title: A_251

value: Severe asthma, non-smoking


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_1_2

status: Public on Dec 09 2016

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: total RNA

organism: Homo sapiens

source_name: Primary solid_tumor

tag: diseasestate

value: Untreated primary (de novo) GBM

tag: organismpart

value: Brain

tag: Sex

value: Male

tag: age

tag: clinical diagnosis

value: GBM

tag: individual

tag: pathologic status

value: MALIGNANT

tag: tissue anatomic site

value: TEMPORAL LOBE

tag: histologic diagnosis

value: GLIOBLASTOMA MULTIFORME


title: topal-00039: US82800149_251643612343_S01_miRNA_105_Dec08_2_1

scan_protocol: See mage-tab files linked to series entry for additional details


title: topal-00039: US82800149_251643612365_S01_miRNA_105_Dec08_2_3

data_processing: See mage-tab files linked to series entry for additional details

value: NOT SPECIFIED


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_1_4

label_protocol: See mage-tab files linked to series entry for additional details

value: PARIETAL LOBE


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_1_2

extract_protocol: See mage-tab files linked to series entry for additional details

value: Female


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643610877_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_1_3

value: Treated primary GBM


title: topal-00039: US82800149_251643612350_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_1_2


title: A_220

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Standard procedure for Affymetrix® GeneTitan™ running Affymetrix GeneChip® Command Console 2.0.

data_processing: Scans were imported into ArrayStudio V8.0 and pre-processed using the default RMA pipeline

label: biotin

source_name: Blood

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: RNA was extracted from blood collected in PAXgene tubes using the PAXgene blood miRNA kit

tag: cohort

tag: gender

value: male

tag: race

tag: tissue

value: blood


title: topal-00039: US82800149_251643612334_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_1_1

value: OVERLAPPING LESION OF BRAIN


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612362_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_2_1

value: FRONTAL LOBE


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612355_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643610883_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643610873_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612340_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_1_2

source_name: Solid normal_tissue


title: topal-00039: US82800149_251643612359_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612334_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US82800149_251643612353_S01_miRNA_105_Dec08_1_2


title: MDA_231_IMPI

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

country: China

institute: Shantou University Medical College

description: LncRNA expression profiles of IMP1-expression MDA231 cells

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization  Kit  (Cat#5188‐5242,  Agilent  technologies,  Santa  Clara,  CA,  US)  in Hybridization  Oven  (Cat#G2545A,  Agilent  technologies,  Santa  Clara,  CA,  US), according  to  the  manufacturer’s  instructions.  The experiment was performed by the ' Shanghai Biotechnology Corporation ' in Shanghai, China.

scan_protocol: Slides  were  scanned  by  Agilent  Microarray  Scanner  (Cat#G2565CA,  Agilent technologies,  Santa  Clara,  CA, US) with  default  settings, Dye  channel: Green,  Scan resolution=3μm,  20bit.

data_processing: Data were  extracted with  Feature  Extraction  software  10.7 (Agilent  technologies,  Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).  The analysis was performed in the Shanghai Biotechnology Corporation in Shanghai, China.

label_protocol: Total  RNA  was  amplified  and  labeled  by  Low  Input  Quick  Amp  Labeling  Kit, One‐Color  (Cat#5190‐2305, Agilent  technologies, Santa  Clara,  CA, US),  following  the manufacturer’s  instructions.  Cy3-Labeled  cRNA  were  purified  by  RNeasy  mini  kit (Cat#74106, QIAGEN, GmBH, Germany).  Labeling was performed by the  Shanghai Biotechnology Corporation in Shanghai, China.

growth_protocol: Cells were cultured in cultured DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol: Total RNA from cultured cells was extracted using RNAsimple Total RNA Kit（Tiangen, Beijing，China) according to the manufacturer's instructions.

tag: cell line

value: MDA231 (parental)

tag: cell type

value: breast cancer cells

tag: genotype/variation


title: MDA_231_GFP

description: LncRNA expression profiles of IMP1-nonexpression MDA231 cells


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_2_1

value: Untreated primary (de novo) GBM


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_1_1

value: Brain


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_2_3

value: Male


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_1_2

value: GBM


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612230_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612355_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_2_2

value: MALIGNANT


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_2_2

value: TEMPORAL LOBE


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_1_4

value: GLIOBLASTOMA MULTIFORME


title: topal-00039: US82800149_251643612359_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_1_4

value: GLIOMA MIXED


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_1_2

value: PARIETAL LOBE


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_1_1

value: Female


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_2_2

value: NOT SPECIFIED


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612356_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612340_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643610865_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610863_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643610873_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612356_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_1_4

value: OCCIPITAL LOBE


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_2_4


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_1_4


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610868_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612350_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612356_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610870_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610870_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612347_S01_miRNA_105_Dec08_1_1

value: Treated primary GBM


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612365_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_2_3


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643610867_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643612234_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US45102955_251643610865_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612334_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610866_S01_miRNA-v1_95_May07_2_1

value: OVERLAPPING LESION OF BRAIN


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_2_1

value: FRONTAL LOBE


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612347_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_2_3


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610871_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610870_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612352_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612362_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643610875_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610883_S01_miRNA-v1_95_May07_1_2

value: CEREBRUM


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610876_S01_miRNA-v1_95_May07_1_2

value: GLIOBLASTOMA


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_1_3

value: Untreated primary (de novo) GBM


title: topal-00039: US45102955_251643610875_S01_miRNA-v1_95_May07_1_2

value: Brain


title: topal-00039: US45102955_251643610877_S01_miRNA-v1_95_May07_1_2

value: Male


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_1_1

value: GBM


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_1_2

value: MALIGNANT


title: topal-00039: US45102955_251643610876_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610877_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612366_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643610866_S01_miRNA-v1_95_May07_1_3

value: TEMPORAL LOBE


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610876_S01_miRNA-v1_95_May07_1_4

value: GLIOBLASTOMA MULTIFORME


title: topal-00039: US45102955_251643610865_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610868_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643610864_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643611185_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612343_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612352_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612366_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US45102955_251643610873_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610868_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612353_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US82800149_251643612334_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643610871_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643610864_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612234_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643611185_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643610865_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612353_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643611184_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610865_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611184_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612365_S01_miRNA_105_Dec08_2_2


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_1_1

value: ANAPLASTIC ASTROCYTOMA


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610864_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612380_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_2_2

value: PARIETAL LOBE


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610875_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_2_3

value: Female


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US45102955_251643610870_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612347_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643611181_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643611185_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612356_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610860_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_2_3

value: NOT SPECIFIED


title: topal-00039: US82800149_251643612352_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612365_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612334_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612359_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610875_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610860_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643612037_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612230_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612365_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643610883_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_2_3


title: topal-00039: US82800149_251643612340_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612336_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643611185_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612352_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612355_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612034_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_2_3

value: BRAIN, NOS


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643610883_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612346_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US45102955_251643610860_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_2_3


title: topal-00039: US14702406_251643612132_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_1_1


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_1_4


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612231_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643610864_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612350_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US45102955_251643612234_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610868_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643610867_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643610871_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612379_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610870_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612337_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612234_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612362_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_1_2


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612350_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_1_2

value: Untreated primary (De Nova) GBM


title: topal-00039: US82800149_251643612353_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610871_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610867_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612343_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612344_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_2_2

value: OVERLAPPING LESION OF BRAIN


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612363_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610863_S01_miRNA-v1_95_May07_1_3

value: FRONTAL LOBE


title: topal-00039: US45102955_251643612230_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_2_2


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612333_S01_miRNA-v1_10_Apr08_1_1


title: topal-00039: US82800149_251643612338_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_1_4


title: topal-00039: US45102955_251643611184_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612366_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612169_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612367_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612364_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US82800149_251643612357_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643611182_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610864_S01_miRNA-v1_95_May07_1_3

value: Treated primary GBM


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_2_1


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_2_3


title: topal-00039: US82800149_251643612353_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612349_S01_miRNA_105_Dec08_1_2


