title: ATL_Sample164

first: Aiko

last: Sato-Otsubo

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Genomic DNA was digested by NspI, PCR amplified, fragmented, labeled and hybridized to the 250K Nsp array according to manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip(R)  scanner 3000.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0. Full data deposited contains whole genotype and intensity data of chromosome 9.

source_name: ATL primary specimen

label_protocol: Affymetrix standard protocol

extract_protocol: Genomic DNA was extracted using QIAamp DNA Kit (QIAGEN) or equivalent from isolated PBMC or lymph node cells of ATL patients.

tag: disease

value: ATL


title: ATL #28

status: Public on Feb 23 2012

type: RNA

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

description: mRNA expression in ATL

hyb_protocol: 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent)  for 1min at 37C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol : GE1-v5_95_Feb07  and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng total RNA using the Low RNA Linear Amplification Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations.  The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from ATL patients and healthy volunteers was subjected to PBMC isolation. Then PBMC from healthy donor was further subjected to isolation of CD4+ T-cells by negative isolation.

tag: cell type

value: Adult T-cell Leukemia (ATL) cells

tag: atl subtype

value: Chronic

tag: age (y)

tag: gender

value: M

tag: disease state

value: Adult T-cell Leukemia (ATL)


title: ATL_Sample162

type: genomic

description: Hybridized to 250K_Nsp

label: Biotin

molecule: genomic DNA


title: ATL_Sample160

description: Hybridized to 250K_Nsp


title: ATL_Sample158

description: Hybridized to 250K_Nsp


title: ATL_Sample166

description: Hybridized to 250K_Nsp


title: ATL_Sample165

description: Hybridized to 250K_Nsp


title: ATL_Sample167

description: Hybridized to 250K_Nsp


title: ATL_Sample150

description: Hybridized to 250K_Nsp


title: ATL_Sample145

description: Hybridized to 250K_Nsp


title: ATL_Sample154

description: Hybridized to 250K_Nsp


title: ATL_Sample157

description: Hybridized to 250K_Nsp


title: ATL_Sample168

description: Hybridized to 250K_Nsp


title: ATL_Sample155

description: Hybridized to 250K_Nsp


title: ATL_Sample152

description: Hybridized to 250K_Nsp


title: ATL_Sample147

description: Hybridized to 250K_Nsp


title: ATL_Sample142

description: Hybridized to 250K_Nsp


title: ATL_Sample161

description: Hybridized to 250K_Nsp


title: ATL_Sample163

description: Hybridized to 250K_Nsp


title: ATL_Sample143

description: Hybridized to 250K_Nsp


title: ATL_Sample144

description: Hybridized to 250K_Nsp


title: ATL_Sample153

description: Hybridized to 250K_Nsp


title: ATL_Sample159

description: Hybridized to 250K_Nsp


title: ATL_Sample156

description: Hybridized to 250K_Nsp


title: ATL_Sample151

description: Hybridized to 250K_Nsp


title: ATL_Sample146

description: Hybridized to 250K_Nsp


title: ATL_Sample141

description: Hybridized to 250K_Nsp


title: ATL_Sample149

description: Hybridized to 250K_Nsp


title: ATL_Sample148

description: Hybridized to 250K_Nsp


title: ATL_Sample140

description: Hybridized to 250K_Nsp


title: ATL_Sample139

description: Hybridized to 250K_Nsp


title: ATL_Sample135

description: Hybridized to 250K_Nsp


title: ATL_Sample137

description: Hybridized to 250K_Nsp


title: ATL_Sample133

description: Hybridized to 250K_Nsp


title: ATL_Sample129

description: Hybridized to 250K_Nsp


title: ATL_Sample126

description: Hybridized to 250K_Nsp


title: ATL_Sample120

description: Hybridized to 250K_Nsp


title: ATL_Sample127

description: Hybridized to 250K_Nsp


title: ATL_Sample116

description: Hybridized to 250K_Nsp


title: ATL_Sample132

description: Hybridized to 250K_Nsp


title: ATL_Sample138

description: Hybridized to 250K_Nsp


title: ATL_Sample110

description: Hybridized to 250K_Nsp


title: ATL_Sample118

description: Hybridized to 250K_Nsp


title: ATL_Sample114

description: Hybridized to 250K_Nsp


title: ATL_Sample124

description: Hybridized to 250K_Nsp


title: ATL_Sample134

description: Hybridized to 250K_Nsp


title: ATL_Sample131

description: Hybridized to 250K_Nsp


title: ATL_Sample115

description: Hybridized to 250K_Nsp


title: ATL_Sample125

description: Hybridized to 250K_Nsp


title: ATL_Sample122

description: Hybridized to 250K_Nsp


title: ATL_Sample121

description: Hybridized to 250K_Nsp


title: ATL_Sample123

description: Hybridized to 250K_Nsp


title: ATL_Sample113

description: Hybridized to 250K_Nsp


title: ATL_Sample130

description: Hybridized to 250K_Nsp


title: ATL_Sample117

description: Hybridized to 250K_Nsp


title: ATL_Sample136

description: Hybridized to 250K_Nsp


title: ATL_Sample111

description: Hybridized to 250K_Nsp


title: ATL_Sample112

description: Hybridized to 250K_Nsp


title: ATL_Sample128

description: Hybridized to 250K_Nsp


title: ATL_Sample109

description: Hybridized to 250K_Nsp


title: ATL_Sample119

description: Hybridized to 250K_Nsp


title: ATL_Sample102

description: Hybridized to 250K_Nsp


title: ATL_Sample100

description: Hybridized to 250K_Nsp


title: ATL_Sample104

description: Hybridized to 250K_Nsp


title: ATL_Sample105

description: Hybridized to 250K_Nsp


title: ATL_Sample86

description: Hybridized to 250K_Nsp


title: ATL_Sample95

description: Hybridized to 250K_Nsp


title: ATL_Sample99

description: Hybridized to 250K_Nsp


title: ATL_Sample88

description: Hybridized to 250K_Nsp


title: ATL_Sample97

description: Hybridized to 250K_Nsp


title: ATL_Sample106

description: Hybridized to 250K_Nsp


title: ATL_Sample108

description: Hybridized to 250K_Nsp


title: ATL_Sample107

description: Hybridized to 250K_Nsp


title: ATL_Sample94

description: Hybridized to 250K_Nsp


title: ATL_Sample83

description: Hybridized to 250K_Nsp


title: ATL_Sample91

description: Hybridized to 250K_Nsp


title: ATL_Sample96

description: Hybridized to 250K_Nsp


title: ATL_Sample103

description: Hybridized to 250K_Nsp


title: ATL_Sample84

description: Hybridized to 250K_Nsp


title: ATL_Sample93

description: Hybridized to 250K_Nsp


title: ATL_Sample101

description: Hybridized to 250K_Nsp


title: ATL_Sample81

description: Hybridized to 250K_Nsp


title: ATL_Sample79

description: Hybridized to 250K_Nsp


title: ATL_Sample80

description: Hybridized to 250K_Nsp


title: ATL_Sample90

description: Hybridized to 250K_Nsp


title: ATL_Sample82

description: Hybridized to 250K_Nsp


title: ATL_Sample87

description: Hybridized to 250K_Nsp


title: ATL_Sample85

description: Hybridized to 250K_Nsp


title: Tobacco-leaves-Tianzhu-Kaiyang, biological rep2

city: Beibei

first: Kun

last: Lu

state: Chongqing

address: 2 Tiansheng Road

department: College of Agronomy and Biotechnology

country: China

institute: Southwest University

description:
TZ-KY-rep2
Biological replicate 2 of 2. tobacco leaves Tianzhu vs Kaiyang

hyb_protocol: Hybridization was preformed at 42°C for 16 h in a CapitalBio BioMixer II Hybridization Station (CapitalBio Crop.).

scan_protocol: Microarray slides were scanned with a LuxScan 10KA confocal laser scanner (CapitalBio Crop.) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: The obtained images were analyzed using LuxScan 3.0 software (CapitalBio Crop.), which employed the LOWESS (locally weighted scatter plot smoothing regression) method to minimize differences in dye incorporation efficiency in a two-channel microarray platform. Spots showing the fluorescent signal intensities were less than 800 units after subtracting the background in both channels were regarded as empty spots and not included in the downstream analysis. DEGs were selected on fold change < 0.5 or fold change > 2 and probe wise P value < 0.05, which was calculated for the microarray data using Students t-test. Comparison of transcription profiles between WN and TZ (WN/TZ) were indirectly analyzed based on the microarray data of WN/KY and TZ/KY.

organism: Nicotiana tabacum

source_name: tobacco leaves from Tianzhu

label_protocol: Labeling reactions were performed using the CapitalBio cRNA Amplification and Labeling Kit (CapitalBio Corp.) in the presence of a fluorescent dye (Cy5 and Cy3-dCTP) . RNA reference sample from KY was labeled with Cy3, and the samples from WN and TZ were labeled with Cy5. To rule out dye bias, the labeling of samples with these dyes was reversed (day swap method) .

growth_protocol: Three different growing regions of Guizhou Province in China, including a medium aroma tobacco region Longgang town, Kaiyang county (26°52′24.8″ N, 107°06′40.8″ E, 1130 m a.s.l., KY) and two light aroma tobacco regions Niupeng town, Weining county (27°06′40.8″ N, 103°48′57.3″ E, 2111 m a.s.l., WN) and Shexue town, Tianzhu county (26˚57′15″ N, 109˚15′30″ E, 640 m a.s.l., TZ) were chosen for plant cultivation in 2009, according to the production standard of high quality tobacco leaves routinely used in the locality. For gene expression analysis, middle portions of mature leaves (about 65 cm in length) from three individual plants each region were harvested at 70 days after transplanting.

