample 2


title: MiddleL03

description: lung at 16 to 24 postovulatory weeks,sample 3


title: MiddleL04

description: lung at 16 to 24 postovulatory weeks,sample 4


title: MiddleL05

description: lung at 16 to 24 postovulatory weeks,sample 5


title: 82-65vs83-2


title: EarlyL10

description: lung at 6 to 8 postovulatory weeks,sample 10

source_name: lung at 6 to 8 postovulatory weeks

value: lung at 6 to 8 postovulatory weeks


title: EarlyL06

description: lung at 6 to 8 postovulatory weeks,sample 6


title: MiddleL01

description: lung at 16 to 24 postovulatory weeks,sample 1


title: MiddleL02

description: lung at 16 to 24 postovulatory weeks,sample 2


title: EarlyL09

description: lung at 6 to 8 postovulatory weeks,sample 9


title: EarlyL03

description: lung at 6 to 8 postovulatory weeks,sample 3


title: CPMpos VAFECs

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

hyb_protocol: A total of 10 ug of cRNA was hybridized for 16 hours at 45C on the GeneChip Human Genome U133 Plus 2.0 Array, followed by washing and staining in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were quantified and normalized according to the MAS5.0 algorithm. The trimmed mean target intensity of each chip was arbitrarily set to 500.

source_name: 201B7-derived CPMpos VAFECs

label_protocol: Biotinylated cRNA was synthesized using the GeneChip 3'IVT Express Kit (Affymetrix) from 250 ng of total RNA according to the manufacturer's instructions.

growth_protocol: When 201B7 hiPSCs reached 70% confluence (Day 0), the cells were incubated in 10 microM of Y-27632 (Wako) for one hour followed by deprivation of STO feeder cells with CTK dissociation solution containing 0.25% trypsin (Life Technologies), 0.1% collagenase IV (Life Technologies), 20% KSR (Life Technologies) and 1mM of CaCl2 in PBS. The cells were subsequently rinsed carefully with PBS and, incubated in Accutase (Innovative Cell Technologies) for 20 minutes at 37°C. The detached 201B7 hiPSCs were then dissociated into single cells via pipetting, incubated on a 0.1% gelatin-coated plate for 30 minutes at 37°C and seeded on Matrigel-coated plates (BD Biosciences) at a density of 1.1 x105 cells/cm2 in the Step 1 medium containing RPMI1640 medium (Nacalai Tesque), 1x B27 supplements (Life Technologies, #17504-044), and 50 U/ml of penicillin/streptomycin, 100 ng/ml of human activin A (R&D systems), 1 microM of CHIR99021 (Axon Medchem), supplemented with 10 microM of Y-27632 (Day 0) and 0.25mM (Day 1) and 0.125mM (Day 2-6) of sodium butyrate. On day 6, the medium was changed to Step 2 medium, containing basal medium of DMEM/F12 plus Glutamax (Life Technologies), 1x B27 and N2 supplements (Life Technologies, #17502-048), 50 U/ml of penicillin/streptomycin, 0.05 mg/ml of L-ascorbic acid (Sigma-Aldrich), 0.4 mM of monothioglycerol (Wako), 100 ng/ml of human recombinant noggin (R&D systems) and 10 microM of SB-431542 (R&D systems). On day 10, the medium was changed to Step 3 medium, containing 100 ng/ml of human recombinant BMP4 (Humanzyme), 0.05 microM of all-trans retinoic acid (ATRA) (Sigma-Aldrich) and 2.5 microM of CHIR99021. The ventral anterior foregut cells (VAFECs) are obtained on day 14. Each medium was replaced every two days throughout the differentiation process.

extract_protocol: Total RNA was isolated using the PureLink RNA Mini Kit (Life Technologies) according to the manufacturer’s manual.

treatment_protocol: Induced AFECs and VAFECs were washed twice with PBS supplemented with 0.5 mM of EDTA and dissociated with Accutase at 37°C for 20 minutes. After resuspending the detached cells in four times the volume of DMEM/F12 containing 2% FBS, the cell clumps were removed using a cell strainer. For FACS, the dissociated cells were washed in 1% BSA/PBS, centrifuged at 800 rpm for five minutes, resuspended and incubated in mouse anti-human CPM antibody (Leica Microsystems) labeled with the Alexa 647-conjugated Fab fragment (Life Technologies) and FITC-conjugated mouse anti-human EpCAM antibody (BD Biosciences) at 4°C for 15 minutes. After rinsing with 1% BSA/PBS twice, the EpCAM+CPM+ and EpCAM+CPM- cells were sorted using the BD FACSAria II flowcytometer (BD Biosciences).  For MACS, the dissociated cells were resuspended and incubated in mouse anti-human CPM antibody solution at 4°C for 15 minutes. After washing twice with 0.5% BSA/PBS with 2mM EDTA, the labeled cells were incubated in anti-mouse IgG1 microbeads solution at 4°C for 15 minutes. After washing twice with the same buffer, the CPM+ cells were separated using a magnetic stainless column (Miltenyi Biotec).

value: endoderm

value: CPM+ VAFECs


title: EPCAMposCPMneg VAFECs replicate 3

source_name: 201B7-derived EPCAMposCPMneg VAFECs

value: EPCAM+CPM- VAFECs


title: EarlyL07

description: lung at 6 to 8 postovulatory weeks,sample 7


title: EPCAMposCPMneg VAFECs replicate 2


title: EarlyL04

description: lung at 6 to 8 postovulatory weeks,sample 4


title: EPCAMposCPMpos VAFECs replicate 3

source_name: 201B7-derived EPCAMposCPMpos VAFECs

value: EPCAM+CPM+ VAFECs


title: EPCAMposCPMneg VAFECs replicate 1


title: EPCAMposCPMpos VAFECs replicate 1


title: EarlyL08

description: lung at 6 to 8 postovulatory weeks,sample 8


title: EarlyL05

description: lung at 6 to 8 postovulatory weeks,sample 5


title: EPCAMposCPMpos VAFECs replicate 2


title: VAFECs

source_name: 201B7-derived VAFECs

value: VAFECs


title: CTL-d7-IgG

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

institute: Kazusa DNA Research Institute

description: gene expression on day 7 in CTL-treated tumor with control Rat IgG

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software v9.5 using default parameters (protocol GE1-v5_95_Feb07). The dataset was normalized using the 75 percentile median shift method.

source_name: tumor, day7, CTL-treated, IgG (pooled, n=3)

label_protocol: 500 ng of total RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

extract_protocol: Total RNA was extracted  from tumor tissues using the TRIzol (Invitrogen) according to manufacturer's instructions, and quantified using a NanoDrop-1000 spectrophotometer. Total RNA extracted from 3-4 tumor tissues in each group was pooled and used for gene chip analysis.

