title: EmbryonicPeripheralBud_Age13 rep 4

description:
laser microdissected sample
E13.5PB_004

value: Peripheral Bud


title: >=5% myeloblast bone marrow 39

status: Public on Jul 01 2011

type: genomic

city: Cleveland

first: Kwok Peng

last: Ng

state: OH

address: 9500 Euclid Avenue

department: Ophthalmic Research

country: USA

institute: Cleveland Clinic

description:
genomic DNA from bone marrow aspirates
HIGH39

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Cancer Panel 1 Methylation Microarray using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: MDS or AML bone marrow aspirates

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from bone marrow aspirates samples using Qiagen DNeasy Kit according to standard instructions

tag: cells

value: bone marrow aspirates

tag: who diagnosis

value: RAEB


title: lung cancer tissue_LCA011

type: RNA

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description: lung cancer tissue

hyb_protocol: standard affymetrix hybridisation protocol

scan_protocol: standard affymetrix scanning protocol with affymetrix 3000 7G Scanner

data_processing: The data were analyzed with GCOS version 1.1.1.052 using Affymetrix default analysis settings. Scaling was performed using Mask Files provided by Affymetrix (HGU133Anorm.msk for U133A arrays, HGU133_plus_2norm.msk for U133 Plus 2.0 arrays). The mean target intensity was arbitrarily set to 1200 (U133A) or 850 (U133 Plus 2.0). All samples were normalized with RMA algorithm.

label: Biotin

molecule: total RNA

source_name: lung cancer tissue

label_protocol: standard affymetrix labeling protocol

extract_protocol: standard qiagen isolation protocol

tag: cell type

value: adenocarcinoma


title: >=5% myeloblast bone marrow 38

description:
genomic DNA from bone marrow aspirates
HIGH38


title: EmbryonicPeripheralBud_Age13 rep 5

city: Bethesda

first: Kurt

last: Musselmann

state: MD

address: 30 Convent Dr, Room 426

department: Laboratory of Cell and Developmental Biology

institute: NIDCR

description:
laser microdissected sample
E13.5PB_005

hyb_protocol: Standard Agilent hybridization protocol: 1.5 mg of labeled RNA were fractionated and hybridized overnight (17h) at 60C, followed by washing according to Agilent's instructions.

scan_protocol: Standard Agilent scan using Agilent Microarray Scanner.  Sensitivities used were 10 and 100%

data_processing: GeneSpring 11.0, Quantile normalization of microarray data

organism: Mus musculus

source_name: Salivary gland, replicate 5

label_protocol: MessageAMP 2 AA labeling protocol, however, ratio of aaUTP to UTP was reduced from 1:1 to 1:3 to reduce background signal.  The RNA was then labeles following the manufacturers instructions.

extract_protocol: The RNA from the isolated cell samples were extracted using either Trizol or Rneasy Micro (Qiagen), and the RNA precipitated using glycogen as a carrier.  The samples were then amplified using MessageAMP 2AA, and the spike ins incorporated at the start of the 2nd round.

treatment_protocol: No special treatment of pregnant mice.  Embryos were isolated from timed pregnancies, the salivary glands isolated and embedded in OCT on top of nucleopore filters.  The filters were removed, and the salivary glands sectioned at 10um.  The sections were stained, and specific locations isolated by laser microdissection.

tag: strain

value: ICR

tag: collection method

value: laser microdissection

tag: age

value: Embryonic day E13

tag: tissue

value: salivary gland

tag: salivary gland domain


title: >=5% myeloblast bone marrow 37

description:
genomic DNA from bone marrow aspirates
HIGH37


title: 2w old FHH untreated female (4160685018_J)

city: Utrecht

first: Sebastiaan

last: Wesseling

address: Heidelberglaan 100

department: Nephrology & Hypertension

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: Signal is developed with streptavidin-Cy3.

scan_protocol: The BeadChip is scanned with the Illumina BeadArray Reader, which is a two-channel, 0.8 μm resolution confocal laser scanner. During the scan process, the BeadChip barcode is scanned, ensuring effective data management.

data_processing: The raw bead files (each file contained about 1 million beads) was reorganized into non-normalized data files using T4Illumina (see www.nephrogenomics.net/UMCUtrecht/Tools/). The data were log2-transformed and quantile normalized using the program FlexArray (see gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e). The statistical program CyberT was used to signify change in gene expression between any two groups (e.g. Molsidomine-vs-Untreated FHH of 2 days old). P<0.05 was considered significant. In our analysis we use Array_Address_ID, instead of ID_Ref, as identities for the genes because they contain more unique probe codes.

organism: Rattus norvegicus

source_name: rat kidney

label_protocol: The samples amplified and labeled using Illumina TotalPrep RNA Amplification Kit (Ambion, cat. nr. IL1791).

growth_protocol: 2w old FHH untreated female

extract_protocol: Kidneys was homogenized in TRIzol using beadbeater. Then RNA was extracted from Trizol and purified using NucleoSpin® RNA II kit from Macherey-Nagel (cat. #: 740 955). The purified RNA was sent to ServiceXS.com who processed the samples as recommended by Illumina.

treatment_protocol: Fawn-Hooded Hypertensive (FHH) rats were bred. Pregnant female FHH was treated with NO donor molsidomine in drinking water (120 mg/L) two weeks before to four weeks after birth. The offspring were sacrificed at 2d, 2w and 36w/42w (male/female respectively) old. The kidneys were isolated from these rats and subjected to BeadChip Illumina RatRef-12. Molsidomine-treated rats were compared to age- and gender-matched untreated FHH rats.

value: Fawn-Hooded Hypertensive

value: 2 weeks

value: kidney

tag: gender

value: female

tag: treatment

value: Untreated


title: 2w old FHH untreated female (4160685015_I)


title: 42w old FHH untreated female (4256273084_C)

description: Adult-untreated-female

growth_protocol: 42w old FHH untreated female

value: 42 weeks


title: >=5% myeloblast bone marrow 36

description:
genomic DNA from bone marrow aspirates
HIGH36


title: EmbryonicPeripheralBud_Age13 rep 3

description:
laser microdissected sample
E13.5PB_003

source_name: Salivary gland, replicate 3


title: >=5% myeloblast bone marrow 35

description:
genomic DNA from bone marrow aspirates
HIGH35


title: 2w old FHH untreated female (4160685013_A)


title: lung cancer tissue_LCA003

description: lung cancer tissue

value: squamous cell carcinoma


title: EmbryonicPeripheralBud_Age13 rep 1

description:
laser microdissected sample
E13.5PB_001

source_name: Salivary gland, replicate 1


title: 2w old FHH untreated female (4160685006_F)


title: lung cancer tissue_LCA010

description: lung cancer tissue

value: metastasis of a colon carcinoma


title: Z138_2_sensitive

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA in Bioconductor.

label: biotin

source_name: Mantel cell lymphoma cell line, sensitive to ABT-737

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

value: Mantel Cell Lymphoma

tag: cell line


title: EmbryonicPeripheralBud_Age13 rep 2

description:
laser microdissected sample
E13.5PB_002

source_name: Salivary gland, replicate 2

value: Peripheral Bud


title: EmbryonicMainDuct_Age12 rep 5

description:
laser microdissected sample
E12.5MD_005

value: Embryonic day E12

value: Main Duct


title: 2w old FHH untreated female (4160685004_C)


title: >=5% myeloblast bone marrow 34

description:
genomic DNA from bone marrow aspirates
HIGH34

value: bone marrow aspirates

value: AML


title: lung cancer tissue_LCA008

description: lung cancer tissue


title: Z138_1_sensitive


title: EmbryonicMainDuct_Age12 rep 4

description:
laser microdissected sample
E12.5MD_004

source_name: Salivary gland, replicate 4

value: ICR

value: laser microdissection


title: >=5% myeloblast bone marrow 33

description:
genomic DNA from bone marrow aspirates
HIGH33


title: 2w old FHH untreated male (4160685018_L)

growth_protocol: 2w old FHH untreated male

value: male


title: >=5% myeloblast bone marrow 32

description:
genomic DNA from bone marrow aspirates
HIGH32


title: EmbryonicMainDuct_Age12 rep 3

description:
laser microdissected sample
E12.5MD_003

value: salivary gland


title: >=5% myeloblast bone marrow 31

description:
genomic DNA from bone marrow aspirates
HIGH31


title: 2w old FHH untreated male (4256273078_K)

value: Fawn-Hooded Hypertensive

value: 2 weeks


title: 2w old FHH untreated male (4160685015_G)

value: kidney


title: UPN1_1_resistant

source_name: Mantel cell lymphoma cell line, resistant to ABT-737


title: EmbryonicMainDuct_Age12 rep 1

description:
laser microdissected sample
E12.5MD_001


title: >=5% myeloblast bone marrow 30

description:
genomic DNA from bone marrow aspirates
HIGH30


title: UPN1_2_resistant


title: REC1_2_resistant


title: EmbryonicMainDuct_Age12 rep 2

description:
laser microdissected sample
E12.5MD_002


title: >=5% myeloblast bone marrow 29

description:
genomic DNA from bone marrow aspirates
HIGH29


title: 2w old FHH untreated male (4160685013_L)

value: Untreated


title: EmbryonicCleft_Age12 rep 5

description:
laser microdissected sample
E12.5Cl_005

value: Cleft


title: EmbryonicCleft_Age12 rep 4

description:
laser microdissected sample
E12.5Cl_004


title: 2w old FHH untreated male (4160685010_I)


title: >=5% myeloblast bone marrow 28

description:
genomic DNA from bone marrow aspirates
HIGH28


title: EmbryonicCleft_Age12 rep 3

description:
laser microdissected sample
E12.5Cl_003


title: >=5% myeloblast bone marrow 27

description:
genomic DNA from bone marrow aspirates
HIGH27


title: MINO_2_sensitive

value: MINO


title: 2w old FHH untreated male (4160685006_B)


title: REC1_1_resistant


title: MINO_1_sensitive


title: 2d old FHH molsidomine female (4160685018_H)

growth_protocol: 2d old FHH molsidomine female

value: 2 days

value: female

value: molsidomine


title: EmbryonicCleft_Age12 rep 2

description:
laser microdissected sample
E12.5Cl_002

value: Embryonic day E12


title: L128_1_resistant

value: Mantel Cell Lymphoma


title: >=5% myeloblast bone marrow 26

description:
genomic DNA from bone marrow aspirates
HIGH26

value: bone marrow aspirates


title: 2d old FHH molsidomine female (4160685015_L)


