title: P114 replicate

status: Public on May 31 2012

type: RNA

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate 2 of 2

hyb_protocol: The hybridization was performed with canine-specific AMADID Release GE 4x44K microarrays (Agilent, USA) using Gene Expression Hybridization Kit (Agilent, USA) according to the manufacturer`s protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Canis lupus familiaris

source_name: P114 co-culture with MQ

label_protocol: The Quick Amp Labeling Kit (Agilent, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA) for oligo microarrays used in gene expression profiling and other downstream analyses.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL–1), and fungizone (2.5 mg mL–1) (reagents obtained from Sigma Aldrich, USA), in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol.

treatment_protocol: Cancer cells were grown and sorted monocytes were then layered on the top of each cell line. CMTMR was used to stain the cancer cells population prior to addition of the sorted monocyte population. The co-culture was maintained for at least 72 hrs. After the 72 hrs of co-culture the cells were harvested by trypsynization and sorted using FACS Aria II (Becton Dickinson, USA) into two tubes: not-stained macrophages and stained cancer cells.

tag: culture conditions

value: P114 co-culture with MQ

tag: cell line (sorted)

source_name: P114 single culture [control]

value: P114 single culture

tag: cell line


title: MQ P114 replicate

description: Biological replicate 2 of 2

source_name: MQ single culture [control]

value: MQ single culture

tag: cell type

value: macrophages

source_name: MQ co-cultured with P114

value: MQ co-cultured with P114

tag: cell type (sorted)


title: MQ CMT-U27 replicate

description: Biological replicate 2 of 2

source_name: MQ co-cultured with CMT-U27

value: MQ co-cultured with CMT-U27


title: MQ CMT-W2

description: Biological replicate 1 of 2

source_name: MQ co-cultured with CMT-W2

value: MQ co-cultured with CMT-W2


title: MQ CMT-U309

description: Biological replicate 1 of 2

source_name: MQ co-cultured with CMT-U309

value: MQ co-cultured with CMT-U309


title: MQ P114

description: Biological replicate 1 of 2


title: CMT-W1

description: Biological replicate 1 of 2

source_name: CMT-W1 single culture [control]

value: CMT-W1 single culture

source_name: CMT-W1 co-culture with MQ

value: CMT-W1 co-culture with MQ


title: CMT-U309

description: Biological replicate 1 of 2

source_name: CMT-U309 single culture [control]

value: CMT-U309 single culture

source_name: CMT-U309 co-culture with MQ

value: CMT-U309 co-culture with MQ


title: MQ CMT-U309 replicate

description: Biological replicate 2 of 2


title: MQ CMT-W1 replicate

description: Biological replicate 2 of 2

source_name: MQ co-cultured with CMT-W1

value: MQ co-cultured with CMT-W1


title: CMT-W2 replicate

description: Biological replicate 2 of 2

source_name: CMT-W2 co-culture with MQ

value: CMT-W2 co-culture with MQ

source_name: CMT-W2 single culture [control]

value: CMT-W2 single culture


title: CMT-W1 replicate

description: Biological replicate 2 of 2


title: Novel song replicate 4 [e15]

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

country: USA

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

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

data_processing: Data were background-subtracted and values < 0.5 were set to 0.5. Spots with -100 flags were filtered out before print-tip loess normalization. A scale between-array normalization was performed, then arrays with the reference in the Cy5 channel were inverted by multiplying by -1 to make all log ratios test/reference.

organism: Taeniopygia guttata

source_name: universal SoNG reference

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Trizol following manufacturer's protocol and DNase-treated with TURBO DNase (Ambion). 500ng total RNA was amplified using using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: European starling males were acoustically isolated then exposed to either silence control or 30 minutes of novel song, then sacrificed and Als (auditory lobules) were collected and flash frozen.

tag: song exposure

tag: brain region

value: Telencephalon

tag: gender

value: Male and female

tag: age

value: Adult

organism: Sturnus vulgaris

source_name: Novel song

value: 30 minutes of novel song

value: AL (auditory lobule)

value: Male


title: CMT-U27 replicate

description: Biological replicate 2 of 2

source_name: CMT-U27 co-culture with MQ

value: CMT-U27 co-culture with MQ

source_name: CMT-U27 single culture [control]

value: CMT-U27 single culture


title: CMT-U309 replicate

description: Biological replicate 2 of 2


title: P114

description: Biological replicate 1 of 2

source_name: P114 single culture [control]

value: P114 single culture

source_name: P114 co-culture with MQ

value: P114 co-culture with MQ


title: Silence replicate 4 [e15]

source_name: Silence

value: silence


title: Silence replicate 6 [e15]


title: MQ CMT-W1

description: Biological replicate 1 of 2

value: macrophages

source_name: MQ single culture [control]

value: MQ single culture


title: Novel song replicate 6 [e15]

value: 30 minutes novel song


title: Novel song replicate 5 [e15]


title: CMT-W2

description: Biological replicate 1 of 2


title: Novel song replicate 3 [e15]


title: Silence replicate 3 [e15]


title: Novel song replicate 1 [e15]


title: Silence replicate 1 [e15]


title: MQ CMT-W2 replicate

description: Biological replicate 2 of 2

source_name: MQ co-cultured with CMT-W2

value: MQ co-cultured with CMT-W2


title: MQ CMT-U27

description: Biological replicate 1 of 2

source_name: MQ co-cultured with CMT-U27

value: MQ co-cultured with CMT-U27


title: Autumn STI replicate 4 [e14]

description: print batch: 4/2/2007

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chamber, and incubated O/N at 42ûC. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

organism: Melospiza melodia

source_name: Autumn Experimental

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 46C for 16 h in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; 0.5µg total RNA was amplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the autumn (mid November, 2005 to late January, 2006; the non-breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live caged male song sparrow decoy and recorded male conspecific songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

tag: season

value: Autumn

tag: intrusion treatment

value: Simulated Territorial Intrusion

value: hypothalamus

value: male

treatment_protocol: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

tag: intrustion treatment

value: telencephalon

value: male and female


title: Autumn Control replicate 4 [e14]

description: print batch: 4/2/2007

source_name: Autumn Control

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the autumn (mid November, 2005 to late January, 2006; the non-breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a control territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live  caged male white-crowned sparrow decoy and recorded white-crowned sparrow songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

value: Control


title: Silence replicate 5 [e15]

value: Telencephalon

value: Male and female

value: Adult

value: AL (auditory lobule)

value: Male


title: Spring STI replicate 4 [e14]

description: print batch: 4/2/2007

source_name: Spring Experimental

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the spring (mid to late June, 2005; the breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live caged male song sparrow decoy and recorded male conspecific songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.

value: Spring


title: Novel song replicate 2 [e15]


title: Autumn Control replicate 3 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 3 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 7 [e14]

description: print batch: 4/2/2007

source_name: Spring Control

treatment_protocol: Free-ranging male song sparrow (Melospiza melodia morphna) were tested in the spring (mid to late June, 2005; the breeding season) in one the following 7 sites in western Washington State (48ºN): Crescent Lake, Cherry Valley, Prison Farm, Spencer Island (all in Snohomish county), Skagit Valley (Skagit county), Pack Forest (Pierce county), Stillwater (King county). To simulate a control territorial intrusion, a free-ranging territorial male (focal bird) was presented with a live  caged male white-crowned sparrow decoy and recorded white-crowned sparrow songs. During the first 10 minutes of the STI, the following behaviors were recorded from the focal bird: 1) number of songs, 2) number of flights directed at the decoy, 3) closest approach to the decoy, and 4) time spent within 5 meters (m) of the decoy.  The STI was continued for additional 20 min and then the bird was quickly captured with a mist net. Immediately after capture, the bird was anesthetized with isoflurane (10%) and decapitated.  Hypothalamus was quickly dissected out and quickly frozen on dry ice and subsequently stored at -80 ºC.  Due to the location and structural association of the pars tuberalis in avian species, it was impossible to accurately dissect out pars tuberalis from the hypothalamus, therefore all samples were collected along with pars tuberalis for consistency; however, other parts of the pituitary were removed.


