title: 14228064 - ch1 Stressed 1 vs ch1 Acclimated-Stressed 1

hyb_protocol: ch1 Acclimated-Stressed 1 Cy5 / ch1 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Acclimated-Stressed 1

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 8 weeks for under control conditions. Plants were then transfered for two days under acclimation conditions and two days under stress conditions. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimation conditions: Media=compost hygrometry=70-80 % Temperature=16°C/19°C Ligh=450 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: ch1 Acclimated-Stressed 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

value: columbia (col0)

value: PSII antenna-deficient mutant (ch1)

source_name: ch1 Stressed 1

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 8 weeks under control conditions. Plants were then transfered for two days in a chamber at 900 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 10°C/14°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: ch1 Stressed 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: MCF7-I6 highly invasive cells

status: Public on Dec 10 2011

type: RNA

city: Coleraine

first: Anthony

last: Bjourson

state: Northern Ireland

address: Cromore Road

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Ulster

description: Gene expression data from subclone MCF7-I6 of MCF7 breast cancer cell line (3 replicates).

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data normalization was performed using GeneSpring software. All 3 unscaled CHP files were used for the analysis. Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. A per-gene normalization to specific samples (control samples) was applied. The control value was the mean of the three control replicates. The Cross Gene Error Model (CGEM) was established based on replicates.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Highly invasive subclone of MCF7 breast cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneCHip Expression Analysis, Technical Manual, 701021 Rev. 5).

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

treatment_protocol: The Matrigel-coated membranes from the invasion assay inserts were aseptically removed and placed in the bottom of a companion plate. MCF7 cells (2.5x10E5) were loaded into the top well of the Matrigel invasion assay and incubated for 72h. On completion of the assay the invading cells were collected as follows: (a) Cells that had degraded the Matrigel matrix and migrated to the underside of the membrane were scraped off using a cell scraper (Corning, Netherlands) and transferred to a single well of a 6 well plate containing 1 ml of complete culture medium. (b) Cells that had degraded the Matrigel matrix and migrated into the bottom well and adhered to the inserts in the bottom of the companion plate were also collected. These inserts in the bottom of the companion plate were aseptically transferred to a 6 well plate and 1ml culture medium placed in the companion plate of the invasion assay. (c) MCF7 cells were loaded into the top well of an additional Matrigel invasion assay and incubated for 72h. Cells that had degraded the Matrigel matrix and migrated into the bottom well and adhered to the bottom of the companion plate were collected. These invaded subclones were cultured by replacing the culture medium every 2-3 days to give rise to 3 MCF7 subclones: (a) bottom insert, (b) insert and (c) bottom plate. Once sufficient numbers of these subclones were achieved, they were introduced into another Matrigel invasion assay with the parental MCF7 cells as a control. The invaded subclones were isolated and re-introduced into an invasion assay.

tag: tissue

value: breast cancer

tag: cell line

tag: subclone


title: wild type, rep3

status: Public on Dec 09 2011

type: mixed

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

description: SL1344 3

hyb_protocol: Slides were blocked with DCE according to protocol at PMID 11266573. For hybridization and washing protocols, see  http://www.ifr.ac.uk/safety/Microarrays/protocols.html

scan_protocol: Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using block median normalization.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium SL1344 wild type

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Cultures were grown aerobically in LB to early stationary phase (OD 600=2.3).

extract_protocol: Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: strain

tag: genotype

value: wild type

tag: growth phase

value: early stationary

molecule: genomic DNA

source_name: S. Typhimurium genomic DNA


title: 14228065 - ch1 Acclimated 3 vs ch1 Stressed 3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant

hyb_protocol: ch1 Stressed 3 Cy5 / ch1 Acclimated 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: ch1 Stressed 3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

extract_protocol: ch1 Stressed 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Stressed - environmental treatment - light,light:time 2day .  Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days in a chamber at 900 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 10°C/14°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light.

