title: MicMa067_Agilent

description: biopsy of breast carcinoma

source_name: MicMa067_Agilent with Cy5


title: MicMa085_Agilent

status: Public on Nov 30 2005

type: RNA

city: Foster City

first: Yulei

last: Wang

state: CA

address: 850 Lincoln Centre Dr

country: USA

institute: Applied Biosystems

description: biopsy of breast carcinoma

hyb_protocol: cRNA hybridized according to standard Agilent protocols

scan_protocol: arrays were scanned according to standard Agilent protocols

data_processing: Data processed with FeatureExtraction v7.5.1

molecule: total RNA

organism: Homo sapiens

source_name: MicMa085_Agilent with Cy5

label_protocol: Amplified and labeled according to standard Agilent protocols

extract_protocol: not provided

tag: early stage, breast carcinoma

source_name: Universal Human Reference (Stratagene) with Cy3

tag: Common Reference

value: Universal Human Reference RNA sample (Stratagene)


title: MicMa031_Agilent

description: biopsy of breast carcinoma

source_name: MicMa031_Agilent with Cy5


title: MicMa132_Agilent

description: biopsy of breast carcinoma

source_name: MicMa132_Agilent with Cy5


title: MicMa632_Agilent

description: biopsy of breast carcinoma

source_name: MicMa632_Agilent with Cy5


title: MicMa020_Agilent

description: biopsy of breast carcinoma

source_name: MicMa020_Agilent with Cy5


title: MicMa065_Agilent

description: biopsy of breast carcinoma

source_name: MicMa065_Agilent with Cy5


title: B128A genomic vs Tigr/Astra Ref 4

status: Public on Oct 20 2005

type: genomic

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7913.gif

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

molecule: genomic DNA

organism: Helicobacter pylori

source_name: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug B128A genomic DNA

tag: 2 ug B128A genomic DNA


title: MicMa267_Agilent

description: biopsy of breast carcinoma

source_name: MicMa267_Agilent with Cy5


title: J99-C6 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10857.gif

source_name: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug J99-C6 genomic DNA

tag: 2 ug J99-C6 genomic DNA


title: MicMa088_Agilent

description: biopsy of breast carcinoma

source_name: MicMa088_Agilent with Cy5


title: MicMa122_Agilent

description: biopsy of breast carcinoma

source_name: MicMa122_Agilent with Cy5


title: J99-C10-3 vs Tigr/Astra references (250 ug)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17833.gif

source_name: 250 ng Tigr/Astra genomic DNA

tag: 250 ng Tigr/Astra genomic DNA

source_name: 250 ng J99-C10 genomic DNA

tag: 250 ng J99-C10 genomic DNA


title: MicMa053_Agilent

description: biopsy of breast carcinoma

source_name: MicMa053_Agilent with Cy5


title: MicMa101_Agilent

description: biopsy of breast carcinoma

source_name: MicMa101_Agilent with Cy5


title: MicMa148_Agilent

description: biopsy of breast carcinoma

source_name: MicMa148_Agilent with Cy5

source_name: Universal Human Reference (Stratagene) with Cy3


title: SS200 vs Tigr/Astra reference 65degC

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/7056.gif

source_name: 1 ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug SS2000 genomic DNA

tag: 2 ug SS2000 genomic DNA


title: MicMa042_Agilent

description: biopsy of breast carcinoma

source_name: MicMa042_Agilent with Cy5


title: MicMa079_Agilent

description: biopsy of breast carcinoma

source_name: MicMa079_Agilent with Cy5


title: MicMa146_Agilent

description: biopsy of breast carcinoma

source_name: MicMa146_Agilent with Cy5


title: MicMa091_Agilent

description: biopsy of breast carcinoma

source_name: MicMa091_Agilent with Cy5


title: J99-C10 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10859.gif

tag: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug J99-C10 genomic

tag: 2 ug J99-C10 genomic


title: M1.16 genomic vs Tigr/Astra Ref 4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7914.gif

source_name: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug M1.16 genomic

tag: 2 ug M1.16 genomic


title: MicMa263_Agilent

description: biopsy of breast carcinoma

source_name: MicMa263_Agilent with Cy5


title: MicMa709_Agilent

description: biopsy of breast carcinoma

source_name: MicMa709_Agilent with Cy5


title: J99-C6 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10856.gif

source_name: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug J99-C6 genomic DNA