title: JVM2_2_resistant


title: 2d old FHH molsidomine female (4160685013_F)


title: EmbryonicBud_Age12 rep 5

description:
laser microdissected sample
E12.5MB_005

value: Bud


title: EmbryonicBud_Age12 rep 3

description:
laser microdissected sample
E12.5MB_003

value: ICR


title: >=5% myeloblast bone marrow 25

description:
genomic DNA from bone marrow aspirates
HIGH25

value: AML


title: JVM2_1_resistant


title: L128_2_resistant


title: JEKO_2_resistant

value: JEKO


title: EmbryonicCleft_Age12 rep 1

description:
laser microdissected sample
E12.5Cl_001

value: laser microdissection

value: salivary gland


title: 2d old FHH molsidomine female (4160685006_D)

value: Fawn-Hooded Hypertensive


title: >=5% myeloblast bone marrow 24

description:
genomic DNA from bone marrow aspirates
HIGH24


title: 2d old FHH molsidomine female (4160685010_B)

value: kidney


title: >=5% myeloblast bone marrow 21

description:
genomic DNA from bone marrow aspirates
HIGH21


title: >=5% myeloblast bone marrow 22

description:
genomic DNA from bone marrow aspirates
HIGH22


title: >=5% myeloblast bone marrow 19

description:
genomic DNA from bone marrow aspirates
HIGH19


title: JEKO_1_resistant


title: >=5% myeloblast bone marrow 20

description:
genomic DNA from bone marrow aspirates
HIGH20


title: >=5% myeloblast bone marrow 23

description:
genomic DNA from bone marrow aspirates
HIGH23


title: HBL2_2_sensitive


title: IRM2_2_resistant


title: 2d old FHH molsidomine male (4160685018_B)

growth_protocol: 2d old FHH molsidomine male

value: male


title: proliferating leaf, control, 24h, biological rep3

city: Gent

first: aleksandra

last: skirycz

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: Ghent University

description: leaf size around 0.1mm2

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

organism: Arabidopsis thaliana

source_name: Wild type, proliferating leaf, control, 24h

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on nylon mesh (PROSEP) overlaying 0.5MS medium (control) under 16 h light/ 8 h dark cycle at 22°C, at 9DAS seedlings were transferred to control media

extract_protocol: Proliferating leaves were disected in RNAlater, Trizol extraction (Invitrogen) followed by clean-up by RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

tag: ecotype

value: 3rd true leaf

value: leaf 3_10DAS plants

tag: genotype

value: wild-type


title: >=5% myeloblast bone marrow 18

description:
genomic DNA from bone marrow aspirates
HIGH18


title: 2d old FHH molsidomine male (4160685015_F)

value: 2 days


title: EmbryonicBud_Age12 rep 4

description:
laser microdissected sample
E12.5MB_004


title: HBL2_1_sensitive


title: 2d old FHH molsidomine male (4160685010_L)

value: molsidomine


title: proliferating leaf, mannitol, 24h, biological rep1

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress, 24h

growth_protocol: plant were grown on nylon mesh (PROSEP) overlaying 0.5MS medium (control) under 16 h light/ 8 h dark cycle at 22°C, at 9DAS seedlings were transferred to mannitol (25mM) containing media


title: 2d old FHH molsidomine male (4160685004_G)


title: EmbryonicBud_Age12 rep 2

description:
laser microdissected sample
E12.5MB_002

value: Embryonic day E12


title: EmbryonicBud_Age12 rep 1

description:
laser microdissected sample
E12.5MB_001


title: >=5% myeloblast bone marrow 17

description:
genomic DNA from bone marrow aspirates
HIGH17


title: proliferating leaf, control, 24h, biological rep1

description: leaf size around 0.1mm2

treatment_protocol: plant were grown on nylon mesh (PROSEP) overlaying 0.5MS medium (control) under 16 h light/ 8 h dark cycle at 22°C, at 9DAS seedlings were transferred to control media


title: proliferating leaf, control, 24h, biological rep2

description: leaf size around 0.1mm2


title: 2d old FHH untreated female (4160685018_I)

growth_protocol: 2d old FHH untreated female

value: female

value: Untreated


title: proliferating leaf, mannitol, 12h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress, 12h

treatment_protocol: plant were grown on nylon mesh (PROSEP) overlaying 0.5MS medium (control) under 16 h light/ 8 h dark cycle at 22°C, at 9DAS seedlings were transferred to mannitol (25mM) containing media

value: leaf 3_9DAS plants


title: G519_1_sensitive

value: Mantel Cell Lymphoma


title: 2d old FHH molsidomine female (4160685004_I)


title: G519_2_sensitive


title: 2d old FHH untreated female (4160685018_D)


title: IRM2_1_resistant


title: >=5% myeloblast bone marrow 16

description:
genomic DNA from bone marrow aspirates
HIGH16

value: bone marrow aspirates

value: AML


title: >=5% myeloblast bone marrow 14

description:
genomic DNA from bone marrow aspirates
HIGH14


title: 2d old FHH untreated female (4160685013_C)


title: 2d old FHH untreated female (4160685010_F)


title: >=5% myeloblast bone marrow 15

description:
genomic DNA from bone marrow aspirates
HIGH15


title: proliferating leaf, mannitol, 12h, biological rep2

description: leaf size around 0.1mm2


title: MDA-MB-231 cells repressing a scramble sequence-rep2

city: brussels

first: Françoise

last: Rothé

address: boulevard de waterloo 127

institute: Jules Bordet Institute

description:
MDAMB231_mircontrol_2
Gene expression data from MDA-MB-231 control cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome Array (U133Plus2.0). 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 GCOS Manager 4.0 using Affymetrix default analysis settings. The data were RMA-normalized and log2 transformed using BRB Array Tools software.

source_name: MDA-MB-231 cells repressing a scramble sequence (negative control)

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

growth_protocol: MCF7 and MDA-MB-231 cells were obtained from the ATCC and cultured under standard conditions.

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

tag: estrogen-receptor status

value: ER-negative

tag: genotype/variation

value: control (for miR-210 repression)


title: proliferating leaf, mannitol, 12h, biological rep1

description: leaf size around 0.1mm2


title: >=5% myeloblast bone marrow 12

description:
genomic DNA from bone marrow aspirates
HIGH12


title: >=5% myeloblast bone marrow 10

description:
genomic DNA from bone marrow aspirates
HIGH10


title: >=5% myeloblast bone marrow 11

description:
genomic DNA from bone marrow aspirates
HIGH11


title: proliferating leaf, control, 12h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, control, 12h


title: proliferating leaf, control, 12h, biological rep2

description: leaf size around 0.1mm2


title: 2d old FHH untreated male (4160685015_B)

growth_protocol: 2d old FHH untreated male

value: Fawn-Hooded Hypertensive


title: 2d old FHH untreated female (4160685006_I)

value: kidney


title: MDA-MB-231 cells repressing miR-210-rep1

description:
MDAMB231_miR210_1
Gene expression data from MDA-MB-231 cells repressing miR-210

source_name: MDA-MB-231 cells repressing miR-210

value: miR-210 repression


title: 2d old FHH untreated male (4160685018_K)

value: male


title: MDA-MB-231 cells repressing a scramble sequence-rep1

description:
MDAMB231_mircontrol_1
Gene expression data from MDA-MB-231 control cells


title: >=5% myeloblast bone marrow 13

description:
genomic DNA from bone marrow aspirates
HIGH13


title: MDA-MB-231 cells repressing miR-210-rep2

description:
MDAMB231_miR210_2
Gene expression data from MDA-MB-231 cells repressing miR-210


title: proliferating leaf, mannitol, 3h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress, 3h

value: 3rd true leaf


title: proliferating leaf, control, 12h, biological rep1

description: leaf size around 0.1mm2

value: wild-type


title: MCF7 cells overexpressing miR-210-rep2

description:
MCF7_miR210_2
Gene expression data from MCF7 cells overexpressing miR-210

source_name: MCF7 cells overexpressing miR-210

value: ER-positive

value: miR-210 overexpression


title: 2d old FHH untreated male (4160685013_J)

value: 2 days


title: MCF7 cells overexpressing a scramble sequence-rep1

description:
MCF7_mircontrol_1
Gene expression data from MCF7 control cells

source_name: MCF7 cells overexpressing a scramble sequence (negative control)

value: control (for miR-210 overexpression)


title: MCF7 cells overexpressing a scramble sequence-rep2

description:
MCF7_mircontrol_2
Gene expression data from MCF7 control cells


title: >=5% myeloblast bone marrow 9

description:
genomic DNA from bone marrow aspirates
HIGH9

source_name: MDS or AML bone marrow aspirates


title: MCF7 cells overexpressing miR-210-rep1

description:
MCF7_miR210_1
Gene expression data from MCF7 cells overexpressing miR-210


title: >=5% myeloblast bone marrow 8

description:
genomic DNA from bone marrow aspirates
HIGH8


title: proliferating leaf, mannitol, 3h, biological rep1

description: leaf size around 0.1mm2


title: >=5% myeloblast bone marrow 7

description:
genomic DNA from bone marrow aspirates
HIGH7


title: >=5% myeloblast bone marrow 5

description:
genomic DNA from bone marrow aspirates
HIGH5


title: 2d old FHH untreated male (4160685006_G)

source_name: rat kidney

value: Untreated


title: >=5% myeloblast bone marrow 3

description:
genomic DNA from bone marrow aspirates
HIGH3


title: 2d old FHH untreated male (4160685004_A)


title: proliferating leaf, mannitol, 3h, biological rep2

description: leaf size around 0.1mm2

value: leaf 3_9DAS plants


title: >=5% myeloblast bone marrow 2

description:
genomic DNA from bone marrow aspirates
HIGH2


title: proliferating leaf, control, 3h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, control, 3h


title: >=5% myeloblast bone marrow 4

description:
genomic DNA from bone marrow aspirates
HIGH4


title: proliferating leaf, control, 3h, biological rep2

description: leaf size around 0.1mm2


title: >=5% myeloblast bone marrow 1

description:
genomic DNA from bone marrow aspirates
HIGH1


title: proliferating leaf, control, 1.5h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, control, 1.5h


title: PER-403, post NUT siRNA, rep 2

city: boston

first: Chris

middle: A

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

description:
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with NUT siRNA
per403_nut_siRNA_2.CEL

hyb_protocol: Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.

