title: Testis_MEHP_treatmentA3_Rep1

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating,278.34mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating, 278.34 mg/l.


title: Testis_Bisphenol_treatmentC3_Rep2

status: Public on Jun 01 2010

type: RNA

city: Madrid

first: Luis

middle: A.

last: Lopez-Fernandez

address: Dr. Esquerdo 46

department: Pharmacy

country: Spain

institute: Hospital General Universitario Gregorio Marañon

description:
Dye-Swap replicates were performed: one slide hybridized with experimental and control targets labeled with Cy3 and Cy5, respectively; and the second slide with the same type of targets but inversely labeled. Target refers to labeled aRNA while probe refers to the oligonucleotides spotted on the microarray platform.
Imaging and data generation were carried out using a GenePix 4000B (Axon Instruments) and associated software from Axon Instruments, Inc. The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5. Images were captured in TIFF files. Information extraction for a given spot was based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots. The Cy3 and Cy5 fluorescence signal intensities were normalized.

hyb_protocol: Prehybridization was performed at 42ºC for 30-45 minutes in 6X SSC, 0.5% SDS and 1% BSA. Slides were rinsed five times with destilled water. Cy5 and Cy3 amplified RNA (aRNA) probes were mixed (150 pmol of each label) with 10 µg of PolyA (Sigma) and 1 µg of Cot-DNA (Invitrogen) in a final volume of 40 µl of hybridization buffer (50% formamide, 6X SSC, 0.5% SDS, 5X Denhardt’s). The probe was denatured at 95ºC for 5 minutes and applied to the slide using a coverslip. Slides were then incubated at 42ºC for 16h in hybridization chambers (Array-It). After incubation, slides were washed twice with 0.1X SSC, 0.1% SDS for 5 minutes each, three times with 0.1X SSC for 5 minutes and finally in distilled water for 10 seconds. Slides were dried by centrifugation at 563g for 1 minute.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with an Axon 4000B scanner (Axon Instruments) and spots quantified using GenePix 5.1 software (Axon). GPR files were then included in almaZen database software (Bioalma). Signals were background subtracted, and normalized by total intensity and lowess_print_tip_group.

data_processing: GPR files with raw data were introduced in almaZen database software (http://www.Bioalma.com). Signals were background subtracted, and normalized by total intensity and Print_tip_group_Lowess.

molecule: total RNA

organism: Mus musculus

label_protocol: Starting with total RNA from pools (Three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies)

extract_protocol: Total RNA from testes of animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories).

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.

tag: strain

tag: gender

value: Male

tag: tissue

value: Testis

tag: age

value: four weeks

tag: agent

value: not exposed to chemical compounds.

label_protocol: Starting with total RNA from pools (three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies).

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 200 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_Bisphenol_treatmentC1_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.5 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth


title: Testis_MEHP_treatmentC2_Rep1

treatment_protocol: Mothers were exposed to MEHP (in DMSO) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 139.17 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth

value: Mothers were exposed to MEHP (in DMSOl) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth,139.17 mg/l .

extract_protocol: Total RNA from testes of animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories)

value: not exposed to chemical compounds


title: Testis_MEHP_treatmentA1_Rep1

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating,27.83 mg/l. Then, administration was interrupted. Male offspring were sacrificed to obtain the testis four weeks after birth.

value: Mothers were exposed to MEHP (in DMSO) two weeks before mating, 27.83 mg/l.


title: Testis_MEHP_treatmentA2_Rep2

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated

treatment_protocol: Mothers were exposed to MEHP for two weeks before mating, 27.83 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to MEPH (in DMSO) two weeks before mating, 27.83 mg/l.


title: Testis_Bisphenol_treatmentB1_Rep1

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating and maintained during pregnancy, 0.5 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating and maintained during pregnancy, 0.5 mg/l.


title: Testis_Bisphenol_treatmentC1_Rep1

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 0.5 mg/l.. Male offspring were sacrificed to obtain the testis four weeks after birth


title: Testis_Bisphenol_treatmentB3_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating and maintained during pregnancy, 200 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating and maintained during pregnancy, 200 mg/l.


title: Testis_Bisphenol_treatmentB2_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating and maintained during pregnancy, 50 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating and maintained during pregnancy, 50 mg/l.


title: Testis_MEHP_treatmentA1_Rep2

treatment_protocol: Mothers were exposed to MEHP  for two weeks before mating, 27.83 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.


title: Testis_Bisphenol_treatmentA3_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating, 200 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, 200 mg/l.


title: Testis_Bisphenol_treatmentB2_Rep1


title: Testis_MEHP_treatmentA3_Rep2

value: Mothers were exposed to MEPH (in DMSO) two weeks before mating, 278.34 mg/l


title: Testis_Bisphenol_treatmentC2_Rep1

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 50 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: Testis_Bisphenol_treatmentA3_Rep1


title: Testis_Bisphenol_treatmentA2_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating, 50 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, 50 mg/l.


title: Testis_Bisphenol_treatmentA2_Rep1


title: Testis_Bisphenol_treatmentB3_Rep1


title: Testis_Bisphenol_treatmentB1_Rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating and maintained during pregnancy, 0.5 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.


title: Testis_Bisphenol_treatmentA1_rep2

treatment_protocol: Mothers were exposed to Bisphenol A for two weeks before mating, 0.5 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

value: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, 0.5 mg/l.


title: Testis_Bisphenol_treatmentA1_Rep1

treatment_protocol: Mothers were exposed to Bisphenol A  for two weeks before mating, 0.5 mg/l. Then, administration was interrupted. Male offspring were sacrified to obtain the testis four weeks after birth.

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.


title: Testis_Control_rep2

extract_protocol: Total RNA from testes of controls animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories).


title: Testis_Control_rep1

label_protocol: Starting with total RNA from pools described above, full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies).


title: RPaSMC exposed to GSNO for 2 hours, microarray1

city: Boston

first: Andrea

middle: U

last: Steinbicker

state: MA

address: 55 Fruit Street

country: USA

institute: Massachusetts General Hospital

description: Gene expression data of rat pulmonary artery smooth muscle cells exposed to GSNO for 2 hours.

hyb_protocol: Labeled cRNA (40 mg) was fragmented in fragmentation buffer (40 mmol/L Tris, pH 8.1, 100 mmol/L potassium acetate, 30 mmol/L magnesium acetate) for 35 min at 94oC. Following confirmation of cRNA quality by hybridization to a test chip (Affymetrix), fragmented cRNA was hybridized to Affymetrix rat U-34A GeneChips containing 8798 gene elements in the GeneChip Fluidics Station 450.

scan_protocol: Gene Chips were scanned using the GeneChip® Scanner 3000.

data_processing: Affymetrix GeneChip 5.0 software was used for scanning and data analysis according to Affymetrix protocols.

label: biotin

organism: Rattus norvegicus

source_name: Rat pulmonary artery smooth muscle cells (RPaSMC) exposed to GSNO for 2 hours

label_protocol: Biotin-labeled cRNA was generated from the double-stranded cDNA by in vitro transcription using the ENZO Bioarray High Yield transcript labeling method (Affymetrix Inc., Santa Clara, CA).

growth_protocol: Cultures of primary rat pulmonary artery smooth muscle cells (RPaSMC) were prepared from explants of endothelium- and adventitia-stripped pulmonary arteries of adult Sprague-Dawley rats, as described previously [Takata, M. et al., Am J Physiol Lung Cell Mol Physiol., 280, L272-282, 2001].

extract_protocol: Total RNA from RPaSMC was extracted using Trizol® reagent (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: Rat pulmonary artery smooth muscle cells were either untreated or exposed to GSNO (100 mmol/L) for 1, 2, and 4 hours.

