title: Wild Type Time 1 replicate 2

status: Public on Jul 15 2005

city: London

first: Fiona

middle: M

last: Watt

address: 44 Lincolns Inn Fields

department: Keratinocyte

country: United Kingdom

institute: Cancer Research UK

description:
Total RNA was isolated from wild type C57BL/6 mice treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell

source_name: Total skin


title: Wild Type Time 1 replicate 3

type: RNA

description:
Total RNA was isolated from a wild type C57BL/6 mouse treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell

molecule: total RNA

organism: Mus musculus


title: 0 hours

status: Public on Jul 18 2005

city: Boston

first: Damian

last: LaGamba

state: MA

address: 220 Longwood Ave.

department: Cell Biology

country: USA

institute: Harvard Medical School

description:
Palate medial edge epithelium from CF-1 ED13.5 mouse embryos.
Epithelium was isolated using Dispase II (Roche) enzyme.
RNA extraction was performed using RNeasy Mini kit (Qiagen).
RNA amplification and labeling was performed using RiboAmp RNA amplification kit (Arcturus) and ENZO Bioarray high yield labeling kit (Affymetrix). Hybridization, fluidics, scanning were performed at the Biopolymers facility at Harvard Medical School: Department of Genetics. Data analysis was conducted with Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics) software.

source_name: Unfused palate medial edge epithelium


title: Wild Type Time 7 replicate 1

description:
Total RNA was isolated from a wild type C57BL/6 mouse treated for 7 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell


title: Wild Type Time 7 replicate 2


title: 12 hours

description:
Palate medial edge epithelium from CF-1 ED13.5 mouse embryos.
Palatal shelves were placed together in culture for 12 hours post initial contact.
Epithelium was isolated using Dispase II (Roche) enzyme.
RNA isolation was performed using RNeasy Mini kit (Qiagen).
RNA amplification and labeling was performed using RiboAmp RNA amplification kit (Arcturus) and ENZO Bioarray high yield labeling kit (Affymetrix). Hybridization, fluidics, scanning were performed at the Biopolymers facility at Harvard Medical School: Department of Genetics. Data analysis was conducted with Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics) software.

source_name: Fused palate medial edge epithelium


title: Wild Type Time 1 replicate 1


title: K14deltaNB-cateninER  Time 7 replicate 1

description:
Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 7 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell


title: Wild Type Time 0 replicate 3

description:
Total RNA was isolated from wild type C57BL/6 mice treated for 0 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell


title: K14deltaNB-cateninER  Time 7 replicate 2


title: Wild Type Time 0 replicate 2


title: K14deltaNB-cateninER Time 0 replicate 1

description:
Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 0 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell


title: Comparison aft1 vs aft1aft2 experiment 2

city: Paris

first: Pierre-Louis

last: Blaiseau

address: 2 Place Jussieu

country: France

institute: Institute Jacques Monod

description:
Strains were grown exponentially in Bio101#4027-122, and total RNA was extracted using the hot phenol method. Yeast Genefilters Microarrays were used to hybridize the resulting RNA according to the manufacturer's instructions. Five micrograms of total RNA were reverse-transcribed, and hybridizations were done in duplicate using two separate GeneFilters. The membranes were exposed to a phosphor imaging screen for 3 days. Images were acquired by using a Storm 860 (Molecular Dynamics), and analyzed by using the PATHWAYS 3 (Research Genetics) software.
Keywords = iron metabolism
Keywords = transcription factor

organism: Saccharomyces cerevisiae

source_name: Y18 (aft1) minus iron

source_name: Y18aft2delta (aft1aft2) minus iron


title: Wild Type Time 0 replicate 1


title: K14deltaNB-cateninER  Time 7 replicate 3


title: Comparison aft1 vs aft1aft2 experiment 1


title: K14deltaNB-cateninER  Time 1 replicate 3

description:
Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell


title: K14deltaNB-cateninER  Time 1 replicate 2


title: Comparison wt vs aft1aft2 experiment 1

source_name: CM3260 (wt) minus iron


title: K14deltaNB-cateninER  Time 1 replicate 1


title: K14deltaNB-cateninER Time 0 replicate 2


title: Comparison wt vs aft1 experiment 2


title: Comparison wt vs aft1aft2 experiment 2


title: Comparison wt vs aft1 experiment 1


title: 12 Week Jejunum 230B Low Fe Group 2

status: Public on Jul 11 2005

city: Tucson

first: James

middle: Forrest

last: Collins

state: AZ

address: PO Box 245073, 1501 N. campbell Ave.

department: Pediatrics

institute: University of Arizona Health Sciences Center

description: mRNA purified from jejunal scrape

organism: Rattus norvegicus

source_name: Jejunal Scrape


title: 12 Week Jejunum 230B Low Fe Group 1

description: mRNA purified from jejunal scrape


title: 12 Week Jejunum 230B Low Fe Group 3

description: mRNA purified from jejunal scrape


title: 12 Week Jejunum 230B High Fe Group 1

description: mRNA purified from jejunal scrape


title: 12 Week Jejunum Low Fe Group 2

description:
mRNA purified from Rat Jejunal Mucosal Scrape
Keywords = iron-deficiency
Keywords = anemia


title: 12 Week Jejunum 230B High Fe Group 3

description: mRNA purified from jejunal scrape


title: Neisseria gonorrhoeae gene expression in response to iron availability  Array #0304

city: Oklahoma City

first: Thomas

middle: Francis

last: Ducey

state: OK

address: 975 NE 10th Street, BRC 366

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

description:
Microarray experiment using pan-Neisseria array.  Array hybridized with cDNA labeled with Cy3 (Iron Deplete) and Cy5 (Iron Replete). cDNA generated from random nonamers.

Array #0304.

organism: Neisseria gonorrhoeae

source_name: Iron Replete CDM

source_name: Iron Deplete CDM


title: 12 Week Jejunum 230B High Fe Group 2

description: mRNA purified from jejunal scrape

source_name: jejunal scrape


title: 12 Week Jejunum Low Fe Group 3


title: Expression profile of patient 229-A

status: Public on Jul 06 2005

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

description:
Pancreatic ductal cells were purified from pancreatic juice of the patients.
Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc).

organism: Homo sapiens

source_name: Patient 229


title: Expression profile of patient 224-A

source_name: Patient 224


title: Neisseria gonorrhoeae gene expression in response to iron availability Array #0290

description: Microarray experiment using pan-Neisseria array. Array hybridized with cDNA labeled with Cy3 (Iron Deplete) and Cy5 (Iron Replete). cDNA generated using random nonamers.  Array #0290.


title: 12 Week Jejunum High Fe Group 3


title: Expression profile of patient 234-A

source_name: Patient 234


title: 12 Week Jejunum High Fe Group 2


title: Expression profile of patient 217-A

source_name: Patient 217


title: Neisseria gonorrhoeae gene expression in response to iron availability Array #0291

description: Microarray experiment using pan-Neisseria array. Array hybridized with cDNA labeled with Cy3 (Iron Deplete) and Cy5 (Iron Replete). cDNA generated using random nonamers.  Array #0291.


title: 12 Week Jejunum High Fe Group 1

source_name: Rat Jejunal Mucosal Scrape


title: Neisseria gonorrhoeae gene expression in response to iron availability Array #0305

description:
Microarray experiment using pan-Neisseria array.  Array hybridized with cDNA labeled with Cy3 (Iron Deplete) and Cy5 (Iron Replete). cDNA generated from random nonamers.

