title: Expression data of Dukes' C_33

status: Public on Aug 31 2010

type: RNA

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description: Recurrence(+)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Automated processing of image scans to absolute expression analysis was done using the Microarray Suite 5.0 software (Affymetrix, Santa Clara, CA). The software provided for each transcript "detection call," which predicted if the gene was present at levels detectable by the array. The call indicates that whether the transcript is detected (Present), undetected (Absent), or at the limit of detection (Marginal). These raw data including expression data and detection call data were loaded to GeneSpring™ software version 7.2 (Silicongenetics, Redwood, California). Gene expression data was normalized in two ways: "per chip normalization" and "per gene normalization". For "per chip normalization" all expression data on a chip is normalized to the 50th percentile of all values with detection call Present or Marginal on that chip.  For "per gene normalization" the data for a given gene is normalized to the median expression level of that gene across all samples.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: Tissue

value: Colorecal Cancer


title: Expression data of Dukes' C_29

description: Recurrence(-)


title: Expression data of Dukes' C_36

description: Recurrence(+)


title: Expression data of Dukes' C_18

description: Recurrence(-)


title: Expression data of Dukes' C_31

description: Recurrence(+)


title: Expression data of Dukes' C_34

description: Recurrence(-)


title: Expression data of Dukes' C_25

description: Recurrence(+)


title: Expression data of Dukes' C_32

description: Recurrence(-)


title: Expression data of Dukes' C_20

description: Recurrence(+)


title: Expression data of Dukes' C_21

description: Recurrence(-)


title: Expression data of Dukes' C_27

description: Recurrence(-)


title: Expression data of Dukes' C_12

description: Recurrence(-)


title: Expression data of Dukes' C_30

description: Recurrence(+)


title: Expression data of Dukes' C_19

description: Recurrence(-)


title: Expression data of Dukes' C_22

description: Recurrence(-)


title: Expression data of Dukes' C_14

description: Recurrence(-)


title: Expression data of Dukes' C_23

description: Recurrence(-)


title: Expression data of Dukes' C_24

description: Recurrence(-)


title: Expression data of Dukes' C_28

description: Recurrence(+)


title: Expression data of Dukes' C_35

description: Recurrence(-)


title: Expression data of Dukes' C_15

description: Recurrence(-)


title: Expression data of Dukes' C_17

description: Recurrence(-)


title: Expression data of Dukes' C_26

description: Recurrence(-)


title: Expression data of Dukes' C_16

description: Recurrence(-)


title: Expression data of Dukes' C_13

description: Recurrence(-)


title: Expression data of Dukes' C_10

description: Recurrence(+)


title: Expression data of Dukes' C_11

description: Recurrence(-)


title: Expression data of Dukes' C_08

description: Recurrence(-)


title: Apoptotic bodies

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

description: miRNAs from HUVEC apoptotic bodies

hyb_protocol: Hybridization was performed with mirVana miRNA Bioarrays (Ambion).

scan_protocol: The Cy3 fluorescence on the arrays was scanned at an excitation wavelength of 532nm using a Affymetrix 428 Array scanner. (MWG AG)

data_processing: Scanned data were quantified by ImaGene 5.5.4 (Bio Discovery). Resulting signal intensities were background corrected and normalized using the global Variance Stabilization Normalization (VSN; Huber et al., 2002).

source_name: Apoptotic bodies from human umbilical vein endothelial cells (HUVECs)

label_protocol: miRNAs were labeled using the mirVana miRNA labeling kit (Ambion).

growth_protocol: HUVECs were grown in endothelial cells medium (Promocell) and apoptotic bodies were isolated from the supernatant by sequential centrifugation steps after serum- and growth factor starvation for 24 hours.

extract_protocol: Material was isolated using the mirVana miRNA isolation kit (Ambion).


title: Human umbilical vein endothelial cells

description: miRNAs from HUVECS

source_name: Human umbilical vein endothelial cells(HUVECs)

treatment_protocol: HUVECs were grown in endothelial cells medium (Promocell)


title: Expression data of Dukes' C_09

description: Recurrence(+)


title: Expression data of Dukes' C_05

description: Recurrence(+)


title: Expression data of Dukes' C_03

description: Recurrence(-)


title: Expression data of CC_LN50

description: Training-Lymph(+)

data_processing: Affymetrix Microarray Suite version 5.0


title: Expression data of CC_LN47

description: Training-Lymph(-)


title: Expression data of CC_LN51

description: Training-Lymph(+)


title: Expression data of CC_LN65

description: Training-Lymph(-)


title: Expression data of Dukes' C_04

description: Recurrence(-)


title: Expression data of CC_LN83

description: Test-Lymph(+)


title: Expression data of Dukes' C_06

description: Recurrence(+)


title: Expression data of CC_LN14

description: Training-Lymph(+)


title: Expression data of CC_LN44

description: Training-Lymph(-)


title: Expression data of Dukes' C_01

description: Recurrence(+)


title: Expression data of CC_LN70

description: Test-Lymph(-)


title: Expression data of Dukes' C_02

description: Recurrence(+)


title: Expression data of CC_LN02

description: Training-Lymph(-)


title: Expression data of CC_LN64

description: Training-Lymph(-)


title: Expression data of CC_LN42

description: Training-Lymph(-)


title: Expression data of CC_LN84

description: Test-Lymph(-)


title: E coli LY180_del_yqhC_w 0.5g/L Furfural

status: Public on Aug 24 2010

city: Gainesville

first: Peter

middle: Christopher

last: Turner

state: FL

address: Bldg 981, Museum Road

department: Micro and Cell Science

country: USA

institute: University of Florida

description: OID 20404

hyb_protocol: Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Escherichia coli

source_name: LY180 del yqhC + furfural

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown in AM1 medium with 14% xylose to OD 550 = 1.5 (0.66 g dcw/liter). 4 replicate 350 ml fermentors per strain.

extract_protocol: Cells were chilled in dry ice/ethanol, centrifuged, and the pellet resuspended in RNA Later (Qiagen) before storing at –80 C. Total RNA was extracted using the RNeasy Mini kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

treatment_protocol: Samples were taken at OD = 1.5, then furfural added to 0.5 g/L. Samples were taken at 15 min after furfural addition.

tag: strain

tag: genotype

value: engineered yqhC deletion mutant


title: E coli LY180_w 0.5g/L Furfural

description: OID 20404

source_name: LY180 + furfural

value: wild-type (ethanologenic)


title: E coli LY180 del yqhC

description: OID 20404

source_name: LY180 del yqhC


title: E coli LY180

description: OID 20404


title: Expression data of CC_LN05

description: Training-Lymph(-)


title: Control healthy individual 40 peripheral blood cells

status: Public on Aug 21 2010

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42ﾟC. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2 ratios of Cy3 to Cy5 were calculated and normalized by the method of global ratio median normalization.

source_name: peripheral blood cells from healthy individual 40

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3/Cy5.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion according to the manufacturer`s instructions.

tag: gender

value: male

tag: age

tag: disease

value: healthy individual

tag: tissue

value: peripheral blood

source_name: Total RNA from pooled whole blood of 45 healthy individuals

tag: sample type

value: pooled control


title: liver from fasted rats

status: Public on Aug 28 2010

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

description: Gene expression data from male rat liver fasted overnight

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 array

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA

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

organism: Rattus norvegicus

source_name: Liver RNA

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

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit.

treatment_protocol: Fasted overnight

value: liver from fasted rats

tag: stain

value: Wistar

value: 2 months


title: liver from postprandial rats

description: Gene expression data from male rat liver after 5 ml olive oil meal

treatment_protocol: Fasted overnight and then fed 5 ml extra virgin olive oil

value: liver from postprandial rats


title: Control healthy individual 43 peripheral blood cells

source_name: peripheral blood cells from healthy individual 43


title: Control healthy individual 37 peripheral blood cells

source_name: peripheral blood cells from healthy individual 37


title: Control healthy individual 36 peripheral blood cells

source_name: peripheral blood cells from healthy individual 36


title: Control healthy individual 32 peripheral blood cells

source_name: peripheral blood cells from healthy individual 32


title: Control healthy individual 28 peripheral blood cells

source_name: peripheral blood cells from healthy individual 28


title: Control healthy individual 38 peripheral blood cells

source_name: peripheral blood cells from healthy individual 38

value: female


title: Control healthy individual 33 peripheral blood cells

source_name: peripheral blood cells from healthy individual 33


title: Control healthy individual 39 peripheral blood cells

source_name: peripheral blood cells from healthy individual 39


title: Control healthy individual 24 peripheral blood cells

source_name: peripheral blood cells from healthy individual 24


title: Control healthy individual 26 peripheral blood cells

source_name: peripheral blood cells from healthy individual 26


title: Control healthy individual 44 peripheral blood cells

source_name: peripheral blood cells from healthy individual 44


title: Control healthy individual 29 peripheral blood cells

source_name: peripheral blood cells from healthy individual 29


title: Control healthy individual 35 peripheral blood cells

source_name: peripheral blood cells from healthy individual 35


title: Control healthy individual 42 peripheral blood cells

source_name: peripheral blood cells from healthy individual 42


title: Control healthy individual 34 peripheral blood cells

source_name: peripheral blood cells from healthy individual 34


title: Control healthy individual 27 peripheral blood cells

source_name: peripheral blood cells from healthy individual 27

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: Control healthy individual 45 peripheral blood cells