title: Autumn STI replicate 8 [e14]

description: print batch: 4/2/2007


title: Spring Control replicate 3 [e14]

description: print batch: 5/31/2006


title: Silence replicate 2 [e15]

value: silence


title: Spring STI replicate 8 [e14]

description: print batch: 4/2/2007


title: CMT-U27

description: Biological replicate 1 of 2

value: CMT-U27 single culture

value: CMT-U27 co-culture with MQ


title: Autumn Control replicate 8 [e14]

description: print batch: 4/2/2007


title: Spring STI replicate 3 [e14]

description: print batch: 5/31/2006


title: Autumn Control replicate 7 [e14]

description: print batch: 5/31/2006


title: Autumn Control replicate 2 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 7 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 6 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 2 [e14]

description: print batch: 5/31/2006


title: Spring STI replicate 7 [e14]

description: print batch: 5/31/2006


title: Autumn Control replicate 6 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 6 [e14]

description: print batch: 5/31/2006


title: Autumn Control replicate 1 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 1 [e14]

description: print batch: 5/31/2006


title: Spring STI replicate 2 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 5 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 2 [e14]

description: print batch: 5/31/2006


title: Autumn STI replicate 5 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 1 [e14]

description: print batch: 5/31/2006


title: Autumn Control replicate 5 [e14]

description: print batch: 5/31/2006


title: Spring STI replicate 1 [e14]

description: print batch: 5/31/2006


title: Spring STI replicate 5 [e14]

description: print batch: 5/31/2006


title: Spring Control replicate 4 [e14]

description: print batch: 5/31/2006


title: Day 45 Male replicate 8 [e13]

description: Biological replicate 8 of 8 Male Post-hatch day 45

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chamber, and incubated O/N at 42˚C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon Genepix 6.0

source_name: Day 45 Male

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70°C for 10 min, then reversed transcribed at 46°C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 500ng total RNA wasamplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: LMAN punches were taken from frozen brain sections of Taeniopygia guttata males at post-hatch days 25 and 45.

value: LMAN

value: Post-hatch day 45

tag: treatment protocol

value: LMAN punch dissection

value: Male and Female

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: Day 25 Male replicate 8 [e13]

description: Biological replicate 8 of 8 Male Post-hatch day 25

source_name: Day 25 Male

value: Post-hatch day 25


title: Day 45 Male replicate 5 [e13]

description: Biological replicate 5 of 8 Male Post-hatch day 45


title: Day 25 Male replicate 7 [e13]

description: Biological replicate 7 of 8 Male Post-hatch day 25


title: Day 25 Male replicate 6 [e13]

description: Biological replicate 6 of 8 Male Post-hatch day 25


title: Day 45 Male replicate 7 [e13]

description: Biological replicate 7 of 8 Male Post-hatch day 45


title: Day 45 Male replicate 6 [e13]

description: Biological replicate 6 of 8 Male Post-hatch day 45


title: Day 25 Male replicate 5 [e13]

description: Biological replicate 5 of 8 Male Post-hatch day 25


title: Day 45 Male replicate 4 [e13]

description: Biological replicate 4 of 8 Male Post-hatch day 45


title: Day 45 Male replicate 3 [e13]

description: Biological replicate 3 of 8 Male Post-hatch day 45


title: Day 25 Male replicate 3 [e13]

description: Biological replicate 3 of 8 Male Post-hatch day 25


title: Day 25 Male replicate 4 [e13]

description: Biological replicate 4 of 8 Male Post-hatch day 25


title: Day 45 Male replicate 1 [e13]

description: Biological replicate 1 of 8 Male Post-hatch day 45


title: Day 45 Male replicate 2 [e13]

description: Biological replicate 2 of 8 Male Post-hatch day 45


title: Spring STI replicate 6 [e14]

description: print batch: 5/31/2006

value: telencephalon

value: male and female

value: Simulated Territorial Intrusion

value: hypothalamus

value: male


title: Silence replicate 6 [e12]

extract_protocol: Experimental samples: Total RNA was extracted using RNAqueous Mini kit (Ambion) and DNase treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng total RNA was amplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Post-hatch day 20 male zebra finches that had been raised in acoustic isolation with a foster female were placed in a song playback chamber. The next day, birds heard either silence (control) or 30 minutes of novel song. Birds were then sacrificed and the AL (auditory lobule) was dissected and flash frozen.

value: adult

value: Silence

value: AL (auditory lobule)

value: day 20 post-hatch


title: Silence replicate 3 [e12]

value: Male


title: Novel song replicate 1 [e12]

value: 30 minutes of Novel song

value: Telencephalon

value: Male and female

value: Adult


title: Silence replicate 5 [e12]


title: Day 25 Male replicate 1 [e13]

description: Biological replicate 1 of 8 Male Post-hatch day 25

value: Male and Female

value: LMAN

value: LMAN punch dissection


title: Novel song replicate 3 [e12]

value: telencephalon


title: Silence replicate 1 [e12]


title: Novel song replicate 5 [e12]


title: Novel song replicate 4 [e12]


title: Novel song replicate 2 [e12]

value: male and female


title: Silence replicate 4 [e12]


title: Day 25 Male replicate 2 [e13]

description: Biological replicate 2 of 8 Male Post-hatch day 25

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: Post-hatch day 25


title: Silence replicate 2 [e12]

value: male


title: AL of Adult silence control replicate 6 [e11]

source_name: Silence control

treatment_protocol: Adult male zebra finches (Taeniopygia guttata) were acoutically isolated in playback chambers overnight. The next day (day1), one group of birds heard 30 minutes of a novel song (e.g. SongA), sacrificed and tissue collected and flash frozen. Silence control birds were taken at the equivalent time of day1 as novel song birds, but heard no song playback. The birds hearing familiar song were isolated as the others, but on the first day heard 180 min of SongA, remained in the chambers a second night, and heard 30 min of SongA again the follwing day (day2).

tag: song playback experience

value: Silence control


title: AL of Adult silence control replicate 5 [e11]

source_name: universal SoNG reference


title: AL of Adult novel song replicate 5 [e11]

source_name: Novel song

value: 30 min of novel song


title: AL of Adult male familiar song replicate 5 [e11]

source_name: Familiar song

value: AL (auditory lobule)

value: Trained 180 min with song on day1, heard 30 min of same song on day2


title: AL of Adult novel song replicate 6 [e11]

value: Male


title: AL of Adult male familiar song replicate 6 [e11]


title: AL of Adult silence control replicate 3 [e11]


title: AL of Adult novel song replicate 3 [e11]


title: Novel song replicate 6 [e12]

value: adult

value: 30 minutes of Novel song

value: day 20 post-hatch


title: AL of Adult silence control replicate 2 [e11]

value: Adult

value: Telencephalon

value: Male and female


title: AL of Adult male familiar song replicate 4 [e11]


title: AL of Adult silence control replicate 4 [e11]


title: AL of Adult male familiar song replicate 3 [e11]


title: AL of Adult novel song replicate 2 [e11]


title: AL of Adult silence control replicate 1 [e11]


title: Adult female NCM after 90 min novel song playback replicate 1 [e10]

extract_protocol: Experimental: Total RNA was extracted from NCM and L2a tissue punches using the Absolutely RNA kit (Stratagene). 500ng were amplified one round using the MessageAmp II kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Adult female zebra finches were acoustically isolated overnight, then 30' of playback was presented that consisted of a repeated medley of 3 zebra finch songs over 15 followed by a 45 interval  of silence. 30 min samples were collected at this time; birds remained in the chamber for an additional 60 min to collect the 90 min samples. Silence control birds were acoustically isolated but heard no playback the next day.

value: NCM

value: 90 minutes after onset of novel song

value: Female


title: AL of Adult male familiar song replicate 1 [e11]


title: Adult female NCM after 30 min novel song playback replicate 1 [e10]

value: 30 minutes after onset of novel song


title: AL of Adult novel song replicate 1 [e11]


title: Adult female L2a silence replicate 4 [e10]


title: Adult female L2a after 90 min novel song playback replicate 5 [e10]


title: Adult female NCM after 90 min novel song playback replicate 5 [e10]


title: Adult female NCM after 30 min novel song playback replicate 5 [e10]


title: AL of Adult novel song replicate 4 [e11]


title: AL of Adult male familiar song replicate 2 [e11]


title: Adult female NCM silence replicate 5 [e10]


title: Adult female NCM after 90 min novel song playback replicate 3 [e10]


title: Adult female NCM silence replicate 4 [e10]


title: Adult female L2a after 30 min novel song playback replicate 4 [e10]


title: Adult female NCM silence replicate 1 [e10]


title: Adult female NCM after 30 min novel song playback replicate 3 [e10]


title: Adult female NCM silence replicate 6 [e10]


title: Adult female NCM silence replicate 2 [e10]


title: Adult female L2a after 30 min novel song playback replicate 5 [e10]


title: Adult female NCM after 90 min novel song playback replicate 4 [e10]


title: Adult female NCM silence replicate 3 [e10]


title: Adult female L2a after 90 min novel song playback replicate 4 [e10]


