title: gastric tumor Gastric0113

description: gene expression data from gastric tumor Gastric0113

source_name: gastric tumor Gastric0113


title: gastric tumor Gastric0109

status: Public on Jul 05 2012

type: RNA

city: Singapore

first: Zhengdeng

last: Lei

address: 8 College Road

country: Singapore

institute: Duke-NUS graduate medical school

description: gene expression data from gastric tumor Gastric0109

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were RMA normalized with R package affy.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: gastric tumor Gastric0109

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: gastric tumor tissue.

extract_protocol: Total RNA was extracted from primary tumors using RNeasy mini spin columns (Qiagen) according to the instructions of the manufacturer.

treatment_protocol: gastric tumor tissue.

tag: tissue

value: gastric adenocarcinoma

tag: subtype

value: Invasive


title: liver-HCV-Non Tumor-rep4 [miRNA]

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

country: USA

institute: Washington University in St.Louis

hyb_protocol: Samples were hybridized onto beadchips according to microRNA expression profiling protocol from Illumina.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.  Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

data_processing: The data were normalized using quantile normalization implemented in Illumina Genome studio version 1.7.0.

source_name: liver-HCV-Non Tumor

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

growth_protocol: The study was approved by the Institutional Review Board at Washington University in St. Louis and all patients were enrolled after informed consent.

extract_protocol: Liver biopsy that were snap frozen obtained from HCV or control normal liver, were used to isolate RNA using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

value: liver

tag: tissue subtype

value: Non Tumor


title: Gastric tumor 4351_Stom_Tum_U133B

first: Wu

last: Yonghui

state: Choose your state

institute: NCCS

description: gene expression data from gastric tumor 4351_Stom_Tum_U133B

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were RMA normalized with BRB-ArrayTools.

label: Biotin

source_name: Gastric tumor 4351_Stom_Tum_U133B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

extract_protocol: Total RNA was extracted from gastric tissues using RNeasy mini spin columns (Qiagen) according to the instructions of the manufacturer.

value: Gastric tumor

tag: intra-tumoral stroma


title: liver-Tumor-rep3 [miRNA]

source_name: liver-Tumor

value: Tumor


title: liver-HCV-Non Tumor-rep3 [miRNA]


title: liver-HCV-rep4 [miRNA]

source_name: liver-HCV

value: HCV


title: Gastric tumor 4350_Stom_Tum_U133B_ab3_R1

description: gene expression data from gastric tumor 4350_Stom_Tum_U133B_ab3_R1


title: liver-HCV-Non Tumor-rep2 [miRNA]


title: Gastric non-malignant 4348_Norm_Stom_U133B

description: gene expression data from gastric non-malignant 4348_Norm_Stom_U133B

value: Gastric non-malignant


title: liver-HCV-rep3 [miRNA]


title: liver-Normal-Post reperfusion-rep1 [miRNA]

source_name: liver-Normal-Post reperfusion

value: Normal


title: human islets, ID66

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the software “Expression Console” (Affymetrix).

source_name: Islets from cadaver donor ID66

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to RNA preparation.

value: pancreatic islets

tag: Sex

value: Female

tag: age

tag: bmi

tag: status

value: non-diabetic donors


title: human islets, ID65

source_name: Islets from cadaver donor ID65

value: Male

value: T2D donors


title: human islets, ID63

source_name: Islets from cadaver donor ID63


title: Gastric tumor 4349_Stom_Tum_U133B

description: gene expression data from gastric tumor 4349_Stom_Tum_U133B

source_name: Gastric tumor 4349_Stom_Tum_U133B


title: Gastric non-malignant 4347_Norm_Stom_U133B

description: gene expression data from gastric non-malignant 4347_Norm_Stom_U133B


title: human islets, ID64

source_name: Islets from cadaver donor ID64


title: Gastric non-malignant 4346_Norm_Stom_U133B

description: gene expression data from gastric non-malignant 4346_Norm_Stom_U133B


title: liver-Normal-rep3 [miRNA]

source_name: liver-Normal


title: Gastric non-malignant 4345_Norm_Stom_U133B

description: gene expression data from gastric non-malignant 4345_Norm_Stom_U133B


title: gastric tumor Gastric0101

description: gene expression data from gastric tumor Gastric0101

source_name: gastric tumor Gastric0101


title: human islets, ID61

source_name: Islets from cadaver donor ID61


title: human islets, ID62

source_name: Islets from cadaver donor ID62


title: gastric tumor Gastric0097

description: gene expression data from gastric tumor Gastric0097

source_name: gastric tumor Gastric0097


title: gastric tumor Gastric0103

description: gene expression data from gastric tumor Gastric0103

source_name: gastric tumor Gastric0103

value: Proliferative


title: gastric tumor Gastric0105

description: gene expression data from gastric tumor Gastric0105

source_name: gastric tumor Gastric0105


title: human islets, ID60

source_name: Islets from cadaver donor ID60


title: Gastric non-malignant 4344_Norm_Stom_U133B

description: gene expression data from gastric non-malignant 4344_Norm_Stom_U133B


title: gastric tumor Gastric0099

description: gene expression data from gastric tumor Gastric0099

source_name: gastric tumor Gastric0099


title: Gastric non-malignant 3866_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3866_Norm_Stom_U133B_ab2


title: gastric tumor 20020849-GC

description: gene expression data from gastric tumor 20020849-GC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: gastric tumor 20020849-GC

value: gastric tumor


title: gastric tumor Gastric0096

description: gene expression data from gastric tumor Gastric0096

source_name: gastric tumor Gastric0096


title: gastric tumor Gastric0093

description: gene expression data from gastric tumor Gastric0093

source_name: gastric tumor Gastric0093

value: Metabolic


title: human islets, ID59

source_name: Islets from cadaver donor ID59


title: liver-Normal-rep2 [miRNA]


title: human islets, ID58

source_name: Islets from cadaver donor ID58


title: liver-Normal-rep1 [miRNA]


title: liver-HCV-rep2 [miRNA]

source_name: liver-HCV


title: Gastric tumor 3864_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3864_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3864_Stom_Tum_U133B_ab2


title: Gastric tumor 3865_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3865_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3865_Stom_Tum_U133B_ab2


title: human islets, ID56

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID56


title: human islets, ID57

source_name: Islets from cadaver donor ID57


title: liver-HCV-rep1 [miRNA]


title: liver-Tumor-rep1 [miRNA]

source_name: liver-Tumor


title: Gastric tumor 3863_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3863_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3863_Stom_Tum_U133B_ab2


title: liver-HCV-Non Tumor-rep1 [miRNA]

source_name: liver-HCV-Non Tumor


title: Gastric tumor 3862_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3862_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3862_Stom_Tum_U133B_ab2


title: Gastric tumor 3861_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3861_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3861_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0091

description: gene expression data from gastric tumor Gastric0091

source_name: gastric tumor Gastric0091

value: gastric adenocarcinoma


title: gastric tumor Gastric0095

description: gene expression data from gastric tumor Gastric0095

source_name: gastric tumor Gastric0095


title: human islets, ID54

source_name: Islets from cadaver donor ID54


title: human islets, ID53

source_name: Islets from cadaver donor ID53


title: gastric tumor Gastric0089

description: gene expression data from gastric tumor Gastric0089

source_name: gastric tumor Gastric0089

value: Invasive


title: gastric tumor Gastric0086

description: gene expression data from gastric tumor Gastric0086

source_name: gastric tumor Gastric0086


title: human islets, ID55

source_name: Islets from cadaver donor ID55


title: Gastric tumor 3860_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3860_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3860_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0082

description: gene expression data from gastric tumor Gastric0082

source_name: gastric tumor Gastric0082


title: Gastric tumor 3858_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3858_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3858_Stom_Tum_U133B_ab2


title: human islets, ID51

source_name: Islets from cadaver donor ID51


title: human islets, ID52

source_name: Islets from cadaver donor ID52


title: gastric tumor Gastric0083

description: gene expression data from gastric tumor Gastric0083

source_name: gastric tumor Gastric0083


title: gastric tumor Gastric0087

description: gene expression data from gastric tumor Gastric0087

source_name: gastric tumor Gastric0087


title: liver-Tumor-rep2 [miRNA]

source_name: liver-Tumor

value: liver


title: gastric tumor Gastric0079

description: gene expression data from gastric tumor Gastric0079

source_name: gastric tumor Gastric0079


title: anther-LCM-premeiotic-cells 1mm anthers mac1_heterozygote Rep1 Cy3

city: Stanford

first: Timothy

last: Kelliher

state: Ca

address: 385 Serra Mall

department: Biology

institute: Stanford University

description:
compare pre-meiotic cells in 1mm anthers between mac1 mutant and its wildtype
Cy3-180_3
raw data file: US84703594_251604710180_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing:
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, intensities for each channel from Feature Extraction were normalized using lowess.  Average intensities were then calculated for each sample type for comparison.
The limma package (v.3.8.3) of R (v.2.13) was used to normalize the median intensities for each channel as follows: within each array using loess and between arrays using quantile method. Sample data table contains the absolute values for cy3 or cy5 after normalization.

organism: Zea mays

label_protocol: Total RNA (50 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: For whole anthers, total RNA was extracted from 30 - 60 mg of frozen tissues with TRIzol, digested with DNase I, and cleaned up with Qiagen RNeasy Mini kit. For laser microdissection, a PALM microbeam LCM was used for dissection, and RNA was extracted and cleaned up with a PicoPure column (Arcturus), treated with Dnase I, and resuspended in dH2O.

