title: proNGF-KR 4h /untreated (2)

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: PC12 cells were treated for 4h with 20 ng/ml of furin-cleavage resistant proNGF-KR

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 825 ng of Cyanine 3-labelled and 825 ng of Cyanine 5-labelled cRNA per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit with the 4X44K whole rat genome chip (G4131F). After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitrile for one minute at room temperature.

scan_protocol: Chips were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1) and the GE2-v4_91 extraction protocol.

data_processing:
The signal values used for the subsequent analysis (for both channels) are median feature signals, non background substracted, and corrected using multiple detrending. Microsoft Excel software was used to filter out unreliable features (essentially features with expression values smaller than background + 3 Standard deviations of the background) and to perform the dye swap normalization. Agilent GeneSpring GX Software (v 7.3) was used for the LOWESS normalization. To select differentially expressed genes, up- and down-regulated features were selected both from the dye-swap normalized data and from the LOWESS normalized data, then these two sets were intersected.
VALUE in Sample Tabe below represents LOWESS normalized Log2 ratio (Cy5/Cy3, treated/untreated) for each single sample. Only filtered features were normalized.

organism: Rattus norvegicus

source_name: Rat pheochromocytoma PC12 cells, SB subclone

label_protocol: 500ng of Poly A+RNA were labelled, using Cyanine 3-CTP or Cyanine 5-CTP (Perkin Elmer) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns

growth_protocol: Rat pheochromocytoma PC12 cells (Greene and Tischler, 1976) (PC12 SB subclone) were maintained with RPMI 1640 Medium (InVitrogen) and grown as monolayer cultures on Falcon dishes, supplemented with 10% Horse Serum (InVitrogen) and 5% Foetal Calf Serum (Invitrogen), in a humidified atmosphere at 37° C and 5% CO2.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions.

treatment_protocol: For differentiation, PC12 cells were plated at a concentration of 10E6/dish (100mm plates, BD Falcon) and kept in culture for 12 hours. For microarray mRNA expression analysis, half volume of medium was replaced with fresh medium and the naive PC12 cells were treated for 1h or 4h with 10ng/ml NGF, 20ng/ml of wild type proNGF-WT or 20 ng/ml of furin-cleavage resistant proNGF-KR. A negative control with no neurotrophin addition was performed.

tag: treatment group

value: Untreated cells

tag: developmental stage

value: Differentiating cells

tag: tissue

value: Rat pheochromocytoma

value: PC12 + proNGF-KR 4h


title: 46.d0

status: Public on Jan 09 2012

type: protein

city: Irvine

first: David

middle: Huw

last: Davies

state: CA

address: Med Surge II

department: Medicine

country: USA

institute: University of California Irvine

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

hyb_protocol: Human sera were used at 1/100 dilution in protein array blocking buffer (Whatman) containing E. coli lysate (Antigen Discovery Inc, Irvine CA) to a final concentration of 10mg/ml protein to block anti-E. coli antibodies.   Sera were preincubated at RT for 30 minutes with constant mixing prior to applying to the arrays in triplicate and incubating overnight at 4oC with gentle agitation.   After washing in TBS + 0.05% Tween 20% (T-TBS), biotinylated anti-human IgG (Jackson) was used as secondary antibody followed after washing in T-TBS by streptavidin-PBXL3 conjugate (Martek Biosciences), both at 1/200 in blocking buffer.

scan_protocol: After washing five times, slides were air dried by brief centrifugation and then scanned and analyzed using a Perkin Elmer ScanArray Express HT microarray scanner (PerkinElmer).   Fluorescence intensities were quantified from tiff images by using ProScanArray Express software (PerkinElmer).

data_processing: Data analysis was performed using the R (http://www.r-project.org) statistical software.   In order to stabilize the variance observed in microarray signals, the vsn normalization was implemented as part of the Bioconductor suite (www.bioconductor.org) to the quantified array intensities using the 'no DNA' spots (IVTT reactions lacking the template DNA) as normalization controls.  Inter-group comparisons were performed using a Bayes regularized t-test adapted from Cyber-T for protein arrays (Baldi and Hatfield, 2002; Baldi and Long, 2001).    To account for multiple comparison conditions, p-values were corrected by the Benjamini and Hochberg (pBH) method  to control the false discovery rate (Benjamini and Hochberg, 1995).    After correction, p-values < 0.05 were considered significant.  An individual was defined as a responder if the ratio of retransformed signal intensities before and after DVX vaccination (d28/d0) was >2.0 for 2 or more of 6 signature antigens (WR101/H3L, WR113/D8L, WR148, WR150/A27L, WR070/I1L, and WR118/D13L).  Seroprevalence rates on d0 and d28 were determined for each antigen based on a cut off defined as the averaged+2SD of the naïve take population (n=50).   Individuals positive for one or more of the 6 signature antigens were considered seropositive.

label: biotin

molecule: protein

organism: Homo sapiens

source_name: serum

label_protocol: Biotinylated anti-human IgG (Jackson) was used as secondary antibody followed after washing in T-TBS by streptavidin-PBXL3 conjugate (Martek Biosciences), both at 1/200 in blocking buffer.

extract_protocol: serum samples

tag: donor id

tag: vaccination status

value: naïve

tag: skin take

value: yes

tag: nih clinical trial #

tag: time

tag: vaccine type

value: DVX

tag: vaccine dilution

value: Undiluted Dryvax


title: proNGF-KR 4h /untreated (1)

type: RNA

country: Italy

molecule: total RNA


title: 45.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W88.R

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Liver sample at the time of rejection  BX.W88.R

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: Liver biopsy sample

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

growth_protocol: Liver sample at the time of rejection

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: liver sample group

value: Non-TOL REJ

tag: demographic origin center

value: Hospital Clinic


title: Liver biopsy sample :Non-TOL member: BX.W41.P

description: Liver biopsy before immunosuppressive therapy BX.W41.P

value: Non-TOL


title: 47.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W89.R

description: Liver sample at the time of rejection  BX.W89.R


title: 44.d0


title: proNGF 4h /untreated (2)

description: PC12 cells were treated for 4h with 20ng/ml of wild type proNGF-WT

value: PC12 + proNGF 4h


title: proNGF 4h /untreated (1)


title: Liver biopsy sample :Non-TOL member: BX.W83.P

description: Liver biopsy before immunosuppressive therapy BX.W83.P


title: 41.d0


title: 42.d0


title: NGF 4h /untreated (1)

description: PC12 cells treated for 4h with 10ng/ml NGF

value: PC12 + NGF 4h


title: NGF 4h /untreated (2)


title: proNGF-KR 1h /untreated (2)

description: PC12 cells were treated for 1h with 20 ng/ml of furin-cleavage resistant proNGF-KR

value: PC12 + proNGF-KR 1h


title: 39.d0


title: 38.d0


title: 43.d0


title: 37.d0


title: 35.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W15.R

description: Liver sample at the time of rejection  BX.W15.R


title: 36.d0


title: proNGF-WT 1h /untreated (2)

description: PC12 cells were treated for 1h with 20ng/ml of wild type proNGF-WT

value: PC12 + proNGF-WT 1h


title: Liver biopsy sample :TOL member: BX.W111.P

description: Liver biopsy before immunosuppressive therapy BX.W111.P

value: TOL


title: proNGF-WT 1h /untreated (1)


title: Liver biopsy sample :Non-TOL member: BX.W12.P

description: Liver biopsy before immunosuppressive therapy BX.W12.P


title: Liver biopsy sample :TOL member: BX.W113.P

description: Liver biopsy before immunosuppressive therapy BX.W113.P


title: NGF 1h /untreated (2)

description: PC12 cells treated for 1h with 10ng/ml NGF

value: PC12 + NGF 1h


title: proNGF-KR 1h /untreated (1)

value: Untreated cells


title: 33.d0


title: Liver biopsy sample :TOL member: BX.W10.P

description: Liver biopsy before immunosuppressive therapy BX.W10.P


title: 40.d0


title: Liver biopsy sample :Non-TOL REJ member: BX.W81.R

description: Liver sample at the time of rejection  BX.W81.R


title: Liver biopsy sample :TOL member: BX.W8.P

description: Liver biopsy before immunosuppressive therapy BX.W8.P


title: 34.d0

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.


title: Liver biopsy sample :TOL member: BX.W20.P

description: Liver biopsy before immunosuppressive therapy BX.W20.P


title: Liver biopsy sample :Non-TOL REJ member: BX.W12.R

description: Liver sample at the time of rejection  BX.W12.R


title: untreated /untreated

description: untreated PC12 cells

value: Differentiating cells

value: untreated cells


title: 32.d0


title: NGF 1h /untreated (1)

value: Rat pheochromocytoma


title: 31.d0

value: naïve


title: 30.d0

value: yes


title: Liver biopsy sample :TOL member: BX.W4.P

description: Liver biopsy before immunosuppressive therapy BX.W4.P


title: 29.d0

value: DVX


title: Liver biopsy sample :Cont-Tx member: BX.P23.AVA

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P23.AVA

value: Cont-Tx


title: 28.d0

value: Undiluted Dryvax


title: 26.d0


title: 25.d0


title: 23.d28

value: no

value: APSV

value: 1:5 dilution


title: 27.d0


title: 20.d28

value: 1:32 dilution


title: 22.d28


title: 21.d28

value: 1:10 dilution


title: 24.d0


title: 19.d28

value: 1:100 dilution


title: Liver biopsy sample :Cont-Tx member: BX.P22.AND

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P22.AND

value: Hospital Clinic


title: 18.d28


title: 17.d28


title: Liver biopsy sample :Cont-Tx member: BX.P17.MOR

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P17.MOR


title: 15.d28


title: Liver biopsy sample :HEPC member: BX.P16.SAL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P16.SAL

