title: D20_B1

description:
D20_B1_R620G520_50313.gpr
Single sperm from donor#D20


title: E. coli control (biological replicate 2)

status: Public on Jul 25 2008

type: RNA

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

country: Australia

institute: University of Tasmania

description: The sucrose and NaCl hyperosmotic treatment data were compared to the no treatment control data separately.

hyb_protocol: Hybridization of the fragmented, biotinylated cDNA to a chip, washing, and staining of the chip was done on an Affymetrix workstation as described previously (Expression Analysis Technical Manual; Affymetrix, Inc., Santa Clara, Calif.). Detailed method is equivalent to that described by Soupene and colleagues: http://nature.berkeley.edu/%7eopaliy/papers/MG1655/MAprotocol.pdf

scan_protocol: Scanning of the chip were done on an Affymetrix workstation as described previously (Expression Analysis Technical Manual; Affymetrix, Inc., Santa Clara, Calif.).

data_processing: Background correction, normalization and calculation of the expression measures were performed using RMA procedure with the WebArray platform (http://bioinformatics.skcc.org/webarray/). Subsequently the program EDGE (http://www.biostat.washington.edu/software/jstorey/edge/) was used to estimate the conditional false discovery rate (FDR), the expected proportion of false positives conditioned on having k 'significant' findings.

label: biotin

molecule: total RNA

organism: Escherichia coli

source_name: E. coli Frag1 (biological replicate 2)

label_protocol: Gene expression was assessed on Affymetrix E. coli Genome GeneChip arrays (Affymetrix, Inc., Santa Clara, Calif.). Briefly, total RNA was prepared from E. coli cells by phenol-chloroform extraction, and ~10 µg of total RNA was used to synthesize cDNA. After purification with a Qiagen cDNA purification kit (Qiagen, Inc.), the cDNA was fragmented with DNase I. The fragmented cDNA was end biotinylated by terminal transferase with biotinylated ddATP.

growth_protocol: Grown in Davis's Mineral Salts medium (Gibco BRL Life Technologies Inc.) with 0.1% D-glucose at 25 C (100 r.p.m. shaking) until an OD (550 nm) of 0.6.

extract_protocol: RNA was obtained using the RNAeasy MIDI RNA extraction kit (Qiagen) using lysis buffer containing 0.1% beta-mercaptoethanol. RNA was extracted from lysates and purified according to the manufacturer’s standard protocol and subsequently stored at -80°C. RNA quality was assessed with electrophoresis using a RNA bioanalyser 2100 and Lab RNAChip (Agilent Technologies) before progression to microarray hybridization.

treatment_protocol: No treatment (control sample).

tag: E. coli, strain Frag1


title: D20_A6

type: genomic

city: Piscataway

first: Minjie

last: Luo

state: NJ

address: 675 Hoes Lane

department: Microbiology & Molecular Genetics

country: USA

institute: University of Medicine and Dentistry of New Jersey

description:
D20_A6_R630G530_50313.gpr
Single sperm from donor#D20

hyb_protocol: Hybridization was done with 1x hybridization solution (5x Denhart's solution, 0.5% SDS, 5x SSC, 20 µL of ssDNA/1000 microarray spots) in a Hybridization Chamber (Corning) at 56°C for 2.5-4 h. After hybridization, the slide was washed at 56°C with 1x SSC and 0.1% SDS for 10 min, twice with 0.5x SSC for 30 sec, and twice with 0.2x SSC for 30 sec.

scan_protocol: Microarrays were scanned with GenePix 4000B (Axon Instruments)

data_processing: The resulting images were analyzed with either the GenePix Pro (Axon Instruments) or ImaGene (BioDiscovery) software.

molecule: genomic DNA

organism: Homo sapiens

source_name: Semen donor #D20

label_protocol: Probes were labeled in 25 µL of labeling solution containing  Sequenase buffer), 0.5 units/µL Sequenase (Amersham Pharmacia Biosciences), Cy3-ddATP and Cy5-ddGTP (PE Biosystems) for AG probes, and Cy3-ddUTP and Cy5-ddCTP for CT probes (750 nM each). The reaction was incubated at 70°C for 10 min. The slide was washed under conditions as described above.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The procedures for multiplex amplification and genotype determination are illustrated in Figure 1. First, multiplex PCR (Fig. 1A) was performed in 30 µL of PCR mix containing 1x PCR buffer (50 mM KCl, 100 mM Tris-HCl at pH 8.3, 1.5 mM MgCl2, and 100 µg/mL gelatin), four dNTPs (200 µM each; Invitrogen), primers (20 nM each) for all SNPs in the multiplex group, 6 units of HotStar Taq DNA polymerase (QIAGEN), and 5 ng of DNA or single sperm. The samples were first heated to 94°C for 15 min to activate the Taq DNA polymerase followed by 40 PCR cycles. Each PCR cycle consisted of 40 sec at 94°C for denaturation and 2 min at 55°C followed by 5 min of ramping from 55°C to 70°C for annealing and extension. A final extension step was carried out at 72°C for 3 min at the end of the 40-th cycle. PCR amplifications were performed with thermal cyclers capable of ramping as slow as 0.01°C/sec. ssDNA was generated in both directions by using the same conditions for multiplex PCR except: (1) 1-2 µL of product from the multiplex PCR was used as templates, (2) only one primer for each SNP; and (3) 45 PCR cycles.

tag: Single sperm prepared by flow cytometry


title: D20_A4

description:
D20_A4_R700G600_50313.gpr
Single sperm from donor#D20


title: D20_A2

description:
D20_A2_R640G540_50313.gpr
Single sperm from donor#D20


title: D18_C4

description:
D18_C4ag_R640G540_50320.gpr
Single sperm from donor#D18

source_name: Semen donor #D18


title: D20_A11

description:
D20_A11_R610G510_50313.gpr
Single sperm from donor#D20


title: D18_C2

description:
D18_C2ag_R640G540_50320.gpr
Single sperm from donor#D18


title: D18_C3

description:
D18_C3ag_R640G540_50320.gpr
Single sperm from donor#D18


title: D20_A1

description:
D20_A1_R640G540_50313.gpr
Single sperm from donor#D20


title: D18_C1

description:
D18_C1_R600G500_50312.gpr
Single sperm from donor#D18


title: D18_B1

description:
D18_B1_R640G540_50312.gpr
Single sperm from donor#D18


title: D18_A9

description:
D18_A9_R640G540_50312.gpr
Single sperm from donor#D18


title: D18_A8

description:
D18_A8_R600G500_50312.gpr
Single sperm from donor#D18


title: D18_A7

description:
D18_A7_R580G480_50312.gpr
Single sperm from donor#D18


title: D17_B7

description:
D17_B7_R600G500_50312.gpr
Single sperm from donor#D17

source_name: Semen donor #D17


title: D18_A6

description:
D18_A6_R580G480_50312.gpr
Single sperm from donor#D18


title: D17_B8

description:
D17_B8_R580G480_50312.gpr
Single sperm from donor#D17


title: D17_B9

description:
D17_B9_R590G490_50312.gpr
Single sperm from donor#D17


title: D18_A5

description:
D18_A5_R640G540_50312.gpr
Single sperm from donor#D18


title: D18_A3

description:
D18_A3_R600G500_50312.gpr
Single sperm from donor#D18


title: D18_A2

description:
D18_A2_R590G490_50312.gpr
Single sperm from donor#D18


title: D17_B6

description:
D17_B6_R580G480_50312.gpr
Single sperm from donor#D17


title: D17_B5

description:
D17_B5_R570G470_50312.gpr
Single sperm from donor#D17


title: D17_B4

description:
D17_B4_R580G480_50312.gpr
Single sperm from donor#D17


title: D17_B3

description:
D17_B3_R580G480_50312.gpr
Single sperm from donor#D17


title: D18_A4

description:
D18_A4_R600G500_50312.gpr
Single sperm from donor#D18


title: AC09_D7

description:
AC09_D7_R630G530_50312.gpr
Single sperm from donor#AC09

source_name: Semen donor #AC09


title: AC09_C10

description:
AC09_C10_R600G500_50312.gpr
Single sperm from donor#AC09


title: D17_B2

description:
D17_B2_R590G490_50312.gpr
Single sperm from donor#D17


title: D17_B1

description:
D17_B1_R580G480_50312.gpr
Single sperm from donor#D17


title: AC09_D8

description:
AC09_D8_R630G530_50312.gpr
Single sperm from donor#AC09


title: D17_B10

description:
D17_B10_R590G490_50312.gpr
Single sperm from donor#D17


title: AC09_D3

description:
AC09_D3_R600G500_50312.gpr
Single sperm from donor#AC09


title: AC09_D4

description:
AC09_D4_R630G530_50312.gpr
Single sperm from donor#AC09


title: AC09_D10

description:
AC09_D10_R600G500_50312.gpr
Single sperm from donor#AC09


title: AC09_C9

description:
AC09_C9_R580G480_50312.gpr
Single sperm from donor#AC09


title: AC09_D11

description:
AC09_D11ag_R640G540_50320.gpr
Single sperm from donor#AC09


title: AC09_C8

description:
AC09_C8_R580G480_50312.gpr
Single sperm from donor#AC09


title: AB027_C6-AG

description:
AB027_C6ag_R650G550_50320.gpr
Single sperm from donor#AB027

source_name: Semen donor #AB027


title: AC09_C7

description:
AC09_C7_R580G480_50312.gpr
Single sperm from donor#AC09


title: AB027_C7-AG

description:
AB027_C7ag_R650G550_50320.gpr
Single sperm from donor#AB027


title: AB027_C4

description:
AB027_C4_R590G490_50311.gpr
Single sperm from donor#AB027


title: AB027_C5-AG

description:
AB027_C5ag_R620G520_50320.gpr
Single sperm from donor#AB027


title: AB027_B9

description:
AB027_B9_R560G460_50311.gpr
Single sperm from donor#AB027


title: AB027_B7

description:
AB027_B7_R590G490_50311.gpr
Single sperm from donor#AB027


title: AB027_B11

description:
AB027_B11_R610G510_50311.gpr
Single sperm from donor#AB027


title: AB027_A9

description:
AB027_A9_R570G470_50311.gpr
Single sperm from donor#AB027


title: AB027_B10

description:
AB027_B10_R610G510_50311.gpr
Single sperm from donor#AB027


title: AB027_A8

description:
AB027_A8_R580G480_50311.gpr
Single sperm from donor#AB027


title: AB027_A10

description:
AB027_A10_R640G540_50311.gpr
Single sperm from donor#AB027


title: AB027_A7

description:
AB027_A7_R580G480_50311.gpr
Single sperm from donor#AB027


title: AB027_A11

description:
AB027_A11_R590G490_50311.gpr
Single sperm from donor#AB027


title: H9_AB012

description:
H9_sperm_R550G450_50201.gpr
Single sperm from donor#AB012

source_name: Semen donor #AB012


title: H7_AB012

description:
H7_sperm_R540G440_50201.gpr
Single sperm from donor#AB012


title: AB027_C8-AG

description:
AB027_C8ag_R600G500_50320.gpr
Single sperm from donor#AB027


title: H8_AB012

description:
H8_sperm_R540G440_50201.gpr
Single sperm from donor#AB012


title: AB027_C10-AG

description:
AB027_C10ag_R620G520_50320.gpr
Single sperm from donor#AB027


title: H6_AB012

description:
H6_sperm_R560G460_50201.gpr
Single sperm from donor#AB012


title: H3_AB012

description:
H3_sperm_R530G430_50201.gpr
Single sperm from donor#AB012


title: H4_AB012

description:
H4_sperm_R560G460_50201.gpr
Single sperm from donor#AB012


title: H2_AB012

description:
H2_sperm_R550G450_50201.gpr
Single sperm from donor#AB012


title: H1_AB012

description:
H1_sperm_R550G450_50201.gpr
Single sperm from donor#AB012


title: G7_AB012

description:
G7_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: G9_AB012

description:
G9_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: G8_AB012

description:
G8_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: H11_AB012

description:
H11_sperm_R550G450_50201.gpr
Single sperm from donor#AB012


title: LEC 1h VEGFC - trial 2

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

hyb_protocol: Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Scan protocol Chemiluminescent Detection Kit (P/N 4339627) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescent Digoxigenin-UTP labeled cRNA

source_name: Human primary dermal microvascular lymphatic endothelial cell (LEC) isolated from neonatal human foreskin

