title: blastomere 16 from embryo 2 E2.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 2


title: blastomere 15 from embryo 2 E2.C15

status: Public on Apr 05 2013

type: genomic

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

description: frozen-thawed day-4 embryo

hyb_protocol: Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome 24Sure Protocol, www.cytochip.com).

scan_protocol: The slides were  scanned using an Agilent dual laser DNA microarray scanner G2566AA (Agilent technologies, Palo Alto, CA, USA).

data_processing: The scan images were analysed using BlueFuse Software (BlueGnome).

molecule: genomic DNA

organism: Homo sapiens

source_name: blastomere 15 from embryo 2

extract_protocol: Blastomeres were collected  and the genomic DNA  was amplified using the SurePlex DNA Amplification System (BlueGnome, Cambridge, UK), according to the manufacturer’s instructions.

treatment_protocol: All blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected and arrayed.

tag: age

value: day 4 embryo

tag: cell type

value: blastomere

tag: sample type

value: blastomere from frozen-thawed day-4 embryo

source_name: Control genomic DNA

tag: gender

value: male


title: blastomere 13 from embryo 3 E3.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 3

label_protocol: Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome 24Sure Protocol, www.cytochip.com).


title: blastomere 9 from embryo 2 E2.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 2


title: blastomere 7 from embryo 2 E2.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 2


title: blastomere 13 from embryo 2 E2.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 2


title: blastomere 17 from embryo 2 E2.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 2


title: blastomere 8 from embryo 13 E14.C8

description: fresh PGD day-4 embryo

source_name: blastomere 8 from embryo 13

value: blastomere from fresh PGD day-4 embryo


title: blastomere 9 from embryo 13 E14.C9

description: fresh PGD day-4 embryo

source_name: blastomere 9 from embryo 13


title: blastomere 11 from embryo 2 E2.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 2


title: blastomere 1 from embryo 2 E2.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 2


title: blastomere 7 from embryo 13 E14.C7

description: fresh PGD day-4 embryo

source_name: blastomere 7 from embryo 13


title: blastomere 6 from embryo 13 E14.C6

description: fresh PGD day-4 embryo

source_name: blastomere 6 from embryo 13


title: blastomere 21 from embryo 13 E14.C21

description: fresh PGD day-4 embryo

source_name: blastomere 21 from embryo 13


title: blastomere 14 from embryo 2 E2.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 2


title: blastomere 18 from embryo 13 E14.C18

description: fresh PGD day-4 embryo

source_name: blastomere 18 from embryo 13


title: blastomere 19 from embryo 13 E14.C19

description: fresh PGD day-4 embryo

source_name: blastomere 19 from embryo 13


title: blastomere 2 from embryo 13 E14.C2

description: fresh PGD day-4 embryo

source_name: blastomere 2 from embryo 13


title: blastomere 20 from embryo 13 E14.C20

description: fresh PGD day-4 embryo

source_name: blastomere 20 from embryo 13

source_name: Control genomic DNA


title: blastomere 26 from embryo 13 E14.C26

description: fresh PGD day-4 embryo

source_name: blastomere 26 from embryo 13


title: blastomere 27 from embryo 13 E14.C27

description: fresh PGD day-4 embryo

source_name: blastomere 27 from embryo 13


title: blastomere 4 from embryo 13 E14.C4

description: fresh PGD day-4 embryo

source_name: blastomere 4 from embryo 13


title: blastomere 23 from embryo 13 E14.C23

description: fresh PGD day-4 embryo

source_name: blastomere 23 from embryo 13


title: blastomere 3 from embryo 13 E14.C3

description: fresh PGD day-4 embryo

source_name: blastomere 3 from embryo 13


title: blastomere 17 from embryo 13 E14.C17

description: fresh PGD day-4 embryo

source_name: blastomere 17 from embryo 13


title: blastomere 5 from embryo 13 E14.C5

description: fresh PGD day-4 embryo

source_name: blastomere 5 from embryo 13


title: blastomere 16 from embryo 13 E14.C16

description: fresh PGD day-4 embryo

source_name: blastomere 16 from embryo 13


title: blastomere 15 from embryo 13 E14.C15

description: fresh PGD day-4 embryo

source_name: blastomere 15 from embryo 13


title: blastomere 14 from embryo 13 E14.C14

description: fresh PGD day-4 embryo

source_name: blastomere 14 from embryo 13


title: blastomere 13 from embryo 13 E14.C13

description: fresh PGD day-4 embryo

source_name: blastomere 13 from embryo 13


title: blastomere 10 from embryo 2 E2.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 2


