title: Alternate splicing in LPS Stimulated BMMs replicate2

status: Public on Jan 15 2007

type: RNA

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

description: Pairwise comparison of expression of alternate splicing in the Tlr4 pathway using custom designed Combimatix oligonucleotide arrays. Scanned on an Axon4000b scanner.

hyb_protocol: Followed protocol from Combimatrix

data_processing: Combimatrix image analysis, Lowess normalised (Genespring 7.0))

molecule: polyA RNA

organism: Mus musculus

source_name: 7hr LPS treated BMMs

label_protocol: Kreatech mRNA labelling kit

tag: Bone marrow derived macrophages (BMMs) from C57Bl6/J mice (6 wks male) exposed to LPS (10ng/ml) for 7hrs.

molecule: total RNA

source_name: Unstimulated BMMs

tag: Bone marrow derived macrophages (BMMs) from C57Bl6/J mice (6 wks male).


title: Alternate splicing in LPS Stimulated BMMs replicate4


title: Alternate splicing in LPS Stimulated BMMs replicate1


title: Alternate splicing in LPS Stimulated BMMs replicate3


title: HES P7 V P4_4

status: Public on Jan 11 2007

description: Pairwise comparison of two immunosorted HES cell populations. Scanned on an Agilent dual colour scanner.

data_processing: Imagene image analysis Lowess Normalisation, Normalisation between arrays

organism: Homo sapiens

source_name: HES P7 population

tag: HES P7 population

source_name: HES P4 population

tag: HES P4 population


title: HES P7 V P5_1

tag: HES P5 population

source_name: HES P5 population


title: HES P6 V P4_3

source_name: HES P6 population

tag: HES P6 population


title: HES P7 V P6_2


title: HES P5 V P4_3


title: HES P6 V P4_1


title: HES P7 V P6_1


title: HES P7 V P4_3


title: HES P7 V P5_2


title: HES P7 V P4_1

description: Pairwise comparison of two immunosorted HES cell populations.

data_processing: Imagene image analysis, Lowess Normalisation, Normalisation between arrays


title: HES P5 V P4_2

source_name: HES P4  population


title: HES P7 V P6_3


title: HES P5 V P6_4


title: HES P7 V P5_3


title: HES P5 V P6_2


title: non-activated regulatory T-cells

status: Public on Jan 09 2007

city: Berlin

first: Reinhard

last: Wanner

address: Arnimallee 22

department: Inst. of Molecular Biology and Bioinformatics

country: Germany

institute: Charite-CBF

description: untreated regulatory T-cells freshly isolated from human blood using MACS. Data in files "not-activated regulatory T-cells" and "activated regulatory T-cells" stem from the same donor.

scan_protocol: GenChip Scanner 3000

data_processing: GCOS 1.2

label: biotinylated UTP/CTP; SAPE-solution; biotinylated goat anti-streptavidin; 2nd SAPE-solution;

source_name: regulatoy T-cells freshly isolated from human blood

tag: anonymous healthy blood donor


title: HES P7 V P4_2


title: HES P6 V P4_2


title: HES P5 V P6_1

description:
Pairwise comparison of two immunosorted HES cell populations.
Scanned on an Agilent dual colour scanner.


title: P1-2_P1-1

status: Public on Jul 29 2006

city: Minamidai, Kawagoe

first: Toshiro

last: Saito

state: Saitama

department: Life Science Group

country: Japan

institute: Hitachi, Ltd.

description: Sample Tissue: peripheral blood

data_processing: Global Normalization and Lowess

tag: after monotonous VTR, patients with type 2 diabetes (diabetic nephropathy -)

tag: before monotonous VTR, patients with type 2 diabetes (diabetic nephropathy -)


title: HES P7 V P4_5


title: HES P5 V P6_3


title: P1-4_P1-3

description: Sample Tissue: peripheral blood

tag: after comedy show, patients with type 2 diabetes (diabetic nephropathy -)

tag: before comedy show, patients with type 2 diabetes (diabetic nephropathy -)


title: activated regulatory T-cells

description: Regulatory T-cells freshly isolated from human blood using MACS were activated by temorary contact to monocyte-derived Dendritic cells. Data in files "activated regulatory T-cells" and "not-activated regulatory T-cells" stem from the same donor.


title: N-4_N-3

description: Sample Tissue: peripheral blood

tag: after comedy show, normal subject

tag: before comedy show, normal subject


title: AG825-treated, 6h after UV, Replicate B

status: Public on Jul 01 2006

city: Omaha

first: Laura

middle: A

last: Hansen

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

country: USA

institute: Creighton University School of Medicine

description: AG825-treated, harvested 6h after UV exposure

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Average (RMA) of Affymetrix CEL file

label: biotin

source_name: dorsal mouse skin

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

extract_protocol: Total RNA was extracted from the shaved dorsal skin using Trizol (Invitrogen) followed by RNeasy kit (Qiagen).

tag: DMSO-treated, sham UV exposed


title: AG825-treated, 24h after UV, Replicate A

description: AG825-treated, harvested 24h after UV exposure


title: AG825-treated, 6h after UV, Replicate E


title: P2-2_P2-1

description: Sample Tissue: peripheral blood

tag: after monotonous VTR, patients with type 2 diabetes (diabetic nephropathy +)

tag: before monotonous VTR, patients with type 2 diabetes (diabetic nephropathy +)


title: P2-3_N-3

description: Sample Tissue: peripheral blood

tag: before comedy show, patients with type 2 diabetes (diabetic nephropathy +)


title: AG825-treated, 24h after UV, Replicate B


title: AG825-treated, Sham UV, Replicate C

description: AG825-treated, harvested 6h after Sham UV exposure


title: AG825-treated, 24h after UV, Replicate C


title: AG825-treated, 6h after UV, Replicate D


title: P2-4_P2-3

description: Sample Tissue: peripheral blood

tag: after comedy show, patients with type 2 diabetes (diabetic nephropathy +)


title: AG825-treated, Sham UV, Replicate E


title: AG825-treated, 6h after UV, Replicate A


title: AG825-treated, Sham UV, Replicate D


title: AG825-treated, Sham UV, Replicate B


title: HES P5 V P4_1


title: P1-3_N-3

description: Sample Tissue: peripheral blood


title: N-2_N-1

description: Sample Tissue: peripheral blood

tag: after monotonous VTR, normal subject

tag: before monotonous VTR, normal subject


title: DMSO-treated, 24h after UV, Replicate C

description: DMSO-treated, harvested 24h after UV exposure


title: DMSO-treated, 24h after UV, Replicate E


title: DMSO-treated, 6h after UV, Replicate G

description: DMSO-treated, harvested 6h after UV exposure


title: DMSO-treated, 24h after UV, Replicate A


title: DMSO-treated, Sham UV, Replicate B

description: DMSO-treated, harvested 6h after Sham UV exposure


title: DMSO-treated, 24h after UV, Replicate B


title: DMSO-treated, 6h after UV, Replicate C


title: DMSO-treated, Sham UV, Replicate C


title: DMSO-treated, Sham UV, Replicate D


title: DMSO-treated, 6h after UV, Replicate E


title: DMSO-treated, 6h after UV, Replicate F


title: S_pyogenes_NZ131_rgg_early-stat_6.21.05

status: Public on Jun 01 2006

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

description: End-terminus biotin-labeled cDNA (1.86 µg) was hybridized to S. pyogenes GeneChip genome arrays following the prokaryotic hybridization protocol recommended in the Affymetrix GeneChip Expression Analysis Technical Manual available at the Website http://www.affymetrix.com/support/technical/manual/expressionmanual.affx.

hyb_protocol: The GeneChips were hybridized with 1.86 ug of biotin end-terminus labeled cDNA in 1X hybridization buffer [100 mM Mes, 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20 (Pierce Chemical, Rockford, IL), 50 pM control oligonucleotide B2 (Affymetrix), 20 ug herring sperm DNA (Promega, Madison, WI), 100 ug acetylated bovine serum albumin (Invitrogen)] for 16 h at 45°C on a rotisserie at 60 r.p.m.  Following hybridization, the hybridization cocktail was removed and the GeneChip filled with non-stringent buffer A [0.9 M sodium chloride, 60 mM sodium phosphate, 6 mM EDTA, and 0.01% Tween 20].  GeneChips were post-processed on the automated Affymetrix GeneChip Fluidics Station 450 using the following protocol: Wash 1: 10 cycles of 2 mixes/cycle with non-stringent buffer A at 25°C; Wash 2: 4 cycles of 15 mixes/cycles with stringent buffer B [100 mM Mes, 0.1 M NaCl, and 0.01% Tween 20] at 45°C; First stain: stain probe array for 10 min at 25°C in streptavidin-phycoerythrin (SAPE) solution [1x Mes stain buffer (100 mM Mes, 1 M NaCl, and 0.05% Tween 20), 2 mg/ml acetylated BSA, and 10 ug/ml SAPE (Molecular Probes, Eugene, OR)] post stain: wash 10 cycles of 4 mixes/cycle with non-stringent buffer A at 300C; second stain: stain probe array for 10 min in antibody solution [1x Mes stain buffer, 2 mg/ml acetylated BSA, 0.1 mg/ml normal goat IgG (Sigma-Aldrich, St. Louis, MO), and 3 ug/ml biotinylated antibody (Vector Laboratories, Burlingame, CA); third stain: stain probe array for 10 min in SAPE solution at 25°C; final wash: 15 cycles of 4 mixes/cycle with non-stringent buffer A at 30°C.

scan_protocol: The probed arrays were scanned at 570 nm at a resolution of 1.56 µm using a confocal GC3000 laser scanner (Affymetrix)

data_processing: Gene expression levels were calculated with GeneSpring 7 software (Silicon Genetics, Redwood City, CA)

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes, NZ131 rgg isogenic mutant strain, early-stationary phase of growth

label_protocol: The 3' terminus of the fragmented cDNA was labeled with Biotin-N6-ddATP (ENZO, New York, NY) at 37°C for 2 h using 50 U of terminal deoxynucleotide transferase (New England Biolabs, Ipswich, MA)

growth_protocol: The strain was grown in Todd-Hewitt broth to A600=0.7

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA). cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carsbad, CA)

tag: Strain

value: NZ131 rgg isogenic mutant


title: S_pyogenes_NZ131_rgg_early-stat_6.9.05


title: U937_vs_MO-exp_01

status: Public on May 10 2006

type: mixed

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Comparative hybridization of MCIp-enriched methylated DNA-fragements from leukemia versus normal

hyb_protocol: Ten microgram of each fluorescently labeled and purified DNA amplicon) in 300 µl DIG Easy Hyp Solution (Roche) supplemented with 25 µg Cot-1 DNA (Invitrogen) and 30 µg Yeast tRNA were hybridized to Human CpG 12K Arrays (HCGI12K, Microarray Centre, UHN, Toronto, Canada) in 60x21 mm Gene Frames (ABgene) at 37°C for o/n. Slides were washed three times in 1x SSC, 0.1% SDS at 50°C for 10 min.