title: Adult female L2a after 30 min novel song playback replicate 1 [e10]


title: Adult female L2a silence replicate 1 [e10]


title: Adult female NCM after 90 min novel song playback replicate 6 [e10]


title: Adult female NCM after 90 min novel song playback replicate 2 [e10]


title: Adult female NCM after 30 min novel song playback replicate 4 [e10]


title: Adult female L2a after 90 min novel song playback replicate 1 [e10]


title: Adult female L2a silence replicate 5 [e10]


title: Adult female NCM after 30 min novel song playback replicate 2 [e10]


title: Adult female L2a silence replicate 6 [e10]


title: Adult female L2a after 90 min novel song playback replicate 6 [e10]


title: Adult female L2a silence replicate 3 [e10]


title: Adult female L2a after 90 min novel song playback replicate 2 [e10]


title: Adult female L2a after 90 min novel song playback replicate 3 [e10]


title: HVC replicate 3 [e09]

source_name: HVC

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Brain regions HVC and Shelf were laser-capture microdissected from brain sections of adult male zebra finches

value: HVC


title: Adult female NCM after 30 min novel song playback replicate 6 [e10]


title: HVC replicate 6 [e09]


title: Shelf replicate 3 [e09]

source_name: Shelf

value: Shelf


title: RA at 56 Short Days and Intact replicate 5 [e08]

source_name: unviversal SoNG reference

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 300ng total RNA was amplified once using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Area X, HVC, POA and RA were collected from adult male European starlings (Sturnus vulgaris) that were gonadally-intact and photostimulated (7 and 21 days on long days, 16:8 light: dark), castrated and photostimulated (7 days on long days), and photorefractory (56 days on long days), with short-day control (56 days on short days, 11:13 light:dark).

tag: light cycle

tag: gonad

tag: photoperiod

value: RA

value: 11:13 light:dark

tag: gonads

value: Intact

value: Control


title: Shelf replicate 6 [e09]

value: Male


title: RA at 56 Short Days and Intact replicate 3 [e08]


title: RA at 7 Long Days and Intact replicate 1 [e08]

value: 16:8 light:dark

value: Photostimulated


title: RA at 7 Long Days and Intact replicate 2 [e08]


title: Adult female L2a after 30 min novel song playback replicate 3 [e10]


title: HVC replicate 4 [e09]


title: RA at 7 Long Days and Castrated replicate 3 [e08]

value: Castrated


title: Adult female L2a silence replicate 2 [e10]

value: Silence control

value: Adult


title: Shelf replicate 5 [e09]

value: Telencephalon

value: Male and female


title: RA at 7 Long Days and Intact replicate 5 [e08]


title: RA at 56 Short Days and Intact replicate 1 [e08]


title: HVC replicate 1 [e09]


title: Shelf replicate 2 [e09]


title: Shelf replicate 1 [e09]


title: Shelf replicate 4 [e09]


title: Adult female L2a after 30 min novel song playback replicate 6 [e10]


title: HVC replicate 5 [e09]


title: Adult female L2a after 30 min novel song playback replicate 2 [e10]


title: HVC replicate 2 [e09]


title: RA at 7 Long Days and Castrated replicate 5 [e08]


title: RA at 7 Long Days and Castrated replicate 1 [e08]


title: RA at 56 Long Days and Intact replicate 4 [e08]

value: Photorefractory


title: RA at 21 Long Days and Intact replicate 2 [e08]


title: RA at 21 Long Days and Intact replicate 3 [e08]


title: POA at 56 Short Days and Intact replicate 6 [e08]

value: POA


title: RA at 56 Long Days and Intact replicate 5 [e08]


title: POA at 7 Long Days and Intact replicate 3 [e08]


title: POA at 56 Long Days and Intact replicate 1 [e08]


title: HVC at 56 Short Days and Intact replicate 1 [e08]


title: HVC at 7 Long Days and Intact replicate 1 [e08]


title: POA at 7 Long Days and Intact replicate 4 [e08]


title: POA at 21 Long Days and Intact replicate 4 [e08]


title: POA at 7 Long Days and Castrated replicate 5 [e08]


title: HVC at 7 Long Days and Castrated replicate 5 [e08]


title: HVC at 56 Short Days and Intact replicate 4 [e08]


title: POA at 56 Long Days and Intact replicate 4 [e08]


title: HVC at 7 Long Days and Intact replicate 5 [e08]


title: POA at 21 Long Days and Intact replicate 1 [e08]


title: POA at 21 Long Days and Intact replicate 3 [e08]


title: POA at 7 Long Days and Castrated replicate 1 [e08]


title: HVC at 7 Long Days and Intact replicate 2 [e08]


title: HVC at 56 Short Days and Intact replicate 3 [e08]


title: POA at 7 Long Days and Intact replicate 1 [e08]


title: POA at 7 Long Days and Castrated replicate 3 [e08]


title: RA at 21 Long Days and Intact replicate 1 [e08]


title: POA at 56 Short Days and Intact replicate 3 [e08]


title: RA at 56 Long Days and Intact replicate 3 [e08]


title: POA at 56 Long Days and Intact replicate 3 [e08]


title: POA at 56 Short Days and Intact replicate 5 [e08]


title: HVC at 7 Long Days and Castrated replicate 3 [e08]


title: HVC at 7 Long Days and Castrated replicate 1 [e08]


title: Area X at 7 Long Days and Castrated replicate 3 [e08]

value: Area X


title: Area X at 7 Long Days and Intact replicate 6 [e08]


title: HVC at 21 Long Days and Intact replicate 5 [e08]

value: HVC


title: Area X at 7 Long Days and Intact replicate 3 [e08]


title: HVC at 21 Long Days and Intact replicate 1 [e08]


title: Area X at 56 Long Days and Intact replicate 5 [e08]


title: HVC at 21 Long Days and Intact replicate 3 [e08]


title: RA at 56 Short Days and Intact replicate 4 [e08]


title: HVC at 56 Long Days and Intact replicate 4 [e08]


title: Area X at 56 Short Days and Intact replicate 5 [e08]


title: RA at 7 Long Days and Intact replicate 3 [e08]


title: RA at 56 Short Days and Intact replicate 2 [e08]


title: Area X at 56 Short Days and Intact replicate 6 [e08]


title: HVC at 56 Long Days and Intact replicate 1 [e08]


title: Area X at 7 Long Days and Castrated replicate 1 [e08]


title: Area X at 56 Long Days and Intact replicate 1 [e08]


title: HVC at 56 Long Days and Intact replicate 3 [e08]


title: RA at 56 Short Days and Intact replicate 6 [e08]


title: Area X at 7 Long Days and Intact replicate 5 [e08]


title: RA at 7 Long Days and Castrated replicate 2 [e08]


title: Area X at 7 Long Days and Castrated replicate 5 [e08]


title: Area X at 21 Long Days and Intact replicate 1 [e08]


title: Area X at 56 Long Days and Intact replicate 3 [e08]


title: Area X at 21 Long Days and Intact replicate 3 [e08]


title: RA at 7 Long Days and Intact replicate 4 [e08]


title: RA at 7 Long Days and Intact replicate 6 [e08]


title: Area X at 21 Long Days and Intact replicate 5 [e08]


title: RA at 7 Long Days and Castrated replicate 6 [e08]


title: RA at 56 Long Days and Intact replicate 6 [e08]


title: RA at 7 Long Days and Castrated replicate 4 [e08]


title: RA at 56 Long Days and Intact replicate 1 [e08]


title: RA at 21 Long Days and Intact replicate 4 [e08]


title: POA at 7 Long Days and Intact replicate 5 [e08]


title: POA at 7 Long Days and Intact replicate 2 [e08]


title: POA at 7 Long Days and Castrated replicate 4 [e08]


title: RA at 56 Long Days and Intact replicate 2 [e08]


title: POA at 56 Short Days and Intact replicate 4 [e08]


title: POA at 56 Short Days and Intact replicate 2 [e08]


title: POA at 56 Long Days and Intact replicate 2 [e08]


title: POA at 7 Long Days and Castrated replicate 6 [e08]


title: POA at 56 Long Days and Intact replicate 5 [e08]


title: POA at 7 Long Days and Castrated replicate 2 [e08]


title: POA at 7 Long Days and Intact replicate 6 [e08]


title: POA at 56 Long Days and Intact replicate 6 [e08]


title: POA at 21 Long Days and Intact replicate 6 [e08]


title: HVC at 56 Short Days and Intact replicate 6 [e08]


title: HVC at 7 Long Days and Intact replicate 3 [e08]


title: RA at 21 Long Days and Intact replicate 6 [e08]