source_name: peripheral blood cells from healthy individual 45


title: Control healthy individual 41 peripheral blood cells

source_name: peripheral blood cells from healthy individual 41


title: Control healthy individual 25 peripheral blood cells

source_name: peripheral blood cells from healthy individual 25


title: Control healthy individual 30 peripheral blood cells

source_name: peripheral blood cells from healthy individual 30


title: Control healthy individual 22 peripheral blood cells

source_name: peripheral blood cells from healthy individual 22


title: Control healthy individual 31 peripheral blood cells

source_name: peripheral blood cells from healthy individual 31


title: Control healthy individual 21 peripheral blood cells

source_name: peripheral blood cells from healthy individual 21


title: Expression data of Dukes' C_07

description: Recurrence(-)


title: Control healthy individual 23 peripheral blood cells

source_name: peripheral blood cells from healthy individual 23


title: Control healthy individual 20 peripheral blood cells

source_name: peripheral blood cells from healthy individual 20


title: Control healthy individual 16 peripheral blood cells

source_name: peripheral blood cells from healthy individual 16


title: Control healthy individual 18 peripheral blood cells

source_name: peripheral blood cells from healthy individual 18


title: Control healthy individual 19 peripheral blood cells

source_name: peripheral blood cells from healthy individual 19


title: Control healthy individual 14 peripheral blood cells

source_name: peripheral blood cells from healthy individual 14


title: Control healthy individual 17 peripheral blood cells

source_name: peripheral blood cells from healthy individual 17


title: Control healthy individual 15 peripheral blood cells

source_name: peripheral blood cells from healthy individual 15


title: Control healthy individual 10 peripheral blood cells

source_name: peripheral blood cells from healthy individual 10


title: Control healthy individual 13 peripheral blood cells

source_name: peripheral blood cells from healthy individual 13

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: Control healthy individual 5 peripheral blood cells

source_name: peripheral blood cells from healthy individual 5


title: Control healthy individual 12 peripheral blood cells

source_name: peripheral blood cells from healthy individual 12


title: Control healthy individual 11 peripheral blood cells

source_name: peripheral blood cells from healthy individual 11


title: Control healthy individual 8 peripheral blood cells

source_name: peripheral blood cells from healthy individual 8


title: Control healthy individual 4 peripheral blood cells

source_name: peripheral blood cells from healthy individual 4


title: Control healthy child 8 peripheral blood cells

source_name: peripheral blood cells from healthy child 8

value: healthy child


title: Control healthy individual 6 peripheral blood cells

source_name: peripheral blood cells from healthy individual 6


title: Control healthy child 6 peripheral blood cells

source_name: peripheral blood cells from healthy child 6


title: Control healthy individual 3 peripheral blood cells

source_name: peripheral blood cells from healthy individual 3


title: Control healthy individual 9 peripheral blood cells

source_name: peripheral blood cells from healthy individual 9


title: Control healthy individual 2 peripheral blood cells

source_name: peripheral blood cells from healthy individual 2


title: Control healthy child 2 peripheral blood cells

source_name: peripheral blood cells from healthy child 2


title: sJIA patient 51 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 51

value: systemic-onset juvenile idiopathic arthritis


title: Control healthy child 3 peripheral blood cells

source_name: peripheral blood cells from healthy child 3


title: Control healthy child 5 peripheral blood cells

source_name: peripheral blood cells from healthy child 5


title: Control healthy individual 7 peripheral blood cells

source_name: peripheral blood cells from healthy individual 7


title: Control healthy individual 1 peripheral blood cells

source_name: peripheral blood cells from healthy individual 1

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: sJIA patient 48 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 48


title: Control healthy child 4 peripheral blood cells

source_name: peripheral blood cells from healthy child 4


title: sJIA patient 47 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 47


title: sJIA patient 49 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 49


title: sJIA patient 46 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 46


title: Control healthy child 1 peripheral blood cells

source_name: peripheral blood cells from healthy child 1


title: sJIA patient 44 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 44


title: sJIA patient 43 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 43


title: sJIA patient 50 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 50


title: Control healthy child 7 peripheral blood cells

source_name: peripheral blood cells from healthy child 7


title: sJIA patient 38 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 38


title: sJIA patient 41 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 41


title: sJIA patient 37 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 37


title: sJIA patient 45 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 45


title: sJIA patient 42 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 42


title: sJIA patient 39 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 39


title: sJIA patient 40 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 40

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: sJIA patient 33 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 33


title: sJIA patient 29 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 29


title: sJIA patient 36 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 36


title: sJIA patient 35 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 35


title: sJIA patient 24 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 24


title: sJIA patient 26 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 26


title: sJIA patient 27 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 27


title: sJIA patient 30 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 30


title: sJIA patient 34 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 34


title: sJIA patient 32 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 32


title: sJIA patient 31 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 31


title: sJIA patient 28 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 28


title: sJIA patient 22 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 22


title: sJIA patient 21 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 21


title: sJIA patient 25 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 25


title: sJIA patient 15 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 15


title: sJIA patient 19 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 19

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: sJIA patient 14 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 14


title: sJIA patient 11 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 11


title: sJIA patient 10 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 10


title: sJIA patient 20 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 20


title: sJIA patient 16 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 16


title: sJIA patient 17 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 17


title: sJIA patient 9 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 9


title: sJIA patient 8 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 8


title: sJIA patient 18 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 18


title: sJIA patient 7 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 7


title: sJIA patient 12 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 12


title: sJIA patient 4 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 4


title: polyJIA patient 4 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 4

value: polyarticular type juvenile idiopathic arthritis


title: sJIA patient 3 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 3


title: sJIA patient 5 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 5


title: polyJIA patient 2 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 2


title: sJIA patient 13 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 13

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: sJIA patient 2 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 2


title: polyJIA patient 5 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 5


title: sJIA patient 1 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 1


title: SLE patient 11 peripheral blood cells

source_name: peripheral blood cells from SLE patient 11

value: systemic lupus erythematosus


title: SLE patient 10 peripheral blood cells

source_name: peripheral blood cells from SLE patient 10


title: polyJIA patient 6 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 6


title: SLE patient 8 peripheral blood cells

source_name: peripheral blood cells from SLE patient 8


title: polyJIA patient 1 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 1


title: SLE patient 12 peripheral blood cells

source_name: peripheral blood cells from SLE patient 12


title: SLE patient 7 peripheral blood cells

source_name: peripheral blood cells from SLE patient 7


title: SLE patient 9 peripheral blood cells

source_name: peripheral blood cells from SLE patient 9


title: SLE patient 5 peripheral blood cells

source_name: peripheral blood cells from SLE patient 5


title: SLE patient 3 peripheral blood cells

source_name: peripheral blood cells from SLE patient 3


title: SLE patient 2 peripheral blood cells

source_name: peripheral blood cells from SLE patient 2


title: SLE patient 6 peripheral blood cells

source_name: peripheral blood cells from SLE patient 6


title: RA patient 111 peripheral blood cells

source_name: peripheral blood cells from RA patient 111

value: rheumatoid arthritis


title: polyJIA patient 3 peripheral blood cells

source_name: peripheral blood cells from polyJIA patient 3

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: SLE patient 1 peripheral blood cells

source_name: peripheral blood cells from SLE patient 1


title: RA patient 103 peripheral blood cells

source_name: peripheral blood cells from RA patient 103


title: RA patient 112 peripheral blood cells

source_name: peripheral blood cells from RA patient 112


title: RA patient 109 peripheral blood cells

source_name: peripheral blood cells from RA patient 109


title: RA patient 108 peripheral blood cells

source_name: peripheral blood cells from RA patient 108


title: RA patient 107 peripheral blood cells

source_name: peripheral blood cells from RA patient 107


title: RA patient 104 peripheral blood cells

source_name: peripheral blood cells from RA patient 104


title: RA patient 110 peripheral blood cells

source_name: peripheral blood cells from RA patient 110


title: RA patient 106 peripheral blood cells

source_name: peripheral blood cells from RA patient 106


title: SLE patient 4 peripheral blood cells

source_name: peripheral blood cells from SLE patient 4


title: RA patient 100 peripheral blood cells

source_name: peripheral blood cells from RA patient 100


title: RA patient 102 peripheral blood cells

source_name: peripheral blood cells from RA patient 102


title: RA patient 99 peripheral blood cells

source_name: peripheral blood cells from RA patient 99


title: RA patient 105 peripheral blood cells

source_name: peripheral blood cells from RA patient 105


title: RA patient 97 peripheral blood cells

source_name: peripheral blood cells from RA patient 97


title: RA patient 92 peripheral blood cells

source_name: peripheral blood cells from RA patient 92


title: RA patient 91 peripheral blood cells

source_name: peripheral blood cells from RA patient 91

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: RA patient 90 peripheral blood cells

