title: cy3:SHR treated w/ nifedipine and then washed out, biological rep 2g; cy5:pool of 6 WKY control rats


title: AML sample 48 diagnosis paired with sample 93

status: Public on Apr 11 2007

type: genomic

city: London

first: Manoj

last: Raghavan

address: Charterhouse Square

department: Centre for Medical Oncology, Institute of Cancer

country: United Kingdom

institute: Barts and the London, Queen Mary's School of Medicine and Dentistry

description: SNP genotype data from AML patient at diagnosis

hyb_protocol: Affymetrix 10K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: AML blood/marrow cells relapse

label_protocol: Affymetrix 10K mapping assay protocol

growth_protocol: Not applicable

extract_protocol: Phenol chloroform

treatment_protocol: AML cells collected from blood or bone marrow. Ficoll separation, and cryopreserved in liquid nitrogen.

tag: FAB type = M1

tag: cytogenetics = 46,XX


title: cy3:SHR treated w/ nifedipine and then washed out, biological rep 4g; cy5:pool of 6 WKY control rats

type: RNA

city: Seattle

first: Lynn

middle: M

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: 60 C for 17 hours

scan_protocol: Agilent DNA Microarray scanner

data_processing: images analyzed with Agilent Feature Extraction v7.1,

molecule: total RNA

organism: Rattus norvegicus

source_name: medial layer of thorassic and abdominal aorta from pool of 6 WKY control rats

label_protocol: fluorescent linear amplification kit from Agilent

extract_protocol: Qiagen RNeasy kit

tag: mean systolic blood pressure = 107+/-8 mm HG

source_name: medial layer of thorassic and abdominal aorta from SHR rat treated w/ nifedipine and then washed out

tag: mean systolic blood pressure = 151+/-4 mm HG


title: cy5:SHR treated w/ nifedipine and then washed out, biological rep 2r; cy3:pool of 6 WKY control rats


title: cy5:SHR treated w/ nifedipine and then washed out, biological rep 1r; cy3:pool of 6 WKY control rats


title: AML sample 30 remission paired with sample 29

source_name: AML marrow cells remission

tag: FAB type = NA


title: cy5:SHR treated w/ nifedipine and then washed out, biological rep 6r; cy3:pool of 6 WKY control rats


title: AML sample 29 diagnosis paired with sample 30

tag: FAB type = M2


title: AML sample 92 remission paired with sample 59

tag: cytogenetics = not analysed


title: AML sample 59 diagnosis paired with sample 92

tag: FAB type = M4


title: AML sample 93 remission paired with sample 48


title: AML sample  97 remission paired with sample 58


title: cy3:WKY control, biological rep 6g; cy5:pool of 6 WKY control rats

source_name: medial layer of thorassic and abdominal aorta from untreated WKY rat


title: cy5:WKY control, biological rep 5r; cy3:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine and then washed out, biological rep 6g; cy5:pool of 6 WKY control rats


title: cy5:WKY control, biological rep 6r; cy3:pool of 6 WKY control rats


title: AML sample 91 remission paired with GSM173411


title: cy5:SHR treated w/ nifedipine and then washed out, biological rep 5r; cy3:pool of 6 WKY control rats


title: cy3:WKY control, biological rep 5g; cy5:pool of 6 WKY control rats


title: AML sample 58 diagnosis paired with sample 97

tag: cytogenetics = 47,XX, inv(16)(p13q22),+22


title: cy3:WKY control, biological rep 4g; cy5:pool of 6 WKY control rats


title: AML sample 32 diagnosis paired with sample 96

tag: cytogenetics = 46,XY,+8


title: cy5:WKY control, biological rep 4r; cy3:pool of 6 WKY control rats


title: AML sample 311 diagnosis paired with sample 81

tag: FAB type = M3


title: AML sample 13 diagnosis paired with sample 90


title: AML sample 81 remission paired with sample 311

tag: cytogenetics = 46,XY


title: AML sample 96 remission paired with sample 32


title: cy3:WKY control, biological rep 1g; cy5:pool of 6 WKY control rats


title: AML sample 26 remission paired with GSM173401


title: AML sample 107 remission paired with sample 35


title: cy5:WKY control, biological rep 2r; cy3:pool of 6 WKY control rats


title: cy5:WKY control, biological rep 1r; cy3:pool of 6 WKY control rats


title: AML sample 28 remission paired with sample 27


title: AML sample 27 diagnosis paired with sample 28

tag: FAB type = M6


title: cy3:WKY treated w/ angtiotensin, biological rep 5g; cy5:pool of 6 WKY control rats

source_name: medial layer of thorassic and abdominal aorta from WKY rat treated w/ angiotensin

tag: mean systolic blood pressure = 188+/-12  mm HG


title: AML sample 90 remission paired with sample 13


title: cy3:WKY control, biological rep 3g; cy5:pool of 6 WKY control rats


title: cy5:WKY control, biological rep 3r; cy3:pool of 6 WKY control rats


title: cy5:WKY treated w/ angtiotensin, biological rep 5r; cy3:pool of 6 WKY control rats


title: cy3:WKY control, biological rep 2g; cy5:pool of 6 WKY control rats


title: cy3:WKY treated w/ angtiotensin, biological rep 6g; cy5:pool of 6 WKY control rats


title: AML sample 44 remission paired with sample 10


title: AML sample 35 diagnosis paired with sample 107

source_name: AML blood/marrow cells diagnosis


title: AML sample 10 diagnosis paired with sample 44

tag: FAB type = M5

tag: cytogenetics = 46,XX,dic(7;22),+8


title: cy5:WKY treated w/ angtiotensin, biological rep 4r; cy3:pool of 6 WKY control rats


title: cy5:WKY treated w/ angtiotensin, biological rep 6r; cy3:pool of 6 WKY control rats


title: AML sample 89 remission paired with sample 16


title: cy5:WKY treated w/ angtiotensin, biological rep 3r; cy3:pool of 6 WKY control rats


title: AML sample 21 remission paired with sample 22


title: AML sample 132 remission paired with GSM173397


title: AML sample 21 diagnosis paired with sample 22


title: AML sample 16 diagnosis paired with sample 89


title: cy5:WKY treated w/ angtiotensin, biological rep 2r; cy3:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine, biological rep 6g; cy5:pool of 6 WKY control rats

source_name: medial layer of thorassic and abdominal aorta from SHR rat treated w/ nifedipine

tag: mean systolic blood pressure = 145+/-9 mm HG


title: cy5:WKY treated w/ angtiotensin, biological rep 1r; cy3:pool of 6 WKY control rats


title: cy3:WKY treated w/ angtiotensin, biological rep 3g; cy5:pool of 6 WKY control rats


title: AML sample 45 diagnosis paired with sample 24


title: cy5:SHR treated w/ nifedipine, biological rep 6r; cy3:pool of 6 WKY control rats


title: cy3:WKY treated w/ angtiotensin, biological rep 2g; cy5:pool of 6 WKY control rats


title: cy3:WKY treated w/ angtiotensin, biological rep 4g; cy5:pool of 6 WKY control rats