scan_protocol: Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.

data_processing: Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm

source_name: PER-403, post NUT siRNA, rep 2

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).

extract_protocol: Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.

treatment_protocol: Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.

value: NMC cell line PER-403

tag: agent

value: NUT siRNA


title: proliferating leaf, mannitol, 1.5h, biological rep1

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress, 1.5h


title: proliferating leaf, control, 1.5h, biological rep2

description: leaf size around 0.1mm2


title: >=5% myeloblast bone marrow 6

description:
genomic DNA from bone marrow aspirates
HIGH6

value: bone marrow aspirates

value: AML


title: proliferating leaf, mannitol, 1.5h, biological rep2

description: leaf size around 0.1mm2


title: PER-403, post NUT siRNA, rep 1

description:
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with NUT siRNA
per403_NUT_siRNA_1.CEL

source_name: PER-403, post NUT siRNA, rep 1


title: patient55_OXFU_2197

description: MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.

hyb_protocol: Hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations (Ambion).

scan_protocol: Hybridization signals were detected at 532 nm using a GenePix 4000B scanner and quantified by GenePix Pro 4.0 software.

data_processing: The signal intensity of each spot was calculated by subtracting the local background from the mean signal. After averaging replicate spots, a global scaling normalization was applied, as suggested by Ambion. This normalization consisted of the following steps: 1) thresholding, for which intensities below the background (set to 2 times the signal of empty spots) were set to 1; 2) scaling, which involved ranking the intensities of each sample separately and dividing them by the 30th intensity value; and 3) log 2 transformation. The normalized intensities were used for further analyses.

source_name: primary breast cancer

label_protocol: 7.5 µg total RNA was labeled with Cy3 dye using the miRVana labeling kit according to the manufacturer's instructions (Ambion).

extract_protocol: Total RNA was prepared from tumor cryostat sections using the Trizol method according to the manufacturer's instructions.

value: primary breast cancer

tag: age at operation

tag: menopause status

value: post

tag: histology

value: infiltrating ductal

tag: tumor size

tag: histological grade

tag: estrogen receptor status

tag: nodal status

tag: rfs status


title: proliferating leaf, mannitol, 1.5h, biological rep3

description: leaf size around 0.1mm2

tag: tissue

tag: age


title: patient56_OXFU_4550

tag: treatment

value: pre


title: proliferating leaf, control, 3h, biological rep1

description: leaf size around 0.1mm2


title: PER-403, POST-TSA, rep 2

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-2-1567H.CEL

source_name: PER-403, POST-TSA, rep 2

tag: cell line

value: trichostatin (TSA)


title: PER-403, post control siRNA, rep 2

description:
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with scrambled control siRNA
per403_CTRL_siRNA_2.CEL

source_name: PER-403, post control siRNA, rep 2

value: scrambled control siRNA


title: PER-403, POST-ETOH, rep3

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-3-1567L.CEL

source_name: PER-403, POST-ETOH, rep3

value: ethanol vehicle control


title: PER-403, POST-TSA, rep 1

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-1-1567G.CEL

source_name: PER-403, POST-TSA, rep 1


title: patient54_OXFU_1993


title: PER-403, post control siRNA, rep 1

description:
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with scrambled control siRNA
per403_CTRL_siRNA_1.CEL

source_name: PER-403, post control siRNA, rep 1


title: <5% myeloblast bone marrow 26

description:
genomic DNA from bone marrow aspirates
LOW26

tag: cells

tag: who diagnosis

value: RCMD


title: <5% myeloblast bone marrow 27

description:
genomic DNA from bone marrow aspirates
LOW27

value: RARS


title: patient53_OXFU_1373

tag: genomic grade


title: <5% myeloblast bone marrow 25

description:
genomic DNA from bone marrow aspirates
LOW25


title: patient52_OXFU_1248


title: proliferating leaf, mannitol, 24h, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress, 24h

tag: ecotype

value: 3rd true leaf

value: leaf 3_10DAS plants

tag: genotype

value: wild-type


title: PER-403, POST-TSA, rep 3

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-3-1567I.CEL

source_name: PER-403, POST-TSA, rep 3

tag: agent


title: patient51_OXFU_1192

tag: age at operation

tag: menopause status


title: proliferating leaf, mannitol, 24h, biological rep2

description: leaf size around 0.1mm2


title: <5% myeloblast bone marrow 24

description:
genomic DNA from bone marrow aspirates
LOW24


title: <5% myeloblast bone marrow 22

description:
genomic DNA from bone marrow aspirates
LOW22


title: PER-403, POST-ETOH, rep1

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-1-1567J.CEL

source_name: PER-403, POST-ETOH, rep1


title: <5% myeloblast bone marrow 23

description:
genomic DNA from bone marrow aspirates
LOW23


title: proliferating leaf, control, 1.5h, biological rep1

description: leaf size around 0.1mm2

value: leaf 3_9DAS plants


title: patient50_OXFU_1065

tag: histology

tag: tumor size


title: <5% myeloblast bone marrow 21

description:
genomic DNA from bone marrow aspirates
LOW21


title: RatSpinalCord-Sham 7 day-4

city: Toledo

first: Rodrigo

middle: M

last: Maza

state: Toledo

address: Finca La Peraleda s/n

department: Unidad de Neurología Experimental

institute: Hospital Nacional de Parapléjicos (SESCAM)

hyb_protocol: Following the Exiqon protocols included in the miRCURY LNA™ microRNA Array kit v.11.0

scan_protocol: Arrays were scanned by the Genomic Service of the Madrid Science Park using a GenePix4000B scanner, the GenePix Pro 5.0.1.24 software, and the specific GAL file for the miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno. Scanner settings are detailed in every raw data file.

data_processing: Data provided in the matrix spreadsheet was normalized following the Variance Stabilization Method developed by Huber and developed in R language by the Bioconductor facility.

source_name: spinal cord, sham, 7 days after surgery

label_protocol: Using the reactives and protocols included in the miRCURY LNA™ microRNA Power labeling kit, Hy3 dye.

extract_protocol: RNAlater (Qiagen) preservation followed by miRNeasy Mini kit (Qiagen) extraction

treatment_protocol: Controls: no treatment; Injuried: laminectomy and 200 Kdynes contusion injury at T8 level; Sham: laminectomy at T8 level but no contussion. Contussions using Contusor IH Spinal Cord Impactor (Precision System & Instrumentation, LLC, Va)

tag: tissue type

value: spinal cord

tag: gender

value: female

tag: strain

value: Wistar

value: Sham

tag: time point

value: 7 days after surgery


title: PER-403, POST-ETOH, rep2

description:
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-2-1567K.CEL

source_name: PER-403, POST-ETOH, rep2

value: NMC cell line PER-403


title: RatSpinalCord-Sham 7 day-5


title: TC-797, post NUT siRNA, rep 2

description:
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with NUT siRNA
797_NUT_siRNA_2.cel

source_name: TC-797, post NUT siRNA, rep 2

value: NMC cell line TC-797

value: NUT siRNA


title: TC-797, post NUT siRNA, rep 1

description:
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with NUT siRNA
797_NUT_siRNA_1.CEL

source_name: TC-797, post NUT siRNA, rep 1


title: RatSpinalCord-Sham 7 day-3


title: <5% myeloblast bone marrow 20

description:
genomic DNA from bone marrow aspirates
LOW20

source_name: MDS or AML bone marrow aspirates

value: bone marrow aspirates


title: patient48_OXFU_1006

description: MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.

tag: tissue

value: primary breast cancer

value: pre

value: infiltrating ductal

tag: histological grade

tag: estrogen receptor status

tag: nodal status

tag: rfs status


title: RatSpinalCord-Sham 7 day-1

tag: treatment


title: TC-797, post-TSA, rep 3

description:
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-3-1567C.CEL

source_name: TC-797, post-TSA, rep 3

tag: cell line

value: trichostatin (TSA)


title: RatSpinalCord-Sham 7 day-2


title: patient47_OXFU_963


title: <5% myeloblast bone marrow 19

description:
genomic DNA from bone marrow aspirates
LOW19

tag: cells

tag: who diagnosis

value: RCMD


title: RatSpinalCord-Injury 7 day-5

source_name: spinal cord, injuried, 7 days after surgery

value: Injuried


title: patient49_OXFU_1049

tag: age at operation

value: post


title: patient46_OXFU_957

tag: menopause status


title: RatSpinalCord-Injury 7 day-4


title: TC-797, post control siRNA, rep 2

description:
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with scrambled control siRNA
797_CTRL_siRNA_2.CEL

source_name: TC-797, post control siRNA, rep 2

tag: agent

value: scrambled control siRNA


title: <5% myeloblast bone marrow 18

description:
genomic DNA from bone marrow aspirates
LOW18


title: <5% myeloblast bone marrow 17

description:
genomic DNA from bone marrow aspirates
LOW17


title: TC-797, post control siRNA, rep 1

description:
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with scrambled control siRNA
797_CTRL_siRNA_1.CEL

