title: HepaRG_Chol_3

source_name: HepaRG, Cholangiocyte, day10, replicate3


title: HepaRG_cHep_2

status: Public on Oct 28 2013

type: RNA

city: Rennes

first: Hélène

last: Dubois-Pot-Schneider

address: Hopital Pontchaillou, rue Henri Le Guilloux

country: France

institute: INSERM UMR 991

description: Gene expression of HepaRG-committed hepatocyte (10 days of normal culture conditions)

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 manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE_1-107_sep09_ssSurogates and Grid: 028004_D_F_20110325. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 100% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

molecule: total RNA

organism: Homo sapiens

source_name: HepaRG, committed Hepatocyte, day10, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fischer Scientific, Waltham, MA).  amplification yield was 4.04 ± 0.53 µg cRNA and specific activity was 11.97 ± 0.98 pmol Cy3 per µg cRNA.

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations. RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

treatment_protocol: hESC (WA09, WiCell) were maintained on irradiated mouse embryonic fibroblast feeder cells, in DMEM/F12 medium supplemented with 20% knockout serum replacement, 1mM L-glutamine, 1% non essential amino acids, 0.1 mM beta-mercaptoethanol, and 4 ng/ml bFGF.

tag: differentiation state

value: committed hepatocyte


title: HepaRG_HB_3

description: Gene expression of HepaRG-hepatoblast (4 days of culture)

source_name: HepaRG, Hepatoblast, day4, replicate3

tag: origin cell line

value: HepaRG

value: Hepatoblast

tag: time

value: 4 days


title: bone marrow_case_rep1 [2784]

status: Public on Oct 29 2013

type: genomic

city: Shanghai

first: xiaoqin

last: wang

address: 12 wulumuqi road central

country: China

institute: Huashan  hospital

description: patient bone marrow

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software 2011.1

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purifiedusing QIAamp DNA Mini Kit according to standard instructions

tag: gender

value: male

tag: tissue

value: bone marrow

tag: disease state

value: myelodysplastic syndrome

tag: age


title: HepaRG_HB_2

source_name: HepaRG, Hepatoblast, day4, replicate2


title: bone marrow_case_rep2 [5157]

description: patient bone marrow

value: female


title: HepaRG_cHep_1

source_name: HepaRG, committed Hepatocyte, day10, replicate1


title: HepaRG_Chol_2

description: Gene expression of HepaRG-cholangiocyte (10 days of culture)

source_name: HepaRG, Cholangiocyte, day10, replicate2

value: Cholangiocyte

value: 10 days


title: hESC_Chol_2

description: Gene expression of hESC-Cholangiocyte (23 days of culture)

source_name: hESC, Cholangiocyte, day23, replicate2

value: hESC

value: 23 days


title: hESC_Chol_5

source_name: hESC, Cholangiocyte, day23, replicate5


title: hESC_Chol_4

source_name: hESC, Cholangiocyte, day23, replicate4


title: hESC_Chol_3

source_name: hESC, Cholangiocyte, day23, replicate3


title: HepaRG_HB_1

source_name: HepaRG, Hepatoblast, day4, replicate1


title: bone marrow_control_rep4 [H]

description: normal bone marrow

value: normal


title: hESC_Chol_1

source_name: hESC, Cholangiocyte, day23, replicate1


title: bone marrow_control_rep1 [B]

description: normal bone marrow


title: hESC_HB_5

description: Gene expression of hESC-Hepatoblast (10 days of culture)

source_name: hESC, Hepatoblast,  day10, replicate5


title: hESC_HB_4

source_name: hESC, Hepatoblast,  day10, replicate4


title: bone marrow_control_rep2 [E]

description: normal bone marrow


title: Total Homogenate_Control_12 - Outlier

city: Austin

first: Dana

last: Moat

state: Texas

address: 2500 Speedway, MBB 1.138

department: Waggoner center for alcohol and addiction research

country: USA

institute: University of Texas at Austin

description:
TH19
Control mice were given a 24-hour access for 30 days to two bottle of water

hyb_protocol: According to manufacturer’s instructions.

data_processing:
The data were preprocessed using variance stabilization transformation (variance within array) (Dunning, Ritchie et al. 2008, Lin, Du et al. 2008), quantile normalized (variance between arrays), and background subtracted using ‘Lumi’ package (Du, Kibbe et al. 2007, Du, Kibbe et al. 2008). Quality measures were taken before and after preprocessing using the array quality metrics package (Kauffmann, Gentleman et al. 2009, Kauffmann and Huber 2010) to remove outliers based on at least two out of the three tests in the package and taking care that the normalization did not skew the data (only two TH samples, out of 42 total arrays, failed to pass the cut off and so were removed from the analysis). This package was also used to generate the Principle component analysis. We determined the transcripts detected on 80% of the arrays with a p < 0.05.
The data tables contain Illumina dentifiers, raw or normalized (scaled) signal count and  detection p-values. Each normalized sheet contains data that was normalized using a specific group of samples. The normalized data is presented for the transcripts that had a detection p-value < 0.05 for atleast 80% of the samples.

label: biotin

organism: Mus musculus

source_name: Total Homogenates (the standard prep) from extended amygdala

label_protocol: RNA samples were processed at the University of Texas Southwestern Medical Center microarray facility in Dallas. mRNA was amplified and biotin-labeled using the Illumina TotalPrep RNA Amplification kit (Ambion, TX) and hybridized to Mouse WG-6 v2.0 Expression BeadChips (Illumina, CA). Each array contained SN and paired TH samples from control and alcohol-treated mice. These were assigned randomly to each array.

growth_protocol: Adult (two month old) C57BL/6J female mice were maintained at the University of Texas at Austin Animal Research Center. Mice were given a one-week acclimation period in combined housing and another week to acclimate to the bottle position in individual housing. Food and water were provided ad libitum and monitored daily, as were the temperature and light/dark cycles.

extract_protocol: We extracted total RNA from the extended amygdala of 8 alcohol treated mice and 13 controls and 42 microarrays were used for the alcohol-control analysis, 21 SN and 21 paired TH.   Total RNA was extracted from the SN and TH with the Direct-Zol RNA extraction kit (Zymo, Japan), using the small IC extraction columns according to manufacturer’s instructions. The RNA was quantified using nanodrop (NanoDrop 1000, Thermo Fisher Scientific Inc., IL) and assayed for quality using Agilent 2100 Tape Station (Agilent Technologies, CA). The cut-off criteria were set on 280/260 > 1.7, RIN > 6.5, and amount of total RNA > 500ng. We used two validation methods for the preparation:  flow cytometer analysis of SN filtration according to (Gylys, Fein et al. 2004, Sokolow, Henkins et al. 2012) and immunocytochemistry (Gylys, Fein et al. 2004, Williams, Mehrian Shai et al. 2009).

treatment_protocol: Mice were given a 24-hour/day access to a two-bottle choice protocol using bottles containing water and/or 20% ethanol and the volume consumed from both bottles was recorded daily as described by (Osterndorff-Kahanek, Ponomarev et al. 2013). Bottle positions were changed daily to control for position preferences. All procedures were approved by the Institutional Animal Care and Use Committee and adhere to NIH Guidelines. The brains were removed and washed for one minute with 1ml of ice-cold-Homogenizing Buffer (HB) containing Hepes [20mM], EDTA [1mM](pH 7.4), RNAseOut, phosphatase and protease inhibitors (from Invitrogen, Sigma, Roche, respectively). Brains were then placed in a coronal Zivic-mouse-brain-slicer (previously washed with HB) with a 0.5mm resolution (Zivic Instruments, PA) and sliced in the following coordinates in order to isolate extended amygdala-containing slices: coronal level 56-66 [Bregma (-0.18)-(-1.155)] and 66-80 [Bregma (-1.155)-(-2.55)]. The extended amygdala was dissected and placed in a tube containing ice-cold HB (250) and homogenized using a VWR homogenizer. To minimize homogenate loss, the pestles were washed with 50ml HB after use and the wash was collected and added to the sample. 10% of the homogenate (30ml) was snap frozen in liquid nitrogen and stored at -80°C for RNA total homogenate (TH) analysis. The rest of the homogenate (270ml) was filtered with a 100um-pore filter and a 5um-pore filter (Millipore) (filters were washed with HB before use for protection from RNAse). To maximize yield, the filters were washed with 50ml HB after use and the wash was collected and added. The homogenate was then centrifuged at 14,000g for 20 minutes at 4°C in order to pellet the cell fraction containing SN (Quinlan, Philpot et al. 1999, Raab-Graham, Haddick et al. 2006, Sosanya, Huang et al. 2013). The supernatant was removed and the pellet snap frozen and stored at -80°C for SN RNA analysis.

tag: background strain

value: 2 months


title: Total Homogenate_Control_13

description:
TH21
Control mice were given a 24-hour access for 30 days to two bottle of water

scan_protocol: According to manufacturer’s instructions.


title: Total Homogenate_Control_10

description:
TH32
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_11 - Outlier

description:
TH28
Control mice were given a 24-hour access for 30 days to two bottle of water


title: bone marrow_case_rep4 [10677]

description: patient bone marrow


title: Total Homogenate_Control_7

description:
TH27
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_6

description:
TH31
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_3

description:
TH25
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_9

description:
TH26
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_5

description:
TH22
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Control_4

description:
TH34
Control mice were given a 24-hour access for 30 days to two bottle of water


title: hESC_HB_3

source_name: hESC, Hepatoblast,  day10, replicate3


title: hESC_3

description: Gene expression of hESC

source_name: hESC, H9, replicate3

value: hESC H9

value: control


title: miR-29a inhibitor, biological rep3

city: New Haven

first: Pei

last: Zhang

address: 10 Amistad

institute: Yale University

description: Gene expression in the presence of miRNA-29a inhibitor.

hyb_protocol: Samples were hybridized for 16 hours at 45°C to the Affymetrix Whole Transcript GeneChip Human Gene 1.0 ST array using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G using the Affymetrix GeneChip Command Console for image processing, following the user manual's instructions.

data_processing: Data were analyzed with the Affymetrix Expression Console Software 1.2, using the GC-RMA processing algorithm, following the user manual's instructions.

source_name: dermal fibroblasts, miR-29a inhibitor

label_protocol: In order to generate sense-strand cDNA, samples (250ng total RNA) were processed using The Ambion® WT Expression Kit (Applied Biosystems), followed by the GeneChip® WT Terminal Labeling Kit (Affymetrix) for fragmentation and biotin labeling, according to the manufacturer’s protocol.

growth_protocol: Human dermal fibroblast cells were grown in 10% FBS/DMEM media at 80% confluency.

extract_protocol: Trizol extraction of total RNA including miRNA was performed according to the manufacturer's instructions (QIAGEN miRNeasy kit).

treatment_protocol: Cells were treated with 90nM miRNA inhibitor (Dharmacon) with oligofectamine (Invitrogen) in Opti-MEM media for 15h. Then media were replaced by fresh 10% FBS/DMEM for 48h before RNA being harvested.