scan_protocol: After two more rinses with 0.1xSSC, slides were dried and scanned using the Affymetrix 428 Scanner. Images were analyzed using the ImaGene 5.6 and Gene Sight Lite software (BioDiscovery, Inc.)

data_processing: LOWESS normalization was used to normalize Cy3 and Cy5 signals.

molecule: genomic DNA

source_name: human histiocytic lymphoma U937

label_protocol: four microgram of MCIp-amplicon were directly labeled with Cy3-dUTP using the BioPrime® Array CGH Genomic Labeling System (Invitrogen)

growth_protocol: The human histiocytic lymphoma cell line U937 was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany)

extract_protocol: Mse I digested genomic DNA was subjected to Methyl-CpG immunoprecipitation (MCIp), and amplified by LM-PCR

treatment_protocol: untreated

tag: established from the pleural effusion of a 37-year-old man with generalized diffuse histiocytic lymphoma in 1974; cells were described to express markers and properties of monocytes

source_name: freshly isolated human blood monocytes

label_protocol: four microgram of MCIp-amplicon were directly labeled with Cy5-dUTP using the BioPrime® Array CGH Genomic Labeling System (Invitrogen)

growth_protocol: Peripheral blood mononuclear cells were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque. Monocytes were isolated from mononuclear cells by countercurrent centrifugal elutriation in a J6M-E centrifuge (Beckman, München, Germany)

tag: healthy donor gender male age 27


title: S_pyogenes_NZ131_rgg_mid-exp_3.17.05

source_name: Streptococcus pyogenes, NZ131 rgg isogenic mutant strain, mid-exponential phase of growth

growth_protocol: The strain was grown in Todd-Hewitt broth to A600=0.3


title: S_pyogenes_NZ131_rgg_late-exp_6.9.05

source_name: Streptococcus pyogenes, NZ131 rgg isogenic mutant strain, late-exponential phase of growth

growth_protocol: The strain was grown in Todd-Hewitt broth to A600=0.6


title: KG-1_vs_MO-exp_01

source_name: human acute myeloid leukemia KG-1

growth_protocol: The human myeloid leukaemia cell line KG-1, and was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany)

tag: established from the bone marrow of a 59-year-old man with erythroleukemia that developped into acute myeloid leukemia (AML) at relapse in 1977; cells were described to form colonies in soft-agar in response to colony-stimulating factor


title: S_pyogenes_NZ131_wt_early-stat_6.21.05

source_name: Streptococcus pyogenes, NZ131 wild-type strain, early-stationary phase of growth

tag: Disease

value: acute streptococcal glomerulonephritis


title: THP-1_vs_MO-exp_01

source_name: human acute monocytic leukemia THP-1

growth_protocol: The human acute monocytic leukemia THP-1, and was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany)

tag: established from the peripheral blood of a 1-year-old boy with acute monocytic leukemia (AML) at relapse in 1978; the cells can be used for induction of differentiation studies; the cells were described to produce lysozyme and to be phagocytic


title: U937_vs_MO-exp_03


title: KG-1_vs_MO-exp_02


title: THP-1_vs_MO-exp_02


title: S_pyogenes_NZ131_wt_mid-exp_3.17.05

source_name: Streptococcus pyogenes, NZ131 wild-type strain, mid-exponential phase of growth


title: S_pyogenes_NZ131_rgg_mid-exp_5.2.05


title: U937_vs_MO-exp_02


title: KG-1

status: Public on May 31 2006

description: expression profile of KG-1 cells.

data_processing: GCOS, MAS5

source_name: human acute myeloid leukemia

label_protocol: one cycle (Affymetrix standard protocol)

extract_protocol: RNA Midi Kit from Qiagen


title: KG-1_vs_MO-exp_03


title: THP-1_vs_MO-exp_03


title: normal Monocytes (MO)

description: This experiment was designed to test the properties of the platform. The same sample (normal human monocytes) was labeled with both Cy3 and Cy5.

tag: healthy donor

tag: gender male

tag: age 27


title: THP-1

description: expression profile of THP-1 cells.

source_name: human acute monocytic leukemia


title: S_pyogenes_NZ131_wt_early-stat_6.9.05


title: S_pyogenes_NZ131_wt_mid-exp_5.2.05


title: human blood monocytes

description: expression profile of peripheral human blood monocytes. used as a reference for leukemia cell lines


title: U937

description: expression profile of U937 cells.

source_name: human histiocytic lymphoma


title: LRRC3B tumor vs SNU-601 #1

city: Daejeon

first: Mirang

last: Kim

address: 52 Eoeun-dong

department: human genome center

country: South Korea

institute: KRIBB

description: GenePix Pro 4.0 program (Axon Instruments)

hyb_protocol: Genisphere 3DNA Expression Array Detection kit

scan_protocol: GenePix 4000B Scanner (Axon Instruments)

data_processing: print-tip Lowess method (bioconductor.org)

source_name: xenograft LRRC3B tumor

extract_protocol: RNeasy midi-prep (Qiagen)

tag: Total RNA from Xenograft tumor of SNU-601-LRRC3B

tag: Total RNA from gastric cancer cell, SNU-601


title: control tumor vs SNU-601 #1

hyb_protocol: Genisphere 3DNA Expression Array Detection Kit (Genisphere, Hatfield, PA)

source_name: xenograft control tumor

tag: total RNA from xenograft tumor of SNU-601-pcDNA3.1

extract_protocol: RNeasy midi-prep (Qiagen, Chatsworth, CA)

tag: total RNA from SnU-601 cells


title: control tumor vs SNU-601 #2

label_protocol: Genisphere 3DNA Expression Array Detection kit

tag: Total RNA from Xenograft tumor of SNU-601-pcDNA3.1


title: control tumor vs SNU-601 #3

tag: Total RNA from Xenograft tumor#3 of SNU-601-pcDNA3.1


title: LRRC3B tumor vs SNU-601 #3


title: LRRC3B tumor vs SNU-601 #2

tag: Total RNA from Xenograft tumor #2 of SNU-601-LRRC3B


title: RNAi -Transgenic replicate 6

status: Public on May 01 2006

city: Philadelphia

first: Hung

last: Tseng

state: PA

address: 415 Curie Boulevard Room 242B

department: Dermatology

institute: University of Pennsylvania

description: mouse fully-grown (GV) oocytes

data_processing: GC-RMA

source_name: oocyte

label_protocol: Approximately 15 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: RNA was extracted from 50 oocytes isolated from a single mouse

tag: mouse B6xCF-1  RNAi transgenic


title: RNAi -Transgenic replicate 11

description: mouse fully-grown (GV) oocytes


title: Non-Transgenic replicate 8

description: mouse fully-grown (GV) oocytes


title: Non-Transgenic replicate 1

description: mouse fully-grown (GV) oocytes

tag: mouse B6xCF-1  Non-transgenic (control-1)


title: RNAi -Transgenic replicate 12

description: mouse fully-grown (GV) oocytes


title: RNAi -Transgenic replicate 5

description: mouse fully-grown (GV) oocytes


title: Non-Transgenic replicate 2

description: mouse fully-grown (GV) oocytes

tag: mouse B6xCF-1  Non-transgenic (control-2)


title: iA50clone6-

city: Muenster

first: Thorsten

last: Mueller

address: Domgakstr. 19

department: University Hospital Muenster

institute: Institute of Neuropathology

description: Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain

data_processing: GeneData Expressionist raw data

source_name: SHEP-SF neuroblastoma

tag: induction of AICD


title: iFA50clone8-

tag: induction of AICD and Fe65


title: ORNL 5wk Hr(n) mice skin array 4

status: Public on Apr 18 2006

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

description: Dye coupling and hybridization was done according to the standard protocols from TIGR.

data_processing: Data has been nomalized with Lowess after flooring, omitting low expression, removing flagged spots

source_name: Heterozygous mutant

tag: Total RNA is extracted from dorsal skin of 5 week-old heterozygous Hr(n) mutant mice

source_name: wild type mice

tag: Total RNA is extracted from dorsal skin of 5 week-old wild type mice


title: ORNL 5wk Hr(n) mice skin array 3


title: ORNL 5wk Hr(n) mice skin array 6


title: ORNL 5wk Hr(n) mice skin array 5


title: ORNL 5wk Hr(n) mice skin array 7


title: iFA50clone8+

tag: suppressed induction of AICD and Fe65


title: iA50clone9+

source_name: SHEP-SF neuroblastom

tag: suppressed induction of AICD


title: Non -Transgenic replicate 7

description: mouse fully-grown (GV) oocytes

tag: mouse B6xCF-1  Non-transgenic (control-3)


title: ORNL 5wk Hr(n) mice skin array 2


title: iA50clone6+

description: Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain (AICD)

data_processing: GeneData Expressionist


title: iA50clone9-


title: Hr(Rh-R) mouse cutaneous array 4

source_name: sample

tag: The total RNA was extracted from the skin of Hr(Rh-R)/Hr(Rh-R) mice at 10 days of age.

source_name: control

tag: The total RNA was extracted from the skin of Hr(Rh-R)/+ mice at 10 days of age.


title: Hr(Rh-R) mouse cutaneous array 2

tag: The total RNA was extracted from the skin of Hr(Rh-R)/Hr(Rh-R) mice at 10 days of age


title: Hr(Rh-R) mouse cutaneous array 6


title: Hr(Rh-R) mouse cutaneous array 3


title: Hr(Rh-R) mouse cutaneous array 5


title: Hr(Rh-R) mouse cutaneous array 1


title: ORNL 5wk Hr(n) mice skin array 1


title: DMSO-treated, Sham UV, Replicate A

source_name: dorsal mouse skin

tag: DMSO-treated, sham UV exposed


title: Near naked hairless mice skin array 5

source_name: Sample

tag: This is the channel used skin RNA from homozygous near naked mutant mice at 7 days of age.

tag: This is the channel used skin RNA from wild-type mice at 7 days of age.


title: Near naked hairless mice skin array 8


title: PC xenograft PC339 after castration replicate_1

status: Public on Apr 01 2006

city: Wageningen

first: Peter

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

country: Netherlands

institute: Wageningen University & Research

description: The prostate cancer xenografts have been described by van Weerden and Romijn (Prostate 2000; 43:263-271). The xenografts were serially passaged subcutaneously in both shoulders of male Swiss nude mice.

data_processing: Normalization was performed using R-routines (Lowess method; http://cmfdb.nki.nl/). All spots with an R-value below 3 or with an average intensity less than 0.4 of the median spot intensity per subarray were considered to be insufficiently reliable and were excluded from the data analysis.

source_name: xenograft

tag: Androgen-independent xenograft, without expression of a functional androgen receptor, 7 days after castration of male host mouse.

source_name: common reference of 13 cell lines

tag: 13 cell lines that originated from prostate cancer (Du145 and LNCaP), breast (MCF7 and ZR75.1), bone (MG63), colon (HT29), endothelium (Ea-hy926), ovary (A2780), skin (SK-MEL-28), B-cell leukemia (Raji), T-cell lymphoblastoma (Jurkat) and fibroblasts (N92-19N and N92-19T).


