title: 00058463

description:
Date:2006/02/17
I0 vs N0

source_name: Infected, day=0

tag: Infected, day=0

source_name: Non-Infected, day=0

tag: Non-Infected, day=0


title: Gastric mucosal scrapings #1

status: Public on Nov 22 2006

type: RNA

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

state: CA

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

country: USA

institute: UCLA

description: Manufacturer's scanner and feature extraction - normalization software

hyb_protocol: Agilent 44K hybridization, 17 hrs

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing: Genespring 7.3

molecule: total RNA

organism: Rattus norvegicus

source_name: rat gastric mucosa

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: NucleoSpin RNA II (BD Biosciences, USA)

treatment_protocol: free access to food and water

tag: gastric mucosal scrapings, mixed homogenate total RNA isolate


title: Fasting gastric mucosal scrapings #2

treatment_protocol: 24 hr fasted rats, free access to water

tag: gastric mucosal scrapings from 24 hr fasted rats, mixed homogenate total RNA isolate


title: Rat gastric ECL cells (95% purity), normal conditions #2

tag: Homogeneous (95%) ECL cell suspensions, purified by counterflow elutriation and FACS using acridine orange as marker


title: Kidney / Reference

status: Public on Oct 30 2006

city: Las Vegas

first: Sheri

last: Holmen

state: NV

address: 10441 W. Twain Ave.

department: Drug Development

institute: Nevada Cancer Institute

description: Gene expression data from cell type: Kidney

hyb_protocol: Hybridization was performed at 50C and 35% formamide for 16 hours.

scan_protocol: Microarrays were scanned using the Agilent G2505B scanner.

data_processing: log2 ratio of Cy5/Cy3

organism: Mus musculus

source_name: Kidney

label_protocol: Direct incorporation of CyDye labeled dCTP by reverse transcription.

extract_protocol: Trizol

tag: Kidney

source_name: Mouse Embryo Reference

tag: Reference


title: Fasting gastric mucosal scrapings #1


title: Rat gastric PC cells (99% purity), normal conditions #1

tag: Homogeneous (99%) PC cell suspensions, purified by counterflow elutriation and FACS using autofluorescense as marker


title: NRAS_MEL / Reference

description: Gene expression data from cell type: C3 Nras

tag: C3 Nras


title: Rat gastric ECL cells (95% purity), normal conditions #3


title: Rat gastric ECL cells (95% purity), 24 hrs fasting #1

treatment_protocol: No access to food for 24 hrs.

tag: Homogeneous (95%) ECL cell suspensions, purified by counterflow elutriation and FACS using acridine orange as marker from rats fasted for 24 hrs.


title: Liver / Reference

description: Gene expression data from cell type: Liver

source_name: Liver

tag: Liver


title: Lung / Reference

description: Gene expression data from cell type: Lung

source_name: Lung

tag: Lung


title: Rat gastric ECL cells (95% purity), normal conditions #1


title: Rat gastric PC cells (99% purity), normal conditions #2


title: Fasting gastric mucosal scrapings #3


title: D6_MEL / Reference

description: Gene expression data from cell type: C3


title: Heart / Reference

description: Gene expression data from cell type: Heart

source_name: Heart

tag: Heart


title: KRAS_MEL / Reference

description: Gene expression data from cell type: C3 Kras

tag: C3 Kras


title: 3T3 / Reference

description: Gene expression data from cell type: 3T3


title: 00058462

status: Public on Jan 17 2007

type: other

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Date:2006/02/17
N0 vs I0

hyb_protocol: Agilent : 750.0 ng at 50 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000A fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: No normalization performed : VALUE column is the "Ratio of Medians (635/532)" column of Genepix6.0 .gpr file.

molecule: other

organism: Homo sapiens

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana


title: Melan A / Reference

description: Gene expression data from cell type: Melan A

source_name: Melan A

tag: Melan A


title: HRAS_MEL / Reference

description: Gene expression data from cell type: 862


title: VA_475 / Reference

description: Gene expression data from cell type: B475


title: Rat gastric ECL cells (95% purity), 24 hrs fasting #3


title: VA_MEF / Reference

description: Gene expression data from cell type: BAKE

tag: BAKE


title: NHF1-hTERT_1.5Gy_24h_C3_20182

status: Public on Feb 01 2007

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

institute: Gentris Corperation

description: The gene expression level was presented as ratio of sample intensity against reference intensity.

hyb_protocol: 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology.

data_processing: Microarray images were analyzed using Agilent Feature Extraction Software (v7.1). Expression patterns and significant genes were extracted using Extracting Microarray Gene Expression Patterns and Identifying Biologically Significant genes (EPIG)

source_name: Sample RNA

label_protocol: 1 µg of sample RNA was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy3-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was e

growth_protocol: Fibroblasts were cultured in DMEM (Invitrogen) supplemented with 2 mM L-glutamine (Invitrogen) and 10% fetal bovine serum (Sigma). All cell lines were maintained at 37oC in a humidified atmosphere of 5% CO2.

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells were harvested 24 hr after 1.5 Gy iozining radiation treatment

tag: Normal human fibroblast

source_name: Reference RNA

label_protocol: 1 µg of global reference RNA (Stratagene) was converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with Cy5-dUTP (Agilent’s Low RNA Input Linear Amplification Kit). The quality of

extract_protocol: Stratagene protocol for preparation of reference RNA

tag: global reference RNA


title: siKlf4/EB5 #2(16012165010178)

status: Public on Sep 30 2006

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.   The manual can be found at  https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961,  or through a WEB search on the manual title.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: siKlf4/EB5 #2

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

growth_protocol: ES cells grow without feeders on gelatin coated in complete ES medium. Cells were incubated at 37 0C; 5% CO2. Medium was exchanged on day1 with puromysin. On the day 2 Trizol was added and RNA were extracted.

extract_protocol: TROZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used. 1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using a glass-Teflon® or power homogenizer (Polytron, or Tekmar's TISSUMIZER® or equivalent). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8°C. 6. REDISSOLVING THE RNA At the end of the procedure, briefly dry the RNA pellet (ai

treatment_protocol: EB5 ES cells were transfected with siRNA and pCAGEGFP-IP plasmid. After transfection, cells were cultured for 24 hours, following to drag selection for more 24 hours in the presence of puromycin to ensure concentration of transfectants.

tag: embryonic stem cell 129/Ola male  Transgenic and Knock down

source_name: Universal Mouse Reference RNA

growth_protocol: The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: siKlf4/EB5 #1(16012165010177)

source_name: siKlf4/EB5 #1


title: HCC827(B)

status: Public on May 16 2006

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250

label: biotin

source_name: lung cancer cell line

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 5 microgram total RNA

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment

tag: Histology

value: adenocarcinoma (BAC features)

tag: Age

tag: Sex

value: F

tag: Race

value: caucasian


title: HCC4006(B)

value: adenocarcinoma

tag: Age:

value: M


title: HCC1195(B)

value: adenocarcinoma (mixed)

value: black


title: H3255(B)


title: HCC366(B)

value: adenosquamous

tag: Race:


title: HCC515(B)


title: HCC1359(B)

value: large cell carcinoma


title: H820(B)

value: Bronchoalveolar


title: H2882(B)

value: NSCLC


title: H2122(B)


title: HCC95(B)

value: squamous cell carcinoma


title: H460(B2)


title: H2126(B)


title: HCC44(B)


title: HCC461(B)


title: H358(B)

value: asian


title: H441(B)


title: HCC1171(B)


title: HCC15(B2)


title: HCC78(B)


title: HCC2935(B)


title: H2347(B)


title: H2887(B)


title: HCC2279(B)


title: Rat gastric PC cells (99% purity), normal conditions #3

tag: Homogeneous (99%) PC cell suspensions, purified by counterflow elutriation and FACS using autofluorescense as marker


title: H2009(B)


title: H2087(B)


title: H1975(B)


title: H1819(B)


title: H1993(B)


title: H1672(B2)

value: SCLC


title: Calu-3(B)


title: H1666(B)


title: H1648(B)


title: H157(B)


title: A549(B)


title: H1650(B)


title: H1299(B)


title: 243_PyPn_4_Cy5_vs_EtOH_4_Cy3_REV

status: Public on Mar 31 2006

city: Ottawa

first: Helen

middle: Rose

last: Jensen

state: Ontario

address: 30 Marie-Curie street

department: Ottawa-Carleton Institute of Biology

country: Canada

institute: University of Ottawa

description: This dye-reversal hybridization compared the gene expression profiles after 6 hours of Drosophila treated with a synergistic insecticidal combination of Piper nigrum and natural pyrethrin to the expression of insects treated with 99% ethanol (carrier solvent).