title: H15 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6453.gif

source_name: 1ug Tigr genomic DNA + 1 ug Astra DNA

tag: 1ug Tigr genomic DNA + 1 ug Astra DNA

source_name: 2 ug H15 genomic DNA

tag: 2 ug H15 genomic DNA


title: B128A genomic vs Tigr/Astra Ref 3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7910.gif

tag: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug B128A genomic DNA


title: H15 vs. Tigr/Astra reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8427.gif

source_name: 1ug genomic DNATigr + 1 ug Astra genomic DNA


title: M1.16 genomic vs Tigr/Astra Ref 3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7911.gif


title: H34 genomic DNA vs Tigr/Astra reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/8133.gif

source_name: 2ug H34 genomic DNA

tag: 2ug H34 genomic DNA


title: CA19 genomic DNA vs. Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10269.gif

source_name: 1 ug 26695 genomic DNA + 1ug J99 genomic DNA

source_name: 2 ug CA19 genomic DNA

tag: 2 ug CA19 genomic DNA


title: 27616 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6457.gif

source_name: 2 ug 27616 genomic DNA

tag: 2 ug 27616 genomic DNA


title: 27571 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6458.gif

source_name: 2 ug 27571 genomic DNA

tag: 2 ug 27571 genomic DNA


title: 51407 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6460.gif

source_name: 2 ug 51407 genomic DNA

tag: 2 ug 51407 genomic DNA


title: CPY3401 Genomic DNA vs TIGR/Astra Trial 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4560.gif

source_name: TIGR/Astra Reference DNA

tag: TIGR/Astra Reference DNA

source_name: CPY3401 Test DNA

tag: CPY3401 Test DNA


title: 27616 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11922.gif


title: 27741 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6459.gif

source_name: 2 ug 27741 genomic DNA

tag: 2 ug 27741 genomic DNA


title: 51407 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11924.gif


title: TR20-2 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6451.gif

source_name: 2 ug TR20-2 genomic DNA

tag: 2 ug TR20-2 genomic DNA


title: 27741 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11923.gif


title: AR32 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6456.gif

source_name: 2 ug AR32 genomic DNA

tag: 2 ug AR32 genomic DNA


title: TR20-4 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6455.gif

source_name: 2 ug TR20-4 genomic DNA

tag: 2 ug TR20-4 genomic DNA


title: AR28 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11921.gif

source_name: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug AR28 genomic DNA

tag: 2 ug AR28 genomic DNA


title: 27571 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11920.gif

tag: 1ug Tigr genomic DNA + 1ug Astra genomic DNA


title: AR32 genomic DNA vs. Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2807.gif

source_name: 1ug Tigr genomic DNA and 1ug Astra genomic DNA

source_name: 2ug AR32 genomic DNA

tag: 2ug AR32 genomic DNA


title: TR75-7 genomic DNA vs. Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3110.gif

source_name: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug TR75-7 genomic DNA

tag: 2ug TR75-7 genomic DNA


title: H34 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6454.gif

source_name: 1ug Tigr genomic DNA + 1 ug Astra DNA

tag: 1ug Tigr genomic DNA + 1 ug Astra DNA

source_name: 2 ug H34 genomic DNA

tag: 2 ug H34 genomic DNA


title: M1.16 genomic vs Tigr/Astra Ref 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7601.gif

source_name: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug M1.16 genomic

tag: 2 ug M1.16 genomic


title: TR20-1 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6447.gif

source_name: 2 ug TR20-1 genomic DNA

tag: 2 ug TR20-1 genomic DNA


title: TR13-4 genomic DNA vs. Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3108.gif

tag: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug TR 13-4 genomic DNA

tag: 2ug TR 13-4 genomic DNA


title: CPY3401 Genomic DNA vs TIGR/Astra Trial 1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4126.gif

source_name: TIGR/Astra Reference DNA

source_name: CPY3401 Test DNA


title: 29011 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11913.gif

source_name: 2 ug 29011 genomic DNA

tag: 2 ug 29011 genomic DNA


title: AR28 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6448.gif


title: 29011 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11910.gif


title: 316a vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11918.gif

source_name: 2 ug 316a genomic DNA

tag: 2 ug 316a genomic DNA


title: 316a vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11919.gif


title: 314a vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11916.gif

source_name: 2 ug 314a genomic DNA

tag: 2 ug 314a genomic DNA


title: 315a vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11917.gif

source_name: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug 315a genomic DNA