title: AML sample 24 remission paired with sample 45


title: cy3:SHR treated w/ nifedipine, biological rep 5g; cy5:pool of 6 WKY control rats


title: AML sample 40 diagnosis paired with sample 41


title: AML sample 41 remission paired with sample 40


title: AML sample 49 diagnosis paired with sample 106

tag: FAB type = M1


title: AML sample 106 remission paired with sample 49


title: cy5:SHR treated w/ nifedipine, biological rep 5r; cy3:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine, biological rep 4g; cy5:pool of 6 WKY control rats


title: cy5:SHR treated w/ nifedipine, biological rep 3r; cy3:pool of 6 WKY control rats


title: cy3:WKY treated w/ angtiotensin, biological rep 1g; cy5:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine, biological rep 3g; cy5:pool of 6 WKY control rats


title: cy5:SHR treated w/ nifedipine, biological rep 4r; cy3:pool of 6 WKY control rats


title: AML sample 95 remission paired with GSM173396

tag: cytogenetics = 46,XX


title: AML sample 53 diagnosis paired with sample 88

tag: FAB type = M0

tag: cytogenetics = 47,XY,+19 and del 1x ABL homologue


title: AML sample 94 remission paired with sample 69

tag: FAB type = NA


title: AML sample 69 diagnosis paired with sample 94

tag: cytogenetics = 46,XY,+3,+10


title: AML sample 131 remission paired with sample 72


title: cy3:SHR treated w/ nifedipine, biological rep 2g; cy5:pool of 6 WKY control rats

tag: mean systolic blood pressure = 107+/-8 mm HG


title: AML sample 104  remission paired with sample 71


title: AML sample 88 remission paired with sample 53


title: cy5:SHR treated w/ nifedipine, biological rep 2r; cy3:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine, biological rep 1g; cy5:pool of 6 WKY control rats


title: cy5:SHR treated w/ nifedipine, biological rep 1r; cy3:pool of 6 WKY control rats


title: AML sample 72 diagnosis paired with sample 131


title: cy3:SHR control, biological rep 6g; cy5:pool of 6 WKY control rats

source_name: medial layer of thorassic and abdominal aorta from untreated SHR rat

tag: mean systolic blood pressure = 184+/-13 mm HG


title: cy5:SHR control, biological rep 6r; cy3:pool of 6 WKY control rats


title: AML sample 71  diagnosis paired with sample 104


title: cy5:SHR control, biological rep 5r; cy3:pool of 6 WKY control rats


title: lymphoblasts from normal male control S83

status: Public on Apr 10 2007

city: Baltimore

first: tao

last: wang

state: MD

address: 733 N. Broadway, BRB513

institute: Johns Hopkins University

description: Total RNA samples prepared from lymphoblasts of 6 unrelated males with normal cognitive function were used as controls. Total RNA from individual patients and controls were labeled with Cy3, which were hybridized against the same reference RNA labeled with Cy5.

scan_protocol: (http://oncweb1.onc.jhmi.edu/microarray) using an Axon GenePix 4000A scanner (Axon Instruments, Foster City, CA)

data_processing: The data from individual patient and 6 controls were grouped together and processed in the following way.  The signal intensity ratios, (R/G or Cy5/Cy3), were computed and log transformed on the base 2.  The print-tip loess method was used to make within microarray normalization on M=log2(R/G) by assessing the relationship of M=log2(R/G) vs. A= 1/2*log2(R*G) in which A is the average of the log intensities, i.e., A=1/2*[log2(R)+log2(G)]. To achieve expression value consistency between microarrays, we normalized microarray data with Bioconductor package limma (www.bioconductor.org) using the ‘Scale’ method that ensures the same medium-absolute-deviation (MAD) of the log ratios across microarrays.

label_protocol: Following a standard labeling protocol (http://oncweb1.onc.jhmi.edu/microarray) using a PowerScrip Fluorecent-labeling kit (Clontech)

growth_protocol: Lymphoblasts cultured in RPMI1640 with 15% fetal calf serum in 5% CO2 at 37o C and harvested at log phase growth.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen) and RNeasy Midi-RNA preparation kit (Qiagen) (http://oncwebl.onc.jhmi.edu/microarray).

tag: total RNA from lymphoblasts cultured at log phase from the indicated individual

source_name: lymphoblasts from normal males as reference

growth_protocol: Lymphoblasts cultured in RPMI1640 with 15% fetal calf serum in 5% CO2 at 37o C and harvested during log phase growth.

tag: pooled total RNA from reference lymphoblasts cultured at log phase growth


title: lymphoblasts from normal male control S82


title: lymphoblasts from normal male control S84


title: lymphoblasts from normal male control S36


title: cy3:SHR control, biological rep 5g; cy5:pool of 6 WKY control rats


title: lymphoblasts from normal male control S76


title: lymphoblasts from normal male control S81


title: AML sample 14 diagnosis paired with sample 105

tag: FAB type = M2


title: cy3:SHR control, biological rep 3g; cy5:pool of 6 WKY control rats


title: cy5:SHR control, biological rep 2r; cy3:pool of 6 WKY control rats


title: cy5:SHR control, biological rep 3r; cy3:pool of 6 WKY control rats


title: cy5:SHR control, biological rep 1r; cy3:pool of 6 WKY control rats


title: AML sample 105 remission paired with sample 14


title: cy3:SHR control, biological rep 1g; cy5:pool of 6 WKY control rats


title: cy3:SHR control, biological rep 2g; cy5:pool of 6 WKY control rats


title: lymphoblasts_XLMR Male_S87

source_name: Lymphoblasts from patient S87

tag: total RNA from lymphoblasts cultured at log phase from the indicated patient


