title: sugar, female 48h, chip 6

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_023


title: sugar, male 48h, chip 2

status: Public on Nov 01 2004

type: RNA

city: Karlsruhe

first: Michael

middle: J.

last: Pankratz

department: Institute of Genetics

country: Germany

institute: Forschungszentrum Karlsruhe

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_027

molecule: total RNA

organism: Drosophila melanogaster

source_name: normal

source_name: 48h sugar


title: sugar, male 24h, chip 5

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_021

source_name: 24h sugar


title: starvation, male 24h, chip 6

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_030

source_name: 24h starved


title: sugar, male 24h, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_016


title: starvation, male 24h, chip 3

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_029


title: sugar, male 24h, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_020


title: starvation, male 24h, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_024


title: starvation, male 24h, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_012


title: sugar, female 48h, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_018


title: sugar, female 48h, chip 5

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_019


title: sugar, male 24h, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_017


title: starvation, male 24h, chip 5

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_025


title: starvation, male 24h, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_013


title: sugar, female 48h, chip 3

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_022


title: sugar, female 48h, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_045


title: starvation, female 48h, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_021

source_name: 48h starved


title: starvation, female 48h, chip 5

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_024


title: sugar, female 48h, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_047


title: starvation, female 24h, chip 3

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_031


title: starvation, female 24h, chip 6

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_032


title: CEA_SGF:ALY019_ASP

city: EVRY

first: Michèle

middle: T

last: Martin

address: 2, rue Gaston Crémieux

department: DSV/DRR

country: France

institute: CEA

description:
Human mammary skin biopsies were obtained from plastic surgery, from the Tissue Bank for Research (AFM-BTR, hôpital La Pitié Salpétrière, Paris) and keratinocytes were isolated with trypsin. Primary cultures were initiated in complete KGM2 semi-defined medium (Clonetics) on flasks coated with collagen type I (Falcon Biocoat). Sub-confluent cultures were re-plated to allow amplification through a second passage. Third passage cultures were seeded at 40 000 cells/cm2 and were grown at 37°C and 5% CO2. Cultures were confluent at day 5 and cells were further incubated for 3 days post-confluence in order to reach a morphological differentiated state.
Differentiated cultures were then irradiated with a 60 Co source at two different dose rates: 28 cGy/min and 2 cGy/min to deliver 10 mGy and 2 Gy, respectively. Sham irradiated cells received the same treatment, except for irradiation. Cultures were then returned to the incubator and harvested at 3,6,15,24,48 and 72 hours following irradiation in order to prepare RNA extracts. Media was changed the day before irradiation and renewed every two days. Total RNA was amplified using the MessageAmp RNA Kit (Ambion). One round of amplification was performed. Amplified RNA was labeled by coupling with aminoallyl-modified dUTP (Sigma), followed by a subsequent incorporation of monofunctionnal Cy3 or Cy5-N-succinimide esters (Amersham Biosciences). For each labeling experiment, amplified RNA (2 µg) was reverse-trancribed using random hexamers in the presence of 200 µM aminoallyl-dUTP, 500 µM each dATP, dCTP, dGTP, 300 µM dTTP, 400 U of Superscript II polymerase (Invitrogen) in a final volume of 30 µl. After incubation at 42°C for 2 hours, RNA was hydrolyzed by adding 2 units of DNAse-free RNAse H (Invitrogen) and incubating at 37°C for 15 minutes. The volume was adjusted to 400 µl with H20, aminoallyl-cDNA was purified by centrifugation in a microcon (YM-30 Millipore Amicon), eluted with 20 µl of water and then dried in a vacuum to 10µl. One µl sodium bicarbonate 0.5 M was added to aminoallyl-cDNA and subsequently mixed with vacuum-dried monofunctional dye. Coupling reaction was performed during 1 hour at room temperature in the dark. Labeled cDNAs were purified with a nucleospin column (Macherey Nagel), eluted with 100 µl of TE, mixed with 10 µg of human Cot-1 DNA, 10µg poly(A) and 10µg of yeast tRNA, then precipitated with 1 volume of 5 M ammonium acetate in chilled ethanol.
The microarray slides were pre-hybridized in 3,5x SSC, 0,1% SDS and 1% BSA for 30 mn at 50°C. The labeled extract pellet was suspended in the hybridization solution (formamide 50%, 2,5x Denhardt, 0,5% SDS, 0,6% SSPE). The solution was heated to 95°C, added onto the prehybridized microarray slides, and hybridized at 42°C in a humidified chamber for 16 to 18 hours. Microarray glass slides were washed with 0,1X SSC / 0,1 % SDS at room temperature for 15 minutes and then twice with 0,1X SSC in the same conditions.

