title: Breast tumor sample 125

description: Gene expression data from breast cancer


title: Breast tumor sample 123

status: Public on Jul 23 2008

type: RNA

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre

description: Gene expression data from breast cancer

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Affymetrix).

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

tag: Tissue

value: breast


title: Breast tumor sample 122

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 44

description: Gene expression data from breast cancer (test set)

hyb_protocol: The biotin- labelled cRNA (20 µg) was fragmented at 94oC for 60 min to generate 50 to 200-base fragments. Following fragmentation, Array was hydrated with water and incubated at 65oC for 10 min prior to priming with pre-hybridization solution at 45oC for 30 min.  Biotin-labelled fragmented cRNAs (5 µg, 50 ng/µl) were hybridized to the array and incubated at 45oC for 16 hours with gentle rotation.

scan_protocol: GeneChips were scanned using the GenePix 4000B scanner

data_processing:
The data were analyzed with Microarray Imager software and customized program.

The related GPL5022 Platform includes only ~200 gene signatures, which vary from sample to sample in breast cancer. In other words, these samples are supposed to show various median expression levels based on the small scale of 200 genes. For this reason, control genes are used for normalization, rather than global normalization.

source_name: breast cancer sample

label_protocol: Synthesis of biotin-labeled cRNA from cDNA was performed using the GeneChip Expression 3’ Amplification Reagents IVT labelling kit (Affymetrix, Inc., Santa Clara, CA) at 37oC for 16 hours. Total RNA clean-up was performed using the Qiagen RNeasy kit (Qiagen, Inc., Valenica, CA) prior to synthesis of double stranded cDNA.


title: Breast tumor sample (test) 45


title: Breast tumor sample 120

description: Gene expression data from breast cancer


title: Breast tumor sample 121

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 47


title: Breast tumor sample (test) 43


title: Breast tumor sample 116

description: Gene expression data from breast cancer


title: Breast tumor sample 118

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 42


title: Breast tumor sample (test) 41


title: Breast tumor sample 117

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 39


title: Breast tumor sample (test) 40


title: Breast tumor sample (test) 38


title: Breast tumor sample (test) 36


title: Breast tumor sample (test) 37


title: Breast tumor sample 115

description: Gene expression data from breast cancer


title: Breast tumor sample 114

description: Gene expression data from breast cancer


title: Breast tumor sample 112

description: Gene expression data from breast cancer


title: Breast tumor sample 172

description: Gene expression data from breast cancer


title: Breast tumor sample 110

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 34


title: colon tumor sample 2

description: Gene expression data from colon cancer

source_name: colon tumor sample

value: colon


title: Breast tumor sample (test) 35


title: Breast tumor sample 111

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 32


title: Breast tumor sample (test) 33


title: Breast tumor sample (test) 31


title: Breast tumor sample 113

description: Gene expression data from breast cancer


title: Breast tumor sample 106

description: Gene expression data from breast cancer


title: Breast Normal sample 8

description: Gene expression data from breast cancer

source_name: Breast Normal sample


title: Breast tumor sample 109

description: Gene expression data from breast cancer


title: Breast Normal sample 12

description: Gene expression data from breast cancer


title: Breast tumor sample 107

description: Gene expression data from breast cancer


title: Breast tumor sample 105

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 30


title: Breast tumor sample (test) 29


title: Breast tumor sample 103

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 27


title: Breast tumor sample (test) 23


title: Breast tumor sample (test) 24


title: Breast tumor sample 102

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 28


title: Breast tumor sample 100

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 20


title: Breast tumor sample 97

description: Gene expression data from breast cancer


title: Breast tumor sample 98

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 26


title: Breast tumor sample (test) 18


title: Breast tumor sample (test) 17


title: Breast tumor sample (test) 16


title: Breast tumor sample (test) 25


title: Breast tumor sample (test) 15


title: Breast tumor sample 94

description: Gene expression data from breast cancer


title: Breast tumor sample 95

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 21


title: Breast tumor sample (test) 22


title: Breast tumor sample 101

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 14


title: Breast tumor sample 88

description: Gene expression data from breast cancer


title: Breast tumor sample 90

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 12


title: Breast tumor sample 89

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 13


title: Breast tumor sample (test) 11


title: Breast tumor sample (test) 8


title: Breast tumor sample 87

description: Gene expression data from breast cancer


title: Breast tumor sample 85

description: Gene expression data from breast cancer


title: Breast tumor sample 83

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 3


title: Breast tumor sample (test) 9


title: Breast tumor sample (test) 7


title: Breast tumor sample 81

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 5


title: Breast tumor sample 84

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 4


title: Breast tumor sample (test) 2


title: Breast tumor sample 80

description: Gene expression data from breast cancer


title: Breast tumor sample 82

description: Gene expression data from breast cancer


title: Breast tumor sample 78

description: Gene expression data from breast cancer


title: Breast tumor sample (training) 16

description: Gene expression data from breast cancer (training set)


title: Breast tumor sample 77

description: Gene expression data from breast cancer


title: Breast tumor sample 74

description: Gene expression data from breast cancer


title: Breast tumor sample 73

description: Gene expression data from breast cancer


title: Breast tumor sample 76

description: Gene expression data from breast cancer


title: Breast tumor sample 79

description: Gene expression data from breast cancer


title: Breast tumor sample (training) 14


title: Breast tumor sample (training) 15


title: Breast tumor sample 72

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 1


title: Breast tumor sample (training) 13


title: Breast tumor sample (training) 12


title: Breast tumor sample (training) 11


title: Breast tumor sample (test) 10


title: Breast tumor sample 75

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 6


title: Breast tumor sample (training) 9


title: Breast tumor sample (training) 10


title: Breast tumor sample (training) 8


title: Breast tumor sample 70

description: Gene expression data from breast cancer


title: Breast tumor sample 71

description: Gene expression data from breast cancer


title: Breast tumor sample (training) 7


title: Breast tumor sample 67

description: Gene expression data from breast cancer


title: Breast tumor sample 69

description: Gene expression data from breast cancer


title: Adult hind limb suspension vs. control Sample 3 Swap

city: Little Rock

first: Radhakrishnan

last: Nagarajan

state: AR

address: 4301 W Markham, Slot 781, Room: 3234

department: Department of Biostatistics

country: USA

institute: University of Arkansas for Medical Sciences

hyb_protocol: Hybridizations were performed on the Discovery Hybridization Station (Ventana Medical Systems, Tucson, AZ).

scan_protocol: Arrays were scanned using Perkin Elmer ScanArray 5000 (Perkin Elmer Life and Analytical Sciences, Boston, MA).

data_processing: Image analysis was performed using the adaptive circle method in ScanArray Express (Perkin Elmer). The (Cy3, Cy5) channels were subsequently LOWESS normalized to minimize systematic bias.

organism: Rattus norvegicus

source_name: soleus muscle

label_protocol: RNA from soleus muscle of control animals was labeled with Cy3 and those hindlimb suspended were labeled with Cy5. These were reveresed in the dye-swap

extract_protocol: Soleus muscle from one leg was frozen in liquid nitrogen and stored at -80ºC for RNA and protein isolation, and soleus muscle from the other leg was embedded in a freezing medium, frozen in liquid nitrogen-cooled isopentane, and stored at -80°C for determination of mean fiber cross sectional area (CSA).

tag: Strain

value: Brown Norway/F344, Gender:Male; Age:6 months, hindlimb suspension

value: Brown Norway/F344, Gender:Male; Age:6 months, control


title: Breast tumor sample 68

description: Gene expression data from breast cancer


title: Breast tumor sample 63

description: Gene expression data from breast cancer


title: Adult hind limb suspension vs. control Sample 3


title: Breast tumor sample (training) 6


title: Breast tumor sample 119

description: Gene expression data from breast cancer


title: Breast tumor sample 64

description: Gene expression data from breast cancer


title: Breast tumor sample 65

description: Gene expression data from breast cancer


title: Adult hind limb suspension vs. control Sample 2 Swap


title: Breast tumor sample 62

description: Gene expression data from breast cancer


title: Breast tumor sample 60

description: Gene expression data from breast cancer


title: Breast tumor sample 61

description: Gene expression data from breast cancer


title: Breast tumor sample (training) 5


title: Adult hind limb suspension vs. control Sample 2


title: Breast tumor sample 58

description: Gene expression data from breast cancer


title: Breast tumor sample 167

description: Gene expression data from breast cancer


title: Breast tumor sample (training) 4


title: Breast tumor sample (training) 3


title: Breast tumor sample (training) 2


title: Breast tumor sample (training) 1

data_processing:
The data were analyzed with Microarray Imager software and customized program.