title: blastomere 1 from embryo 13 E14.C1

description: fresh PGD day-4 embryo

source_name: blastomere 1 from embryo 13


title: blastomere 11 from embryo 13 E14.C11

description: fresh PGD day-4 embryo

source_name: blastomere 11 from embryo 13


title: blastomere 10 from embryo 13 E14.C10

description: fresh PGD day-4 embryo

source_name: blastomere 10 from embryo 13


title: blastomere 9 from embryo 12 E13.C9

description: fresh PGD day-4 embryo

source_name: blastomere 9 from embryo 12


title: blastomere 4 from embryo 12 E13.C4

description: fresh PGD day-4 embryo

source_name: blastomere 4 from embryo 12

source_name: Control genomic DNA


title: blastomere 12 from embryo 13 E14.C12

description: fresh PGD day-4 embryo

source_name: blastomere 12 from embryo 13


title: blastomere 21 from embryo 12 E13.C21

description: fresh PGD day-4 embryo

source_name: blastomere 21 from embryo 12


title: blastomere 14 from embryo 12 E13.C14

description: fresh PGD day-4 embryo

source_name: blastomere 14 from embryo 12


title: blastomere 3 from embryo 12 E13.C3

description: fresh PGD day-4 embryo

source_name: blastomere 3 from embryo 12


title: blastomere 12 from embryo 12 E13.C12

description: fresh PGD day-4 embryo

source_name: blastomere 12 from embryo 12


title: blastomere 2 from embryo 12 E13.C2

description: fresh PGD day-4 embryo

source_name: blastomere 2 from embryo 12


title: blastomere 17 from embryo 12 E13.C17

description: fresh PGD day-4 embryo

source_name: blastomere 17 from embryo 12


title: blastomere 13 from embryo 12 E13.C13

description: fresh PGD day-4 embryo

source_name: blastomere 13 from embryo 12


title: blastomere 8 from embryo 12 E13.C8

description: fresh PGD day-4 embryo

source_name: blastomere 8 from embryo 12


title: blastomere 11 from embryo 12 E13.C11

description: fresh PGD day-4 embryo

source_name: blastomere 11 from embryo 12


title: blastomere 20 from embryo 12 E13.C20

description: fresh PGD day-4 embryo

source_name: blastomere 20 from embryo 12


title: blastomere 6 from embryo 11 E12.C6

description: fresh PGD day-4 embryo

source_name: blastomere 6 from embryo 11


title: blastomere 10 from embryo 12 E13.C10

description: fresh PGD day-4 embryo

source_name: blastomere 10 from embryo 12


title: blastomere 41 from embryo 11 E12.C41

description: fresh PGD day-4 embryo

source_name: blastomere 41 from embryo 11


title: blastomere 37 from embryo 11 E12.C37

description: fresh PGD day-4 embryo

source_name: blastomere 37 from embryo 11


title: blastomere 4 from embryo 11 E12.C4

description: fresh PGD day-4 embryo

source_name: blastomere 4 from embryo 11


title: blastomere 9 from embryo 11 E12.C9

description: fresh PGD day-4 embryo

source_name: blastomere 9 from embryo 11

source_name: Control genomic DNA


title: blastomere 38 from embryo 11 E12.C38

description: fresh PGD day-4 embryo

source_name: blastomere 38 from embryo 11


title: blastomere 39 from embryo 11 E12.C39

description: fresh PGD day-4 embryo

source_name: blastomere 39 from embryo 11


title: blastomere 35 from embryo 11 E12.C35

description: fresh PGD day-4 embryo

source_name: blastomere 35 from embryo 11


title: blastomere 40 from embryo 11 E12.C40

description: fresh PGD day-4 embryo

source_name: blastomere 40 from embryo 11


title: blastomere 18 from embryo 12 E13.C18

description: fresh PGD day-4 embryo

source_name: blastomere 18 from embryo 12


title: blastomere 36 from embryo 11 E12.C36

description: fresh PGD day-4 embryo

source_name: blastomere 36 from embryo 11


title: blastomere 34 from embryo 11 E12.C34

description: fresh PGD day-4 embryo

source_name: blastomere 34 from embryo 11


title: blastomere 33 from embryo 11 E12.C33

description: fresh PGD day-4 embryo

source_name: blastomere 33 from embryo 11


title: blastomere42 from embryo 11 E12.C42

description: fresh PGD day-4 embryo

source_name: blastomere42 from embryo 11


title: blastomere 32 from embryo 11 E12.C32

description: fresh PGD day-4 embryo

source_name: blastomere 32 from embryo 11


title: blastomere 31 from embryo 11 E12.C31

description: fresh PGD day-4 embryo

source_name: blastomere 31 from embryo 11


title: blastomere 7 from embryo 11 E12.C7

description: fresh PGD day-4 embryo

source_name: blastomere 7 from embryo 11


title: blastomere 28 from embryo 11 E12.C28

description: fresh PGD day-4 embryo

source_name: blastomere 28 from embryo 11


title: blastomere 27 from embryo 11 E12.C27

description: fresh PGD day-4 embryo

source_name: blastomere 27 from embryo 11


title: blastomere 25 from embryo 11 E12.C25

description: fresh PGD day-4 embryo

source_name: blastomere 25 from embryo 11


title: blastomere 22 from embryo 11 E12.C22

description: fresh PGD day-4 embryo

source_name: blastomere 22 from embryo 11


title: blastomere 24 from embryo 11 E12.C24

description: fresh PGD day-4 embryo

source_name: blastomere 24 from embryo 11

source_name: Control genomic DNA


title: blastomere 21 from embryo 11 E12.C21

description: fresh PGD day-4 embryo

source_name: blastomere 21 from embryo 11


title: blastomere 16 from embryo 11 E12.C16

description: fresh PGD day-4 embryo

source_name: blastomere 16 from embryo 11


title: blastomere 2 from embryo 11 E12.C2

description: fresh PGD day-4 embryo

source_name: blastomere 2 from embryo 11


title: blastomere 17 from embryo 11 E12.C17

description: fresh PGD day-4 embryo

source_name: blastomere 17 from embryo 11


title: blastomere 19 from embryo 11 E12.C19

description: fresh PGD day-4 embryo

source_name: blastomere 19 from embryo 11


title: blastomere 20 from embryo 11 E12.C20

description: fresh PGD day-4 embryo

source_name: blastomere 20 from embryo 11


title: blastomere 3 from embryo 11 E12.C3

description: fresh PGD day-4 embryo

source_name: blastomere 3 from embryo 11


title: blastomere 12 from embryo 11 E12.C12

description: fresh PGD day-4 embryo

source_name: blastomere 12 from embryo 11


title: blastomere 12 from embryo 11 E12.C11

description: fresh PGD day-4 embryo


title: blastomere 15 from embryo 11 E12.C15

description: fresh PGD day-4 embryo

source_name: blastomere 15 from embryo 11


title: blastomere 1 from embryo 11 E12.C1

description: fresh PGD day-4 embryo

source_name: blastomere 1 from embryo 11


title: blastomere 7 from embryo 10 E11.C7

description: fresh PGD day-4 embryo

source_name: blastomere 7 from embryo 10


title: blastomere 22 from embryo 10 E11.C22

description: fresh PGD day-4 embryo

source_name: blastomere 22 from embryo 10


title: blastomere 9 from embryo 10 E11.C9

description: fresh PGD day-4 embryo

source_name: blastomere 9 from embryo 10


title: blastomere 5 from embryo 10 E11.C5

description: fresh PGD day-4 embryo

source_name: blastomere 5 from embryo 10


title: blastomere 6 from embryo 10 E11.C6

description: fresh PGD day-4 embryo

source_name: blastomere 6 from embryo 10


title: blastomere 21 from embryo 10 E11.C21

description: fresh PGD day-4 embryo

source_name: blastomere 21 from embryo 10


title: blastomere 13 from embryo 11 E12.C13

description: fresh PGD day-4 embryo

source_name: blastomere 13 from embryo 11

source_name: Control genomic DNA


title: blastomere 3 from embryo 10 E11.C3

description: fresh PGD day-4 embryo

source_name: blastomere 3 from embryo 10


title: blastomere 10 from embryo 11 E12.C10

description: fresh PGD day-4 embryo

source_name: blastomere 10 from embryo 11


title: blastomere 20 from embryo 10 E11.C20

description: fresh PGD day-4 embryo

source_name: blastomere 20 from embryo 10


title: blastomere 26 from embryo 11 E12.C26

description: fresh PGD day-4 embryo

source_name: blastomere 26 from embryo 11


title: blastomere 23 from embryo 11 E12.C23

description: fresh PGD day-4 embryo

source_name: blastomere 23 from embryo 11


title: blastomere 19 from embryo 10 E11.C19

description: fresh PGD day-4 embryo

source_name: blastomere 19 from embryo 10


title: blastomere 2 from embryo 10 E11.C2

description: fresh PGD day-4 embryo

source_name: blastomere 2 from embryo 10


title: blastomere 17 from embryo 10 E11.C17

description: fresh PGD day-4 embryo

source_name: blastomere 17 from embryo 10


title: blastomere 14 from embryo 10 E11.C14

description: fresh PGD day-4 embryo

source_name: blastomere 14 from embryo 10


title: blastomere 16 from embryo 10 E11.C16

description: fresh PGD day-4 embryo

source_name: blastomere 16 from embryo 10


title: blastomere 10 from embryo 10 E11.C10

description: fresh PGD day-4 embryo

source_name: blastomere 10 from embryo 10


title: blastomere 13 from embryo 10 E11.C13

description: fresh PGD day-4 embryo

source_name: blastomere 13 from embryo 10


title: blastomere 1 from embryo 10 E11.C1

description: fresh PGD day-4 embryo

source_name: blastomere 1 from embryo 10


title: blastomere 10 from embryo 9 E10.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 9


title: blastomere 12 from embryo 10 E11.C12

description: fresh PGD day-4 embryo

source_name: blastomere 12 from embryo 10


title: blastomere 10 from embryo 9 E10.C7

description: frozen-thawed day-4 embryo


title: blastomere 3 from embryo 9 E10.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 9


title: blastomere 6 from embryo 9 E10.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 9

source_name: Control genomic DNA


title: blastomere 17 from embryo 9 E10.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 9


title: blastomere 2 from embryo 9 E10.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 9


title: blastomere 14 from embryo 9 E10.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 9


title: blastomere 10 from embryo 9 E10.C9

description: frozen-thawed day-4 embryo


title: blastomere 15 from embryo 9 E10.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 9


title: blastomere 4 from embryo 9 E10.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 9


title: blastomere 15 from embryo 10 E11.C15

description: fresh PGD day-4 embryo

source_name: blastomere 15 from embryo 10


title: blastomere 11 from embryo 10 E11.C11

description: fresh PGD day-4 embryo

source_name: blastomere 11 from embryo 10


title: blastomere 8 from embryo 10 E11.C8

description: fresh PGD day-4 embryo

source_name: blastomere 8 from embryo 10


title: blastomere 8 from embryo 1 E1.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 1


title: blastomere 16 from embryo 9 E10.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 9


title: blastomere 13 from embryo 9 E10.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 9


title: blastomere 7 from embryo 1 E1.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 1


title: blastomere 11 from embryo 9 E10.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 9


title: blastomere 1 from embryo 9 E10.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 9


title: blastomere 5 from embryo 1 E1.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 1


title: blastomere 10 from embryo 9 E10.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 9


title: blastomere 12 from embryo 9 E10.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 9

source_name: Control genomic DNA


title: blastomere 9 from embryo 1 E1.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 1


title: blastomere 16 from embryo 1 E1.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 1


title: blastomere 18 from embryo 1 E1.C18

description: frozen-thawed day-4 embryo

source_name: blastomere 18 from embryo 1


title: blastomere 2 from embryo 1 E1.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 1


title: blastomere 17 from embryo 1 E1.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 1


title: blastomere 12 from embryo 1 E1.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 1


title: blastomere 11 from embryo 1 E1.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 1


title: blastomere 6 from embryo 1 E1.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 1


title: blastomere 14 from embryo 1 E1.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 1


title: codY-rsh double mutant replicate 3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description:
codY-rsh_rep3
codY-rsh_cy3 vs pool gDNA_cy5 2_3b
Newman codY-rsh

hyb_protocol: A mixture of RNA from WT or mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

molecule: total RNA

organism: Staphylococcus aureus

source_name: Newman codY-rsh

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in CYPG (10 g/l casamino acids, 10 g/l yeast extract, 5 g/l NaCl, 0.5% glucose and 0.06 M phosphoglycerate).

extract_protocol:
Briefly, bacteria were lysed in 1 ml of Trizol reagent (Invitrogen Life Technologies, Karlsruhe, Germany) with 0.5 ml zirconia-silica beads (0.1 mm-diameter) in a high-speed homogenizer (Savant Instruments, Farmingdale, NY). RNA was isolated as described in the instructions provided by the manufacturer of Trizol. RNA isolation after phagocytosis was performed as described in the instructions provided by the manufacturer of the RNA isolation kit (ExpressArt RNAready, AmpTec) with the modification adding an inhibitor removal buffer (high pure viral nucleic acid kit, Roche diagnostics) in the first step. Then DNA digestion was performed as instructed by the RNA isolation kit.
Purified genomic DNA from the different sequenced strains used for the design of the microarray was extracted (DNeasy; Qiagen)

tag: strain background

value: Newman

tag: genotype/variation

value: codY-rsh mutant

label: cyanine 5

source_name: genomic DNA pool

value: Staphylococcus aureus gDNA mixture


title: codY-rsh double mutant replicate 2

description:
codY-rsh_rep2
codY-rsh_cy3 vs pool gDNA_cy5 2_4a
Newman codY-rsh


title: codY-rsh double mutant replicate 1

description:
codY-rsh_rep1
codY-rsh_cy3 vs pool gDNA_cy5 2_3a
Newman codY-rsh


title: blastomere 13 from embryo 1 E1.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 1