title: lymphoblasts_XLMR Male_S88

source_name: Lymphoblasts from patient S88


title: lymphoblasts_XLMR Male_S79

source_name: Lymphoblasts from patient S79


title: lymphoblasts_XLMR Male_S80

source_name: Lymphoblasts from patient S80


title: lymphoblasts_XLMR Male_S86

source_name: Lymphoblasts from patient S86


title: cy5:SHR control, biological rep 4r; cy3:pool of 6 WKY control rats


title: cy3:SHR control, biological rep 4g; cy5:pool of 6 WKY control rats


title: lymphoblasts_XLMR Male_S75

source_name: Lymphoblasts from patient S75


title: lymphoblasts_XLMR Male_S74

source_name: Lymphoblasts from patient S74


title: willem170605-42_WT42_dB42

city: Wageningen

first: Menno

middle: van der

last: Voort

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

description: 200ng cDNA was hybridised

data_processing: lowess-normalisation, performed in Feature Extract, Agilent

organism: Bacillus cereus ATCC 14579

source_name: wild-type, BHI, 42 degrees

tag: mid-exponential, OD600 0.4-0.6 at 30 degrees, 10 minutes 42 degrees

source_name: DeltaSigB, BHI, 42 degrees


title: 290605WTDsigB42_GEO

description: 200ng cDNA was hybridised

tag: mid-exponential, OD600 0.4-0.6 at 30degrees, 10 minutes 42 degrees

source_name: Wild type, BHI, 42 degrees


title: 099_1_dY42_WT42

description: 200ng cDNA was hybridised

source_name: DeltaRsbY, BHI, 42 degrees

tag: mid-exponential, OD600 0.4-0.6 at 30 degrees, 10 minutes at 42 degrees

source_name: Wild-type, BHI, 42degrees


title: lymphoblasts_XLMR Male_S71

source_name: Lymphoblasts from patient S71


title: 029_2_WT42_30

description: 200ng cDNA was hybridised

source_name: Wild-type BHI 42degrees

source_name: Wild-type BHI 30degrees

tag: mid-exponential, OD600 0.4-0.6 at 30 degrees


title: 099_2_WT42_dY42

description: 200ng cDNA was hybridised

tag: mid-exponential, OD600 0.4-0.6 at 30degrees, 10 minutes at 42 degrees


title: lymphoblasts_XLMR Male_S73

source_name: Lymphoblasts from patient S73


title: 029_1_WT30_42

description: 200ng cDNA was hybridised

source_name: Wild type BHI 42degrees

tag: midexponential, OD600 0.4-0.6 at 30 degrees, 10 minutes 42 degrees


title: lymphoblasts_XLMR Male_S69

source_name: Lymphoblasts from patient S69

source_name: lymphoblasts from normal males as reference


title: lymphoblasts_XLMR Male_S68

source_name: lymphoblasts_XLMR Male_S68


title: 004_2_WT42_dB42

description: 200ng cDNA was hybridised

source_name: Wild Type BHI 42degrees

source_name: deltaSigB BHI 42degrees


title: lymphoblasts_XLMR Male_S70

source_name: Lymphoblasts from patient S70


title: lymphoblasts_XLMR Male_S72

source_name: Lymphoblasts from patient S72


title: lymphoblasts_XLMR Male_S67

source_name: lymphoblasts from patient S67


title: lymphoblasts_XLMR Male_S62

source_name: lymphoblasts from patient S62


title: lymphoblasts_XLMR Male_S65

source_name: lymphoblasts from patient S65


title: lymphoblasts_XLMR Male_S58

source_name: lymphoblasts from patient S58


title: lymphoblasts_XLMR Male_S56

source_name: lymphoblasts from patient S56


title: lymphoblasts_XLMR Male_S59

source_name: lymphoblasts from patient S59


title: lymphoblasts_XLMR Male_S63

source_name: lymphoblasts from patient S63


title: lymphoblasts_XLMR Male_S57

source_name: lymphoblasts from patient S57


title: lymphoblasts_XLMR Male_S61

source_name: lymphoblasts from patient S61


title: lymphoblasts_XLMR Male_S53

source_name: lymphoblasts from patient S53


title: lymphoblasts_XLMR Male_S50

source_name: lymphoblasts from patient S50

tag: pooled total RNA from lymphoblasts cultured at log phase growth


title: lymphoblasts_XLMR Male_S54

source_name: lymphoblasts from patient S54

source_name: lymphoblasts from normal males as reference


title: lymphoblasts_XLMR Male_S55

source_name: lymphoblasts from patient S55


title: lymphoblasts_XLMR Male_S49

source_name: lymphoblasts from patient S49


title: lymphoblasts_XLMR Male_S48

source_name: lymphoblasts from patient S48


title: lymphoblasts_XLMR Male_S52

source_name: lymphoblasts from patient S52


title: lymphoblasts_XLMR Male_S46

source_name: lymphoblasts from patient S46


title: lymphoblasts_XLMR Male_S51

source_name: lymphoblasts from patient S51


title: lymphoblasts_XLMR Male_S33

source_name: lymphoblast from patient S33


title: lymphoblasts_XLMR Male_S30

source_name: lymphoblast from patient S30


title: lymphoblasts_XLMR Male_S47

source_name: lymphoblasts from patient S47


title: lymphoblasts_XLMR Male_S43

source_name: lymphoblast from patient S43


title: lymphoblasts_XLMR Male_S34

source_name: lymphoblast from patient S34


title: lymphoblasts_XLMR Male_S44

source_name: lymphoblast from patient S44


title: lymphoblasts_XLMR Male_S29

source_name: lymphoblast from patient S29


title: lymphoblasts_XLMR Male_S28

description: Total RNA samples prepared from lymphoblasts of 6 unrelated males with normal cognitive function were used as controls.  Total RNA from individual patients and controls were labeled with Cy3, which were hybridized against the same reference RNA labeled with Cy5.

data_processing: The data from individual patient and 6 controls were grouped together and processed in the following way.  The signal intensity ratios, (R/G or Cy5/Cy3), were computed and log transformed on the base 2.  The print-tip loess method was used to make within microarray normalization on M=log2(R/G) by assessing the relationship of M=log2(R/G) vs. A= 1/2*log2(R*G) in which A is the average of the log intensities, i.e., A=1/2*[log2(R)+log2(G)].  To achieve expression value consistency between microarrays, we further normalized microarray data with Bioconductor package limma (www.bioconductor.org) using the ‘Scale’ method that ensures the same medium-absolute-deviation (MAD) of the log ratios across microarrays.

source_name: lymphoblast from patient S28


title: lymphoblasts_XLMR Male_S27

source_name: lymphoblast from patient S27

source_name: : lymphoblasts from normal males as reference


title: lymphoblasts_XLMR Male_S31

source_name: lymphoblast from patient S31

source_name: lymphoblasts from normal males as reference


title: Human Ntera2 cells, KAP1 Replicate 1

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human Ntera2 cells

hyb_protocol: Cy-labedled ChIP Samples

scan_protocol: NimbleScan

data_processing: log base 2 ratios

source_name: Ntera2 cells

label_protocol: Cy dye

extract_protocol: ChIP-chip

tag: KAP1 antibody

tag: control total input


title: lymphoblasts_XLMR Male_S23

description: Total RNA prepared from lymphoblasts of 6 normal unrelated males were used as controls.  Total RNA from individual patients and controls were labeled with Cy3, which were hybridized against the same reference RNA labeled with Cy5.

source_name: lymphoblasts from patient S23

extract_protocol: Total RNA was prepared using Trizol (Invitrogen) and followed by RNeasy Midi-RNA preparation kit (Qiagen) (http://oncwebl.onc.jhmi.edu/microarray).

tag: total RNA from lymphoblasts cultured at log phase from a patient

tag: Provider


title: Human Ntera2 cells, KAP1 Replicate 2

description: Human Ntera2 cells


title: HCT116 Mock 24h a2 vs. HCT116 KIAA1387 esiRNA3 10nM-24 a2

city: Carlsbad

first: Aimee

last: Jackson

state: CA

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: R. Kittler, V. Surendranath, A.-K. Heninger, M. Slabicki, M. Theis, G. Putz, K. Franke, A. Caldareli, H. Grabner, K. Kozak, J. Wagner, E. Rees, B. Korn, C. Sachse, B. Sonnichsen, J. Guo, J. Schelter, J. Burchard, P.S. Linsley, A.L. Jackson, B. Habermann, and F. Buchholz, Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies, 2007, Nature Methods