The related GPL5022 Platform includes only ~200 gene signatures, which vary from sample to sample in breast cancer. In other words, these samples are supposed to show various median expression levels based on the small scale of 200 genes. For this reason, control genes are used for normalization, rather than global normalization..

The related GPL5022 Platform includes only ~200 gene signatures, which vary from sample to sample in breast cancer. In other words, these samples are supposed to show various median expression levels based on the small scale of 200 genes. For this reason, control genes are used for normalization, rather than global normalization.


title: Adult hind limb suspension vs. control Sample 1 Swap


title: Breast tumor sample 57

description: Gene expression data from breast cancer


title: Breast tumor sample 56

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 6 Swap

value: Brown Norway/F344, Gender:Male; Age:32 months, hindlimb suspension

value: Brown Norway/F344, Gender:Male; Age:32 months, control


title: Breast tumor sample 66

description: Gene expression data from breast cancer


title: Breast tumor sample 51

description: Gene expression data from breast cancer


title: Adult hind limb suspension vs. control Sample 1


title: Breast tumor sample 48

description: Gene expression data from breast cancer


title: Breast tumor sample 46

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 5


title: Breast tumor sample 47

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 5 Swap


title: Breast tumor sample 45

description: Gene expression data from breast cancer


title: Breast tumor sample 54

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 4 Swap


title: Breast tumor sample 50

description: Gene expression data from breast cancer


title: Breast tumor sample 53

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 6


title: Breast tumor sample 44

description: Gene expression data from breast cancer


title: Breast tumor sample 41

description: Gene expression data from breast cancer


title: Breast tumor sample 42

description: Gene expression data from breast cancer


title: Breast tumor sample 43

description: Gene expression data from breast cancer


title: Breast tumor sample 55

description: Gene expression data from breast cancer


title: Breast tumor sample 40

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 4


title: Breast tumor sample 38

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 3


title: Aged hind limb suspension vs. control Sample 3 Swap


title: Aged hind limb suspension vs. control Sample 2 Swap


title: Breast tumor sample 32

description: Gene expression data from breast cancer


title: Breast tumor sample 39

description: Gene expression data from breast cancer


title: Breast tumor sample 35

description: Gene expression data from breast cancer


title: Breast tumor sample 34

description: Gene expression data from breast cancer


title: Breast tumor sample 33

description: Gene expression data from breast cancer


title: Breast tumor sample 30

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 1


title: Breast tumor sample (test) 19


title: Aged hind limb suspension vs. control Sample 2


title: Breast tumor sample 23

description: Gene expression data from breast cancer


title: Breast tumor sample 22

description: Gene expression data from breast cancer


title: Aged hind limb suspension vs. control Sample 1 Swap


title: Breast tumor sample 24

description: Gene expression data from breast cancer


title: Breast tumor sample 27

description: Gene expression data from breast cancer


title: Breast tumor sample 29

description: Gene expression data from breast cancer


title: Breast tumor sample 16

description: Gene expression data from breast cancer


title: Breast tumor sample 19

description: Gene expression data from breast cancer


title: Breast tumor sample 14

description: Gene expression data from breast cancer


title: Breast tumor sample 26

description: Gene expression data from breast cancer


title: Thyroid tissue cultured with 1 microM amiodarone medium for 5 days

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

country: Japan

institute: Tokyo Women's Medical University

description: Thyroid follicles were cultured with or without Amiodarone for 5 days

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

scan_protocol: Images were quantified using AgilentMicroarray Scanner and Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: human thyroid follicles - untreated

label_protocol: 0.5 µg of total RNA were primed with 2 µl of 100 µM T16P7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10-8M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without Amiodarone (1microM) for 5 days.

tag: Amiodarone (-)

source_name: human thyroid follicles - amiodarone 1 microM treated

tag: Amiodarone 1 microM


title: Breast tumor sample 10

description: Gene expression data from breast cancer


title: Breast tumor sample 11

description: Gene expression data from breast cancer


title: Breast tumor sample 15

description: Gene expression data from breast cancer


title: Breast tumor sample 7

description: Gene expression data from breast cancer


title: Breast tumor sample 8

description: Gene expression data from breast cancer


title: Breast tumor sample 5

description: Gene expression data from breast cancer


title: Breast tumor sample 9

description: Gene expression data from breast cancer


title: Breast tumor sample 17

description: Gene expression data from breast cancer


title: Breast tumor sample 4

description: Gene expression data from breast cancer


title: Breast tumor sample 59

description: Gene expression data from breast cancer


title: Breast tumor sample 2

description: Gene expression data from breast cancer


title: mouse tendon-1

city: Baltimore

first: Shukti

last: Chakravarti

state: MD

address: 720 Rutland Ave

department: Medicine

institute: Johns Hopkins University School of Medicine

description: Detail could be found in " Differential gene expression patterns of the developing and adult mouse cornea compared to the lens and tendon" Experimental Eye Research. 2008 in press.

hyb_protocol: using standard Affymetrix procedures

scan_protocol: using standard Affymetrix procedures

data_processing:
The expression values of all probe sets are scaled to 150 of Target Intensity by using Affymetrix Microarray Suite 5.0. Two replicates of tendon were analyzed.
The model-based DNA-Chip Analyzer (dChip) software (http://www.dchip.org/) was used to normalize the data from the image files for array-to-array comparison (Li and Wong 2001).
The data table below reports both the MAS5.0- and dChip-calculated data.

organism: Mus musculus

source_name: mouse tendon

label_protocol: Targets were produced using standard Affymetrix procedures from 5ug of total RNA.

extract_protocol: Total RNA was extracted from pooled mouse tendons using TRIzol reagent.

tag: The Flexor digitorum longus tendons were dissected from 7-8 weeks old CD-1 mouse.


title: wt 502_24h

status: Public on Jul 22 2008

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: To compare the transcriptomes of T-cells from Gfi1-knockout cells with wildtype cells, spleenocytes  from wildtype and Gfi-knockout C57Bl/6 mice were isolated using panT-cell kit  in an AutoMACS device (Miltenyi). Cells were cultured with anti-CD3 plus anti-CD28 antibodies (2 µg antibody/ml) for the indicated time period. Total RNAs was isolated and subjected to microarray analysis on Affymetrix MOE430A_2.0 arrays.

hyb_protocol: Following fragmentation, 7.5 microgram of cRNA were hybridized for 16 hr at 45C on MOE430A_2.0A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GCOS version 1.4 (MAS5 algorithm) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000

label: Biotin

source_name: murine T-cells from wildtype mice activated by anti-CD3 plus anti-CD28 for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 1 microgram of total RNA (Expression Analysis Technical Manual, version2, Affymetrix).

extract_protocol: Isolation of total RNA was performed with TRIzol (Stratagene) according to the manufacturer's instructions

tag: AutoMACS (panT-cell kit) separated T-cells from wt mice


title: mouse tendon-2

tag: The flexor digitorum longus tendons were dissected from 7-8 weeks old CD-1 mouse.


title: adult mouse Lens-2

data_processing:
The expression values of all probe sets are scaled to 150 of Target Intensity by using Affymetrix Microarray Suite 5.0. Two replicates of Lens were analyzed.
The model-based DNA-Chip Analyzer (dChip) software (http://www.dchip.org/) was used to normalize the data from the image files for array-to-array comparison (Li and Wong 2001).
The data table below reports both the MAS5.0- and dChip-calculated data.

source_name: mouse Lens

extract_protocol: Total RNA was extracted from pooled mouse lens using TRIzol reagent.

tag: Lens were dissected from 7-8 weeks old CD-1 mouse.


title: wt 502_4h

source_name: murine T-cells from wildtype mice activated by anti-CD3 plus anti-CD28 for 4h


title: ko 501_24h

source_name: murine T-cells from Gfi1-knockout mice activated by anti-CD3 plus anti-CD28 for 24h

tag: AutoMACS (panT-cell kit) separated T-cells from Gfi1 knockout mice


title: ko 501_0h

source_name: murine T-cells from Gfi1-knockout mice

treatment_protocol: untreated control


title: wt 502_0h

source_name: murine T-cells from wildtype mice


title: wt CD4 M

description: Aim: to compare the transcriptomes of naïve CD4+ and CD8+ T-cells from Gfi1-knockout mice with wildtype cells, spleenocytes  from wildtype and Gfi-knockout C57Bl/6 mice were isolated, stained with CD44, CD4 and CD8 antibodies and separated by using a FACS Diva (Becton Dickinson). Total RNAs isolated from 2 mice each (approximately 2xE06 cells) were pooled and subjected to microarray analysis on Affymetrix MOE430A_2.0 arrays.