tag: genotype/variation

value: laser microdissected pre-meiotic cells

tag: anther length

value: 1 mm


title: human islets, ID50

source_name: Islets from cadaver donor ID50


title: Gastric tumor 3859_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3859_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3859_Stom_Tum_U133B_ab2

value: Gastric tumor


title: human islets, ID49

source_name: Islets from cadaver donor ID49


title: Gastric tumor 3857_Stom_Tum_U133B_ab2_R1

description: gene expression data from gastric tumor 3857_Stom_Tum_U133B_ab2_R1


title: Gastric non-malignant 3856_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3856_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3855_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3855_Norm_Stom_U133B_ab2


title: anther-LCM-premeiotic-cells 1mm anthers mac1_mutant Rep1 Cy5

description:
compare pre-meiotic cells in 1mm anthers between mac1 mutant and its wildtype
Cy5-180_3
raw data file: US84703594_251604710180_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

value: mac1 mutant


title: anther-LCM-premeiotic-cells 700micron anthers wildtype_W23 Rep2 Cy5

description:
compare whole anther to premeiotic cells for W23 inbred at 700micron anther length
Cy5-207_4
raw data file: US84703594_251604710207_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

value: wild type

value: 701 micron


title: human islets, ID48

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID48

value: pancreatic islets


title: anther-whole 700micron anthers wildtype_W23 Rep2 Cy3

description:
compare whole anther to premeiotic cells for W23 inbred at 700micron anther length
Cy3-207_4
raw data file: US84703594_251604710207_S01_GE2-v5_95_Feb07_2_JF_1_4.txt

source_name: anther-whole 700micron wildtype_W23

value: whole anthers


title: Gastric non-malignant 3854_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3854_Norm_Stom_U133B_ab2

value: Gastric non-malignant


title: human islets, ID46

source_name: Islets from cadaver donor ID46

value: Male

value: non-diabetic donors


title: gastric tumor Gastric0073

description: gene expression data from gastric tumor Gastric0073

source_name: gastric tumor Gastric0073


title: gastric tumor Gastric0068

description: gene expression data from gastric tumor Gastric0068

source_name: gastric tumor Gastric0068


title: anther-LCM-premeiotic-cells 700micron anthers wildtype_W23 Rep1 Cy3

description:
compare whole anther to premeiotic cells for W23 inbred at 700micron anther length
Cy3-207_3
raw data file: US84703594_251604710207_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

value: 700 micron


title: human islets, ID44

source_name: Islets from cadaver donor ID44

value: Female


title: Gastric non-malignant 3853_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3853_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0080

description: gene expression data from gastric tumor Gastric0080

source_name: gastric tumor Gastric0080

value: Proliferative


title: Gastric non-malignant 3852_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3852_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3851_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3851_Norm_Stom_U133B_ab2


title: human islets, ID47

source_name: Islets from cadaver donor ID47


title: human islets, ID43

source_name: Islets from cadaver donor ID43


title: gastric tumor Gastric0070

description: gene expression data from gastric tumor Gastric0070

source_name: gastric tumor Gastric0070

value: gastric adenocarcinoma


title: gastric tumor Gastric0074

description: gene expression data from gastric tumor Gastric0074

source_name: gastric tumor Gastric0074

value: Metabolic


title: gastric tumor Gastric0072

description: gene expression data from gastric tumor Gastric0072

source_name: gastric tumor Gastric0072

value: Invasive


title: Q of C3KO Y mouse H4-2

city: San Sebastian

first: Amets

last: Saenz

state: Gipuzkoa

address: Pº dr Begiristain s/n

country: Spain

institute: Donostia Hospital

description:
1-3-97-Q-C3KO
Gene expression data from quadriceps of C3KO mouse H4-2 (2-3months)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and with the Robust Multichip Average (RMA) algorithm in Bioconductor

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: strain

value: 129 SvEvBrd x C57BL/6 heterozygotes

value: Quadriceps muscle

value: Y (2-3 months)


title: soleus of C3KO Y mouse H4-2

description:
1-4-1-S-C3KO
Gene expression data from soleus of C3KO mouse H4-2 (2-3months)

source_name: soleus of C3KO mouse H4-2 (2-3months)

value: Soleus muscle


title: gastric tumor Gastric0063

description: gene expression data from gastric tumor Gastric0063

source_name: gastric tumor Gastric0063


title: human islets, ID42

source_name: Islets from cadaver donor ID42

value: T2D donors


title: Gastric non-malignant 3850_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3850_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0065

description: gene expression data from gastric tumor Gastric0065

source_name: gastric tumor Gastric0065


title: anther-whole 700micron anthers wildtype_W23 Rep1 Cy5

description:
compare whole anther to premeiotic cells for W23 inbred at 700micron anther length
Cy5-207_3
raw data file: US84703594_251604710207_S01_GE2-v5_95_Feb07_2_JF_1_3.txt

value: wild type


title: gastric tumor Gastric0062

description: gene expression data from gastric tumor Gastric0062

source_name: gastric tumor Gastric0062


title: human islets, ID41

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID41

value: pancreatic islets


title: human islets, ID40

source_name: Islets from cadaver donor ID40


title: Gastric non-malignant 3848_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3848_Norm_Stom_U133B_ab2


title: Q of C3KO A mouse U2-2

description:
1-3-9-Q-C3KO
Gene expression data from quadriceps of C3KO mouse U2-2 (11-12months)

value: A (11-12 months)


title: soleus of C3KO Y mouse H4-1

description:
1-3-87-S-C3KO
Gene expression data from soleus of C3KO mouse H4-1 (2-3months)

source_name: soleus of C3KO mouse H4-1 (2-3months)


title: gastric tumor Gastric0060

description: gene expression data from gastric tumor Gastric0060

source_name: gastric tumor Gastric0060


title: soleus of wt Y mouse F4-4

description:
1-3-82-S-WT
Gene expression data from soleus of wt mouse F4-4 (2-3months)

source_name: soleus of wt mouse F4-4 (2-3months)

value: wild-type


title: Q of C3KO Y mouse H4-1

description:
1-3-84-Q-C3KO
Gene expression data from quadriceps of C3KO mouse H4-1 (2-3months)


title: Gastric non-malignant 3847_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3847_Norm_Stom_U133B_ab2

value: Gastric non-malignant


title: Gastric non-malignant 3849_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3849_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3846_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3846_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0058

description: gene expression data from gastric tumor Gastric0058

source_name: gastric tumor Gastric0058


title: Gastric non-malignant 3845_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3845_Norm_Stom_U133B_ab2


title: human islets, ID37

source_name: Islets from cadaver donor ID37

value: Male

value: non-diabetic donors


title: Gastric non-malignant 3844_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3844_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0057

description: gene expression data from gastric tumor Gastric0057

source_name: gastric tumor Gastric0057


title: human islets, ID36

source_name: Islets from cadaver donor ID36


title: Q of wt Y mouse F4-4

description:
1-3-79-Q-WT
Gene expression data from quadriceps of wt mouse F4-4 (2-3months)

source_name: quadriceps of wt mouse F4-4 (2-3months)


title: gastric tumor Gastric0055

description: gene expression data from gastric tumor Gastric0055

source_name: gastric tumor Gastric0055


title: human islets, ID39

source_name: Islets from cadaver donor ID39


title: gastric tumor Gastric0053

description: gene expression data from gastric tumor Gastric0053

source_name: gastric tumor Gastric0053


title: soleus of wt Y mouse F4-3

description:
1-3-77-S-WT
Gene expression data from soleus of wt mouse F4-3 (2-3months)

source_name: soleus of wt mouse F4-3 (2-3months)


title: Q of wt Y mouse F4-3

description:
1-3-74-Q-WT
Gene expression data from quadriceps of wt mouse F4-3 (2-3months)

source_name: quadriceps of wt mouse F4-3 (2-3months)


title: gastric tumor Gastric0052

description: gene expression data from gastric tumor Gastric0052

source_name: gastric tumor Gastric0052


title: Gastric non-malignant 3843_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3843_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0051

description: gene expression data from gastric tumor Gastric0051

source_name: gastric tumor Gastric0051


title: human islets, ID35

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID35

value: Female


title: human islets, ID34

source_name: Islets from cadaver donor ID34


title: Q of wt Y mouse F4-2

description:
1-3-69-Q-WT
Gene expression data from quadriceps of wt mouse F4-2 (2-3months)

source_name: quadriceps of wt mouse F4-2 (2-3months)


title: human islets, ID33

source_name: Islets from cadaver donor ID33


title: human islets, ID32

source_name: Islets from cadaver donor ID32


title: gastric tumor Gastric0050

description: gene expression data from gastric tumor Gastric0050

source_name: gastric tumor Gastric0050


title: soleus of wt Y mouse F4-2

description:
1-3-72-S-WT
Gene expression data from soleus of wt mouse F4-2 (2-3months)

source_name: soleus of wt mouse F4-2 (2-3months)


title: soleus of wt Y mouse F4-1

description:
1-3-67-S-WT
Gene expression data from soleus of wt mouse F4-1 (2-3months)

source_name: soleus of wt mouse F4-1 (2-3months)


title: Gastric non-malignant 3842_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3842_Norm_Stom_U133B_ab2


title: human islets, ID31

source_name: Islets from cadaver donor ID31


title: Gastric non-malignant 3841_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3841_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3823_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3823_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3822_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3822_Norm_Stom_U133B_ab2


title: Q of wt Y mouse F4-1

description:
1-3-64-Q-WT
Gene expression data from quadriceps of wt mouse F4-1 (2-3months)

source_name: quadriceps of wt mouse F4-1 (2-3months)


title: soleus of C3KO A mouse U2-1

description:
1-3-6-S-C3KO
Gene expression data from soleus of C3KO mouse U2-1 (11-12months)

source_name: soleus of C3KO mouse U2-1 (11-12months)


title: gastric tumor Gastric0049

description: gene expression data from gastric tumor Gastric0049

source_name: gastric tumor Gastric0049

value: Proliferative


title: human islets, ID29

source_name: Islets from cadaver donor ID29


title: gastric tumor Gastric0047

description: gene expression data from gastric tumor Gastric0047

source_name: gastric tumor Gastric0047

value: gastric adenocarcinoma


title: human islets, ID38

source_name: Islets from cadaver donor ID38


title: Gastric tumor 3820_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3820_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3820_Stom_Tum_U133B_ab2

value: Gastric tumor


title: Gastric non-malignant 3821_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3821_Norm_Stom_U133B_ab2


title: human islets, ID28

source_name: Islets from cadaver donor ID28


title: Gastric tumor 3819_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3819_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3819_Stom_Tum_U133B_ab2


title: human islets, ID27

source_name: Islets from cadaver donor ID27


title: soleus of C3KO Y mouse J4-2

description:
1-3-52-S-C3KO
Gene expression data from soleus of C3KO mouse J4-2 (2-3months)

source_name: soleus of C3KO mouse J4-2 (2-3months)


title: Q of C3KO Y mouse J4-2

description:
1-3-49-Q-C3KO
Gene expression data from quadriceps of C3KO mouse J4-2 (2-3months)


title: gastric tumor Gastric0046

description: gene expression data from gastric tumor Gastric0046

source_name: gastric tumor Gastric0046


title: gastric tumor Gastric0043

description: gene expression data from gastric tumor Gastric0043

source_name: gastric tumor Gastric0043


title: gastric tumor Gastric0041

description: gene expression data from gastric tumor Gastric0041

source_name: gastric tumor Gastric0041

value: Invasive


title: Q of C3KO Y mouse J4-1

description:
1-3-44-Q-C3KO
Gene expression data from quadriceps of C3KO mouse J4-1 (2-3months)

value: 129 SvEvBrd x C57BL/6 heterozygotes


title: Gastric tumor 3818_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3818_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3818_Stom_Tum_U133B_ab2