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 0.5 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.

growth_protocol: LEC were seeded onto fibronectin-coated culture dishes (10 µg/ml; BD Biosciences, Bedford, MA) and were cultured in endothelial cell basal medium (EBM; Cambrex Bio Science, Walkersville, MD) supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY), 2 mM L glutamine, antibiotic-antimycotic solution, 10 µg/ml hydrocortisone  and N6,2'-O-dibutyryl-adenosine 3',5'-cyclic monophosphate (25 µg/ml; all from Fluka, Buchs, Switzerland) for up to 7 passages.

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

treatment_protocol: Primary LEC were serum starved overnight in EBM supplemented with 0.2% bovine serum albumin. Cells were treated or not for 1h, 4h, 8h or 24h with recombinant human VEGF-A165 (R&D Systems; 20 ng/ml) or mature human VEGF-C (R&D Systems; 500 ng/ml).

tag: CD45-/CD34-/CD31+ Human Lymphatic Endothelial Cell (LEC)


title: G6_AB012

description:
G6_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: G5_AB012

description:
G5_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: H10_AB012

description:
H10_sperm_R550G450_50201.gpr
Single sperm from donor#AB012


title: G4_AB012

description:
G4_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: E. coli sucrose hyperosmotic treatment (biological replicate 1)

description: The sucrose and NaCl hyperosmotic treatment data were compared to the no treatment control data separately.

source_name: E.coli Frag1, sucrose hyperosmotic treatment (biological replicate 1)

treatment_protocol: Cell suspension was ammended with 1.25 M sucrose to an osmotic pressure of 2.7 Os kg-1 for 10 minutes. The biomass was centrifuged at 4000 rpm and the pellet treated with RNAProtect (Qiagen) following the manufacturer's protocol.


title: G2_AB012

description:
G2_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: H5_AB012

description:
H5_sperm_R560G460_50201.gpr
Single sperm from donor#AB012


title: F8_AB012

description:
F8_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: F5_AB012

description:
F5_sperm_R580G480_50114.gpr
Single sperm from donor#AB012


title: F6_AB012

description:
F6_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: F7_AB012

description:
F7_sperm_R620G520_50114.gpr
Single sperm from donor#AB012


title: F4_AB012

description:
F4_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: G1_AB012

description:
G1_sperm_R640G540_50114.gpr
Single sperm from donor#AB012


title: F3_AB012

description:
F3_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: F9_AB012

description:
F9_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: G3_AB012

description:
G3_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: F1_AB012

description:
F1_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: E5_AB012

description:
E5_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: E3_AB012

description:
E3_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: E11_AB012

description:
E11_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: E2_AB012

description:
E2_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: D9_AB012

description:
D9_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: D6_AB012

description:
D6_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: D3_200

description:
D3_200nm_r590g490_41222.gpr
Single sperm from donor#AB012


title: D7_AB012

description:
D7_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: D10_AB012

description:
D10_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: D11_AB012

description:
D11_sperm_R600G500_50114.gpr
Single sperm from donor#AB012


title: C9_AB012

description:
C9_sperm_R580G490_41229.gpr
Single sperm from donor#AB012


title: E9_AB012

description:
E9_sperm_R630G530_50114.gpr
Single sperm from donor#AB012


title: F2_AB012

description:
F2_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: C7_AB012

description:
C7_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: C6_AB012

description:
C6_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: D5_AB012

description:
D5_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: C4_AB012

description:
C4_sperm_R580G490_41229.gpr
Single sperm from donor#AB012


title: B9_AB012

description:
B9_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: C11_AB012

description:
C11_sperm_R650G550_50114.gpr
Single sperm from donor#AB012


title: B6_AB012

description:
B6_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: B7_AB012

description:
B7_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: C10_AB012

description:
C10_sperm_R580G490_41229.gpr
Single sperm from donor#AB012


title: B2_AB012

description:
B2_sperm_R600G510_41229.gpr
Single sperm from donor#AB012


title: C5_AB012

description:
C5_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: B4_AB012

description:
B4_sperm_R600G510_41229.gpr
Single sperm from donor#AB012


title: B1_AB012

description:
B1_sperm_R600G510_41229.gpr
Single sperm from donor#AB012


title: A8_AB012

description:
A8_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: A10_AB012

description:
A10_sperm_R600G510_41229.gpr
Single sperm from donor#AB012


title: A4_AB012

description:
A4_200nm_r590g490_41222.gpr
Single sperm from donor#AB012


title: A7_AB012

description:
A7_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: A9_AB012

description:
A9_sperm_R550G460_41229.gpr
Single sperm from donor#AB012


title: AB011_B3

description:
AB011_B3_R580G480_50311.gpr
Single sperm from donor#AB011

source_name: Semen donor #AB011


title: AB011_A5

description:
AB011_A5_R590G480_50311.gpr
Single sperm from donor#AB011


title: AB011_A8

description:
AB011_A8_R570G470_50311.gpr
Single sperm from donor#AB011


title: AB011_A6

description:
AB011_A6_R570G470_50311.gpr
Single sperm from donor#AB011


title: AB011_A4

description:
AB011_A4_R610G510_50311.gpr
Single sperm from donor#AB011


title: AB011_A2

description:
AB011_A2_R590G490_50311.gpr
Single sperm from donor#AB011


title: AB011_A3

description:
AB011_A3_R610G510_50311.gpr
Single sperm from donor#AB011


title: AB011_A12

description:
AB011_A12_R580G490_50311.gpr
Single sperm from donor#AB011


title: AB011_A1

description:
AB011_A1_R590G490_50311.gpr
Single sperm from donor#AB011


title: AB005_F8

description:
AB005_F8ag_R670G570_50320.gpr
Single sperm from donor#AB005

source_name: Semen donor #AB005


title: AB005_E7

description:
AB005_E7ag_R600G500_50320.gpr
Single sperm from donor#AB005


title: A11_AB012

description:
A11_sperm_R600G510_41229.gpr
Single sperm from donor#AB012


title: AB005_E4

description:
AB005_E4ag_R580G480_50320.gpr
Single sperm from donor#AB005


title: AB005_E5

description:
AB005_E5ag_R580G480_50320.gpr
Single sperm from donor#AB005


title: AB005_E3

description:
AB005_E3ag_R580G480_50320.gpr
Single sperm from donor#AB005


title: AB005_F7

description:
AB005_F7_R580G480_50311.gpr
Single sperm from donor#AB005


title: AB005_F6

description:
AB005_F6_R570G470_50311.gpr
Single sperm from donor#AB005


title: C8_AB012

description:
C8_sperm_R580G490_41229.gpr
Single sperm from donor#AB012


title: AB005_F1

description:
AB005_F1_R600G500_50311.gpr
Single sperm from donor#AB005


title: AB005_F4

description:
AB005_F4_R590G490_50311.gpr
Single sperm from donor#AB005


title: AB005_E11

description:
AB005_E11_R600G500_50311.gpr
Single sperm from donor#AB005


title: AB005_F11

description:
AB005_F11_R600G500_50311.gpr
Single sperm from donor#AB005


title: #012_E6

description:
#012_E6ag_R640G540_50320.gpr
Single sperm from donor#12

source_name: Semen donor #12


title: #012_D10

description:
#012_D10ag_R640G540_50320.gpr
Single sperm from donor#12


title: AB011_A10

description:
AB011_A10_R570G470_50311.gpr
Single sperm from donor#AB011


title: #012_D9

description:
#012_D9ag_R640G540_50320.gpr
Single sperm from donor#12


title: #12_C5

description:
#12_C5ag_R670G570_50320.gpr
Single sperm from donor#12


title: #012_C4

description:
#012_C4ag_R590G490_50320.gpr
Single sperm from donor#12


title: #12_C3

description:
#12_C3_R640G540_50313.gpr
Single sperm from donor#12


title: #12_D12

description:
#12_D12_R640G540_50313.gpr
Single sperm from donor#12


title: AB005_F5

description:
AB005_F5_R570G470_50311.gpr
Single sperm from donor#AB005


title: #12_C11

description:
#12_C11_R660G560_50313.gpr
Single sperm from donor#12


title: #12_C9

description:
#12_C9_R640G540_50313.gpr
Single sperm from donor#12


title: #12_B9

description:
#12_B9_R600G500_50313.gpr
Single sperm from donor#12


title: #12_A10

description:
#12_A10_R600G500_50313.gpr
Single sperm from donor#12


title: #12_A9

description:
#12_A9_R640G540_50313.gpr
Single sperm from donor#12


title: C t=32 Cy3

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: Biological replicate 3 of 3.

hyb_protocol: Samples were mixed (18 uL total) with 42.6 uL of hybridization mix (45% formamide, 5X SSC, 0.1% SDS) and applied to prehybridized (1% BSA, 5X SSC, 0.1% SDS 40 min followed by 3X washes in water and 1X wash in isopropanol) microarrays. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 20 h at 42°C in hybridization cassettes (Array-It), and washed 5 min, 2X SSC, 0.1% SDS; 20 min, 0.1X SSC, 0.1% SDS, 5X 0.1X SSC and dried.

scan_protocol: Scanned on an GenePix 4000B. Images were quantified using GenePix Pro 6.0.

data_processing: Background calculated and subtracted using morphological opening followed by closing in GenePix 6.0, LOWESS normalization in GenespringGX 7.3.

organism: Saccharolobus solfataricus

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-3 (green) at t=32 h post infection.