value: Sprague-Dawley

value: Pulmonary artery smooth muscle cells


title: RPaSMC exposed to GSNO for 2 hours, microarray2


title: RPaSMC exposed to GSNO for 1 hour, microarray1

description: Gene expression data of rat pulmonary artery smooth muscle cells exposed to GSNO for 1 hour.

source_name: Rat pulmonary artery smooth muscle cells (RPaSMC) exposed to GSNO for 1 hour


title: RPaSMC control, microarray 2

description: Gene expression data of untreated rat pulmonary artery smooth muscle cells

source_name: Rat pulmonary artery smooth muscle cells (RPaSMC) untreated


title: RPaSMC exposed to GSNO for 4 hours, microarray2

description: Gene expression data of rat pulmonary artery smooth muscle cells exposed to GSNO for 4 hours.

source_name: Rat pulmonary artery smooth muscle cells (RPaSMC) exposed to GSNO for 4 hours


title: RPaSMC exposed to GSNO for 4 hours, microarray1


title: RPaSMC control, microarray 1


title: Sinorhizobium meliloti Rm1021, biological rep2

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: Rm1021, cells harvested at OD600 of 0.84

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: For each biological replicate, a single bacterial colony was inoculated into 20 milliliters of TY broth, supplemented with streptomycin at 500 micrograms per microliter, and grown with shaking at 200 rpm at 30 degrees celsius in a 250 milliliter baffled flask.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: genotype/variation

tag: lab of origin

value: Max Teplitski


title: Sinorhizobium meliloti hfq deletion mutant, biological rep2

source_name: hfq deletion mutant, cells harvested at OD600 of 0.84


title: Sinorhizobium meliloti Rm1021, biological rep3


title: RPaSMC exposed to GSNO for 1 hour, microarray2


title: Sinorhizobium meliloti Rm1021, biological rep1

source_name: Rm1021, cells harvested at OD600 of 0.83


title: Sinorhizobium meliloti hfq deletion mutant, biological rep3


title: Sinorhizobium meliloti hfq deletion mutant, biological rep1

source_name: hfq deletion mutant, cells harvested at OD600 of 0.87


title: Esophageal Adenocarcinoma MRC/OEA0872BJ5

first: Paul

last: Grosu

address: 33 Avenue Louis Pasteur

institute: Microsoft/Merck

description: Individual esophageal adenocarcinoma tissue specimen

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Homo sapiens

source_name: Stratagene Universal Human Reference RNA

label_protocol: Custom automated version of the aminoallyl MessageAmp II kit from Ambion.  Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

extract_protocol: Total RNA was extracted from 10x 15 μm sections using Trizol™ according to Invitrogen's instructions

treatment_protocol: Human tissue specimens were surgically excised and snap frozen in liquid nitrogen

tag: sample type

value: Reference RNA Pool

value: Human esophageal adenocarcinoma

tag: patient id

value: Male

tag: survival days

tag: positive nodes

tag: tumor histology

value: Oesophageal adenocarcinoma

tag: tumor differentiation

value: Moderate

tag: tumour length cm

tag: tumour width cm

tag: tumor volume mm3


title: Esophageal Adenocarcinoma MRC/OEA0842CJ1

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber

value: Poor


title: Esophageal Adenocarcinoma MRC/OEA0645CJ4

value: Female

value: Gastric adenocarcinoma


title: Esophageal Adenocarcinoma MRC/OEA1202CJ0


title: Esophageal Adenocarcinoma MRC/OEA0972CJ1


title: Esophageal Adenocarcinoma MRC/OEA1372BJ4


title: Esophageal Adenocarcinoma MRC/OEA0995CJ4


title: Esophageal Adenocarcinoma MRC/OEA0635CJ4


title: Esophageal Adenocarcinoma MRC/OEA0682CJ2


title: Esophageal Adenocarcinoma MRC/OEA1625CJ4


title: Esophageal Adenocarcinoma MRC/OEA1612CJ2


title: Esophageal Adenocarcinoma MRC/OEA0532CJ0


title: Esophageal Adenocarcinoma MRC/OEA1602CJ3


title: Esophageal Adenocarcinoma MRC/OEA0652AJ1

value: Well


title: Esophageal Adenocarcinoma MRC/OEA1645CJ4


title: Esophageal Adenocarcinoma MRC/OEA0602BJ2


title: Esophageal Adenocarcinoma MRC/OEA1392CJ0


title: Esophageal Adenocarcinoma MRC/OEA0962BJ0


title: Esophageal Adenocarcinoma MRC/OEA1362CJ0


title: Esophageal Adenocarcinoma MRC/OEA0745CJ4


title: Esophageal Adenocarcinoma MRC/OEA1562CJ2


title: Esophageal Adenocarcinoma MRC/OEA1282BJ0


title: Esophageal Adenocarcinoma MRC/OEA1172CJ1


title: Esophageal Adenocarcinoma MRC/OEA1272CJ5


title: Esophageal Adenocarcinoma MRC/OEA1235BJ4


title: Esophageal Adenocarcinoma MRC/OEA1342BJ0


title: Esophageal Adenocarcinoma MRC/OEA1135BJ4


title: Esophageal Adenocarcinoma MRC/OEA1382CJ0


title: Esophageal Adenocarcinoma MRC/OEA1212BJ0


title: Esophageal Adenocarcinoma MRC/OEA0735BJ4


title: Esophageal Adenocarcinoma MRC/OEA1152BJ2


title: Esophageal Adenocarcinoma MRC/OEA1552AJ1


title: Esophageal Adenocarcinoma MRC/OEA0985BJ4


title: Esophageal Adenocarcinoma MRC/OEA1012BJ0


title: Esophageal Adenocarcinoma MRC/OEA0725BJ4


title: Esophageal Adenocarcinoma MRC/OEA0322CJ3


title: Esophageal Adenocarcinoma MRC/OEA0785CJ4


title: Esophageal Adenocarcinoma MRC/OEA0381CJ5

value: Squamous cell carcinoma


title: Esophageal Adenocarcinoma MRC/OEA0272CJ1


title: Esophageal Adenocarcinoma MRC/OEA0341CJ5


title: Esophageal Adenocarcinoma MRC/OEA1521CJ4


title: Esophageal Adenocarcinoma MRC/OEA1165AJ4


title: Esophageal Adenocarcinoma MRC/OEA0281BJ5


title: Esophageal Adenocarcinoma MRC/OEA0752BJ2


title: Esophageal Adenocarcinoma MRC/OEA0022CJ5


title: Esophageal Adenocarcinoma MRC/OEA0201BJ5


title: Esophageal Adenocarcinoma MRC/OEA0011BJ5


title: Esophageal Adenocarcinoma MRC/OEA0192BJ3


title: Esophageal Adenocarcinoma MRC/OEA0162CJ1


title: Esophageal Adenocarcinoma MRC/OEA0512BJ0


title: Esophageal Adenocarcinoma MRC/OEA0862BJ0


title: Esophageal Adenocarcinoma MRC/OEA0032CJ5


title: Esophageal Adenocarcinoma MRC/OEA1662BJ1


title: Esophageal Adenocarcinoma MRC/OEA0151AJ5


title: Esophageal Adenocarcinoma MRC/OEA0292CJ2


title: Esophageal Adenocarcinoma MRC/OEA0312CJ4


title: Esophageal Adenocarcinoma MRC/OEA0362CJ3


title: Esophageal Adenocarcinoma MRC/OEA0252BJ0


title: Esophageal Adenocarcinoma MRC/OEA0392CJ0


title: Esophageal Adenocarcinoma MRC/OEA0372AJ0


title: Esophageal Adenocarcinoma MRC/OEA0232AJ1


title: Esophageal Adenocarcinoma MRC/OEA0242CJ5


title: Esophageal Adenocarcinoma MRC/OEA0042BJ1


title: Esophageal Adenocarcinoma MRC/OEA0502BJ0


title: Esophageal Adenocarcinoma MRC/OEA0792BJ0


title: Rat Liver Biotin deficient 2

status: Public on May 31 2010

city: MEXICO, D.F.