value: skin

tag: cell type

value: dermal fibroblasts

tag: treatment

value: miR-29a inhibitor


title: Total Homogenate_Alcohol_8

description:
TH15
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: miR-29a inhibitor, biological rep2


title: bone marrow_control_rep3 [G]

description: normal bone marrow


title: Total Homogenate_Control_2

description:
TH29
Control mice were given a 24-hour access for 30 days to two bottle of water


title: ctr miRNA, biological rep1

description: Gene expression in the presence of ctr miRNA inhibitor.

source_name: dermal fibroblasts, ctr miRNA inhibitor

value: control miRNA inhibitor


title: Total Homogenate_Control_1

description:
TH20
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Alcohol_6

description:
TH4
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Total Homogenate_Control_8

description:
TH33
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Alcohol_7

description:
TH7
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: hESC_2

description: Gene expression of hESC

source_name: hESC, H9, replicate2


title: hESC_HB_2

description: Gene expression of hESC-Hepatoblast (10 days of culture)

source_name: hESC, Hepatoblast,  day10, replicate2

value: Hepatoblast


title: hESC_HB_1

source_name: hESC, Hepatoblast,  day10, replicate1


title: miR-29a inhibitor, biological rep1


title: hESC_1

description: Gene expression of hESC

source_name: hESC, H9, replicate1


title: ctr miRNA, biological rep2


title: Total Homogenate_Alcohol_2

description:
TH8
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Total Homogenate_Alcohol_3

description:
TH17
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Total Homogenate_Alcohol_5

description:
TH9
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Total Homogenate_Alcohol_1

description:
TH14
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Control_13

description:
SN21
Control mice were given a 24-hour access for 30 days to two bottle of water

source_name: Synaptoneurosomes from extended amygdala


title: Synaptoneurosome_Control_12

description:
SN19
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Total Homogenate_Alcohol_4

description:
TH13
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Control_11

description:
SN28
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_9

description:
SN26
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_8

description:
SN33
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_6

description:
SN31
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_7

description:
SN27
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_5

description:
SN22
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_3

description:
SN25
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_2

description:
SN29
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Control_1

description:
SN20
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Alcohol_8

description:
SN15
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Alcohol_7

description:
SN7
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Alcohol_6

description:
SN4
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Alcohol_5

description:
SN9
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: WT #2

city: Dallas

first: Nicolai S.C.

last: van Oers

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was processed without normalization using GenomeStudio and exported as probe profile .txt file compatible with GeneSpring GX 11. Raw data was normalized once exported to GeneSpring.

label: Biotin

source_name: Thymus

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

growth_protocol: Total thymocytes were isolated from the wild type and miR-185 Tg mice.

extract_protocol: RNA was extracted using the Ambion RNAqueous micro RNA Isolation kit according to the manufacturer's instructions, followed by and DNase treatment. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: DN3 thymcoytes were sorted gating on CD44- CD25+ CD4- CD8- B220- NK1.1- TCRgd- CD11b- CD11c- population.

tag: strain

value: Sorted DN3 thymocytes

tag: genotype/variation

value: wild type


title: LVEC Scramble, array A

city: Boston

first: Sharon

last: Shechter

state: MA

address: 99 Brookline ave.

department: Pathology

institute: Beth Israel Deaconess

description: Gene expression data from human primary lymphatic endothelial cells transfected with scramble siRNA

hyb_protocol: cRNA were hybridized for 16h at 45C on Affymetrix Human Genome U133 A&B Arrays. GeneChips were washed and stained in the Affymetrix Fluidics station 400.

scan_protocol: Standard Affymetrix Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human Primary Lymphatic Endothelial Cell, scramble siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: BVECs and LVECs were grown in pre-coated plates with collagen I in MCDB131 medium (CellGro) supplemented with L-Alanyl-L-Glutamine (CellGro, 2mM) and MVGS supplement (Cascade Biologics)

extract_protocol: Total RNAs were isolated using RNeasy Kit and treated by DNase I during extraction steps according to the manufacturer's instructions (Qiagen)

treatment_protocol: siRNA transfection in BVECs and LVECs was performed using HMVEC-L Nucleofector kit (Lonza). Confluent cells were harvested with trypsin-EDTA, washed in PBS and added to nucleofection solution (100 µl per 1x106 cells). Program S-005 was used for transfection. Cells were removed from the cuvette and plated into a pre-coated 6 well culture plate. Final siRNA concentration was 50 µM in plate.

value: male

value: foreskin

value: LVEC


title: BVEC silenced VEZF1, array A

description: Gene expression data from human primary blood endothelial cells transfected with siRNA targeting VEZF1

source_name: Human Primary Blood Endothelial Cell, VEZF1 siRNA

value: BVEC

value: siRNA targeting VEZF1


title: miR-185 Tg #1

value: miR-185 Tg


title: miR-185 Tg #3


title: LVEC silenced RhoB, array A

description: Gene expression data from human primary lymphatic endothelial cells transfected with siRNA targeting RhoB

source_name: Human Primary Lymphatic Endothelial Cell, RhoB siRNA

value: siRNA targeting RhoB


title: Synaptoneurosome_Alcohol_4

description:
SN13
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol

value: 2 months

value: female


title: WT #3


title: miR-185 Tg #2


title: LVEC silenced VEZF1, array A

description: Gene expression data from human primary lymphatic endothelial cells transfected with siRNA targeting VEZF1

source_name: Human Primary Lymphatic Endothelial Cell, VEZF1 siRNA


title: Synaptoneurosome_Control_10

description:
SN32
Control mice were given a 24-hour access for 30 days to two bottle of water


title: Synaptoneurosome_Alcohol_2

description:
SN8
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: Synaptoneurosome_Control_4

description:
SN34
Control mice were given a 24-hour access for 30 days to two bottle of water


title: BVEC Scramble, array A

description: Gene expression data from human primary blood endothelial cells transfected with scramble siRNA

source_name: Human Primary Blood Endothelial Cell, scramble siRNA

value: control


title: WT #1


title: Synaptoneurosome_Alcohol_1

description:
SN14
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: ctr miRNA, biological rep3

description: Gene expression in the presence of ctr miRNA inhibitor.

value: skin


title: BVEC silenced RhoB, array A

description: Gene expression data from human primary blood endothelial cells transfected with siRNA targeting RhoB1

source_name: Human Primary Blood Endothelial Cell, RhoB siRNA


title: Synaptoneurosome_Alcohol_3

description:
SN17
Alcohol treated mice were given a 24-hour access for 30 days to a two-bottle choice, using a bottle containing water and a bottle containing 20% ethanol


title: 48H rep2

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

description: replicate 2

data_processing: The data were normalized using RSN normalisation with lumi package in R

source_name: AGS cells, 48h MPA treatment

label_protocol: Biotinylated cRNA were prepared with the Illumina TargetAmp-Nano labeling kit as per the manufacturer’s instructions

extract_protocol: Total RNA was extracted from AGS cells using a magnetic beads RNA extraction kit (Jinfiniti Biosciences, Augusta, GA). Extracted RNA was analyzed for quantity and quality using the Agilent 2100 Bioanalyzer system (Agilent Technologies, Palo Alto, CA).

tag: cell line

value: AGS

tag: disease

value: gastric adenocarcinoma


title: 72H rep2

description: replicate 2

source_name: AGS cells, 72h MPA treatment


title: 72H rep1

description: replicate 1


title: 48H rep1

description: replicate 1


title: Lean 2

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

institute: INSERM

description: Exploration of the CAZyme genes encoded by the human distal gut bacteria

hyb_protocol: After removing the unreacted dye, 9 µl of each labeled DNA sample (250 ng) was mixed with 25 µL of the hybridization master mix that corresponded to Agilent 8 x microarray format.After removing the non-reacted dye, 9 µl of each labeled DNA sample was mixed with 25 µL of the hybridization master mix that corresponded to Agilent 8 x microarray format. For each DNA sample, an amount of 250 ng was used for hybridization with a degree of Cy-3 labeling that varied from 1.64% to 3.1% throughout the eight samples which indicated an optimal degree of labeling as considered in the manufacturing protocol (between 1.75% and 3.5%).  The hybridization master mix was prepared with 0.5 µl of Agilent 100X CGH Blocking Agent and 25 µl of Agilent 2X CGH Hybridization Buffer per hybridization (8 samples). The final volume for each hybridization mixture was 34 µl after adding the Agilent CGH Blocking Agent. The hybridization mixture was applied directly to the gasket slide, and the active side of the microarray slide was placed on top of the gasket to form a “sandwich slide pair”. The microarray slide was placed immediately in a hybridization oven set to 65°C for 46 hours with a rotation of 20 rpm as recommended by the manufacturer. To clean the microarray, a series of washes was performed using Oligo aCGH Wash Buffer 1 and Oligo aCGH Wash Buffer 2 (Agilent Technologies).

scan_protocol: After hybridization and cleaning, the arrays were immediately scanned using an Agilent Microarray Scanner with Agilent Scanner Control software v7.0 with a resolution of 3 μm. The scanned images were analyzed by quantifying the pixel density (intensity) of each spot using the Agilent Feature Extraction (AFE) software v9.5. The mean signal was determined for each spot of the eight hybridized arrays.

data_processing: The local median background signals were subtracted from the mean spot intensity using the “backgroundCorrect” function and “half” method implemented in the 'limma' package available from the Bioconductor website (http://www.bioconductor.org/).The signal values of all spots were then normalized between the arrays using the “limma” function “normalizeBetweenArrays” and the “quantile” method. We used AFE to assess all spots (probes) and determine errors in signal quantification, and non-uniform features were filtered out. To identify the significant signals or successful hybridizations, many criteria were taken into account. The feature mean signal had to be distinguishable from the local background signal. To do so, the two-sided Student’s t-test had to be significant, and the background-corrected mean signal had to be greater than 2.6 times the standard deviation (SD) of the local background. Because the degree of freedom was large enough, the pixel intensities were believed to vary following a normal distribution. Therefore, we used an additive error model to measure the significance of signals. The background signal distribution was assumed to be approximately 0 with one error, which was defined as one standard deviation (1 SD) from the probability of 0 and equal to a p-value of 0.01. Thus, to ensure that the pixels of interest were contained within the rejection boundaries of a 99% confidence interval (p-value ≤ 0.01), the corrected mean signal of the corresponding feature had to be greater than 2.6 times the SD background (for more details on the statistical models, see the AFE reference guide at URL: http://www.chem.agilent.com/Library/usermanuals/Public/ReferenceGuide_050416.pdf).  The probe mean signal had to be significantly different from the mean of the negative controls (> mean negative control + 1.5 x the standard deviation of the negative controls). Accordingly, the following probes were filtered out: (1) the control probes, (2) the probes with a signal that was not significant above background, (3) the probes with a signal that was not higher than the controls and finally, (4) the probes with non-uniformity outliers (if the pixel noise of the corresponding feature exceeded a threshold established for uniformity based on statistical deviation from the expected noise).