title: PC xenograft PC324 replicate_1

tag: Androgen-independent xenograft, without expression of a functional androgen receptor, on intact mouse.


title: PC xenograft PC339 replicate_1


title: Near naked hairless mice skin array 3

source_name: Control


title: Near naked hairless mice skin array 2

tag: This is the channel used skin RNA from homozygous near naked mutant mice at 7 days of age

tag: This is the channel used skin RNA from wild-type mice at 7 days of age


title: PC xenograft PC135 after castration replicate_2

tag: Androgen-independent xenograft, without expression of a functional androgen receptor, 14 days after castration of male host mouse.


title: PC xenograft PC339 after castration replicate_2


title: Near naked hairless mice skin array 6


title: Near naked hairless mice skin array 4


title: Near naked hairless mice skin array 7


title: PC xenograft PC324 after castration replicate_2

tag: Androgen-independent xenograft, without expression of a functional androgen receptor, 10 days after castration of male host mouse.


title: PC xenograft PC135 replicate_2


title: PC xenograft PC135 after castration replicate_1


title: PC xenograft PC339 replicate_2


title: PC xenograft PC324 replicate_2


title: PC xenograft PC133 replicate_2


title: Near naked hairless mice skin array 1


title: RNAi -Transgenic replicate 13

description: mouse fully-grown (GV) oocytes

tag: mouse B6xCF-1 RNAi transgenic


title: PC xenograft PC324 after castration replicate_1


title: PC xenograft PC133 after castration replicate_1


title: Mouse sarcoma replicate 1

description: mouse sarcoma that developed spontaneously on an intact mouse. This was used as a control for contamination of the human xenografts with mouse stromal cells.

source_name: mouse sarcoma


title: PC xenograft PC133 after castration replicate_2

tag: Androgen-independent xenograft, without expression of a functional androgen receptor, 15 days after castration of male host mouse.


title: RNAi -Transgenic replicate 4

description: mouse fully-grown (GV) oocytes

tag: mouse B6xCF-1  RNAi transgenic


title: PC xenograft PC374 after castration replicate_2

tag: Androgen-independent xenograft, androgen receptor expressing, 9 days after castration of male host mouse.


title: PC xenograft PC135 replicate_1


title: Mouse sarcoma replicate 2

tag: mouse sarcoma that developed spontaneously on an intact mouse. This was used as a control for contamination of the human xenografts with mouse stromal cells.


title: PC xenograft PC133 replicate_1


title: PC xenograft PC374 replicate_2

tag: Androgen-independent xenograft, androgen receptor expressing, on intact mouse.


title: PC xenograft PC346B after castration replicate_2

tag: Androgen-independent xenograft, androgen receptor expressing, 6 days after castration of male host mouse.


title: PC xenograft PC346 after castration replicate_1

tag: Androgen-responsive xenograft, androgen receptor expressing, 10 days after castration of male host mouse.


title: PC xenograft PC374 after castration replicate_1

tag: Androgen-independent xenograft, androgen receptor expressing, 8 days after castration of male host mouse.


title: PC xenograft PC346B replicate_1


title: PC xenograft PC346B after castration replicate_1

tag: Androgen-independent xenograft, androgen receptor expressing, 13 days after castration of male host mouse.


title: PC xenograft PC374 replicate_1


title: PC xenograft PC346I after castration replicate_2


title: PC xenograft PC310 after castration replicate_1

tag: Androgen-dependent xenograft, androgen receptor expressing, 12 days after castration of male host mouse.


title: PC xenograft PC329 replicate_1

tag: Androgen-dependent xenograft, androgen receptor expressing, on intact mouse.

tag: 13 cell lines that originated from prostate cancer (Du145 and LNCaP), breast (MCF7 and ZR75.1), bone (MG63), colon (HT29), endothelium (Ea-hy926), ovary (A2780), skin (SK-MEL-28), B-cell leukemia (Raji), T-cell lymphoblastoma (Jurkat) and fibroblasts (N92-19N and N92-19T).


title: PC xenograft PC310 after castration replicate_2

tag: Androgen-dependent xenograft, androgen receptor expressing, 14 days after castration of male host mouse.


title: PC xenograft PC346BI replicate_1


title: PC xenograft PC346BI replicate_2


title: PC xenograft PC346 replicate_2

tag: Androgen-responsive xenograft, androgen receptor expressing, on intact mouse.


title: PC xenograft PC346 replicate_1


title: PC xenograft PC346BI after castration replicate_1

tag: Androgen-independent xenograft, androgen receptor expressing, 15 days after castration of male host mouse.


title: PC xenograft PC346I replicate_2


title: PC xenograft PC346I after castration replicate_1


title: PC xenograft PC310 replicate_1


title: PC xenograft PC346B replicate_2


title: PC xenograft PC346 after castration replicate_2

tag: Androgen-responsive xenograft, androgen receptor expressing, 6 days after castration of male host mouse.


title: PC xenograft PC295 after castration replicate_1

tag: Androgen-dependent xenograft, androgen receptor expressing, 9 days after castration of male host mouse.


title: PC xenograft PC82 replicate_2


title: PC xenograft PC295 after castration replicate_2

tag: Androgen-dependent xenograft, androgen receptor expressing, 6 days after castration of male host mouse.


title: PC xenograft PC295 replicate_1


title: PC xenograft PC82 after castration replicate_2


title: PC xenograft PC295 replicate_2


title: PC xenograft PC310 replicate_2


title: PC xenograft PC329 replicate_2


title: PC xenograft PC346I replicate_1


title: PC xenograft PC346BI after castration replicate_2


title: LNCaP_8h_R1881_rep1

description: The LNCaP cell line was maintained in RPMI media with 10% fetal calf serum and penicillin/streptomycin. Before R1881 treatment, cells were androgen-deprived by culture for 72 h in medium containing 10% dextran-filtered, charcoal-stripped fetal calf serum with a medium replacement after 36 h. After androgen deprivation, the medium was supplemented with R1881 to a final concentration of 1 nM. R1881 was dissolved in ethanol. The final concentration of ethanol in the media was 0.1%. In the control, ethanol was added to the same final concentration.

hyb_protocol: The probe was heated for 2 min at 95 °C, mixed with 72 µl hybridization buffer no. 1 from Ambion and applied on the cDNA microarray. Hybridization was performed o/n at 45 °C.

scan_protocol: After hybridization, the microarrays were washed and scanned (ScanArray Express HT, PerkinElmer, Boston, MA). Fluorescence intensities on scanned images were quantified using Imagene 5.1 (BioDiscovery, Marina del Rey, CA).

source_name: LNCaP 8h ethanol

tag: Prostate cancer cell line LNCaP treated for 8 h with 0.1% ethanol (carrier control).

source_name: LNCaP 8h +R1881

tag: Prostate cancer cell line LNCaP treated for 8 h with R1881.


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 3 - Slide 4/4

status: Public on Mar 17 2006

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

institute: University of Amsterdam

description: Amplified mRNA from fractionated polysomes (membrane-bound or free) was labeled with CyDye and applied to the array.

data_processing: Printtip LOESS & Scaling between arrays (median absolute deviation). VALUE represents log2(channel 1/channel 2).

molecule: other

organism: Arabidopsis thaliana

source_name: Membrane-bound polysomes (MBP)

tag: Aboveground parts of two weeks old seedlings (Col-0)

source_name: Free polysomes (FP)


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 3 - Slide 3/4


title: bhh treated 2

status: Public on Mar 31 2006

city: New York

first: Curtis

middle: R

last: Altmann

state: NY

address: 599 Lexington Avenue

institute: Goodwin Procter LLP

description: St 24 bhh treated pronephric explants

data_processing: Affymetrix Microarray Suite version 5.0

organism: Xenopus laevis

source_name: pronephric explant

label_protocol: 1 µg of total RNA was processed using MessageAmp™ aRNA Amplification Kit (AMBION) to produce biotinylated cRNA targets.

extract_protocol: Pronephric region explants were prepared from stage 24 embryos using a gastromaster (Xenotek) with the tip set to a width of 70 microns. Rectangular explants, approximately 70 microns (dorsal to ventral) x 100 microns (anteriorposterior) and 70 microns (laterally) were cut from the flanks of both sides of embryos. 300 explants were extracted with Trizol (Gibco)

tag: Wild type, Stage 24 pronephric explant


title: Untreated 3

description: St 24 untreated pronephric explants


title: bhh treated 1

description: St 24 bhh treated pronephric explants


title: LNCaP_2h_R1881_rep2

source_name: LNCaP 2h -R1881

treatment_protocol: Total RNA was isolated with RNAzolB. Three µg of RNA was used for a T7 based linear mRNA amplification protocol as described before. After first and second strand cDNA synthesis, RNA was amplified using the T7 Megascript kit (Ambion Inc., Austin, TX) for 6 h at 37 °C according to manufacturer’s instructions. RNAs were purified using RNeasy columns (Qiagen).

tag: Prostate cancer cell line LNCaP treated for 2 h with 0.1% ethanol (carrier control).

source_name: LNCaP 2h +R1881

tag: Prostate cancer cell line LNCaP treated for 2 h with R1881


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 2 - Slide 3/4


title: LNCaP_8h_R1881_rep2


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 1 - Slide 4/4


title: LNCaP_2h_R1881_rep1

treatment_protocol:
Total RNA was isolated with RNAzolB. Three µg of RNA was used for a T7 based linear mRNA amplification protocol as described before. After first and second strand cDNA synthesis, RNA was amplified using the T7 Megascript kit (Ambion Inc., Austin, TX) for 6 h at 37 °C according to manufacturer’s instructions. RNAs were purified using RNeasy columns (Qiagen).
Two micrograms of amplified RNA were used to produce Cy3- or Cy5-labeled cDNA. The reaction mix of 30 µl further contained 10 mM dithiothreitol, 0.5 mM of dATP, dGTP, dTTP, 0.05 mM dCTP, 0.1 mM of either Cy3-dCTP or Cy5-dCTP (final concentrations), 3 µg of random hexamers (Amersham Biosciences, Roosendaal, The Netherlands), 6 µl first strand buffer (5x), 40 u ribonuclease inhibitor and 200 U Superscript II reverse transcriptase. The cDNA synthesis was performed for 2 h at 42 °C, followed by 5 min at 70 °C. Samples to be co-hybridized on the same arrays were pooled and first purified on a PCR clean up column (Qiagen) and then concentrated to approximately 5 µl on a YM-30 microcon column (Millipore Corporation, Bedford, MA).

tag: Prostate cancer cell line LNCaP treated for 2 h with R1881.

source_name: LNCaP 2h ethanol


title: PC xenograft PC82 after castration replicate_1

tag: Androgen-dependent xenograft, androgen receptor expressing, 15 days after castration of male host mouse.


title: bhh treated 3

description: St 24 bhh treated pronephric explants


title: LNCaP_4h_R1881_rep2

source_name: LNCaP 4h ethanol

tag: Prostate cancer cell line LNCaP treated for 4 h with 0.1% ethanol (carrier control).

source_name: LNCaP 4h +R1881

tag: Prostate cancer cell line LNCaP treated for 4 h with R1881.