source_name: peripheral blood cells from RA patient 90


title: RA patient 93 peripheral blood cells

source_name: peripheral blood cells from RA patient 93


title: RA patient 95 peripheral blood cells

source_name: peripheral blood cells from RA patient 95


title: RA patient 96 peripheral blood cells

source_name: peripheral blood cells from RA patient 96


title: RA patient 94 peripheral blood cells

source_name: peripheral blood cells from RA patient 94


title: RA patient 101 peripheral blood cells

source_name: peripheral blood cells from RA patient 101


title: RA patient 87 peripheral blood cells

source_name: peripheral blood cells from RA patient 87


title: sJIA patient 23 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 23


title: RA patient 88 peripheral blood cells

source_name: peripheral blood cells from RA patient 88


title: RA patient 86 peripheral blood cells

source_name: peripheral blood cells from RA patient 86


title: RA patient 83 peripheral blood cells

source_name: peripheral blood cells from RA patient 83


title: RA patient 84 peripheral blood cells

source_name: peripheral blood cells from RA patient 84


title: RA patient 82 peripheral blood cells

source_name: peripheral blood cells from RA patient 82


title: RA patient 78 peripheral blood cells

source_name: peripheral blood cells from RA patient 78


title: RA patient 77 peripheral blood cells

source_name: peripheral blood cells from RA patient 77


title: RA patient 79 peripheral blood cells

source_name: peripheral blood cells from RA patient 79


title: RA patient 76 peripheral blood cells

source_name: peripheral blood cells from RA patient 76

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: RA patient 81 peripheral blood cells

source_name: peripheral blood cells from RA patient 81


title: RA patient 73 peripheral blood cells

source_name: peripheral blood cells from RA patient 73


title: RA patient 72 peripheral blood cells

source_name: peripheral blood cells from RA patient 72


title: RA patient 70 peripheral blood cells

source_name: peripheral blood cells from RA patient 70


title: RA patient 67 peripheral blood cells

source_name: peripheral blood cells from RA patient 67


title: RA patient 64 peripheral blood cells

source_name: peripheral blood cells from RA patient 64


title: RA patient 75 peripheral blood cells

source_name: peripheral blood cells from RA patient 75


title: RA patient 65 peripheral blood cells

source_name: peripheral blood cells from RA patient 65


title: RA patient 66 peripheral blood cells

source_name: peripheral blood cells from RA patient 66


title: RA patient 61 peripheral blood cells

source_name: peripheral blood cells from RA patient 61


title: RA patient 62 peripheral blood cells

source_name: peripheral blood cells from RA patient 62


title: RA patient 85 peripheral blood cells

source_name: peripheral blood cells from RA patient 85


title: RA patient 74 peripheral blood cells

source_name: peripheral blood cells from RA patient 74


title: RA patient 68 peripheral blood cells

source_name: peripheral blood cells from RA patient 68


title: RA patient 80 peripheral blood cells

source_name: peripheral blood cells from RA patient 80


title: RA patient 59 peripheral blood cells

source_name: peripheral blood cells from RA patient 59


title: RA patient 60 peripheral blood cells

source_name: peripheral blood cells from RA patient 60

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: RA patient 63 peripheral blood cells

source_name: peripheral blood cells from RA patient 63


title: RA patient 89 peripheral blood cells

source_name: peripheral blood cells from RA patient 89


title: RA patient 55 peripheral blood cells

source_name: peripheral blood cells from RA patient 55


title: RA patient 53 peripheral blood cells

source_name: peripheral blood cells from RA patient 53


title: RA patient 71 peripheral blood cells

source_name: peripheral blood cells from RA patient 71


title: RA patient 69 peripheral blood cells

source_name: peripheral blood cells from RA patient 69


title: RA patient 51 peripheral blood cells

source_name: peripheral blood cells from RA patient 51


title: RA patient 54 peripheral blood cells

source_name: peripheral blood cells from RA patient 54


title: RA patient 47 peripheral blood cells

source_name: peripheral blood cells from RA patient 47


title: RA patient 42 peripheral blood cells

source_name: peripheral blood cells from RA patient 42


title: RA patient 50 peripheral blood cells

source_name: peripheral blood cells from RA patient 50


title: RA patient 43 peripheral blood cells

source_name: peripheral blood cells from RA patient 43


title: RA patient 48 peripheral blood cells

source_name: peripheral blood cells from RA patient 48


title: RA patient 52 peripheral blood cells

source_name: peripheral blood cells from RA patient 52


title: RA patient 58 peripheral blood cells

source_name: peripheral blood cells from RA patient 58


title: RA patient 37 peripheral blood cells

source_name: peripheral blood cells from RA patient 37


title: RA patient 38 peripheral blood cells

source_name: peripheral blood cells from RA patient 38

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: RA patient 46 peripheral blood cells

source_name: peripheral blood cells from RA patient 46


title: RA patient 57 peripheral blood cells

source_name: peripheral blood cells from RA patient 57


title: RA patient 49 peripheral blood cells

source_name: peripheral blood cells from RA patient 49


title: RA patient 44 peripheral blood cells

source_name: peripheral blood cells from RA patient 44


title: RA patient 40 peripheral blood cells

source_name: peripheral blood cells from RA patient 40


title: RA patient 45 peripheral blood cells

source_name: peripheral blood cells from RA patient 45


title: RA patient 36 peripheral blood cells

source_name: peripheral blood cells from RA patient 36


title: RA patient 39 peripheral blood cells

source_name: peripheral blood cells from RA patient 39


title: RA patient 35 peripheral blood cells

source_name: peripheral blood cells from RA patient 35


title: RA patient 41 peripheral blood cells

source_name: peripheral blood cells from RA patient 41


title: S058 vs L035

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

description: Gene expression data from European maize inbred lines (14 dent, 7 flint)

hyb_protocol: The hybridization and post-hybridization followed the protocol of the Maize Oligo Array Project (http://www.maizearray.org/).

scan_protocol: The slides were scanned using an AppliedPrecision ArrayWorx Scanner (Applied Precision Inc., USA).

data_processing: Raw data from microarray hybridization, exported from GenePix suites 6.0 (Axon, USA), was imported into LIMMA. The background was corrected by normexp method with offset 50. Background-corrected signal intensities were normalized using a two-step normalization: print-tip group loss (within-array normalization) and then between-array scale normalization.

organism: Zea mays

label_protocol: Aminoallyl-RNA was labeled with Cy5 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).

growth_protocol: Regulated growth conditions (25℃ 16h-day, 21℃ 8h-night, 70% air humidity) in a climate chamber (Percival Scientific Inc., Perry, USA) for seven days.

extract_protocol: Total RNA was extracted with an extraction buffer (200 mM NaCl, 50mM Tris pH 9, 5 mM EDTA pH 8, 1% SDS), phenol/chloroform and selective LiCl (4M) precipitation.

tag: inbred line

tag: cultivar

value: dent

value: seedling

value: 7 day

value: pool of 5 biological replicates

label_protocol: Aminoallyl-RNA was labeled with Cy3 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).