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643610860_S01_miRNA-v1_95_May07_2_1

value: OCCIPITAL LOBE


title: topal-00039: US82800149_251643612366_S01_miRNA_105_Dec08_1_2


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_1_2

value: Untreated primary (de novo) GBM


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_2_2

value: Brain


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_1_1

value: Male


title: topal-00039: US82800149_251643612369_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610859_S01_miRNA-v1_95_May07_1_2

value: GBM


title: topal-00039: US45102955_251643610876_S01_miRNA-v1_95_May07_1_1

value: MALIGNANT


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643610877_S01_miRNA-v1_95_May07_1_1

value: TEMPORAL LOBE


title: topal-00039: US82800149_251643612366_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643611184_S01_miRNA-v1_95_May07_1_3

value: GLIOBLASTOMA MULTIFORME


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612328_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US82800149_251643612347_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_2_1


title: topal-00039: US45102955_251643612135_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610862_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612036_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643610883_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612368_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612329_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US82800149_251643612371_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612038_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612358_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612168_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612035_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612345_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643610875_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612340_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612361_S01_miRNA_105_Dec08_2_1


title: topal-00039: US45102955_251643612130_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643612150_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US45102955_251643611184_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643610873_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US82800149_251643612343_S01_miRNA_105_Dec08_2_2


title: topal-00039: US82800149_251643612342_S01_miRNA_105_Dec08_1_3


title: topal-00039: US82800149_251643612344_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612225_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643611183_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612226_S01_miRNA-v1_95_May07_1_3


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_2_1


title: topal-00039: US82800149_251643612354_S01_miRNA_105_Dec08_1_4


title: topal-00039: US82800149_251643612351_S01_miRNA_105_Dec08_2_3


title: topal-00039: US45102955_251643612151_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612039_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US45102955_251643610861_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US82800149_251643612331_S01_miRNA-v1_10_Apr08_1_3


title: topal-00039: US45102955_251643612233_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612330_S01_miRNA-v1_10_Apr08_2_3


title: topal-00039: US45102955_251643612234_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643610867_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643610866_S01_miRNA-v1_95_May07_1_4


title: topal-00039: US45102955_251643612032_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612356_S01_miRNA_105_Dec08_1_1


title: topal-00039: US82800149_251643612370_S01_miRNA_105_Dec08_2_3


title: topal-00039: US82800149_251643612341_S01_miRNA_105_Dec08_1_3


title: topal-00039: US45102955_251643612033_S01_miRNA-v1_95_May07_2_3


title: topal-00039: US45102955_251643610863_S01_miRNA-v1_95_May07_2_2


title: topal-00039: US45102955_251643612129_S01_miRNA-v1_95_May07_1_2


title: topal-00039: US45102955_251643612128_S01_miRNA-v1_95_May07_1_1


title: topal-00039: US45102955_251643612227_S01_miRNA-v1_95_May07_1_1


title: Caucasian patient 9

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

description:
Gene expression data from benign prostate epithelium
EA_9

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with Affy and Oligo packages from Bioconductor

source_name: Laser capture microdissected prostate benign epithelium

label_protocol: Labeling followed the Encore Biotin Module protocol (NuGEN, USA)

extract_protocol:
[collection protocol] 10 micron sections of fresh frozen prostate were laser capture microdissected. Samples stored in lysis buffer at -80C until extraction
RNA extracted using RNAqueous-Micro kit (Ambion, USA) and used the RNAqueous -Micro Procedure for LCM protocol with DNase treatment. RNA was whole transcriptome amplified using Ovation PicoSL WTA System V2 (NuGEN, USA)

value: Prostate

tag: ancestry

value: European American


title: Caucasian patient 8

description:
Gene expression data from benign prostate epithelium
EA_8


title: Caucasian patient 5

description:
Gene expression data from benign prostate epithelium
EA_5


title: Caucasian patient 12

description:
Gene expression data from benign prostate epithelium
EA_12


title: African American patient 10

description:
Gene expression data from benign prostate epithelium
AA_10

value: African American


title: Caucasian patient 3

description:
Gene expression data from benign prostate epithelium
EA_3


title: Caucasian patient 4

description:
Gene expression data from benign prostate epithelium
EA_4


title: Caucasian patient 2

description:
Gene expression data from benign prostate epithelium
EA_2


title: African American patient 8

description:
Gene expression data from benign prostate epithelium
AA_8


title: Caucasian patient 13

description:
Gene expression data from benign prostate epithelium
EA_13


title: African American patient 9

description:
Gene expression data from benign prostate epithelium
AA_9


title: Caucasian patient 1

description:
Gene expression data from benign prostate epithelium
EA_1


title: Caucasian patient 6

description:
Gene expression data from benign prostate epithelium
EA_6


title: Caucasian patient 11

description:
Gene expression data from benign prostate epithelium
EA_11


title: African American patient 11

description:
Gene expression data from benign prostate epithelium
AA_11


title: African American patient 5

description:
Gene expression data from benign prostate epithelium
AA_5


title: African American patient 2

description:
Gene expression data from benign prostate epithelium
AA_2


title: Caucasian patient 7

description:
Gene expression data from benign prostate epithelium
EA_7


title: African American patient 4

description:
Gene expression data from benign prostate epithelium
AA_4


title: Caucasian patient 10

description:
Gene expression data from benign prostate epithelium
EA_10


title: African American patient 12

description:
Gene expression data from benign prostate epithelium
AA_12


title: African American patient 1

description:
Gene expression data from benign prostate epithelium
AA_1


title: African American patient 3

description:
Gene expression data from benign prostate epithelium
AA_3


title: African American patient 13

description:
Gene expression data from benign prostate epithelium
AA_13


title: CD4+cells_HealthyControl_Subject5

city: Chengdu

first: Ting

last: Wang

state: Sichuan

address: No. 37 Guo Xue Xiang

department: Respiratory and Critical Care Medicine

institute: West China Hospital, Sichuan University

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 5)

hyb_protocol: Cy3 labeled, linearly amplified complementary RNA was synthesized and hybridized to Sureprint G3 Human Gene Expression 8 x 60K (Agilent) microarrays according to manufacturer's protocol.

scan_protocol: Arrays were scanned using Agilent G2505C Microarray Scanner

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction v10.7.3.1 software with the protocol GE1_107_Sep09 and Grid 028004_D_F_20110325, to obtain spatially detrended signal intensities.

source_name: peripheral blood CD4+ T cells

label_protocol: Labeling was performed with Cy3 according to the manufacturer protocol for one color microarray based gene expression analysis (Agilent)

extract_protocol: Isolated CD4+ cells was frozen in Trizol for RNA extraction using chloroform purification and isopropanol extraction.

treatment_protocol: Venous blood samples were collected and lymphocyte were freshly isolated using Lymphoprep (Axis-Shield PoC AS, Oslo, Norway). Human CD4+ cells were isolated by means of immunomagnetic depletion with the human CD4+ T cell Isolation Kit II (Miltenyi Biotec, Rostock, Germany).

