title: MCF7

description: Untreated

value: Breast


title: EA08079_80512_MDAMB175

status: Public on Apr 28 2014

type: RNA

city: Macclesfield

first: Mark

last: Wappett

address: Alderley Park

department: Oncology

country: United Kingdom

institute: AstraZeneca

description: Untreated

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analysed with the robust multichip analysis algorithm.  The data is returned in log2 normalised format. The RMA version used was from the bioconductor package affy, stable release version number 1.40.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: AZ GENE EXPRESSION

label_protocol: Affymetrix protocol

extract_protocol: RNA was extracted from cell lines using the Qiagen RNeasy kit as per the manufacturer's instructions. RNA quantity was determined using a Nanodrop spectrophotometer and both 260/280 and 260/230 ratios were evaluated. RNA quality was assessed using an Agilent RNA 6000 Nano Chip and the RNA Integrity Number (RIN) value of each sample was determined.

tag: cell line

tag: tissue


title: LP1 ghp280606

description: Untreated

value: Hematopoietic System

tag: disease

value: Myeloma


title: LoVo_1

description: Untreated

value: LOVO

value: Colon

value: colorectal adenocarcinoma


title: Bx051b_003 HG2

description: Untreated

source_name: Kudos 95 Cell Panel


title: Bx058-11 HG2

description: Untreated

value: Brain

value: malignant glioblastoma; glioma; glial cell


title: EA09076_118376_HG-U133_PLUS_2_CO015_06

description: Untreated

value: colorectal carcinoma


title: SR5062_HUMAN_U133_PLUS2_250310

description: Untreated

value: LNCAPCASRESNEWCASTLE

value: Prostate


title: LoVo

description: Untreated


title: LnCap

description: Untreated

value: LNCAPCLONEFGC

value: carcinoma Derived from metastatic site:left supraclavicular lymph node


title: Bx042-049

description: Untreated


title: Bx051b_053 HG2

description: Untreated


title: SB11010-2_D4S1C0044R_(HG-U133_Plus_2)

description: Untreated

value: Lung

value: SqLC


title: Bx058-09 HG2

description: Untreated

value: glioblastoma


title: LS174T

description: Untreated


title: SR5061_HUMAN_U133_PLUS2_250310

description: Untreated

value: LNCAPAI


title: SR5065_HUMAN_U133_PLUS2_250310

description: Untreated

value: LNCAPCASRES


title: Bx058-08 HG2

description: Untreated

value: glioblastoma; glioma


title: LB-61 nsclc ghp030206

description: Untreated

value: NSCLC


title: SR5060_HUMAN_U133_PLUS2_250310

description: Untreated

value: LNCAP


title: Bx042-009

description: Untreated

value: Colon


title: SB11010-2_D4S1C0037R_(HG-U133_Plus_2)

description: Untreated


title: A1631-04

description: Untreated

value: Breast


title: L363 ghp280606

description: Untreated

value: Hematopoietic System

value: Myeloma


title: Bx051b_102 HG2

description: Untreated

value: Esophagus

value: invasive esophageal squamous cell carcinoma


title: SBCG2008008-D3S1CO007R

description: Untreated

value: Esophageal cancer


title: KYSE-30 ap270406

description: Untreated

value: asian squamous cell carcinoma


title: KU812 ghp231105

description: Untreated

value: CML (Chronic Myeloid Leukemia)


title: A1385-14

description: Untreated

value: Pancreas


title: A1631-12

description: Untreated

value: Prostate


title: Bx030_006 HG2

description: Untreated


title: A1631-05

description: Untreated


title: 121 KK47

description: Untreated

value: Bladder


title: SR5069_HUMAN_U133_PLUS2_250310

description: Untreated


title: SB11010-1-2_D4S1C0031R_(HG-U133_Plus_2)

description: Untreated

value: Lung

value: SqLC


title: SBCG2008008-D3S1CO008R

description: Untreated


title: KB ap270406

description: Untreated

value: KB

value: Nasopharynx

value: Epidermoid carcinoma with HeLa markers (poss contamination)


title: KYSE-450 ap270406

description: Untreated

value: squamous cell carcinoma


title: KG-1 ghp231105

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: Bx051b_077 HG2

description: Untreated


title: KMS12BM ghp280606

description: Untreated

value: Hematopoietic System


title: Bx056_11 HG2

description: Untreated

value: KATOIII

value: Stomach

value: gastric carcinoma


title: SBCG2008008-D3S1CO006R

description: Untreated

value: Esophagus

value: Esophageal cancer


title: KG-1a ghp231105

description: Untreated


title: EA10068_111342

description: Untreated

value: AML


title: SBCG2008008-D1S1CO14R

description: Untreated

value: Gastric Cancer


title: SBCG2008008-D3S1C0005R

description: Untreated


title: Bx030_023 HG2

description: Untreated


title: Bx030_014 HG2

description: Untreated


title: KARPAS-422 ghp231105

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLBL (Diffuse Large B-cell Lymphoma )


title: Karpas620 ghp280606

description: Untreated

value: Myeloma


title: A1631-06

description: Untreated

value: Breast


title: K562 ghp231105

description: Untreated

value: CML (Chronic Myeloid Leukemia)


title: Karpas1106 ghp280606

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma)


title: Bx030_011 HG2

description: Untreated


title: Bx030_022 HG2

description: Untreated


title: JVM-2 ghp221105

description: Untreated

value: B-CLL (Chronic Lymphocytic B-Leukemia )


title: JVM-3 ghp221105

description: Untreated


title: JEKO ghp280606

description: Untreated

value: B-NHL (B-cell non-Hodgkins Lymphoma) (Mantle Cell)


title: A1385-06

description: Untreated

value: Pancreas


title: JJN3 ghp280606

description: Untreated


title: SBCG2008008-D1S1CO27R

description: Untreated


title: HUT78

description: Untreated

value: lymphoma


title: Bx051b_021 HG2

description: Untreated

value: Ovary

value: Carcinoma


title: Jurkat ghp280606

description: Untreated

value: JURKAT

value: Hematopoietic System

value: T-cell leukemia


title: 82 J82 Creteil

description: Untreated

value: Bladder


title: SBCG2008008-D1S1CO30R

description: Untreated

value: Stomach


title: IM9 ghp280606

description: Untreated


title: EA08079_80514_JIMT-1

description: Untreated


title: Bx051b_067 HG2

description: Untreated

value: Adenocarcinoma


title: SBCG2008008-D2S1C0031R

description: Untreated

value: Liver

value: Liver Cancer


title: Hx-147 re-hyb

description: Untreated

value: Lung

value: Lung Large Cell Carcinoma


title: SR5073_HUMAN_U133_PLUS2_250310

description: Untreated


title: HT29_1

description: Untreated

value: Colon

value: colorectal adenocarcinoma


title: SR5081_HUMAN_U133_PLUS2_250310

description: Untreated


title: SBCG2008008-D2S1CO28R

description: Untreated


title: HT29

description: Untreated


title: Bx042-037

description: Untreated


title: Bx051b_016 HG2

description: Untreated


title: SR5078_HUMAN_U133_PLUS2_250310

description: Untreated


title: HT ghp280606

description: Untreated

value: HT

value: B-NHL (B-cell non-Hodgkins Lymphoma) / DLCL (Diffuse Large Cell Lymphoma)


title: Hs840.T ap200406

description: Untreated

value: Pharynx

value: papilloma


title: Bx040_0007_R

description: Untreated

value: Pancreas

value: Carcinoma


title: Bx051b_075 HG2

description: Untreated

value: Papilloma


title: Bx051b_091 HG2

description: Untreated


title: SBCG2008008-D1S1CO32R

description: Untreated

value: Gastric Cancer


title: Bx051b_041 HG2

description: Untreated

value: Breast

value: Carcinoma; mammary gland


title: Bx058-10 HG2

description: Untreated

value: Brain

value: glioma


title: Bx040_0006_R

description: Untreated

value: HPAFII


title: HOP-62 ghp030206

description: Untreated

value: Lung

value: NSCLC


title: EA09076_118375_HG-U133_PLUS_2_CO015_05

description: Untreated

value: Colon

value: Colorectal carcinoma


title: Bx051b_014 HG2

description: Untreated

value: large cell carcinoma


title: A1385-05

description: Untreated


title: Hs578T

description: Untreated

value: carcinoma


title: EA10068_203543_HG-U133_PLUS_2_HLY-1

description: Untreated

value: Hematopoietic System

value: DLBCL


title: HN5 ap150606

description: Untreated

value: Tongue

value: Squamous Cell Carcinoma


title: SBCG2008008-D2S1CO29R

description: Untreated

value: HLF

value: Liver

value: Liver Cancer


title: Bx040_0005_R

description: Untreated

value: HPAC

value: Pancreas

value: Adenocarcinoma


title: Bx051b_089 HG2

description: Untreated

value: HPAFII

value: adenocarcinoma


title: Bx051b_095 HG2

description: Untreated

value: squamous cell carcinoma


title: Bx051b_051 HG2

description: Untreated

value: Lung


title: HL60

description: Untreated

value: acute promyelocytic leukemia


title: Bx051b_087 HG2

description: Untreated

value: Larynx

value: Epidermoid carcinoma with HeLa markers (poss contamination)


title: Bx056_16 HG2

description: Untreated

value: HELA

value: Cervix


title: EA10068_111346

description: Untreated

value: Hematopoietic System

value: AML


title: HL 60 ghp221105

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: KARPAS-231 ghp231105

description: Untreated

value: B-ALL (B-cell Acute Lymphoblastic Leukemia )


title: HEP2 ap270406

description: Untreated


title: SBCG2008008-D2S1C0012R

description: Untreated

value: Liver

value: Liver Cancer


title: SBCG2008008-D2S1CO27R

description: Untreated

value: HLE


title: HEL 92.1.7 ghp221105

description: Untreated

value: Erythroleukemia


title: SBCG2008008-D2S1C0033R

description: Untreated


title: SBCG2008008-D1S1CO13R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx056_09 HG2

description: Untreated

value: gastric carcinoma


title: HCT8_1

description: Untreated

value: Colon

value: ileocecal colorectal adenocarcinoma


title: HCT8

description: Untreated


title: Bx056_15 HG2

description: Untreated

value: Kidney

value: primary human embryonal kidney transformed by sheared human adenovirus type 5 (Ad 5) DNA


title: HCT15

description: Untreated

value: colorectal adenocarcinoma


title: Bx051b_024 HG2

description: Untreated

value: colorectal carcinoma


title: A1631-02

description: Untreated

value: Breast


title: HCT116_1

description: Untreated


title: Bx051b_029 HG2

description: Untreated


title: SB11010-2_D4S1C0047R_(HG-U133_Plus_2)