tag: ecotype

tag: genotype/variation

tag: age

tag: boyes leaf development stage (boyes et al. plant cell 2001)

source_name: ch1 Acclimated 3

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 8 weeks under control conditions. Plants were then transfered for two days in a chamber at 450 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 16°C/19°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimated conditions : Media=compost hygrometry=70-80 % Temperature=16°C/19°C Light=450 µmol m-2s-1

extract_protocol: ch1 Acclimated 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Acclimated - environmental treatment - light,light:time 2day . Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days in a chamber at 450 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 16°C/19°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light.


title: Rhesus macaque - cerebellar cortex - 1487 days old

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 1487 days old Rhesus macaque individual
Mml_1487days_batch1

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >70% of human, chimpanzee or macaque individuals.

organism: Macaca mulatta

source_name: Dissected Rhesus macaque post-mortem cerebellar cortex

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cerebellar cortex.

value: 1487 days

tag: gender

value: m

value: cerebellar cortex of the brain

tag: post-mortem interval (hours)

tag: rna integrity number (rin)

tag: batch


title: wild type, rep2

description: SL1344 2


title: 14228067 - ch1 Acclimated-Stressed 3 vs ch1 Stressed 3

hyb_protocol: ch1 Stressed 3 Cy5 / ch1 Acclimated-Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Acclimated-Stressed 3

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 8 weeks under control conditions. Plants were then transfered for two days under acclimation conditions and two days under stress conditions. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimation conditions: Media=compost hygrometry=70-80 % Temperature=16°C/19°C Ligh=450 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: ch1 Acclimated-Stressed 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: Name:Acclimated-Stressed - environmental treatment - light,light:time 2day . Plants of Arabidopsis thaliana were grown for 4 or 8 weeks for respectively the Col0 and the ch1 mutant, under control conditions. Plants were then transfered for two days under acclimation conditions and two days under stress conditions. Plants were harvested at 11 am after two hours of light.


title: Rhesus macaque - cerebellar cortex - 16 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 16 days old Rhesus macaque individual
Mml_16days_batch1

value: 16 days


title: Rhesus macaque - cerebellar cortex - 1 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 1 days old Rhesus macaque individual
Mml_1days_batch2

value: 1 days


title: wild type, rep1

description: SL1344 1


title: F. nucleatum DSMZ 25586 monolayer

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

description: This sample is of wild-type F. nucleatum DSMZ 25586 adherent cells/monolayer.

hyb_protocol: Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

scan_protocol: Scanning was performed with the DNA Microarray Scanner (Agilent) at a resolution of 5 µm and NimbleScanTM version 2.4 software

data_processing: The raw data (.pair file) were checked for inhomogenous hybridization. Probes with a high intensity caused by wash artefacts were deleted. In the case of GSM714207-GSM714212, remaining technical replicates were averaged. In the case of GSM714213-GSM714218, probes not belonging to S. mutans or RANDOM were excluded from analysis. Additionally, probes identified as interspecies cross-hybridizing biological false positive probes, identified on GSM714212, were also excluded from analysis. The remaining probes were quantile normalized, background corrected and sumarized with NimbleScan Software RMA, and subsequently analysed with GeneSpring GX 11.0, Agilent Technologies.

organism: Fusobacterium nucleatum

source_name: F. nucleatum DSMZ 25586

label_protocol: Labeling with Cy3 was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

growth_protocol: Bacterial cells were cultured under anaerobic conditions (10% CO2; 10% H2; 80% N2) at 37°C in chemical defined medium supplemented with 50 mM sucrose or in artificial saliva supplemented with 50 mM galactose for 24 h.

extract_protocol: RNA was extracted out of 100 mg harvested cells using the Fast RNA Pro Blue Kit (MP Biomedicals, Solon, Ohio, USA) following manufacturers instructions. Removal of DNA was performed by DNase digenstion for 1 hour at 37 °C.