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment


title: HCT116 Mock 24h a2 vs. HCT116 KIAA1387-2656 10nM-24 a2


title: lymphoblasts_XLMR Male_S24

source_name: lymphoblast from patient S24


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA1 10nM 24h a


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA2 10nM-24 a2


title: HCT116 Mock 24h a2 vs. HCT116 KIAA1387-1512 10nM-24 a2


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-2473 10nM 24h a


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA1 10nM-24 a2


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA3 10nM-24 a2


title: HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA1 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA2 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-1512 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA3 10nM 24h a


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14-793 10nM-24 a2


title: HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA3 10nM 24h a


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14-542 10nM-24 a2


title: HCT116 Mock 24h a2 vs. HCT116 KIAA1387-2473 10nM-24 a2


title: HCT116 Mock 24h a2 vs. HCT116 MAPK14-569 10nM-24 a2


title: HCT116 Mock 24h a vs. HCT116 KIAA1387-2656 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA2 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 MAPK14-569 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 MAPK14-542 10nM 24h a


title: HCT116 Mock 24h a vs. HCT116 MAPK14-793 10nM 24h a


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA2 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA1 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-1512 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA3 10nM 24h b2


title: HeLa, mock, 24 hr vs. Hela, MAPK14 569, 10 nM, 24 hr

source_name: HeLa

tag: HeLa, mock, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-2, 10 nM, 24 hr

tag: HeLa, KIAA1387_esRNA-2, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 24 hr (-DNase)

tag: HeLa, KIAA1387_esRNA-3, 10 nM, 24 hr (-DNase)


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 24 hr

tag: HeLa, KIAA1387_esRNA-3, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-1, 10 nM, 24 hr

tag: HeLa, KIAA1387_esRNA-1, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 2656, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-3, 10 nM, 24 hr

tag: Hela, MAPK14_esRNA-3, 10 nM, 24 hr


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-2473 10nM 24h b2


title: HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-1, 10 nM, 24 hr

tag: Hela, MAPK14_esRNA-1, 10 nM, 24 hr


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA1 10nM 24h b2


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 2473, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, KIAA1387 1512, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. Hela, MAPK14 542, 10 nM, 24 hr


title: HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-2, 10 nM, 24 hr

tag: Hela, MAPK14_esRNA-2, 10 nM, 24 hr


title: HCT116 Mock 24h b vs. HCT116 MAPK14-569 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-2656 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA2 10nM 24h b2


title: HCT116 Mock 24h b vs. HCT116 MAPK14-542 10nM 24h b2


title: HeLa, mock, 24 hr. vs. HeLa, MAPK14 793, 10nM, 24hr b

tag: HeLa, mock, 24 hr.


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA3 10nM 24h b2


title: ACC 27

city: Phoenix

first: Elizabeth

middle: A

last: Stephan

state: AZ

address: 445 North 5th Street

department: Genetic Basis of Human Disease

institute: Translational Genomics Research Institute

hyb_protocol: Agilent Protocol

scan_protocol: Agilent Protocol

data_processing: Raw Data

source_name: ACC Tumor Sample 27

label_protocol: Agilent Protocol

extract_protocol: Qiagen DNeasy Blook and Tissue Kit

tag: Male with Nonfunctioning disease, unknown size and weight, grade 2, unknown age and survival

source_name: Control DNA

tag: Male Genomic DNA - Promega G1471


title: ACC 28

source_name: ACC Tumor Sample 28

tag: Female with Cushings, Regional disease, 9cm, 153.8g, grade 2, 58.00 yrs at operation, unknown survival


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA3 10nM 24h b


title: ACC 26

source_name: ACC Tumor Sample 26

tag: Female with Cushings, unknown disease, unknown size and weight, grade 3, unknown age and survival


title: HCT116 Mock 24h b2 vs. HCT116 MAPK14-793 10nM 24 b2


title: ACC 24

source_name: ACC Tumor Sample 24

tag: Male with Nonfunctioning disease, Localized disease, 21.5cm, 2880g, grade 4, 43.03 yrs at operation, survival >3.62yrs


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-3, 10 nM, 12 hr

tag: HeLa, mock, 12 hr

tag: HeLa, MAPK14_esRNA-3, 10 nM, 12 hr


title: ACC 20

source_name: ACC Tumor Sample 20

tag: Female with Nonfunctioning Disease, Localized disease, 15cm, 1115g, grade 4, 62.34 yrs at operation, survival unknown


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA1 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 569, 10 nM, 12 hr


title: ACC 18

source_name: ACC Tumor Sample 18

tag: Male with Cushings, Localized disease, 17cm, 1345g, grade 3, 77.68 yrs at operation, survival 0.18yrs


title: ACC 21

source_name: ACC Tumor Sample 21

tag: Female with Cushings, Localized disease, 6.5cm, unknown weight, grade 4, 36.88 yrs at operation, survival >8.09yrs


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA2 10nM 24h b


title: ACC 19

source_name: ACC Tumor Sample 19

tag: Male with Cushings, Localized disease, 9cm, 195g, grade 3, 48.46 yrs at operation, survival 3.11yrs


title: ACC 25

source_name: ACC Tumor Sample 25

tag: Female with unknown hormone, Localized of disease, 4cm, 20.5g, grade 3, 35.21 yrs at operation, survival >1.84yrs


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-2473 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-2, 10 nM, 12 hr

tag: HeLa, MAPK14_esRNA-2, 10 nM, 12 hr


title: ACC 22

source_name: ACC Tumor Sample 22

tag: Female with Nonfunctioning Disease, Localized disease, 10cm, 230g, grade 2, 67.30 yrs at operation, survival >0.01yrs


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-2656 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-1, 10 nM, 12 hr

tag: HeLa, MAPK14_esRNA-1, 10 nM, 12 hr


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 542, 10 nM, 12 hr


title: ACC MPI3

source_name: ACC Tumor Sample MPI3

tag: Female with unknown hormone levels, Metastatic disease, unknown size and grade, 37.00 yrs at operation, survival unknown


title: HeLa, mock, 12 hr vs. HeLa, MAPK14 793, 10 nM, 12 hr


title: ACC 17

source_name: ACC Tumor Sample 17

tag: Female with Nonfunctioning Disease, Localized disease, 3cm, unknown g, grade 7, 26.71 yrs at operation, survival >10.36yrs


title: ACC 13

source_name: ACC Tumor Sample 13

tag: Male with Cushings, Metastatic disease, 12cm, 235g, grade 4, 46.92 yrs at operation, survival 0.01yrs


title: HCT116 Mock 24h b vs. HCT116 KIAA1387-1512 10nM 24h b


title: ACC 5

source_name: ACC Tumor Sample 5

tag: Female with Nonfunctioning Disease, Localized disease, 19cm, 1100g, grade 3, 23.28 yrs at operation, survival 3.05yrs

tag: Male Genomic DNA - Promega G1471


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA1 10nM 24h b


title: ACC 2

source_name: ACC Tumor Sample 2

tag: Male with Nonfunctional Tumor, Localized disease, 7cm, 60g, grade 2, 66.50 yrs at operation, survival >2.67yrs