description: Untreated

value: Lung

value: SqLC


title: Bx042-036

description: Untreated


title: HCT15_1

description: Untreated


title: SBCG2008008-D2S1CO03R

description: Untreated


title: SBCG2008008-D2S1C0030R

description: Untreated


title: HCT116

description: Untreated


title: Bx051b_088 HG2

description: Untreated

value: invasive ductal carcinoma


title: EA08079_80491_HCC1954

description: Untreated


title: Bx051b_013 HG2

description: Untreated

value: primary ductal carcinoma


title: Bx051b_040 HG2

description: Untreated


title: EA08079_80503_HCC1937

description: Untreated


title: EA08079_81807_HCC1569

description: Untreated


title: SB11010-2_D4S1C0036R_(HG-U133_Plus_2)

description: Untreated


title: Bx051b_022 HG2

description: Untreated

value: Primary Acantholytic Squamous Cell Carcinoma


title: EA08079_80511_HCC1500

description: Untreated


title: EA08079_80496_HCC1419

description: Untreated


title: EA08079_80500_HCC1806

description: Untreated


title: Bx051b_081 HG2

description: Untreated

value: Primary Metaplastic Carcinoma


title: Bx051b_033 HG2

description: Untreated

value: Mucinous colon carcinoma


title: EA08079_80506_HCC1395

description: Untreated


title: EA08079_80499_HCC1187

description: Untreated


title: SB11010-2_D4S1C0035R_(HG-U133_Plus_2)

description: Untreated


title: Bx051b_054 HG2

description: Untreated


title: EA10068_203542_HG-U133_PLUS_2_HBL1

description: Untreated

value: Hematopoietic System

value: DLBCL


title: SB11010-2_D4S1C0043R_(HG-U133_Plus_2)

description: Untreated

value: HARAB


title: Bx056_12 HG2

description: Untreated

value: Stomach

value: gastric carcinoma


title: Bx030_016 HG2

description: Untreated


title: EA09076_118374_HG-U133_PLUS_2_CO015_04

description: Untreated

value: Colon

value: Adenocarcinoma


title: Bx042-031

description: Untreated

value: Colon Adenocarcinoma


title: EA10068_203557_HG-U133_PLUS_2_FARAGE

description: Untreated

value: FARAGE


title: Bx051b_010 HG2

description: Untreated

value: Breast


title: SBCG2008008-D1S1COO1R

description: Untreated

value: Gastric Cancer


title: Bx051b_015 HG2

description: Untreated

value: Primary Ductal Carcinoma


title: FaDu ap270406

description: Untreated

value: FADU

value: Pharynx

value: Squamous Cell Carcinoma


title: G361 ap071105

description: Untreated

value: Skin

value: malignant melanoma


title: Bx051b_098 HG2

description: Untreated


title: SB11010-2_D4S1C0042R_(HG-U133_Plus_2)

description: Untreated

value: HARA

value: Lung

value: SqLC


title: A1631-01

description: Untreated

value: EVSAT


title: SB11010-2_D4S1C0045R_(HG-U133_Plus_2)

description: Untreated


title: DOHH-2 ghp221105

description: Untreated

value: Hematopoietic System

value: B-NHL (B-cell non-Hodgkins Lymphoma) / FL (Follicular Lymphoma)


title: EA10068_111339

description: Untreated

value: CEL


title: Bx030_003 HG2

description: Untreated

value: ESKOL


title: EA10068_111347

description: Untreated

value: CML


title: EHEB ghp221105

description: Untreated

value: EHEB

value: B-CLL (Chronic Lymphocytic B-Leukemia )


title: Bx042-028

description: Untreated

value: Colon

value: Mucinous colon carcinoma


title: DOK ap200406

description: Untreated

value: DOK

value: Tongue

value: Dysplastic oral keratinocyte


title: SR5063_HUMAN_U133_PLUS2_250310

description: Untreated

value: Prostate


title: DMS114 ap071105

description: Untreated

value: carcinoma; small cell lung cancer


title: 83 EJ 138

description: Untreated

value: Bladder


title: Du145

description: Untreated

value: carcinoma Derived from metastatic site:brain


title: DMS114

description: Untreated

value: Lung


title: Bx051b_074 HG2

description: Untreated

value: Pharynx

value: Carcinoma


title: EA08073_86095_BX062-07

description: Untreated


title: EA08079_80497_HCC202

description: Untreated

value: Breast


title: Bx030_021 HG2

description: Untreated

value: Hematopoietic System


title: Daudi ghp221105

description: Untreated

value: DAUDI

value: Burkitts lymphoma


title: Bx042-042

description: Untreated

value: Colon carcinoma


title: Detroit 562 ap270406

description: Untreated

value: carcinoma from pleural effusion


title: Bx051b_039 HG2

description: Untreated

value: small cell lung cancer; carcinoma


title: Bx042-018

description: Untreated

value: Colon

value: colorectal adenocarcinoma


title: Bx042-026

description: Untreated


title: CTV-1 ghp221105

description: Untreated

value: AML (Acute Myeloid Leukemia)


title: COLO205

description: Untreated


title: CCRFCEM

description: Untreated

value: CCRFCEM

value: acute lymphoblastic leukemia


title: Colo320DM

description: Untreated


title: Bx058-20 HG2

description: Untreated

value: Brain

value: astrocytoma


title: Capan 1 ap071105

description: Untreated

value: Pancreas

value: adenocarcinoma Derived from metastatic site:liver


title: A1385-03

description: Untreated


title: Bx030_001 HG2

description: Untreated

value: CMK


title: EA09076_118373_HG-U133_PLUS_2_CO015_03

description: Untreated

value: adenocarcinoma


title: Bx030_020 HG2

description: Untreated

value: Hematopoietic System


title: Bx042-015

description: Untreated


title: COLO205_2

description: Untreated


title: Bx051b_052 HG2

description: Untreated

value: Lung

value: anaplastic carcinoma


title: Bx040_0004_R

description: Untreated

value: Carcinoma


title: EA08079_80510_CAMA-1

description: Untreated

value: Breast


title: Bx051b_086 HG2

description: Untreated

value: ductal adenocarcinoma; cystic fibrosis


title: Bx042-006

description: Untreated

value: Colon


title: Bx042-014

description: Untreated

value: rectum adenocarcinoma


title: Bx051b_072 HG2

description: Untreated


title: A1385-02

description: Untreated


title: Bx051b_078 HG2

description: Untreated


title: CaLu-6

description: Untreated


title: CaLu 1 ap071105

description: Untreated

value: epidermoid carcinoma


title: Bx051b_062 HG2

description: Untreated

value: Tongue

value: Squamous Cell Carcinoma


title: Bx051b_058 HG2

description: Untreated

value: Adenocarcinoma


title: EA09076_118372_HG-U133_PLUS_2_CO015_02

description: Untreated


title: EA09076_118371_HG-U133_PLUS_2_CO015_01

description: Untreated


title: CaLu-1 ghp030206

description: Untreated


title: Bx042-058

description: Untreated


title: CaLu-3 ap050706

description: Untreated


title: Bx056_07 HG2

description: Untreated


title: CAL27 ap270406

description: Untreated


title: Bx042-003

description: Untreated

value: colorectal adenocarcinoma


title: Bx042-002

description: Untreated


title: Bx042-056

description: Untreated


title: Bx042-012

description: Untreated


title: BxPC3 ap121105

description: Untreated

value: Pancreas


title: Bx042-057

description: Untreated


title: Bx040_0002_R

description: Untreated


title: EA09076_118382_HG-U133_PLUS_2_CO015_12

description: Untreated


title: EA09076_118381_HG-U133_PLUS_2_CO015_11

description: Untreated


title: EA08079_80502_BT-549

description: Untreated


title: BT474 ap071105

description: Untreated

value: ductal carcinoma


title: EA08079_80498_BT-20

description: Untreated


title: BT474C ap071105

description: Untreated

value: Breast Ductal Carcinoma


title: Bx051b_096 HG2

description: Untreated


title: SBCG2008008-D1S1CO21R

description: Untreated

value: Stomach

value: Gastric Cancer


title: Bx030_010 HG2

description: Untreated

value: Hematopoietic System


title: Bx051b_011 HG2

description: Untreated

value: Ductal Carcinoma


title: EA08079_80494_BT-474

description: Untreated


title: BE

description: Untreated

value: BE

value: Colon carcinoma


title: SR5071_HUMAN_U133_PLUS2_250310

description: Untreated

value: Bladder


title: A1631-13

description: Untreated

value: Prostate


title: Bx051b_045 HG2

description: Untreated

value: Colon

value: Carcinoma


title: SBCG2008008-D2S1CO08R

description: Untreated

value: Liver

value: Liver Cancer


title: SBCG2008008-D1S1COO3R

description: Untreated


title: SBCG2008008-D2S1CO11R

description: Untreated


title: Bx051b_035 HG2

description: Untreated

value: Breast


title: Bx051b_103 HG2

description: Untreated

value: Adenocarcinoma


title: Bx051b_005 HG2

description: Untreated


title: Bx056_13 HG2

description: Untreated

value: AGS

value: gastric adenocarcinoma


title: Bx030_019 HG2

description: Untreated


title: A549_2

description: Untreated

value: Lung

value: carcinoma


title: Bx051b_037 HG2

description: Untreated


title: SBCG2008008-D1S1CO005R

description: Untreated

value: Stomach

value: Gastric Cancer


title: A427 ghp030206

description: Untreated


title: ARH77 ghp280606

description: Untreated

value: Hematopoietic System

value: Myeloma


title: SBCG2008008-D2S1CO04R

description: Untreated


title: A1385-01

description: Untreated

value: Pancreas


title: Bx040_0001_R

description: Untreated

value: adenocarcinoma Derived from metastatic site:ascites


title: A2780 ap101105

description: Untreated

value: Ovary

value: Ovarian Carcinoma


title: A549-R ghp030206

description: Untreated

value: Carcinoma


title: AMO1 ghp280606

description: Untreated


title: Lymphoma_6

city: Grand Rapids

first: David

last: Cherba

state: MI

address: 333 Bostwick Ave

department: Bioinformatics and Biostatistic Core

country: USA

institute: Van Andel Institute

description: mRNA from tumor sample

hyb_protocol: Amplified cDNA samples generated with the NuGen Ovation Pico WTA system were used for fragmentation and labelling process using the NuGen Encore Biotin Module (Cat # 4200-12). The resulting fragmented and labeled cDNA was used for Affymetrix Canine 2.0 array hybridization. Samples were hybridized to Canine Genome Version 2.0 Affymetrix oligonucleotide arrays according to manufacturer's instructions (Affymetrix, Santa Clara, CA) at Clinical Reference Laboratory (a CLIA facility at Lenexa, KS).