label_protocol: 2-5 µg of total RNA were primed with 5 ug random primer (hexamer) at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 20 µM dCTP, 80 µM aminoallyl-dUTP (Sigma), and DTT. RNA was then degraded with 200nM EDTA and 1M NaOH, and labeled with CyDye Reactive Dye, post labeling (GE Healthcare) and cDNAs were purified using MinElute Enzymatic Cleanup Kit (Qiagen).

extract_protocol: mirVana total RNA extraction (Ambion)

tag: Strain 2-2-12

tag: t=32 h post infection

source_name: S. solfataricus + STIV labeled with Cyanine-5 (red) at t=32 h post infection.

treatment_protocol: Infection of cells with STIV at an MOI of approx. 1.5.

tag: t=32 post infection


title: B t=32 Cy5

description: Biological replicate 2 of 3.

source_name: S. solfataricus + STIV labeled with Cyanine-3 (green) at t=32 h post infection.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-5 (red) at t=32 h post infection.


title: B t=32 Cy3

description: Biological replicate 2 of 3.


title: A t=32 Cy5

description: Biological replicate 1 of 3.


title: C t=32 Cy5

description: Biological replicate 3 of 3.


title: A t=32 Cy3

description: Biological replicate 1 of 3.


title: #12_B10

description:
#12_B10_R600G500_50313.gpr
Single sperm from donor#12


title: #11_D5

description:
#11_D5_R640G540_50313.gpr
Single sperm from donor#11

source_name: Semen donor #11


title: AB005_E10

description:
AB005_E10ag_R620G520_50320.gpr
Single sperm from donor#AB005


title: #11_D4

description:
#11_D4_R640G540_50313.gpr
Single sperm from donor#11


title: C t=24 Cy3

description: Biological replicate 3 of 3.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-3 (green) at t=24 h post infection.

tag: t=24 h post infection

source_name: S. solfataricus + STIV labeled with Cyanine-5 (red) at t=24 h post infection.

tag: t=24 post infection


title: #11_C8

description:
#11_C8_R600G500_50313.gpr
Single sperm from donor#11


title: #11_C9

description:
#11_C9_R600G500_50313.gpr
Single sperm from donor#11


title: B t=24 Cy3

description: Biological replicate 2 of 3.


title: B t=24 Cy5

description: Biological replicate 2 of 3.

source_name: S. solfataricus + STIV labeled with Cyanine-3 (green) at t=24 h post infection.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-5 (red) at t=24 h post infection.


title: #11_C11

description:
#11_C11_R630G530_50313.gpr
Single sperm from donor#11


title: #11_C5

description:
#11_C5_R600G500_50313.gpr
Single sperm from donor#11


title: #11_B9

description:
#11_B9_R620G520_50313.gpr
Single sperm from donor#11


title: A t=24 Cy3

description: Biological replicate 1 of 3.


title: C t=24 Cy5

description: Biological replicate 3 of 3.


title: #11_B8

description:
#11_B8_R610G510_50313.gpr
Single sperm from donor#11


title: #11_B11

description:
#11_B11_R640G540_50313.gpr
Single sperm from donor#11


title: S002_E11

description:
S002_E11_R580G470_50309.gpr
Single sperm from donor#002

source_name: Semen donor #002


title: C t=16 Cy3

description: Biological replicate 3 of 3.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-3 (green) at t=16 h post infection.

tag: t=16 h post infection

source_name: S. solfataricus + STIV labeled with Cyanine-5 (red) at t=16 h post infection.

tag: t=16 post infection


title: B t=16 Cy5

description: Biological replicate 2 of 3.

source_name: S. solfataricus + STIV labeled with Cyanine-3 (green) at t=16 h post infection.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-5 (red) at t=16 h post infection.


title: B t=16 Cy3

description: Biological replicate 2 of 3.


title: S002_C11

description:
S002_C11_R580G470_50309.gpr
Single sperm from donor#002


title: A t=16 Cy5

description: Biological replicate 1 of 3.


title: S002_A11

description:
S002_A11_R580G470_50309.gpr
Single sperm from donor#002


title: S002_A10

description:
S002_A10_R580G470_50309.gpr
Single sperm from donor#002


title: A t=16 Cy3

description: Biological replicate 1 of 3.


title: A t=24 Cy5

description: Biological replicate 1 of 3.


title: B t=8 Cy5

description: Biological replicate 2 of 3.

source_name: S. solfataricus + STIV labeled with Cyanine-3 (green) at t=8 h post infection.

tag: t=8 h post infection

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-5 (red) at t=8 h post infection.

tag: t=8 post infection


title: C t=8 Cy3

description: Biological replicate 3 of 3.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-3 (green) at t=8 h post infection.

source_name: S. solfataricus + STIV labeled with Cyanine-5 (red) at t=8 h post infection.


title: C t=16 Cy5

description: Biological replicate 3 of 3.


title: B t=8 Cy3

description: Biological replicate 2 of 3.


title: C t=8 Cy5

description: Biological replicate 3 of 3.


title: #11_B10

description:
#11_B10_R600G500_50313.gpr
Single sperm from donor#11


title: S002_D6

description:
S002_D6_R580G470_50309.gpr
Single sperm from donor#002


title: S002_A8

description:
S002_A8_R580G470_50309.gpr
Single sperm from donor#002


title: A t=8 Cy5

description: Biological replicate 1 of 3.


title: A t=8 Cy3

description: Biological replicate 1 of 3.


title: S002_A6

description:
S002_A6_R580G470_50309.gpr
Single sperm from donor#002


title: S002_A9

description:
S002_A9_R580G470_50309.gpr
Single sperm from donor#002


title: S002_A7

description:
S002_A7_R580G470_50309.gpr
Single sperm from donor#002


title: S002_A4

description:
S002_A4_R570G460_50309.gpr
Single sperm from donor#002


title: S002_A2

description:
S002_A2_R590G480_50309.gpr
Single sperm from donor#002


title: C t=0 Cy3

description: Biological replicate 3 of 3.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-3 (green) at t=0 h post infection.

tag: t=0 h post infection

source_name: S. solfataricus + STIV labeled with Cyanine-5 (red) at t=0 h post infection.

tag: t=0 post infection


title: #002_B9

description:
#002_B9_R620G520_50313.gpr
Single sperm from donor#002


title: B t=0 Cy5

description: Biological replicate 2 of 3.

source_name: S. solfataricus + STIV labeled with Cyanine-3 (green) at t=0 h post infection.

source_name: Total RNA from S. solfataricus control cells labeled with Cyanine-5 (red) at t=0 h post infection.


title: #002_B8

description:
#002_B8_R620G520_50313.gpr
Single sperm from donor#002


title: #002_B6

description:
#002_B6_R630G530_50313.gpr
Single sperm from donor#002


title: #002_B5

description:
#002_B5_R630G530_50313.gpr
Single sperm from donor#002


title: #002_B7

description:
#002_B7_R620G520_50313.gpr
Single sperm from donor#002


title: B t=0 Cy3

description: Biological replicate 2 of 3.


title: S002_A1

description:
S002_A1_R590G480_50309.gpr
Single sperm from donor#002


title: A t=0 Cy3

description: Biological replicate 1 of 3.


title: #002_B2

description:
#002_B2_R640G540_50313.gpr
Single sperm from donor#002


title: #002_B1

description:
#002_B1_R640G540_50313.gpr
Single sperm from donor#002


title: A t=0 Cy5

description: Biological replicate 1 of 3.


title: Semen_S002-AG

description:
S002-2_AG_Semen_590G490_50320.gpr
semen sample 11 detected from AG direction

source_name: Semen samples collected from Dr. David Seifer’s infertility test laboratory

tag: Semen


title: Semen_D18-AG

description:
D18_AG_Semen_600G500_50320.gpr
semen sample 9 detected from AG direction


title: Semen_D20-AG

description:
D20_AG_Semen_600G500_50320.gpr
semen sample 10 detected from AG direction


title: Semen_AC09-AG

description:
AC09_AG_Semen_590G490_50320.gpr
semen sample 7 detected from AG direction


title: 3T3L1_DMSO_36hr_rep2

city: Berkeley

first: Jason

middle: T

last: Huff

state: CA

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

description: The second biological replicate of DMSO vehicle treatment for 36hr versus pooled reference.

hyb_protocol: 2 days at 63 °C

scan_protocol: Axon Scanner 4000B; SpotReader (Niles Scientific) was used to extract intensities

data_processing: The ratios of probe intensities were normalized without background subtraction using the 'printtiploess' method of the "limma" package (Smyth, 2004) in BioConductor (Gentleman et al., 2004).

organism: Mus musculus

source_name: 3T3L1, treated with DMSO for 36hr

label_protocol: cDNA was generated by one cycle of reverse transcription (Superscript II, Invitrogen) using 15 ug of total RNA. Cy5 NHS ester was coupled to amino allyl dU in cDNA.

extract_protocol: Total RNA was extracted with QIAshredder and RNeasy kits (Qiagen).

source_name: pooled reference

label_protocol: cDNA was generated by one cycle of reverse transcription (Superscript II, Invitrogen) using 15 ug of total RNA. Cy3 NHS ester was coupled to amino allyl dU in cDNA.


title: 3T3L1_DMSO_36hr_rep3

description: The third biological replicate of DMSO vehicle treatment for 36hr versus pooled reference.


title: 3T3L1_DMSO_36hr_rep4

description: The fourth biological replicate of DMSO vehicle treatment for 36hr versus pooled reference.


title: 3T3L1_DMSO_36hr_rep1

description: The first biological replicate of DMSO vehicle treatment for 36hr versus pooled reference.


title: 3T3L1_dex_36hr_rep3

description: The third biological replicate of dex treatment for 36hr versus pooled reference.

source_name: 3T3L1, treated with dex for 36hr


title: Semen_AB011-AG

description:
AB011_AG_Semen_590G490_50320.gpr
semen sample 4 detected from AG direction


title: Semen_AB027-AG

description:
AB027_AG_Semen_600G500_50320.gpr
semen sample 6 detected from AG direction


title: 3T3L1_dex_36hr_rep1

description: The first biological replicate of dex treatment for 36hr versus pooled reference.


title: 3T3L1_dex_36hr_rep2

description: The second biological replicate of dex treatment for 36hr versus pooled reference.


title: Semen_D17-AG

description:
D17_AG_Semen_590G490_50320.gpr
semen sample 8 detected from AG direction


title: Semen_AB012-AG

description:
AB012-2_AG_Semen_600G500_50320.gpr
semen sample 5 detected from AG direction


title: Semen_AB005-AG

description:
AB005_AG_Semen_590G490_50320.gpr
semen sample 3 detected from AG direction


title: Semen_#12-AG

description:
#12_AG_Semen_600G500_50320.gpr
semen sample 2 detected from AG direction


title: 3T3L1_dex_36hr_rep4

description: The fourth biological replicate of dex treatment for 36hr versus pooled reference.


title: 3T3L1_DMSO_2hr_rep2

description: The second biological replicate of DMSO vehicle treatment for 2hr versus pooled reference.

source_name: 3T3L1, treated with DMSO for 2hr


title: 3T3L1_DMSO_2hr_rep4

description: The  fourth biological replicate of DMSO vehicle treatment for 2hr versus pooled reference.