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 2 - Slide 4/4


title: LNCaP_6h_R1881_rep2

source_name: LNCaP 6h +R1881

tag: Prostate cancer cell line LNCaP treated for 6 h with R1881.

source_name: LNCaP 6h ethanol

tag: Prostate cancer cell line LNCaP treated for 6 h with 0.1% ethanol (carrier control).


title: LNCaP_6h_R1881_rep1


title: LNCaP_4h_R1881_rep1

description: The LNCaP cell line was maintained in RPMI media with 10% fetal calf serum and penicillin/streptomycin. Before R1881 treatment, cells were androgen-deprived by culture for 72 h in medium containing 10% dextran-filtered, charcoal-stripped fetal calf serum with a medium replacement after 36 h. After androgen deprivation, the medium was supplemented with R1881 to a final concentration of 1 nM. R1881 was dissolved in ethanol. The final concentration of ethanol in the media was 0.1%. In the control, ethanol was added to the same final concentration


title: Untreated 2

description: St 24 untreated pronephric explants


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 3 - Slide 2/4


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 1 - Slide 2/4


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 1 - Slide 3/4


title: PC xenograft PC82 replicate_1

tag: Androgen-dependent xenograft, androgen receptor expressing, on intact mouse.

tag: 13 cell lines that originated from prostate cancer (Du145 and LNCaP), breast (MCF7 and ZR75.1), bone (MG63), colon (HT29), endothelium (Ea-hy926), ovary (A2780), skin (SK-MEL-28), B-cell leukemia (Raji), T-cell lymphoblastoma (Jurkat) and fibroblasts (N92-19N and N92-19T).


title: Untreated 1

description: St 24 untreated pronephric explants


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 2 - Slide 2/4

source_name: Membrane-bound polysomes


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 1 - Slide 1/4

tag: Aboveground parts of two weeks old seedlings  (Col-0)


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 3 - Slide 1/4


title: M8-Cy5_2

status: Public on Mar 01 2006

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process. Quality Controls of IVT transcription: Double stranded cDNA (ds-cDNA) and amplified RNA (aRNA) products were analyzed for purity and concentration by UV spectrophotometry, using the Ultrospec3100 pro and 5-mm cuvettes (GE Healthcare, USA). The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Three metrics were considered based on the A260 measurement. First, efficiency of the reverse transcription (ds-cDNA quantity/total RNA quantity) and IVT (aRNA quantity/ds-cDNA quantity) reaction efficiencies were computed. The yield of amplification was quantified (aRNA quantity/mRNA quantity), with the assumption that total RNA contains 2% of mRNA. Finally, an aliquot (1 µl) of the IVT reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol. An mRNA nano assay was run on the chip, and the size of the aRNA was compared with the molecular weight markers. On one hand, ds-cDNA product with unsatisfactory reverse transcription reaction efficiency (RT ≤ 0.4) and purity (A260:A280 ratios ≤ 1.6) were removed from the IVT reaction pipeline. On the other hand, aRNA products with unsatisfactory yield of amplification (amplification < 1,000) and integrity (mean size < 1,000 nucleotides) were removed from subsequent analyses. Only samples that reached the expected purity and integrity parameters described above were introduced within the microarray labeling and hybridization pipelines. Quality Controls of Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

hyb_protocol: A mixture of equimolar aliquots (20 pmol) of each labeled target (DATA and REF) was incubated at 95°C for 4 min in the presence of 1.5 µg Oligo-A80 (Eurogentec, USA) and 1 µg human Cot-I DNA® (Invitrogen, USA). Fragmented labeled cDNA was then placed onto 11K_VJF-ARRAY slides in a 30 µl hybridization solution (50% formamide, GE Healthcare, USA) and covered by a coverslip. The slides were subsequently hybridized in a humid hybridization cabinet (GE Healthcare, USA) for 16 hr at 42°C. Then the hybridized slides were washed in 1xSSC, 0.2% SDS for 10 min at 55°C, twice in 0.1x SSC, 0.2% SDS for 10 min at 55°C and twice in 0.1x SSC for 1 min at room temperature.

scan_protocol: After washing and drying, the arrays were scanned at 532 nm (PMT 600 V) and 635 nm (PMT 650 V) using a 3rd generation array scanner (GE Healthcare, USA) and independent grayscale images (8 bits, Tiff) were generated for each pair of samples to be compared.

data_processing: Foreground (raw) data - ARMDens - were local background-subtracted (corners between spots - median value) and normalized using a Lowess (locally weighted linear regression) transformation. The following selection criteria were applied: all spots having a mean signal (after background subtraction) less than that of the background and below that of the negative controls in both Cy3 and Cy5 channels were systematically excluded; the data were also filtered to exclude spots flagged as missing or corrupted in one array. We next calculated the expression ratios (DATA/REF) in all analyses; the provided VALUE corresponds to the log, base 2 ratios. Replicate spots on the array (n=2) are considered separately.

label_protocol: Linear Amplification: One-round of RNA amplification was performed on total RNA as described in [Van Gelder et al., 1990; Eberwine et al., 1992] with some modifications. Amplified RNA products were air dried, resuspended in 10µl RNase-free water and then stored at -80°C; 1 µl of the reaction (1/10) was stored to perform quality assessment (Purity, size, yield). Labeling protocol: Targets were synthesized using 1.0 µg amplified RNA, 1 µl anchored oligo-(dT) and 2 µl random nonamers (GE Healthcare, USA) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield). Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled aRNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration.

extract_protocol: see Provider description

tag: Universal Reference RNA

extract_protocol: Frozen tissue samples specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure, including an additional treatment step to remove residual DNA contamination with 30 units RNase-free DNase I.

tag: Patient

tag: Gender

value: female;

tag: Age at onset

value: 68 years;

tag: Disease

value: Advanced colorectal (CRC) cancer;

tag: Tumor stage

value: stade IV (UICC);

tag: Tissue

value: liver metastasis;

tag: Response status of the patient

value: Sensitive (S)


title: Membrane-bound polysomes (MBP) versus free polysomes (FP) - Fractionation 2 - Slide 1/4

tag: Aboveground parts of two weeks old seedlings (Col-0)


title: T7-Cy5

value: male;

value: 65 years;

value: tumor colon;

value: Resistant (R)


title: T10-Cy5

value: 50 years;


title: T13-2-Cy5

value: 71 years;

value: tumor colon, 2nd biopsy;


title: N13-Cy5

value: adjacent non tumoral colon;


title: T8-Cy5


title: N9-Cy5

value: 60 years;


title: N1-Cy5

value: 61 years;


title: N3-Cy5


title: N12-Cy5

value: 62 years;


title: T13-1-Cy5

value: tumor colon, 1st biopsy;


title: M5a-Cy5_2

value: 48 years;

value: liver metastasis, 1st biopsy;


title: T12-Cy5

value: Advanced colorectal (CRC) cancer;

value: stade IV (UICC);


title: M8-Cy5_1

value: female;

value: 68 years;

value: liver metastasis;

value: Sensitive (S)


title: T3-Cy5

value: tumor colon;


title: M7-Cy5

value: male;

value: 65 years;

value: Resistant (R)


title: M5b-Cy5_1

value: liver metastasis, 2nd biopsy;


title: M6-Cy5

value: 49 years;


title: M5b-Cy5_2


title: M4-Cy5

value: 53 years;


title: N8-Cy5

value: adjacent non tumoral colon;


title: M9-Cy5

value: 60 years;


title: M11-2-Cy5

value: 67 years;


title: M1-Cy5

value: 61 years;


title: T9-Cy5

value: Advanced colorectal (CRC) cancer;


title: M5a-Cy5_1

value: 48 years;

value: stade IV (UICC);

value: liver metastasis, 1st biopsy;


title: T3-Cy3

value: female;

value: 68 years;


title: M10-Cy5

value: 50 years;

value: liver metastasis;

value: Sensitive (S)


title: M12-Cy5

value: male;

value: 62 years;

value: Resistant (R)


title: T13-2-Cy3

value: 71 years;

value: tumor colon, 2nd biopsy;


title: N9-Cy3

value: 60 years;

value: adjacent non tumoral colon;

tag: Universal reference RNA


title: T6-Cy5

value: 49 years;

value: tumor colon;


title: T6-Cy3

value: Advanced colorectal (CRC) cancer;


title: M11-1-Cy5

value: 67 years;

value: stade IV (UICC);


title: T9-CY3


title: T12-Cy3


title: T10-Cy3

value: female;


title: N8-Cy3

value: 68 years;


title: N12-Cy3


title: N1-Cy3

value: 61 years;


title: M9-Cy3

value: liver metastasis;


title: T7-Cy3

value: 65 years;


title: N3-Cy3

value: Sensitive (S)


title: N13-Cy3

value: male;


title: T8-Cy3


title: M2-Cy5

value: Resistant (R)


title: M7-Cy3


title: M5b-Cy3_1

value: 48 years;

value: liver metastasis, 2nd biopsy;


title: M6-Cy3


title: M8-Cy3


title: M5b-Cy3_2


title: T13-1-Cy3

value: 71 years;

value: tumor colon, 1st biopsy;


title: M4-Cy3

value: 53 years;

value: Resistant(R)


title: M5a-Cy3

value: Advanced colorectal (CRC) cancer;

value: liver metastasis, 1st biopsy;


title: M2-Cy3

value: stade IV (UICC);


title: M11-1-Cy3

data_processing: Foreground (raw) data - ARMDens - were local background-subtracted (corners between spots - median value) and normalized using a Lowess (locally weighted linear regression) transformation. The following selection criteria were applied: all spots having a mean signal (after background subtraction) less than that of the background and below that of the negative controls in both Cy3 and Cy5 channels were systematically excluded; the data were also filtered to exclude spots flagged as missing or corrupted in one array. We next calculated the expression ratios (DATA/REF) in all analyses; the provided VALUE corresponds to the log, base 2 ratios. Replicate spots on the array (n=2) are considered separately

value: 67 years;

value: liver metastasis, 1st biospy;


title: M1-Cy3

value: female;

value: 61 years;


title: M11-2-Cy3


title: M10-Cy3

description:
Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process.