first: Pablo Antonio

last: Velázquez-Arellano

address: Av. IMAN No. 1, 4th floor

department: Molecular Biology and Biotechnology

country: Mexico

institute: Institute for Biomedical Research, UNAM

description: Gene expression data from Rat Liver fed with avidin and low biotin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C with rotation (60 rpm) on the array (Affymetrix, Santa Clara, CA). GeneChips were washed and stained using Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin, and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays were scanned using Affymetrix Gene Array Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with Affymetrix GCOS 1.4 software by comparing means of signals intensity from RNA samples derived from biotin sufficient and deficient organisms.

source_name: Rat fed with a commercial biotin-deficient diet containing 30% of white egg as source of avidin

label_protocol: Total RNA (5 ug) was reverse transcribed using One Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA) and the obtained double-stranded cDNA was purified with GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). The obtained cDNA was used as a template for in vitro transcription using GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Five male rats (Wistar strain) aged 21 days and 50g of weight were made biotin-deficient and another five rats, of similar gender age and weight, served as controls. Biotin deficiency was induced by feeding them with a commercial biotin-deficient diet containing 30% of white egg as source of avidin (TD.81079 ICN Nutritional Biochemicals, Cleveland, OH). The control animals were fed with a similar diet that lacked avidin (TD.97126 ICN Nutritional Biochemicals, Cleveland, OH). Each rat was housed individually in an air-filtered cage on 12h light/dark cycles and was allowed for free access to water. Control and deficient rats were sacrificed at 6–7 weeks and the tissues were removed

extract_protocol: RNA was extracted was extracted with the TRIzol® method (Invitrogen) according to the manufacturer’s instructions. RNA was subsequently loaded onto RNA-binding columns from QIAGEN’s RNeasy kit (Qiagen, Valencia, CA) to remove contamination with genomic DNA and proteins before further processing.

treatment_protocol: Tissues were removed immediately after sacrifice and resuspended in PBS pH 7.0 buffer.

value: Wistar

value: 21 days

tag: animal weight

value: Liver

tag: environmental factor

value: biotin deficient diet


title: Esophageal Adenocarcinoma MRC/OEA0432BJ0

tag: gender


title: Rat Liver Control 3

description: Gene expression data from Rat Liver fed with enough biotin

source_name: Rat fed with a commercial diet with sufficent Biotin and that lacked avidin

tag: strain

tag: tissue

value: biotin sufficient diet


title: Esophageal Adenocarcinoma MRC/OEA0262CJ1


title: Rat Liver Biotin deficient 1

tag: age


title: Esophageal Adenocarcinoma MRC/OEA0472CJ1


title: Esophageal Adenocarcinoma MRC/OEA0221BJ5


title: Rat Liver Control 2


title: Rat Liver Biotin deficient 3


title: Yeast growth at 8 nM of biotin 2

description: Gene expression data from Yeast growth in minimal media with 8 nM of biotin and harvested in log phase.

organism: Saccharomyces cerevisiae

source_name: Yeast growth in Minimal Media with glucose and with biotin at 8 nM

growth_protocol: Yeast cells were grown overnight in a defined synthetic minimal (SD) media with dextrose (2 %), (NH4)2SO4, aminoacids, minerals and vitamins as complements but without biotin. Cells were centrifuged, washed, and used to inoculate cultures in MMY with 0.4 nM and 8nM of biotin adjusted to an A600 absorbance of 0.04.

treatment_protocol: Cells were harvested when cultures reached an A600 absorbance of 0.6 -0.8 and resuspended in 50% (v/v) of RNAlater Soln. (Ambion) and SD media.

tag: genome/variation


title: Esophageal Adenocarcinoma MRC/OEA1032AJ2


title: Yeast growth at 8 nM of biotin 3


title: Yeast growth at 8 nM of biotin 1


title: Esophageal Adenocarcinoma MRC/OEA0522CJ1


title: Yeast growth at 0.4 nM of biotin 1

description: Gene expression data from Yeast growth in minimal media with 0.4 nM of biotin and harvested in log phase.

source_name: Yeast growth in Minimal Media with glucose and with biotin at 0.4 nM


title: Esophageal Adenocarcinoma MRC/OEA0121CJ5


title: Yeast growth at 0.4 nM of biotin 3


title: Esophageal Adenocarcinoma MRC/OEA0415BJ4


title: Esophageal Adenocarcinoma MRC/OEA1412CJ1


title: Yeast growth at 0.4 nM of biotin 2


title: Rat Liver Control 1


title: PTC1_SDD_rep1

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

description: Gene expression data from yeast.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Signals were calculated by Affymetrix GeneChip Operating Software Version 1.4.

source_name: PTC1 with SDS and DON

label_protocol: Approximately 4 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

extract_protocol: Each sample of total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Strains BY4743 and PTC1 were grown in YPD medium including 0.01% SDS, or 0.01% SDS with 25 ppm deoxynivalenol.

value: PTC1 mutant

tag: condition

value: grown in YPD with SDS and deoxynivalenol


title: PTC1_SDD_rep2

description: Gene expression data from yeast.


title: Esophageal Adenocarcinoma MRC/OEA0052BJ1

tag: sample type

value: Reference RNA Pool


title: PTC1_SD_rep3

description: Gene expression data from yeast.

source_name: PTC1 with SDS

value: grown in YPD with SDS


title: Esophageal Adenocarcinoma MRC/OEA0402BJ0

value: Human esophageal adenocarcinoma

tag: patient id

value: Male


title: PTC1_SDD_rep3

description: Gene expression data from yeast.


title: PTC1_SD_rep2

description: Gene expression data from yeast.


title: Control_SDD_rep2

description: Gene expression data from yeast.

source_name: BY4743 with SDS and DON


title: Control_SDD_rep3

description: Gene expression data from yeast.


title: Control_SDD_rep1

description: Gene expression data from yeast.


title: Control_SD_rep2

description: Gene expression data from yeast.

source_name: BY4743 with SDS


title: Caenorhabditis elegans in biotin deficiency 3

description: Gene expression data from Caenorhabditis elegans grown with deficient biotin

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans in grown in minimal media with conditions of biotin deficiency

growth_protocol: Biotin deficiency for C. elegans strain N2 was achieved by feeding nematodes synchronized in L1 stage with an overnight culture of E.coli biotin auxotrophic (MG1655bioB:kan, kindly donated by Dr. Cronan) grown in minimal medium (MM) with 5 and 0.05 nM of biotin (sufficient and deficient, respectively). To generate deficiency in worms, avidin (2U/ml) was added at each condition. Worms were allowed to grow until the L4 stage.

treatment_protocol: Caenorhabditis elegans were collected and resuspended in PBS pH 7.0 buffer.

tag: developmental stage

value: L4 stage


title: PTC1_SD_rep1

description: Gene expression data from yeast.


title: Control_SD_rep3

description: Gene expression data from yeast.


title: Caenorhabditis elegans in biotin deficiency 2


title: Control_SD_rep1

description: Gene expression data from yeast.


title: Caenorhabditis elegans in biotin deficiency 1


title: Caenorhabditis elegans grown with sufficient Biotin 2

description: Gene expression data from Caenorhabditis elegans grown with sufficient biotin

source_name: Caenorhabditis elegans in grown in minimal media with conditions of biotin sufficiency


title: Caenorhabditis elegans grown with sufficient Biotin 1

value: biotin suffficient diet


title: C57 non-infarct at day 5, biological rep 4

status: Public on May 01 2010

city: La Jolla

first: Darlene

middle: L

last: Hunt

address: 9500 Gilman Drive #0412

department: Bioengineering

institute: UC San Diego

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an MOE430A microarray (one sample per array for a total of 46 arrays). Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were analyzed using the GC-RMA package available in R (www.bioconductor.org).