value: F. nucleatum DSMZ 25586

value: wt

tag: single species biofilm / culture

value: yes

tag: two-species biofilm

value: no


title: 14228068 - ch1 Stressed 3 vs ch1 Acclimated-Stressed 3

hyb_protocol: ch1 Acclimated-Stressed 3 Cy5 / ch1 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228066 - ch1 Stressed 3 vs ch1 Acclimated 3

hyb_protocol: ch1 Acclimated 3 Cy5 / ch1 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Rhesus macaque - cerebellar cortex - 1135 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 1135 days old Rhesus macaque individual
Mml_1135days_batch2

value: 1135 days


title: Rhesus macaque - cerebellar cortex - 10220 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 10220 days old Rhesus macaque individual
Mml_10220days_batch1

value: f


title: Rhesus macaque - cerebellar cortex - 151 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 151 days old Rhesus macaque individual
Mml_151days_batch2

value: 151 days


description: This sample is of wild-type A. actinomycetemcomitans HK1651 monolayer.

source_name: A. actinomycetemcomitans HK1651

value: A. actinomycetemcomitans HK1651


title: Rhesus macaque - cerebellar cortex - 153 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 153 days old Rhesus macaque individual
Mml_153days_batch1

value: 153 days


title: 14228062 - ch1 Stressed 1 vs ch1 Acclimated 1

hyb_protocol: ch1 Acclimated 1 Cy5 / ch1 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Acclimated 1

extract_protocol: ch1 Acclimated 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

value: columbia (col0)

value: PSII antenna-deficient mutant (ch1)


title: 14228060 - col0 Stressed 2 vs col0 Control 2

hyb_protocol: col0 Control 2 Cy5 / col0 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Control 2

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under controlled conditions : 250 µmol m-2 s-1, photoperiod of 8h/16h, temperature of 22°C/18°C and 55% of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1

extract_protocol: col0 Control 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

treatment_protocol: no treatment

value: wild type

source_name: col0 Stressed 2

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under control conditions. Plants were then transfered for two days in a chamber at 900 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 10°C/14°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Stress conditions : Media=compost hygrometry=70-80% Temperature=10°C/14°C Light=900 µmol m-2s-1

extract_protocol: col0 Stressed 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228063 - ch1 Acclimated-Stressed 1 vs ch1 Stressed 1

hyb_protocol: ch1 Stressed 1 Cy5 / ch1 Acclimated-Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228061 - ch1 Acclimated 1 vs ch1 Stressed 1

hyb_protocol: ch1 Stressed 1 Cy5 / ch1 Acclimated 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228057 - ch1 Acclimated-Stressed 2 vs ch1 Stressed 2

hyb_protocol: ch1 Stressed 2 Cy5 / ch1 Acclimated-Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Stressed 2

extract_protocol: ch1 Stressed 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

source_name: ch1 Acclimated-Stressed 2

extract_protocol: ch1 Acclimated-Stressed 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228058 - ch1 Stressed 2 vs ch1 Acclimated-Stressed 2

hyb_protocol: ch1 Acclimated-Stressed 2 Cy5 / ch1 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228055 - ch1 Acclimated 2 vs ch1 Stressed 2

hyb_protocol: ch1 Stressed 2 Cy5 / ch1 Acclimated 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Acclimated 2

extract_protocol: ch1 Acclimated 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228054 - ch1 Stressed 2 vs ch1 Control 2

hyb_protocol: ch1 Control 2 Cy5 / ch1 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Control 2