title: POA at 21 Long Days and Intact replicate 5 [e08]


title: POA at 56 Short Days and Intact replicate 1 [e08]


title: RA at 21 Long Days and Intact replicate 5 [e08]


title: HVC at 56 Short Days and Intact replicate 2 [e08]


title: POA at 21 Long Days and Intact replicate 2 [e08]


title: HVC at 7 Long Days and Intact replicate 4 [e08]


title: HVC at 56 Short Days and Intact replicate 5 [e08]


title: HVC at 7 Long Days and Intact replicate 6 [e08]


title: HVC at 56 Long Days and Intact replicate 5 [e08]


title: HVC at 7 Long Days and Castrated replicate 4 [e08]


title: HVC at 56 Long Days and Intact replicate 2 [e08]


title: HVC at 21 Long Days and Intact replicate 2 [e08]


title: HVC at 21 Long Days and Intact replicate 4 [e08]


title: HVC at 21 Long Days and Intact replicate 6 [e08]


title: HVC at 7 Long Days and Castrated replicate 2 [e08]


title: HVC at 7 Long Days and Castrated replicate 6 [e08]


title: HVC at 56 Long Days and Intact replicate 6 [e08]


title: Area X at 56 Short Days and Intact replicate 1 [e08]


title: Area X at 7 Long Days and Intact replicate 2 [e08]


title: Area X at 7 Long Days and Intact replicate 1 [e08]


title: Area X at 7 Long Days and Castrated replicate 4 [e08]


title: Area X at 56 Short Days and Intact replicate 3 [e08]


title: Area X at 56 Long Days and Intact replicate 4 [e08]


title: Area X at 7 Long Days and Castrated replicate 2 [e08]


title: Area X at 56 Short Days and Intact replicate 4 [e08]


title: Area X at 7 Long Days and Intact replicate 4 [e08]


title: Area X at 56 Long Days and Intact replicate 2 [e08]


title: Area X at 7 Long Days and Castrated replicate 6 [e08]


title: Area X at 56 Short Days and Intact replicate 2 [e08]


title: Day 55 TAF replicate 2 [e07]

source_name: Day 55 TAF

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 500ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: HVC of post-hatch day 55 and adult male zebra finches were collected after 20 days of food ad libitum or Timed Access to Food (TAF) to assess singing-driven differences in gene expression.

tag: development

value: Post-hatch day 55

value: Day 55 post-hatch male with Timed Access to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle

value: Male and Female

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: Area X at 21 Long Days and Intact replicate 6 [e08]

value: Intact


title: Area X at 21 Long Days and Intact replicate 4 [e08]

value: Male


title: Area X at 56 Long Days and Intact replicate 6 [e08]

value: 16:8 light:dark


title: Day 55 TAF replicate 6 [e07]


title: Day 55 TAF replicate 1 [e07]

value: Day 55 post-hatch male with Timed accesss to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle


title: Area X at 21 Long Days and Intact replicate 2 [e08]

value: Photostimulated


title: Day 55 ad lib replicate 5 [e07]

source_name: Day 55 ad lib

value: Day 55 post-hatch male with food acces ad libitum


title: Adult ad lib replicate 5 [e07]

source_name: Adult ad lib

value: Adult

value: Adult male with food acces ad libitum


title: Adult TAF replicate 4 [e07]

source_name: Adult TAF

value: Adult male with Timed Access to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle

value: Telencephalon


title: Adult ad lib replicate 1 [e07]


title: Day 55 ad lib replicate 4 [e07]

source_name: Day 55ad lib


title: Adult TAF replicate 2 [e07]

value: Adult male with Timed accesss to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle


title: Day 55 ad lib replicate 2 [e07]

value: Day 55 post-hatch male with food access ad libitum


title: Day 55 TAF replicate 4 [e07]

value: HVC


title: Adult ad lib replicate 3 [e07]

value: Adult male with food access ad libitum


title: Day 55 ad lib replicate 1 [e07]

value: Post-hatch day 55


title: Day 55 ad lib replicate 3 [e07]

value: Male and Female


title: Day 55 ad lib replicate 6 [e07]

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: Day 55 TAF replicate 3 [e07]

value: Day 55 post-hatch male with Timed Access to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle


title: Day 55 TAF replicate 5 [e07]

value: Male


title: Adult ad lib replicate 2 [e07]


title: HVC 24hr +T replicate 7 [e06]

extract_protocol: Experimental samples: Total RNA was extracted using RNAqueous Mini kit (Ambion) and DNAse treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng total RNA was amplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: HVCs of adult male house finches (Carpodacus mexicanus) were collected on short days (8:16 light:dark cycle) at Time 0 (control), 24 and 48 hours after implantation with Testosterone silastic capsule.

tag: hormone treatment

value: Male and female

organism: Haemorhous mexicanus

source_name: HVC 24hr +T

value: 24 hours +Testosterone


title: Adult ad lib replicate 6 [e07]

value: Adult male with food accesss ad libitum


title: HVC 24hr +T replicate 5 [e06]


title: Adult TAF replicate 6 [e07]


title: HVC 24hr +T replicate 8 [e06]


title: Adult ad lib replicate 4 [e07]


title: Adult TAF replicate 1 [e07]


title: HVC 24hr +T replicate 6 [e06]


title: HVC Control T(0) replicate 5 [e06]

source_name: HVC Control

value: Control (no Testosterone)


title: HVC 48hr +T replicate 5 [e06]

value: Adult

source_name: HVC 48hr +T

value: 48 hours +Testosterone


title: Adult TAF replicate 5 [e07]

value: Adult male with Timed Access to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle


title: HVC 48hr +T replicate 7 [e06]

value: Telencephalon


title: Adult TAF replicate 3 [e07]

value: Adult male with Timed accesss to Food (TAF); 3g of seed presented 8 hours after lights on in a 14:10 light:dark cycle


title: HVC 48hr +T replicate 6 [e06]


title: HVC Control T(0) replicate 8 [e06]

source_name: HVC control


title: HVC 48hr +T replicate 3 [e06]


title: HVC 48hr +T replicate 8 [e06]


title: HVC Control T(0) replicate 6 [e06]


title: HVC Control T(0) replicate 7 [e06]


title: HVC Control T(0) replicate 2 [e06]


title: HVC 24hr +T replicate 1 [e06]


title: HVC 48hr +T replicate 1 [e06]


title: HVC Control T(0) replicate 1 [e06]


title: HVC 24hr +T replicate 3 [e06]


title: HVC 48hr +T replicate 2 [e06]


title: HVC 24hr +T replicate 2 [e06]


title: HVC 48hr +T replicate 4 [e06]


title: HVC Control T(0) replicate 3 [e06]


title: p7 e-silastic replicate 4 [e05]

source_name: p7 e-silastic

treatment_protocol: Taeniopygia guttata females were implanted on hatch day with estrogen-containing silastic capsules or blank controls, then sacrified and whole telencephalons collected after 1 day and 7 days.

value: day 7 post-hatch

value: Female

value: synthetic estrogen capsule


title: p7 e-silastic replicate 1 [e05]


title: HVC 24hr +T replicate 4 [e06]

value: HVC


title: p7 e-silastic replicate 6 [e05]


title: HVC Control T(0) replicate 4 [e06]


title: p1 e-silastic replicate 6 [e05]

source_name: p1 e-silastic

value: day 1 post-hatch


title: p7 e-silastic replicate 3 [e05]

source_name: universal SoNG reference


title: p7 e-silastic replicate 2 [e05]


title: p7 e-silastic replicate 5 [e05]


title: p1 e-silastic replicate 1 [e05]


title: p1 e-silastic replicate 3 [e05]


title: p7 blank control replicate 5 [e05]

source_name: p7 blank control

value: blank capsule


title: p1 e-silastic replicate 4 [e05]


title: p1 e-silastic replicate 2 [e05]


title: p1 e-silastic replicate 5 [e05]


title: p7 blank control replicate 2 [e05]


title: p1 blank control replicate 5 [e05]

source_name: p1 blank control


title: p1 blank control replicate 1 [e05]


title: p1 blank control replicate 4 [e05]


title: p7 blank control replicate 1 [e05]


title: Day 45 Female replicate 1 [e04]

description:
Biological replicate 1 of 6 Female Post-hatch Day 45
Print batch: 3/28/06

data_processing: The probes with fluorescence intensities under 50 were filtered out. For each developmental stage, the genes with hybridization intensities above 50 in more than 50% of arrays were used for further analysis. The “expression ratios” (ratios of the sample to reference fluorescence intensities) were quantile normalized in the statistical environment R 2.8.0 using the “affy” package (www.rproject.org) and used for the analyses.