source_name: Non-infarct region of C57 left ventricle 5 days post-MI

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Mice were anesthetized with 5% isoflurane and the chest was opened to expose the heart. Hearts were excised and immediately placed in an ice-cold hyperkalemic solution containing 2,3-Butanedione monoxime to stop the beating and delay the onset of contracture. Hearts were cut along the septum to spread flat, and the infarct and non-infarct regions were separated using a biopsy punch and immediately snap frozen with liquid nitrogen. The snap-frozen heart samples were quickly homogenized using Retsch Mix Mill MM 300 and RNA was isolated using Qiagen's RNeasy mini kit according to the manufacturer's instructions. The quality of extracted RNA was confirmed using the Agilent Bioanalyzer.

treatment_protocol: Mice were anesthetized with 5% isoflurane, the trachea was exposed, and animals were intubated and mechanically ventilated with a mixture of 2% isoflurane and 100% oxygen. The chest was opened through the third intercostal space, and the left coronary artery was occluded using a 7-0 silk suture 1.5 mm below the left atrial appendage. The lungs were overinflated and the ribs closed using 6-0 prolene suture, the pectoralis muscles were returned to their original positions, and the skin was closed. Animals were given buprenorphine as an analgesic before being removed from ventilation and recovering consciousness. Mice survived for 1 or 5 days before being sacrificed.

value: male

value: 15-20 weeks

value: heart


title: C57 infarct at day 5, biological rep 4

source_name: Infarct and border region of C57 left ventricle 5 days post-MI


title: MRL infarct at day 5, biological rep 4

source_name: Infarct and border region of MRL left ventricle 5 days post-MI

value: MRL/MpJ


title: MRL non-infarct at day 5, biological rep 3

source_name: Non-infarct region of MRL left ventricle 5 days post-MI


title: MRL non-infarct at baseline, biological rep 4

source_name: MRL LV at baseline (no MI) in the same region as non-infarct tissue in post-MI hearts


title: MRL infarct at day 1, biological rep 4

source_name: Infarct and border region of MRL left ventricle 1 day post-MI


title: MRL infarct at baseline (day 0), biological rep 4

source_name: MRL LV at baseline (no MI) in the same region as the infarct in post-MI hearts


title: C57 non-infarct at baseline (day 0), biological rep 3

source_name: C57 LV at baseline (no MI) in the same region as non-infarct tissue in post-MI hearts


title: MRL non-infarct at day 5, biological rep 4


title: C57 infarct at baseline (day 0), biological rep 3

source_name: C57 LV at baseline (no MI) in the same region as the infarct in post-MI hearts


title: MRL infarct at day 5, biological rep 3


title: C57 infarct at day 1, biological rep 4

source_name: Infarct and border region of C57 left ventricle 1 day post-MI


title: MRL non-infarct at day 1, biological rep 4

source_name: Non-infarct region of MRL left ventricle 1 day post-MI


title: C57 non-infarct at day 1, biological rep 3

source_name: Non-infarct region of C57 left ventricle 1 day post-MI


title: C57 infarct at day 5, biological rep 3


title: MRL infarct at day 1, biological rep 3


title: C57 non-infarct at day 5, biological rep 3


title: MRL non-infarct at baseline, biological rep 3


title: C57 non-infarct at day 1, biological rep 1


title: MRL non-infarct at day 1, biological rep 3


title: C57 non-infarct at day 1, biological rep 4


title: C57 infarct at day 1, biological rep 3


title: MRL non-infarct at day 1, biological rep 2


title: MRL infarct at day 1, biological rep 2


title: C57 infarct at day 1, biological rep 2


title: MRL non-infarct at day 5, biological rep 2


title: MRL non-infarct at baseline, biological rep 1


title: MRL infarct at day 5, biological rep 2


title: MRL infarct at baseline (day 0), biological rep 3


title: C57 infarct at baseline (day 0), biological rep 1


title: C57 non-infarct at baseline (day 0), biological rep 2


title: C57 infarct at baseline (day 0), biological rep 2


title: C57 non-infarct at day 5, biological rep 1


title: MRL non-infarct at baseline, biological rep 2


title: C57 infarct at day 5, biological rep 2


title: MRL non-infarct at day 5, biological rep 1


title: MRL infarct at day 5, biological rep 1


title: MRL infarct at day 1, biological rep 1


title: C57 infarct at day 1, biological rep 1

source_name: Infarct and border region of C57 left ventricle (LV) 1 day post-myocardial infarction (MI)


title: MRL non-infarct at day 1, biological rep 1


title: C57 non-infarct at baseline (day 0), biological rep 1


title: C57 non-infarct at day 5, biological rep 2


title: C57 non-infarct at day 1, biological rep 2


title: MRL infarct at baseline (day 0), biological rep 1


title: MRL infarct at baseline (day 0), biological rep 2


title: C57 infarct at day 5, biological rep 1


title: Arabidopsis seedling, mSPL13, rep2

status: Public on Apr 30 2010

city: Corvallis

first: Hiro

last: Nonogaki

state: OR

address: 4017 ALS Bldg, Dept. of Horticulture, Oregon State University

department: Horticulture

institute: Oregon State University

description: Independent biological replicate of Col-0, SPL13, mSPL13 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on agar medium containing MS salts and 1% w/v sucrose and incubated at 4°C for 3 days in the dark and at 22°C for 3 days under the light.

hyb_protocol: Twenty-five μg of cRNAs were purified and fragmented prior to hybridization in the Affymetrix GeneChip® Hybridization Oven 640, washing in the Affymetrix GeneChip® Fluidics Station 450, and then staining the arrays with biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University, Corvallis OR.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570 nm and signal values were obtained using statistical algorithms on Affymetrix GeneChip® Operating (GCOS) software (Affymetrix).

data_processing: Expression data generated with GCOS software (MAS5.0 method) with a scale factor of 500.

organism: Arabidopsis thaliana

source_name: mSPL13 in Col-0 3 days seedling

label_protocol: Biotinylated cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase and a biotin-conjugated pseudouridine containing nucleotide mixture provided in the IVT Labeling Kit (Affymetrix, Santa Clara, CA) .

growth_protocol: Seeds were plated on agar medium containing MS salts and 1% w/v sucrose, incubated at 4°C for 3 days in the dark and at 22°C for 3 days under the light.

extract_protocol: Total RNA was extracted from 3 days seedling using standard phenol-SDS extraction as described before (Sambrook et al., 1989), and then checked for RNA integrity with Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). Ten μg of total RNA was used to produce double-strand cDNAs which were transcribed to cRNAs.

treatment_protocol: The mutant SPL13 (mSPL13) and non-mutated gene (SPL13) driven by the native promoter were used to transform Arabidopsis Col-0.

tag: mSPL13 in Col-0 background, 3 days seedling, three independent seed lots, m7B


title: Arabidopsis seedling, mSPL13, rep1

tag: mSPL13 in Col-0 background, 3 days seedling, three independent seed lots, m2D


title: Arabidopsis seedling, SPL13, rep3

source_name: SPL13 in Col-0 3 days seedling

tag: SPL13 in Col-0 background, 3 days seedling, three independent seed lots, S5B


title: Arabidopsis seedling, mSPL13, rep3

tag: mSPL13 in Col-0 background, 3 days seedling, three independent seed lots, m12C


title: Arabidopsis seedling, Col-0, rep1

source_name: Wild-type Col-0 3 days seedling

tag: Wild-type Col-0, 3 days seedling, three independent seed lots, rep1


title: Arabidopsis seedling, SPL13, rep2

tag: SPL13 in Col-0 background, 3 days seedling, three independent seed lots, S4C


title: Arabidopsis seedling, Col-0, rep2

tag: Wild-type Col-0, 3 days seedling, three independent seed lots, rep2


title: Arabidopsis seedling, Col-0, rep3

tag: Wild-type Col-0, 3 days seedling, three independent seed lots, rep3


title: Arabidopsis seedling, SPL13, rep1

tag: SPL13 in Col-0 background, 3 days seedling, three independent seed lots, S2B


title: T-13_N_Mapping250K_Nsp

status: Public on Apr 29 2010

type: genomic

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0 After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).