organism: human gut metagenome

source_name: Fecal DNA from lean and healthy individual

label_protocol: The genomic DNA ULS (Universal Linkage System) Labeling Kit™ and the ULS-Cy3 (Agilent Technologies) reagent were used to perform the DNA labeling following the supplier’s instructions for an 8x60K microarray. For the eight samples, the same amount of DNA (250 ng in a volume of 8 µL of nuclease-free water) was utilized for the labeling. Before labeling, the extracted genomic DNA was fragmented by heating at 95°C in a PCR thermocycler for 10 minutes, followed immediately by a 3-minutes hold at 4°C. Such a protocol usually results in DNA fragments of at least 10 KB (see for more details the protocol of “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”, version 3.1, August 2009, manual part number G4410-90020). The fragmented DNA was labeled with a one-color fluorescence dye (Cyanine 3). A total of 2 µL of Agilent Labeling Master Mix was added to 8 µL of DNA fragments. For each reaction, the Labeling Master Mix contained 0.75, 0.25, and 1 µL of nuclease-free water, ULS-Cy3 and 10x labeling solution, respectively. The eight reaction mixtures were incubated at 85°C for 30 minutes and then transferred immediately on ice for 3 minutes. The removal of unreacted ULS-Cyanine 3 was performed using Agilent KREApure columns (the Genomic DNA Purification Module). The efficiency of the DNA labeling was measured using a NanoDrop ND-1000 spectrophotometer to determine the absorbance at A260 nm for the labeled DNA and at A550 nm for Cy3 dye. The degree of labeling was calculated as indicated by the manufacturing protocol as follow:   Degree of Labeling =(340 x pmol per µL dye)/(ng per µL genomic DNA x 100)  x 100.

extract_protocol: The human fecal bacteria DNA was obtained using phenol-chloroform extraction based on the protocol adapted by Zoetendal et al. (2006) (Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat Protoc 1: 870-873.)

tag: individual

value: human female

tag: bmi

tag: sample type

value: distal gut bacteria from individual's fecal sample


title: 24H rep2

description: replicate 2

source_name: AGS cells, 24h MPA treatment


title: 12H rep2

description: replicate 2

source_name: AGS cells, 12h MPA treatment


title: 24H rep1

description: replicate 1


title: Lean 1


title: Anorexic 2

source_name: Fecal DNA from anorexic individual

value: Anorexic (9.8)


title: Control rep4

description: replicate 4

source_name: AGS cells, 0h MPA treatment


title: Epididymal adipose tissue_Acute Cpn-infected 14wk_rep1

city: Helsinki

first: Kati

last: Hyvärinen

address: Biomedicum Helsinki 1, Haartmaninkatu 8

country: Finland

institute: Institute of Dentistry, University of Helsinki

description:
Sample name: 5511109057_A FinalReport_nonorm_nobkgd.txt EPIVIII3
replicate 1

hyb_protocol: Standard Illumina hybridization protocol. 5 µg of cRNA from each sample was hybridized at 58 °C overnight using the Illumina Whole-Genome Gene Expression Direct Hybridization Assay system with the six-sample BeadChip platform.

scan_protocol: Standard Illumina scannig protocol.

data_processing:
Quantile normalization. The software used to to perform quantile normalization were Anduril [1] and R [2].
1: Kristian Ovaska, Marko Laakso et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Medicine 2010, 2:65.
2: R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

label_protocol: Standard Illumina labeling protocol. The cDNA was in vitro transcripted into cRNA using biotin-labeled nucleoside triphosphates.

growth_protocol: The mice were fed regular mouse chow ab libitum and maintained in a germ-free environment

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). DNase treatment was performed on a column using the RNase-Free DNase Set (Qiagen) and again after RNA extraction using the DNA-free™ Kit (Ambion). The RNA concentration was determined using a NanoDrop 1000 spectrophotometer (Thermo Scientific). The quality of total RNA was assessed by an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano Kit (Agilent Technologies).

value: B6.129P2- Apoetm1Unc/Crl

value: apoE-deficient

tag: infection

value: Acute Cpn-infected

value: Epididymal adipose tissue

value: 14 weeks


title: Anorexic 3

value: Anorexic (10)


title: 12H rep1

description: replicate 1


title: Control rep2

description: replicate 2


title: Epididymal adipose tissue_Acute Cpn-infected 14wk_rep2

description:
Sample name: 5511109057_B FinalReport_nonorm_nobkgd.txt EPIVIII4
replicate 2

value: male


title: Epididymal adipose tissue_control 14wk_rep3

description:
Sample name: 5511109057_F FinalReport_nonorm_nobkgd.txt EPIIX5
replicate 3

source_name: Epididymal adipose tissue_control 14wk


title: Control rep1

description: replicate 1


title: Anorexic 1

value: Anorexic (13.7)


title: Control rep3

description: replicate 3


title: Epididymal adipose tissue_Chronic Cpn-infected 14wk_rep2

description:
Sample name: 5511109020_E FinalReport_nonorm_nobkgd.txt EPIVII4
replicate 2

value: Chronic Cpn-infected


title: Epididymal adipose tissue_control 24wk_rep2

description:
Sample name: 5511109020_B FinalReport_nonorm_nobkgd.txt EPIIV5
replicate 2

source_name: Epididymal adipose tissue_control 24wk

value: 24 weeks


title: Obese 3

source_name: Fecal DNA from obese individual

value: Obese (35)


title: Epididymal adipose tissue_control 14wk_rep1

description:
Sample name: 5511109057_D FinalReport_nonorm_nobkgd.txt EPIIX2
replicate 1

value: control


title: Epididymal adipose tissue_Chronic Cpn-infected 14wk_rep3

description:
Sample name: 5511109020_F FinalReport_nonorm_nobkgd.txt EPIVII5
replicate 3


title: Epididymal adipose tissue_Acute Cpn-infected 14wk_rep3

description:
Sample name: 5511109057_C FinalReport_nonorm_nobkgd.txt EPIVIII7
replicate 3


title: Epididymal adipose tissue_control 14wk_rep2

description:
Sample name: 5511109057_E FinalReport_nonorm_nobkgd.txt EPIIX3
replicate 2


title: Obese 2


title: Epididymal adipose tissue_control 24wk_rep3

description:
Sample name: 5511109020_C FinalReport_nonorm_nobkgd.txt EPIIV8
replicate 3


title: Epididymal adipose tissue_control 24wk_rep1

description:
Sample name: 5511109020_A FinalReport_nonorm_nobkgd.txt EPIIV2
replicate 1


title: Obese 1


title: Epididymal adipose tissue_Cpn+Aa-infected 24wk_rep3

description:
Sample name: 5511109053_F FinalReport_nonorm_nobkgd.txt EPIIII6
replicate 3

value: Cpn+Aa-infected


title: Epididymal adipose tissue_Cpn+Aa-infected 24wk_rep2

description:
Sample name: 5511109053_E FinalReport_nonorm_nobkgd.txt EPIIII2
replicate 2


title: OSC19_TC

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Human H&N cell line

hyb_protocol: According to Affemetix protocol.

scan_protocol: According to Affemetix protocol.

data_processing: The images was processed using Affymetrix software, GeneChip Operating Software (GCOS).

label_protocol: According to Affemetix protocol.

growth_protocol: Residual tumor at the time of surgery was taken from 30 previously untreated patients undergoing definitive surgery and 4 patients undergoing surgical salvage for HNSCC and transported immediately upon arrival in the pathology suite to the animal facility in sterile RPMI medium.  For tumors measuring < 0.5 cm3, the entire tumor was implanted into mice (Figure 1).  For samples measuring >0.5 cm3, the tumor (F0 generation) was divided and either snap-frozen, immersed and stored in RNAlater (Life Technologies, Carlsbad, CA), or implanted.  The tumor tissue used for implantation was minced into 2-mm3 pieces and subcutaneously engrafted into the flanks of anesthetized 6-week-old Nu/Nu female mice.  Once tumors grew to 1 cm3 the tumor (F1 generation) was resected and divided as with the primary tumor and passaged into 5 mice (F2 generation).  The process was repeated to generate subsequent generations.  All research was performed in accordance with the Institutional Animal Care and Use Committee's policies and approved by the Institutional Review Board.

extract_protocol: RNA was extracted from original patient tumors, xenografts, and cell lines using an RNAeasy mini kit (Qiagen, Valencia, CA). The integrity of the RNA from each sample was measured by using the RNA 6000 Nano labchip and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The quality and concentration of RNA was assessed with use of the NanoDrop ND-1000 (Wilmington, DE) spectrophotometer. The Affymetrix (Santa Clara, CA) GeneChip U133 Plus 2.0 was used without RNA amplification.

value: Human H&N cell line


title: Epididymal adipose tissue_Chronic Cpn-infected 14wk_rep1

description:
Sample name: 5511109020_D FinalReport_nonorm_nobkgd.txt EPIVII3
replicate 1


title: TU167_TC

description: Human H&N cell line


title: HOSC1_3D_TC

description: HOSC3D (HOSC1 Cell line cultured in 3D)

value: HOSC3D (HOSC1 Cell line cultured in 3D)


title: Epididymal adipose tissue_Cpn+Aa-infected 24wk_rep1

description:
Sample name: 5511109053_D FinalReport_nonorm_nobkgd.txt EPIIII1
replicate 1


title: Epididymal adipose tissue_Cpn-infected 24wk_rep3

description:
Sample name: 5511109053_C FinalReport_nonorm_nobkgd.txt EPIII7
replicate 3

value: Cpn-infected


title: HOSC1_TC

description: HOSC1Cell line (derived from F7 HOSC1 transplanted tumor, 2D culture)


title: 462 cell line, siEZH2

description:
462 cell line, siEZH2
462 siEZH2 (GFS640)

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: Gene expression values derived from Illumina GenomeStudio software were subject to quantile normalization.

source_name: 462 cell line, siEZH2

label_protocol: According to Illumina protocol.

growth_protocol: MPNST cell lines were cultured in DMEM medium with 10% FBS.

extract_protocol: According to Illumina protocol.

treatment_protocol: For siRNA knockdown and short-hairpin RNA–mediated gene knockdown, negative control siRNA or siRNA targeting EZH2 (Dharmacon) and empty vector or two different shRNA constructs targeting EZH2 (Origen) were transfected to MPNST cells with lipofectamine 2000 (Invitrogen) according to the manufacturer’s protocol. Cells with siRNAs were harvested after 48 hour and subjected to gene array analyses.