source_name: murine CD4+ CD44lo T-cells from wildtype mice

treatment_protocol: untreated

tag: FACS Diva sorted CD4+ CD44lo T-cells from wildtype mice


title: ko 501_8h

source_name: murine T-cells from Gfi1-knockout mice activated by anti-CD3 plus anti-CD28 for 8h


title: wt 502_8h

source_name: murine T-cells from wildtype mice activated by anti-CD3 plus anti-CD28 for 8h


title: ko 501_4h

source_name: murine T-cells from Gfi1-knockout mice activated by anti-CD3 plus anti-CD28 for 4h


title: wt CD8 M

source_name: murine CD8+ CD44lo T-cells from wildtype mice

tag: FACS Diva sorted CD8+ CD44lo T-cells from wildtype mice


title: Gene expression changes associated with the anti-angiogenic effect of KLK3 in HUVECs

city: Helsinki

first: Hannu

last: Koistinen

address: PO Box 63

department: Clinical Chemistry

country: Finland

institute: University of Helsinki

hyb_protocol: According to manufacturer's instructions (Agilent Technologies)

scan_protocol: Agilent

data_processing: Feature Extraction software (v 7.5.1)

source_name: Human umbilical vein endothelial cells treated with PSA (KLK3) for 18h

label_protocol: RNA input fluorescent linear amplification Kit (Agilent Technologies)

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: Cells cultured on top of basement membrane preparation

source_name: Control (i.e., buffer treated) human umbilical vein endothelial cells


title: K5601_WCE

status: Public on Jul 21 2008

type: genomic

city: London

first: claudio

last: d'ambrosio

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4)

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Input DNA from Schizosaccharomyces pombe cells from unbound fraction

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells in YE4S were cycling in a logaritmically growing phase

extract_protocol: Extraction was performed as previously described (Katou et al. 2003).

tag: Schizosaccharomyces pombe (972 background)

tag: Genotype

value: PY457 h90 rad21-HA3 leu1 ade6-M216

tag: logaritmically growing cells

tag: Starin

tag: Antibody

value: anti-PK


title: 057_IP1

source_name: ChIP DNA from yeast Schizosaccharomyces pombe cells

growth_protocol: Cells in YE4S were synchronized in metaphase by inactivation of nda3 for 6 hours at 20ºC

treatment_protocol: Extraction was performed as previously described (Katou et al. 2003)

value: Cnd2-9PK-kanR nda3-KM311

tag: nda3 arrest for 6 hours at 20ºC


title: adult mouse Lens-1

source_name: lens


title: normal murine lung biopsy_rep1

city: Detroit

first: Kami

last: Moin

state: MI

address: 540 E. Canfield

department: Pharmacology

institute: Wayne State University

description: Tissue sample

hyb_protocol: Following fragmentation, 6.5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Custom Protease520066F Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with Auto Loader.  Expression analysis settings at All Probe Sets Scale Factor 500, Normalization = 1.0, No Masking.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  Expression analysis settings were All Probe Sets Scale Factor 500, Normalization = 1.0, No Masking.

source_name: normal mouse lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, rev. 2 of 2004, Affymetrix).

growth_protocol: not relevant

extract_protocol: Trizol extraction of total RNA followed by RNA purification & DNase treatment with Qiagen RNeasy kit was performed according to the manufacturer's instructions.

treatment_protocol: no treatments

tag: Strain

value: Rag-2 null/C57Bl/6


title: normal murine lung biopsy_rep3

description: Tissue sample


title: normal murine mammary fat pad biopsy_rep4

description: Tissue sample

source_name: normal mammary fat pad, thorasic, Rag1 retired breeder

tag: Rag-1 tm1Mom retired female breeder at >6 weeks post lactation


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vitro on plastic_rep1

description: Tissue sample

growth_protocol: Standard growth conditions recommended by ATCC. Log phase cells were harvested.

tag: human breast carcinoma cell line_ATCC# HTB-26


title: ko CD8 N

source_name: murine CD8+ CD44lo T-cells from Gfi knockout mice

tag: FACS Diva sorted CD8+ CD44lo T-cells from Gfi1 knockout mice


title: Gene expression changes associated with the anti-angiogenic effect of KLK3 (PSA) on HUVECs replicate 3

source_name: KLK3 treated HUVECS replicate 3

tag: HUVECs grown on  basement membrane preparation

source_name: Control HUVECS replicate 3


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vitro on plastic_rep3

description: Tissue sample


title: ko CD4 N

source_name: murine CD4+ CD44lo T-cells from Gfi1 knockout mice

tag: FACS Diva sorted CD4+ CD44lo T-cells from Gfi1 knockout mice


title: Gene expression changes associated with the anti-angiogenic effect of KLK3 (PSA) on HUVECs replicate 2

source_name: KLK3 treated HUVECs data set 2

tag: Cells grown on basement membrane preparation

source_name: Control HUVECs data set 2


title: normal murine lung biopsy_rep2

description: Tissue sample


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vitro on plastic_rep2

description: Tissue sample


title: Universal reference standard RNA from mouse_SuperArray Bioscience Corp. Xpress Ref. GA005_Rep3

description: Tissue sample

source_name: Universal reference standard RNA

tag: See


title: Universal reference standard RNA from H. sapiens_SuperArray Bioscience Corp. Xpress Ref. GA004_Rep1

description: Tissue sample


title: Universal reference standard RNA from mouse_SuperArray Bioscience Corp. Xpress Ref. GA005_Rep2

description: Tissue sample


title: normal human breast tissue biopsy_rep10

description: Tissue sample

source_name: normal breast tissue

tag: Normal human mammary tissue biopsy from univolved area


title: normal human breast tissue biopsy_rep13

description: Tissue sample


title: Universal reference standard RNA from H. sapiens_SuperArray Bioscience Corp. Xpress Ref. GA004_Rep2

description: Tissue sample


title: Universal reference standard RNA from H. sapiens_SuperArray Bioscience Corp. Xpress Ref. GA004_Rep3

description: Tissue sample


title: normal human breast tissue biopsy_rep12

description: Tissue sample

tag: Normal human mammary tissue biopsy from reduction mamioplasty


title: normal murine mammary fat pad biopsy_rep1

description: Tissue sample

source_name: normal mammary fat pad, abdominal, Rag1 retired breeder


title: normal murine mammary fat pad biopsy_rep3

description: Tissue sample


title: normal murine mammary fat pad biopsy_rep2

description: Tissue sample


title: Histone H4 ChIP-chip data of Wild Type

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: Histone H4 ChIP fraction from Wild type cells.

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Data was processed following the protocol provided by Affymetrix (GCOS ver 1.4).

source_name: Histone H4 ChIP fraction

label_protocol: DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin‐N11‐ddATP (NEL508).

extract_protocol: We disrupted 1.5 x 10^8 cells byMulti-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-H4(Upstate)was used for chromatin immunoprecipitation.

tag: Chromatin was prepared from wild type S.pombe cells. Chromatin-IP was carried out by pan-Histone H4 antibody.