scan_protocol: scanned using the Affymetrix gene chip scanner 3000 7G

data_processing: Affymetrix .CEL files containing the raw, probe-level signal intensities were analyzed using Affymetrix Gene Console build version 1.3.1.187 and MAS 5.0 normalization

organism: Canis lupus

source_name: tumor biospy

label_protocol: cDNA synthesis and amplification were accomplished using the NuGen Ovation Pico WTA System (Cat # 3300-12).  Fifty nanograms of total RNA was used for cDNA synthesis using the following steps as per the Ovation Pico WTA System protocol: First Strand cDNA synthesis, second strand cDNA synthesis, cDNA purification, SPIA cDNA amplification, and amplified SPIA cDNA purification

extract_protocol: Tumors were stored in RNAlater (ambion AM7020#). RNA extracted using Qiagen Rneasy Micro Kit (74004) and quality assement using Agilen Bionanalyzer for 260/280 ratio >=1.8 and RIN >= 8.0

tag: diagnosis

value: Lymphoma


title: A2058

description: Untreated

value: Skin

value: melanoma Derived from metastatic site:lymph node


title: A549

description: Untreated


title: Melanoma_3

description: mRNA from tumor sample

value: Melanoma


title: Lymphoma_5

description: mRNA from tumor sample


title: Melanoma_4

description: mRNA from tumor sample


title: A375

description: Untreated

value: malignant melanoma


title: A431

description: Untreated

value: epidermoid carcinoma


title: Bx051b_055 HG2

description: Untreated

value: Ovarian carcinoma


title: TCC_2

description: mRNA from tumor sample

value: TCC


title: Bx058-12 HG2

description: Untreated

value: Brain

value: glioblastoma


title: Sarcoma_1

description: mRNA from tumor sample

value: Sarcoma


title: Nasal Tumor

description: mRNA from tumor sample

value: Nasal Tumor


title: Bx051b_092 HG2

description: Untreated


title: Lymphoma_4

description: mRNA from tumor sample


title: TCC_1

description: mRNA from tumor sample


title: SR5077_HUMAN_U133_PLUS2_250310

description: Untreated

value: Bladder


title: HSA

description: mRNA from tumor sample

value: HSA


title: SR5066_HUMAN_U133_PLUS2_250310

description: Untreated

value: Prostate


title: Lymphoma_1

description: mRNA from tumor sample


title: Melanoma_2

description: mRNA from tumor sample


title: Melanoma_1

description: mRNA from tumor sample


title: Lymphoma_2

description: mRNA from tumor sample


title: Bx058-03 HG2

description: Untreated

value: Astrocytoma


title: SBCG2008008-D1S1CO26R

description: Untreated

value: Stomach

value: Gastric Cancer


title: SR5076_HUMAN_U133_PLUS2_250310

description: Untreated


title: STS_0

description: mRNA from tumor sample

value: STS


title: Hepatocelluar Carcinoma

description: mRNA from tumor sample

value: Hepatocelluar Carcinoma


title: TCC_0

description: mRNA from tumor sample


title: STS_1

description: mRNA from tumor sample


title: A1631-07

description: Untreated


title: Bx056_08 HG2

description: Untreated

value: gastric adenocarcinoma


title: SCNT sample 5

status: Public on Apr 27 2014

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
Chip no. 6004838015; Array C
NTb.AVG_Signal

hyb_protocol: Hybridization according to Illumina protocols on Illumina HumanHT-12 v4 Expression BeadChip. Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal. Background was subtracted using GenomeStudio v2009.1.

source_name: somatic cell nuclear transfer (SCNT)

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit. Two rounds of amplification

growth_protocol: human nuclear transfer oocytes were cultured in Global medium

extract_protocol: Picopure RNA isolation (kit PN 12204-01, Actrurus, lot 143413)

treatment_protocol: a human MII oocyte was enucleated and a somatic cell genome transferred by Sendai virus. Oocytes were activated artificially and allowed to develop until collection and analysis at the cleavage stage.

tag: host cell type

value: enucleated MII oocytes

tag: transferred with

value: adult somatic cells


title: GASmuscle_cSix1 rep1

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

country: France

institute: Cochin institut

description: Microarrays analysis of GP muscles of cSix1

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

organism: Mus musculus

source_name: C56BL6N gastrocnemius muscle

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

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

treatment_protocol: Gastrocnemius muscles were collected from cSix1 KO and control mice. Total RNAs were extracted by Trizol Reagent (Invitrogen) according to manufacturer's instruction.

value: Gastrocnemius muscle

tag: age

value: 8 weeks old

tag: strain

tag: genotype/variation

value: cSix1 KO


title: Lymphoma_0

description: mRNA from tumor sample

value: Lymphoma


title: GASmuscle_cSix1 rep3


title: Histiocytic Sarcoma

description: mRNA from tumor sample

value: Histiocytic Sarcoma


title: SCNT sample 11

description:
Chip no. 6004838015; Array A
Nta.AVG_Signal


title: cells stimulated with 10uM OA [gene-level]

city: Irapuato

first: Gertrud

last: Lund

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Genetic Engineering

country: Mexico

institute: CINVESTAV Irapuato

description: SZai-Ext-06-95-HuEx-1_0-st v2-a1.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Software: Affymetrix Expression Console;  Normalization: RMA gene extended and RMA exon all
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.extended.mps (gene level) and HuEx-1_0-st-v2.r2.dt1.hg18.full.mps (exon level)

source_name: THP-1 monocytes

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

growth_protocol: THP-1 monocytes cultured as in standard protocol

extract_protocol: RNA was extracted by the Trizol method, followed by cDNA synthesis and amplification by commercial kits (Affymetrix).

treatment_protocol: not applicable

tag: agent

value: 10 uM OA


title: GASmuscle_ctl rep2

value: wild type


title: GASmuscle_ctl rep3


title: TAmuscle_shlincMYH rep2

description: Microarrays analysis of TA muscles electroporated by shlinc- MYH

source_name: C56BL6N TA muscle, shlincMYH

treatment_protocol: Ten μg of shRNA-expressing vector were introduced into TA muscles of 8 week-old mice by electroporation. Two weeks following electroporation, TA myofibres expressing GFP were dissected under a Nikon SMZ1500 stereo microscope and frozen in liquid nitrogen before processing.

value: TA muscle

value: shlincMYH


title: NT hybrid sample

description:
Chip no. 6004838015; Array E
Hybrid 1027.AVG_Signal

source_name: nuclear transfer but no enucleation

value: MII oocyte

value: somatic cell genome


title: cells stimulated with 100uM AA [gene-level]

description: SZai-Ext-04-93-HuEx-1_0-st v2-a1.CEL

value: 100 uM AA


title: TAmuscle_shlincMYH rep1


title: BJ fibroblast cell line

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene expression data from BJ fibroblasts

hyb_protocol: Affymetrix protocol, 11 µg cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: BJ fibroblast cell line

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit (5 PRIME)

value: BJ fibroblasts

tag: gender

value: Male

tag: cell type

value: Fibroblasts


title: 1018-NT-ES

description: Gene expression data from 1018-NT-ES

source_name: Nuclear-transfer embryonic stem cell line derived from adult fibroblasts of a type 1 diabetic subject

value: Female

value: Undifferentiated nuclear-transfer embryonic stem cells


title: Melanoma_0

description: mRNA from tumor sample

value: Melanoma


title: BJ-NT-ES-8

description: Gene expression data from BJ-NT-ES-8

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 8


title: Lymphoma_3

description: mRNA from tumor sample


title: TAmuscle_ctl rep1

source_name: C56BL6N TA muscle, control vector

value: 8 weeks old

value: control vector


title: unstimulated cells [gene-level]

description: SZai-Ext-01-90-HuEx-1_0-st v2-a1.CEL

value: unstimulated control


title: TAmuscle_ctl rep2


title: cells stimulated with 1uM OA [gene-level]

description: SZai-Ext-05-94-HuEx-1_0-st v2-a1.CEL

value: 1 uM OA


title: cells stimulated with 1uM AA [gene-level]

description: SZai-Ext-02-91-HuEx-1_0-st v2-a1.CEL

value: 1 uM AA


title: Sarcoma_0

description: mRNA from tumor sample

value: Sarcoma


title: GASmuscle_ctl rep1

value: Gastrocnemius muscle

value: wild type


title: BJ-NT-ES-5

description: Gene expression data from BJ-NT-ES-5

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 5


title: cells stimulated with 100uM OA [exon-level]

description: SZai-Ext-07-96-HuEx-1_0-st v2-a1.CEL

value: 100 uM OA


title: cells stimulated with 10uM AA [gene-level]

description: SZai-Ext-03-92-HuEx-1_0-st v2-a1.CEL

value: 10 uM AA


title: SR5070_HUMAN_U133_PLUS2_250310

description: Untreated

value: Bladder


title: atorvastatin treated 1

status: Public on Apr 26 2014

city: Oslo

first: Camilla

last: Stormo

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

description: hepatoblastoma cell line

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing:
The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization. Exon array data were filtered to include only those probe sets derived from the core meta-probe list.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin-labeled

source_name: atorvastatin treated 1

label_protocol: Total RNA (100 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

growth_protocol: The human hepatoblastoma cell line HepG2 (American Type Culture Collection, Manassas, VA, USA) was maintained in collagen I-coated tissue culture flasks (BD Biosciences, San Jose, CA, USA) and modified Eagle’s minimal essential medium (MEM; ATCC) supplemented with 10% heat inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin-glutamine mixture (Sigma-Aldrich, St Louis, MO, USA).

extract_protocol: The cells were lysed by adding 700 µL QIAzol Lysis Reagent. Phase Lock Gel Heavy 2 mL (5PRIME Inc., Gaithersburg, MD, USA) was applied for phase-separation. RNA was then purified from the aqueous upper phase using miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) according to manufacturer’s instructions

treatment_protocol: Cells were seeded at 2 x 10e5 cells/mL in a 12-well collagen I-coated plate (BD Biosciences). The following day, medium was changed to 1 mL growth medium containing 3 mg/mL of human lipoprotein deficient serum (LPDS; Millipore, Billerica, MA, USA) instead of FBS. Cells were treated with or without 10 µM of water dissolve (3S, 5S)-Atorvastatin Sodium Salt (Toronto Research Chemicals North York, Ontario, Canada) for 24 hrs in triplicates


title: atorvastatin treated 3

description: hepatoblastoma cell line

source_name: atorvastatin treated 3


title: non-treated Ctr 1

description: hepatoblastoma cell line

source_name: non-treated Ctr 1


title: atorvastatin treated 2

description: hepatoblastoma cell line

source_name: atorvastatin treated 2


title: WB_AR19

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

description: discovery

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. Equilibrate probe array to room temperature immediately before use.  Then, heat the hybridization cocktail to 99°C for 5 minutes in heatblock.  Next, wet the array by filling it through one of the septa with appropriate volume of 1X MES Hybridization Buffer using a micropipettor and appropriate tips. Last, incubate the probe array for 10 minutes at 45°C in the hybridization oven with rotation.