extract_protocol: Total RNA was extracted from 100 mg of tobacco leaves using the Plant RNA Mini Kit (Watson Biotechnologies, Inc., Shanghai, China) according to the manufacturer’s instructions. RNA samples were collected from three biological replicates. DNase digestion was performed with RNase-free DNase I (TaKaRa) for removal of any residual DNA.

treatment_protocol: Middle portions of mature leaves from three individual plants each region were collected when plants were 3 months old. All samples were immediately frozen in liquid nitrogen and sent to the CapitalBio Corporation (Beijing, China) for microarray analysis.

tag: cultivar

value: Yunyan 85

tag: growing region

value: light aroma tobacco regions

tag: age

value: 3 month-old

tag: tissue

value: middle portions of mature leaves

source_name: tobacco leaves from Kaiyang

value: medium aroma tobacco regions


title: ATL_Sample98

description: Hybridized to 250K_Nsp


title: Tobacco-leaves-Tianzhu-Kaiyang, biological rep1

description:
TZ-KY-rep1
Biological replicate 1 of 2. tobacco leaves Tianzhu vs Kaiyang


title: ATL_Sample92

description: Hybridized to 250K_Nsp


title: Tobacco-leaves-Weining-Kaiyang, biological rep2

description:
WN-KY-rep2
Biological replicate 2 of 2. tobacco leaves Weining vs Kaiyang

source_name: tobacco leaves from Weining


title: ATL_Sample89

description: Hybridized to 250K_Nsp


title: Normal-#20

description: miRNA expression in healthy donor

hyb_protocol: 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 5min and with GE Wash buffer 2 (Agilent)  for 5min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K miRNA microarray slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: US45103006_251911810135_S01_H_grid) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD4+ T-cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and Hybridization Kit (Agilent) according to the manufacturer's instructions.

value: whole blood

tag: disease status

value: healthy control


title: Normal-#21

description: miRNA expression in healthy donor


title: Normal-#22

description: miRNA expression in healthy donor


title: Tobacco-leaves-Weining-Kaiyang, biological rep1

description:
WN-KY-rep1
Biological replicate 1 of 2. tobacco leaves Weining vs Kaiyang


title: Normal-#19

description: miRNA expression in healthy donor


title: ATL_Sample76

description: Hybridized to 250K_Nsp


title: Normal-#18

description: miRNA expression in healthy donor


title: ATL_Sample78

description: Hybridized to 250K_Nsp


title: Normal-#16

description: miRNA expression in healthy donor


title: ATL_Sample60

description: Hybridized to 250K_Nsp


title: Normal-#17

description: miRNA expression in healthy donor


title: ATL_Sample75

description: Hybridized to 250K_Nsp


title: ATL_Sample70

description: Hybridized to 250K_Nsp


title: ATL_Sample74

description: Hybridized to 250K_Nsp


title: ATL_Sample69

description: Hybridized to 250K_Nsp


title: ATL_Sample71

description: Hybridized to 250K_Nsp


title: ATL_Sample61

description: Hybridized to 250K_Nsp


title: ATL_Sample63

description: Hybridized to 250K_Nsp


title: ATL_Sample72

description: Hybridized to 250K_Nsp


title: ATL_Sample65

description: Hybridized to 250K_Nsp


title: ATL_Sample67

description: Hybridized to 250K_Nsp


title: ATL_Sample68

description: Hybridized to 250K_Nsp


title: ATL_Sample64

description: Hybridized to 250K_Nsp


title: Normal-#12

description: miRNA expression in healthy donor


title: Normal-#13

description: miRNA expression in healthy donor


title: Normal-#15

description: miRNA expression in healthy donor


title: ATL_Sample58

description: Hybridized to 250K_Nsp


title: ATL_Sample66

description: Hybridized to 250K_Nsp


title: Normal-#9

description: miRNA expression in healthy donor


title: Normal-#14

description: miRNA expression in healthy donor


title: Normal-#11

description: miRNA expression in healthy donor


title: ATL_Sample57

description: Hybridized to 250K_Nsp


title: Normal-#10

description: miRNA expression in healthy donor


title: Normal-#8

description: miRNA expression in healthy donor


title: Normal-#7

description: miRNA expression in healthy donor


title: ATL_Sample53

description: Hybridized to 250K_Nsp


title: Normal-#6

description: miRNA expression in healthy donor


title: Normal-#5

description: miRNA expression in healthy donor


title: ATL_Sample77

description: Hybridized to 250K_Nsp


title: ATL_Sample54

description: Hybridized to 250K_Nsp


title: Normal-#3

description: miRNA expression in healthy donor


title: Normal-#4

description: miRNA expression in healthy donor


title: ATL_Sample52

description: Hybridized to 250K_Nsp


title: Normal-#1

description: miRNA expression in healthy donor


title: ATL_Sample59

description: Hybridized to 250K_Nsp


title: ATL-#52

description: miRNA expression in ATL

source_name: PBMC


title: ATL_Sample73

description: Hybridized to 250K_Nsp


title: ATL_Sample62

description: Hybridized to 250K_Nsp


title: ATL-#51

description: miRNA expression in ATL


title: ATL_Sample51

description: Hybridized to 250K_Nsp


title: ATL-#50

description: miRNA expression in ATL


title: ATL-#48

description: miRNA expression in ATL


title: ATL-#47

description: miRNA expression in ATL


title: Normal-#2

description: miRNA expression in healthy donor


title: ATL_Sample56

description: Hybridized to 250K_Nsp


title: ATL-#43

description: miRNA expression in ATL


title: ATL-#44

description: miRNA expression in ATL


title: ATL_Sample50

description: Hybridized to 250K_Nsp


title: ATL_Sample46

description: Hybridized to 250K_Nsp


title: ATL-#42

description: miRNA expression in ATL


title: ATL_Sample48

description: Hybridized to 250K_Nsp


title: ATL_Sample43

description: Hybridized to 250K_Nsp


title: ATL-#46

description: miRNA expression in ATL


title: ATL-#41

description: miRNA expression in ATL


title: ATL_Sample45

description: Hybridized to 250K_Nsp


title: ATL_Sample42

description: Hybridized to 250K_Nsp


title: ATL_Sample44

description: Hybridized to 250K_Nsp


title: ATL_Sample35

description: Hybridized to 250K_Nsp


title: ATL_Sample55

description: Hybridized to 250K_Nsp


title: ATL-#45

description: miRNA expression in ATL


title: ATL-#37

description: miRNA expression in ATL


title: ATL-#40

description: miRNA expression in ATL


title: ATL-#36

description: miRNA expression in ATL


title: ATL_Sample36

description: Hybridized to 250K_Nsp


title: ATL-#39

description: miRNA expression in ATL


title: ATL-#35

description: miRNA expression in ATL


title: ATL_Sample39

description: Hybridized to 250K_Nsp


title: ATL_Sample34

description: Hybridized to 250K_Nsp


title: ATL_Sample49

description: Hybridized to 250K_Nsp


title: ATL_Sample37

description: Hybridized to 250K_Nsp


title: ATL_Sample38

description: Hybridized to 250K_Nsp


title: ATL-#33

description: miRNA expression in ATL


title: ATL-#38

description: miRNA expression in ATL


title: ATL_Sample40

description: Hybridized to 250K_Nsp


title: ATL-#32

description: miRNA expression in ATL


title: ATL_Sample33

description: Hybridized to 250K_Nsp


title: ATL_Sample41

description: Hybridized to 250K_Nsp


title: ATL-#31

description: miRNA expression in ATL


title: ATL-#30

description: miRNA expression in ATL


title: ATL-#29

description: miRNA expression in ATL


title: ATL-#28

description: miRNA expression in ATL


title: ATL-#34

description: miRNA expression in ATL


title: ATL_Sample47

description: Hybridized to 250K_Nsp


title: ATL-#26

description: miRNA expression in ATL


title: ATL_Sample28

description: Hybridized to 250K_Nsp


title: ATL_Sample30

description: Hybridized to 250K_Nsp


title: ATL-#24

description: miRNA expression in ATL


title: ATL-#22

description: miRNA expression in ATL


title: ATL_Sample32

description: Hybridized to 250K_Nsp


title: ATL_Sample29

description: Hybridized to 250K_Nsp


title: ATL-#21

description: miRNA expression in ATL


title: ATL_Sample31

description: Hybridized to 250K_Nsp


title: ATL-#23

description: miRNA expression in ATL


title: ATL_Sample26

description: Hybridized to 250K_Nsp


title: ATL_Sample25

description: Hybridized to 250K_Nsp


title: ATL-#20

description: miRNA expression in ATL


title: ATL_Sample23

description: Hybridized to 250K_Nsp


title: ATL_Sample27

description: Hybridized to 250K_Nsp


title: A673/TR/siDAX clone2

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

description: Ewing sarcoma

hyb_protocol: Ten ug of cRNA were fragmented by heating at 94ºC for 20 min in fragmentation buffer, subsequently diluted in hybridization buffer  and hybridized to Human Whole Genome CodeLink Bioarrays for 20 hours at 37ºC in an Innova 40 shaking incubator (New Brunswick). After hybridization, microarrays were washed in 0.75 x TNT buffer (1 x TNT = 0.15 mol/L NaCl, 0.05% Tween 20, 0.1 mol/L Tris-HCl, pH 7.6) for 1 h at 46ºC, incubated with Cy5-streptavidin for 30 min at room temperature, washed in 1 x TNT four times for 5 minutes each, followed by two rinses in 0.1 x SSC, 0.05% Tween 20, and then dried by centrifugation.