value: HEPC


title: Liver biopsy sample :HEPC member: BX.P15.MEL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P15.MEL


title: Liver biopsy sample :REJ member: BX.P12.TAL7

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P12.TAL7

value: REJ


title: 16.d28

value: 1:3.2 dilution


title: 14.d28


title: Liver biopsy sample :REJ member: BX.P10.BUI

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P10.BUI


title: 13.d28


title: 12.d28


title: 11.d28


title: 10.d28


title: Liver biopsy sample :REJ member: BX.P14.RUB

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P14.RUB


title: Liver biopsy sample :HEPC member: BX.P4.BAL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P4.BAL


title: 9.d28

value: undiluted


title: Liver biopsy sample :HEPC member: BX.P9.MON

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P9.MON


title: 7.d28


title: 6.d28

value: Undiluted


title: Liver biopsy sample :Cont-Tx member: BX.P21.ASB

description: liver sample from transplant recipient under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation BX.P21.ASB


title: 8.d28

value: naïve


title: Liver biopsy sample :REJ member: BX.P2.RAM

description: liver sample with typical acute cellular rejection taking place during the immediate post-transplant period  BX.P2.RAM


title: PFC R control 4

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

description: Gene expression data from the Pre-Frontal cortex of naïve AChE-R mice

hyb_protocol: Microarray procedures followed manufacturer’s instructions. Each array was hybridized with pooled RNA from 3-4 mice, except for one of the TgS MPTP injected groups, containing tissue from only two mice.

scan_protocol: The microarrays were scanned using GeneChip® Scanner 3000.

data_processing: The probe sets were summarized with Affymetrix Power Tools (APT) through Expression Console (EC) using RMA.

organism: Mus musculus

source_name: Pre-Frontal cortex of naïve AChE-R mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNA was extracted from frozen CPu and PFC using the RNeasy lipid tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, with DNAse treatment.

treatment_protocol: Transgenic strains and MPTP Exposure experiment: all experiments were carried out in accordance with the Animal Care and Use Committee of the Hebrew University of Jerusalem (approval # MD-80.03-3), and the Safety Regulations of the Hebrew University. Na\357ere employed in 4 different experiments. These included the parent strain FVB/N, TgS (transgenic mice expressing the human AChE-S variant) and TgR (transgenic mice expressing human AChE-R) mice, whose brain regions before and after exposure were used for microarray and qRT-PCR analyses. Mice were kept on a 12h dark/12h light diurnal schedule. MPTP-HCl (Sigma, Rehovot, Israel) was dissolved in saline and injected in four doses of 20mg/Kg at 2h intervals for a cumulative dose of 80 mg/Kg. We injected 6 mice from each of the three strains with saline and 6 mice with MPTP, a total of 36 mice (Protocol 1). 4 days after injection, mice were decapitated following Isoflurane (Rhodia, Bristol, UK) anaesthesia, and CPu and PFC were dissected on ice and immediately stored at -80 C for subsequent tests. Brain sections: For histology, left hemispheres were dissected on ice and immediately transferred to 4% PBS-Paraformaldehyde (pH 7.4) for at least 72 hours prior to sectioning. Paraffin-embedded blocks were prepared, and coronal sections of 7um thickness were made on SuperFrost\256enzel-Glaser, Germany). Striatal sections were made in the rostral to caudal direction, starting at Bregma +1.1 coordinates.

tag: treatment

tag: transgenic variant

value: AChE-R

value: Pre-Frontal Cortex

tag: genetic background

value: FVB/N


title: 4.d28

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

value: DVX


title: Liver biopsy sample :HEPC member: BX.P1.DEL

description: liver sample with chronic hepatitis due to recurrent hepatitis C virus infection  BX.P1.DEL


title: Liver biopsy sample :Non-TOL member: BX.W106.P

description: Liver biopsy before immunosuppressive therapy BX.W106.P

value: Non-TOL

value: University Tor Vergata Rome


title: Liver biopsy sample :Non-TOL member: BX.W104.P

description: Liver biopsy before immunosuppressive therapy BX.W104.P


title: PFC S control 4

description: Gene expression data from the Pre-Frontal cortex of naïve AChE-S mice

source_name: Pre-Frontal cortex of naïve AChE-S mice

value: AChE-S


title: 3.d28

value: no


title: Liver biopsy sample :Non-TOL member: BX.W75.P

description: Liver biopsy before immunosuppressive therapy BX.W75.P


title: 5.d28


title: 1.d28

value: 1:10 dilution


title: PFC S control 3


title: Liver biopsy sample :Non-TOL member: BX.W71.P

description: Liver biopsy before immunosuppressive therapy BX.W71.P

value: University Hospitals Leuven


title: PD4S3

description: PD patient post-DBS off stimulation

hyb_protocol: Samples were hybridized using Affymetrix® hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GCOS and Expression Console software tools. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized. RMA signal estimates from Expression Console version 1_1_2 are provided in the data table.
probe group file: probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Blood leukocytes, PD patient, post-DBS off stimulation

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix® GeneChip® WT Terminal Labeling Kit

extract_protocol: Venous blood samples (9ml) were collected (9ml blood into 4.5 ml EDTA (anti-coagulant) tubes). The blood was filtered within up to 10 minutes using the LeukoLock fractionation and stabilization kitTM (Ambion, Applied Biosystems, Inc., Foster City, CA). These filters allow immediate separation of leukocytes. Separated leukocytes were immediately incubated in RNALater (Ambion) for RNA protection (in http://www.affymetrix.com/support/technical/technotes/blood_technote.pdf). Stabilized filters were kept at room temperature up to 12 hours and stored at -80⁰C. An aliquote of each serum sample was stored at -80⁰C (within 12 hours post collection). RNA extraction followed the LeukoLock manufacturers’ alternative protocol instructions. Briefly, cells were flushed from the filter using TRI-Reagent TM (Ambion) into 1-Bromo-3-chloropropane (BCP)-containing 15ml tubes, shaken (30 seconds), stored (room temperature) and centrifuged to acquire the aqueous phase. For RNA extraction, water and ethanol were added at 0.5 and 1.25 volume. Samples were filtered through spin cartridges using centrifugation and were stored in pre-heated (80 ⁰C) 150 µl of EDTA. RNA integrity, concentration and purity were assessed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). None of the samples included RNA degradation products or DNA contamination. RNA immediately stored at -80 ⁰C until microarray hybridization.

tag: gender

value: male

value: Blood leukocytes

tag: disease stage

value: post-DBS off stimulation


title: 23.d0

value: APSV

value: 1:5 dilution


title: PFC FVB/N control 3

description: Gene expression data from the Pre-Frontal cortex of naïve FVB/N mice

source_name: Pre-Frontal cortex of naïve FVB/N mice


title: PFC R control 3


title: PD7S2

description: PD patient post-DBS on stimulation

source_name: Blood leukocytes, PD patient, post-DBS on stimulation

value: post-DBS on stimulation


title: PD7S3

description: PD patient post-DBS off stimulation


title: PFC FVB/N control 4

value: naïve


title: CPU R MPTP 1

description: Gene expression data from the Caudate-Putamen of MPTP-exposed AChE-R mice

value: MPTP

value: AChE-R

value: Caudate-Putamen


title: 22.d0


title: 21.d0

value: DVX


title: PD6S3

description: PD patient post-DBS off stimulation


title: Liver biopsy sample :Non-TOL member: BX.W22.P

description: Liver biopsy before immunosuppressive therapy BX.W22.P

value: Non-TOL

value: Hospital Clinic


title: CPU R control 2

description: Gene expression data from the Caudate-Putamen of naive AChE-R mice

source_name: Caudate-Putamen of naive AChE-R mice

value: FVB/N


title: HC3

description: Healthy control

source_name: Blood leukocytes, Healthy control

value: healthy control


title: CPU R control 1


title: Liver biopsy sample :Non-TOL REJ member: BX.W19.R

description: Liver sample at the time of rejection  BX.W19.R

value: Non-TOL REJ


title: Liver biopsy sample :Non-TOL member: BX.W70.P

description: Liver biopsy before immunosuppressive therapy BX.W70.P

value: University Hospitals Leuven


title: HC5

description: Healthy control

source_name: Blood leukocytes, healthy control

value: male


title: Liver biopsy sample :Non-TOL member: BX.W85.P

description: Liver biopsy before immunosuppressive therapy BX.W85.P


title: PD5S1

description: PD patient pre-DBS

source_name: Blood leukocytes, PD patient, pre-DBS

value: Blood leukocytes

value: pre-DBS


title: PD7S1

description: PD patient pre-DBS


title: Liver biopsy sample :Non-TOL member: BX.W81.P

description: Liver biopsy before immunosuppressive therapy BX.W81.P


title: 20.d0

value: no

value: APSV

value: 1:32 dilution


title: HC6

description: Healthy control


title: 18.d0

value: naïve

value: 1:100 dilution


title: 19.d0


title: HC2

description: Healthy control


title: 2.d28

value: Undiluted


title: CPU S MPTP 2

description: Gene expression data from the Caudate-Putamen of MPTP-exposed AChE-S mice

value: MPTP

value: AChE-S

value: Caudate-Putamen


title: Liver biopsy sample :Non-TOL member: BX.W40.P

description: Liver biopsy before immunosuppressive therapy BX.W40.P

value: Non-TOL

value: Hospital Clinic


title: CPU S control 2

description: Gene expression data from the Caudate-Putamen of naive AChE-S mice

source_name: Caudate-Putamen of naive AChE-S mice

value: FVB/N


title: 16.d0

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

value: 1:3.2 dilution


title: Liver biopsy sample :Non-TOL REJ member: BX.W66.R

description: Liver sample at the time of rejection  BX.W66.R

value: Non-TOL REJ


title: 17.d0

value: DVX


title: PD6S2

description: PD patient post-DBS on stimulation

value: male

value: Blood leukocytes

value: post-DBS on stimulation


title: PD5S2

description: PD patient post-DBS on stimulation


title: HC4

description: Healthy control

value: healthy control


title: CPU S control 1


title: Liver biopsy sample :Non-TOL REJ member: BX.W21.R

description: Liver sample at the time of rejection  BX.W21.R


title: CPU FVB/N MPTP 2

description: Gene expression data from the Caudate-Putamen of MPTP-exposed FVB/N mice


title: 14.d0

value: no

value: APSV

value: 1:32 dilution


title: PD6S1

description: PD patient pre-DBS

value: pre-DBS


title: CPU S MPTP 1

source_name: Caudate-Putamen of MPTP-exposed AChE-S mice

value: MPTP


title: PD3S3

description: PD patient post-DBS off stimulation

value: post-DBS off stimulation


title: E9.5 MafF-/-: MafG+/+: MafK-/- embryos (no.3)