title: rsh mutant replicate 3

description:
rsh_rep3
rsh_cy3 vs pool gDNA_cy5 1_3b
Newman rsh

source_name: Newman rsh

value: rsh mutant


title: blastomere 10 from embryo 1 E1.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 1


title: blastomere 4 from embryo 1 E1.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 1


title: blastomere 3 from embryo 1 E1.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 1


title: codY mutant replicate 2

description:
codY_rep2
codY_cy3 vs pool gDNA_cy5 2_2a
Newman codY

source_name: Newman codY

value: codY mutant


title: rsh mutant replicate 1

description:
rsh_rep1
rsh_cy3 vs pool gDNA_cy5 1_3a
Newman rsh


title: rsh mutant replicate 2

description:
rsh_rep2
rsh_cy3 vs pool gDNA_cy5 1_4a
Newman rsh


title: codY mutant replicate 1

description:
codY_rep1
codY_cy3 vs pool gDNA_cy5 2_1a
Newman codY


title: blastomere 1 from embryo 1 E1.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 1

source_name: Control genomic DNA


title: blastomere 15 from embryo 2 E1.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 2


title: codY mutant replicate 3

description:
codY_rep3
codY_cy3 vs pool gDNA_cy5 2_1b
Newman codY


title: Wild type strains replicate 3

description:
WT_rep3
WT_cy3 vs pool gDNA_cy5 1_1b
Newman WT

source_name: Newman WT

value: WT


title: IB009.076

type: RNA

city: St John's

first: Tiago

last: Hori

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences Centre

country: Canada

institute: Memorial University of Newfoundland

description: 10ppb dietary TCDD treated compared to control group (wk4)

hyb_protocol: The cDNAs for each “TCDD vs. control” comparison were combined and incubated at 50°C until being hybridized to consortium for Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays (http://web.uvic.ca/grasp/microarray/array.html, batch number IB009) platform version 2.1. Prior to hybridization, arrays were washed in 0.1 % SDS (2 x 5 min), rinsed in RNase-free water (5 x 1 min) in 50 ml conical tubes (BD Falcon, Franklin Lakes, NJ), and then immersed in 95°C RNase-free water (1 x 3 min) to denature the probes. Slides were dried by centrifugation (2000 rpm for 5 min, room temperature) and kept at 50°C until use. Hybridization was performed using HybriSlips coverslips (Sigma, St. Louis, MO) and Corning microarray hybridization chambers (Corning, Tewksbury, MA) in a water bath at 50°C for 16 h; the first hybridization used LNA dT blocker (vial 9 in the Array 900 kit) and formamide-based hybridization buffer (vial 7 in the Array 900 kit) as directed in the Array 900 manual. Following the first hybridization, arrays were washed in 2X SSC (Ambion, Austin, TX), 0.2% SDS solution (Ambion, Austin, TX) at 50°C (1 x 15 min), 2X SSC (1 x 15 min) at room temperature, then 0.2X SSC (1 x 15 min) at room temperature; all microarray wash solutions were made using RNase-free water. The fluorescence labeling hybridization (50 °C for 4 h) utilized the Genisphere 3DNA Cy3 and Cy5 Capture Reagents in formamide-based hybridization buffer (vial 7). After the second hybridization, the arrays were washed and dried.

scan_protocol: Microarrays were scanned at 10 µm resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer).

data_processing: Fluorescence intensity data for Cy3 and Cy5 channels were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery Inc., El Segundo, CA). Background correction, data transformation (setting background corrected values < 0.01 to 0.01), Lowess normalization, and analysis (e.g. fold-change calculations) were performed using GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA). Transcripts with reproducible 2-fold or greater differences in expression between TCDD exposed and control RNA samples in all slides of a given comparison were identified with GeneSpring.

organism: Oncorhynchus mykiss

source_name: pooled RNA of 10ppb dietary TCDD treated trout wk4

label_protocol: For target synthesis, purified RNA samples from 10 individual fish from the same group were pooled with each fish contributing an equal quantity (1 µg) of RNA to a given pool. cDNA was synthesized from 1 μg of pooled RNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, CA) and the Array 900 Expression Array Detection kit (Genisphere, Hatfield, PA) according to the Array 900 protocol. Briefly, for each microarray target, 1 µg of pooled RNA was denatured at 80°C for 5 min in the presence of oligo (dT) primers with 5’-prime unique sequences complementary to the Cy3 or Cy5 Capture Reagents, then reverse transcribed at 42°C for 2.5 h (see the Array 900 manual for details regarding the labeling system chemistry). The reverse transcription reactions were stopped, denatured (with degradation of RNA), and neutralized following the Array 900 manual.

growth_protocol: Eyed trout eggs were ordered from Fish and Wildlife Service of Ennis National Fish Hatchery (MT), reared in 10 ℃ dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility, and 45 days after hatching TCDD dietary exposures were initiated.

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Briefly, individual whole fish were homogenized in 1 ml of TRIzol reagent with a PowerGen 500 homogenizer (Fisher Scientific, Pittsburgh, PA). Chloroform (Fisher Scientific, Pittsburg, PA) (0.2 ml) was added for phase separation and mixed by inverting the tubes by hand for 15 s. The samples were then centrifuged at 11400 rpm for 15 min at 8°C. The upper aqueous phase was transferred to a clean 1.5 ml microcentrifuge tube, and 0.5 ml of isopropyl alcohol (PHARMCO-AAPER, Brookfield, CT) was added. RNA was precipitated at room temperature (10 min) and pelleted by centrifugation at 11400 rpm for 15 min at 8°C. The supernatant was removed and the pellet was washed with 1 ml 75% ethanol. The samples were centrifuged at 11400 rpm for 5 min at 8°C, supernatants were removed, and RNA pellets were air-dried and dissolved in RNase-free water (Gibco, Grand Island, NY). Total RNA samples (< 45 µg in a total volume of 100 µl) were digested with 2.5 µl DNase I (1500 U) for 10 min at room temperature and further column RNA purification was performed using the RNeasy MiniElute cleanup kit (Qiagen, MD) following the manufacturer’s protocol. The purity and quantity of RNA were examined using A260/A230 and A260/A280 ratios calculated by the ND-1000 NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and quality and integrity of RNA was examined by 1% TAE agarose gel electrophoresis.

treatment_protocol: Rainbow trout were fed BioDiet starter #2 (Bio-Oregon, Inc., Longview, WA) at 4% of body weight per day with TCDD added at 0, 0.1, 1, 10 and 100 ppb (nominal concentration, ethanol as a vehicle) starting at 45 days after hatching (0.18 ± 0.01 g, average ± SEM). The rainbow trout in 10 ppb group were collected at 7, 14, 28 and 42 days for microarray experiments after initiation of the exposure.

tag: tissue

value: 10 whole fish

source_name: pooled RNA of trout in control diet group at 4 weeks


title: IB009.078

description: 10ppb dietary TCDD treated compared to control group (wk6)

source_name: pooled RNA of 10ppb dietary TCDD treated trout wk6

source_name: pooled RNA of trout in control diet group at 6 weeks


title: Wild type strains replicate 1

description:
WT_rep1
WT_cy3 vs pool gDNA_cy5 1_1a
Newman WT


title: IB009.077


title: IB009.080


title: Wild type strains replicate 2

description:
WT_rep2
WT_cy3 vs pool gDNA_cy5 1_2a
Newman WT


title: IB009.065

description: 10ppb dietary TCDD treated compared to control group (wk1)

source_name: pooled RNA of 10ppb dietary TCDD treated trout wk1

source_name: pooled RNA of trout in control diet group at 1 week


title: blastomere 30 from embryo 11 E12.C30

description: fresh PGD day-4 embryo

source_name: blastomere 30 from embryo 11


title: IB009.079


title: IB009.066


title: IB009.072

description: 10ppb dietary TCDD treated compared to control group (wk2)

source_name: pooled RNA of trout in control diet group at 2 week

source_name: pooled RNA of 10ppb dietary TCDD treated trout wk2


title: IB009.081


title: IB009.073


title: IB009.071

source_name: pooled RNA of trout in control diet group at 2 weeks


title: IB009.069


title: SLC7A1.3.2

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA SLC7A1

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies, Cat. #: 5188-5242).  Hybridizations were performed on SureHyb chambers on a rotator oven at 65C for 17 hours.

scan_protocol: Agilent G2565BA

data_processing: log2 transformation of signal intensity, quantile normalization

source_name: SW480; Transf2.2.SLC7A1.3

label_protocol: Quick Amp Labeling Kit (Agilent Technologies, Cat. #: 5190-0442), including MMLV-RT and oligo dT-Promoter primers for cDNA sinthesis, and T7 RNA Polymerase, Cy3-CTP and NTPs for labeling.

extract_protocol: RNeasy Mini Kit (Qiagen) + RNase-Free DNase Set (Qiagen)

tag: cell line

value: colorectal cancer cells

tag: sirna

tag: sirna no.

tag: rep. no.


title: POLR1D.3.3

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA POLR1D

source_name: SW480; Transf2.3.POLR1D.3


title: SLC7A1.2.1

source_name: SW480; Transf1.1.SLC7A1.2


title: IB009.067


title: MC_SH2-rep3

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

description: HeLa cells were transduced for 6 hours with filtered supernatant containing shRNAs targeting FANCD2 recombinant lentiviral particles.