scan_protocol: Slides were scanned with an Axon GenePix Scanner

data_processing: Data were processed using the CodeLink Expression Analysis Software v4.0 (GE Healthcare)

label: biotin

source_name: A673/TR/siDAX clone2, + doxycycline 72 hr

label_protocol: Double-stranded cDNA and biotin-labeled cRNA were generated following the manufacturer's instructions, except that biotin-16-UTP (Roche Applied Biosystems) was used instead of biotin-11-UTP. Biotin-labeled cRNA was purified on an Rneasy column (Qiagen), quantified by UV spectrophotometry , and analyzed for integrity using an Agilent 21200 Bioanalyzer

growth_protocol: Cells were cultured in DMEM suplemented with 10% tetracycline-free fetal bovine serum and antibiotics.

extract_protocol: Total RNA was isolated with TRI reagent (Sigma Aldrich) and its integrity was assessed using an Agilent 2100 Bioanalyzer

treatment_protocol: Cells were cultured in the presence of doxycycline (1 ug/ml) for 72 hours to induce the expression of GFP (control), EWS/FLI1 and DAX1-specific siRNAs

tag: cell line

tag: transgene

tag: sample type

value: clone


title: ATL-#19

description: miRNA expression in ATL


title: A673/TR/siDAX pool

description: Ewing sarcoma

source_name: A673/TR/siDAX pool, + doxycycline 72 hr

value: pool


title: ATL-#18

description: miRNA expression in ATL


title: ATL_Sample24

description: Hybridized to 250K_Nsp


title: A673/TR/siDAX clone1

description: Ewing sarcoma

source_name: A673/TR/siDAX clone1, + doxycycline 72 hr


title: ATL_Sample22

description: Hybridized to 250K_Nsp


title: ATL-#17

description: miRNA expression in ATL


title: A673/TR/siEF clone3

description: Ewing sarcoma

source_name: A673/TR/siEF clone3, + doxycycline 72 hr


title: ATL_Sample21

description: Hybridized to 250K_Nsp


title: A673/TR/siEF pool

description: Ewing sarcoma

source_name: A673/TR/siEF pool, + doxycycline 72 hr


title: ATL_Sample17

description: Hybridized to 250K_Nsp


title: ATL_Sample20

description: Hybridized to 250K_Nsp


title: ATL-#12

description: miRNA expression in ATL


title: ATL-#9

description: miRNA expression in ATL


title: A673/TR/siEF clone1

description: Ewing sarcoma

source_name: A673/TR/siEF clone1, + doxycycline 72 hr


title: A673/TR/siGFP clone3

description: Ewing sarcoma

source_name: A673/TR/siGFP clone3, + doxycycline 72 hr

value: GFP


title: A673/TR/siGFP pool

description: Ewing sarcoma

source_name: A673/TR/siGFP pool, + doxycycline 72 hr


title: ATL_Sample19

description: Hybridized to 250K_Nsp


title: ATL_Sample15

description: Hybridized to 250K_Nsp


title: ATL-#8

description: miRNA expression in ATL


title: A673/TR/siDAX clone3

description: Ewing sarcoma

source_name: A673/TR/siDAX clone3, + doxycycline 72 hr


title: ATL_Sample11

description: Hybridized to 250K_Nsp


title: A673/TR/siGFP clone2

description: Ewing sarcoma

source_name: A673/TR/siGFP clone2, + doxycycline 72 hr


title: ATL_Sample18

description: Hybridized to 250K_Nsp


title: ATL-#4

description: miRNA expression in ATL


title: ATL_Sample16

description: Hybridized to 250K_Nsp


title: ATL_Sample13

description: Hybridized to 250K_Nsp


title: CaseI (myeloma) 0 minutes [BM]

city: Be'er Yacob

first: Yossi

last: Cohen

address: Zeriffin

department: Hematology

country: Israel

institute: Asaf Harofeh University Hospital

description:
bone marrow
CaseI_bone-marrow_0_minutes.CEL

hyb_protocol: Biotin-labeled cRNA was hybridized onto 1.0 ST Expression Bead Chips

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed Affymetrix gene expression console

source_name: CaseI (myeloma) 0 minutes

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

growth_protocol: Cultured bone marrow cells were grown in high cell density imposing cell-cell contact

extract_protocol: Frozen samples were lyzed by adding 300 µl lysis buffer to tubes. Samples stored in RNAlater were fractionated and lyzed by x10 volumes (v/v) lysis buffer. RNA was isolated by MagNA Pure LC RNA Isolation procedure using MagNA Pure instrument (Roche). Integrity of RNA was examined by Agilent 2100 Bioanalyzer.

value: myeloma

tag: sample source

value: bone marrow

tag: protocol

value: Immediate fixation following aspiration

tag: time

value: 0 minutes


title: WT mouse lung, biological rep2

city: Los Angeles

first: Aik

middle: T

last: Ooi

address: 650 Charles E Young Dr S, Factor 9-240

department: Pediatrics

country: USA

institute: UCLA

description: Gene expression data from mouse lung upper left lobe

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained according to standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to standard protocol.

data_processing: The data was analyzed using Matlab R2011b with Bioinformatics Toolbox to read in Affymetrix microarray data and normalize the data using Robust Multi-array Average procedure. Filter to remove probes yielding maximum intensity levels below 100 was applied.

organism: Mus musculus

source_name: WT mouse lung

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

treatment_protocol: Mice were given doxycycline-treated (final concentration 2 mg/mL) water for 7 days. After 7 days, mice were euthanized and the left upper lobes of the lungs were removed for RNA extraction.

value: mouse lung upper left lobe

tag: strain

tag: genotype/variation

value: wildtype

value: 6-10 weeks old mouse


title: ATL-#2

description: miRNA expression in ATL

value: ATL


title: ATL_Sample9

description: Hybridized to 250K_Nsp

source_name: ATL primary specimen

tag: disease


title: CaseJ (myeloma) 660 minutes [BM]

description:
bone marrow
CaseJ_bone-marrow_660_minutes.CEL

source_name: CaseJ (myeloma) 660 minutes

value: Delayed fixation following aspiration

value: 660 minutes


title: CaseI (myeloma) 180 minutes [BM]

description:
bone marrow
CaseI_bone-marrow_180_minutes.CEL

source_name: CaseI (myeloma) 180 minutes

value: 180 minutes


title: A673/TR/siGFP clone1

description: Ewing sarcoma

source_name: A673/TR/siGFP clone1, + doxycycline 72 hr


title: CaseH (myeloma) 120 minutes [BM]

description:
bone marrow
CaseH_bone-marrow_120_minutes.CEL

source_name: CaseH (myeloma) 120 minutes

value: 120 minutes


title: ATL-#6

description: miRNA expression in ATL

source_name: PBMC

value: whole blood


title: WT mouse lung, biological rep1


title: ATL_Sample5

description: Hybridized to 250K_Nsp


title: ATL_Sample14

description: Hybridized to 250K_Nsp


title: ATL_Sample10

description: Hybridized to 250K_Nsp


title: CaseH (myeloma) 0 minutes [BM]

description:
bone marrow
CaseH_bone-marrow_0_minutes.CEL

source_name: CaseH (myeloma) 0 minutes


title: CaseG (myeloma) 480 minutes [BM]

description:
bone marrow
CaseG_bone-marrow_480_minutes.CEL

source_name: CaseG (myeloma) 480 minutes

value: 480 minutes


title: WT mouse lung, biological rep3


title: ATL-#1

description: miRNA expression in ATL


title: ATL_Sample8

description: Hybridized to 250K_Nsp


title: ATL_Sample6

description: Hybridized to 250K_Nsp


title: WT mouse lung, biological rep4


title: ATL_Sample4

description: Hybridized to 250K_Nsp


title: CaseG (myeloma) 120 minutes [BM]

description:
bone marrow
CaseG_bone-marrow_120_minutes.CEL

source_name: CaseG (myeloma) 120 minutes


title: CaseG (myeloma) 0 minutes [BM]

description:
bone marrow
CaseG_bone-marrow_0_minutes.CEL

source_name: CaseG (myeloma) 0 minutes


title: JEC21-1 hr, rep2 swap

city: Murfreesboro

first: Erin

last: McClelland

state: TN

address: 1301 East Main Street, P.O. Box 60

department: Biology

institute: Middle Tennessee State University

description: JEC21 incubated with mAb 18B7 or MOPC for 1 hour at 37 C

hyb_protocol: 2ug of each aRNA was paired, then fragmented according to manufacturer’s protocol (Fragmentation Reagents; ABI-Ambion).  Each paired, fragmented sample was normalized to 13ul, then suspended in Formamide-based hybridization buffer (vial 7-Genisphere) (26ul) and Kreablock (Kreatech Diagnostics) (13ul).  The hybridization solution was heated to 70C for 5 minutes, then allowed to cool to room temperature.  48ul of hybridization solution was added to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Slides were gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays were treated with Dyesaver (Genisphere).

scan_protocol: The microarray slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer, San Mateo, CA) to detect Cy3 and Cy5 fluorescence.  Laser power was kept constant and photomultiplier tube values were set for optimal intensity with minimal background.  An additional scan (low PMT) was done for each slide with the PMT such that <1% of the elements were saturating in order to characterize spots which were saturated at the higher PMT setting.

data_processing: Background subtracted raw intensity values were extracted from the .gpr files from each of the channels. The box plots showed minimum variability of the expression values and therefore no normalization was required. The data has been transformed into two-class unpaired data format as required by Significance Analysis of Microarrays (SAM) software. Two files corresponding to strain 24067 at time course of 2 h and 4 h that offered comparison between 18b7 and MOPC types have been created. Similarly, three files corresponding to time course 1, 2  and 4 h that offered comparison between 18b7 and MOPC types were created for strain JEC21. Using t-statistic as the test statistic, 100 random permutations, k-Nearest neighbor imputer and 10 neighbors, we selected probes with false discovery rate 0 or an insignificant value.