treatment_protocol: C57BL/6 mice were challenged with 1x106 B16F10 tumor cells. 9 days later (day 0), tumor bearing mice received 1x107 in vitro activated B16-specific (gp100-specific) CD90.1+ CTLs. Tumor tissues from untreated or ACT mice were harvested on day 1, 3, 5 and 7. Anti-IFNg or control Rat IgG antibodies were injected intraperitoneally on day 0 and 2 after CTL transfer.

value: tumor (B16F10)


title: EarlyL01

description: lung at 6 to 8 postovulatory weeks,sample 1


title: EarlyL02

description: lung at 6 to 8 postovulatory weeks,sample 2


title: AFECs

source_name: 201B7-derived AFECs

value: AFECs


title: OE7-C [roots]

city: Hong Kong

first: Boon Leong

last: Lim

address: 5N01, Kaddorie Biological Sciences Building, the University of Hong Kong, Pokafulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Normalized expression values are generated using a standard quantile normalization matrix (Bolstad et al., 2003) and Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003a; Irizarry et al., 2003b)

organism: Arabidopsis thaliana

source_name: Arabidopsis 20-day-old roots

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Arabidopsis (Col-0) seeds were germinated on MS medium supplemented with 2% (w/v) sucrose and grew under 12 hours light/12 hours at 21-23°C for 10 days and then transferred to soil under a 16 hours light (22°C) and 8 hours dark (18°C) cycle in plant growth chamber. Arabidopsis root were collected in the middle of day and grinded in liquid nitrogen.

extract_protocol: Total RNA extraction was manipulated using the RNeasy Mini Kit (Qiagen, USA) and quantified by the Bioanalyzer 2100 (Agilent Technologies, USA). First strand cDNA synthesis was performed with oligo dT primer using 10 μg total RNA. Double strand DNA synthesis and Cy 3 labeling from three biological replicates were performed by NimbleGen Systems, Inc. (USA).

treatment_protocol: Wild type, AtPAP2 T-DNA mutant line, AtPAP2 overexpression lines

value: AtPAP2 overexpression OE7

tag: cultivar

value: 20-day-old roots


title: OE21-B [roots]

value: AtPAP2 overexpression OE21


title: OE7-B [roots]


title: T-DNA-C [roots]

value: AtPAP2 T-DNA mutant


title: CTL-d7-aIFNg

description: gene expression on day 7 in CTL-treated tumor with anti-IFNg mAb

source_name: tumor, day7, CTL-treated, aIFNg (pooled, n=3)


title: OE7-A [roots]


title: OE21-C [roots]


title: T-DNA-A [roots]


title: Untreated-d7

description: gene expression on day 7 in untreated control tumor

source_name: tumor, day7, untreated (pooled, n=4)


title: CTL-d5-IgG

description: gene expression on day 5 in CTL-treated tumor with control Rat IgG

source_name: tumor, day5, CTL-treated, IgG (pooled, n=3)


title: OE21-A [roots]


title: T-DNA-B [roots]


title: CTL-d5

description: gene expression on day 5 in CTL-treated tumor

source_name: tumor, day5, CTL-treated (pooled, n=4)


title: CTL-d7

description: gene expression on day 7 in CTL-treated tumor

source_name: tumor, day7, CTL-treated (pooled, n=4)


title: CTL-d5-aIFNg

description: gene expression on day 5 in CTL-treated tumor with anti-IFNg mAb

source_name: tumor, day5, CTL-treated, aIFNg (pooled, n=3)


title: OE21-C [shoots]

source_name: Arabidopsis 20-day-old shoots

growth_protocol: Arabidopsis (Col-0) seeds were germinated on MS medium supplemented with 2% (w/v) sucrose and grew under 12 hours light/12 hours at 21-23°C for 10 days and then transferred to soil under a 16 hours light (22°C) and 8 hours dark (18°C) cycle in plant growth chamber. Arabidopsis shoot and root were collected in the middle of day and grinded in liquid nitrogen.

value: 20-day-old shoots


title: CTL-d3-IgG

description: gene expression on day 3 in CTL-treated tumor with control Rat IgG

source_name: tumor, day3, CTL-treated, IgG (pooled, n=3)


title: WT-C [roots]

value: WT


title: WT-B [roots]


title: CTL-d3-aIFNg

description: gene expression on day 3 in CTL-treated tumor with anti-IFNg mAb

source_name: tumor, day3, CTL-treated, aIFNg (pooled, n=3)


title: CTL-d3

description: gene expression on day 3 in CTL-treated tumor

source_name: tumor, day3, CTL-treated (pooled, n=4)


title: WT-A [roots]


title: OE21-A [shoots]


title: Untreated-d1

description: gene expression on day 1 in untreated control tumor

source_name: tumor, day1, untreated (pooled, n=4)


title: Untreated-d5

description: gene expression on day 5 in untreated control tumor

source_name: tumor, day5, untreated (pooled, n=4)


title: OE21-B [shoots]


title: CTL-d1

description: gene expression on day 1 in CTL-treated tumor

source_name: tumor, day1, CTL-treated (pooled, n=4)


title: OE7-B [shoots]


title: Untreated-d3

description: gene expression on day 3 in untreated control tumor

source_name: tumor, day3, untreated (pooled, n=4)


title: T-DNA-C [shoots]


title: OE7-A [shoots]


title: OE7-C [shoots]


title: apl3

city: Helsinki

first: Ykä

last: Helariutta

address: Viikinkaari 1

department: University of Helsinki

country: Finland

institute: Institute of Biotechnology

description: Gene expression data from apl Phloem

hyb_protocol: Labeling and hybridisation was done according to Affymetrics protocols (http://www.affymetrix.com)

scan_protocol: standard Affymetrix protocol, Scanning and Data-processing was done according to the protocols of the VIB nucleomics core facility (http://www.nucleomics.be).

source_name: apl mutant phloem

growth_protocol: Plants were grown on square plates (Greiner Labortechnik) with solid medium derived from standard MS medium incubated in a growth chamber under continuous light (110 μE.m-2.s-1 photosynthetically active radiation, supplied by cool-white fluorescent tungsten tubes; Osram) at 22°C.

extract_protocol: Root tissues were protoplasted according to [Iyer-Pascuzzi, A. S. & Benfey, P. N. Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol. 655, 313-319 (2010)].

value: phloem

tag: genotype

value: apl mutant

tag: ecotype

value: Columbia


title: WT-A [shoots]


title: apl2

description: Gene expression data from apl Phloem

data_processing: standard Affymetrix protocol, Scanning and Data-processing was done according to the protocols of the VIB nucleomics core facility (http://www.nucleomics.be).

label_protocol: Labeling and hybridisation was done according to Affymetrics protocols (http://www.affymetrix.com)

treatment_protocol: Root tissues were protoplasted according to [Iyer-Pascuzzi, A. S. & Benfey, P. N. Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol. 655, 313-319 (2010)].