Array #0305.


title: Expression profile of patient 203-A

source_name: Patient 203


title: Expression profile of patient 162-A

source_name: Patient 162


title: Expression profile of patient 218-A

source_name: Patient 218


title: 12 Week Jejenum Low Fe Group 1


title: Expression profile of patient 227-A

source_name: Patient 227


title: Expression profile of patient 202-A

source_name: Patient 202


title: Expression profile of patient 174-A

source_name: Patient 174


title: Expression profile of patient 152-A

source_name: Patient 152


title: Expression profile of patient 151-A

source_name: Patient 151


title: Expression profile of patient 225-A

source_name: Patient 225


title: Expression profile of patient 146-A

source_name: Patient 146


title: Expression profile of patient 144-A

source_name: Patient 144


title: Expression profile of patient 147-A

source_name: Patient 147


title: Expression profile of patient 142-A

source_name: Patient 142


title: Expression profile of patient 141-A

source_name: Patient 141


title: Expression profile of patient 140-A

source_name: Patient 140


title: Expression profile of patient 135-A

source_name: Patient 135


title: Expression profile of patient 134A

source_name: Patient 134


title: Expression profile of patient 137-A

source_name: Patient 137


title: Expression profile of patient 133-A

source_name: Patient 133


title: Expression profile of patient 128-A

source_name: Patient 128


title: Expression profile of patient 131-A

source_name: Patient 131


title: Expression profile of patient 120-A

source_name: Patient 120


title: Expression profile of patient 121-A

source_name: Patient 121


title: Expression profile of patient 125-A

source_name: Patient 125


title: Expression profile of patient 122-A

source_name: Patient 122


title: Expression profile of patient 117-A

source_name: Patient 117


title: Expression profile of patient 118-A

source_name: Patient 118


title: Expression profile of patient 103-A

source_name: Patient 103


title: Expression profile of patient 130-A

source_name: Patient 130


title: Expression profile of patient 102-A

source_name: Patient 102


title: Expression profile of patient 119-A

source_name: Patient 119


title: Expression profile of patient 124-A

source_name: Patient 124


title: Expression profile of patient 116-A

source_name: Patient 116


title: Expression profile of patient 096-A

source_name: Patient 096


title: Expression profile of patient 090-A

source_name: Patient 090


title: Expression profile of patient 086-A

source_name: Patient 086


title: Expression profile of patient 084-A

source_name: Patient 084


title: Expression profile of patient 088-A

source_name: Patient 088


title: Expression profile of patient 093-A

source_name: Patient 093


title: Expression profile of patient 098-A

source_name: Patient 098


title: Expression profile of patient 072-A

description: Pancreatic ductal cells were purified from pancreatic juice of the patients. Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc).

source_name: Patient 072


title: Expression profile of patient 227-B

source_name: Patient 227


title: Expression profile of patient 089-A

source_name: Patient 089


title: Expression profile of patient 229-B

source_name: Patient 229


title: Expression profile of patient 092-A

source_name: Patient 092


title: Expression profile of patient 225-B

source_name: Patient 225


title: Expression profile of patient 234-B

source_name: Patient 234


title: Expression profile of patient 073-A

source_name: Patient 073


title: Expression profile of patient 203-B

source_name: Patient 203


title: Expression profile of patient 218-B

source_name: Patient 218


title: Expression profile of patient 224-B

source_name: Patient 224


title: Expression profile of patient 217-B

source_name: Patient 217


title: Expression profile of patient 162-B

source_name: Patient 162


title: Expression profile of patient 146-B

source_name: Patient 146


title: Expression profile of patient 152-B

source_name: Patient 152


title: Expression profile of patient 147-B

source_name: Patient 147


title: Expression profile of patient 151-B

source_name: Patient 151


title: Expression profile of patient 202-B

source_name: Patient 202


title: Expression profile of patient 144-B

source_name: Patient 144


title: Expression profile of patient 174-B

source_name: Patient 174


title: Expression profile of patient 135-B

source_name: Patient 135


title: Expression profile of patient 141-B

source_name: Patient 141


title: Expression profile of patient 134-B

source_name: Patient 134


title: Expression profile of patient 137-B

source_name: Patient 137


title: Expression profile of patient 140-B

source_name: Patient 140


title: Expression profile of patient 121-B

source_name: Patient 121


title: Expression profile of patient 142-B

source_name: Patient 142


title: Expression profile of patient 120-B

source_name: Patient 120


title: Expression profile of patient 130-B

source_name: Patient 130


title: Expression profile of patient 133-B

source_name: Patient 133


title: Expression profile of patient 124-B

source_name: Patient 124


title: Expression profile of patient 119-B

source_name: Patient 119


title: Expression profile of patient 122-B

source_name: Patient 122


title: Expression profile of patient 125-B

source_name: Patient 125


title: Expression profile of patient 095-A

source_name: Patient 095


title: Expression profile of patient 118-B

source_name: Patient 118


title: Expression profile of patient 117-B

source_name: Patient 117


title: Expression profile of patient 131-B

source_name: Patient 131


title: Expression profile of patient 128-B

source_name: Patient 128


title: Expression profile of patient 103-B

source_name: Patient 103


title: Expression profile of patient 116-B

source_name: Patient 116


title: Expression profile of patient 098-B

source_name: Patient 098


title: Expression profile of patient 096-B

source_name: Patient 096


title: Expression profile of patient 095-B


title: Expression profile of patient 089-B

source_name: Patient 089-B


title: Expression profile of patient 086-B

source_name: Patient 086


title: Expression profile of patient 102-B

source_name: Patient 102


title: Expression profile of patient 093-B

source_name: Patient 093


title: Expression profile of patient 092-B

source_name: Patient 092


title: Expression profile of patient 084-B

source_name: Patient 084


title: ovarian tissue

status: Public on Jul 05 2005

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

description:
microRNA expression profile
Keywords = microRNA
Keywords = miRNA
Keywords = Danio rerio
Keywords = development

organism: Danio rerio

source_name: Danio rerio


title: Expression profile of patient 090-B

source_name: Patient 090-B


title: testis tissue


title: eye tissue


title: Expression profile of patient 072-B

source_name: Patient 072-B


title: heart tissue


title: gut tissue


title: muscle tissue


title: Expression profile of patient 073-B

source_name: Patient 073


title: skin tissue


title: liver tissue


title: Expression profile of patient 088-B

source_name: Patient 088-B


title: fin


title: brain tissue


title: gill tissue


title: 56 hrs development

status: Public on Jul 04 2005

description:
miRNA expression during early zebrafish development
Keywords = microRNA
Keywords = miRNA
Keywords = Danio rerio
Keywords = development