title: ACC 9

source_name: ACC Tumor Sample 9

tag: Male with Nonfunctioning Disease, Localized disease, 8cm, 195g, grade 2, 53.18 yrs at operation, survival >7.35yrs


title: ACC 1

source_name: ACC Tumor Sample 1

tag: Male with Feminizing hormone, Regional disease, 5cm, 32g, grade 3, 69.50 yrs at operation, survival >12.44yrs


title: ACC 11

source_name: ACC Tumor Sample 11

tag: Female with Aldosterone, Localized disease, 15cm, 890g, grade 1, 54.22 yrs at operation, survival >6.82yrs

source_name: Control DNA


title: ACC 23

source_name: ACC Tumor Sample 23

tag: Female with Cushings, Localized disease, 8cm, 149g, grade 2, 27.72 yrs at operation, survival >5.29yrs


title: ACC 14

source_name: ACC Tumor Sample 14

tag: Male with Cushings, Regional disease, 21cm, 1160g, grade 3, 35.66 yrs at operation, survival 0.50yrs


title: ACC 15

source_name: ACC Tumor Sample 15

tag: Male with Nonfunctioning Disease, Localized disease, 9cm, 120g, grade 3, 64.86 yrs at operation, survival 0.44yrs

source_name: c


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 12 hr

source_name: HeLa

tag: HeLa, mock, 12 hr

tag: HeLa, KIAA1387_esRNA-3, 10 nM, 12 hr


title: ACC 6

source_name: ACC Tumor Sample 6

tag: Male with Nonfunctioning Disease, Metastatic disease, 10cm, 130g, grade 3, 60.36 yrs at operation, survival 0.90yrs


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA3 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-1, 10 nM, 12 hr

tag: HeLa, KIAA1387_esRNA-1, 10 nM, 12 hr


title: ACC 10

source_name: ACC Tumor Sample 10

tag: Male with Nonfunctioning Disease, Localized disease, 7.6cm, 150g, grade 4, 67.77 yrs at operation, survival 1.60yrs


title: HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA2 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 2473, 10 nM, 12 hr


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-2, 10 nM, 12 hr

tag: HeLa, KIAA1387_esRNA-2, 10 nM, 12 hr


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 2656, 10 nM, 12 hr


title: HCT116 Mock 24h b vs. HCT116 MAPK14-542 10nM 24h b


title: ACC 8

source_name: ACC Tumor Sample 8

tag: Female with Nonfunctioning Disease, Metastatic disease, 9cm, 190g, grade 4, 56.48 yrs at operation, survival 0.59yrs


title: HCT116 Mock 24h b vs. HCT116 MAPK14-569 10nM 24h b


title: HeLa, mock, 12 hr vs. HeLa, KIAA1387 1512, 10 nM, 12 hr


title: ACC 12

source_name: ACC Tumor Sample 12

tag: Male with Cushings, Metastatic disease, 9.5cm, 175g, grade 4, 72.15 yrs at operation, survival 0.35yrs


title: HCT116 Mock 24h b vs. HCT116 MAPK14-793 10nM 24h b


title: HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-5, 24hr

tag: HeLa, mock, 24 hr.

tag: HeLa, Pool of siRNAs 1-5, 24hr


title: HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-3, 24hr

tag: HeLa, Pool of siRNAs 1-3, 24hr


title: HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-12, 24hr

tag: HeLa, Pool of siRNAs 1-12, 24hr


title: HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 8.3nM, 24hr

tag: HeLa, MAPK14-1, 8.3nM, 24hr


title: HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 33nM, 24hr

tag: HeLa, MAPK14-1, 33nM, 24hr


title: renal_vesicle_wild_type_4

city: Cincinnati

first: Steven

last: Potter

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

description: No other informatin required.

hyb_protocol: Standard Affymetrix hybridization protocols, using five micrograms of target

scan_protocol: Standard Affymetrix scan protocols.

data_processing: Expression values generated with GCOS affymetrix software using all probe sets scaling factor 1500

organism: Mus musculus

source_name: renal vesicle from E12.5 wild type kidney

label_protocol: Used two round Epicentre kit, as per Potter GUDMAP.ORG protocols

extract_protocol: According to GUDMAP  Potter laboratory protocols (GUDMAP.ORG)

treatment_protocol: Was prepared according to GUDMAP Potter protocols (GUDMAP.ORG)

tag: strain CD-1


title: renal_vesicle_wild_type_1

description: No other informatin required.

tag: strain CD-1 mouse. RV was isolated by laser capture microdissection.


title: HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-9, 24hr

tag: HeLa, Pool of siRNAs 1-9, 24hr


title: renal_vesicle_wild_type_3

description: No other informatin required.

tag: Strain CD-1


title: renal_vesicle_wild_type_2

description: No other informatin required.


title: HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 11nM, 24hr

tag: HeLa, MAPK14-1, 11nM, 24hr


title: HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 20nM, 24hr

tag: HeLa, MAPK14-1, 20nM, 24hr


title: HeLa, mock, 24 hr vs. HeLa, MAPK14 793, 10 nM, 24 hr

tag: HeLa, mock, 24 hr


title: renal_vesicle_wild_type_5

description: No other informatin required.