tag: diagnosis

value: Healthy Control

value: peripheral blood

value: female

tag: age (y)


title: CD4+cells_HealthyControl_Subject4

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 4)


title: African American patient 7

description:
Gene expression data from benign prostate epithelium
AA_7


title: CD4+cells_HealthyControl_Subject3

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 3)


title: African American patient 6

description:
Gene expression data from benign prostate epithelium
AA_6


title: CD4+cells_HealthyControl_Subject6

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 6)


title: CD4+cells_Depression_Subject6

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 6)

value: Depression


title: CD4+cells_Depression_Subject4

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 4)


title: CD4+cells_Depression_Subject1

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 1)


title: CD4+cells_DepressiveAsthma_Subject6

description: gene expression of peripheral blood CD4+ T cells in depression without asthma (subject 6)

value: Depressive Asthma


title: CD4+cells_HealthyControl_Subject1

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 1)


title: CD4+cells_Non-depressiveAsthma_Subject4

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 4)

value: Non-depressive Asthma


title: CD4+cells_DepressiveAsthma_Subject5

description: gene expression of peripheral blood CD4+ T cells in asthmatic with depression (subject 5)


title: CD4+cells_DepressiveAsthma_Subject2

description: gene expression of peripheral blood CD4+ T cells in asthmatic with depression (subject 2)


title: CD4+cells_HealthyControl_Subject2

description: gene expression of peripheral blood CD4+ T cells in healthy control (subject 2)


title: CD4+cells_Depression_Subject2

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 2)


title: CD4+cells_Depression_Subject3

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 3)


title: CD4+cells_Non-depressiveAsthma_Subject6

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 6)


title: CD4+cells_DepressiveAsthma_Subject4

description: gene expression of peripheral blood CD4+ T cells in asthmatic with depression (subject 4)


title: CD4+cells_Non-depressiveAsthma_Subject2

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 2)


title: CD4+cells_Non-depressiveAsthma_Subject5

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 5)


title: CD4+cells_DepressiveAsthma_Subject1

description: gene expression of peripheral blood CD4+ T cells in asthmatic with depression (subject 1)


title: CD4+cells_Non-depressiveAsthma_Subject1

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 1)


title: L47, human PDAC tissue

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

description: Gene expreesion data

hyb_protocol: Labeled RNA was hybridized to a Agilent human geneexpression microarray according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Agilent G2565CA manufacturer's instructions.

data_processing: Probe intensities were extracted using FeatureExtraction software (Agilent). Value definition Probe intensities were background corrected and normalized (quantile normalization) using the LIMMA package in R.

source_name: Tumor pancreatic tissue

label_protocol: Total RNA (100 ng)Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA of normal pancreatic specimens were purchased commercially. Trizol extraction of total RNA was performed on PDAC and adjacent benign specimens according to the manufacturer's instructions.

value: Pancreas

tag: disease state

value: PDAC


title: L46, human PDAC tissue

description: Gene expreesion data


title: L48, human PDAC tissue

description: Gene expreesion data


title: L50, human PDAC tissue

description: Gene expreesion data


title: CD4+cells_Depression_Subject5

description: gene expression of peripheral blood CD4+ T cells in depression patient (subject 5)


title: L45, human PDAC tissue

description: Gene expreesion data


title: L44, human PDAC tissue

description: Gene expreesion data


title: L49, human PDAC tissue

description: Gene expreesion data


title: whole lung_treated_8

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description:
9377360006_H
tissue

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: NEQC normalized implemented in beadarray package.

organism: Mus musculus

source_name: whole lung_treated

label_protocol: standard biotin Ambion labeling - Illumina

growth_protocol: Specific pathogen-free C57Bl/6 mice were purchased from Harlan Sprague-Dawley (Horst, the Netherlands) and housed in a controlled environemt on 12h/12h light/dark cycles.

extract_protocol: Rneasy kit procedures including DNAse digestion.

treatment_protocol: Mice were treated with broad-spectrum antibiotics (ampicillin1 g ml−1, Mediatech; neomycin sulfate 1 g ml−1, Calbiochem; metronidazole 1 g ml−1, Fluka; and vancomycin 0.5 g ml−1, Sigma) in drinking water for 3 weeks.

tag: strain

tag: treatment

value: antibiotic

value: whole lung


title: L43, human PDAC tissue

description: Gene expreesion data


title: L41, human PDAC tissue

description: Gene expreesion data


title: CD4+cells_Non-depressiveAsthma_Subject3

description: gene expression of peripheral blood CD4+ T cells in asthmatic without depression (subject 3)


title: whole lung_untreated_8

description:
9377360006_G
tissue

source_name: whole lung_untreated


title: alveolar macrophage_untreated_8

description:
9377360006_F
cell

source_name: alveolar macrophage_untreated

value: alveolar macrophage


title: L39, human PDAC tissue

description: Gene expreesion data


title: L38, human PDAC tissue

description: Gene expreesion data


title: whole lung_untreated_7

description:
9377360006_D
tissue


title: alveolar macrophage_treated_8

description:
9377360004_H
cell

source_name: alveolar macrophage_treated


title: alveolar macrophage_untreated_7

description:
9377360006_C
cell


title: whole lung_treated_6

description:
9377360006_B
tissue


title: whole lung_treated_7

description:
9377360006_E
tissue


title: L36, human PDAC tissue

description: Gene expreesion data


title: L40, human PDAC tissue

description: Gene expreesion data


title: L30, human PDAC tissue

description: Gene expreesion data


title: whole lung_untreated_6

description:
9377360004_D
tissue


title: L33, human PDAC tissue

description: Gene expreesion data


title: L35, human PDAC tissue

description: Gene expreesion data


title: whole lung_treated_5

description:
9377360006_A
tissue


title: L42, human PDAC tissue

description: Gene expreesion data


title: L32, human PDAC tissue

description: Gene expreesion data


title: alveolar macrophage_treated_6

description:
9377360004_B
cell


title: alveolar macrophage_treated_7

description:
9377360004_F
cell


title: whole lung_treated_4

description:
9377360004_G
tissue


title: alveolar macrophage_untreated_5

description:
9377360004_C
cell


title: alveolar macrophage_untreated_6

description:
9377360004_E
cell


title: L29, human PDAC tissue

description: Gene expreesion data


title: L31, human PDAC tissue

description: Gene expreesion data


title: alveolar macrophage_treated_5

description:
9377360004_A
cell


title: whole lung_untreated_5

description:
9377360001_G
tissue


title: L27, human PDAC tissue

description: Gene expreesion data


title: L25, human PDAC tissue

description: Gene expreesion data


title: alveolar macrophage_untreated_3

description:
9377360001_B
cell


title: L20, human benign pancreatic tissue

description: Gene expreesion data

source_name: Benign pancreatic tissue

value: benign


title: alveolar macrophage_treated_2

description:
9377360001_C
cell


title: alveolar macrophage_treated_3

description:
9377360001_D
cell


title: alveolar macrophage_treated_4

description:
9377360001_H
cell


title: L26, human PDAC tissue

description: Gene expreesion data


title: whole lung_treated_3

description:
9377360001_E
tissue


title: L23, human benign pancreatic tissue

description: Gene expreesion data


title: whole lung_untreated_4

description:
9340020021_H
tissue


title: alveolar macrophage_untreated_2

description:
9340020021_C
cell


title: L22, human benign pancreatic tissue

description: Gene expreesion data


title: L24, human PDAC tissue

description: Gene expreesion data


title: whole lung_treated_1

description:
9340020021_F
tissue


title: whole lung_untreated_3

description:
9340020021_E
tissue


title: L21, human benign pancreatic tissue

description: Gene expreesion data


title: alveolar macrophage_treated_1

description:
9377360001_A
cell


title: whole lung_untreated_2

description:
9340020021_D
tissue


title: L19, human benign pancreatic tissue

description: Gene expreesion data


title: L16, human benign pancreatic tissue

description: Gene expreesion data


title: L17, human benign pancreatic tissue

description: Gene expreesion data


title: L18, human benign pancreatic tissue

description: Gene expreesion data


title: 200 rosy-vs-hang (dye flip)