organism: Cryptococcus neoformans

source_name: JEC21 after 1 hour

label_protocol: RNA transcripts were first amplified by T7 linear amplification using MessageAmpII aRNA amplification kit; (ABI-Ambion, cat#AM 1751).   700ng of RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol. aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns (Kreatech Diagnostics) according to manufacturer’s protocol.  The labeled RNAs were then quantitated on a NanoDrop spectrophotometer.

growth_protocol: C. neoformans strains 24067 (serotype D) or JEC21 (serotype D) were grown from frozen stocks in Yeast Peptone Dextrose (YPD) media for 24-36 hours (mid-log phase) at 37 ºC and then washed three times with phosphate buffered saline (PBS).  Approximately 4 x 107 cells were aliquoted into a 6-well plate and allowed to settle to the bottom of the plate for 10-30 minutes at room temperature.

extract_protocol: RNA was extracted using the Rneasy Midi Kit and genomic DNA removed using the Message Clean Kit from GenHunter.

treatment_protocol: Near-saturating concentrations of mAb 18B7 or the control mAb MOPC were added slowly so as not to disturb the cell monolayer and promote aggregation. Cells+mAb were incubated for 1, 2 or 4 hours at 37 C.

tag: treatment

value: 1 h

source_name: JEC21 after 1 hours


title: CaseF (myeloma) 420 minutes [BM]

description:
bone marrow
CaseF_bone-marrow_420_minutes.CEL

source_name: CaseF (myeloma) 420 minutes

value: 420 minutes


title: TG mouse lung, biological rep1

source_name: TG mouse lung

value: CC10-rtTA-IL13 transgenic (TG)


title: ATL_Sample12

description: Hybridized to 250K_Nsp


title: CaseF (myeloma) 120 minutes [BM]

description:
bone marrow
CaseF_bone-marrow_120_minutes.CEL

source_name: CaseF (myeloma) 120 minutes

value: myeloma


title: ATL_Sample3

description: Hybridized to 250K_Nsp


title: A673/TR/siEF clone2

description: Ewing sarcoma

source_name: A673/TR/siEF clone2, + doxycycline 72 hr

value: clone


title: JEC21-1 hr, rep1


title: CaseF (myeloma) 0 minutes [BM]

description:
bone marrow
CaseF_bone-marrow_0_minutes.CEL

source_name: CaseF (myeloma) 0 minutes

value: bone marrow

value: Immediate fixation following aspiration


title: JEC21-2 hrs, rep2 swap

description: JEC21 incubated with mAb 18B7 or MOPC for 2 hours at 37 C

source_name: JEC21 after 2 hours

value: 2 h


title: ATL_Sample2

description: Hybridized to 250K_Nsp

source_name: ATL primary specimen


title: CaseJ (myeloma) 0 minutes [BM]

description:
bone marrow
CaseJ_bone-marrow_0_minutes.CEL

source_name: CaseJ (myeloma) 0 minutes

value: 0 minutes


title: CaseD (myeloma) 0 minutes [BM]

description:
bone marrow
CaseD_bone-marrow_0_minutes.CEL

source_name: CaseD (myeloma) 0 minutes


title: ATL_Sample1

description: Hybridized to 250K_Nsp


title: CaseD (myeloma) 120 minutes [BM]

description:
bone marrow
CaseD_bone-marrow_120_minutes.CEL

source_name: CaseD (myeloma) 120 minutes


title: ATL_Sample7

description: Hybridized to 250K_Nsp


title: CaseC (myeloma) 270 minutes [PF]

description:
pleural fluid
CaseC_Pleural-fluid_270_minutes.CEL

source_name: CaseC (myeloma) 270 minutes

value: pleural fluid

value: Delayed fixation following spread of malignant cell sediment from the bottom tube

value: 270 minutes


title: CaseE (myeloma) 120 minutes [BM]

description:
bone marrow
CaseE_bone-marrow_120_minutes.CEL

source_name: CaseE (myeloma) 120 minutes

value: Delayed fixation following aspiration


title: CaseE (myeloma) 0 minutes [BM]

description:
bone marrow
CaseE_bone-marrow_0_minutes.CEL

source_name: CaseE (myeloma) 0 minutes


title: TG mouse lung, biological rep2

description: Gene expression data from mouse lung upper left lobe

value: mouse lung upper left lobe

value: 6-10 weeks old mouse


title: JEC21-1 hr, rep2


title: CaseC (myeloma) 120 minutes [culture]

description:
culture
CaseC_Culture_120_minutes.CEL

source_name: CaseC (myeloma) 120 minutes

value: bone marrow culture

value: Delayed fixation following spread from the bottom well

value: 120 minutes


title: CaseC (myeloma) 0 minutes [PF]

description:
pleural fluid
CaseC_Pleural-fluid_0_minutes.CEL

source_name: CaseC (myeloma) 0 minutes

value: Immediate fixation following spread of malignant cell sediment from the bottom tube


title: JEC21-2 hrs, rep2


title: CaseC (myeloma) 0 minutes [culture]

description:
culture
CaseC_Culture_0_minutes.CEL

value: Immediate fixation following spread from the bottom well


title: CaseB (remission) 120 minutes [BM]

description:
bone marrow
CaseB_remission_bone-marrow_120_minutes.CEL

source_name: CaseB (remission) 120 minutes

value: remission


title: CaseC (myeloma) 300 minutes  [BM]

description:
bone marrow
CaseC_bone-marrow_300_minutes.CEL

source_name: CaseC (myeloma) 300 minutes

value: myeloma

value: 300 minutes


title: CaseC (myeloma) 0 minutes [BM]

description:
bone marrow
CaseC_bone-marrow_0_minutes.CEL

value: bone marrow

value: Immediate fixation following aspiration


title: 24067-2 hrs, rep2

description: 24067 incubated with mAb 18B7 or MOPC for 2 hours at 37 C

source_name: 24067 after 2 hours

value: 2 h


title: CaseB (remission) 0 minutes [BM]

description:
bone marrow
CaseB_remission_bone-marrow_0_minutes.CEL

source_name: CaseB (remission) 0 minutes

value: 0 minutes


title: JEC21-2 hrs, rep1


title: 24067-1 hr, rep4

description: 24067 incubated with mAb 18B7 or MOPC for 1 hour at 37 C

hyb_protocol: Each sample pair (~24ul) is resuspended in formamide-based  hybridization buffer (vial 7-Genisphere) (26ul),  and Array 50dT blocker (Genisphere) (2ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity in the dark.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and nuclease-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.

data_processing: The gene expression data were averaged across the RNA pools and analyzed (GeneSpring 7.2, Agilent, Redwood City, CA) taking into account the local background intensity and the Cy3/Cy5 dye swap. Twenty percent of the data were used to calculate the Lowess fit at each point and then a Lowess curve was fit to the log-intensity versus log-ratio plot.  After this, the mean signal to Lowess-adjusted controlled ratios was calculated.  The cross-chip averages were derived from the antilog of the mean of the natural log ratios across the two microarrays.  The data were then filtered in the following manner.  First, oligonucleotide elements that received a “present” call by the ScanArray software in half of the high PMT scans in either dye were identified for each condition and all others were excluded from the analysis.  Second, the data were filtered for genes in which the mean of the replicates had > 2-fold change and p<0.05. The Benjamini & Hoechberg false discovery rate for multiple testing corrections was then done for all genes showing changes in gene expression (p<0.01).

source_name: 24067 after 1 hour

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere).  Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer.  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 2ug of total RNA and the solution is incubated at 80C for 5 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (0.5ul), 5X first strand buffer (2ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (0.5ul), 0.1M DTT (1ul), and Superscript II RNase H- Reverse Transcriptase (0.5ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 1.0M NaOH/ 100mM EDTA (1.0ul) and incubation at 65C for 10 minutes then neutralized with 2M Tris-HCL, pH 7.5 (1.2ul).  For RNA expression level comparison, samples are paired.

value: 1 h


title: JEC21-2 hrs, rep1 swap


title: 24067-2 hrs, rep1


title: JEC21-4 hrs, rep2 swap

description: JEC21 incubated with mAb 18B7 or MOPC for 4 hours at 37 C

source_name: JEC21 after 4 hours

value: 4 h


title: CaseB (myeloma) 120 minutes [BM]

description:
bone marrow
CaseB_bone-marrow_120_minutes.CEL

source_name: CaseB (myeloma) 120 minutes

value: Delayed fixation following aspiration


title: 24067-2 hrs, rep1 swap


title: 24067-1 hr, rep4 swap


title: CaseB (myeloma) 0 minutes [culture]

description:
culture
CaseB_Culture_0_minutes.CEL

source_name: CaseB (myeloma) 0 minutes


title: CaseB (myeloma) 0 minutes [BM]

description:
bone marrow
CaseB_bone-marrow_0_minutes.CEL


title: 24067-2 hrs, rep2 swap


title: CaseB (myeloma) 540 minutes [BM]

description:
bone marrow
CaseB_bone-marrow_540_minutes.CEL

source_name: CaseB (myeloma) 540 minutes

value: 540 minutes


title: 24067-1 hr, rep3 swap


title: 24067-4 hrs, rep2

description: 24067 incubated with mAb 18B7 or MOPC for 4 hours at 37 C

source_name: 24067 after 4 hours


title: JEC21-4 hrs, rep2


title: CaseA (myeloma) 17 minutes [BM]

description:
bone marrow
CaseA_bone-marrow_17_minutes.CEL

source_name: CaseA (myeloma) 17 minutes

value: 17 minutes


title: DC_KO_MOCK_rep2

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: Gene expression data from Nlrp10 deficient DCs

hyb_protocol: Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.