label: biotin phytoerythrin

molecule: genomic DNA

source_name: MPD specimens

label_protocol: Affymetrix standard

extract_protocol: standard DNA extraction

tag: disease category

value: blast phase_PV


title: T-09_N_Mapping250K_Nsp


title: T-12_N_Mapping250K_Nsp

value: blast phase_PMF


title: T-10_N_Mapping250K_Nsp


title: T-11_N_Mapping250K_Nsp

value: blast phase_ET


title: sAML-F9_N_Mapping250K_Nsp


title: tMPD-K011_N_Mapping250K_Nsp


title: tMPD-K017_N_Mapping250K_Nsp


title: tMPD-K012_N_Mapping250K_Nsp


title: sAML-F7932_N_Mapping250K_Nsp


title: T-04_N_Mapping250K_Nsp


title: T-07_N_Mapping250K_Nsp


title: T-05_N_Mapping250K_Nsp


title: sAML-F7_N_Mapping250K_Nsp


title: T-01_N_Mapping250K_Nsp


title: sAML-F8_N_Mapping250K_Nsp


title: T-02_N_Mapping250K_Nsp


title: T-06_N_Mapping250K_Nsp


title: T-08_N_Mapping250K_Nsp


title: T-14_N_Mapping250K_Nsp


title: T-03_N_Mapping250K_Nsp


title: sAML-F6_N_Mapping250K_Nsp


title: sAML-F7412_N_Mapping250K_Nsp


title: sAML-F7775_N_Mapping250K_Nsp


title: sAML-F7126_N_Mapping250K_Nsp


title: tMPD-K029_N_Mapping250K_Nsp


title: sAML-F44_N_Mapping250K_Nsp


title: sAML-F5_N_Mapping250K_Nsp


title: sAML-F41_N_Mapping250K_Nsp


title: sAML-F4_N_Mapping250K_Nsp


title: MPD86MMM_X_Mapping50K_Xba240


title: sAML-F36_N_Mapping250K_Nsp


title: sAML-F3_N_Mapping250K_Nsp


title: sAML-F5781_N_Mapping250K_Nsp


title: sAML-F43_N_Mapping250K_Nsp


title: sAML-F31_N_Mapping250K_Nsp


title: sAML-F32_N_Mapping250K_Nsp


title: sAML-F29_N_Mapping250K_Nsp


title: sAML-F38_N_Mapping250K_Nsp


title: sAML-F34_N_Mapping250K_Nsp


title: sAML-F26_N_Mapping250K_Nsp


title: sAML-F37_N_Mapping250K_Nsp


title: sAML-F27_N_Mapping250K_Nsp


title: sAML-F2_N_Mapping250K_Nsp


title: sAML-F28_N_Mapping250K_Nsp


title: sAML-F33_N_Mapping250K_Nsp


title: sAML-F39_N_Mapping250K_Nsp


title: sAML-F24_N_Mapping250K_Nsp


title: sAML-F30_N_Mapping250K_Nsp


title: MPD84_X_Mapping50K_Xba240


title: MPD78PV_X_Mapping50K_Xba240


title: sAML-F25_N_Mapping250K_Nsp


title: sAML-F23_N_Mapping250K_Nsp


title: MPD5ET_X_Mapping50K_Xba240


title: sAML-F42_N_Mapping250K_Nsp


title: MPD56_X_Mapping50K_Xba240


title: MPD457_X_Mapping50K_Xba240


title: MPD485_X_Mapping50K_Xba240


title: MPD461_X_Mapping50K_Xba240


title: sAML-F20_N_Mapping250K_Nsp


title: sAML-F21_N_Mapping250K_Nsp


title: sAML-F1_N_Mapping250K_Nsp


title: sAML-F19_N_Mapping250K_Nsp


title: MPD459_X_Mapping50K_Xba240


title: MPD446_X_Mapping50K_Xba240


title: sAML-F35_N_Mapping250K_Nsp


title: sAML-F18_N_Mapping250K_Nsp


title: sAML-F17_N_Mapping250K_Nsp


title: sAML-F16_N_Mapping250K_Nsp


title: sAML-F14_N_Mapping250K_Nsp


title: sAML-F15_N_Mapping250K_Nsp


title: sAML-F22_N_Mapping250K_Nsp


title: sAML-F12_N_Mapping250K_Nsp


title: sAML-518_N_Mapping250K_Nsp


title: MPD442_X_Mapping50K_Xba240


title: sAML-F10_N_Mapping250K_Nsp


title: MPD374_X_Mapping50K_Xba240


title: sAML-F11_N_Mapping250K_Nsp


title: MPD375_X_Mapping50K_Xba240


title: MPD354_X_Mapping50K_Xba240


title: s-AML08-1883_N_Mapping250K_Nsp


title: MPD327_X_Mapping50K_Xba240


title: s-AML08-1776_N_Mapping250K_Nsp


title: sAML-F13_N_Mapping250K_Nsp


title: s-AML05-2223_N_Mapping250K_Nsp


title: AML-MPDK052_N_Mapping250K_Nsp


title: MPD325_X_Mapping50K_Xba240


title: MPD314_X_Mapping50K_Xba240


title: MPD330_X_Mapping50K_Xba240


title: s-AML06-7227_N_Mapping250K_Nsp


title: s-AML07-6749_N_Mapping250K_Nsp


title: MPD313_X_Mapping50K_Xba240


title: AML-MPDK055_N_Mapping250K_Nsp


title: s-AML07-19990_N_Mapping250K_Nsp


title: AML-MPDK054_N_Mapping250K_Nsp


title: AML-MPDK046_N_Mapping250K_Nsp


title: AML-MPDK051_N_Mapping250K_Nsp


title: MPD29MMM_X_Mapping50K_Xba240


title: MPD307_X_Mapping50K_Xba240


title: AML-MPDK045_N_Mapping250K_Nsp


title: AML-MPDK049_N_Mapping250K_Nsp


title: MPD298_X_Mapping50K_Xba240


title: MPD281_X_Mapping50K_Xba240


title: MPD287_X_Mapping50K_Xba240


title: MPD285_X_Mapping50K_Xba240


title: AML-MPDK044_N_Mapping250K_Nsp


title: MPD272_X_Mapping50K_Xba240


title: AML-MPDK047_N_Mapping250K_Nsp


title: MPD271_X_Mapping50K_Xba240


title: AML-MPDK042_N_Mapping250K_Nsp


title: MPD249_X_Mapping50K_Xba240


title: AML-MPDK039_N_Mapping250K_Nsp


title: MPD240_X_Mapping50K_Xba240


title: AML-MPDK043_N_Mapping250K_Nsp


title: MPD196_X_Mapping50K_Xba240


title: MPD191_X_Mapping50K_Xba240


title: MPD186_X_Mapping50K_Xba240


title: MPD183_X_Mapping50K_Xba240


title: AML-MPDK027_N_Mapping250K_Nsp


title: AML-MPDK032_N_Mapping250K_Nsp


title: AML-MPDK033_N_Mapping250K_Nsp


title: AML-MPDK038_N_Mapping250K_Nsp


title: MPD175_X_Mapping50K_Xba240


title: MPD201_X_Mapping50K_Xba240


title: MPD172_X_Mapping50K_Xba240


title: MPD122_X_Mapping50K_Xba240


title: AML-MPDK026_N_Mapping250K_Nsp


title: AML-MPDK024_N_Mapping250K_Nsp


title: MPD115ET_X_Mapping50K_Xba240


title: MPD1138MM_X_Mapping50K_Xba240


title: AML-MPDK030_N_Mapping250K_Nsp


title: AML-MPDK028_N_Mapping250K_Nsp


title: MPD120_X_Mapping50K_Xba240


title: AML-MPDK035_N_Mapping250K_Nsp


title: MPD114ET_X_Mapping50K_Xba240


title: AML-MPDK022_N_Mapping250K_Nsp


title: AML-MPDK031_N_Mapping250K_Nsp


title: AML-MPDK020_N_Mapping250K_Nsp


title: MPD-1972_X_Mapping50K_Xba240


title: AML-MPDK007_N_Mapping250K_Nsp


title: MPD109_X_Mapping50K_Xba240


title: AML-MPDK005_N_Mapping250K_Nsp


title: AML-MPDK016_N_Mapping250K_Nsp


title: AML-MPDK004_N_Mapping250K_Nsp


title: MPD-1768_X_Mapping50K_Xba240


title: MPD-1442_X_Mapping50K_Xba240


title: MPD-1464_X_Mapping50K_Xba240


title: AML-MPDK002_N_Mapping250K_Nsp


title: 07-4374_N_Mapping250K_Nsp


title: AML-MPDK015_N_Mapping250K_Nsp


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 3

status: Public on Apr 01 2010

city: Barcelona

first: Isabel

last: Novoa

address: Dr. Aiguader, 88

department: Gene Regulation

institute: Center for Genomic Regulation

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 3 of 3. Technical replicate 1 of 2.

hyb_protocol: Three biological replicate experiments were performed for each of the three conditions (control shRNA, CPEB1 shRNA and CPEB4 shRNA expressing cells). For each condition SHORT fraction mRNAs was used as the common reference to compare with ALL fraction mRNAs. For all three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to six microarray hybridizations were processed for each of the two comparisons - ALL fraction mRNAs versus SHORT fraction mRNAs of control shRNA expressing cells; ALL fraction mRNAs versus SHORT fraction mRNAs of CPEB1 shRNA expressing cells; ALL fraction mRNAs versus SHORT fraction mRNAs of CPEB4 shRNA expressing cells. Thus, a total number of 18 microarray hybridizations were processed.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 110% PMT 110% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization with reduced weights in control and poor quality spots, followed by scaling across chips. Differential expression analysis was performed using SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