source_name: TC-797, post control siRNA, rep 1


title: TC-797, post-TSA, rep 2

description:
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-2-1567B.CEL

source_name: TC-797, post-TSA, rep 2


title: RatSpinalCord-Injury 7 day-3

value: spinal cord


title: TC-797, post-etoh, rep 2

description:
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-2-1567E.CEL

source_name: TC-797, post-etoh, rep 2

value: ethanol vehicle control


title: TC-797, post-TSA, rep 1

description:
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-1-1567A.CEL

source_name: TC-797, post-TSA, rep 1


title: TC-797, post-etoh, rep 3

description:
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-3-1567F.CEL

source_name: TC-797, post-etoh, rep 3


title: <5% myeloblast bone marrow 16

description:
genomic DNA from bone marrow aspirates
LOW16


title: <5% myeloblast bone marrow 15

description:
genomic DNA from bone marrow aspirates
LOW15

value: RARS/T


title: patient45_OXFU_869

source_name: primary breast cancer

tag: histology

value: tubular

tag: tumor size

tag: genomic grade


title: <5% myeloblast bone marrow 14

description:
genomic DNA from bone marrow aspirates
LOW14


title: <5% myeloblast bone marrow 13

description:
genomic DNA from bone marrow aspirates
LOW13


title: patient44_OXFU_819

value: Phylloides


title: <5% myeloblast bone marrow 12

description:
genomic DNA from bone marrow aspirates
LOW12


title: patient41_OXFU_573


title: patient39_OXFU_559


title: patient42_OXFU_598


title: patient43_OXFU_608


title: patient40_OXFU_567


title: RatSpinalCord-Sham 3 day-4

source_name: spinal cord, sham, 3 days after surgery

tag: tissue type

tag: gender

value: female

tag: strain

value: Wistar

value: Sham

value: 3 days after surgery


title: RatSpinalCord-Injury 7 day-2

tag: time point

value: 7 days after surgery


title: RatSpinalCord-Injury 7 day-1


title: RatSpinalCord-Sham 3 day-5


title: <5% myeloblast bone marrow 11

description:
genomic DNA from bone marrow aspirates
LOW11

value: bone marrow aspirates


title: RatSpinalCord-Sham 3 day-3


title: <5% myeloblast bone marrow 10

description:
genomic DNA from bone marrow aspirates
LOW10

value: RARS


title: <5% myeloblast bone marrow 9

description:
genomic DNA from bone marrow aspirates
LOW9


title: <5% myeloblast bone marrow 8

description:
genomic DNA from bone marrow aspirates
LOW8

value: RA


title: <5% myeloblast bone marrow 7

description:
genomic DNA from bone marrow aspirates
LOW7


title: <5% myeloblast bone marrow 6

description:
genomic DNA from bone marrow aspirates
LOW6


title: <5% myeloblast bone marrow 5

description:
genomic DNA from bone marrow aspirates
LOW5


title: <5% myeloblast bone marrow 4

description:
genomic DNA from bone marrow aspirates
LOW4


title: RatSpinalCord-Sham 3 day-2


title: RatSpinalCord-Sham 3 day-1


title: patient34_OXFU_547

description: MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.

tag: tissue

value: primary breast cancer

value: pre

value: infiltrating ductal

tag: histological grade

tag: estrogen receptor status


title: patient33_OXFU_544

tag: treatment

value: post

tag: nodal status

tag: rfs status


title: patient37_OXFU_556


title: patient36_OXFU_554


title: patient35_OXFU_549

value: infiltrating lobular


title: patient38_OXFU_557


title: patient31_OXFU_535


title: RatSpinalCord-Sham 1 day-5

source_name: spinal cord, sham, 1 day after surgery

value: spinal cord

value: 1 day after surgery


title: RatSpinalCord-Injury 3 day-1

source_name: spinal cord, injuried, 3 days after surgery

value: Injuried


title: patient32_OXFU_543


title: TC-797, post-etoh, rep 1

description:
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-1-1567D.CEL

source_name: TC-797, post-etoh, rep 1

tag: cell line

value: NMC cell line TC-797

value: ethanol vehicle control


title: <5% myeloblast bone marrow 3

description:
genomic DNA from bone marrow aspirates
LOW3

tag: cells

tag: who diagnosis


title: RatSpinalCord-Injury 3 day-3

value: female

value: Wistar


title: RatSpinalCord-Injury 3 day-4

value: 3 days after surgery


title: <5% myeloblast bone marrow 2

description:
genomic DNA from bone marrow aspirates
LOW2


title: patient29_OXFU_533

tag: age at operation

tag: menopause status


title: patient30_OXFU_534

tag: histology

tag: tumor size


title: RatSpinalCord-Injury 3 day-2

tag: tissue type


title: Renal Cell Carcinoma Cell line SN12C19

city: Houston

first: Nanyue

last: Chen

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description: Gene expression data from human renal cancer cell line SN12C19

hyb_protocol: Hybridization was performed using established Affymetrix protocols.

scan_protocol: Scanning was performed as recommended by Affymetrix protocols.

data_processing: Probe normalization and summarization was performed using the PerfectMatch software suite utilizing the PDNN algorithm

source_name: Renal Carcinoma Cell line

label_protocol: Labeling was performed using established Affymetrix protocols.

extract_protocol: RNA was extracted from cultured renal carcinoma cells using a miRNeasy Mini Kit


title: RatSpinalCord-Sham 1 day-3

tag: gender

value: Sham


title: RatSpinalCord-Sham 1 day-2

tag: strain


title: RatSpinalCord-Injury 3 day-5

tag: time point


title: <5% myeloblast bone marrow 1

description:
genomic DNA from bone marrow aspirates
LOW1

value: bone marrow aspirates


title: RatSpinalCord-Sham 1 day-4


title: patient28_OXFU_530

tag: tissue

tag: genomic grade


title: Renal Cell Carcinoma Cell line SN19(3i)YY

description: Gene expression data from human renal cancer cell line SN19(3i)YY containing an introduced normal chromosome 3P fragment which suppressed tumorigenicity in athymic nude mice


title: Patient 4-Tumor

description: pancreatic adenocarcinoma

hyb_protocol: Hybridizaiton was performed using Affymetrix protocols provided by the manufacturer

scan_protocol: Scanning was performed using Affymetrix protocols provided by the manufacturer

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

source_name: Pancreatic tumor tissue

label_protocol: Labeling was performed using Affymetrix protocols provided by the manufacturer.

extract_protocol: RNA was extracted from frozen pancreatic tumors and adjacent normal samples using a miRNeasy Mini Kit

tag: patient

tag: age

tag: disease state

value: Pancreatic tumor tissue

tag: diagnosis

value: Poorly differentiated pancreatic adenocarcinoma; no metastasis to lymph nodes


title: Patient 5-Normal

description: pancreatic tissue adjacent to pancreatic adenocarcinoma

source_name: Pancreas

value: adjacent normal tissue

value: control


title: Patient 7-Tumor

description: pancreatic cancer

value: male

value: Pancreatic cancer


title: Patient 6-Normal


title: Patient 4-Normal


title: Patient 8-Normal


title: Patient 8-Tumor

description: pancreatic adenocarcinoma

value: Pancreatic adenocarinoma with advanced metastasis


title: Patient 7-Normal


title: Patient 5-Tumor

description: pancreatic adenocarcinoma

value: Well differentiated pancreatic adenocarcinoma; no metastasis to lymph node


title: Patient 3-Normal


title: Patient 3-Tumor

description: pancreatic adenocarcinoma

value: Well differentiated pancreatic adenocarinoma with metastasis to lymph nodes


title: Patient 6-Tumor

description: pancreatic adenocarcinoma

value: Pancreatic mucinous cystadenocarcinoma with perineural invasion


title: normal bone marrow 42

description:
genomic DNA from bone marrow aspirates
NORMAL42

source_name: normal bone marrow aspirates

value: NORMAL


title: patient27_OXFU_522

value: primary breast cancer

tag: treatment

value: post

value: mucinous

tag: estrogen receptor status

tag: nodal status

tag: rfs status


title: patient26_OXFU_491

tag: age at operation

tag: menopause status

value: infiltrating ductal

tag: histological grade


title: normal bone marrow 40

description:
genomic DNA from bone marrow aspirates
NORMAL40

tag: cells

tag: who diagnosis


title: patient25_OXFU_484

tag: histology

tag: tumor size


title: RatSpinalCord-Injury 1 day-5

source_name: spinal cord, injuried, 1 day after surgery

tag: tissue type

value: spinal cord

tag: gender

value: female

tag: strain

value: Wistar

value: Injuried

tag: time point

value: 1 day after surgery


title: RatSpinalCord-Sham 1 day-1

value: Sham


title: RatSpinalCord-Injury 1 day-4


title: normal bone marrow 41

description:
genomic DNA from bone marrow aspirates
NORMAL41

value: bone marrow aspirates


title: normal bone marrow 38

description:
genomic DNA from bone marrow aspirates
NORMAL38


title: RatSpinalCord-Injury 1 day-3


title: RatSpinalCord-Injury 1 day-2


title: Patient 2-Tumor

description: pancreatic adenocarcinoma

tag: patient

tag: age

tag: disease state

value: Pancreatic tumor tissue

value: Undifferentiated small cell carcinoma of the pancreas with metastasis to lymph nodes


title: patient23_OXFU_476

tag: tissue

tag: treatment

value: infiltrating lobular

tag: genomic grade


title: Patient 2-Normal

value: adjacent normal tissue

tag: diagnosis

value: control


title: normal bone marrow 39

description:
genomic DNA from bone marrow aspirates
NORMAL39

value: NORMAL


title: Patient 1-Tumor

description: pancreatic adenocarcinoma

value: male

value: Moderately differentiated pancreatic adenocarcinoma with metastasis to lymph nodes


title: patient21_OXFU_373

value: primary breast cancer

tag: age at operation

tag: menopause status

value: post

value: mixed

tag: estrogen receptor status

tag: nodal status

tag: rfs status


title: Patient 1-Normal


title: patient24_OXFU_478

tag: histology

value: medullary

tag: tumor size


title: normal bone marrow 37

description:
genomic DNA from bone marrow aspirates
NORMAL37

tag: cells

tag: who diagnosis


title: RatSpinalCord-Injury 1 day-1

tag: tissue type

value: spinal cord

tag: gender

value: female

tag: strain

value: Wistar

tag: time point


title: RatSpinalCord-Control-5

source_name: spinal cord, control

value: Control


title: normal bone marrow 35

description:
genomic DNA from bone marrow aspirates
NORMAL35

value: bone marrow aspirates


title: patient20_OXFU_366

tag: tissue

value: infiltrating ductal

tag: histological grade


title: RatSpinalCord-Control-4

tag: treatment


title: normal bone marrow 34

description:
genomic DNA from bone marrow aspirates
NORMAL34


title: RatSpinalCord-Control-3


title: patient19_OXFU_360

value: pre

tag: genomic grade


title: HUVEC non-stimulated, 0h biological rep 2

city: Berlin

first: Gürkan

last: Bal

address: Augustenburger Platz 1

department: Institute for Transfusion Medicine

institute: Charité - Universitätsmedizin Berlin

description: Gene expression data from interlekin stimulated HUVEC vs. BSA control stimulation in time course

hyb_protocol: Fragmented cRNA (10 μg) were hybridized to HG-U133 plus 2.0 gene chips for 16 hours at 45°C.

scan_protocol: Following washing and staining, gene chips were scanned with the GeneArray scanner controlled by the Affymetrix GCOS 1.4 software.

data_processing: Raw data were processed and normalized by applying the GCOS 1.4 software according to Affymetrix recommendations and by the MAS5.0 normalization method.