source_name: Day 45 Female

treatment_protocol:
Whole telencephalon isolated from an individual bird forty five days post-hatch
Whole telencephalon isolated from an individual bird forty five days post-hatch

tag: tissue

tag: developmental stage

value: Post-hatch Day 45

treatment_protocol:
Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country
Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: telencephalon

value: Male and Female


title: p7 blank control replicate 4 [e05]

value: Male and female


title: p7 blank control replicate 3 [e05]


title: p7 blank control replicate 6 [e05]


title: p1 blank control replicate 3 [e05]


title: p1 blank control replicate 2 [e05]


title: Day 45 Male replicate 1 [e04]

description:
Biological replicate 1 of 6 Male Post-hatch Day 45
Print batch: 3/28/06

source_name: Day 45 Male

value: Male


title: Day 25 Female replicate 5 [e04]

description:
Biological replicate 5 of 6 Female Post-hatch Day 25
Print batch: 3/28/06

source_name: Day 25 Female

treatment_protocol:
Whole telencephalon isolated from an individual bird twenty five days post-hatch
Whole telencephalon isolated from an individual bird twenty five days post-hatch

value: Post-hatch Day 25


title: Day 1 Male replicate 3 [e04]

description:
Biological replicate 3 of 6 Male Post-hatch Day 1
Print batch: 3/28/06

value: Adult

source_name: Day 1 Male

treatment_protocol:
Whole telencephalon isolated from an individual bird one day post-hatch
Whole telencephalon isolated from an individual bird one day post-hatch

value: Post-hatch Day 1


title: Adult Female replicate 2 [e04]

description:
Biological replicate 2 of 6 Female Adult
Print batch: 3/28/06

source_name: Adult Female

treatment_protocol:
Whole telencephalon isolated from an individual bird more than ninety days post-hatch
Whole telencephalon isolated from an individual bird more than ninety days post-hatch


title: p1 blank control replicate 6 [e05]


title: Day 45 Female replicate 3 [e04]

description:
Biological replicate 3 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Adult Female replicate 3 [e04]

description:
Biological replicate 3 of 6 Female Adult
Print batch: 3/28/06


title: Day 25 Male replicate 6 [e04]

description:
Biological replicate 6 of 6 Male Post-hatch Day 25
Print batch: 3/28/06

source_name: Day 25 Male


title: Adult Male replicate 6 [e04]

description:
Biological replicate 6 of 6 Male Adult
Print batch: 3/28/06

source_name: Adult Male


title: Day 45 Male replicate 5 [e04]

description:
Biological replicate 5 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 1 Male replicate 5 [e04]

description:
Biological replicate 5 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 25 Female replicate 4 [e04]

description:
Biological replicate 4 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 45 Female replicate 2 [e04]

description:
Biological replicate 2 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 25 Female replicate 3 [e04]

description:
Biological replicate 3 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 1 Female replicate 4 [e04]

description:
Biological replicate 4 of 6 Female Post-hatch Day 1
Print batch: 3/28/06

source_name: Day 1 Female


title: Adult Male replicate 2 [e04]

description:
Biological replicate 2 of 6 Male Adult
Print batch: 3/28/06


title: Day 1 Male replicate 2 [e04]

description:
Biological replicate 2 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 45 Male replicate 4 [e04]

description:
Biological replicate 4 of 6 Male Post-hatch Day 45
Print batch: 8/8/05


title: Adult Female replicate 4 [e04]

description:
Biological replicate 4 of 6 Female Adult
Print batch: 8/8/05


title: Day 45 Male replicate 6 [e04]

description:
Biological replicate 6 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 25 Male replicate 3 [e04]

description:
Biological replicate 3 of 6 Male Post-hatch Day 25
Print batch: 3/28/06


title: Day 45 Female replicate 5 [e04]

description:
Biological replicate 5 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Day 1 Male replicate 6 [e04]

description:
Biological replicate 6 of 6 Male Post-hatch Day 1
Print batch: 8/8/05


title: Day 25 Female replicate 6 [e04]

description:
Biological replicate 6 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Adult Male replicate 5 [e04]

description:
Biological replicate 5 of 6 Male Adult
Print batch: 8/8/05


title: Day 1 Female replicate 3 [e04]

description:
Biological replicate 3 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 45 Female replicate 4 [e04]

description:
Biological replicate 4 of 6 Female Post-hatch Day 45
Print batch: 3/28/06


title: Adult Male replicate 3 [e04]

description:
Biological replicate 3 of 6 Male Adult
Print batch: 3/28/06


title: Day 25 Male replicate 5 [e04]

description:
Biological replicate 5 of 6 Male Post-hatch Day 25
Print batch: 3/28/06


title: Adult Female replicate 6 [e04]

description:
Biological replicate 6 of 6 Female Adult
Print batch: 3/28/06


title: Day 45 Male replicate 2 [e04]

description:
Biological replicate 2 of 6 Male Post-hatch Day 45
Print batch: 3/28/06


title: Day 1 Female replicate 1 [e04]

description:
Biological replicate 1 of 6 Female Post-hatch Day 1
Print batch: 3/28/06


title: Day 1 Male replicate 1 [e04]

description:
Biological replicate 1 of 6 Male Post-hatch Day 1
Print batch: 3/28/06


title: Day 1 Male replicate 4 [e04]

description:
Biological replicate 4 of 6 Male Post-hatch Day 1
Print batch: 8/8/05


title: Day 25 Male replicate 4 [e04]

description:
Biological replicate 4 of 6 Male Post-hatch Day 25
Print batch: 8/8/05


title: Day 25 Female replicate 1 [e04]

description:
Biological replicate 1 of 6 Female Post-hatch Day 25
Print batch: 3/28/06


title: Day 25 Male replicate 2 [e04]

description:
Biological replicate 2 of 6 Male Post-hatch Day 25
Print batch: 8/8/05


title: Adult Female replicate 5 [e04]

description:
Biological replicate 5 of 6 Female Adult
Print batch: 8/8/05


title: Day 1 Female replicate 5 [e04]

description:
Biological replicate 5 of 6 Female Post-hatch Day 1
Print batch: 8/8/05


title: Day 1 Female replicate 2 [e04]

description:
Biological replicate 2 of 6 Female Post-hatch Day 1
Print batch: 8/8/05


title: Adult Male replicate 4 [e04]

description:
Biological replicate 4 of 6 Male Adult
Print batch: 8/8/05


title: Day 25 Female replicate 2 [e04]

description:
Biological replicate 2 of 6 Female Post-hatch Day 25
Print batch: 8/8/05


title: Adult Male replicate 1 [e04]

description:
Biological replicate 1 of 6 Male Adult
Print batch: 8/8/05


title: RCb on Short Days Roudybush plus replicate 6 [e03]

organism: Loxia curvirostra

source_name: RCb SD Roudybush plus

extract_protocol: Experimental samples: Total RNA was extracted using Trizol following manufacturer's protocol and DNase-treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng total RNA was amplified using using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Diencephalons were collected under short days (8:16 light:dark) from birds on either standard or enriched diets, in 2 species that differ in effects of diet on reproductive behavior (responsive red crossbills, non-responsive house finches). Red crossbills on a standard diet and long days (20:4 light:dark) were also compared to the short day group to assess effects of photostimulation in this species.

value: Diencephalon

value: 8:16 Light:Dark

tag: food

value: Diencephalon from RCb after 2 days on Short Days (8:16 Light:Dark cycle) and Roudybush plus pine nuts and sunflower seeds, ad lib