hyb_protocol: Hybridization protocol as specified in Neal et al. (2003), Genome 46: 879-892. 80 μg of total RNA from the control and treated samples were hybridized.

scan_protocol: Scan protocol using the ScanArray 4000 XL (GSI Lumonics/Packard Biochips) as specified in Neal et al. (2003), Genome 46: 879-892.

data_processing: Quantarray Microarray Analysis Software version 3.0 (Packard BioScience, copyright 2001) was used to quantify image data. Spot and background intensity were measured using the adaptive circle quantification method. Gene TrafficTM Duo, version 2.8 (Iobion Informatics, copyright 2002) was used for further analysis. Data normalization was performed on background subtracted spots on a subgrid basis using the Locally Weighted Scatter Plot Smoother (LOWESS) algorithm with a smoothing factor of 20. Spots with intensity values less than 100 units and spots with intensity values below the average background intensity value and/or below the local background intensity value were excluded from normalization and analysis. Data was filtered so as to exclude all genes with less than two-thirds of spots being usable as defined by quality filters and by a mean differential expression ratio with a coefficient of variance higher than 100%.

organism: Drosophila melanogaster

label_protocol: 80 μg of total RNA was labeled using the direct labeling protocol as specified in Neal et al. (2003), Genome 46: 879-892.

extract_protocol: Total RNA from approximately 240 adult female Drosophila was isolated using the acid guanidium thiocyanate-phenol-choloroform extraction method (Chomczynski and Sacchi, 1987). Samples were homogenized in 200 μL of solution D using a Kontes pestle and further homogenized with 3 short sonicator pulses after adding an additional 800 μL of solution D. Insoluble material was removed from samples by centrifuging at 16 000 x g for 3 minutes and transferring the supernatant to new microtubes. Three washes with cold 80% EtOH were performed to ensure the removal of red coloured eye pigments and organic contaminants from the RNA pellet. RNA samples with (A260/A280) values between 1.8 and 2.0 were considered suitable for microarray analysis.

treatment_protocol: Treatment: 2 mL of 99% ethanol, application was topical using a Potter's tower and the time elapsed between application and sampling was 6 hours.

tag: Strain

value: Oregon-R

value: Female

value: 4-10 days (after adult emergence)

tag: Temperature:23 degrees Celsius

tag: Relative Humidity

tag: Label type

value: Reverse

treatment_protocol: Treatment: 2 mL of 0.1 mg/mL Piper nigrum seed ethylacetate extract +0.004 mg/mL pyrethrin formulated in 99% ethanol, application was topical using a Potter's tower and the time elapsed between application and sampling was 6 hours.


title: H1437(B)


title: Calu-6(B)

value: F


title: H1355(B)

value: caucasian


title: 240_PyPn_6_Cy5_vs_EtOH_1_Cy3_REV


title: Calu-1(B)


title: 228_PyPn_6_Cy3_vs_EtOH_1_Cy5

description: This hybridization compared the gene expression profiles after 6 hours of Drosophila treated with a synergistic insecticidal combination of Piper nigrum and natural pyrethrin to the expression of insects treated with 99% ethanol (carrier solvent).

value: Normal


title: 226_PyPn_2_Cy3_vs_EtOH_2_Cy5


title: 241_PyPn_2_Cy5_vs_EtOH_2_Cy3_REV


title: 215_Pyr_4_Cy3_vs_EtOH_4_Cy5

description: This hybridization compared the gene expression profiles after 6 hours of Drosophila treated with the botanical insecticide pyrethrin to the expression of insects treated with 99% ethanol (carrier solvent).

treatment_protocol: Treatment: 2 mL of 0.04 mg/mL pyrethrin formulated in 99% ethanol, application was topical using a Potter's tower and the time elapsed between application and sampling was 6 hours.


title: 225_PyPn_5_Cy3_vs_EtOH_3_Cy5

treatment_protocol:
Treatment: 2 mL of 99% ethanol
Type: topical mist application using a Potter's tower
Time elapsed between application and sampling: 6 hours

treatment_protocol:
Treatment: 2 mL of 0.1 mg/mL Piper nigrum seed ethylacetate extract +0.004 mg/mL pyrethrin formulated in 99% ethanol
Type: topical mist application using a Potter's tower
Time elapsed between application and sampling: 6 hours


title: H1395(B)

value: adenocarcinoma


title: 185_Pyr_1_Cy3_vs_EtOH_3_Cy5


title: 186_Pyr_2_Cy3_vs_EtOH_3_Cy5


title: 214_Pyr_5_Cy3_vs_EtOH_4_Cy5


title: DC #2(16012165010109)

status: Public on Jan 23 2006

description: differentiated cells

source_name: DC #2

growth_protocol: Grown on gelatin in DMEM (GIBCO 11965) with 10%FCS, 2mM Glutamine, 1μM RA and p/s.

extract_protocol: not supplied

treatment_protocol: By culturing in differentiation promoting conditions, NS5 cells were turned into differentiated neural cells (DC).

tag: neural stem/progenitor cells CD1 male


title: E12.5 Placenta1, 5 pooled(16012165010116)

description: E12.5 Placenta

source_name: E12.5 Placenta1, 5 pooled

extract_protocol:
not supplied
TROZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used. 1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using a glass-Teflon® or power homogenizer (Polytron, or Tekmar's TISSUMIZER® or equivalent). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8°C. 6. REDISSOLVING THE RNA At the end of the procedure, briefly dry the RNA pellet (ai

treatment_protocol: Pregnant female mice from timed matings were sacrificed by cervical dislocation at 12.5 days post-coitus.  Decidua were removed to 1x PBS on ice, and embryos/placentas were dissected and transferred to iced PBS.  For each litter, embryos were combined in one tube, while placentas were combined in another.  Tubes were snap frozen on dry ice and stored at -80°C.

tag: placenta C57BL/6 mixed sex embryo


title: DC #1(16012165010108)

description: differentiated cells

source_name: DC #1

tag: neural stem/progenitor cells CD1 unknown sex


title: HCC193(B)


title: 183_Pn_3_Cy3_vs_EtOH_3_Cy5

description: This hybridization compared gene expression profiles of Drosophila treated with an insecticidal extract of Piper nigrum seeds to a control group of Drosophila treated with the carrier solvent ethanol.

treatment_protocol:
Treatment: 2 mL of 0.2 mg/mL Piper nigrum seed ethylacetate extract formulated in 99% ethanol
Type: topical mist application using a Potter's tower
Time elapsed between application and sampling: 6 hours


title: DC #3(16012165010110)

description: differentiated cells

source_name: DC #3


title: 224_PyPn_4_Cy3_vs_EtOH_4_Cy5


title: 184_Pn_4_Cy3_vs_EtOH_4_Cy5


title: E12.5 Placenta2, 5 pooled(16012165010118)

description: E12.5 Placenta

source_name: E12.5 Placenta2, 5 pooled


title: 178_Pn_2_Cy5_vs_EtOH_2_Cy3_REV

description: A hybridization with reversed fluorescent labeling of identical biological samples.  This hybridization compared gene expression profiles of Drosophila treated with an insecticidal extract of Piper nigrum seeds to a control group of Drosophila treated with the carrier solvent ethanol.