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: Cells were cultured in Earl´s M199 medium (Biochrom, Berlin, Germany) supplemented with 16% fetal bovine serum (FBS, Hyclone, South Logan, UT, USA), 4% human serum from healthy volunteers, 2 mM L-glutamine, 0.15 mg/mL endothelial growth factor supplement (Intracel; Rockville, MD, USA), 0.015 mg/mL heparin and 1% fungicide.

extract_protocol: Following stimulation of HUVEC with the various interleukins, cells were harvested by collagenase treatment (0.1% in PBS). Total RNA was isolated from stimulated cells obtained at the various time points via a Qiagen RNeasy Mini Kit in accordance to the manufacturer’s protocols.

treatment_protocol: Confluent monolayer ECs from the third passage were stimulated for either 4, 8 or 16 hours with 100 U/mL IL-1ß, or for 4, 8, 16 and 48 hours with 100 U/mL IL-3 or IL-6, and 0.01 % BSA. Medium only controls were also performed at 0 and 16 hours.

tag: cell type

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: cell culture

value: Passage 3

tag: pooling

value: pooled from 7 individual

tag: treatment group

value: non-stimulated, 0h biological rep 2


title: HUVEC simulated 48h with IL-6(100 U)

value: simulated 48h with IL-6(100 U)


title: normal bone marrow 36

description:
genomic DNA from bone marrow aspirates
NORMAL36

value: NORMAL


title: patient22_OXFU_449

description: MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.

value: primary breast cancer

tag: age at operation

tag: menopause status

value: infiltrating lobular

tag: estrogen receptor status

tag: nodal status

tag: rfs status


title: HUVEC non-stimulated, 0h biological rep 1

value: non-stimulated, 0h biological rep 1


title: HUVEC non-stimulated, 16h

value: non-stimulated, 16h


title: normal bone marrow 33

description:
genomic DNA from bone marrow aspirates
NORMAL33

tag: cells

tag: who diagnosis


title: patient17_OXFU_320

tag: histology

tag: tumor size


title: patient18_OXFU_348

tag: tissue

value: post


title: RatSpinalCord-Control-2

tag: tissue type

value: spinal cord

tag: gender

value: female

tag: strain

tag: time point


title: RatSpinalCord-Control-1

value: Wistar

tag: treatment

value: Control


title: HUVEC simulated 16h with IL-6(100 U)

tag: cell type

tag: cell culture

tag: pooling

value: simulated 16h with IL-6(100 U)


title: normal bone marrow 31

description:
genomic DNA from bone marrow aspirates
NORMAL31

value: bone marrow aspirates


title: HUVEC simulated 8h with IL-6(100 U)

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: treatment group

value: simulated 8h with IL-6(100 U)


title: normal bone marrow 30

description:
genomic DNA from bone marrow aspirates
NORMAL30


title: HUVEC simulated 4h with IL-6(100 U)

value: Passage 3

value: pooled from 7 individual

value: simulated 4h with IL-6(100 U)


title: patient15_OXFU_294

tag: age at operation

tag: menopause status

value: infiltrating ductal

tag: histological grade

tag: estrogen receptor status


title: HUVEC simulated 16h with IL-3(100 U)

value: simulated 16h with IL-3(100 U)


title: HUVEC simulated 48h with IL-3(100 U)

value: simulated 48h with IL-3(100 U)


title: normal bone marrow 29

description:
genomic DNA from bone marrow aspirates
NORMAL29

tag: cells

tag: who diagnosis

value: NORMAL


title: patient16_OXFU_316

value: primary breast cancer

value: pre

tag: histology

tag: tumor size

tag: genomic grade

tag: nodal status

tag: rfs status


title: normal bone marrow 32

description:
genomic DNA from bone marrow aspirates
NORMAL32


title: patient14_OXFU_281

tag: tissue

value: post


title: patient13_OXFU_247

tag: treatment


title: normal bone marrow 28

description:
genomic DNA from bone marrow aspirates
NORMAL28


title: normal bone marrow 27

description:
genomic DNA from bone marrow aspirates
NORMAL27


title: patient12_OXFU_245


title: patient11_OXFU_220


title: HUVEC simulated 4h with IL-3(100 U)

tag: cell type

value: simulated 4h with IL-3(100 U)


title: normal bone marrow 26

description:
genomic DNA from bone marrow aspirates
NORMAL26


title: normal bone marrow 25

description:
genomic DNA from bone marrow aspirates
NORMAL25


title: HUVEC simulated 8h with IL-3(100 U)

tag: cell culture

value: simulated 8h with IL-3(100 U)


title: normal bone marrow 24

description:
genomic DNA from bone marrow aspirates
NORMAL24


title: HUVEC simulated 8h with IL-1beta(100 U)

tag: pooling

value: simulated 8h with IL-1beta(100 U)


title: normal bone marrow 23

description:
genomic DNA from bone marrow aspirates
NORMAL23


title: patient10_OXFU_181


title: HUVEC simulated 16h with % 0.01 BSA

tag: treatment group

value: simulated 16h with % 0.01 BSA


title: normal bone marrow 22

description:
genomic DNA from bone marrow aspirates
NORMAL22

value: bone marrow aspirates


title: HUVEC simulated 48h with % 0.01 BSA

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: simulated 48h with % 0.01 BSA


title: normal bone marrow 21

description:
genomic DNA from bone marrow aspirates
NORMAL21


title: patient8_OXFU_150

tag: age at operation


title: patient7_OXFU_145

tag: menopause status


title: HUVEC simulated 8h with % 0.01 BSA

value: Passage 3

value: simulated 8h with % 0.01 BSA


title: HUVEC simulated 16h with IL-1beta(100 U)

value: pooled from 7 individual

value: simulated 16h with IL-1beta(100 U)


title: patient6_OXFU_138

value: infiltrating ductal

tag: histological grade


title: patient9_OXFU_162

tag: estrogen receptor status


title: normal bone marrow 20

description:
genomic DNA from bone marrow aspirates
NORMAL20

tag: cells


title: T. virens after contact

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

description: Trichoderma virens during overgrowth with a potential prey (the plant pathogen Rhizoctonia solani)

hyb_protocol: 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scaning.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner and the TIFF images extracted using the Agilent Feature Extraction software (version 10.5.1.1) using the 20 bit coding ability.

data_processing: Data pretreatment was applied on each result file to discard flagged spots by Feature Extraction software. The data were normalised without background subtraction by the global Lowess method performed with the Goulphar software (Lemoine, 2006).

organism: Trichoderma virens

source_name: Total RNA extracted from T virens after contact with Rhizoctonia solani

label_protocol: 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy5.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.

extract_protocol: Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).

treatment_protocol: For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm.

tag: condition

value: after contact with Rhizoctonia solani

source_name: Total RNA extracted from T virens control

treatment_protocol: As control T. virens was confronted with itself and harvested at contact.

value: Control


title: patient5_OXFU_127

value: primary breast cancer

tag: histology


title: HUVEC simulated 4h with IL-1beta(100 U)

description: Gene expression data from interlekin stimulated HUVEC vs. BSA control stimulation in time course

value: simulated 4h with IL-1beta(100 U)


title: patient4_OXFU_104

description: MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.

value: post

value: mixed

tag: tumor size


title: MS patient 12, technical replicate 2

city: Cambridge

first: Anu

last: Kemppinen

address: Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: University of Cambridge

description: Gene expression data from MS patients

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array for 16 hours at 45°C and 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 GC-RMA normalized and analyzed with GeneSpring 7.3 GX (Agilent Technologies, CA, US). After normalization and data filtering MS_11_REPL2 and MS_12_REPL2 were excluded from analysis.

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Peripheral blood mononuclear cells were isolated from whole blood using BD Vacutainer® CPT™ Cell Preparation Tubes (Becton, Dickinson and Company, NJ, USA) according to the manufacturer's recommendations. Cells were homogenized in TRIzol® (Invitrogen, CA, US) and samples were stored in -80°C until RNA isolation.

value: peripheral blood mononuclear

tag: disease state

value: multiple sclerosis


title: normal bone marrow 19

description:
genomic DNA from bone marrow aspirates
NORMAL19

tag: who diagnosis

value: NORMAL


title: normal bone marrow 18

description:
genomic DNA from bone marrow aspirates
NORMAL18

value: bone marrow aspirates


title: MS patient 12, technical replicate 1

description: Gene expression data from MS patients


title: T. virens after contact - dye switch

description: Trichoderma virens during overgrowth with a potential prey (the plant pathogen Rhizoctonia solani) dye switch


title: patient3_OXFU_90

value: infiltrating lobular

tag: genomic grade

tag: nodal status

tag: rfs status


title: patient1_OXFU_37

tag: tissue

tag: treatment

value: pre


title: patient2_OXFU_88


title: normal bone marrow 17

description:
genomic DNA from bone marrow aspirates
NORMAL17


title: normal bone marrow 16

description:
genomic DNA from bone marrow aspirates
NORMAL16


title: normal bone marrow 13

description:
genomic DNA from bone marrow aspirates
NORMAL13


title: normal bone marrow 15

description:
genomic DNA from bone marrow aspirates
NORMAL15


title: T. virens during contact

description: Trichoderma virens during first physical contact with a potential prey (the plant pathogen Rhizoctonia solani)

source_name: Total RNA extracted from T virens during contact with Rhizoctonia solani

treatment_protocol: For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were at contact of the mycelia of the host fungus Rhizoctonia solani.