title: soleus of C3KO Y mouse J4-1

description:
1-3-47-S-C3KO
Gene expression data from soleus of C3KO mouse J4-1 (2-3months)

source_name: soleus of C3KO mouse J4-1 (2-3months)


title: gastric tumor Gastric0045

description: gene expression data from gastric tumor Gastric0045

source_name: gastric tumor Gastric0045


title: gastric tumor Gastric0039

description: gene expression data from gastric tumor Gastric0039

source_name: gastric tumor Gastric0039


title: human islets, ID26

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID26


title: Gastric tumor 3817_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3817_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3817_Stom_Tum_U133B_ab2


title: Gastric tumor 3816_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3816_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3816_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0037

description: gene expression data from gastric tumor Gastric0037

source_name: gastric tumor Gastric0037


title: human islets, ID25

source_name: Islets from cadaver donor ID25


title: human islets, ID24

source_name: Islets from cadaver donor ID24


title: soleus of wt A mouse X2-2

description:
1-3-37-S-WT
Gene expression data from soleus of wt mouse X2-2 (11-12months)

source_name: soleus of wt mouse X2-2 (11-12months)


title: gastric tumor Gastric0036

description: gene expression data from gastric tumor Gastric0036

source_name: gastric tumor Gastric0036


title: Gastric tumor 3813_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3813_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3813_Stom_Tum_U133B_ab2


title: Q of wt A mouse X2-3

description:
1-3-39-Q-WT
Gene expression data from quadriceps of wt mouse X2-3 (11-12months)

value: Quadriceps muscle


title: human islets, ID23

source_name: Islets from cadaver donor ID23


title: Q of wt A mouse X2-2

description:
1-3-34-Q-WT
Gene expression data from quadriceps of wt mouse X2-2 (11-12months)


title: human islets, ID22

source_name: Islets from cadaver donor ID22


title: human islets, ID21

source_name: Islets from cadaver donor ID21


title: soleus of wt A mouse X2-3

description:
1-3-42-S-WT
Gene expression data from soleus of wt mouse X2-3 (11-12months)

source_name: soleus of wt mouse X2-3 (11-12months)


title: soleus of wt A mouse W2-3

description:
1-3-32-S-WT
Gene expression data from soleus of wt mouse W2-3 (11-12months)

source_name: soleus of wt mouse W2-3 (11-12months)


title: Gastric tumor 3812_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3812_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3812_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0033

description: gene expression data from gastric tumor Gastric0033

source_name: gastric tumor Gastric0033


title: Q of C3KO A mouse U2-1

description:
1-3-3-Q-C3KO
Gene expression data from quadriceps of C3KO mouse U2-1 (11-12months)


title: Gastric tumor 3815_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3815_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3815_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0031

description: gene expression data from gastric tumor Gastric0031

source_name: gastric tumor Gastric0031


title: gastric tumor Gastric0032

description: gene expression data from gastric tumor Gastric0032

source_name: gastric tumor Gastric0032

value: Metabolic


title: gastric tumor Gastric0034

description: gene expression data from gastric tumor Gastric0034

source_name: gastric tumor Gastric0034


title: human islets, ID20

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID20


title: Q of wt A mouse W2-3

description:
1-3-29-Q-WT
Gene expression data from quadriceps of wt mouse W2-3 (11-12months)


title: Gastric non-malignant 3808_Norm_Stom_Mus_U133B_ab2

description: gene expression data from gastric non-malignant 3808_Norm_Stom_Mus_U133B_ab2


title: gastric tumor Gastric0029

description: gene expression data from gastric tumor Gastric0029

source_name: gastric tumor Gastric0029


title: gastric tumor Gastric0028

description: gene expression data from gastric tumor Gastric0028

source_name: gastric tumor Gastric0028


title: Q of wt A mouse W2-2

description:
1-3-24-Q-WT
Gene expression data from quadriceps of wt mouse W2-2 (11-12months)


title: Gastric tumor 3810_Stom_Tum_U133B_ab3

description: gene expression data from gastric tumor 3810_Stom_Tum_U133B_ab3

source_name: Gastric tumor 3810_Stom_Tum_U133B_ab3


title: Gastric non-malignant 3807_Norm_Stom_Mus_U133B_ab2

description: gene expression data from gastric non-malignant 3807_Norm_Stom_Mus_U133B_ab2


title: human islets, ID15

source_name: Islets from cadaver donor ID15


title: gastric tumor Gastric0026

description: gene expression data from gastric tumor Gastric0026

source_name: gastric tumor Gastric0026


title: human islets, ID16

source_name: Islets from cadaver donor ID16


title: Gastric tumor 3811_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3811_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3811_Stom_Tum_U133B_ab2


title: Q of wt A mouse W2-1

description:
1-3-19-Q-WT
Gene expression data from quadriceps of wt mouse W2-1 (11-12months)


title: Gastric non-malignant 3806_Norm_Stom_Mus_U133B_ab2

description: gene expression data from gastric non-malignant 3806_Norm_Stom_Mus_U133B_ab2


title: gastric tumor Gastric0023

description: gene expression data from gastric tumor Gastric0023

source_name: gastric tumor Gastric0023


title: soleus of wt A mouse W2-1

description:
1-3-22-S-WT
Gene expression data from soleus of wt mouse W2-1 (11-12months)

source_name: soleus of wt mouse W2-1 (11-12months)

value: Soleus muscle


title: human islets, ID11

source_name: Islets from cadaver donor ID11

value: T2D donors


title: human islets, ID13

source_name: Islets from cadaver donor ID13


title: Gastric tumor 3803_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3803_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3803_Stom_Tum_U133B_ab2


title: human islets, ID12

source_name: Islets from cadaver donor ID12


title: Gastric non-malignant 3805_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3805_Norm_Stom_U133B_ab2


title: human islets, ID14

source_name: Islets from cadaver donor ID14


title: Gastric non-malignant 3802_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3802_Norm_Stom_U133B_ab2


title: soleus of C3KO A mouse U2-2

description:
1-3-12-S-C3KO
Gene expression data from soleus of C3KO mouse U2-2 (11-12months)

source_name: soleus of C3KO mouse U2-2 (11-12months)


title: Q of C3KO A mouse U2-3

description:
1-3-14-Q-C3KO
Gene expression data from quadriceps of C3KO mouse U2-3 (11-12months)


title: Q of C3KO A mouse Q2-4

description:
1-1-98-Q-C3KO
Gene expression data from quadriceps of C3KO mouse Q2-4 (11-12months)


title: gastric tumor Gastric0020

description: gene expression data from gastric tumor Gastric0020

source_name: gastric tumor Gastric0020


title: gastric tumor Gastric0021

description: gene expression data from gastric tumor Gastric0021

source_name: gastric tumor Gastric0021


title: soleus of C3KO A mouse Q2-4

description:
1-3-1-S-C3KO
Gene expression data from soleus of C3KO mouse Q2-4 (11-12months)

source_name: soleus of C3KO mouse Q2-4 (11-12months)


title: gastric tumor Gastric0019

description: gene expression data from gastric tumor Gastric0019

source_name: gastric tumor Gastric0019


title: Gastric non-malignant 3804_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3804_Norm_Stom_U133B_ab2


title: Gastric non-malignant 3801_Norm_Stom_Mus_U133B_ab2

description: gene expression data from gastric non-malignant 3801_Norm_Stom_Mus_U133B_ab2


title: human islets, ID10

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID10


title: gastric tumor Gastric0018

description: gene expression data from gastric tumor Gastric0018

source_name: gastric tumor Gastric0018


title: Q of C3KO A mouse Q2-3

description:
1-1-93-Q-C3KO
Gene expression data from quadriceps of C3KO mouse Q2-3 (11-12months)


title: human islets, ID9

source_name: Islets from cadaver donor ID9


title: Gastric non-malignant 3799_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3799_Norm_Stom_U133B_ab2


title: soleus of C3KO A mouse Q2-3

description:
1-1-96-S-C3KO
Gene expression data from soleus of C3KO mouse Q2-3 (11-12months)

source_name: soleus of C3KO mouse Q2-3 (11-12months)


title: human islets, ID8

source_name: Islets from cadaver donor ID8


title: soleus of C3KO A mouse Q2-2

description:
1-1-79-S-C3KO
Gene expression data from soleus of C3KO mouse Q2-2 (11-12months)

source_name: soleus of C3KO mouse Q2-2 (11-12months)


title: Gastric non-malignant 3800_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3800_Norm_Stom_U133B_ab2


title: Gastric tumor 3798_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3798_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3798_Stom_Tum_U133B_ab2


title: human islets, ID7

source_name: Islets from cadaver donor ID7


title: Q of C3KO A mouse Q2-2

description:
1-1-76-Q-C3KO
Gene expression data from quadriceps of C3KO mouse Q2-2 (11-12months)


title: human islets, ID6

source_name: Islets from cadaver donor ID6


title: Gastric non-malignant 3797_Norm_Stom_U133B_ab2

description: gene expression data from gastric non-malignant 3797_Norm_Stom_U133B_ab2


title: gastric tumor Gastric0014

description: gene expression data from gastric tumor Gastric0014

source_name: gastric tumor Gastric0014


title: Gastric tumor 3794_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3794_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3794_Stom_Tum_U133B_ab2


title: Q of C3KO A mouse Q2-1

description:
1-1-71-Q-C3KO
Gene expression data from quadriceps of C3KO mouse Q2-1 (11-12months)


title: gastric tumor Gastric0012

description: gene expression data from gastric tumor Gastric0012

source_name: gastric tumor Gastric0012


title: Gastric tumor 3796_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3796_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3796_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0016

description: gene expression data from gastric tumor Gastric0016

source_name: gastric tumor Gastric0016


title: human islets, ID5

source_name: Islets from cadaver donor ID5


title: gastric tumor Gastric0010

description: gene expression data from gastric tumor Gastric0010

source_name: gastric tumor Gastric0010


title: soleus of C3KO A mouse Q2-1

description:
1-1-74-S-C3KO
Gene expression data from soleus of C3KO mouse Q2-1 (11-12months)

source_name: soleus of C3KO mouse Q2-1 (11-12months)


title: Q of wt A mouse M2-2

description:
1-1-66-Q-WT
Gene expression data from quadriceps of wt mouse M2-2 (11-12months)


title: gastric tumor Gastric0008

description: gene expression data from gastric tumor Gastric0008

source_name: gastric tumor Gastric0008


title: soleus of wt A mouse M2-2

description:
1-1-69-S-WT
Gene expression data from soleus of wt mouse M2-2 (11-12months)

source_name: soleus of wt mouse M2-2 (11-12months)