tag: 2 ug 315a genomic DNA


title: TR75-3 genomic DNA vs. Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3109.gif

source_name: 2ug TR 75-3genomic DNA

tag: 2ug TR 75-3genomic DNA


title: B128A genomic vs Tigr/Astra Ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7597.gif

tag: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA

source_name: 2 ug B128A genomic DNA

tag: 2 ug B128A genomic DNA


title: TR13-7 genomic DNA vs. Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3107.gif

source_name: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug TR 13-7 genomic DNA

tag: 2ug TR 13-7 genomic DNA


title: M1.16 genomic vs Tigr/Astra Ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7598.gif


title: 29041 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11909.gif

tag: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug 29041genomic DNA

tag: 2 ug 29041genomic DNA


title: 26255 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11903.gif

source_name: 2 ug 26255 genomic DNA

tag: 2 ug 26255 genomic DNA


title: T98

status: Public on Apr 13 2005

city: New York

first: Veronique

last: Bourdon

state: NY

department: Human Genetics

institute: Memorial Sloan Kettering Cancer Center

description: mCGH of cervical cancer

source_name: Placenta


title: 314a 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15969.gif

source_name: 0.5 ug Tigr/Astra reference

tag: 0.5 ug Tigr/Astra reference

source_name: 2ug 314a genomic DNA

tag: 2ug 314a genomic DNA


title: B128A genomic vs Tigr/Astra Ref 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7599.gif

source_name: 1ug Tigr genomic DNA + 1 ug Astra genomic DNA


title: 315a 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15970.gif

source_name: 2ug 315a genomic DNA

tag: 2ug 315a genomic DNA


title: 316a 3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15971.gif

source_name: 2ug 316a genomic DNA

tag: 2ug 316a genomic DNA


title: AR32 vs Tigr/Astra reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6488.gif

source_name: 2ug AR32 genomic DNA

tag: 2ug AR32 genomic DNA


title: 26255 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11904.gif


title: j166 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15968.gif

source_name: 2ug J166 genomic DNA

tag: 2ug J166 genomic DNA


title: 29061 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11914.gif

source_name: 2 ug 29061 genomic DNA

tag: 2 ug 29061 genomic DNA


title: Syd (A.L.) vs Tigr/Astra reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5683.gif

source_name: 0.7 ug Tigr genomic DNA + 0.7 ug Astra genomic DNA

source_name: 2 ug SS1 (AL) genomic DNA

tag: 2 ug SS1 (AL) genomic DNA


title: TR75-7 vs Tigr/Astra reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6489.gif

source_name: 2ug TR75-7 genomic DNA

tag: 2ug TR75-7 genomic DNA


title: J166 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11915.gif

source_name: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug J166 genomic DNA

tag: 2 ug J166 genomic DNA


title: T984

description: mCGH of cervical cancer


title: "J166 ure+, 0.25 ug "

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24494.gif

source_name: 0.25 ug Tigr/Astra reference

tag: 0.25 ug Tigr/Astra reference

source_name: 0.25 ug J166 ure+ genomic DNA

tag: 0.25 ug J166 ure+ genomic DNA


title: "J166 ure+, 0.25 ug 2"

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24497.gif


title: 29041 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11906.gif

source_name: 2 ug 29041genomic DNA


title: T892

description: mCGH of cervical cancer

source_name: Placenta


title: T1051

description: mCGH of cervical cancer


title: T954

description: mCGH of cervical cancer


title: T92

description: mCGH of cervical cancer


title: T86

description: mCGH of cervical cancer


title: T1068

description: mCGH of cervical cancer


title: T66

description: mCGH of cervical cancer


title: T968

description: mCGH of cervical cancer


title: T966

description: mCGH of cervical cancer


title: T82

description: mCGH of cervical cancer


title: T939

description: mCGH of cervical cancer


title: T79

description: mCGH of cervical cancer


title: T80

description: mCGH of cervical cancer


title: T869

description: mCGH of cervical cancer


title: T117

description: mCGH of cervical cancer


title: T52

description: mCGH of cervical cancer


title: T24

description: mCGH of cervical cancer


title: J99-C10  vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10861.gif

source_name: 2 ug J99-C10 genomic

tag: 2 ug J99-C10 genomic


title: J99-C12 vs Tigr/Astra Reference

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10862.gif

source_name: 2 ug J99-C12 genomic DNA

tag: 2 ug J99-C12 genomic DNA


title: Control 7:8vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10866.gif