treatment_protocol: Treatment: 2 mL of 99% ethanol

treatment_protocol: Treatment: 2 mL of 0.2 mg/mL Piper nigrum seed ethylacetate extract formulated in 99% ethanol


title: E12.5 Placenta3, 3 pooled(16012165010120)

description: E12.5 Placenta

source_name: E12.5 Placenta3, 3 pooled


title: NS1 #1(16012165010088)

description: doublet cells

treatment_protocol: Cells isolated from the forebrain periventricular zone were cultured to form neurospheres. The neurospheres were dissociated into single cells and passaged to a new culture dish. After one day in culture (1DIV), cells that divided and formed doublets were harvested as NS1.


title: TS #3(16012165010087)

description: GFP-Exe TS cells

source_name: TS #3

treatment_protocol: grown on TC plastic, 70cond+Fgf4+Heparin, p35, GFP sort, p22

tag: trophoblast stem cell B5/GFP unknown sex  GFP transgenic


title: 182_Pn_2_Cy3_vs_EtOH_2_Cy5


title: TS #1(16012165010085)

description: GFP-Exe TS cells

source_name: TS #1

treatment_protocol: grown on TC plastic, 70cond+Fgf4+Heparin, p28, DNA/GFP sort, p4


title: NS5 #1(16012165010105)

description: neural stem cells

treatment_protocol: Cells isolated from the forebrain periventricular zone were cultured to form neurospheres. The neurospheres were dissociated into single cells and passaged to a new culture dish. After 5 days in culture (5DIV), cells that divided and formed doublets were harvested as NS5.


title: 177_Pn_1_Cy5_vs_EtOH_1_Cy3_REV


title: 181_Pn_1_Cy3_vs_EtOH_1_Cy5


title: NS5 #3(16012165010107)

description: neural stem cells


title: ES_R1 #3(16012165010084)

description: R1 ES cells passaged on gelatin, p12

treatment_protocol: Passaged on gelatin, p12

tag: embryonic stem cell 129X1/Sv male


title: NS1 #2(16012165010089)

description: doublet cells

tag: Universale Mouse Reference


title: TS #2(16012165010086)

description: GFP-Exe TS cells

source_name: TS #2


title: ES_R1 #2(16012165010083)

description: R1 ES cells passaged on gelatin, p12


title: ES_R1 #1(16012165010082)

description: R1 ES cells passaged on gelatin, p12


title: NS1 #3(16012165010090)

description: doublet cells


title: NS5 #2(16012165010106)

description: neural stem cells


title: P19 4-1(16012165010046)

growth_protocol: Grown on gelatin in DMEM (GIBCO 11965) with 10%FCS, 2mM Glutamine and p/s.

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin.

tag: embryonic stem cell C3H/He male


title: P19 RA 1-1(16012165010047)

description: P19 RA

treatment_protocol: To induce neural differentiation of P19 cells, they were aggregated in presence of 1μM all-trans-retinoic acid (RA, Sigma) in 100 mm bacteriological dishes (Fisher). The RA stock solution (10mM) was made with anhydrous ethanol. Cultures were fed with fresh media containing RA after 2 days. P19 cell aggregates were cultured for following 2days.


title: P19 RA 4-1(16012165010049)

description: P19 RA


title: P19 1-1(16012165010036)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin.


title: P19 RA 3-1(16012165010048)

description: P19 RA


title: P19 3-1(16012165010045)


title: F9 1-1(16012165010021)

tag: embryonic stem cell 129 unknown sex


title: F9 4-1(16012165010024)


title: F9 3-1(16012165010022)


title: N2_d1 #1(16012165010067)

description: N2 day1

source_name: brain control (meth) #3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 1 day.

tag: embryonic stem cell 129/Sv male


title: N2_d3 #1(16012165010069)

description: N2 day3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 3 days.


title: N2_d4 #1(16012165010070)

description: N2 day4

source_name: brain 24h post-T3 induction #2

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 4 days.

tag: embryonic stem cell 129/Sv


title: N2_d1 #2(16012165010074)

description: N2 day1

source_name: brain 48h post-T3 induction #2


title: N2_d5 #1(16012165010071)

description: N2 day5

source_name: brain 24h post-T3 induction #3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 5 days.


title: N2_d4 #2(16012165010079)

description: N2 day4


title: N2_d2 #2(16012165010075)

description: N2 day2

source_name: brain 48h post-T3 induction #3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 2 days.


title: EB(4-/3+) #2(16012165010064)

treatment_protocol: Embryoid bodies were grown for 4 days without LIF at 5 x 106 cells per 100 mm bacteriological dish and then treated for 3 days with 1 μM RA.

source_name: Universal Mouse Reference RNA


title: ES_129b #2(16012165010073)

treatment_protocol: Undifferentiated 129 ES cells (2.5 x 106 cells) were cultured in gelatin-coated T25 flasks in ES standard medium with LIF for 24h.


title: N2_d6 #1(16012165010072)

description: N2 day6

source_name: brain 24h post-T3 induction #4

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 6 days.


title: ES_129b #1(16012165010066)

source_name: brain control (meth) #2


title: N2_d2 #1(16012165010068)

description: N2 day2


title: N2_d3 #2(16012165010078)

description: N2 day3

source_name: brain 48h post-T3 induction #4


title: N2_d5 #2(16012165010080)

description: N2 day5


title: EB(4-/2+) #2(16012165010063)

treatment_protocol: Embryoid bodies were grown for 4 days without LIF at 5 x 106 cells per 100 mm bacteriological dish and then treated for 2 days with 1 μM RA.


title: 242_PyPn_5_Cy5_vs_EtOH_3_Cy3_REV

treatment_protocol: Treatment: 2 mL of 99% ethanol, application was topical using a Potter's tower and the time elapsed between application and sampling was 6 hours.

tag: Sex

tag: Age

treatment_protocol: Treatment: 2 mL of 0.1 mg/mL Piper nigrum seed ethylacetate extract +0.004 mg/mL pyrethrin formulated in 99% ethanol, application was topical using a Potter's tower and the time elapsed between application and sampling was 6 hours.


title: EB(4-/1+) #2(16012165010062)

treatment_protocol: Embryoid bodies were grown for 4 days without LIF at 5 x 106 cells per 100 mm bacteriological dish and then treated for 1 days with 1 μM RA.


title: EB(4-) #2(16012165010059)

treatment_protocol: Embryoid bodies were grown for 4 days without LIF at 5 x 106 cells per 100 mm bacteriological dish


title: EB(4-/4+) #2(16012165010065)

source_name: brain control (meth) #1


title: EB(4-/3+) #1(16012165010056)


title: ES_129a #1(16012165010050)

treatment_protocol: Undifferentiated embryonic stem cells, 129.3 (129/SvEv) was cultivated on gelatin-coated 100 mm-dishes in DMEM supplemented with 15% FBS, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, Penicillin-Streptomycin and 103 unit/ml of LIF.


title: EB(4-) #1(16012165010051)


title: EB(4-/1+) #1(16012165010054)


title: EB(4-/4+) #1(16012165010057)

treatment_protocol: Embryoid bodies were grown for 4 days without LIF at 5 x 106 cells per 100 mm bacteriological dish and then treated for 4 days with 1 μM RA.


title: Drosophila_T0-2

status: Public on Jan 01 2006

city: Marseille cedex 9

first: Fanny

last: PILOT

address: Campus de Luminy case 907

department: Institut de Biologie du Développement de Marseille (IBDM)

institute: UMR6545 CNRS-Université de la Méditerrannée

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. File T0-2.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45oC 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: The image data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotine

source_name: Drosophila embryos before nuclear cycle 9 (maternal transcripts)

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

growth_protocol: 30 min egg collections of OreR and yw flies at 25°C were aged at room temperature (RT) according to the different temporal classes T0-T4.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer’s instructions.