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vivo orthotopically in murine mammary fat pad_rep2

description: Tissue sample

organism:
Homo sapiens
Mus musculus

source_name: xenograft, MDA-MB-231

growth_protocol: 5-6 weeks growth in vivo post implantation into the mammary fat pad of 6-8 week old females

value: Rag-1 tm1Mom


title: human ductal breast carcinoma biopsy_rep18

description: Tissue sample

source_name: breast carcinoma

tag: Human breast tumor_ductal histology_stage III


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vivo orthotopically in murine mammary fat pad_rep1

description: Tissue sample


title: MDA-MB-231 human mammary carcinoma cell line_ grown in vivo orthotopically in murine mammary fat pad_rep3

description: Tissue sample


title: Histone H4 ChIP data of mcl1 deletion mutant

description: Histone H4 ChIP data for mcl1 deletion mutant.

tag: Chromatin was prepared from mcl1 deletion mutant S.pombe cells. Chromatin-IP was carried out by pan-Histone H4 antibody.


title: normal human breast tissue biopsy_rep11

description: Tissue sample


title: Universal reference standard RNA from mouse_SuperArray Bioscience Corp. Xpress Ref. GA005_Rep1

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 66 S2)

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: No additional information.

hyb_protocol: Arrays were hybridized according to Agilent’s Hybridization Procedure for 22k microarrays (cDNA labeled Targets) (Agilent 60-mer Oligo Microarray Processing Protocol v. 4.1, Agilent); however, the 17 hr incubation was performed at 65 degrees C. Washing of the arrays was performed according to Agilent’s Wash Procedure with Stabilization and Drying Solution (Two-Color Microarray-Based Gene Expression Analysis v. 4.0.1, Agilent). Removal of microarrays from the final Stabilization and Drying Solution wash was immediately repeated for slides that were not completely dry.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution and PMTs were set to 60 and 10.

data_processing: Microarrays were scanned using a G2565BA Agilent Microarray Scanner (Agilent) at 10 microm resolution. Scans were performed using Agilent’s eXtended Dynamic Range technique. Each array was scanned twice: once at photomultiplier tube gain of 100%, and again at a 10% gain. Information from both scans was processed by Agilent Feature Extraction software (v. 9.1), used to assess spot quality and obtain feature intensity statistics; duplicate spots were averaged. Background-subtracted data were normalized using a segmental nearest neighbor logarithmic expression ratio-of-the mean (SNN-LERM) approach (Yang et al., PNAS 2003; 100:1122-1127).

organism: Clostridium acetobutylicum

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain collected at several timepoints.

label_protocol: An indirect labeling approach was followed where cDNA was first made in the presence of nucleotides and aminoallyl dUTP, purified, and then the aminoallyl dUTP groups were coupled to a monoreactive dye (Cy3 or Cy5) as described previously (Alsaker et al. 2005. Biotechnology and Bioprocess Engineering 10: 432-443).

growth_protocol: Colonies of C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA, USA) were grown on agar-solidifed 2xYTG plates and used to start preinoculum cultures as previously described (Alsaker et al. 2005. Biotechnology and Bioprocess Engineering 10: 432-443). Preinoculum cultures were grown to OD(600 nm) of 0.2 and transferred to a 3.6 liter working volume reactors (Bioflow II and  Bioflow 110, New Brunswick Scientific, Edison, NJ) in a 10-fold dilution of CGM. The fermentation was pH controlled at a low end of 5.0 with 6N NH4OH. Anaerobic conditions were maintained with nitrogen at flow rates of 125 ml/min (for an OD(600 nm) below 1.0) and 25 ml/min (for an OD(600 nm) above 1.0).

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min at 4 degrees C, and stored at -80 degrees C until the RNA was isolated. Immediately prior to RNA isolation, cells were washed in 1 mL of SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) and collected by centrifuging at 5,000xg for 10 min at 4 degrees C. Cell pellets were then suspended in 220 microL SET buffer containing 20 mg/mL lysozyme (Sigma, St. Louis, MO, USA) and 4.55 U/ml proteinase K (Roche Applied Science, Indianapolis, IN, USA). The sample was incubated at room temperature for 6 min followed by 4 min continuous vortexing at room temperature. 1 mL of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions (RNeasy Lipid Tissue Handbook, Qiagen); buffer RW1 was incubated for 4 minutes at room temperature to minimize genomic DNA contamination. Isolated RNA was eluted in 30-40 microL RNase-free water and quantified using a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8 and RNA integrity was verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA was stored at -85 degrees C and used within one week of purification.

treatment_protocol: A RNA pool was generated by combining 25 microg of RNA from isolations from samples taken from the Bioflow II reactor at 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation.

tag: Clostridium acetobutylicum ATCC 824

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 66 hours after bioreactor inoculation.

label_protocol: Same as channel 1

growth_protocol: Same as channel 1

extract_protocol: Same as channel 1

treatment_protocol: Sample taken 66 hours after bioreactor inoculation.


title: normal human breast tissue biopsy_rep9

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep17

description: Tissue sample

tag: Human breast tumor_ductal histology_stageII


title: normal human breast tissue biopsy_rep8

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep15

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep16

description: Tissue sample


title: normal human breast tissue biopsy_rep7

description: Tissue sample


title: normal human breast tissue biopsy_rep5

description: Tissue sample


title: normal human breast tissue biopsy_rep6

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 54 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 54 hours after bioreactor inoculation.

treatment_protocol: Sample taken 54 hours after bioreactor inoculation.


title: Histone AcH4 ChIP-chip data of Wild Type

description: Histone AcH4 binding profile of Wild Type.

source_name: Distribution of Histone AcH4 in wild type.

extract_protocol: We disrupted 1.5 x 10^8 cells byMulti-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-pan Ac-H4(Upstate)was used for chromatin immunoprecipitation.

tag: Chromatin was prepared from wild type S.pombe cells. Chromatin-IP was carried out by pan Ac-H4 antibody.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 58 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 58 hours after bioreactor inoculation.

treatment_protocol: Sample taken 58 hours after bioreactor inoculation.


title: human ductal breast carcinoma biopsy_rep14

description: Tissue sample

tag: Human breast tumor_ductal histology_stage II


title: normal human breast tissue biopsy_rep4

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep12

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep13

description: Tissue sample


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model_rep4

description: Tissue sample

source_name: breast carcinoma, MMTV-PymT+

growth_protocol: spontaneous tumors (14-16 week old mice) harvested by macroscopic dissection

tag: Strain

value: FVB/n, Polyoma Virus Middle T antigen transgene driven by the Murine Mammary Tumor Virus promotor


title: Clostridium acetobutylicum ATCC 824 time course (Hour 48 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 48 hours after bioreactor inoculation.

treatment_protocol: Sample taken 48 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 66 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 40 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 40 hours after bioreactor inoculation.

treatment_protocol: Sample taken 40 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 44 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 44 hours after bioreactor inoculation.

treatment_protocol: Sample taken 44 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 38 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 38 hours after bioreactor inoculation.

treatment_protocol: Sample taken 38 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 66 S3 Discarded)

description: No additional information.


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model_rep3

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 38 S3 Discarded)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 44 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 36 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 36 hours after bioreactor inoculation.

treatment_protocol: Sample taken 36 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 58 S2)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 36 S2)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 54 S2)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 48 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 38 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 40 S2)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 34 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 34 hours after bioreactor inoculation.

treatment_protocol: Sample taken 34 hours after bioreactor inoculation.


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model_rep2

description: Tissue sample


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with wild type UPARAP_rep4

description: Tissue sample

source_name: breast carcinoma, MMTV-PymT+/uPARAP+/+

value: FVB/n, Polyoma Virus Middle T antigen transgene driven by the Murine Mammary Tumor Virus promotor, with wildtype UPARAP locus


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model_rep1

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 34 S1)

description: No additional information.


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with UPARAP gene knockout_rep2

description: Tissue sample

source_name: breast carcinoma, MMTV-PymT+/uPARAP-/-

value: FVB/n, Polyoma Virus Middle T antigen transgene driven by the Murine Mammary Tumor Virus promotor, with UPARAP gene knockout


title: normal human breast tissue biopsy_rep2

description: Tissue sample

source_name: normal breast tissue


title: human ductal breast carcinoma biopsy_rep11

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep9

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep8

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep10

description: Tissue sample


title: normal human breast tissue biopsy_rep1

description: Tissue sample


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with UPARAP gene knockout_rep1

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 32 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 32 hours after bioreactor inoculation.

treatment_protocol: Sample taken 32 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 32 S3 Discarded)

description: No additional information.


title: human ductal breast carcinoma biopsy_rep7

description: Tissue sample

source_name: breast carcinoma


title: Clostridium acetobutylicum ATCC 824 time course (Hour 26 S2)

description: No additional information.

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain collected at several timepoints.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 26 hours after bioreactor inoculation.

treatment_protocol: Sample taken 26 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 30 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 30 hours after bioreactor inoculation.

treatment_protocol: Sample taken 30 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 28 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 28 hours after bioreactor inoculation.

treatment_protocol: Sample taken 28 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 32 S1)

description: No additional information.


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with wild type UPARAP_rep3

description: Tissue sample

growth_protocol: spontaneous tumors harvested by macroscopic dissection


title: Clostridium acetobutylicum ATCC 824 time course (Hour 26 S1)

description: No additional information.