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: RCb on Short Days Roudybush replicate 4 [e03]

source_name: RCb SD Roudybush

tag: brain region

value: Roudybush

value: Diencephalon from RCb after 2 days on Short Days (8:16 Light:Dark cycle) and Roudybush, ad lib

value: Telencephalon


title: Day 25 Male replicate 1 [e04]

description:
Biological replicate 1 of 6 Male Post-hatch Day 25
Print batch: 8/8/05

tag: gender


title: RCb on Short Days Roudybush replicate 3 [e03]


title: RCb on Short Days Roudybush plus replicate 4 [e03]

value: Roudybush plus pine nuts and sunflower seeds


title: Day 45 Male replicate 3 [e04]

description:
Biological replicate 3 of 6 Male Post-hatch Day 45
Print batch: 8/8/05


title: RCb on Short Days Roudybush replicate 6 [e03]


title: RCb on Short Days Roudybush replicate 2 [e03]


title: RCb on Long Days Roudybush replicate 6 [e03]

source_name: RCb LD Roudybush

value: 20:4 Light:Dark

value: Diencephalon from RCb after 2 days on Long Days (16:8 Light:Dark cycle) and Roudybush, ad lib


title: RCb on Short Days Roudybush replicate 5 [e03]


title: RCb on Short Days Roudybush plus replicate 5 [e03]


title: RCb on Long Days Roudybush replicate 4 [e03]


title: RCb on Long Days Roudybush replicate 3 [e03]


title: RCb on Short Days Roudybush plus replicate 3 [e03]


title: RCb on Long Days Roudybush replicate 2 [e03]


title: HF on Short Days Roudybush replicate 2 [e03]

source_name: HF SD Roudybush

value: Diencephalon from HF after 2 days on Short Days (8:16 Light:Dark cycle) and Roudybush, ad lib


title: RCb on Long Days Roudybush replicate 5 [e03]

value: Male and Female


title: HF on Short Days Roudybush plus replicate 2 [e03]

source_name: HF SD Roudybush plus

value: Diencephalon from HF after 2 days on Short Days (8:16 Light:Dark cycle) and Roudybush plus pine nuts and sunflower seeds, ad lib


title: RCb on Short Days Roudybush plus replicate 2 [e03]

value: Male


title: Day 45 Female replicate 6 [e04]

description:
Biological replicate 6 of 6 Female Post-hatch Day 45
Print batch: 3/28/06

value: telencephalon

value: Post-hatch Day 45

value: Female


title: HF on Short Days Roudybush plus replicate 3 [e03]

value: Adult

value: Diencephalon


title: HF on Short Days Roudybush replicate 3 [e03]

value: 8:16 Light:Dark


title: HF on Short Days Roudybush replicate 1 [e03]

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: HF on Short Days Roudybush plus replicate 1 [e03]


title: RCb on Short Days Roudybush replicate 1 [e03]

value: Roudybush


title: RCb on Long Days Roudybush replicate 1 [e03]


title: familiar tutor replicate 4 [e02]

source_name: familiar tutor

extract_protocol: Experimental samples: Total RNA was extracted using RNAqueous Mini kit (Ambion) and treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng of total RNA was amplified using Agilent's Low-input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Zebrafinch (Taeniopygia guttata) males were acoustically isolated at day 30 post-hatch, then at day 35 post-hatch they were placed next to a stimulus female and exposed to no tutor, father (familiar) tutor, or unfamiliar tutor for two hours, then sacrificed.

value: Area x

tag: tutor experience

value: familiar tutor

value: male

tag: age

value: 35 days post-hatch

value: male and female


title: familiar tutor replicate 3 [e02]

source_name: universal SoNG reference

value: Telencephalon


title: no tutor replicate 4 [e02]

source_name: no tutor

value: no tutor


title: unfamiliar tutor replicate 5 [e02]

source_name: unfamiliar tutor

value: unfamiliar tutor


title: no tutor replicate 2 [e02]


title: unfamiliar tutor replicate 3 [e02]


title: no tutor replicate 1 [e02]


title: no tutor replicate 3 [e02]


title: unfamiliar tutor replicate 4 [e02]


title: familiar tutor replicate 5 [e02]


title: 21LD+T.RA replicate 1 [e01]

organism: Zonotrichia leucophrys gambelii

treatment_protocol: Gambel's White crowned sparrows were castrated and synchronized to a Short Day (SD) state to ensure regressed song nuclei, basal levels of Testosterone (T) typical of the non-breeding season, low song rates and unstereotyped song structure, and a low intrinsic spontaneous firing rate in the robust nucleus of the arcopalluim (RA). Then, on Day 0 of the experiment we sacrificed 6 birds. This group of birds, referred to as SD long-term, represents the steady-state of the regressed song control system and served as a baseline for all other groups. We implanted the rest of the birds with a subcutaneous Silastic capsule of T, and shifted them to Long Day (LD) photoperiod. To measure gene expression while the song control system was actively changing from a nonbreeding to a breeding phenotype, 6 birds were sacrificed on each of days 3, 7, and 21 (3LD+T, 7LD+T, and 21LD+T, respectively). By day 21, the song control system has reached its full breeding phenotype, and this time point represents the breeding-state song control system. On Day 21, the subcutaneous T capsules were removed from the remaining birds and they were shifted overnight to SD photoperiod to induce regression of the song control system back to the non-breeding state. On each of days 22 and 23 we sacrificed 6 birds (1SD-T and 2SD-T, respectively) to measure gene expression while the song control system is actively regressing. To control for circadian patterns of gene expression, all birds were sacrificed during the three hour period following their subjective dawn (i.e., lights on).

value: RA

tag: light

value: Dark cycle:20:4

tag: testosterone at sacrifice

value: Yes

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.

value: Dark cycle:NA


title: familiar tutor replicate 2 [e02]

value: Adult


title: 2SD-T.RA replicate 2 [e01]

value: Dark cycle:8:16

value: No

tag: treatment protocol

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.

value: telencephalon


title: unfamiliar tutor replicate 6 [e02]

value: Area x


title: unfamiliar tutor replicate 2 [e02]

value: male


title: unfamiliar tutor replicate 1 [e02]

value: 35 days post-hatch


title: 7LD+T.RA replicate 1 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.

value: male and female

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: familiar tutor replicate 1 [e02]

value: Telencephalon

value: familiar tutor


title: no tutor replicate 5 [e02]

value: no tutor


title: 1SD-T.RA replicate 2 [e01]

value: RA

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: SD.RA replicate 2 [e01]

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.

value: Dark cycle:NA


title: 3LD+T.RA replicate 6 [e01]

value: Dark cycle:20:4

value: Yes

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 2SD-T.HVC replicate 5 [e01]

value: telencephalon

value: HVC

value: Dark cycle:8:16

value: No

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 21LD+T.HVC replicate 5 [e01]

value: male and female

value: male

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: Adult Female replicate 1 [e04]

description:
Biological replicate 1 of 6 Female Adult
Print batch: 3/28/06

value: Telencephalon

value: Adult

value: Female

value: Male and Female


title: 3LD+T.HVC replicate 1 [e01]

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 1SD-T.HVC replicate 2 [e01]

value: Dark cycle:NA

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: Day 1 Female replicate 6 [e04]

description:
Biological replicate 6 of 6 Female Post-hatch Day 1
Print batch: 3/28/06

value: Post-hatch Day 1


title: SD.HVC replicate 5 [e01]

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: SD.HVC replicate 6 [e01]

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.

value: telencephalon


title: 7LD+T.HVC replicate 1 [e01]

value: HVC

value: Dark cycle:20:4

value: Yes

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: 7LD+T.HVC replicate 2 [e01]

value: male and female

value: male


title: 2SD-T.RA replicate 4 [e01]

value: RA

value: Dark cycle:8:16

value: No

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 21LD+T.HVC replicate 3 [e01]

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 21LD+T.RA replicate 6 [e01]

value: Dark cycle:NA

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 7LD+T.RA replicate 3 [e01]


title: 2SD-T.HVC replicate 4 [e01]


title: 7LD+T.HVC replicate 5 [e01]


title: 21LD+T.RA replicate 4 [e01]


title: SD.RA replicate 6 [e01]

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 1SD-T.RA replicate 1 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 2SD-T.RA replicate 3 [e01]

value: telencephalon

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 3LD+T.RA replicate 3 [e01]

value: Dark cycle:20:4

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 21LD+T.HVC replicate 2 [e01]

value: HVC

value: Yes


title: CMT-W1

description:
Biological replicate 1 of 2
338379.txt

hyb_protocol: Before hybridization, dog-specific oligonucleotide microarray slides Canis familiaris V1.0.1 AROS (Operon, USA) with 25 383 probes were prepared according to the manufacturer’s  protocol. The hybridization mixture contained hybridization buffer (Agilent, USA) and the same  amount of stained nucleic acids of examined cells and reference.  Two replicates were performed (dye-swap). Hybridization was performed using automatic hybridization  station HybArray12 (PerkinElmer,  USA).

scan_protocol: Acquisition and analysis of hybridization intensities  were performed using microarray scanner  ScanArray HT and ScanExpress software  (PerkinElmer, USA).

data_processing: Different types of values were obtained for quantification of the dot intensity. Due to experimental variations in specific activity of oligo-nucleotide target preparations or exposure time that might alter the signal intensity, hybridization data were automatically normalized (LOWESS method) (Oshlack et al. 2007) by ScanExpress software. Dye swap experiments were scanned recording control (reference) probe as a Ch1 and examined probe as Ch2.