Quality Controls of IVT transcription: Double stranded cDNA (ds-cDNA) and amplified RNA (aRNA) products were analyzed for purity and concentration by UV spectrophotometry, using the Ultrospec3100 pro and 5-mm cuvettes (GE Healthcare, USA). The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Three metrics were considered based on the A260 measurement. First, efficiency of the reverse transcription (ds-cDNA quantity/total RNA quantity) and IVT (aRNA quantity/ds-cDNA quantity) reaction efficiencies were computed. The yield of amplification was quantified (aRNA quantity/mRNA quantity), with the assumption that total RNA contains 2% of mRNA. Finally, an aliquot (1 µl) of the IVT reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol. An mRNA nano assay was run on the chip, and the size of the aRNA was compared with the molecular weight markers.
On one hand, ds-cDNA product with unsatisfactory reverse transcription reaction efficiency (RT ≤ 0.4) and purity (A260:A280 ratios ≤ 1.6) were removed from the IVT reaction pipeline. On the other hand, aRNA products with unsatisfactory yield of amplification (amplification < 1,000) and integrity (mean size < 1,000 nucleotides) were removed from subsequent analyses. Only samples that reached the expected purity and integrity parameters described above were introduced within the microarray labeling and hybridization pipelines.

Quality Controls of Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

label_protocol:
Linear Amplification: One-round of RNA amplification was performed on total RNA as described in [Van Gelder et al., PNAS, 1990; Eberwine et al., PNAS, 1992] with some modifications. Amplified RNA products were air dried, resuspended in 10µl RNase-free water and then stored at -80°C; 1 µl of the reaction (1/10) was stored to perform quality assessment (Purity, size, yield).
Labeling protocol: Targets were synthesized using 1.0 µg amplified RNA, 1 µl anchored oligo-(dT) and 2 µl random nonamers (GE Healthcare, USA) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield).
Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled aRNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration.

value: 50 years;

value: liver metastasis;


title: Patient5 before agaricus treatment

status: Public on Feb 20 2006

city: Oslo

first: Bjorn

last: Grinde

state: Oslo

address: Geitmyrsveien 75

department: Infectious Disease Control

country: Norway

institute: Norwegian Institute of Public Health

description: Part of experiment to find systemic effects of oral administration of agaricus extract

data_processing: Using J-Express: Controls and flagged spots filtered away, reporters with same probe merged, reporters with signal to noise < 3 removed, intensities of the different arrays normalized using the Quantile Normalize All Arrays function

label: Applied Biosystems Expression Array System

source_name: PAX-tube blood

tag: From patient with chronic hepatitis C


title: Patient2 before agaricus treatment


title: Patient4 after agaricus treatment


title: Patient2 after agaricus treatment


title: Patient3 before agaricus treatment


title: Patient5 after agaricus treatment


title: M12-Cy3

value: male;

value: 62 years;


title: Patient4 before agaricus treatment


title: Ad infected murine liver-MO30k-(232)-6hpi

status: Public on Feb 15 2006

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Sample is C3KO murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

hyb_protocol: Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

data_processing: VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.

source_name: Cy5 labeled Liver RNA

label_protocol: The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols

extract_protocol: RNA isolation was accomplished by homogenizing liver in liquid nitrogen, then extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was purified using an RNeasy Kit (Qiagen) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: C57/BL6 C3KO murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.

source_name: Murine Reference RNA

tag: Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.


title: Ad infected murine liver-MO30k-(230)-6hpi

description: Sample is C57/Bl6 C3KO liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

tag: C57/BL6 C3KO murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock).


title: Ad infected murine liver-MO30k-(231)-6hpi


title: Ad infected murine liver-MO30k-(228)-6hpi


title: Ad infected murine liver-MO30k-(229)-6hpi


title: H4del(2-26) CSM rep3

status: Public on Feb 10 2006

city: Albany

first: Randall

middle: Heywood

last: Morse

institute: Wadsworth Center

description: H4del(2-26) yeast grown in CSM

hyb_protocol: Per Affy instructions

data_processing: MAS 5.1

label: phycoerythrin

organism: Saccharomyces cerevisiae

source_name: H4del(2-26) yeast grown in CSM

label_protocol: Ambion kit

growth_protocol: Grown to mid-log in complete synthetic medium lacking tryptophan and uracil

extract_protocol: Masterpure RNA purification kit from Epicenter Technology

tag: Strain NSY438


title: Mock infected murine liver-MO30k-(275)-6hpi

description: Sample is C57/Bl6 C3KO murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.


title: Mock infected murine liver-MO30k-(272)-6hpi


title: H4 wild type CSM rep3

description: H4 wild type strain grown in CSM

source_name: H4 wild type strain grown in CSM

tag: Strain NSY429


title: H4 wild type CSM rep1

description: H4 wild type strain grown in CSM


title: H4del(2-26) CSM rep1

description: H4del(2-26) yeast grown in CSM


title: H4 wild type CSM rep2

description: H4 wild type strain grown in CSM


title: Patient3 after agaricus treatment


title: H4del(2-26) CSM rep2

description: H4del(2-26) yeast grown in CSM


title: H3 wild type CSM rep3

description: H3 wild type grown in CSM

source_name: H3 wild type grown in CSM

growth_protocol: Grown to mid-log in complete synthetic medium lacking leucine and uracil

tag: Strain CY1-4C


title: H3 wild type CSM rep4

description: H3 wild type grown in CSM


title: Mock infected murine liver-MO30k-(211)-6hpi


title: Mock infected murine liver-MO30k-(210)-6hpi


title: Mock infected murine liver-MO30k-(209)-6hpi


title: Mock infected murine liver-MO30k-(270)-6hpi


title: H3del(1-28)_CSM_rep4

description: H3 tail mutant grown in CSM

source_name: H3 tail mutant grown in CSM

extract_protocol: Yeast Masterpure RNA purification kit from Epicenter Technology

tag: Strain CY2-4C


title: Ad infected murine liver-MO30k-(233)-6hpi


title: H3del(1-28)_CSM_rep2

description: H3 tail deletion mutant grown in CSM

source_name: H3 tail deletion mutant grown in CSM


title: H3 wild type CSM rep1

description: H3 wild type grown in CSM


title: H3del(1-28)_CSM_rep3

description: H3 tail mutant grown in CSM


title: H3 wild type CSM rep2

description: H3 wild type grown in CSM


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 2

status: Public on Feb 03 2006

type: genomic

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

description: Chromatin immunoprecipitated DNA (Cy5) was co-hybridized with total genomic DNA (Cy3). The ratio between Cy5 and Cy3 signal was calculated for all high quality features.

data_processing: The acquired microarray image was analyzed with GenePix Pro 6.0 software. After excluding the spots flagged for bad quality, signal ratios were log2 transformed and normalized using intensity-dependent normalization.

source_name: MCF7 cells_Immunoprecipitated

tag: MCF7 cells, anti-diMeH3K9-immunoprecipitated DNA

source_name: MCF7 cells_Input

tag: MCF7 cells, total input DNA


title: H3del(1-28)_CSM_rep1

description: H3 tail deletion mutant grown in CSM

extract_protocol: Yeast Masterpure RNA Purification Kit (Epicenter Technology)

tag: Strain CY2-4C grown in complete synthetic medium lacking leucine and uracil


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 2

tag: MCF7 cells, anti-AcH3K9-immunoprecipitated DNA


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with diMe-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with ERa antibody, replicate 2

tag: MCF7 cells, anti-ERa-immunoprecipitated DNA


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with ERa antibody, replicate 1


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with ERa antibody, replicate 1


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with ERa antibody, replicate 2


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 0hr, immunoprecipitated with ERa antibody, replicate 2


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with ERa antibody, replicate 1


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 1


title: MCF7 cells treated with estradiol for 12hr, immunoprecipitated with ERa antibody, replicate 1


title: MCF7 cells treated with estradiol for 3hr, immunoprecipitated with Ac-H3-K9 antibody, replicate 2


title: MCF7 cells treated with estradiol for 24hr, immunoprecipitated with ERa antibody, replicate 2


title: HW_437

status: Public on Feb 01 2006

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

description: trained wt animal for the identification of genotype specific training induced gene expression response

hyb_protocol: 15 ug of each cRNA sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Microarray Suite Version 5.0 software (Affymetrix).

label: biotin labeled

source_name: trained wt

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality was checked by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL Biol, Berlin, Germany) one to three micrograms of total RNA were used for the synthesis of double-stranded cDNA (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix, Santa Clara, CA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment [40 mmol/L Tris-acetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate] at 94°C for 35 minutes.

growth_protocol: standard animal care

extract_protocol: TRIzol Reagent (Invitrogen), standard protocol

treatment_protocol: training: mice were put into a 30 x 50, 20 cm deep container filled with warm (35 C) water equipped with a floating rotating wheel. Swimming duration was continously increased from 5 minutes to 90 minutes daily (6 times per week) swimming. Mice were stimulated to swim as sonn as they began floating to maximize activity in the water.

tag: strain

tag: gender

value: male

tag: age

value: 6 months

tag: tissue

value: right ventricle

tag: genotype

value: wt


title: HW_436

description: trained plakoglobin (+/-) animal for the identification of genotype specific training induced gene expression response

source_name: trained plakoglobin (+/-)

value: plakoglobin (+/-)


title: HW_475

value: female


title: HW_450


title: 1hr Experiment 1

city: Evanston

first: Xijin

last: Ge

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute

description: Jurkat Cells are exposed to nanosecond pulsed electric fields (nsPEFs). Two consecutive 10 ns pulses at 280kV/cm are applied to the cells. Cells are collected for RNA extraction after 30 minutes and 60 minutes.

data_processing: Axon Acuity 3.0 analysis software. Median normalized.

source_name: 1hr Experiment 1, Jurkat Cells after nanosecond pulsed electric fields

tag: Jurkat Cells


title: 1hr Control 3

source_name: 1hr Control 3, Jurkat Cells after nanosecond pulsed electric fields


title: HW_449


title: 1hr Experiment 2

source_name: 1hr Experiment 2, Jurkat Cells after nanosecond pulsed electric fields


title: HW_1090

description: untrained plakoglobin (+/-) control animal for training induced gene expression response

source_name: untrained plakoglobin (+/-)

treatment_protocol: untrained

value: 10 months


title: HW_476

hyb_protocol: 15 ug of each cRNA sample was hybridized for 16 hours at 45°C to rat expression Affymetrix RAE 230A GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

data_processing: Microarray Suite Version 5.0 software (Affymetrix)

label: bioton labeled

treatment_protocol: training: mice were put into a 30 x 50, 20 cm deep container filled with warm water (35 C) equipped with a floating rotating wheel. Swimming duration was continously increased from 5 minutes to 90 minutes daily (6 times per week) swimming. Mice were stimulated to swim as soon as they began floating to maximize activity in the water.


title: 1hr Experiment 3

source_name: 1hr Experiment 3, Jurkat Cells after nanosecond pulsed electric fields


title: HW_453


title: HW_1089

description: untrained wt control animal for training induced gene expression response

source_name: untrained wt


title: 1hr Control 2

source_name: 1hr Control 2, Jurkat Cells after nanosecond pulsed electric fields


title: 30min Experiment 3

source_name: 30min Experiment 3, Jurkat Cells after nanosecond pulsed electric fields


title: Controlvs.treated_LAQ-824_5hrs_rep4

city: Research Triangle Park

middle: D.