source_name: Danio rerio embryo


title: 64 hrs development


title: adult male


title: 40 hrs development


title: 48 hrs development


title: 96 hrs development


title: 12 hrs development


title: 32 hrs development


title: 20 hrs development


title: 28 hrs development


title: 24hrs development


title: 16 hrs development


title: 8 hrs development


title: 4 hrs development


title: 0 hrs development


title: Glucose Sample B

city: Berkely

first: Sanchita

last: Bhattacharya

state: CA

address: 1 Cyclotron Rd

institute: MIT

description:
Yeast was grown in YPGlucose medium
Total RNA was isolated from cells at OD 600 of 1.0

source_name: Saccharomyces cerevisiae ATCC 4126


title: adult female


title: Glucose Sample A


title: Round cell 3

status: Public on Jul 01 2005

first: Namali

last: Fernando

department: Surgical Oncology

institute: Massachusetts General Hospital

description: Round cell sample

source_name: sarcoma tissue


title: Galactose Sample C

description:
Yeast was grown in YPGalacatose medium
Total RNA was isolated from cells at OD 600 of 1.0


title: UR552

city: San Francisco

first: Ekaterini

last: Blaveri

address: 2340 Sutter street

department: Laboratory Medicine

institute: UCSF Comprehensive Cancer Center

description: stage pT4                     Transitional Cell Carcinoma

source_name: Bladder tumor

source_name: Reference pool RNA from 11 cancer cell lines


title: Galactose Sample B

description:
Yeast was grown in YPGalacatose medium
Total RNA was isolated from cells at OD 600 of 1.0.


title: Synovial sarcoma 3

description: Synovial sarcoma sample


title: UR448


title: Synovial sarcoma 2

description: Synovial sarcoma sample


title: UR553


title: UR509


title: UR507


title: UR441


title: Synovial sarcoma 1

description: Synovial sarcoma sample


title: UR497


title: UR513


title: UR485


title: UR350


title: MFH 7

description: MFH sample


title: MFH 8

description: MFH sample


title: Round cell 2

description: Round cell sample


title: Round cell 4

description: Round cell sample


title: MFH 9

description: MFH sample


title: MFH 6

description: MFH sample


title: UR403


title: Round cell 1

description: Round cell sample


title: UR539

description: stage pT3                     Transitional Cell Carcinoma


title: MFH 4

description: MFH sample


title: MFH 5

description: MFH sample


title: UR463


title: UR406


title: Lipo dediff 4

description: lipo dediff sample


title: UR435


title: UR446


title: Lipo pleo 2

description: lipo pleo sample


title: Lipo pleo 3

description: lipo pleo sample


title: Lipo pleo 1

description: lipo pleo sample


title: MFH 3

description: MFH sample


title: MFH 2

description: MFH sample


title: UR405


title: UR554


title: Leiomyosarcoma 6

description: leiomyosarcoma sample


title: MFH 1

description: MFH sample


title: Leiomyosarcoma 5

description: leiomyosarcoma sample


title: Lipo dediff 3

description: lipo dediff sample


title: Lipo dediff 2

description: lipo dediff sample


title: UR383


title: UR465


title: Leiomyosarcoma 4

description: leiomyosarcoma sample


title: Lipo dediff 1

description: lipo dediff sample


title: Leiomyosarcoma 2

description: leiomyosarcoma sample


title: Leiomyosarcoma 3

description: leiomyosarcoma sample


title: UR503


title: Leiomyosarcoma 1

description: leiomyosarcoma sample


title: GIST 2

description: gastrointestinal stromal tumor sample


title: GIST 1

description: gastrointestinal stromal tumor sample


title: Synovial sarcoma 4

description: Synovial sarcoma sample


title: UR353

description:
stage pT3
Transitional Cell Carcinoma


title: UR419

description:
stage pT3
Transitional Cell Carcinoma


title: fibrosarcoma 7

description: fibrosarcoma sample


title: UR256

description:
stage pT3
Transitional Cell Carcinoma


title: UR500

description:
stage pT3
Transitional Cell Carcinoma


title: UR506

description:
stage pT3
Transitional Cell Carcinoma


title: spleen

description: normal tissue

source_name: normal tissue


title: UR357

description:
stage pT3
Squamous Cell Carcinoma


title: fibrosarcoma 4

description: fibrosarcoma sample


title: UR372

description:
stage pT3

Squamous Cell Carcinoma


title: fibrosarcoma 3

description: fibrosarcoma sample


title: fibrosarcoma 5

description: fibrosarcoma sample


title: UR482

description:
stage pT3

Transitional Cell Carcinoma


title: kidney

description: normal tissue


title: lung

description: normal tissue


title: liver

description: normal tissue


title: fibrosarcoma 1

description: fibrosarcoma sample


title: fibrosarcoma 6

description: fibrosarcoma sample


title: fibrosarcoma 2

description: fibrosarcoma sample


title: skeletal muscle

description: normal tissue


title: connective tissue

description: normal tissue


title: small intestine

description: normal tissue


title: adrenal

description: normal tissue


title: heart

description: normal tissue


title: skin

description: normal tissue


title: UR376

description:
stage pT2
Squamous Cell Carcinoma


title: prostate

description: normal tissue


title: UR546

description:
stage pT2
Squamous Cell Carcinoma


title: stomach

description: normal tissue


title: colon

description: normal tissue


title: UR456

description:
stage pT2
Transitional Cell Carcinoma


title: pancreas

description: normal tissue


title: UR487

description:
stage pT2
Transitional Cell Carcinoma


title: brain

description: normal tissue


title: UR515

description:
stage pT2
Transitional Cell Carcinoma


title: UR449

description:
stage pT2
Transitional Cell Carcinoma


title: UR524

description:
stage pT2
Transitional Cell Carcinoma


title: MCI-014

city: Omaha

first: Yaozhong

last: Liu

state: NE

address: 601 N 30th Street, Suite 6730

department: Osteoporosis Research Center

institute: Creighton University

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-014 was from a postmenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR

source_name: monocytes


title: MCI-018

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-018 was from a premenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-011

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-011 was from a postmenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: UR361

description:
stage pT2
Transitional Cell Carcinoma


title: MCI-020

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-020 was from a postmenopausal high BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: UR351

description:
stage pT3
Transitional Cell Carcinoma


title: MCI-021

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-021 was from a postmenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-006

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-006 was from a postmenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-016

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-016 was from a premenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-015

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-015 was from a premenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-002

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-002 was from a postmenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-013

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-013 was from a postmenopausal high BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-009

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-009 was from a postmenopausal low BMD woman.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-017

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-017 was from a premenopausal low BMD woman.

Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: UR044

description:
stage pT3
Transitional Cell Carcinoma


title: MCI-010

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-010 was from a postmenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: UR445

description:
stage pT2
Transitional Cell Carcinoma


title: UR438

description:
stage pT2
Transitional Cell Carcinoma


title: UR106

description:
stage pT2
Transitional Cell Carcinoma


title: MCI-019

description:
Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-019 is from a premenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-004

description:
Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-004 is the sample from a premenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-003

description:
Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-003 is the sample from a premenopausal high BMD subjects.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-007

description:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-007 is from a postmenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-005

description:
Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-005 is the sample from a premenopausal high BMD subjects.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: MCI-001

description:
Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-001 is the sample from a premenopausal high BMD women.
Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR


title: UR356

description:
stage pT2
Transitional Cell Carcinoma


title: UR325

description:
stage pTa
High grade
Transitional Cell Carcinoma


title: UR179

description:
stage pTa
Low grade
Transitional Cell Carcinoma


title: UR119

description:
stage pT1
Transitional Cell Carcinoma


title: UR498

description: stage pT3


title: UPN5259 CALM-AF10 negative T-cell lymphoblastic leukemia sample

last: DELABESSE

address: 149-161, rue de Sèvres

department: Department of Haematology

institute: Hôpital Necker

description:
Peripheral blood sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 96% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1

source_name: Peripheral blood


title: UPN3973 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 99% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1

source_name: Bone marrow


title: UPN5105 CALM-AF10 negative T-cell lymphoblastic leukemia sample


title: UPN5558 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Peripheral blood sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 98% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN3776 CALM-AF10 negative T-cell lymphoblastic leukemia sample


title: UPN2586 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 96% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN3580 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 97% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN1147 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Peripheral blood sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 97% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN0792 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
CD3- sorted bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 95% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1

source_name: CD3- sorted bone marrow cells


title: UPN4925 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
CD34+ sorted cells from peripheral blood sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 92% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR468

description:
stage pT2
Squamous Cell Carcinoma


title: UR263

description:
stage pTa
Transitional Cell Carcinoma


title: UPN4871 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
Peripheral blood sample of CALM-AF10 positive T-cell lymphoblastic leukemia with a content of 96% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR367


title: UR479

description:
stage pT1
Transitional Cell Carcinoma


title: UPN3954 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
CD3- sorted cells from bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 99% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1

source_name: CD3- sorted cells from bone marrow


title: UPN0226 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 91% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN3188 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 positive T-cell lymphoblastic leukemia with a content of 97% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UPN1439 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
CD3- sorted bone marrow sample of CALM-AF10 positive T-cell lymphoblastic leukemia with a content of 95% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: T135 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of less than 90% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR477

description:
stage pT1
Transitional Cell Carcinoma


title: UPN0094 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 95% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR250

description:
stage pT1
Transitional Cell Carcinoma


title: T080 CALM-AF10 negative T-cell lymphoblastic leukemia sample


title: T053 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 90% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR467

description:
stage pT1
Transitional Cell Carcinoma


title: UPN4516 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 positive T-cell lymphoblastic leukemia with a content of 98% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: T043 CALM-AF10 negative T-cell lymphoblastic leukemia sample

description:
Peripheral blood sample of CALM-AF10 negative T-cell lymphoblastic leukemia with a content of 96% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: UR286

description:
stage pT1
Transitional Cell Carcinoma


title: UPN4105 CALM-AF10 positive T-cell lymphoblastic leukemia sample

description:
Bone marrow sample of CALM-AF10 positive T-cell lymphoblastic leukemia with a content of 99% of blasts.
Keywords = CALM-AF10, HOXA9, MEIS1, BMI1


title: T011 CALM-AF10 negative T-cell lymphoblastic leukemia sample


title: UR520

description:
stage pT1
Transitional Cell Carcinoma


title: UR254

description:
stage pT1
Transitional Cell Carcinoma


title: UR404

description:
stage pTa
Low grade
Transitional Cell Carcinoma


title: UR556


title: UR461

description:
stage pT4
Transitional Cell Carcinoma


title: WKY20-3

city: University of OULU

first: Jaana

last: Rysä

address: PO BOX 5000

department: Pharmacology and toxicology

country: Finland

institute: University of Oulu

description:
Left ventricular gene expression profiles from 12-, 16- and 20-months old spontaneously hypertensive rats (SHRs) were compared with left ventricular profiles seen in age-matched Wistar-Kyoto (WKY) rats by screening Affymetrix U34A arrays (there are 4 samples in each timepoint except 3 samples of 20-months old WKYs).
Keywords = heart
Keywords = microarray
Keywords = SHR
Keywords = heart failure

source_name: Rat left ventricle


title: WKY12-3


title: WKY20-4


title: WKY20-2


title: UR151


title: UR343

description:
stage pT1
Transitional Cell Carcinoma


title: WKY12-4


title: WKY16-3


title: WKY16-1


title: UR581


title: WKY16-4


title: WKY16-2


title: UR396


title: WKY12-2


title: UR516

description:
stage pTa
Low Malignant Potential
Transitional Cell Carcinoma


title: SHR20-3


title: WKY12-1


title: SHR20-4

source_name: Rat eft ventricle


title: SHR20-1


title: UR523

description: stage pTa High grade       Transitional Cell Carcinoma


title: UR530


title: UR240

description: stage pTa Low grade       Transitional Cell Carcinoma


title: UR540


title: SHR16-4


title: SHR16-3


title: UR354


title: UR514


title: SHR20-2


title: SHR16-2


title: UR394

description:
stage pTa
High grade
Transitional Cell Carcinoma


title: UR261

description:
stage pT3
Transitional Cell Carcinoma


title: UR558

description:
stage pT3
Transitional Cell Carcinoma

source_name: Reference Pool RNA from 11 cancer cell lines


title: UR591

description:
stage pT3
Transitional Cell Carcinoma


title: UR534

description:
stage pT3
Transitional Cell Carcinoma


title: SHR12-1

description:
Left ventricular gene expression profiles from 12-, 16- and 20-months old spontaneously hypertensive rats (SHRs) were compared with left ventricular profiles seen in age-matched Wistar-Kyoto (WKY) rats by screening Affymetrix U34A arrays (there are 4 samples in each timepoint except 3 samples of 20-months old WKYs).
Keywords = heart
Keywords = microarray
Keywords = SHR
Keywords = microarray
Keywords = heart failure


title: SHR16-1


title: UR496

description:
stage pT2
Squamous Cell Carcinoma


title: SHR12-3


title: SHR12-4


title: UR531

description:
stage pT3

Transitional Cell Carcinoma


title: UR590

description:
stage pT3
Transitional Cell Carcinoma


title: UR437

description:
stage pTa High grade
Transitional Cell Carcinoma


title: SHR12-2


title: Brain Injury after 3 hours

city: Memphis

first: Eldon

middle: E

last: Geisert

state: TN

address: 855 Monroe Avenue

department: Ophthalmology

institute: University of Tennesse

description: RNA samples were prepared from ipsilateral hippocampi 3 hr and 24 hr following lateral cortical impact injury and compared to samples from sham-operated controls.  For details please see Matzilevich et al., J Neuros Res, 2002.

source_name: Rat injured hippocampus


title: Brain Injury after 24 hours

source_name: Injured rat hippocampus after 24 hours


title: Brain injury sham

description: RNA samples were prepared from ipsilateral hippocampi 3 hr and 24 hr following lateral cortical impact injury and compared to samples from sham-operated controls.