value: flint


title: L024 vs S058


title: RA patient 98 peripheral blood cells

source_name: peripheral blood cells from RA patient 98

value: male

value: peripheral blood


title: L043 vs S046


title: RA patient 33 peripheral blood cells

source_name: peripheral blood cells from RA patient 33

value: pooled control


title: S036 vs L043


title: RA patient 32 peripheral blood cells

source_name: peripheral blood cells from RA patient 32


title: RA patient 28 peripheral blood cells

source_name: peripheral blood cells from RA patient 28


title: RA patient 34 peripheral blood cells

source_name: peripheral blood cells from RA patient 34


title: sJIA patient 6 peripheral blood cells

source_name: peripheral blood cells from sJIA patient 6


title: RA patient 30 peripheral blood cells

source_name: peripheral blood cells from RA patient 30

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: S058 vs F047


title: L035 vs S036


title: RA patient 26 peripheral blood cells

source_name: peripheral blood cells from RA patient 26


title: RA patient 25 peripheral blood cells

source_name: peripheral blood cells from RA patient 25


title: F047 vs S067


title: S049 vs L024


title: RA patient 24 peripheral blood cells

source_name: peripheral blood cells from RA patient 24


title: RA patient 27 peripheral blood cells

source_name: peripheral blood cells from RA patient 27


title: L024 vs P066


title: L043 vs P066


title: S044 vs F047


title: P063 vs L043


title: P066 vs L035


title: F047 vs S049


title: S067 vs F043


title: RA patient 22 peripheral blood cells

source_name: peripheral blood cells from RA patient 22


title: RA patient 21 peripheral blood cells

source_name: peripheral blood cells from RA patient 21


title: RA patient 17 peripheral blood cells

source_name: peripheral blood cells from RA patient 17


title: RA patient 16 peripheral blood cells

source_name: peripheral blood cells from RA patient 16


title: F043 vs S044


title: S049 vs F043


title: S028 vs F043


title: RA patient 19 peripheral blood cells

source_name: peripheral blood cells from RA patient 19


title: F043 vs S050


title: RA patient 15 peripheral blood cells

source_name: peripheral blood cells from RA patient 15


title: RA patient 23 peripheral blood cells

source_name: peripheral blood cells from RA patient 23


title: RA patient 18 peripheral blood cells

source_name: peripheral blood cells from RA patient 18


title: RA patient 14 peripheral blood cells

source_name: peripheral blood cells from RA patient 14


title: F039 vs S067


title: P040 vs F047


title: P046 vs L035


title: F039 vs S046


title: L043 vs P046


title: F047 vs P048


title: S050 vs F039


title: P048 vs L024


title: S044 vs F039


title: L035 vs P048


title: P063 vs F039


title: L024 vs P040


title: F043 vs P040


title: RA patient 13 peripheral blood cells

source_name: peripheral blood cells from RA patient 13


title: RA patient 12 peripheral blood cells

source_name: peripheral blood cells from RA patient 12


title: RA patient 11 peripheral blood cells

source_name: peripheral blood cells from RA patient 11


title: RA patient 9 peripheral blood cells

source_name: peripheral blood cells from RA patient 9

source_name: Total RNA from pooled whole blood of 45 healthy individuals


title: P033 vs L043


title: RA patient 10 peripheral blood cells

source_name: peripheral blood cells from RA patient 10


title: S028 vs F037


title: P033 vs L024


title: S046 vs F037


title: L035 vs P033


title: F037 vs S050


title: RA patient 8 peripheral blood cells

source_name: peripheral blood cells from RA patient 8


title: P046 vs F037


title: RA patient 6 peripheral blood cells

source_name: peripheral blood cells from RA patient 6


title: RA patient 7 peripheral blood cells

source_name: peripheral blood cells from RA patient 7


title: RA patient 4 peripheral blood cells

source_name: peripheral blood cells from RA patient 4


title: L043 vs S058


title: S050 vs L043


title: S067 vs F037


title: RA patient 5 peripheral blood cells

source_name: peripheral blood cells from RA patient 5


title: RA patient 3 peripheral blood cells

source_name: peripheral blood cells from RA patient 3


title: F037 vs S036


title: S058 vs S067


title: L035 vs S049


title: S049 vs S050


title: RA patient 2 peripheral blood cells

source_name: peripheral blood cells from RA patient 2


title: S046 vs L035


title: RA patient 56 peripheral blood cells

source_name: peripheral blood cells from RA patient 56


title: RA patient 1 peripheral blood cells

source_name: peripheral blood cells from RA patient 1


title: S044 vs S046


title: L024 vs S044


title: S028 vs S036


title: F047 vs S028


title: S036 vs L024


title: P066 vs F047


title: P046 vs P048


title: P048 vs F043


title: F039 vs P046


title: P063 vs P066


title: F043 vs P063


title: F039 vs S028


title: RA patient 20 peripheral blood cells

source_name: peripheral blood cells from RA patient 20


title: P040 vs F039


title: F037 vs P033


title: F037 vs P063


title: P162.150min

status: Public on Aug 19 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: tumor biopsy of patient P162 with 2:30 h RNA degradation

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide Whole Human Genome Microarray (4x44K, Agilent Technologies) for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner, and data were extracted using the Feature Extraction software version 9.5.3.1 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: 2:30 h RNA degradation

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Gaithersburg, MD), and purified using the RNeasy Mini kit (Qiagen, Germantown, MD).  A detailed protocol can be found at www.riedlab.nci.nih.gov/.  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number between 9.0 and 10.0 were considered for further analysis.

treatment_protocol: Tumor biopsies from three patients with locally advanced rectal cancer were taken prior to the preoperative radio-chemotherapy. The biopsies were immediately stored in RNAlater (Qiagen, Hilden, Germany) for subsequent extraction of nucleic acids. RNA isolation was performed using TRIZOL (Invitrogen, Carlsbad, CA) following standard procedures as previously described [Grade06] (details can be found at http://www.riedlab.nci.nih.gov/protocols.asp) and stored at -80°C. RNA Degradation and Quality Control Heat-induced degradation was carried out at 60°C on a thermal block (Eppendorf Thermomixer). For each of the three patients, four different time points were defined for the analysis of degradation-state, namely 0:00h; 1:45h; 2:30h; and 3:15h respectively.

tag: patient id

tag: tissue type

value: tumor

tag: rna degradation time

tag: experimentor

value: Rong Gö


title: P033 vs P040


title: 12_pyometra

status: Public on Aug 20 2010

city: Uppsala

first: Gunnar

last: Pejler

address: BMC, Box 575

department: Anatomy, Physiology and Biochemistry

country: Sweden

institute: SLU

description: Gene expression in uterine tissue from dog with pyometra disease.

hyb_protocol: Affymetrix GeneChip® expression arrays (Canine Genome 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with the robust multi-array average (RMA) method using default analysis settings.

organism: Canis lupus familiaris

source_name: Canine uterine tissue, pyometra disease

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Total RNA was prepared from cross-sections of frozen uterus samples, using Nucleospin RNA II (Macherey-Nagel, Düren, Germany).

value: uterus

value: pyometra disease


title: P162.195min

description: tumor biopsy of patient P162 with 3:15 h RNA degradation

source_name: 3:15 h RNA degradation


title: 7_control

description: Gene expression in healthy uterine tissue.

source_name: Canine uterine tissue, healthy


title: 5_control


title: 11_pyometra


title: 16_pyometra


title: 6_control


title: 13_pyometra


title: 8_control


title: P162.105min

description: tumor biopsy of patient P162 with 1:45 h RNA degradation

source_name: 1:45 h RNA degradation


title: P162.000min

description: tumor biopsy of patient P162 with 0:00 h RNA degradation

source_name: 0:00 h RNA degradation


title: P159.000min

description: tumor biopsy of patient P159 with 0:00 h RNA degradation


title: P160.195min

description: tumor biopsy of patient P160 with 3:15 h RNA degradation


title: P160.000min

description: tumor biopsy of patient P160 with 0:00 h RNA degradation


title: 6h Low Interferon alpha MHH1

status: Public on Aug 18 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Cultured for 6h with low dosage of Interferon alpha.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

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 150.

source_name: PBMC, 5 male healthy humans

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

growth_protocol: 6h RPMI, 10% human AB serum, 100 U/ml penicillin, 100 µg/ml streptomycin, 37°C, 5%CO2

extract_protocol: RNAeasy

treatment_protocol: 1 ng/ml recombinant IFNa-2b

value: blood

tag: cell type

value: natural killer cells

tag: treatment

value: recombinant IFNa-2b

tag: dosage

value: 1 ng/ml


title: P160.150min

description: tumor biopsy of patient P160 with 2:30 h RNA degradation


title: P159.150min

description: tumor biopsy of patient P159 with 2:30 h RNA degradation


title: P159.105min

description: tumor biopsy of patient P159 with 1:45 h RNA degradation


title: 6h High Interferon alpha MHH1

description: Cultured for 6h with high dosage of Interferon alpha.

treatment_protocol: 100 ng/ml recombinant IFNa-2b

value: 100 ng/ml


title: P159.195min

description: tumor biopsy of patient P159 with 3:15 h RNA degradation


title: P160.105min

description: tumor biopsy of patient P160 with 1:45 h RNA degradation


title: 6h Medium MHH1

description: Cultured for 6h without Interferon alpha.

treatment_protocol: w/o recombinant IFNa-2b


title: 0h MHH1

description: Cultured for 0h.

growth_protocol: ex vivo


title: wild type vs fixK mutant (comparison 1, slide 2)

status: Public on Aug 16 2010

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: The software package IcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Two calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides each (except for one of the calibration experiments ; 9 slides total) were used to generate each data set.

hyb_protocol: Prior to performing hybridizations, the array slides were incubated in prehybridization buffer at 65oC for 45 min in prehybridization buffer (3X SSC [1X SSC is 0.15M NaCl plus 0.015M sodium citrate], 0.3% sodium dodecyl sulfate (SDS), and 1% bovine serum albumin). The two labeled cDNA samples to be compared were mixed, and 20X SSC (final concentration ,3X), 10mg/ml salmon sperm DNA (Invitrogen; final concentration, 0.8 mg/ml), and 5% SDS (final concentration 0.3%) were added to the sample. This hybridization mixture was divided into two tubes, incubated at 95oC for 3 minutes, and the mixture in each tube was applied to prehybridized slides that had been covered with Lifterslips (Erie Scientific Company, NH). The slides were assembled with hybridization chambers (Corning, NY) and submerged in a 65oC water bath for 14-16 hours. After hybridization the slides were washed with 1X SSC and 0.2% SDS for 5 minutes, 0.1X SSC and 0.2% SDS for 5 minutes, and 0.1 SSC for 5 minutes. The slides were dried by centrifugation (200 X g for 5 minutes).