source_name: ALL fraction CPEB4 KD - 3

label_protocol: 100 ng of mRNA (ALL fraction mRNA or SHORT fraction mRNA) were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions.

growth_protocol: HeLa cells were maintained in DMEM high glucose + 10% FCS + penicillin/streptomycin supplement.

extract_protocol: RNA was extracted using standard total RNA extraction protocol. Then for each condition total RNA was purified by two different procedures: poly(U) chromatography and oligo(dT)-chromatography. Poly(U)-chromatography (Jacobson, 1987): 100 μg of total RNA were bound to poly(U)-sepharose (Sigma) and eluted at 35ºC to isolate mRNAs with short poly(A) tail (<30As, SHORT fraction). Oligo(dT) chromatography: mRNAs were purified independently of their poly(A) tail length with Ambion Poly(A)Purist kit from 20 μg total RNA (ALL fraction).  Jacobson, A. Purification and fractionation of poly(A)+ RNA. Methods in Enzymology (1987) 152: 254-261.

treatment_protocol: HeLa cells expressing the different shRNAs were synchronized with double thymidine blockade (12 hours with 2 mM thymidine, 12 hours release, and 12 hours with 2 mM thymidine),  and cells were taken after 8 hours release (G2/M phase).

tag: cell type

value: HeLa

tag: shrna

source_name: SHORT fraction CPEB4 KD - 3


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 3 dye-swap

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 3 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction CPEB1 KD - 3

source_name: ALL fraction CPEB1 KD - 3


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 2 dye-swap

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 2 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction CPEB1 KD - 2

source_name: ALL fraction CPEB1 KD - 2


title: 07-8747_N_Mapping250K_Nsp


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 2 dye-swap

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 2 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction CPEB4 KD - 2

source_name: ALL fraction CPEB4 KD - 2


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 1 dye-swap

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 1 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction CPEB1 KD - 1

source_name: ALL fraction CPEB1 KD - 1


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 3

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 3 of 3. Technical replicate 1 of 2.


title: 07-15031_N_Mapping250K_Nsp


title: AML-MPDK001_N_Mapping250K_Nsp


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 1 dye-swap

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 1 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction CPEB4 KD - 1

source_name: ALL fraction CPEB4 KD - 1


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 3 dye-swap

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 3 of 3. Technical replicate 2 of 2.


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 2

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 2 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown replicate 1

description: ALL fraction mRNAs CPEB4 knockdown versus SHORT fraction mRNAs CPEB4 knockdown biological replicate 1 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 1

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 1 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown replicate 2

description: ALL fraction mRNAs  CPEB1 knockdown versus SHORT fraction mRNAs CPEB1 knockdown biological replicate 2 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 3

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 3 of 3. Technical replicate 1 of 2.

source_name: ALL fraction wild type - 3

value: control

source_name: SHORT fraction wild type - 3


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 3 dye-swap

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 3 of 3. Technical replicate 2 of 2.


title: 07-0425_N_Mapping250K_Nsp


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 2

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 2 of 3. Technical replicate 1 of 2.

source_name: ALL fraction wild type - 2

source_name: SHORT fraction wild type - 2


title: S phase versus G2/M phase replicate 1 dye-swap

description: S phase versus G2/M phase biological replicate 1 of 3. Technical replicate 2 of 2.

hyb_protocol: Three biological replicate experiments were performed to compare the expression  of mRNAs between S phase (2 hours release after double thymidine blockade) and G2/M phase (8 hours release after double thymidine blockade). For all three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, in total six microarray hybridizations were processed.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization with reduced weights in control and poor quality spots, followed by scaling across chips. Differential expression analysis was performed using empirical Bayes statistics (Limma package, Smyth 2004) and SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

source_name: G2/Mphase 8 hours - 1

label_protocol: 100 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions.

extract_protocol: RNA was extracted using standard total RNA extraction protocol. Then mRNAs were purified with Ambion Poly(A)Purist kit from 20 μg total RNA.

treatment_protocol: HeLa cells were synchronized with double thymidine blockade (12 hours with 2 mM thymidine, 12 hours release, and 12 hours with 2 mM thymidine),  and cells were taken after 2 hour release (S phase) and 8 hour release (G2/M phase).

source_name: Sphase 2 hours - 1


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 1 dye-swap

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 1 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction wild type - 1

source_name: ALL fraction wild type - 1


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 2 dye-swap

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 2 of 3. Technical replicate 2 of 2.


title: S phase versus G2/M phase replicate 2 dye-swap

description: S phase versus G2/M phase biological replicate 2 of 3. Technical replicate 2 of 2.

source_name: G2/Mphase 8 hours - 2

source_name: Sphase 2 hours - 2


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 2

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 2 of 3. Technical replicate 1 of 2.

hyb_protocol: Three biological replicate experiments were performed and SHORT fraction mRNAs was used as the common reference to compare with ALL fraction mRNAs. For all three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to six microarray hybridizations were processed for each of the two comparisons - ALL fraction mRNAs versus SHORT fraction mRNAs at S phase (2 hours release after double thymidine blockade) and ALL fraction mRNAs versus SHORT fraction mRNAs at G2/M phase (8 hours release after double thymidine blockade)-, totalling 12 array datasets.

molecule: polyA RNA

source_name: ALL fraction 8h - 2

treatment_protocol: HeLa cells were synchronized with double thymidine blockade (12 hours with 2 mM thymidine, 12 hours release, and 12 hours with 2 mM thymidine),  and cells were taken after 2 hours release (S phase) and 8 hours release (G2/M phase).

tag: cell line

tag: molecule

value: ALL fraction RNA

source_name: SHORT fraction 8h - 2

value: SHORT fraction RNA


title: S phase versus G2/M phase replicate 3 dye-swap

description: S phase versus G2/M phase biological replicate 3 of 3. Technical replicate 2 of 2.

source_name: G2/Mphase 8 hours - 3

source_name: Sphase 2 hours - 3


title: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type replicate 1

description: ALL fraction mRNAs wild type versus SHORT fraction mRNAs wild type biological replicate 1 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 3

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 3 of 3. Technical replicate 1 of 2.

source_name: ALL fraction 8h - 3

source_name: SHORT fraction 8h - 3


title: S phase versus G2/M phase replicate 2

description: S phase versus G2/M phase biological replicate 2 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 3 dye-swap

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 3 of 3. Technical replicate 2 of 2.


title: S phase versus G2/M phase replicate 1

description: S phase versus G2/M phase biological replicate 1 of 3. Technical replicate 1 of 2.


title: S phase versus G2/M phase replicate 3

description: S phase versus G2/M phase biological replicate 3 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 1 dye-swap

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 1 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction 8h - 1

source_name: ALL fraction 8h - 1


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 1

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 1 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 3 dye-swap

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours biological replicate 3 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction 2h - 3

source_name: ALL fraction 2h - 3


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 3

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours biological replicate 3 of 3. Technical replicate 1 of 2.


title: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours replicate 2 dye-swap

description: ALL fraction mRNAs 8 hours versus SHORT fraction mRNAs 8 hours biological replicate 2 of 3. Technical replicate 2 of 2.


title: 06-12200_N_Mapping250K_Nsp

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

source_name: MPD specimens


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 2 dye-swap

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours biological replicate 2 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction 2h - 2

source_name: ALL fraction 2h - 2


title: 06-1972_N_Mapping250K_Nsp


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 1 dye-swap

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours  biological replicate 1 of 3. Technical replicate 2 of 2.

source_name: SHORT fraction 2h - 1

source_name: ALL fraction 2h - 1


title: 06-11091_N_Mapping250K_Nsp


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 2

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours biological replicate 2 of 3. Technical replicate 1 of 2.


title: 06-1484_N_Mapping250K_Nsp


title: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours replicate 1

description: ALL fraction mRNAs 2 hours versus SHORT fraction mRNAs 2 hours biological replicate 1 of 3. Technical replicate 1 of 2.


title: KBCP2

city: Baltimore

first: Xiaofei

last: Chang

state: MD

address: 1550 Orleans Street, CRBII, Rm574A

department: Otolaryngology

institute: Johns Hopkins University

description: Gene expression data from KB CP clone 2 cells treated with vehicle for 5 days

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

growth_protocol: Cell lines were grown in DMEM with 4.5 g/l glucose and L-glutamine/10% fetal bovine serum/penicillin-streptomycin. Media for SCC-25 and SCC-25/CP cells was supplemented with hydrocortisone (0.04 g/ml). KB-CP resistant cell lines were chronically maintained in media supplemented with cisplatin 5 microg/ml while SCC-25/CP cells are stably cisplatin resistant.

extract_protocol: Total cellular RNA was isolated using Trizol and the RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Cells were split to low density (1,000,000 per T-75 flask) 12 to 24 hours before treatment. Cells were then treated with freshly prepared 5 microM 5-Aza-dC dissolved in 50% acetic acid/50% PBS or were mock treated with the same volume of vehicle (50% acetic acid/50% PBS) in the media for 5 days (media changed on day 3).

value: KB/CP

value: Epidermoid


title: SCC aza

description: Gene expression data from SCC cells treated with 5 microM 5-aza-dC for 5 days

value: Squamous


title: KBCP1

description: Gene expression data from KB CP clone 1 cells treated with vehicle for 5 days


title: KB aza-2

description: Gene expression data from KB cells treated with 5 microM 5-aza-dC for 5 days

value: KB


title: KB aza-1

source_name: KB cells treated with 5 microM 5-aza-dC for 5 days


title: SCC

description: Gene expression data from SCC cells treated with vehicle for 5 days


title: Roots: Terese non-acclimated 5 days

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité Scientifique SN2/302

department: Stress Abiotiques et Différenciation des Végétaux Cultivés

country: France

institute: UMR  USTL / INRA 1281

description: Images were analyzed with GenePix Pro 6.0 software (Axon).

hyb_protocol: 14-18 h hybridization (DigEasy hybridization buffer; Roche) at 42°C in a Corning chamber. Slides were washed successively in 4x, 2x (with SDS 0.1x), 0.2x, and 0.1x SSC.

scan_protocol: Images were acquired with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA, USA)

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. Three biological replicates were mixed and used for two individual hybridizations.

organism: Lathyrus oleraceus

source_name: roots of Terese non-acclimated 5 days

label_protocol: Twenty-five μg of total RNA were used for each experiment. Reverse transcription and fluorochrome incorporation were performed in a MJ PTC-200 Peltier Thermal Cycler, using oligo-dT (Roche), the Superscript II Kit (Invitrogen) and CY3- and CY5-labelled d-CTP (Amersham). The QIAquick PCR Purification Kit (Qiagen) was used for target purification.

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery). The phase of acclimation was excluded and the phase of nursery was prolonged in order to attempt the same stage of development as acclimated plants (5 days) on the basis of number of degrees x days (Eteve and Derieux, 1982; Ney and Turc, 1993).

extract_protocol: Total RNA was extracted using a Tri reagent kit (Euromedex). RNA quantification was done by capillary electrophoresis (Experion, Biorad).

treatment_protocol: non-acclimated plants, corresponding to 5 days

tag: variety

value: Terese

tag: tissue

value: roots

source_name: roots of Terese without treatment (d0)

treatment_protocol: Without temperature treatment (d0)


title: Roots: Terese non-acclimated 10 days

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. Three biological replicates were mixed and used for  hybridization.

source_name: roots of Terese non-acclimated 10 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery). The phase of acclimation was excluded and the phase of nursery was prolonged in order to attempt the same stage of development as acclimated plants (10 days) on the basis of number of degrees x days (Eteve and Derieux, 1982; Ney and Turc, 1993).

treatment_protocol: non-acclimated plants, corresponding to 10 days


title: SCCCP

description: Gene expression data from SCC CP cells treated with vehicle for 5 days


title: KBCP1 aza

description: Gene expression data from KB CP clone 1 cells treated with 5 microM 5-aza-dC for 5 days


title: KB-1

description: Gene expression data from KB cells treated with vehicle for 5 days


title: Roots: Terese non-acclimated 2 days

source_name: roots of Terese non-acclimated 2 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery). The phase of acclimation was excluded and the phase of nursery was prolonged in order to attempt the same stage of development as acclimated plants (2 days) on the basis of number of degrees x days (Eteve and Derieux, 1982; Ney and Turc, 1993).

treatment_protocol: non-acclimated plants, corresponding to 2 days


title: Roots: Terese acclimated 20 days

source_name: roots of Terese acclimated 20 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery) following of 20 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).

treatment_protocol: Low temperature treatment 20 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery).


title: KB-2

source_name: KB cells treated with vehicle for 5 days


title: mesocarp_36h_1-MCP_17a

city: Padova

first: Livio

last: Trainotti

address: Via Ugo Bassi 58/B

country: Italy

institute: University of Padova

description: The fine tuning of the excitation/emission settings has been possible due to the presence of control probes on the platform.