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

country: Germany

institute: Humboldt University Berlin

description:
hangover mutant vs. rosy control, replicate 5
dye flip experiment to biological replicate 1/3

hyb_protocol: Klebes et al., 2003

scan_protocol: GenePix 4000A Microarray Scanner (Axon Instruments, Union City, CA)

data_processing: raw data, global median normalized

organism: Drosophila melanogaster

source_name: heads from male rosy PZ[+]  flies

label_protocol: Klebes et al., 2002

growth_protocol: standard Drosophila culture

extract_protocol: Trizol RNA extraction

treatment_protocol: collection of app 1000 fly heads of male flies per probe

value: male

value: heads

value: rosy PZ[+]

source_name: heads from male hangover mutants

value: hangover mutant (hangAE10)


title: L15, human benign pancreatic tissue

description: Gene expreesion data


title: L14, human benign pancreatic tissue

description: Gene expreesion data


title: 195 hang-vs-rosy

description:
hangover mutant vs. rosy control, replicate 4
biological replicate 3/3


title: 159 hang-vs-rosy

description:
hangover mutant vs. rosy control, replicate 2
biological replicate 2/3 with 1 round of RNA amplification


title: 194 rosy-vs-hang (dye flip)

description:
hangover mutant vs. rosy control, replicate 3
dye flip experiment to biological replicate 3/3


title: L28, human PDAC tissue

description: Gene expreesion data


title: 117 hang-vs-rosy

description:
hangover mutant vs. rosy control, replicate 1
biological replicate 1/3 with 1 round of RNA amplification


title: CD4+cells_DepressiveAsthma_Subject3

description: gene expression of peripheral blood CD4+ T cells in asthmatic with depression (subject 3)


title: L13, human benign pancreatic tissue

description: Gene expreesion data


title: L8, human normal pancreatic tissue

description: Gene expreesion data

source_name: Normal pancreatic tissue

value: normal

tag: manufacturer

value: Clontech

tag: catalog #


title: L10, human benign pancreatic tissue

description: Gene expreesion data


title: L12, human benign pancreatic tissue

description: Gene expreesion data


title: L3, human normal pancreatic tissue

description: Gene expreesion data

value: Ambion


title: L9, human benign pancreatic tissue

description: Gene expreesion data


title: L5, human normal pancreatic tissue

description: Gene expreesion data


title: L2, human normal pancreatic tissue

description: Gene expreesion data


title: L11, human benign pancreatic tissue

description: Gene expreesion data


title: 22Rv1-norm_solvent_3

status: Public on Dec 08 2016

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Prostate cancer

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

growth_protocol: The cells were incubated in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 1% L-glutamine under a 5% CO2 atmosphere at 37°C.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Exponentially growing cells were plated and incubated for 2 days. Cells were harvested at 70-80 % confluence and subjected to RNA extraction.

tag: histology

value: Radiation sensitive

value: untreated


title: alveolar macrophage_untreated_1

description:
9340020021_B
cell


title: L6, human normal pancreatic tissue

description: Gene expreesion data

value: Stratagen


title: L7, human normal pancreatic tissue

description: Gene expreesion data


title: L1, human normal pancreatic tissue

description: Gene expreesion data


title: whole lung_untreated_1

description:
9340020021_A
tissue


title: 22Rv1-hyp_vorinostat_2

value: vorinostat  (1 uM, 24h) and hypoxia (0.2% O2, 24h) exposed


title: 22Rv1-norm_vorinostat_3

value: vorinostat exposed (1 uM, 24h)


title: 22Rv1-hyp_solvent_3

value: hypoxia exposed (0.2% O2, 24h)


title: 22Rv1-hyp_vorinostat_3


title: L4, human normal pancreatic tissue

description: Gene expreesion data

value: Pancreas


title: 22Rv1-norm_vorinostat_2


title: 22Rv1-hyp_vorinostat_1


title: 22Rv1-norm_vorinostat_1


title: 22Rv1-norm_solvent_2


title: 22Rv1-hyp_solvent_1


title: 22Rv1-norm_solvent_1


title: PC-3-norm_vorinostat_3


title: PC-3-hypo_solvent_3


title: Wholebood_HP_7_rep1

city: Seoul

first: In-Wha

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy and Research Institute of Pharmaceutical Sciences

country: South Korea

institute: Seoul National University

description: miRNA expression in patients with high PTH

hyb_protocol: 1.5 ug of Hy3-labelled cRNA (specific activity >10.0 pmol Hy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 15 hours at 56°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 2 minute at 56°C with Wash Buffer 1 (20x salt buffer 60 ml, 10% detergent solution 12 ml, nuclease-free water 528 ml), 2 minute at room temperature Wash buffer 2 (20x salt buffer 20 ml, nuclease-free water 285 ml), and 2 minute at room temperatureWash buffer C (20x salt buffer 2 ml, nuclease-free water 198 ml), then dried immediately.

scan_protocol: Slides were scanned immediately after drying on the Agilent G2565CA DNA Microarray Scanner using one color scan setting.

data_processing:
The scanned images were analyzed with Agilent Feature Extraction software version 10.7.3.1 using default parameters  to obtain background subtracted and spatially detrended processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Quantile normalized expression values were obtained with GeneSpring software PX 13.1.

label_protocol: The first step included a Calf Intestinal Alkaline Phosphatase for removal of 5’-phosphates from terminal of the microRNAs. In the second step, a fluorescent label was attached enzymatically to the 3’-end of the microRNAs in the total RNA sample.

extract_protocol: Total RNA including miRNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: A 2.5 mL sample of whole blood from PD patient was drawn directly to a PAXGene Blood miRNA Kit .

value: whole blood

value: chronic kidney disease


title: Wholebood_HP_8_rep1


title: PC-3-norm_solvent_3


title: Wholebood_HP_5_rep1


title: PC-3-hypo_solvent_2


title: PC-3-hypo_solvent_1


title: PC-3-norm_vorinostat_2


title: PC-3-hypo_vorinostat_3


title: DU145-hypo_solvent_3

description: DU 145-hyp_solvent_3

value: Radiation resistant


title: DU145-norm_vorinostat_2

description: DU 145-norm_vorinostat_2


title: alveolar macrophage_untreated_4

description:
9377360001_F
cell

value: alveolar macrophage


title: DU145-norm_solvent_2

description: DU 145-norm_solvent_2


title: PC-3-hypo_vorinostat_2


title: DU145-hypo_vorinostat_1

description: DU 145-hyp_vorinostat_1


title: DU145-hypo_vorinostat_3

description: DU 145-hyp_vorinostat_3


title: DU145-hypo_vorinostat_2

description: DU 145-hyp_vorinostat_2


title: PC-3-norm_solvent_1


title: DU145-norm_solvent_3

description: DU 145-norm_solvent_3


title: Wholebood_HP_6_rep1


title: PC-3-norm_vorinostat_1


title: Wholebood_HP_2_rep1


title: PC-3-norm_solvent_2


title: Wholebood_LP_7_rep1

description: miRNA expression in patients with low PTH


title: Wholebood_HP_3_rep1


title: Wholebood_LP_5_rep1


title: DU145-hypo_solvent_2

description: DU 145-hyp_solvent_2


title: Wholebood_LP_4_rep1


title: Wholebood_LP_6_rep1


title: Wholebood_HP_4_rep1


title: DU145-hypo_solvent_1

description: DU 145-hyp_solvent_1


title: Wholebood_LP_3_rep1


title: Wholebood_HP_1_rep1


title: Wholebood_LP_2_rep1


title: Wholebood_LP_1_rep1


title: DU145-norm_solvent_1

description: DU 145-norm_solvent_1


title: strue-00134: BRCA1_FF4826a_U133B

source_name: human RNA

tag: tissue type

value: human RNA


title: strue-00134: BRCA1_FF3521c_U133B


title: strue-00134: BRCA1_FG0149a_U133B


title: strue-00134: BRCA1_TC4583a2_U133B


title: strue-00134: BRCA1_FF4229a_U133B


title: strue-00134: BRCA1_FG0757a_U133B


title: strue-00134: BRCA1_FF5114a_U133B


title: strue-00134: BRCA1_FF6051a_U133B


title: whole lung_treated_2

description:
9340020021_G
tissue

value: antibiotic

value: whole lung


title: strue-00134: BRCA1_FG0148c_U133B


title: DU145-norm_vorinostat_1

description: DU 145-norm_vorinostat_1


title: strue-00134: BRCA1_FF7720a_U133B


title: strue-00134: BRCA1_FF8135a_U133B


title: strue-00134: BRCA1_FF9748a_U133B


title: strue-00134: BRCA1_FF4266a_U133B


title: strue-00134: BRCA1_TC4514a_U133B


title: strue-00134: BRCA1_FG1009a_U133B


title: strue-00134: BRCA1_F4414a_U133B


title: strue-00134: BRCA1_FF2888a_U133B


title: PE5 (Cy5) Onconase (Cy3) - OVCAR8

city: Girona

first: Maria

last: Vilanova Brugués

address: Maria Aurèlia Capmany  40

department: Biologia

country: Spain

institute: Universitat de Girona

description: RNA of PE5-treated OVCAR8 cells (biological replicate 1) was labeled with Cy5, RNA of Onconase-treated OVCAR8 cells (biological replicate 4) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