title: Ovarian_Tumor_Serous_UM-OS-09

status: Public on Apr 09 2007

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

description: ovarian tumor: serous

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

value: Serous

tag: stage

tag: grade


title: Ovarian_Tumor_Serous_KU-OS-015

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_UM-OS-07

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-022

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_UM-OS-10

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_UM-OS-11

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-018

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_UM-OS-02

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-021

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-011

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-012

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-013

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-009

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-005

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-003

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-002

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CU-OS-05

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-089

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CU-OS-04

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-081

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-001

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-072

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-093

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_KU-OS-007

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-048

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-046

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-098

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-020

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-044

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-018

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-029

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-011

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-068

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-041

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-003

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-038

description: ovarian tumor: serous


title: Ovarian_Tumor_Mucinous_UM-OM-03

description: ovarian tumor: mucinous

value: Mucinous


title: Ovarian_Tumor_Serous_CHTN-OS-002

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-053

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-010

description: ovarian tumor: serous


title: Ovarian_Tumor_Mucinous_KU-OM-007

description: ovarian tumor: mucinous

value: I c


title: Ovarian_Tumor_Mucinous_KU-OM-003

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Serous_CHTN-OS-055

description: ovarian tumor: serous


title: Ovarian_Tumor_Serous_CHTN-OS-009

description: ovarian tumor: serous


title: Ovarian_Tumor_Mucinous_CHTN-OM-036

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_KU-OM-004

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_CHTN-OM-029

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_CHTN-OM-007

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_KU-OM-006

description: ovarian tumor: mucinous

value: I a


title: Ovarian_Tumor_Mucinous_UM-OM-01

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_CHTN-OM-017

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_CHTN-OM-035

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Mucinous_CHTN-OM-032

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Endometrioid_UM-OE-1T

description: ovarian tumor: endometrioid

value: Endometrioid

value: Y

value: N

value: present

value: absent


title: Ovarian_Tumor_Endometrioid_KU-OE-003

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Mucinous_CHTN-OM-023

description: ovarian tumor: mucinous


title: Ovarian_Tumor_Endometrioid_KU-OE-007

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_KU-OE-004

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_JH-OE-2T

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-087

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-092

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-082

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-080

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-077

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-065

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-069

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-061

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-076

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-060

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-054

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-047

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-056

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-039

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-046

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-042

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-038

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-048

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-059

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-036

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-053

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-029

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-018

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-035

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-033

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-019

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-023

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-017

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-011

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-040

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-014

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_Endometrioid_CHTN-OE-005

description: ovarian tumor: endometrioid


title: Ovarian_Tumor_ClearCell_KU-OC-006

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_KU-OC-003

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_CHTN-OC-012

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_KU-OC-004

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_KU-OC-005

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_CHTN-OC-004

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_CHTN-OC-028

description: ovarian tumor: clear cell


title: Ovarian_Tumor_ClearCell_KU-OC-007

description: ovarian tumor: clear cell


title: Tropheryma whipplei CGH microarray_Slow1B vs Twist_rep1

status: Public on Apr 06 2007

city: Marseille

first: My-Van

last: La

address: 27 BD Jean Moulin

country: France

institute: Unité des Rickettsies (CNRS-UMR 6020)

description: The data filtering and normalization were then processed with the Microsoft Excel software. Spots with background-corrected signal intensity (median) in both channels lower than two-fold the background intensity (median) were discarded from further analysis.

hyb_protocol: Following a post processing step, 7 μg labeled DNA of each reference and test sample were pooled for hybridization onto microarrays as previously described (Crapoulet et al. 2006). After 18-hour incubation at 42°C, the slides were washed then dried with compressed nitrogen, and then scanned with ScanArray®Express (Perkin Elmer, Boston, MA, USA).

scan_protocol: The signal intensity, local background for both fluorescence channels of each spot, and the preliminary exclusion of irrelevant values, as flagged, were determined from TIF images using the QuantArray® Microarray Analysis Software version 3.0.0.0 (Packard BioScience).

data_processing: The background-subtracted signals derived from the remaining spots were normalized by global median method, and then the normalized log ratio of test/reference signal for each spot was recorded. For each ORF and in each comparative strain analysis, the median value of 12 normalized log ratios of test/reference signal was used for GACK analysis (Charlie Kim, Stanford University) (Kim et al. 2002). Trinary output was then applied to determine an ORF as present, uncertain, absent or divergent. A gene was designated as present (assigned ‘+1’) when its deduced estimated probability of presence (EPP) was of 100%, and absent or divergent (assigned ‘-1’) when its EPP was found null. When EPP was ranging between 0% and 100%, if the gene was present or absent/divergent remained uncertain.

organism: Tropheryma whipplei

source_name: Test (Slow1B)

label_protocol: DNA of T. whipplei Twist strain was used as reference sample whereas the DNA from other isolates was referred as test DNA. DNA was labeled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences, Piscataway, NJ, USA) for test and reference samples, respectively, using the BioPrime® Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA, USA). For each hybridization, 1 µg of T. whipplei Twist DNA and of test DNA were primed with random octamers and Cy3- or Cy5-labeled probes were generated under the extension and the fluorescent nucleotide incorporation activity of exo-Klenow polymerase. The levels of incorporation were quantified by absorbance measurement at 550 nm and 650 nm, and samples processed for hybridization on microarray when incorporation levels are ≥ 50 pmol of fluorochromes per μg of DNA.

growth_protocol: The T. whipplei isolates (n = 16) used in this study were grown under axenic conditions as previously described (Renesto et al. 2003)

extract_protocol: Eighteen days-old bacterial cultures (300 ml) were collected by centrifugation 16,900 × g for 10 min at 4°C. Resulting pellets were resuspended in 3 ml PBS and stored at -20°C. DNA was then extracted using QIAamp® DNA mini kit according to the manufacturer’s instruction (Qiagen, Courtaboeuf, France) and its concentration was determined by UV absorbance at 260 nm.

tag: Strain Slow1B

tag: Eighteen days-old axenic culture

source_name: Reference (Twist)

tag: Strain Twist


title: Tumor_262

status: Public on Apr 07 2007

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71349.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 13:50:04; Parameter PMT Volts = 560; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15861; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 13:50:04; Parameter PMT Volts = 600; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258609; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Universal Human Reference

label_protocol: Human Cy3 - Chen et al; Incorporation of Cy3-labeled deoxynucleotides was as described (Chen et al., Mol Biol Cell,2002).; Protocol Type = Labeling; Performer: Adam,,Adler

extract_protocol:
StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Adam,,Adler
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Adam,,Adler

tag: Universal Human Reference

label_protocol: Human Cy5 - Chen et al; Incorporation of Cy5-labeled deoxynucleotides was as described (Chen et al., Mol Biol Cell, 2002).; Protocol Type = Labeling; Performer: Adam,,Adler

extract_protocol:
Primary Tumor; RNA was obtained from primary tumor sample.; Protocol Type = Biological Sample; Performer: Adam,,Adler
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Slow1B vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Slow1B vs Twist_rep3


title: Tropheryma whipplei CGH microarray_DigNeuro18 vs Twist_rep1

source_name: Test (DigNeuro18)

tag: Strain DigNeuro18


title: Tropheryma whipplei CGH microarray_DigNeuro18 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_DigNeuro18 vs Twist_rep3


title: Tumor_261

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71348.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 5200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 12:36:04; Parameter PMT Volts = 540; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15787; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.02; Parameter Scan Time = 12:36:04; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258536; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_253

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71347.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.87; Parameter Scan Time = 12:28:16; Parameter PMT Volts = 540; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15779; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.87; Parameter Scan Time = 12:28:16; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258528; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_224

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71345.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.42; Parameter Scan Time = 13:32:41; Parameter PMT Volts = 550; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15843; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.42; Parameter Scan Time = 13:32:41; Parameter PMT Volts = 600; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258592; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_DigMusc17 vs Twist_rep2

source_name: Test (DigMusc17)

tag: Strain DigMusc17


title: Tropheryma whipplei CGH microarray_DigMusc17 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_DigMusc17 vs Twist_rep3


title: Tumor_289

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71353.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 14:27:35; Parameter PMT Volts = 560; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15897; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 14:27:35; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258646; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Dig15 vs Twist_rep2

source_name: Test (Dig15)

tag: Strain Dig15


title: Tropheryma whipplei CGH microarray_DigNeuro14 vs Twist_rep3

source_name: Test (DigNeuro14)

tag: Strain DigNeuro14


title: Tumor_193

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71344.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 12:11:18; Parameter PMT Volts = 530; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15762; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.50; Parameter Scan Time = 12:11:18; Parameter PMT Volts = 580; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258511; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_387

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71357.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 15:25:47; Parameter PMT Volts = 540; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15956; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 15:25:47; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258704; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_127

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71339.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:08:15; Parameter PMT Volts = 490; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15699; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:08:15; Parameter PMT Volts = 520; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_283