last: Mattie

address: Five Moore Drive

department: Genomics Research

institute: GlaxoSmithKline

description: Quantitations are based on the images (ratios of median fluorescence intensity were the primary study measurements). Genepix 3.0 produces both feature and background intensity and ratio measurements for the Cy3 and Cy5 channels and notes if data are flagged by the analyst.

hyb_protocol: Briefly, 200 ng of enriched miRNA was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene).  Arrays were washed as follows:  Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge.  The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius.  Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius.

scan_protocol: Images were acquired using an Axon 4000b confocal laser scanner with Genepix 3.0 software (Axon, Foster City, CA).

data_processing: Only Genepix median ratios for non-flagged spots were used for the analysis.  Genepix data was uploaded to the NOMAD relational database (http://derisilab.ucsf.edu), median ratio information was downloaded after linear normalization of Cy3 and Cy5 signals (equal average intensity of each fluorescent channel).  Data were formatted for the Cluster (http://rana.lbl.gov) algorithm, which was used after log base 2 transformation of ratios, and filtering to exclude genes flagged in more than 20% of the arrays.

source_name: Untreated SKBr3 cells

label_protocol: Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc.

growth_protocol: Standard growth conditions.

extract_protocol: MicroRNA was isolated from the untreated SKBr3 cells using the mirVana microRNA isolation kit from Ambion

treatment_protocol: Control cells were not treated.

tag: Untreated SKBr3 breast cancer cell line

source_name: Treated SKBr3 cells

growth_protocol: Standard growth conditions

treatment_protocol: SKBr3 cells were treated with 20 uM LAQ-824 for 5 hours

tag: SKBr3 breast cancer cell line treated with LAQ-824, a histone deacetylase inhibitor


title: 1hr Control 1

source_name: 1hr Control 1, Jurkat Cells after nanosecond pulsed electric fields


title: Controlvs.treated_LAQ-824_5hrs_rep1

source_name: Control SKBr3 cells

source_name: LAQ-824 treated SKBr3 cells

label_protocol: MicroRNA was isolated from the treated SKBr3 cells using the mirVana microRNA isolation kit from Ambion


title: Controlvs.treated_LAQ-824_5hrs_rep3

hyb_protocol: Briefly, 200 ng of enriched miRNA was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene).  Arrays were washed as follows:  Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge.  The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius.  Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius. Images were acquired using an Axon 4000b confocal laser scanner with Genepix 3.0 software (Axon, Foster City, CA).


title: 30min Control 1

source_name: 30min Control 1, Jurkat Cells after nanosecond pulsed electric fields


title: M48_Rep3

status: Public on Jan 31 2006

city: Seattle

first: Renata

middle: Fava

last: Ditt

state: WA

address: Hitchcock Hall Box 355325

institute: University of Washington

description: Arabidopsis thaliana cell cultures sub-cultured every week. Agrobacterium- or mock-inoculated 3 days after sub-culture. Inoculated samples co-hybridized with reference RNA. Reference RNA: pool of RNA samples from mock-treated cell cultures.

data_processing: Lowess normalization (Cui et al., 2003) done in Matlab, analysis done with SAM (Tusher et al., 2001).

source_name: Mock-inoculated, 48h, replication 3

tag: Arabidopsis thaliana cell suspension culture, LER ecotype.

tag: Collected 48h after mock-inoculation.

source_name: Reference RNA

tag: Reference RNA.


title: 30min Control 2

source_name: 30min Control 2, Jurkat Cells after nanosecond pulsed electric fields


title: Controlvs.treated_LAQ-824_5hrs_rep2


title: 30min Experiment 1

source_name: 30min Experiment 1, Jurkat Cells after nanosecond pulsed electric fields


title: M48_Rep2

source_name: Mock-inoculated, 48h, replication 2


title: M04_Rep3

source_name: Mock-inoculated, 4h, replication 3

tag: Collected 4h after mock-inoculation.


title: HW_447

source_name: trained plakoglobin (+/-)


title: 30min Control 3

source_name: 30min Control 3, Jurkat Cells after nanosecond pulsed electric fields


title: 30min Experiment 2

source_name: 30min Experiment 2, Jurkat Cells after nanosecond pulsed electric fields


title: M24_Rep1

source_name: Mock-inoculated, 24h, replication 1

tag: Collected 24h after mock-inoculation.


title: M48_Rep1

source_name: Mock-inoculated, 48h, replication 1


title: M24_Rep2

source_name: Mock-inoculated, 24h, replication 2


title: M24_Rep4

source_name: Mock-inoculated, 24h, replication 4


title: M04_Rep4

source_name: Mock-inoculated, 4h, replication 4


title: M12_Rep4

source_name: Mock-inoculated, 12h, replication 4

tag: Collected 12h after mock-inoculation.


title: M12_Rep3

source_name: Mock-inoculated, 12h, replication 3


title: M12_Rep2

source_name: Mock-inoculated, 12h, replication 2


title: M04_Rep1

source_name: Mock-inoculated, 4h, replication 1


title: M04_Rep2

source_name: Mock-inoculated, 4h, replication 2

source_name: Reference RNA


title: M48_Rep4

source_name: Mock-inoculated, 48h, replication 4


title: A48_Rep4

source_name: Agrobacterium-inoculated, 48h, replication 4

tag: Collected 48h after inoculation with Agrobacterium tumefaciens strain A348.


title: A24_Rep4

source_name: Agrobacterium-inoculated, 24h, replication 4

tag: Collected 24h after inoculation with Agrobacterium tumefaciens strain A348.


title: A24_Rep3

source_name: Agrobacterium-inoculated, 24h, replication 3


title: M24_Rep3

source_name: Mock-inoculated, 24h, replication 3


title: A48_Rep2

source_name: Agrobacterium-inoculated, 48h, replication 2


title: A48_Rep1

source_name: Agrobacterium-inoculated, 48h, replication 1


title: A48_Rep3

source_name: Agrobacterium-inoculated, 48h, replication 3


title: S. cerevisiae WT +HU 2hr

status: Public on Jan 30 2006

first: Bonita

middle: J

last: Brewer

department: Genome Sciences

description: S. cerevisiae WT HM14-3a (MATa bar1 trp1-289 leu2-3,112 ura3-52::URA3 his6) cells

data_processing: Background subtracted median values from the two channels were used to calculate the ratio of Cy3:Cy5 as the raw ratio of ssDNA (S/G1) (in table below).  The raw ratio was then normalized by the total amount of ssDNA in both the G1 and S phase samples by slot blotting and hybridization experiments (Table 1 in GSE4099).  The raw normalized ratios of ssDNA for all genomic locations were then smoothed over a 4kb window by Fourier transformation (Table 2 in GSE4099).

source_name: WT G1 phase

label_protocol: Five micrograms of genomic DNA were digested with EcoRI for 3 hours at 37oC, followed by ethanol precipitation.  The DNA was then used as template for random primed labeling at 37oC for 2.5 hours.  The reaction contains 50 mM Tris-HCl, pH 6.8; 5 mM MgCl2; 10 mM -mercaptoethanol; 300 ug/ml random hexamers; 0.12 mM of each dATP, dCTP, and dGTP; 0.06 mM dTTP; 1 mM Tris-HCl, pH 8.0; 3 ul of Cy5-conjugated dUTP (Amersham) and 50 units of exonuclease deficient Klenow.  The labeling reaction was performed WITHOUT denaturing the template DNA. The labeled DNA was purified through a sephadex G50 column.

extract_protocol: genomic DNA extracted as described on http://fangman-brewer.genetics.washington.edu/DNA_prep.html

treatment_protocol: Log phase cells were arrested in G1 phase by 200 nM alpha factor until the unbudded cells reach over 95%

tag: ssDNA in WT G1 phase

source_name: WT +HU 2hr

label_protocol: Five micrograms of genomic DNA were digested with EcoRI for 3 hours at 37oC, followed by ethanol precipitation.  The DNA was then used as template for random primed labeling.  The reaction contains 50 mM Tris-HCl, pH 6.8; 5 mM MgCl2; 10 mM -mercaptoethanol; 300 ug/ml random hexamers; 0.12 mM of each dATP, dCTP, and dGTP; 0.06 mM dTTP; 1 mM Tris-HCl, pH 8.0; 3 ul of Cy3-conjugated dUTP (Amersham) and 50 units of exonuclease deficient Klenow.  The labeling reaction was performed WITHOUT denaturing the template DNA.  The labeled DNA was purified through a sephadex G50 column.

treatment_protocol: Alpha factor arrested cells were released by addition of pronase  at 0.02 mg/ml into media containing 200 mM HU.  Cells were collected at 1hr post release.

tag: ssDNA in WT +HU 2hr S phase


title: M12_Rep1

source_name: Mock-inoculated, 12h, replication 1


title: A24_Rep2

source_name: Agrobacterium-inoculated, 24h, replication 2


title: S. cerevisiae rad53 +HU 2hr

description: S. cerevisiae rad53 in HM14-3a background (MATa bar1 trp1-289 leu2-3,112 ura3-52::URA3 his6 RAD53::rad53K227A(KanMX4)) cells

source_name: rad53 G1 phase

tag: ssDNA in rad53 G1 phase

source_name: rad53 +HU 2hr

tag: ssDNA in rad53 +HU 2hr S phase


title: A12_Rep2

source_name: Agrobacterium-inoculated, 12h, replication 2

tag: Collected 12h after inoculation with Agrobacterium tumefaciens strain A348.


title: A24_Rep1

source_name: Agrobacterium-inoculated, 24h, replication 1


title: A04_Rep3

description:
Arabidopsis thaliana cell cultures sub-cultured every week. Agrobacterium- or mock-inoculated 3 days after sub-culture.
Inoculated samples co-hybridized with reference RNA.
Reference RNA: pool of RNA samples from mock-treated cell cultures.

source_name: Agrobacterium-inoculated, 4h, replication 3

tag: Collected 4h after inoculation with Agrobacterium tumefaciens strain A348.

source_name: Reference RNA


title: S. cerevisiae rad53 +HU 1hr

source_name: rad53 +HU 1hr

tag: ssDNA in rad53 +HU 1hr S phase


title: S. cerevisiae rad53 +HU 30min

source_name: rad53 +HU 30min

tag: ssDNA in rad53 +HU 30min S phase


title: A12_Rep3

source_name: Agrobacterium-inoculated, 12h, replication 3


title: S. cerevisiae WT +HU 1hr

source_name: WT +HU 1hr

tag: ssDNA in WT +HU 1hr S phase


title: S. cerevisiae WT +HU 3hr

source_name: WT +HU 3hr

tag: ssDNA in WT +HU 3hr S phase


title: A04_Rep4

description:
Arabidopsis thaliana cell cultures sub-cultured every week. Agrobacterium- or mock-inoculated 3 days after sub-culture. Inoculated samples co-hybridized with reference RNA.
Reference RNA: pool of RNA samples from mock-treated cell cultures.

source_name: Agrobacterium-inoculated, 4h, replication 4

tag: Arabidopsis thaliana cell suspension culture, LER ecotype.