hyb_protocol: Labeled cRNA (antisense) was hybridized to the oligonucleotide microarray at 65ºC for 17 h. After hybridization, microarrays were washed sequentially.

scan_protocol: Microarrays were scanned on a G2565CA Microarray Scanner updated to 2 micron resolution (Agilent Technologies, USA). Data were extracted from the resulting TIFF-images using the Feature Extraction software v. 10.7 (Agilent Technologies, USA).

data_processing:
Raw microarray data were statistically analysed using the software packages Marray, pcaMethods, Limma, and RankProd from Bioconductor (www.bioconductor.org), which uses the R statistical environment and programming language. Specifically, the non-specific signal was removed from the total intensity using the Normexp background correction method with an offset of 20. Then intra-slide normalization was done using the Loess method to make intensities consistent within each array, and inter-slide normalization was performed employing the Aquantiles method to achieve consistency between arrays. After each of these analyses, a quality control analysis of microarray data (RG density plot, MA plot and M boxplot) was performed. Following normalization, the RankProd method was applied to identify differentially expressed genes.
Processed/normalized log2 ratios (test/control) are provided. These values were calculated using both samples of each comparison: samples A and B for the comparison between PE5-treated and control NCI/ADR-RES cells (PE5 vs Control - NCI/ADR-RES), samples C and D for the comparison between onconase-treated and control NCI/ADR-RES cells (Onconase vs Control - NCI/ADR-RES), samples E and F for the comparison between onconase- and PE5-treated NCI/ADR-RES cells (Onconase vs PE5 - NCI/ADR-RES), samples G and H for the comparison between PE5-treated and control OVCAR8 cells (PE5 vs Control - OVCAR8), samples I and J for the comparison between onconase-treated and control OVCAR8 cells (Onconase vs Control - OVCAR8), and samples K and L for the comparison between onconase- and PE5-treated OVCAR8 cells (Onconase vs PE5 - OVCAR8). Therefore, 6 final sets of processed/normalized data are provided, one for each comparison. Only those probes with an FDR adjusted p-value < 0.05 were considered significant.

source_name: PE5-treated OVCAR8 cells. Biological replicate 1

label_protocol: Sample preparation and microarray processing procedures were done according to the Two-Color Microarray-Based Gene Expression Analysis v. 6.5 (Agilent Technologies, USA). Briefly, 200 ng of total RNA was used to synthesize double-stranded cDNA with AffinityScript-Reverse Transcriptase and Oligo dT-Promoter Primer. cDNA was simultaneously amplified and transcribed into cyanine 3- or cyanine 5-labeled cRNA employing T7 RNA Polymerase in presence of cyanine 3-CTP or cyanine 5-CTP. Labeled cRNA (antisense) was then purified and evaluated using a ND-1000 Spectrophotometer (NanoDrop) (Thermo Fisher Scientific, USA).

growth_protocol: NCI/ADR-RES cells were grown at 37°C in a humidified atmosphere of 5% CO2 in DMEM (Gibco, Germany) supplemented with 10% fetal bovine serum (Gibco, Germany), 50 U/ml penicillin, 50 μg/ml streptomycin (Gibco, Germany), and 1.84 μM doxorubicin (Tedec-Meijic Farma, Spain). OVCAR8 cells were grown at 37ºC in a humidified atmosphere of 5% CO2 in RPMI (Gibco, Germany) supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin. Cells remained free of Mycoplasma and were propagated according to established protocols.

extract_protocol: After treatment, cells were harvested at 400 xg for 5 min at 4ºC and washed twice with cold PBS. Total RNA was extracted using the mirVana miRNA isolation kit (Applied Biosystems/Ambion, USA) according to the manufacturer’s instructions. RNA was then evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and a ND-1000 Spectrophotometer (NanoDrop) (Thermo Fisher Scientific, USA).

treatment_protocol: NCI/ADR-RES cells (2 x 105 per well) and OVCAR8 cells (5 x 104 per well) were seeded into 6-well plates and treated for 36 h with concentrations of PE5 or onconase that caused a 10% decrease of cell proliferation (12 µM PE5 or 0.5 µM onconase for NCI/ADR-RES cells and 0.45 µM PE5 or 0.06 µM onconase for OVCAR8 cells). Four independent biological replicates were performed for each cell line.

value: ovarian cancer cells

source_name: Onconase-treated OVCAR8 cells. Biological replicate 4

value: Onconase


title: Control (Cy5) Onconase (Cy3) - OVCAR8

description: RNA of control OVCAR8 cells (biological replicate 4) was labeled with Cy5, RNA of Onconase-treated OVCAR8 cells (biological replicate 1) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Control OVCAR8 cells. Biological replicate 4

value: Control (untreated)

source_name: Onconase-treated OVCAR8 cells. Biological replicate 1


title: strue-00134: BRCA1_FF6930a_U133B


title: PE5 (Cy5) Control (Cy3) - OVCAR8

description: RNA of PE5-treated OVCAR8 cells (biological replicate 3) was labeled with Cy5, RNA of control OVCAR8 cells (biological replicate 2) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: PE5-treated OVCAR8 cells. Biological replicate 3

source_name: Control OVCAR8 cells. Biological replicate 2


title: PE5 (Cy5) Onconase (Cy3) - NCI/ADR-RES

description: RNA of PE5-treated NCI/ADR-RES cells (biological replicate 1) was labeled with Cy5, RNA of Onconase-treated NCI/ADR-RES cells (biological replicate 4) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: PE5-treated NCI/ADR-RES cells. Biological replicate 1

value: NCI/ADR-RES

value: MDR ovarian cancer cells

source_name: Onconase-treated NCI/ADR-RES cells. Biological replicate 4


title: Onconase (Cy5) Control (Cy3) - NCI/ADR-RES

description: RNA of Onconase-treated NCI/ADR-RES cells (biological replicate 2) was labeled with Cy5, RNA of control NCI/ADR-RES cells (biological replicate 3) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Onconase-treated NCI/ADR-RES cells. Biological replicate 2

source_name: Control NCI/ADR-RES cells. Biological replicate 3


title: PE5 (Cy5) Control (Cy3) - NCI/ADR-RES

description: RNA of PE5-treated NCI/ADR-RES cells (biological replicate 3) was labeled with Cy5, RNA of control NCI/ADR-RES cells (biological replicate 2) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: PE5-treated NCI/ADR-RES cells. Biological replicate 3

source_name: Control NCI/ADR-RES cells. Biological replicate 2


title: Control (Cy5) Onconase (Cy3) - NCI/ADR-RES

description: RNA of control NCI/ADR-RES cells (biological replicate 4) was labeled with Cy5, RNA of Onconase-treated NCI/ADR-RES cells (biological replicate 1) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Control NCI/ADR-RES cells. Biological replicate 4