title: 3T3L1_DMSO_2hr_rep1

description: The first biological replicate of DMSO vehicle treatment for 2hr versus pooled reference.


title: 3T3L1_DMSO_2hr_rep3

description: The  third biological replicate of DMSO vehicle treatment for 2hr versus pooled reference.


title: Semen_#11-AG

description:
#11_AG_Semen_590G490_50320.gpr
semen sample 1 detected from AG direction


title: 3T3L1_dex_2hr_rep4

description: The fourth biological replicate of dex treatment for 2hr versus pooled reference.

source_name: 3T3L1, treated with dex for 2hr


title: 3T3L1_dex_2hr_rep2

description: The second biological replicate of dex treatment for 2hr versus pooled reference.


title: Semen_S002-CT

description:
S002-2_seman_R590G480_50309.gpr
semen sample 11 detected from CT direction


title: Semen_D17-CT

description:
D17_Semen_R580G480_50312.gpr
semen sample 8 detected from CT direction


title: Semen_D18-CT

description:
D18_Semen_R580G480_50312.gpr
semen sample 9 detected from CT direction


title: Semen_AB027-CT

description:
AB027_Semen_R580G480_50311.gpr
semen sample 6 detected from CT direction


title: Semen_D20-CT

description:
D20_Semen_R600G500_50312.gpr
semen sample 10 detected from CT direction


title: Semen_AC09-CT

description:
AC09_Semen_R560G460_50312.gpr
semen sample 7 detected from CT direction


title: Semen_AB012-CT

description:
AB012_2_R600G500_50114.gpr
semen sample 5 detected from CT direction


title: 3T3L1_dex_2hr_rep1

description: The first biological replicate of dex treatment for 2hr versus pooled reference.


title: S. cerevisiae EC1118 continuous culture D=0.05 at 30ºC rep2

city: Santiago

first: Francisco

middle: J

last: Pizarro

address: Av. Vicuna Mackenna 4860

department: Chemical and Bioprocess Engineering

country: Chile

institute: Universidad Catolica de Chile

description: Transcriptional response in laboratory and wine strains of S. cerevisiae to growth temperature

hyb_protocol: Affymetrix standard protocol (overnight)

scan_protocol: Affymetrix standard protocol using Affymetirix Fluidics 400 and Scanner 3000

data_processing: Acquisition and primary data analysis of array images was performed using the Affymetrix Microarray suite v5.0 and dChip 2005 software packages. dChip was used to normalize the data. All arrays were globally scaled to a target value of 120 using the invariant set normalization method. Probe summarization was made using only the perfect match (PM) values. From the 10765 transcript features on the Yeast genome 2.0 arrays, a filter was applied to extract 5814 unique S. cerevisiae open reading frames.

label: Biotin

molecule: polyA RNA

organism: Saccharomyces cerevisiae

label_protocol: mRNA extraction, cDNA synthesis, cRNA synthesis and labeling as well as hybridization to Affymetrix Yeast Genome 2.0 arrays, were performed with the GeneChip one cycle target labeling kit as described in the Affymetrix users’ manual

extract_protocol: Samples for RNA isolation were taken by rapidly sampling 20 mL of culture into a tube with 35-40 mL of crushed ice, decreasing sample temperature to below 2ºC in less than 10 seconds. Cells were pelleted (4500 RPM at 0ºC for 2 minutes), instantly frozen in liquid nitrogen and stored at -80ºC until further use. Total RNA was extracted using FastRNA Pro RED kit (QBiogene, Inc, USA) according to manufacturer’s instructions after thawing samples on ice. Samples with good RNA integrity and quality, assessed by the RNA 6000 Nano LabChip kit ran on an Agilent 2100 Bioanalyzer, were hybridized.

tag: Strain

value: S. cerevisiae EC1118 (Industrial Wine Strain)

tag: Growth conditions

value: Steady state chemostat cultures, N-limited, anaerobic at D=0.05h-1, 30ºC in Minimal Media supplemented with anaerobic factors.


title: S. cerevisiae EC1118 continuous culture D=0.05 at 15ºC rep3

value: Steady state chemostat cultures, N-limited, anaerobic at D=0.05h-1, 15ºC in Minimal Media supplemented with anaerobic factors.


title: S. cerevisiae EC1118 continuous culture D=0.05 at 30ºC rep3


title: C t=0 Cy5

description: Biological replicate 3 of 3.


title: Semen_AB005-CT

description:
AB005_Semen_R580G480_50311.gpr
semen sample 3 detected from CT direction


title: S. cerevisiae EC1118 continuous culture D=0.05 at 30ºC rep1


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 30ºC rep2

value: S. cerevisiae CEN.PK113-7D


title: S. cerevisiae EC1118 continuous culture D=0.05 at 15ºC rep2


title: Semen_AB011-CT

description:
AB011_Semen_R580G480_50311.gpr
semen sample 4 detected from CT direction


title: Semen_#12-CT

description:
#12_Semen_R600G500_50312.gpr
semen sample 2 detected from CT direction


title: S. cerevisiae EC1118 continuous culture D=0.05 at 15ºC rep1


title: 3T3L1_dex_2hr_rep3

description: The third biological replicate of dex treatment for 2hr versus pooled reference.


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 30ºC rep3


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 30ºC rep1


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 15ºC rep2


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 15ºC rep3


title: HD6-10

description:
HD6-10_DNA_R620G520_50312.gpr
Genomic DNA sample 40

source_name: Genomic DNA purchased from the Coriell Institute for Medical Research

tag: from American Indian


title: HD6-8

description:
HD6-8_DNA_R600G500_50312.gpr
Genomic DNA sample 38


title: HD6-9

description:
HD6-9_DNA_R620G520_50312.gpr
Genomic DNA sample 39


title: Semen_#11-CT

description:
#11_Semen_R600G500_50312.gpr
semen sample 1 detected from CT direction


title: HD6-7

description:
HD6-7_DNA_R660G560_50311.gpr
Genomic DNA sample 37


title: S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 15ºC rep1


title: HD6-6

description:
HD6-6_AG_DNA_R700G600_50320.gpr
Genomic DNA sample 36


title: mouse brain from 13.5 dpc embryo, T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, 430B

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: expression data from 13.5 dpc embryonic brain

hyb_protocol: Following fragmentation, 10 micrograms of fragmented target cRNA was hybridized for 16 hr at 45° C on GeneChipR Mouse Expression Array 430B.  Genechips were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Gen/Array Scanner G2500A.

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as the normalization method.

label_protocol: Labeling, hybridization, scanning and data processing were performed at the UC Irvine DNA and Protein Microarray Facility.  Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 9 µg total RNA (GeneChipR Expression Analysis Technical Manual, 2001, Affymetrix, Inc., Santa Clara, CA).

growth_protocol: Neonatal mice and embryos were bred and identified as described  (Buettner, VL, et al., Mammalian Genome, volume 16, 219-227 (2005).

extract_protocol: RNA was prepared by use of Trizol followed by the RNeasy Mini Kit as described in the manufacturers' instructions.

tag: Genotype

value: T9H/+ heterozygotes


title: HD6-4

description:
HD6-4_DNA_R590G490_50311.gpr
Genomic DNA sample 34


title: HD6-5

description:
HD6-5_AG_DNA_R700G600_50320.gpr
Genomic DNA sample 35


title: HD6-3

description:
HD6-3_AG_DNA_R640G540_50320.gpr
Genomic DNA sample 33


title: HD6-2

description:
HD6-2_DNA_R600G500_50311.gpr
Genomic DNA sample 32


title: HD6-1

description:
HD6-1_DNA_R530G430_50306.gpr
Genomic DNA sample 31


title: HD4-8

description:
HD4-8_AG_DNA_R580G480_50320.gpr
Genomic DNA sample 28

tag: from African American


title: HD4-10

description:
HD4-10_DNA_R610G510_50313.gpr
Genomic DNA sample 30


title: neonatal cerebellum, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, 430B

description: expression data from neonatal cerebellum


title: HD4-7

description:
HD4-7_DNA_R530G430_50306.gpr
Genomic DNA sample 27


title: HD4-9

description:
HD4-9_DNA_R610G510_50313.gpr
Genomic DNA sample 29


title: HD4-6

description:
HD4-6_DNA_R590G480_50309.gpr
Genomic DNA sample 26


title: mouse brain from 15.5 dpc embryo, T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, 430B

description: expression data from 15.5 dpc embryonic brain


title: mouse brain from 13.5 dpc embryo, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, 430B


title: HD4-5

description:
HD4-5_DNA_R530G430_50306.gpr
Genomic DNA sample 25


title: HD4-4

description:
HD4-4_DNA_R510G410_50306.gpr
Genomic DNA sample 24


title: HD4-2

description:
HD4-2_DNA_R550G450_50306.gpr
Genomic DNA sample 22


title: HD4-3

description:
HD4-3_DNA_R520G420_50306.gpr
Genomic DNA sample 23


title: HD2-9

description:
HD2-9_DNA_R550G450_50306.gpr
Genomic DNA sample 19

tag: from Chinese


title: HD2-10

description:
HD2-10_DNA_R640G540_50312.gpr
Genomic DNA sample 20


title: HD2-8

description:
HD2-8_DNA_R600G500_50312.gpr
Genomic DNA sample 18


title: neonatal cerebellum, T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, 430B


title: neonatal cortex,T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, 430B

description: expression data from neonatal cortex (forebrain)


title: neonatal cortex, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, 430B


title: mouse brain from 13.5 dpc embryo,  T9H/+  matdup proximal Chr 7, patdup proximal Chr 15, 430A

description: expression data from 13.5 dpc embryonic brain

hyb_protocol: Following fragmentation, 10 micrograms of fragmented target cRNA was hybridized for 16 hr at 45° C on GeneChipR Mouse Expression Array 430A.  Genechips were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.