title: S. cerevisiae WT +HU 30min

source_name: WT +HU 30min

tag: ssDNA in WT +HU 30min S phase


title: S. cerevisiae rad53 +HU 3hr

description: Saccharomyces cerevisiae rad53 in HM14-3a background (MATa bar1 trp1-289 leu2-3,112 ura3-52::URA3 his6 RAD53::rad53K227A(KanMX4)) cells

source_name: rad53 +HU 3hr

tag: ssDNA in rad53 +HU 3hr S phase


title: A12_Rep1

source_name: Agrobacterium-inoculated, 12h, replication 1

tag: Reference RNA.


title: A12_Rep4

source_name: Agrobacterium-inoculated, 12h, replication 4


title: A04_Rep2

source_name: Agrobacterium-inoculated, 4h, replication 2


title: S. pombe cds1delta

description: S. pombe cds1delta cells (h-)

data_processing: Background subtracted median values from the two channels were used to calculate the ratio of Cy3:Cy5 as the raw ratio of ssDNA (S/G1) (in table below).  The raw ratio was then normalized by the total amount of ssDNA in both the G1 and S phase samples by slot blotting and hybridization experiments (Table 3 in GSE4099).  The raw normalized ratios of ssDNA for all genomic locations were then smoothed over a 4kb window by Fourier transformation (Table 4 in GSE4099).

organism: Schizosaccharomyces pombe

source_name: cds1delta G1 phase

treatment_protocol: Log phase cells were arrested in G1 phase by nitrogen starvation

tag: ssDNA in cds1delta G1 phase

source_name: cds1delta +HU early S phase

treatment_protocol: Log phase cells were arrested in early S phase by treatment of 12 mM HU for 3 hours at 30oC

tag: ssDNA in cds1delta in early S phase in HU


title: S. pombe WT

description: S. pombe WT cells (h-)

source_name: WT G1 phase

source_name: WT +HU early S phase

tag: ssDNA in WT in early S phase in HU


title: medial prefrontal cortex long access to cocaine replicate 3

status: Public on Jan 26 2006

city: La Jolla

first: Lena

middle: Dina

last: van der Stap

state: CA

address: 10550 N. Torrey Pines Rd.

department: Neuropharmacology

institute: The Scripps Research Institute

description: long access to cocaine ,medial prefrontal cortex, 6 hrs/day access to cocaine

organism: Rattus norvegicus

source_name: medial prefrontal cortex

label_protocol: Approximately 1 to 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNAs of regions of interest were prepared with an RNeasy miniprep kit according to manufacturer's (Qiagen, Valencia, CA) protocol. RNA was quantified by using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Palo Alta, CA) and with agarose gel electrophoresis. Depending on the brain region, between 1 and 5 µg of total RNA was used to prepare double-stranded cDNA with a cDNA synthesis kit (GIBCO/BRL) for first and second strand. Biotinylated cRNA was generated from these cDNAs with a BioArray high-yield RNA transcript labeling kit (Enzo Life Sciences). It was then purified with RNeasy spin columns (Qiagen) and fragmented before hybridization

tag: Male, Wistar, 6 hrs/day access to cocaine, medial prefrontal cortex


title: medial prefrontal cortex long access to cocaine replicate 2


title: medial prefrontal cortex cocaine naive replicate 3

description: cocaine naive,medial prefrontal cortex, 0 hrs/day access to cocaine

tag: Male, Wistar, 0 hrs/day access to cocaine, medial prefrontal cortex


title: medial prefrontal cortex short access to cocaine replicate 2

description: short access to cocaine ,medial prefrontal cortex, 1 hr/day access to cocaine

tag: Male, Wistar, 1 hr/day access to cocaine, medial prefrontal cortex


title: medial prefrontal cortex short access to cocaine replicate 3


title: septum long access to cocaine replicate 3

description: long access to cocaine, septum, 6 hrs/day access to cocaine

source_name: septum

tag: Male, Wistar, 6hrs/day access to cocaine, septum


title: ventral tegmental area cocaine naive replicate 1

description: cocaine naive, ventral tegmental area, 0 hrs/day access to cocaine

source_name: ventral tegmental area

tag: Male, Wistar, 0 hrs/day access to cocaine, ventral tegmental area


title: ventral tegmental area cocaine naive replicate 2


title: medial prefrontal cortex cocaine naive replicate 2


title: medial prefrontal cortex cocaine naive replicate 1


title: medial prefrontal cortex short access to cocaine replicate 1


title: septum long access to cocaine replicate 2


title: medial prefrontal cortex long access to cocaine replicate 1


title: ventral tegmental area short access to cocaine replicate 2

description: short access to cocaine, ventral tegmental area, 1 hr/day access to cocaine

tag: Male, Wistar, 1 hr/day access to cocaine, ventral tegmental area


title: ventral tegmental area short access to cocaine replicate 1


title: ventral tegmental area long access to cocaine replicate 3

description: long access to cocaine, ventral tegmental area, 6 hrs/day access to cocaine

tag: Male, Wistar, 6 hrs/day access to cocaine, ventral tegmental area


title: ventral tegmental area short access to cocaine replicate 3


title: ventral tegmental area long access to cocaine replicate 1


title: septum long access to cocaine replicate 1


title: ventral tegmental area cocaine naive replicate 3


title: 3005day0K

status: Public on Jan 29 2006

description: THP-1 cells, untreated control

hyb_protocol: according to affymetrix

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: GCOS 1.4.0.036 scaled to 500

source_name: THP-1 cells untreated

label_protocol: one cycle target labeling assay

growth_protocol: cultivated in RPMI1640 medium, 10% FCS, 1mM L-glutamine, 1% penicillin/streptomycin

extract_protocol: RNeasy Mini-Kit including Qiashredder columns (Qiagen)

tag: myelomonocytic leukemia cell line


title: 0606day7_20K

description: THP-1 cells, untreated control, cultivated for 7 days


title: 1409day720Gy

description: THP-1 cells harvested 7 days post irradiation

source_name: THP-1 cells irradiated

treatment_protocol:
irradiated with 20Gy
day 7 post irradiation


title: 3005day3_20Gy

description: THP-1 cells harvested 3 days post irradiation

treatment_protocol:
irradiated with 20Gy
day 3 post irradiation


title: 0709day0K

description: THP-1 cells, untreated control


title: 2408day7_20Gy

treatment_protocol: irradiated with 20Gy


title: septum short access to cocaine replicate 3

description: short access to cocaine, septum, 1 hr/day access to cocaine

tag: Male, Wistar, 1hr/day access to cocaine, septum


title: septum short access to cocaine replicate 2


title: septum no access to cocaine replicate 3

description: cocaine naive, septum, 0 hrs/day access to cocaine

tag: Male, Wistar, 0 access to cocaine, septum


title: lateral hypothalamus long access to cocaine replicate 4

description: long access to cocaine, lateral hypothalamus, 6 hrs/day access to cocaine

source_name: lateral hypothalamus

tag: Male, Wistar, 6hrs/day access to cocaine, lateral hypothalamus


title: septum short access to cocaine replicate 1


title: septum no access to cocaine replicate 1


title: septum no access to cocaine replicate 2


title: ventral tegmental area long access to cocaine replicate 2


title: 0606day7_20G


title: lateral hypothalamus long access to cocaine replicate 2


title: amygdala short access to cocaine replicate 4

description: short access to cocaine, amygdala, 1 hr/day access to cocaine

source_name: amygdala

tag: Male, Wistar, 1hr/day access to cocaine, amygdala


title: A04_Rep1

description:
Arabidopsis thaliana cell cultures sub-cultured every week. Agrobacterium- or mock-inoculated 3 days after sub-culture.
Inoculated samples co-hybridized with reference RNA.
Reference RNA: pool of RNA samples from mock-treated cell cultures.

source_name: Agrobacterium-inoculated, 4h, replication 1

tag: Arabidopsis thaliana cell suspension culture, LER ecotype.

tag: Collected 4h after inoculation with Agrobacterium tumefaciens strain A348.

source_name: Reference RNA


title: 2408day7_K


title: lateral hypothalamus no access to cocaine replicate 2

description: cocaine naive, lateral hypothalamus, 0 hrs/day access to cocaine

tag: Male, Wistar, 0 access to cocaine, lateral hypothalamus


title: lateral hypothalamus long access to cocaine replicate 1


title: lateral hypothalamus short access to cocaine replicate 2

description: short access to cocaine, lateral hypothalamus, 1 hr/day access to cocaine

tag: Male, Wistar, 1hr/day access to cocaine, lateral hypothalamus


title: lateral hypothalamus no access to cocaine replicate 1


title: lateral hypothalamus short access to cocaine replicate 3


title: lateral hypothalamus short access to cocaine replicate 4


title: lateral hypothalamus no access to cocaine replicate 3


title: amygdala long access to cocaine replicate 2

description: long access to cocaine, amygdala, 6 hrs/day access to cocaine

tag: Male, Wistar, 6hrs/day access to cocaine, amygdala


title: amygdala long access to cocaine replicate 1


title: lateral hypothalamus long access to cocaine replicate 3


title: lateral hypothalamus no access to cocaine replicate 4


title: lateral hypothalamus short access to cocaine replicate 1


title: amygdala short access to cocaine replicate 2


title: amygdala short access to cocaine replicate 1


title: amygdala short access to cocaine replicate 3


title: amygdala long access to cocaine replicate 4


title: amygdala long access to cocaine replicate 3


title: amygdala no access to cocaine replicate 4

description: cocaine naive, amygdala, 0 hrs/day access to cocaine

tag: Male, Wistar, 0 access to cocaine, amygdala


title: amygdala no access to cocaine replicate 3


title: nucleus accumbens long access to cocaine replicate 4

description: long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine

source_name: nucleus accumbens

tag: Male, Wistar, 6hrs/day access to cocaine, nucleus accumbens


title: amygdala no access to cocaine replicate 1


title: nucleus accumbens long access to cocaine replicate 2


title: amygdala no access to cocaine replicate 2


title: nucleus accumbens long access to cocaine replicate 3


title: nucleus accumbens short access to cocaine replicate 4

description: short access to cocaine, nucleus accumbens, 1 hr/day access to cocaine

tag: Male, Wistar, 1hr/day access to cocaine, nucleus accumbens


title: nucleus accumbens short access to cocaine replicate 2


title: nucleus accumbens short access to cocaine replicate 3


title: nucleus accumbens short access to cocaine replicate 1


title: nucleus accumbens long access to cocaine replicate 1


title: nucleus accumbens ctrl replicate 3

description: cocaine naive, nucleus accumbens, 0 hrs access to cocaine

tag: Male, Wistar, 0 access to cocaine, nucleus accumbens


title: nucleus accumbens ctrl replicate 1


title: nucleus accumbens ctrl replicate 2


title: nucleus accumbens ctrl replicate 4


title: HCC108 Cy3 - mAdbID:59871

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

description: mAdb experiment ID: 59871

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Pooled Normal Liver Sample - Cy5