value: during contact with Rhizoctonia solani


title: normal bone marrow 12

description:
genomic DNA from bone marrow aspirates
NORMAL12


title: normal bone marrow 14

description:
genomic DNA from bone marrow aspirates
NORMAL14


title: normal bone marrow 10

description:
genomic DNA from bone marrow aspirates
NORMAL10


title: normal bone marrow 9

description:
genomic DNA from bone marrow aspirates
NORMAL9


title: normal bone marrow 11

description:
genomic DNA from bone marrow aspirates
NORMAL11


title: HUVEC simulated 4h with % 0.01 BSA

tag: cell type

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: cell culture

value: Passage 3

tag: pooling

value: simulated 4h with % 0.01 BSA


title: normal bone marrow 8

description:
genomic DNA from bone marrow aspirates
NORMAL8


title: Bmpr2-Delx4 2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)

data_processing: Data was normalized (RMA) using Expression Console

source_name: PMVEC isolated from mice carrying TetO7-Bmpr2-delx4, immortomouse and Rosa26-rtTA transgenes

growth_protocol: Normoxic PMVEC, approximately 50% confluent in 10% serum

extract_protocol: RNA was extracted from freshly cultured PMVEC using a Qiagen RNEasy kit

treatment_protocol: Full serum, not confluent

tag: strain

value: FVB/N

tag: genotype/variation

value: Bmpr2-delx4+ mutation

value: pulmonary vascular microendothelial cells (PMVEC)


title: MS patient 11, technical replicate 2

description: Gene expression data from MS patients


title: Bmpr2-R899X 2

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)

source_name: PMVEC isolated from mice carrying TetO7-Bmpr2-R899X, immortomouse and Rosa26-rtTA transgenes

value: Bmpr2-R899X mutation


title: MS patient 10

description: Gene expression data from MS patients


title: MS patient 5

description: Gene expression data from MS patients


title: MS patient 7

description: Gene expression data from MS patients


title: MS patient 9

description: Gene expression data from MS patients


title: MS patient 6

description: Gene expression data from MS patients


title: normal bone marrow 7

description:
genomic DNA from bone marrow aspirates
NORMAL7


title: Control 2

source_name: PMVEC isolated from mice carrying immortomouse and Rosa26-rtTA transgenes

label_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)

value: Wild-type


title: Hippocampi Naive replicate 3

city: Girona

first: Gemma

last: Huguet

address: Campus de Montilivi

institute: Universitat de Girona

description: Biological replicate 3 of 4. Hippocampi of naive rats versus brain tissue pool of reference.

hyb_protocol: After fragmentation, 825 ng of labeled cRNA from each of the two samples were co-hybridized in in situ hybridization buffer (Agilent) for 17 h at 65ºC and washed at rt 1 min in 6X SSPE (Saline Sodium Phosphate-EDTA) pH 7.4 + 0.005% Sarcosine, 1 min at rt in Gene Expression WashBuffer 1 (GE WB1 - Agilent), 1 min at 37 ºC with GE WB2 (Agilent).

scan_protocol: Scanned on an Agilent G2565AA scanner. Quantified using GenePix 6.0 (Molecular Devices-MDS Analytical Technologies, Silicon Valley, CA). The  quality  of  each  individual  hybridization  was  assessed  with  the  Feature  Extraction  software 10.5  (Agilent).

data_processing: Raw  data  was  corrected  for  background  noise  using  the  normexp method.  Global  Lowess  normalization  was  applied  (intra-chip  normalization).  Scaling of the normalized log2 ratios (inter-chip  normalization)  was applied to assure  comparability  across  samples.

source_name: Hippocampi of naive rats

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy5-CTP or Cy3-CTP using the Low Input RNA labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Tissues were conserved in RNA later (Ambion, Austin, TX) for 48 h at 4ºC. Total RNAs were prepared with an RNeasy Lipid Tissue Mini kit according to manufacturer’s protocol (Quiagen, Valencia, CA)

treatment_protocol: Naive rats, handling process similar to stimulated animals.

value: naïve

tag: sample type

value: Male albino Wistar rats.

tag: gender

value: male

value: albino Wistar

tag: age

value: 12 weeks old.

value: Hippocampi dissected from slices between Bregma levels -2 and -4.

tag: pool

value: Pooled  from three rats.

source_name: Brain tissue of reference

value: Brain pooled tissue consisting of hippocampal, thalamic and cortical brain tissue.

value: Pooling:naive (n=4), sham-operated (n=5) and stimulated (n=4) rats


title: MS patient 3

description: Gene expression data from MS patients

value: peripheral blood mononuclear

value: multiple sclerosis


title: MS patient 2

description: Gene expression data from MS patients


title: Bmpr2-R899X 1


title: normal bone marrow 6

description:
genomic DNA from bone marrow aspirates
NORMAL6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Cancer Panel 1 Methylation Microarray using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

extract_protocol: genomic DNA was extracted and purified from bone marrow aspirates samples using Qiagen DNeasy Kit according to standard instructions

tag: cells

value: bone marrow aspirates

value: NORMAL


title: normal bone marrow 5

description:
genomic DNA from bone marrow aspirates
NORMAL5


title: MS patient 11, technical replicate 1

description: Gene expression data from MS patients

tag: disease state


title: Hippocampi Naive replicate 2

description: Biological replicate 2 of 4. Hippocampi of naive rats versus brain tissue pool of reference.


title: Control 15

description: Gene expression data from controls representing the general population.

value: healthy


title: Control 14


title: MS patient 4

description: Gene expression data from MS patients


title: MS patient 1

description: Gene expression data from MS patients


title: normal bone marrow 4

description:
genomic DNA from bone marrow aspirates
NORMAL4

tag: who diagnosis


title: Control 13


title: Hippocampi Naive replicate 1

description: Biological replicate 1 of 4. Hippocampi of naive rats versus brain tissue pool of reference.


title: PTEN+/- ep_A

city: Vienna

first: Andreas

last: Birbach

address: Schwarzspanierstrasse 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University of Vienna

description:
1036
Gene expression data from PTEN+/- (ep) lateral prostate.

hyb_protocol: According to standard Affymetrix protocol.

data_processing: RMA analysis using Affymetrix Expression Console 1.1.

source_name: lateral prostate, PTEN+/- epithelium, 12 months

extract_protocol: Lateral prostates were dissected from euthanized mice at 12 months of age by use of a stereomicroscope and placed in RNAlater solution. Tissues were homogenized using a Polytron homogenizer. Total RNA was extrected using RNeasy (QIAGEN).

tag: genotype

value: PTEN+/- (epithelium)

value: 12 months

value: lateral prostate


title: T. virens during contact - dye switch

description: Trichoderma virens during first physical contact with a potential prey (the plant pathogen Rhizoctonia solani) dye switch

tag: condition

value: Control

value: during contact with Rhizoctonia solani


title: MS patient 8

description: Gene expression data from MS patients


title: PTEN+/-IKK2ca/ca ep_C

description:
1020
Gene expression data from PTEN+/- IKK2ca/ca (ep) lateral prostate.

scan_protocol: According to standard Affymetrix protocol.

source_name: lateral prostate, PTEN+/- IKK2ca/ca epithelium, 12 months

value: PTEN+/- IKK2ca/ca (epithelium)


title: T. virens before contact - dye switch

description: Trichoderma virens before confrontation with a potential prey (the plant pathogen Rhizoctonia solani) dye switch

source_name: Total RNA extracted from T virens before contact with Rhizoctonia solani

treatment_protocol: For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart the host fungus Rhizoctonia solani.

value: before contact with Rhizoctonia solani


title: T. virens before contact

description: Trichoderma virens before confrontation with a potential prey (the plant pathogen Rhizoctonia solani)


title: PTEN+/- ep_C

description:
1121
Gene expression data from PTEN+/- (ep) lateral prostate.

label_protocol: According to standard Affymetrix protocol.


title: Hippocampi Sham replicate 4

description: Biological replicate 4 of 4. Hippocampi of sham rats versus brain tissue pool of reference.

source_name: Hippocampi of sham rats

treatment_protocol: Rats with electrode placement but without stimulation, handling process similar to stimulated animals

value: sham

value: Male albino Wistar rats.

value: male

value: albino Wistar

value: 12 weeks old.


title: Control 12

value: peripheral blood mononuclear


title: Control 1

value: FVB/N

value: Wild-type

value: pulmonary vascular microendothelial cells (PMVEC)


title: normal bone marrow 1

description:
genomic DNA from bone marrow aspirates
NORMAL1

source_name: normal bone marrow aspirates

label_protocol: Standard Illumina Protocol

value: bone marrow aspirates

value: NORMAL


title: normal bone marrow 2

description:
genomic DNA from bone marrow aspirates
NORMAL2


title: cord blood isolated CD34+ cells 9

description:
genomic DNA from isolated CD34+ cells
NCD34_9

source_name: cord blood isolated CD34+ cells

value: cord blood isolated CD34+ cells


title: PTEN+/-IKK2ca/ca ep_B

description:
928
Gene expression data from PTEN+/- IKK2ca/ca (ep) lateral prostate.

value: 12 months

value: lateral prostate


title: MOLM-14 DZNep, biological rep2

city: Singapore

first: Jianbiao

last: Zhou

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description: MOLM-14 cells were treated with DZNep

hyb_protocol: Biotinylated samples were hybridized onto the array for 16hrs and 60rpm in a GeneChip Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G

data_processing: The data were analyzed with Genespring GX. Raw signals were converted to expression value using RMA algorithm.

source_name: MOLM-14 DZNep treated

label_protocol: 200ng of total RNA were amplified and labeled using Affymetrix Whoe Transcript Sense Target Labeling and control reagents kit (Affymetrix)

extract_protocol: miRNeasy Kit (Qiagen)

treatment_protocol: DMSO or DZNep

tag: cell line

tag: disease type

value: acute myeloid leukemia (AML)


title: PTEN+/-IKK2ca/ca ep_A

description:
986
Gene expression data from PTEN+/- IKK2ca/ca (ep) lateral prostate.

value: PTEN+/- IKK2ca/ca (epithelium)

tag: tissue


title: Control 11

tag: cell type

value: healthy


title: Hippocampi Sham replicate 3

description: Biological replicate 3 of 4. Hippocampi of sham rats versus brain tissue pool of reference.

tag: treatment

value: sham

value: Hippocampi dissected from slices between Bregma levels -2 and -4.

value: Pooled  from three rats.

value: Brain pooled tissue consisting of hippocampal, thalamic and cortical brain tissue.

value: Pooling:naive (n=4), sham-operated (n=5) and stimulated (n=4) rats


title: 8069-TCDD 48 h

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

hyb_protocol: Labeled RNA was mixed with 33 hybridization buffer (Ambion), heated to 95 C for 3 min, and incubated with the miRdicator array for 12–16 hr

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner Bundle (Agilent Technologies, Santa Clara, CA) at a resolution of 10 mm at 100% power. Array images were analyzed using SpotReader software (Niles Scientific, Portola Valley, CA).