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with wild type UPARAP_rep2

description: Tissue sample


title: spontaneous murine mammary carcinoma_MMTV-polyoma middle T model with wild type UPARAP_rep1

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 24 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 24 hours after bioreactor inoculation.

treatment_protocol: Sample taken 24 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 22 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 22 hours after bioreactor inoculation.

treatment_protocol: Sample taken 22 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 24 S1)

description: No additional information.


title: human ductal breast carcinoma biopsy_rep5

description: Tissue sample

treatment_protocol: no treatments


title: human ductal breast carcinoma biopsy_rep4

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 22 S1)

description: No additional information.

treatment_protocol: A RNA pool was generated by combining 25 microg of RNA from isolations from samples taken from the Bioflow II reactor at 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 30 S1)

description: No additional information.


title: human ductal breast carcinoma biopsy_rep3

description: Tissue sample


title: Clostridium acetobutylicum ATCC 824 time course (Hour 28 S2)

description: No additional information.


title: Histone Ac H4 ChIP fraction in mcl1 deletion mutant

description: Histone AcH4 profile data for mcl1 deletion mutant.

extract_protocol: We disrupted 1.5 x 10^8 cells byMulti-beads shocker (MB400U, Yasui Kikai) using glass beads. pan-Ac H4 antibody (Upstate)was used for chromatin immunoprecipitation.

tag: Chromatin was prepared from mcl1 deletion mutant of S.pombe cells. Chromatin-IP was carried out by pan-Ac Histone H4 antibody.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 18 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 18 hours after bioreactor inoculation.

treatment_protocol: Sample taken 18 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 18 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 20 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 20 hours after bioreactor inoculation.

treatment_protocol: Sample taken 20 hours after bioreactor inoculation.


title: human ductal breast carcinoma biopsy_rep6

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep2

description: Tissue sample


title: human ductal breast carcinoma biopsy_rep1

description: Tissue sample


title: A549 human lung carcinoma cell line_ grown in vivo orthotopically in lung_rep1

description: Rag-2 mice were used due to their lack of mature B and T lymphocytes and suitability for transplantation studies.  Remaining NK cells were eliminated by non-lethal irradiation with 400 rads/mouse using a cesium g source.

source_name: A549, xenografts

growth_protocol: 6-week old mice were injected with 1 x 106 A549 cells into the lung via the trachea and tumors formed after 6 weeks


title: A549 human lung carcinoma cell line_ grown in vivo orthotopically in lung_rep12


title: A549 human lung carcinoma cell line_ grown in vivo orthotopically in lung_rep3


title: A549 human lung carcinoma cell line_ grown in vitro on plastic_rep2

description: Cells were cultured in F-12 Nutrient Mixture (Kaighn's modification) with 2mM L-glutamine (Gibco BRL, Long Island, NY) supplemented with 1.5 g/L sodium bicarbonate, 10% fetal calf serum and at 37°C, 5% CO2.

source_name: A549, cultured cells

tag: Human lung carcinoma cell line_ATCC #CCL-185


title: Clostridium acetobutylicum ATCC 824 time course (Hour 20 S1)

description: No additional information.


title: A549 human lung carcinoma cell line_ grown in vitro on plastic_rep1


title: E81_IP

organism: Saccharomyces cerevisiae

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells

growth_protocol: Cells in YP + 2% glucose were synchronized in metaphase with the spindle depolymerising drug nocodazole

treatment_protocol: Extraction was performed as previously described (Katou et al. 2003)

tag: Saccharomyces cerevisiae (W303 background)

tag: Genotype

value: MATa Scc2-9PK

tag: 2 hours nocodazole arrested cells

tag: Antibody


title: Clostridium acetobutylicum ATCC 824 time course (Hour 14 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 14 hours after bioreactor inoculation.

treatment_protocol: Sample taken 14 hours after bioreactor inoculation.


title: 021_SUP

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction

growth_protocol: Cells in YP + 2% raffinose were synchronized in G1 with alpha factor for 2 hours and released in nocodazole for 2 hours

value: MATa Scc1-HA6

value: anti-HA


title: Clostridium acetobutylicum ATCC 824 time course (Hour 12 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 12 hours after bioreactor inoculation.

treatment_protocol: Sample taken 12 hours after bioreactor inoculation.


title: K5601_BrdU_IP

growth_protocol: Cells in YP + 2% glucose were synchronized in alpha-factor (2µM) and released into 200 mM HU for 60 minutes at 23°C. For the simultaneous analysis of BrdU incorporation, BrdU was added to the culture 30 minutes before from G1 arrest to a final concentration of 200 µg/ml.

value: MATa GPD-TK

tag: Yeast cells synchronized in alpha-factor (2µM) and released into 200 mM HU for 60 minutes at 23°C. For the simultaneous analysis of BrdU incorporation, BrdU was added to the culture 30 minutes before from G1 arrest to a final concentration of 200 µg/ml.

value: anti-BrdU monoclonal antibody


title: C6_IPHu_2315

growth_protocol: Cells in YP + 2% glucose were synchronized in hydroxyurea after release from G1 arrest

value: MATa Smc4-9PK

tag: 2 hours hydroxyurea arrested cells


title: C12_IP_2565_NOC

treatment_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl)

tag: 2 hours alpha factor arrested cells


title: Clostridium acetobutylicum ATCC 824 time course (Hour 14 S1)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 14 S3 Discarded)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 16 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 16 hours after bioreactor inoculation.

treatment_protocol: Sample taken 16 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 12 S2)

description: No additional information.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 10 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 10 hours after bioreactor inoculation.

treatment_protocol: Sample taken 10 hours after bioreactor inoculation.


title: C5N_IP_2315


title: Newborn normal melanocytes NBMEL_rep1 (RNA)

city: New Haven

first: Annette

last: Molinaro

state: CT

address: 60 College St

institute: Yale University

description: This expression dataset has been used in association with the DNA-methylation data reported in GSE12096. The purpose of this study is the evaluation of the effectiveness of a new DNA methylation estimate in capturing the transcriptional repression associated with promoter hyper methylation (Pelizzola et al, 2008).

hyb_protocol: Standard Nimblegen protocol

scan_protocol: Standard Nimblegen protocol

data_processing:
Within (Loess based) and between (Quantile based) normalization methods available in the
Limma Bioconductor/R library as standard methods for two-channel microarrays are applied
(Ihaka et al. 1996, Gentleman et al. 2004, Smyth et al. 2003, Smyth 2005).

molecule: polyA RNA

source_name: Newborn normal melanocytes

label_protocol: NimbleGen human Whole genome expression microarray (array 2005-04-20_Human_60mer_1in2) were used for hybridization. The array hybridizations and data captures were performed by personnel at  NimbleGen Systems Iceland LLc. Vínlandsleið 2-4, 113 Reykjavik, Iceland (currently Roche Applied Science, Basel, Switzerland).

extract_protocol: Approximately 20–30 million cells (normal human melanocytes and melanoma cells/each) were used for mRNA extraction. High-quality total RNA was prepared with the TRIzol reagent (Invitrogen Life Technologies, Inc., Invitrogen Corp., Carlsbad, CA). The quality of RNA products was determined visually by 1% denaturing agarose gel, and RNA concentration was measured using a spectrophotometer. Poly(A) mRNA was further isolated from 150-300 µg total RNA/sample using the PolyATtract mRNA isolation system IV (Pro-mega, Madison, WI) following the manufacturer’s instructions, and reversed transcribed to double stranded cDNA. This additional step is required to eliminate the melanin present in the total RNA preparation that suppresses PCR hybridization reactions.

tag: Newborn normal melanocytes


title: Clostridium acetobutylicum ATCC 824 time course (Hour 09 S2)

description: No additional information.