organism: Homo sapiens

source_name: Differentiated primary keratinocyte culture, 3 hours, 2 Gy

source_name: Differentiated primary keratinocyte culture, 6 hours, 0 Gy


title: sugar, female 24, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_022


title: starvation, female 48h, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_050


title: starvation, female 24h, chip 5

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_028


title: sugar, female 24, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_019


title: starvation, female 24h, chip 2

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_027


title: larval development, 100h AEL, chip 4

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 100h AEL timepoint resulted from a 99-101h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP6_012

source_name: 100h AEL

source_name: 40h AEL


title: starvation, female 24h, chip 4

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_015


title: starvation, female 48h, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 48h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_049


title: larval development, 100h AEL, chip 1

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 100h AEL timepoint resulted from a 99-101h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. Only regulations that are in the 99.5% confidence interval are included. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP6_006


title: larval development, 100h AEL, chip 3

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 100h AEL timepoint resulted from a 99-101h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP6_011


title: larval development, 88h AEL, chip 4

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 88h AEL timepoint resulted from a 87-89h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_009

source_name: 88h AEL


title: larval development, 76h AEL, chip 6

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_008

source_name: 76h AEL


title: larval development, 76h AEL, chip 3

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_003


title: larval development, 76h AEL, chip 4

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_009


title: larval development, 88h AEL, chip 2

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 88h AEL timepoint resulted from a 87-89h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_004


title: larval development, 76h AEL, chip 5

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_022


title: starvation, female 24h, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS soaked filterpaper only for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_014


title: larval development, 100h AEL, chip 2

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 100h AEL timepoint resulted from a 99-101h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_011


title: larval development, 88h AEL, chip 1

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 88h AEL timepoint resulted from a 87-89h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_005


title: larval development, 88h AEL, chip 3

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 88h AEL timepoint resulted from a 87-89h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_010


title: larval development, 64h AEL, chip 4

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 64h AEL timepoint resulted from a 63-65h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_021

source_name: 64h AEL


title: larval development, 76h AEL, chip 1

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_004


title: larval development, 64h AEL, chip 5

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 64h AEL timepoint resulted from a 63-65h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_007


title: larval development, 64h AEL, chip 3

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 64h AEL timepoint resulted from a 63-65h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_008


title: larval development, 76h AEL, chip 2

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 76h AEL timepoint resulted from a 75-77h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_019


title: larval development, 64h AEL, chip 2

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 64h AEL timepoint resulted from a 63-65h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_018


title: larval development, 52h AEL, chip 6

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_006

source_name: 52h AEL


title: larval development, 52h AEL, chip 5

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations.  For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_020


title: larval development, 52h AEL, chip 3

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP5_001


title: larval development, 52h AEL, chip 2

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_017


title: larval development, 64h AEL, chip 1

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 64h AEL timepoint resulted from a 63-65h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_003


title: sugar, female 24, chip 1

description:
OregonR flies were kept in 50 ml PS-tubes flat bottom (Greiner) at 25¡C on standard fly food. For the control flies were moved to tubes containing yeast paste on PBS soaked filterpaper (normal), starved flies were obtained by putting them in tubes with PBS + 20% sucrose soaked filterpaper for 24h. For further details see publication.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP2_018


title: larval development, 52h AEL, chip 4

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_007


title: larval development, 52h AEL, chip 1

description:
OregonR larvae were kept on apple juice agar plates with yeast at 25¡C. For the control larvae were collected 39-41h AEL (40h AEL). Larvae of the 52h AEL timepoint resulted from a 51-53h collection.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. . Both copies and all hybridisation repeats were used for normalisation, MY_VALUE therefore has the same value for these copies in all relevant hybridisations. For additional information see publication and web link.
Keywords = nutrient response, starvation, anti-aging, longevity
Lot batch = FP3_002