title: mouse brain from 13.5 dpc embryo,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, 430A


title: HD2-7

description:
HD2-7_DNA_R530G430_50306.gpr
Genomic DNA sample 17


title: HD2-6

description:
HD2-6_DNA_R560G460_50201.gpr
Genomic DNA sample 16


title: HD2-4

description:
HD2-4_DNA_R560G460_50201.gpr
Genomic DNA sample 14


title: HD2-3

description:
HD2-3_DNA_R530G430_50201.gpr
Genomic DNA sample 13


title: HD2-5

description:
HD2-5_DNA_R560G460_50201.gpr
Genomic DNA sample 15


title: mouse brain from 15.5 dpc embryo,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep2, 430A


title: mouse brain from 15.5 dpc embryo,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep1, 430A


title: mouse brain from 15.5 dpc embryo,  T9H/+  matdup proximal Chr 7, patdup proximal Chr 15, biological rep1, 430A


title: mouse brain from 15.5 dpc embryo,  T9H/+  matdup proximal Chr 7, patdup proximal Chr 15, biological rep2, 430A


title: HD2-2

description:
HD2-2_DNA_R580G480_50312.gpr
Genomic DNA sample 12


title: HD1-10

description:
HD1-10_DNA_R710G600_50309.gpr
Genomic DNA sample 10

tag: from Northern European


title: HD1-8

description:
HD1-8_DNA_R560G460_50201.gpr
Genomic DNA sample 8


title: HD1-9

description:
HD1-9_AG_DNA_R610G510_50320.gpr
Genomic DNA sample 9


title: HD2-1

description:
HD2-1_DNA_R540G440_50201.gpr
Genomic DNA sample 11


title: neonatal cerebellum,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep2, 430A

description: expression data from neonatal cerebellum


title: HD1-7

description:
HD1-7_DNA_R590G490_50201.gpr
Genomic DNA sample 7


title: neonatal cerebellum,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep1, 430A


title: HD1-6

description:
HD1-6_DNA_R550G450_50201.gpr
Genomic DNA sample 6


title: HD1-4

description:
HD1-4_DNA_R550G450_50201.gpr
Genomic DNA sample 4


title: mouse P10 Cornea_2

city: Baltimore

first: Shukti

last: Chakravarti

state: MD

address: 720 Rutland Ave

department: Medicine

institute: Johns Hopkins University School of Medicine

description:
Detail could be found in " Differential gene expression patterns of the developing and adult mouse cornea compared to the lens and tendon" Experimental Eye Research. 2008 in press.
Keywords = cornea	maturation

hyb_protocol: using standard Affymetrix procedures

scan_protocol: using standard Affymetrix procedures

data_processing:
The expression values of all probe sets are scaled to 150 of Target Intensity by using Affymetrix Microarray Suite 5.0. Two replicates of Lens were analyzed.
The model-based DNA-Chip Analyzer (dChip) software (http://www.dchip.org/) was used to normalize the data from the image files for array-to-array comparison (Li and Wong 2001).
The data table below reports both the MAS5.0- and dChip-calculated data.

source_name: corneal stroma

label_protocol: Targets were produced using standard Affymetrix procedures from 5ug of total RNA.

extract_protocol: Total RNA was extracted using TRIzol reagent.

tag: Corneal stroma was dissected from postnatal 10 days CD-1 mouse.


title: HD1-5

description:
HD1-5_DNA_R550G450_50201.gpr
Genomic DNA sample 5


title: mouse P10 Cornea_1


title: neonatal cerebellum,  T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, biological rep2, 430A


title: HD1-2

description:
HD1-2_R600G500_50114.gpr
Genomic DNA sample 2


title: neonatal cortex,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep2, 430A

description: expression data from neonatal cortex (forebrain)


title: mouse Adult cornea_3

tag: Corneal stroma was dissected from 7-8 weeks old CD-1 mouse.


title: neonatal cerebellum,  T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, biological rep1, 430A


title: HD1-1

description:
HD1-1_R600G500_50114.gpr
Genomic DNA sample 1


title: HD1-3

description:
HD1-3_DNA_R550G450_50201.gpr
Genomic DNA sample 3


title: Growth stage control_2.5hr

status: Public on Jul 24 2008

city: St. Paul

first: Zhigang

last: Zhang

state: MN

address: 1479 Gortner Avenue, Suite 140

department: BioTechnology Institute

institute: University of Minnesota

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between time-point samples (2.5hr) during the normal growth in BG-11 medium  and mid-exponential growth phase cell samples (OD730nm=0.6)

hyb_protocol: Microarray hybridization and washing conditions were based on E. coli cDNA microarray protocols (Khodursky, Bernstein et al. 2003) with some modifications. To reduce cross-hybridization, a pre-hybridization step was performed for Synechocystis slides as follows: 45ml pre-hybridization solution (containing 4.5 ml of 20× SSC, 1.1 ml of HEPES (pH 7), 250 μl of salmon sperm DNA and 250 μl of BSA) was preheated to 65 oC in a water bath. Then microarray slides were incubated vertically in the preheated solution for 45 min at 65 oC. The slides were washed 3 times in sterile dH2O and were spin-dried for 2 min at 600 rpm. The slides were then immediately used for hybridization. The hybridization mixture (total volume 21 μl) contained on-column cleaned Cy3-dUTP and Cy5-dUTP labelled samples, 3 μl of 20×SSC, 0.5 μl of 1M HEPES buffer (pH 7), 2 μl of BSA and 2 μl of salmon sperm DNA as blocking agent and 0.75 μl of 5% SDS. The hybridizations were carried out under a 20×20 flat cover-slip in hybridization chambers (Monterey Industries) submerged in a 65°C water bath for 5 to 6 hours. Slides were washed sequentially in each of the following solutions: Chamber 1: 330 ml of dH2O, 15 ml of 20× SSC, 10 ml of 10% SDS; Chamber 2: 350 ml of dH2O and 1 ml of 20× SSC; and Chamber 3: 350 ml of dH2O and 0.5 ml of 20× SSC. After the washes, the slides were air dried by centrifugation for 3 min at 600 rpm.

scan_protocol: Scanned on an Axon GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA) at the resolution of 10 µm per pixel. The scanned 16-bit TIFF images were analyzed by using the software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, CA).

data_processing: The original fluorescence intensity gene expression data were pre-processed using lowess smoothing and an ANOVA linear model. The data were centered. The normalized Cy-5/Cy-3 log2(ratio) values were taken to reflect the relative gene expression level changes. The statistically significant genes were identified by using significance analysis of microarray (SAM) (Tusher et al. 2001) with a false discovery rate lower than 1%.

organism: Synechocystis sp. PCC 6803

source_name: Control sample (mid-exponential phase cells)

label_protocol: Direct fluorescent labelling of reverse-transcribed cDNA was performed. The labelling reaction consisted of 8-15 μg of purified total RNA, 5-10 μg of random hexamer (pdN6), 3μl of dNTP mix (1 mM dATP, 1 mM dCTP, 1 mM dGTP and 0.4 mM dTTP), 1.0 µl of 1mM Cy3- or Cy5-dUTP, 1× superscript buffer, 3.0 µl of 0.1M DTT, and 1µl Superscript II (Invitrogen). The reactions were incubated at room temperature for 10min before transferring to 42oC for 1hr 50min. labeled cDNA was purified using a Microcon YM-30 column (Millipore).

extract_protocol: The bacterial samples were fixed by a stop solution (see above) and centrifuged at 4oC. The cell pellets were snap-frozen in liquid nitrogen before storing at -80oC until required. Total RNA was isolated using standard hot phenol-chloroform method with 1×TE sucrose buffer (10mM Tris, 1mM EDTA, 0.5M sucrose, pH 8) at 50oC instead of using TE buffer (10mM Tris, 1mM EDTA, pH 8) at 25oC. Residual DNA was removed by DNase I digestion.

tag: Control cells (mid-log, 0hr)

source_name: Growth stage control sample

tag: Growth stage control_2.5hr


title: Growth stage control_4hr

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between time-point samples (4hr) during the normal growth in BG-11 medium  and mid-exponential growth phase cell samples (OD730nm=0.6)

tag: Growth stage control_4hr


title: Growth stage control_11hr

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between time-point samples (11hr) during the normal growth in BG-11 medium  and mid-exponential growth phase cell samples (OD730nm=0.6)

tag: Growth stage control_11hr


title: neonatal cortex, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, biological rep2, 430A


title: mouse Adult cornea_1

hyb_protocol: using standard Affymetrix protocol

scan_protocol: using standard Affymetrix protocol


title: neonatal cortex,  T9H/+ patdup proximal Chr 7, matdup proximal Chr 15, biological rep1, 430A


title: neonatal cortex, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, biological rep1, 430A


title: mouse Adult cornea_2


title: Growth stage control_1hr

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between time-point samples (1hr) during the normal growth in BG-11 medium  and mid-exponential growth phase cell samples (OD730nm=0.6)

tag: Growth stage control_1hr


title: Sulfate deprivation (-SO4/+HEPES) time course 24hr_rep2

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 24hr after  sulfate deprivation (with HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium

source_name: Sulfate deprived (-SO4/+HEPES)  cells


title: Sulfate deprivation (-SO4/+HEPES) time course 24hr_rep1


title: Sulfate deprivation (-SO4/+HEPES) time course 12hr_rep2

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 12hr after  sulfate deprivation (with HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/+HEPES) time course 1hr_rep1

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 1hr after  sulfate deprivation (with HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/+HEPES) time course 1hr_rep2


title: Sulfate deprivation (-SO4/+HEPES) time course 12hr_rep1


title: Sulfate deprivation (-SO4/-HEPES) time course 72hr_rep2

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 72hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium

source_name: Sulfate deprived (-SO4/-HEPES)  cells


title: HD4-1

description:
HD4-1_DNA_R530G430_50306.gpr
Genomic DNA sample 21


title: Sulfate deprivation (-SO4/-HEPES) time course 72hr_rep1


title: Sulfate deprivation (-SO4/-HEPES) time course 24hr_rep1

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 24hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 48hr_rep1

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 48hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 24hr_rep2


title: Sulfate deprivation (-SO4/-HEPES) time course 12hr_rep1

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 12hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 12hr_rep2


title: Chip 68 volatile+herbivory

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

description: On the day of collection, each leaf was excised at the petiole, photographed, and then placed in a labeled coin envelope and submerged directly into liquid N2. Each photograph also contained a standard of known area, from which leaf area and % damage calculations were determined (Sigma Scan 500, Systat Software Inc.). Herbivore Larvae consumed statistically similar amounts on the treatment and control leaves (24 hours: z3HAC-treated leaves: 4.7 ± 1.8 cm2; controls: 4.3 ± 1.7 cm2). The snap-frozen leaves were stored at -80oC until grinding. Each leaf was ground in an individual mortar and pestle under liquid N2. Ground tissue was weighed into vials for RNA extraction.