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain collected at several timepoints.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 9 hours after bioreactor inoculation.

treatment_protocol: Sample taken 9 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 08 S3 Discarded)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 8 hours after bioreactor inoculation.

treatment_protocol: Sample taken 8 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 10 S1)

description: No additional information.


title: C8_IP_2200_a_SC

growth_protocol: Cells in YP + 2% glucose were synchronized in G1 with alpha factor for 2 hours

value: MATa Brn1-9PK


title: Clostridium acetobutylicum ATCC 824 time course (Hour 08 S2)

description: No additional information.


title: Newborn normal melanocytes NBMEL_rep2 (RNA)


title: Clostridium acetobutylicum ATCC 824 time course (Hour 06 S3 Discarded)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 6 hours after bioreactor inoculation.

treatment_protocol: Sample taken 6 hours after bioreactor inoculation.


title: Clostridium acetobutylicum ATCC 824 time course (Hour 07 S2)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 7 hours after bioreactor inoculation.

treatment_protocol: Sample taken 7 hours after bioreactor inoculation.


title: C6_IPa_2315


title: Clostridium acetobutylicum ATCC 824 time course (Hour 09 S1)

description: No additional information.


title: DNA control 3

status: Public on Jul 19 2008

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

hyb_protocol: Per Affymetrix recommendation

scan_protocol: Scanned using Affymetrix 7G scanner

data_processing: CEL  and GRD files created from Affymetrix GCOS software; Affymetrix Tiling Array Software used to create .bar files

source_name: DNase treated genomic DNA

label_protocol: biotinylated with Biotin-N6-ddATP using terminal deoxynucleotidyl transferase

growth_protocol: Grown in YPD to mid-log phase at 30 C

extract_protocol: Chromatin was digested with micrococcal nuclease to yield predominantly mononucleosomal DNA

tag: Strain BY4741


title: Clostridium acetobutylicum ATCC 824 time course (Hour 08 S1)

description: No additional information.


title: DNA control 2


title: Clostridium acetobutylicum ATCC 824 time course (Hour 07 S1)

description: No additional information.


title: DNA control 1


title: Bj_Arabinose supplemented chemoautotrophy vs. Chemoautotrophy_Rep3

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

description:
Transcriptional profiling of chemoautotrophically cultured cells compared to arabinose supplemented chemoautotrophically cultured cells.
VALUE = Normalized Log2 (Arabinose supplemented chemoautotrophy/Chemoautotrophy) ratio

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 1.5-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Arabinose supplemented chemoautotrophy Replication 3

label_protocol: 10 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Two micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: Cells cultured chemoautotrophically supplemented with arabinose under an artificial atmosphere consisting of 1% oxygen, 5% carbon dioxide, 10% Hydrogen and 84% nitrogen gas.

source_name: Chemoautotrophy Replication 3

tag: Cells cultured chemoautotrophically under an artificial atmosphere consisting of 1% oxygen, 5% carbon dioxide, 10% Hydrogen and 84% nitrogen gas.


title: Bj_Arabinose supplemented chemoautotrophy vs. Chemoautotrophy_Rep1

source_name: Arabinose supplemented chemoautotrophy Replication 1

source_name: Chemoautotrophy Replication 1


title: aCGH_ IL1403versusMG1363_slideIL48-7

status: Public on Jul 20 2008

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

hyb_protocol: For aCGH comparison, the labeled purified DNA fragments of two L. lactis strains were mixed and hybridized to L. lactis IL1403 DNA microarrays as described for transcriptome experiments [Kuipers OP, et al. 2002. Antonie Van Leeuwenhoek, 82:113-122; van Hijum SAFT, et al. 2005. BMC Genomics, 6:77]. After overnight hybridization at 40 ºC, slides were washed in [2x SSC, 0.5% SDS] at room temperature and subsequently for 5 min in [1x SSC, 0.25% SDS] to remove non-specifically hybridized DNAs. Slide scanning and spot intensity quantization were done as described earlier [van Hijum SAFT, et al. 2005. BMC Genomics, 6:77].

scan_protocol: See: van Hijum SAFT, et al. 2005. BMC Genomics, 6:77

data_processing: See manuscript: van Hijum, SAFT et al. Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons.

organism: Lactococcus lactis subsp. lactis Il1403

source_name: IL1403 wild type

label_protocol: Chromosomal DNAs (1 – 2 µg) of L. lactis cells were randomly labeled and linearly amplified using the BioPrime DNA Labeling System (Invitrogen, Breda, the Netherlands) according to the manufacturers’ instructions, with the following modifications. For labeling, 5 μL 10x dNTP-mix (1.2 mM dATP, dGTP and dCTP; 0.6 mM dTTP; in 10 mM Tris, 1 mM EDTA, pH 8.0), 3 μL Cy3- or Cy5-dUTP (Amersham Bioscience Europe, Freiburg, Germany) and 1 μL Klenow enzyme were used. The DNA-primer hybrid elongation and labeling reaction was performed by incubation for 2 h at 37°C in a Bio-Rad iCycler Thermal Cycler (Bio-Rad Life Science, Veenendaal, the Netherlands). The Cy-dye-labeled DNA fragments were purified using the QiaGen QiaQuick Nucleotide Removal Kit (Qiagen Benelux BV, Venlo, the Netherlands).

growth_protocol: L. lactis cells were grown statically at 30°C in M17 broth [Terzaghi BE, Sandine WE. 1975. Appl Microbiol, 29:807-813] supplemented with 0.5% glucose (GM17). Cells were grown until the late-exponential phase of growth (OD600 ~1.5 - 2) and harvested for chromosomal DNA isolation.

extract_protocol: Chromosomal DNA isolation was performed as described [Leenhouts KJ, et al. 1990. Appl Environ Microbiol, 56:2726-2735].

tag: L. lactis subsp lactis IL1403 (Lac-; Prt- ; plasmid–free derivative of IL594) [Chopin A, et al. 1984. Plasmid 11:260-263; Bolotin A, et al. 2001. Genome Res. 11:731-753].

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: MG1363 wild type

label_protocol: See Channel 1.

growth_protocol: See Channel 1.

extract_protocol: See Channel 1

tag: L. lactis subsp cremoris MG1363 (Lac-; Prt- ; plasmid–free derivative of NCDO712) [Gasson MJ. 1983. J Bacteriol, 154:1-9; Wegmann U et al. 2007. J Bacteriol, 189:3256-3270].


title: Clostridium acetobutylicum ATCC 824 time course (Hour 06 S2)

description: No additional information.

tag: Clostridium acetobutylicum ATCC 824


title: aCGH_MG1363versusIL1403_slideIL47-10


title: Clostridium acetobutylicum ATCC 824 time course (Hour 06 S1)

description: No additional information.


title: Bj_Chemoautotrophy vs. Heterotrophy_Rep2

description:
Transcriptional profiling of heterotrophically cultured cells compared to chemoautotrophically cultured cells.
VALUE = Normalized Log2 (Chemoautotrophy/Heterotrophy) ratio

source_name: Chemoautotrophy Replication 2

source_name: Heterotrophy Replication 2

tag: Cells cultured heterotrophically on arabinose under ambient atmosphere.


title: Bj_Chemoautotrophy vs. Heterotrophy_Rep1

source_name: Heterotrophy Replication 1


title: Bj_Chemoautotrophy vs. Arabinose supplemented chemoautotrophy_Rep2

source_name: Arabinose supplemented chemoautotrophy Replication 2


title: Bj_Heterotrophy vs. Chemoautotrophy_Rep1


title: Bj_Chemoautotrophy vs. Arabinose supplemented chemoautotrophy_Rep3


title: Bj_Arabinose supplemented chemoautotrophy vs. heterotrophy _Rep3

description:
Transcriptional profiling of heterotrophically cultured cells compared to arabinose supplemented chemoautotrophically cultured cells.
VALUE = Normalized Log2 (Arabinose supplemented chemoautotrophy/Heterotrophy) ratio

tag: Cells cultured chemoautotrophically with arabinose under an artificial atmosphere consisting of 1% oxygen, 5% carbon dioxide, 10% Hydrogen and 84% nitrogen gas.

source_name: Heterotrophy Replication 3

tag: Cells cultured heterotrophically on arabinose under ambient atmosphere


title: aCGH_IL1403versusMG1363_slideIL47-11


title: Bj_Chemoautotrophy vs. Arabinose supplemented chemoautotrophy_Rep1


title: Bj_Arabinose supplemented chemoautotrophy vs. heterotrophy _Rep1

source_name: Arabinose supplemented chemoautotrophy_Replication 1


title: Bj_Arabinose supplemented chemoautotrophy vs. Chemoautotrophy_Rep2


title: LW05set3_coi1_mock_24h

status: Public on Jul 18 2008

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: coi1 infiltrated with water, harvested 24h after infiltration in set3 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing:
Note that each Sample corresponds to two GPR files (we use low PMT and high PMT, then combine them).