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52361)

status: Public on Oct 29 2004

city: New Haven

first: Paul

last: Bertone

state: CT

country: USA

institute: Yale University

description:
Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals was obtained from Ambion (Austin, TX). First-strand cDNA was generated from 4 µg RNA/rxn with (RNase H-) M-MLV reverse transcriptase, primed with equimolar concentrations of oligo(dT18) and random decamers. The reactions were carried out at 42°C for 2 hours in the presence of 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.15 mM dTTP and 0.15 mM amino-allyl dUTP to facilitate the secondary labeling of an amine-reactive fluorescent conjugate.
Following reverse transcription the products were heated at 95°C for 5 minutes to denature the RNA:DNA hybrids and heat-inactivate the reverse transcriptase, after which the RNA template was hydrolyzed by incubating in 0.2 M NaOH at 65°C for 15 minutes. The reaction was then neutralized in 0.3 M HEPES (pH 7.0). Reverse transcription products from 20 separate reactions were produced in this manner and pooled to reduce technical variability between samples.
The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs. Following incubation at room temperature for 1 hour, the labeled cDNAs were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ) and isopropanol-precipitated.
Microarrays were hybridized with 2-3 µg labeled cDNA in 320 µL hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 20 hours at 50°C. Hybridizations were performed in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation.
After hybridization, the arrays were washed on an orbital platform in non-stringent buffer (6× SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45°C. This was followed by a 5-minute wash in non-stringent buffer and a 4-minute wash in 0.2X SSC.
The arrays were dried with compressed nitrogen. Fluorescence micrographs were acquired with an Axon 4000B laser scanner at 5 µm resolution and intensity data were extracted with NimbleScan software (NimbleGen Systems).
Keywords = liver tissue, poly(A)+ RNA

source_name: Alexa555-labeled cDNA derived from human liver poly(A)+ RNA


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52375)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52178)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52377)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30228)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52358)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52437)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30229)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52353)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52395)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52439)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30152)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30231)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30071)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52472)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52352)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30222)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30237)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30146)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52441)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29118)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30074)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30220)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30221)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_52473)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29074)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30091)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30140)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30213)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29035)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29112)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29095)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30162)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29033)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25100)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_30212)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24906)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24938)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25089)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24610)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20266)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_29030)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25093)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25061)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_19824)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25075)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_18517)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24940)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24949)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_18601)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24946)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24943)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_18605)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17915)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25094)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_18373)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_25070)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_24942)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20338)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17911)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17916)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17918)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20344)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14313)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20289)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14316)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14308)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14293)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14307)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14288)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20275)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14297)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_16306)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14309)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14289)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14310)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14294)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14311)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14292)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14277)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14276)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14318)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14326)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14317)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_20282)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14278)


title: JMV-1-SA3-9897-3-1-ME-1-RML_Signal

status: Public on Sep 26 2005

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
To measure S. aureus gene expression during growth phase and/or S. aureus–PMN interaction.
This sample is also known as JMV-1-SA3-9897-3-1-ME-1-RML_Signal

organism: Staphylococcus aureus

source_name: Sa and PMN interaction


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14267)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14274)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17913)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_17996)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14273)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14287)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14269)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14261)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14263)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14285)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14272)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12813)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14262)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14284)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12867)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14280)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14270)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14271)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13242)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12859)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12846)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_14259)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13107)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12825)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13289)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13111)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13051)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12866)


title: Estrogen actions in human breast cancer cells - 32 hrs (dye swap)

status: Public on Oct 27 2004

city: Avellino

first: Angelo

last: Facchiano

address: via Roma 52A/C

country: Italy

institute: Institute of Food Science

description:
Cell Culture and RNA purification
Human breast cancer ZR-75.1 cells were propagated in DMEM medium supplemented with 10% FBS and antibiotics
(100U/ml Penicillin, 100?g/ml Streptomycin and 250ng/ml Amphotericin-B). Before use, cells were plated at
20-40% confluence and maintained for 4 days in steroid-free medium (Phenol red-free DMEM medium, with 5%
charcoal-stripped FBS and antibiotics), before stimulation with 5x10-8M 17?-estradiol (E2). At the indicated
times, total cellular RNA was extracted from control (0, - E2) or E2–stimulated (+E2) cultures. 6 culture
plates (150mm) were used for each time-point, and the experiment was repeated three times within two weeks.
Poly(A)+ RNA was isolated from pools of 2mg total RNA, by batch-wise magnetic separation with Dynabeads
(Oligo (dT)25; Dynal, Oslo, Norway) according to the manufacturer’s instructions, resuspended in diethyl
pyrocarbonate-treated water, quantitated and diluted to a final concentration of 50ng/?l. Before further use,
total and poly(A)+ RNAs were tested by agarose gel electrophoresis.