hyb_protocol: Hybidizations were carried out at Penn State using thier standard procedures: Prehybridization D.1.4. Prehybridize the slide in a Petri dish at room temp on an orbital shaker (50 rpm) for 15 min. D.1.5. Transfer the slide into a 50 ml Falcon tube filled with dH2O. Rock the tube end to end in a roughly horizontal plane, 50 times with DNA side of slide facing up. Replace the H2O, and repeat the procedure twice more. D.1.6. Place the slide into a new Falcon tube filled with ethanol. Dry slides either by spinning (in empty Falcon tubes) at 2,500 rpm for 2 min at room temperature, or by blowing under a heavy stream of filtered air using the Microarray Air Jet. Dry immediately. The slides are ready for hybridization. Do not leave them exposed for more than 1 hr Hybridization D.1.7. Resuspend the labeled cDNAs in an appropriate volume (e.g., 50 μL each) of hybridization buffer and combine. MTU-BRC Tsai Lab Microarray Protocols H:\MTU Microarray Protocols 090407.doc 8 Ideally, the Cy3 and Cy5 targets should have similar FOI and cDNA concentrations after labeling. Mix equal amounts of cDNA targets (each with approximately 50 pmol of incorporated dye when using the random hexamer labeling). D.1.8. Apply hybridization mixture to the slide (non-barcode side), and cover with a piece of parafilm. D.1.9. Place into a humid hybridization chamber (with a 5X SSC-soaked paper towel) pre-set at 60oC to denature any target secondary structure. Immediately re-set the chamber to 39oC for cool-down, and hybridize at that temperature for 20-36 hours. Note: Longer hybridization times can significantly improve the hybridization results as reported by Sartor et al. (2004) and confirmed in our hands with the Tecan automated hybridization station and with manual hybridization. We used to perform hybridization overnight (~16 hr), but are now doing this step for 36 hr, with mixing, if using the Tecan. Reference: Sartor M, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M, and Tomlinson CR (2004) Microarray results improve significantly as hybridization approaches equilibrium. BioTechniques 36:790-796. Washing D.1.10. Immerse the slide in 500 ml Wash solution I prewarmed to 42oC in a beaker. Shake the slide gently to loose the cover slip (approximately 30 sec). Move slide to a second beaker of prewarmed Wash Sol. I, and swirl through the solution, dipping in and out 2-3 times (30 sec). Note: Do not allow the arrays to dry out between washes, as this will result in high background. Protect the slides from light at all times. D.1.11. Move the slide to another beaker containing pre-warmed Wash solution II and repeat washing for 30 sec. D.1.12. Rinse with ddH2O water for 5 seconds. D.1.13. Dry the slide by spinning at 2,500 rpm at room temperature for 2 min, or under heavy stream of filtered air. Exactly how the drying step is conducted with forced air will greatly affect slide background. In general, operate quickly and completely as you blow from the tip toward the base of the slide. Do not leave traces of liquid that you have to re-dry. D.1.14. Scan immediately.

scan_protocol: Scans were performed at Penn State using GenePix image acquisition

data_processing: Raw signal intensity detected for each probe was log2-transformed and normalized by setting the array mean to 0 and standard deviation to 1 using SAS 9.0 (SAS Institute, Cary, NC).

organism: Populus x canadensis

source_name: LPI9 pretreated with z3HAC in dichloromethane solvent (volatile) and then fed on by gypsy moths for 48 hours

label_protocol: Total RNA was labeled using Ambion's Amino Allyl Message Amp II aRNA Amplification Kit (#AM1753) according to the manufacturer's instructions. Briefly, 1 ug of each sample was reversed transcribed using T7-oligo(dT) priming and subsequently second strand cDNA synthesis was performed. The resulting double stranded cDNA was purified and then used as a template for in vitro transcription during which amino allyl-modified UTP was incorporated. The resulting amino allyl-modified cRNA was purified and coupled with Cy3 or Cy5 (GE Amersham, #RPN5661) as appropriate . We used dye swapping to account for potential dye effects. Dye coupled cRNA was purified and 4 ug was fragmented and subsequently dissolved in 60ul of hybridization solution.

growth_protocol: Hybrid poplar (Populus deltoides x nigra, clone “OGY”: Magnoliopsida; Malpighiales; Salicaceae; Aigeiros section of Populus) saplings were grown from cuttings in a walk-in growth chamber maintained at 25oC with a 16:8 photoperiod. Cuttings were planted in five-gallon pots in commercial potting soil (MetroMix 250, SunGro, Bellevue, WA, USA) and watered as necessary. Due to supplements in the soil, fertilization was not required and poplars grew to heights of ~1.5 m in 12-15 weeks. Newly molted 4th instar L. dispar larvae were used for all experiments. Egg masses were obtained from APHIS (Otis Plant Protection Lab, Cape Cod, MA, USA) and reared through 3rd instar on artificial diet. Newly molted 4th instar larvae cleared their gut contents prior to molting.

extract_protocol: Total RNA was extracted from each sample by modifying a cCetyl trimethylammonium bromide (CTAB) method (Chang et al., 1993) for extracting small samples. Briefly, ~150 mg ground tissue was added to 1 ml CTAB solution, heated at 65oC, and double purified with chloroform. RNA in the aqueous extract was precipitated overnight with LiCl, centrifuged, re-dissolved in SSTE, purified with chloroform, and precipitated with 100% EtOH. RNA quality was measured with Agilent Bioanalyzer, and all samples had RNA integrity number (RIN) values >7. Total RNA (5 ug per sample) was treated with DNAse (Turbo DNAse, Ambion) according to the manufacturer's directions. Chang S, Puryear J, Cairney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11: 113-116.

treatment_protocol: All experiments were conducted from March-April 2007 in a single walk-in growth chamber maintained as described above. Poplars were equilibrated to the chamber for 24 hours prior to manipulations. Two fully-expanded source leaves (leaf plastochron index LPI 8 and 9) were isolated per sapling using individual 15x15x1 cm Teflon/glass chambers. These two leaves are non-orthostichous, which means that they do not readily share assimilates or wound signals. Thus, for the purposes of these experiments, treatment leaves did not interact with their respective control leaves. However, the leaves are of slightly different ages and, to control for this potential effect, we randomized which leaf would receive the z3HAC treatment. Flow into each chamber was set at 2.0 L/min, which was sufficient to avoid condensation within the chamber. The experiments were designed to have two consecutive albeit separate treatments: exposure to z3HAC and subsequent application of L. dispar larvae. We used commercially available z3HAC (Sigma-Aldrich), and prepared concentrations to infuse into each septum such that it delivered ~40 ng z3HAC per application. After a pretreatment volatile collection (Day 1 and night starting Day 2), z3HAC-infused rubber septa were placed into the leaf chambers with each treatment leaf (morning of Day 2). Control leaves each received a septum infused with just the dichloromethane solvent. Septa were replaced twice, once before the afternoon collection on Day 2, and before the morning collection on Day 3. All septa were removed during the night of Day 3, since most volatile production stops at night in this hybrid (Fig 5a). On the morning of Day 4, two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf, regardless of whether the leaf received the treatment or control septa on Days 2 and 3. The herbivores remained on the leaves for ~24 hours.

tag: LPI 9 leaf that was pretreated with z3HAC in dichloromethane solvent (volatile) for 3 days. On day 4 two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf. The herbivores remained on the leaves for 24 hours.


title: Chip 67 volatile+herbivory

source_name: LPI8 pretreated with z3HAC in dichloromethane solvent (volatile) and then fed on by gypsy moths for 48 hours

tag: LPI 8 leaf that was pretreated with z3HAC in dichloromethane solvent (volatile) for 3 days. On day 4 two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf. The herbivores remained on the leaves for 24 hours.


title: Chip 68 control+herbivory

source_name: LPI8 pretreated with dichloromethane solvent (control) and then fed on by gypsy moths for 48 hours

tag: LPI 8 leaf that was pretreated with dichloromethane solvent (control) for 3 days. On day 4 two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf. The herbivores remained on the leaves for 24 hours.


title: Chip 67 control+herbivory

source_name: LPI9 pretreated with dichloromethane solvent (control) and then fed on by gypsy moths for 48 hours

treatment_protocol: All experiments were conducted from March-April 2007 in a single walk-in growth chamber maintained as described above. Poplars were equilibrated to the chamber for 24 hours prior to manipulations. Two fully-expanded source leaves (leaf plastochron index LPI 8 and 9) were isolated per sapling using individual 15x15x1 cm Teflon/glass chambers. These two leaves are non-orthostichous, which means that they do not readily share assimilates or wound signals. Thus, for the purposes of these experiments, treatment leaves did not interact with their respective control leaves. However, the leaves are of slightly different ages and, to control for this potential effect, we randomized which leaf would receive the z3HAC treatment. Flow into each chamber was set at 2.0 L/min, which was sufficient to avoid condensation within the chamber. The experiments were designed to have two consecutive albeit separate treatments: exposure to z3HAC and subsequent application of L. dispar larvae. We used commercially available z3HAC (Sigma-Aldrich), and prepared concentrations to infuse into each septum such that it delivered ~40 ng z3HAC per application. After a pretreatment volatile collection (Day 1 and night starting Day 2), z3HAC-infused rubber septa were placed into the leaf chambers with each treatment leaf (morning of Day 2). Control leaves each received a septum infused with just the dichloromethane solvent. Septa were replaced twice, once before the afternoon collection on Day 2, and before the morning collection on Day 3. All septa were removed during the night of Day 3, since most volatile production stops at night in this hybrid (Fig 5a). On the morning of Day 4, two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf, regardless of whether the leaf received the treatment or control septa on Days 2 and 3. The herbivores remained on the leaves for ~24hours.

tag: LPI 9 leaf that was pretreated with dichloromethane solvent (control) for 3 days. On day 4 two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf. The herbivores remained on the leaves for 24 hours.


title: Chip 66 volatile+herbivory


title: Chip 66 control+herbivory


title: mouse brain from 15.5 dpc embryo, T9H/+ matdup proximal Chr 7, patdup proximal Chr 15, 430B

description: expression data from 15.5 dpc embryonic brain


title: Chip 65 volailte+herbivory


title: Sulfate deprivation (-SO4/-HEPES) time course 6hr_rep2

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 6hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 6hr_rep1


title: Sulfate deprivation (-SO4/-HEPES) time course 3hr_rep3

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 3hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 6hr_rep3


title: cell at T05_1.biological rep2

city: Seoul

first: Dong-Wook

last: Kim

address: 221, Heukseok-Dong, Dongjak-Ku

department: Lifescience

country: South Korea

institute: Chung-Ang University

description: Gene expression data from ESP_treated cells for 0hr

hyb_protocol: 750 ng of cRNA was hybridized to a human-8 expression bead array for 16 hr at 58¡É

scan_protocol: Scans are performed on the illumine BeadArray Reader scanner.

data_processing: The data were extracted using the Bead Studio v 2.1.12. Quantile normalization.

source_name: Hucct1 cells after 24hr of ESP treatment

label_protocol: Biotinylated cRNA was prepared using Ambio Illumina RNA amplification kits (Ambion, Austin, TX, USA) according to the manufacturer¡¯s protocols.

growth_protocol: HuCCT1 cells were cultured in RPMI1640 medium

extract_protocol: Total RNA was extracted from the ESP-treated cells using TRIzol according to the manufacturer¡¯s protocols.

treatment_protocol: HuCCT1 cells were gradually depreived of serum by 1% FBS for overnight. These serum-starved cells were treated with 800ng/ml ESP and incubated for the indicated times (T01-T05)

tag: Tissue

value: Bile duct carcinoma


title: Chip 65 control+herbivory

hyb_protocol: D.1.7. Resuspend the labeled cDNAs in an appropriate volume (e.g., 50 μL each) of hybridization labeling. Mix equal amounts of cDNA targets (each with approximately 50 pmol of incorporated dye when using the random hexamer labeling).