scan_protocol: The Probe Array is scanned using the Affymetrix System.  The scanner is controlled by the GeneChip software.  The probe array is scanned after the wash protocols are complete

data_processing:
Quality of arrays was assessed by visual inspection of boxplots, RLE, NUSE and M/A-plots that were produced with the AffyPLM-package (Bolstad et al., 2005) in Bioconductor. The 40 samples were combined with 253 additional Microarray samples from the larger Biomarkers in Transplantation study, and all 293 samples together were background adjusted, normalized and probe information was summarized into probe-sets using the Robust Multi-Array Average (RMA)-procedure from the RefPlus package in Bioconductor (Harbron, Chang, & South, 2007).
References: Bolstad, B., Collin, F., Brettschneider, J., Simpson, K., Cope, L., Irizarry, R., & Speed, T. P. (2005). Quality assessment of Affymetrix GeneChip data. Bioinformatics and computational biology solutions using R and bioconductor, 33   47. AND Harbron, C., Chang, K.-M., & South, M. C. (2007). RefPlus: an R package extending the RMA Algorithm. Bioinformatics, 23(18), 2493   2494

source_name: post-transplant acute rejection (AR) whole blood (WB)

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

extract_protocol: Isolation begins with a centrifugation step to pellet nucleic acids in the PAXgene Blood RNA Tube. The pellet is washed, resuspended, and incubated in optimized buffers containing Proteinase K to digest proteins. A second centrifugation step is carried out to remove residual cell debris, and the supernatant is transferred to a fresh microcentrifuge tube. Ethanol is added to adjust binding conditions, and the lysate is applied to a PAXgene RNA spin column. During a brief centrifugation, RNA is selectively bound to the silica-gel membrane of the spin column as contaminants pass through. Remaining contaminants are removed in three wash steps, and pure RNA is then eluted in Buffer BR5. Generally, DNase digestion is not required for RNA purified with the PAXgene Blood RNA Kit, since PAXgene silica-gel–membrane technology efficiently removes most of the DNA without DNase treatment. However, further DNA removal is recommended for RNA applications that are sensitive to DNA contamination. In these cases, residual DNA can be removed either by using the RNase-Free DNase Set for on-column DNase digestion, or by treating the eluted RNA with DNase.

tag: Sex

value: F

tag: race

value: Caucasian

value: whole blood

tag: procedure status

value: post-transplant acute rejection (AR)

tag: sample group

value: discovery


title: non-treated Ctr 3

description: hepatoblastoma cell line

source_name: non-treated Ctr 3


title: WB_NR20

description: control

source_name: post-transplant non-rejection (NR) whole blood (WB)

value: M

value: Asian Oriental

value: post-transplant non-rejection (NR)

value: control


title: GASmuscle_cSix1 rep2

value: 8 weeks old

value: cSix1 KO


title: WB_AR20

description: discovery


title: WB_NR19

description: control


title: cells stimulated with 10uM OA [exon-level]

description: SZai-Ext-06-95-HuEx-1_0-st v2-a1.CEL

value: 10 uM OA


title: WB_NR17

description: control


title: cells stimulated with 100uM OA [gene-level]

description: SZai-Ext-07-96-HuEx-1_0-st v2-a1.CEL


title: WB_AR18

description: discovery


title: WB_NR18

description: control


title: BJ-NT-ES-6

description: Gene expression data from BJ-NT-ES-6

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 6

value: Male

value: Undifferentiated nuclear-transfer embryonic stem cells


title: WB_AR17

description: discovery


title: WB_AR15

description: discovery


title: cells stimulated with 10uM AA [exon-level]

description: SZai-Ext-03-92-HuEx-1_0-st v2-a1.CEL


title: WB_NR14

description: control


title: WB_AR16

description: discovery


title: WB_NR12

description: control


title: WB_NR16

description: control


title: WB_AR14

description: discovery


title: WB_NR10

description: control

value: Asian Indian


title: WB_AR11

description: discovery


title: WB_AR12

description: discovery


title: cells stimulated with 1uM OA [exon-level]

description: SZai-Ext-05-94-HuEx-1_0-st v2-a1.CEL

value: 1 uM OA


title: WB_NR11

description: control


title: WB_NR9

description: control


title: WB_AR10

description: discovery


title: cells stimulated with 1uM AA [exon-level]

description: SZai-Ext-02-91-HuEx-1_0-st v2-a1.CEL

value: 1 uM AA


title: RNA from C2C12 transfected with control siRNA_1

city: Montreal

first: Imed

last: Gallouzi

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Array Pro software was used to calculate differences in signal intensities and to normalize by Z-score transformation

label_protocol: RNA was reverse transcribed in the presence of [α-33P]dCTP.

growth_protocol: Proliferating C2C12 muscle cells were grown in DMEM supplemented with 20% FBS and 1% Pen/Strep.

extract_protocol: RNA was extracted with phenol/chloroform from C2C12 cell extracts

treatment_protocol: Cells were transfected with siRNA against HuR or a control

value: myoblast


title: RNA from C2C12 transfected with control siRNA_2


title: cells stimulated with 100uM AA [exon-level]

description: SZai-Ext-04-93-HuEx-1_0-st v2-a1.CEL

value: 100 uM AA


title: RNA from C2C12 transfected with siRNA against HuR_2


title: Enro30_2

city: Amsterdam

first: Nadine

last: Händel

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description: This sample is of enrofloxacin resistant Escherichia coli. It is the second of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures that were incubated additionally 30 days without any antibiotic.

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: The slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

organism: Escherichia coli

source_name: E. coli enrofloxacin resistant

label_protocol: Per test sample, 5 µg total RNA combined with 1 µg random octamers (Biolegio) in 4.5 µl was heated to 65°C for 10 min to denature the RNA and was allowed to cool in an ice-waterbath for 10 min. This 4.5 µl was made to 10 µl with a first strand mastermix containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, 1.5 µl of 2.5M NaOH was added to hydrolyze the remaining RNA by heating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 10 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled as the test samples with Cy5 incorporation.

growth_protocol: Cells were cultured overnight, inoculated in fresh Evans medium to an OD of 0.2 with or without the drug, incubated aerobically at 37⁰C and 200rpm and harvested at an OD600 of 1.0.

extract_protocol: Cells were harvested at an OD of 1, flash-frozen with liquid nitrogen and stored at -80⁰C. The total RNA was extracted by adding 500 µl of RNeasy lysis buffer containing 1% mercaptoethanol and incubation at room temperature for 5 minutes. The lysed cells were extracted twice with acid phenol, followed by two chloroform extractions. Subsequently the total RNA was precipitated with isopropanol and incubated over night at -80°C. After centrifugation for 30 minutes at 4°C, the pellet was washed with ice-cold 75% ethanol. Subsequently, the RNA was re-dissolved in 100 µl RNAse free water. Samples were purified with the RNeasy Kit (Qiagen).

treatment_protocol: Drug sensitive and resistant E. coli cells were grown with or without the presence of enrofloxacin or tetracycline. Treated cells were cultured with a drug concentration corresponding to 0.25xMIC (sensitive cells: 0.125 μg/ml enrofloxacin or 0.25 μg/ml tetracycline, resistant: 128 μg/ml enrofloxacin or 16  μg/ml tetracycline).

tag: phenotype

value: Enrofloxacin resistant


title: Enro30_3

description: This sample is of enrofloxacin resistant Escherichia coli. It is the third of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures that were incubated additionally 30 days without any antibiotic.


title: Tetra_exposed_1

description: This sample is of tetracycline resistant Escherichia coli. It is the first of three tetracycline resistant biological replicates used in this experiment, each from separate cultures that were incubated with 16 μg/ml tetracycline.

source_name: E. coli tetracycline resistant

value: Tetracycline resistant


title: RNA from C2C12 transfected with siRNA against HuR_1

tag: cell line


title: WB_AR9

description: discovery

value: Caucasian

tag: tissue

value: whole blood

value: post-transplant acute rejection (AR)

value: discovery


title: Tetra_2

description: This sample is of tetracycline resistant Escherichia coli. It is the first of three tetracycline resistant biological replicates used in this experiment, each from separate cultures.


title: Enro30_1

description: This sample is of enrofloxacin resistant Escherichia coli. It is the first of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures that were incubated additionally 30 days without any antibiotic.


title: Tetra_exposed_3

description: This sample is of tetracycline resistant Escherichia coli. It is the third of three tetracycline resistant biological replicates used in this experiment, each from separate cultures that were incubated with 16 μg/ml tetracycline.


title: Tetra_exposed_2

description: This sample is of tetracycline resistant Escherichia coli. It is the second of three tetracycline resistant biological replicates used in this experiment, each from separate cultures that were incubated with 16 μg/ml tetracycline.


title: unstimulated cells [exon-level]

description: SZai-Ext-01-90-HuEx-1_0-st v2-a1.CEL

source_name: THP-1 monocytes

value: unstimulated control


title: Tetra_3

description: This sample is of tetracycline resistant Escherichia coli. It is the third of three tetracycline resistant biological replicates used in this experiment, each from separate cultures.


title: WB_NR7

description: control

value: M

value: post-transplant non-rejection (NR)

value: control


title: WB_AR8

description: discovery


title: Tetra_1

description: This sample is of tetracycline resistant Escherichia coli. It is the second of three tetracycline resistant biological replicates used in this experiment, each from separate cultures.


title: WB_NR8

description: control

value: F

value: North American Indian


title: Enro_exposed_3

description: This sample is of enrofloxacin resistant Escherichia coli. It is the third of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with 128 μg/ml enrofloxacin.


title: WB_AR6

description: discovery


title: WB_NR6

description: control


title: Enro_exposed_2

description: This sample is of enrofloxacin resistant Escherichia coli. It is the second of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures that were incubated with 128 μg/ml enrofloxacin.


title: Enro_exposed_1

description: This sample is of enrofloxacin resistant Escherichia coli. It is the first of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures that were incubated with 128 μg/ml enrofloxacin.


title: Enro_3

description: This sample is of enrofloxacin resistant Escherichia coli. It is the third of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures.