source_name: Rat brain himppocampus


title: 33_495

status: Public on Jun 30 2005

city: Palo Alto

first: Jennifer

last: King

department: Cardiovascular Medicine

institute: Stanford University

description: Total RNA was isolated from segments of coronary artery using a combination of Trizol reagent (Invitrogen, Carlsbad, California) and RNeasy Mini kit (Qiagen, Valencia, California) techniques

source_name: Human coronary artery RNA

source_name: HUVEC and HeLa RNA


title: cultured rat cortex astrocyte

description: cultured astrocyte from postnatal rat cortex

source_name: Postnatal rat cortex


title: 35_480


title: 35_479


title: 34_496


title: 30_457


title: 32_494


title: 33_478


title: 31_491


title: 30_456


title: 27_477


title: 31_459


title: 27_475


title: 28_497


title: 31_492


title: 31_458


title: 27_476


title: 29_455


title: 32_493


title: 24_451


title: 28_454


title: 28_452


title: 26_474


title: 22_409


title: 15_471


title: 22_410


title: 22_473


title: 10_730


title: 8_408


title: 15_472


title: Vit A deficient 4b

city: Indianapolis

first: Howard

last: Edenberg

state: IN

institute: Indiana University School of Medicine

description:
Liver removed from 74-day old male rat fed special diet for 53 days. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 2ug of total RNA.
Keywords = rat, liver, vitamin A deficiency

source_name: liver


title: 7_406


title: 7_405


title: Vit A deficient 2b


title: 8_407


title: Vit A deficient 1b


title: Vit A deficient 4a

description:
Liver removed from 74-day old male rat fed special diet for 53 days. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.
Keywords = rat, liver, vitamin A deficiency


title: 6_404


title: Vit A deficient 3a


title: Vit A deficient 1a


title: 5_401


title: 4_397


title: 6_402


title: 5_400


title: 6_403


title: Vit A sufficient 4b


title: 5_399


title: Vit A sufficient 2b


title: 3_393


title: 3_392


title: 4_398


title: 4_395


title: Vit A sufficient 1b


title: Vit A deficient 2a


title: 3_394


title: 3_391


title: Vit A sufficient 4a


title: 2_378


title: 3_380


title: Vit A sufficient 2a


title: Vit A sufficient 1a


title: Vit A sufficient 3a


title: 2_379


title: 1_375


title: 2_377


title: 2_376


title: Sham 6

status: Public on Jun 29 2005

city: Durham

first: Maria

last: Mirotsou

state: NC

institute: Duke University

description: Heart from male sham control

source_name: heart left ventricle


title: TAC 1

description: Heart from female TAC operated animal


title: Sham 8

description: Heart from male sham control


title: TAC 5

description: Heart from male TAC operated animal


title: Sham 9

description: Heart from male sham control


title: TAC 4

description: Heart from male TAC operated animal


title: Sham 7

description: Heart from male sham control


title: Sham 4

description: Heart from male sham control


title: Sham 3

description: Heart from female sham control


title: TAC 6

description: Heart from male TAC operated animal


title: TAC 2

description: Heart from female TAC operated animal


title: TAC 3

description: Heart from female TAC operated animal


title: Wild type control_2bV2

status: Public on Jun 15 2005

description: Wild type mouse with normal cardiac phenotype used as control

source_name: cardiac ventricle


title: Wild type control_4bV2


title: Sham 2

description: Heart from female sham control


title: AT1 Tg- cardiac hypertophy_7bV2

description: cardiac specific AT1 transgenic mouse undergoing cardiac hypertrophy


title: Sham 1

description: Heart from female sham control


title: AT1 Tg- cardiac hypertophy_3bV2


title: Wild type control_3bV2


title: AT1 Tg- cardiac hypertophy_6bV2


title: AT1 Tg- cardiac hypertophy_1bV2


title: Wild type control_1bV2


title: AT1 Tg- cardiac hypertrophy_4bV2


title: Wild type control_5bV2


title: AT1 Tg- cardiac failure_3bV2

description: cardiac specific AT1 transgenic mouse undergoing cardiac failure


title: AT1 Tg- cardiac hypertophy_5bV2


title: AT1 Tg- cardiac hypertophy_8bV2


title: AT1 Tg- cardiac failure_2bV2


title: AT1 Tg- cardiac hypertophy_2bV2


title: AT1 Tg- cardiac failure_1bV2


title: Wild type control_2

description: Wild type mouse with normal cardaic phenotype used as control


title: Wild type control_4


title: Wild type control_5


title: AT1 Tg- cardiac hypertophy_8


title: Wild type control_1


title: Sham 5

description: Heart from male sham control


title: AT1 Tg- cardiac hypertophy_6


title: AT1 Tg- cardiac failure_2


title: AT1 Tg- cardiac failure_1


title: AT1 Tg- cardiac failure_3


title: AT1 Tg- cardiac hypertophy_5


title: AT1 Tg- cardiac hypertophy_1


title: AT1 Tg- cardiac hypertophy_4


title: AT1 Tg- cardiac hypertophy_2


title: Wild type control_3


title: AT1 Tg- cardiac hypertophy_7


title: H4 ORF replicate 3

type: genomic

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

description: Labeled total DNA (cy3) and immunoprecipitated DNA (cy5) were mixed and allowed to hybridize at 45 C overnight in hybridization buffer (3x SSC, 0.1% SDS, 25% formamide, Salmon sperm DNA to 300ng/ul).

molecule: genomic DNA

source_name: cy3 total DNA

source_name: cy5 immunoprecipitated DNA


title: H4 intergenic replicate 3


title: AT1 Tg- cardiac hypertophy_3


title: H4 ORF replicate 1


title: H4 ORF replicate 2


title: H4 intergenic replicate 2


title: H4 intergenic replicate 1


title: 24576 MeasuredBioAssayData&DerivedBioAssayData

status: Public on Jun 08 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA).  The ten chimpanzees included five males and five females.  We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1).  For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1).  All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO).  All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day.  To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points.  Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied.
reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999.

PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions.  Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org).  We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).  Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies).  We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples.  After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added.  The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).