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: Genotype

value: yellow white and Oregon R parents

value: embryos younger than nuclear cycle 9, i.e. before pole cells budding


title: EB(4-/2+) #1(16012165010055)


title: Drosophila_T4-1

description: Gene expression data from embryos at the end of germ band elongation. File T4-1.

source_name: Drosophila embryos at the end of germ band elongation

value: yellow white and Oregon R embryos Age :embryos at the end of germ band elongation


title: Drosophila_T3-3

description: Gene expression data from embryos at the beginning of germ band elongation. File T3-3.

source_name: Drosophila embryos at the beginning of germ band elongation

value: yellow white and Oregon R embryos Age :embryos at the beginning of germ band elongation


title: Drosophila_T0-3

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. File T0-3.

value: yellow white and Oregon R parents Age :embryos younger than nuclear cycle 9, i.e. before pole cells budding


title: Drosophila_T1-2

description: Gene expression data from embryos in slow phase of cellularisation. File T1-2.

source_name: Drosophila embryos in slow phase of cellularisation


title: Drosophila_T4-2

description: Gene expression data from embryos at the end of germ band elongation. File T4-2.


title: Drosophila_T2-4

description: Gene expression data from embryos in fast phase of cellularisation. File T2-4.

source_name: Drosophila embryos in fast phase of cellularisation

value: yellow white and Oregon R embryos


title: Drosophila_T1-3

description: Gene expression data from embryos in slow phase of cellularisation. File T1-3.


title: Drosophila_T3-2

description: Gene expression data from embryos at the beginning of germ band elongation. File T3-2.


title: Drosophila_T2-3

description: Gene expression data from embryos in fast phase of cellularisation. File T2-3.


title: Drosophila_T4-3

description: Gene expression data from embryos at the end of germ band elongation. File T4-3.


title: Drosophila_T2-1

description: Gene expression data from embryos in fast phase of cellularisation. File T2-1.


title: Drosophila_T1-1

description: Gene expression data from embryos in slow phase of cellularisation. File T1-1.


title: Drosophila_T3-1

description: Gene expression data from embryos at the beginning of germ band elongation. File T3-1.


title: SENS 1 0hr

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Not applicable

hyb_protocol: According to Buermans HP, et al. Physiol Genomics 2005;21:314-23

data_processing: ImaGene feature extraction (Biodiscovery Ltd, Marina del Rey, CA, USA) was used to record spot intensities. The signal mean was taken to represent the actual spot intensity, after subtraction of the mean background values. All spot were log2 transformed and intensities lower than 10, typical for the empty spots, were classified as missing. Next for each micro-array, the spot intensities were Z score normalized (Cheadle C, et al. J Mol Diagn  2003;5:73-81), while missing values (some 6% overall) were handled so as to minimize their effect on statistics. Specifically, such values were set equal to the mean of the micro-array distribution after Z score normalization, thus equal to zero. So for each micro-array, Z scores were computed for each green labeled spot intensity according to(2log(G) - mu) / sigma, where mu is the mean and sigma the standard deviation of all 2log(G) of the micro-array. Likewise the Z score was computed for each red labeled spot intensity and the result subtracted from the 'green' Z score for each spot on the micro-array. These differences were then again Z score normalized to obtain the so called Z ratio for each spot.This information will soon be available in a publication.

label_protocol: Non-amplified total RNA (75 µg) was used for preparation of labelled cDNA essentially as described (Buermans HP, et al. Physiol Genomics 2005;21:314-23). In brief, anchored oligo-dT [(dT)20-VN] primer was used and SuperScript II Reverse Transcriptase (Invitrogen), with incorporation of amino-allyl dUTP(Ambion, Huntingdon, UK). RNA was hydrolysed with 0.1 mM NaOH (70¦C, 10 min) and after neutralizing with 0.1 mM HCl the samples were diluted in water and transferred onto a Microcon YM-30 filter (Millipore, Billerica, MA, USA) to purify and concentrate the cDNA. Before labelling with the dye, the dry cDNA pellet was dissolved in 9 ml of NaHCO3/NaCO3 (50 mM, pH 9.0) and incubated at room temperature for 1 hr in the dark with 2 ml aliquots Cy 3(Fluorolink Cy 3 Monofunctional Dye (Amersham). Unbound dye was removed using the Qiaquick PCR purification kit (Qiagen, Venlo, the Netherlands)according to the manufacturer's protocol.

treatment_protocol: untreated

tag: lymphoblastoid cell line from F6.04, one out of seven of sensitive group

source_name: Reference pool

label_protocol: see label protocol of ch1 (Cy5 instead of Cy3)

tag: Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.


title: INSENS 7 4hr

description: Not applicable

scan_protocol: According to Buermans HP, et al. Physiol Genomics 2005;21:314-23

data_processing: ImaGene feature extraction (Biodiscovery Ltd, Marina del Rey, CA, USA) was used to record spot intensities. The signal mean was taken to represent the actual spot intensity, after subtraction of the mean background values. All spot were log2 transformed and intensities lower than 10, typical for the empty spots, were classified as missing. Next for each micro-array, the spot intensities were Z score normalized (Cheadle C, et al. J Mol Diagn  2003;5:73-81), while missing values (some 6% overall) were handled so as to minimize their effect on statistics. Specifically, such values were set equal to the mean of the micro-array distribution after Z score normalization, thus equal to zero. So for each micro-array, Z scores were computed for each green labeled spot intensity according to(2log(G) - mu) / sigma, where mu is the mean and sigma the standard deviation of all 2log(G) of the micro-array. Likewise the Z score was computed for each red labeled spot intensity and the result subtract from the ‘green’ Z score for each spot on the micro-array. These differences were then again Z score normalized to obtain the so called Z ratio for each spot.This information will soon be available in a publication.

label_protocol: Non-amplified total RNA (75 µg) was used for preparation of labelled cDNA essentially as described (Buermans HP, et al. Physiol Genomics 2005;21:314-23). In brief, anchored oligo-dT [(dT)20-VN] primer was used and SuperScript II Reverse Transcriptase (Invitrogen), with incorporation of amino-allyl dUTP(Ambion, Huntingdon, UK). RNA was hydrolysed with 0.1 mM NaOH (70°C, 10 min) and after neutralizing with 0.1 mM HCl the samples were diluted in water and transferred onto a Microcon YM-30 filter (Millipore, Billerica, MA, USA) to purify and concentrate the cDNA. Before labelling with the dye, the dry cDNA pellet was dissolved in 9 ml of NaHCO3/NaCO3 (50 mM, pH 9.0) and incubated at room temperature for 1 hr in the dark with 2 ml aliquots Cy 3(Fluorolink Cy 3 Monofunctional Dye (Amersham). Unbound dye was removed using the Qiaquick PCR purification kit (Qiagen, Venlo, the Netherlands)according to the manufacturer’s protocol.

treatment_protocol: bleomycin 4hr 5 mU/ml

tag: lymphoblastoid cell line from T21.01, one out of seven of insensitive group, 50*10e6 cells


title: Drosophila_T0-4

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation. File T0-4.


title: INSENS 7 0hr

description: Not applicable


title: N2_d6 #2(16012165010081)

description: N2 day6


title: SENS 5 4hr

description: Not applicable

tag: lymphoblastoid cell line from T4.02, one out of seven of insensitive group, 50*10e6 cells


title: INSENS 2 0hr

description: Not applicable

tag: lymphoblastoid cell line from F16.01, one out of seven of insensitive group, 50*10e6 cells


title: INSENS 3 4hr

description: Not applicable

tag: lymphoblastoid cell line from T9.01, one out of seven of insensitive group, 50*10e6 cells


title: INSENS 5 4hr

description: Not applicable

treatment_protocol: bleomycin 4hr 5mU/ml

tag: lymphoblastoid cell line from T6.01, one out of seven of insensitive group, 50*10e6 cells


title: SENS 2 0hr

description: Not applicable

source_name: R

tag: lymphoblastoid cell line from R, one out of seven of sensitive group, 50*10e6 cells


title: INSENS 4 0hr

description: Not applicable

tag: lymphoblastoid cell line from F23.05, one out of seven of insensitive group, 50*10e6 cells


title: INSENS 3 0hr

description: Not applicable


title: INSENS 4 4hr

description: Not applicable


title: SENS 2 4hr

description: Not applicable


title: INSENS 5 0hr

description: Not applicable


title: INSENS 6 4hr

description: Not applicable

tag: lymphoblastoid cell line from T3.02, one out of seven of insensitive group, 50*10e6 cells