data_processing: Triplicate spots were combined to produce one signal for each probe by taking the logarithmic mean of reliable spots. All data were log-transformed (base 2) and the analysis was performed in log-space. A reference data vector for normalization R was calculated by taking the median expression level of a subset of all probes (all miRs in mirbase 10) across samples. For each sample data vector S, a 2nd degree polynomial F was found so as to provide the best fit between the sample data and the reference data, such that R≈F(S). For each probe in the sample (element Si in the vector S), the normalized value (in log-space) Mi was calculated from the initial value Si by transforming it with the polynomial function F, so that Mi=F(Si). P-values were calculated using a two-sided t-test on the log-transformed normalized fluorescence signal. The fold-difference (ratio of the median normalized fluorescence) was calculated for each microRNA.

source_name: HepG2 hepatocellular carcinoma cell line

label_protocol: Fifteen micrograms of total RNA was labeled by ligation of an RNAlinker p-rCrU-Cy-dye

growth_protocol: Cells were grown in MEM–Eagle (+Earl's BBS), w/NEAA and 10% FBS with additions of sodium bicarbonate and sodium pyruvate.

extract_protocol: EZ-RNA II kit from Biological Industries, Israel, was used for total RNA extraction from cell lines

treatment_protocol: Cells were treated with TCDD at 10nM concentration for 48h

value: TCDD

tag: time


title: Control 9

value: peripheral blood mononuclear


title: Control 7


title: MOLM-14 Control,  biological rep1

description: MOLM-14 cells were treated with DMSO as control.

source_name: MOLM-14 DMSO treated


title: Hippocampi Sham replicate 2

description: Biological replicate 2 of 4. Hippocampi of sham rats versus brain tissue pool of reference.

value: Male albino Wistar rats.

value: male

tag: strain

value: albino Wistar

value: 12 weeks old.


title: cord blood isolated CD34+ cells 8

city: Cleveland

first: Kwok Peng

last: Ng

address: 9500 Euclid Avenue

institute: Cleveland Clinic

description:
genomic DNA from isolated CD34+ cells
NCD34_8

value: cord blood isolated CD34+ cells

value: NORMAL


title: Hippocampi DBS replicate  3

description: Biological replicate 3 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.

source_name: Hippocampi of stimulated rats

treatment_protocol: Vetrolateral thalamus stimulation 1 hour daily during 14 days

value: deep brain stimulation


title: PTEN+/- ep_B

description:
1103
Gene expression data from PTEN+/- (ep) lateral prostate.

value: PTEN+/- (epithelium)

value: 12 months

value: lateral prostate


title: Control 8

description: Gene expression data from controls representing the general population.

source_name: peripheral blood mononuclear cells

value: healthy


title: neural stem cell line F3

city: Seoul

first: Soon-Tae

last: Lee

address: 28, Yeongon-dong, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Human Gene 1.0 ST arrays for 17 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix expression console software1.1 was used. Gene level expression were summarized from the corrected intensities and then quantile normalized.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: neural stem cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was isolated using Trizol (Invitrogen) according to the manufacturer's instructions.

value: neural stem cells


title: MOLM-14 DZNep, biological rep1

description: MOLM-14 cells were treated with DZNep

value: acute myeloid leukemia (AML)


title: Hippocampi DBS replicate  2

description: Biological replicate 2 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.

value: Hippocampi dissected from slices between Bregma levels -2 and -4.

value: Pooled  from three rats.

value: Brain pooled tissue consisting of hippocampal, thalamic and cortical brain tissue.


title: Hippocampi DBS replicate 4

description: Biological replicate 4 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.

value: Pooling:naive (n=4), sham-operated (n=5) and stimulated (n=4) rats


title: Control 10

value: peripheral blood mononuclear


title: fibroblast cultured in neurosphere culture condition (FB_con)

value: dermal fibroblasts


title: cord blood isolated CD34+ cells 5

description:
genomic DNA from isolated CD34+ cells
NCD34_5


title: 8071-control

value: HepG2 hepatocellular carcinoma cell line

value: control


title: Hippocampi Sham replicate 1

description: Biological replicate 1 of 4. Hippocampi of sham rats versus brain tissue pool of reference.

value: sham

value: Male albino Wistar rats.

value: male

value: albino Wistar

value: 12 weeks old.


title: Control 5


title: cord blood isolated CD34+ cells 4

description:
genomic DNA from isolated CD34+ cells
NCD34_4

value: cord blood isolated CD34+ cells

value: NORMAL


title: MOLM-14 Control, biological rep2


title: Control 6

value: healthy


title: induced neural stem cells (iNS)

source_name: induced neural stem cells

value: neural stem cells

value: iNS


title: cord blood isolated CD34+ cells 3

description:
genomic DNA from isolated CD34+ cells
NCD34_3


title: Control 4


title: fibroblast cultured in DMEM (FB)

source_name: fibroblast cultured in DMEM


title: Control 3


title: cord blood isolated CD34+ cells 2

description:
genomic DNA from isolated CD34+ cells
NCD34_2


title: Control 2


title: Bmpr2-Delx4 1

source_name: PMVEC isolated from mice carrying TetO7-Bmpr2-delx4, immortomouse and Rosa26-rtTA transgenes

value: FVB/N

tag: genotype/variation

value: Bmpr2-delx4+ mutation

value: pulmonary vascular microendothelial cells (PMVEC)


title: Control 1

value: peripheral blood mononuclear


title: cord blood isolated CD34+ cells 1

description:
genomic DNA from isolated CD34+ cells
NCD34_1


title: spf_vs_Control_repl2

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

description: Biological replicate 2 of 3

hyb_protocol: Samples were hybridised to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 0.1×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software

data_processing: The quantified signals were background corrected with offset value 10 and normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithmThe expression data were analysed using the LIMMA framework in Bioconductor (http://www.bioconductor.org) with R v2.11 and LIMMA v3,2.1.

organism: Aliivibrio salmonicida LFI1238

source_name: Aliivibrio salmonicida LFI1238 spf mutant K01

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

value: spf mutant

tag: growth condition

value: with glucose

source_name: Aliivibrio salmonicida LFI1238

value: wild type control


title: spf_vs_Control_repl3

description: Biological replicate 3 of 3 Dye swap


title: Hippocampi DBS replicate 1

description: Biological replicate 1 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.

value: deep brain stimulation

tag: sample type

tag: gender

value: Hippocampi dissected from slices between Bregma levels -2 and -4.

value: Pooled  from three rats.

source_name: Brain tissue of reference

value: Brain pooled tissue consisting of hippocampal, thalamic and cortical brain tissue.

value: Pooling:naive (n=4), sham-operated (n=5) and stimulated (n=4) rats


title: PBMCs_Control_14

city: Lisbon

first: Sofia

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: scan date 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix 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 GeneChip scanner 3000 – 7G.

data_processing: Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.

label_protocol: Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.

tag: affected status

value: control

value: male

tag: age at examination

tag: geographical origin

value: Lisbon

tag: immunosuppressors

value: no


title: HEK293T_miR-neg_FSK4hr_rep2

city: Philadelphia

first: Anthony

middle: O

last: Olarerin-George

state: PA

address: 835 BRB II/III, 421 Curie Blvd

department: Pharmacology

institute: University of Pennsylvania

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: RMA normalized expression values calculated with Affymetrix Expression console

source_name: HEK 293T Human embryonic kidney cells

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1X PSG.

extract_protocol: Total RNA (including small RNAs) was extracted using Trizol (Invitrogen) and the aqueous phase was purified with RNeasy Mini kit (Qiagen) according to the manufacturers’ protocols.

treatment_protocol: Cells were reverse transfected with RNA using Lipofectamine2000 at a final concentration of 50 nM.  Approximately 72hrs post-transfection, cells were treated with 15uM forskolin for 0, 1 or 4 hrs.

tag: transfected rna

value: negative control

tag: agent

value: FSK


title: HEK293T_miR-381_FSK1hr_rep2

tag: cell line


title: spf_vs_Control_repl1

description: Biological replicate 1 of 3


title: HEK293T_miR-132_FSK4hr_rep2


title: PBMCs_Control_13

description: scan date 2

value: Guarda


title: HEK293T_miR-381_FSK4hr_rep2


title: cord blood isolated CD34+ cells 7

description:
genomic DNA from isolated CD34+ cells
NCD34_7

tag: cells

value: cord blood isolated CD34+ cells

tag: who diagnosis

value: NORMAL


title: normal bone marrow 3

description:
genomic DNA from bone marrow aspirates
NORMAL3

value: bone marrow aspirates


title: HEK293T_miR-132_FSK1hr_rep2


title: HEK293T_miR-neg_FSK1hr_rep2


title: HEK293T_miR-132_FSK0hr_rep2

value: untreated


title: Trichoderma reesei during first physical contact with the plant pathogen Rhizoctonia solani

organism: Trichoderma reesei

source_name: Total RNA extracted from T reesei during contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. reesei was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were at contact of the mycelia of the host fungus Rhizoctonia solani.

tag: condition

value: during contact with Rhizoctonia solani

source_name: Total RNA extracted from T reesei control.

treatment_protocol: As control T. reesei was confronted with itself and harvested at contact.

value: Control


title: PBMCs_Control_11

description: scan date 3

value: Aveiro


title: PBMCs_Control_12

description: scan date 3


title: Glioma_PDGFRa+_tumor_NSC-Cre-1

first: Roel

last: Verhaak

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: The tumor sample was dissociated and the PDGFRa+ glioma tumor cells were enriched by immunopanning method and the total RNA was extracted for microarray analysis. Total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex. However, in this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals.

hyb_protocol: The hybridization was followed by the  “Two-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacture (Agilent).

scan_protocol: The images were scanned by a GenePix 4000B scanner and the intensity values were extracted by using the Agilent Feature Extraction Software.

data_processing: After scanning the images by using a GenePix 4000B scanner, the intensity values were extracted by using the Agilent Feature Extraction Software. In this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals. Probe sequences were downloaded from the Agilent website and aligned to a transcript sequence database consisting of 49,040 Mus musculus genes from Ensembl57. After removing probes that did not align, or aligned with more than 5 mismatches (n=19,194), or probes that aligned to multiple genes (n=2,283), 23,006 probes representing 17,585 genes remained. Expression profiles were quantile normalized and log transformed. Expression values for genes represented by multiple probes were collapsed by taking the mean value of the set of probes.