title: gastric tumor Gastric0015

description: gene expression data from gastric tumor Gastric0015

source_name: gastric tumor Gastric0015


title: human islets, ID4

description: Gene expression data from human pancreatic islets

source_name: Islets from cadaver donor ID4


title: human islets, ID3

source_name: Islets from cadaver donor ID3


title: Gastric tumor 3793_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3793_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3793_Stom_Tum_U133B_ab2


title: gastric tumor Gastric0006

description: gene expression data from gastric tumor Gastric0006

source_name: gastric tumor Gastric0006


title: human islets, ID1

source_name: Islets from cadaver donor ID1


title: Gastric tumor 3792_Stom_Tum_U133B_ab2

description: gene expression data from gastric tumor 3792_Stom_Tum_U133B_ab2

source_name: Gastric tumor 3792_Stom_Tum_U133B_ab2


title: Gastric non-malignant 3791_Norm_Stom_Mus_U133B_ab2

description: gene expression data from gastric non-malignant 3791_Norm_Stom_Mus_U133B_ab2


title: gastric tumor Gastric0001

description: gene expression data from gastric tumor Gastric0001

source_name: gastric tumor Gastric0001


title: S of wt A mouse M2-1

description:
1-1-61-Q-WT
Gene expression data from soleus of wt mouse M2-1 (11-12months)

source_name: soleus of wt mouse M2-1 (11-12months)


title: Q of wt A mouse M2-1

description:
1-1-64-S-WT
Gene expression data from quadriceps of wt mouse M2-1 (11-12months)


title: human islets, ID2

source_name: Islets from cadaver donor ID2


title: gastric tumor Gastric0002

description: gene expression data from gastric tumor Gastric0002

source_name: gastric tumor Gastric0002


title: mD1R-expanded KSL cells, biological rep3

status: Public on Jul 04 2012

city: Xian

first: Dengmei

last: Tian

address: Chang-Le Xi Street #17

country: China

institute: Fourth Military Medical University

description: Gene expression data from KSL cells expanded on HUVEC+m5GF in the presence of mD1R for 7 days

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and   Stain  Kit  (Cat#900720,  Affymetrix,  Santa  Clara,  CA,  US)in  Hybridization  Oven  645   (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079,   Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

source_name: KSL cells expanded in the presence of mD1R

label_protocol: Total  RNA  were  amplified,  labeled  and  purified  by  using  GeneChip 3’IVT  Express  Kit   (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to   obtain biotin labeled cRNA

growth_protocol: Purified KSL cells were cultured on HUVEC+m5GF in the presence of PBS or mD1R at 37 °C in 5% CO2 atmosphere for 7 days.

treatment_protocol: KSL cells were sorted from hematopoietic cells expanded on HUVEC+m5GF in the presence of PBS or mD1R for 7 days. Sorted cells were placed on ice in the Trizol solution (GibcoBRL).

value: Bone marrow KSL cells

tag: treatment


title: PBS-expanded KSL cells, biological rep3

description: Gene expression data from KSL cells expanded on HUVEC+m5GF in the presence of PBS for 7 days

source_name: KSL cells expanded in the presence of PBS


title: gastric tumor Gastric0024

description: gene expression data from gastric tumor Gastric0024

source_name: gastric tumor Gastric0024


title: Dox induction at d3.5, replicate 1

city: Minneapolis

first: Fengli

last: Fu

state: MN

address: 312 Church Street SE

institute: University of Minnesota

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition. Etv2 was induced to overexpress from day 3.0 to 3.5 (0.5 microg/ml doxycycline).
KB_D31on

hyb_protocol: Amplified aRNAs were hybridized to Affymetrix mouse 430 2.0 full genome array chips at the BioMedical Genomics Center of the University of Minnesota  BioMedical Genomics Center of the University of Minnesota

scan_protocol: GeneChip were scanned according to Affymetrix standard protocols

data_processing: The data were processed with Affymetrix RMA method using R/Bioconductor

source_name: Mouse ES cell line ER71 A17C, differentiated by EB formation for 3.5 days (Etv2 overexpressed from day 3.0 to day 3.5).

label_protocol: MessageAmpII-Biotin Enhanced Kit

growth_protocol: See Iacovino et al. Stem Cells Dev. 2009;18:783-792., and Dang et al Biotechnol Bioeng. 2002;78:442-453.

extract_protocol: Trizol followed by extraction by 1-butanol and diethyl ether.

treatment_protocol: 0.5 microg/ml doxycycline from day 3.0 to day 3.5

tag: cell line

value: ES cell line ER71 A17C with a doxycycline inducible expression casette of Etv2 (ER71 A2Lox.cre)

value: Day 3.5 of differentiation

value: Etv2 overexpression


title: PBS-expanded KSL cells, biological rep1

value: expanded on HUVEC+m5GF in the presence of PBS for 7 days


title: Control at d3.5, replicate 2

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition
KB_D32off

source_name: Mouse ES cell line ER71 A17C, differentiated by EB formation for 3.5 days.

value: control


title: PBS-expanded KSL cells, biological rep2


title: Control at d3.5, replicate 3

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition
KB_D33off


title: Control at d3.5, replicate 1

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition
KB_D31off


title: mD1R-expanded KSL cells, biological rep1

value: expanded on HUVEC+m5GF in the presence of mD1R for 7 days


title: Dox induction at d3.5, replicate 3

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition. Etv2 was induced to overexpress from day 3.0 to 3.5 (0.5 microg/ml doxycycline).
KB_D33on


title: Dox induction at d3.5, replicate 2

description:
Gene expression data of Flk1 positive cells in Ebs differentiated for 3.5 days in a mesoderm inducing condition. Etv2 was induced to overexpress from day 3.0 to 3.5 (0.5 microg/ml doxycycline).
KB_D32on


title: mD1R-expanded KSL cells, biological rep2


title: cervix cell line HCSC1

city: Manchester

first: Jan

last: Taylor

address: Wilmslow Road

department: Bioinformatics

country: United Kingdom

institute: Paterson Institute for Cancer Research

description: exon array compared to tumour samples exon array for TP63 expression

hyb_protocol: RNA was quantified using a Bioanalyser (Agilent Technologies) and 100 ng amplified using NuGEN WT-Ovation FFPE v2 kit. The WT-Ovation Exon Module V1.0 was used to generate ST-cDNA and 4 µg was hybridised to Affymetrix Human Exon 1.0 ST arrays.

scan_protocol: Affymetrix GeneChip scanner 3000 running GCOS software

data_processing:
Background adjustment, quantile normalisation and summarisation of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm, using R and the Affymetrix Power Tools
probe group file: HuEx-1_0-st-v2.r2.pgf

source_name: cervix cell line HCSC1

label_protocol: The RNA was amplified using the WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module, and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2

growth_protocol: DMEM + 10% calf serum. p63 protein expression was used to classify cell lines as SCC (p63+ve) or AC (p63 -ve)

extract_protocol: RNA was extracted and Dnase treated using RecoverAll Total Nucleic Acid Isolation kit (Ambion)

tag: tissue origin

value: cervix

tag: storage

value: fresh

tag: histology (p63)

value: adenocarcinoma (AC)

tag: data series

value: cell line


title: cervix cell line SKG1

source_name: cervix cell line SKG1

value: squamous cell carcinoma (SCC)


title: cervix cell line ME180

description: exon array compared to tumour samples exon array for TP63 expression. Cell line also put on miRNA array

source_name: cervix cell line ME180


title: cervix cell line SKG2

source_name: cervix cell line SKG2


title: cervix cell line SKG3a

source_name: cervix cell line SKG3a


title: cervix cell line HT3

source_name: cervix cell line HT3


title: cervix cell line MS751

source_name: cervix cell line MS751


title: cervix cell line HSCS2

source_name: cervix cell line HSCS2


title: bladder_tumour_bs_139

source_name: bladder tumour FFPE

tag: organ

value: bladder

tag: tissue type

value: tumour

value: FFPE

tag: ffpe block storage duration (yrs)