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 8 weeks under controlled conditions : 250 µmol m-2 s-1, photoperiod of 8h/16h, temperature of 22°C/18°C and 55% of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1

extract_protocol: ch1 Control 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: 14228059 - col0 Control 2 vs col0 Stressed 2

hyb_protocol: col0 Stressed 2 Cy5 / col0 Control 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 7-day Cy/+ rat kidney

city: Toyoake

first: Kugita

last: Masanori

state: Aichi

address: kutsukake-cho Denngakugakubo 1-98

department: Center of Animal Models for Human Diseases

country: Japan

institute: Fujita Health University

hyb_protocol: 1 μg aliquots of Cy3-labeled RNA obtained from age-matched +/+ kidneys and Cy5-labeled RNA from +/+, Cy/+, or Cy/Cy kidneys were mixed and hybridized onto Agilent Rat Oligo Microarrays (product no. G4130A) according to the manufacturer’s hybridization protocol.

scan_protocol: The microarray slides were examined with an Agilent microarray scanner and software (scanner model G2565BA).

data_processing: Data analysis was performed with Agilent Feature Extraction software (version A.7.1.1) using default settings and Excel 2003 (Microsoft).

organism: Rattus norvegicus

source_name: 7-day +/+ rat kidney

label_protocol: 200 ng aliquots of total RNA obtained from kidneys of 3- or 7-day-old rats were labeled using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Rats were allowed free access to water and food throughout the study.

extract_protocol: RNA was extracted from kidneys of 3- and 7-day-old rats using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol® reagent (Invitrogen Co., Carlsbad, CA, USA) in accordance with their manual, and the samples were incubated with RNase-free DNase I (Ambion, TX, USA).  The quality and concentration of each sample was confirmed by spectrophotometry (NanoDropTM ND-1000; Asahi glass Co. Ltd., Tokyo, Japan).

value: 7 days old

value: Kidney

source_name: 7-day Cy/+ rat kidney

value: Cy/+


title: 14228056 - ch1 Stressed 2 vs ch1 Acclimated 2

hyb_protocol: ch1 Acclimated 2 Cy5 / ch1 Stressed 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228053 - ch1 Control 2 vs ch1 Stressed 2

hyb_protocol: ch1 Stressed 2 Cy5 / ch1 Control 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14228051 - ch1 Control 2 vs ch1 Acclimated 2

hyb_protocol: ch1 Acclimated 2 Cy5 / ch1 Control 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3-day Cy/Cy rat kidney

source_name: 3-day +/+ rat kidney

value: 3 days old

source_name: 3-day Cy/Cy rat kidney

value: Cy/Cy


title: 7-day +/+ rat kidney


title: 14227587 - ch1 Control 1 vs ch1 Acclimated 1

hyb_protocol: ch1 Acclimated 1 Cy5 / ch1 Control 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Control 1

extract_protocol: ch1 Control 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: Chimpanzee - superior frontal gyrus - 525 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 525 days old Chimpanzee individual
Ptr_525days_batch1

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age. Batch 2_2 indicates addition to macaque batch 2.

organism: Pan troglodytes

source_name: Dissected Chimpanzee post-mortem superior frontal gyrus

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cortical region approximately corresponding to Brodmann area 9 of the prefrontal cortex (the superior frontal gyrus). We aimed to make dissections that contain 2:1 grey:white matter (60-70% grey matter).

value: 525 days

value: superior frontal gyrus of the brain


title: Chimpanzee - superior frontal gyrus - 8 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 8 days old Chimpanzee individual
Ptr_8days_batch1

value: 8 days

value: m


title: 14227588 - ch1 Acclimated 1 vs ch1 Control 1

hyb_protocol: ch1 Control 1 Cy5 / ch1 Acclimated 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Chimpanzee - superior frontal gyrus - 4500 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 4500 days old Chimpanzee individual
Ptr_4500days_batch1

value: 4500 days


title: 7-day Cy/Cy rat kidney

source_name: 7-day Cy/Cy rat kidney


title: Chimpanzee - superior frontal gyrus - 4415 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 4415 days old Chimpanzee individual
Ptr_4415days_batch1