value: EZH2 knockdown (siEZH2)


title: Epididymal adipose tissue_Aa-infected 24wk_rep3

description:
Sample name: 5511109056_F FinalReport_nonorm_nobkgd.txt EPII10
replicate 3

value: B6.129P2- Apoetm1Unc/Crl

value: Aa-infected


title: Epididymal adipose tissue_Cpn-infected 24wk_rep1

description:
Sample name: 5511109053_A FinalReport_nonorm_nobkgd.txt EPIII1
replicate 1

value: apoE-deficient


title: 462 cell line, siEZH2, replicate

description:
462 cell line, siEZH2, replicate
462 siEZH2 2 (GFS646)


title: Epididymal adipose tissue_Aa-infected 24wk_rep1

description:
Sample name: 5511109056_D FinalReport_nonorm_nobkgd.txt EPII1
replicate 1

value: Epididymal adipose tissue


title: HOSC19_F1

description: Tumor from transplanted mice

value: Tumor from transplanted mice


title: Epididymal adipose tissue_Cpn-infected 24wk_rep2

description:
Sample name: 5511109053_B FinalReport_nonorm_nobkgd.txt EPIII2
replicate 2


title: HOSC12_F3, biological replicate

description: Tumor from transplanted mice


title: 724 cell line, no treatment, replicate

description:
724 cell line, no treatment (negative control siRNA), replicate
724 NT 2 (GFS643)

source_name: 724 cell line, no treatment

value: control (siRNA control)


title: 724 cell line, siEZH2, replicate

description:
724 cell line, siEZH2, replicate
724 siEZH2 2 (GFS644)

source_name: 724 cell line, siEZH2


title: Epididymal adipose tissue_Aa-infected 24wk_rep2

description:
Sample name: 5511109056_E FinalReport_nonorm_nobkgd.txt EPII8
replicate 2

value: male


title: Inguinal adipose tissue_control 14wk_rep3

description:
Sample name: 5511109056_C FinalReport_nonorm_nobkgd.txt INGIX6
replicate 3

source_name: Inguinal adipose tissue_control 14wk

value: Inguinal adipose tissue

value: 14 weeks


title: Inguinal adipose tissue_control 14wk_rep2

description:
Sample name: 5511109056_B FinalReport_nonorm_nobkgd.txt INGIX5
replicate 2


title: HOSC19_F3

description: Tumor from transplanted mice


title: 724 cell line, siEZH2

description:
724 cell line, siEZH2
724 siEZH2 (GFS638)


title: Inguinal adipose tissue_control 14wk_rep1

description:
Sample name: 5511109056_A FinalReport_nonorm_nobkgd.txt INGIX4
replicate 1


title: Inguinal adipose tissue_Acute Cpn-infected 14wk_rep2

description:
Sample name: 5511109019_E FinalReport_nonorm_nobkgd.txt INGVIII3
replicate 2

value: Acute Cpn-infected


title: Inguinal adipose tissue_Acute Cpn-infected 14wk_rep1

description:
Sample name: 5511109019_D FinalReport_nonorm_nobkgd.txt INGVIII2
replicate 1


title: BVEC Scramble, array B

description: Gene expression data from human primary blood endothelial cells transfected with scramble siRNA

value: foreskin

value: BVEC


title: HOSC12_F1, biological replicate

description: Tumor from transplanted mice


title: LVEC silenced VEZF1, array B

description: Gene expression data from human primary lymphatic endothelial cells transfected with siRNA targeting VEZF1

source_name: Human Primary Lymphatic Endothelial Cell, VEZF1 siRNA

value: LVEC

value: siRNA targeting VEZF1


title: Inguinal adipose tissue_Chronic Cpn-infected 14wk_rep3

description:
Sample name: 5511109019_C FinalReport_nonorm_nobkgd.txt INGVII5
replicate 3

value: Chronic Cpn-infected


title: Inguinal adipose tissue_Cpn+Aa-infected 24wk_rep2

description:
Sample name: 5511109008_B FinalReport_nonorm_nobkgd.txt INGIII7
replicate 2

value: Cpn+Aa-infected

value: 24 weeks


title: HOSC12_F3

description: Tumor from transplanted mice


title: Inguinal adipose tissue_Cpn-infected 24wk_rep3

description:
Sample name: 5528656040_F FinalReport_nonorm_nobkgd.txt INGII7
replicate 3

value: B6.129P2- Apoetm1Unc/Crl

value: Cpn-infected


title: 462 cell line, no treatment

description:
462 cell line, no treatment (negative control siRNA)
462 NT (GFS639)

source_name: 462 cell line, no treatment


title: 724 cell line, no treatment

description:
724 cell line, no treatment (negative control siRNA)
724 NT (GFS637)


title: Inguinal adipose tissue_Chronic Cpn-infected 14wk_rep1

description:
Sample name: 5511109019_A FinalReport_nonorm_nobkgd.txt INGVII1
replicate 1

value: apoE-deficient


title: Inguinal adipose tissue_control 24wk_rep1

description:
Sample name: 5511109008_D FinalReport_nonorm_nobkgd.txt INGIV7
replicate 1

source_name: Inguinal adipose tissue_control 24wk

value: control


title: 724 cell line, siEZH2, replicate, miRNA

description:
724 cell line, siEZH2, replicate
724 cell line, siEZH2 (EZH2 knockdown)

hyb_protocol: Hybridization was carried out on the fifth version of a miRNA-chip (MDACC v5). Each oligo was printed in duplicate.

scan_protocol: Hybridization signals were detected by biotin binding of a Streptavidin-Alexa647 conjugate (one-color signal) using a GenePix 4000B scanner (Axon Instruments). We quantified images using the GenePix Pro 6.0 (Axon Instruments).

data_processing: Gene expression values were subject to quantile normalization.

source_name: 724 cell line, siEZH2, replicate

label_protocol: Briefly, 5 ug of RNA from each tissue sample was labeled with biotin by reverse transcription using random octomers.

extract_protocol: Total RNA, including miRNA, was isolated from cells using TRIZOL (Invitrogen). After quality assurance with a 2100 Bioanalyzer (Agilent), procedures at the genomic core facility at MD Anderson was conducted to result in eventual hybridization and reporting of raw data for the miRNA microarray.

value: siEZH2 (EZH2 knockdown)


title: Inguinal adipose tissue_Cpn-infected 24wk_rep2

description:
Sample name: 5528656040_E FinalReport_nonorm_nobkgd.txt INGII6
replicate 2


title: 462 cell line, no treatment, replicate

description:
462 cell line, no treatment (negative control siRNA), replicate
462 NT 2 (GFS645)

value: control (siRNA control)


title: Inguinal adipose tissue_Cpn+Aa-infected 24wk_rep1

description:
Sample name: 5511109008_A FinalReport_nonorm_nobkgd.txt INGIII3
replicate 1

value: male


title: LVEC silenced RhoB, array B

description: Gene expression data from human primary lymphatic endothelial cells transfected with siRNA targeting RhoB

source_name: Human Primary Lymphatic Endothelial Cell, RhoB siRNA

value: siRNA targeting RhoB


title: Inguinal adipose tissue_control 24wk_rep3

description:
Sample name: 5511109008_F FinalReport_nonorm_nobkgd.txt INGIV9
replicate 3

value: Inguinal adipose tissue


title: HOSC21_F3

description: Tumor from transplanted mice

value: Tumor from transplanted mice


title: HOSC12_F1

description: Tumor from transplanted mice


title: Inguinal adipose tissue_control 24wk_rep2

description:
Sample name: 5511109008_E FinalReport_nonorm_nobkgd.txt INGIV8
replicate 2


title: Inguinal adipose tissue_Cpn+Aa-infected 24wk_rep3

description:
Sample name: 5511109008_C FinalReport_nonorm_nobkgd.txt INGIII10
replicate 3


title: LVEC Scramble, array B

description: Gene expression data from human primary lymphatic endothelial cells transfected with scramble siRNA

source_name: Human Primary Lymphatic Endothelial Cell, scramble siRNA

value: foreskin


title: Inguinal adipose tissue_Chronic Cpn-infected 14wk_rep2

description:
Sample name: 5511109019_B FinalReport_nonorm_nobkgd.txt INGVII4
replicate 2

value: 14 weeks


title: HOSC10_F3

description: Tumor from transplanted mice


title: HOSC1_F10

description: Tumor from transplanted mice


title: HOSC5_F0

description: Tumor originated from human (HOSC human oral squamous carcinoma)


title: 724 cell line, siEZH2, miRNA

description:
724 cell line, siEZH2
724 cell line, siEZH2 (EZH2 knockdown)


title: S462 cell line, siEZH2, replicate, miRNA

description:
S462 cell line, siEZH2, replicate
S462 cell line, siEZH2 (EZH2 knockdown)

source_name: S462 cell line, siEZH2, replicate


title: S462 cell line, siEZH2, miRNA

description:
S462 cell line, siEZH2
S462 cell line, siEZH2 (EZH2 knockdown)

source_name: S462 cell line, siEZH2


title: BVEC silenced RhoB, array B

description: Gene expression data from human primary blood endothelial cells transfected with siRNA targeting RhoB1

source_name: Human Primary Blood Endothelial Cell, RhoB siRNA

value: BVEC


title: BVEC silenced VEZF1, array B

description: Gene expression data from human primary blood endothelial cells transfected with siRNA targeting VEZF1

source_name: Human Primary Blood Endothelial Cell, VEZF1 siRNA

value: siRNA targeting VEZF1


title: 724 cell line, no treatment, replicate, miRNA

description:
724 cell line, no treatment, replicate
724 cell line, no treatment (negative control siRNA)


title: 26T cell line, siEZH2, replicate, miRNA

description:
26T cell line, siEZH2, replicate
26T cell line, siEZH2 (EZH2 knockdown)

source_name: 26T cell line, siEZH2, replicate


title: HOSC30_F0

value: Tumor originated from human (HOSC human oral squamous carcinoma)


title: 26T cell line, siEZH2, miRNA

description:
26T cell line, siEZH2
26T cell line, siEZH2 (EZH2 knockdown)

source_name: 26T cell line, siEZH2


title: 724 cell line, no treatment, miRNA

description:
724 cell line, no treatment
724 cell line, no treatment (negative control siRNA)


title: Inguinal adipose tissue_Aa-infected 24wk_rep3

description:
Sample name: 5528656040_C FinalReport_nonorm_nobkgd.txt INGI6
replicate 3

value: Aa-infected


title: S462 cell line, no treatment, replicate, miRNA

description:
S462 cell line, no treatment, replicate
S462 cell line, no treatment (negative control siRNA)

source_name: S462 cell line, no treatment


title: p25_16h exp2

city: Aarhus C

first: Christine

middle: Lund

last: Kragh

address: Ole Worms Alle 1.170

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Gene expression data from OLN cells expressing alpha-synuclein and p25alpha - RNA isolated 16 hrs after transfection

hyb_protocol: Biotinylated cRNAs (15 µg) generated from independent cell culture preparations were hybridized onto individual Affymetrix RAE230 2.0 oligonucleotide arrays for 16 h at 45°C (Affymetrix) according to the manufacturer´s protocol

scan_protocol: The arrays were scanned with a Hewlett-Packard Gene Array 3000 7G Scanner

data_processing: The data were analyzed using Microarray Suite version 5.0 (MAS 5.0) (Affymetrix)

organism: Rattus norvegicus

source_name: OLN cells transfected with p25 for 16 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were grown at 37C for 24 hrs prior to transfection

extract_protocol: Isolation of total RNA was perfomed using Rneasy Mini Kit (Qiagen)

treatment_protocol: Cells stably expressing alpha-synuclein were transfected (using Fugene-6 transfection reagent) with an empty control vector or p25alpha pcDNA3.1 for 8, 12, or 16 hrs