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71351.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 560, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.57; Parameter Scan Time = 13:58:15; Parameter PMT Volts = 550; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15868; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.57; Parameter Scan Time = 13:58:15; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258617; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_360

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71356.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 4360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.42; Parameter Scan Time = 13:40:36; Parameter PMT Volts = 550; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15851; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.42; Parameter Scan Time = 13:40:36; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258599; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Dig15 vs Twist_rep3


title: Tumor_264

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71350.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 4680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.77; Parameter Scan Time = 11:33:02; Parameter PMT Volts = 530; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15723; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.77; Parameter Scan Time = 11:33:02; Parameter PMT Volts = 580; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258472; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Dig15 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_DigNeuro14 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_DigNeuro14 vs Twist_rep1


title: Tumor_252

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71346.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.46; Parameter Scan Time = 11:20:27; Parameter PMT Volts = 530; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15711; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.46; Parameter Scan Time = 11:20:27; Parameter PMT Volts = 570; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Art1 vs Twist_rep3

source_name: Test (Art1)

tag: Strain Art1


title: Tumor_297

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71355.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 15:08:23; Parameter PMT Volts = 560; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15939; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 15:08:23; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258688; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_179

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71342.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.98; Parameter Scan Time = 11:43:56; Parameter PMT Volts = 470; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.98; Parameter Scan Time = 11:43:56; Parameter PMT Volts = 510; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_184

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71343.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.71; Parameter Scan Time = 12:20:04; Parameter PMT Volts = 540; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15770; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.71; Parameter Scan Time = 12:20:04; Parameter PMT Volts = 600; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258519; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_133

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71340.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 11:52:13; Parameter PMT Volts = 470; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15742; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.10; Parameter Scan Time = 11:52:13; Parameter PMT Volts = 500; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258491; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_291

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71354.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 15:17:47; Parameter PMT Volts = 520; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15948; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 15:17:47; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258697; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tumor_288

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71352.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 14:43:08; Parameter PMT Volts = 560; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15913; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 14:43:08; Parameter PMT Volts = 610; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258662; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Dig10 vs Twist_rep3

description: The data filtering and normalization were then processed with the Microsoft Excel software. Spots with background-corrected signal intensity (median) in both channels lower than two-fold the background intensity (median) were discarded from further analysis.

scan_protocol: The signal intensity, local background for both fluorescence channels of each spot, and the preliminary exclusion of irrelevant values, as flagged, were determined from TIF images using the QuantArray® Microarray Analysis Software version 3.0.0.0 (Packard BioScience).

source_name: Test (Dig10)

tag: Strain Dig10


title: Tropheryma whipplei CGH microarray_DigADP11 vs Twist_rep1

source_name: Test (DigADP11)

tag: Strain DigADP11


title: Tumor_175

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71341.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.26; Parameter Scan Time = 12:00:21; Parameter PMT Volts = 470; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15751; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.26; Parameter Scan Time = 12:00:21; Parameter PMT Volts = 520; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258500; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: Tropheryma whipplei CGH microarray_Art1 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Art1 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_Dig9 vs Twist_rep2

source_name: Test (Dig9)

tag: Strain Dig9


title: Tropheryma whipplei CGH microarray_Dig10 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Dig7 vs Twist_rep2

source_name: Test (Dig7)

tag: Strain Dig7


title: Tropheryma whipplei CGH microarray_DigADP11 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Dig10 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_DigADP11 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Dig9 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Dig7 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_Dig7 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Endo7 vs Twist_rep2

source_name: Test (Endo7)

tag: Strain Endo7


title: Tropheryma whipplei CGH microarray_Dig9 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_Neuro2 vs Twist_rep3

source_name: Test (Neuro2)

tag: Strain Neuro2


title: Tropheryma whipplei CGH microarray_Endo7 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Neuro2 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Endo7 vs Twist_rep1


title: Tropheryma whipplei CGH microarray_Neuro1 vs Twist_rep1

source_name: Test (Neuro1)

tag: Strain Neuro1


title: Tropheryma whipplei CGH microarray_Endo5 vs Twist_rep2

source_name: Test (Endo5)


title: Tropheryma whipplei CGH microarray_Slow2 vs Twist_rep1

source_name: Test (Slow2)

tag: Strain Slow2


title: Tropheryma whipplei CGH microarray_Neuro1 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Endo5 vs Twist_rep1

tag: Strain Endo5


title: Tropheryma whipplei CGH microarray_Twist vs Twist_rep3

source_name: Test

tag: Eighteen days-old axenic culture

source_name: Reference


title: Tropheryma whipplei CGH microarray_Endo5 vs Twist_rep3

source_name: Reference (Twist)

tag: Strain Twist


title: Tropheryma whipplei CGH microarray_Slow2 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Twist vs Twist_rep1


title: Tropheryma whipplei CGH microarray_Twist vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Slow2 vs Twist_rep2


title: Tropheryma whipplei CGH microarray_Neuro1 vs Twist_rep3


title: Tropheryma whipplei CGH microarray_Neuro2 vs Twist_rep1


title: Animal 16 PHx6h

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

hyb_protocol: Reference and experimental probes were combined and competitively hybridized to microarrays for 18 hours at 37C.

scan_protocol: Slides were scanned using ScanArray 5000 fluorescent scanner (GSI Lumonics, Billerica, MA). The resulting images were quantified using ScanArray Express v2.2 software with the Adaptive Threshold segmentation (GSI Lumonics, Billerica, MA).

data_processing: Raw quantitated array data was normalized using the print-tip lowess and scale normalization algorithms

organism: synthetic construct

source_name: Reference RNA

label_protocol: indirect labeling protocol

extract_protocol: RT on empty pT7T3Pac vector

tag: Vector RNA. Hybridizes to all spots evenly

source_name: Animal 16 PHx6h

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: Remnat liver section removed 6 h after 70% partial hepatectomy (t=6h).


title: Animal 16 control

source_name: Animal 16 control

tag: Strain:Sprague-Dawley, Gender:Male

tag: Liver section removed by partial hepatectomy (t=0).


title: Animal 14 control

source_name: Animal 14 control


title: Animal 13 PHx6h

source_name: Animal 13 PHx6h


title: Animal 14 PHx6h

source_name: Animal 14 PHx6h


title: Animal 15 PHx6h

source_name: Animal 15 PHx6h


title: Animal 13 control

source_name: Animal 13 control


title: Animal 10 PHx4h

source_name: Animal 10 PHx4h

tag: Remnat liver section removed 4 h after 70% partial hepatectomy (t=4h).


title: Animal 15 control

source_name: Animal 15 control


title: Animal 11 PHx4h

source_name: Animal 11 PHx4h


title: Animal 11 control

source_name: Animal 11 control


title: Animal 12 control

source_name: Animal 12 control


title: Animal 12 PHx4h

source_name: Animal 12 PHx4h


title: Animal 6 PHx2h

source_name: Animal 6 PHx2h

tag: Remnat liver section removed 2 h after 70% partial hepatectomy (t=2h).