title: WB_AR13

description: discovery


title: Enro_1

description: This sample is of enrofloxacin resistant Escherichia coli. It is the first of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures.


title: Enro_2

description: This sample is of enrofloxacin resistant Escherichia coli. It is the second of three enrofloxacin resistant biological replicates used in this experiment, each from separate cultures.


title: WT_tetra_1

description: This sample is of wildtype Escherichia coli MG1655. It is the first of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with 0.25 μg/ml tetracycline.

source_name: E. coli MG1655 wildtype

value: Drug sensitive


title: WT_enro_1

description: This sample is of wildtype Escherichia coli MG1655. It is the first of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with 0.125 μg/ml enrofloxacin.

organism: Escherichia coli str. K-12 substr. MG1655


title: WT_enro_2

description: This sample is of wildtype Escherichia coli MG1655. It is the second of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with  0.125 μg/ml enrofloxacin.


title: WB_NR5

description: control


title: WB_NR13

description: control

value: Asian Oriental


title: WT_3

description: This sample is of wildtype Escherichia coli MG1655. It is the third of three wildtype biological replicates used in this experiment, each from separate cultures.


title: WT_tetra_2

description: This sample is of wildtype Escherichia coli MG1655. It is the second of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with  0.25 μg/ml tetracycline.


title: WB_AR7

description: discovery


title: WT_tetra_3

description: This sample is of wildtype Escherichia coli MG1655. It is the third of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with  0.25 μg/ml tetracycline.


title: WT_2

description: This sample is of wildtype Escherichia coli MG1655. It is the second of three wildtype biological replicates used in this experiment, each from separate cultures.


title: WB_NR4

description: control


title: WB_AR3

description: discovery

value: Asian Indian


title: lncRNA and mRNA expression changed by calcium oxalate monohydrate crystals treatment for 24h

city: Wuhan

first: BH

last: Wang

address: jiefang road 1095

country: China

institute: Tongji hospital

description: LncRNAs and mRNAs expression after 24h calcium oxalate monohydrate crystals.

hyb_protocol: Each slide was hybridized with Cy3-labeled RNA using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242, Agilent Technologies, Santa Clara, CA, US) in hybridization oven (Agilent p/n G2545A, Agilent Technologies, Santa Clara, CA, US) at 60°C for exactly 30 minutes following the manufacturer's instruction.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent p/n G2565BA, Agilent Technologies, Santa Clara, CA, US) and Agilent Feature Extraction software (version 11.0.1.1, Agilent Technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Agilent GeneSpring Software GX v12.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: HK-2 lncRNAs and mRNA, calcium oxalate monohydrate crystals treatment, 24h

label_protocol: RNA molecule was labeled by Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442, Agilent Technologies, Santa Clara, CA, US) following the manufacturer's instructions.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies, USA) following the manufacturer's instructions. RNA was purified using RNeasy Mini Kit (Qiagen p/n 74104) following the manufacturer's instructions and qualified by NanoDrop ND-1000 (Thermo Fisher Scientific, USA).

treatment_protocol: HK-2 cells were treated with calcium oxalate monohydrate crystals for 0h and 24h.

value: proximal renal tubular cell line

tag: treatment

value: calcium oxalate monohydrate (COM)

tag: treatment duration


title: WT_enro_3

description: This sample is of wildtype Escherichia coli MG1655. It is the third of three wildtype biological replicates used in this experiment, each from separate cultures that were incubated with  0.125 μg/ml enrofloxacin.


title: WT_1

description: This sample is of wildtype Escherichia coli MG1655. It is the first of three wildtype biological replicates used in this experiment, each from separate cultures.


title: WB_AR5

description: discovery


title: WB_AR4

description: discovery


title: Wip1-Tg Neurospheres_14DIV_Secondary

city: Singapore

first: Dmitry

last: Bulavin

address: 61Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description:
gender matched
6285431010_F

hyb_protocol: as described by manufacturer

scan_protocol: as described by manufacturer

data_processing:
I used Bioconductor from R to normalize and analyze these data.
Differential expression analysis after quantile normalization
Differentially expressed genes are those with fold change greater than 1.5, comparing primary wt and Wip1Tg

source_name: Wip1-Tg Neurospheres_14DIV_Secondary

label_protocol: Cy3 labeling as described by manufacturer

growth_protocol: Mouse subventricular zone was microdisected out and trypsinized, culture in neural progenitor medium including EGF and FGF, for 2 weeks. RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

extract_protocol: Standard Trizon RNA extraction

treatment_protocol: No treatment

value: 18 month


title: WB_NR2

description: control


title: WB_AR2

description: discovery


title: lncRNA and mRNA expression changed by calcium oxalate monohydrate crystals treatment for 0h

description: LncRNAs and mRNAs expression after 0h calcium oxalate monohydrate crystals.

source_name: HK-2 lncRNAs and mRNA, calcium oxalate monohydrate crystals treatment, 0h


title: WB_NR3

description: control


title: wt Neurospheres_14DIV_Secondary 2

description:
gender matched
6285431010_E

source_name: wt Neurospheres_14DIV_Secondary

value: wt


title: WB_NR15

description: control

value: Caucasian


title: 02-106_1

status: Public on Apr 25 2014

type: protein

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

description: The symptom number column refers to the number of symptoms each patient was experiencing based on physician-elicited questionnaire.

hyb_protocol: Incubation with the appropriate biotinylated detection antibody cocktail was performed as outlined in the protocol, followed by incubation with streptavidin-PE. Following the final wash step, beads were re-suspended in the designated buffer.

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA).

data_processing: Serum concentrations were interpolated from standard curves for each respective analyte in Bio-Plex Manager 5.0 software. Values out of range below the standard curve were set to zero, while any value out of range above the standard curve was set to 4x the highest observed standard concentration.  For descriptive analyses of the multiplex biomarker data, data were analyzed using the log of the “ratio to cohort average”. This value was computed for each analyte by first setting any value less than 1 pg/mL to 1 pg/mL and then calculating the log base 2 of [(observed value)/(average value in the cohort)].

label: PE

molecule: protein

source_name: serum

label_protocol: Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. All assays were performed using 96-well flat-bottom plates and a Bio-Plex Pro II magnetic wash station. Standards, quality controls and experimental sera were diluted in provided diluents and then incubated with the respective multiplex bead mix according to manufacturer protocol.

extract_protocol: Serum was isolated from coagulated blood using standard protocols.  All sera were frozen and aliquoted within four hours of sampling.

tag: subject id

tag: visit number (1 = baseline)

tag: group

value: Control

tag: acute 2 tier status

value: Negative

tag: elevated liver enzyme

value: N

tag: multiple em

tag: illness duration (days)

tag: symptom number

tag: cd3+, cxcr3+, cd4+

tag: cd3+, cxcr3+, cd8+


title: WB_NR1

description: control

tag: Sex

tag: race

value: whole blood

tag: procedure status


title: 02-105_1

value: M


title: 02-104_1


title: 02-108_1


title: 02-102_1


title: 02-098_1


title: 02-096_1


title: 02-097_1


title: non-treated Ctr 2

description: hepatoblastoma cell line

source_name: non-treated Ctr 2

tag: cell line


title: 02-084_1


title: siBRCA1 + Etoposide 2

type: genomic

city: Belfast

first: Kienan

last: Savage

address: 97 Lisburn Rd

department: Centre for Cancer Research and Cell Biology

institute: Queen's University Belfast

description: BCLAF1 ChIP-chip from 293T cells transfected with BRCA1 targeted siRNAs (siBRCA1) and treated with 1uM etoposide for 16hours.

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: BCLAF1 Chip from 293T cells transfected with siBRCA1 BRCA1 targeted siRNA and treated with 1uM Etoposide for 16 hours

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: 293T cells were reverse transfected with GFP or BRCA1 targeted siRNAs using Lipofectamine RNAiMax as per the manufacturers protocol.  Following transfection, cells were grown for 72 hours in DMEM before fixing for ChIP.

extract_protocol: 5x10E6 cells were fixed with 1.5% formaldehyde Chromatin was cross- linked using 1.5% formaldehyde for 15 minutes at room temperature.  Cells were then washed twice with PBS and collected in 1 mL collection buffer [100mM Tris-HCL (pH 9.4) and 100mM DTT]. The cell suspension was then incubated on ice for 15 minutes. Cells were then lysed sequentially by resuspension and 5-minute centrifugation at 3,000g at 4oC with 1 mL buffer A (10mM EDTA, 0.5mM EGTA, 10mM HEPES, and 0.25% Triton X-100) and 1 mL buffer B (1mM EDTA, 0.5mM EGTA, 10mM HEPES, and 200mM NaCl), and sonicated three times for 10 seconds at maximum settings in 250 mL lysis buffer (10mM EDTA, 50mM Tris-HCl, 1% SDS, and 0.5% Empigen BB). After 15-minute centrifugation, 10 ML of the supernatant was taken as input and the remainder was diluted 5-fold in immunoprecipitation buffer (2mM EDTA, 100mM NaCl, 20mM Tris-HCl, and 0.5% Triton X-100). This was then subjected to immunoprecipitation overnight with specific antibodies after preclearing with pre-immune IgG, 2mg salmon sperm DNA, and 60mL protein A/G Sepharose bead slurry. Precipitate complexes were serially washed with 300 mL washing buffer I (2mM EDTA, 20mM Tris-HCl, 1% SDS, 01% Triton X-100, and 150mM NaCl), washing buffer II (2mM EDTA, 20mM Tris-HCl, 1% SDS, 01% Triton X-100, and 250mM NaCl), washing buffer III (1mM EDTA, 10mM Tris-HCl, 1% NP40, 1% deoxycholate, and 0.25M LiCl) then twice with 1 mM EDTA and 10mM Tris-HCl. Complexes were removed from the beads through subsequent 15-minute incubations, vortexing, and 5-minute centrifugations with 50 ML of 1% SDS, 0.1 mol/L NaHCO3. Cross-linking was reversed overnight at 65oC and the DNA was purified with QIAquick columns (Qiagen). Anti-BCLAF1 antibody (A300-608A Bethyl Labs) was used for ChIPs

treatment_protocol: Treated with 1uM Etoposide for 16 hours

value: 293T cells

value: Etoposide

tag: sirna

source_name: Input from 293T cells transfected with siBRCA1 BRCA1 targeted siRNA and treated with 1uM Etoposide for 16 hours


title: siBRCA1 Untreated 3

description: BCLAF1 ChIP-chip from 293T cells transfected with BRCA1 targeted siRNAs (siBRCA1)

source_name: BCLAF1 Chip from 293T cells transfected with siBRCA1 BRCA1 targeted siRNA siRNA