title: WT-C [shoots]


title: WT4

description: Gene expression data from WT Phloem

source_name: WT Phloem

value: wild type


title: T-DNA-A [shoots]


title: WT3

description: Gene expression data from WT Phloem


title: WT2

description: Gene expression data from WT Phloem


title: WT-B [shoots]


title: apl1

description: Gene expression data from apl Phloem


status: Public on Aug 24 2014

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

description:
Wu229_hGFAPCre_B
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 5

hyb_protocol: as per manufacturer's protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using the oligo (v1.14) package in the R (v2.15) environment. Probeset level expression was derived using Robust Multi-array Average normalization.
probe group file: MoGene-1_1-st-v1.r4.pgf
meta-probeset file: MoGene-1_1-st-v1.r4.mps

source_name: hGFAP:GnasCKO, cerebellar tumor

label_protocol: as per manufacturer's protocol

growth_protocol: Mouse normal cerebellum or cerebellar tumor dissected at endpoint

extract_protocol: Standard total RNA extraction with TRIzol

treatment_protocol: not applicable

value: mixed C57BL/6 x 129

value: cerebellar tumor


description:
Wu235_Oligo1Cre-III
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 7

source_name: Oligo1:GnasCKO, cerebellar tumor


description:
Wu234_Oligo1Cre-2_II
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 6


title: normal adult cerebellum, postnatal day 60, replicate 1

description:
Wu227_P60CBL-ctrl-1
normal adult cerebellum, postnatal day 60

source_name: Wild-type, cerebellum

value: cerebellum

value: Wild-type

tag: age

value: postnatal day 60


description:
Wu226_OG-1T4
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 4


description:
Wu236_Oligo1Cre-5m_IV
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 8


description:
Wu233_Oligo1Cre-G0-4_B2C
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 5


title: normal cerebellum, postnatal day 122

description:
Wu217_CBP122
normal cerebellum, postnatal day 122

value: postnatal day 122


title: normal cerebellum, postnatal day 95

description:
Wu216_CBP95
normal cerebellum, postnatal day 95

value: postnatal day 95


description:
Wu232_hGFAPCre_4m-IV
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 8


title: normal adult cerebellum

description:
Wu218_HXL-1
normal adult cerebellum

value: adult


title: Control C59

city: San Antonio

first: Yury

middle: O.

last: Nunez

state: TX

address: 7703 Floyd Curl Drive MC6220

department: Pharmacy

institute: University of Texas at Austin

description:
5665159077_C
control mouse

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalized using quantile normalization with lumi package in R
The quality of the Illumina bead summary data was assessed using the Bioconductor packages Lumi and arrayQualityMetrics. Data preprocessing included variance stabilization and quantile normalization using the Lumi package. Statistical analysis comparing ethanol-treated and control groups was performed using the Bioconductor package limma, which implements an empirical Bayes approach in R (Smyth 2005). False discovery rate (FDR) was assessed using the Benjamini-Hochberg method.

source_name: control mouse

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was extracted using Ambion's mirVana™ miRNA Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: C57BL/6J x FVB/NJ F1

value: frontal cortex

tag: stress

value: control


description:
Wu224_OG-2A6
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 2


description:
Wu231_hGFAPCre_1-III
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 7


title: Control C66

description:
5665159077_H
control mouse


description:
Wu222_HG-6
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 4


description:
Wu221_HG-5
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 3


description:
Wu225_OG-1T3
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 3


title: Control C62

description:
5665159077_G
control mouse


title: Control C64

description:
5665159077_D
control mouse


title: Control C65

description:
5665159077_F
control mouse


description:
Wu223_OG-2A2
Oligo1:GnasCKO transgenic mouse cerebellar tumor, biological replicate 1


title: Control C60

description:
5665159077_E
control mouse


title: normal cerebellum, embryonic day 15

description:
Wu213_CBE15
normal cerebellum, embryonic day 15

value: embryonic day 15


title: normal cerebellum, embryonic day 18

description:
Wu214_CBE18
normal cerebellum, embryonic day 18

value: embryonic day 18


description:
Wu230_hGFAPCre_3-II
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 6


description:
Wu219_HG-1
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 1


description:
Wu220_HG-3
hGFAP:GnasCKO transgenic mouse cerebellar tumor, biological replicate 2


title: normal adult cerebellum, postnatal day 60, replicate 2

description:
Wu228_P60CBL-ctrl-2
normal adult cerebellum, postnatal day 60


title: normal cerebellum, postnatal day 0

description:
Wu215_CBP0
normal cerebellum, postnatal day 0

value: postnatal day 0


title: Ethanol-treated A32

description:
5665159054_E
treated mouse

source_name: treated mouse

value: ethanol


title: Control C55

description:
5665159057_F
control mouse


title: Control C54

description:
5665159057_D
control mouse


title: Control C56

description:
5665159057_H
control mouse


title: Ethanol-treated A50

description:
5665159057_G
treated mouse


title: Control C57

description:
5665159077_A
control mouse


title: Ethanol-treated A29

description:
5665159054_C
treated mouse


title: Ethanol-treated A34

description:
5665159054_G
treated mouse


title: Ethanol-treated A41

description:
5665159054_D
treated mouse


title: Ethanol-treated A49

description:
5665159057_E
treated mouse


title: Ethanol-treated A47

description:
5665159057_C
treated mouse


title: Ethanol-treated A39

description:
5665159054_B
treated mouse


title: Ethanol-treated A44

description:
5665159054_F
treated mouse


title: Ethanol-treated A45

description:
5665159054_H
treated mouse


title: Ethanol-treated A46

description:
5665159057_A
treated mouse


title: Ethanol-treated A9

description:
5665159043_E
treated mouse


title: Ethanol-treated A28

description:
5665159054_A
treated mouse


title: Ethanol-treated A20

description:
5665159043_F
treated mouse


title: Ethanol-treated A11

description:
5665159043_G
treated mouse


title: Ethanol-treated A3

description:
5665159043_A
treated mouse


title: Ethanol-treated A21

description:
5665159043_H
treated mouse


title: Control C52

description:
5665159057_B
control mouse


title: Ethanol-treated A13

description:
5665159043_B
treated mouse


title: Ethanol-treated A7

description:
5665159043_C
treated mouse


title: Ethanol-treated A19

description:
5665159043_D
treated mouse


title: leaf_HDSN rep3 31 days

city: Guelph

first: Max

last: Misyura

state: ON

address: 50 stone rd

department: Department of Cellular and Molecular Biology

institute: University of Guelph

data_processing: The gpr files were loaded into GeneSpring GX 11 (Agilent Technologies) and the GC-RMA normalization algorithm was applied. A minimum 2-fold change between normalized averages were used as a cut-off point setting for further analysis and Benjamini-Hochberg FDR was applied (p < 0.05).

organism: Oryza sativa

source_name: high density sufficient nitrogen

label_protocol: For global expression analysis, Rice Genome OneArray® Microarray chips were used.  Labelling, hybridization, and scanning of the chips were carried out by the University of Guelph Genomics facility (Guelph, Ontario, Canada) according to the manufacturer’s protocols (www.phalanxbiotech.com).