The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California).  Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.

organism:
Pan troglodytes
Homo sapiens

source_name: pool of 9 human cell lines - Cy3

source_name: human sample - Cy5


title: 24577 MeasuredBioAssayData&DerivedBioAssayData


title: 24563 MeasuredBioAssayData&DerivedBioAssayData

source_name: chimp sample - Cy5


title: 24559 MeasuredBioAssayData&DerivedBioAssayData


title: 24561 MeasuredBioAssayData&DerivedBioAssayData


title: 24575 MeasuredBioAssayData&DerivedBioAssayData


title: 24558 MeasuredBioAssayData&DerivedBioAssayData


title: 24564 MeasuredBioAssayData&DerivedBioAssayData


title: 24562 MeasuredBioAssayData&DerivedBioAssayData


title: SHFC176

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52944.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 29.56; Parameter Scan Time = 12:32:33; Parameter PMT Volts = 550; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.90; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 29.56; Parameter Scan Time = 12:32:33; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: REBA

source_name: aURNA


title: EBV-positive NPC_CGBM1

status: Public on Jun 07 2005

city: Taipei

first: Yuan-Chii

middle: Gladys

last: Lee

department: Graduate Institute of Medical Informatics

country: Taiwan

institute: Taipei Medical University

description: EBV+_CGBM1 cell line vs common reference RNA

source_name: cy5: EBV+_CGBM1 cell line

source_name: cy3: common reference RNA mixture


title: 24552 MeasuredBioAssayData&DerivedBioAssayData


title: SHFB24

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52948.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 14:40:41; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16911; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 14:40:41; Parameter PMT Volts = 620; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16939; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: PENOY


title: 24557 MeasuredBioAssayData&DerivedBioAssayData


title: 24555 MeasuredBioAssayData&DerivedBioAssayData


title: 24560 MeasuredBioAssayData&DerivedBioAssayData


title: SHFC179

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52947.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 29.47; Parameter Scan Time = 14:31:33; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16901; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 29.47; Parameter Scan Time = 14:31:33; Parameter PMT Volts = 630; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16929; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: CLAWS


title: SHFC175

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52943.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 29.13; Parameter Scan Time = 12:16:27; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 29.13; Parameter Scan Time = 12:16:27; Parameter PMT Volts = 610; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: FAYE


title: EBV-positive NPC_TW06

description: EBV+_TW06 cell line vs common reference RNA

source_name: cy5: EBV+_TW06 cell line


title: EBV-positive NPC_TW04

description: EBV+_TW04 cell line vs common reference RNA

source_name: cy5: EBV+_TW04 cell line


title: SHFC122

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52941.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 11:02:37; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16801; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 11:02:37; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16829; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: LILI


title: SHFC123

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52942.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 28.55; Parameter Scan Time = 11:10:30; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16809; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 28.55; Parameter Scan Time = 11:10:30; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-10; Parameter Pixel Size = 10; Parameter Laser on time = 16837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: SHFB25

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52949.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 30.29; Parameter Scan Time = 15:01:28; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16932; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 30.29; Parameter Scan Time = 15:01:28; Parameter PMT Volts = 610; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: 24551 MeasuredBioAssayData&DerivedBioAssayData


title: SHFC177

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52945.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 29.78; Parameter Scan Time = 12:43:41; Parameter PMT Volts = 590; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 29.78; Parameter Scan Time = 12:43:41; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16876; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: SHFC178

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52946.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 30.05; Parameter Scan Time = 12:59:53; Parameter PMT Volts = 530; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 30.05; Parameter Scan Time = 12:59:53; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 16892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: EBV-positive NPC_TW03

description: EBV+_TW03 cell line vs common reference RNA

source_name: cy5: EBV+_TW03 cell line


title: EBV-free NPC_TW06

description: NPC_TW06 (EBV free) vs common reference RNA

source_name: cy5: NPC_TW06 cell line (without EBV)


title: EBV-positive NPC_TW01

description: EBV+_TW01 cell line vs common reference RNA

source_name: cy5: EBV+_TW01 cell line


title: 24550 MeasuredBioAssayData&DerivedBioAssayData


title: 24578 MeasuredBioAssayData&DerivedBioAssayData


title: 24553 MeasuredBioAssayData&DerivedBioAssayData


title: 24554 MeasuredBioAssayData&DerivedBioAssayData


title: EBV-free NPC_TW04

description: NPC_TW04 (EBV free) vs common reference RNA

source_name: Cy5: NPC_TW04 cell line (without EBV)


title: 24556 MeasuredBioAssayData&DerivedBioAssayData

description:
Whole blood (10 ml) for ten unrelated common chimpanzees (Pan troglodytes) was kindly provided by Dr. Harold M. McClure at the Yerkes Regional Primate Center of Emory University (Atlanta, GA).  The ten chimpanzees included five males and five females.  We isolated and transformed lymphocytes with frozen virus stocks by using a standard Epstein-Barr virus transformation protocol (1).  For the human samples, we randomly selected lymphoblastoid cell lines for nine unrelated humans from a collection previously established in our laboratory (reference 1).  All cell lines were maintained at 37 degrees C in 5% CO2, and with DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine (Gibco-BRL, Carlsbad, CA), 100 U/ml penicillin, 100 microg/ml streptomycin (BioWhittaker, East Rutherford, NJ), and 10% FCS (Sigma, St. Louis, MO).  All cell lines were maintained under the same conditions for more than 3 months, and were harvested on the same day.  To minimize differences in growth behavior and morphology between different cell lines, we fed and split them at comparable growth points.  Because growth rates differed between different lines, the splitting schedule and feeding cycle for individual lines varied.
reference 1: Risch N, Spiker D, Lotspeich L, Nouri N, Hinds D, Hallmayer J, Kalaydjieva L, McCague P, Dimiceli S, Pitts T, Nguyen L, Yang J, Harper C, Thorpe D, Vermeer S, Young H, Hebert J, Lin A, Ferguson J, Chiotti C, Wiese-Slater S, Rogers T, Salmon B, Nicholas P, Myers RM, and et al. A genomic screen of autism: evidence for a multilocus etiology. Am J Hum Genet 65: 493-507., 1999.

PolyA+ RNAs were isolated from approximated 107 cells by using the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA) following the manufacturer's instructions.  Equal amounts of poly-A RNA from nine human cell lines were pooled to serve as the common reference sample for each of the individual 19 samples. The human cDNA microarrays used in this study were obtained from the Stanford Functional Genomic Facility (http://www.microarray.org).  We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).  Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ml containing 2 mg mRNA / 4 mg oligo (dT) primer / 0.5 mM each dATP, dCTP, dGTP / 0.2 mM dTTP / 0.1 mM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies).  We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples.  After incubation at 42 degrees C for 2-3 hours, the RNA was degraded by adding 15 ml of 0.1 N NaOH at 70 degrees C for 10 minutes, and was neutralized by adding 15 ml of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 mg Cot1 human DNA (Gibco-BRL), 20 mg PolyA RNA (Sigma, #P9403) and 20 mg tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ml of 20x SSC (BioWhittaker, MD) and 1 ml of 10% SDS were added.  The probes were denatured at 100 degrees C for 3 minutes, incubated at 37 degrees C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).