cDNA microarray probing
cDNA microarray mRNA analysis was carried with UniGEM Human V 2.0 (Incyte Genomics, St. Louis, U.S.A.). 200ng
of each poly(A)+ RNA derived from estrogen stimulated (+E2) cells were used to generate carbocyanine 5
(Cy5)-labeled cDNAs, that was mixed with common reference probes consisting of carbocyanine 3 (Cy3)-labeled
cDNAs prepared from an equal amount of poly(A)+ RNAs purified from quiescent, hormone deprived cultures (-E2),
for competitive hybridization to a cDNA microarray grid containing 9,182 human sequences of known genes and
expressed sequence tags (representing 8,372 unique gene/ESTs clusters) and 192 internal controls (for reverse
transcription, absolute sensitivity and differential expression QCs: human UniGEM V 2.0 screening services;
Incyte Genomics, St. Louis, U.S.A.). cDNA synthesis, labeling and hybridization were generally repeated 3 times
(in three cases 4 times), in separate experiments.

source_name: Estrogen stimulated (32 hrs, + E2)

source_name: Control (0 hr, -E2)


title: Estrogen actions in human breast cancer cells - 28 hrs (dye swap)

source_name: Estrogen stimulated (28 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 20 hrs (dye swap)

source_name: Estrogen stimulated (20 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 12 hrs (dye swap)

source_name: Estrogen stimulated (12 hrs, + E2)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12869)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12801)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12610)


title: Estrogen actions in human breast cancer cells - 16 hrs (dye swap)

source_name: Estrogen stimulated (16 hrs, + E2)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13254)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12783)


title: Estrogen actions in human breast cancer cells - 4 hrs (dye swap)

source_name: Estrogen stimulated (4 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 6 hrs (dye swap)

source_name: Estrogen stimulated (6 hrs, + E2)


title: Estrogen actions in human breast cancer cells -2 hrs (dye swap)

source_name: Estrogen stimulated (2 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 1hr (dye swap)

source_name: Estrogen stimulated (1 hr, + E2)


title: Estrogen actions in human breast cancer cells - 8 hrs (dye swap)

source_name: Estrogen stimulated (8 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 32 hrs


title: Estrogen actions in human breast cancer cells - 28 hrs


title: Estrogen actions in human breast cancer cells - 20 hrs


title: Estrogen actions in human breast cancer cells - 24 hrs

source_name: Estrogen stimulated (24 hrs, + E2)


title: Estrogen actions in human breast cancer cells - 16 hrs (duplicate)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11648)


title: Estrogen actions in human breast cancer cells -2 hrs (duplicate) (dye swap)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12794)


title: Estrogen actions in human breast cancer cells - 16 hrs


title: Estrogen actions in human breast cancer cells - 24 hrs (dye swap)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12807)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11692)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_13243)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11691)


title: Estrogen actions in human breast cancer cells - 12 hrs


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12863)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12808)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12802)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11693)


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11703)


title: Estrogen actions in human breast cancer cells - 8 hrs


title: Estrogen actions in human breast cancer cells - 8 hrs (duplicate)


title: Estrogen actions in human breast cancer cells - 4 hrs


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_12803)