scan_protocol: The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.

data_processing: Raw microarray data in CEL file format were read in and normalized with the RMA method provided by the R oligo package

source_name: Nlrp10 deficient DCs

label_protocol: 10ug of amplified cRNA is placed into a reaction with a random primer and then onto to generate a second cycle of 1st strand sense direction cDNA. The cDNA is purified using the Ambion bead cleanup as described previously and quantitated. 5.5ug of sscDNA is then enzymatically fragmented using ADP and UDG using the Affymetrix Terminal Labeling kit and ran on the Agilent bioanalyzer to ensure proper transcript size. The fragmented material is then labeled using TdT and then placed into a hybridization cocktail.

growth_protocol: Bone marrow cells were plated at 1 x 106 cells/mL in 4 mL per well of 6 well NON-TC treated plates. Cell were fed by removing 1.5 mL and adding 2 mL DC Media on days 2, 4 and 6. DCs were stimulated on day 8. DC media: RPMI-1640 supplemented with Penicillin (100 U/ml) , Streptomycin (100 μg/ml), glutamine (2 mM), 2-mercaptoethanol (50 μM), 10% heat-inactivated FCS, 1% GM-CSF hybridoma media and rmGM-CSF (10 ng/mL)

extract_protocol: RNA was extracted using Qiagen RNeasy MiniKit

treatment_protocol: WT and KO BMDCs were treated with or without LPS (1 μg/mL) overnight. Loosly adherent cells were rinsed from the plate using cold PBS and RNA isolated.

tag: cell type

value: dendritic cell

value: Nlrp10 deficient


title: CaseA (myeloma) 0 minutes [BM]

description:
bone marrow
CaseA_bone-marrow_0_minutes.CEL

source_name: CaseA (myeloma) 0 minutes

tag: disease state


title: DC_KO_MOCK_rep1


title: CaseB (myeloma) 60 minutes [culture]

description:
culture
CaseB_Culture_60_minutes.CEL

source_name: CaseB (myeloma) 60 minutes

value: bone marrow culture

value: Delayed fixation following spread from the bottom well

value: 60 minutes


title: CaseA (myeloma) 120 minutes [BM]

description:
bone marrow
CaseA_bone-marrow_120_minutes.CEL

source_name: CaseA (myeloma) 120 minutes

value: 120 minutes


title: DC_KO_LPS_rep2

description: Gene expression data from Nlrp10 deficient DCs treated with LPS

source_name: Nlrp10 deficient DCs treated with LPS

value: treated with LPS


title: JEC21-4 hrs, rep1 swap


title: 24067-1 hr, rep3


title: DC_WT_LPS_rep2

description: Gene expression data from Wild Type treated with LPS

source_name: Wild Type treated with LPS

value: Wild Type


title: DC_KO_LPS_rep1


title: JEC21-4 hrs, rep1


title: 24067-4 hrs, rep2 swap


title: 24067-1 hr, rep2 swap


title: 24067-1 hr, rep1


title: 24067-1 hr, rep2


title: 24067-1 hr, rep1 swap


title: DC_WT_LPS_rep1


title: 24067-4 hrs, rep1  swap


title: DC_WT_MOCK_rep2

description: Gene expression data from Wild Type

source_name: Wild Type


title: DC_WT_MOCK_rep1

description: Gene expression data from Wild Type


title: WT mouse lung, biological rep3

description: miRNA expression data from mouse lung upper left lobe

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse miRNA Array. GeneChips were washed and stained according to standard Affymetrix protocol.

data_processing: The raw expression data were first processed for background estimation and correction, normalization, and summarization using miRNAQCTools, an Affymetrix software specifically developed for the GeneChip miRNA arrays.

source_name: WT mouse lung

value: mouse lung upper left lobe

value: wildtype

value: 6-10 weeks old mouse


title: WT mouse lung, biological rep4


title: WT mouse lung, biological rep2


title: dt27J, rep3

city: Ottawa

first: Scott

middle: D

last: Ryan

state: ON

address: 501 Smyth Rd

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
2010-07-23_dt_3
P4 dt27j dorsal root ganglia tissue, analysis of pre-phenotype stage.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture, and 100 ul of the mixture was hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37C GE Wash buffer 2 (Agilent), and then air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using the one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 0.10 XDR, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

Raw data were processed using GeneSpring GX (Agilent). Using the gMedian signal transformed to log base 2, the probes were normalized within the sample by quantiles, and the samples were then normalized by baseline transformation through the median of each sample.

source_name: P4 DRG tissue, dt27J

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300ng RNA using the Quick Amp Labeling Kit, one-color kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Animals were housed in a temperature/humidity controlled environment on a 12 hour light-dark cycle.  All animal procedures were performed in accordance with institutional guidelines (Animal Care and Veterinary Services and Ethics, University of Ottawa).

extract_protocol: Total RNA was isolated with the Absolutely RNA Mini-Prep Kit (Stratagene) following the manufacturer's protocol. RNA quantity and quality was assessed with the NanoDrop ND-1000. Integrity of the RNA was determined by agarose gel.

treatment_protocol: Following dissection of dorsal root ganglia, tissue was flash frozen in liquid nitrogen and stored at -80 degees Centigrade until RNA was extracted.

tag: background strain

tag: genotype

value: dorsal root ganglia


title: TG mouse lung, biological rep1

source_name: TG mouse lung

value: CC10-rtTA-IL13 transgenic (TG)

tag: age


title: TG mouse lung, biological rep2

tag: tissue


title: dt27J, rep2

description:
2010-04-08_dt_2
P4 dt27j dorsal root ganglia tissue, analysis of pre-phenotype stage.


title: 24067-4 hrs, rep1

label_protocol:
RNA transcripts were first amplified by T7 linear amplification using MessageAmpII aRNA amplification kit; (ABI-Ambion, cat#AM 1751).   700ng of RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol. aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns (Kreatech Diagnostics) according to manufacturer’s protocol.  The labeled RNAs were then quantitated on a NanoDrop spectrophotometer.
RNA transcripts were first amplified by T7 linear amplification using MessageAmpII aRNA amplification kit; (ABI-Ambion, cat#AM 1751).   700ng of RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol. aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns (Kreatech Diagnostics) according to manufacturer’s protocol.  The labeled RNAs were then quantitated on a NanoDrop spectrophotometer.

value: 4 h


title: WT mouse lung, biological rep1


title: WT, rep3

description:
2010-07-23_wt_3
P4 WT dorsal root ganglia tissue, littermate control.

source_name: P4 DRG tissue, WT

value: WT


title: dt27J, rep1

description:
2010-04-08_dt_1
P4 dt27j dorsal root ganglia tissue, analysis of pre-phenotype stage.


title: WT, rep2

description:
2010-04-08_wt_2
P4 WT dorsal root ganglia tissue, littermate control.


title: WT, rep1

description:
2010-04-08_wt_1
P4 WT dorsal root ganglia tissue, littermate control.


title: Wt rep2

city: Saskatoon

first: Raju

last: Datla

address: 110 Gymnasium Place

institute: NRC-PBI

description: Biological replicate 2 of 2. WT cSAMs

hyb_protocol: 5 µg fragmented Cy5-aRNAs were mixed with hybridization buffer (6xSSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionized formamide, 0.1 mg/mL sheared salmon sperm DNA and 0.04% SDS) and hybridized to the Combimatrix Brassica 90K arrays at 45°C overnight in the dark. After hybridization, stringent washes were performed according to the manufacturer’s instructions, and the slides were immediately coated with an imaging solution (CombiMatrix) prior to scanning.

scan_protocol: Scanning on a GenePix 4000B scanner (Axon Instruments, CA, USA) using 400 PMT, 5µm resolution and 100% laser power.

data_processing: The image analysis was performed using GenePix Pro version 6.0 software (Axon Instruments, CA, USA). After automatic alignment, feature indicators were manually moved, resized and fine-tuned. The local background corrected spot fluorescence intensities for the Cy5 channel were saved as GPR files.    The GPR files were loaded in GeneSpring GX 11.0 (Agilent Technologies Inc. and Strand Life Sciences Pvt. Ltd) with percentile shift normalization and baseline to median of all samples.  Signal intensity cut-off was set to 200. One way ANOVA analysis was carried out with the asymptotic p-value computation method.  Multiple testing correction method is Benjamini-Hochberg FDR. Corrected p-value (Benjamini-Hochberg FDR) cut-off set to 0.05 and fold change is more than 2.

organism: Brassica napus

source_name: cSAMs of WT

label_protocol: RNA amplification was carried out using the MessageAmp aRNA kit (Ambion, Catalog# 1750) according to the supplied protocol. During the second round of in vitro transcription, aminoallyl-UTP was incorporated into the newly synthesized aRNA.Dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: Microspore derived embyros were cultured as outlined in Belmonte et al. 2006 (Physiologia Plantarum 127:690-700)

extract_protocol: RNA was expracted using a RNAqueous Micro, from Ambion

value: Wt

value: shoot meristem


title: Wt rep1

description: Biological replicate 1 of 2. WT cSAMs


title: A5 antisense line with decreased BnSTM expression rep1

description: Biological replicate 1 of 2. A5 cSAMs

source_name: cSAMs of  A5


title: colon_INT_T1003_cardA

status: Public on Feb 22 2012

city: Milano

first: James

middle: F

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare

description: MicroRNA expression data of sporadic colon cancer patient 2108728

data_processing: The cycle threshold (Ct) is defined as the number of cycles required for the fluorescent signal to cross the threshold in qPCR and was quantified using the Sequence Detector System (SDS) software version 2.2.2 (Applied Biosystem, Foster City, CA). The undetermined data were set to the Ct value of 40. Data were normalized data using the mean U6 on each card (4 technical replicates).