The slides were incubated at 65 degrees C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California).  Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.

source_name: pool of 9 human cell lines - Cy3


title: EBV-free NPC_CGBM1

description: NPC_CGBM1 (EBV free) vs common reference RNA

source_name: cy5: NPC_CGBM1 cell line (without EBV)


title: EBV-free NPC_TW03

description: NPC_TW01 (EBV free) vs common reference RNA

source_name: Cy5: NPC_TW03 cell line (without EBV)


title: SHFB26

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52950.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
We used standard direct labeling protocols describes by the Brown lab (http://cmgm.stanford.edu/pbrown/protocols/index.html).
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 = 30.39; Parameter Scan Time = 15:11:10; Parameter PMT Volts = 570; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16942; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
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 = 30.39; Parameter Scan Time = 15:11:10; Parameter PMT Volts = 630; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 16969; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: NPC_TW06

description: NPC cell line (TW06) vs Normal epithelial tissues

source_name: Cy3: Normal epithelial tissues


title: NPC_TW03

description: NPC cell line (TW03) vs Normal epithelial tissues


title: EBV-free NPC cell line (EBV-_TW01)

source_name: Cy5: NPC_TW01 cell line (without EBV)


title: MLO-Y4 OC high - 2

status: Public on Jun 05 2005

city: San Antonio

first: Wuchen

last: Yang

state: TX

address: 7703 Floyd Curl Drive

department: Department of Periodontics

institute: The University of Texas Health Science Center at San Antonio

description:
1) osteoblast vs. osteocytes in vitro;
2) osteocyte with gap junction vs. without gap junction in vitro.
Keywords = osteoblast
Keywords = osteocyte

source_name: Osteocyte cell line derived from a transgenic mouse containing the osteocalcin promoter driving T antigen


title: MLO-Y4 OC high - 3


title: MLO-Y4 OC high - 1


title: NPC_CGBM1

description: NPC cell line (NPC_CGBM1) vs Normal epithelial tissues


title: NPC_TW01

description: NPC cell line (NPC_TW01) vs Normal epithelial tissues


title: 2T3 OB C0 - 1

description:
1) osteoblast vs. osteocytes in vitro;
2) osteoblast low density vs. confluency in vitro.
Keywords = osteoblast
Keywords = osteocyte

source_name: Osteoblast cell line derived from a transgenic mouse containing BMP-2 promoter driving the SV-40 T antigen transgene


title: MLO-Y4 OC low - 3


title: MLO-Y4 OC low - 2


title: 2T3 OB low - 3


title: 2T3 OB low - 2


title: 2T3 OB C0 - 2


title: 2T3 OB C0 - 3


title: MLO-Y4 OC low - 1


title: Polyribosomal transcript study set 3

status: Public on Jun 06 2005

first: David

middle: William

last: Galbraith

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

description: Comparison of transcript profiles of total RNA and polyribosomal RNA. The data represents output (log2 median intensities) from the GenePix Result (GPR) file extracted from TIF images. The data is from hybridization on slide ATv3 01.01.097.

organism: Arabidopsis thaliana

source_name: total RNA from leaf tissue of 5-6 week-old plants

source_name: polyribosomal RNA from leaf tissue of 5-6 week-old plants


title: Polyribosomal transcript study set 4

description: Comparison of transcript profiles of total RNA and polyribosomal RNA. The data represents output (log2 median intensities) from the GenePix Result (GPR) file extracted from TIF images. The data is from hybridization on slide ATv3 01.01.098.


title: Rep 1 number 2

status: Public on Jun 04 2005

city: Saskatoon

first: Matthew

last: Bainbridge

state: SK

address: 20 Campus Drive

department: Computer Science

country: Canada

institute: U of Saskatchewan

description:
Cell-line K562 with gene RIZ1 (prdm2) vs. K562 with no RIZ1
Keywords = riz1


title: Rep 4 number 1


title: Rep 4 number 2


title: IS5KO_Nonmotile_sample_2

status: Public on Jun 02 2005

city: Saint Paul

first: Betsy

last: Martinez-Vaz

state: MN

address: 1479 Gortner Ave

department: Biochemistry , Molecular Biology and Biophysics

institute: University of Minnesota

description: This experiment compared the expression profiles of the non motile E.coli strain to the isogenic E.coli strain with IS5 (usptream of flhDC) deletion.

organism: Escherichia coli

source_name: WT E.coli Non Motile strain

source_name: Sample E.coli strain with IS5 deletion


title: Rep 3 number 1


title: IS5mapping_sample_B7

description:
This is one of the experimental sample for the IS mapping experiment. The reaction was done with primers specific for IS5 and genomic DNA from the NonMotile isolate as the template
Keywords = IS
Keywords = mapping
Keywords = DNA
Keywords = arrays
Keywords = single
Keywords = channel

source_name: PCR product with IS5 primers and genomic DNA from NonMotile isolate as a template


title: IS5mapping_sample_B6


title: IS5mapping_sample_B5


title: IS5mapping_sample_B3


title: 2T3 OB low - 1


title: IS5KO_Nonmotile_sample_1


title: NPC_TW04

description: NPC cell line (NPC_TW04) vs Normal epithelial tissues


title: Rep 3 number 2


title: Rep 2 number 1


title: Rep 1 number 1

description: Cell-line K562 with gene RIZ1 (prdm2) vs. K562 with no RIZ1


title: Polyribosomal transcript study set 2

city: Tucson

description: Comparison of transcript profiles of total RNA and polyribosomal RNA. The data represents output (log2 median intensities) from the GenePix Result (GPR) file extracted from TIF images. The data is from hybridization on slide ATv3 01.01.096.


title: Polyribosomal transcript study set 1

description: Comparison of transcript profiles of total RNA and polyribosomal RNA. The data represents output (log2 median intensities) from the GenePix Result (GPR) file extracted from TIF images. The data is from hybridization on slide ATv3 01.01.095.


title: Rep 2 number 2


title: IS5mapping_sample_B2


title: IS5mapping_sample_A2

description: This is one of the experimental sample for the IS mapping experiment. The reaction was done with primers specific for IS5 and genomic DNA from the Motile isolate as the template

source_name: PCR product with IS5 primers and genomic DNA from Motile isolate as a template


title: IS5mapping_sample_A3


title: IS5mapping_sample_B4


title: IS5mapping_control_2

description: This is the control for the IS5 mapping using single channel hybridizations. Intensities were used to evaluate the data. The control was done in a PCR reaction that did not contain genomic DNA. A purified IS5 fragment obatined in a previous PCR was used as template

source_name: DNA probe produced by labelling a purified IS5 PCR product as PCR template for flourescent labeling reaction


title: IS5mapping_sample_A5

description:
This is one of the experimental sample for the IS mapping experiment. The reaction was done with primers specific for IS5 and genomic DNA from the Motile isolate as the template
Keywords = IS
Keywords = mapping
Keywords = DNA
Keywords = arrays
Keywords = single
Keywords = channel


title: IS5mapping_sample_B1


title: IS5mapping_sample_A4


title: IS5mapping_sampleA1


title: IS5mapping_control_3

source_name: PCR product with IS5 primers and purified IS5 PCR product as template- no genomic DNA present


title: IS5mapping_control_1


title: Motile_NonMotile_sample_5

description:
This experiment compares the expression profile of the motile and Non motile isolates of wildt type E.coli strain MG1655
Keywords = IS
Keywords = mapping
Keywords = DNA
Keywords = arrays

source_name: WT E.coli Motile strain

source_name: WT E.coli NonMotile strain


title: Motile_NonMotile_sample_7

description:
This experiment compares the expression profile of the motile and Non motile isolates of wild type E.coli strain MG1655
Keywords = IS
Keywords = mapping
Keywords = DNA
Keywords = arrays


title: IS5KO_motile_sample_2

description: In this experiment, the expression profile of a strain containing a deletion of the IS5 element upstream of flhDC was compared to expression profile of the wild type motile strain.