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: Partek Genomics Suite v.6.6

label: biotin

source_name: Cells treated with shRNAs targeting FANCD2 recombinant lentiviral particles.

label_protocol: Total mRNA was RNase H reduced and labelled with the SuperScript One-Cycle cDNA Kit following manufacturer's instructions (Invitrogen).

growth_protocol: HeLa cell line was grown in DMEM media supplemented with 10% FBS and were incubated in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted with Trizol or the RNeasy Mini kit with DNAse digestion (Qiagen, Valencia, CA) and resuspended in PCR-grade water. To ensure adequate quality, RNA was analysed with an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA) in the Quebec Genomics Center Microarray core facility.

treatment_protocol: A four-plasmid (pRSV-Rev, pMDLg/pRRE, pMD2.G and pLKO.1) expression system was used for lentiviral production. Different pLKO.1 plasmids carrying shRNAs targeting FANCA (TRCN0000118982), FANCD2 (TRCN0000082840), CtBP1 (TRCN0000013738) or CtBP2 (TRCN0000013744) were purchased from Open Biosystems (Lafayette, CO). A lentiviral control vector, pLKO.1-scrambled was purchased from Addgene (Cambridge, MA). Lentiviral particles were produced via calcium phosphate-mediated transient transfection of the four plasmids into HEK293T cells. Cells were exposed to appropriate lentiviral particles.  In each experiment, HeLa cells were transduced for 6 hours with filtered supernatant containing recombinant lentiviral particles. After transduction, the cells were cultured for 72 hours. Total RNA extracts from 3 different samples of each scrambled, CtBPs and FANCD2 shRNA treated HeLa cells were subjected to gene expression profiling via microarray analysis. Gene expression profiles were determined with Affymetrix GeneChip® Human Gene 1.0.

value: HeLa cells


title: IB009.068


title: POLR1D.3.2

source_name: SW480; Transf2.2.POLR1D.3


title: IB009.074


title: SLC7A1.2.3

source_name: SW480; Transf1.4.SLC7A1.2


title: SLC7A1.3.3

source_name: SW480; Transf2.3.SLC7A1.3


title: SLC7A1.3.1

source_name: SW480; Transf2.1.SLC7A1.3


title: MC_SH_1-rep2

description: HeLa cells were transduced for 6 hours with filtered supernatant containing shRNAs targeting CtBPs recombinant lentiviral particles.

source_name: Cells treated with shRNAs targeting CtBPs recombinant lentiviral particles.


title: SLC7A1.2.2

source_name: SW480; Transf1.2.SLC7A1.2


title: NUPL1.4.1

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA NUPL1

source_name: SW480; Transf2.1.NUPL1.4


title: POLR1D.3.1

source_name: SW480; Transf2.1.POLR1D.3


title: NUPL1.4.2

source_name: SW480; Transf2.2.NUPL1.4


title: MC_SH2-rep2


title: MC_PLKO-rep2

description: HeLa cells were transduced for 6 hours with filtered supernatant containing shRNAs targeting pLKO.1-scrambled recombinant lentiviral particles.

source_name: Cells treated with pLKO.1-scrambled recombinant lentiviral particles.


title: NUPL1.3.2

source_name: SW480; Transf1.2.NUPL1.3


title: NUPL1.3.3

source_name: SW480; Transf1.4.NUPL1.3


title: NUPL1.4.3

source_name: SW480; Transf2.3.NUPL1.4


title: TCDD 100% 2

city: Memphis

first: Lawrence

middle: H

last: Kennedy

state: TN

address: 3700 Walker Ave

department: Biological Sciences

country: USA

institute: University of Memphis

hyb_protocol: Fluidics Station 400

scan_protocol: GeneChip Scanner 3000 7G

data_processing: 5th percentile in region method in dChip, genes with 1.25 fold change or greater between control and TCDD at 100% density were further analyzed by 2 way ANOVA using JMP Genomics

source_name: NHEK - TCDD-100%

label_protocol: GeneChip Whole Transcript Sense Target Labeling assay

extract_protocol: Stat 60 RNA isolation

value: NHEK

value: neonatal foreskin (fifth passage)


title: TCDD 100% 3


title: MC_SH2-rep1


title: NUPL1.1.3

source_name: SW480; Transf2.3.NUPL1.1


title: Control 100% 3

source_name: NHEK - control-100%


title: MC_SH_1-rep3


title: POLR1D.1.3

source_name: SW480; Transf1.4.POLR1D.1


title: IB009.070

source_name: pooled RNA of trout in control diet group at 2 week

source_name: pooled RNA of 10ppb dietary TCDD treated trout wk2


title: NUPL1.3.1

source_name: SW480; Transf1.1.NUPL1.3


title: MC_SH_1-rep1


title: POLR1D.1.2

source_name: SW480; Transf1.2.POLR1D.1


title: fibroblast_patient_SIL_Q-treated_2

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

description:
rep. 2
unpublished data

hyb_protocol: Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). Hybridization was performed overnight in the GeneChip Hybridization Oven 640 at 45C with shaking at 60 rpm; washes and staining of the probe were performed in the GeneChip fluidics station using buffers and protocols provided by the manufacturer. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

scan_protocol: High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

data_processing: Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using PLIER and RMA algorithms at linear scale.

source_name: human fibroblast, Q10 deficient patient SIL supplemented with CoQ10

label_protocol: A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.

growth_protocol: Control fibroblasts and those from Q-deficient patients were cultured at 37°C using DMEM 1 g/L Glucose, L-Glutamine, Pyruvate (Invitrogen, Prat de Llobregat, Barcelona) supplemented with an antibiotic/antimycotic solution (Sigma Chemical Co., St. Louis, Missouri) and 20% fetal bovine serum (FBS, Linus).

extract_protocol: Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4C. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy MinElute Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20C in RNase-free water.

treatment_protocol: Coenzyme Q10 pre-diluted in FBS was added to the plates at a final concentration of 30 micromolar (Coenzyme Q10, Synthetic Minimun 98%, HPLC, Sigma).

tag: patient

value: pathogenic mutation (c.483G>C) in the COQ4 gene, rabdomyolisis, CoQ10 deficiency

value: girl

value: unknown

tag: treatment

value: CoQ10 supplementation


title: Control 100% 2


title: LNX2.1.3

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA LNX2

source_name: SW480; Transf1.4.LNX2.1


title: fibroblast_patient_MSI_Q-treated_2

description:
rep. 2
unpublished data

source_name: human fibroblast, Q10 deficient patient MSI supplemented with CoQ10

value: mother of patient_SIL

value: woman


title: NUPL1.1.1

source_name: SW480; Transf2.1.NUPL1.1


title: fibroblast_patient_ELO_Q-treated_1

description:
rep. 1
unpublished data

source_name: human fibroblast, Q10 deficient patient ELO supplemented with CoQ10

value: mtDNA depletion syndrome and a secondary CoQ10 deficiency

value: boy

value: 1 day old


title: POLR1D.1.1

source_name: SW480; Transf1.1.POLR1D.1


title: LNX2.1.2

source_name: SW480; Transf1.2.LNX2.1


title: fibroblast_patient_ELO_Q-treated_2

description:
rep. 2
unpublished data


title: MC_PLKO-rep1

source_name: Cells treated with pLKO.1-scrambled recombinant lentiviral particles.


title: MC_PLKO-rep3


title: fibroblast_patient_SOF_Q-treated_1

description:
rep. 1
Reference: Salviati, L. et al. Infantile encephalomyopathy and nephropathy with CoQ10 deficiency: a CoQ10-responsive condition. Neurology 65, 606-8 (2005).

source_name: human fibroblast, Q10 deficient patient SOF supplemented with CoQ10

value: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts).


title: Btt1 (2)

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85701.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 7020; Software: type: feature extraction; Performer: Marta,,Del Alamo Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.61; Performer: Marta,,Del Alamo Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.61; Performer: Marta,,Del Alamo

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

organism: Saccharomyces cerevisiae

source_name: total rna WT

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: total rna

source_name: IP rna Btt1

tag: cyclohexamide treatment

tag: genotype

value: wt

tag: tap-tag


title: fibroblast_patient_SIL_Q-treated_1

description:
rep. 1
unpublished data

tag: age


title: TCDD 100% 4

source_name: NHEK - TCDD-100%

tag: cell type


title: Control 100% 4

source_name: NHEK - control-100%


title: KLF5.5.1

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA KLF5

source_name: SW480; Transf2.2.KLF5.5


title: TCDD 100% 1


title: control_fibroblast_2c

description:
rep. 2c
control fibroblasts obtained from healthy volunteers

source_name: human dermal fibroblast, neonatal

value: healthy volunteers

value: neonatal


title: KLF5.5.2

source_name: SW480; Transf2.3.KLF5.5

value: colorectal cancer cells


title: NUPL1.1.2

source_name: SW480; Transf2.2.NUPL1.1


title: fibroblast_patient_GIO_1_2

description:
rep. 1, cRNA 2
unpublished data

source_name: human fibroblast, Q10 deficient patient GIO

value: chromosome 9 deletion containg COQ4 gene, CoQ10 deficiency


title: LNX2.5.3

source_name: SW480; Transf2.3.LNX2.5


title: control_fibroblast_4a

description:
rep. 4a
control fibroblasts obtained from healthy volunteers


title: fibroblast_patient_MEL_Q-treated_1

description:
rep. 1
Reference: PubMed ID #21551238 - Cotan, D. et al. Secondary coenzyme Q10 deficiency triggers mitochondria degradation by mitophagy in MELAS fibroblasts. Faseb J 25, 2669-87 (2011).