title: bladder_tumour_bs_138


title: cervix cell line SW756

source_name: cervix cell line SW756


title: cervix cell line HeLa

source_name: cervix cell line HeLa

value: HeLa


title: bladder_tumour_bs_131


title: bladder_tumour_bs_128


title: cervix cell line SiHa

source_name: cervix cell line SiHa

value: SiHa


title: bladder_tumour_bs_132


title: bladder_tumour_bs_137


title: cervix cell line CaSki

source_name: cervix cell line CaSki

value: CaSki


title: bladder_tumour_bs_135


title: bladder_tumour_bs_133


title: cervix cell line 778

source_name: cervix cell line 778


title: cervix cell line C33a

source_name: cervix cell line C33a


title: bladder_tumour_bs_130


title: bladder_tumour_bs_129


title: cervix cell line 808

source_name: cervix cell line 808


title: bladder_tumour_bs_141


title: bladder_tumour_bs_134


title: cervix cell line BOKU

source_name: cervix cell line BOKU

value: BOKU


title: bladder_tumour_bs_124


title: bladder_tumour_bs_126


title: bladder_tumour_bs_123


title: bladder_tumour_bs_140


title: bladder_tumour_bs_127


title: bladder_tumour_bs_119


title: bladder_tumour_bs_125


title: bladder_tumour_bs_120


title: bladder_tumour_bs_122


title: bladder_tumour_bs_118


title: bladder_tumour_bs_115


title: bladder_tumour_bs_113


title: bladder_tumour_bs_105


title: bladder_tumour_bs_106


title: bladder_tumour_bs_104


title: bladder_tumour_bs_112


title: bladder_tumour_bs_114


title: bladder_tumour_bs_121


title: bladder_tumour_bs_107


title: bladder_tumour_bs_111


title: bladder_tumour_bs_116


title: bladder_tumour_bs_100


title: bladder_tumour_bs_102


title: bladder_tumour_bs_101


title: bladder_tumour_bs_110


title: bladder_tumour_bs_117


title: bladder_tumour_bs_109


title: bladder_tumour_bs_99


title: bladder_tumour_bs_98


title: bladder_tumour_bs_108


title: bladder_tumour_bs_94


title: bladder_tumour_bs_97


title: bladder_tumour_bs_96


title: bladder_tumour_bs_91


title: bladder_tumour_bs_89


title: bladder_tumour_bs_81


title: bladder_tumour_bs_95


title: bladder_tumour_bs_82


title: bladder_tumour_bs_136


title: bladder_tumour_bs_83


title: bladder_tumour_bs_90


title: bladder_tumour_bs_85


title: bladder_tumour_bs_93


title: bladder_tumour_bs_84


title: bladder_tumour_bs_86


title: bladder_tumour_bs_103


title: bladder_tumour_bs_79


title: bladder_tumour_bs_77


title: bladder_tumour_bs_78


title: bladder_tumour_bs_88


title: bladder_tumour_bs_87


title: bladder_tumour_bs_92


title: bladder_tumour_bs_80


title: bladder_tumour_bs_76


title: bladder_tumour_bs_70


title: bladder_tumour_bs_74


title: bladder_tumour_bs_73


title: bladder_tumour_bs_69


title: bladder_tumour_bs_64


title: bladder_tumour_bs_72


title: bladder_tumour_bs_71


title: bladder_tumour_bs_62


title: bladder_tumour_bs_65


title: bladder_tumour_bs_68


title: bladder_tumour_bs_67


title: bladder_tumour_bs_59


title: bladder_tumour_bs_60


title: bladder_tumour_bs_75


title: bladder_tumour_bs_57


title: bladder_tumour_bs_56


title: bladder_tumour_bs_66


title: bladder_tumour_bs_63


title: bladder_tumour_bs_58


title: bladder_tumour_bs_55


title: bladder_tumour_bs_54


title: bladder_tumour_bs_51


title: bladder_tumour_bs_53


title: bladder_tumour_bs_47


title: bladder_tumour_bs_61


title: bladder_tumour_bs_48


title: bladder_tumour_bs_52


title: bladder_tumour_bs_46


title: bladder_tumour_bs_49


title: bladder_tumour_bs_44


title: bladder_tumour_bs_50


title: bladder_tumour_bs_45


title: bladder_tumour_bs_42


title: bladder_tumour_bs_39


title: bladder_tumour_bs_40


title: bladder_tumour_bs_43


title: bladder_tumour_bs_41


title: bladder_tumour_bs_34


title: bladder_tumour_bs_37


title: bladder_tumour_bs_38


title: bladder_tumour_bs_31


title: bladder_tumour_bs_36


title: bladder_tumour_bs_26


title: bladder_tumour_bs_35


title: bladder_tumour_bs_27


title: bladder_tumour_bs_32


title: bladder_tumour_bs_29


title: bladder_tumour_bs_28


title: bladder_tumour_bs_25


title: bladder_tumour_bs_30


title: bladder_tumour_bs_19


title: bladder_tumour_bs_18


title: bladder_tumour_bs_24


title: bladder_tumour_bs_33


title: bladder_tumour_bs_23


title: bladder_tumour_bs_20


title: bladder_tumour_bs_13


title: bladder_tumour_bs_15


title: bladder_tumour_bs_11


title: bladder_tumour_bs_21


title: bladder_tumour_bs_9


title: bladder_tumour_bs_8


title: bladder_tumour_bs_3


title: bladder_tumour_bs_5


title: bladder_tumour_bs_22


title: bladder_tumour_bs_16


title: bladder_tumour_bs_1


title: bladder_tumour_bs_14


title: bladder_tumour_bs_7


title: bladder_tumour_bs_10


title: bladder_tumour_bs_2


title: bladder_tumour_bs_17


title: bladder_tumour_bs_12


title: bladder_tumour_bs_4


title: cervix_tumour_cs2_45

source_name: cervix tumour ffpe series 2

value: formalin-fixed paraffin-embedded (FFPE)

tag: histology

value: OTHER


title: cervix_tumour_cs2_40


title: cervix_tumour_cs2_46


title: cervix_tumour_cs2_44


title: cervix_tumour_cs2_42


title: cervix_tumour_cs2_47


title: cervix_tumour_cs2_43


title: cervix_tumour_cs2_41


title: cervix_tumour_cs2_37


title: cervix_tumour_cs2_48


title: cervix_tumour_cs2_35

description:
CS2_sample_35
samples compared to miRNA: CS2_SCC_4


title: cervix_tumour_cs2_36


title: cervix_tumour_cs2_34


title: cervix_tumour_cs2_33

description:
CS2_sample_33
samples compared to miRNA: CS2_AC_4


title: cervix_tumour_cs2_30


title: cervix_tumour_cs2_26


title: Monoassociated with E. coli 4 (PAMM-073)

city: Chapel Hill

first: Janelle

middle: C

last: Arthur

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: monoassociated + AOM

data_processing: SABiosciences online array analysis pipeline. Cts were normalized to 5 housekeeping genes (Gusb, Hprt, Hsp90ab1, Gapdh, Actb) by arithmetic mean.

label: SYBR green

source_name: distal colon tissue, E. coli

label_protocol: Qiagen First Strand Kit.

extract_protocol: RNA was extracted using the TRIZOL method and further cleaned using DNase treatment and RNeasy columns (Qiagen).

tag: strain/background

tag: genotype

tag: tissue

value: distal colon

tag: monoassociation

value: E. coli NC101

tag: inflammation

value: yes

tag: cancer


title: cervix_tumour_cs2_28

description:
CS2_sample_28
samples compared to miRNA: CS2_SCC_3

value: cervix


title: bladder_tumour_bs_6


title: cervix_tumour_cs2_32


title: cervix_tumour_cs2_22


title: cervix_tumour_cs2_31


title: cervix_tumour_cs2_29


title: Monoassociated with E. coli 3 (PAMM-073)

description: monoassociated + AOM


title: cervix_tumour_cs2_19


title: cervix_tumour_cs2_24


title: cervix_tumour_cs2_25


title: cervix_tumour_cs2_17

description:
CS2_sample_17
samples compared to miRNA: CS2_SCC_2


title: Monoassociated with E. coli 2 (PAMM-073)

description: monoassociated + AOM


title: cervix_tumour_cs2_15

description:
CS2_sample_15
samples compared to miRNA: CS2_SCC_1


title: Monoassociated with E. coli 1 (PAMM-073)

description: monoassociated + AOM


title: Monoassociated with E. faecalis 4 (PAMM-073)

description: monoassociated + AOM

source_name: distal colon tissue, E. faecalis

value: E. faecalis OG1RF

value: no


title: Monoassociated with E. faecalis 2 (PAMM-073)

description: monoassociated + AOM


title: Monoassociated with E. faecalis 3 (PAMM-073)

description: monoassociated + AOM


title: cervix_tumour_cs2_16

description:
CS2_sample_16
samples compared to miRNA: CS2_AC_1

value: adenocarcinoma (AC)


title: Monoassociated with E. faecalis 1 (PAMM-073)

description: monoassociated + AOM


title: cervix_tumour_cs2_13

value: squamous cell carcinoma (SCC)


title: cervix_tumour_cs2_21


title: cervix_tumour_cs2_23


title: Germ-free 4 (PAMM-073)

description: monoassociated + AOM

source_name: distal colon tissue, germ-free

value: germ-free


title: Germ-free 3 (PAMM-073)

description: monoassociated + AOM


title: Germ-free 2 (PAMM-073)

description: monoassociated + AOM


title: Germ-free 1 (PAMM-073)

description: monoassociated + AOM


title: cervix_tumour_cs2_11

value: tumour


title: cervix_tumour_cs2_20

description:
CS2_sample_20
samples compared to miRNA: CS2_AC_2


title: cervix_tumour_cs2_12


title: Monoassociated with E. coli NC101-delta-pks 3

description: Monoassociated + AOM

source_name: distal colon tissue, E. coli NC101-delta-pks

value: E. coli NC101-delta-pks


title: cervix_tumour_cs2_14


title: Monoassociated with E. coli NC101-delta-pks 2

description: Monoassociated + AOM


title: Monoassociated with E. coli NC101-delta-pks 1

description: Monoassociated + AOM


title: cervix_tumour_cs2_7


title: cervix_tumour_cs2_9


title: Monoassociated with E. coli NC101 3

description: Monoassociated + AOM

source_name: distal colon tissue, E. coli NC101


title: Monoassociated with E. coli NC101 2

description: Monoassociated + AOM


title: Germ-free 2

description: Monoassociated + AOM


title: Germ-free 1

description: Monoassociated + AOM


title: Monoassociated with E. coli 4 (PAMM-077)

description: Monoassociated + AOM


title: cervix_tumour_cs2_18


title: Monoassociated with E. coli NC101 1

description: Monoassociated + AOM


title: Monoassociated with E. coli 3 (PAMM-077)

description: Monoassociated + AOM


title: Monoassociated with E. coli 1 (PAMM-077)

description: Monoassociated + AOM


title: cervix_tumour_cs2_39


title: Monoassociated with E. faecalis 3 (PAMM-077)

description: Monoassociated + AOM


title: Monoassociated with E. coli 2 (PAMM-077)

description: Monoassociated + AOM


title: cervix_tumour_cs1_109

source_name: cervix tumour FFPE series 1


title: cervix_tumour_cs2_4


title: cervix_tumour_cs1_113

description:
CS1_sample_113
sample compared to miRNA: CS1_AC_1


title: Monoassociated with E. faecalis 2 (PAMM-077)

description: Monoassociated + AOM


title: cervix_tumour_cs2_5


title: cervix_tumour_cs1_111


title: cervix_tumour_cs2_6


title: cervix_tumour_cs2_8


title: Monoassociated with E. faecalis 4 (PAMM-077)

description: Monoassociated + AOM


title: Germ-free 4 (PAMM-077)

description: Monoassociated + AOM


title: Germ-free 3 (PAMM-077)

description: Monoassociated + AOM


title: cervix_tumour_cs2_10


title: cervix_tumour_cs1_112

description:
CS1_sample_112
sample compared to miRNA: CS1_AC_4


title: Monoassociated with E. faecalis 1 (PAMM-077)

description: Monoassociated + AOM


title: Germ-free 2 (PAMM-077)

description: Monoassociated + AOM


title: Germ-free 1 (PAMM-077)

description: Monoassociated + AOM


title: donor heart tissue [VC-2A4]

city: Christchurch

first: Anna

middle: P

last: Pilbrow

address: 2 Riccarton Avenue

department: Medicine

country: New Zealand

institute: University of Otago Christchurch

description: Gene expression and genotype in normal heart

hyb_protocol: Following fragmentation, 5.5 ug of single stranded  cDNA was hybridized for 17 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner G7 plus.

data_processing: The data were analysed using R version 2.8.1 with Bioconductor.  Aroma Affymetrix was used for background correction, quantile normalization and fitting GCRMA probe level models. Batch effects were corrected with Combat. Limma was used to calculate differential expression and apply Benjamini and Hochberg corection for multiple testing.

source_name: human heart tissue from left ventricular free wall of organ donors with no previous history of heart disease

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100 ng of total RNA ( whole transcript(WT) sense target labeling assay Technical manual version 4 2007, Affymetrix)) using the non ribosomal RNA reduced option. (chapter 4)

extract_protocol: Total RNA and genomic DNA was simultaneously extracted from frozen tissue after automated grinding (Retsch Mixer Mill MM301, Haan, Germany) in TRIzol® (Invitrogen, Carlsbad, CA) and chloroform. RNA was purified using RNeasy Midi columns (Qiagen, Valencia, CA) according to manufacturer’s instructions and tested for quality and quantity with an Experion (Bio-Rad Laboratories, Hercules, CA). Genomic DNA was extracted from the remaining organic and interphase layers of the TRIzol® extract (see protocol at http://genome-www.stanford.edu/DFSP/materials.shtml).