The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. LW01_set1_Col-0_Psm_24h, LW01_set1_eds5_Psm_24h, LW01_set1_mpk3_Psm_24h, LW01_set1_mpk6_Psm_24h, LW01_set1_npr_Psm_24h, LW01_set1_pad4_Psm_24h, LW01_set1_sid2_Psm_24h, LW01_set1_tga_Psm_24h, LW01_set2_Col-0_Psm_24h, LW01_set2_eds5_Psm_24h, LW01_set2_mpk3_Psm_24h, LW01_set2_mpk6_Psm_24h, LW01_set2_npr_Psm_24h, LW01_set2_pad4_Psm_24h, LW01_set2_sid2_Psm_24h, LW01_set2_tga_Psm_24h, LW01_set3_Col-0_Psm_24h, LW01_set3_eds5_Psm_24h, LW01_set3_mpk3_Psm_24h, LW01_set3_mpk6_Psm_24h, LW01_set3_npr_Psm_24h, LW01_set3_pad4_Psm_24h, LW01_set3_sid2_Psm_24h, LW01_set3_tga_Psm_24h, LW02_set1_Col-0_Psm_24h, LW02_set1_SALK023199_Psm_24h, LW02_set1_SALK066990_Psm_24h, LW02_set1_coi1_Psm_24h, LW02_set1_dde2_Psm_24h, LW02_set1_ein2_Psm_24h, LW02_set1_jai1_Psm_24h, LW02_set1_jar1_Psm_24h, LW02_set2_Col-0_Psm_24h, LW02_set2_SALK023199_Psm_24h, LW02_set2_SALK066990_Psm_24h, LW02_set2_coi1_Psm_24h, LW02_set2_dde2_Psm_24h, LW02_set2_ein2_Psm_24h, LW02_set2_jai1_Psm_24h, LW02_set2_jar1_Psm_24h, LW02_set3_Col-0_Psm_24h, LW02_set3_SALK023199_Psm_24h, LW02_set3_SALK066990_Psm_24h, LW02_set3_coi1_Psm_24h, LW02_set3_dde2_Psm_24h, LW02_set3_ein2_Psm_24h, LW02_set3_jai1_Psm_24h, LW02_set3_jar1_Psm_24h, LW03_set1_Col-0_Psm_24h, LW03_set1_Col-0_mock_24h, LW03_set1_SALK018487_Psm_24h, LW03_set1_SALK052422_Psm_24h, LW03_set1_SALK084141_Psm_24h, LW03_set1_SALK143063_Psm_24h, LW03_set1_eds1_Psm_24h, LW03_set1_fmo1_Psm_24h, LW03_set2_Col-0_Psm_24h, LW03_set2_Col-0_mock_24h, LW03_set2_SALK018487_Psm_24h, LW03_set2_SALK052422_Psm_24h, LW03_set2_SALK084141_Psm_24h, LW03_set2_SALK143063_Psm_24h, LW03_set2_eds1_Psm_24h, LW03_set2_fmo1_Psm_24h, LW03_set3_Col-0_Psm_24h, LW03_set3_Col-0_mock_24h, LW03_set3_SALK018487_Psm_24h, LW03_set3_SALK052422_Psm_24h, LW03_set3_SALK084141_Psm_24h, LW03_set3_SALK143063_Psm_24h, LW03_set3_eds1_Psm_24h, LW03_set3_fmo1_Psm_24h, LW05_set1_Col-0_Psm-cor-_24h, LW05_set1_Col-0_Psm_24h, LW05_set1_Col-0_mock_24h, LW05_set1_coi1_Psm-cor-_24h, LW05_set1_coi1_Psm_24h, LW05_set1_coi1_mock_24h, LW05_set1_ndr1_Psm_24h, LW05_set1_pbs3_Psm_24h, LW05_set2_Col-0_Psm-cor-_24h, LW05_set2_Col-0_Psm_24h, LW05_set2_Col-0_mock_24h, LW05_set2_coi1_Psm-cor-_24h, LW05_set2_coi1_Psm_24h, LW05_set2_coi1_mock_24h, LW05_set2_ndr1_Psm_24h, LW05_set2_pbs3_Psm_24h, LW05_set3_Col-0_Psm-cor-_24h, LW05_set3_Col-0_Psm_24h, LW05_set3_Col-0_mock_24h, LW05_set3_coi1_Psm-cor-_24h, LW05_set3_coi1_Psm_24h, LW05_set3_coi1_mock_24h, LW05_set3_ndr1_Psm_24h, and LW05_set3_pbs3_Psm_24h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana coi1, leaves, water-infiltrated, 24h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 24h later.

tag: Tissue

value: leaves

tag: Age

value: 4 week-old

tag: Treatment

value: water

tag: Time point


title: Bj_Arabinose supplemented chemoautotrophy vs. heterotrophy _Rep2


title: Bj_Heterotrophy vs. Arabinose supplemented chemoautotrophy_Rep3


title: Clostridium acetobutylicum ATCC 824 time course (Hour 16 S1)

description: No additional information.

source_name: Clostridium acetobutylicum ATCC 824 time course sample taken 16 hours after bioreactor inoculation.

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain collected at several timepoints.


title: Bj_Heterotrophy vs. Arabinose supplemented chemoautotrophy_Rep2

source_name: Arabinose supplemented chemoautotrophy_Replication 2


title: Bj_Heterotrophy vs. Arabinose supplemented chemoautotrophy_Rep1


title: LW05set3_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 24h

tag: Genotype


title: LW05set3_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae ES4326 and harvested 24h later.


title: LW05set3_coi1_Psm-cor-_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana coi1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-)-infiltrated, 24h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-) and harvested 24h later.


title: LW05set3_Col-0_Psm-cor-_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-)-infiltrated, 24h


title: YUSAC2 melanoma cells YUSAC2_rep1

description: Comparison of MeDIP enrichment and input genomic DNA allows the determination of DNA-methylation, according to Weber et al 2005.

scan_protocol: Standard Nimblegen Protocol

data_processing:
Within (Loess based) and between (Quantile based) normalization methods available in the Limma Bioconductor/R library (Ihaka et al. 1996, Gentleman et al. 2004, Smyth et al. 2003, Smyth 2005) as standard methods for two-channel microarrays are applied to determine M and A values.
Smoothed MeDIP enrichment as well as Absolute and Relative Methylation Score are determined using the MEDME R library (Pelizzola et al, 2008).

source_name: YUSAC2 melanoma, MeDIP

label_protocol: MeDIP was adapted from the previous study (Weber et al. 2005). Genomic DNA was sheared by sonication into 300 to 1200 bp fragments, and methylated DNA was immunoprecipitated by incubating 10 ug of sonicated genomic DNA for 12 hr at 4C with 20 ug of mouse monoclonal antibody against 5-methylcytidine (Eurogentec). Fifty uL of Dynabeads with M-280 sheep antibodies to mouse IgG (Dynal Biotech) were added to the mix and incubated at 4oC for 2hr. Elution was performed two times in 200 uL TE containing 1.0% and 0.67% SDS, respectively, and methylated DNA was then recovered by standard proteinase K/phenol-chlorophorm procedure. DNA was also recovered from the unbound fractions. The remaining DNA from eluted fractions and sonicated input DNA were differentially labeled using fluorescent dyes (Cy3/Cy5) and competitively hybridized to the genomic DNA arrays.

extract_protocol: Melanoma cells (YUSAC2) were established from metastatic melanoma and were grown in basal medium (OptiMEM supplemented with 5% fetal calf serum and penicillin/streptomycin) enriched with the following ingredients required for proliferation: TPA (20 nM, 12-O-tetradecanoyl phorbol-13-acetate), IBMX (0.1 mM, 3-isobutyl-1-methyl xanthin), cholera toxin (2.5 nM), vanadate (1 µm) and dbcAMP (0.1 mM, N6, 2’-O-dibutyryladenosine 3:5-cyclic monophosphate), termed TICVA (Cheng et al. 2006). The samples were collected according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol. Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer’s instructions.

tag: metastatic melanoma

source_name: YUSAC2 melanoma


title: aCGH_MG1363versusIL1403_slideIL48-6

source_name: MG1363 wild type

source_name: IL1403 wild type


title: LW05set3_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana coi1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW05set2_coi1_Psm-cor-_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set2 experiment.


title: LW05set2_ndr1_Psm_24h

description: ndr1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana ndr1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: YUSAC2 melanoma cells YUSAC2_rep2

source_name: Melanoma YUSAC2, MeDIPw

tag: Metastatic melanoma

source_name: Melanoma YUSAC2

tag: Metastatic Melanoma


title: LW05set2_pbs3_Psm_24h

description: pbs3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana pbs3, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: Newborn normal melanocytes NBMEL_rep1 (genomic)

source_name: Newborn normal melanocytes, MeDIP

extract_protocol: Normal human melanocytes were cultured from newborn foreskins (NBMEL) in basal medium (OptiMEM supplemented with 5% fetal calf serum and penicillin/streptomycin) enriched with the following ingredients required for proliferation: TPA (20 nM, 12-O-tetradecanoyl phorbol-13-acetate), IBMX (0.1 mM, 3-isobutyl-1-methyl xanthin), cholera toxin (2.5 nM), vanadate (1 µm) and dbcAMP (0.1 mM, N6, 2’-O-dibutyryladenosine 3:5-cyclic monophosphate), termed TICVA (Cheng et al. 2006). The samples were collected according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol. Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer’s instructions.