tag: 1ug Tigr genomic DNA + 1ug Astra genomic DNA

source_name: 2 ug Control 7:8 genomic DNA

tag: 2 ug Control 7:8 genomic DNA


title: control 7:8 genomic DNA vs. Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10210.gif

source_name: 1 ug 26695 genomic DNA + 1ug J99 genomic DNA

source_name: 2 ug control 7:8 genomic DNA

tag: 2 ug control 7:8 genomic DNA


title: T103

description: mCGH of cervical cancer


title: T102

description: mCGH of cervical cancer


title: J99-C12 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs//10863.gif


title: CASKI

description: mCGH of cervical cancer

source_name: CASKI


title: SIHA

description: mCGH of cervical cancer

source_name: SIHA


title: SW756

description: mCGH of cervical cancer


title: MS751

description: mCGH of cervical cancer


title: i155-680680_TBPB

status: Public on Nov 03 2004

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

description:
Strains were grown in YPD media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC for 15 min. ( by adding an equal volume of heated media for the heat shocked set), or mock treated at 25ûC for 15 min. (by adding an equal volume of 25ûC media for the mock treated set).  After 15 min. incubation, cells were brought back to 25ûC and simultaneously cross-linked with 1% formaldehyde for 2 hours.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

organism: Saccharomyces cerevisiae

source_name: HA-TBP Mock Treated Purified ChIP DNA (CH1)

source_name: HA-TBP Heat Shocked Purified ChIP DNA (CH2)


title: C33

description: mCGH of cervical cancer


title: HT3

description: mCGH of cervical cancer


title: ME180

description: mCGH of cervical cancer


title: i152-680680_NullA

source_name: Null Heat Shocked Purified ChIP DNA (CH1)

source_name: Null Mock Treated Purified ChIP DNA (CH2)


title: i157-680680_TBPD


title: i148-680680_NullC


title: i146-680680_TAF1C

source_name: HA-TAF1 Heat Shocked Purified ChIP DNA (CH1)

source_name: HA-TAF1 Mock Treated Purified ChIP DNA (CH2)


title: i153-680680_Spt3E

source_name: HA-Spt3 Heat Shocked Purified ChIP DNA (CH1)

source_name: HA-Spt3 Mock Treated Purified ChIP DNA (CH2)


title: i142-680680_TAF1A


title: i156-680680_TBPC

source_name: HA-TBP Heat Shocked Purified ChIP DNA (CH1)

source_name: HA-TBP Mock Treated Purified ChIP DNA (CH2)


title: C41

description: mCGH of cervical cancer

source_name: Placenta


title: i151-680680_Spt3D

source_name: HA-Spt3 Mock Treated Purified ChIP DNA (CH1)

source_name: HA-Spt3 Heat Shocked Purified ChIP DNA (CH2)


title: i154-680680_TBPA


title: i159-680680_NullB

source_name: Null Mock Treated Purified ChIP DNA (CH1)

source_name: Null Heat Shocked Purified ChIP DNA (CH2)


title: i147-680680_TAF1D

source_name: HA-TAF1 Mock Treated Purified ChIP DNA (CH1)

source_name: HA-TAF1 Heat Shocked Purified ChIP DNA (CH2)


title: i150-680680_Spt3C


title: i165-680680_Mot1D

source_name: HA-Mot1 Mock Treated Purified ChIP DNA (CH1)

source_name: HA-Mot1 Heat Shocked Purified ChIP DNA (CH2)


title: i143-680680_TAF1B


title: i145-680680_Spt3B


title: i125-650650_InputB

source_name: HA-Spt3 ChIP Input DNA (CH1)

source_name: HA-TAF1 ChIP Input DNA (CH2)


title: i149-680680_NullD


title: i166-680680_Mot1B

source_name: HA-Mot1 Heat Shocked Purified ChIP DNA (CH1)

source_name: HA-Mot1 Mock Treated Purified ChIP DNA (CH2)


title: j99-c10 2 vs tigr/astra ref 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17117.gif