scan_protocol: Slides were scanned with a ScanArray 4000XL scanner (Perkin-Elmer, Boston, MA). Images (Cy3 and Cy5) were captured as TIFF files.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with image preocessing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

organism: Rhodopseudomonas palustris

source_name: wild type (comparison 1, slide 2)

growth_protocol: Cells were grown on PM medium in the dark. Cultures were continuously bubbled with a gas mix (94%N2/6%O2). Flasks were placed on a magnetic stirrer turning at ~100 rpm to allow proper mixing of the cultures. The culture medium was equilibrated with the desired gas mixture for at least 12 hours before inoculation. Cells were harvested at OD660 of 0.25-0.35. Cells were harvested at OD660 of 0.25-0.35.

extract_protocol: RNA was isolated using a modification of the RNeasy midi kit (Qiagen, Chatsworth, CA).

tag: RNA from R. palustris wild type grown microaerobically

source_name: fixK (comparison 1, slide 2)

label_protocol: Labeled cDNA was prepared by direct incorporation of either the Cy3-dCTP or Cy5-dCTP fluorophore (Amersham Biosciences) during a first-strand reverse transcription reaction. Each 45 µl reaction contained 12 µg of total RNA, 13.5 µg of random primers (Invitrogen), 9 µl of 10 mM DTT, 0.5 mM each of dATP, dGTP, and dTTP, 0.2 mM dCTP, 40 U RNasin (Promega, Madison, WI), 3 µl of 1 mM Cy3- or 1 mM Cy5-dCTP, and 600 U of SuperScript II reverse transcriptase (Invitrogen). After a 2 hour incubation at 42ºC, 15 µl of 0.5 M EDTA (pH 8.0) and 15 µl of 1M NaOH were added to the sample, and incubation was continued at 65ºC for 30 minutes. The sample was then neutralized by adding 30 µl of 3M sodium acetate (pH 5.2) and 45 µl of H2O to bring the volume to 150 µl.  The labeled cDNA was purified with the QIAquick PCR purification kit (Qiagen, Chatsworth, CA). The labeling efficiency was calculated by measuring the A260 and either A550 for Cy3 incorporation or A650 for Cy5 incorporation.


title: wild type vs fixK mutant (comparison 3, slide 1)

description: The software package 1cDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Two calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides each (except for one of the calibration experiments ; 9 slides total) were used to generate each data set.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with image preocessing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA)

source_name: fix mutant (comparison 3, slide 1)

growth_protocol: Cells were grown on PM medium in the dark. Cultures were continuously bubbled with a gas mix  (94%N2/6%O2). Flasks were placed on a magnetic stirrer turning at ~100 rpm to allow proper mixing of the cultures. The culture medium was equilibrated with the desired gas mixture for at least 12 hours before inoculation.

tag: RNA from R. palustris fixK mutant grown microaerobically

source_name: wild type (comparison 3, slide 1)


title: wild type vs fixK mutant (comparison 3, slide 2)

source_name: fix K (comparison #3, slide #2)

tag: RNA from R. palustris fixKgrown microaerobically

source_name: wild type (comparison #3, slide #2)


title: wild type vs fixK mutant (comparison 1, slide 1)

source_name: wild type (comparison 1, slide 1)

source_name: fixK (comparison 1, slide 1)


title: calibration 2 slide 2

source_name: calibration 2 slide 2

label_protocol: Labeled cDNA was prepared by direct incorporation of either the Cy3-dCTP or Cy5-dCTP fluorophore (Amersham Biosciences) during a first-strand reverse transcription reaction. Each 45 µl reaction contained 12 µg of total RNA, 13.5 µg of random primers (Invitrogen), 9 µl of 10 mM DTT, 0.5 mM each of dATP, dGTP, and dTTP, 0.2 mM dCTP, 40 U RNasin (Promega, Madison, WI), 3 µl of 1 mM Cy3- or 1 mM Cy5-dCTP, and 600 U of SuperScript II reverse transcriptase (Invitrogen). After a 2 hour incubation at 42ºC, 15 µl of 0.5 M EDTA (pH 8.0) and 15 µl of 1M NaOH were added to the sample, and incubation was continued at 65ºC for 30 minutes. The sample was then neutralized by adding 30 µl of 3M sodium acetate (pH 5.2) and 45 µl of H2O to bring the volume to 150 µl.  The labeled cDNA was purified with the QIAquick PCR purification kit (Qiagen, Chatsworth, CA). The labeling efficiency was calculated by measuring the A260 and either A550 for Cy3 incorporation or A650 for Cy5 incorporation

tag: RNA from R. palustris wild type/fixK grown microaerobically


title: calibration 1 slide 1

source_name: calibration 1 slide #1

tag: RNA from R. palustris wild type/fixK mutant grown microaerobically


title: wild type vs fixK mutant (comparison 2, slide 2)

source_name: wild type (comparison 2, slide 2)

source_name: fixK (comparison 2, slide 2)


title: wild type vs fixK mutant (comparison 2, slide 1)

source_name: wild type (comparison 2, slide 1)

source_name: fixk mutant (comparison 2, slide 1)

tag: RNA from R. palustris fixk mutant grown microaerobically


title: Hs primary aortic endothelial cells grown on 100 nm nanotubes for 24 hrs_rep2

status: Public on Aug 14 2010

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description: no additional information

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome human arrays (platform acc# GPL6480) Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

source_name: Human Aortic Endothelial Cells (HAEC)

label_protocol: 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA  Input Linear Amplification Kit

growth_protocol: Cells from Lonza were cultured according to manufacturer’s instructions using Lonza’s HAEC and HAoSMC complete media in a humidified 95% air/5% CO2 incubator at 37°C.  Cells were passaged less than 15 times.

extract_protocol: Total RNA was extracted using Qiagen's RNA easy kit

treatment_protocol: Cells were seeded onto surfaces with nanotube pore diameters of 30 nm, 100 nm, or flat surfaces at a density of 5 x 10^4 cells/cm^2 for 24 hours.

value: Human Aortic Endothelial Cells (HAEC)

tag: protocol

value: 100 nm nanotubes


title: Hs primary aortic endothelial cells grown on 100 nm nanotubes for 24 hrs_rep3

description: no additional information


title: Hs primary aortic endothelial cells grown on 100 nm nanotubes for 24 hrs_rep4

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on 30 nm nanotubes for 24 hrs_rep1

description: no additional information

source_name: Human Aortic Vascular Smooth Muscle Cell (HAoSMC)

value: 30 nm nanotubes


title: Hs primary aortic vascular smooth muscle cells grown on flat titanium for 24 hrs_rep1

description: no additional information

value: Human Aortic Vascular Smooth Muscle Cell (HAoSMC)

value: flat titanium


title: Hs primary aortic endothelial cells grown on 30 nm nanotubes for 24 hrs_rep4

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on flat titanium for 24 hrs_rep2

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on 30 nm nanotubes for 24 hrs_rep3

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on flat titanium for 24 hrs_rep4

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on flat titanium for 24 hrs_rep3

description: no additional information


title: Hs primary aortic endothelial cells grown on 30 nm nanotubes for 24 hrs_rep2

description: no additional information


title: Hs primary aortic vascular smooth muscle cells grown on 30 nm nanotubes for 24 hrs_rep2

description: no additional information


title: Hs primary aortic endothelial cells grown on flat titanium for 24 hrs_rep3

description: no additional information


title: Hs primary aortic endothelial cells grown on 100 nm nanotubes for 24 hrs_rep1

description: no additional information


title: Hs primary aortic endothelial cells grown on 30 nm nanotubes for 24 hrs_rep3

description: no additional information


title: Hs primary aortic endothelial cells grown on flat titanium for 24 hrs_rep4

description: no additional information


title: Hs primary aortic endothelial cells grown on flat titanium for 24 hrs_rep2

description: no additional information


title: BbreveUCC2003_Glucose_vs_Cellobiose DYE SWAP

status: Public on Aug 11 2010

city: Cork

first: Karina

last: Pokusaeva

address: Western Road

country: Ireland

institute: University College Cork

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5) which performs a lowess normalization.

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in  Escherichia coli  K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control. The log10 ratio's represent Cy5/Cy3.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in mMRS with cellobiose

growth_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of cellobiose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

tag: strain

value: Bifidobacterium breve UCC2003

tag: growth stage

value: exponential

tag: carbon source

value: Cellobiose

source_name: Bifidobacterium breve UCC2003 grown in mMRS with glucose

treatment_protocol: ifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: Glucose


title: Hs primary aortic endothelial cells grown on flat titanium for 24 hrs_rep1

description: no additional information


title: BbreveUCC2003_Glucose_vs_Cellodextrins DYE SWAP

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5), which performs a lowess normalization.

source_name: Bifidobacterium breve UCC2003 grown in mMRS with cellodextrins

label_protocol: DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in  Escherichia coli  K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control. The log10 ratio's represent Cy5/Cy3.