growth_protocol: The plants were grown in Rubbermaid containers (61x41x32 cm) at 450 µmol m-2 s-1, 16h day at 27o C/8h night at 23o C and 75% relative humidity.  High density treatment was defined as 40 plants per container and low density treatment was defined as 6 plants per container, uniformly spaced.  The samples for gene expression and metabolite analysis were collected from 21 and 31 days old plants.  The leaf tissues were frozen immediately in liquid nitrogen.

extract_protocol: Total RNA was isolated from 100mg of frozen leaf tissue with TRIzol reagent (Invitrogen).  RNeasy (Qiagen) columns were used to purify the RNA samples.   1mg of total RNA was converted into cDNA using Superscript (Quanta) kit.  Three biological replicates were used for microarray analysis.

value: 31 days

value: leaf

tag: treatment

value: high density sufficient nitrogen


title: GFAP-Gnas-2

hyb_protocol: DNA were hybridized on aCGH arrays (Nimblegen, Mouse CGH 3x720K Whole-Genome Tiling Array) according to the manufacturer’s protocol.

scan_protocol: not provided

data_processing:
Data from the aCGH arrays were analyzed using the Nexus aCGH software with recommended normalization settings.
Each sample was compared to a distributed baseline to identify amplified and deleted regions using a segmentation algorithm within Nexus Suite using a cutoff with gain (≥ 0.23) and loss (≤ –0.5) and significance threshold = 1.0E–5. Segments showing copy number variation were only reported if they occurred in list those regions of gain or loss with an individual False Discovery Rate (FDR) no greater than 5%.

label_protocol: not provided

extract_protocol: We isolated genomic DNAs from the cerebellum of adult wildtype mice and tumor tissue from individual GFAP-Gnas or Olig1-Gnas mutants (n = 3 for each genotype) using a DNA preparation kit (Zymo Inc.)

value: hGFAPCre+/-,Gnaslox/lox (hGFAP-Gnas)

value: WT


title: leaf_HDLN rep1 31 days

hyb_protocol: Labelling, hybridization, and scanning of the chips were carried out by the University of Guelph Genomics facility (Guelph, Ontario, Canada) according to the manufacturer’s protocols (www.phalanxbiotech.com).

source_name: high density limiting nitrogen

value: high density limiting nitrogen


title: leaf_HDLN rep3 31 days

scan_protocol: Labelling, hybridization, and scanning of the chips were carried out by the University of Guelph Genomics facility (Guelph, Ontario, Canada) according to the manufacturer’s protocols (www.phalanxbiotech.com).


title: leaf_HDSN rep2 31 days


title: GFAP-Gnas-3

value: cerebellum


title: leaf_HDSN rep1 31 days


title: leaf_LDSN rep3 31 days

source_name: low density sufficient nitrogen

value: low density sufficient nitrogen


title: leaf_LDLN rep2 31 days

source_name: low density limiting nitrogen

value: low density limiting nitrogen


title: leaf_HDLN rep2 31 days


title: Olig1-Gnas-3

value: Olig1Cre+/-,Gnaslox/lox (Olig1-Gnas)


title: leaf_HDLN rep2 21 days

value: 21 days


title: leaf_HDSN rep2 21 days


title: leaf_LDLN rep3 21 days


title: GFAP-Gnas-1


title: leaf_HDLN rep3 21 days


title: leaf_HDLN rep1 21 days


title: Control C63

description:
5665159077_B
control mouse

value: C57BL/6J x FVB/NJ F1

value: frontal cortex


title: leaf_LDLN rep3 31 days


title: leaf_LDLN rep1 31 days


title: leaf_HDSN rep1 21 days


title: leaf_HDSN rep3 21 days


title: Olig1-Gnas-2


title: leaf_LDLN rep1 21 days


title: leaf_LDSN rep3 21 days


title: leaf_LDLN rep2 21 days


title: leaf_LDSN rep1 31 days


title: leaf_LDSN rep2 31 days


title: 251486828152-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Between-array normalization using the quantile normalization  in R, using the limma package

source_name: Sunitinib 2

label_protocol: cRNA Agilent

extract_protocol: Chomzynski

value: Xenograft

tag: amount in (µg)

tag: rin number

value: sunitinib (40mg/kg/day)


title: 251486828152-1

source_name: Vehicle 2

value: vehicle


title: Olig1-Gnas-1


title: leaf_LDSN rep2 21 days


title: 251486828153-1

source_name: Vehicle 1


title: 251486828153-2

source_name: Sunitinib 1


title: leaf_LDSN rep1 21 days


title: Mst1/2 -/- hepatocellular carcinoma tumor MST12_HCC_01

status: Public on Aug 23 2014

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 45281 probes on the Illumina MouseWG-6 v2.0 were used.

hyb_protocol: Labeled, amplified material (1500 ng per array) was hybridized to the Illumina MouseWG-6 v2.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: MST12 HCC 01

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 750 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

value: hepatocellular carcinoma tumor


title: Mst1/2 -/- hepatocellular carcinoma tumor MST12_HCC_03

source_name: MST12 HCC 03


title: Mst1/2 -/- Surrounding Liver MST12_ST_02

source_name: MST12 ST 02

value: Surrounding Liver


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_10

source_name: Sav1 HCC 10


title: Mst1/2 -/- hepatocellular carcinoma tumor MST12_HCC_02

source_name: MST12 HCC 02


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_09

source_name: Sav1 HCC 09


title: Mst1/2 -/- hepatocellular carcinoma tumor MST12_HCC_04

source_name: MST12 HCC 04


title: Mst1/2 -/- Surrounding Liver MST12_ST_01

source_name: MST12 ST 01


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_08

source_name: Sav1 HCC 08


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_11

source_name: Sav1 HCC 11


title: Mst1/2 -/- Surrounding Liver MST12_ST_03

source_name: MST12 ST 03


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_07

source_name: Sav1 HCC 07


title: 557245A12 - G2-Gravity_BR2 vs G2-Control_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Cell cycle and cell proliferation are decoupled under altered gravity conditions. We have previously shown that semisolid cell cultures of Arabidopsis suffer overall genome changes in response to altered gravity and also that cell cycle stages duration is altered. By using synchronized cell cultures we will demonstrate the precise alterations in cell cycle duration and also the transcriptional signature in any of them.

hyb_protocol: G2-Control_BR2 Cy5 / G2-Gravity_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: cell culture/primary cell - Media=MSS medium hygrometry=On solution Temperature=27ºC Light=Dark conditions

treatment_protocol: no treatment

tag: cell cycle phase

value: Control

tag: arabidopsis thaliana (columbia)  - age

tag: cell culture

treatment_protocol: Name:Gravity 7h - environmental treatment - abiotic stress,microgravity:time 14hour . We will use 12 samples (two RNA Biological replicate of 3 experimental and 3 control conditions). Material is from Arabidopsis thaliana cell cultures (MM2D) synchronized with Aphidicolin during 24 hours and then exposed to altered gravity or 1g control conditions. Samples description (cell cultures were collected and frozen in liquid nitrogen until RNA extraction, harvesting stage according to Menges M, Murray JA: Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity. Plant J 2002, 30(2):203-212.)