treatment_protocol: Heart specimens were rapidly frozen in liquid nitrogen at the time of harvest and stored at -80°C until use.

tag: rs1333049 genotype

value: GC

tag: age

tag: Sex

value: F

tag: batch


title: cervix_tumour_cs1_110

tag: storage


title: cervix_tumour_cs1_107


title: donor heart tissue [VC-2A1]

value: M


title: donor heart tissue [VC-2A2]


title: donor heart tissue [VC-H12]

value: GG


title: donor heart tissue [VC-2A3]


title: donor heart tissue [VC-H11]

value: CC


title: donor heart tissue [VC-H10]


title: cervix_tumour_cs2_38

value: formalin-fixed paraffin-embedded (FFPE)


title: cervix_tumour_cs1_104


title: cervix_tumour_cs1_108


title: donor heart tissue [VC-H9]


title: cervix_tumour_cs2_1


title: cervix_tumour_cs1_105


title: cervix_tumour_cs1_102


title: cervix_tumour_cs2_2

value: UNKNOWN


title: cervix_tumour_cs1_103


title: cervix_tumour_cs2_27

description:
CS2_sample_27
samples compared to miRNA: CS2_AC_3


title: donor heart tissue [VC-H8]


title: cervix_tumour_cs1_100


title: cervix_tumour_cs2_3


title: donor heart tissue [VC-H7]


title: donor heart tissue [VC-H1]


title: donor heart tissue [VC-G12]


title: cervix_tumour_cs1_106


title: donor heart tissue [VC-G11]


title: donor heart tissue [VC-G10]


title: donor heart tissue [VC-G8]


title: donor heart tissue [VC-H4]


title: donor heart tissue [VC-G9]


title: donor heart tissue [VC-G7]


title: donor heart tissue [VC-H2]


title: donor heart tissue [VC-148]


title: cervix_tumour_cs1_99


title: donor heart tissue [VC-H5]


title: BRCA1 siRNA_MLN4924_26h_3

city: Cambridge

first: Hugues

last: Bernard

state: MA

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

description: Gene expression data from treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133Plus 2.0 Array in an Affymetrix Model 640 hybridization oven . GeneChips were washed and stained on an Affymetrix FS450 station.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console software from Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Cell culture of Melanoma Cell Line - A375

label_protocol: Biotinylated cRNA were prepared using modified MesageAmp-based protocols (Ambion Inc) from 1.5ug total RNA.

growth_protocol: A375 cells were maintained at 37°C in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 100 U/ml penicillin/100 g/ml streptomycin (Invitrogen).

extract_protocol: Cells were precipitated, PBS washed, lysed using Qiagen RLT Buffer, and then RNA was extracted with Ambion MegaMax kit using King Fisher automated platform. All protocoles were executed following manufacturers recommendations.

treatment_protocol: siRNA transfected for 48hrs, then 27,000 A375 cells were treated with 0.065% DMSO, 650nM MLN4924, 5uM Nutlin or 100nM Daunorubicin and incubated for 26 hours before recovery for RNA isolation and Gene Expression.

tag: cell line

tag: transfection

tag: treatment

value: 650nM MLN4924 for 26 hours


title: donor heart tissue [VC-G5]


title: donor heart tissue [VC-147]


title: cervix_tumour_cs1_93

tag: organ

tag: tissue type

value: OTHER

tag: data series


title: BRCA1 siRNA_MLN4924_26h_2

description: Gene expression data from treated cells


title: cervix_tumour_cs1_98

value: cervix

tag: histology

tag: ffpe block storage duration (yrs)


title: cervix_tumour_cs1_96


title: cervix_tumour_cs1_92


title: cervix_tumour_cs1_101


title: donor heart tissue [VC-H3]


title: cervix_tumour_cs1_95


title: cervix_tumour_cs1_97


title: donor heart tissue [VC-144]


title: cervix_tumour_cs1_94


title: BRCA1 siRNA_MLN4924_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-G3]


title: cervix_tumour_cs1_91


title: donor heart tissue [VC-139]


title: BRCA1 siRNA_DMSO_26h_2

description: Gene expression data from treated cells

value: 0.065% DMSO for 26 hours


title: donor heart tissue [VC-G1]


title: donor heart tissue [VC-G2]


title: BRCA1 siRNA_DMSO_26h_3

description: Gene expression data from treated cells


title: donor heart tissue [VC-135]


title: donor heart tissue [VC-F11]


title: donor heart tissue [VC-F12]


title: cervix_tumour_cs1_90


title: BRCA1 siRNA_DMSO_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-F10]


title: donor heart tissue [VC-H6]


title: donor heart tissue [VC-F9]


title: donor heart tissue [VC-130]


title: cervix_tumour_cs1_86


title: donor heart tissue [VC-G6]


title: donor heart tissue [VC-F8]


title: donor heart tissue [VC-128]


title: donor heart tissue [VC-G4]


title: donor heart tissue [VC-141]


title: p53 siRNA_MLN4924_26h_3

description: Gene expression data from treated cells


title: p53 siRNA_MLN4924_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-F6]


title: cervix_tumour_cs1_89


title: cervix_tumour_cs1_87


title: p53 siRNA_MLN4924_26h_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-F7]


title: p53 siRNA_DMSO_26h_2_2

description: Gene expression data from treated cells


title: cervix_tumour_cs1_85


title: donor heart tissue [VC-F5]


title: donor heart tissue [VC-F4]


title: cervix_tumour_cs1_84


title: p53 siRNA_DMSO_26h_3_2

description: Gene expression data from treated cells


title: cervix_tumour_cs1_81


title: cervix_tumour_cs1_82


title: cervix_tumour_cs1_83


title: donor heart tissue [VC-F2]


title: CDT1 siRNA_MLN4924_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-E9]


title: donor heart tissue [VC-E12]


title: donor heart tissue [VC-E11]


title: donor heart tissue [VC-E10]


title: donor heart tissue [VC-E8]


title: p53 siRNA_DMSO_26h_1_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-F1]


title: CDT1 siRNA_MLN4924_26h_2

description: Gene expression data from treated cells


title: CDT1 siRNA_MLN4924_26h_3

description: Gene expression data from treated cells


title: CDT1 siRNA_DMSO_26h_3

description: Gene expression data from treated cells


title: cervix_tumour_cs1_79

description:
CS1_sample_79
sample compared to miRNA: CS1_AC_3


title: donor heart tissue [VC-E6]


title: donor heart tissue [VC-E5]


title: cervix_tumour_cs1_88


title: cervix_tumour_cs1_78


title: cervix_tumour_cs1_80


title: donor heart tissue [VC-D12]


title: cervix_tumour_cs1_76


title: donor heart tissue [VC-E3]


title: donor heart tissue [VC-E4]


title: GL2 siRNA_MLN4924_26h_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-E2]


title: donor heart tissue [VC-D11]


title: CDT1 siRNA_DMSO_26h_2

description: Gene expression data from treated cells


title: GL2 siRNA_MLN4924_26h_3

description: Gene expression data from treated cells


title: cervix_tumour_cs1_77


title: donor heart tissue [VC-E1]


title: donor heart tissue [VC-D10]


title: CDT1 siRNA_DMSO_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-D8]


title: donor heart tissue [VC-D9]


title: donor heart tissue [VC-D4]


title: donor heart tissue [VC-D3]


title: donor heart tissue [VC-D7]


title: donor heart tissue [VC-D2]


title: GL2 siRNA_DMSO_26h_1_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-D6]


title: GL2 siRNA_DMSO_26h_2_2

description: Gene expression data from treated cells


title: GL2 siRNA_MLN4924_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-D1]


title: donor heart tissue [VC-D5]


title: donor heart tissue [VC-F3]


title: p53 siRNA_Nutlin_26h_3

description: Gene expression data from treated cells

value: 5uM Nutlin for 26 hours


title: cervix_tumour_cs1_70


title: cervix_tumour_cs1_71


title: donor heart tissue [VC-C10]


title: cervix_tumour_cs1_72


title: donor heart tissue [VC-C11]


title: p53 siRNA_Nutlin_26h_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-C12]


title: donor heart tissue [VC-C7]


title: donor heart tissue [VC-E7]


title: cervix_tumour_cs1_69


title: donor heart tissue [VC-C9]


title: cervix_tumour_cs1_73


title: cervix_tumour_cs1_75


title: donor heart tissue [VC-C8]


title: GL2 siRNA_Nutlin_26h_3

description: Gene expression data from treated cells


title: cervix_tumour_cs1_65

description:
CS1_sample_65
sample compared to miRNA: CS1_SCC_3


title: donor heart tissue [VC-C5]


title: donor heart tissue [VC-C6]


title: cervix_tumour_cs1_67

description:
CS1_sample_67
sample compared to miRNA: CS1_SCC_4


title: p53 siRNA_Nutlin_26h_1

description: Gene expression data from treated cells


title: GL2 siRNA_Nutlin_26h_2

description: Gene expression data from treated cells


title: GL2 siRNA_DMSO_26h_3-2

description: Gene expression data from treated cells


title: donor heart tissue [VC-C4]


title: donor heart tissue [VC-B12]


title: cervix_tumour_cs1_68


title: donor heart tissue [VC-C2]


title: GL2 siRNA_Nutlin_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-C3]


title: cervix_tumour_cs1_66


title: cervix_tumour_cs1_74


title: donor heart tissue [VC-B11]


title: donor heart tissue [VC-B10]


title: donor heart tissue [VC-C1]


title: p53 siRNA_Daunorubicin_26h_3

description: Gene expression data from treated cells

value: 100nM Daunorubicin for 26 hours


title: p53 siRNA_Daunorubicin_26h_2

description: Gene expression data from treated cells


title: cervix_tumour_cs1_63

value: squamous cell carcinoma (SCC)


title: donor heart tissue [VC-B7]


title: donor heart tissue [VC-B8]


title: donor heart tissue [VC-B9]


title: donor heart tissue [VC-B5]


title: donor heart tissue [VC-B6]


title: cervix_tumour_cs1_60

description:
CS1_sample_60
sample compared to miRNA: CS1_SCC_2


title: cervix_tumour_cs1_62


title: GL2 siRNA_Daunorubicin_26h_2

description: Gene expression data from treated cells


title: donor heart tissue [VC-B4]


title: donor heart tissue [VC-B3]


title: cervix_tumour_cs1_61


title: cervix_tumour_cs1_64


title: GL2 siRNA_Daunorubicin_26h_3

description: Gene expression data from treated cells


title: cervix_tumour_cs1_59

description:
CS1_sample_59
sample compared to miRNA: CS1_SCC_1


title: cervix_tumour_cs1_58


title: donor heart tissue [VC-A11]


title: donor heart tissue [VC-A10]


title: donor heart tissue [VC-A8]


title: p53 siRNA_DMSO_26h_3

description: Gene expression data from treated cells


title: p53 siRNA_DMSO_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-A7]


title: p53 siRNA_Daunorubicin_26h_1

description: Gene expression data from treated cells


title: GL2 siRNA_DMSO_26h_3

description: Gene expression data from treated cells


title: donor heart tissue [VC-A12]


title: GL2 siRNA_Daunorubicin_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-A9]


title: donor heart tissue [VC-A6]


title: donor heart tissue [VC-B1]


title: donor heart tissue [VC-B2]


title: donor heart tissue [VC-A5]


title: GL2 siRNA_DMSO_26h_2

description: Gene expression data from treated cells


title: cervix_tumour_cs1_54


title: cervix_tumour_cs1_51


title: donor heart tissue [VC-A3]


title: p53 siRNA_DMSO_26h_2

description: Gene expression data from treated cells


title: GL2 siRNA_DMSO_26h_1

description: Gene expression data from treated cells


title: donor heart tissue [VC-A1]


title: cervix_tumour_cs1_53


title: cervix_tumour_cs1_57

value: adenocarcinoma (AC)


title: donor heart tissue [VC-A2]


title: Expression data of 145_ACa

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description: CIN-high

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Rubust Multichip Analysis (RMA)

source_name: Patient 145

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer’s instructions.

tag: tissue

value: Colorecal Cancer


title: Nkx3.1CE2/+; Ptenf/f castrated  (4453)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: mice_ID: 4453

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scaning protocol

data_processing: Data were loaded, normalized, and analyzed with Illumina Expression FileCreator and Illumina Normalizer in GenePattern

source_name: Anterior Prostate

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: no treatment

value: anterior prostate

tag: genotype/variation

value: Nkx3.1CE2/+; Ptenf/f

tag: phenotype

value: castrated


title: cervix_tumour_cs1_55

description:
CS1_sample_55
sample compared to miRNA: CS1_AC_2

value: tumour


title: cervix_tumour_cs1_56


title: cervix_tumour_cs1_52


title: Nkx3.1CE2/+; Ptenf/f castrated  (4644)

description: mice_ID: 4644


title: Nkx3.1CE2/+; Ptenf/f castrated  (4450)

description: mice_ID: 4450


title: Expression data of 46_RCa

description: CIN-low

source_name: Patient 46


title: Nkx3.1CE2/+; Ptenf/f castrated  (2282)

description: mice_ID: 2282


title: Expression data of 185_Ca

description: CIN-high

source_name: Patient 185


title: Nkx3.1CE2/+; Ptenf/f castrated  (2859)

description: mice_ID: 2859


title: Nkx3.1CE2/+; Ptenf/f  (2432)

description: mice_ID: 2432

value: intact


title: Nkx3.1CE2/+; Ptenf/f  (2669)

description: mice_ID: 2669


title: Nkx3.1CE2/+; Ptenf/f castrated  (2881)

description: mice_ID: 2881


title: donor heart tissue [VC-A4]

value: CC

value: M


title: cervix_tumour_cs1_46

value: formalin-fixed paraffin-embedded (FFPE)


title: Expression data of 180_SCa

description: CIN-high

source_name: Patient 180


title: Nkx3.1CE2/+; Ptenf/f  (2847)

description: mice_ID: 2847


title: Nkx3.1CE2/+; Ptenf/f  (2865)

description: mice_ID: 2865


title: Expression data of 1_Ca

description: CIN-high

source_name: Patient 1


title: cervix_tumour_cs1_47


title: cervix_tumour_cs1_50


title: Nkx3.1CE2/+; Ptenf/f  (2245)

description: mice_ID: 2245


title: cervix_tumour_cs1_48


title: Expression data of 60_RCa

description: CIN-high

source_name: Patient 60


title: Expression data of 158_TCa

description: CIN-low

source_name: Patient 158


title: Nkx3.1CE2/+  (2430)

description: mice_ID: 2430


title: Nkx3.1CE2/+; Ptenf/f  (3183)

description: mice_ID: 3183


title: cervix_tumour_cs1_45


title: Nkx3.1CE2/+  (2848)

description: mice_ID: 2848


title: cervix_tumour_cs1_49


title: St-0 non-infected control sample 62

city: Valencia

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

institute: CSIC-UPV

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
Babelomics 4.2 (http://babelomics.bioinfo.cipf.es)
Series supplementary file contains Limma normalized signal intensity

organism: Arabidopsis thaliana

source_name: non-infected

label_protocol: standard Agilent protocol

growth_protocol: plants were mantained in a BSL-2 greenhouse at 16:8h light:dark and 24:20 day:night temperature until sample collection on 21 days post infection.

extract_protocol: Quiagen, RNasyPlant Mini kit manufacturer protocol

treatment_protocol: Plants infected with TEV strain previosly adapted to A.thaliana ssp. Ler and non-infected plants as a control

tag: ecotype

value: whole organism

tag: infection

value: non-infected


title: Nkx3.1CE2/+  (2668)

description: mice_ID: 2668


title: Expression data of 178_Ca

description: CIN-low

source_name: Patient 178


title: Ei-2 non-infected control sample 63


title: Expression data of 265_RCa

description: CIN-high

source_name: Patient 265


title: Wt-1 non-infected control sample 64


title: Expression data of 384_RCa

description: CIN-high

source_name: Patient 384


title: Ler-0 non-infected control sample 61


title: cervix_tumour_cs1_44

value: cervix


title: Expression data of 215_ACa

description: CIN-high

source_name: Patient 215


title: Oy-0 non-infected control sample 57


title: St-0 non-infected control sample 60


title: Oy-0 non-infected control sample 56


title: Expression data of 73SCa

description: CIN-high

source_name: Patient 73


title: Di-2 non-infected control sample 59


title: cervix_tumour_cs1_41

source_name: cervix tumour FFPE series 1


title: cervix_tumour_cs1_43


title: Wt-1 non-infected control sample 53


title: Expression data of 61_ACa

description: CIN-low

source_name: Patient 61


title: cervix_tumour_cs1_42


title: Ei-2 non-infected control sample 52


title: Oy-0 non-infected control sample 51


title: Expression data of 218SCa

description: CIN-high

source_name: Patient 218


title: Ler-0 non-infected control sample 55


title: Di-2 non-infected control sample 47


title: St-0 non-infected control sample 50


title: Ler-0 non-infected control sample 46


title: Di-2 non-infected control sample 45


title: St-0 infected replicate 4 sample 48

source_name: infected

value: Tobacco etch potyvirus


title: cervix_tumour_cs1_38


title: Expression data of 181_RCa

description: CIN-high

source_name: Patient 181


title: Expression data of 45_ACa

description: CIN-low

source_name: Patient 45


title: cervix_tumour_cs1_37


title: cervix_tumour_cs1_40


title: cervix_tumour_cs1_39


title: Ei-2 infected replicate 8 sample 42


title: Oy-0 infected replicate 7 sample 41


title: Oy-0 infected replicate 9 sample 44


title: Expression data of 79_Ca_2

description: CIN-high

source_name: Patient 79


title: Expression data of 118_RCa

description: CIN-low

source_name: Patient 118


title: St-0 infected replicate 6 sample 40


title: Ei-2 infected replicate 4 sample 37


title: St-0 infected replicate 3 sample 36


title: Oy-0 infected replicate 5 sample 39


title: Expression data of 227_RCa

description: CIN-high

source_name: Patient 227


title: cervix_tumour_cs1_34


title: Ler-0 non-infected control sample 35


title: Expression data of 153_Ca

description: CIN-high

source_name: Patient 153


title: Ei-2 infected replicate 5 sample 33


title: cervix_tumour_cs1_32


title: Expression data of 162_ACa

description: CIN-high

source_name: Patient 162


title: cervix_tumour_cs1_35


title: cervix_tumour_cs1_36


title: Ei-2 non-infected control sample 32

source_name: non-infected


title: Expression data of 5_Ca

description: CIN-high

source_name: Patient 5


title: cervix_tumour_cs1_33


title: Wt-1 non-infected control sample 31


title: cervix_tumour_cs1_30


title: Ler-0 non-infected control sample 30


title: Di-2 non-infected control sample 29


title: cervix_tumour_cs1_31


title: Expression data of 116_RCa

description: CIN-high

source_name: Patient 116


title: Ei-2 infected replicate 1 sample 27


title: Expression data of 157_Ca

description: CIN-low

source_name: Patient 157


title: Expression data of 50_Ca

description: CIN-high

source_name: Patient 50


title: cervix_tumour_cs1_29


title: Ei-2 infected replicate 6 sample 23


title: St-0 non-infected control sample 20


title: St-0 infected replicate 5 sample 22


title: Expression data of 169_ACa

description: CIN-low

source_name: Patient 169


title: cervix_tumour_cs1_28

source_name: cervix tumour FFPE series 1


title: Oy-0 non-infected control sample 26


title: Ler-0 infected replicate 8 sample 25


title: Ler-0 infected replicate 7 sample 19


title: Di-2 infected replicate 5 sample 17


title: Wt-1 infected replicate 6 sample 18


title: Wt-1 infected replicate 7 sample 24


title: Di-2 infected control sample 16


title: Expression data of 2_Ca

description: CIN-high

source_name: Patient 2


title: Expression data of 128_RCa

description: CIN-high

source_name: Patient 128


title: Wt-1 infected replicate 8 sample 13

source_name: infected


title: Expression data of 106_SCa

description: CIN-high

source_name: Patient 106


title: cervix_tumour_cs1_27


title: Expression data of 148_ACa

description: CIN-low

source_name: Patient 148


title: Expression data of 258_Ca

description: CIN-high

source_name: Patient 258


title: Ler-0 infected replicate 7 sample 12


title: Liver DKO

city: Heidelberg

first: Francesca

last: Tuorto

address: Im Neuenheimer Feld 580

department: Epigenetics

country: Germany

institute: German Cancer Research Center

description: replicate 1

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner.