title: INSENS 1 0hr

description: Not applicable


title: INSENS 2 4hr

description: Not applicable


title: SENS 3 4hr

description: Not applicable

tag: lymphoblastoid cell line from P910, one out of seven of sensitive group, 50*10e6 cells


title: INSENS 6 0hr

description: Not applicable


title: SENS 5 0hr

description: Not applicable

tag: lymphoblastoid cell line from T5.02, one out of seven of sensitive group, 50*10e6 cells


title: Wild-type SeriesB Transition T+2.75 hours

status: Public on Nov 16 2005

city: Newcastle upon Tyne

first: Nicholas

last: Allenby

state: Tyne and Wear

address: Leech Building, Medical School

department: Institute for Cell and Molecular Biosciences

country: United Kingdom

institute: The University of Newcastle upon Tyne

description:
Total RNA was extracted from the wild-type strain (Bacillus subtilis, 168) and phoR and sigB-null mutants before, during (T0) and after transition to phosphate-limited growth.  Cell harvesting, preparation of RNA, synthesis of radioactively labeled  cDNA and hybridization  of B. subtilis macroarrays (Sigma-Genosys, The Woodlands, Tex., USA) were performed as described by Eymann and co-workers (Eymann, C., H. Mach, C. R. Harwood, and M. Hecker. 1996. Phosphate-starvation-inducible proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study. Microbiology 142:3163-70.). Each analysis was carried out twice, using two independently isolated RNA preparations and two different array batches. The arrays were exposed to a phosphorescent screen which was subsequently scanned with a Storm 860 PhosphorImager (Molecular Dynamics, Sunnyvale, CA, USA) at a resolution of 50 µm and a 16-bit color depth. For quantification of the hybridization signals and background subtraction, the ArrayVision software (Version 5.1, Imaging Research, Onteria, Canada) was used. Calculation of normalized intensity values of the individual spots was performed using the over-all-spot-normalization function of ArrayVision. To avoid extreme expression ratios for genes close to or below the detection limit, genes with signal intensity values corresponding to less that twice the background were not counted in the analysis. Subsequently, the average of the normalized intensity values of the duplicate spots of each gene was used to calculate the expression level ratios. Data analysis (statistical analysis, visualization and the generation of lists) was performed using the GeneSpring software (Version 4.2.12, Silicon Genetics, Redwood City, CA).
Keywords = phosphate starvation
Keywords = PhoP regulon
Keywords = signal transduction
Keywords = DNA-array
Keywords = gene expression

organism: Bacillus subtilis

source_name: Total RNA SeriesB


title: SENS 4 4hr

description: Not applicable

tag: lymphoblastoid cell line from F6.01, one out of seven of sensitive group, 50*10e6 cells


title: SENS 1 4hr

description: Not applicable

tag: lymphoblastoid cell line from F6.04, one out of seven of sensitive group, 50*10e6 cells


title: SENS 7 4hr

description: Not applicable


title: SENS 4 0hr

description: Not applicable


title: ES_129a #2(16012165010058)

tag: embryonic stem cell 129/Sv

tag: Universale Mouse Reference


title: SENS 3 0hr

description: Not applicable


title: SENS 7 0hr

description: Not applicable

tag: lymphoblastoid cell line from F1.02, one out of seven of sensitive group, 50*10e6 cells


title: SENS 6 4hr

description: Not applicable


title: total RNA pool: 25% TR076, 75% TR077(16012165010019)

status: Public on Oct 28 2005

description: total RNA pool: 25% TR076, 75% TR077

source_name: total RNA pool: 25% TR076, 75% TR077

tag: C57BL/6 mixed sex embryo


title: E12.5 Placenta1, 5 pooled(16012165010020)

description: E12.5 Placenta

source_name: E12.5 Placentas, 5 pooled

treatment_protocol: Pregnant female mice from timed matings were sacrificed by cervical dislocation at 12.5 days post-coitus.  Decidua were removed to 1x PBS on ice, and embryos/placentas were dissected and transferred to iced PBS.  For each litter, embryos were combined in one tube, while placentas were combined in another.  Tubes were snap frozen on dry ice and stored at -80°C.

tag: mixed C57BL/6 mixed sex embryo


title: total RNA pool: 50% TR076, 50% TR077(16012165010018)

description: total RNA pool: 50% TR076, 50% TR077

source_name: total RNA pool: 50% TR076, 50% TR077


title: TS #3(251279910061)

description: GFP-Exe TS cells

source_name: GFP-Exe TS cells

treatment_protocol: grown on TC plastic, 70cond+Fgf4+Heparin, p35, GFP sort, p22

tag: trophoblast stem cell B5/GFP unknown sex  GFP transgenic

source_name: Universal Mouse Reference Cell Line Pool


title: ES_R1 #2(251279910055)

description: R1 ES cells passaged on gelatin, p12

source_name: R1 ES cells passaged on gelatin, p12

treatment_protocol: Passaged on gelatin, p12

tag: embryonic stem cell 129X1/Sv male


title: E12.5 Placenta2, 5 pooled(251279910051)

description: E12.5 Placenta


title: E12.5 Placenta3, 3 pooled(251279910053)

description: E12.5 Placenta

source_name: E12.5 Placenta, 3 pooled


title: total RNA pool: 75% TR076, 25% TR077(16012165010017)

description: total RNA pool: 75% TR076, 25% TR077

source_name: total RNA pool: 75% TR076, 25% TR077

source_name: Universal Mouse Reference RNA


title: TS #1(251279910059)

description: GFP-Exe TS cells

treatment_protocol: grown on TC plastic, 70cond+Fgf4+Heparin, p28, DNA/GFP sort, p4


title: TS #2(251279910060)

description: GFP-Exe TS cells


title: E12.5 Embryos2, 5 pooled(251279910049)

description: E12.5 Embryos

source_name: E12.5 Embryos, 5 pooled


title: ES_R1 #1(251279910054)

description: R1 ES cells passaged on gelatin, p12


title: E12.5 Embryos3, 3 pooled(251279910052)

description: E12.5 Embryos

source_name: E12.5 Embryo, 3 pooled


title: E12.5 Placenta1, 5 pooled(251279910048)

description: E12.5 Placenta


title: E12.5 Placenta1, 5 pooled(16012165010015)

description: E12.5 Placenta


title: E12.5 Embryos1, 5 pooled(251279910047)

description: E12.5 Embryos


title: ES_R1 #3(251279910058)

description: R1 ES cells passaged on gelatin, p12


title: total RNA pool: 50% TR076, 50% TR077(16012165010013)

description: total RNA pool: 50% TR076, 50% TR077


title: total RNA pool: 25% TR076, 75% TR077(16012165010014)

description: total RNA pool: 25% TR076, 75% TR077


title: E12.5 Embryos1, 5 pooled(16012165010016)

description: E12.5 Embryos


title: E12.5 Embryos1, 5 pooled(16012165010011)

description: E12.5 Embryos


title: SENS 6 0hr

description: Not applicable

tag: lymphoblastoid cell line from F6.06, one out of seven of sensitive group, 50*10e6 cells

tag: Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.


title: total RNA pool: 75% TR076, 25% TR077(16012165010012)

description: total RNA pool: 75% TR076, 25% TR077


title: FVB/NJ pituitary gland rep1

status: Public on Oct 23 2005

city: La Jolla

first: Carrolee

last: Barlow

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

description: Wild type 8 wk old male FVB/NJ mouse pituitary gland

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Lockhart-Barlow expression analysis algorithm

source_name: pituitary gland

label_protocol: 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: pituitary glands  were dissected from five FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).