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.85% (w/v) of cellodextrins solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: Cellodextrins

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .


title: BbreveUCC2003_Glucose_vs_Cellodextrins

label_protocol: DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in  Escherichia coli  K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

treatment_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

extract_protocol: NA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: ifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.85% (w/v) of cellodextrins solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .


title: PDGFRa(+) Sca-1(+)

status: Public on Aug 10 2010

city: Tokyo

first: Fumio

last: Arai

address: 35 Shinano-machi, Shinjuku-ku

institute: School of Medicine, Keio University

description: Gene expression data from PDGFRa(+) Sca-1(+) cells in murine bone marrow.

hyb_protocol: Following fragmentation, 10 μg of cRNA was hybridized for 16 hr at 45°C on GeneChip Mouse Genome Array 430 2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated by the MAS5.0 algorithm using the GeneChip Operating Software (Affymetrix, ver. 1.4).

label: Biotin

organism: Mus musculus

source_name: Murine bone marrow

label_protocol: Biotin-labeled cRNAs were prepared from total RNA using the Affymetrix two-cycle target-labeling assay (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from fractionated bone-derived cells using TRIzol Reagent (Qiagen, GmbH, Hilden, Germany).

tag: phenotype

value: PDGFRa(+) Sca-1(+)

value: endosteal cell


title: PDGFRa(+) Sca-1(-)

description: Gene expression data from PDGFRa(+) Sca-1(-) cells in murine bone marrow.

value: PDGFRa(+) Sca-1(-)


title: PDGFRa(-) Sca-1(-)

description: Gene expression data from PDGFRa(-) Sca-1(-) cells in murine bone marrow.

value: PDGFRa(-) Sca-1(-)


title: ALCAM(-) Sca-1(-)

description: Gene expression data from ALCAM(-) Sca-1(-) cells in murine bone marrow.

value: ALCAM(-) Sca-1(-)


title: muscle_LF_ d56_biorep8

city: Maastricht

first: Janneke

last: de Wilde

address: Universiteitssingel 50

department: Human Biology

country: Netherlands

institute: Maastricht University

description: Before the diet intervention mice (age: 9 weeks) were switched to the LF run-in diet for 3 weeks

hyb_protocol: Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

scan_protocol: Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

data_processing:
Expression levels of probe sets were normalized using GC-RMA(slow) (unlogged scale). Probe sets were redefined according to Dai et al (Nucleic Acids Research, 2005). In this method probes are annotated
using up to date databases and assigned to unique gene identifiers, in this case Entrez ID's, instead of the classic GeneChip probe sets. As selection criteria we used: fold change > 1.3 a  p value < 0.05 and FDR < 0.05

source_name: mouse 148, quadriceps muscle, low fat diet, day 56

label_protocol: Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

growth_protocol: Mice were fed a standard growth diet for 3 weeks prior to switching to the LF run-in diet for 3 weeks. Following the run-in period mice were sacrificed or randomly assigned to the LF or the HF group for 56 days

extract_protocol:
According the manufactures instruction, total RNA was extracted from the quadriceps muscle with Trizol reagent (Invitrogen, Breda, the Netherlands) and purified with the Rneasy Mini Kit
(Qiagen, Venlo, the Netherlands). Contaminating genomic DNA was removed with the RNase-free DNase set (Qiagen, Venlo, the Netherlands) according the manufactures instructions.

treatment_protocol: After 0 days or 56 days of diet intervention, mice were sacrificed, the quadriceps muscle was dissected and snap-frozen in liquid nitrogen

value: low fat diet

tag: time

value: day 56

tag: tissue

value: quadriceps muscle

tag: gender

value: Male

tag: age

value: 20 weeks


title: muscle_HF_ d56_biorep9

source_name: mouse 151, quadriceps muscle, high fat diet, day 56

value: high fat diet


title: muscle_LF_ d56_biorep7

source_name: mouse 154, quadriceps muscle, low fat diet, day 56


title: muscle_HF_ d56_biorep10

source_name: mouse 158, quadriceps muscle, high fat diet, day 56


title: muscle_LF_ d56_biorep10

source_name: mouse 141, quadriceps muscle, low fat diet, day 56


title: muscle_HF_ d56_biorep8

source_name: mouse 152, quadriceps muscle, high fat diet, day 56


title: muscle_LF_ d56_biorep9

source_name: mouse 155, quadriceps muscle, low fat diet, day 56


title: ALCAM(-) Sca-1(+)

description: Gene expression data from ALCAM(-) Sca-1(+) cells in murine bone marrow.

value: ALCAM(-) Sca-1(+)

tag: cell type


title: muscle_HF_ d56_biorep1

source_name: mouse 146, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep6

source_name: mouse 149, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep7

source_name: mouse 157, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep2

source_name: mouse 145, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep3

source_name: mouse 144, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep5

source_name: mouse 143, quadriceps muscle, high fat diet, day 56


title: muscle_HF_ d56_biorep4

source_name: mouse 150, quadriceps muscle, high fat diet, day 56


title: ALCAM(+) Sca-1(-)

description: Gene expression data from ALCAM(+) Sca-1(-) cells in murine bone marrow.

value: ALCAM(+) Sca-1(-)


title: muscle_LF_ d56_biorep5

source_name: mouse 142, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d56_biorep6

source_name: mouse 159, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d56_biorep4

source_name: mouse 160, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d56_biorep3

source_name: mouse 153, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d56_biorep2

source_name: mouse 156, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d56_biorep1

source_name: mouse 147, quadriceps muscle, low fat diet, day 56


title: muscle_LF_ d0_biorep10

source_name: mouse 12, quadriceps muscle, low fat diet, day 0

value: day 0

value: 12 weeks


title: muscle_LF_ d0_biorep9

source_name: mouse 14, quadriceps muscle, low fat diet, day 0


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-lfg_rep2

status: Public on Aug 06 2010

city: Boston

first: Michael

last: Coyne

state: MA

address: 181 Longwood Avenue

department: Medicine

institute: Brigham & Women's Hospital

description: This sample is of Bacteroides fragilis NCTC 9343 delta-lfg. It is the second of three biological replicates of this mutant strain used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Roche NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The normalized values were calulated by NimbleGen Systems Inc. using quantile normalization (Bolstad et al. Bioinformatics 19(2):185) and the RMA algorithm (Irizarry et al. Biostatistics 4(2):249) with tools made available by the Bioconductor project (http://www.bioconductor.org).
Further explanation of Nimblegen data types is available in the NimbleScan User's Guide at: http://www.nimblegen.com/products/lit/nimblescan2.3usersguide.pdf

organism: Bacteroides fragilis NCTC 9343

label_protocol: Labeling was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Bacteroides fragilis NCTC 9343 was grown to mid-log phase (O.D.600nm ~0.75) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: The delta-lfg mutant was constructed by deleting 10,040 bp of DNA affecting nine genes (BF4298 through BF4306 of NC_003228).  The DNA removed by the lfg deletion corresponds to bases 5,103,555 through 5,113,594 of NC_003228.

tag: Accession

tag: GI

tag: Taxname

value: Bacteroides fragilis NCTC 9343

tag: Taxid

tag: This sample is of a multiple deletion mutant in which nine genes (BF4298 through BF4306 of NC_003228) of the lfg locus are deleted.


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-lfg_rep1

description: This sample is of Bacteroides fragilis NCTC 9343 delta-lfg. It is the first of three biological replicates of this mutant strain used in this experiment, each from separate cultures.


title: muscle_LF_ d0_biorep5

source_name: mouse 20, quadriceps muscle, low fat diet, day 0


title: muscle_LF_ d0_biorep8

source_name: mouse 18, quadriceps muscle, low fat diet, day 0


title: muscle_LF_ d0_biorep4

source_name: mouse 16, quadriceps muscle, low fat diet, day 0


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-gmd-fcl_delta-fkp_rep3

description: This sample is of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp. It is the third of three biological replicates of this mutant strain used in this experiment, each from separate cultures.

treatment_protocol: The delta-gmd-fcl mutant was constructed by deleting 2,092 bp of DNA, affecting both of the adjacent genes (BF1887 [fcl] and BF1888 [gmd]).  The DNA removed by the gmd-fcl deletion corresponds to bases 2,205,448 through 2,207,539 of NC_003228.  A second deletion encompassing 2,791 bp of the 2,850 bp fkp gene (BF2607) was introduced into the delta-gmd-fcl background, resulting in the B. fragilis delta-gmd-fcl delta-fkp strain.  The bases deleted by the delta-fkp mutation correspond to 3,033,425 through 3,036,215 of NC_003228.

tag: This sample is from a double deletion mutant in which the adjacent genes gmd (BF1888) and fcl (BF1887) are deleted, and a second deletion removed fkp (BF2607).


title: muscle_LF_ d0_biorep7

source_name: mouse 15, quadriceps muscle, low fat diet, day 0


title: calibration 2 slide 1

source_name: calibration 2 slide 1

tag: RNA from R. palustris wild type/fixK mutant grown microaerobically


title: muscle_LF_ d0_biorep3

source_name: mouse 17, quadriceps muscle, low fat diet, day 0

tag: protocol


title: muscle_LF_ d0_biorep2

source_name: mouse 13, quadriceps muscle, low fat diet, day 0

tag: strain


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-gmd-fcl_delta-fkp_rep2

description: This sample is of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp. It is the second of three biological replicates of this mutant strain used in this experiment, each from separate cultures.