label_protocol: Total RNA was labeled using Ambion's Amino Allyl Message Amp II aRNA Amplification Kit (#AM1753) according to the manufacturer's instructions.  Briefly, 1 ug of each sample was reversed transcribed using T7-oligo(dT) priming and subsequently second strand cDNA synthesis was performed. The resulting double stranded cDNA was purified and then used as a template for in vitro transcription during which amino allyl-modified UTP was incorporated. The resulting amino allyl-modified cRNA was purified and coupled with Cy3 or Cy5 (GE Amersham, #RPN5661) as appropriate . We used dye swapping to account for potential dye effects.  Dye coupled cRNA was purified and 4 ug was fragmented and subsequently dissolved in 60ul of hybridization solution.

tag: LPI 8 leaf that was pretreated with dichloromethane solvent (control) for 3 days. On day 4 two newly molted 3rd or 4th instar gypsy moth larvae were added to each leaf.  The herbivores remained on the leaves for 24 hours.


title: Sulfate deprivation (-SO4/-HEPES) time course 3hr_rep1


title: Sulfate deprivation (-SO4/-HEPES) time course 1hr_rep3

description: Transcriptional profiling of Synechocystis sp. PCC 6803 was compared between cells of 1hr after  sulfate deprivation (without HEPES buffering) and mid-exponential growth phase cells grown in BG-11 medium


title: Sulfate deprivation (-SO4/-HEPES) time course 3hr_rep2


title: cell at T03_1.biological rep2

source_name: Hucct1 cells after 3hr of ESP treatment


title: cell at T04_1.biological rep2

source_name: Hucct1 cells after 9hr of ESP treatment


title: Sulfate deprivation (-SO4/-HEPES) time course 1hr_rep2


title: cell at T03.biological rep1


title: cell at T05.biological rep1


title: cell at T04.biological rep1


title: Sulfate deprivation (-SO4/-HEPES) time course 1hr_rep1


title: Primary-LvMx-rep2

status: Public on Jul 23 2008

city: kamakura

first: yoji

last: ueda

state: Kanagawa

address: 6-10-1 Tebiro

country: Japan

institute: Toray Industries, Inc.

description: Biological replicate 2 of 2.

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray lite (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: Colon26 primary tumours

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Colon26 cells were obtained from Cell Resource Center for Biochemical Research (Tohoku University, Japan) and cultured in RPMI1640 (Nacalai Tesque) containing 10% FCS.  The cells were trypsinized, collected and injected into the rectal submucosa of Balb/c mice.

extract_protocol: RNA samples were collected from Colon26 cells in primary tumours and their liver metastases using TRI reagent (SIGMA).

tag: Colon26 primary tumours

source_name: liver metastases

tag: liver metastases


title: Fascicle Unstrained 1h rep2

city: London

first: Eijiro

last: Maeda

address: Mile End Road

department: Engineering

country: United Kingdom

institute: Queen Mary, University of London

hyb_protocol: According to protocol provided by Illumina

scan_protocol: Scanning procedures were carried out as described by Illumina

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Rattus norvegicus

source_name: Rat tail tendon

label_protocol: biotin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: Wistar, male, 5-month old, no previous injury


title: Fascicle Unstrained 1h rep1


title: Fascicle Strained 1h rep3


title: Fascicle Strained 1h rep2


title: Fascicle Unstrained 1h rep3


title: cell at T02.biological rep1

source_name: Hucct1 cells after 1hr of ESP treatment


title: Fascicle Unstrained 24h rep2


title: Fascicle Strained 24h rep3


title: Fascicle Unstrained 24h rep3


title: Primary-LvMx-rep1

description: Biological replicate 1 of 2.


title: Fascicle Strained 24h rep2


title: Fascicle Strained 24h rep1


title: Fascicle Unstrained 24h rep1


title: Thyroid tumor sample 34

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre

description: Gene expression data from thyroid cancer

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Thyroid tumor sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: thyroid


title: Thyroid tumor sample 35


title: Wpl1-9PK distribution along the whole genome (+NOC)

first: Tamar Tom

last: Rolef Ben-Shahar

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK London Research Institute

description: Wpl1-9PK distribution along the whole genome in metaphase-arrested cells in the presence of nocodazole. [Figure S1]

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Reference: Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4).

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells in YP + 2% Galactose were synchronized in metaphase arrest with nocodazole.

extract_protocol:
Extraction was performed as previously described (Katou et al. 2003).
Reference:
Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

tag: Strain 877 = MATa WPL-9PK::KAN


title: Thyroid normal sample 16

source_name: Thyroid normal sample


title: Thyroid normal sample 15


title: Thyroid tumor sample 31


title: Thyroid tumor sample 32


title: Thyroid tumor sample 28


title: Thyroid normal sample 10


title: Thyroid tumor sample 33


title: Thyroid tumor sample 25


title: Thyroid normal sample 13


title: Thyroid tumor sample 29


title: Thyroid tumor sample 30


title: Thyroid normal sample 12


title: Thyroid tumor sample 27


title: Thyroid normal sample 14


title: Thyroid normal sample 11


title: Thyroid tumor sample 23


title: Fascicle Strained 1h rep1


title: eco1-1

description: S. cerevisiae eco1-1

hyb_protocol: as in D. Gresham et al., Science 311, 1932 (2006). Labeled DNA was mixed with 27 ul water, 150 ul 2x hybe buffer, 15 ul 10 mg/gl BSA, 3 ul 10 mg/ml salmon sperm DNA, 5 ul 3 nM control oligo B2, Incubate 99C 5 min, then at 45C 5 min and spun 5 min. 200 ul probe was added to prehybed Sc03b_MR_v04 chip and incubated to hybe for 20 hours at 45C 60 RPM in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). sample washing was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix), using the EukGE-WS2v4 protocol with standard washA washB buffers, SAPE (stain 1 and 3): 12 ul 1 mg/ml R-streptavidin phycoerythrin (to 10 ug/ml), 240 ul 10 mg/ml BSA, 600 ul 2x stain buffer, water to 1.2 ml, antibody solution (stain 2) 6 ul 10 mg/ml goat IgG, 120 ul 10 mg/ml BSA, 3.6 ul 0.5 mg/ml anti-streptavidin antibody (goat), biotinylated, 300 ul 2x stain buffer, water to 600 ul.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing:
Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4).
Probe level signals were processed using SNPScanner.
Gresham, D. et al. Genome-wide detection of polymorphisms at nucleotide
resolution with a single DNA microarray. Science 311, 1932-1936 (2006).

source_name: S. cerevisiae eco1-1

label_protocol: as in D. Gresham et al., Science 311, 1932 (2006), using BioArray Terminal Labeling Kit (Enzo 42630); To 10 ug of DNAse digested DNA in 1x one-phor-all + 2 mM CoCl2 add at room temperature 20 ul 5x reaction buffer, 10 l 10x CoCl2; 1 ul Biotin-ddUTP, 2 ul Terminal Deoxynucleotide Transferase and water to 100 ul. Incubate at 37C 1 hour, transfer to ice and stop with 5 ul 0.2 M EDTA.

growth_protocol: cells were grown to saturation in YPD media before genomic DNA extraction

extract_protocol: DNA was extrcted using QIAGEN genomic tip G100 according to manufacturers manual

tag: MATα eco1-1 tetOs::URA3 tetR-GFP


title: eco1-1 SUPb2

description: S. cerevisiae eco1-1 with spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPb1

source_name: S. cerevisiae eco1-1 SUPb2

tag: MATα eco1-1 tetOs::URA3 tetR-GFP; spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPb2


title: eco1-1 SUPb1

source_name: S. cerevisiae eco1-1 SUPb1

tag: MATα eco1-1 tetOs::URA3 tetR-GFP; spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPb1


title: Thyroid normal sample 8


title: Thyroid tumor sample 24


title: Thyroid tumor sample 20


title: eco1-1 SUPb3

description: S. cerevisiae eco1-1 with spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPb3

source_name: S. cerevisiae eco1-1 SUPb3

tag: MATα eco1-1 tetOs::URA3 tetR-GFP; spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPb3


title: eco1-1 SUPa

description: S. cerevisiae eco1-1 with spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPa

source_name: S. cerevisiae eco1-1 SUPa

tag: MATα eco1-1 tetOs::URA3 tetR-GFP; spontaneous suppressor mutation for eco1-1 thermosensitive growth SUPa


title: Thyroid normal sample 9


title: Thyroid tumor sample 22


title: Thyroid normal sample 6


title: Thyroid tumor sample 14


title: Thyroid tumor sample 15


title: Thyroid tumor sample 18


title: Thyroid normal sample 4


title: Thyroid tumor sample 21


title: Thyroid normal sample 7


title: Thyroid tumor sample 17


title: Thyroid tumor sample 19


title: Thyroid normal sample 2


title: Thyroid tumor sample 10


title: Thyroid tumor sample 16


title: Thyroid tumor sample 11


title: Thyroid tumor sample 13


title: Thyroid normal sample 5


title: Thyroid tumor sample 7


title: Thyroid tumor sample 8


title: Thyroid normal sample 3


title: Thyroid normal sample 1


title: Thyroid tumor sample 12


title: Thyroid tumor sample 9


title: Patient 076 with adenocarcinoma

status: Public on Apr 01 2009

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: Cy5-sample cRNA and Cy3-common reference cRNA were hybridized to a custom Agilent oligonucleotide microarray, containing a total of 21,619 spots corresponding to 18,175 unique genes, followed by confocal laser scanning (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Primary lung tumor

label_protocol: cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescent Linear Amplification kit (Agilent Technologies, Palo Alto, CA).

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 250 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: Annotation

tag: Position in Figure 1 (L to R)

tag: Age

tag: Sex

value: F

tag: Histology

value: AD

tag: Smoking (BI)

tag: pTNM

tag: pStage

value: IA

tag: Status

value: Dead

tag: Survival (days)

tag: Evidence of relapse

value: Y

tag: Site of relapse

value: Local rec.,Brain

tag: EGFR status

value: Wt

tag: K-ras Status

tag: p53 Status

value: Mut

tag: Gefitinib treatment:

tag: Position in Figure 2 (L to R)

tag: Expression profile-based classification

value: TRU-a

tag: Invasion

value: Definite but focal

tag: Necrosis

value: Negative

tag: Grade

value: Moderately

tag: BAC features

source_name: Total RNA from 20 lung cell lines representing all major histological types of lung cancers, labeled with Cyanine-3 (green).