source_name: human fibroblast, Q10 deficient patient MEL supplemented with CoQ10

value: MELAS (A3243G mutation) with (1) decreased mitochondrial respiratory chain enzyme activities, (2) low CoQ10 level, (3) decreased mitochondrial membrane potential, (4) increased oxidative stress and the activation of mitochondrial permeability, and (5) defective autophagosome elimination in MELAS fibroblasts.


title: BY4741 Ribosome Occupancy YPAD mid-log (3)

description:
Simple annotation: Polysomes, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77668.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan

source_name: RNA not associated with ribosomes

tag: extract

value: RNA not associated with ribosomes

source_name: RNA associated with ribosomes

value: RNA associated with ribosomes


title: Control 100% 1

value: NHEK

value: neonatal foreskin (fifth passage)


title: LNX2.5.2

source_name: SW480; Transf2.2.LNX2.5


title: fibroblast_patient_MSI_Q-treated_1

description:
rep. 1
unpublished data

source_name: human fibroblast, Q10 deficient patient MSI supplemented with CoQ10

value: mother of patient_SIL

tag: gender

value: unknown

value: CoQ10 supplementation


title: LNX2.5.1

source_name: SW480; Transf2.1.LNX2.5


title: BY4741 Ribosome Occupancy YPAD mid-log (1)

description:
Simple annotation: Polysomes, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77666.gif


title: DIS3.3.1

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA DIS3

source_name: SW480; Transf1.2.DIS3.3


title: LNX2.1.1

source_name: SW480; Transf1.1.LNX2.1


title: HUVEC_replicative senescent_rep3

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

description: Gene expression of replicative senescent HUVEC

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity > 6.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute with moderate stirring at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with moderate stirring at 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using scan one color setting  for 4x44k array slide (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and output is 20 bit TIFF).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using protocol: GE1_105_Dec08 and Grid: 014850_D_20070820.

source_name: HUVEC_PD > 48_replicate3

label_protocol: Total RNAs (50ng) were labeled with Cyanine 3-CTP using Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., USA) according to manufacturer’s protocol, followed by RNAeasy mini column purification (Qiagen, Germany). Dye incorporation and cRNA yield were checked with the Nanophotometer (Implen GmbH, Germany).

growth_protocol: HUVECs were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA) and maintained in endothelial cell medium (ECM) supplemented with 5% FBS, 1% endothelial cell growth supplement and 1% of penicillin/streptomycin (ScienCell Research Laboratories), at 37oC in a humidified atmosphere of 95% air/5% CO2.  Young and senescent cells used in experiments are cells with PD < 10 and PD > 48 respectively.

extract_protocol: Total RNAs were isolated from cells using miRNeasy mini kit (Qiagen) according to manufacturer’s protocol. RNA was quantified using Nanophotometer (Implen GmbH, Germany). RNA integrity was accessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA).

treatment_protocol: Not applicable

value: Endothelial cell

value: Umbilical vein

value: HUVEC

tag: Stage

value: replicative senescent


title: fibroblast_patient_SOF_Q-treated_2

description:
rep. 2
Reference: Salviati, L. et al. Infantile encephalomyopathy and nephropathy with CoQ10 deficiency: a CoQ10-responsive condition. Neurology 65, 606-8 (2005).

source_name: human fibroblast, Q10 deficient patient SOF supplemented with CoQ10

value: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts).

value: boy


title: control_fibroblast_4b

description:
rep. 4b
control fibroblasts obtained from healthy volunteers

value: healthy volunteers

value: neonatal


title: fibroblast_patient_GIO_2_1

description:
rep. 2, cRNA 1
unpublished data

value: chromosome 9 deletion containg COQ4 gene, CoQ10 deficiency


title: Membrane bound vs Free/Soluble mRNAs (7) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78992.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 403; Parameter Laser on time = 33334; Parameter Laser Power = 3.59; Parameter Scan Time = 11:04:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.90; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 476; Parameter Scan Power = 100; Parameter Laser on time = 33338; Parameter Laser Power = 3.16; Parameter Scan Time = 11:04:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.90; Performer: Daniel,,Hogan

source_name: free RNA

tag: fraction

value: free RNA

tag: strain

value: wt

source_name: membrane bound RNA

extract_protocol: Del Alamo Subcellular Fractionation and RNA Isolation; Free cytosolic polysomes and membrane-bound polysomes were fractionated by sedimentation velocity exactly as described [34],[85] starting with 250 ml of exponential growth cultures (of WT or ??egd1/egd2) in YPD. Total RNA from free and membrane-associated polysomes was purified with RNeasy Mini Columns Kit (Qiagen).; Protocol Type = Biological Sample; Performer: Daniel,,Hogan

value: membrane bound RNA


title: fibroblast_patient_GIO_2_2

description:
rep. 2, cRNA 2
unpublished data


title: Btt1 (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85702.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 7020; Software: type: feature extraction; Performer: Marta,,Del Alamo Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.61; Performer: Marta,,Del Alamo Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.89; Performer: Marta,,Del Alamo

source_name: total rna WT

value: total rna

source_name: IP rna Btt1


title: BY4741 Ribosome Occupancy YPAD mid-log (2)

description:
Simple annotation: Polysomes, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77667.gif

value: RNA not associated with ribosomes

value: RNA associated with ribosomes


title: Membrane bound vs Free/Soluble mRNAs (6) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78991.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 439; Parameter Laser on time = 33316; Parameter Laser Power = 3.58; Parameter Scan Time = 10:46:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.65; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 478; Parameter Scan Power = 100; Parameter Laser on time = 33320; Parameter Laser Power = 3.17; Parameter Scan Time = 10:46:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.65; Performer: Daniel,,Hogan


title: Btt1 (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85700.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5960; Software: type: feature extraction; Performer: Marta,,Del Alamo Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.40; Performer: Marta,,Del Alamo Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.40; Performer: Marta,,Del Alamo


title: A2

city: Madison

first: Caitlin

middle: Aran

last: Brennan

state: WI

address: 1550 Linden Drive

department: MMI

institute: University of Wisconsin

description: Gene expression data from the V. fischeri flrA deletion mutant DM159, grown to mid-log phase in SWT

hyb_protocol: Following fragmentation, cDNA was labeled with biotin and hybridized to the Custom Vibrio fischeri GeneChip Array at 45C for 16 hours. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The array data were processed using the GeneChip Operation Software (GCOS, Affymetrix).

label: Biotin

organism: Aliivibrio fischeri

source_name: flrA deletion V. fischeri culture

label_protocol: Procedures for total RNA labeling were performed based on the protocols from the E. coli Genome Project at the University of Wisconsin-Madison.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were grown in seawater tryptone (SWT) at 28 degrees C with shaking, to an OD600 of ~0.5


title: fibroblast_patient_GIO_1_1

description:
rep. 1, cRNA 1
unpublished data

source_name: human fibroblast, Q10 deficient patient GIO

value: unknown


title: DIS3.1.1

source_name: SW480; Transf2.1.DIS3.1

tag: cell line

value: colorectal cancer cells


title: fibroblast_patient_ELO_2_1

description:
rep. 2, cRNA 1
Reference: Montero, R. et al. Analysis of Coenzyme Q10 in muscle and fibroblasts for the diagnosis of CoQ10 deficiency syndromes. Clinical Biochemistry 41, 697-700 (2008).

source_name: human fibroblast, Q10 deficient patient ELO

value: mtDNA depletion syndrome and a secondary CoQ10 deficiency

value: 1 day old


title: FA009.016

description: 100ppb groups compares to control group

hyb_protocol: The cDNAs for each “TCDD vs. control” comparison were combined and incubated at 50°C until being hybridized to consortium for Genomics Research on All Salmonids Project (cGRASP) 16K cDNA microarrays (http://web.uvic.ca/grasp/microarray/array.html, batch number FA009) platform version 2.1. Prior to hybridization, arrays were washed in 0.1 % SDS (2 x 5 min), rinsed in RNase-free water (5 x 1 min) in 50 ml conical tubes (BD Falcon, Franklin Lakes, NJ), and then immersed in 95°C RNase-free water (1 x 3 min) to denature the probes. Slides were dried by centrifugation (2000 rpm for 5 min, room temperature) and kept at 50°C until use. Hybridization was performed using HybriSlips coverslips (Sigma, St. Louis, MO) and Corning microarray hybridization chambers (Corning, Tewksbury, MA) in a water bath at 50°C for 16 h; the first hybridization used LNA dT blocker (vial 9 in the Array 900 kit) and formamide-based hybridization buffer (vial 7 in the Array 900 kit) as directed in the Array 900 manual. Following the first hybridization, arrays were washed in 2X SSC (Ambion, Austin, TX), 0.2% SDS solution (Ambion, Austin, TX) at 50°C (1 x 15 min), 2X SSC (1 x 15 min) at room temperature, then 0.2X SSC (1 x 15 min) at room temperature; all microarray wash solutions were made using RNase-free water. The fluorescence labeling hybridization (50 °C for 4 h) utilized the Genisphere 3DNA Cy3 and Cy5 Capture Reagents in formamide-based hybridization buffer (vial 7). After the second hybridization, the arrays were washed and dried.