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_wild-type_rep3

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Bacteroides fragilis NCTC 9343

treatment_protocol: None (wild-type)

tag: wild-type sample


title: muscle_LF_ d0_biorep6

source_name: mouse 19, quadriceps muscle, low fat diet, day 0


title: muscle_LF_ d0_biorep1

source_name: mouse 11, quadriceps muscle, low fat diet, day 0


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-gmd-fcl_delta-fkp_rep1

description: This sample is of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp. It is the first of three biological replicates of this mutant strain used in this experiment, each from separate cultures.


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_delta-lfg_rep3

description: This sample is of Bacteroides fragilis NCTC 9343 delta-lfg. It is the third of three biological replicates of this mutant strain used in this experiment, each from separate cultures.


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_wild-type_rep2

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: BWH_Comstock_B_fragilis_9343_glycoprotein_study_wild-type_rep1

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: SRC-5AZA-2

city: Chicago

first: Christopher

middle: A

last: Hamm

state: IL

address: 2430 N. Halsted Street

department: Cancer Biology and Epigenomics

institute: Children’s Memorial Research Center

description: This sample is of Swarm Rat Chondrosarcoma cells treated with 5-aza-2-deoxycytidine for five passages. It is the second of two biologic replicates, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Swarm Rat chondrosarcoma Cell line treated with 5-aza-2-deoxycytidine

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Swarm rat chondrosarcoma cells were cultured in DMEM high glucose (4.5g glucose/ml) supplemented with 10% FBS and Penicillin/Streptomycin.

extract_protocol: Total RNA was isolated using Trizo (Invitrogen), RNA was treated with TURBO DNA-free (Ambion).

treatment_protocol: Experimental cells: Swarm Rat Chondrosarcoma cells treated with 5-aza-2-deoxycytidine(0.1uM) for five passages.

value: Rat chondrosarcoma

tag: cell line

value: Swarm cells

tag: treatment

value: 0.1uM 5-aza-2-deoxycytidine


title: SCR-No-Treat-3

description: This sample is of Swarm Rat Chondrosarcoma grown for five passages with no drug treatment.  It is the third of three biologic replicates, each from separate cultures.

source_name: Swarm Rat chondrosarcoma Cell line untreated

treatment_protocol: Control cells: Swarm Rat Chondrosarcoma grown for five passages with no drug treatment.

value: No drug treatment


title: SRC-5AZA-1

description: This sample is of Swarm Rat Chondrosarcoma cells treated with 5-aza-2-deoxycytidine for five passages. It is the first of two biologic replicates, each from separate cultures.


title: SCR-No-Treat-2

description: This sample is of Swarm Rat Chondrosarcoma grown for five passages with no drug treatment.  It is the second of three biologic replicates, each from separate cultures.


title: SCR-No-Treat-1

description: This sample is of Swarm Rat Chondrosarcoma grown for five passages with no drug treatment.  It is the first of three biologic replicates, each from separate cultures.


title: BbreveUCC2003_Glucose_vs_Cellobiose

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5) which performs a lowess normalization.

source_name: Bifidobacterium breve UCC2003 grown in mMRS with glucose

value: Bifidobacterium breve UCC2003

tag: growth stage

value: exponential

tag: carbon source

value: Glucose

source_name: Bifidobacterium breve UCC2003 grown in mMRS with cellobiose

treatment_protocol: ifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of cellobiose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: Cellobiose


title: 0.6% vs. 50% air saturation Replicate 4

status: Public on Aug 05 2010

city: Bronx

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

description: Biological replicate 4 of 5.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner . Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis MC2 155

source_name: Chemostat culture slow 0.6% air saturation

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: Prior to each experiment bacteria were loop inoculated from a cryo-culture (-80°C) onto a LBT plate and incubated for 3 days at 37°C.  A colony was picked from the plate and inoculated into the 5 ml batch medium in a 30 ml glass universal and incubacted at 37°C on a rotary shaker at 200 rpm. At an OD between 0.3 - 0.5 a sample was withdrawn to inoculate the bioreactor (700 ml) to a starting OD600 of 0.005. The culture was then left in batch mode under oxystatic condition (maintaining an air saturation of 50% i.e. 10% dissolved oxygen concentration) until OD600 reached around 80% of maximum OD600 and then turned in to chemostat mode either at a dilution rate of 4.6 h-1 or 69 h-1. The chemostat was then left running for at least two volume changes before harvest.

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

tag: culture doubling time

value: 69 hours

source_name: Chemostat culture slow 50% air saturation


title: 2.5% vs. 50% air saturation Replicate 3

description: Biological replicate 3 of 5.

source_name: Chemostat culture slow 2.5% air saturation


title: 2.5% vs. 50% air saturation Replicate 2

description: Biological replicate 2 of 5.


title: 0.6% vs. 50% air saturation Replicate 5

description: Biological replicate 5 of 5.


title: 2.5% vs. 50% air saturation Replicate 5

description: Biological replicate 5 of 5.


title: Slow vs. Fast Replicate 5

description: Biological replicate 5 of 5.

source_name: Chemostat culture fast 50% air saturation

value: 4.6 hours


title: 0.6% vs. 50% air saturation Replicate 3

description: Biological replicate 3 of 5.


title: 0.6% vs. 50% air saturation Replicate 1

description: Biological replicate 1 of 5.


title: 2.5% vs. 50% air saturation Replicate 4

description: Biological replicate 4 of 5.


title: Slow vs. Fast Replicate 4

description: Biological replicate 4 of 5.


title: 2.5% vs. 50% air saturation Replicate 1

description: Biological replicate 1 of 5.


title: 0.6% vs. 50% air saturation Replicate 2

description: Biological replicate 2 of 5.


title: Slow vs. Fast Replicate 3

description: Biological replicate 3 of 5.


title: Rg1_HUVEC_rep2

type: other

city: Hong Kong

first: Patrick

middle: YK

last: Yue

address: Waterloo Road

department: Biology

country: Hong Kong

institute: Hong Kong Baptist University

description: Analysis used miRNA of normal HUVEC as control samples for comparison to the Rg1-treated HUVEC.

hyb_protocol: Firstly, polyadenylated miRNA was hybridized onto microarray at 52oC for 16 h, then these tagged miRNA were fluorescently labeled by binding with comlementary branched DNA polyers carried Alexa Fluor 3 or 5 in the second round of hybridization carried out at 62oC for 4 h.

scan_protocol: Microarrays were scanned using the ScanArray 5000 confocal laser scanner (Parkard Biochip Technologies/GSI Lumonics).

data_processing: Data analysis was carried out using QuantArray® Quantitative Microarray Analysis Software (GSI Lumonics) and GeneSpring GX software (Version 7.3.1; Agilent Technologies) by means of LOWESS normalization method.

molecule: other

source_name: HUVEC cultured in medium

label_protocol: Labelled with Alexa Fluor 3 or 5 using NCodeTM miRNA Labeling System (Invitrogen) as manufacturers instructions.

growth_protocol: HUVEC were grown in M199 medium supplemented with 20% heat-inactivated FBS, 20 μg/ml ECGS, 90 μg /ml heparin, 1% PS on 0.1% gelatin-coated culture flasks. All cells were maintained in a humidified incubator at 37℃ with 5% CO2.

extract_protocol: Total RNA of HUVEC was extracted by using TRIzol® Reagent according to the manufacturer’s protocol. By using PureLinkTM miRNA Isolation Kit, small RNA from control and Rg1-treated groups total RNA were further isolated and enriched.

treatment_protocol: Cells were induced with 150 nM Rg1 for 48 hours. A control group was performed in parallel by culturing cells in culture medium without Rg1.

value: human umbilical vein endothelial cells (HUVEC)

tag: agent

value: control

source_name: HUVEC treated with Rg1


title: Rg1_HUVEC_rep3

tag: cell type


title: Rg1_HUVEC_rep1


title: Slow vs. Fast Replicate 1

description: Biological replicate 1 of 5.