source_name: E.coli strain with IS5 deletion


title: IS5KO_motile_sample_5

source_name: Sample IS5 deletion


title: IS5KO_motile_sample_1


title: Motile_NonMotile_sample_6


title: Motile_NonMotile_sample_4


title: Motile_NonMotile_sample_3


title: Motile_NonMotile_sample_2


title: Motile_NonMotile_sample_1


title: IS5KO_motile_sample_6


title: IS5KO_motile_sample_3


title: FoxM1 A

status: Public on May 31 2005

first: Diane

last: Wonsey

institute: Wyeth Research

description: cells transfected with siRNA targeting FoxM1, replicate 1 of 3

source_name: BT-20 cells


title: mock B

description: mock transfection, replicate 2 of 3


title: IS5KO_motile_sample_4

source_name: E.coli IS5 deletion


title: mTert 1

city: Madrid

first: Peter

last: Klatt

department: Molecular Oncology Program

country: Spain

institute: Spanish National Cancer Center (CNIO)

description: mouse embryonic fibroblasts retrovirally transfected with pBabePuro containing the catalytic subunit of mouse telomerase (mTert)

source_name: mouse embryonic fibroblasts


title: FoxM1 B

description: cells transfected with siRNA targeting FoxM1, replicate 2 of 3


title: mTert 2


title: GFP C

description: cells transfected with siRNA targeting GFP, replicate 3 of 3


title: GFP B

description: cells transfected with siRNA targeting GFP, replicate 2 of 3


title: GFP A

description: cells transfected with siRNA targeting GFP, replicate 1 of 3


title: FoxM1 C

description: cells transfected with siRNA targeting FoxM1, replicate 3 of 3


title: control 2

description: mouse embryonic fibroblasts retrovirally transfected with pBabePuro (empty virus)


title: mock C

description: mock transfection, replicate 3 of 3


title: mock A

description: mock transfection, replicate 1 of 3

source_name: BT-20 cell line


title: hSF-ChIP Chromatin-B-IP1-1

status: Public on May 30 2005

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

description: Chromatin Immunopurification with anti-Heat Shock Facotor from heat shocked Drosophila embryos

organism: Drosophila melanogaster

source_name: anti-HSF enriched chromatin

source_name: pre-immune sera chromatin


title: hSF-ChIP Chromatin-B-IP2


title: hSF-ChIP Chromatin-A-IP3-2


title: hSF-ChIP Chromatin-A-IP4-2


title: hSF-ChIP Chromatin-A-IP2-3


title: HSF-ChIP Chromatin-C-IP1-2


title: control 1


title: HSF-ChIP Chromatin-A-IP2-1


title: HSF-ChIP Chromatin-A-IP1-4


title: HSF-ChIP Chromatin-B-IP1-2


title: hSF-ChIP Chromatin-A-IP2-2


title: HSF-ChIP Chromatin-C-IP1-1


title: hSF-ChIP Chromatin-A-IP4-1


title: hSF-ChIP Chromatin-A-IP2-4


title: HSF-ChIP Chromatin-A-IP1-3


title: Motile_NonMotile_sample_8


title: HSF-ChIP ChromatinA-IP1-1


title: BeWo E

city: Madison

middle: W

last: Burleigh

state: WI

address: 1220 Capital Court

institute: Wisconsin National Primate Research Center

description:
BeWo choriocarcinoma cell line total RNA
Keywords = trophoblast
Keywords = BeWo
Keywords = placenta
Lot batch = 4001570

source_name: BeWo cell line


title: ChromatinC1-IP1

city: Cambridge

description: Genomic tiling array interogated with heat shock factor immunopurified chromatin.


title: BeWo A


title: hSF-ChIP Chromatin-A-IP3-1


title: ChromatinB2-IP1


title: ChromatinC1-IP2


title: Htt14A2.5-PA_replicate 4

city: Irvine

first: Barbara

last: Apostol

department: Psychiratry and Human Behavior

institute: University of California Irvine

description:
PC12 cells, stably expressing inducible truncated mutant exon 1 of human Huntingtin, cells were induced with ponasterone (PA) for 48 hrs
Keywords = huntingtin
Keywords = PC12

source_name: line Htt14A2.5 (see below)


title: Htt14A2.5+PA_replicate 2

source_name: Htt14A2.5 line


title: chromatinB1-IP2


title: BeWo B


title: ChromatinB2-IP2


title: Htt14A2.5-PA_replicate 3


title: BeWo D


title: chromatinA1-IP2


title: Htt14A2.5-PA_replicate 1


title: Htt14A2.5+PA_replicate 4


title: Htt14A2.5-PA_replicate 2


title: ChromatinB1-IP1


title: Htt14A2.5+PA_replicate 1


title: ChromatinA1-IP1


title: JEG3 A

description:
JEG3 choriocarcinoma cell line total RNA
Keywords = trophoblast
Keywords = JEG3
Keywords = placenta
Lot batch = 4001570

source_name: JEG3 cell line


title: JEG3 C


title: HSF-ChIP Chromatin-A-IP1-2


title: Htt14A2.5+PA_replicate 3


title: ChromatinA2-IP1


title: BeWo C


title: ChromatinA2-IP2


title: array-CGH - sGBM3

status: Public on May 27 2005

first: Markus

last: Bredel

institute: Stanford University School of Medicine

description:
Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51525.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 33.59; Parameter Scan Time = 15:44:29; Parameter PMT Volts = 550; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 83196; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 33.59; Parameter Scan Time = 15:44:29; Parameter PMT Volts = 720; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 152674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

source_name: male reference


title: WLPBS3

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description:
Total RNA from whole lung
no amplification-cDNA
PBS

source_name: Ref Pool 2


title: WLOVA5

description:
Total RNA from whole lung
no amplification-cDNA
OVA


title: WLPBS2


title: WLPBS1


title: array-CGH - sGBM2

description:
Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51555.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 32.13; Parameter Scan Time = 16:29:21; Parameter PMT Volts = 530; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 85315; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 32.13; Parameter Scan Time = 16:29:21; Parameter PMT Volts = 700; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 154793; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel


title: WLPBS4


title: WLOVA2


title: WLOVA4


title: WLPBS5


title: WLOVA1


title: WLOVA6


title: array-CGH - O5

description:
Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51533.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 33.99; Parameter Scan Time = 16:44:52; Parameter PMT Volts = 510; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 83256; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 33.99; Parameter Scan Time = 16:44:52; Parameter PMT Volts = 700; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 152734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel


title: array-CGH - O2

description:
Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51532.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 34.02; Parameter Scan Time = 17:00:38; Parameter PMT Volts = 510; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 83272; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 34.02; Parameter Scan Time = 17:00:38; Parameter PMT Volts = 700; Parameter Scan Date = 2004-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 152749; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel