title: Ulcerative colitis repl10

city: Cincinnati

first: Lee

last: Denson

state: OH

address: 3333 Burnet Avenue

institute: CCHMC

description: gene expression data from human colon

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the human HG-U133 Plus 2.0 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8) , then normalized to the internal control for each batch and the mean of the healthy control reference samples.

source_name: human colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Plus Mini kit (QIAGEN, Hilden, Germany)

tag: ulcerative colitis replicate sample


title: DMSO-treated

status: Public on Mar 12 2009

type: RNA

city: Chicago

first: Atsushi

last: Kato

state: IL

address: 240 E. Huron St.

department: Allergy-Immunology Division

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Human peripheral blood-derived mast cells were sensitized with 1 ug/ml human myeloma IgE (Calbiochem) for 48 hours. After washing, the mast cells were preincubated with 1 uM DEX (dexamethasone), 0.1 uM FK506 or 0.01% DMSO for 1 hour and then stimulated with 1.5 ug/ml anti-IgE antibody (DakoCytomation, Denmark) for 6 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (Affymetrix) using Affymetrix default analysis settings. To normalize the variations in staining intensity among chips, the 'Average Difference' values for all genes on a given chip were divided by the median value for expression of all genes on the chip.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: Total RNA was extracted with RNeasy (Qiagen) and digested with DNase I (Qiagen) according to the manufacturer's instructions.

tag: cell type

value: peripheral blood-derived mast cells

tag: agent

value: treated with vehicle control DMSO


title: Low Early-Life SES Subject # 795

status: Public on Mar 11 2009

city: Vancouver

first: Gregory

middle: E

last: Miller

state: BC

address: 2136 W Mall

department: Psychology

country: Canada

institute: UBC

hyb_protocol: RNA was hybridized to Illumina HumanRef-8 v3.0 Expression Beadchips following manufacturer's instructions

scan_protocol: Chips were scanned on an Illumina Beadstation 500 at the McGill University and Génome Québec Innovation Centre.

data_processing: None - these are raw hybridization intensities, averaged across the 30 bead replicates, provided by Illumina Beadstudio

label: biotin

source_name: PBMC

label_protocol: Used the Illumina TotalPrep RNA  Amplification Kit following manufacturer's instructions

extract_protocol: PBMC were then homogenized in QiaShredder Spin Columns (Qiagen) and the lysates were frozen at -80° C until RNA was extracted using AllPrep DNA/RNA kits (Qiagen; Mississauga, ON).

treatment_protocol: Leukocytes were collected by antecubtial  venipuncture and PBMC were then isolated by density-gradient centrifugation

tag: socio-economic status

value: Low Early-Life SES

value: PBMC


title: High Early-Life SES Subject # 786

value: High Early-Life SES


title: High Early-Life SES Subject # 787


title: High Early-Life SES Subject # 773


title: High Early-Life SES Subject # 778


title: Low Early-Life SES Subject # 774


title: High Early-Life SES Subject # 770


title: Ulcerative colitis repl7

description: gene expression data from human colon


title: High Early-Life SES Subject # 772


title: Ulcerative colitis repl9

description: gene expression data from human colon


title: High Early-Life SES Subject # 768


title: High Early-Life SES Subject # 782


title: Ulcerative colitis repl8

description: gene expression data from human colon


title: High Early-Life SES Subject # 767


title: Ulcerative colitis repl3

description: gene expression data from human colon


title: High Early-Life SES Subject # 765


title: High Early-Life SES Subject # 763


title: Ulcerative colitis repl2

description: gene expression data from human colon


title: Ulcerative colitis repl6

description: gene expression data from human colon


title: Ulcerative colitis repl1

description: gene expression data from human colon


title: Low Early-Life SES Subject # 769


title: Ulcerative colitis repl4

description: gene expression data from human colon


title: Healthy control repl10

description: gene expression data from human colon

tag: healthy control replicate sample


title: High Early-Life SES Subject # 762


title: Ulcerative colitis repl5

description: gene expression data from human colon


title: Healthy control repl11

description: gene expression data from human colon


title: P06_0350U2H

status: Public on Mar 29 2009

city: Sunnyvale

first: Ljubomir

last: Buturovic

state: CA

address: 1196 Borregas Avenue

department: Application Development

institute: Pathwork Diagnostics

description: Metastatic malignant melanoma

hyb_protocol: Affymetrix GeneChip standard protocol

scan_protocol: Affymetrix GeneChip standard protocol

data_processing: Pathwork standardization (Dumur et al., JMD 2008, Vol. 10, No. 1)

source_name: Skin

label_protocol: Affymetrix GeneChip 1-cycle IVT labeling and cDNA synthesis kits

extract_protocol: Qiagen RNEasy kit

tag: Anatomical sites

value: Small Bowel

tag: gender

value: F

tag: age

tag: TNM


title: Healthy control repl8

description: gene expression data from human colon


title: Healthy control repl9

description: gene expression data from human colon


title: Low Early-Life SES Subject # 761


title: Healthy control repl7

description: gene expression data from human colon


title: High Early-Life SES Subject # 757


title: High Early-Life SES Subject # 758


title: Healthy control repl6

description: gene expression data from human colon


title: High Early-Life SES Subject # 752


title: Low Early-Life SES Subject # 756


title: Healthy control repl3

description: gene expression data from human colon


title: High Early-Life SES Subject # 750


title: Low Early-Life SES Subject # 754


title: Healthy control repl4

description: gene expression data from human colon


title: Internal control repl3

description: gene expression data from human colon

tag: internal control replicate sample


title: Low Early-Life SES Subject # 751


title: High Early-Life SES Subject # 744


title: Internal control repl5

description: gene expression data from human colon


title: Internal control repl4

description: gene expression data from human colon


title: Ileo-colonic CD repl18

description: gene expression data from human colon

tag: ileo-colonic crohn's disease replicate sample


title: Low Early-Life SES Subject # 749


title: Internal control repl2

description: gene expression data from human colon


title: Internal control repl1

description: gene expression data from human colon


title: Healthy control repl2

description: gene expression data from human colon


title: Low Early-Life SES Subject # 747


title: Low Early-Life SES Subject # 741


title: Low Early-Life SES Subject # 748


title: Healthy control repl1

description: gene expression data from human colon


title: Ileo-colonic CD repl17

description: gene expression data from human colon


title: Low Early-Life SES Subject # 738


title: High Early-Life SES Subject # 728


title: High Early-Life SES Subject # 726


title: Ileo-colonic CD repl15

description: gene expression data from human colon


title: High Early-Life SES Subject # 732


title: Low Early-Life SES Subject # 731


title: Ileo-colonic CD repl16

description: gene expression data from human colon


title: Low Early-Life SES Subject # 737


title: Healthy control repl5

description: gene expression data from human colon


title: High Early-Life SES Subject # 717


title: Low Early-Life SES Subject # 735


title: Low Early-Life SES Subject # 719


title: Ileo-colonic CD repl14

description: gene expression data from human colon


title: Ileo-colonic CD repl12

description: gene expression data from human colon


title: Ileo-colonic CD repl13

description: gene expression data from human colon


title: Ileo-colonic CD repl9

description: gene expression data from human colon


title: Low Early-Life SES Subject # 742


title: Ileo-colonic CD repl10

description: gene expression data from human colon


title: Ileo-colonic CD repl11

description: gene expression data from human colon


title: Low Early-Life SES Subject # 712


title: Ileo-colonic CD repl8

description: gene expression data from human colon


title: Low Early-Life SES Subject # 715


title: Ileo-colonic CD repl6

description: gene expression data from human colon


title: Ileo-colonic CD repl7

description: gene expression data from human colon


title: Low Early-Life SES Subject # 727


title: Low Early-Life SES Subject # 710


title: Ileo-colonic CD repl4

description: gene expression data from human colon


title: Ileo-colonic CD repl3

description: gene expression data from human colon


title: Ileo-colonic CD repl5

description: gene expression data from human colon


title: Ileo-colonic CD repl2

description: gene expression data from human colon


title: Ileo-colonic CD repl1

description: gene expression data from human colon


title: P7 vs P28, rep2

city: Dallas

first: Steve

last: Kernie

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Gene expression in P7 and P28 dentate gyrus neural progenitors. The P7 sample is the control.

hyb_protocol: Equal amounts of corresponding Cy3 and Cy5 labeled cDNAs were combined and hybridized overnight on topic-defined PIQOR Stem Cell Microarrays Mouse Antisense using the a-Hyb hybridization station (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

scan_protocol: Fluorescence signals of the hybridized PIQOR Microarray were detected using the laser scanner ScanArray Lite (PerkinElmer Life Sciences).  Mean signal and mean local background intensities were obtained for each spot of the micrarray images using the ImaGene software (Biodiscovery Inc). Spots located in areas in which hybridization artefacts (e.g. air bubbles) occur are flagged and excluded for further analysis. Since each gene is spotted on 4 different positions on the array, even if one or two spots are flagged, still sufficient replicates for valid data analysis remain on the slide.

data_processing:
Low quality spots were flagged and excluded for data analysis.  Unflagged spots were analyzed using the PIQOR Analyzer software (Miltenyi Biotec).  The PIQOR analyzer allows automated data processing of the raw data text files derived from the ImaGene software.  This includes background subtraction to obtain the net signal intensity, data normalization and calculation of the Cy5/Cy3 ratios.  As an additional quality filtering only those spots/genes are taken into account for the calculation of the Cy5/Cy3 ratio for which at least in one channel the signal intensity greater than 1 fold than the mean background. Data were Lowess-normalized.

The complete “ratio list of all genes” with all Cy5/Cy3 ratios and the respective coefficient of variation (CV, in %) is provided in the table (CV herein refers to the average of the expression ratios for 4 spot replicates. A "minus" % indicates that only 1 out of the 4 spots/gene could be evaluated and therefore no CV could be determined). To discriminate questionable results from relevant results in the ratio list, the cells in the output “ratio list table” of spots/genes having very low signal intensities (<1-fold above average signal intensities of negative controls in both channels Cy3 and Cy5) are blank.

molecule: polyA RNA

organism: Mus musculus

source_name: P7 neural progenitor

label_protocol: 250 ng of each cDNA was used as template for Cy3 and Cy5 labeling, which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: Samples were lysed using SuperAmp Lysis Buffer at 4 degrees and were shipped on dry ice to MiltenyiBiotec.

tag: strain

value: mix

source_name: P28 neural progenitor


title: Low Early-Life SES Subject # 708


title: High Early-Life SES Subject # 706


title: High Early-Life SES Subject # 707


title: P7 vs P28, rep1


title: Low Early-Life SES Subject # 702


title: P7 vs P28, rep3


title: High Early-Life SES Subject # 701


title: Low Early-Life SES Subject # 705


title: Colon-only CD repl13

description: gene expression data from human colon

tag: colon-only crohn's disease replicate sample


title: Colon-only CD repl11

description: gene expression data from human colon


title: Colon-only CD repl12

description: gene expression data from human colon


title: Colon-only CD repl7

description: gene expression data from human colon


title: Colon-only CD repl14

description: gene expression data from human colon


title: Colon-only CD repl9

description: gene expression data from human colon


title: Dll3tm1Rbe_9.5dpc_Somites_rep3

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

description: Target labeling, hybridization and data analysis carried out at the Children's Hospital of Philadelphia, PA.  Microarray data analysis carried out at the School of Life Sciences, Arizona State University, Tempe, AZ.

hyb_protocol: Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.

scan_protocol: Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value = 150.

data_processing: CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent).  CHP files were generated using MAS5.0.

source_name: somites, 9.5 dpc

label_protocol: Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).

extract_protocol: Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.

treatment_protocol: Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and the level corresponding to the recently-formed somite. The remainder of the embryo was cut at the level of the otic placode, and the heart and endodermal tissues removed to generate the somite level tissues, which was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.

value: 9.5 days post coitum embryo

tag: tissue

value: somite-level tissues

tag: genotype

value: Dll3-tm1Rbe/tm1Rbe or Dll3neo/neo


title: Colon-only CD repl10

description: gene expression data from human colon


title: Colon-only CD repl6

description: gene expression data from human colon


title: Dll3tm1Rbe_9.5dpc_Somites_rep1


title: Colon-only CD repl2

description: gene expression data from human colon


title: Colon-only CD repl4

description: gene expression data from human colon


title: Colon-only CD repl5

description: gene expression data from human colon


title: WT_9.5dpc_Somites_rep3

treatment_protocol: Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and most recently-formed somite. The remainder of the embryo was cut at the level of the otic placode, and the heart and endodermal tissues removed to generate the somite level tissues, which was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.

value: wild-type


title: WT_9.5dpc_Somites_rep1


title: Dll3tm1Rbe_9.5dpc_Somites_rep2


title: Balb/c KO1738

city: Columbus

first: Terry

last: Camerlengo

address: Biological Research Tower 12 ave

department: Biomedical Informatics

institute: Ohio State University

hyb_protocol: 18 hours overnight at 45C

scan_protocol: Genepix scanner/@10 microns with pmt of 650 and 100% power.

data_processing: Genepix to align GAL file to image. Values are F635 Median - background.

label: Biotinylated - random hexamer

source_name: Low density Bone Marrow cells

label_protocol: RT primer

extract_protocol: Trizol

value: Balb/c

value: low density bone marrow


title: Colon-only CD repl3

description: gene expression data from human colon


title: WT_9.5dpc_Somites_rep2


title: C57Bl/6 KO1267


title: Balb/c WT424


title: Colon-only CD repl1

description: gene expression data from human colon


title: Dll3tm1Rbe_9.5dpc_PSM_rep3

source_name: presomitic mesoderm 9.5 dpc

treatment_protocol: Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and the area corresponding to the most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.

value: presomitic mesoderm


title: Dll3tm1Rbe_9.5dpc_PSM_rep1


title: C57Bl/6 WT535


title: WT_9.5dpc_PSM_rep3

treatment_protocol: Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.


title: 95970 Sun1KO/WT-MEFs-2

city: Bethesda

first: Ya-Hui

last: Chi

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

hyb_protocol: Buffer (30 mM sodium citrate, 300 mM sodium chloride, 50% formamide, 0.4% SDS, pH 7.0) was held at 42 deg. C. Twelve ul was added to each sample along with 3 ul of 1:1 salmon sperm/tRNA blocker, heated for 2 min at 98 deg. C, centrifuged for 3 min at 14,000 x g, and then  20 ul was transferred into a microarray hybridization chamber (MAUI Mixer, Biomicro Systems).  After overnight hybridization at  45 deg. C, slides were inserted into a jig and submerged in Buffer A, comprised of 1X SSC and 0.05% SDS. The adhesive MAUI Mixer lid was removed and the slide placed in a rack in a jar containing fresh Buffer A. Once all slides were in the rack, they were agitated for 1 min, transferred to fresh Buffer A, agitated 2 min, transferred to Buffer B (0.1X SSC) for 2 min and then into fresh Buffer B. Slides were  centrifuged for 5 min starting at 220 rpm and increasing to 580 in increments of approximately 100 rpm. Once dry, the slides were removed from the centrifuge and scanned on a GenePix4000B Scanner (Axon Instrumets / Molecular Devices).

scan_protocol: Image analysis was performed using GenePix Pro software (version 5.1, Axon Instruments/Molecular Devices). Relative mRNA expression levels measured by each probe spot were estimated by using median pixel intensity minus the median background intensity. Log (base 2) transformation was applied to the Cy5/Cy3 ratios before further analysis. Arrays were normalized using the median spot intensity in each channel as a scaling factor.

data_processing: Feature pixel median minus background pixel median; Ratio set to missing where image analysis flag set to "absent" or "bad" or "not found." Normalization performed by subtracting array-median log2 ratio.

source_name: WT

label_protocol: RNA was labeled following the protocol of the Microarray Research Facility at the National Institute of Allergy and Infectious Diseases, including the addition of RNase inhibitor.  Briefly, for each sample, 25 ug of RNA were reverse-transcribed/labeled with Cy3, and 25 ug were reverse-transcribed/labeled with Cy5. Dyes were obtained from Amersham Biosciences; all other reagents were from Invitrogen.  Cy3- and Cy5- labeled samples were mixed and then concentrated in a Vivaspin 500 centrifigal concentrator (10,000 MW cut-off; Vivascience). 400 ul TE buffer was added (10 mM Tris, 1 mM EDTA, pH 8.0), and the samples were then centrifuged for 8 min at 12,000 x g. The flow-through was discarded and 400 ul fresh TE was added to each tube and mixed by pipette. These spinning and washing steps were repeated 3 more times, the sample transferred to a new Vivaspin 500, washed with TE buffer, and centrifuged twice more. The flow-through was again discarded, and sample was transferred to a fresh tube and its volume adjusted to 9 ul by adding TE or by vacuum centrifugation, as appropriate. Samples were then held on ice.

extract_protocol: RNA extracted using Trizol and purified with the RNeasy Mini-kit (Qiagen).

tag: day

value: E14.5  strain:WT Tissue:embryonic fibroblasts

value: E14.5  strain: Sun1 (-/-)  Tissue:embryonic fibroblasts


title: 95969 Sun1KO/WT-MEFs-1

department: National Institute of Allergy and Infectious Disease


title: 95974 Sun1KO/WT-MEFs-3


title: 95966 Sun1KO/WT-P9-7

value: P9  strain:WT Tissue:whole testes

value: P9  strain: Sun1 (-/-)  Tissue:whole testes


title: 95965 Sun1KO/WT-P9-6


title: C57Bl/6 KO2100


title: C57Bl/6 WT582


title: C57Bl/6 WT741


title: WT_9.5dpc_PSM_rep1


title: Ago-1 IP small RNAs from mouse brain

status: Public on Mar 10 2009

type: other

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: RNA species in the immunoprecipitations smaller than 500 bases were enriched with the mirVana miRNA isolation kit (Ambion, Austin, Texas, USA). The RNA sample was then separated on a denaturing 15% polyacrylamide (PAA) gel and stained with SYBRgreenII. The population of small RNA with a length of 19-29 bases was obtained by passive elution of the RNA from the gel. The eluted RNA was first poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the RNA. First-strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. The resulting cDNAs were then PCR-amplified to about 30 ng/ul using a high fidelity Taq DNA polymerase. The barcoded primers used for PCR amplification were designed for amplicon sequencing according to the instructions of 454 Live Sciences. The resulting cDNAs were obtained by fractionation on preparative 6% PAA-gels. cDNAs of the correct size were eluted, finally extracted with phenol/chloroform and precipitated with Ethanol. These gel-purified cDNAs were submitted to 454 sequencing.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: adapter sequences (ctATCGgaccttggctgtcactca and polyA) were trimmed and inserts longer than 18 nt were mapped to the mouse genome.

label: not applicable

molecule: other

source_name: Ago-1 IP small RNAs from mouse brain

label_protocol: not applicable

extract_protocol: Brain tissue was lysed with lysis buffer (2% Triton X-100 and Complete protease inhibitor cocktail (Roche) in PBS) for 30 min at 4oC. The high-speed supernatant was incubated with the antibody, after 4h protein G-Agarose beads were added. After an over night at 4oC the beads were washed 3x with 0.1% Triton X-100 in PBS.

tag: E14.5 mouse brain, IP with an anti-Ago-1 antibody (provided by Gunter Meister / Munich)


title: WT_9.5dpc_PSM_rep2


title: 95964 Sun1KO/WT-P9-5


title: 92384 SUN1KO/WT-P14-3

value: P14  strain:WT Tissue:whole testes

value: P14  strain: Sun1 (-/-)  Tissue:whole testes


title: OS25_3day-differentiation_rep1

city: Bron

first: Clémence

last: Kress

address: 18 avenue du Doyen Lépine

country: France

institute: INRAE, Inserm

description: No additional information

hyb_protocol: Equivalent amounts of cDNAs (1-2µg cDNA corresponding to about 100pmol of incorporated dye) from undifferentiated and differentiated cells labelled with a different dye were precipitated together with 10µg of salmon sperm DNA, 500µg of yeast tRNA and resuspended in 45µL of hybridization buffer (50% deionized formamide, 5x SSC, 5x Denhardt, 0.1% SDS). This hybridisation mix was denaturated for 8min at 94°C and pipetted onto the prewarmed microarray slide. Hybridisation was overnight under a 22x64 mm coverslip in a humid chamber floating in a 42°C waterbath. Slides were washed with gentle shaking as follow: 2x 5min in 2x SSC, 0.1% SDS at 42°C, 2x 5min in 0.2x SSC at room temperature, 2x 5min in 0.1x SSC at room temperature, 30s in 0.01x SSC at room temperature. Slides were dried by centrifugation 5min at 1000rpm at room temperature.

scan_protocol: Slides were scanned using the Genepix scanner (Axon Instruments).

data_processing: Analyzis was done with BlueFuse software (Cambridge BlueGnome). Bad spots (with high backgound or not correctly located by the software) were manually excluded before normalization. Normalization between the two channels was done by global Lowess to obtain the value of normalized Log2ratio (differentiated / undifferentiated cells cDNA).

source_name: OS25 ES cells, differentiated

label_protocol: 10µg of total RNA were reverse-transcribed using SuperScript Direct cDNA labeling kit (Invitrogen) to produce oligo dT primed cDNAs labeled with Cy3-dCTP (Amersham). cDNAs were purified with Qiagen PCR purification kit and checked and quantified with a Nanodrop ND-1000 spectrophotometer.

growth_protocol: OS25 ES cells were cultured as previously described (Chambeyron and Bickmore, 2004; Morey et al., 2007).

extract_protocol: Total RNA was extracted from cells with TriReagent (Sigma).

treatment_protocol: Differentiation was induced by plating the cells at low-density without LIF or hygromycin for 1 day. 5x10-6 M retinoic acid (RA) was then added for 2 days.

tag: cell line

source_name: OS25 ES cells, undifferentiated

label_protocol: 10µg of total RNA were reverse-transcribed using SuperScript Direct cDNA labeling kit (Invitrogen) to produce oligo dT primed cDNAs labeled with Cy5-dCTP (Amersham). cDNAs were purified with Qiagen PCR purification kit and checked and quantified with a Nanodrop ND-1000 spectrophotometer.

treatment_protocol: Cells were kept undifferentiated in the appropriate culture conditions (with LIF) as previously described.


title: 92383 SUN1KO/WT-P14-2


title: TRIM32 IP small RNAs from mouse brain

data_processing: adapter sequences (ctCAATgaccttggctgtcactca and polyA) were trimmed and inserts longer than 18 nt were mapped to the mouse genome.

source_name: TRIM32 IP small RNAs from mouse brain

tag: E14.5 mouse brain, IP with an anti-TRIM32 antibody.


title: OS25_3day-differentiation_rep2

description: No additional information

data_processing: Analyzis was done with BlueFuse software (Cambridge BlueGnome). Bad spots (with high backgound or not correctly located by the software) were manually excluded before normalization. Normalization between the two channels was done by global Lowess to obtain the value of normalized Log2ratio (undifferentiated /differentiated cells cDNA).


title: muscle_active_N04-113

city: FAIRBANKS

first: Anna

last: Goropashnaya

state: AK

address: 311 Irving I Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

description: skeleton muscle tissue from summer active black bear

hyb_protocol: The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Ursus americanus

source_name: skeleton muscle, summer active

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

tag: tissue type

value: skeleton muscle

value: male


title: muscle_active_N04-104


title: muscle_active_N03-152


title: muscle_active_N05-131


title: muscle_active_N05-132


title: muscle_active_N05-131_rep2


title: 92382 SUN1KO/WT-P14-1


title: muscle_hibernating_N07-027

description: skeleton muscle tissue from hibernating black bear

source_name: skeleton muscle, hibernating


title: total small RNAs from mouse brain

description: Small RNA were enriched with the mirVana miRNA isolation kit (Ambion, Austin, Texas, USA). The RNA sample was then separated on a denaturing 15% polyacrylamide (PAA) gel and stained with SYBRgreenII. The population of small RNA with a length of 19-29   bases was obtained by passive elution of the RNA from the gel. The eluted RNA was first poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5'-phosphate of the RNA. First-strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. The resulting cDNAs were then PCR-amplified to about 30 ng/ul using a high fidelity Taq DNA polymerase. The barcoded primers used for PCR amplification were designed for amplicon sequencing according to the instructions of 454 Live Sciences. The resulting cDNAs were obtained by fractionation on preparative 6% PAA-gels. cDNAs of the correct size were eluted, finally extracted with phenol/chloroform and precipitated with Ethanol. These gel-purified cDNAs were submitted to 454 sequencing.

data_processing: adapter sequences (ctACTAgaccttggctgtcactca and polyA) were trimmed and inserts longer than 18 nt were mapped to the mouse genome.

source_name: total small RNAs from mouse brain

extract_protocol: Brain tissue was lysed with lysis buffer (2% Triton X-100 and Complete protease inhibitor cocktail (Roche) in PBS) for 30 min at 4oC. Total RNA was isolated using the mirVana miRNA isolation kit (Ambion, Austin, Texas, USA).

tag: E14.5 mouse brain


title: control IP small RNAs from mouse brain

data_processing: adapter sequences (ctAGGTgaccttggctgtcactca and polyA) were trimmed and inserts longer than 18 nt were mapped to the mouse genome.

source_name: control IP small RNAs from mouse brain

tag: E14.5 mouse brain, IP with anti-TRIM32 antibody that was preincubated and thereby blocked with the antigenic TRIM32 peptide.


title: muscle_hibernating_N05-034_rep2


title: muscle_hibernating_N05-034


title: muscle_hibernating_N05-035


title: Dll3tm1Rbe_9.5dpc_PSM_rep2


title: liver_active_N05-132

description: liver tissue from summer active black bear

source_name: liver, summer active

value: liver


title: liver_active_N05-131_rep2


title: liver_active_N04-113


title: liver_active_N05-131


title: muscle_hibernating_N04-047


title: liver_active_N04-104_rep2


title: muscle_hibernating_N06-030


title: liver_hibernating_N05-034

description: liver tissue from hibernating black bear

source_name: liver, hibernating


title: liver_active_N04-104


title: liver_hibernating_N05-035


title: liver_hibernating_N07-027


title: liver_hibernating_N04-047_rep2


title: C57Bl/6 K01727


title: liver_hibernating_N04-047


title: liver_hibernating_N03-056


title: liver_active_N03-152


title: Human dorsolateral prefrontal cortex 47.4 years old, rep39

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 47.4 years old human individual

hyb_protocol: Hybridization to Affymetrix HG-U133 Plus 2.0 GeneChip arrays was carried out following standard Affymetrix protocols.

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. For summarizing the expression data, we used custom chip definition files (Custom CDF, v. 11) based on Ensembl gene annotation rather than Affymetrix annotation (Dai et al., PMID: 16284200). Further, we only accepted probes that perfectly matched both the human, the chimpanzee and the rhesus macaque genomes at a single location (hg18, panTro2, and rheMac2, respectively; see Khaitovich et al., PMID: 16141373), which correspond to 31% of probes on the microarray. Further, we did not include probesets with less than 8 probes in our analysis. The list of exluded probes is supplied as supplement to the CDF file. This list can be used in combination with the removeprobe function in the customCDF package (http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#CustomCDF) to create CDF environments with masked probes. We used the R Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters. Note that, for analyses of gene expression changes during postnatal development in humans and chimpanzees only, it is advisable to use CDF files masked for mismatches to the human and chimpanzee genomes, and for analyses involving humans only, to use non-masked CDF files. This is because masking out probes strongly decreases statistical power.

source_name: Dissected human post-mortem dorsolateral prefrontal cortex

label_protocol: Biotinylated cRNA were prepared from 1 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.

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). The majority of chimpanzees used in this study belonged to the Western chimpanzee population. Rhesus macaque samples were obtained from the German Primate Center (DPZ)(Goettingen, Germany). 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. The human prefrontal cortex samples were taken from the middle third of the middle frontal gyrus: a cortical region approximately corresponding to Brodmann area 46, and from the equivalent region in the non-human primates. For all samples special care was taken to dissect primarily grey matter (in the order of 90-95% of the total sample). The human caudate nucleus samples were taken from the central part of the nucleus in order to avoid any cross-contamination by adjacent brain structures. See publication for a more detailed description of the samples.

tag: sex

value: Male

value: dorsolateral prefrontal cortex of the brain


title: Human dorsolateral prefrontal cortex 75 years old, rep40

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 75 years old human individual


title: Human dorsolateral prefrontal cortex 42.9 years old, rep37

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 42.9 years old human individual


title: Human dorsolateral prefrontal cortex 77 years old, rep41

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 77 years old human individual

value: Female


title: Human dorsolateral prefrontal cortex 38.4 years old, rep36

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 38.4 years old human individual


title: Human dorsolateral prefrontal cortex 36 years old, rep35

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 36 years old human individual


title: liver_hibernating_N06-030_rep2

tag: gender


title: Human dorsolateral prefrontal cortex 25.4 years old, rep34

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 25.4 years old human individual

tag: age

value: 9262 days


title: Human dorsolateral prefrontal cortex 23.6 years old, rep32

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 23.6 years old human individual

value: 8623 days


title: Human dorsolateral prefrontal cortex 24.9 years old, rep33

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 24.9 years old human individual

value: 9098 days


title: Human dorsolateral prefrontal cortex 22.9 years old, rep31

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 22.9 years old human individual

value: 8364 days


title: Human dorsolateral prefrontal cortex 17.7 years old, rep27

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 17.7 years old human individual

value: 6456 days


title: Human dorsolateral prefrontal cortex 17.8 years old, rep28

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 17.8 years old human individual

value: 6505 days


title: Human dorsolateral prefrontal cortex 20.1 years old, rep29

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 20.1 years old human individual

value: 7350 days


title: Human dorsolateral prefrontal cortex 46.2 years old, rep38

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 46.2 years old human individual


title: Human dorsolateral prefrontal cortex 21.9 years old, rep30

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 21.9 years old human individual

value: 8006 days


title: Human dorsolateral prefrontal cortex 17 years old, rep26

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 17 years old human individual

value: 6222 days


title: 220 days after flowering R5+CK5_repeat2

city: Wuhan

first: Qing

last: Liu

address: Shizishan street NO.1

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

description: Identification of bud mutation-related genes in citrus fruits by suppression subtracted hybridization and microarray analysis

hyb_protocol: Cy5/Cy3-labeled cDNA were hybridized with the microarray at 42 °C overnight. Following hybridization, the arrays were washed with 0.2% SDS, 2×SSC at 42 °C for 5 min, and 0.2% SSC for 5 min at room temperature.

scan_protocol: Arrays were scanned with a confocal laser scanner, LuxScan™ 10K (CapitalBio Corp.)

data_processing: LOWESS

organism: Citrus sinensis

source_name: Anliu

label_protocol: An aliquot of 5 μg total RNA was used to produce Cy5-labled cDNA employing a RNA amplification combined with Klenow enzyme labeling strategy according to a previous published protocol(Guo et al., 2005)

extract_protocol: Total RNA was extracted from fruits following Liu et al.(2006). RNA degradation and quality were evaluated on 1.2% agarose gel and spectrophotometrically between 180 and 340 nm. Isolated RNA was treated with DNase I at 37°C for one hour to remove genomic DNA contamination.

tag: 220 days after flowering, the wild type

source_name: Hong Anliu

label_protocol: An aliquot of 5 μg total RNA was used to produce Cy3-labled cDNA employing a RNA amplification combined with Klenow enzyme labeling strategy according to a previous published protocol(Guo et al., 2005)

tag: 220 days after flowering, the mutant


title: Colon-only CD repl8

description: gene expression data from human colon

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Hs133P_Hs_REFSEQ_8) , then normalized to the internal control for each batch and the mean of the healthy control reference samples.

source_name: human colon


title: 220 days after flowering R5+CK5_repeat1

source_name: Hong anliu


title: Human dorsolateral prefrontal cortex 13 years old, rep24

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 13 years old human individual

value: 4733 days


title: Human dorsolateral prefrontal cortex 16.7 years old, rep25

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 16.7 years old human individual

value: 6090 days


title: 190 days after flowering R4+CK4_repeat2

tag: 190 days after flowering, the wild type

tag: 190 days after flowering, the mutant


title: 170 days after flowering R3+CK3_repeat2

tag: 170 days after flowering, the wild type

tag: 170 days after flowering, the mutant


title: 190 days after flowering R4+CK4_repeat1


title: RD_with_pK1_with_30nM4-OHT_rep3

city: Philadelphia

first: Frederic

last: Barr

state: PA

address: 422 Curie Blvd

institute: University of Pennsylvania

description: Embryonal Rhabdomyosarcoma cell line transduced with pK1 vector

scan_protocol: Standard protocol for Affymetrix GeneChip Human Genome U133A array performed in the Penn Microarray Facility using the Affymetrix GCS 2500 Scanner

data_processing: The scanned .CEL files were analyzed using Affymetrix GCOS software.  The .CHP files were generated using the MAS5 algorithm

source_name: RD cell line transduced with pK1 vector with 30nM 4-hydroxy-tamoxifen (4-OHT)

growth_protocol: DMEM with 10% FBS and 1% antibiotics

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: with 30nM 4-OHT treatment for 24 hours

value: Embryonal Rhabdomyosarcoma


title: RD_with_pK1_with_30nM4-OHT_rep2

hyb_protocol: Standard protocol for Affymetrix GeneChip Human Genome U133A array performed in the Penn Microarray Facility


title: RD_with_pK1_with_30nM4-OHT_rep1

label_protocol: Standard protocol for Affymetrix GeneChip Human Genome U133A array performed in the Penn Microarray Facility


title: 170 days after flowering R3+CK3_repeat1


title: 150 days after flowering R2+CK2_repeat2

tag: 150 days after flowering, the wild type

tag: 150 days after flowering, the mutant


title: Human dorsolateral prefrontal cortex 8 years old, rep20

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 8 years old human individual

value: 2920 days

tag: tissue


title: Human dorsolateral prefrontal cortex 11.5 years old, rep22

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 11.5 years old human individual

value: 4213 days


title: Human dorsolateral prefrontal cortex 8 years old, rep21


title: Human dorsolateral prefrontal cortex 4.6 years old, rep17

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 4.6 years old human individual

value: 1692 days

value: Male


title: Human dorsolateral prefrontal cortex 5.4 years old, rep19

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 5.4 years old human individual

value: 1969 days

value: dorsolateral prefrontal cortex of the brain


title: liver_hibernating_N06-030

description: liver tissue from hibernating black bear

value: liver

value: male


title: Human dorsolateral prefrontal cortex 4.9 years old, rep18

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 4.9 years old human individual

value: 1773 days


title: Human dorsolateral prefrontal cortex 2.7 years old, rep16

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 2.7 years old human individual

value: 990 days

value: Female


title: RD_with_pK1_without_4-OHT_rep3

source_name: RD cell line transduced with pK1 without 4-hydroxy-tamoxifen (4-OHT)

treatment_protocol: without 4-OHT treatment

tag: cell line


title: 120 days after flowering R1+CK1_repeat2

tag: 120 days after flowering, the wild type

tag: 120 days after flowering, the mutant


title: 150 days after flowering R2+CK2_repeat1


title: RD_with_pK1_without_4-OHT_rep2


title: Human dorsolateral prefrontal cortex 2.2 years old, rep14

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 2.2 years old human individual

value: 801 days


title: RD_with_pK1_without_4-OHT_rep1

source_name: RD cell line transduced with pK1 vector without 4-hydroxy-tamoxifen (4-OHT)


title: Human dorsolateral prefrontal cortex 2.4 years old, rep15

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 2.4 years old human individual

value: 893 days


title: 120 days after flowering R1+CK1_repeat1

tag: 120 days after flowering, the bud mutant


title: Human dorsolateral prefrontal cortex 0.9 years old, rep13

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.9 years old human individual

value: 332 days


title: Human dorsolateral prefrontal cortex 0.5 years old, rep10

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.5 years old human individual

value: 188 days


title: Human dorsolateral prefrontal cortex 0.8 years old, rep12

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.8 years old human individual

value: 301 days


title: Human dorsolateral prefrontal cortex 0.5 years old, rep11

value: 198 days


title: RD_with_PAX3-FKHR-ER_with_30nM4-OHT_rep2

description: Embryonal Rhabdomyosarcoma cell line transduced with PAX3-FKHR joined to the modified estrogen receptor ligand binding domain

source_name: RD cell line transduced with PAX3-FKHR-ER with 30nM 4-hydroxy-tamoxifen (4-OHT)

value: Embryonal Rhabdomyosarcoma


title: Human dorsolateral prefrontal cortex 0.4 years old, rep9

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.4 years old human individual

value: 141 days


title: Human dorsolateral prefrontal cortex 0.3 years old, rep7

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.3 years old human individual

value: 118 days


title: PLN_20w_5

city: Stanford

first: Keiichi

last: Kodama

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

description: PLN_20w_5; VALUE=LOG10(NOD/NOD.B10)

hyb_protocol: as described in In situ Hybridization kit-plus

scan_protocol: Agilent scanner, manufacturer's protocol

data_processing: Agilent Feature Extraction software 8.5

source_name: NOD

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Qiagen RNeasy

tag: tissue type

value: pancreatic lymph nodes

value: 20 weeks

tag: disease state

value: diabetic

value: control


title: PLN_20w_3

description: PLN_20w_3; VALUE=LOG10(NOD/NOD.B10)


title: Human dorsolateral prefrontal cortex 0.4 years old, rep8

value: 139 days

tag: sex

value: Male

value: dorsolateral prefrontal cortex of the brain


title: Human dorsolateral prefrontal cortex 0.3 years old, rep6

tag: age

value: 92 days

value: Female


title: RD_with_PAX3-FKHR-ER_with_30nM4-OHT_rep1


title: PLN_20w_2

description: PLN_20w_2; VALUE=LOG10(NOD/NOD.B10)


title: Human dorsolateral prefrontal cortex 0.2 years old, rep4

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.2 years old human individual

value: 62 days


title: Human dorsolateral prefrontal cortex 0.2 years old, rep5

value: 89 days


title: Human dorsolateral prefrontal cortex 0.2 years old, rep3

value: 56 days


title: Rhesus macaque-superior frontal gyrus-28 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 28 years old rhesus macaque individual

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols.

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 >1/3 of human or chimpanzee individuals. For further analysis, we mapped the transcript IDs to Ensemble Genes using the table provided at the Affymetrix support site (“http://www.affymetrix.com/analysis/downloads/na26/wtgene/HuGene-1_0-st-v1.na26.hg18.transcript.csv.zip”). For 127 expressed genes with multiple transcripts, we calculated the means across transcripts.

organism: Macaca mulatta

source_name: Dissected rhesus macaque post-mortem superior frontal gyrus

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

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: female

value: superior frontal gyrus of the brain


title: PLN_16w_6

description: PLN_16w_6; VALUE=LOG10(NOD/NOD.B10)

value: 16 weeks


title: Human dorsolateral prefrontal cortex 0.1 years old, rep1

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.1 years old human individual

value: 39 days


title: Human dorsolateral prefrontal cortex 0.1 years old, rep2

value: 54 days


title: PLN_20w_1

description: PLN_20w_1; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes


title: Rhesus macaque-superior frontal gyrus-26 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 26 years old rhesus macaque individual

value: 9518 days

value: male


title: PLN_20w_4

description: PLN_20w_4; VALUE=LOG10(NOD/NOD.B10)

value: 20 weeks

value: diabetic

value: control


title: RD_with_PAX3-FKHR-ER_with_30nM4-OHT_rep3

value: Embryonal Rhabdomyosarcoma


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

description: Gene expression data from post-mortem superior frontal gyrus of a 20 years old rhesus macaque individual

value: 7391 days


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

description: Gene expression data from post-mortem superior frontal gyrus of a 22 years old rhesus macaque individual

value: 8104 days


title: Mus spretus whole brain 56 days old, rep3

description: Gene expression data from the whole brain of a 56 days old Mus spretus individual

hyb_protocol: Hybridization to Affymetrix MG-430 2.0 GeneChip arrays was carried out following standard Affymetrix protocols.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. For summarizing the expression data, we used Custom Chip Definition Files (Custom CDF, version 11) based on Ensembl gene annotation rather than Affymetrix annotation (Dai et al., PMID: 16284200). Further, we masked out probes that which were estimated to show genotype differences between M.musculus and M.spretus, by employing a method which utilizes the discrepancy between the expression levels of pairs of probes within a probe set (e.g. see Khaitovich et al., PMID: 15289471). 19% of all probes are thus masked. Further, we did not include probesets with less than 8 probes in our analysis. The list of exluded probes is supplied as supplement to the CDF file. We used the R Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters. Note that, for analyses of gene expression changes during postnatal development within a single species, it is advisable to use non-masked CDF files. This is because masking out probes decreases statistical power.

organism: Mus spretus

source_name: Dissected Mus spretus whole brain

label_protocol: Biotinylated cRNA were prepared from 5 micrograms of total RNA following standard Affymetrix protocols.

growth_protocol: WSB/EiJ (Mus musculus) and SPRET/EiJ (Mus spretus) strain mice were purchased from the Jackson Laboratory (Bar Harbor, Maine, USA) and bred in at the MPI-EVA facility under standard conditions.

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

treatment_protocol: We dissected whole brains (excluding the ofactory bulb) of mice at three age stages: neonates within the first postnatal day, pups at 14 days of age, and adults at 56 days of age.

value: 56 days after birth

value: Male

value: whole brain


title: Mus spretus whole brain 14 days old, rep3

description: Gene expression data from the whole brain of a 14 days old Mus spretus individual

value: 14 days after birth


title: Mus spretus whole brain 56 days old, rep2


title: Rhesus macaque-superior frontal gyrus-9 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 9 years old rhesus macaque individual

value: 3389 days

value: superior frontal gyrus of the brain


title: PLN_16w_3

description: PLN_16w_3; VALUE=LOG10(NOD/NOD.B10)

value: 16 weeks


title: PLN_16w_5

description: PLN_16w_5; VALUE=LOG10(NOD/NOD.B10)


title: PLN_16w_4

description: PLN_16w_4; VALUE=LOG10(NOD/NOD.B10)


title: PLN_16w_2

description: PLN_16w_2; VALUE=LOG10(NOD/NOD.B10)


title: Rhesus macaque-superior frontal gyrus-0.8 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.8 years old rhesus macaque individual

value: 310 days


title: Mus spretus whole brain 56 days old, rep1


title: PLN_16w_1

description: PLN_16w_1; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes


title: Mus spretus whole brain 0 days old, rep2

description: Gene expression data from the whole brain of a 0 days old Mus spretus individual

value: 0 days after birth


title: Mus spretus whole brain 14 days old, rep1


title: iPS cells from episomal vectors (Defined Factor) DF19_3 (set of 16)

status: Public on Mar 27 2009

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s instructions.

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: IPS cells treated with episomal vectors

tag: cell type


title: Mus spretus whole brain 0 days old, rep3


title: Mus spretus whole brain 0 days old, rep1


title: Mus musculus whole brain 56 days old, rep3

description: Gene expression data from the whole brain of a 56 days old Mus musculus individual

source_name: Dissected Mus musculus whole brain


title: Rhesus macaque-superior frontal gyrus-0.1 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.1 years old rhesus macaque individual

value: 20 days

value: male


title: Mus musculus whole brain 56 days old, rep2


title: PLN_12w_6

description: PLN_12w_6; VALUE=LOG10(NOD/NOD.B10)

value: 12 weeks

value: diabetic


title: Mus musculus whole brain 14 days old, rep3

description: Gene expression data from the whole brain of a 14 days old Mus musculus individual


title: Rhesus macaque-superior frontal gyrus-16 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 0 years old rhesus macaque individual

value: 16 days


title: Mus musculus whole brain 56 days old, rep1


title: PLN_12w_5

description: PLN_12w_5; VALUE=LOG10(NOD/NOD.B10)

value: control


title: Chimpanzee-superior frontal gyrus-44 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 44 years old chimpanzee individual

organism: Pan troglodytes

source_name: Dissected chimpanzee post-mortem superior frontal gyrus

value: female


title: Mus musculus whole brain 14 days old, rep2


title: Mus musculus whole brain 0 days old, rep3

description: Gene expression data from the whole brain of a 0 days old Mus musculus individual


title: PLN_12w_4

description: PLN_12w_4; VALUE=LOG10(NOD/NOD.B10)


title: Mus musculus whole brain 14 days old, rep1


title: Chimpanzee-superior frontal gyrus-35 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 35 years old chimpanzee individual


title: Mus musculus whole brain 0 days old, rep1


title: RD_with_PAX3-FKHR-ER_without_4-OHT_rep3

description: Embryonal Rhabdomyosarcoma cell line transduced with PAX3-FKHR joined to the modified estrogen receptor ligand binding domain

source_name: RD cell line transduced with PAX3-FKHR-ER without 4-hydroxy-tamoxifen (4-OHT)

value: Embryonal Rhabdomyosarcoma


title: PLN_12w_3

description: PLN_12w_3; VALUE=LOG10(NOD/NOD.B10)


title: Human caudate nucleus 46.2 years old, rep13

description: Gene expression data from post-mortem caudate nucleus of a 46.2 years old human individual

source_name: Dissected human post-mortem caudate nucleus

value: Male

value: caudate nucleus of the brain


title: Mus musculus whole brain 0 days old, rep2

value: whole brain


title: Human caudate nucleus 38.6 years old, rep12

description: Gene expression data from post-mortem caudate nucleus of a 38.6 years old human individual


title: Chimpanzee-superior frontal gyrus-12 years old (2)

description: Gene expression data from post-mortem superior frontal gyrus of a 12 years old chimpanzee individual

value: 4480 days


title: Human caudate nucleus 25.4 years old, rep11

description: Gene expression data from post-mortem caudate nucleus of a 25.4 years old human individual

value: 9253 days

value: Female


title: Human caudate nucleus 24.9 years old, rep10

description: Gene expression data from post-mortem caudate nucleus of a 24.9 years old human individual

value: 9098 days


title: Chimpanzee-superior frontal gyrus-12 years old (1)

value: 4415 days

value: superior frontal gyrus of the brain


title: RD_with_PAX3-FKHR-ER_without_4-OHT_rep1


title: Human caudate nucleus 22.9 years old, rep9

description: Gene expression data from post-mortem caudate nucleus of a 22.9 years old human individual

value: 8364 days


title: PLN_12w_2

description: PLN_12w_2; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes


title: Human caudate nucleus 17.5 years old, rep8

description: Gene expression data from post-mortem caudate nucleus of a 17.5 years old human individual

value: 6384 days


title: PLN_12w_1

description: PLN_12w_1; VALUE=LOG10(NOD/NOD.B10)

value: 12 weeks

value: diabetic


title: Human caudate nucleus 17 years old, rep7

description: Gene expression data from post-mortem caudate nucleus of a 17 years old human individual

value: 6222 days


title: PLN_8w_4

description: PLN_8w_4; VALUE=LOG10(NOD/NOD.B10)

value: 8 weeks

value: control


title: PLN_12w_7

description: PLN_12w_7; VALUE=LOG10(NOD/NOD.B10)


title: Human caudate nucleus 12.4 years old, rep5

description: Gene expression data from post-mortem caudate nucleus of a 12.4 years old human individual

value: 4534 days

value: Male


title: Human caudate nucleus 2.4 years old, rep4

description: Gene expression data from post-mortem caudate nucleus of a 2.4 years old human individual

value: 893 days

value: caudate nucleus of the brain


title: Chimpanzee-superior frontal gyrus-0.1 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.1 years old chimpanzee individual

value: 39 days

value: male


title: Chimpanzee-superior frontal gyrus-6 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 6 years old chimpanzee individual

value: 2313 days

value: female


title: Human caudate nucleus 0.9 years old, rep3

description: Gene expression data from post-mortem caudate nucleus of a 0.9 years old human individual

value: 332 days


title: Human caudate nucleus 13 years old, rep6

description: Gene expression data from post-mortem caudate nucleus of a 13 years old human individual

value: 4738 days

value: Female


title: Chimpanzee-superior frontal gyrus-1 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 1 years old chimpanzee individual

value: 525 days

value: superior frontal gyrus of the brain


title: PLN_8w_3

description: PLN_8w_3; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes

value: diabetic


title: PLN_8w_2

description: PLN_8w_2; VALUE=LOG10(NOD/NOD.B10)

value: 8 weeks


title: PLN_8w_1

description: PLN_8w_1; VALUE=LOG10(NOD/NOD.B10)

value: control


title: Human dorsolateral prefrontal cortex 12.4 years old, rep23

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 12.4 years old human individual

value: 4534 days

value: dorsolateral prefrontal cortex of the brain


title: Human caudate nucleus 0.4 years old, rep1

description: Gene expression data from post-mortem caudate nucleus of a 0.4 years old human individual

value: 128 days

value: Male


title: Human caudate nucleus 0.4 years old, rep2

value: 141 days

value: caudate nucleus of the brain


title: Chimpanzee-superior frontal gyrus-1 day old

description: Gene expression data from post-mortem superior frontal gyrus of a 0 years old chimpanzee individual

value: 1 day


title: Rhesus macaque dorsolateral prefrontal cortex 17.9 years old, rep9

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 17.9 years old rhesus macaque individual

source_name: Dissected rhesus macaque post-mortem dorsolateral prefrontal cortex

value: 6524 days


title: Chimpanzee-superior frontal gyrus-8 days old

value: 8 days

value: male


title: PLN_4w_6

description: PLN_4w_6; VALUE=LOG10(NOD/NOD.B10)

value: 4 weeks


title: Rhesus macaque dorsolateral prefrontal cortex 17.1 years old, rep8

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 17.1 years old rhesus macaque individual

value: 6230 days

value: Female


title: Rhesus macaque dorsolateral prefrontal cortex 17.1 years old, rep7


title: Rhesus macaque dorsolateral prefrontal cortex 7.7 years old, rep5

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 7.7 years old rhesus macaque individual

value: 2816 days


title: PLN_4w_5

description: PLN_4w_5; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes

value: diabetic


title: Human-superior frontal gyrus-66 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 66 years old human individual

source_name: Dissected human post-mortem superior frontal gyrus

value: superior frontal gyrus of the brain


title: PLN_4w_4

description: PLN_4w_4; VALUE=LOG10(NOD/NOD.B10)

value: control


title: Rhesus macaque dorsolateral prefrontal cortex 7.7 years old, rep4

value: 2814 days

value: dorsolateral prefrontal cortex of the brain


title: Human-superior frontal gyrus-53 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 53 years old human individual


title: Rhesus macaque dorsolateral prefrontal cortex 3.5 years old, rep2

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 3.5 years old rhesus macaque individual

value: 1269 days

value: Male


title: Rhesus macaque dorsolateral prefrontal cortex 4.8 years old, rep3

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 4.8 years old rhesus macaque individual

value: 1760 days


title: Rhesus macaque dorsolateral prefrontal cortex 1.3 years old, rep1

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 1.3 years old rhesus macaque individual

value: 467 days


title: Human-superior frontal gyrus-14 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 14 years old human individual

value: 5105 days


title: Human-superior frontal gyrus-25 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 25 years old human individual

value: 9277 days


title: Chimpanzee dorsolateral prefrontal cortex 44.2 years old, rep14

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 44.2 years old chimpanzee individual

source_name: Dissected chimpanzee post-mortem dorsolateral prefrontal cortex


title: Rhesus macaque dorsolateral prefrontal cortex 13.4 years old, rep6

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 13.4 years old rhesus macaque individual

value: 4894 days


title: PLN_4w_1

description: PLN_4w_1; VALUE=LOG10(NOD/NOD.B10)

value: 4 weeks


title: Chimpanzee dorsolateral prefrontal cortex 35 years old, rep13

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 35 years old chimpanzee individual


title: PLN_4w_2

description: PLN_4w_2; VALUE=LOG10(NOD/NOD.B10)


title: Chimpanzee dorsolateral prefrontal cortex 12.3 years old, rep12

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 12.3 years old chimpanzee individual

value: 4480 days


title: Human-superior frontal gyrus-8 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 8 years old human individual

value: 2922 days

value: male


title: Rhesus macaque-superior frontal gyrus-0.4 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.4 years old rhesus macaque individual

value: 153 days


title: Chimpanzee dorsolateral prefrontal cortex 11.9 years old, rep10

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 11.9 years old chimpanzee individual

value: 4361 days


title: Chimpanzee dorsolateral prefrontal cortex 12.1 years old, rep11

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 12.1 years old chimpanzee individual

value: 4415 days


title: Chimpanzee dorsolateral prefrontal cortex 6.7 years old, rep9

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 6.7 years old chimpanzee individual

value: 2447 days


title: Human-superior frontal gyrus-0.6 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.6 years old human individual

value: 204 days

value: superior frontal gyrus of the brain


title: Human-superior frontal gyrus-0.1 years old

description: Gene expression data from post-mortem superior frontal gyrus of a 0.1 years old human individual

value: 34 days


title: PLN_10d_7

description: PLN_10d_7; VALUE=LOG10(NOD/NOD.B10)

value: pancreatic lymph nodes

value: 10 days

value: diabetic

value: control


title: Human-superior frontal gyrus-4 days old

description: Gene expression data from post-mortem superior frontal gyrus of a 0 years old human individual

value: 4 days


title: Chimpanzee dorsolateral prefrontal cortex 1.4 years old, rep7

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 1.4 years old chimpanzee individual

value: 525 days

value: Female

value: dorsolateral prefrontal cortex of the brain


title: Chimpanzee dorsolateral prefrontal cortex 0.5 years old, rep6

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.5 years old chimpanzee individual

value: 186 days

value: Male


title: Chimpanzee dorsolateral prefrontal cortex 0.1 years old, rep5

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0.1 years old chimpanzee individual

value: 45 days


title: Human-superior frontal gyrus-1 day old

value: 1 day

value: male


title: PLN_10d_2

description: PLN_10d_2; VALUE=LOG10(NOD/NOD.B10)


title: PLN_10d_4

description: PLN_10d_4; VALUE=LOG10(NOD/NOD.B10)


title: PLN_10d_6

description: PLN_10d_6; VALUE=LOG10(NOD/NOD.B10)


title: PLN_10d_5

description: PLN_10d_5; VALUE=LOG10(NOD/NOD.B10)


title: Mus spretus whole brain 14 days old, rep2

description: Gene expression data from the whole brain of a 14 days old Mus spretus individual

value: 14 days after birth

value: whole brain


title: WGACON-216 (relatedness outlier by IBS PLINK MDS examination)

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

description: Human Cortex from neurologically normal control, Caucasian, male.