title: MEF_rep2_Cy5labeled

status: Public on Aug 04 2010

city: Storrs

first: Mark

middle: Gerald

last: Carter

state: CT

address: 1392 Storrs Road

department: Center for Regenerative Biology

institute: University of Connecticut

description: Mouse Embryonic Fibroblast cells, replicate 2, HyperCy5-labeled

hyb_protocol: Slides were plunged into 0.2% SDS 10 times, incubated 2-3 minutes with gentle shaking, and rinsed in a series of 5 milli-Q water baths. Slides were dried by immersion in isopropanol for 10-15 sec. followed by centrifugation at 1,000 rpm in a hanging bucket rotor. Slides were prehybridized in 5X SSC, 0.1% SDS, 1% bovine serum albumin at 42°C for 1 hour, washed and dried as before. Combined C3/Cy5 target mixes were hybridized in 50% Formamide, 10X SSC, 0.2% SDS for 40 hours at 42°C. Hybridized slides were sequentially washed in (1X SSC, 0.2% SDS), (0.1X SSC, 0.2% SDS), and 0.1X SSC for 4 minutes each, dried by centrifugation, and stored in argon gas until scanned.

scan_protocol: Washed slides were scanned using GenePix Pro 6.1 software on an MD Axon 4000B scanner, at 33% laser power, and 10 μm resolution. Automatic PMT adjustment was used, set at 0.05% saturated features. Images were saved as two-channel TIFF files.

data_processing: Two-channel TIFF scan images were overlayed with GAL file spot grids in GenePix Pro 6.1, irregular blocks and spots were manually adjusted when necessary, and unflagged bad features were manually flagged. Normalized, background-subtracted intensity data was exported to GPR files.

source_name: Stratagene Universal Mouse Reference

label_protocol: following stratagene's instructions

extract_protocol: following stratagene's instructions

tag: passage number

value: unknown

value: mixed

source_name: mouse embryonic fibroblast cells, inactivated

label_protocol: Ten micrograms of each total RNA sample was reverse transcribed, and remaining RNA was removed by adding 10 μl 1M NaOH, incubation at 65 °C for 15 min, followed by addition of 10 μl 1M HCl for pH neutralization. cDNA was purified using a modified QIAquick PCR purification kit protocol, spectrophotometer quantitated, then dried completely in a speed-vac and stored at -80°C until use. Cy dyes were conjugated to aminoallyl-labeled cDNA by resuspending each cDNA in 4.5 μl 0.1 M sodium carbonate buffer, combining with 4.5 μl of Cy3 or Hyper-Cy5 NHS-ester monoreactive dye in Dimethyl Sulphoxide (DMSO) and incubated in the dark at room temperature for approximately 1 hr, and then purified with a QIAquick PCR purification kit. Labeled cDNA target mixes were quantitated with a NanoDrop 1000 spectrophotometer (Thermo Scientific), combined in Cy-3/HyperCy-5 pairs and dried to 40 μl total volume in a Speed-vac.

growth_protocol: ES Cell lines, which were derived from blastocysts and preblastocysts in three different media, KDMEM, LG-MEMα, and HG-MEMα, were cultured to passage 8 on feeders, then lysed in TriZol (Invitrogen) and stored at -80 until RNA extraction.

extract_protocol: Total RNA was extracted as described in TriZol manufacturer's protocol. Approximately 100 ug of each total RNA preparation was further purified for microarray analysis using RNeasy Mini columns (Qiagen) as indicated by the manufacturer for total RNA purification, spectrophotometer-quantitated, and stored at -80 oC in 10 ug aliquots (1 ug/ul).

value: mouse embryonic fibroblasts


title: MEF_rep1_Cy5labeled

description: Mouse Embryonic Fibroblast cells, replicate 1, HyperCy5-labeled


title: ES_preblastocyst_LG-MEMa_rep2_Cy3labeled

description: ES cells, preblastocyst-derived in low-glucose MEMa, replicate 2, cy3-labeled

source_name: ES cells derived from preblastocyst in low-glucose MEMa

value: ES cells derived from preblastocyst

value: (CBS/CaJ X C57BL/6J) X (C57BL/6XDBA/2)F1


title: ES_preblastocyst_LG-MEMa_rep1_Cy5labeled

description: ES cells, preblastocyst-derived in low-glucose MEMa, replicate 1, HyperCy5-labeled


title: MEF_rep1_Cy3labeled

description: Mouse Embryonic Fibroblast cells, replicate 1, cy3-labeled


title: MEF_rep2_Cy3labeled

description: Mouse Embryonic Fibroblast cells, replicate 2, cy3-labeled


title: ES_preblastocyst_LG-MEMa_rep2_Cy5labeled

description: ES cells, preblastocyst-derived in low-glucose MEMa, replicate 2, HyperCy5-labeled


title: ES_preblastocyst_LG-MEMa_rep1_Cy3labeled

description: ES cells, preblastocyst-derived in low-glucose MEMa, replicate 1, cy3-labeled


title: ES_preblastocyst_KDMEM_rep2_Cy3labeled

description: ES cells, preblastocyst-derived in KnockOut DMEM, replicate 2, cy3-labeled

source_name: ES cells derived from preblastocyst in KnockOut DMEM


title: ES_preblastocyst_KDMEM_rep1_Cy5labeled

description: ES cells, preblastocyst-derived in KnockOut DMEM, replicate 1, HyperCy5-labeled


title: ES_blastocyst_LG-MEMa_rep2_Cy3labeled

description: ES cells, blastocyst-derived in low-glucose MEMa, replicate 2, cy3-labeled

source_name: ES cells derived from blastocyst in low-glucose MEMa

value: ES cells derived from blastocyst


title: ES_preblastocyst_KDMEM_rep1_Cy3labeled

description: ES cells, preblastocyst-derived in KnockOut DMEM, replicate 1, cy3-labeled


title: ES_blastocyst_LG-MEMa_rep1_Cy5labeled

description: ES cells, blastocyst-derived in low-glucose MEMa, replicate 1, HyperCy5-labeled


title: ES_preblastocyst_HG-MEMa_rep1_Cy3labeled

description: ES cells, preblastocyst-derived in high-glucose MEMa, replicate 1, cy3-labeled

source_name: ES cells derived from preblastocyst in high-glucose MEMa


title: ES_blastocyst_LG-MEMa_rep2_Cy5labeled

description: ES cells, blastocyst-derived in low-glucose MEMa, replicate 2, HyperCy5-labeled


title: ES_preblastocyst_HG-MEMa_rep2_Cy5labeled

description: ES cells, preblastocyst-derived in high-glucose MEMa, replicate 2, HyperCy5-labeled


title: ES_preblastocyst_HG-MEMa_rep1_Cy5labeled

description: ES cells, preblastocyst-derived in high-glucose MEMa, replicate 1, HyperCy5-labeled


title: ES_preblastocyst_HG-MEMa_rep2_Cy3labeled

description: ES cells, preblastocyst-derived in high-glucose MEMa, replicate 2, cy3-labeled


title: ES_blastocyst_KDMEM_rep2_Cy5labeled

description: ES cells, blastocyst-derived in KnockOut DMEM, replicate 2, HyperCy5-labeled

data_processing: Two-channel TIFF scan images were overlayed with GAL file spot grids in GenePix Pro 6.1, irregular blocks and spots were manually adjusted when necessary, and unflagged bad features were manually flagged. Normalized, background-subtracted intensity data was exported from GPR files.

source_name: ES cells derived from blastocyst in KnockOut DMEM


title: ES_blastocyst_LG-MEMa_rep1_Cy3labeled

description: ES cells, blastocyst-derived in low-glucose MEMa, replicate 1, cy3-labeled


title: ES_blastocyst_KDMEM_rep2_Cy3labeled

description: ES cells, blastocyst-derived in KnockOut DMEM, replicate 2, cy3-labeled


title: ES_blastocyst_KDMEM_rep1_Cy3labeled

description: ES cells, blastocyst-derived in KnockOut DMEM, replicate 1, cy3-labeled


title: ES_blastocyst_KDMEM_rep1_Cy5labeled

description: ES cells, blastocyst-derived in KnockOut DMEM, replicate 1, HyperCy5-labeled


title: ES_blastocyst_HG-MEMa_rep2_Cy3labeled

description: ES cells, blastocyst-derived in high-glucose MEMa, replicate 2, cy3-labeled

source_name: ES cells derived from blastocyst in high-glucose MEMa


title: ES_blastocyst_HG-MEMa_rep2_Cy5labeled

description: ES cells, blastocyst-derived in high-glucose MEMa, replicate 2, HyperCy5-labeled


title: ES_blastocyst_HG-MEMa_rep1_Cy3labeled

description: ES cells, blastocyst-derived in high-glucose MEMa, replicate 1, cy3-labeled


title: ES_blastocyst_HG-MEMa_rep1_Cy5labeled

description: ES cells, blastocyst-derived in high-glucose MEMa, replicate 1, HyperCy5-labeled