value: oligodendroglial cell line stably expressing alpha-synuclein

value: expressing alpha-synuclein and p25alpha

value: 16 hrs


title: HOSC1_F3

description: Tumor from transplanted mice


title: HOSC29_F0


title: mock_16h exp1

description: Gene expression data from OLN cells expressing solely alpha-synuclein - RNA isolated 16 hrs after transfection

source_name: OLN cells transfected with mock for 16 hrs

value: expressing solely alpha-synuclein


title: HOSC3_F0


title: Inguinal adipose tissue_Cpn-infected 24wk_rep1

description:
Sample name: 5528656040_D FinalReport_nonorm_nobkgd.txt INGII1
replicate 1

value: B6.129P2- Apoetm1Unc/Crl

value: apoE-deficient

value: Cpn-infected

value: 24 weeks


title: HOSC25_F0


title: HOSC23_F0


title: Inguinal adipose tissue_Aa-infected 24wk_rep1

description:
Sample name: 5528656040_A FinalReport_nonorm_nobkgd.txt INGI2
replicate 1

value: male


title: Inguinal adipose tissue_Aa-infected 24wk_rep2

description:
Sample name: 5528656040_B FinalReport_nonorm_nobkgd.txt INGI3
replicate 2

value: Inguinal adipose tissue


title: HOSC2_F0

description: Tumor originated from human (HOSC human oral squamous carcinoma)


title: HOSC20_F0


title: p25_12h exp2

description: Gene expression data from OLN cells expressing alpha-synuclein and p25alpha - RNA isolated 12 hrs after transfection

source_name: OLN cells transfected with p25 for 12 hrs

value: 12 hrs


title: Inguinal adipose tissue_Acute Cpn-infected 14wk_rep3

description:
Sample name: 5511109019_F FinalReport_nonorm_nobkgd.txt INGVIII5
replicate 3

value: Acute Cpn-infected


title: HOSC22_F0


title: S462 cell line, no treatment, miRNA

description:
S462 cell line, no treatment
S462 cell line, no treatment (negative control siRNA)

value: control (siRNA control)


title: 26T cell line, no treatment, replicate, miRNA

description:
26T cell line, no treatment, replicate
26T cell line, no treatment (negative control siRNA)

source_name: 26T cell line, no treatment


title: p25_16h exp1


title: HOSC18_F0


title: mock_16h exp2


title: p25_8h exp1

description: Gene expression data from OLN cells expressing alpha-synuclein and p25alpha - RNA isolated 8 hrs after transfection

source_name: OLN cells transfected with p25 for 8 hrs

value: 8 hrs


title: mock_12h exp1

description: Gene expression data from OLN cells expressing solely alpha-synuclein - RNA isolated 12 hrs after transfection

source_name: OLN cells transfected with mock for 12 hrs


title: 26T cell line, no treatment, miRNA

description:
26T cell line, no treatment
26T cell line, no treatment (negative control siRNA)


title: p25_12h exp1


title: mock_12 exp2


title: HOSC15_F0


title: HOSC13_F0


title: mock_8h exp2

description: Gene expression data from OLN cells expressing solely alpha-synuclein - RNA isolated 8 hrs after transfection

source_name: OLN cells transfected with mock for 8 hrs


title: HOSC14_F0


title: HOSC17_F0


title: HOSC21_F0


title: p25_8h exp2


title: HOSC10_F0


title: mock_8h exp1


title: Lung-PC infected-CD4 depleted-IFNg KO-rep2

status: Public on Oct 27 2013

city: Bozeman

first: Steve

middle: D

last: Swain

state: MT

address: 560 Technology Blvd

department: Immunology & Infectious Disease

institute: Montana State University

description: Gene expression data of IFN-gamma deficient CD4-depleted Pneumocystis-infected lung

hyb_protocol: The labeled cRNA was purified, fragmented, and hybridized to the arrays at 45°C for 16 hours with constant rotational mixing at 60 rpm. Washing and staining of the arrays was performed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 7G and GCOS software version 1.4.

data_processing: Microarray data was analyzed using FlexArray version 1.5. The Affymetrix CEL files were imported and normalized using gc-RMA.Three data filters were applied: (1) signal intensities of at least 50 in one biological replicate; (2) at least one condition called “present” by GCOS; (2) minimal fold-change of 2 in any comparison. Statistical significance between conditions was determined using ANOVA, resulting in a final gene list of 406 genes.

source_name: IFN-gamma knockout mouse lung, Pneumocystis infected, depleted of CD4 cells 10 days, d38 post-infection.

label_protocol: Biotinylated cRNA was made from 500 ng total RNA using the Ambion Message Amp Premier RNA amplification kit

growth_protocol: All mice were kept in conditions of 12:12 photoperiod, ad libitum food and HEPA-filtered air exchange.

extract_protocol: Total RNA was extracted from samples using Qiagen RNeasy Maxi-kit following  manufacturer's instructions.

treatment_protocol: Mice were euthanized, the lung vasculature was perfused with sterile buffer before the tissue was homogenized with RNAse free rotors and immediately used for extraction

value: Lung

value: BALB/c

tag: genotype

value: IFN-gamma knockout

tag: pathogen

value: Pneumocystis

tag: immune status

value: CD4 T-cell depleted


title: HOSC1_F0

tag: tissue

value: Tumor originated from human (HOSC human oral squamous carcinoma)


title: Lung-Control-BALB/c-rep1

description: Gene expression data of wildtype immune competent non-infected lung

source_name: BALB/c mouse lung, no treatments, age-matched to other groups.

value: wildtype

value: Normal


title: Lung-PC infected-CD4 depleted-BALB/c-rep3

description: Gene expression data of wildtype CD4-depleted Pneumocystis-infected lung

source_name: BALB/c mouse lung, Pneumocystis infected, depleted of CD4 cells 10 days, d38 post-infection


title: Lung-Control-BALB/c-rep3


title: Lung-PC infected-CD4 depleted-IFNg KO-rep1


title: Lung-PC infected-CD4 depleted-BALB/c-rep2


title: Lung-PC infected-CD4 depleted-IFNg KO-rep3


title: Lung-Control-BALB/c-rep2


title: Lung-PC infected-BALB/c-rep2

description: Gene expression data of wildtype immune competent Pneumocystis-infected lung

source_name: BALB/c mouse lung, Pneumocystis infected, d38 post-infection.


title: Lung-PC infected-CD4 depleted-BALB/c-rep1


title: Lung-PC infected-BALB/c-rep1

source_name: BALB/c mouse lung, Pneumocystis infected, d38 post-infection.  BALB/c mouse lung, Pneumocystis infected, d38 post-infection.


title: 1752 cell line

status: Public on Oct 26 2013

city: Freiburg

first: Jaga

last: Virayah

address: Am Flughafen 12-14

country: Germany

institute: Oncotest GmbH

description: Gene expression data from cell-line

hyb_protocol: Standard Affymetix protocol for 3' IVT design

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

data_processing: The data were analysed using RMAExpress (v. 1.04, written by Ben Bolstad)

source_name: Medical Center Freiburg

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

extract_protocol: Extraction of total RNA was performed using the mirVana® kit (Ambion) according to the manufacturer’s instructions

tag: gender

tag: differentiation

value: not known

tag: origin

value: primary


title: 698 cell line

description: Gene expression data from cell-line

tag: age


title: MOLT-4 cell line

description: Gene expression data from cell-line

source_name: ATCC

value: poor


title: Lung-PC infected-BALB/c-rep3


title: KCL-22 cell line

description: Gene expression data from cell-line

source_name: DSMZ

value: female


title: 251 cell line

description: Gene expression data from cell-line

value: male


title: 276 cell line

description: Gene expression data from cell-line

value: metastasis


title: 526 cell line

description: Gene expression data from cell-line


title: 269 cell line

description: Gene expression data from cell-line


title: NCI-H460 cell line

description: Gene expression data from cell-line

source_name: NCI

value: Not available


title: NCI-H929 cell line

description: Gene expression data from cell-line


title: 486 cell line

description: Gene expression data from cell-line


title: KG-1 cell line

description: Gene expression data from cell-line


title: Saos-2 cell line

description: Gene expression data from cell-line


title: 546 cell line

description: Gene expression data from cell-line

value: good


title: RAJI cell line

description: Gene expression data from cell-line

value: RAJI


title: PC-3M cell line

description: Gene expression data from cell-line

source_name: NCI / Oncotest


title: 94 cell line

description: Gene expression data from cell-line

value: moderate


title: JURL-MK1 cell line

description: Gene expression data from cell-line


title: 289 cell line

description: Gene expression data from cell-line


title: 1781 cell line

description: Gene expression data from cell-line

value: recurrent


title: 1121 cell line

description: Gene expression data from cell-line


title: 1341 cell line

description: Gene expression data from cell-line


title: IM-9 cell line

description: Gene expression data from cell-line


title: K-562 cell line

description: Gene expression data from cell-line


title: 462 cell line

description: Gene expression data from cell-line


title: 1183 cell line

description: Gene expression data from cell-line


title: 520 cell line

description: Gene expression data from cell-line


title: T-24 cell line

description: Gene expression data from cell-line


title: PL-21 cell line

description: Gene expression data from cell-line


title: MDA-MB-231 cell line

description: Gene expression data from cell-line


title: LP-1 cell line

description: Gene expression data from cell-line


title: RKO cell line

description: Gene expression data from cell-line

value: RKO


title: HL-60 cell line

description: Gene expression data from cell-line


title: NIH:OVCAR-3 cell line

description: Gene expression data from cell-line


title: 575 cell line

description: Gene expression data from cell-line

source_name: San Diego, R.Taettle


title: JURKAT cell line

description: Gene expression data from cell-line

value: JURKAT


title: 22Rv1 cell line

description: Gene expression data from cell-line


title: 401 cell line

description: Gene expression data from cell-line


title: 1657 cell line

description: Gene expression data from cell-line


title: U-937 cell line

description: Gene expression data from cell-line


title: 899 cell line

description: Gene expression data from cell-line


title: HT-29 cell_line

description: Gene expression data from cell-line


title: MCF-7 cell line

description: Gene expression data from cell-line


title: DU-145 cell line

description: Gene expression data from cell-line


title: EM-2 cell line

description: Gene expression data from cell-line


title: CAL-27 cell line

description: Gene expression data from cell-line


title: S8 (sample 37) vs V8 (sample 6)

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Sterile37_8week vs. V6_8week

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequentially.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix6.0

data_processing: Spot intensities were quantified from scanned microarray images with GenePix Pro 6.0 using default settings and manual correction and flagging of ambiguous spots. Subsequently, we followed a standard microarray analysis procedure, guided by the documentation of the Bioconductor limma package (Gentleman et al. 2004; Smyth 2004; Smyth et al. 2005). In brief, median signal and background levels were extracted for each cDNA spot. The limma 3.2.1 package (Smyth 2004) in R 2.10.1 (The R Development Core Team 2007) was used for Normexp background correction, Print-tip Loess normalization within arrays, and Aquantile normalization between arrays (Smyth & Speed 2003).

organism: Cardiocondyla obscurior

source_name: S8 (pooled RNA from two queens)