treatment_protocol: Untreated

tag: treatment

value: untreated

source_name: Input from 293T cells transfected with siBRCA1 BRCA1 targeted siRNA siRNA


title: 02-083_1

value: F


title: WB_AR1

description: discovery

source_name: post-transplant acute rejection (AR) whole blood (WB)

tag: tissue

value: post-transplant acute rejection (AR)

tag: sample group

value: discovery


title: Wip1-Tg Neurospheres_14DIV_Primary 1

description:
gender matched
6285431010_B

source_name: Wip1-Tg Neurospheres_14DIV_Primary

tag: genotype/variation

tag: age


title: siGFP Untreated 2

description: BCLAF1 ChIP-chip from 293T cells transfected with control siRNAs (siGFP)

source_name: BCLAF1 Chip from 293T cells transfected with siGFP control siRNA

value: siGFP

source_name: Input from 293T cells transfected with siGFP control siRNA


title: siBRCA1 Untreated 2


title: siBRCA1 + Etoposide 1


title: 02-103_1

tag: subject id

tag: visit number (1 = baseline)

tag: group

tag: acute 2 tier status


title: wt Neurospheres_14DIV_Primary

description:
gender matched
6285431010_A

source_name: wt Neurospheres_14DIV_Primary


title: Wip1-Tg Neurospheres_14DIV_Primary 2

description:
gender matched
6285431010_C


title: siGFP + Etoposide 3

description: BCLAF1 ChIP-chip from 293T cells transfected with control siRNAs (siGFP) treated with 1uM Etoposide for 16 hours

source_name: BCLAF1 Chip from 293T cells transfected with siGFP control siRNA and treated with 1uM Etoposide for 16 hours

source_name: Input from 293T cells transfected with siGFP control siRNA and treated with 1uM Etoposide for 16 hours


title: siGFP + Etoposide 2


title: siGFP + Etoposide 1


title: siBRCA1 + Etoposide 3


title: siGFP Untreated 1


title: siBRCA1 Untreated 1


title: siGFP Untreated 3


title: 02-060_1

tag: elevated liver enzyme

value: Y

tag: multiple em

tag: illness duration (days)

tag: symptom number


title: 02-058_1

tag: Sex

tag: cd3+, cxcr3+, cd4+

tag: cd3+, cxcr3+, cd8+


title: 02-057_1


title: wt Neurospheres_14DIV_Secondary 1

description:
gender matched
6285431010_D


title: 02-022_1


title: 02-061_1


title: 02-056_1


title: 02-055_1


title: 01-052_1

value: Case

value: Positive


title: 01-053_1


title: 01-054_1


title: 01-051_1


title: 02-019_1


title: 02-059_1


title: 02-041_1


title: 01-050_1


title: 01-044_1

value: Converter


title: 01-040_1


title: 01-048_1


title: 01-047_1


title: 01-042_1


title: 01-046_1


title: 02-018_1


title: 01-049_1


title: 01-045_1


title: 01-037_1


title: 01-034_1


title: 01-036_1


title: 01-033_1


title: 01-032_1


title: 01-031_1


title: 01-028_1


title: 01-029_1


title: 01-030_1


title: 01-027_1


title: 01-024_1


title: 01-026_1


title: 01-023_1


title: 01-020_1


title: 01-039_1


title: 01-025_1


title: 01-017_1


title: 01-014_1


title: 01-016_1


title: 01-011_1


title: 01-009_1


title: 01-007_1


title: 01-005_1


title: 01-012_1


title: 01-006_1


title: 01-003_1


title: 01-002_1


title: 01-001_1


title: 01-013_1


title: 01-004_1


title: 01-010_1


title: GEK-50

type: SRA

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Vriesea carinata

source_name: leaf

growth_protocol: Adult individual

extract_protocol: Total RNA were isolated from Vriesea carinata leaves using Trizol reagent (Invitrogen, CA, USA), according to manufacturer’s protocol and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. One mRNA library was constructed and it was sequenced by Illumina HiSeq2000. Briefly, the construction of the small RNA libraries consisted of the following successive steps: acrylamide gel purification of the RNA bands corresponding to the size range 20-30 nt, ligation of the 3p and 5p adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification, cDNA synthesis followed by acrylamide gel purification, and a final step of PCR amplification to generate a cDNA colony template library for Illumina sequencing.

tag: sample

value: single

value: adult

value: leaf

tag: molecule subtype

value: Small RNA


title: posterior HH6 PPR, Set 3

city: London

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

institute: King's College Londonn

description: Gene expression data

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 18 Hours at 45oC on GeneChip Gallus gallus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. as per Nugen Inc Instructions for Nugen Ovation V2

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Probe set values were generated with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and a user defined scale factor of 1.0

organism: Gallus gallus

source_name: HH5-7 Chick embryo posterior PPR

label_protocol: Nugen Ovation V2 and Biotin Module

growth_protocol: Embryos were incubated until they had reached HH5-7 and harvested in Tyrode's saline. PPR tissue was dissected manually using fine insect pins and stored on ice until processing.

extract_protocol: Absolutely RNA Stratagene

treatment_protocol: Embryos were incubated until they had reached HH5-7 and harvested in Tyrode's saline. PPR tissue was dissected manually using fine insect pins and stored on ice until setting up in collagen cultures. Explants were embedded in rat tail collagen and cultured for 5 hours before being processed.

tag: Stage

value: HH5-7 embryo

tag: tissue

value: Posterior Pre Placodal Region


title: cultured pPPR Set 1

description: Gene expression data

source_name: HH5-7 Chick embryo cultured posterior PPR

value: Cultured Posterior Pre Placodal Region


title: anterior HH6 PPR, Set 3

description: Gene expression data

source_name: HH5-7 Chick embryo anterior PPR

value: Anterior Pre Placodal Region


title: PE-5

city: Shreveport

first: Yuping

state: LA

address: 1501 Kings Hwy

department: OB/GYN

institute: LSUHSC-Shreveport

hyb_protocol: Following fragmentation, 1 ug of labeled product was hybridized for 18 hr at 48° C on GeneChip miRNA 2.0 arrays . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console 1.2 using RMA + DABG as the normalization method.

source_name: placenta

label_protocol: Biotinylated template was prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTag Biotin HSR RNA Labeling Kit, Affymetrix).

extract_protocol: Trizol was used to extract total RNA.

value: villous tissue

value: preeclamptic


title: PE-6


title: N-1

value: normal


title: N-2


title: Hepa 1-6 actinomycin D-treated 2

city: North Grafton

first: Arlin

middle: B

last: Rogers

state: MA

address: 200 Westoboro Road

department: Biomedical Sciences

institute: Tufts Cummings School of Vet Med

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software pattern 014868 was used for background subtraction and LOWESS normalization.

source_name: Hepa 1-6 actinomycin D-treated

label_protocol: 10 µg of total RNA primed with 2 µl of 100 µM DNA primers at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: For maintenance, cells were grown in DMEM with 10% fetal bovine serum; AML12 cells also were supplemented with dexamethasone and insulin according to ATCC guidelines.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Serum and all other additives were withdrawn from DMEM media overnight, and cells subsequently exposed to 200 ng/mL pituitary-derived ovine prolactin (PRL) or 10 ug/mL actinomycin D (ActD; both Sigma) for 8 hr prior to harvest.

tag: cell line

value: Hepa 1-6

tag: cell source

value: Hepatoma

tag: agent

value: actinomycin D

source_name: Universal Mouse Reference RNA (Agilent)

tag: source type

value: reference comprising 11 mouse cell lines


title: PE-4

tag: group


title: N-3


title: N-4


title: posterior HH6 PPR, Set 2

description: Gene expression data


title: PE-2


title: PE-1


title: anterior HH6 PPR, Set 2

description: Gene expression data


title: cultured aPPR Set 1

description: Gene expression data

source_name: HH5-7 Chick embryo cultured anterior PPR

value: Cultured Anterior Pre Placodal Region


title: cultured pPPR Set 2

description: Gene expression data


title: posterior HH6 PPR, Set 1

description: Gene expression data


title: anterior HH6 PPR, Set 1

description: Gene expression data


title: Resistant Leishmania infected (18h)

city: Kolkata

first: Syamal

last: Roy

state: West Bengal

address: 4, Raja SC Mullick Road

department: Infectious Disease and Immunology

country: India

institute: Indian Institute of Chemical Biology

description:
MicroRNA expression data
SAMPLE 5

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

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

data_processing: The data were analyzed with Expression Console and Gene springGX 12.0 using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: Resistant Leishmania infected (18h)

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

growth_protocol: Macrophages grown in 60 mm plates

extract_protocol: Total RNA prepared using Trizol according to manufacturer's instructions

treatment_protocol: Infected with an MOI 10 of Leishmania donovani

tag: strain

value: Balb/c

tag: cell type

value: Primary macrophage

tag: stress

value: infection by Leishmania [antimonial drug (sodium stibogluconate) resistant]

tag: time


title: Sensitive Leishmania infected (24h)

description:
MicroRNA expression data
SAMPLE 6

source_name: Sensitive Leishmania infected (24h)

value: infection by Leishmania [antimonial drug (sodium stibogluconate) sensitive]


title: Resistant Leishmania infected (24h)

description:
MicroRNA expression data
SAMPLE 7

source_name: Resistant Leishmania infected (24h)


title: Normal

description:
MicroRNA expression data
SAMPLE 1

source_name: Normal

value: normal control (not Leishmania-infected)

value: control


title: cultured aPPR Set 2

first: David

description: Gene expression data

value: HH5-7 embryo


title: LPS

description:
MicroRNA expression data
SAMPLE 8

source_name: LPS

value: LPS challenge (not Leishmania-infected)


title: Sensitive Leishmania infected (12h)

description:
MicroRNA expression data
SAMPLE 2

source_name: Sensitive Leishmania infected (12h)


title: Resistant Leishmania infected (12h)

description:
MicroRNA expression data
SAMPLE 3

source_name: Resistant Leishmania infected (12h)


title: Sensitive Leishmania infected (18h)

description:
MicroRNA expression data
SAMPLE 4

source_name: Sensitive Leishmania infected (18h)


title: PE-3


title: 02-021_1

source_name: serum

tag: subject id

tag: visit number (1 = baseline)

value: Control

value: F

tag: acute 2 tier status

value: Negative

tag: elevated liver enzyme

value: N

tag: multiple em

tag: illness duration (days)

tag: symptom number


title: Hepa 1-6 actinomycin D-treated 1

value: Hepa 1-6


title: AML12 actinomycin D-treated 2

source_name: AML12 actinomycin D-treated

value: Hepatoma


title: AML12 serum-free control 2

source_name: AML12 serum-free control

value: serum-free control


title: Hepa 1-6 prolactin-treated 1

source_name: Hepa 1-6 prolactin-treated

value: prolactin

value: reference comprising 11 mouse cell lines


title: AML12 actinomycin D-treated 1

value: actinomycin D


title: Hepa 1-6 prolactin-treated 2


title: PC3 cells stably overexpressing ERG treated with I-BET762 Replicate 1 PC3_ERG_IBET762_rep1