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in E9.5 MafF-/-: MafG+/+: MafK-/- embryos  in mixed background

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Agilent Feature Extraction Software

source_name: E9.5 MafF-/-: MafG+/+: MafK-/- whole embryos

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole embryos using Isogen (Nippon Gene).

tag: genotype

value: whole embryo


title: CPU FVB/N MPTP 1

source_name: Caudate-Putamen of MPTP-exposed FVB/N mice

value: Caudate-Putamen


title: Liver biopsy sample :Non-TOL member: BX.W21.P

description: Liver biopsy before immunosuppressive therapy BX.W21.P

value: Non-TOL

value: Hospital Clinic


title: CPU FVB/N control 2

source_name: Caudate-Putamen of naive FVB/N mice

value: naïve

value: FVB/N


title: 13.d0

value: DVX

value: 1:100 dilution


title: 15.d0


title: Liver biopsy sample :Non-TOL member: BX.W6.P

description: Liver biopsy before immunosuppressive therapy BX.W6.P


title: PD4S2

description: PD patient post-DBS on stimulation

value: male

value: Blood leukocytes


title: E10.5 MafF-/-: MafG+/+: MafK-/- embryos  (no.2)

description: Gene expression in E10.5 MafF-/-: MafG+/+: MafK-/- embryos  in mixed background

source_name: E10.5 MafF-/-: MafG+/+: MafK-/- whole embryos

tag: developmental stage


title: Liver biopsy sample :Non-TOL member: BX.W15.P

description: Liver biopsy before immunosuppressive therapy BX.W15.P


title: 12.d0

source_name: serum


title: PD3S1

description: PD patient pre-DBS

tag: tissue


title: Liver biopsy sample :Non-TOL REJ member: BX.W2.R

description: Liver sample at the time of rejection  BX.W2.R

source_name: Liver biopsy sample

value: Non-TOL REJ


title: CPU FVB/N control 1

description: Gene expression data from the Caudate-Putamen of naive FVB/N mice


title: E10.5 MafF-/-: MafG-/-: MafK-/- embryos (no.1)

description: Gene expression in E10.5 MafF-/-: MafG-/-: MafK-/- embryos in mixed background

source_name: E10.5 MafF-/-: MafG-/-: MafK-/- whole embryos


title: 11.d0

tag: donor id

value: no

value: 1:10 dilution


title: PFC S MPTP 2

description: Gene expression data from the Pre-Frontal contex of MPTP-exposed AChE-S mice

value: AChE-S

value: Pre-Frontal Cortex


title: Liver biopsy sample :TOL member: BX.W87.P

description: Liver biopsy before immunosuppressive therapy BX.W87.P

value: TOL


title: Liver biopsy sample :TOL member: BX.W129.P

description: Liver biopsy before immunosuppressive therapy BX.W129.P


title: 10.d0

tag: vaccination status

value: APSV


title: PD4S1

description: PD patient pre-DBS

value: pre-DBS


title: PD2S1

description: PD patient pre-DBS


title: 9.d0

tag: skin take

value: undiluted


title: PD5S3

description: PD patient post-DBS off stimulation

value: post-DBS off stimulation


title: PFC S MPTP 1

source_name: Pre-Frontal contex of MPTP-exposed AChE-S mice

value: MPTP


title: 8.d0

value: naïve

tag: nih clinical trial #


title: PFC R MPTP 2

description: Gene expression data from the Pre-Frontal contex of MPTP-exposed AChE-R mice

value: AChE-R

value: FVB/N


title: 7.d0

tag: time

value: DVX


title: PFC R MPTP 1

source_name: Pre-Frontal contex of MPTP-exposed AChE-R mice


title: Liver biopsy sample :TOL member: BX.W63.P

description: Liver biopsy before immunosuppressive therapy BX.W63.P

value: Hospital Clinic


title: Liver biopsy sample :TOL member: BX.W18.P

description: Liver biopsy before immunosuppressive therapy BX.W18.P


title: PFC FVB/N MPTP 2

description: Gene expression data from the Pre-Frontal contex of MPTP-exposed FVB/N mice


title: PD2S3

description: PD patient post-DBS off stimulation

source_name: Blood leukocytes, PD patient, post-DBS off stimulation

value: male

value: Blood leukocytes


title: Liver biopsy sample :TOL member: BX.W64.P

description: Liver biopsy before immunosuppressive therapy BX.W64.P


title: Trim33-KD-SB-2

city: New York

first: Qiaoran

last: Xi

state: NY

address: 1275, York ave.

department: Cancer biology and genetics

institute: MSKCC

description: Gene expression data from differentiated mouse ESCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Differentially expressed genes were identified using a Bayes model Implemented by the limma package of R.

source_name: Ebs at Day2.5 were treated with SB431542 for 2 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ebs were set up by growing mouse ESCs in medium without LIF in ultra-low attachment dishes.

extract_protocol: preEase RNA spin kit.

treatment_protocol: The Ebs at Day 2.5 were treated with Activin(50ng/ml) or 10 mM SB431542.

tag: strain

tag: cell type

value: EBs

tag: genotype/variation


title: Liver biopsy sample :TOL member: BX.W9.P

description: Liver biopsy before immunosuppressive therapy BX.W9.P

tag: liver sample group

tag: demographic origin center


title: PFC FVB/N MPTP 1

source_name: Pre-Frontal contex of MPTP-exposed FVB/N mice

tag: treatment

tag: transgenic variant


title: Trim33-KD-ac-2

source_name: Ebs at Day2.5 were treated with Activin for 2 h


title: Smad4-null-ac-2


title: WT-SB-2

value: WT


title: 5.d0

description:
References:
Baldi, P., and Hatfield, G.W. (2002). DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press
Baldi, P., and Long, A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289--300.
Hermanson, G., Chun, S., Felgner, J., Tan, X., Pablo, J., Nakajima-Sasaki, R., Molina, D.M., Felgner, P.L., Liang, X., and Davies, D.H. (2011). Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax((R)) using proteome microarrays and development of recombinant protein ELISAs. Vaccine 30, 614-625.
Long, A.D., Mangalam, H.J., Chan, B.Y., Tolleri, L., Hatfield, G.W., and Baldi, P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276, 19937-19944.

value: no

tag: vaccine type

tag: vaccine dilution

value: Undiluted


title: Liver biopsy sample :TOL member: BX.W58.P

description: Liver biopsy before immunosuppressive therapy BX.W58.P

value: TOL

value: University Tor Vergata Rome


title: PFC R control 2

description: Gene expression data from the Pre-Frontal contex of naïve AChE-R mice

source_name: Pre-Frontal contex of naïve AChE-R mice

value: Pre-Frontal Cortex

tag: genetic background


title: 6.d0


title: Smad4-null-SB-2


title: WT-ac-2


title: PD1S3

description: PD patient post-DBS off stimulation

tag: gender

tag: disease stage


title: Liver biopsy sample :TOL member: BX.W39.P

description: Liver biopsy before immunosuppressive therapy BX.W39.P


title: PFC R control 1

tag: tissue


title: PD1S2

description: PD patient post-DBS on stimulation

source_name: Blood leukocytes, PD patient, post-DBS on stimulation

value: post-DBS on stimulation


title: Smad4-null-SB-1


title: HC1

description: Healthy control

source_name: Blood leukocytes, Healthy control

value: healthy control


title: 3.d0

tag: donor id

tag: vaccination status

value: 1:10 dilution


title: PD3S2

description: PD patient post-DBS on stimulation


title: Smad4-null-ac-1


title: PFC FVB/N control 2

description: Gene expression data from the Pre-Frontal contex of naïve FVB/N mice

source_name: Pre-Frontal contex of naïve FVB/N mice

value: naïve


title: 1.d0

tag: skin take

tag: nih clinical trial #


title: PD2S2

description: PD patient post-DBS on stimulation


title: PFC FVB/N control 1


title: Liver biopsy sample :TOL member: BX.W14.P

description: Liver biopsy before immunosuppressive therapy BX.W14.P


title: PFC S control 1

description: Gene expression data from the Pre-Frontal contex of naïve AChE-S mice

source_name: Pre-Frontal contex of naïve AChE-S mice

value: AChE-S


title: Trim33-KD-ac-1

tag: strain


title: PFC S control 2

value: FVB/N


title: PD1S1

description: PD patient pre-DBS

source_name: Blood leukocytes, PD patient, pre-DBS

value: pre-DBS


title: Liver biopsy sample :TOL member: BX.W1.P

description: Liver biopsy before immunosuppressive therapy BX.W1.P

value: Hospital Clinic


title: WT-ac-1

tag: cell type


title: WT-SB-1

tag: genotype/variation


title: Liver biopsy sample :TOL member: BX.W3.P

description: Liver biopsy before immunosuppressive therapy BX.W3.P

tag: liver sample group


title: Trim33-KD-SB-1


title: G9a knockdown cells, rep3

status: Public on Jan 07 2012

city: Lexington

first: Binhua

middle: P

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

description: Gene expression array of less metastatic breast tumor cell line.

hyb_protocol: Hybridization was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

scan_protocol: Scanning was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

data_processing: Data processing was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

label: Biotin

source_name: MDA-MB231 cells, G9a knockdown

label_protocol: Labeling was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

growth_protocol: Cells were grown in DMEM/F12 plus 10%FBS in 5%CO2 at 37C. Cells were trypsinized and harvested when in log-growth phase.

extract_protocol: Total RNA was extracted from cells using the Qiagen RNA purification kit following the manfacturer's protocol.

tag: cell line

value: G9a knockdown

value: less metastatic breast cancer cells


title: G9a knockdown cells, rep1

institute: University of Kentucky School of Medicine

tag: treatment


title: Control cells, rep3

description: Gene expression array of metastatic breast tumor cell line.

source_name: MDA-MB231 cells, control

value: metastatic breast cancer cells


title: 4.d0

source_name: serum

tag: time

value: DVX


title: G9a knockdown cells, rep2


title: Control cells, rep1


title: Control cells, rep2


title: NSCB_CGH1018036_FTi20_p9

type: genomic

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

hyb_protocol: Step 1. Prepare the Samples 1. Set the Hybridization System to 42°C. With the cover closed, allow at least 3 hours for the temperature to stabilize. 2. Resuspend the dried sample pellet in 3.3 ul Sample Tracking Control. Use a unique STC to resuspend each sample to be hybridized. Record which STC is used for each sample. If you are not using Sample Tracking Controls, resuspend the dried sample pellet in the equivalent volume of water. 3. Vortex well and spin to collect contents in bottom of the tube. 4. Using components from a NimbleGen Hybridization Kit, prepare the hybridization solution master mix - 88.5 ul of 2x Hybridization Buffer (vial 1), 35.4 ul of  Hybridization Component A (vial 2), 3.6 ul of Alignment Oligo (vial 3).  The amount listed is sufficient to hybridize all arrays on one slide. To hybridize multiple slides, adjust the amounts accordingly. 5. Add 8.7 ul of hybridization solution to each sample pair. 6. Vortex well (approximately 15 seconds) and spin to collect contents in bottom of the tube. Incubate at 95°C for 5 minutes, protected from light. 7. Place tubes at 42°C (in the Hybridization System sample block or heat block) for at least 5 minutes or until ready for sample loading. Vortex and spin prior to loading. Step 2. Prepare Mixers 1. Locate an HX12 mixer. Remove from its package. For best results, use a compressed gas nozzle to gently blow compressed nitrogen or argon gas across the mixer and slide to remove any dust or debris. The use of canned aerosol compressed air for this purpose is not recommended and could compromise array and data quality. Load samples within 30 minutes of opening the vacuum-packaged mixer to prevent the formation of bubbles during loading and/or hybridization. 2. Position the Precision Mixer Alignment Tool (PMAT) with its hinge on the left. Open the PMAT. 3. Snap the mixer onto the two alignment pins on the lid of the PMAT with the tab end of the mixer toward the inside hinge and the mixer’s adhesive gasket facing outward. 4. While pushing back the plastic spring with a thumb, place the slide in the base of the PMAT so that the barcode is on the right and the corner of the slide sits against the plastic spring. The NimbleGen logo and barcode number should be readable. Remove your thumb and make sure the spring is engaging the corner of the slide and the entire slide is registered to the edge of the PMAT to the rightmost and closest to you. In addition, be sure that the slide is lying flat against the PMAT. Gently blow compressed nitrogen or argon gas across the mixer and slide to remove dust. Take care to align the slide correctly in the PMAT. Incorrectly aligned slides may result in inaccurate attachment of the mixer and may affect the array features, or may not fit well into the Mixer Disassembly Tool used to remove the mixers after hybridization. 5. Using forceps, remove the backing from the adhesive gasket of the mixer and close the lid of the PMAT so that the gasket makes contact with the slide. 6. Lift the lid by grasping the long edges of the PMAT while simultaneously applying pressure with a finger through the window in the lid of the PMAT to free the mixer-slide assembly from the alignment pins. 7. Remove the mixer-slide assembly from the PMAT. 8. Place the mixer-slide assembly on the back of a 42°C heating block for 5 minutes to facilitate adhesion of the mixer to the slide. 9. Rub the Mixer Brayer over the mixer with moderate pressure to adhere the adhesive gasket and remove any bubbles. For HX12 mixers, first use a corner of the Mixer Brayer to rub the borders between the arrays and then rub around the outside of the arrays. The adhesive gasket will become clear when fully adhered to both surfaces. 10. Place the mixer-slide assembly in the slide bay of the Hybridization System. Step 3. Load & Hybridize Samples 1. Keep the following in mind before loading sample: • When pipetting the sample before loading, leave residual volume in the sample tube to avoid introducing bubbles. The volumes listed in the table below allow for this residual volume. • After aspirating the designated sample volume, inspect the pipette tip for air bubbles. Dispense and reload the pipette if bubbles exist. Keep the following in mind when loading sample: • Keep the pipette tip perpendicular to the slide to avoid possible leakage at the fill port. • Apply gentle pressure of the tip into the port to ensure a tight seal while loading the sample. 2. Using the appropriate Gilson Microman pipette, slowly dispense the appropriate sample volume into the fill port. Load samples and seal mixer ports as described below for each array format: •For 12x135K arrays: a. Load 6 ul using a CP10 Pipette tip into a fill port. Due to the close proximity of the fill and vent ports, do not overfill the arrays. Load sample until it enters the vent port channel. Do not allow sample to come to the surface of the HX12 mixer. Dry any overflow from the fill and vent ports with a cotton swab after loading the array. It is not unusual for small bubbles to form in the corners of the mixer-slide assembly during loading. These bubbles will dissipate upon mixing and will not compromise the data. b. Use one mixer port seal to cover both the fill and vent ports on the mixers, filling and sealing one chamber at a time. Press the mixer port seal, using uniform pressure across the seal to adhere. Mixer port seals are now used to seal fill and vent ports on HX12 mixers instead of mixer multi-port seals. c. Use forceps to press the mixer port seal around the fill and vent ports to ensure it is adhered in those areas. 4. Close the bay clamp. 5. Turn on the Mixing Panel on the Hybridization System, set the mix mode to B, and press the mix button to start mixing. Confirm that the Hybridization System recognizes the slide in each occupied bay (its indicator light becomes green). 6. Approximately 10 minutes after starting the Hybridization System: • Ensure the mix mode is set to B. • Ensure a green light is displayed for all occupied stations. 7. Hybridize sample at 42°C to the array(s) for the following incubation times: • For  12x135K arrays: 40 - 72 hours Roche NimbleGen has found that longer hybridization times result in higher signal-to-noise ratios, which may be beneficial for some experiments. 7.11. Array Washing 7.11.1. Turn on GenePix 4000B to warm up lasers prior to beginning wash procedure. 7.11.2. Disassemble and wash arrays according to NimbleGen™ Arrays User Guide (CGHv Analysis v5.0) with the following exceptions: 7.11.2.1. Heat both Wash Buffer I solutions to 42ºC. 7.11.2.2. Agitate array in Wash Buffer I for 3 minutes. 7.11.2.3. Follow 1 minute agitation in Wash Buffer 2 with a 2 minute incubation. 7.11.3. Perform washes protecting arrays from light and ozone. 7.11.4. Place array in corresponding case and wrap case in aluminum foil. 7.11.4.1. Label with CGH number. 7.11.5. Scan arrays immediately after washing (ref: SOP-CH-309). 7.12. Array Storage 7.12.1. Store scanned arrays in the dessicator.

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction: NimbleScan provided by NimbleGen is used to extract signal data from image files (*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization: Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification: Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization: CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

molecule: genomic DNA

label_protocol:
7.7. Labeling
7.7.1. Cy3/Cy5 Labeling
7.7.1.1. Verify that the DNA concentration is between 25 and 30ng/ul for all test and reference samples.
7.7.1.2. Thaw the Cy3/Cy5 random nonamers on ice, protected from light.
7.7.1.3. Add 1μg of sonicated test DNA to 40 μl Cy3 dye. Bring to volume in 80 μl VWR water. Repeat for all test samples to be labeled.
7.7.1.4. Add 1 μg of sonicated reference DNA to 40 μl Cy5 dye. Bring to volume in 80 μl VWR water. Repeat for all reference samples to be labeled.
7.7.1.5. Vortex and quickly centrifuge test and reference DNA samples.
7.7.1.6. Incubate samples for 10 minutes at 98ºC protecting from light.
7.7.1.7. Rapidly transfer samples to an ice-water bath for 5 minutes protecting from light.
7.7.1.8. Prepare 20μl of the following aha-dNTP/Klenow Master Mix for each test and reference sample.
7.7.1.8.1. aha-dNTP/Klenow Master Mix per Sample
7.7.1.8.1.1. Thaw all reagents and aha-dNTP/Klenow master mix on ice.
7.7.1.8.1.2. Add 9μl VWR water to 0.2ml PCR tube.
7.7.1.8.1.3. Add 10μl 50X aha-dNTP Mix.
7.7.1.8.1.4. Add 1μl Klenow (50U/μl). DO NOT vortex. Total amount of solution is 20μl.
7.7.1.9. Add 20μl of the aha-dNTP/Klenow Master Mix to each of the cooled samples. Keep on ice.
7.7.1.10. Pipette to mix (15 times). DO NOT vortex.
7.7.1.11. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.12. Incubate the samples for 2 hours 15 minutes at 37°C in thermocycler protected from light.
7.7.1.13. Remove samples from thermocycler, keep at room temperature. Heat thermocycler to 98ºC. Place samples back into thermocycler and incubate for 10 minutes at 98ºC.
7.7.1.14. Rapidly transfer samples to an ice-water bath for 5 minutes protecting samples from light.
7.7.1.15. Add 1 μl of Klenow (50U/μl) to each sample.
7.7.1.16. Pipette to mix (15 times). DO NOT vortex.
7.7.1.17. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.18. Place samples in thermocycler at 37ºC for overnight amplification.
7.7.2. First DNA Precipitation
7.7.2.1. Set Roche Nimblegen Hybridization System 12 to 48ºC if proceeding to hybridization in the same day to allow for at least 3 hours of stabilization.
7.7.2.2. Cool centrifuge to 4ºC.
7.7.2.3. Add 10μl of 0.5M EDTA to each sample to stop the overnight amplification reaction.
7.7.2.4. Add 11.5 μl of 5M NaCl to each sample, then vortex for 10 seconds.
7.7.2.5. Briefly centrifuge samples using a tabletop centrifuge.
7.7.2.6. Transfer each sample into a 1.5ml tube containing 200 μl of isopropanol.
7.7.2.7. Vortex samples for 20 seconds.
7.7.2.8. Incubate at room temperature for 10 minutes, protected from light.
7.7.2.9. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.2.10. Aspirate supernatant.
7.7.2.11. Rinse pellet with 500μl of 80% ice-cold ethanol. As you rinse, gently wash pellet from tube wall.
7.7.2.12. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.2.13. Aspirate supernatant.
7.7.2.14. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.2.15. Proceed to Alexa Fluor Labeling or store labeled samples at -20°C, protected from light.
7.7.2.15.1. Frozen samples are stable for up to 2 weeks at -20ºC.
7.7.3. Alexa Fluor Labeling
7.7.3.1. Thaw one vial of Alexa Fluor 555 dye per Cy3-labeled test DNA sample on ice. Keep protected from light.
7.7.3.2. Thaw one vial of Alexa Fluor 647 dye per Cy5-labeled reference DNA sample on ice. Keep protected from light.
7.7.3.3. Thaw Alexa Fluor Labeling Buffer on ice.
7.7.3.4. Add 5 μl VWR water to each DNA sample.
7.7.3.5. Place samples in thermocycler at 42ºC for 5 minutes.
7.7.3.6. Add 3 μl Labeling Buffer to each DNA sample.
7.7.3.7. Vortex and quickly centrifuge DNA samples.
7.7.3.8. Add 2 μl DMSO to one of the vials of Alexa Fluor dye (either 555 or 647).
7.7.3.9. Vortex for 10 seconds to dissolve Alexa Fluor dye.
7.7.3.10. Immediately add 8 μl of corresponding DNA to the dissolved dye.
7.7.3.11. Pipette up and down to further dissolve dye pellet, replace lid and vortex briefly to mix.
7.7.3.12. Incubate at room temperature, protected from light for 1 hour.
7.7.3.13. Repeat steps 7.7.3.8.-7.7.3.12 for each Cy-labeled DNA to be labeled with Alexa Fluor dyes.
7.7.4. Second DNA Precipitation
7.7.4.1. Add 100 μl VWR water to each labeled DNA sample.
7.7.4.2. Add 11.5 μl of 5M NaCl to each sample.
7.7.4.3. Vortex for 10 seconds.
7.7.4.4. Briefly centrifuge samples using a tabletop centrifuge.
7.7.4.5. Transfer each sample into 1.5ml tubes containing 200 μl each of isopropanol.
7.7.4.6. Vortex samples for 20 seconds.
7.7.4.7. Incubate at room temperature for 10 minutes, protected from light.
7.7.4.8. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.4.9. Aspirate supernatant.
7.7.4.10. Add 500μl of 80% ice-cold ethanol to the pellet and gently wash pellet from tube wall by pipetting.
7.7.4.11. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.4.12. Aspirate supernatant.
7.7.4.13. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.4.14. Proceed to ‘Specific Activity Calculation’ or store labeled samples at -20°C, protected from light. Frozen samples are stable for up to 2 weeks at -20ºC.

extract_protocol:
1. Cells arrived pelleted and frozen in 1.5mL microcentrifuge tubes, which were stored at -80C until extraction.
2. Thaw samples in 37C waterbath for ~5 min. until completely thawed.
3. Resuspend pellet in PBS
4. Add cell solution to 5mL PBS in 15mL centrifuge tube and resuspend to wash cells
5. Centrifuge the tube for 5 minutes at 1000 RPM.
6. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
7. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by vortexing. It is important that the solution is immediately and thoroughly mixed by vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
8. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload the spin column. The maximum number of hES cells that should be used in a DNA extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
9. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C) Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
10. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.

tag: sample type

value: human induced pluripotent stem (hiPSC) cell line CTR#4600, CGH#1018036

extract_protocol:
7.5. Dispase the Cells
7.5.1. Heat the Circulating Waterbath to 70C
7.5.2. Warm buffer AW2 for at least 10 minutes in the 37C waterbath.
7.5.3. Aspirate the media from each well to be extracted.
7.5.4. Add 1ml of Accumax to each well of four 6-well plates at a time.
7.5.4.1.This may be staggered according to number of people performing the extraction.
7.5.5. Return the plate to the 37C incubator for 9-11 minutes.
7.5.6. Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
7.5.7. Gently wash the cells from the surface of the well with a serological pipette, using the previously added 1ml of dispase.
7.5.8. Transfer the dispased cells from two 6-well plates to a 50ml centrifuge tube containing 25ml of PBS. Repeat as needed for additional plates.
7.5.9. Gently resuspend cells in PBS using a serological pipette.
7.5.10. Wash well(s) with 1-2ml of the resuspended cell solution to ensure complete cell removal.
7.5.11. Gently pipette solution up and down to mix thoroughly.
7.5.12. Centrifuge the tube for 5 minutes at 1000 RPM.
7.5.13. Aspirate the supernatant.
7.5.14. Add 30 ml of PBS and resuspend the cell pellet gently to wash.
7.5.15. Centrifuge the tube for 5 minutes at 1000 RPM.
7.5.16. Aspirate the supernatant.
7.5.17. Add 2 ml of PBS to each cell pellet and gently resuspend, using a serological pipette.
7.5.18. Keep tubes on ice until all plates are extracted and resuspended..
7.6. Digest Protein and RNA
7.6.1. Vortex Qiagen protease .
7.6.2. Prepare one 15 ml centrifuge tube for each 50 ml conical tube.
7.6.3. Add 200μl Qiagen protease to each 15 ml centrifuge tube.
7.6.4. Transfer 2ml of cells in PBS from one 50 ml conical tube to one 15 ml centrifuge tube containing Qiagen protease and pipette to resuspend.
7.6.4.1. Repeat for additional 50 ml conical tubes.
7.6.5. Add 20μl RNase A to each tube and vortex.
7.6.6. Incubate at room temperature for 3 minutes.
7.6.7. Add 2.4 ml Buffer AL, and mix thoroughly by inverting the tubes 15 times, followed by additional vigorous shaking for at least 1 minute.
7.6.7.1. Do not add Qiagen protease directly to buffer AL
7.6.7.2. Buffer AL may form a precipitate upon storage. If a precipitate has formed,
incubate the buffer at 55C until the precipitate has fully dissolved.
7.6.8. Close caps and incubate in a 70C waterbath for 10 minutes.
7.6.8.1. Monitor the waterbath rack during incubation to insure samples remain above the water level.
7.7. Precipitate DNA and Separate Cellular Components
7.7.1. Add 2 ml ethanol (200 proof) to each tube, and mix by inverting tubes 10 times, followed by additional vigorous shaking for 1 minute.
7.7.2. Carefully transfer one half (approx. 3.5 ml) of the solution onto the labeled QIAamp Midi columns placed into 15 ml centrifuge tubes.
7.7.3. Close the caps and centrifuge at 3000 rpm for 3 minutes.
7.7.4. Remove the columns, discard the filtrate, and place the columns back into the 15 ml centrifuge tubes.
7.7.4.1. Wipe off any spillage from the thread of the tubes before re-inserting the
columns.
7.7.5. Load the remainder of the solution onto the columns.
7.7.6. Close the caps and centrifuge again at 3000 rpm for 3 minutes.
7.8. Wash the DNA
7.8.1. Remove the columns, discard the filtrate, and place the columns back into the 15 ml centrifuge tubes.
7.8.1.1. Wipe off any spillage from the thread of the tubes before re-inserting the
columns.
7.8.2. Add 2 ml of Buffer AW1 to the columns, without moistening the rim.
7.8.3. Close the caps and centrifuge at 5000 rpm for 1 minute.
7.8.3.1. Do not discard the flow-through at this stage.
7.8.4. Add 2 ml of warm Buffer AW2 to the columns, without moistening the rim.
7.8.5. Centrifuge at 5000 rpm for 15 minutes.
7.8.5.1. If the centrifugal force is below 5000 rpm, incubating the column for 10 minutes in an incubator or waterbath to evaporate residual ethanol is recommended.
7.8.6. Remove the columns, discard the filtrate, and place the columns back into 15ml centrifuge tubes.
7.8.6.1. Wipe off any spillage from the thread of the tube before re-inserting the column.
7.8.7. Remove caps and place tubes in the 70ºC waterbath for 10 minutes.
7.9. Elute the DNA
7.9.1. Place the columns in clean, labeled 15ml centrifuge tubes (provided in kit) and discard the collection tube.
7.9.2. Pipette 300μl Buffer AE directly onto the membrane of the columns, close the caps and incubate at room temperature for 5 minutes.
7.9.3. Centrifuge at 5000 rpm for 2 minutes to elute.
7.9.4. Transfer eluate to labeled 1.5ml microcentrifuge tubes and proceed to spectrophotometry.
7.9.5. Store columns/15 ml elution tubes at 4ºC until spectrophotometric results are obtained.
7.9.5.1. Additional AE buffer may be added to columns pending spectrophotometric
results.
7.10. Perform UV Spectrophotometry
7.10.1. Choose the ND-1000 icon from the desktop of the lab computer and select “Nucleic
Acid”.
7.10.2. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.3. Use a p2 micropipetter and carefully load 1.5μl of nuclease-free water into the bottom pedestal of the NanoDrop and gently lower the top pedestal. Click “OK”.
7.10.4. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.5. Load 1.5μl of AE Buffer onto the bottom pedestal, close the top, and click “Blank”.
7.10.6. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.7. Enter the DNA # (DNAXXX), tube#, and elution description of the sample you are
quantifying into the Sample ID box.
7.10.8. Vortex and quick spin the sample and load 1.5μl onto the bottom pedestal of the NanoDrop.
7.10.9. Close the top and click “Measure”.
7.10.10. Verify that the DNA absorbance ratios meet the requirements: 260/280 ≥ 1.75, 260/230 ≥
1.85 (as seen in SOP-CH-014).
7.10.10.1. If the ratios are do not meet the requirements, add 300ul fresh AE buffer to columns/15ml elution tubes and incubate at room temperature for 5 minutes.
7.10.10.2. Centrifuge at 5000 rpm for 2 minutes to elute.
7.10.10.3. Transfer eluate to new, labeled 1.5 ml microcentrifuge tubes and proceed to spectrophotometry.
7.10.10.4. If the ratios are still do not meet requirements, add the original eluate to a new column/15 ml elution tube. If necessary, dilute with additional AE buffer and
incubate at room temperature for 5 minutes.
7.10.10.5. Centrifuge at 5000 rpm for 2 minutes to elute.
7.10.11. Verify that the DNA concentration is between 250-1000ng/ul.
7.10.12. Discard samples that do not meet required ratios.
7.10.13. Click “Show Report” and check that all samples are recorded.
7.10.13.1. Use the “Data” tab to delete or rename samples.
7.10.14. Click “Reports” “Save Reports” “Full Report” and save the report with the naming convention Date, DNA#(s) (Ex:052207.DNA145.146.147) under In-House CGH/CGH Reference Standard.
7.11. Perform Agarose Gel Electrophoresis and Imaging
7.11.1. Prepare and run samples for DNA Gel Electrophoresis and Imaging (ref SOP-CH-007).
7.11.2. Analyze gel image to verify that there is no RNA contamination or degradation of DNA.
7.11.3. DO NOT use samples that have RNA contamination or degradation of DNA.
7.12. Aliquot and Store Samples
7.12.1. In ND-1000 software, load the previous report containing uncombined samples.
7.12.2. Combine all samples with acceptable ratios and dilute with AE buffer until a
concentration of 200-250 μg/ml is achieved.
7.12.3. Print report by clicking “Load Report Format”, choose “notebook.ndf”. Click “Reports” “Print Report”.
7.12.4. Tape the printout into the lab notebook.
7.12.5. Enter the absorbance ratios (260/280 and 260/230) and the concentration into the DNA Extraction Log form under the appropriate DNA# previously entered. Save the DNA Extraction Log.
7.12.6. If DNA does NOT meet the above acceptable ratio requirements and/or does not yield a minimum of 450ug, it must be re-extracted.
7.12.7. Labe

value: human embryonic stem (hES) cell line WA09 [reference]


title: 2.d0

value: no

tag: vaccine type

tag: vaccine dilution

value: Undiluted


title: NSCB_CGH1018034_FTi19_p10

value: human induced pluripotent stem (hiPSC) cell line CTR#4599, CGH#1018034


title: NSCB_CGH1018030_FTC1_p4

value: human induced pluripotent stem (hiPSC) cell line CTR#4597, CGH#1018030

value: human embryonic stem (hES) cell line WA01 [reference]


title: Bone marrow cells_ RANKlowFmshigh

city: Nagano

first: Toshihide

last: Mizoguchi

address: 1780 Gobara, Hiro-oka, Shiojiri

institute: Matsumoto Dental Univ.

description: Gene expression data from RANKlowFmshigh

hyb_protocol: 1.8 ug of biotin-labeled sense-strand cDNA were hybridized for 18 hours at 45°C on Affymetrix GeneChipR mouse gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip system confocal scanner 3000.

data_processing: CEL files were obtained by the Affymetrix GeneChip operating software (GCOS 1.4). To enable a comparison between chips, data were normalized to a global intensity by GeneSpring GX software (Agilent Technologies) using the RMA (Robust Multi-array Average) procedure.

source_name: RANKlowFmshigh

label_protocol: Complementary DNA (cDNA) was prepared from the total RNA by using the WT-Ovation Pico RNA Amplification System (NuGen Technologies). Biotin-labeled sense-strand cDNA was prepared by using WT-Ovation Exon Module (NuGen Technologies) and FL-Ovation cDNA Biotin Module V2 (NuGen Technologies).

growth_protocol: Bone marrow cells were prepared from 6-week-old ddY mice, and layered onto a lympholyte-M (Cedarlane) gradient. After centrifugation, mononuclear cells were collected.

extract_protocol: FACS-sorted cells were lysed with Trizol (Invitrogen), and total RNA was extracted from the lysate using a PureLink RNA Mini Kit (Applied Biosystems/Ambion).

treatment_protocol: Mononuclear cells were stained with the PE-conjugated anti-RANK (eBioscience) and Biotin-conjugated anti-c-Fms antibodies (eBioscience). After 2 washes, they were incubated with Streptavidin FITC conjugate. Cells were sorted using a FACS Vantage SE (BD Biosciences).

value: Bone marrow

value: RANKlowFmshigh

value: ddY


title: Bone marrow cells_RANKhighFmslow

description: Gene expression data from RANKhighFmslow

source_name: RANKhighFmslow

value: RANKhighFmslow


title: Intestine_KO_day8_3

city: Baltimore

first: Tai-Chung

last: Huang

state: MD

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: Samples were hybridized with GeneChip miRNA array (Affymetrix) and scanned at the Johns Hopkins Microarray Core Facility.

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

data_processing: Our data was processed with "Affymetrix miRNA QC Tool version 1.0", within which background subtraction and quantile normalization were done. The summarized probe set data was log2 transformed. The statistical analysis was performed using GeneSpring GX 10.

source_name: small intestine (jejunum)

label_protocol: FlashTag Biotin HSR RNA labeling kit

growth_protocol: Conditional knockout of Dicer exon 21 & 22 in C57B/6 mice of 8 weeks of age

extract_protocol: miRNeasy Mini (Qiagen)

treatment_protocol: Tamoxifen gavage to induce conditional knockout

value: Dicer KO

tag: age

value: 8 weeks


title: a16011-WT-FVB

status: Public on Jan 08 2012

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description: Amygdala

hyb_protocol: Following fragmentation of 15.0 mg of the labeled cRNA, a hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array.  The array was hybridized 16 hours

scan_protocol: The array was stained using the EukGEws2v5 protocol on the Fluidics Station 450.  The stained array was scanned on the Affymetrix GeneChip Scanner 3000

data_processing:
The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.1 and scale factor of 500. Subsequently, R based analysis using exonmap package and rma normalization
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na27.mm9.mps

source_name: WT

label_protocol: Total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the in vitro transcription reaction, producing biotin-labeled

growth_protocol: Mice were bred and tissue was harvested from animals at 6 weeks of life

extract_protocol: Total RNA was extracted from the amygdala of 6 weeks old male mice using TRIzol reagent, DNaseI treated, and purified using the RNeasy mini kit, all according to the manufacturers protocols

treatment_protocol: No treatments were applied

tag: genotype

value: WT

tag: genetic background

value: FVB

value: Amygdala


title: Intestine_ctrl_day8_3

value: wildtype CTRL


title: Liver biopsy sample :TOL member: BX.W37.P

description: Liver biopsy before immunosuppressive therapy BX.W37.P

source_name: Liver biopsy sample

value: TOL

tag: demographic origin center

value: Hospital Clinic


title: BM_CMP_rep1

city: St. Louis

first: Amy

middle: M.

last: Becker

state: MO

address: 660 S. Euclide Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

description: replicate 1

hyb_protocol: Used standard Affymetrix hybiridization protocol

scan_protocol: Used standard Affymetrix scanning protocol.

data_processing: Background subtraction and quantiles-based normalization was performed using the GCRMA algorithm, available from Bioconductor.org.

source_name: mouse bone marrow

label_protocol: RNA was amplified and biotin-lableled using the amplified using Affymetrix Two-Cycle Amplification and IVT kits (Affymetrix).

extract_protocol: CDP or CMP were double sorted from the bone marrow of C57BL/6 mice. Total RNA was extracted using Trizol (Invitrogen) and linear acrylamide (Ambion) according to the manufacturer's instructions.

tag: tissue

value: bone marrow

value: wild type

value: common myeloid progenitors (Lineage-c-kithiSca-1-CD11c- CD34+ Flk2+CD16/32-CD115-)


title: Intestine_ctrl_day8_2


title: a16013-WT-FVB

description: Amygdala


title: a16509-TG3

description: Amygdala

source_name: Mecp2 TG

value: Mecp2 TG


title: BM_CMP_rep2

description: replicate 2


title: a15966-TG3

description: Amygdala


title: Intestine_ctrl_day8_1


title: a16508-TG3

description: Amygdala


title: a16009-WT-FVB

description: Amygdala


title: a15964-WT-FVB

description: Amygdala


title: a16010-TG3

description: Amygdala


title: a15965-WT-FVB

description: Amygdala


title: a15959-TG3

description: Amygdala


title: 56 day 13cisRA Treatment: 1129

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

country: Germany

institute: HelmholtzZentrum

description: Gene expression data from transplanted rat kidneys

hyb_protocol: We used standard Affymetrix procedures for hybridization

scan_protocol: Reactions were performed essentially according to the Affymetrix protocol.

data_processing: The resultant CEL files were analyzed using the ChipInspector software V.0.92 (CI; Genomatix Software GmbH, Munich, Germany)

source_name: 56 day 13cisRA Treatment (1129)

label_protocol: 20µg of total RNA were reverse-transcribed and used for biotinylation.

extract_protocol: Total RNA was isolated by the method of Chomczynski and Sacci. RNA quality was characterized using a RNA6000 Nanochip (Agilent)

treatment_protocol:
Inbred male rats were purchased from Charles River Laboratories GmbH (Sulzfeld, Germany) and were used in all experiments. Kidney transplantation was performed by a modified technique originally described by Lee (1967) under general ether anaesthesia. Unlike the original model, the recipient's right kidney was left in place and no immunosuppressive agent was given, in order to enhance the contribution of rejection to CAD. In the13cisRA Treatment group rats were13cisRA Treated with 13cisRA 2mg/kg/body weight
Placebo rats were not13cisRA Treated with any medication including Cyclosporine A.

tag: transplants

value: F344 RT1lvl

tag: recipients

value: LEW RT1l

value: kidney


title: a15921-WT-B6

description: Amygdala


title: a15955-WT-B6

description: Amygdala


title: a15953-Mecp2-NULL

description: Amygdala

source_name: Mecp2 -/-

value: Mecp2 -/-


title: 14 day 13cisRA Treatment: 527

source_name: 14  day 13cisRA Treatment (527)


title: a15957-WT-B6

description: Amygdala


title: a15952-Mecp2-NULL

description: Amygdala


title: Intestine_KO_day8_2

tag: strain


title: CM_CDP_rep3

description: replicate 3

tag: cell type

value: common dendritic cell progenitors (Lin-c-kitintSca-1-CD34+Flk2+CD16/32-CD115+)


title: 56 day 13cisRA Treatment: 1131

source_name: 56 day 13cisRA Treatment (1131)


title: BM_CDP_rep1

description: replicate 1


title: a15925-Mecp2-NULL

description: Amygdala


title: 14 day 13cisRA Treatment: 564

source_name: 14  day 13cisRA Treatment (564)


title: 56 day 13cisRA Treatment: 1132

source_name: 56 day 13cisRA Treatment (1132)


title: a15951-Mecp2-NULL

description: Amygdala


title: 14 day 13cisRA Treatment: 760

source_name: 14  day 13cisRA Treatment (760)


title: 56 day 13cisRA Treatment: 1083

source_name: 56 day 13cisRA Treatment (1083)


title: 14 day 13cisRA Treatment: 561

source_name: 14  day 13cisRA Treatment (561)


title: 7 day 13cisRA Treatment: 1466

source_name: 7  day 13cisRA Treatment (1466)


title: a15956-WT-B6

description: Amygdala


title: 7 day 13cisRA Treatment: 1464

source_name: 7  day 13cisRA Treatment (1464)


title: 7 day 13cisRA Treatment: 1448

source_name: 7  day13cisRA Treatment (1448)


title: shRNA-Control/EGFP-transfected LS174T cells

city: Chongqing

first: Rongquan

last: Wang

state: Chongqing

address: Gaotanyan Main Street 30#

department: Department of Gastroenterology

country: China

institute: Southwest Hospital

description:
shRNA-Ctr/LS174T cells
Stable shRNA-Ctr/EGFP-transfected LS174T cells, harvested after several passages.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to the array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Scanned on an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA). Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Replicated miRNAs were averaged, and miRNAs with intensities >50 in all samples were chosen for calculating the normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change (>=2.0) filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

The lists of differentially expressed genes are linked to the GSE34926 record as supplementary files.

source_name: LS174T cells, stably transfected with shRNA-Ctr/EGFP vector

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: The shRNA-Ascl2/HT-29 cells, shRNA-Ctr/HT-29 cells, shRNA-Ascl2/LS174T cells and shRNA-Ctr/LS174T cells were maintained in McCoy’s 5A medium (Sigma, USA) containing 10% fetal bovine serum (FBS; HyClone, USA), and 0.4 mg/ml G418 for HT-29 transfectants or 0.2 mg/ml G418 for LS174T transfectants, at 37ºC and 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and the miRNeasy mini kit (QIAGEN) according to the manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity were measured by using a Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies), and RNA integrity was determined by gel electrophoresis.

value: colon cancer

tag: stable transfection

value: shRNA-Ctr/EGFP vector


description:
shRNA-Ascl2/LS174T cells
Stable shRNA-Ascl2/EGFP-transfected LS174T cells, harvested after several passages.

source_name: LS174T cells, stably transfected with shRNA-Ascl2/EGFP vector

value: shRNA-Ascl2/EGFP vector


title: shRNA-Control/EGFP-transfected HT-29 cells

description:
shRNA-Ctr/HT-29 cells
Stable shRNA-Ctr/EGFP-transfected HT-29 cells, harvested after several passages.

source_name: HT-29 cells, stably transfected with shRNA-Ctr/EGFP vector


title: Intestine_ctrl_day8_3 [gene-level]

description: THua-DIC-Cre_TA_ctrl-3a-mmExon1_(MoEx-1_0-st-v1).CEL

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

data_processing:
affymetrix-algorithm-name = rma-gene-extended
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935
program-company = Affymetrix
The statistical analysis was performed using GeneSpring GX 10.

source_name: small intestine (jejunum)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

tag: genotype/variation

value: 8 weeks


title: Intestine_ctrl_day8_2 [gene-level]

description: THua-DIC-Cre_TA_ctrl-2a-mmExon1_(MoEx-1_0-st-v1).CEL


title: Intestine_ctrl_day8_1 [gene-level]

description: THua-DIC-Cre_TA_ctrl-1a-mmExon1_(MoEx-1_0-st-v1).CEL


title: BM_CDP_rep2

description: replicate 2

source_name: mouse bone marrow


title: Intestine_KO_day8_3 [gene-level]

description: THua-DIC-Cre_TA_1014-3a-mmExon1_(MoEx-1_0-st-v1).CEL

value: Dicer KO


title: 14 day 13cisRA Treatment: 563

source_name: 14  day 13cisRA Treatment (563)


title: 7 day 13cisRA Treatment: 1357

source_name: 7  day13cisRA Treatment (1357)


title: Intestine_KO_day8_1


title: Intestine_KO_day8_2 [gene-level]

description: THua-DIC-Cre_TA_1014-2a-mmExon1_(MoEx-1_0-st-v1).CEL


title: Intestine_KO_day8_1 [gene-level]

description: THua-DIC-Cre_TA_1014-1a-mmExon1_(MoEx-1_0-st-v1).CEL


description:
shRNA-Ascl2/HT-29 cells
Stable shRNA-Ascl2/EGFP-transfected HT-29 cells, harvested after several passages.

source_name: HT-29 cells, stably transfected with shRNA-Ascl2/EGFP vector

tag: cell line


title: NH Osteoblasts and T47D coculture A

status: Public on Jan 06 2012

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86234.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4100A 01

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

source_name: stratagene human reference plus doping controls.

label_protocol:
StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)

extract_protocol: MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions

tag: reference

source_name: NH Osteoblasts and T47D coculture A plus doping controls.

label_protocol: Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)

growth_protocol: osteoblast co-culture; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Walkersville, MD) were expanded in mammary epithelial basal medium that was supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Walkersville, MD). MCF-7, T47D, MDA-MB231, SKBR-3, Hs578T, (ATCC, Atlanta, GA) were propagated in DMEM with 4.5% glucose (Gibco, Grand Island, NY) that was supplemented with 10% FBS (HyClone, Logan, UT), glutamine, 100 U/ml penicillin and 100 ??g/ml streptomycin (Gibco, Grand Island, NY). Normal human Osteoblasts (NHOST) (Lonza Walkersville, Walkersville, MD) were expanded in Clonetics Osteoblast Basal Medium (OBM???) (Lonza Walkersville, Walkersville, MD) supplemented with osteoblast growth medium (OGM TM) SingleQuots?? (Lonza Walkersville, Walkersville, MD) with 10 % FBS. For the co-culture experiments, the cells were cultivated for 48 hours at equal density of 30???000 cells/cm2 (15???000 tumor cells /cm2 and 15???000 normal human Osteoblast cells /cm2) in Clonetics Osteoblast Basal Medium (OBM???) supplemented with 0.2% FBS without any further additives. This medium served as a good universal media for all the cells in the study

extract_protocol:
RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions

tag: cells

value: normal human osteoblasts and T47D coculture A plus doping controls.


title: NH Osteoblasts and T47D coculture B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86235.gif

value: stratagene human reference plus doping controls.

source_name: NH Osteoblasts and T47D coculture B plus doping controls.

value: normal human osteoblasts and T47D coculture B plus doping controls.


title: db/db mouse sample 400

city: Ann Arobr

first: Manjusha

last: Pande

address: 2800 Plymouth Rd.

department: BRCF

institute: University of Michigan

description:
Feldman_400.CEL
Gene expression data from 8 week db/db mouse sciatic nerve

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: The Affymetrix CEL files were initially analyzed using a local version of the GenePattern genomic analysis platform from the Broad Institute.  The samples were Robust Multi-array Average (RMA) normalized using the BrainArray Custom CDF version 12. Since the RNA amplification and hybridization was performed in two batches, normalized, log2 transformed expression values from the two batches of microarrays were adjusted for batch effect bias using the Distance Weighted Discrimination (DWD) batch effect correction method.