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

growth_protocol: Each colony was started with 20 adult workers, 10 worker pupae, brood (8 larvae of each of the three stages, cf. Schrempf & Heinze 2006) and a single not-yet sclerotized queen pupae (Fig. 1). Colonies were housed in petri-dishes (∅ = 10cm) with plaster-flooring in which small cavities have been carved to serve as nest sites.  Colonies were fed three times a week with chopped cockroaches, Drosophila and diluted honey. We observed each colony of the 8 week old queens three times a week for developing male and queen pupae which we removed to avoid re-mating (although unlikely in Cardiocondyla) or mistaking a young queen for the original one. We provisioned the colonies with brood and worker pupae from random chosen stock donor colonies, when necessary. After one or eight weeks, respectively, queens were collected individually in 1.5ml microcentrifuge tubes, immediately snap-frozen in liquid N2 and stored at -80°C.

extract_protocol: We extracted total RNA from whole queens with the Trizol Reagent (Invitrogen, Carlsbad, CA), following the manufacturers protocol. Tissue was homogenized with ceramic beads (Quackenbush) using a Fastprep bead shaker. Extraction of two queens resulted in a total RNA yield of 25 – 40µg after DNAse treatment (Ambion DNA-free, Austin, TX) and subsequent Microcon purification (Millipore, Billerica, MA). Extracted RNA was dried at 50°C in a vacuum centrifuge and re-dissolved in 12µl H2O. 10µl of total RNA was used for amplification (MessageAmp II aRNA Amplification Kit, Ambion, Austin, TX) yielding 110-1625µg of amplified RNA (aRNA) for each sample.

treatment_protocol: We sampled one and eight week old queens that have been subjected to one of three mating treatments. We analyzed 7 and 9 biological replicates for each treatment (M, S and V) at the respective time point (one and eight week old queens). To reduce inter-individual variation within replicate, we pooled two queens per sample for each treatment at each time point. Thus, in total, we sampled 42 one-week-old and 54 eight-week-old queens resulting in a total of 96 experimental colonies.For the treatment with sterilized males we collected males one to two days after eclosion and exposed them, individually placed in 100ul cups, to x-ray (120 Gy; 2,95 ± 0.12 Gy/min, ca 40min) which results in sperm degradation (Schrempf et al 2005), a dose that also induces sterility in similar-sized braconidae wasps (Grosch and Sullivan 1954). After irradiation we immediately returned the males to their colony. At this stage the queens were between 2 and 3 days old. Some males (~ 10%) died within the first few hours after irradiation, showing black cuticular pigmentation and spastic body movements. Other males were initially disorientation compared to non-treated males. Males that survived the first 24h appeared to recover and showed typical male behaviour, such as patrolling the nest. Observations of attempted mating confirmed the sexual functionality of these males. Colonies in which males (of both mated and dummy mated treatment) did not survive for more than 10 days were excluded to further ensure for the functionality of the males. After 10 days all males were removed. S and M queens shed their wings within days after mating and therefore we excluded the few cases where queens remained winged, indicating that something unexpected happened, i.e either the queens or their mating partners did not engage in full mating behavior.

tag: matingstatus

value: ShamMated

tag: timesincemating

value: 8 weeks

source_name: V8 (pooled RNA from two queens)

value: Virgin


title: 1118 cell line

description: Gene expression data from cell-line


title: M8 (sample 68) vs S8 (sample 37)

description: M68_8week vs. Sterile37_8week

source_name: M8 (pooled RNA from two queens)

value: Mated


title: V8 (sample 6) vs M8 (sample 68)

description: V6_8week vs. M68_8week


title: M8 (sample 68) vs M1 (sample 23)

description: M68_8week vs. M23_1week

source_name: M1 (pooled RNA from two queens)

value: 1 weeks


title: HCT-116 cell_line

description: Gene expression data from cell-line

value: not known


title: M8 (sample 69) vs M1 (sample 24)

description: M69_8week vs. M24_1week


title: M1 (sample 24) vs M8 (sample 69)

description: M24_1week vs. M69_8week


title: M8 (sample 70) vs M1 (sample 62)

description: M70_8week vs. M62_1week


title: MV4-11 cell line

description: Gene expression data from cell-line


title: 1138 cell line

description: Gene expression data from cell-line

value: poor


title: M1 (sample 62) vs M8 (sample 70)

description: M62_1week vs. M70_8week


title: 1218 cell line

description: Gene expression data from cell-line

value: female


title: TE671 cell line

description: Gene expression data from cell-line

source_name: ECACC


title: NOMO-1 cell line

description: Gene expression data from cell-line


title: HUT-78 cell line

description: Gene expression data from cell-line

value: male


title: 1352 cell line

description: Gene expression data from cell-line

value: metastasis


title: M8 (sample 67) vs M1 (sample 21)

description: M67_8week vs. M21_1week


title: PANC-1 cell line

description: Gene expression data from cell-line


title: M8 (sample 66) vs M1 (sample 20)

description: M66_8week vs. M20_1week


title: 1792 cell line

description: Gene expression data from cell-line

source_name: Oncotest


title: 1103 cell line

description: Gene expression data from cell-line


title: M1 (sample 23) vs M8 (sample 68)

description: M23_1week vs. M68_8week


title: M1 (sample 21) vs M8 (sample 67)

description: M21_1week vs. M67_8week


title: M1 (sample 20) vs M8 (sample 66)

description: M20_1week vs. M66_8week


title: OCI-AML2 cell line

description: Gene expression data from cell-line


title: MEG-01 cell line

description: Gene expression data from cell-line

value: primary


title: S8 (sample 39) vs V8 (sample 5)

description: Sterile39_8week vs. V5_8week


title: LNCaP cell line

description: Gene expression data from cell-line

value: LNCaP


title: M8 (sample 65) vs S8 (sample 39)

description: M65_8week vs. Sterile39_8week


title: 393 cell line

description: Gene expression data from cell-line


title: L-363 cell line

description: Gene expression data from cell-line


title: S8 (sample 54) vs V8 (sample 2)

description: Sterile54_8week vs. V2_8week


title: S8 (sample 40) vs V8 (sample 1)

description: Sterile40_8week vs. V1_8week


title: M8 (sample 67) vs S8 (sample 54)

description: M67_8week vs. Sterile54_8week


title: DiFi cell line

description: Gene expression data from cell-line

value: DiFi

value: good


title: 3011 cell line

description: Gene expression data from cell-line

source_name: Seoul National University


title: 983 cell line

description: Gene expression data from cell-line


title: V8 (sample 5) vs M8 (sample 65)

description: V5_8week vs. M65_8week


title: V8 (sample 2) vs M8 (sample 67)

description: V2_8week vs. M67_8week


title: V8 (sample 7) vs M8 (sample 69)

description: V7_8week vs. M69_8week


title: JHH-6 cell line

description: Gene expression data from cell-line

source_name: JCRB

value: undifferentiated


title: V8 (sample 1) vs M8 (sample 66)

description: V1_8week vs. M66_8week


title: M8 (sample 66) vs S8 (sample 40)

description: M66_8week vs. Sterile40_8week


title: 529 cell line

description: Gene expression data from cell-line


title: JHH-2 cell line

description: Gene expression data from cell-line


title: 629 cell line

description: Gene expression data from cell-line


title: OCUM-1 cell line

description: Gene expression data from cell-line


title: V8 (sample 41) vs M8 (sample 70)

description: V41_8week vs. M70_8week


title: S8 (sample 56) vs V8 (sample 7)

description: Sterile56_8week vs. V7_8week


title: RPMI8226 cell line

description: Gene expression data from cell-line


title: MKN45 cell line

description: Gene expression data from cell-line


title: JHH-4 cell line

description: Gene expression data from cell-line


title: M8 (sample 69) vs S8 (sample 56)

description: M69_8week vs. Sterile56_8week


title: NUGC-4 cell line

description: Gene expression data from cell-line


title: V8 (sample 4) vs M8 (sample 64)

description: V4_8week vs. M64_8week


title: IM95 cell line

description: Gene expression data from cell-line

value: moderate


title: S8 (sample 57) vs V8 (sample 41)

description: Sterile57_8week vs. V41_8week


title: SNU-449 cell line

description: Gene expression data from cell-line

source_name: KCLB


title: SNU-761 cell line

description: Gene expression data from cell-line


title: M8 (sample 74) vs S8 (sample 60)

description: M74_8week vs. Sterile60_8week


title: S8 (sample 38) vs V8 (sample 4)

description: Sterile38_8week vs. V4_8week


title: SNU-423 cell line

description: Gene expression data from cell-line


title: M8 (sample 64) vs S8 (sample 38)

description: M64_8week vs. Sterile38_8week


title: SNU-878 cell line

description: Gene expression data from cell-line


title: SNU-739 cell line

description: Gene expression data from cell-line


title: V8 (sample 11) vs M8 (sample 74)

description: V11_8week vs. M74_8week


title: S1 (sample 76) vs M1 (sample 19)

description: Sterile76_1week vs. M19_1week

source_name: S1 (pooled RNA from two queens)


title: S8 (sample 60) vs V8 (sample 11)

description: Sterile60_8week vs. V11_8week


title: FU97 cell line

description: Gene expression data from cell-line


title: SNU-475 cell line

description: Gene expression data from cell-line


title: M8 (sample 71) vs S8 (sample 58)

description: M71_8week vs. Sterile58_8week


title: M8 (sample 70) vs S8 (sample 57)

description: M70_8week vs. Sterile57_8week


title: V8 (sample 9) vs M8 (sample 71)

description: V9_8week vs. M71_8week


title: CCRF-CEM-VCR cell line

description: Gene expression data from cell-line

source_name: Not available

value: CCRF-CEM-VCR


title: S8 (sample 58) vs V8 (sample 9)

description: Sterile58_8week vs. V9_8week

value: ShamMated


title: SNU-1076 cell line

description: Gene expression data from cell-line

value: Not available


title: M1 (sample 19) vs V1 (sample 29)

description: M19_1week vs. V29_1week

source_name: V1 (pooled RNA from two queens)

value: Virgin


title: V1 (sample 29) vs S1 (sample 76)

description: V29_1week vs. Sterile76_1week


title: 498 cell line

description: Gene expression data from cell-line


title: S1 (sample 50) vs M1 (sample 17)

description: Sterile50_1week vs. M17_1week

value: Mated


title: M1 (sample 17) vs V1 (sample 15)

description: M17_1week vs. V15_1week

value: 1 weeks


title: CCRF-CEM cell line

description: Gene expression data from cell-line

source_name: ATCC

value: CCRF-CEM

value: not known


title: V1 (sample 15) vs S1 (sample 50)

description: V15_1week vs. Sterile50_1week


title: SNU-899 cell line

description: Gene expression data from cell-line


title: S1 (sample 52) vs M1 (sample 24)

description: Sterile52_1week vs. M24_1week


title: V1 (sample 32) vs S1 (sample 52)

description: V32_1week vs. Sterile52_1week


title: M1 (sample 24) vs V1 (sample 32)

description: M24_1week vs. V32_1week


title: M1 (sample 23) vs V1 (sample 31)

description: M23_1week vs. V31_1week


title: S1 (sample 49) vs M1 (sample 21)

description: Sterile49_1week vs. M21_1week


title: S1 (sample 51) vs M1 (sample 23)

description: Sterile51_1week vs. M23_1week


title: MKN7 cell line

description: Gene expression data from cell-line


title: MKN1 cell line

description: Gene expression data from cell-line


title: V1 (sample 31) vs S1 (sample 51)

description: V31_1week vs. Sterile51_1week


title: Gastric Cancer T1

city: Sagamihara

first: Akira

last: Ema

state: Kanagawa

address: Kitasato 1-15-1, Minami-ku

department: Department of Surgery

country: Japan

institute: Kitasato University School of Medicine

description: High ND T1

hyb_protocol: The biotinylated cRNA was fragmented and hybridized for 16h at 45 degrees with the Human Genome U133 plus 2.0 array (Affymetrix).  The arrays were washed, stained with streptavidin-phycoerythrin, and scanned using an Fludics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The fluorescence intensity of each probe was quantified using the computer program GeneChip operating software, GCOS version 1.4 (Affymetrix). The intensity was nomalized as the mean target intensity of each array was 100.