value: Gravity


title: 557245A11 - G2-Control_BR2 vs G2-Gravity_BR2

hyb_protocol: G2-Gravity_BR2 Cy5 / G2-Control_BR2 Cy3 : 30pmol.


title: 557245A02 - 14hr-Gravity_BR1 vs 14hr-Control_BR1

hyb_protocol: 14hr-Control_BR1 Cy5 / 14hr-Gravity_BR1 Cy3 : 30pmol.

source_name: 14hr-Control_BR1 (Asynchronous cells)

tag: time

source_name: 14hr-Gravity_BR1 (Asynchronous cells)

treatment_protocol: Name:Gravity 14h - environmental treatment - abiotic stress,microgravity:time 14hour . We will use 12 samples (two RNA Biological replicate of 3 experimental and 3 control conditions). Material is from Arabidopsis thaliana cell cultures (MM2D) synchronized with Aphidicolin during 24 hours and then exposed to altered gravity or 1g control conditions. Samples description (cell cultures were collected and frozen in liquid nitrogen until RNA extraction, harvesting stage according to Menges M, Murray JA: Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity. Plant J 2002, 30(2):203-212.)


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_06

source_name: Sav1 HCC 06


title: 557245A07 - G1-Control_BR2 vs G1-Gravity_BR2

hyb_protocol: G1-Gravity_BR2 Cy5 / G1-Control_BR2 Cy3 : 30pmol.


title: 557245A05 - G1-Control_BR1 vs G1-Gravity_BR1

hyb_protocol: G1-Gravity_BR1 Cy5 / G1-Control_BR1 Cy3 : 30pmol.


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_05

source_name: Sav1 HCC 05


title: 557245A10 - G2-Control_BR1 vs G2-Gravity_BR1

hyb_protocol: G2-Gravity_BR1 Cy5 / G2-Control_BR1 Cy3 : 30pmol.


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_04

source_name: Sav1 HCC 04


title: 557245A04 - 14hr-Gravity_BR2 vs 14hr-Control_BR2

hyb_protocol: 14hr-Control_BR2 Cy5 / 14hr-Gravity_BR2 Cy3 : 30pmol.

source_name: 14hr-Control_BR2 (Asynchronous cells)

source_name: 14hr-Gravity_BR2 (Asynchronous cells)


title: 557245A09 - G2-Gravity_BR1 vs G2-Control_BR1

hyb_protocol: G2-Control_BR1 Cy5 / G2-Gravity_BR1 Cy3 : 30pmol.


title: 557245A08 - G1-Gravity_BR2 vs G1-Control_BR2

hyb_protocol: G1-Control_BR2 Cy5 / G1-Gravity_BR2 Cy3 : 30pmol.


title: 557245A01 - 14hr-Control_BR1 vs 14hr-Gravity_BR1

hyb_protocol: 14hr-Gravity_BR1 Cy5 / 14hr-Control_BR1 Cy3 : 30pmol.


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_03

source_name: Sav1 HCC 03


title: 557245A06 - G1-Gravity_BR1 vs G1-Control_BR1

hyb_protocol: G1-Control_BR1 Cy5 / G1-Gravity_BR1 Cy3 : 30pmol.


title: 557245A03 - 14hr-Control_BR2 vs 14hr-Gravity_BR2

hyb_protocol: 14hr-Gravity_BR2 Cy5 / 14hr-Control_BR2 Cy3 : 30pmol.


title: AR112Q-KRKR + vehicle 2

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 3510 MSRB I 1150 W Medical Center Dr

department: Pathology

institute: University of Michigan

description: Gene expression data from PC12 cells expression AR112Q-KRKR in the absence of androgen

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene 2.1 ST Array Strips using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment 3.0.0. RMA was used to normalize the data and fit log2 transformed expression values.

organism: Rattus norvegicus

source_name: PC12 cells expressing AR112Q-KRKR in the absence of androgen

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3).

growth_protocol: AR10Q, AR112Q, and AR112QKRKR PC12 cells were cultured at 37ºC at 10% CO2.

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

treatment_protocol: PC12 cells were induced to express each AR variant with doxycycline in the presence of 10nM R1881 or ethanol vehicle for 24 hours.

value: pheochromocytoma (PC12)

tag: genotype/variation

tag: agent

value: control


title: AR112Q-KRKR + ligand 1

description: Gene expression data from PC12 cells expression AR112Q-KRKR in the presence of androgen

source_name: PC12 cells expressing AR112Q-KRKR in the presence of androgen

tag: cell line

value: synthetic androgen R1881


title: AR112Q + ligand 3

description: Gene expression data from PC12 cells expression AR112Q in the presence of androgen

source_name: PC12 cells expressing AR112Q in the presence of androgen


title: Wt Normal Liver NL_07

source_name: NL 07

value: Wt

tag: tissue

value: Normal Liver


title: Sav1 -/- Surrounding Liver Sav1_ST_01

source_name: Sav1 ST 01


title: AR112Q-KRKR + vehicle 3


title: Sav1 -/- Surrounding Liver Sav1_ST_02

source_name: Sav1 ST 02


title: Mst1/2 flox Normal Liver NL_04

source_name: NL 04

value: Mst1/2 flox


title: AR112Q + ligand 2


title: Sav1 -/- Surrounding Liver Sav1_ST_03

source_name: Sav1 ST 03


title: AR112Q-KRKR + ligand 3


title: AR112Q-KRKR + vehicle 1


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_02

source_name: Sav1 HCC 02


title: Sav1 -/- hepatocellular carcinoma tumor Sav1_HCC_01

source_name: Sav1 HCC 01


title: AR112Q + ligand 1


title: Sav1 -/- Surrounding Liver Sav1_ST_06

source_name: Sav1 ST 06


title: Sav1 -/- Surrounding Liver Sav1_ST_05

source_name: Sav1 ST 05


title: Wt Normal Liver NL_08

source_name: NL 08


title: Sav1 -/- Surrounding Liver Sav1_ST_07

source_name: Sav1 ST 07


title: AR112Q-KRKR + ligand 2


title: Mst1/2 flox Normal Liver NL_05

source_name: NL 05


title: Mst1/2 flox Normal Liver NL_06

source_name: NL 06


title: Sav1 flox Normal Liver NL_01

source_name: NL 01

value: Sav1 flox


title: Sav1 flox Normal Liver NL_03

source_name: NL 03


title: AR112Q + vehicle 3

description: Gene expression data from PC12 cells expression AR112Q in the absence of androgen

source_name: PC12 cells expressing AR112Q in the absence of androgen


title: Sav1 flox Normal Liver NL_02

source_name: NL 02


title: AR112Q + vehicle 2


title: babA

city: Yufu

first: Katsuhiro

last: Hanada

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Faculty of Medicine

institute: Oita University

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: AGS_H. pylori TN2gf6 babA mutant

label_protocol: The cRNA was amplified and labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc. CA, USA).

growth_protocol: Cells were cultred in RPMI+10%FBS at 37 degree C with 5% carbon dioxide.