label: FAM dye

source_name: Colon, RNA

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

tag: type

value: T

tag: patient

tag: Stage

value: II

tag: status

value: NED

tag: cea

tag: apc

tag: kras


title: colon_INT_N143_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2535254

value: N


title: colon_INT_T64_cardA

description: MicroRNA expression data of sporadic colon cancer patient 8103314

value: III

value: ED


title: colon_INT_T1005_cardA

description: MicroRNA expression data of sporadic colon cancer patient 9927424


title: colon_INT_N1004_cardA


title: colon_INT_N153_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2618350


title: colon_INT_N1002_cardA


title: colon_INT_N1000_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2901136


title: colon_INT_N35_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2507524


title: colon_INT_T1001_cardA

value: IV


title: colon_INT_N15_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523788


title: colon_INT_N75_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2514062


title: S101 sense line with increased BnSTM expression rep1

description: Biological replicate 1 of 2. S101 cSAMs

source_name: cSAMs of  S101


title: S101 sense line with increased BnSTM expression rep2

description: Biological replicate 2 of 2. S101 cSAMs


title: JEC21-1 hr, rep1 swap

description: JEC21 incubated with mAb 18B7 or MOPC for 1 hour at 37 C

source_name: JEC21 after 1 hour

tag: strain

tag: time

value: 1 h

source_name: JEC21 after 1 hours


title: colon_INT_T80_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2525570


title: A5 antisense line with decreased BnSTM expression rep2

description: Biological replicate 2 of 2. A5 cSAMs


title: colon_INT_N101_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2525403


title: colon_INT_N149_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2800128


title: colon_INT_N25_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2510059


title: colon_INT_T28_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2502694


title: colon_INT_T6_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2517863


title: colon_INT_T26_cardA


title: colon_INT_T150_cardA

value: I


title: colon_INT_N95_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2510751


title: colon_INT_N27_cardA


title: colon_INT_N54_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2507980


title: colon_INT_N155_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2914433


title: colon_INT_T156_cardA


title: colon_INT_T92_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2506571


title: colon_INT_N71_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2522853


title: colon_INT_N159_cardA

description: MicroRNA expression data of sporadic colon cancer patient 9016328


title: colon_INT_N17_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2527001


title: colon_INT_N13_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2521269


title: colon_INT_N3_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523478


title: colon_INT_T154_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2618350


title: colon_INT_T146_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2713204


title: colon_INT_T88_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2507219


title: colon_INT_T16_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523788


title: colon_INT_T106_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2436469


title: colon_INT_T152_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2120580


title: colon_INT_N87_cardA


title: colon_INT_T59_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523477


title: colon_INT_N105_cardA


title: colon_INT_T110_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2103972


title: colon_INT_T14_cardA


title: colon_INT_N91_cardA


title: colon_INT_N145_cardA


title: colon_INT_T100_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2534321


title: colon_INT_N49_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2520527


title: colon_INT_N99_cardA


title: colon_INT_T4_cardA


title: colon_INT_N151_cardA


title: colon_INT_N147_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2629057


title: colon_INT_T50_cardA


title: colon_INT_T108_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2437932


title: colon_INT_T160_cardA


title: colon_INT_N5_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2517863


title: colon_INT_T12_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2519163


title: colon_INT_T144_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2535254


title: colon_INT_N157_cardA

description: MicroRNA expression data of sporadic colon cancer patient 9111362


title: colon_INT_T96_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2510751


title: colon_INT_T158_cardA


title: colon_INT_T18_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2527001


title: colon_INT_N11_cardA


title: colon_INT_T36_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2507524


title: colon_INT_T55_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2519768


title: colon_INT_T1005_cardB

description: MicroRNA expression data of sporadic colon cancer patient 9927424


title: colon_INT_N1002_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2108728


title: colon_INT_T1003_cardB


title: colon_INT_N35_cardB


title: colon_INT_N15_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523788


title: colon_INT_N1000_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2901136


title: colon_INT_T1001_cardB


title: colon_INT_T112_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2435300


title: colon_INT_T90_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2515795


title: colon_INT_N1004_cardB


title: colon_INT_T102_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2525403


title: colon_INT_N107_cardA


title: colon_INT_N111_cardA


title: colon_INT_N89_cardA


title: colon_INT_T64_cardB

description: MicroRNA expression data of sporadic colon cancer patient 8103314


title: colon_INT_N143_cardB


title: colon_INT_N79_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2525570


title: colon_INT_T76_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2514062


title: colon_INT_N60_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523477


title: colon_INT_T72_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2522853


title: colon_INT_N75_cardB


title: colon_INT_T53_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2507980


title: colon_INT_T80_cardB


title: colon_INT_N101_cardB


title: colon_INT_T26_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2510059


title: colon_INT_N56_cardA


title: colon_INT_N153_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2618350


title: colon_INT_N63_cardA


title: colon_INT_N25_cardB


title: colon_INT_T6_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2517863


title: colon_INT_N109_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2103972


title: colon_INT_N67_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2523712


title: colon_INT_N149_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2800128


title: colon_INT_N71_cardB


title: colon_INT_N54_cardB


title: colon_INT_T150_cardB


title: colon_INT_N145_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2713204


title: colon_INT_T148_cardA

description: MicroRNA expression data of sporadic colon cancer patient 2629057


title: colon_INT_N27_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2502694


title: colon_INT_N95_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2510751


title: colon_INT_T28_cardB


title: colon_INT_N155_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2914433


title: colon_INT_T68_cardA


title: colon_INT_T156_cardB


title: colon_INT_T16_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523788


title: Methylation in 0 min dnaC2 rep2

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

country: Germany

institute: Synmikro

hyb_protocol: 12.5 µl of labeld DpnI cut and non cut DNA was mixed with 5 µl 12x MES, 12 µl 5M Sodium chloride, 12 µl formamide, 2.5 µl EDTA and 6 µl 10% Triton X-100. 45µl of this hybridization mix was used for in each chamber of the gasket slide. Arrays were hybridized in an Agilent hybridisation oven at 55 °C for about 36 h and washed with washbuffer I (300 ml 20x SSPE; 0.5 ml 10% N-Lauroylsarcosine, 700ml water) and washbuffer II (3 ml 20x SSPE, 1.8 ml PEG200, 995 ml water) for 5 min each.

scan_protocol: Arrays were scanned on an Agilent SureScan High-Resolution Scanner per manufacturer's protocol

data_processing: Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis.

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

source_name: Methylation in 0 min dnaC2 rep2

label_protocol: ~200ng of DNA used for labeling with Cy3 (DpnI cut) or Cy5-dCTP (no DpnI cut) using the BioPrime kit from Invitrogen.

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 0min before crosslinking.

extract_protocol: 500 ng chrom. DNA was digested with 10U of MseI (NEB) in 10μL volume for 3h at 37°C and heat inactivated for 20 min at 65°C. To prepare adapters 100pmol of MseIlong (AGTGGGATTCCGCATGCTAGT) and MseIshortnewNo (TAACTAGCATGC)  were annealed in 8µl ddH2O by heating to 95°C for 3 min and than cooling to 70°C and subsequently to 15°C with 1°C per min. At 15°C 10µl MseI digested DNA, 2µl ligase buffer and 400U T4-ligase (NEB) were added and ligated over night. Ligase was inactivated at 65°C for 10 min. One halve of the ligation mix was digested with 20 U DpnI for 2h at 37°C in a volume of 50µl and the other halve treated similar with water instead of DpnI as control. 5µl of the DNA was amplified in a 50 µl PCR reaction with 0.2mM dNTPs, 0.5µM primer MseIlong, 10µl Phusion HF buffer and 1U Phusion DNA polymerase (Finnzymes) with the program 30sec 98°C, 20x(30sec 98°C, 30 sec 62°C, 60sec 72°C), 10 min 72°C. DNA was purified with a Qiagen PCR cleanup kit.

treatment_protocol: Cell cultures were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected from 15 ml by centrifugation and washed twice with cold TBS (pH7.5).The pellet wa resuspended in 300μL TE with 40 μl 10% SDS and 3 μl 0.5 M EDTA. After incubation for 5 min at 65°C 750μl isopropanole was added before centrifugation at 15600 rcf for 5 min. The pellet was resuspended in 500μL TE and 3μL RNase A (25mg/ml) was added and incubated for 30 min at 65°C. Subsequently, 100μL proteinase K (25 mg/ml) was added and samples incubated at  42°C for 2 h and 65°C for 6 h to reverse the crosslink followed by phenol extraction and precipitation with ethanol and Na-acetate. Precipitated DNA was resuspended in 50μL dH2O.

value: DpnI digested DNA

organism: Escherichia coli

source_name: untreated control

value: control


title: colon_INT_T88_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2507219


title: colon_INT_N159_cardB

description: MicroRNA expression data of sporadic colon cancer patient 9016328


title: Methylation in 0 min dnaC2 rep1

source_name: Methylation in 0 min dnaC2 rep1

treatment_protocol: 10 ml of cell culture was mixed with 5 ml ice cold killing buffer (20mM Tris and 5mM MgCl2 and 20mM NaN3) and cells collected by centrifugation (8000g, 4C, 3min). The supernatant was discarded and the pellet resuspended in 300μL TE with 40 μl 10% SDS and 3 μl 0.5 M EDTA. After incubation for 5 min at 65°C 750μl isopropanole was added before centrifugation at 15600 rcf for 5 min. The pellet was resuspended in 500μL TE and 2μL RNase A (25mg/ml) was added and incubated for 30 min at 65°C. Subsequently, 2μL proteinase K (25 mg/ml) was added and samples incubated at 37°C for 15 min followed by phenol extraction and precipitation with ethanol and Na-acetate. Precipitated DNA was resuspended in 50μL dH2O.