source_name: pooled RNA of trout in control diet group

treatment_protocol: Rainbow trout were fed BioDiet starter #2 (Bio-Oregon, Inc., Longview, WA) at 4% of body weight per day with TCDD added at 0, 0.1, 1, 10 and 100 ppb (nominal concentration, ethanol as a vehicle) starting at 45 days after hatching (0.18 ± 0.01 g, average ± SEM). The rainbow trout were collected after 28 days after initiation of the exposure.

tag: tissue

value: 10 whole fish

source_name: pooled RNA of 100ppb dietary TCDD treated trout


title: KLF5.3.2

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA KLF5

source_name: SW480; Transf1.2.KLF5.3

tag: sirna

tag: sirna no.


title: GPR180.5.3

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA GPR180

tag: rep. no.


title: fibroblast_patient_ELO_1_2

description:
rep. 1, cRNA 2
Reference: Montero, R. et al. Analysis of Coenzyme Q10 in muscle and fibroblasts for the diagnosis of CoQ10 deficiency syndromes. Clinical Biochemistry 41, 697-700 (2008).

tag: patient

tag: treatment


title: Membrane bound vs Free/Soluble mRNAs (8) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78993.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 419; Parameter Laser on time = 33350; Parameter Laser Power = 3.59; Parameter Scan Time = 11:19:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.11; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-03-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 478; Parameter Scan Power = 100; Parameter Laser on time = 33353; Parameter Laser Power = 3.16; Parameter Scan Time = 11:19:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.11; Performer: Daniel,,Hogan


title: ES2

description: Gene expression data from wild-type V. fischeri ES114, grown to mid-log phase in SWT

source_name: Wild-type V. fischeri culture


title: KLF5.3.1

source_name: SW480; Transf1.1.KLF5.3


title: fibroblast_patient_ELO_1_1

description:
rep. 1, cRNA 1
Reference: Montero, R. et al. Analysis of Coenzyme Q10 in muscle and fibroblasts for the diagnosis of CoQ10 deficiency syndromes. Clinical Biochemistry 41, 697-700 (2008).


title: HUVEC_young_rep2

description: Gene expression of young HUVEC

source_name: HUVEC_PD <10_replicate 2

value: Endothelial cell

value: Umbilical vein

value: HUVEC

value: young


title: DIS3.1.2

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA DIS3

source_name: SW480; Transf2.2.DIS3.1


title: HUVEC_replicative senescent_rep2

description: Gene expression of replicative senescent HUVEC

source_name: HUVEC_PD > 48_replicate2

value: replicative senescent


title: fibroblast_patient_ELO_2_2

description:
rep. 2, cRNA 2
Reference: Montero, R. et al. Analysis of Coenzyme Q10 in muscle and fibroblasts for the diagnosis of CoQ10 deficiency syndromes. Clinical Biochemistry 41, 697-700 (2008).

value: boy


title: Membrane bound vs Free/Soluble mRNAs (5) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-01/78251.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 12160; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-01-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 537; Parameter Laser on time = 24149; Parameter Laser Power = 3.54; Parameter Scan Time = 11:40:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-01-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 505; Parameter Scan Power = 100; Parameter Laser on time = 24152; Parameter Laser Power = 3.18; Parameter Scan Time = 11:40:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Daniel,,Hogan

value: free RNA


title: DIS3.1.3

source_name: SW480; Transf2.3.DIS3.1


title: Membrane bound vs Free/Soluble mRNAs (2) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78839.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-02-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 490; Parameter Laser on time = 26127; Parameter Laser Power = 3.58; Parameter Scan Time = 11:09:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.50; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-02-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 476; Parameter Scan Power = 100; Parameter Laser on time = 26131; Parameter Laser Power = 3.18; Parameter Scan Time = 11:09:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.50; Performer: Daniel,,Hogan

source_name: free RNA

value: wt


title: A1


title: GPR180.1.3


title: 1st instar larvae_wildtype_replicate_F

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description: Gene expression data from 1st instar larvae

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Raw data was normalized using RMA (R and Bioconductor).

organism: Drosophila melanogaster

source_name: 1st instar larvae_wildtype_replicate_F

label_protocol: Standard Affymetrix

growth_protocol: Flies were cultivated and crossed in vials with potato-yeast-agar medium at 25 ̊ C.

extract_protocol:
Each replicate contains 200 1st instar larvae. The larvae were collected approximately 48 hours after egg laying and frozen in -70 ̊ C prior to RNA extraction
Total RNA was isolated using TRIzol reagent (Invitrogen) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers.

tag: genotype/variation

value: wildtype

tag: developmental stage

value: 1st instar larvae, approximately 48 hours after egg laying


title: HUVEC_young_rep1

description: Gene expression of young HUVEC

source_name: HUVEC_PD <10_replicate 1


title: HUVEC_replicative senescent_rep1

source_name: HUVEC_PD > 48_replicate1


title: GPR180.1.2


title: FA009.012

description: 10ppb groups compares to control group

scan_protocol: Microarrays were scanned at 10 µm resolution using a ScanArray Express (PerkinElmer Life Sciences, Inc, Boston, MA). The photomultiplier tube settings (PMT) for Cy3 and Cy5 were 70 and 65-66, respectively. TIFF images of arrays were generated with ScanArray Express software (PerkinElmer).

source_name: pooled RNA of 10ppb dietary TCDD treated trout


title: SRP54 IP YPAD mid-log phase 5mM MgCl2/cyclohexamide (9)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77583.gif

source_name: total rna extract

tag: reference

value: total rna

source_name: affinity purified RNA

tag: cyclohexamide treatment

tag: genotype

tag: tap-tag


title: FA009.010

description: 10ppb groups compares to control group


title: FA009.009

description: 10ppb groups compares to control group


title: GPR180.5.2

scan_protocol: Agilent G2565BA

tag: cell type


title: ES1


title: FA009.014

description: 100ppb groups compares to control group


title: GPR180.5.1


title: Membrane bound vs Free/Soluble mRNAs (3) -- glass beads

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78840.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 6040; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-02-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 476; Parameter Laser on time = 26145; Parameter Laser Power = 3.58; Parameter Scan Time = 11:27:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.78; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-02-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 488; Parameter Scan Power = 100; Parameter Laser on time = 26148; Parameter Laser Power = 3.16; Parameter Scan Time = 11:27:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.78; Performer: Daniel,,Hogan

source_name: membrane bound RNA

value: membrane bound RNA


title: SRP54 IP YPAD mid-log phase 5mM MgCl2/cyclohexamide (8)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76833.gif


title: FA009.013

description: 100ppb groups compares to control group

source_name: pooled RNA of trout in control diet group


title: GPR180.1.1


title: 1st instar larvae_wildtype_replicate_D

source_name: 1st instar larvae_wildtype_replicate_D


title: FA009.008

description: 1ppb groups compares to control group

source_name: pooled RNA of 1ppb dietary TCDD treated trout


title: FA009.015

description: 100ppb groups compares to control group

source_name: pooled RNA of 100ppb dietary TCDD treated trout


title: SRP54 IP YPAD mid-log phase 5mM MgCl2/cyclohexamide (10)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77584.gif


title: 1st instar larvae_wildtype_replicate_E

source_name: 1st instar larvae_wildtype_replicate_E


title: FA009.007

description: 1ppb group compares to control group


title: SRP54 IP YPAD mid-log phase 5mM MgCl2/cyclohexamide (7)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/76830.gif


title: POMP.4.2

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA POMP

source_name: SW480; Transf2.2.POMP.4

value: POMP


title: FA009.006

description: 1ppb group compares to control group


title: POMP.2.3

source_name: SW480; Transf1.4.POMP.2

value: colorectal cancer cells


title: Iliac artery necropsy_Estradiol treatment_rep3

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Approval for all animal procedures was obtained from the Institutional Animal Care and Use Committee.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

organism: Macaca fascicularis

source_name: Iliac artery necropsy_high fat diet_Estradiol treatment

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 0.275 micrograms total RNA starting material.

extract_protocol: The iliac artery samples were obtained at necropsy.  The artery samples were placed in RNAlater (Ambion) in the surgical suite.  For processing, RNAlater was blotted off and the artery sample was minced with scalpels, and homogenized in TRI reagent (MRC) with a Polytron (Brinkmann).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Cynomolgus monkey

tag: age

value: greater than 11 years

tag: gender

value: female

tag: high fat diet

value: 6.5 years

tag: ovariectomized

value: ~4 years

value: iliac artery necropsy

value: Estradiol

tag: duration

value: 8 months

tag: atherosclerotic plaque size pretreatment

tag: atherosclerotic plaque size postreatment

tag: animal id


title: POMP.4.1

source_name: SW480; Transf2.1.POMP.4

tag: cell line

tag: sirna

tag: sirna no.

tag: rep. no.


title: POMP.4.3

source_name: SW480; Transf2.3.POMP.4


title: FA009.005

description: 1ppb group compares to control group

tag: tissue

value: 10 whole fish


title: 271_8

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
271_8_Cy3
271-4_271-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_4
This Sample represents one channel of a dual-channel array.

hyb_protocol: According to the manufacturer's recommendations.

data_processing: Data was imported into R and analyzed with the BioConductor limma package. Data was quantile normalized.

source_name: hBMSCs, old donor, passage 8

label_protocol: Cy3 and Cy5, following the manufacturer's recommendations.