title: Animal 10 control

source_name: Animal 10 control


title: Animal 9 PHx4h

source_name: Animal 9 PHx4h


title: Animal 7 PHx2h

source_name: Reference RNA

source_name: Animal 7 PHx2h


title: Animal 9 control

source_name: Animal 9 control


title: Animal 4 PHx1h

source_name: Animal 4 PHx1h

tag: Remnat liver section removed 1 h after 70% partial hepatectomy (t=1h).


title: Animal 3 control

source_name: Animal 3 control


title: Animal 5 control

source_name: Animal 5 control


title: Animal 8 control

source_name: Animal 8 control


title: Animal 4 control

source_name: Animal 4 control


title: Animal 5 PHx2h

tag: RT on empty pT7T3Pac vector

source_name: Animal 5 PHx2h


title: Animal 3 PHx1h

source_name: Animal 3 PHx1h


title: Animal 7 control

source_name: Animal 7 control


title: Animal 2 PHx1h

source_name: Animal 2 PHx1h


title: Animal 1 control

source_name: Animal 1 control


title: Animal 8 PHx2h

source_name: Animal 8 PHx2h


title: Animal 6 control

source_name: Animal 6 control


title: Animal 1 PHx1h

source_name: Animal 1 PHx1h


title: Animal 2 control

source_name: Animal 2 control


title: WT.37C.40|mex67-5.37C.40

status: Public on Apr 04 2007

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

description: see PMID: 17388687

hyb_protocol: Competitive hybridization at 65oC for 12h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 4.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: Genotype

tag: Temperature (C)

tag: Time (min)

value: matched WT for mex67-5


title: mex67-5.37C.0|WT.37C.0

description: see PMID: 17388687


title: mex67-5.37C.5|WT.37C.5

description: see PMID: 17388687


title: mex67-5.37C.40|WT.37C.40

description: see PMID: 17388687


title: mex67-5.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.30|mex67-5.37C.30

description: see PMID: 17388687


title: WT.37C.0|rna14-64.37C.0

description: see PMID: 17388687

value: matched WT for rna14-64


title: WT.37C.10|mex67-5.37C.10

description: see PMID: 17388687


title: mex67-5.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.0|mex67-5.37C.0

description: see PMID: 17388687


title: mex67-5.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.90|rna14-64.37C.90

description: see PMID: 17388687


title: WT.37C.20|mex67-5.37C.20

description: see PMID: 17388687


title: rna14-64.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.30|rna14-64.37C.30

description: see PMID: 17388687


title: rna14-64.37C.0|WT.37C.0

description: see PMID: 17388687


title: rna14-64.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.5|mex67-5.37C.5

description: see PMID: 17388687


title: WT.37C.20|rna14-64.37C.20

description: see PMID: 17388687


title: rna14-64.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.60|rna14-64.37C.60

description: see PMID: 17388687


title: WT.37C.10|rna14-64.37C.10

description: see PMID: 17388687


title: WT.37C.5|sub2-1.37C.5

description: see PMID: 17388687

value: matched WT for sub2-1


title: rna14-64.37C.60|WT.37C.60

description: see PMID: 17388687


title: WT.37C.0|sub2-1.37C.0

description: see PMID: 17388687


title: rna14-64.37C.90|WT.37C.90

description: see PMID: 17388687


title: WT.37C.40|sub2-1.37C.40

description: see PMID: 17388687


title: sub2-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: sub2-1.37C.5|WT.37C.5

description: see PMID: 17388687


title: sub2-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: sub2-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: yra1-1.37C.5|WT.37C.5

description: see PMID: 17388687

value: matched WT for yra1-1


title: sub2-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: WT.37C.20|sub2-1.37C.20

description: see PMID: 17388687


title: WT.37C.10|sub2-1.37C.10

description: see PMID: 17388687


title: WT.37C.10|yra1-1.37C.10

description: see PMID: 17388687


title: yra1-1.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.30|yra1-1.37C.30

description: see PMID: 17388687


title: WT.37C.30|sub2-1.37C.30

description: see PMID: 17388687


title: WT.37C.20|yra1-1.37C.20

description: see PMID: 17388687


title: yra1-1.37C.10|WT.37C.10

description: see PMID: 17388687


title: sub2-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.40|yra1-1.37C.40

description: see PMID: 17388687


title: WT.37C.5|yra1-1.37C.5

description: see PMID: 17388687


title: yra1-1.37C.40|WT.37C.40

description: see PMID: 17388687


title: prp8-101.37C.30|WT.37C.30

description: see PMID: 17388687

value: matched WT for prp8-101


title: yra1-1.37C.20|WT.37C.20

description: see PMID: 17388687


title: WT.37C.0|yra1-1.37C.0

description: see PMID: 17388687


title: prp8-101.37C.10|WT.37C.10

description: see PMID: 17388687


title: WT.37C.20|prp8-101.37C.20

description: see PMID: 17388687


title: prp8-101.37C.20|WT.37C.20

description: see PMID: 17388687


title: prp8-101.37C.0|WT.37C.0

description: see PMID: 17388687


title: WT.37C.30|prp8-101.37C.30

description: see PMID: 17388687


title: WT.37C.10|prp8-101.37C.10

description: see PMID: 17388687


title: WT.37C.0|snu114-60.37C.0

description: see PMID: 17388687

value: matched WT for snu114-60


title: WT.37C.0|prp8-101.37C.0

description: see PMID: 17388687


title: WT.37C.5|prp8-101.37C.5

description: see PMID: 17388687


title: yra1-1.37C.30|WT.37C.30

description: see PMID: 17388687


title: WT.37C.20|snu114-60.37C.20

description: see PMID: 17388687


title: prp8-101.37C.5|WT.37C.5

description: see PMID: 17388687


title: WT.37C.10|snu114-60.37C.10

description: see PMID: 17388687


title: WT.37C.30|snu114-60.37C.30

description: see PMID: 17388687


title: Transcript Mapping for Human HeLa Total RNA Sample 2

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description:
Total RNA for HeLa S3 cells was obtained from Ambion (Austin, TX). All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.

scan_protocol: Scanned according to manufacturers procedures (http://www.affymetrix.com/).

data_processing: The value determined calculated from log (max [1, PM-MM] ) for each biological replicate separately.

source_name: Human HeLa S3 Cells

extract_protocol: First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C. The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia). Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel.

tag: Total RNA from Human HeLa S3 Cells.  All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.


title: WT.37C.90|snu114-60.37C.90

description: see PMID: 17388687


title: WT.37C.60|snu114-60.37C.60

description: see PMID: 17388687


title: snu114-60.37C.0|WT.37C.0

description: see PMID: 17388687


title: snu114-60.37C.30|WT.37C.30

description: see PMID: 17388687


title: snu114-60.37C.60|WT.37C.60

description: see PMID: 17388687


title: Transcript Mapping for Human HeLa Poly(A)+ RNA Sample 2

description:
PolyA RNA for HeLa S3 cells was obtained from Ambion (Austin, TX). All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.

molecule: polyA RNA

tag: Triple selected Poly(A)+ RNA from Human HeLa S3 Cells.  All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.


title: snu114-60.37C.20|WT.37C.20

description: see PMID: 17388687