source_name: Specimens of gastric cancer with 13th pStage III (high ND)

label_protocol: 200ng of mRNA was used to generate first-strand cDNA using T7-linked oligo-(dT) primer.  After second-strand synthesis, the cDNA was subjected to in vitro transcription in the presence of biotinylated uridine triphosphate, using an IVT labering kit (Affymetrix).

extract_protocol: Harvested cells were washed three times with Phosphate Buffer Saline (PBS) solution and homogenized using QIA Shredder (QIAGEN).  Total RNA from homogenized tissues was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: Each sample of excised gastric tissue was immediately immersed in RNAlater RNA stabilization Reagent (QIAGEN Sciences), and the samples were homogenized for 60 seconds at 6000 rpm using a MagNA Lyser (Roche diagnostics Inc.).

tag: tissue type

value: gastric cancer

value: Male

value: 75 years old

tag: Stage

value: stage III

tag: phenotype

value: Famous oncogenes such as Nkx2.1, CHST9, FGFR2, and EGFR were expressed in high ND tumors.


title: Gastric Cancer T2

description: Low ND T2

source_name: Specimens of gastric cancer with 13th pStage III (low ND)

value: 66 years old

value: Specific oncogene was not expressed in low ND tumors.


title: Gastric Cancer T5

description: High ND T5

value: 80 years old

value: Famous oncogenes such as Nkx2.1, CHST9, FGFR4, and EGFR were expressed in high ND tumors.


title: Gastric Cancer T7

description: Low ND T7

value: 48 years old


title: Gastric Cancer T20

description: Low ND T20

value: 70 years old


title: Gastric Cancer N18

description: Normal tissue N18

source_name: Normal mucosa specimens

value: normal mucosa


title: PSM05_LN4D6 CREB3L1 cells

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

description: Gene expression data from LN4D6 CREB3L1 cells

hyb_protocol: cRNA was hybridized and stained using the Genechip hybridization, stain and wash kit according to manufacturers instructions.

scan_protocol: Gene chips were scanned using Genechip Scanner 3000 7G

data_processing: The data was analyzed with Partek Genomics Suite v6.6 using RMA (data in log2)

source_name: LN4D6 CREB3L1 cells

label_protocol: Biotin labelling was prepared using the 3' IVT Express Kit according to manufacturers instructions.

growth_protocol: Cells were grown in 5% CO2 at 37C

extract_protocol: RNA was extracted using the Qiagen RNA extraction kit according to manufacturers instructions.

tag: cell line

tag: cell type

value: rat mammary tumor cells

tag: tansfected with


title: PSM06_LN4D6 CREB3L1 cells


title: V1 (sample 16) vs S1 (sample 49)

description: V16_1week vs. Sterile49_1week

value: Virgin

value: ShamMated


title: PSM02_LN4D6 cells

description: Gene expression data from LN4D6 cells

source_name: LN4D6 cells


title: PSM01_LN4D6 cells

description: Gene expression data from LN4D6 cells


title: RB cells (Y79), Duplicate

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Suspension cell line

hyb_protocol: The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water. The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: miRNA based normalization was done using GeneSpring GX 11.5 Software. 90th Percentile Shift Normalization

source_name: Eye/ retina

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hr.

extract_protocol: RNA was prepared using the mirVana kit from Ambion as per manufacturer's protocol.

value: Female

tag: age (years)

value: Retinoblastoma cells (Y79)

tag: genotype/variation

value: control


title: RB cells (Y79) treated with anti-HMGA2 siRNA , Duplicate

description: Suspension cell line

value: anti-HMGA2 siRNA


title: Gastric Cancer T11

description: High ND T11

value: gastric cancer

value: Male

value: 65 years old

value: Famous oncogenes such as Nkx2.1, CHST9, FGFR3, and EGFR were expressed in high ND tumors.


title: Gastric Cancer N17

description: Normal tissue N17


title: M1 (sample 21) vs V1 (sample 16)

description: M21_1week vs. V16_1week

value: Mated

value: 1 weeks


title: S1 (sample 42) vs M1 (sample 20)

description: Sterile42_1week vs. M20_1week


title: PSM04_LN4D6 CREB3L1 cells


title: Gastric Cancer T9

description: High ND T9

value: 69 years old

value: stage III

value: Famous oncogenes such as Nkx2.1, CHST9, FGFR5, and EGFR were expressed in high ND tumors.


title: Gastric Cancer T4

description: Low ND T4

value: 74 years old

value: Specific oncogene was not expressed in low ND tumors.


title: M1 (sample 20) vs V1 (sample 14)

description: M20_1week vs. V14_1week

value: Virgin


title: PSM03_LN4D6 cells

description: Gene expression data from LN4D6 cells

value: rat mammary tumor cells


title: V1 (sample 14) vs S1 (sample 42)

description: V14_1week vs. Sterile42_1week

value: ShamMated


title: RB cells (Y79) treated with anti-HMGA2 siRNA

description: Suspension cell line

value: Female

value: Retinoblastoma cells (Y79)


title: S1 (sample 53) vs M1 (sample 62)

description: Sterile53_1week vs. M62_1week


title: RB cells (Y79)

description: Suspension cell line

value: control


title: M1 (sample 62) vs V1 (sample 46)

description: M62_1week vs. V46_1week


title: V1 (sample 46) vs S1 (sample 53)

description: V46_1week vs. Sterile53_1week


title: TG 1

city: Chicago

first: Waddah

last: Alrefai

state: IL

address: 820 S Damen Ave

department: Medicine

institute: University of Illinois at Chicago/Jesse Brown VA Medical Center

description: jejunum of ISR2 mouse (8-10 weeks of age)

hyb_protocol: Hybridization at 45 C for 18 hrs, Affymetrix wash protocol FS450_0007

scan_protocol: Affymetrix GeneChip 7G scanner

data_processing: RMA

source_name: Mucosal scraping from the jejunum

label_protocol: Affymetrix WT target labeling protocol

growth_protocol: Mice were housed in a controlled 12h dark and 12h light cycles/day up to 8-10 weeks of age

extract_protocol: Total RNA was extracted from tissues utilizing RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Mice were fed regular chow diet and had free access to food and water

value: Jejunal mucosa

tag: strain

value: Transgenic mouse ISR2 (C57/BL)

value: 8-10 weeks


title: TG 2


title: Control 1

description: jejunum of wild type mouse (8-10 weeks of age)

value: Mouse (C57/BL)


title: TG 3


title: Control 2


title: Control 3


title: Experimantal rat 4 after 3 months of experiment

status: Public on Oct 25 2013

city: Warsaw

first: Hanna

last: Oszkiel

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: WARSAW UNIVERSITY OF LIFE SCIENCES – SGGW  (WULS-SGGW)

hyb_protocol: according to the Agilent manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: liver tissue from experimental group

growth_protocol: Animals were divided into two groups: a control group and an experimental group.Rats from both groups were receiving semi-synthetic diets formulated according to the nutritional requirements for laboratory animals and described in. The application of the semi-synthetic diet allowed elimination of the additional impact of biologically active compounds contained in commercially available diets. To experimental  diet the following biologically active compounds were added: 6% of salmon fat replacing lard (to increase the level of unsaturated fatty acids), 8% of hydrolysed water extract from small-leaved linden (Tilia cordata) inflorescence (as a source of antioxidant compounds), 8% puree from giant pumpkin (Curcubita macima) (the source of beta-carotene) and 1% of two strains of bacteria with documented probiotic activity: Lactobacillus acidophilus LA-5 and Bifidobacterium animals ssp. lactis. The dry matter content of both diets was the same.

extract_protocol: Total RNA extracted using RNeasy Lipid Tissue Mini Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: not applicable

tag: diet

value: diet enriched with biologicaly active compunds

tag: duration of the experiment

value: 3 months

value: liver

source_name: common reference sample compsed of total RNAs isolated from 10-week healthy rats not participating in the experiment, haused for two weeks in the same room with experimental rats

tag: group

value: common reference


title: Experimantal rat 6 after 14 months of experiment

label_protocol: according to the Agilent manufacturer's protocol

value: 14 months

tag: tissue


title: Experimantal rat 1 after 14 months of experiment


title: Control rat 3 after 14 months of experiment

source_name: liver tissue from control group

value: control diet


title: Experimantal rat 5 after 3 months of experiment


title: Control rat 2 after 14 months of experiment


title: Control rat 4 after 14 months of experiment


title: Experimantal rat 4 after 14 months of experiment


title: Control rat 6 after 14 months of experiment


title: Experimantal rat 3 after 14 months of experiment


title: Experimantal rat 3 after 3 months of experiment


title: Experimantal rat 5 after 14 months of experiment


title: Control rat 5 after 14 months of experiment


title: HLE cell line

description: Gene expression data from cell-line

value: HLE

tag: gender

value: male

tag: differentiation

value: undifferentiated

tag: origin

value: not known


title: Control rat 1 after 14 months of experiment


title: Control rat 4 after 3 months of experiment


title: Experimantal rat 2 after 3 months of experiment


title: Control rat 3 after 3 months of experiment


title: Control rat 1 after 3 months of experiment


title: Experimantal rat 2 after 14 months of experiment


title: Control rat 2 after 3 months of experiment


title: Experimantal rat 1 after 3 months of experiment


title: Mayo 92

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: FFPE samples from chemotherapy-naïve hormone-receptor-negative breast cancer annotated with distant recurrence information.