source_name: Non-purified secondary glioma sample, induced by NSC-Cre

label_protocol: Total RNA from all samples were labeled with either Cy3 or Cy5 following the “Two-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacture (Agilent).

growth_protocol: All samples were from fresh tumor tissue.

extract_protocol: Tumor tissue or purified cells were homogenized into 50 ul TRIZOL. Immediately add 450 ul TRIzol and incubate the homogenized samples for 5 minutes at 15 to 30°C. Freeze samples at -80°C until used for RNA extraction.  Thaw samples, immediately add 100 ul of chloroform. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 g for 15 minutes at 4°C.  Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL used for homogenization.  Remove aqueous phase (around 280 ul) and transfer to new 1.5 ml tube. Add 5 ug (1 ul) polyacrylamide to sample. Add 250 ul of isopropyl alcohol. Invert a few time to mix. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 °— g for 10 minutes at 4°C.  Remove the supernatant with a 1 ml pipet tip, leaving no more than around 10 ul at the bottom of the tube. Add 950 ul 75% ethanol (room temperature) to the RNA pellet. Mix the sample by inverting and centrifuge at 7,500 g for 5 minutes at 4°C.  Remove the supernatant with 1 ml pipet tip. Quick spin to collect all residual liquid at the bottom. Remove ALL the residual liquid with 20 ul pipet tip.  Dry the RNA pellet for 1-2 minutes and then pipet 6.5 ul RNase free water onto the pellet. Let sample stand for 2 minutes, then pipet gently to completely re-suspend pellet.  Measure RNA concentration using 2.0 ul sample on Nanodrop.

treatment_protocol: Tumor tissue isolation. All dissection tools were sterilized by soaking in Cidex (Allegromedical, Cat 189980) for 10 minutes and then rinsed with autoclaved distilled water prior to dissection. The tools were kept in 70% ethanol between usages. Tumor-carrying mice were euthanized by cervical dislocation, sprayed down with 70% ethanol and then wiped with Betadine to remove loosed fur. The head was cut off with a pair of large dissection scissors and then soaked in 70% ethanol for 45 seconds to 1 minute. The skin down the midline of the head was sliced through with a razor blade. The skull was cut open using a pair of small dissection scissors. Brain tissue was then lift from the skull and washed once with sterilized cold PBS before being embedded into chilled but still liquid 4% low-melting temperature agarose (prepared in 1X PBS) on ice. After the agarose became solid, the brain was sliced into 1mm thick coronal sections and kept in cold SMEM (Invitrogen, #11380) in a Petri Dish on ice. Under a fluorescence dissection scope, tumors were easily identified because of their strong fluorescence. The tumor region was dissected out with a 22.5o straight microsurgical knife (Sharpoint, #72-2201) and then either immediately lyzed in TRYZOL for RNA extraction or further used for purification of OPC-like tumor cells (see below). Adjacent brain slices containing some tumor tissue were preserved in 4% PFA immediately after dissection. These slices were sent for immunohistochemistry and H&E staining for tumor pathology.    OPC-like glioma cells were purified as following:  Purification of OPC-like tumor cells from fresh glioma samples T1, T2 and T3 was performed according to the PDGFRa immunopanning methods previously described for normal OPC cell purification (B. A. Barres et al., Cell 70, 31 (1992); J. D. Cahoy et al., J Neurosci 28, 264 (2008)) with minor modification.     Panning plates preparation        BSL-1 plates: Two Petri dishes (100 x 10 mm, BD Biosciences-Falcon 351058) were incubated with BSL-1 solution (Vector Laboratories, Burlingame, CA, L-1100, 25?g BSL-1 in 10ml DPBS for each plate). The solution was swirled carefully to ensure that each whole Petri dish was completely coated with solution prior to incubation overnight at 4 oC. The next morning, the BSL-1 solution was removed from the plates and 20ml 0.2% BSA (in DPBS) was added to block the plates at room temperature until panning (usually more than 4 hours).         PDGFR? immunopanning plates: Two Petri dishes (100 x 10 mm) were incubated with 10 ml each of a secondary antibody solution containing Tris buffer solution (50 mM pH8.5 Tris-Cl) and 75 µg (30?l) goat anti-rat IgG H+L chain (112-005-167) overnight at 4 oC. The next morning, the secondary antibody solution was removed and the plates were washed three times with 1X DPBS. Subsequently, a primary antibody solution containing 10?l Rat-anti-PDGFR? antibody (CD140a clone APA5, BD Biosciences-Pharmingen, 558774) in 10ml DPBS with 0.1% BSA was added to each plate. The plates were then incubated at room temperature until used. The plates were washed directly before immunopanning.          The whole procedure can be divided into two major parts: cell dissociation and immunopanning, with details described as follows.  Cell dissociation         The dissected tumor tissue was transferred to a 60 mm Petri dish containing 5ml Papain solution and diced into ~1 mm3 pieces. The papain solution includes 1X EBSS (Sigma E7510), 0.5mM EDTA (Sigma E7510), 10mM HEPES (Gibco 15630-080), 26mM NaHCO3 (Sigma S5761-500g, cell culture grade), 0.16mg/ml L-Cysteine (Sigma C-7477, 25g), 20Unit/ml Papain, 1mg/ml DNase (Sigma, DN-25) and was carefully balanced in 5% CO2 at 37oC for at least 30 minutes before use.        The tumor tissue was incubated in Papain solution at 37oC 5% CO2 for 90 minutes (gently agitated every 15 minutes). Afterwards it was transferred into a sterile 15ml Conical polystyrene tube (BD BioScience #352095) and allowed to settle to the bottom of the tube (We used 10ml serological pipette to transfer the tissue to avoid losing the cells at this step). The Papain solution was then pipetted off and 2ml Diluted trypsin inhibitor buffer was added. Diluted trypsin inhibitor includes 1X EBSS, 10mM HEPES, 26mM NaHCO3, 1mg/ml ovomucoid (Sigma T9253-1G), 1mg/ml BSA (Sigma A-9418) and was carefully balanced in 5% CO2 at 37oC for at least 30 minutes before use. After the tissue settled down (~2 minutes), the Diluted trypsin inhibitor buffer was replaced by 2ml fresh Diluted trypsin inhibitor buffer. The tissue was then triturated 8 times with a 5ml Pasteur pipette. After the tissue settled, 1ml of supernatant (containing dissociated cells) was carefully transferred to a new 15ml Conical polystyrene tube and set aside. 1ml fresh Diluted trypsin inhibitor buffer was added to the original tissue, and the trituration procedure was repeated. After the tissue settled, 1ml of supernatant was removed and combined with the other set aside supernatant.  The trituration was repeated until all the Diluted trypsin inhibitor buffer was used (10ml total). The last two rounds of trituration were performed with a 1ml pipette tip to ensure all the visible tissue chunks were fully dissociated into single cells.         Once the tissue was dissociated, 4ml Standard Trypsin inhibitor solution (10mg/ml BSA in Diluted Tripsin inhibitor buffer) was placed in a new 15ml Conical polystyrene tube. Dissociated cell suspension was carefully layered on top of Standard Trypsin inhibitor solution. The layered solution was centrifuged at 220g for 15 minutes followed by immediate removal of the supernatant. Cells were re-suspended in 6ml Panning solution (0.02% BSA, 1mg/ml DNase in 1X DPBS, Invitrogen 14040-182) using a 5ml pipette and centrifuged at 220g for 10 minutes. Cells were re-suspended in 12 ml Panning buffer and passed through a 70?m cell strainer (Fisher 08-771-23) before performing immunopanning.  Immunopanning          The first BSL-1 coated plate was washed 2X with PBS and 1X with DPBS. 100?l of single cell suspension was set aside for cell number counting and cell culture. The remaining cell suspension was poured onto the first BSL-1 plate and incubated at room temperature for 15 minutes. During that incubation time, we counted the living cell number using the Trypan Blue Method and a hemacytometer. The second BSL-1 coated plate was washed 2X with PBS and 1X with DPBS before the supernatant from the first plate was transferred to it.             During the second BSL-1 panning plate, one primary antibody coated plate was washed 3X with 20ml DPBS. The supernatant from the second BSL-1 plate was transferred to the washed primary antibody plate and incubated for 45min. The plate was swirled very gently every 15 min. During the first primary antibody panning plate, the second primary antibody coated plate was washed 3X with 20ml DPBS to deplete the remaining OPC-like tumor cells (Used to collect tumor cells not presenting PDGFR? antigen). During the second primary antibody panning plate, the first primary antibody panning plate was washed 6-8 times with DPBS to remove the non-binding cells. At the end of the last wash the plate was checked under the microscope to visualize floating cells. Additional washes were performed until there were almost zero and certainly less than 5% floating cells.         Cells were collected by incubating the first primary antibody panning plate with 2ml pre-balanced TrypLE (Invitrogen 12605-010) in 5% CO2 at 37oC for 7 minutes. The reaction was then stopped by adding 2ml trypsin inhibitor solution (2mg/ml Ovomucoid, 0.4% BSA in 1X DPBS). Tumor cells were dislodged from the plate surface by squirting with a 1 ml pipette tip. We collected the cells and also the supernatant from the second primary antibody plate and transferred them separately to new 15ml conical polystyrene tubes which were pre-coated with 0.4% BSA at 37C for 1 hour to prevent adherence of cells to the tubes. After centrifuged at 220g for 10min, the cells were washed one time with NSC medium (see cell culture section for recipes) before re-suspension in the same medium for further use (RNA extraction or allografting).

tag: age

value: 5 months

tag: genotype

value: MADM, p53-/-, NF1-/-, hGFAP-Cre

tag: tissue

value: Non-purified secondary glioma, induced by NSC-Cre

tag: purification

value: Immunopanned

tag: tumor type

value: Primary

tag: genetic background

value: mixed, significant portion CD1 outbred

source_name: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex

tag: sample age

value: brain neocortex

value: wild type


title: Glioma_PDGFRa+_tumor_NSC-Cre-2

value: 3.5 months

value: MADM, p53-/-, NF1-/-, Nestin-Cre

tag: sample type

value: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex


title: PBMCs_Control_9

description: scan date 4

tag: affected status

value: control

tag: gender

value: male

tag: age at examination

value: no


title: PBMCs_Control_10

description: scan date 4

tag: geographical origin

tag: immunosuppressors