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

treatment_protocol: Cells were infected with H. pylori and incubated for 24 hours. Then cells were fixed with TRizol.

value: AGS

tag: cell type

value: gastric cancer cell line

tag: infected with

value: H. pylori TN2gf6 babA mutant


title: low miR-146a_patient 8412_5q- syndrome

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: For each sample a hybridization cocktail was created that includes a total of 2.5 micrograms of fragmented cDNA. Probe arrays were filled with hybridization cocktail and placed in a GeneChip® Hybridization Oven 640 (Affymetrix) for 18 hours. Arrays were then washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G. All files including .dat, .cel, and .chp files were created by the scanning and analysis software, the Genechip Operating Software (Affymetrix).

data_processing: Use RMA to normalize all arrays (samples) for a project. Average means of samples in the same group, i.e. miR-146 low versus miR-146a high groups. Create interpretations to compare miR-146 low versus miR-146a high groups. Filter raw data to remove entities (genes) not being expressed. The processed data set was used for gene set enrichment analysis and gene ontology.

source_name: low miR-146a, patient 8412, 5q- syndrome

label_protocol: Assays from NuGEN were used to create biotin-labeled cDNA target. Specifically the WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) was used to prepare target cDNA.  Then the WT-Ovation Exon Module v1.0 (NuGEN) was used to create sense-strand cDNA targets. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragmented and labeled the sense-strand cDNA targets.

growth_protocol: Bone marrow aspiration were prepared from MDS/AML patients with deletion of chromosome 5q. Red blood cells were lysed, and the mononuclear bone marrow cells were used for RNA extraction.

extract_protocol: Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

treatment_protocol: The patients haven't received any chemotherapy at the time of bone marrow aspiration.

tag: phenotype

value: 5q- syndrome

tag: gender

value: female

tag: mir-146a expression

value: low

value: bone marrow


title: high miR-146a_patient 4982_RCMD-RS

source_name: high miR-146a, patient 4982, RCMD-RS

value: RCMD-RS

value: male

value: high


title: VacA_cagPAI

source_name: AGS_H. pylori TN2gf6 vacA cag PAI mutant

value: H. pylori TN2gf6 vacA cag PAI mutant


title: high miR-146a_patient 5534_sAML

source_name: high miR-146a, patient 5534, sAML

value: sAML


title: VacA

source_name: AGS_H. pylori TN2gf6 vacA mutant

value: H. pylori TN2gf6 vacA mutant


title: AR112Q + vehicle 1

value: pheochromocytoma (PC12)

value: control


title: AGS_TN_2

source_name: AGS_H. pylori TN2gf6 strain

value: H. pylori TN2gf6 strain


title: low miR-146a_patient 8839_RCMD

source_name: low miR-146a, patient 8839, RCMD

value: RCMD


title: AGS_cagA

source_name: AGS_H. pylori TN2gf6 cagA mutant

value: AGS

value: H. pylori TN2gf6 cagA mutant


title: AR10Q + ligand 2

description: Gene expression data from PC12 cells expression AR10Q in the presence of androgen

source_name: PC12 cells expressing AR10Q in the presence of androgen

value: synthetic androgen R1881


title: high miR-146a_patient 7957_RA

source_name: high miR-146a, patient 7957, RA

value: RA


title: AGS_TN_1

value: gastric cancer cell line


title: AR10Q + ligand 1


title: low miR-146a_patient 8285_RCMD

source_name: low miR-146a, patient 8285, RCMD

value: low


title: AR10Q + ligand 3


title: low miR-146a_patient 4233_5q- syndrome

source_name: low miR-146a, patient 4233, 5q- syndrome

value: 5q- syndrome

value: female

value: bone marrow


title: AGS_NT

value: none (control)


title: high miR-146a_patient 4688_RAEB

source_name: high miR-146a, patient 4688, RAEB

value: male

value: high


title: Sav1 -/- Surrounding Liver Sav1_ST_04

source_name: Sav1 ST 04

tag: genotype

value: Surrounding Liver


title: AR10Q + vehicle 2

description: Gene expression data from PC12 cells expression AR10Q in the absence of androgen

source_name: PC12 cells expressing AR10Q in the absence of androgen

value: pheochromocytoma (PC12)


title: AGS_PAI

source_name: AGS_H. pylori TN2gf6 cag PAI mutant

value: H. pylori TN2gf6 cag PAI mutant


title: AR10Q + vehicle 1

value: control


title: low miR-146a_patient 5284_sAML

source_name: low miR-146a, patient 5284, sAML

value: sAML


title: AR10Q + vehicle 3


title: Serbian_Serbia9

status: Public on Aug 22 2014

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Serbian

value: blood

tag: region

value: Serbia


title: Serbian_Serbia5


title: Serbian_Serbia16


title: Serbian_Serbia3


title: Serbia_Serbia19


title: Bosnian_8

value: Bosniac

value: Bosnia and Herzegovina


title: Bosnian_6


title: Bosnian_2


title: Serbian_Serbia10


title: Serbian_B-H9


title: Bosnian_5


title: Serbian_Serbia4


title: Bosnian_4


title: Bosnian_7


title: Serbian_B-H4


title: Bosnian_12


title: Serbian_Serbia7


title: Serbian_B-H11


title: Bosnian_15


title: Bosnian_14


title: Serbian_Serbia11


title: Serbian_Serbia12


title: Bosnian_13


title: Serbian_Serbia2


title: Serbian_Serbia6


title: Serbian_Serbia1


title: Bosnian_3


title: Bosnian_16


title: Serbian_Serbia18


title: Serbian_B-H7


title: Montenegro19

value: Montenegrin

value: Monte Negro


title: Montenegro9


title: Montenegro10


title: Bosnian_1


title: Montenegro20


title: Kosovo15

value: Kosovar

value: Kosovo


title: Montenegro11


title: Montenegro14


title: Bosnian_11


title: Montenegro7


title: Montenegro6


title: Montenegro4


title: Montenegro15


title: Montenegro21


title: Kosovo18


title: Kosovo7


title: Kosovo8


title: Macedonian9

value: Macedonian

value: FYR Macedonia


title: Kosovo14


title: Montenegro1


title: Kosovo12


title: Kosovo1


title: Montenegro17


title: Kosovo16


title: MGHc198

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated with High Pure RNA paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: disease state