source_name: co-culture with CAF

label_protocol: For each microarray slide, total RNA (10 μg) of each cell line growing as a co-culture and as a single culture was reverse-transcribed using SuperScript Plus Direct cDNA Labeling System (Invitrogen, USA) according to the manufacturer’s protocol. Single-strand cDNA were stained with Alexa 647 and Alexa 555 (Invitrogen). The efficiency of dye incorporation was measured using NanoDrop (NanoDrop Technologies, USA).  For each slide, the RNA of cells from a different  passage was used.

treatment_protocol: Carcinoma-associated fibroblasts (CAFs) were grown and cancer cells were then layered on the top of them. CMTMR was used to stain the CAFs population prior to addition of the cancer cells population. The co-culture was maintained for at least 72 hrs. After the 72 hrs of co-culture the cells were harvested by trypsynization and sorted using FACS Aria II (Becton Dickinson, USA) into two tubes: not-stained cancer cells and stained CAFs.

tag: cell line

source_name: single culture


title: 7LD+T.RA replicate 6 [e01]

value: male

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.

value: male and female


title: CMT-W1 replicate

description:
Biological replicate 2 of 2
338382.txt


title: 1SD-T.HVC replicate 3 [e01]

value: Dark cycle:8:16

value: No

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: CMT-U309

description:
Biological replicate 1 of 2
339340.txt


title: CMT-U309 replicate

description:
Biological replicate 2 of 2
339344.txt


title: RCb on Short Days Roudybush plus replicate 1 [e03]

value: Telencephalon

value: Male and Female

tag: light cycle

value: Adult

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: Diencephalon

value: Male

value: 8:16 Light:Dark

value: Diencephalon from RCb after 2 days on Short Days (8:16 Light:Dark cycle) and Roudybush plus pine nuts and sunflower seeds, ad lib


title: CMT-W2 replicate

description:
Biological replicate 2 of 2
338400.txt


title: CMT-W2

description:
Biological replicate 1 of 2
338480.txt


title: 3LD+T.HVC replicate 2 [e01]

value: Dark cycle:20:4

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.

value: telencephalon

value: Dark cycle:NA


title: 2SD-T.RA replicate 1 [e01]

value: male

value: RA

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: SD.HVC replicate 4 [e01]

value: male and female

value: HVC

value: Dark cycle:8:16

value: No

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: CMT-U27

description:
Biological replicate 1 of 2
338381.txt


title: SD.RA replicate 5 [e01]

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 3LD+T.RA replicate 2 [e01]

value: Yes


title: CMT-U27 replicate

description:
Biological replicate 2 of 2
338343.txt


title: P114 replicate

description:
Biological replicate 2 of 2
339345.txt


title: SD.HVC replicate 2 [e01]

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 1SD-T.RA replicate 4 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: SD.RA replicate 1 [e01]


title: P114

description:
Biological replicate 1 of 2
339339.txt


title: 1SD-T.HVC replicate 6 [e01]

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 2SD-T.HVC replicate 1 [e01]


title: 1SD-T.HVC replicate 5 [e01]


title: 2SD-T.HVC replicate 2 [e01]

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: hippocampus_medip_control_57_rep2

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description:
57_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

hyb_protocol: All of the steps of hybridization and washing were performed following the Agilent protocol for ChIP-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The data were background subtracted, and quantile normalized in R using the limma package from the Bioconductor project.

molecule: genomic DNA

organism: Homo sapiens

source_name: hippocampus, MeDIP, control group

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions, respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive elements.

extract_protocol: Samples were dissected at 4C, snap-frozen on dry ice, and stored in plastic vials at -80C until analysis. DNA (2.g) was sonicated on ice for a total of 3 min, using 5 sec pulses with 15 sec resting times, to fragment the DNA to between 200 bp and 700 bp, as verified subsequently on a 1.5% agarose gel. After denaturing, 1/10th of each sample was removed as input DNA. The remainder of the sample was then precleared with sepharose beads, bound to anti-5 methylcytosine antibody (Calbiochem), washed, and eluted. PCR was performed to assess relative enrichment of an unmethylated plasmid DNA (GFP) versus an in vitro methylated plasmid DNA (Luciferase). Samples were PCR purified (GenScript) and quantified by Nanodrop, and for each sample, 100ng of input and immunoprecipitated DNA were subjected to whole genome amplification (Sigma). Samples were again quantified to assess the results of WGA, and then labeled with Cy3 (Input) or Cy5 (meDIP) prior to hybridization to the microarray.

value: hippocampus

tag: group

value: control

tag: individual identifier

tag: medip antibody

value: anti-5 methylcytosine antibody

tag: antibody vendor

value: Calbiochem

tag: antibody catalog number

tag: antibody lot#

source_name: hippocampus, input DNA, control group


title: 21LD+T.HVC replicate 6 [e01]

tag: tissue

value: telencephalon

value: Dark cycle:NA

value: male

value: Dark cycle:20:4

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 1SD-T.RA replicate 5 [e01]

value: RA

value: Dark cycle:8:16

value: No

value: male and female


title: 7LD+T.HVC replicate 6 [e01]

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: HVC

value: Yes

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: hippocampus_medip_abuse_43_rep1

description:
43_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

source_name: hippocampus, MeDIP, abuse group

value: hippocampus

value: abuse

source_name: hippocampus, input DNA, abuse group


title: hippocampus_medip_abuse_9_rep1

description:
9_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: anti-5 methylcytosine antibody


title: hippocampus_medip_control_57_rep1

description:
57_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: control

value: Calbiochem


title: hippocampus_medip_abuse_9_rep3

description:
9_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_8_rep1

description:
8_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_57_rep3

description:
57_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 21LD+T.RA replicate 3 [e01]

value: telencephalon

value: Dark cycle:NA


title: hippocampus_medip_abuse_8_rep2

description:
8_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_43_rep2

description:
43_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 7LD+T.RA replicate 2 [e01]

value: male

value: Dark cycle:20:4


title: 3LD+T.HVC replicate 5 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: SD.RA replicate 4 [e01]

value: RA

value: Dark cycle:8:16

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 3LD+T.RA replicate 4 [e01]

value: male and female

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: hippocampus_medip_abuse_39_rep3

description:
39_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_4_rep1

description:
4_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 2SD-T.HVC replicate 6 [e01]

value: HVC

value: No

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: hippocampus_medip_abuse_4_rep2

description:
4_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: hippocampus

value: abuse


title: hippocampus_medip_abuse_39_rep2

description:
39_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: anti-5 methylcytosine antibody


title: 2SD-T.RA replicate 5 [e01]


title: 1SD-T.HVC replicate 4 [e01]

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: SD.HVC replicate 1 [e01]

value: telencephalon


title: hippocampus_medip_control_36_rep3

description:
36_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: control

value: Calbiochem


title: hippocampus_medip_control_36_rep2

description:
36_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_39_rep1

description:
39_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 1SD-T.RA replicate 3 [e01]

value: male

value: Dark cycle:NA


title: hippocampus_medip_control_31_rep2

description:
31_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_31_rep1

description:
31_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 21LD+T.RA replicate 2 [e01]

value: RA

value: Dark cycle:20:4

value: Yes

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: hippocampus_medip_abuse_37_rep2

description:
37_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_36_rep1

description:
36_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 7LD+T.RA replicate 5 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.

value: male and female

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: hippocampus_medip_abuse_30_rep2

description:
30_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_31_rep3

description:
31_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_29_rep2

description:
29_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_29_rep3

description:
29_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: 21LD+T.HVC replicate 1 [e01]

value: HVC


title: brain quail SSP rep2

city: Durham

first: Miriam

middle: Virtudes

last: Rivas

state: NC

address: 451 Bryan Research Building

department: Neurobiology

institute: Duke University Medical Center

description: gene expression brain

hyb_protocol: From the amplified cDNA reactions, 1.5 mg of amplified labeled product (probe) was denatured and hybridized to our custom designed songbird oligo spotted arrays (Agilent Technologies; Whitney et al, in preparation) containing oligos designed from over 44,000 relatively unique cDNA transcripts, including some splice variants. More detailed information on the arrays is available at http://aviangenomes.org/main/zebrafincholigoarray.

scan_protocol: After hybridization, the microarrays were scanned with the Axon GenePix 4000B scanner to acquire and analyze the expression data (Molecular Devices).

data_processing: For analysis, signal intensity on an axon array scanner was obtained in Agilent oligoarray format. The data was extracted in R using the Agi4x44PreProcess Bioconductor library. The values were normalized using median centered log2 transformation. Raw and normalized expression distributions were evaluated for sample quality control using the normalization centering profile, the normalization factor, and a cross-sample correlation analysis. Normalization was evaluated with VSN (variance stabilization normalization)-Scale Factor package in R (R Foundation for Statistical Computing, Vienna, Austria). VSN-Scale Factor was chosen because it performed the least manipulation of the original intensity profiles, and normalizes samples among themselves.