source_name: 8 week db/db mouse sciatic nerve

label_protocol: Of the total RNA, 75 ng from each sample was amplified and biotin-labeled using the Ovation™ Biotin-RNA Amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s protocol

extract_protocol: Total RNA was isolated from sciatic nerve using a commercially available silica gel-based isolation protocol (RNeasy Mini Kit, QIAGEN Inc., Valencia, CA) including an on-column DNase digestion following the manufacturer's protocol.  RNA quantity and quality was measured by microfluid electrophoresis using the RNA 6000 Pico LabChip® on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: BKS

value: db/db

value: sciatic nerve


title: db/db mouse sample 402

description:
Feldman_402.CEL
Gene expression data from 8 week db/db mouse sciatic nerve


description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86220.gif

source_name: NH Osteoblasts and MDA-MB-231 coculture A plus doping controls.

value: normal human osteoblasts and MDA-MB-231 coculture A plus doping controls.


title: SKBR3 sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86239.gif

source_name: SKBR3 sample B plus doping controls.

value: SKBR3 sample B plus doping controls.


title: SKBR3 sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86238.gif

source_name: SKBR3 sample A plus doping controls.

value: SKBR3 sample A plus doping controls.


title: db/db mouse sample 399

description:
Feldman_399.CEL
Gene expression data from 8 week db/db mouse sciatic nerve


title: MDA-MB-231 sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86217.gif

source_name: MDA-MB-231 sample B plus doping controls.


title: T47D sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86230.gif

source_name: T47D sample A

value: T47D sample A


title: Intestine_KO_day8_3 [exon-level]

data_processing:
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935
program-company = Affymetrix
The statistical analysis was performed using GeneSpring GX 10.


title: NH Osteoblasts and SKBR3 coculture A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86242.gif

source_name: NH Osteoblasts and SKBR3 coculture A plus doping controls.

value: normal human osteoblasts and SKBR3 coculture A plus doping controls.


description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86222.gif

source_name: NH Osteoblasts and MDA-MB-231 coculture B plus doping controls.

value: normal human osteoblasts and MDA-MB-231 coculture B plus doping controls.


title: NH Osteoblasts sample B2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86227.gif

source_name: NH Osteoblasts sample B2  plus doping controls.

value: normal human osteoblasts sample B2  plus doping controls.


title: NH Osteoblasts and MCF-7 coculture B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86233.gif

source_name: NH Osteoblasts and MCF-7 coculture B plus doping controls.

value: normal human osteoblasts and MCF-7 coculture B plus doping controls.


title: T47D sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86231.gif

source_name: T47D sample B

value: T47D sample B


title: MCF-7 sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86229.gif

source_name: MCF-7 sample B plus doping controls.

value: MCF-7 sample B plus doping controls.


title: NH Osteoblasts and Hs578t coculture A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86218.gif

source_name: NH Osteoblasts and Hs578t coculture A plus doping controls.

value: normal human osteoblasts and Hs578t coculture A plus doping controls.


title: NH Osteoblasts and SKBR3 coculture B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86243.gif

source_name: NH Osteoblasts and SKBR3 coculture B plus doping controls.

value: normal human osteoblasts and SKBR3 coculture B plus doping controls.


title: db/db mouse sample 344

description:
Feldman_344.CEL
Gene expression data from 8 week db/db mouse sciatic nerve

value: 8 weeks


title: MCF-7 sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86228.gif

source_name: stratagene human reference plus doping controls.

source_name: MCF-7 sample A plus doping controls.

value: MCF-7 sample A plus doping controls.


title: Intestine_ctrl_day8_2 [exon-level]

description: THua-DIC-Cre_TA_ctrl-2a-mmExon1_(MoEx-1_0-st-v1).CEL

source_name: small intestine (jejunum)

value: wildtype CTRL


title: MDA-MB-231 sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86216.gif

value: stratagene human reference plus doping controls.

source_name: MDA-MB-231 sample A plus doping controls.


title: NH Osteoblasts sample A2

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86226.gif

source_name: NH Osteoblasts sample A2  plus doping controls.

value: normal human osteoblasts sample A2  plus doping controls.


title: Intestine_ctrl_day8_3 [exon-level]

description: THua-DIC-Cre_TA_ctrl-3a-mmExon1_(MoEx-1_0-st-v1).CEL


title: db/db mouse sample 343

description:
Feldman_343.CEL
Gene expression data from 8 week db/db mouse sciatic nerve

source_name: 8 week db/db mouse sciatic nerve

value: BKS

value: db/db

value: sciatic nerve


title: db/db mouse sample 342

description:
Feldman_342.CEL
Gene expression data from 8 week db/db mouse sciatic nerve


title: db/db mouse sample 346

description:
Feldman_346.CEL
Gene expression data from 8 week db/db mouse sciatic nerve


title: db/+ mouse sample 398

description:
Feldman_398.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve

source_name: 8 week db/+ mouse sciatic nerve

value: db/+


title: db/db mouse sample 341

description:
Feldman_341.CEL
Gene expression data from 8 week db/db mouse sciatic nerve


title: NH Osteoblasts and MCF-7 coculture A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86232.gif

source_name: NH Osteoblasts and MCF-7 coculture A plus doping controls.

value: normal human osteoblasts and MCF-7 coculture A plus doping controls.


title: NH Osteoblasts and Hs578t coculture B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86219.gif

source_name: NH Osteoblasts and Hs578t coculture B plus doping controls.

value: normal human osteoblasts and Hs578t coculture B plus doping controls.


title: db/+ mouse sample 397

description:
Feldman_397.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: Hfq virulence regulation in enterohemorhagic Escherichia coli O157:H7 strain 86-24

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli O157:H7

source_name: 86-24 wild type

extract_protocol: Ambion RiboPure RNA Isolation

value: wild-type

tag: growth protocol

value: grown to OD600 = 1.0


title: Hfq virulence regulation in enterohemorhagic Escherichia coli O157:H7 strain 86

scan_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: 86-24 delta hfq

tag: hfq mutant


title: Hs578t sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86214.gif

source_name: Hs578t sample A plus doping controls.

value: Hs578t sample A plus doping controls.


title: NH Osteoblasts sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86212.gif

source_name: NH Osteoblasts sample A

value: normal human osteoblasts sample A


title: db/+ mouse sample 339

description:
Feldman_339.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: db/+ mouse sample 340

description:
Feldman_340.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: db/+ mouse sample 395

description:
Feldman_395.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: BNA10ROU

city: Montreal

first: Bernard

last: Robaire

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

description:
IG090820BRE164-2_01.CEL
Gene expression data from round spermatids from aged rats

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat 230 2.0 genome array chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Genespring v11.0.

source_name: Round spermatids from 18 month old rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit

treatment_protocol: Testicular germ cells were isolated using a collagenase and trypsin digest followed by a STAPUT density gradient to isolate fractions of round spermatids with a purity of greater than 83%

value: Brown Norway (BN)

value: aged

value: Round spermatids


title: Intestine_KO_day8_1 [exon-level]

description: THua-DIC-Cre_TA_1014-1a-mmExon1_(MoEx-1_0-st-v1).CEL

value: Dicer KO

value: 8 weeks


title: BNA09ROU

description:
IG090820BRE163-2_01.CEL
Gene expression data from round spermatids from aged rats


title: db/+ mouse sample 337

description:
Feldman_337.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: db/+ mouse sample 335

description:
Feldman_335.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve


title: BNA03ROU

description:
IG090820BRE160-2_01.CEL
Gene expression data from round spermatids from aged rats


title: Hs578t sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86215.gif

value: stratagene human reference plus doping controls.

source_name: Hs578t sample B plus doping controls.

value: Hs578t sample B plus doping controls.


title: NH Osteoblasts sample A3

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86236.gif

source_name: NH Osteoblasts sample A3  plus doping controls.

value: normal human osteoblasts sample A3  plus doping controls.


title: BNA08ROU

description:
IG090820BRE162-2_01.CEL
Gene expression data from round spermatids from aged rats


title: db/+ mouse sample 336

description:
Feldman_336.CEL
Gene expression data from 8 week db/+ mouse sciatic nerve

value: BKS


title: HMEC sample A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86240.gif

source_name: HMEC sample A plus doping controls.

value: HMEC sample A plus doping controls.


title: NH Osteoblasts and HMEC coculture A

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86244.gif

source_name: stratagene human reference plus doping controls.

source_name: NH Osteoblasts and HMEC coculture A plus doping controls.

value: normal human osteoblasts and HMEC coculture A plus doping controls.


title: BNY11ROU

description:
IG090820BRE157-2_01.CEL
Gene expression data from round spermatids from young rats

source_name: Round spermatids from 4 month old rats

value: young


title: NH Osteoblasts sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86213.gif

source_name: NH Osteoblasts sample B plus doping controls.

value: normal human osteoblasts sample B plus doping controls.


title: BNA05ROU

description:
IG090820BRE161-2_01.CEL
Gene expression data from round spermatids from aged rats


title: BNA08PACH

description:
IG090820BRE174-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats

hyb_protocol: Following fragmentation

source_name: Pachytene spermatocytes from 18 month old rats

treatment_protocol: Testicular germ cells were isolated using a collagenase and trypsin digest followed by a STAPUT density gradient to isolate fractions of pachytene spermatocytes and round spermatids with a purity of greater than 83%

value: Pachytene spermatocytes


title: Intestine_ctrl_day8_1 [exon-level]

description: THua-DIC-Cre_TA_ctrl-1a-mmExon1_(MoEx-1_0-st-v1).CEL

source_name: small intestine (jejunum)

value: wildtype CTRL