value: hepatitis C virus (HCV)-related liver cirrhosis

value: liver

tag: prognostic prediction

value: Good


title: MGHc197

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: MGHc200

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Poor


title: MGHc196


title: MGHc195

value: Intermediate


title: Macedonian7


title: MGHc192


title: MGHc194


title: MGHc187


title: MGHc188


title: Bosnian_10


title: Macedonian6


title: MGHc182


title: MGHc189


title: MGHc181


title: Macedonian8


title: MGHc184


title: MGHc191


title: MGHc180


title: MGHc178


title: MGHc179


title: MGHc175


title: Montenegro5


title: MGHc174


title: MGHc172


title: Kosovo11


title: MGHc173


title: MGHc166


title: MGHc164


title: MGHc167


title: MGHc162


title: MGHc160


title: MGHc161


title: MGHc183


title: MGHc165


title: MGHc158


title: MGHc156


title: MGHc159


title: MGHc153


title: MGHc149


title: MGHc150


title: MGHc152


title: MGHc148


title: MGHc147


title: MGHc143


title: MGHc141


title: MGHc145


title: MGHc138


title: Macedonian3


title: MGHc177


title: MGHc136


title: MGHc135


title: MGHc139


title: MGHc134


title: MGHc133


title: MGHc132


title: MGHc190


title: MGHc137


title: Macedonian22


title: MGHc131


title: MGHc186


title: MGHc163


title: Macedonian21


title: MGHc123


title: MGHc124


title: MGHc129


title: MGHc128


title: MGHc121


title: MGHc117


title: MGHc115


title: MGHc120


title: MGHc151


title: MGHc112


title: MGHc114


title: MGHc111


title: MGHc106


title: MGHc105


title: MGHc104


title: MGHc118


title: MGHc170


title: MGHc101


title: MGHc100


title: MGHc176


title: MGHc098


title: Macedonian14


title: MGHc092


title: MGHc095


title: MGHc122


title: MGHc088


title: MGHc089


title: MGHc087


title: MGHc084


title: Macedonian19


title: Macedonian20


title: MGHc090


title: MGHc085


title: MGHc081


title: MGHc073


title: MGHc078


title: MGHc075


title: MGHc079


title: MGHc080


title: MGHc077


title: MGHc074


title: MGHc082


title: MGHc072


title: MGHc097


title: MGHc076


title: MGHc071


title: Macedonian2


title: MGHc070


title: MGHc069


title: Macedonian17b-d


title: MGHc061


title: MGHc064


title: MGHc063


title: MGHc065


title: Macedonian10


title: MGHc057


title: MGHc058


title: MGHc052


title: MGHc055


title: MGHc060


title: MGHc045


title: MGHc046


title: MGHc050


title: MGHc051


title: MGHc043


title: MGHc040


title: MGHc044


title: MGHc038


title: MGHc039


title: MGHc036


title: MGHc037


title: MGHc034


title: MGHc033


title: Macedonian12


title: MGHc054


title: MGHc026


title: MGHc027


title: MGHc041


title: MGHc020


title: MGHc021


title: MGHc022


title: MGHc017


title: MGHc018


title: MGHc024


title: MGHc016


title: MGHc015


title: MGHc014


title: MGHc012


title: MGHc008


title: MGHc011


title: MGHc007


title: MGHc009


title: MGHc006


title: MGHc002


title: MGHc001


title: MGHc025


title: MGHc004


title: MGHc019


title: lc_330

extract_protocol: RNA was isolated with TRIzol LS reagent (Invitrogen) according to manufacturer’s protocol.


title: lc_322


title: lc_329


title: lc_319


title: lc_318


title: lc_311


title: lc_314


title: lc_309


title: lc_310


title: lc_307


title: lc_297


title: lc_305


title: lc_304


title: lc_291


title: lc_282


title: lc_294


title: lc_284


title: lc_279


title: lc_273


title: lc_266


title: lc_274


title: lc_265


title: lc_263


title: lc_277


title: lc_258


title: lc_255


title: lc_254


title: lc_256


title: lc_306


title: lc_253


title: lc_245


title: lc_287


title: lc_241


title: lc_244


title: lc_276


title: lc_240


title: lc_234


title: lc_232


title: lc_233


title: lc_229


title: Patient4_explant_Lt

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

value: hepatitis C virus (HCV)-infected


title: lc_222


title: lc_217


title: ECM Bioconditioned gelfoam

city: Temple

first: Carl

middle: A

last: Gregory

state: Texas

address: 5701 Airport Road

department: Molecular and Cellular Medicine

institute: Texas A&M Health Sciences Center

description: abbreviated sample name BGF

hyb_protocol: Total of 12.5 ug of labeled aRNA was fragmented and hybridized (GeneChip Hybridization Oven 640, Affymetrix) onto a human array (HG-U133 Plus 2.0, Affymterix) followed by washing and staining (GeneChip Fluidics Station 450, Affymetrix) with GeneChip Wash and Stain Kit (Affymetrix) using the Command Console software (Affymetrix)

scan_protocol: Array was scanned with 7G GeneChip Scanner (Affymetrix) using the Command Console software (Affymetrix) and the image were checked for quality.

data_processing: The CHP file was created using the Expression Console software (Affymetrix) and MAS5 analysis.

source_name: MSCs_ECM coated gelfoam

label_protocol: Total of 200 ng of RNA sample was used to prepared labeled aRNA according to manufacturer’s instructions for GeneChip 3’ IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from the cranial bones using a total RNA isolation kit (High Pure, Roche). Bones were incubated in RNA extraction buffer at ambient temperature for 4 h and processed in accordance with the protocol.

treatment_protocol: As per Zeitouni et al.  Human mesenchymal stem cell-derived matrices for enhanced osteoregeneration. Sci Transl Med. 2012;4(132):132ra55. and Clough et al 2014 "Bone regeneration with osteogenically enhanced mesenchymal stem cells and their extracellular matrix proteins." Journal of Bone and Mineral Research , in Press

value: Adult human mesenchymal stem cells (MSCs)

tag: cultured on

value: ECM-coated gelfoam for 5days


title: Gelfoam only

description: abbreviated sample name G

growth_protocol: As per Zeitouni et al.  Human mesenchymal stem cell-derived matrices for enhanced osteoregeneration. Sci Transl Med. 2012;4(132):132ra55.

value: standard gelfoam for 5days


title: lc_236


title: Patient4_explant_Rt

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: lc_216


title: Patient3_severe_Bx2

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: Patient3_severe_Bx1


title: Patient2_mild_Bx2


title: lc_228


title: Patient1_mild_Bx1


title: Patient2_mild_Bx1


title: Patient2_mild_Bx1_duplicate


title: Patient1_mild_Bx2


title: AK6

city: Lund

first: Jenny

last: Karlsson

address: BMC C13

department: Clinical genetics

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: Data was normalized with the quantile normalisation algorithm in the BeadStudio (Illumina) software

source_name: Non-neoplastic tissue

label_protocol: Illumina Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v1.1)

extract_protocol:
Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions. Quality control was performed with Agilent Bioanalyzer.
Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions. Quality control was performed with Agilent Bioanalyzer.

value: Adult kidney

tag: age


title: 66_Lund_AS_sample Secondary

first: Emelie

last: Styring

address: Skanes University Hospital

department: Dept of Orthopedics

description: Secondary

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: Gene expression data were uploaded and processed in the GenomeStudio software (Illumina, San Diego, CA). Data were normalized using background correction and the cubic spline method.