title: Estrogen actions in human breast cancer cells - 6 hrs


title: ME7-end-10

status: Public on Oct 13 2004

city: Winnipeg

first: Garrett

last: Sorensen

country: Canada

institute: Canadian Science Centre for Human and Animal Health

description:
C57BL/6 mice were inoculated intracerebrally with 20 µl of 1% brain homogenate which was obtained from the TSE Resource Centre, Institute for Animal Health, Compton, UK.  Mock-infected control mice were inoculated intra-cerebrally with 20 µl of PBS.  The brains were removed at the appropriate time-points and stored at -80 C in RNALater (Ambion) until all experimental time points were completed.
Total RNA was isolated from the stored tissue samples by homogenization in Trizol reagent (Invitrogen). RNA was further purified using RNeasy columns (Qiagen) according to the manufacturers instructions. 10 µg of total RNA as a template for oligo -dT primed reverse transcription and incorporated amino allyl -dUTP (Sigma) into the cDNA, essentially following the Institute for Genomic Research, Rockville, MD, USA (TIGR) published protocol http://pga.tigr.org/sop/M004_1a.pdf
The remaining RNA template was hydrolysed and the cDNA product purified using the QIAquick PCR purification system (Qiagen). cDNA was dried down, then resuspended in 0.1 M Na2CO3, pH9.0 buffer, and incubated for 1 hour in either an Alexa Fluor555 (AF555) or Alexa Fluor647(AF647) mono-functional reactive dye (Molecular Probes) made up in DMSO.  Labelled cDNA was also purified using QIAquick PCR purification columns.
Labelled cDNA was dried down and resuspended in 60 µl DIG Easy Hyb hybridisation buffer (Roche) containing calf thymus DNA (Sigma) and yeast tRNA (Life Technologies). The labelled cDNAs were applied to arrays under M Series Lifter Slips (Erie Scientific Company) and the slides incubated in a hybridisation chamber at 42oC for 16 hours. Following hybridisation lifter slips were removed and the arrays washed a total of 3 times for 5 minutes first in1 X SSC, 0.2% SDS, and then 3 times for 5 minutes in 0.1 X SSC, 0.2% SDS pre-warmed to 42°C. A final wash in 0.1 X SSC at room temperature was performed, and slides centrifuged to dry. Slides were immediately scanned using a VersArray scanner (BioRad) at appropriate laser power and PhotoMultiplier Tube settings so that high intensity spots were not saturated. Spots were quantitated and background signals removed using ArrayPro software (Media Cybernetics, Inc).

organism: Mus musculus

source_name: Mock infected, endpoint


title: 79a-end-7


title: 79a-end-4


title: ME7-end-9


title: 79a-end-3


title: estrogen actions in human breast cancer cells - 1 hr

source_name: Estrogen stimulated (1hr, + E2)


title: Estrogen actions in human breast cancer cells - 2 hrs


title: 79a-end-5


title: ME7-end-4


title: ME7-end-8


title: 79a-end-6


title: ME7-end-5


title: ME7-end-6


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11690)


title: ME7-end-3


title: Triple-selected poly(A)+ human liver tissue RNA pooled from several individuals (HS_11650)


title: ME7-end-2


title: 79a-100dpi-9

source_name: Mock infected, 100 d.p.i.


title: 79a-end-8


title: 79a-100dpi-8


title: 79a-end-2


title: 79a-100dpi-7


title: ME7-end-1


title: 79a-100dpi-10


title: 79a-100dpi-1


title: 79a-100dpi-2


title: 79a-100dpi-3


title: ME7-100dpi-9


title: 79a-100dpi-4


title: 79a-100dpi-6


title: 79a-100dpi-5


title: ME7-100dpi-6


title: ME7-100dpi-10


title: ME7-100dpi-7


title: Native RPE #5

city: Baltimore

first: James

last: Handa

state: MD

address: 600 N. Wolfe St.

department: Wilmer Eye Institute

institute: Johns Hopkins Medical Institutes

description:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. Sample #5 is from a 95 year old WF with a death to enucleation time of 3 hours, 5 min.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

source_name: Native RPE #5


title: ME7-100dpi-5


title: ME7-100dpi-8


title: ME7-100dpi-4


title: ME7-100dpi-3


title: Native RPE #4

description:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. Sample #4 is from a 74 year old WF with a death to enucleation time of 3 hours, 35 min.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

source_name: Native RPE #4


title: 79a-21dpi-7

source_name: Mock infected, 21 d.p.i.


title: Subconfluent RPE, in serum #2

description:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

source_name: Subconfluent RPE, in serum #2


title: Native RPE #3

description:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. Sample #3 is from a 45 year old WM with a death to enucleation time of 4 hours, 45 min.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

source_name: Native RPE #3


title: Native RPE #1

description:
Description
I.	Exp Design
1.	Type of experiment: Comparison of native versus cultured RPE cells
2.	Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions
3.	How many hybridizations in exp: 20
4.	If a common reference used for all the hybs: no
5.	Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE
6.	Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. Sample #1 is from a 60 year old WM donor with a death to enucleation time of 4 hours.

II.	Samples used, extract prep, and labeling
1.	Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells.
2.	Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium).
3.	Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4.	Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5.	No external controls were added.

III.	Hybridization procedures and parameters
1.	Sample, array type, batch and serial # used
2.	Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with  Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV.	Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.

source_name: Native RPE #1


title: 79a-21dpi-6


title: Subconfluent RPE, in serum #3

source_name: Subconfluent RPE, in serum #3


title: 79a-21dpi-8


title: Subconfluent RPE, in serum #1

source_name: Subconfluent RPE, in serum #1