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Total RNA from PC3 cells stably overexpressing ERG treated with I-BET762

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-label or Cy3-label.

growth_protocol: Cells were cultured in ATCC recommended media supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using miRNeasy Kit (Invitrogen) following to the manufacturer’s instructions.

tag: treatment

value: prostate cancer cells

tag: transduced with

value: ERG lentivirus

tag: genotype/variation

value: AR negative

source_name: Total RNA from PC3 cells stably overexpressing ERG treated with DMSO


title: PC3 cells stably overexpressing ERG treated with I-BET762 Replicate 2 PC3_ERG_IBET762_rep2_swap

tag: cell line


title: AML12 prolactin-treated 2

source_name: AML12 prolactin-treated

tag: cell source

tag: agent

tag: source type


title: Hepa 1-6 serum-free control 1

source_name: Hepa 1-6 serum-free control

source_name: Universal Mouse Reference RNA (Agilent)


title: PC3 cells stably overexpressing ERG treated with JQ1 Replicate 2 PC3_ERG_JQ1_rep2_swap

source_name: Total RNA from PC3 cells stably overexpressing ERG treated with JQ1

tag: cell type


title: PC3 cells stably overexpressing ERG treated with I-BET762 Replicate 1 PC3_ERG_IBET762_rep1_swap


title: AML12 serum-free control 1


title: Hepa 1-6 serum-free control 2


title: AML12 prolactin-treated 1


title: PC3 cells stably overexpressing ERG Replicate 2 PC3_ERG_rep2_swap

source_name: Total RNA from PC3 cells stably overexpressing ERG

value: PC3 cells stably overexpressing ERG

value: LacZ control lentivirus


title: PC3 cells stably overexpressing ERG treated with JQ1 Replicate 2 PC3_ERG_JQ1_rep2


title: PC3 cells stably overexpressing ERG Replicate 1 PC3_ERG_rep1_swap


title: PC3 cells stably overexpressing ERG treated with JQ1 Replicate 1 PC3_ERG_JQ1_rep1_swap


title: PC3 cells stably overexpressing ERG Replicate 1 PC3_ERG_rep1


title: PC3 cells stably overexpressing ERG treated with I-BET762 Replicate 2 PC3_ERG_IBET762_rep2


title: RWPE cells stably overexpressing ERG treated with JQ1 Replicate 1 RWPE_ERG_JQ1_rep1_swap

source_name: Total RNA from RWPE cells stably overexpressing ERG treated with JQ1

value: RWPE

value: Benign prostate cells

source_name: Total RNA from RWPE cells stably overexpressing ERG treated with DMSO


title: PC3 cells stably overexpressing ERG Replicate 2 PC3_ERG_rep2


title: RWPE cells stably overexpressing ERG treated with I-BET762 Replicate 1 RWPE_ERG_IBET762_rep1_swap

source_name: Total RNA from RWPE cells stably overexpressing ERG treated with I-BET762


title: RWPE cells stably overexpressing ERG treated with I-BET762 Replicate 2 RWPE_ERG_IBET762_rep2


title: PC3 cells stably overexpressing ERG treated with JQ1 Replicate 1 PC3_ERG_JQ1_rep1


title: RWPE cells stably overexpressing ERG treated with I-BET762 Replicate 1 RWPE_ERG_IBET762_rep1


title: RWPE cells stably overexpressing ERG treated with JQ1 Replicate 2 RWPE_ERG_JQ1_rep2_swap


title: RWPE cells stably overexpressing ERG treated with JQ1 Replicate 2 RWPE_ERG_JQ1_rep2


title: RWPE cells stably overexpressing ERG treated with I-BET762 Replicate 2 RWPE_ERG_IBET762_rep2_swap


title: RWPE cells stably overexpressing ERG treated with JQ1 Replicate 1 RWPE_ERG_JQ1_rep1


title: RWPE cells stably overexpressing ERG Replicate 1 RWPE_ERG_rep1_swap

source_name: Total RNA from RWPE cells stably overexpressing ERG

value: RWPE cells stably overexpressing ERG

source_name: Total RNA from RWPE cells stably overexpressing LacZ control


title: RWPE cells stably overexpressing ERG Replicate 2 RWPE_ERG_rep2_swap


title: Starved LNCaP cells treated with Bic. followed by DHT Replicate 2 LNCaP_DHT+Bic_rep2

source_name: Total RNA from Starved LNCaP cells treated with Bic. followed by DHT

value: Bic. followed by DHT

value: LNCaP

value: non

value: AR positive, ETV1 fusion positive

source_name: Total RNA from Starved LNCaP cells treated with vehicel control


title: RWPE cells stably overexpressing ERG Replicate 1 RWPE_ERG_rep1


title: Starved LNCaP cells treated with JQ1 followed by DHT Replicate 2 LNCaP_DHT+JQ1_rep2

source_name: Total RNA from Starved LNCaP cells treated with JQ1 followed by DHT

value: JQ1 followed by DHT


title: Starved LNCaP cells treated with MDV followed by DHT Replicate 1 LNCaP_DHT+MDV3100_rep1

source_name: Total RNA from Starved LNCaP cells treated with MDV followed by DHT

value: MDV followed by DHT


title: Starved LNCaP cells treated with MDV followed by DHT Replicate 2 LNCaP_DHT+MDV3100_rep2


title: Starved LNCaP cells treated with JQ1 followed by DHT Replicate 1 LNCaP_DHT+JQ1_rep1


title: RWPE cells stably overexpressing ERG Replicate 2 RWPE_ERG_rep2


title: Starved LNCaP cells treated with Bic. followed by DHT Replicate 1 LNCaP_DHT+Bic_rep1


title: Starved VCaP cells treated with Bic. followed by DHT Replicate 2 VCaP_DHT+Bic_rep2

source_name: Total RNA from Starved VCaP cells treated with Bic. followed by DHT

value: VCaP

value: AR positive, ERG fusion positive

source_name: Total RNA from Starved VCaP cells treated with vehicle control


title: Starved LNCaP cells treated with DHT Replicate 2 LNCaP_DHT_rep2

source_name: Total RNA from Starved LNCaP cells treated with DHT

value: DHT


title: Starved VCaP cells treated with MDV followed by DHT Replicate 1 VCaP_DHT+MDV_rep1

source_name: Total RNA from Starved VCaP cells treated with MDV followed by DHT

value: prostate cancer cells


title: Starved VCaP cells treated with Bic. followed by DHT Replicate 1 VCaP_DHT+Bic_rep1


title: Wild type, 1mM phosphate, 8 hours. Rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Wild type plants supplemented with 30μM phosphate (8 hours). Replicate 2

hyb_protocol: 10µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, SantaClara, CA). Each sample was added to a hybridization solution containing 100mM2-(N-morpholino) ethanesulfonic acid, 1M Na+,and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, 2006). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003).

label: Biotin

organism: Arabidopsis thaliana

source_name: Wild type, 1mM phosphate, 8 hours

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents(Affymetrix, Santa Clara, CA) to produce biotin-labeled cRNA. The cRNA preparations (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Plants were grown on Johnson medium with 1 mM Pi (7 days), transferred to -Pi medium (2 days).

extract_protocol: RNA was isolated from three independent biological samples for each condition using the RNeasy Plant Mini Kit (Qiagen). Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).

treatment_protocol: Plants were transferred to liquid medium supplemented with 30 μM As(V), 30 μM Pi, 1mM Pi (or not supplemented) for indicated times.

tag: ecotype

tag: genotype

value: Wild Type

tag: supplement

value: Phosphate (1mM)

value: 8 hours


title: Starved LNCaP cells treated with DHT Replicate 1 LNCaP_DHT_rep1


title: Wild type, 30μM phosphate, 8 hours. Rep3

description: Wild type plants supplemented with 30μM phosphate (8 hours). Replicate 3

source_name: Wild type, 30μM phosphate, 8 hours

value: Phosphate (30μM)

tag: time


title: DU145 cells treated with JQ1 Replicate 2 DU145_JQ1_0.5µM_rep2

source_name: Total RNA from DU145 cells treated with JQ1

value: AR negative

source_name: Total RNA from DU145 cells treated with DMSO


title: Wild type, 30μM phosphate, 8 hours. Rep2


title: Wild type, 30μM arsenate, 8 hours. Rep3

description: Wild type plants supplemented with 30μM arsenate (8 hours). Replicate 3

source_name: Wild type, 30μM arsenate, 8 hours

value: Arsenate (30μM)


title: Starved VCaP cells treated with DHT Replicate 1 VCaP_DHT_rep1

source_name: Total RNA from Starved VCaP cells treated with DHT


title: Starved VCaP cells treated with JQ1 followed by DHT Replicate 1 VCaP_DHT+JQ1_rep1

source_name: Total RNA from Starved VCaP cells treated with JQ1 followed by DHT


title: Wild type, 1mM phosphate, 8 hours. Rep1

description: Wild type plants supplemented with 30μM phosphate (8 hours). Replicate 1


title: Wild type, 1mM phosphate, 8 hours. Rep3


title: Wild type, 30μM arsenate, 8 hours. Rep2

description: Wild type plants supplemented with 30μM arsenate (8 hours). Replicate 2


title: Starved VCaP cells treated with MDV followed by DHT Replicate 2 VCaP_DHT+MDV_rep2


title: Wild type, 30μM arsenate, 8 hours. Rep1

description: Wild type plants supplemented with 30μM arsenate (8 hours). Replicate 1


title: Starved VCaP cells treated with JQ1 followed by DHT Replicate 2 VCaP_DHT+JQ1_rep2


title: Wild type, 30μM phosphate, 8 hours. Rep1


title: Wild type, control (not supplemented). Rep3

description: Wild type plants control (not supplemented). Replicate 3

source_name: Wild type, control (not supplemented)

value: not supplemented


title: DU145 cells treated with JQ1 Replicate 1 DU145_JQ1_0.5µM_rep1

value: AR positive


title: Starved VCaP cells treated with DHT Replicate 2 VCaP_DHT_rep2


title: 22RV1 cells treated with JQ1 Replicate 2 22RV1_JQ1_0.5µM_rep2

source_name: Total RNA from 22RV1 cells treated with JQ1

source_name: Total RNA from 22RV1 cells treated with DMSO


title: Wild type, control (not supplemented). Rep1

description: Wild type plants control (not supplemented). Replicate 1


title: 22RV1 cells treated with JQ1 Replicate 1 22RV1_JQ1_0.5µM_rep1


title: Wild type, control (not supplemented). Rep2

description: Wild type plants control (not supplemented). Replicate 2


title: 36hr MTF rep B

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

description: 30 pooled zebrafish embryos

hyb_protocol: The samples were hybridized to a the Agilent 4x44K feature zebrafish microarray using the Agilent In situ Hybridization Kit Plus. Labeled cDNA was combined with the Agilent 10x Control Targets (to identify microarray corners). Microarray hybridizations were performed by Genome Technology Core at the Whitehead Institute for Biomedical Research (Cambridge, MA)

scan_protocol: Post-hybridization, microarray slides were washed as per the Agilent In situ Hybridization Kit Plus. Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Extraction of raw microarray results was performed using Agilent’s Feature Extraction software with background detrending (spatial and multiplicative). The data were normalized using a non-linear scaling method based on rank invariant probes. Cy3 signal saturated probes and probes not above background in all replicated were then removed prior to statistical analysis.