title: colon_INT_N105_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2436469


title: colon_INT_N13_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2521269


title: colon_INT_N3_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523478


title: colon_INT_T154_cardB


title: colon_INT_T110_cardB


title: Methylation in 15 min dnaC2 rep2

source_name: Methylation in 15 min dnaC2 rep2

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 15min before crosslinking.


title: colon_INT_T4_cardB


title: colon_INT_N91_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2506571


title: colon_INT_N87_cardB


title: colon_INT_T106_cardB


title: colon_INT_T59_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523477


title: Methylation in 15 min dnaC2 rep1

source_name: Methylation in 15 min dnaC2 rep1


title: colon_INT_T14_cardB


title: colon_INT_N49_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2520527


title: colon_INT_N99_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2534321


title: colon_INT_N151_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2120580


title: colon_INT_N17_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2527001


title: colon_INT_T152_cardB


title: colon_INT_T146_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2713204


title: colon_INT_T50_cardB


title: colon_INT_T108_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2437932


title: colon_INT_N111_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2435300


title: colon_INT_N107_cardB


title: colon_INT_N5_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2517863


title: colon_INT_T158_cardB

description: MicroRNA expression data of sporadic colon cancer patient 9111362


title: colon_INT_T144_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2535254


title: colon_INT_N157_cardB


title: colon_INT_T12_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2519163


title: colon_INT_T100_cardB


title: colon_INT_T55_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2519768


title: colon_INT_T112_cardB


title: colon_INT_N147_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2629057


title: colon_INT_T90_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2515795


title: colon_INT_T36_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2507524


title: colon_INT_N11_cardB


title: colon_INT_T102_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2525403


title: colon_INT_T96_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2510751


title: colon_INT_N79_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2525570


title: colon_INT_N89_cardB


title: Trial 2. Clone 6_MTZ_(Eh_Eia520620F_Eh), biological replicate 2

city: Shinjuku-ku

first: Gil

middle: Mallari

last: Penuliar

state: Tokyo

address: Toyama 1-23-1

department: Parasitology

institute: National Institute of Infectious Diseases

description: Gene expression data from MTZ-treated wild-type trophozoites.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Eh_Eia520620F_Eh Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw probe intensities were generated by the GeneChip Operating Software (GCOS) and GeneTitan Instrument. Resulting expression values were analyzed by GeneSpring GX 10.0.2 to identify differentially expressed genes.

organism: Entamoeba histolytica

source_name: Entamoeba histolytica, wild-type, MTZ treated

growth_protocol: (1) Wild-type amoeba were selected for metronidazole resistance by exposure to sublethal and gradual increase in drug concentration. (2) Wild-type and resistant amoeba were cultured in the absence or presence of metronidazole.

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

treatment_protocol: Cells were treated with 12 micromolar metronidazole.

value: whole body

tag: phenotype

value: wild-type

value: metronidazole


title: colon_INT_T76_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2514062


title: Trial 2. MTZR_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from untreated MTZ-resistant trophozoites.

source_name: Entamoeba histolytica, MTZR, untreated

value: metronidazole resistant

tag: treatment


title: Trial 1. Clone 6_MTZ_(Eh_Eia520620F_Eh), biological replicate 1


title: Trial 2. Clone 6_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from untreated wild-type trophozoites.

source_name: Entamoeba histolytica, wild-type, untreated


title: Trial 1. MTZR_MTZ_(Eh_Eia520620F_Eh), biological replicate 1

description: Gene expression data from MTZ-treated MTZ-resistant trophozoites.

source_name: Entamoeba histolytica, MTZR, MTZ treated


title: Trial 1. MTZR_(Eh_Eia520620F_Eh), biological replicate 1


title: colon_INT_N60_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523477


title: Trial 2. MTZR_MTZ_(Eh_Eia520620F_Eh), biological replicate 2


title: colon_INT_N63_cardB

description: MicroRNA expression data of sporadic colon cancer patient 8103314


title: Trial 1. Clone 6_(Eh_Eia520620F_Eh), biological replicate 1


title: colon_INT_T53_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2507980


title: SeqA in 15 min dnaC2 LB dam++ rep2

hyb_protocol: 25 µl of labeld IP and input DNA was mixed with 10 µl 12x MES, 24 µl 5M Sodium chloride, 24 µl formamide, 5 µl EDTA and 12 µl 10% Triton X-100. Arrays were hybridized in an Agilent hybridisation oven at 55 °C for about 36 h and washed with washbuffer I (300 ml 20x SSPE; 0.5 ml 10% N-Lauroylsarcosine, 700ml water) and washbuffer II (3 ml 20x SSPE, 1.8 ml PEG200, 995 ml water) for 5 min each.

data_processing: Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction and normalized to the array wide average. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis.

source_name: SeqA ChIP DNA

label_protocol: Usually DNA from six parallel immuno precipitations (each with 800 µl extract as described) was joint and labeled with Cy3-dCTP or Cy5-dCTP using the BioPrime kit from Invitrogen (random priming thie Klenow). A similar ammount of input DNA was labeld with Cy5-/Cy3-dCTP. The labeled ChIP DNA was purified using a Quiagen PCR purification kit.

extract_protocol: Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml lysozyme) and incubation at 37 °C for 30 min C followed by addition of 4 ml IP buffer cells were sonicated on ice with 12 times 30 sec and 30 sec breaks at an UP 400s Ultrasonic processor (Dr. Hielscher GmbH) with 100% power. After centrifugation for 10 min at 9000 g, 800 µl aliquotes of the supernatant were stored at -20 °C. 800 µl of sonicated cell extract (see above) were incubated with 20 µl protein A/G agarose beads (Ultralink) and antibody rotating at 4 °C. Washing was done with 500 µl buffer (2 x 500 µl IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X 100, 0.1 % Sodium deoxycholate, 0.1 % SDS], 1 x IP buffer with 500mM NaCl, 1 x wash buffer [10mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Sodium deoxycholate] and 1 x TE) followed by rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation. For elution, 100 µl elution buffer (50 mM Tris (pH 7.5), 10 mM EDTA, 1% SDS) was added to the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. After reversion of crosslink the DNA was purified with phenol/chloroform.

value: dnaC2, pMQ430

tag: chip antibody

value: SeqA

source_name: input DNA


title: SeqA in 50 min dnaC2 rep1

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 50min before crosslinking.


title: PE01

city: St Leonards, Sydney

first: Casina

last: Kan

state: NSW

address: RNSH, Pacific Hwy

department: Hormones and Cancer Group

country: Australia

institute: Kolling Institute of Medical Research

hyb_protocol: Samples were processed by the Adelaide Microarray Consortium

data_processing: Normalization was carried out by the Peter Wills Bioinformatics Centre

source_name: serous ovarian cancer cell line PE01

label_protocol: miRNA expression profiling was performed on RNA from the cell lines using 2-color (Cy-3 versus Cy-5) Exiqon MiRCURYTM Locked Nucleic Acid arrays (Geneworks Pty Ltd., Thebarton, SA, Australia; miRBase 8.2 for human; Adelaide Microarray Centre, SA, Australia). Triplicate arrays (including 1 dye-swap) were performed on the HOSE cell line and duplicate arrays (including 1 dye-swap) were performed on the SEOC cell lines. RNA from the cancer and HOSE cell lines were compared to a pool of total RNA (Ambion FirstChoice Human Total RNA Survey Panel, Applied Biosystems).

growth_protocol: All SEOC cell lines were cultured in RPMI 1640 (Gibco, Life Technologies Australia Pty Ltd, Mulgrave, VIC, Australia) supplemented with 10% (volume/volume) fetal bovine serum (SAFC Bioscience, Brooklyn, VIC, Australia) at 37°C with 5% CO2. Cells were grown to 80% confluence prior to harvesting for RNA extraction.

extract_protocol: RNA for miRNA microarray expression profiling of cell lines was extracted using Trizol (Invitrogen, Life Technologies Australia Pty Ltd), followed by LiCl precipitation (Ambion, Applied Biosystems) according to the manufacturers’ protocols. RNA quality was assessed by a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Australia, Scoresby, VIC, Australia) and Agilent Bioanalyzer (Agilent Technologies Australia, Forest Hills, VIC, Australia). Samples with RNA Integrity Numbers > 9 were used for further analyses.

treatment_protocol: The HOSE cell line expresses a temperature sensitive mutant of the SV40 large T-antigen, which enables it to proliferate at 34°C. The large T-antigen is inactivated when this cell line is cultured at 39°C [27]. HOSE was cultured in MCDB 105:Medium 199 (1:1) (Sigma-Aldrich Corporation, Sydney, NSW, Australia) and supplemented with 15% fetal bovine serum (SAFC Bioscience) at 34°C in 5% CO2. After plating, cells were allowed to attach for 24 hours at 34°C before incubating at 39°C in 5% CO2 for 72 hours prior to RNA extraction.

tag: cell line

tag: cell type

value: serous ovarian cancer

tag: reference


title: SeqA in 15 min dnaC2 LB

tag: genotype


title: OVCAR-3

scan_protocol: Samples were processed by the Adelaide Microarray Consortium

source_name: serous ovarian cancer cell line OVCAR-3

source_name: pool of total RNA (Ambion FirstChoice Human Total RNA Survey Panel, Applied Biosystems)


title: HOSE

source_name: human surface epithelial cells (HOSE)

value: HOSE

value: human surface epithelial

value: pool of total RNA (Ambion FirstChoice Human Total RNA Survey Panel, Applied Biosystems)


title: OV167

source_name: serous ovarian cancer cell line OV167


title: colon_INT_T72_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2522853

source_name: Colon, RNA

value: T


title: SeqA in 50 min dnaC2 rep2


title: OV202

source_name: serous ovarian cancer cell line OV202


title: SeqA in 15 min dnaC2 LB dam++ rep1


title: SeqA in 35 min dnaC2 rep2

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 35min before crosslinking.