source_name: Onconase-treated NCI/ADR-RES cells. Biological replicate 1


title: Control (Cy5) PE5 (Cy3) - NCI/ADR-RES

description: RNA of control NCI/ADR-RES cells (biological replicate 1) was labeled with Cy5, RNA of PE5-treated NCI/ADR-RES cells (biological replicate 4) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Control NCI/ADR-RES cells. Biological replicate 1

source_name: PE5-treated NCI/ADR-RES cells. Biological replicate 4


title: Onconase (Cy5) PE5 (Cy3) - OVCAR8

description: RNA of Onconase-treated OVCAR8 cells (biological replicate 3) was labeled with Cy5, RNA of PE5-treated OVCAR8 cells (biological replicate 2) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Onconase-treated OVCAR8 cells. Biological replicate 3

source_name: PE5-treated OVCAR8 cells. Biological replicate 2


title: strue-00134: BRCA1_TC4515a_U133B

source_name: human RNA


title: Onconase (Cy5) Control (Cy3) - OVCAR8

description: RNA of Onconase-treated OVCAR8 cells (biological replicate 2) was labeled with Cy5, RNA of control OVCAR8 cells (biological replicate 3) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Onconase-treated OVCAR8 cells. Biological replicate 2

source_name: Control OVCAR8 cells. Biological replicate 3


title: Onconase (Cy5) PE5 (Cy3) - NCI/ADR-RES

description: RNA of Onconase-treated NCI/ADR-RES cells (biological replicate 3) was labeled with Cy5, RNA of PE5-treated NCI/ADR-RES cells (biological replicate 2) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Onconase-treated NCI/ADR-RES cells. Biological replicate 3

source_name: PE5-treated NCI/ADR-RES cells. Biological replicate 2


title: strue-00134: BRCA1_TC4498a_U133B


title: Control(Cy5) PE5 (Cy3) - OVCAR8

description: RNA of control OVCAR8 cells (biological replicate 1) was labeled with Cy5, RNA of PE5-treated OVCAR8 cells (biological replicate 4) was labeled with Cy3, and both RNAs were hybridized to the same microarray.

source_name: Control OVCAR8 cells. Biological replicate 1

source_name: PE5-treated OVCAR8 cells. Biological replicate 4


title: strue-00134: BRCA1_F4021a_U133B


title: strue-00134: BRCA1_FF6309a_U133B


title: strue-00134: BRCA1_FF8772a_U133B


title: Cortex from Diabetic BKS db/db mouse 5

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene expression data from Diabetic db/db Cortex (24 weeks old)

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using  RMA method and Mouse Entrez Gene custom CDF annotation version 10 was used for the normalization

source_name: Cortex from Diabetic mouse

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

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany)

value: Cortex

value: diabetic


title: M6

city: Regensburg

first: Christoph

middle: Andreas

last: Klein

state: Bavaria

address: Franz-Josef-Strauß-Allee 11

department: Experimental Medicine and Therapy Research

institute: University of Regensburg

hyb_protocol: cDNA was hybridized to Operon-Microarray-Chips (Eurofins MWG Operon, Alabama, USA). Sample labeling and array hybridization were performed as described previously (Hartmann CH, Klein CA. Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic acids research. 2006;34(21):e143).

scan_protocol: Slides were scanned on a GenePix 4000A Array Scanner. Images were gridded and spots were quantified using GenePix Pro 4.1 software. Features and areas of obvious defects were manually flagged and excluded.

data_processing: Gene expression analysis was performed for 10 normal, 7 ADH, 19 primary tumor and 7 lung metastatic tissue samples. Libraries chosen for gene expression analysis demonstrated good expression of GAPDH, beta-actin and CD30 . cDNA was hybridized to Operon-Microarray-Chips (Eurofins MWG Operon, Alabama, USA). Sample labeling and array hybridization were performed as described previously (Hartmann and Klein 2006). Microarray data pre-processing was performed in R using the limma package (Smyth and Speed, 2003). Raw probe intensities were background corrected by applying the ‘normexp’ method (Smyth and Speed, 2003). Analyses were restricted to cy5 intensities, since cy3 intensities did not capture fold changes correctly in spike-in experiments of single-cell expression assays (not shown). Loess normalization was used in M versus A plots of individual cy5 intensities of a given transcript in a given array and the median cy5 intensity across all arrays of the same transcript. Log2 ratios were calculated from the normalized intensities and quantile normalization was applied across arrays. All further analysis was based on normalized log ratios. Transcripts present at significantly different levels between groups were identified using standardized linear models as implemented in the limma package (Wettenhall and Smyth 2004). Transcripts were considered differentially expressed when their corresponding adjusted p-value (Benjamini, et al 2001) was p<=0.05.

molecule: polyA RNA

source_name: metastasis

label_protocol: After cDNA synthesis the 3'-end was labeled with dGTP, so that a 3'-oligo-dG flanking region was generated. In the fourth step the whole transcriptome was amplified sequence-independent by PCR with a single primer. cDNA libraries were tested for CD30 and housekeeping gene expression by RT-PCR.

growth_protocol: not applicable

extract_protocol: Laser microdissection (PALM MicroBeam from Carl Zeiss MicroImaging GmbH) was performed to dissect metastatic lesions from lung, primary tumors, epithelial layers of mammary glands of BALB-NeuT mice at the time point of ADH, and BALB/c mice at different age. Small pieces summing up to 100,000 um2 for each sample were catapulted into a cap with 10 ul paramagnetic oligo-dT bead suspension and lysis buffer. The extraction of mRNA and microarray experiments were performed as described previously (Klein et al., 2002).

treatment_protocol: Transgenic Balb-NeuT mouse model of breast cancer (untreated)

tag: source

value: lung metastasis tissue


title: Cortex from Diabetic BKS db/db mouse 4


title: M3


title: M7


title: M4


title: P19

source_name: primary tumor

value: tumor tissue


title: 22Rv1-hyp_solvent_2

source_name: Prostate cancer

value: Radiation sensitive

value: hypoxia exposed (0.2% O2, 24h)


title: M1


title: Cortex from Diabetic BKS db/db mouse 2


title: strue-00134: BRCA1_FF2889a_U133B


title: M5


title: Cortex from non diabetic BKS db/m mouse 3

description: Gene expression data from nondiabetic db/m Cortex (24 weeks old)

source_name: Cortex from nondiabetic littermate control mouse

value: non-diabetic


title: strue-00134: BRCA1_FF6475a_U133B


title: strue-00134: BRCA1_FF6461a_U133B


title: strue-00134: BRCA1_FF6467a2_U133A


title: M2


title: Cortex from Diabetic BKS db/db mouse 3


title: Cortex from non diabetic BKS db/m mouse 5


title: strue-00134: BRCA1_TC4656a_U133A


title: strue-00134: BRCA1_TC4656a_U133B


title: Cortex from non diabetic BKS db/m mouse 4


title: strue-00134: BRCA1_FF8135a_U133A


title: Cortex from non diabetic BKS db/m mouse 2


title: P15

value: tumor center tissue


title: strue-00134: BRCA1_FF6994a_U133B


title: Cortex from Diabetic BKS db/db mouse 1


title: strue-00134: BRCA1_FF8120a_U133B


title: strue-00134: BRCA1_FF8151a_U133B


title: strue-00134: BRCA1_FG0207a_U133B


title: strue-00134: BRCA1_F4414a_U133A


title: P16


title: P17


title: P14


title: strue-00134: BRCA1_FF6461a_U133A


title: strue-00134: BRCA1_FF8151a_U133A


title: strue-00134: BRCA1_FF6467a_U133B


title: strue-00134: BRCA1_FF6061a_U133B


title: DU145-norm_vorinostat_3

description: DU 145-norm_vorinostat_3

value: Radiation resistant

value: vorinostat exposed (1 uM, 24h)