tag: Wild type 8 wk old male


title: C57BL/6J pituitary gland rep2

description: Wild type 8 wk old male C57BL/6J mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ pituitary gland rep2

description: Wild type 8 wk old male C3H/HeJ mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J pituitary gland rep2

description: Wild type 8 wk old male A/J mouse pituitary gland

extract_protocol: pituitary glands was dissected from five A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ periaqueductal gray rep1

description: Wild type 8 wk old male FVB/NJ mouse periaqueductal gray

source_name: periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac pituitary gland rep2

description: Wild type 8 wk old male 129S6/SvEvTac mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ pituitary gland rep1


title: 129S6/SvEvTac pituitary gland rep1


title: C57BL/6J periaqueductal gray rep2

description: Wild type 8 wk old male C57BL/6J mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J periaqueductal gray rep1


title: FVB/NJ periaqueductal gray rep2

extract_protocol: periaqueductal gray regions were dissected from two FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J pituitary gland rep1


title: DBA/2J periaqueductal gray rep1

description: Wild type 8 wk old male DBA/2J mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ pituitary gland rep2

extract_protocol: pituitary glands  were dissected from five FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ periaqueductal gray rep1

description: Wild type 8 wk old male C3H/HeJ mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J periaqueductal gray rep2


title: INSENS 1 4hr

description: Not applicable

tag: lymphoblastoid cell line from T4.02, one out of seven of insensitive group, 50*10e6 cells


title: 129S6/SvEvTac periaqueductal gray rep2

description: Wild type 8 wk old male 129S6/SvEvTac mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac periaqueductal gray rep1


title: C3H/HeJ periaqueductal gray rep2


title: FVB/NJ hypothalamus rep2

description: Wild type 8 wk old male FVB/NJ mouse hypothalamus

source_name: hypothalamus

extract_protocol: hypothalami were dissected from one FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J pituitary gland rep2

description: Wild type 8 wk old male DBA/2J mouse pituitary gland

extract_protocol: pituitary glands  were dissected from five DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J periaqueductal gray rep2

description: Wild type 8 wk old male A/J mouse periaqueductal gray

extract_protocol: periaqueductal gray was dissected from one A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J pituitary gland rep1


title: FVB/NJ hypothalamus rep1

extract_protocol: hypothalami were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hypothalamus rep2

description: Wild type 8 wk old male DBA/2J mouse hypothalamus

extract_protocol: hypothalami were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J pituitary gland rep1

extract_protocol: pituitary glands  were dissected from five A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ hypothalamus rep2

description: Wild type 8 wk old male C3H/HeJ mouse hypothalamus

extract_protocol: hypothalami were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hypothalamus rep2

description: Wild type 8 wk old male C57BL/6J mouse hypothalamus

extract_protocol: hypothalami were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hypothalamus rep1


title: DBA/2J hippocampus rep2

description: Wild type 8 wk old male DBA/2J mouse hippocampus

source_name: hippocampus

extract_protocol: Hippocampi were dissected from one DBA/2J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac hypothalamus rep2

description: Wild type 8 wk old male 129S6/SvEvTac mouse hypothalamus

extract_protocol: hypothalami were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac hypothalamus rep1


title: FVB/NJ hippocampus rep1

description: Wild type 8 wk old male FVB/NJ mouse hippocampus

extract_protocol: Hippocampi were dissected from one FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hypothalamus rep2

description: Wild type 8 wk old male A/J mouse hypothalamus

extract_protocol: hypothalami were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hippocampus rep2

description: Wild type 8 wk old male A/J mouse hippocampus

extract_protocol: Hippocampi were dissected from one A/J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J hippocampus rep1


title: A/J hypothalamus rep1


title: C57BL/6J hypothalamus rep1


title: C3H/HeJ hippocampus rep2

description: Wild type 8 wk old male C3H/HeJ mouse hippocampus

extract_protocol: Hippocampi were dissected from one C3H/HeJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hippocampus rep2

description: Wild type 8 wk old male C57BL/6J mouse hippocampus

extract_protocol: Hippocampi were dissected from one C57BL/6J mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ cingulate cortex rep1

description: Wild type 8 wk old male FVB/NJ mouse cingulate cortex

source_name: cingulate cortex

label_protocol: 50 ng of total RNA was processed to produce biotinylated cRNA targets using two rounds of cDNA synthesis and in vitro transcription.

extract_protocol: Cingulate cortices were dissected from two FVB/NJ mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J hippocampus rep1


title: C3H/HeJ hypothalamus rep1


title: C3H/HeJ hippocampus rep1


title: FVB/NJ cingulate cortex rep2

extract_protocol: Cingulate cortices were dissected from one FVB/NJ mouse. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J hippocampus rep1


title: DBA/2J cingulate cortex rep2

description: Wild type 8 wk old male DBA/2J mouse cingulate cortex

extract_protocol: Cingulate cortices were dissected from one DBA/2J mouse. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J cingulate cortex rep1

extract_protocol: Cingulate cortices were dissected from two DBA/2J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac hippocampus rep1

description: Wild type 8 wk old male 129S6/SvEvTac mouse hippocampus

extract_protocol: Hippocampi were dissected from one 129S6/SvEvTac mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ cingulate cortex rep1

description: Wild type 8 wk old male C3H/HeJ mouse cingulate cortex

extract_protocol: Cingulate cortices were dissected from two C3H/HeJ mice. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ cingulate cortex rep2

extract_protocol: Cingulate cortices were dissected from one C3H/HeJ mouse. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J cingulate cortex rep2

description: Wild type 8 wk old male C57BL/6J mouse cingulate cortex

extract_protocol: Cingulate cortices were dissected from two C57BL/6J mice. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J cingulate cortex rep3

description: Wild type 8 wk old male A/J mouse cingulate cortex

extract_protocol: Cingulate cortices were dissected from one A/J mouse under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac hippocampus rep2


title: A/J cingulate cortex rep1

extract_protocol: Cingulate cortices were dissected from two A/J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J bed nucleus of the stria terminalis rep2

description: Wild type 8 wk old male C57BL/6J mouse bed nucleus of the stria terminalis

source_name: bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three C57BL/6J mice under a dissection microscope. The samples were frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ bed nucleus of the stria terminalis rep1

description: Wild type 8 wk old male C3H/HeJ mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from two C3H/HeJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ bed nucleus of the stria terminalis rep2

description: Wild type 8 wk old male FVB/NJ mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three FVB/NJ mouse under a dissection microscope. The samples were frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac cingulate cortex rep2

description: Wild type 8 wk old male 129S6/SvEvTac mouse cingulate cortex

extract_protocol: Cingulate cortices were dissected from two 129S6/SvEvTac. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ bed nucleus of the stria terminalis rep1

extract_protocol: bed nuclei of the stria terminalis were dissected from two FVB/NJ mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ hippocampus rep2

extract_protocol: Hippocampi were dissected from one FVB/NJ mouse under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J cingulate cortex rep1


title: DBA/2J bed nucleus of the stria terminalis rep2

description: Wild type 8 wk old male DBA/2J mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C57BL/6J bed nucleus of the stria terminalis rep1

extract_protocol: bed nuclei of the stria terminalis were dissected from two C57BL/6J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J bed nucleus of the stria terminalis rep1

extract_protocol: bed nuclei of the stria terminalis were dissected from two DBA/2J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ bed nucleus of the stria terminalis rep3


title: C3H/HeJ bed nucleus of the stria terminalis rep2

extract_protocol: bed nuclei of the stria terminalis were dissected from three C3H/HeJ mice under a dissection microscope. The samples were frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J periaqueductal gray rep1

description: Wild type 8 wk old male A/J mouse periaqueductal gray

extract_protocol: periaqueductal gray regions were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J bed nucleus of the stria terminalis rep2

description: Wild type 8 wk old male A/J mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac bed nucleus of the stria terminalis rep2

description: Wild type 8 wk old male 129S6/SvEvTac mouse bed nucleus of the stria terminalis

extract_protocol: bed nuclei of the stria terminalis were dissected from three 129S6/SvEvTac mice. The samples were frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J bed nucleus of the stria terminalis rep1

extract_protocol: bed nuclei of the stria terminalis were dissected from two A/J mice under a dissection microscope. The samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac bed nucleus of the stria terminalis rep1

extract_protocol: bed nuclei of the stria terminalis were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 129S6/SvEvTac cingulate cortex rep1