growth_protocol: The cells were cultured in minimum essential alpha-medium (αMEM) supplemented with 20mM HEPES, 10% heat-inactivated fetal bovine serum (FBS), 2mM L-glutamine and 100 units/ml penicillin and 100 μg/ml streptomycin (all from Gibco, Paisley, UK). Same serum lot was used throughout the study. The medium was renewed twice a week and the cells were harvested when 70-80% confluent and plated further at density of 1000 cells/cm2. Cells were cultured until senescence was reached.

extract_protocol: RNA was extracted using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. no. 80204, Qiagen, CA, USA) and a Qiagen supplementary protocol “Purification of total RNA containing miRNA from animal cells using the RNeasy Plus Mini Kit (cat. no. 74134).

value: bone marrow-derived mesenchymal stem cells

tag: passage

value: 75 years

tag: subject id


title: 1st instar larvae_wildtype_replicate_A

source_name: 1st instar larvae_wildtype_replicate_A

tag: genotype/variation

value: wildtype

tag: developmental stage


title: 271_4

description:
271_4_Cy5
271-4_271-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_4
This Sample represents one channel of a dual-channel array.

scan_protocol: According to the manufacturer's recommendations.

source_name: hBMSCs, old donor, passage 4

tag: cell type

tag: age


title: 194_8

description:
194_8_Cy5
194-4_194-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_3
This Sample represents one channel of a dual-channel array.

value: 82 years


title: 1st instar larvae_Su(var)3-9evo/Su(var)3-906_replicate_C

value: 1st instar larvae, approximately 48 hours after egg laying


title: 1st instar larvae_wildtype_replicate_C

source_name: 1st instar larvae_wildtype_replicate_C


title: 1st instar larvae_wildtype_replicate_B

source_name: 1st instar larvae_wildtype_replicate_B


title: Iliac artery necropsy_Estradiol treatment_rep2

tag: strain

tag: gender

tag: high fat diet

tag: treatment


title: FA009.004

description: 0.1ppb group compares to control group

source_name: pooled RNA of 0.1ppb dietary TCDD treated trout


title: AllStar.3.10

description: aneuploid, colon adenocarcinoma cell line (SW480), transfected with siRNA AllStar

source_name: SW480; Transf2.3.AllStar3

value: AllStar (negative control siRNA)


title: Iliac artery necropsy_Estradiol treatment_rep4

tag: ovariectomized

tag: duration

tag: atherosclerotic plaque size pretreatment

tag: atherosclerotic plaque size postreatment


title: FA009.003

description: 0.1ppb group compares to control group

source_name: pooled RNA of trout in control diet group


title: FA009.001

description: 0.1ppb group compares to control group


title: Iliac artery necropsy_Estradiol treatment_rep1

tag: animal id


title: POMP.2.2

source_name: SW480; Transf1.2.POMP.2

tag: cell line

tag: sirna

value: POMP

tag: sirna no.

tag: rep. no.


title: 1st instar larvae_Su(var)3-9evo/Su(var)3-906_replicate_A

tag: genotype/variation


title: 194_4

description:
194_4_Cy3
194-4_194-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_3
This Sample represents one channel of a dual-channel array.

tag: passage

tag: subject id


title: POMP.2.1

source_name: SW480; Transf1.1.POMP.2

tag: cell type

value: colorectal cancer cells


title: 1st instar larvae_Setdb110.1/ Setdb110.1_replicate_C

tag: developmental stage


title: 172_4

description:
172_4_Cy5
172-4_172-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_2
This Sample represents one channel of a dual-channel array.

tag: age

value: 79 years


title: 172_8

description:
172_8_Cy3
172-4_172-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_2
This Sample represents one channel of a dual-channel array.


title: 1st instar larvae_Su(var)3-9evo/Su(var)3-906_replicate_B


title: AllStar.1.7

source_name: SW480; Transf2.2.AllStar1


title: FA009.002

description: 0.1ppb group compares to control group

tag: tissue


title: AllStar.3.8

source_name: SW480; Transf1.1.AllStar3


title: 092_8

description:
092_8_Cy3
092-4_092-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_4
This Sample represents one channel of a dual-channel array.

source_name: hBMSCs, young donor, passage 8

value: 23 years


title: 164_8

description:
164_8_Cy5
164-4_164-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_1
This Sample represents one channel of a dual-channel array.


title: AllStar.3.9

source_name: SW480; Transf2.1.AllStar3


title: AllStar.1.5

source_name: SW480; Transf1.4.AllStar1


title: 1st instar larvae_Setdb110.1/ Setdb110.1_replicate_B

description: Gene expression data from 1st instar larvae


title: 092_4

description:
092_4_Cy5
092-4_092-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_4
This Sample represents one channel of a dual-channel array.

source_name: hBMSCs, young donor, passage 4


title: 1st instar larvae_HP1a04 PofD119/HP1a05 PofD119_replicate_C

value: HP1a04 PofD119/HP1a05 PofD119


title: 1st instar larvae_Setdb110.1/ Setdb110.1_replicate_A


title: 091_8

description:
091_8_Cy5
091-4_091-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_3
This Sample represents one channel of a dual-channel array.


title: 164_4

description:
164_4_Cy3
164-4_164-8_US23502401_252800414962_S01_GE2_1100_Jul11_1_1
This Sample represents one channel of a dual-channel array.


title: AllStar.1.4

source_name: SW480; Transf1.2.AllStar1


title: 089_4

description:
089_4_Cy5
089-4_089-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_2
This Sample represents one channel of a dual-channel array.

value: 24 years


title: 1st instar larvae_HP1a04 PofD119/HP1a05 PofD119_replicate_A


title: 1st instar larvae_HP1a04 PofD119/HP1a05 PofD119_replicate_B


title: AllStar.0.3

source_name: SW480; Transf3.AllStar


title: 1st instar larvae_HP1a04/HP1a05_replicate_B


title: AllStar.1.6

source_name: SW480; Transf2.1.AllStar1


title: AllStar.0.2

source_name: SW480; Transf2.AllStar


title: 091_4

description:
091_4_Cy3
091-4_091-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_3
This Sample represents one channel of a dual-channel array.


title: AllStar.0.1

source_name: SW480; Transf1.AllStar


title: Sertoli cell cloned embryo, Blastocyst stage, biological rep5

city: Tokyo

first: Feng

last: Cao

address: 1-1-1 Sakuraoka, Setagaya-ku

department: Bioscience

country: Japan

institute: Tokyo University of Agriculture

description: Time-lapse gene expression data of Sertoli cell cloned embryos throughout preimplantation stages.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000

data_processing: The data were analyzed by GeneSpring GX 12.0 with RMA summarization algorithm and baseline to the median of all samples.

organism: Mus musculus

source_name: Mouse Sertoli cell cloned embryo, Blastocyst stage

label_protocol: cRNA amplify and label using Two-cycle target synthesis kit provided by Affymetrix with some modification for single embryos analysis (refer to Plos One, Fukuda, Cao, et al., 2010)

growth_protocol: Embryos incubated in drops of KSOM medium at 37C, 5% CO2,5%O2 and 90%N2 until collect.

extract_protocol: Total RNA is extract by Rneasy Micro kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Embryos were washed 3 times by PBS, transfer into 50μl lysis buffer included 1% 2-mercaptoethanol and store at -80℃ until use.

tag: method

value: Sertoli cell nuclear transfer

tag: Stage

value: Blastocyst stage

tag: strain

value: donor cell:B6CBF1, recipient oocyte:B6D2F1


title: 1st instar larvae_HP1a04/HP1a05_replicate_C


title: 088_4

description:
088_4_Cy3
088-4_088-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_1
This Sample represents one channel of a dual-channel array.

value: 21 years


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S2, triplicate repeat 3

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

description: Sample 9

hyb_protocol: 10ug of fragmented biotinylated cRNA was hybridised for 16hrs at 45oC on a Drosophila Genome 2.0 GeneChip. After 16hrs, GeneChips were washed on a FS_450 Fluidics Station using the Midi_euk_2 v3 script.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and data extraction performed in GCOS v1.2.

data_processing: CHP files were generated in GCOS 1.2 and normalised by global scaling (MAS5) to a value of 500. Experimental and control lines were compared by both a student t-test and log2 ratios.

source_name: Heads, newly eclosed, male, rCAG.rCUG100, S2

label_protocol: Biotinylated cRNA were prepared using the One-Cycle Target Labelling and Control Reagents Kit, according to the manufacturer's protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the Drosophila stocks and flies were maintained in vials containing Fortified (FI) medium and kept at 25°C. The FI medium was composed of 1% agar, 18.75% compressed yeast, 10% polenta, 10% treacle, 1.5% acid mix and 2.5% tegosept.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer's protocol. Total RNA was further purified using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Samples were frozen in liquid nitrogen and homogenised in Trizol reagent (Invitrogen).

tag: line

value: newly eclosed

tag: gender

value: male

value: head


title: 1st instar larvae_HP1a04/HP1a05_replicate_A


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S2, triplicate repeat 1

description: Sample 7


title: 088_8

description:
088_8_Cy5
088-4_088-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_1
This Sample represents one channel of a dual-channel array.

value: bone marrow-derived mesenchymal stem cells


title: Sertoli cell cloned embryo, Blastocyst stage, biological rep4


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S2, triplicate repeat 2

description: Sample 8


title: 089_8

description:
089_8_Cy3
089-4_089-8_US23502401_252800414962_S01_GE2_1100_Jul11_2_2
This Sample represents one channel of a dual-channel array.