source_name: 0.25 ug tigr/astra reference

tag: 0.25 ug tigr/astra reference

source_name: 0.25 ug j99-c10 genomic DNA

tag: 0.25 ug j99-c10 genomic DNA


title: 023-680680

status: Public on Mar 01 2004

description:
Strains were grown in CSM media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC with an equal volume of heated media.  After 5 min. at 37ûC, cells were cooled back to 25ûC and cross-linked with 1% formaldehyde for 15 minutes.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

source_name: Un-tagged Strain Purified ChIP DNA (CH1)

source_name: Un-tagged Strain Reference/un-purified DNA (CH2)


title: i169-680680_Bdf1C

source_name: HA-Bdf1 Heat Shocked Purified ChIP DNA (CH1)

source_name: HA-Bdf1 Mock Treated Purified ChIP DNA (CH2)


title: i162-680680_Mot1A


title: 021-680680

source_name: HA-TBP Reference/un-purified DNA (CH1)

source_name: HA-TBP Purified ChIP DN (CH2)


title: i163-680680_Bdf1A

source_name: HA-Bdf1 Mock Treated Purified ChIP DNA (CH1)

source_name: HA-Bdf1 Heat Shocked Purified ChIP DNA (CH2)


title: 041-680680

source_name: HA-TBP Purified ChIP DNA (CH1)

source_name: HA-TBP Reference/un-purified DNA (CH2)


title: i164-680680_Mot1C


title: 140-720680

description:
Strains were grown in CSM media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC with an equal volume of heated media.  After 5 min. at 37ûC, cells were cooled back to 25ûC and cross-linked with 1% formaldehyde for 20 hours.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  Chromatin immunprecipitation, non-specific amplification and intergenic array hybridization were performed as described in Basehour 2003.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

source_name: HA-Spt3 Reference/un-purified DNA (CH1)

source_name: HA-Spt3 Purified ChIP DNA (CH2)


title: i161-680680_InputD

source_name: HA-Spt3 ChIP Input DNA (CH1)

source_name: HA-TAF1 ChIP Input DNA (CH2)


title: i123-680680_InputC

source_name: HA-TAF1 ChIP Input DNA (CH1)

source_name: HA-Spt3 ChIP Input DNA (CH2)


title: i124-650650_InputA


title: 040-680680


title: i167-680680_Bdf1B


title: i171-680680_Bdf1D


title: 024-680680

source_name: Untagged Strain Reference/un-purified DNA (CH1)

source_name: Untagged Strain Purified ChIP DNA (CH2)


title: patient PV14 - hyb 2

status: Public on Feb 01 2008

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: Cirrhotic liver taken away from a Hepatocellular Carcinoma

hyb_protocol: Hybridization of the [α 33P]-labelled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

source_name: HCV-associated peritumoral cirrhosis liver

label_protocol: Within each RNA preparation prepared as above the target poly(A) mRNAs were labelled as follows : 10μg total RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg 5'(dT23)VN3' oligonucleotide were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labelled cDNAs were immediately used for hybridization.

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.

tag: 66 years old man with hepatitis C


title: S. paradoxus Heat shock (37oC) 90 minutes 2

status: Public on Mar 31 2006

city: Rehovot

first: Naama

last: Barkai

address: Hertzel

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

hyb_protocol: none provided

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet's DNA microarray scanner and image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed. Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as 'missing values' (along with other genes which were flagged by the image analysis software or removed by manual inspection).

organism: Saccharomyces paradoxus

label_protocol: The cDNA from heat shock treated and untreated cells was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

growth_protocol: Cells were grown on YPD to log phase at 30oC prior to heat shock and then transferred to 37oC

extract_protocol: 5 O.D. units of cells were collected, pelleted and immediately frozen. Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: Strain

value: NRRL Y-17217 wild type, diploid

source_name: S. paradoxus grown in YPD at 30oC

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

extract_protocol: The RNA (20 ?g) was annealed with 4 ?g oligo dT12-18, and reverse-transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2h at 45?C in the presence of 2.5mM MgCl2,  0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. After hydrolysis of RNA in 0.2 M NaOH (30min, 65oC), Tris was removed from the reaction with a Microcon-30 concentrator.

tag: For reference we used the same culture prior to pertubation in which cells were grown to log phase in YPD at 30oC.