organism: Danio rerio

source_name: 30 pooled zebrafish embryos

label_protocol: For each RNA sample, a single microarray was hybridized with 750 ng Cy3 labeled cDNA using Agilent’s standard conditions for single-color microarrays. The Agilent Low-Input QuickAmp Labeling Kit was used for labeling.

growth_protocol: The TL (Tupfel/Long fin mutations) wild-type strain of zebrafish was used for all experiments. Fertilized eggs were obtained from multiple group breedings from a Mass Embryo Production System (Aquatic Habitats, Apopka, FL) with ~200 fish at a ratio of 2 female per 1 male fish.  Procedures used in these experiments were approved by the Animal Care and Use Committee of the University of Alabama, Tuscaloosa, Alabama, USA.

extract_protocol: Total RNA was prepared using the RNA STAT60 protocol (Tel-Test, Inc., TX).  RNA was quantified using a Nanodrop 2000C spectrophotometer and assessed for quality using an Agilent 2100 Bioanalyzer Lab-on-chip system. Only samples with RNA integrity number (RIN) between 9.8-10 were used for microarray analysis.

treatment_protocol: A Narishige IM-300 microinjector was used to microinject 1-2 cell embryos with ~100 pg of dnMTF-1 IVT mRNA (~2.1 nL microinjection volume with a concentration 50 ng/µL IVT mRNA), or ~100 pg of enhanced green fluorescent protein (eGFP) IVT mRNA.  The dnMTF-1 is an eGFP fusion protein so proper microinjection and distribution throughout the embryo could be visualized by fluorescent microscopy.  Immediately after microinjection, embryos from each treatment were divided into 4 replicates of 30 pooled embryos and held in 25 mL of 0.3X Danieau’s at 28.5°C under a 14 hour light/10 hour dark cycle.  eGFP positive embryos (dnMTF-1 and eGFP) were collected at 28 and 36 hpf and flash frozen in liquid nitrogen for future RNA isolation and microarray hybridization.

tag: developmental stage

value: embryo

value: injected at the 1-2 cell stage with ~100 pg of dnMTF-1 IVT mRNA

tag: sampling time

value: 36 hours post-fertilization (hpf)

tag: replicate


title: VCaP cells treated with JQ1 Replicate 1 VCaP_JQ1_0.5µM_rep1

source_name: Total RNA from VCaP cells treated with JQ1

value: non

source_name: Total RNA from VCaP cells treated DMSO


title: 36hr MTF rep D

description: 30 pooled zebrafish embryos


title: 36hr MTF rep A

description: 30 pooled zebrafish embryos


title: Col-0 (wt)

city: Valencia

first: Pablo

last: Vera

email: vera@ibmcp.upv.es, oliveros@cnb.csic.es

state: Valencia

address: Camino de Vera s/n

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP) UPV-CSIC

description: old project missing .CEL data

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the standard Affymetrix GeneChip Scanner

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by MAS5 suite (Affymetrix)

source_name: five-weeks-old-plant-wt

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds of csb3 mutant and wild-type Arabidopsis thaliana were kept at 4°C for 3 days and sown in jiffy7 peat pellets (Clause-Tezier Ibérica, Paterna, Spain). Plants were grown in a growth phytochamber for 5 weeks with a light intensity of approximately 150-200 µE m-2s-1 at 23°C under 10 h light/14 h dark cycles and 60% humidity.

extract_protocol: RNA was isolated with Tri-Reagent (Invitrogen) following manufacture´s instructions. High-quality RNA was obtained by using RNeasy Plant Mini Kit (Qiagen).

value: Columbia (Col-0)

value: wild type

tag: tissue

value: whole plant


title: 36hr GFP rep D

description: 30 pooled zebrafish embryos

value: injected at the 1-2 cell stage with ~100 pg of enhanced green fluorescent protein (eGFP) IVT mRNA


title: 36hr MTF rep C

description: 30 pooled zebrafish embryos


title: 36hr GFP rep B

description: 30 pooled zebrafish embryos


title: LNCaP cells treated with JQ1 Replicate 1 LNCaP_JQ1_0.5µM_rep1

source_name: Total RNA from LNCaP cells treated with JQ1

value: LNCaP

value: prostate cancer cells

value: AR positive, ETV1 fusion positive

source_name: Total RNA from LNCaP cells treated with DMSO


title: 28hr MTF rep C

description: 30 pooled zebrafish embryos

value: 28 hours post-fertilization (hpf)


title: VCaP cells treated with JQ1 Replicate 2 VCaP_JQ1_0.5µM_rep2

value: VCaP

value: AR positive, ERG fusion positive


title: 36hr GFP rep C

description: 30 pooled zebrafish embryos


title: csb3 mutant

description: old project missing .CEL data


title: U87-EV human glioblastoma xenograft - Bevacizumab treated 2

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: U87-EV human glioblastoma xenograft tumour stroma component

hyb_protocol: Target cDNA generated from each sample was then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization to Affymetrix Mouse Genome 430 2.0 arrays. Arrays were then washed and stained with streptavidin-phycoerythrin, before imaging on an Affymetrix GeneChip (3000) scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/Downloads/GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v4.pdf.

scan_protocol: Affymetrix GeneChip (3000) scanner

data_processing: Following scanning, .DAT files were processed using Affymetrix GCOS, 1.1.1.052, to generate .CEL files. Subsequent data processing was performed on these data using the affy, simpleaffy and GCRMA packages from BioConductor and R (V.2.11). mRNA was estimated using GCRMA, quantile normalized and log2 transformed.

source_name: U87-EV human glioblastoma xenograft_Bevacizumab

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer’s recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, 10 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in ~100-fold amplification of RNA. A complete description of procedures is available at:  http://bioinf.picr.man.ac.uk/mbcf/Downloads/GeneChip_Target_Prep_Protocol-CR-UK_v4.pdf

growth_protocol: All protocols were carried out under Indiana University Institutional Animal Care and Use Committee (IACUC), and UK Home Office approved protocols and regulations. 107 Human glioblastoma U87GM cells were were subcutaneously implanted into 7 to 8-week-old female BALB/c SCID mice (Harlan Sprague Dawley, Inc., Indiana), 100μl of cell suspension mixed with an equal volume of matrigel (BD Bioscience). Each group consisted of 5 mice. Tumor growth was measured using a caliper and calculated from the formula: “V = L x W x H x π / 0.52”.

extract_protocol: Xenograft samples were placed in RNAlater (Ambion, USA) overnight before storage at -80oC. RNA was extracted using Tri-reagant (Sigma-Aldrich) and washed using the Qiagen Spin column (Qiagen). RNA quality and quantity were confirmed using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: When tumors reached the size of 0.35-0.45 cm3, the mice were treated by intraperitoneal injection (i.p.) of Bevacizumab (10mg/kg body weight), dibenzazepine (DBZ; Syncom Groningen, The Netherlands) (8.1mmol/kg) (Li et al., 2011) or phosphate buffered saline (PBS) as a control. After 3 days, a second dose of Bevacizumab or DBZ was given and, 4h later, the mice were sacrificed and the tumors were collected. Half of each tumor sample was freshly frozen in liquid nitrogen and subsequently used for RNA extraction.

value: U87-EV human glioblastoma xenograft

tag: host

value: BALB/c SCID mouse

tag: treated with

value: Bevacizumab (10mg/kg body weight)


title: U87-EV human glioblastoma xenograft - Bevacizumab treated 3


title: U87-EV human glioblastoma xenograft - Bevacizumab treated 1


title: LNCaP cells treated with JQ1 Replicate 2 LNCaP_JQ1_0.5µM_rep2

tag: treatment

tag: transduced with


title: U87-EV human glioblastoma xenograft - Bevacizumab treated 4


title: 36hr GFP rep A

description: 30 pooled zebrafish embryos

value: embryo


title: 28hr MTF rep B

description: 30 pooled zebrafish embryos

value: injected at the 1-2 cell stage with ~100 pg of dnMTF-1 IVT mRNA


title: 28hr MTF rep A

description: 30 pooled zebrafish embryos


title: U87-EV human glioblastoma xenograft - dibenzazepine treated 4

source_name: U87-EV human glioblastoma xenograft_dibenzazepine

value: dibenzazepine (DBZ) (8.1mmol/kg)


title: 28hr MTF rep D

description: 30 pooled zebrafish embryos


title: U87-EV human glioblastoma xenograft - dibenzazepine treated 5


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 3 [HG-U133_Plus_2]

description: tumor tissue includes mouse host stroma cells

hyb_protocol: Target cDNA generated from each sample was then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).   Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization to HGU133plus2 arrays. Arrays were then washed and stained with streptavidin-phycoerythrin, before imaging on an Affymetrix GeneChip (3000) scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/Downloads/GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v4.pdf.

data_processing: Following scanning, .DAT files were processed using Affymetrix GCOS, 1.1.1.052, to generate .CEL files. Subsequent data processing was performed on these data using the affy, simpleaffy and GCRMA packages from BioConductor and R. mRNA was estimated using GCRMA and log2 values were used.

source_name: Bevacizumab treated

tag: specific-host

tag: tissue type

value: U87-EV human glioblastoma xenograft tumour


title: 28hr GFP rep D

description: 30 pooled zebrafish embryos


title: U87-EV human glioblastoma xenograft - dibenzazepine treated 2


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 2 [HG-U133_Plus_2]


title: U87-EV human glioblastoma xenograft - dibenzazepine treated 3


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 1 [HG-U133_Plus_2]