label_protocol: Cy5 Sample Labeling Protocol - generic

extract_protocol:
CsCl Extraction Protocol
Extraction method: ultracentrifugation

tag: Tissue

value: liver

tag: Developmental stage

value: adult

tag: Cell type

value: Hepatocyte

source_name: HCC108 - Cy3

label_protocol: Cy3 Sample Labeling Protocol - generic

tag: Gender

tag: Age

tag: Disease state

value: Hepatocellular carcinoma

tag: Individual


title: HCC111 Cy5 - mAdbID:59512

description: mAdb experiment ID: 59512

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC111 - Cy5


title: HCC103 Cy3 - mAdbID:59865

description: mAdb experiment ID: 59865

source_name: HCC103 - Cy3


title: HCC110 Cy5 - mAdbID:59484

description: mAdb experiment ID: 59484

source_name: HCC110 - Cy5


title: HCC092 Cy5 - mAdbID:59536

description: mAdb experiment ID: 59536

source_name: HCC092 - Cy5


title: HCC108 Cy5 - mAdbID:59870

description: mAdb experiment ID: 59870

source_name: HCC108 - Cy5


title: HCC109 Cy3 - mAdbID:59095

description: mAdb experiment ID: 59095

source_name: HCC109 - Cy3


title: HCC110 Cy3 - mAdbID:59487

description: mAdb experiment ID: 59487

source_name: HCC110 - Cy3


title: HCC092 Cy3 - mAdbID:59537

description: mAdb experiment ID: 59537

source_name: HCC092 - Cy3


title: HCC105 Cy5 - mAdbID:59088

description: mAdb experiment ID: 59088

source_name: HCC105 - Cy5


title: HCC107 Cy3 - mAdbID:59093

description: mAdb experiment ID: 59093

source_name: HCC107 - Cy3


title: HCC100 Cy5 - mAdbID:57694

description: mAdb experiment ID: 57694

source_name: HCC100 - Cy5


title: HCC099 Cy5 - mAdbID:57692

description: mAdb experiment ID: 57692

source_name: HCC099 - Cy5


title: HCC101 Cy5 - mAdbID:57696

description: mAdb experiment ID: 57696

source_name: HCC101 - Cy5


title: HCC109 Cy5 - mAdbID:59094

description: mAdb experiment ID: 59094

source_name: HCC109 - Cy5


title: HCC103 Cy5 - mAdbID:59864

description: mAdb experiment ID: 59864

source_name: HCC103 - Cy5


title: HCC111 Cy3 - mAdbID:59515

description: mAdb experiment ID: 59515

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC111 - Cy3


title: HCC105 Cy3 - mAdbID:59089

description: mAdb experiment ID: 59089

source_name: HCC105 - Cy3


title: HCC100 Cy3 - mAdbID:57695

description: mAdb experiment ID: 57695

source_name: HCC100 - Cy3


title: HCC091 Cy3 - mAdbID:59535

description: mAdb experiment ID: 59535

source_name: HCC091 - Cy3


title: HCC104 Cy5 - mAdbID:59866

description: mAdb experiment ID: 59866

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC104 - Cy5


title: HCC102 Cy5 - mAdbID:57698

description: mAdb experiment ID: 57698

source_name: HCC102 - Cy5


title: HCC106 Cy5 - mAdbID:59090

description: mAdb experiment ID: 59090

source_name: HCC106 - Cy5


title: HCC102 Cy3 - mAdbID:57699

description: mAdb experiment ID: 57699

source_name: HCC102 - Cy3


title: HCC104 Cy3 - mAdbID:59867

description: mAdb experiment ID: 59867

source_name: HCC104 - Cy3


title: HCC106 Cy3 - mAdbID:59091

description: mAdb experiment ID: 59091

source_name: HCC106 - Cy3


title: HCC091 Cy5 - mAdbID:59534

description: mAdb experiment ID: 59534

source_name: HCC091 - Cy5


title: HCC099 Cy3 - mAdbID:57693

description: mAdb experiment ID: 57693

source_name: HCC099 - Cy3


title: HCC107 Cy5 - mAdbID:59092

description: mAdb experiment ID: 59092

source_name: HCC107 - Cy5


title: HCC101 Cy3 - mAdbID:57697

description: mAdb experiment ID: 57697

source_name: HCC101 - Cy3


title: HCC098 Cy3 - mAdbID:57661

description: mAdb experiment ID: 57661

source_name: HCC098 - Cy3


title: HCC097 Cy3 - mAdbID:57659

description: mAdb experiment ID: 57659

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC097 - Cy3


title: HCC098 Cy5 - mAdbID:57660

description: mAdb experiment ID: 57660

source_name: HCC098 - Cy5


title: HCC096 Cy5 - mAdbID:57656

description: mAdb experiment ID: 57656

source_name: HCC096 - Cy5


title: HCC095 Cy5 - mAdbID:57654

description: mAdb experiment ID: 57654

source_name: HCC095 - Cy5


title: HCC096 Cy3 - mAdbID:57657

description: mAdb experiment ID: 57657

source_name: HCC096 - Cy3


title: HCC095 Cy3 - mAdbID:57655

description: mAdb experiment ID: 57655

source_name: HCC095 - Cy3


title: HCC097 Cy5 - mAdbID:57658

description: mAdb experiment ID: 57658

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC097 - Cy5


title: HCC139 Cy3 - mAdbID:56992

description: mAdb experiment ID: 56992

source_name: HCC139 - Cy3


title: HCC094 Cy5 - mAdbID:57651

description: mAdb experiment ID: 57651

source_name: HCC094 - Cy5


title: HCC094 Cy3 - mAdbID:57652

description: mAdb experiment ID: 57652

source_name: HCC094 - Cy3


title: HCC134 Cy5 - mAdbID:56981

description: mAdb experiment ID: 56981

source_name: HCC134 - Cy5


title: HCC132 Cy3 - mAdbID:56978

description: mAdb experiment ID: 56978

source_name: HCC132 - Cy3


title: HCC132 Cy5 - mAdbID:56977

description: mAdb experiment ID: 56977

source_name: HCC132 - Cy5


title: HCC139 Cy5 - mAdbID:56991

description: mAdb experiment ID: 56991

source_name: HCC139 - Cy5


title: HCC140 Cy5 - mAdbID:56993

description: mAdb experiment ID: 56993

source_name: HCC140 - Cy5


title: HCC130 Cy3 - mAdbID:56974

description: mAdb experiment ID: 56974

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC130 - Cy3


title: HCC138 Cy5 - mAdbID:56989

description: mAdb experiment ID: 56989

source_name: HCC138 - Cy5


title: HCC138 Cy3 - mAdbID:56990

description: mAdb experiment ID: 56990

source_name: HCC138 - Cy3


title: HCC140 Cy3 - mAdbID:56994

description: mAdb experiment ID: 56994

source_name: HCC140 - Cy3


title: HCC135 Cy3 - mAdbID:56984

description: mAdb experiment ID: 56984

source_name: HCC135 - Cy3


title: HCC130 Cy5 - mAdbID:56973

description: mAdb experiment ID: 56973

source_name: HCC130 - Cy5


title: HCC127 Cy5 - mAdbID:56967

description: mAdb experiment ID: 56967

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC127 - Cy5


title: HCC129 Cy3 - mAdbID:56972

description: mAdb experiment ID: 56972

source_name: HCC129 - Cy3


title: HCC137 Cy5 - mAdbID:56987

description: mAdb experiment ID: 56987

source_name: HCC137 - Cy5


title: HCC136 Cy5 - mAdbID:56985

description: mAdb experiment ID: 56985

source_name: HCC136 - Cy5


title: HCC134 Cy3 - mAdbID:56982

description: mAdb experiment ID: 56982

source_name: HCC134 - Cy3


title: HCC131 Cy5 - mAdbID:56975

description: mAdb experiment ID: 56975

source_name: HCC131 - Cy5


title: HCC137 Cy3 - mAdbID:56988

description: mAdb experiment ID: 56988

source_name: HCC137 - Cy3


title: HCC128 Cy5 - mAdbID:56969

description: mAdb experiment ID: 56969

source_name: HCC128 - Cy5


title: HCC136 Cy3 - mAdbID:56986

description: mAdb experiment ID: 56986

source_name: HCC136 - Cy3


title: HCC133 Cy3 - mAdbID:56980

description: mAdb experiment ID: 56980

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC133 - Cy3


title: HCC127 Cy3 - mAdbID:56968

description: mAdb experiment ID: 56968

source_name: HCC127 - Cy3


title: HCC133 Cy5 - mAdbID:56979

description: mAdb experiment ID: 56979

source_name: HCC133 - Cy5


title: HCC135 Cy5 - mAdbID:56983

description: mAdb experiment ID: 56983

source_name: HCC135 - Cy5


title: HCC131 Cy3 - mAdbID:56976

description: mAdb experiment ID: 56976

source_name: HCC131 - Cy3


title: HCC125 Cy5 - mAdbID:56963

description: mAdb experiment ID: 56963

source_name: HCC125 - Cy5


title: HCC124 Cy3 - mAdbID:56962

description: mAdb experiment ID: 56962

source_name: HCC124 - Cy3


title: HCC123 Cy5 - mAdbID:56959

description: mAdb experiment ID: 56959

source_name: Pooled Normal Liver Sample - Cy3

source_name: HCC123 - Cy5


title: HCC124 Cy5 - mAdbID:56961

description: mAdb experiment ID: 56961

source_name: HCC124 - Cy5


title: HCC129 Cy5 - mAdbID:56971

description: mAdb experiment ID: 56971

source_name: HCC129 - Cy5


title: HCC126 Cy3 - mAdbID:56966

description: mAdb experiment ID: 56966

source_name: HCC126 - Cy3


title: HCC126 Cy5 - mAdbID:56965

description: mAdb experiment ID: 56965

source_name: HCC126 - Cy5


title: HCC122 Cy5 - mAdbID:56957

description: mAdb experiment ID: 56957

source_name: HCC122 - Cy5


title: HCC120 Cy3 - mAdbID:56954

description: mAdb experiment ID: 56954

source_name: HCC120 - Cy3


title: HCC122 Cy3 - mAdbID:56958

description: mAdb experiment ID: 56958

source_name: HCC122 - Cy3


title: HCC121 Cy5 - mAdbID:56955

description: mAdb experiment ID: 56955

source_name: HCC121 - Cy5


title: HCC128 Cy3 - mAdbID:56970

description: mAdb experiment ID: 56970

source_name: Pooled Normal Liver Sample - Cy5

source_name: HCC128 - Cy3


title: HCC120 Cy5 - mAdbID:56953

description: mAdb experiment ID: 56953

source_name: HCC120 - Cy5


title: HCC118 Cy3 - mAdbID:56948

description: mAdb experiment ID: 56948

source_name: HCC118 - Cy3


title: HCC114 Cy3 - mAdbID:56928

description: mAdb experiment ID: 56928

source_name: HCC114 - Cy3