extract_protocol: Cingulate cortices were dissected from two 129S6/SvEvTac mice. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ amygdala rep2

description: Wild type 8 wk old male FVB/NJ mouse amygdala

source_name: amygdala

extract_protocol: Amygdalae were dissected from two FVB/NJ mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J amygdala rep2

description: Wild type 8 wk old male DBA/2J mouse amygdala

extract_protocol: Amygdalae were dissected from one DBA/2J mouse under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ amygdala rep1

description: Wild type 8 wk old male C3H/HeJ mouse amygdala

extract_protocol: Amygdalae were dissected from two C3H/HeJ mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: DBA/2J amygdala rep1

extract_protocol: Amygdalae were dissected from two DBA/2J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: C3H/HeJ amygdala rep2

extract_protocol: Amygdalae were dissected from one C3H/HeJ mouse under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: FVB/NJ amygdala rep1


title: C57BL/6J amygdala rep2

description: Wild type 8 wk old male C57BL/6J mouse amygdala

extract_protocol: Amygdalae were dissected from two C57BL/6J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J amygdala rep1

description: Wild type 8 wk old male A/J mouse amygdala

extract_protocol: Amygdalae were dissected from two A/J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: A/J amygdala rep2

extract_protocol: Amygdalae were dissected from one A/J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: TS cells, sample #2(16011321011191)

status: Public on Aug 30 2005

description: TS cells

source_name: TS cells

growth_protocol: The cells derived form ICR E3.5 blastocysts and the extraembryonic ectoderm of E6.5 embryos, cultured in the presence of feeder-conditioned medium with FGF4; see Tanaka et al. Science 1998.

extract_protocol: Using the QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA), total RNA was extracted from the diploid-sorted TS cell lines derived from ICR E3.5 blastcysts and the extraembryonic ectoderm of E6. 5 embryos, cultured in the presence of feeder-conditioned medium with FGF4 (details on Tanaka et al. 1998. Science 282: 2072-2075).

tag: TS cells 129/Sv male  gene knock in

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts


title: 129S6/SvEvTac amygdala rep1

description: Wild type 8 wk old male 129S6/SvEvTac mouse amygdala

extract_protocol: Amygdalae were dissected from two 129S6/SvEvTac mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: ES cells, sample #1(16011321011187)

description: ES cells R1

source_name: ES cells R1

growth_protocol: The cells were derived from F1 hybrid mouse between 129X1/SvJ and 129S1/Sv, cultreed on gelatin with LIF; see Nagy et al. Proc. Natl. Acad. Sci. 1993.

tag: ES cells 129/Sv male


title: ES cells, sample #3(16011321011189)

description: ES cells R1


title: C57BL/6J amygdala rep1


title: ES cells, sample #2(16011321011188)

description: ES cells R1


title: 129S6/SvEvTac amygdala rep3

extract_protocol: Amygdalae were dissected from one 129S6/SvEvTac mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: MIN6 growth at 5.5 mM of glucose and not treated with amylin (control)

status: Public on Apr 12 2005

city: Barcelona

first: Silvia

last: Casas Fontdevila

address: Villarroel, 170

country: Spain

institute: IDIBAPS

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was not treated with human amylin

hyb_protocol: According to Affymetrix protocol (biotin labeled cRNA)

scan_protocol: According to Affymetrix protocol

data_processing: Raw data was background adjusted, normalized and summarized by RMA (Affy package version 1.12.2, R version 2.4.0)

source_name: MIN6, 5.5 mM of glucose, not treated with amylin

label_protocol: According to Affymetrix protocol (biotin)

extract_protocol: According to the protocol enclosed with the RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Not treated with amylin


title: MIN6 growth at 5.5 mM of glucose and treated at 20 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 12h

source_name: MIN6, 5.5 mM of glucose,treated at 20 uM of amylin during 12h

treatment_protocol: Treated at 20 uM of amylin during 12h


title: TS cells, sample #1(16011321011190)

description: TS cells


title: MIN6 growth at 5.5 mM of glucose and treated at 20 uM of amylin during 24h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 24h

source_name: MIN6, 5.5 mM of glucose,treated at 20 uM of amylin during 24h

treatment_protocol: Treated at 20 uM of amylin during 24h


title: 129S6/SvEvTac amygdala rep2


title: TS cells, sample #3(16011321011192)

description: TS cells


title: MIN6 growth at 22.7 mM of glucose and treated at 10 uM of amylin during 24h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 24h

source_name: MIN6, 22.7 mM of glucose, treated at 10 uM of amylin during 24h

treatment_protocol: Treated at 10 uM of human amylin during 24h


title: MIN6 growth at 5.5 mM of glucose and treated at 20 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 2h

source_name: MIN6, 5.5 mM of glucose,treated at 20 uM of amylin during 2h

treatment_protocol: Treated at 20 uM of amylin during 2h


title: MIN6 growth at 5.5 mM of glucose and treated at 10 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 12h

source_name: MIN6, 5.5 mM of glucose,treated at 10 uM of amylin during 12h

treatment_protocol: Treated at 10 uM of amylin during 12h


title: MIN6 growth at 5.5 mM of glucose and treated at 1 uM of amylin during 24h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 24h

source_name: MIN6, 5.5 mM of glucose,treated at 1 uM of amylin during 24h

treatment_protocol: Treated at 1 uM of amylin during 24h


title: MIN6 growth at 22.7 mM of glucose and treated at 10 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 12h

source_name: MIN6, 22.7 mM of glucose, treated at 10 uM of amylin during 12h


title: MIN6 growth at 5.5 mM of glucose and treated at 1 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 2h

source_name: MIN6, 5.5 mM of glucose,treated at 1 uM of amylin during 2h

treatment_protocol: Treated at 1 uM of amylin during 2h


title: MIN6 growth at 5.5 mM of glucose and treated at 1 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 12h

source_name: MIN6, 5.5 mM of glucose,treated at 1 uM of amylin during 12h

treatment_protocol: Treated at 1 uM of amylin during 12h


title: MIN6 growth at 5.5 mM of glucose and treated at 10 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 5.5 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 2h

source_name: MIN6, 5.5 mM of glucose,treated at 10 uM of amylin during 2h

treatment_protocol: Treated at 10 uM of amylin during 2h


title: MIN6 growth at 22.7 mM of glucose and treated at 20 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 2h

source_name: MIN6, 22.7 mM of glucose,treated at 20 uM of amylin during 2h


title: MIN6 growth at 22.7 mM of glucose and treated at 20 uM of amylin during 12h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 12h

source_name: MIN6, 22.7 mM of glucose,treated at 20 uM of amylin during 12h


title: MIN6 growth at 22.7 mM of glucose and treated at 10 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 10 uM of human amylin during 2h

source_name: MIN6, 22.7 mM of glucose, treated at 10 uM of amylin during 2h


title: MIN6 growth at 22.7 mM of glucose and treated at 1 uM of amylin during 24h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 24h

source_name: MIN6, 22.7 mM of glucose, treated at 1 uM of amylin during 24h


title: MIN6 growth at 22.7 mM of glucose and not treated with amylin (control)

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was not treated with human amylin

source_name: MIN6, 22.7 mM of glucose, not treated with amylin


title: MIN6 growth at 22.7 mM of glucose and treated at 1 uM of amylin during 2h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 1 uM of human amylin during 2h

source_name: MIN6, 22.7 mM of glucose, treated at 1 uM of human amylin during 2h

treatment_protocol: Treated at 1 uM of human amylin during 2h


title: A/J cingulate cortex rep2

description: Wild type 8 wk old male A/J mouse cingulate cortex

source_name: cingulate cortex

extract_protocol: Cingulate cortices were dissected from two A/J mice under a dissection microscope. The samples were frozen in the RNALater buffer and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).