title: SeqA in 35 min dnaC2 rep1


title: JB27

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet.
Raw data were log2-transformed. Data were inverted to facilitate use of HTqPCR (R/Bioconductor) for subsequent analysis. Quantile normalization was performed, and data were inverted to approximate log2 of abundance.

source_name: PBMC

label_protocol:
none (detection probe is labeled with a proprietary molecular barcode)
RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Johns Hopkins Microarray Core Facility

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from fresh blood using a standard Ficoll protocol. Total RNA was extracted from ten million PBMCs using the miRvana isolation kit (Ambion) per the manufacturer's protocol. RNA was eluted in 100 ul nuclease-free water.

tag: tissue

value: PBMC

tag: infection status

value: Uninfected Control


title: colon_INT_N109_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2103972

tag: type

value: N

tag: patient


title: JB24


title: colon_INT_T148_cardB

tag: Stage

value: II

tag: status

value: NED


title: JB23


title: JB26


title: colon_INT_N67_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2523712

tag: cea

tag: apc


title: JB22


title: colon_INT_T68_cardB

value: III

tag: kras


title: SeqA in 17 min dnaC2 rep2

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 17min before crosslinking.

tag: strain


title: SeqA in 16 min dnaC2 rep2

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 16min before crosslinking.


title: JB21

value: HIV-1 Elite Suppressor


title: SeqA in 16 min dnaC2 rep1


title: SeqA in 17 min dnaC2 rep1


title: SeqA in 15 min dnaC2 rep3


title: colon_INT_N56_cardB

description: MicroRNA expression data of sporadic colon cancer patient 2519768


title: SeqA in 15 min dnaC2 rep2


title: JB20


title: SeqA in 15 min dnaC2 rep1


title: JB16


title: JB15


title: JB22

description: Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards (2 per sample). Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNAs.

data_processing:
SDS software (Applied Biosystems) was used to collect data.
Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using HTqPCR (R/Bioconductor) and quantile normalization.

label: FAM

label_protocol: 100 ng total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.


title: JB14

value: HIV-1 Viremic


title: JB21


title: JB16


title: JB18


title: JB15


title: JB27


title: JB12


title: JB24


title: JB14


title: JB18


title: SeqA in 5 min dnaC2 rep2

growth_protocol: Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 5min before crosslinking.


title: JB13


title: JB11


title: JB10


title: SeqA in 0 min dnaC2 rep2

description: these data are to examine the effect of limited RNA digestion. We shortened the incubation to 30 min with an otherwise unchanged protocol to the parallel microarray data sets. This led to a high background signal!


title: SeqA in 0 min dnaC2 rep1


title: JB13


title: SeqA in 5 min dnaC2 rep1


title: SeqA in ter GATC cluster rep1

growth_protocol: Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking.


title: SeqA in ter GATC cluster rep2


title: SeqA in srlA GATC cluster rep2


title: SeqA in srlA GATC cluster rep1

description: these data are a comparison of crosslinked/ reversed with non crosslinked chromosomal DNA to assess the effect of crosslinking. The experimental set up did not include any ChIP.


title: JB12


title: Ezh2-null 2'MLL-AF9 BM-Cells, biological rep5

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.

scan_protocol: GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.

data_processing: RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).

source_name: Sorted GFP+/YFP+ bone marrow cells, Ezh2-null

label_protocol: Amplified cDNA was labeled using the NuGEN Encore Biotin Module.

growth_protocol: Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression.  Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.

extract_protocol: Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).

treatment_protocol: Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.

tag: background strain

tag: disease state

value: MLL-AF9-induced acute myeloid leukemia (AML)

value: sorted GFP+/YFP+ bone marrow cells


title: SeqA in hisA GATC cluster rep2

description: these data are a control experiment for the SeqA ChIP with wildtype E. coli

tag: chip antibody


title: JB08


title: JB07


title: JB10


title: JB09


title: JB07


title: JB05


title: JB06


title: JB06


title: JB11


title: SeqA in hisA GATC cluster rep1

description: these data are produced with an unmodiefied ChIP-Chip method which was found to give a high background signal!


title: JB05


title: JB04


title: SeqA in tnaA GATC cluster rep1


title: JB04


title: Ezh2-null 2'MLL-AF9 BM-Cells, biological rep3


title: WT 2'MLL-AF9 BM-Cells, biological rep3

source_name: Sorted GFP+/YFP+ bone marrow cells, WT

value: WT


title: Ezh2-null 2'MLL-AF9 BM-Cells, biological rep2


title: SeqA in tnaA GATC cluster rep2

value: SeqA


title: Ezh2-null 2'MLL-AF9 BM-Cells, biological rep1


title: SeqA in AB acetate rep2

growth_protocol: Cells were grown at 37 °C to an OD450 of about 0.15 in 100 ml AB acetate medium before crosslinking.

value: wildtype


title: SeqA in AB acetate rep1


title: Ezh2-null 2'MLL-AF9 BM-Cells, biological rep4


title: WT 2'MLL-AF9 BM-Cells, biological rep4


title: sars_mu_lung_STAT_Day5_novirus_#2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US23502338_251486818898_S01_GE1-v5_95_Feb07_1_3.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

source_name: lung

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 10-week-old mice were infected intranasally with either phosphate-buffered saline (PBS) alone (Invitrogen, Carlsbad, CA) or 1 × 10^5 PFU rMA15-PBS. Lungs were harvested for microarray at 2, 5 and 9 days-post infection for microarray.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: The left lobe of the lung from each animal was harvested, homogenized using TRIzol and stored at -80 degrees C prior to RNA extraction.

tag: genotype/variation

tag: virus infection

value: mock-infected (PBS)

tag: sample collection time post infection

value: 5 days

tag: biological replicate

value: lung


title: WT 2'MLL-AF9 BM-Cells, biological rep1

tag: genotype

tag: cell type


title: sars_mu_lung_STAT_Day5_novirus_#1

description: US23502338_251486818919_S01_GE1-v5_95_Feb07_1_1.txt

tag: tissue


title: sars_mu_lung_STAT_Day5_novirus_#3

description: US23502338_251486818896_S01_GE1-v5_95_Feb07_1_4.txt


title: JB01

tag: infection status


title: sars_mu_lung_STAT_Day9_rMA15_#2

description: US23502338_251486818922_S01_GE1-v5_95_Feb07_1_4.txt

value: SARS rMA15

value: 9 days


title: WT 2'MLL-AF9 BM-Cells, biological rep2


title: Eed-null MLL-AF9 BM-cells, biological rep3

source_name: Sorted GFP+/YFP+ bone marrow cells, Eed-null

growth_protocol: Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression.

treatment_protocol: Bone marrow cells from leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.

value: Eed-null


title: Eed-null MLL-AF9 BM-cells, biological rep2


title: CPTR treated CEM-ss

city: Hamburg

first: Nicole

last: Walz

address: Martinistr. 52

institute: Heinrich-Pette-Institut

description: treated with CPTR  vs. untreated CEM-ss cells

hyb_protocol: Equal amounts of control and sample RNA (825 ng each) were competitively hybridized. The array was hybridized for 17 h at 65°C rotating at 10 rpm. Arrays were washed as instructed by the Agilent Two-color Microarray-Based Gene Expression Analysis protocol (Version 5.0.1, August 2006).

scan_protocol: Arrays were scanned on a GenePix Personal 4100A scanner (Axon Instruments).

data_processing: Analysis and normalization was conducted using the GenePix Pro 6.0 software (Axon Instruments). Briefly, the DNA gene expression array grid template was adjusted to the array and subsequently all features were aligned and analyzed. Integrated settings were further used to flag features as 'good' when fulfilling the 'fair feature' criteria. For normalization all 'good' flagged spots were included, whereas control spots were excluded [11,111 ID_REFs]. Normalization was performed so that the mean of the ratio of medians of all normalization features is equal to 1. The standard deviation of all spots was calculated using Excel. A twofold change in the expression level was selected as cut off to determine differentially expressed genes.

source_name: CPTR treated CEM-ss

label_protocol: Total RNA was labeled as instructed by the Agilent Two-color Microarray-Based Gene Expression Analysis protocol (Version 5.0.1, August 2006). Labeling of 1 µg control and sample RNA was performed using the Agilent two-color Quick Amp Labeling Kit (5190-0444).

growth_protocol: Cells were maintained in RPMI 1640 ( 89%; PSN antibiotics (Gibco), 1%; fetal bovine serum, 10%).

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

treatment_protocol: 2x10^6 CEM-ss cells were starved for two hours in serum-free medium and subsequently treated with or without 1 µM cell permeable Tre-recombinase (CPTR) for 5 h. After protein transduction cells were maintained for 48 h in normal growth medium prior to RNA extraction.

tag: cell line

value: Human T4-Lymphoblastoid cell line (NIH, Cat. No. 776)

tag: treatment

value: treated with CPTR

source_name: Untreated CEM-ss

value: untreated


title: Ezh2-null MLL-AF9 BM-cells, biological rep4


title: sars_mu_lung_STAT_Day9_rMA15_#1

description: US23502338_251486818899_S01_GE1-v5_95_Feb07_1_1.txt


title: sars_mu_lung_STAT_Day9_rMA15_#3

description: US23502338_251486818896_S01_GE1-v5_95_Feb07_1_3.txt