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

source_name: Liver DKO

label_protocol: cRNA samples were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 200 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 70 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

extract_protocol: RNA was extracted with Trizol reagent, Quality control was performed with Agilent Bioanalyser.

value: liver

tag: age

value: 2 months

value: DKO

tag: strain

value: CBA/C57BL6j x B6;129


title: cervix_tumour_cs1_24

value: adenocarcinoma (AC)


title: Liver Nsun2

description: replicate 1

source_name: Liver Nsun2-/-


title: cervix_tumour_cs1_26

value: squamous cell carcinoma (SCC)


title: Expression data of 217_ACa

description: CIN-high

source_name: Patient 217

value: Colorecal Cancer


title: cervix_tumour_cs1_25


title: Expression data of 31_RCa

description: CIN-low

source_name: Patient 31


title: cervix_tumour_cs1_23


title: cervix_tumour_cs1_21


title: Wt-1 infected replicate 6 sample 11


title: Di-2 infected replicate 5 sample 10


title: Liver wt

description: replicate 1

source_name: Liver wildtype

value: wildtype


title: Liver Dnmt2

description: replicate 1

source_name: Liver Dnmt2-/-


title: MEFs DKO

description: replicate 1

source_name: MEFs DKO

value: MEFs

value: Embryos 13.5


title: Wt-1 non-infected control sample 6

source_name: non-infected


title: cervix_tumour_cs1_17

value: tumour


title: Di-2 infected replicate 4 sample 7


title: Expression data of 123_SCa

description: CIN-high

source_name: Patient 123


title: cervix_tumour_cs1_19


title: St-0 infected replicate 4 sample 5


title: MEFs Dnmt2

description: replicate 1

source_name: MEFs Dnmt2-/-


title: MEFs Nsun2

description: replicate 1

source_name: MEFs Nsun2-/-


title: cervix_tumour_cs1_16

source_name: cervix tumour FFPE series 1


title: MEFs wt

description: replicate 1

source_name: MEFs wildtype


title: Ler-0 infected replicate 3 sample 3

source_name: infected


title: D425-control, t=96

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
NB195
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Cells were cultured in MEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.

value: Medulloblastoma cell line D425

tag: protocol

value: control

tag: time

value: 96 hrs


title: D425-control, t=16

description:
NB192
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

tag: cell line

value: 16 hrs


title: D425-control, t=24

description:
NB193
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 24 hrs


title: Di-2 infected replicate 1 sample 1

value: whole organism

value: Tobacco etch potyvirus


title: H9-c

city: Berlin

first: Katharina

last: Drews

address: Ihnestr. 63-73

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

description: replicate 3

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation after background subtraction using the Gene Expression Module 1.8.0 of GenomeStudio V2010.3 (Illumina).

source_name: hESCs H9, un-treated

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using the RNeasy Mini Kit (Qiagen), including RNase-free Dnase (Qiagen) digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

value: H9 (purchased from WiCell Research Inst.)

tag: passage

value: undifferentiated hESCs


title: D425-control, t=48

description:
NB194
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 48 hrs


title: Expression data of 358_SCa

description: CIN-high

source_name: Patient 358


title: cervix_tumour_cs1_13

value: cervix

tag: storage

value: formalin-fixed paraffin-embedded (FFPE)


title: cervix_tumour_cs1_20

tag: organ

value: squamous cell carcinoma (SCC)


title: H1-c

description: replicate 3

source_name: hESCs H1, un-treated

value: H1 (purchased from WiCell Research Inst.)

tag: treatment


title: Wt-1 infected replicate 2 sample 2


title: Tkv expression 24APF_5

city: Seattle

first: Laura

last: Buttitta

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Hybridization was performed by the FHCRC microarray facility, follwing Nimblegen standard hybridization protocol (see www.nimblegen.com)

scan_protocol: Scanning was performed by the FHCRC microarray facility, follwing Nimblegen standard scanning protocol (see www.nimblegen.com)

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package

organism: Drosophila melanogaster

source_name: dissected wing

label_protocol: Labeling was performed by the FHCRC microarray facility, follwing Nimblegen standard operating protocol (see www.nimblegen.com)

growth_protocol: Drosophila were grown on standard cornmeal, molasses media at 18oC until transgene induction

extract_protocol: 10 wings of the indicated stages were dissected and total RNA was extracted using a Qiagen RNAeasy kit.

treatment_protocol: Gal4/UAS transgene expression (or mock controls) were shifted to 28oC, permissive for Gal4/UAS driven expression without excessive cell death, for 10 hours before dissection. For pupal stages, all animals were staged from white-prepupae collected at 0hr APF.

value: dissected wing

tag: developmental stage

value: 24 hours after pupa formation

tag: transgene

value: Tkv


title: D425-control, t=8

description:
NB191
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: Medulloblastoma cell line D425

value: 8 hrs


title: Tkv expression 24APF_4


title: H9-b

description: replicate 2


title: cervix_tumour_cs1_22

tag: tissue type

value: tumour

tag: histology

tag: data series

tag: ffpe block storage duration (yrs)


title: Tkv expression 24APF_3

tag: tissue


title: D425-shOTX2_3, t=96

description:
NB172
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: doxycyline inducible shRNA against OTX2

value: 96 hrs

tag: time course


title: cervix_tumour_cs1_12


title: cervix_tumour_cs1_15

value: OTHER


title: D425-control, t=0

description:
NB190
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: control

value: 0 hrs


title: H9-a

description: replicate 1

value: H9 (purchased from WiCell Research Inst.)

value: undifferentiated hESCs


title: D425-shOTX2_3, t=48

description:
NB171
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 48 hrs


title: H1-b

description: replicate 2


title: cervix_tumour_cs1_ac_4

hyb_protocol: GeneChip Eukaryotic Hybridization Control Kit - Genisphere standard protocol

data_processing:
Background adjustment and quantile normalisation using Affymetrix miRNA QC Tool (v.1.1.1.0)
probe group file: miRNA-2_0_v2.pgf

label: FlashTag-Biotin-HSR

source_name: cervix tumour FFPE series 1 ac

label_protocol: Genisphere FlashTag Biotin HSR RNA labelling Kit

growth_protocol: Cell lines were grown in DMEM + 10% FCS. Cell lines were classified as SCC or AC according to P63 protein expression

extract_protocol: RNA was extracted and Dnase treated using RecoverAll Total Nucleic Acid Isolation kit (Ambion).

tag: tissue source

value: clinical cervical tumour sample

value: formalin-fixed paraffin-embedded (FFPE)

tag: classification

value: adenocarcinoma (AC)

tag: ffpe block storage duration time (yrs)


title: cervix_tumour_cs1_ac_3


title: cervix_tumour_cs1_18

value: cervix

value: squamous cell carcinoma (SCC)


title: cervix_tumour_cs1_14


title: cervix_tumour_cs1_10


title: cervix_tumour_cs1_scc_4

source_name: cervix tumour FFPE series 1 scc


title: D425-shOTX2_3, t=24

description:
NB170
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

tag: protocol

tag: time

value: 24 hrs


title: Tkv expression 24APF_1

value: dissected wing

value: 24 hours after pupa formation

value: Tkv


title: H1-a

description: replicate 1

tag: cell line

value: H1 (purchased from WiCell Research Inst.)

tag: passage


title: iB5-b

description: replicate 2

source_name: iPSCs line 5 from BJ, un-treated

value: iB5-b derived from BJ

value: undifferentiated iPSCs


title: control 24_4


title: cervix_tumour_cs1_scc_3

value: tumour

tag: storage


title: D425-shOTX2_3, t=16

description:
NB169
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: Medulloblastoma cell line D425

value: doxycyline inducible shRNA against OTX2

value: 16 hrs


title: cervix_tumour_cs1_11

tag: organ


title: cervix_tumour_cs1_scc_2


title: iB5-a

description: replicate 1

value: iB5-a derived from BJ

tag: treatment


title: control 24_3

tag: developmental stage

tag: transgene


title: control 24_5


title: iB4-b

description: replicate 2

source_name: iPSCs line 4 from BJ, un-treated

value: iB4-b derived from BJ


title: cervix_tumour_cs1_9

tag: tissue type

value: formalin-fixed paraffin-embedded (FFPE)

tag: histology


title: cervix_tumour_cs1_scc_1

value: clinical cervical tumour sample

tag: data series


title: cervix_tumour_cs1_7

value: cervix

tag: ffpe block storage duration (yrs)


title: D425-shOTX2_2, t=96

description:
NB166
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 96 hrs

tag: time course


title: D425-shOTX2_3, t=0

description:
NB167
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 0 hrs


title: iB4-a

description: replicate 1

value: iB4-a derived from BJ

tag: tissue


title: cervix_tumour_cs1_ac_1

tag: tissue source

tag: classification

value: adenocarcinoma (AC)


title: control 24_2

value: dissected wing

value: 24 hours after pupa formation


title: Tkv expression 24APF_2

value: Tkv


title: cervix_tumour_cs1_4

value: squamous cell carcinoma (SCC)


title: D425-shOTX2_2, t=48

description:
NB165
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

tag: protocol

value: 48 hrs


title: control 24_1


title: iPS2-b

description: replicate 2

source_name: iPSCs line 2 from HFF1, un-treated

value: iPS2-b derived from HFF1

value: undifferentiated iPSCs


title: cervix_tumour_cs2_ac_4

source_name: cervix tumour FFPE series 2 ac

value: tumour

tag: ffpe block storage duration time (yrs)


title: Tkv expression L3_5

value: wandering 3rd larval instar


title: iPS4-b

description: replicate 2

source_name: iPSCs line 4 from HFF1, un-treated

tag: cell line

value: iPS4-b derived from HFF1


title: cervix_tumour_cs1_ac_2

value: formalin-fixed paraffin-embedded (FFPE)


title: iPS2-a

description: replicate 1

value: iPS2-a derived from HFF1

tag: passage


title: D425-shOTX2_3, t=8

description:
NB168
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: Medulloblastoma cell line D425

value: doxycyline inducible shRNA against OTX2

tag: time

value: 8 hrs


title: cervix_tumour_cs1_6

tag: organ

value: cervix

tag: storage


title: cervix_tumour_cs1_5


title: iPS4-a

description: replicate 1

value: iPS4-a derived from HFF1

tag: treatment


title: D425-shOTX2_2, t=16

description:
NB163
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 16 hrs


title: D425-shOTX2_2, t=8

description:
NB162
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.


title: cervix_tumour_cs2_scc_3

source_name: cervix tumour FFPE series 2 scc

value: clinical cervical tumour sample


title: cervix_tumour_cs1_8


title: D425-shOTX2_2, t=24

description:
NB164
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 24 hrs


title: cervix_tumour_cs1_3

value: squamous cell carcinoma (SCC)


title: Tkv expression L3_3

value: dissected wing

tag: developmental stage

tag: transgene

value: Tkv


title: cervix_tumour_cs2_ac_3

tag: tissue type

value: adenocarcinoma (AC)


title: cervix_tumour_cs2_ac_2

value: tumour

tag: data series