value: 4415 days


title: 3-day Cy/+ rat kidney

source_name: 3-day Cy/+ rat kidney


title: 14228052 - ch1 Acclimated 2 vs ch1 Control 2

hyb_protocol: ch1 Control 2 Cy5 / ch1 Acclimated 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Chimpanzee - superior frontal gyrus - 39 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 39 days old Chimpanzee individual
Ptr_39days_batch1

value: 39 days


title: Chimpanzee - superior frontal gyrus - 4361 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 4361 days old Chimpanzee individual
Ptr_4361days_batch1

value: 4361 days


title: Chimpanzee - superior frontal gyrus - 2447 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2447 days old Chimpanzee individual
Ptr_2447days_batch1

value: 2447 days

value: f


title: Chimpanzee - superior frontal gyrus - 2313 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2313 days old Chimpanzee individual
Ptr_2313days_batch1

value: 2313 days


title: 14227584 - ch1 Stressed 3 vs ch1 Control 3

description: To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant

hyb_protocol: ch1 Control 3 Cy5 / ch1 Stressed 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Control 3

extract_protocol: ch1 Control 3:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)

value: columbia (col0)

value: PSII antenna-deficient mutant (ch1)

source_name: ch1 Stressed 3


title: 14227583 - ch1 Control 3 vs ch1 Stressed 3

hyb_protocol: ch1 Stressed 3 Cy5 / ch1 Control 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: second BR for sample2

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

country: USA

institute: NCI/NIH

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the NCI Frederick Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Affymetrix Human Exon ST1.  0 platform was used for the microarray analysis.  Raw data in CEL files were preprocessed using Affymetrix Expression Console software with ‘RMA polish/RMA’ option and its median normalization method.  ‘Core’ confidence was used for the exon annotation.  We profiled expression of each sample in biological duplicates.  The exon-level value was taken to be the average of the two biological replicates.

source_name: second biological replicate for control stim 1hr

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with cDNA Synthesis Kit (Affymetrix)

growth_protocol: HEK293 cells were grown in RPMI medium supplemented with 10% FCS and 100 U/mL penicillin and streptomycin (Invitrogen) in a humidified atmosphere at 37 °C with 5% CO2

extract_protocol: Total RNA was prepared using the Qiagen RNAeasy Kit following the manufacturer’s instructions

treatment_protocol: HEK293 WT and ELL KD cells were stimulated with EGF (50 ng/mL) (Peprotech) for 1 hr

tag: cell type

value: Human embryonic kidney cell


title: Chimpanzee - superior frontal gyrus - 16131 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 16131 days old Chimpanzee individual
Ptr_16131days_batch1

tag: tissue


title: shELL stim 1hr

source_name: shELL stim 1hr

tag: cell line


title: 14227582 - ch1 Acclimated 3 vs ch1 Control 3

hyb_protocol: ch1 Control 3 Cy5 / ch1 Acclimated 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Acclimated 3


title: Rhesus macaque - superior frontal gyrus - 9518 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 9518 days old Rhesus macaque individual
Mml_9518days_batch1

source_name: Dissected Rhesus macaque post-mortem superior frontal gyrus

value: 9518 days


title: second BR for sample3

source_name: second biological replicate for shELL unstim


title: second BR for sample1

source_name: second biological replicate for control unstim


title: Chimpanzee - superior frontal gyrus - 1 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 1 days old Chimpanzee individual
Ptr_1days_batch1

value: 1 days


title: second BR for sample4

source_name: second biological replicate for shELL stim 1hr


title: Rhesus macaque - superior frontal gyrus - 9291 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 9291 days old Rhesus macaque individual
Mml_9291days_batch2

value: 9291 days


title: Chimpanzee - superior frontal gyrus - 0 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 0 days old Chimpanzee individual
Ptr_0days_batch1

value: 0 days


title: 14227581 - ch1 Control 3 vs ch1 Acclimated 3

hyb_protocol: ch1 Acclimated 3 Cy5 / ch1 Control 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3-day +/+ rat kidney

value: 3 days old

value: Kidney


title: Fasted Cnot3het liver, biological rep1

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

description: Gene expression data from Cnot3+/- liver

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16hr at 45C on Gene Chip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA as normalization method.