source_name: FFPE tumor tissue

label_protocol: Standard Illumina labeling protocol (Ligated products were PCR-amplified and labeled with a universal Cy3-coupled primer, after which single-stranded labeled products were precipitated and then hybridized to WG gene expression BeadChips as previously described (Kuhn et al. 2004).)

extract_protocol: Non-necrotic tumor areas were macro-dissected from FFPE blocks and RNA extraction was performed from three 10-µm sections using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia) according to the manufacturer's instructions.

tag: Sex

value: f

tag: year of birth

tag: year of breast cancer

value: Unknown

tag: year of angiosarcoma

tag: previous radiotherapy to tumor area

value: Yes


title: 64_Lund_AS_sample Secondary

description: Secondary


title: 68_Lund_AS_sample

tag: replicate

value: Techn repl (sample 68 :sample 21)


title: 69_Lund_AS_sample Primary

description: Primary

value: Not applicable

value: No


title: 65_Lund_AS_sample Primary

description: Primary

value: m


title: 70_Lund_AS_sample Secondary

description: Secondary


title: lc_212

value: hepatitis C virus (HCV)-related liver cirrhosis

tag: tissue


title: lc_199

value: liver


title: 63_Lund_AS_sample Primary

description: Primary

value: Biol repl B1


title: lc_203

value: Good


title: AK5


title: 67_Lund_AS_sample Primary

description: Primary


title: lc_196


title: 60_Lund_AS_sample Secondary

description: Secondary


title: 59_Lund_AS_sample Primary

description: Primary


title: AK3


title: 58_Lund_AS_sample Secondary

description: Secondary


title: AK1


title: AK2


title: FK4

description: Clontech  CatNo 636584 LotNo 8082007A

extract_protocol:
NA
Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions. Quality control was performed with Agilent Bioanalyzer.

value: Fetal kidney

value: 12-31 weeks


title: AK4


title: 56_Lund_AS_sample Primary

description: Primary


title: lc_195


title: lc_193


title: lc_198


title: 57_Lund_AS_sample Secondary

description: Secondary


title: lc_187

value: Intermediate


title: 55_Lund_AS_sample Secondary

description: Secondary


title: 54_Lund_AS_sample Primary

description: Primary


title: FK3

description: Stratagene CatNo 540169

value: M

value: 18 and 22 weeks


title: FK1

description: BioChain CatNo R1244142-10, LotNo A507218

value: F

value: 30 weeks


title: lc_186


title: lc_172


title: lc_189


title: CCSK36

source_name: Tumour tissue

value: Clear cell sarcoma of the kidney

value: 1 year


title: lc_170


title: 61_Lund_AS_sample Secondary

description: Secondary

value: f

value: Yes


title: Liver_KO_hypoglycemic_P1, replicate 4

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (8x60K) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chambers were disassembled in Wash Buffer 1 and the slides were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on an Agilent High Resolution C Scanner (G2565CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages from Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for at least 12 out of 15 microarrays or with a weight of 1 in 2 microarrays from at least one experimental group. Additionally, we replaced by NA all values which were flagged with gFeatNonUniOL==1. The filtered data were then stored as an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33709 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver, hypoglycaemic KO, P1

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice with a maternally-inherited deletion of the miR-379/miR-410 cluster and wild-type littermates on a C57BL/6J genetic background were housed at room temperature on a 12h light/dark cycle (lights on at 8:00 am) and had free access to food (standard rodent chow) and tap water.

extract_protocol: Immediately following euthanasia, liver was removed, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with Tri-reagent (Euromedex) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Breeding was performed overnight. Animals were obtained by natural delivery. The day of delivery was considered P0. Animals were studied on postnatal day 1 (P1)

tag: strain

tag: blood glucose (mg/dl)


title: Liver_KO_hypoglycemic_P1, replicate 6


title: FK2

description: BioChain CatNo R1244142-10, LotNo A507217

tag: gender


title: 53_Lund_AS_sample Secondary

description: Secondary

value: Unknown


title: 51_Lund_AS_sample Secondary

description: Secondary

value: Biol repl G1


title: CCSK37

value: 4 years


title: Liver_KO_hypoglycemic_P1, replicate 3

value: liver


title: lc_169

value: hepatitis C virus (HCV)-related liver cirrhosis

value: Poor


title: Liver_KO_hypoglycemic_P1, replicate 1


title: CCSK35


title: Liver_KO_hypoglycemic_P1, replicate 7


title: Liver_KO_normoglycemic_P1, replicate 3

source_name: Liver, normoglycemic KO, P1


title: CCSK34

value: 2 years


title: lc_167


title: CCSK31

value: 3 months


title: lc_166


title: 50_Lund_AS_sample Primary

description: Primary

value: Not applicable

value: Biol repl B2

value: No


title: CCSK30

value: M


title: 46_Lund_AS_sample Secondary

description: Secondary

value: Biol repl D2


title: 47_Lund_AS_sample Secondary

description: Secondary

value: Biol repl H1


title: lc_164


title: Liver_KO_hypoglycemic_P1, replicate 5


title: 45_Lund_AS_sample Secondary

description: Secondary


title: lc_154

value: Intermediate


title: 44_Lund_AS_sample Secondary

description: Secondary

value: f


title: Liver_WildType_P1, replicate 4

source_name: Liver, Wild-type, P1


title: CCSK28

value: Clear cell sarcoma of the kidney


title: Liver_WildType_P1, replicate 5


title: Liver_KO_normoglycemic_P1, replicate 2


title: lc_153


title: Liver_KO_normoglycemic_P1, replicate 1


title: CCSK29

value: 8 months


title: 52_Lund_AS_sample Primary

description: Primary

value: m


title: 41_Lund_AS_sample Primary

description: Primary


title: 48_Lund_AS_sample Secondary

description: Secondary

value: Biol repl E1

value: Yes


title: 43_Lund_AS_sample Primary

description: Primary


title: CCSK27

value: F

value: 9 months


title: Liver_WildType_P1, replicate 3

value: liver


title: Liver_WildType_P1, replicate 2


title: lc_149

value: hepatitis C virus (HCV)-related liver cirrhosis

value: Poor


title: Liver_KO_hypoglycemic_P1, replicate 2


title: CCSK23

value: 2 years


title: lc_145

value: Good


title: Liver_WildType_P1, replicate 1


title: lc_144


title: CCSK26

value: M


title: lc_146


title: lc_141


title: 40_Lund_AS_sample Secondary

description: Secondary


title: 39_Lund_AS_sample Primary

description: Primary

value: Not applicable

value: No


title: 38_Lund_AS_sample Secondary

description: Secondary

value: Biol repl G2


title: CCSK21


title: CCSK25

value: 1 year


title: CCSK22

value: Clear cell sarcoma of the kidney

value: 3 years


title: CCSK19


title: 37_Lund_AS_sample Primary

description: Primary

value: f


title: lc_140


title: lc_139