title: P18


title: Cortex from non diabetic BKS db/m mouse 1


title: strue-00134: BRCA1_FF6061a_U133A

value: human RNA


title: strue-00134: BRCA1_FF2878a_U133B


title: P13


title: strue-00134: BRCA1_FF7012a2_U133B


title: PC-3-hypo_vorinostat_1

value: vorinostat  (1 uM, 24h) and hypoxia (0.2% O2, 24h) exposed


title: strue-00134: BRCA1_FF3521b_U133A


title: strue-00134: BRCA1_FG1009a_U133A


title: strue-00134: BRCA1_FG0885a_U133A


title: strue-00134: BRCA1_F4021a_U133A


title: strue-00134: BRCA1_FG0885a_U133B


title: strue-00134: BRCA1_FF6192a_U133B


title: strue-00134: BRCA1_FG0207a_U133A


title: strue-00134: BRCA1_FF3479a_U133B


title: strue-00134: BRCA1_FF9161a_U133B


title: strue-00134: BRCA1_FF6475a2_U133A


title: P10

value: tumor margin tissue


title: P12


title: strue-00134: BRCA1_TC4583a_U133A


title: P11


title: strue-00134: BRCA1_FF6442a_U133B


title: strue-00134: BRCA1_AC6172a_U133A


title: P8


title: P9


title: P6


title: P4


title: P7


title: P5


title: strue-00134: BRCA1_FF3479a2_U133A


title: strue-00134: BRCA1_FF9161a_U133A


title: strue-00134: BRCA1_FF2886a_U133B


title: strue-00134: BRCA1_FF2878a_U133A


title: strue-00134: BRCA1_TC4514a_U133A


title: CG4EPOR 8D_LIFlow_20h_rep3

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

country: United Kingdom

institute: Brighton & Sussex Medical School

hyb_protocol: Amplified labeled RNA was hybridised onto Single Color Rat miRNA Microarray Slides

scan_protocol: Slides were scanned immediately after washing on the Agilent C microarray Scanner (G2505B) for G3 microarray format scan setting for array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Red and Green PMT).

data_processing: The scanned images were analysed with Feature Extraction software v10.7.3.1 to generate the array data from the images

organism: Rattus norvegicus

source_name: CG4EPOR cells, 20h, LIFlow

label_protocol: RNA was amplified and labeled with Cyanine-3 (Cy3)

growth_protocol: CG4-EPOR cells were cultured in growth medium (DMEM+N1+FGF 5ng/ml+PDGF 1ng/ml+biotin 10ng/ml+B104-conditioned medium 30%), then differentiated in differentiation medium (DMEM/F12+progesterone 3ng/ml+putrescine 5µg/ml+sodium selenite 4µg/ml+insulin 12.5µg/ml+transferrin 50µg/ml+biotin 10ng/ml+thyroxine 0.4µg/ml+glucose 0.3%). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Cells were lysed with QIAzol (QIAGEN) and total RNA was extracted by using the miRNeasy system and protocol (QIAGEN)

treatment_protocol: Cells were treated with EPO 10ng/ml (EPO), LIF 0.2ng/ml (LIFlow), LIF 10ng/ml (LIF) or the combination of EPO and LIF both at 10 ng/ml for 1h and 20h.

value: rat glial precursor cell line

value: CG4-EPOR oligodendrocytes

value: LIFlow

tag: time


title: stegm-00394: 48NT72H1

source_name: Bone marrow

value: Lymphoma


title: CG4EPOR 8C_LIFlow_20h_rep2


title: strue-00134: BRCA1_FF2886a_U133A


title: CG4EPOR 3D_LIFlow_1h_rep3

source_name: CG4EPOR cells, 1h, LIFlow


title: stegm-00394: 48NT48H2


title: stegm-00394: 48T24H1


title: CG4EPOR 11C_undif_rep3

source_name: CG4EPOR cells, undifferentiated

value: undifferentiated

value: control


title: strue-00134: BRCA1_FF6442a_U133A


title: CG4EPOR 11B_undif_rep2


title: N6

source_name: normal

value: normal tissue


title: P3


title: N8


title: N7


title: strue-00134: BRCA1_FF5114a_U133A

source_name: human RNA


title: P2


title: P1


title: N5


title: CG4EPOR 10D_EPO+LIF_20h_rep4

source_name: CG4EPOR cells, 20h, EPO+LIF

value: EPO+LIF


title: stegm-00394: 48NT72H2


title: N3


title: N9


title: N2


title: strue-00134: BRCA1_FF8120a_U133A


title: N4


title: stegm-00394: 48T72H2


title: CG4EPOR 7D_EPO_20h_rep4

source_name: CG4EPOR cells, 20h, EPO

value: EPO


title: strue-00134: BRCA1_FF7720a_U133A


title: stegm-00394: 48NT48H1


title: CG4EPOR 6D_ctr_20h_rep4

source_name: CG4EPOR cells, 20h, control


title: strue-00134: BRCA1_FF6192a_U133A


title: N1


title: stegm-00394: 48T24H2


title: CG4EPOR 11A_undif_rep1


title: strue-00134: BRCA1_FG0757a_U133A


title: strue-00134: BRCA1_FF6930a_U133A


title: stegm-00394: 48Nt24H1


title: stegm-00394: 48T48H1


title: strue-00134: BRCA1_TC4515a_U133A


title: A6

source_name: ADH

value: ADH tissue


title: A7


title: CG4EPOR 8B_LIFlow_20h_rep1


title: CG4EPOR 5D_EPO+LIF_1h_rep4

source_name: CG4EPOR cells, 1h, EPO+LIF


title: stegm-00394: 48NT24H2


title: CG4EPOR 4D_LIF_1h_rep4

source_name: CG4EPOR cells, 1h, LIF

value: LIF


title: CG4EPOR 3B_LIFlow_1h_rep1


title: stegm-00394: 48NT12H2


title: strue-00134: BRCA1_FF6051a_U133A


title: strue-00134: BRCA1_FG0149a_U133A


title: CG4EPOR 1D_ctr_1h_rep4

source_name: CG4EPOR cells, 1h, control


title: CG4EPOR 3C_LIFlow_1h_rep2


title: strue-00134: BRCA1_FF4826a_U133A


title: A5


title: stegm-00394: 48Nt12H1


title: CG4EPOR 2D_EPO_1h_rep4

source_name: CG4EPOR cells, 1h, EPO


title: stegm-00394: 48T72H1


title: A3


title: A4


title: A2


title: A1


title: stegm-00394: 48T48H2


title: strue-00134: BRCA1_FF6309a_U133A


title: CG4EPOR 10C_EPO+LIF_20h_rep3


title: N10


title: strue-00134: BRCA1_FF9748a_U133A


title: CG4EPOR 9C_LIF_20h_rep3

source_name: CG4EPOR cells, 20h, LIF


title: strue-00134: BRCA1_FG0148c2_U133A


title: strue-00134: BRCA1_FF8772a_U133A


title: strue-00134: BRCA1_FF4229a_U133A


title: strue-00134: BRCA1_FF4266a_U133A


title: stegm-00394: 480H2


title: stegm-00394: 480H1


title: CG4EPOR 7C_EPO_20h_rep3


title: strue-00134: BRCA1_FF2888a_U133A


title: CG4EPOR 4C_LIF_1h_rep3


title: CG4EPOR 5C_EPO+LIF_1h_rep3


title: strue-00134: BRCA1_TC4498a2_U133A


title: strue-00134: BRCA1_FF6994a_U133A


title: CG4EPOR 6C_ctr_20h_rep3


title: strue-00134: BRCA1_FF2889a2_U133A


title: CG4EPOR 2C_EPO_1h_rep3


title: stegm-00394: AML1-ETO_Amx_d4-1

value: Acute Myeloid Leukemia


title: stegm-00394: siGL_d4-1


title: glp-4(bn2); let-7(mn112)_3

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

hyb_protocol: hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix)