label: Biotin

organism: Mus musculus

source_name: Mouse liver, 8-week-old, 24hr Fasted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Mice were housed in cages, maintained on a 12-hr light-dark cycle, and had access to water ad libitum. Mice were fed a normal chow diet (CA-1, CLEA Japan Inc.).

extract_protocol: Total RNA were extracted with ISOGEN according to manufacture's protocol (Nippon Gene) and purified with RNeasy Kit (Qiagen).

treatment_protocol: For fasting, mice were housed individually and deprived of food.

value: Male

value: liver


title: Fasted Cnot3het liver, biological rep2


title: Chimpanzee - superior frontal gyrus - 12784 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 12784 days old Chimpanzee individual
Ptr_12784days_batch1

value: m

value: superior frontal gyrus of the brain


title: shELL unstim

source_name: shELL unstim


title: Rhesus macaque - superior frontal gyrus - 9125 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 9125 days old Rhesus macaque individual
Mml_9125days_batch2

value: 9125 days


title: control stim 1hr

source_name: control stim 1hr


title: 14227578 - ch1 Control 1 vs ch1 Stressed 1

hyb_protocol: ch1 Stressed 1 Cy5 / ch1 Control 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Stressed 1

extract_protocol: ch1 Stressed 1:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: Rhesus macaque - superior frontal gyrus - 7 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 7 days old Rhesus macaque individual
Mml_7days_batch2_2

value: 7 days


title: Fasted wild-type liver, biological rep2

description: Gene expression data from wild-type liver

value: Wild-type


title: control unstim

source_name: control unstim


title: 14227579 - ch1 Stressed 1 vs ch1 Control 1

hyb_protocol: ch1 Control 1 Cy5 / ch1 Stressed 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ch1 Control 1


title: Rhesus macaque - superior frontal gyrus - 8104 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 8104 days old Rhesus macaque individual
Mml_8104days_batch1

value: 8104 days


title: Rhesus macaque - superior frontal gyrus - 739 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 739 days old Rhesus macaque individual
Mml_739days_batch1

value: 739 days


title: Rhesus macaque - superior frontal gyrus - 7673 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 7673 days old Rhesus macaque individual
Mml_7673days_batch2

value: 7673 days


title: 14227224 - col0 Acclimated 2 vs col0 Control 2

hyb_protocol: col0 Control 2 Cy5 / col0 Acclimated 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col0 Control 2

value: columbia (col0)

value: wild type

source_name: col0 Acclimated 2

growth_protocol: aerial - Plants of Arabidopsis thaliana were grown for 4 weeks under control conditions. Plants were then transfered for two days in a chamber at 450 µmol m-2 s-1, with a photoperiod of 8h/16h, a temperature of 16°C/19°C and 70-80 % of humidity. Plants were harvested at 11 am after two hours of light. Control conditions : Media=compost  hygrometry=55%  Temperature=22°C/18°C  Ligh=250 µmol m-2s-1 Acclimated conditions : Media=compost hygrometry=70-80 % Temperature=16°C/19°C Light=450 µmol m-2s-1

extract_protocol: col0 Acclimated 2:15ug. (Macherey-Nagel_TotalRNAPlant.pdf)


title: Fasted wild-type liver, biological rep1


title: Rhesus macaque - superior frontal gyrus - 607 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 607 days old Rhesus macaque individual
Mml_607days_batch2

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.

value: 607 days


title: Rhesus macaque - superior frontal gyrus - 7391 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 7391 days old Rhesus macaque individual
Mml_7391days_batch1

value: 7391 days


title: 24090 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 24090 days old human individual

hyb_protocol: The hybridization mix was prepared using the Human miRNA Microarray kit (Agilent Technologies) following the manufacturer's instructions. Labeled miRNA from each sample was hybridized to one Agilent-021827 Human microRNA Microarray (v3, based on the Sanger miRBase Release 12.0). Hybridization was performed at 55C for 20h. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions. For human and chimpanzee, the microarray experiments were carried out in two batches. Batches were balanced with respect to samples' age.