data_processing:
CT values for target genes are non-detected if there is a lack of gene amplification within 40 thermocycles.
ddCT values for target genes are generated by first normalizing to two reference genes (PPIG and NUP214), then to a universal human reference RNA (Stratagene) that was amplified with the same genes. Samples assayed in the same batch are normalized to a corresponding RNA reference; altogether, six RNA references were employed. CPMC samples are normalized to RP_1. Guy's Hospital samples: 5037-057, 5037-228, 5040-026, 5040-042, 5040-047, 5040-057, 5040-058, 5040-060, 5040-087, 5040-093, 5040-100, 5040-103, 5040-112, 5040-154, 5040-173, 5040-178, 5040-193, 5040-197, 5040-253, 5040-255 are normalized to RP_2, the remaining Guy's hospital samples are normalized to RP_3, Mayo clinic samples: Mayo 06, Mayo 15, Mayo 16, Mayo 18, Mayo 20, Mayo 27, Mayo 30, Mayo 31, Mayo 33, Mayo 36, Mayo 38, Mayo 40, Mayo 41, Mayo 44, Mayo 48, Mayo 54, Mayo 65, Mayo 66, Mayo 82, Mayo 88, Mayo 90, Mayo 93 are normalized to RP_4. Mayo clinic samples: Mayo 03, Mayo 08, Mayo 12, Mayo 14, Mayo 17, Mayo 21, Mayo 23, Mayo 24, Mayo 25, Mayo 26, Mayo 32, Mayo 35, Mayo 43, Mayo 45, Mayo 52, Mayo 55, Mayo 57, Mayo 62, Mayo 63, Mayo 64, Mayo 71, Mayo 73, Mayo 84, Mayo 86, Mayo 89, Mayo 92 are normalized to RP_5. All remaining Mayo clinic samples are normalized to RP_6.
ddCT values of target gene signatures are median-centered and scaled to standard deviation of 1 within each of the sample sources (California Pacific Medical Center, Guy's Hospital, Mayo Clinic).

label: Multiplexed - NED, VIC, Quasar 670, 6FAM

source_name: Primary breast cancer, hormone receptor negative, chemotherapy naive

label_protocol: The probe for each gene within a multiplex is labeled with a unique fluorophore with the exception of the two reference genes, which were both labeled with NED in the same mix. Amplifications were performed with AmpliTaq Gold in a buffer containing 15 mM Tris-HCl, 50 mM KCl, pH 8.0 , 2.5 mM MgCl2, 200 uM dAGC, 400 uM dUTP, and uracil-N-glycolysis.

extract_protocol: Total RNA was extracted from 10 micron FFPE sections using a modified commercially available isolation kit (Zymo Research). The FFPE sections were digested with proteinase K for 18-24 hours at 55°C, spun down and the supernatant treated with a mixture of 100% ethanol and a GuSCN-based extraction buffer. The extracted material was purified on Zymo-Spin II columns, eluted with TE buffer and the RNA reverse transcribed into cDNA using random hexamers and the High Capacity cDNA kit (Life Technologies).

value: primary breast tumor

tag: sample source

value: Guy's Hospital

tag: er (0

tag: pr (0

tag: her2 (1

value: positive, 0:negative or equivocal):NA

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: Mayo 93


title: Mayo 88


title: Mayo 90


title: day8 hermaphrodite utx-1 RNAi -males rep 3

city: Stanford

first: Travis

middle: Justin

last: Maures

address: 300 Pasteur Drive Alway

department: Genetics

institute: Stanford University

description: C. elegans hermaphrodites utx-1 RNAi (no males) 3

hyb_protocol: according to Affymetrix protocols

scan_protocol: according to Affymetrix protocols

data_processing: Data processing and analysis from the worm transcriptomes from the three independent experiments was performed in the R software (http://www.r-project.org/), using packages 'affy' (PMID14960456) and recently published batch-correction algorithm ComBat (Johnson et al 2007). Briefly, raw probe fluorescence values were subjected to RMA normalization, and then the batch covariates were used to adjust for batch effects as previously described (PMID16632515). To estimate the reliability of biological replicates after the processing, sample clustering was performed using the Pvclust algorithm using its R package 'pvclust' implementation (PMID16595560). Parameters chosen for the clustering step were the Euclidean distance as a similarity measure, and the use of complete linkage hierarchical clustering. To estimate robustness and P-values, experiments were conducted with 10, 000 bootstrap replications of the clustering step. To identify significantly regulated genes between the -male/+male conditions, we used the Rank Products methods (R package 'RankProd') (PMID16595560), using the batch information to adujst for experiment specific biases, and set a False Discovery Rate (FDR) threshold for discovery of genes of 5%. From this analysis, 341 probes on the array were significantly up-regulated in the male treated samples, and 289 were significantly down-regulated. Functional annotation enrichment was performed using DAVID software portal as described previously (PMID19131956).

organism: Caenorhabditis elegans

source_name: day8 hermaphrodite utx-1 RNAi -males

label_protocol: according to affymetrix GeneChip DNA Labeling Reagent protocol

growth_protocol: glp-1(e2141) embryos were grown at 15 C and sychronized by bleaching. From the bleaching 250 glp-1(e2141) L1 hermaphrodites (to avoid production of progeny) were placed in the presence of 250 wild-type males (L4-adult day 1) for 8 days on a 10 cm NGM plate seeded with OP50. As a control for worm number, 500 L1 glp-1(e2141) hermaphrodites were placed on a 10 cm NGM plate seeded with OP50 for 8 days. Both conditions were incubated at 25°C, the restrictive temperature for the glp-1(e2141) worms throughout the experiment. On day 8, male worms were removed from the plate and RNA was extracted from 200 hermaphrodites from each condition.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA from the trizol extraction was then purified further using RNeasy kit according to the manufacturer's instructions

tag: genotype/variation

value: glp-1(e2141) sterile

value: utx-1 knockdown via RNAi

tag: age

value: hermaphrodites day 8

value: whole worm lysis at day 8


title: day8 hermaphrodite utx-1 RNAi -males rep 1

description: C. elegans hermaphrodites utx-1 RNAi (no males) 1


title: day8 hermaphrodite +males rep 3

description: C. elegans hermaphrodites (with males) 3

source_name: day8 hermaphrodite +males


title: Mayo 86


title: day8 hermaphrodite utx-1 RNAi +males rep 1

description: C. elegans hermaphrodites utx-1 RNAi (with males) 1

source_name: day8 hermaphrodite utx-1 RNAi +males


title: Mayo 89

value: positive, 0:negative or equivocal):1


title: day8 hermaphrodite -males rep 1

description: C. elegans hermaphrodites (no males) 1

source_name: day8 hermaphrodite -males


title: day8 hermaphrodite -males rep 3

description: C. elegans hermaphrodites (no males) 3


title: day8 hermaphrodite +males rep 1

description: C. elegans hermaphrodites (with males) 1


title: day8 hermaphrodite utx-1 RNAi -males rep 2


title: Mayo 84


title: day8 hermaphrodite utx-1 RNAi +males rep 3

description: C. elegans hermaphrodites utx-1 RNAi (with males) 2


title: Dyeflip-BS-BioRep2-Slide42

first: Jasmine

middle: L.

last: Loveland

state: California

address: 371 Serra Mall Rm 320

department: Biology

description: Dyeflip: RNA labeling was swapped (compared to other slides) to control for dye effects. DW2/pFLP-Bs Biological replicate 2 of 2. Time point for RNA harvest was when the optical density of cells in liquid culture reached 0.5

hyb_protocol: cDNA from DW2/pFLP-Bs and DW2/pFLP-Ec were cohybridized to slides containing 70-mer oligos representing 4,290 annotated ORFs in E. coli MG1655. The hybridization solution (20 μl of cDNA mixture, 30 μl of 2X SDS based hybridization buffer, 3 μl of LNA dT Blocker, 8 μl of nuclease-free water) was placed over a pre-warmed microarray slide and covered with a Corning 22 x 60 mm coverslip. The slide was then sealed in a hybridization chamber (Genehyb) and submerged for 2-3 days in a 58°C water bath. Microarray slides were washed for 10 min at room temperature starting with pre-warmed (42°C) 2X SSC (Ambion) followed by 0.2% SDS, 10 min in 2X SSC at room temperature, and lastly 10 min in 0.2X SSC at room temperature. Slides were dried by centrifugation at 1000 rpm, 2 min. For the second hybridization to allow the 3DNA capture reagent to bind to the complementary Cy3- or Cy5-specific 3DNA capture sequences ligated to the cDNAs, each slide received 60 μl of hybridization solution (2.5 μl of Cy3 capture reagent, 2.5 μl of Cy5 capture reagent, 30 μl of 2X SDS-based hybridization buffer, 25 μl of nuclease-free water) and was hybridized as before by submersion for 3 to 4 hrs in a 65°C water.

scan_protocol: GenePix Pro v.4.1 software (Axon Instruments, Inc.). Photomultiplier tube voltage was altered for the initial scanning to ensure proper channel balance and to decrease background.

data_processing: Data from the five slides were normalized by a Lowess fit using GProcessor. Using this program we calculated the mean of log2 ratios and median of log2 ratios across all five slides; and used the median of ratios for further analysis. Data was merged using GEPAS and a t-test was performed by GProcessor to select genes that were differentially expressed based on all good replicate spots.  across five slides; only genes with p-values <0.01 were analyzed further.

organism: Escherichia coli

source_name: DW2/pFLP-Bs cells in exponential growth phase

label_protocol: The synthesis, labeling of cDNA with Cy3 or Cy5, and hybridization to microarray slides were performed using the 3DNA Array 900MPX Expression Array Detection Kit (Genisphere) with 2 μg of total RNA for each strain.

growth_protocol: From a glycerol stock, cells were streaked onto LB-agar plates supplemented with kanamycin. Using a sterile toothpick a single colony was picked and placed into 100 ml of LB broth with kanamycin. Optical readings were taken and cells were pelleted for RNA harvest when the liquid culture reached an OD of 0.5

extract_protocol: Total RNA extracted using phenol:chloroform method followed by two DNase I treatments (Qiagen DNase I and Ambion Dnase Turbo).

tag: strain

source_name: DW2/pFLP-Ec cells in exponential growth phase


title: BS-BioRep1-Slide28

description: DW2/pFLP-Bs Biological replicate 1 of 2. Time point for RNA harvest was when the optical density of cells in liquid culture reached 0.5


title: day8 hermaphrodite -males rep 2

description: C. elegans hermaphrodites (no males) 2


title: day8 hermaphrodite +males rep 2

description: C. elegans hermaphrodites (with males) 2


title: Mayo 83


title: Mayo 73


title: BS-BioRep2-Slide47

description: DW2/pFLP-Bs Biological replicate 2 of 2. Time point for RNA harvest was when the optical density of cells in liquid culture reached 0.5


title: Mayo 82


title: BS-BioRep2-Slide41


title: Mayo 71


title: Mayo 70


title: BS-BioRep2-Slide44

data_processing:
Data from the five slides were normalized by a Lowess fit using GProcessor. Using this program we calculated the mean of log2 ratios and median of log2 ratios across all five slides; and used the median of ratios for further analysis. Data was merged using GEPAS and a t-test was performed by GProcessor to select genes that were differentially expressed based on all good replicate spots.  across five slides; only genes with p-values <0.01 were analyzed further.

Raw data is not available for this sample.


title: Mayo 68

value: positive, 0:negative or equivocal):0


title: Mayo 66


title: Control rat 5 after 3 months of experiment

tag: diet

tag: duration of the experiment

value: 3 months

value: liver

tag: group


title: Mayo 65

tag: tissue


title: Mayo 64


title: Mayo 62


title: Mayo 59


title: Mayo 57


title: Mayo 63