title: 4 week old ERM knockout testis

status: Public on Apr 01 2005

city: St. Louis

first: Kenneth

middle: Martin

last: Murphy

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: ERM knockout 4 week old testis

source_name: testis


title: Primary Mouse ERM knockout 10 week old Sertoli Cells

description: ERM knockout Sertoli cells at 10 weeks

source_name: Primary Mouse Sertoli cells, 10 week ERM knockout


title: MIN6 growth at 22.7 mM of glucose and treated at 20 uM of amylin during 24h

description: Murine pancreatic beta cell line MIN6 was growth at 22.7 mM of glucose, 37 ºC, 5% CO2 and was treated at 20 uM of human amylin during 24h

source_name: MIN6, 22.7 mM of glucose,treated at 20 uM of amylin during 24h


title: HeLa transfected with miR-124mut9-10 versus control transfected HeLa, 24 hours

status: Public on Jan 31 2005

city: Seattle

first: Lee

last: Lim

state: WA

institute: Rosetta Inpharmatics

description:
100nM Oligofectamine transfection of duplexes as described in Lim et al., submitted to Nature, 2004
Sample author: Jason,M,Johnson
Keywords = microRNA

source_name: HeLa transfected with miR-124mut9-10 duplex, 24 hours

source_name: Mock transfected HeLa, 24 hours


title: HeLa transfected with miR-373/hes3 versus control transfected HeLa, 12 hours

description:
100nM Oligofectamine transfection of duplexes as described in Lim et al., submitted to Nature, 2004
Keywords = microRNA

source_name: HeLa transfected with miR-373/hes3 duplex, 12 hours

source_name: Mock transfected HeLa, 12 hours


title: TM4 cell line with transfection of ERM

description: TM4 cell line with transfection of ERM

source_name: TM4-ERM cell line


title: HeLa transfected with miR-124mut9-10 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR-124mut9-10 duplex, 12 hours


title: 42. activated blastocysts lot 3(16011321011228)

status: Public on Aug 04 2004

description: activated blastocysts

source_name: Act.3 RNA

label_protocol: Three batches of 100 blastocysts were collected for dormant and activated blastocysts respectively, and mRNA was extracted from each batch using a Quickprep micro poly-A RNA Extraction Kit (Amersham Biosciences). mRNA aliquots equivalent to 24 blastocysts from each mRNA subset were labeled with Cy3 dyes by two-round linear amplification labeling reactions for cRNA targets using Fluorescent Linear Amplification Kits (Agilent Technologies). Briefly, mRNA was used to synthesize double-stranded cDNA with moloney murine leukemia virus (MMLV) reverse transcriptase in a reaction scaled down to a total volume of 4 ul, with half the standard T7-oligo-dT primer concentration and 125 ng/ul ofT4gp32 single-stranded DNA-binding protein (United States Biochemical,  Cleveland, OH). Linear amplification (in vitro transcription) was performed in a total volume of 16 ul, with half the standard NTP concentration and no labeled CTP. For the second round of amplification, the product of the first reaction was divided in half, and labeled using the manufacturers standard protocol, with the addition of T4gp32 in the cDNA synthesis reaction. Quality and size distribution of targets was determined by an RNA 6000 Nano Lab-on-chip Assay (Agilent Technologies), and quantitation was determined using a NanoDrop microscale spectrophotometer (NanoDrop, Wilmington, DE). cRNA targets were assembled into hybridizations on the NIA 22K 60-mer oligo microarray (manufactured by Agilent Technologies)

extract_protocol: Three batches of 100 blastocysts were collected for dormant and activated blastocysts respectively, and mRNA was extracted from each batch using a Quickprep micro poly-A RNA Extraction Kit (Amersham Biosciences). mRNA aliquots equivalent to 24 blastocysts from each mRNA subset were labeled with Cy3 dyes by two-round linear amplification labeling reactions for cRNA targets using Fluorescent Linear Amplification Kits (Agilent Technologies). The quality and size distribution of targets were determined by RNA 6000 Nano Lab-on-chip Assay (Agilent), and quantitation was determined using a microscale spectrophotometer (NanoDrop).

source_name: Universal Mouse Reference RNA


title: HeLa transfected with miR-373/hes3 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR-373/hes3 duplex, 24 hours


title: Primary Mouse ERM knockout 4 week old Sertoli Cells

description: ERM knockout Sertoli cells at 4 weeks

source_name: Primary Mouse Sertoli cells, 4 week ERM knockout


title: Primary Mouse wild type 4 week old Sertoli Cells

description: Wild type Sertoli cells at 4 weeks

source_name: Primary Mouse Sertoli cells, 4 week wild type


title: HeLa transfected with miR-124mut5-6 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR-124mut5-6 duplex, 24 hours


title: HeLa transfected with miR-124 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR-124 duplex, 12 hours


title: HeLa transfected with chimiR-124-1 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with chimiR-124-1 duplex, 24 hours


title: HeLa transfected with miR-124mut5-6 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR-124mut5-6 duplex, 12 hours


title: 40. activated blastocysts lot 1(16011321011226)

description: activated blastocysts

source_name: Act.1 RNA


title: TM4 cell line without transfection of ERM

source_name: TM4 cell line


title: HeLa transfected with miR-1 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR-1 duplex, 12 hours


title: 39. dormant blastocysts lot 3(16011321011225)

description: dormant blastocysts

source_name: Dor.3 RNA


title: HeLa transfected with chimiR-1-124 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with chimiR-1-124 duplex, 24 hours

source_name: Mock transfected HeLa, 24 hours


title: 38. dormant blastocysts lot 2(16011321011224)

description: dormant blastocysts

source_name: Dor.2 RNA


title: 41. activated blastocysts lot 2(16011321011227)

description: activated blastocysts

source_name: Act.2 RNA


title: HeLa transfected with miR-1 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR-1 duplex, 24 hours


title: HeLa transfected with chimiR-124-1 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with chimiR-124-1 duplex, 12 hours

source_name: Mock transfected HeLa, 12 hours


title: HeLa transfected with chimiR-1-124 versus control transfected HeLa, 12 hours

source_name: HeLa transfected with chimiR-1-124 duplex, 12 hours


title: HeLa transfected with miR-124 versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR-124 duplex, 24 hours


title: H-P1

status: Public on Aug 01 2003

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: photosynthetic conditions

organism: Cereibacter sphaeroides

source_name: University of Texas Health Science Center at Houston


title: H-D2

description: DMSO conditions


title: H-S2

description: semiaerobic conditions


title: H-D1

description: DMSO conditions


title: H-3R

description: aerobic conditions, mutant...


title: H-S4

description: semiaerobic conditions


title: H-P2

description: photosynthetic conditions


title: H-4R

description: 2-nd replicate of Rebecca's mutant


title: H-A1

description: aerobic conditions


title: 4 week old Wild type testis 1

description: wild type 4 week old testis

source_name: testis


title: H-1R

description: aerobic conditions


title: H-A4

description: aerobic conditions


title: Inflammatory myopathy specimen GEIM4

status: Public on Jan 21 2003

city: Boston

first: Steven

middle: Alan

last: Greenberg

state: MA

address: 75 Francis Street

department: Neurology

institute: Brigham and Women's Hospital

description: RNA from muscle biopsy specimen

source_name: Muscle


title: 37. dormant blastocysts lot 1(16011321011223)

description: dormant blastocysts

source_name: Dor.1 RNA

source_name: Universal Mouse Reference RNA


title: H-2R

description: aerobic conditions


title: S2

status: Public on Mar 11 2003

description: Semiaerobic conditions (3% oxygen). Bead-beater 2x DNAse.

source_name: University of Wyoming


title: S3


title: CT22;liver;NONE;C57/BL6;37447

status: Public on Feb 08 2007

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: Circadian Liver_48hr_gcrma

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine

data_processing: gcRMA

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.


title: Rat gastric ECL cells (95% purity), 24 hrs fasting #2

status: Public on Nov 22 2006

city: Los Angeles

first: Nils

last: Lambrecht

institute: UCLA

description: Manufacturer's scanner and feature extraction - normalization software

source_name: rat gastric mucosa

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: NucleoSpin RNA II (BD Biosciences, USA)

treatment_protocol: No access to food for 24 hrs.

tag: Homogeneous (95%) ECL cell suspensions, purified by counterflow elutriation and FACS using acridine orange as marker from rats fasted for 24 hrs.