scan_protocol: Arrays were scanned by a DNA microarray scanner (Agilent G2565BA).

data_processing: The Agilent G4462AA Feature Extraction software (v10.7.3.1) was used for image analysis with default settings. In the original analysis we processed the data using the following steps (i) the data was log2 transformed and normalized, separately for each brain region dataset, (ii) we removed samples with low detection values (total detected miRNAs <200) and two samples that appeared as outliers in a principle components analysis (samples Ptr_CBC_525days_indv12_batch1, Hsa_CBC_1630days_indv5_batch2, Hsa_CBC_2922days_indv31_batch2, Hsa_CBC_8364days_indv32_batch2, Mml_CBC_3389days_indv25_batch1, Hsa_CBC_2days_indv1_batch2),  (iii) we removed any batch effects by equalizing the mean expression level across batches, (iv) we calculated the mean profile per biological replicate, (v) we excluded any miRNAs that showed any sequence difference in their mature sequences among the 3 species. For this, we first extracted miRNA precursor sequences in chimpanzee and macaque genomes (panTro3 and rheMac2, respectively) corresponding to human precursors using BLAT (Kent 2002) and then aligned these by ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2) to extract the orthologous mature sequences. The processed miRNA datasets are available as supplementary files on the Series record.

source_name: Dissected post-mortem human cerebellar cortex

label_protocol: 100 ng of dephosphorylated RNA was labeled with Cyanine 3-pCp following standard Agilent protocols.

extract_protocol: Total RNA was extracted from dissected CBC and PFC samples (humans, n=14; chimpanzees, n=11; macaques, n=8, respectively; Table S1), using the Ambion® mirVana miRNA isolation kit. Two individuals in human PFC and CBC sets and 5 individuals in chimpanzee PFC and CBC sets were measured in both batches to estimate the technical variance.

treatment_protocol: We used prefrontal cortex (PFC) and cerebellar cortex (CBC) samples from postmortem brains of human, chimpanzee, and rhesus macaque individuals of different age. Human samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands, and the Chinese Brain Bank Center, Wuhan, China. Informed consent for use of human tissues for research was obtained in writing from all donors or their next of kin. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state. Chimpanzee samples were obtained from the Yerkes Primate Center, GA, USA, the Anthropological Institute & Museum of the University of Zürich-Irchel, Switzerland, and the Biomedical Primate Research Centre, the Netherlands. Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All non-human primates used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used. CBC dissections were made from the cerebellar cortex. PFC dissections were made from the frontal part of the superior frontal gyrus. All samples contained an approximately 2:1 grey matter to white matter volume ratio.

value: 24090 days old

tag: Sex

value: M

value: cerebellar cortex of the brain

tag: individual no


title: Fed wild-type liver, biological rep2

source_name: Mouse liver, 8-week-old, Fed

value: Male

tag: strain

tag: genotype


title: 24090 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 24090 days old human individual

source_name: Dissected post-mortem human prefrontal cortex

value: prefrontal cortex of the brain


title: 12784 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 12784 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee cerebellar cortex

value: 12784 days old


title: Rhesus macaque - superior frontal gyrus - 449 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 449 days old Rhesus macaque individual
Mml_449days_batch2

value: 449 days

value: m

value: superior frontal gyrus of the brain


title: Rhesus macaque - superior frontal gyrus - 3389 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 3389 days old Rhesus macaque individual
Mml_3389days_batch1

value: 3389 days


title: 14228078 - col0 Control 2 vs col0 Acclimated 2

description: To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant

hyb_protocol: col0 Acclimated 2 Cy5 / col0 Control 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype


title: 12784 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 12784 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee prefrontal cortex


title: Rhesus macaque - superior frontal gyrus - 2936 days old (batch2_2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2936 days old Rhesus macaque individual
Mml_2936days_batch2_2

source_name: Dissected Rhesus macaque post-mortem superior frontal gyrus

value: 2936 days


title: Rhesus macaque - superior frontal gyrus - 310 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 310 days old Rhesus macaque individual
Mml_310days_batch1

value: 310 days


title: Rhesus macaque - superior frontal gyrus - 2936 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2936 days old Rhesus macaque individual
Mml_2936days_batch2


title: Rhesus macaque - superior frontal gyrus - 237 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 237 days old Rhesus macaque individual
Mml_237days_batch2

value: 237 days


title: Rhesus macaque - superior frontal gyrus - -30 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a -30 days old Rhesus macaque individual
Mml_-30days_batch2_2

value: -30 days (prenatal individual; predicted to be ~30 days before birth)


title: Rhesus macaque - superior frontal gyrus - 5478 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 5478 days old Rhesus macaque individual
Mml_5478days_batch2

value: 5478 days


title: Rhesus macaque - superior frontal gyrus - 22 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 22 days old Rhesus macaque individual
Mml_22days_batch2

value: 22 days


title: Cnot3het liver, biological rep2

description: Gene expression data from Cnot3+/- liver

source_name: Mouse liver, 12-week-old, 24hr Fasted

value: Cnot3 heterozygotes

value: liver


title: 29200 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 29200 days old human individual

value: 29200 days old

value: M


title: Wild-type liver, biological rep2

description: Gene expression data from wild-type liver

value: Male

value: Wild-type


title: Fed wild-type liver, biological rep1


title: 32120 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 32120 days old human individual

value: 32120 days old

value: prefrontal cortex of the brain


title: 32120 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 32120 days old human individual

value: cerebellar cortex of the brain


title: Cnot3het liver, biological rep1


title: Rhesus macaque - superior frontal gyrus - 207 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 207 days old Rhesus macaque individual
Mml_207days_batch1

value: 207 days

value: m

value: superior frontal gyrus of the brain


title: Rhesus macaque - superior frontal gyrus - 179 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 179 days old Rhesus macaque individual
Mml_179days_batch2

value: 179 days


title: Rhesus macaque - superior frontal gyrus - 1 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 1 days old Rhesus macaque individual
Mml_1days_batch2_2

value: 1 days


title: 16131 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 16131 days old chimpanzee individual

value: 16131 days old

value: F


title: Rhesus macaque - superior frontal gyrus - -15 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a -15 days old Rhesus macaque individual
Mml_-15days_batch2_2

value: -15 days (prenatal individual; predicted to be ~15 days before birth)


title: Rhesus macaque - superior frontal gyrus - 16 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 16 days old Rhesus macaque individual
Mml_16days_batch1

value: 16 days


title: Rhesus macaque - superior frontal gyrus - 16 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 16 days old Rhesus macaque individual
Mml_16days_batch2


title: 16131 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 16131 days old chimpanzee individual


title: Rhesus macaque - superior frontal gyrus - 1487 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 1487 days old Rhesus macaque individual
Mml_1487days_batch1

value: 1487 days


title: Rhesus macaque - superior frontal gyrus - 20 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 20 days old Rhesus macaque individual
Mml_20days_batch1

value: 20 days


title: 10220 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 10220 days old macaque individual

source_name: Dissected post-mortem macaque prefrontal cortex

value: 10220 days old


title: Rhesus macaque - superior frontal gyrus - 151 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 151 days old Rhesus macaque individual
Mml_151days_batch2

value: 151 days


title: Rhesus macaque - superior frontal gyrus - 1135 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 1135 days old Rhesus macaque individual
Mml_1135days_batch2

value: 1135 days