organism: Coturnix japonica

source_name: SSP quail

label_protocol: Samples were labeled with Cy3-dCTP using the uMACS SuperAmp Kit (Miltenyi Biotec).

extract_protocol: After laser capture of the samples onto the CapSure HS LCM caps (Molecular Devices), the membrane withcaptured brain nuclei was carefully peeled away from the cap and placed in a 0.65 ml tube of the PicoPure RNA isolation kit which contained 50ul of disruption buffer (Molecular Devices). Tubes were placed on a 42oC heat block for 30 min then placed in a -80 oC freezer until all desired samples were captured. Total RNA was then isolated according to the remaining protocol steps in the PicoPure isolation kit instructions (Molecular Devices). The concentration and integrity of total RNA were measured on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA USA) using the RNA Pico 6000 kit according to manufacturer instructions (Agilent Technologies).

tag: cell type

value: Supra-spinal SSP Motor Neuron

value: Male

value: Adult

tag: organism

value: Japanese quail


title: hippocampus_medip_abuse_29_rep1

description:
29_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: hippocampus

value: abuse

value: anti-5 methylcytosine antibody


title: hippocampus_medip_control_28_rep1

description:
28_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

value: control

value: Calbiochem


title: brain Anna's hummingbird 12 rep3

description: gene expression brain

organism: Calypte anna

source_name: 12 hummingbird

value: 12th Motor Neuron

tag: gender

value: Anna's hummingbird


title: brain Anna's hummingbird SSP rep3

description: gene expression brain

source_name: SSP hummingbird


title: brain quail 12 rep2

description: gene expression brain

source_name: 12 quail


title: brain Anna's hummingbird 12 rep2

description: gene expression brain


title: hippocampus_medip_control_28_rep2

description:
28_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_26_rep3

description:
26_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_21_rep5

description:
21_medip_5
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain Anna's hummingbird SSP rep2

description: gene expression brain


title: brain dove 12 rep2

description: gene expression brain

organism: Streptopelia risoria

source_name: 12 dove

value: Ring dove


title: brain quail SSP rep1

description: gene expression brain


title: brain dove SSP rep2

description: gene expression brain

source_name: SSP dove


title: hippocampus_medip_abuse_21_rep2

description:
21_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_20_rep5

description:
20_medip_5
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain quail 12 rep1

description: gene expression brain


title: hippocampus_medip_control_17_rep3

description:
17_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain dove SSP rep1

description: gene expression brain


title: hippocampus_medip_control_20_rep3

description:
20_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain budgerigar SSP rep3

description: gene expression brain

organism: Melopsittacus undulatus

source_name: SSP budgerigar

value: Budgerigar


title: brian budgerigar 12 rep2

description: gene expression brain

source_name: 12 budgeriger


title: brain budgerigar SSP rep2

description: gene expression brain


title: brain dove 12 rep1

description: gene expression brain


title: hippocampus_medip_control_16_rep4

description:
16_medip_4
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_17_rep2

description:
17_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_16_rep1

description:
16_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_abuse_21_rep3

description:
21_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain budgerigar SSP rep1

description: gene expression brain


title: hippocampus_medip_control_17_rep1

description:
17_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_16_rep3

description:
16_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain budgerigar 12 rep3

description: gene expression brain


title: brain budgerigar 12 rep1

description: gene expression brain


title: brain quail 12 rep3

description: gene expression brain


title: hippocampus_medip_control_14_rep2

description:
14_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_11_rep2

description:
11_medip_2
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: hippocampus_medip_control_11_rep3

description:
11_medip_3
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain quail SSP rep3

description: gene expression brain


title: hippocampus_medip_control_14_rep1

description:
14_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.


title: brain dove SSP rep3

description: gene expression brain


title: brain zebra finch SSP rep4

description: gene expression brain

source_name: SSP zebra finch

value: Zebra Finch


title: brain dove 12 rep3

description: gene expression brain


title: ime2_6hr_rep2

city: Detroit

first: George

last: Brush

state: MI

address: 110 E. Warren Ave.

department: School of Medicine

institute: Wayne State University

description: Gene expression 6hr after cells were induced to enter meiosis

hyb_protocol: 0.6 ug of Alexa555-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 1x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40ul hybridized to Agilent Yeast 8x15K microarrays (G4813A) for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 with 0.005% Triton X-102 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 with  0.005% Triton X-102  (Agilent).

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505A) using one color scan settings with the photo multiplier tube (PMT) set to extended dynamic range for the green channel (Hi 100% and Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 016322_D_F_20070321).  Spatially detrending was used to obtain green processed signal intensities. Signal intensities were normalized within GeneSpring on a per-chip basis using the 50th percentile.

organism: Saccharomyces cerevisiae

source_name: ime2D cells, 6hr, replicate 2

label_protocol: Alexa555 labeled cRNA was prepared from 500ng total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Alexa Dye (Invitrogen/Molecular Probes, Eugen OR) incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in rich media under standard pre-sporulation conditions and then induced to enter meiosis synchronously through transfer to a sporulation medium.

extract_protocol: Total RNA was prepared using a rapid hot phenol procedure developed for yeast.

tag: whole cells

value: yeast

tag: strain

tag: genotype/variation

tag: time


title: WT_4hr_rep2

description: Gene expression 4hr after cells were induced to enter meiosis

source_name: WT cells, 4hr, replicate 2

value: wild type


title: WT_6hr_rep2

source_name: WT cells, 6hr, replicate 2


title: brain zebra finch 12 rep2

description: gene expression brain

source_name: 12 zebra finch

tag: age


title: ime2_4hr_rep2

source_name: ime2D cells, 4hr, replicate 2


title: brain zebra finch 12 rep3

description: gene expression brain


title: 3LD+T.HVC replicate 4 [e01]

value: male

value: HVC

tag: light

value: Dark cycle:20:4

tag: testosterone at sacrifice

value: Yes

tag: treatment protocol

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.

source_name: universal SoNG reference

value: male and female

value: telencephalon

value: Dark cycle:NA

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: WT_2hr_rep2

description: Gene expression 2hr after cells were induced to enter meiosis

source_name: WT cells, 2hr, replicate 2


title: ime2_0hr_rep2

description: Gene expression 0hr after cells were induced to enter meiosis

source_name: ime2D cells, 0hr, replicate 2


title: WT_0hr_rep2

source_name: WT cells, 0hr, replicate 2


title: ime2_6hr_rep1

source_name: ime2D cells, 6hr, replicate 1


title: ime2_2hr_rep2

source_name: ime2D cells, 2hr, replicate 2


title: 3LD+T.RA replicate 1 [e01]

value: RA


title: 7LD+T.HVC replicate 3 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: brain zebra finch SSP rep3

description: gene expression brain

value: 12th Motor Neuron

value: Male

value: Adult


title: brain zebra finch SSP rep2

description: gene expression brain

value: Supra-spinal SSP Motor Neuron

value: Zebra Finch


title: SD.RA replicate 3 [e01]

value: Dark cycle:8:16

value: No

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: WT_6hr_rep1

source_name: WT cells, 6hr, replicate 1

value: yeast

value: wild type


title: ime2_4hr_rep1

source_name: ime2D cells, 4hr, replicate 1


title: 21LD+T.RA replicate 5 [e01]

value: male

value: Dark cycle:20:4

value: Yes

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: SD.HVC replicate 3 [e01]

value: male and female

value: telencephalon

value: Dark cycle:NA

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: HVC


title: 1SD-T.RA replicate 6 [e01]

value: RA

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 2SD-T.RA replicate 6 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: ime2_2hr_rep1

source_name: ime2D cells, 2hr, replicate 1


title: WT_0hr_rep1

source_name: WT cells, 0hr, replicate 1


title: WT_4hr_rep1

source_name: WT cells, 4hr, replicate 1


title: 2SD-T.HVC replicate 3 [e01]

value: Dark cycle:8:16


title: 3LD+T.RA replicate 5 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 1SD-T.HVC replicate 1 [e01]

value: No


title: 21LD+T.HVC replicate 4 [e01]


title: 7LD+T.RA replicate 4 [e01]

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: WT_2hr_rep1

source_name: WT cells, 2hr, replicate 1

value: yeast

value: wild type


title: 7LD+T.HVC replicate 4 [e01]

value: male

value: Dark cycle:20:4


title: ime2_0hr_rep1

source_name: ime2D cells, 0hr, replicate 1