title: Thyroid tumor sample 2

tag: Tissue


title: Thyroid tumor sample 1


title: Thyroid tumor sample 4


title: Oesophagus tumor sample 15

description: Gene expression data from Oesophagus cancer

source_name: Oesophagus tumor sample

value: Oesophagus


title: Oesophagus tumor sample 14


title: Thyroid tumor sample 5


title: Oesophagus normal sample 9

source_name: Oesophagus normal sample


title: Oesophagus tumor sample 13


title: Oesophagus tumor sample 9


title: Thyroid tumor sample 6


title: Oesophagus tumor sample 12


title: Oesophagus normal sample 13


title: Oesophagus normal sample 10


title: Oesophagus normal sample 8


title: Thyroid tumor sample 3


title: Oesophagus normal sample 11


title: Oesophagus tumor sample 16


title: Oesophagus normal sample 12


title: Oesophagus normal sample 7


title: Oesophagus tumor sample 8


title: Oesophagus tumor sample 10


title: Oesophagus tumor sample 7


title: Oesophagus normal sample 6


title: Oesophagus tumor sample 11


title: Thyroid tumor sample 26


title: Oesophagus normal sample 2


title: Oesophagus tumor sample 3


title: lung normal sample 12

description: Gene expression data from lung cancer

source_name: lung normal sample

value: lung


title: Oesophagus normal sample 5


title: Oesophagus tumor sample 6


title: Oesophagus tumor sample 1


title: Oesophagus normal sample 1


title: Oesophagus tumor sample 4


title: lung tumor sample 15

description: Gene expression data from lung cancer

source_name: lung tumor sample


title: Oesophagus normal sample 4


title: lung normal sample 8

description: Gene expression data from lung cancer


title: lung normal sample 9

description: Gene expression data from lung cancer


title: lung tumor sample 18

description: Gene expression data from lung cancer


title: Oesophagus tumor sample 2


title: lung tumor sample 14

description: Gene expression data from lung cancer


title: Oesophagus normal sample 3


title: lung normal sample 11

description: Gene expression data from lung cancer


title: lung normal sample 10

description: Gene expression data from lung cancer


title: lung tumor sample 16

description: Gene expression data from lung cancer


title: Oesophagus tumor sample 5


title: lung tumor sample 17

description: Gene expression data from lung cancer


title: lung normal sample 6

description: Gene expression data from lung cancer


title: lung tumor sample 13

description: Gene expression data from lung cancer


title: lung normal sample 7

description: Gene expression data from lung cancer


title: lung tumor sample 12

description: Gene expression data from lung cancer


title: lung tumor sample 11

description: Gene expression data from lung cancer


title: lung tumor sample 10

description: Gene expression data from lung cancer


title: lung tumor sample 9

description: Gene expression data from lung cancer


title: lung tumor sample 7

description: Gene expression data from lung cancer


title: lung normal sample 2

description: Gene expression data from lung cancer


title: lung tumor sample 5

description: Gene expression data from lung cancer


title: lung normal sample 4

description: Gene expression data from lung cancer


title: lung normal sample 3

description: Gene expression data from lung cancer


title: lung normal sample 5

description: Gene expression data from lung cancer


title: lung tumor sample 6

description: Gene expression data from lung cancer


title: lung tumor sample 3

description: Gene expression data from lung cancer


title: lung normal sample 1

description: Gene expression data from lung cancer


title: lung tumor sample 8

description: Gene expression data from lung cancer


title: Liver tumor sample 8

description: Gene expression data from liver cancer

source_name: Liver tumor sample

value: liver


title: lung tumor sample 4

description: Gene expression data from lung cancer


title: lung tumor sample 2

description: Gene expression data from lung cancer


title: lung tumor sample 1

description: Gene expression data from lung cancer


title: Liver tumor sample 6

description: Gene expression data from liver cancer


title: Liver normal sample 8

description: Gene expression data from liver cancer

source_name: Liver normal sample


title: Liver normal sample 7

description: Gene expression data from liver cancer


title: Liver normal sample 6

description: Gene expression data from liver cancer


title: Liver tumor sample 7

description: Gene expression data from liver cancer


title: Liver normal sample 4

description: Gene expression data from liver cancer


title: Liver tumor sample 2

description: Gene expression data from liver cancer


title: colon tumor sample 9

description: Gene expression data from colon cancer

source_name: colon tumor sample

value: colon


title: colon normal sample 9

description: Gene expression data from colon cancer

source_name: colon normal sample


title: Liver tumor sample 5

description: Gene expression data from liver cancer


title: Liver normal sample 2

description: Gene expression data from liver cancer


title: colon normal sample 8

description: Gene expression data from colon cancer


title: Liver tumor sample 3

description: Gene expression data from liver cancer


title: colon normal sample 7

description: Gene expression data from colon cancer


title: Liver normal sample 5

description: Gene expression data from liver cancer


title: Liver tumor sample 4

description: Gene expression data from liver cancer


title: Liver tumor sample 1

description: Gene expression data from liver cancer


title: colon tumor sample 4

description: Gene expression data from colon cancer


title: colon normal sample 6

description: Gene expression data from colon cancer


title: colon tumor sample 7

description: Gene expression data from colon cancer


title: colon normal sample 4

description: Gene expression data from colon cancer


title: colon normal sample 2

description: Gene expression data from colon cancer


title: colon normal sample 5

description: Gene expression data from colon cancer


title: colon tumor sample 8

description: Gene expression data from colon cancer


title: Liver normal sample 3

description: Gene expression data from liver cancer


title: colon tumor sample 5

description: Gene expression data from colon cancer


title: colon tumor sample 1

description: Gene expression data from colon cancer


title: Liver normal sample 1

description: Gene expression data from liver cancer


title: colon tumor sample 3

description: Gene expression data from colon cancer


title: Breast Normal sample 13

description: Gene expression data from breast cancer

source_name: Breast Normal sample

value: breast


title: colon tumor sample 6

description: Gene expression data from colon cancer


title: colon normal sample 3

description: Gene expression data from colon cancer


title: Breast Normal sample 11

description: Gene expression data from breast cancer


title: colon normal sample 1

description: Gene expression data from colon cancer


title: Liver tumor sample 9

description: Gene expression data from liver cancer


title: Breast Normal sample 6

description: Gene expression data from breast cancer


title: Breast Normal sample 2

description: Gene expression data from breast cancer


title: Breast Normal sample 1

description: Gene expression data from breast cancer


title: Breast Normal sample 5

description: Gene expression data from breast cancer


title: Breast Normal sample 7

description: Gene expression data from breast cancer


title: Breast tumor sample 181

description: Gene expression data from breast cancer

source_name: Breast tumor sample


title: Breast tumor sample 180

description: Gene expression data from breast cancer


title: Breast Normal sample 3

description: Gene expression data from breast cancer


title: Breast tumor sample 183

description: Gene expression data from breast cancer


title: Breast Normal sample 4

description: Gene expression data from breast cancer


title: Breast tumor sample 182

description: Gene expression data from breast cancer


title: Breast tumor sample 177

description: Gene expression data from breast cancer


title: Breast tumor sample 171

description: Gene expression data from breast cancer


title: Breast tumor sample 174

description: Gene expression data from breast cancer


title: Breast tumor sample 173

description: Gene expression data from breast cancer


title: Breast tumor sample 170

description: Gene expression data from breast cancer


title: Breast tumor sample 176

description: Gene expression data from breast cancer


title: Breast tumor sample 168

description: Gene expression data from breast cancer


title: Breast tumor sample 165

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 83

description: Gene expression data from breast cancer (test set)

hyb_protocol: The biotin- labelled cRNA (20 µg) was fragmented at 94oC for 60 min to generate 50 to 200-base fragments. Following fragmentation, Array was hydrated with water and incubated at 65oC for 10 min prior to priming with pre-hybridization solution at 45oC for 30 min.  Biotin-labelled fragmented cRNAs (5 µg, 50 ng/µl) were hybridized to the array and incubated at 45oC for 16 hours with gentle rotation.

scan_protocol: GeneChips were scanned using the GenePix 4000B scanner

data_processing:
The data were analyzed with Microarray Imager software and customized program.

The related GPL5022 Platform includes only ~200 gene signatures, which vary from sample to sample in breast cancer. In other words, these samples are supposed to show various median expression levels based on the small scale of 200 genes. For this reason, control genes are used for normalization, rather than global normalization.

source_name: breast cancer sample

label_protocol: Synthesis of biotin-labeled cRNA from cDNA was performed using the GeneChip Expression 3’ Amplification Reagents IVT labelling kit (Affymetrix, Inc., Santa Clara, CA) at 37oC for 16 hours. Total RNA clean-up was performed using the Qiagen RNeasy kit (Qiagen, Inc., Valenica, CA) prior to synthesis of double stranded cDNA.


title: Breast tumor sample (test) 81


title: Breast tumor sample 166

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 82


title: Breast tumor sample (test) 79


title: Breast tumor sample (test) 80


title: Breast tumor sample (test) 78


title: Breast tumor sample 159

description: Gene expression data from breast cancer


title: Breast tumor sample 158

description: Gene expression data from breast cancer


title: Breast tumor sample 162

description: Gene expression data from breast cancer


title: Breast tumor sample 153

description: Gene expression data from breast cancer


title: Breast tumor sample 157

description: Gene expression data from breast cancer


title: Breast tumor sample 155

description: Gene expression data from breast cancer


title: Breast tumor sample 164

description: Gene expression data from breast cancer


title: Breast tumor sample 154

description: Gene expression data from breast cancer


title: Breast tumor sample 156

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 77


title: Breast tumor sample (test) 74


title: Breast tumor sample (test) 76


title: Breast tumor sample (test) 75


title: Breast tumor sample (test) 73


title: Breast tumor sample (test) 72


title: Breast tumor sample 150

description: Gene expression data from breast cancer


title: Breast tumor sample 148

description: Gene expression data from breast cancer


title: Breast tumor sample 169

description: Gene expression data from breast cancer


title: Breast Normal sample 9

description: Gene expression data from breast cancer


title: Breast Normal sample 10

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 69


title: Breast tumor sample (test) 71


title: Breast tumor sample (test) 70


title: Breast tumor sample (test) 68


title: Breast tumor sample 146

description: Gene expression data from breast cancer


title: Breast tumor sample 147

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 67


title: Breast tumor sample (test) 66


title: Breast tumor sample 144

description: Gene expression data from breast cancer


title: Breast tumor sample 143

description: Gene expression data from breast cancer


title: Breast tumor sample 142

description: Gene expression data from breast cancer


title: Breast tumor sample 140

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 65


title: Breast tumor sample 141

description: Gene expression data from breast cancer


title: Breast tumor sample 137

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 61


title: Breast tumor sample (test) 59


title: Breast tumor sample (test) 58


title: Breast tumor sample (test) 63


title: Breast tumor sample (test) 64


title: Breast tumor sample (test) 62


title: Breast tumor sample (test) 57


title: Breast tumor sample 131

description: Gene expression data from breast cancer


title: Breast tumor sample 136

description: Gene expression data from breast cancer


title: Breast tumor sample 133

description: Gene expression data from breast cancer


title: Breast tumor sample 138

description: Gene expression data from breast cancer


title: Breast tumor sample 132

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 55


title: Breast tumor sample (test) 60


title: Breast tumor sample (test) 54


title: Breast tumor sample (test) 56


title: Breast tumor sample 128

description: Gene expression data from breast cancer


title: Breast tumor sample 135

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 53


title: Breast tumor sample 130

description: Gene expression data from breast cancer


title: Breast tumor sample 129

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 52


title: Breast tumor sample (test) 51


title: Breast tumor sample (test) 50


title: Breast tumor sample (test) 49


title: Breast tumor sample 126

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 48


title: Breast tumor sample 124

description: Gene expression data from breast cancer


title: Breast tumor sample (test) 46