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S1, triplicate repeat 3

description: Sample 6

source_name: Heads, newly eclosed, male, rCAG.rCUG100, S1


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S1, triplicate repeat 2

description: Sample 5


title: LNCaP_siCtrl

city: Chicago

first: Hong-Jian

last: Jin

state: IL - Illinois

address: 303 E Superior St

department: Medicine

institute: Northwestern University

description:
SAMPLE 1
No replicates.

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The bead-level data were preprocessed using GenomeStudio (Illumina) and the expression data was analyzed using the beadarray package in Bioconductor,quantile normalized using the beadarray package.

source_name: LNCaP

growth_protocol: LNCaP and 22RV1 cell lines were maintained in RPMI supplemented with 10% FBS.In some experiments Cells were grown in charcoal stripped medium for 3 days followed by treated with 1 nM R1881 for 24hours followed by RNA isolation.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

value: LNCaP

value: control

tag: construct

value: siRNA


title: PC-3M FoxA1

description: SAMPLE 2

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

growth_protocol: PC-3M control and FoxA1 stable cell lines were maintained in RPMI supplemented with 10% FBS

tag: cell line

value: FoxA1 overexpression


title: Sertoli cell cloned embryo, Blastocyst stage, biological rep2


title: Drosophila heads_elavII>rCAG.rCUG100_independent line S1, triplicate repeat 1

description: Sample 4


title: Sertoli cell cloned embryo, Blastocyst stage, biological rep1


title: Sertoli cell cloned embryo, Blastocyst stage, biological rep3


title: 22RV1_shFoxA1

description:
SAMPLE 4
No replicates.

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: FoxA1 knockdown

value: shRNA


title: Sertoli cell cloned embryo, Morula stage, biological rep1

source_name: Mouse Sertoli cell cloned embryo, Morula stage

value: Morula stage


title: Sertoli cell cloned embryo, Morula stage, biological rep4


title: 22RV1_shCtrl

description:
SAMPLE 3
No replicates.


title: PC-3M Ctrl

description: SAMPLE 1


title: Drosophila heads_elavII>4xUAS, triplicate repeat 2

description: Sample 2

source_name: Heads, newly eclosed, male, 4xUAS

tag: sample type


title: Drosophila heads_elavII>4xUAS, triplicate repeat 1

description: Sample 1


title: Sertoli cell cloned embryo, Morula stage, biological rep5


title: Sertoli cell cloned embryo, Morula stage, biological rep2


title: Drosophila heads_elavII>4xUAS, triplicate repeat 3

description: Sample 3


title: Sertoli cell cloned embryo, Morula stage, biological rep3


title: LNCaP_shCtrl_hormone-deprived

hyb_protocol: The arrays were processed at Cleveland Clinic Genomics Core (Cleveland, Ohio) according to manufacturer’s protocol.

growth_protocol: LNCaP cell lines were maintained in RPMI supplemented with 10% FBS. Both shCtrl and shFoxA1 cells were grown in charcoal stripped medium for 3 days followed by treated with 1 nM R1881 for 24hours followed by RNA isolation.


title: LNCaP_shFoxA1_hormone-deprived

scan_protocol: The arrays were processed at Cleveland Clinic Genomics Core (Cleveland, Ohio) according to manufacturer’s protocol.


title: LNCaP_siFoxA1

description:
SAMPLE 2
No replicates.


title: Sertoli cell cloned embryo, 8-cell stage, biological rep5

source_name: Mouse Sertoli cell cloned embryo, 8-cell stage

value: 8-cell stage


title: Sertoli cell cloned embryo, 8-cell stage, biological rep3


title: fibroblast_patient_4_C

description: reference: PubMed ID #21551238 - Cotan, D. et al. Secondary coenzyme Q10 deficiency triggers mitochondria degradation by mitophagy in MELAS fibroblasts. Faseb J 25, 2669-87 (2011).

hyb_protocol: Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). Hybridization was performed overnight in the GeneChip Hybridization Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of the probe were performed in the GeneChip fluidics station using buffers and protocols provided by the manufacturer. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

scan_protocol: High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

data_processing: Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.

source_name: human fibroblast, Q10 deficient patient, MELAS, rep. 3

extract_protocol: Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.

value: fibroblast

tag: clinical phenotype

value: MELAS (A3243G mutation).

tag: cell phenotype

value: (1) decreased mitochondrial respiratory chain enzyme activities, (2) low CoQ10 level, (3) decreased mitochondrial membrane potential, (4) increased oxidative stress and the activation of mitochondrial permeability, and (5) defective autophagosome elimination in MELAS fibroblasts.


title: LNCaP_shCtrl_R1881

description:
SAMPLE 5
replicate 3

label_protocol: The arrays were processed at Cleveland Clinic Genomics Core (Cleveland, Ohio) according to manufacturer’s protocol.

tag: genotype/variation


title: LNCaP_shFoxA1_R1881

description:
SAMPLE 6
replicate 3


title: Sertoli cell cloned embryo, 8-cell stage, biological rep2

value: Sertoli cell nuclear transfer

value: donor cell:B6CBF1, recipient oocyte:B6D2F1


title: fibroblast_patient_5_B

description: reference: unpublished (sister of patient 3; reference 16116126 PubMed ID)

source_name: human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 2

value: girl


title: Sertoli cell cloned embryo, 4-cell stage, biological rep5

source_name: Mouse Sertoli cell cloned embryo, 4-cell stage

value: 4-cell stage


title: LNCaP_shFoxA1_rep2

description:
SAMPLE 4
replicate 2


title: LNCaP_shFoxA1_rep1

description:
SAMPLE 2
replicate 1


title: fibroblast_patient_4_A

source_name: human fibroblast, Q10 deficient patient, MELAS, rep. 1


title: fibroblast_patient_5_A

source_name: human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 1


title: Sertoli cell cloned embryo, 8-cell stage, biological rep1


title: fibroblast_patient_5_C

source_name: human fibroblast, Q10 deficient patient COQ2 mutant (sister), rep. 3


title: fibroblast_patient_3_A

description: reference: Salviati, L. et al.  Neurology 65, 606-8 (2005)

source_name: human fibroblast, Q10 deficient patient COQ2 mutant, rep. 1

value: boy

value: dermal fibroblasts.

value: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts).

tag: treatment

value: Oral CoQ10 improved the neurologic picture, but do not improved the renal dysfunction.


title: fibroblast_patient_4_B

source_name: human fibroblast, Q10 deficient patient, MELAS, rep. 2


title: fibroblast_patient_3_C

description: reference: 16116126 PubMed ID

source_name: human fibroblast, Q10 deficient patient COQ2 mutant, rep. 3

value: (1) corticosteroid-resistant nephrotic syndrome, (2) progressive encephalomyopathy later developed, and (3) CoQ10 was decreased (muscle and fibroblasts)


title: Sertoli cell cloned embryo, 8-cell stage, biological rep4


title: Sertoli cell cloned embryo, 4-cell stage, biological rep2


title: Sertoli cell cloned embryo, 4-cell stage, biological rep4


title: Sertoli cell cloned embryo, 4-cell stage, biological rep3


title: Sertoli cell cloned embryo, 4-cell stage, biological rep1


title: control_fibroblast_B

source_name: human fibroblast, neonatal, rep. 2

value: Human dermal fibroblast (primary culture of cells) obtained from healthy voluntiers.

value: neonatal


title: LNCaP_shCtrl_rep2

description:
SAMPLE 3
replicate 2

value: LNCaP

value: control

value: shRNA


title: fibroblast_patient_3_B

description: reference: 16116126 PubMed ID

source_name: human fibroblast, Q10 deficient patient COQ2 mutant, rep. 2


title: AC_RR_rep2

city: Wageningen

first: Ruud

middle: A

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45C in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

organism: Solanum lycopersicum

source_name: tomato fruit_red ripe

label_protocol: RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands.  corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, total RNA (100 ng) was used for whole transcript cDNA synthesis using the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands), and subsequently labeled using the Affymetrix GeneChip WT Terminal Labeling Kit [catalog number 901524] (Affymetrix, Santa Clara, CA).

growth_protocol: Tomato plants were grown in a greenhouse on rockwool with liquied nutrient solution

extract_protocol: Total RNA was extracted using an InviTrap Spin Plant RNA mini kit (Stratec, Berlin)

treatment_protocol: Fruits kept at -80C untill further use, and ground in liquied nitrogen before RNA extraction

tag: variety

value: Ailsa Craig

value: ripening tomato fruit

tag: ripening stage

value: red ripe (RR)


title: LNCaP_shCtrl_rep1

description:
SAMPLE 1
replicate 1


title: AC_RR_rep1


title: control_fibroblast_A

source_name: human fibroblast, neonatal, rep. 1

tag: cell type


title: total RNA dEgd1/dEgd2 (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88468.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.44; Performer: Marta,,Del Alamo Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.44; Performer: Marta,,Del Alamo

source_name: total rna WT

tag: genotype

value: WT

source_name: total rna dEgd1/dEgd2

value: :egd1 egd2


title: AC_RR_rep3

tag: tissue


title: AC_T_rep2

source_name: tomato fruit_turning/breaker

value: turning/breaker (T)