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing:
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probe group file: probeId_to_tr_min10probes.tab

organism: Caenorhabditis elegans

source_name: staged L4 worms

label_protocol: RNA was processed according to the Affymetrix GeneChip WT Amplified Double Stranded cDNA Synthesis Kit, fragmented with the Affymetrix GeneChip WT Double-Stranded DNA Terminal Labeling Kit and Biotin labeled using the GeneChip WT Genechip WT Terminal Labeling Kit

growth_protocol: Worms were grown until the late L4 stage (glp-4(bn2); let-7(wild-type): 33h 25°C; glp-4(bn2); let-7(mn112): 34h 25°C)

extract_protocol: RNA  was extracted using TRI Reagent (MRC)

treatment_protocol: whole worms were harvested in M9 and transferred to TRI Reagent (MRC)


title: glp-4(bn2); let-7(mn112)_1


title: stegm-00394: siGL_d4-2


title: stegm-00394: siGL_Amx-d4-1


title: stegm-00394: Kasumi_d4-3


title: CG4EPOR 1C_ctr_1h_rep3


title: CG4EPOR 5B_EPO+LIF_1h_rep2


title: CG4EPOR 7B_EPO_20h_rep2


title: CG4EPOR 6B_ctr_20h_rep2


title: CG4EPOR 10B_EPO+LIF_20h_rep2


title: glp-4(bn2); let-7(wild-type)_3

value: glp-4(bn2); let-7(wild-type)


title: CG4EPOR 2B_EPO_1h_rep2


title: CG4EPOR 4B_LIF_1h_rep2


title: strue-00134: BRCA1_FF7012a_U133A


title: stegm-00394: AML1-ETO_Amx_d4-3


title: stegm-00394: siGL_d4-3


title: CG4EPOR 1B_ctr_1h_rep2


title: glp-4(bn2); let-7(wild-type)_2


title: glp-4(bn2); let-7(wild-type)_1


title: stegm-00394: Kas_Amx_d4-1


title: CG4EPOR 10A_EPO+LIF_20h_rep1


title: CG4EPOR 9B_LIF_20h_rep2


title: CG4EPOR 9A_LIF_20h_rep1


title: stegm-00394: Kasumi_d4-1


title: CG4EPOR 7A_EPO_20h_rep1


title: glp-4(bn2); let-7(mn112)_2


title: stegm-00394: AML1-ETO_d4-2


title: CG4EPOR 6A_ctr_20h_rep1


title: stegm-00394: AML1-ETO_d4-1


title: stegm-00394: siGL_Amx-d4-2


title: HeLa shControl

status: Public on Dec 07 2016

city: Atlixco

first: Verónica

last: Vallejo-Ruiz

state: Puebla

address: Km 4.5 Carretera Federal Atlixco-Metepec

department: Centro de Investigación Biomédica de Oriente

country: Mexico

institute: Instituto Mexicano del Seguro Social

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate.

data_processing:
For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.
Data were then normalized and analyzed with genArise software (Institute of Cellular Physiology, UNAM). Genes with a Z score ≥ 2 or ≤ -2 were considered with altered expression (Table z score).

source_name: HeLa cell

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555  and 650 nm for Alexa647.

growth_protocol: HeLa human cervical carcinoma cells (American Type Culture Collection, ATCC, USA) were maintained in Dulbecco Modiﬁed Eagle medium  (DMEM); compania) supplemented with 10% Fetal Bovine Serum containing penicillin (100 U/ml), and streptomycin (100 µg/ml) (compania). The cells were grown in 25-cm2 tissue culture ﬂasks in a (5% CO2) at 37°C and routinely passaged when conﬂuent.

extract_protocol: Total RNA was extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research)  following manufacturer's instructions.

treatment_protocol: Gene silencing was obtained by cloning the shRNA sequence 5’-CTAACACTGGGTTATACAA-3’ into the pLVX-sh vector (pLVX-shE6/E7), (Clontech Laboratories). The 19 nucleotide sequence targets the E6 and E7 bicistronic mRNA (Butz et al. 2003). As control, the sequence 5’-GACTTCATAAGGCGCATGC-3’ (Zongli Qi et al. 2010) was cloned into the pLVX-sh vector (pLVX-shControl). Next, to obtain recombinant lentiviral particles carrying the constructs, Lenti-X 293T Cells (Clontech Laboratories) were co-transfected either with pLVX-shControl or pLVX-shE6/E7 and Lenti-X HTX Packaging Mix (Clontech Laboratories). In brief, Lentivirus were harvested from the supernatant and filtered. Presence of viral particles in the filtered was confirmed by using the LentiX-Gostik kit (Clontech Laboratories). Then supernatants bearing lentivirus pLVX-shControl or pLVX-shE6/E7 were used to transduce HeLa cells. Puromycin (1 µg/µl) selection of transduced cells was perfomed for a week. When the culture reached 60% of confluence, cells were tripsinized and diluted to obtain monoclonal cultures. Then, real time PCR analysis (Step OneTM Life Technologies) was carry out to evaluate the E6 and E7 gene silencing on those cultures. Total RNA from transduced monoclonal HeLa cultures were obtained by using the NucleoSpinII RNA kit (Macherey-Nagel). Then, cDNA was sintethized with random primers and the RevertAid First-Strand cDNA Synthesis kit (cat no. K1621; Thermo Fisher Scientific). Sequences of VPH18 E6 forward (5´-GCGACCCTACAAGCTACCTGAT-3´) and reverse (5´-GCACCGCAGGCACCTTAT-3´); VPH18 E7 forward (5´-TGTCACGAGCAATTAAGCGACT-3´) and reverse (5´CACACAAAGGACAGGGTGTTC-3) were used to quantify the respective cDNAs expression levels. Results were normalized to the level of HPRT expression (forward 5´CCTGGCGTCGTGATTAGTGATGAT3´, reverse 5´CGAGCAAGACGTTCAGTCCTGTC3´) and evaluated using the CT method. Finally, clones which exhibited the best silencing degree were selected to perform the microarray assay.


title: HeLa shE6/E7

value: HeLa human cervical carcinoma cells (American Type Culture Collection, ATCC, USA)


title: hepatic caecom of B. belcheri

city: Beihai

first: Xin

last: Liao

state: Guangxi

address: 2# JinHaian Road

department: School of Life Sciences

institute: Nanjing University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Branchiostoma belcheri

source_name: hepatic caecom RNA of five amphioxus

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

growth_protocol: Amphioxus (B. belcheri) were obtained from the sandy bottom of the sea near Zhanjiang at Guangdong, China, and cultured in Beihai Marine Station of Nanjing University at Beihai, Guangxi, China. They were fed on chlorella and isochrysis with well-aerated circulating filtered seawater at 26 ±2°C.

extract_protocol: Total RNA for each tissue was extracted using trizol reagent (Invitrogen, Carlsbad, CA, USA)according to the manufacturer’s protocol.

treatment_protocol: Five adults of amphioxus were used to harvest the gill, intestine and hepatic caecum, and the tissues were rapidly frozen by liquid nitrogen for further RNA extraction.

value: hepatic caecom


title: stegm-00394: AML1-ETO_d4-3

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Bone marrow


title: CG4EPOR 2A_EPO_1h_rep1


title: CG4EPOR 4A_LIF_1h_rep1


title: intestine of B. belcheri

source_name: intestine RNA of five amphioxus

value: intestine


title: gill of B. belcheri

source_name: gill RNA of five amphioxus mixture

value: gill


title: CG4EPOR 1A_ctr_1h_rep1

value: rat glial precursor cell line


title: CG4EPOR 5A_EPO+LIF_1h_rep1

value: CG4-EPOR oligodendrocytes