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract, log10 transformation before analysis

source_name: neuropathologically normal frozen temporal parietal cortex

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)


title: Chimpanzee dorsolateral prefrontal cortex 0 years old, rep2

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 0 years old chimpanzee individual

value: 1 days


title: WGACON-194 (ethnicity outlier by Structure examination)

description: Human Cortex from neurologically normal control, Caucasian, female.

source_name: neuropathologically normal frozen temporal cortex


title: Chimpanzee dorsolateral prefrontal cortex 0 years old, rep3

value: 8 days


title: Chimpanzee dorsolateral prefrontal cortex 0.1 years old, rep4

value: 40 days


title: Chimpanzee dorsolateral prefrontal cortex 0 years old, rep1

value: 0 days


title: Human dorsolateral prefrontal cortex 83 years old, rep44

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 83 years old human individual

source_name: Dissected human post-mortem dorsolateral prefrontal cortex


title: Cercariae differentially expressed gene compare to adult worm 1

city: shanghai

first: yuan

last: chunxiu

institute: shanghai research institute of domestic animal parasitolgy

description:
Adult worm were obtained by perfusion of the hepatic portal system of infected rabbits (7 weeks post-infection), and cercariae were released from infected snails and concentrated by centrifugation.Adult worm and cercariae were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from adult worm RNA and cercariae RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = adult worm
Keywords = cercariae
Keywords = differentially expressed gene

organism: Schistosoma japonicum

source_name: Adult worm

source_name: Cercariae


title: WGACON-185 (ethnicity outlier by Structure examination)

source_name: neuropathologically normal frozen frontal cortex


title: Cercariae differentially expressed gene compare to egg 1

description:
Egg were recovered from infected liver of rabbits (7 weeks post-infection), and and cercariae were released from infected snails and concentrated by centrifugation.Egg and cercariae were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from egg RNA and cercariae RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray4000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = egg
Keywords = cercariae
Keywords = differentially expressed gene

source_name: Egg


title: 20 day sporocysts (conditioned)

type: SAGE

anchor: NlaIII

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

description: Recombinant pGEM3Z clones produced by SAGE were purified using GeneMachines RevPrep Orbit (San Carlos, CA) and were sequenced on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster City, CA).

data_processing: Sequences collected were analyzed with software created for SAGE analysis.  The SAGE software extracts ditag sequences from the ABI 3730xl results according to the SAGE sequence grammar, parses out individual SAGE tags, excludes tags with sequence ambiguities, and reduces all SAGE tags to a table of unique SAGE tag sequences and their observed frequencies.  Multiple instances of ditag sequences were ignored in the data processing – only a single instance contributed to tag frequencies.

organism: Schistosoma mansoni

source_name: Schistosoma mansoni 20 day sporocysts, conditioned

growth_protocol: Schistosoma mansoni (NMRI strain) eggs were recovered from the livers of mice at 7-8 weeks post-infection as described by Yoshino and Laursen (J Parasitol 1995, 81:714-22).  Miracidia were hatched from the eggs in sterile artificial pond water and concentrated on ice in conical polypropylene centrifuge tubes.  Cold-immobilized miracidia were either centrifuged for 1 min at 500 g and immediately harvested for total RNA or were transferred to a 24-well culture plate to permit transformation into primary sporocysts followed by culturing for 6 or 20 days under normoic conditions at 26°C in either S. mansoni sporocyst medium (SM; Proc Natl Acad Sci 1999, 96:4965-70) or SM conditioned with Biomphalaria glabrata embryonic (Bge) cells.

extract_protocol: RNA was extracted using TRIZOL.

treatment_protocol: Conditioned SM was used in these larval SAGE studies to determine the effect of snail-derived components on sporocyst gene expression. Media were changed in both the control and conditioned wells of sporocysts at two-day intervals.  At 6d and 20d developmental time points total RNA was isolated from all cultured sporocysts (6d control, 6d conditioned, 20d control and 20d conditioned).

tag: Strain

value: NMRI


title: Human dorsolateral prefrontal cortex 81 years old, rep43

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 81 years old human individual


title: 20 day sporocysts (unconditioned)

source_name: Schistosoma mansoni 20 day sporocysts, unconditioned


title: WGACON-149 (relatedness outlier by IBS PLINK MDS examination)


title: Egg differentially expressed gene compare to adult worm 1

description:
Egg were recovered from infected liver of rabbits (7 weeks post-infection), and adult worm were obtained by perfusion of the hepatic portal system of infected rabbits. Egg and adult worm were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from Egg RNA and adult worm RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from adult worm were labeled with Cy3-dUTP and those from egg with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = egg
Keywords = adult worm
Keywords = differentially expressed gene


title: WGACON-107 (relatedness outlier by IBS PLINK MDS examination)


title: Cercariae differentially expressed gene compare to egg


title: PLN_10d_1

description: PLN_10d_1; VALUE=LOG(NOD/NOD.B10)

source_name: NOD

value: pancreatic lymph nodes

value: 10 days

value: diabetic

value: control


title: Schistosoma japonicum adult worm 1

description:
Egg were recovered from infected liver of rabbits (7 weeks post-infection), and adult worm were obtained by perfusion of the hepatic portal system of infected rabbits, and a part of mixed-sex worm were separated manually to get male.Egg and male worm were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from male worm RNA and egg RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = male
Keywords = egg
Keywords = differentially expressed gene

source_name: Male


title: Human dorsolateral prefrontal cortex 78 years old, rep42

description: Gene expression data from post-mortem dorsolateral prefrontal cortex of a 78 years old human individual

value: dorsolateral prefrontal cortex of the brain


title: 6 day sporocysts (conditioned)

source_name: Schistosoma mansoni 6 day sporocysts, conditioned


title: WGACON-101 (relatedness outlier by IBS PLINK MDS examination)


title: 6 day sporocysts (unconditioned)

source_name: Schistosoma mansoni 6 day sporocysts, unconditioned


title: WGACON-66 (ethnicity outlier by Structure examination)


title: PLN_10d_3

description: PLN_10d_3; VALUE=LOG10(NOD/NOD.B10)


title: SWR/J SWR-J_88-9

status: Public on Mar 09 2009

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: Hematopoietic stem/progenitor cells

hyb_protocol: The samples were applied to MouseWG-6 v1.1 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity. (See manuscript)

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader. (See manuscript)

data_processing: quantile normalization

label_protocol: IVT (see manuscript)

extract_protocol: Trizol LS

tag: Hematopoietic stem/progenitor cells


title: PL/J PL-J_118-9

description: Hematopoietic stem/progenitor cells


title: SJL/J SJL_J_124-5

description: Hematopoietic stem/progenitor cells


title: NZB/BlNJ NZB-B1NJ_62-3

description: Hematopoietic stem/progenitor cells


title: SJL/J SJL_J_134-5

description: Hematopoietic stem/progenitor cells


title: NZB/BlNJ NZB-B1NJ_64-5

description: Hematopoietic stem/progenitor cells


title: Miracidia

source_name: Schistosoma mansoni miracidia


title: WGACON-2 (relatedness outlier by IBS PLINK MDS examination)


title: NZB/BlNJ NZB-B1NJ_66-7

description: Hematopoietic stem/progenitor cells


title: Male differentilly expressed gene compare to egg

description:
Egg and male worm were ground into a fine powder in a 10 cm ceramic mortar (RNase-free).  Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China).  After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase.  The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from male worm RNA and egg RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP.  The two color probes were then mixed and diluted to 500uL with TE, and concentrated using  Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr.  Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass.  Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature.Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3  median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69.  Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis.
Keywords = male
Keywords = egg
Keywords = differentially expressed gene


title: SWR/J SWR-J_140-1

description: Hematopoietic stem/progenitor cells


title: PL/J PL-J_102-3

description: Hematopoietic stem/progenitor cells


title: PL/J PL-J_110-1

description: Hematopoietic stem/progenitor cells


title: SWR/J SWR-J_28-9

description: Hematopoietic stem/progenitor cells


title: NOD/LtJ NOD-ShiltJ_98-9

description: Hematopoietic stem/progenitor cells


title: NOD/LtJ NOD-ShiltJ_112-3

description: Hematopoietic stem/progenitor cells


title: LG/J LG-J_58-9

description: Hematopoietic stem/progenitor cells


title: LG/J LG-J_60-1

description: Hematopoietic stem/progenitor cells


title: LG/J LG-J_76-77

description: Hematopoietic stem/progenitor cells


title: KK/HlJ KK_H1J_56-7

description: Hematopoietic stem/progenitor cells


title: FVB/NJ FVB-NJ_16-7

description: Hematopoietic stem/progenitor cells


title: FVB/NJ FVB-NJ_20-1

description: Hematopoietic stem/progenitor cells


title: DBA/2J DBA2-J_130-1

description: Hematopoietic stem/progenitor cells


title: FVB/NJ FVB-NJ_18-9

description: Hematopoietic stem/progenitor cells


title: C58/J C58_J_158-9

description: Hematopoietic stem/progenitor cells


title: DBA/2J DBA2-J_126-7

description: Hematopoietic stem/progenitor cells