tag: Newborn normal melanocytes

source_name: Newborn normal melanocytes


title: Fully Methylated DNA rep1

source_name: Fully methylated DNA, MeDIP

label_protocol:
UA whole-genome amplification was applied for producing an unmethylated copy of genomic DNA of normal human melanocytes (REPLI-g Mini Kit, QIAGEN). The amplified unmethylated DNA was treated with CpG methyltransferase (M. SssI, NEB) to add methyl-groups to all cytosine residues within CpG dinucleotides, in order to obtain fully methylated genomic DNA. This has been verified by bisulfite DNA sequencing for eight genomic loci. We confirmed 0% mCpG in unmethylated genomic DNA and 90-100% mCpG in fully methylated DNA
MeDIP was adapted from the previous study (Weber et al. 2005). Genomic DNA was sheared by sonication into 300 to 1200 bp fragments, and methylated DNA was immunoprecipitated by incubating 10 ug of sonicated genomic DNA for 12 hr at 4C with 20 ug of mouse monoclonal antibody against 5-methylcytidine (Eurogentec). Fifty uL of Dynabeads with M-280 sheep antibodies to mouse IgG (Dynal Biotech) were added to the mix and incubated at 4oC for 2hr. Elution was performed two times in 200 uL TE containing 1.0% and 0.67% SDS, respectively, and methylated DNA was then recovered by standard proteinase K/phenol-chlorophorm procedure. DNA was also recovered from the unbound fractions. The remaining DNA from eluted fractions and sonicated input DNA were differentially labeled using fluorescent dyes (Cy3/Cy5) and competitively hybridized to the genomic DNA arrays.

tag: Fully methylated DNA

source_name: Fully Methylated DNA

tag: Fully Methylated DNA


title: LW05set2_coi1_mock_24h

description: coi1 infiltrated with water, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana coi1, leaves, water-infiltrated, 24h


title: LW05set3_ndr1_Psm_24h

description: ndr1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.


title: LW05set1_ndr1_Psm_24h

description: ndr1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW05set1_coi1_mock_24h

description: coi1 infiltrated with water, harvested 24h after infiltration in set1 experiment.


title: LW05set2_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 24h


title: LW05set1_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW05set2_Col-0_Psm-cor-_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set2 experiment.


title: LW05set2_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW05set1_pbs3_Psm_24h

description: pbs3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW05set2_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW05set1_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW05set1_Col-0_Psm-cor-_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-)-infiltrated, 24h


title: LW03set3_fmo1_Psm_24h

description: fmo1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana fmo1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: Thyroid tissue cultured with 10 microM amiodarone medium for 5 days

description: Thyroid follicles were cultured with or without Amiodarone for 5 days

source_name: human thyroid follicles - untreated

label_protocol: 0.5 µg of total RNA were primed with 2 µl of 100 µM T16P7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10-8M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without Amiodarone (10microM) for 5 days.

tag: Amiodarone (-)

source_name: human thyroid follicles - amiodarone 10 microM treated

tag: Amiodarone 10 microM


title: LW03set3_SALK143063_Psm_24h

description: SALK143063 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK143063, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW03set3_SALK018487_Psm_24h

description: SALK018487 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK018487, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW03set3_SALK084141_Psm_24h

description: SALK084141 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK084141, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW03set3_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.


title: LW03set2_fmo1_Psm_24h

description: fmo1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW03set3_SALK052422_Psm_24h

description: SALK052422 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK052422, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW05set1_coi1_Psm-cor-_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-), harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana coi1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326 COR(-)-infiltrated, 24h


title: LW03set2_SALK084141_Psm_24h

description: SALK084141 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW03set2_eds1_Psm_24h

description: eds1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana eds1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW03set3_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set3 experiment.


title: LW03set3_eds1_Psm_24h

description: eds1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.


title: LW03set2_SALK052422_Psm_24h

description: SALK052422 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW03set2_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: Bj_Heterotrophy vs. Chemoautotrophy_Rep2

description:
Transcriptional profiling of heterotrophically cultured cells compared to chemoautotrophically cultured cells.
VALUE = Normalized Log2 (Chemoautotrophy/Heterotrophy) ratio

source_name: Heterotrophy Replication 2

source_name: Chemoautotrophy Replication 2

tag: Cells cultured chemoautotrophically under an artificial atmosphere consisting of 1% oxygen, 5% carbon dioxide, 10% Hydrogen and 84% nitrogen gas.


title: LW03set2_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set2 experiment.


title: LW03set2_SALK018487_Psm_24h

description: SALK018487 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW03set2_SALK143063_Psm_24h

description: SALK143063 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW03set1_eds1_Psm_24h

description: eds1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_fmo1_Psm_24h

description: fmo1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_SALK052422_Psm_24h

description: SALK052422 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_SALK084141_Psm_24h

description: SALK084141 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_SALK018487_Psm_24h

description: SALK018487 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW03set1_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set1 experiment.


title: LW02set3_jar1_Psm_24h

description: jar1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana jar1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set3_jai1_Psm_24h

description: jai1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana jai1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set3_dde2_Psm_24h

description: dde2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana dde2, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set3_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana coi1, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set3_ein2_Psm_24h

description: ein2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana ein2, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set2_jai1_Psm_24h

description: jai1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set3_SALK066990_Psm_24h

description: SALK066990 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK066990, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set3_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set2_jar1_Psm_24h

description: jar1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set3_SALK023199_Psm_24h

description: SALK023199 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana SALK023199, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW03set1_SALK143063_Psm_24h

description: SALK143063 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW02set2_dde2_Psm_24h

description: dde2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set2_ein2_Psm_24h

description: ein2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set2_SALK066990_Psm_24h

description: SALK066990 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set2_SALK023199_Psm_24h

description: SALK023199 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set2_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set2_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set2 experiment.


title: LW02set1_dde2_Psm_24h

description: dde2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW02set1_jar1_Psm_24h

description: jar1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW02set1_coi1_Psm_24h

description: coi1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: Highly metastatic 468GFP-LN biorep1

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

country: Canada

institute: London Regional Cancer program

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP-LN, Second biological replicate

hyb_protocol: Following fragmentation, 7.5 micrograms of Ligation mediated PCR amplified genomic DNA was hybridized as per standard affymetrix protocols for Human Promoter 1.0R arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin/SAPE

label_protocol: Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays

growth_protocol: Cells were grown out to three passages in alpha-MEM containing 10% FBS in 5% CO2 to 70 % confluency

extract_protocol: Genomic DNA was extracted using Sigma GeneElute kit using the Manufacturer's protocol

treatment_protocol: No treatment


title: LW05set1_Col-0_mock_24h

description: Col-0 infiltrated with water, harvested 24h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 24h


title: LW02set1_SALK023199_Psm_24h

description: SALK023199 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: Poorly metastatic 468GFP biorep3

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP, Third biological replicate

tag: Parental Cell line 468GFP, third biological replicate


title: LW02set1_SALK066990_Psm_24h

description: SALK066990 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: Highly metastatic 468GFP-LN biorep3

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP-LN, Third biological replicate


title: Poorly metastatic 468GFP biorep2

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP, second biological replicate

source_name: Parental Cell line 468GFP, Second biological replicate


title: LW01set3_sid2_Psm_24h

description: sid2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana sid2, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW01set3_npr_Psm_24h

description: npr infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana npr, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h

value: npr


title: Poorly metastatic 468GFP biorep1

description:
Ligation mediated PCR amplified genomic DNA, after restriction with HhaI
Promoter array data from Parental Cell line 468GFP, First biological replicate


title: LW02set1_jai1_Psm_24h

description: jai1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW02set1_ein2_Psm_24h

description: ein2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW01set3_mpk3_Psm_24h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW02set1_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.


title: LW01set3_Col-0_Psm_24h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.


title: LW01set3_pad4_Psm_24h

description: pad4 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pad4, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h


title: LW01set3_mpk6_Psm_24h

description: mpk6 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana mpk6, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h