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm. Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 90-100 pmol of Cy3- and Cy5-labelled target cDNAs. The hybridisation solution was kept in place by means of a microarray gene frame (ABgene, UK), while the glass slides were placed in a hybridisation chamber (HybChamber, by Genomic Solutions, USA) kept on a rotary oven for at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing:
Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data.
Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones.
The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”, keeping as reference the Cy3 channel. The “IA” and “IB” values have been used to determine log2(IB/IA) reported in the “VALUE” column.
Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses. Since each comparison (air vs 1-MCP and 1-MCP vs air –“dye-swap”-) was repeated twice, and a “percentage cutoff filter”, set to 75%, was used to eliminate those gene with less than 3 data points, there were at least 3 values for each gene to be used in the SAM analysis. Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of about 5%.

organism: Prunus persica

label_protocol: Total RNA (15 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dye: the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) stored in air and used as control.

extract_protocol: Total RNA was extracted following the protocol described by Chang et al. (1993). RNA yield and purity were checked by means of UV absorption spectra, whereas RNA integrity was ascertained by electrophoresis in agarose gel followed by ethidium bromide staining.

treatment_protocol: One hundred fruit, homogeneous for size and position on the plant, were placed in a sealed 30-L plastic jars (50 fruit each) for 12 h at 25 °C without 1-MCP (air controls). At the end of treatment, temperature, ethylene and CO2 concentration within the jar were determined. Fruit were then transferred in a growth chamber at 25°C for 24 hours.For molecular analyses, mesocarp from a pool of 10 fruit per class was frozen in liquid nitrogen and stored at -80°C until use.

tag: experimental protocol

value: mesocarp

label_protocol: Total RNA (15 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dye: the red-fluorescent cyanine5 (Cy5) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) treated with 1-methylcyclopropene (1-MCP).

extract_protocol: As in channel 1

treatment_protocol: One hundred fruit, homogeneous for size and position on the plant, were placed in a sealed 30-L plastic jars (50 fruit each). SmartFreshTM (AgroFresh Inc., Philadelphia, PA, USA), a commercial powder containing 0.14% (w/w) 1-MCP a.i., was prepared as a 10-fold concentrated stock solution following the technical bulletin of the company, and injected as 10 mL of air (final concentration 1 µL/L equivalent to 1 ppm). At the end of treatment, temperature, ethylene and CO2 concentration within the jars were determined. Fruit were then transferred in a growth chamber at 25°C for 24 hours.For molecular analyses, mesocarp from a pool of 10 fruit per class was frozen in liquid nitrogen and stored at -80°C until use.


title: SCCCP aza

description: Gene expression data from SCC CP cells treated with 5 microM 5-aza-dC for 5 days


title: KBCP2 aza

description: Gene expression data from KB CP clone 2 cells treated with 5 microM 5-aza-dC for 5 days


title: Roots: Terese acclimated 2 days

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. Three biological replicates were mixed and used for hybridization.

source_name: roots of Terese acclimated 2 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery) following of 2 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).

treatment_protocol: Low temperature treatment 2 days


title: Roots: Terese acclimated 10 days

source_name: roots of Terese acclimated 10 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery) following of 10 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).

treatment_protocol: Low temperature treatment 10 days


title: Roots: Terese acclimated 5 days

source_name: roots of Terese acclimated 5 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery) following of 5 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).

treatment_protocol: Low temperature treatment 5 days


title: Roots: Champagne non-acclimated 10 days

source_name: roots of Champagne non-acclimated 10 days

value: Champagne

source_name: roots of Champagne without treatment (d0)


title: Roots: Champagne d0 vs Terese d0

source_name: Roots Champagne d0

treatment_protocol: without treatment (d0)

source_name: Roots Terese d0

treatment_protocol: without treatment


title: mesocarp_36h_1-MCP_16a

value: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) stored in air and used as control.

value: Nectarines (Prunus persica cv ‘Stark Red Gold’) at ripening stage 4 class 0 (as identified in Ziosi et al., 2008) treated with 1-methylcyclopropene (1-MCP).


title: Roots: Champagne acclimated 5 days

source_name: roots of Champagne acclimated 5 days


title: Roots: Champagne acclimated  2 days

source_name: roots of Champagne acclimated 2 days


title: Roots: Champagne acclimated 10 days

source_name: roots of Champagne acclimated 10 days


title: mesocarp_36h_1-MCP_16b

description:
The fine tuning of the excitation/emission settings has been possible due to the presence of control probes on the platform.
Technical replicate of "mesocarp_36h_1-MCP_16a"


title: Roots: Champagne acclimated 20 days

source_name: roots of Champagne acclimated 20 days


title: Roots: Champagne non-acclimated 2 days

source_name: roots of Champagne non-acclimated 2 days


title: Leaves: Terese non-acclimated 20 days

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. Three biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of six hybridizations per condition.

source_name: aerial tissues of Terese non-acclimated 20 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery). The phase of acclimation was excluded and the phase of nursery was prolonged in order to attempt the same stage of development as acclimated plants (20 days) on the basis of number of degrees x days (Eteve and Derieux, 1982; Ney and Turc, 1993).

treatment_protocol: non-acclimated plants, corresponding to 20 days

value: leaves (aerial)

source_name: aerial tissues of Terese without treatment (d0)


title: HCR_rep11

city: Jyväskylä

first: Heikki

last: Kainulainen

address: Seminaarinmäki

department: Department of Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

description:
replicate 11
RAT 23

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization from the affy package of Bioconductor (www.bioconductor.org) in R statistical programming language.

source_name: Rat gastrocnemius muscle

label_protocol: Biotinylated cRNA was prepared with the Illumina RNA TotalPrep Amplification kit (Ambion, # IL1791).

growth_protocol: Artificial breeding from a genetically heterogeous rat population (N:NIH stock) was used to produce rat strains differing in inherent aerobic capacity. The procedure was previously described in detail (Koch and Britton, Physiol Genomics. 2001; 5:45-52, PMID: 11161005).

extract_protocol: Total RNA was isolated from gastrocnemius muscle using Trizol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer's protocol.

tag: strain

value: high intrinsic aerobic capacity runners

tag: generation

tag: gender

value: female

value: musculus gastrocnemius

tag: age

value: 8 months


title: HCR_rep9

description:
replicate 9
RAT 19


title: LCR_rep11

description:
replicate 11
RAT 21

value: low intrinsic aerobic capacity runners


title: LCR_rep10

description:
replicate 10
RAT 18


title: HCR_rep12

description:
replicate 12
RAT 24


title: Leaves: Terese non-acclimated 10 days

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. A total of four hybridizations were done per condition.

source_name: aerial tissues of Terese non-acclimated 10 days


title: Leaves: Terese non-acclimated 5 days

source_name: aerial tissues of Terese non-acclimated 5 days


title: HCR_rep8

description:
replicate 8
RAT 16


title: HCR_rep10

description:
replicate 10
RAT 20


title: Roots: Champagne non-acclimated 5 days

source_name: roots of Champagne non-acclimated 5 days


title: LCR_rep12

description:
replicate 12
RAT 22


title: HCR_rep7

description:
replicate 7
RAT 15


title: LCR_rep9

description:
replicate 9
RAT 17


title: Leaves: Terese acclimated 2 days

data_processing: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles. Two biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of four hybridizations per condition.

source_name: aerial tissues of Terese acclimated 2 days

treatment_protocol: acclimated plants, corresponding to 2 days


title: Leaves: Terese acclimated 10 days

source_name: aerial tissues of Terese acclimated 10 days

treatment_protocol: acclimated plants, corresponding to 10 days


title: Leaves: Terese acclimated 5 days

source_name: aerial tissues of Terese acclimated 5 days

treatment_protocol: acclimated plants, corresponding to 5 days


title: Leaves: Terese non-acclimated 2 days

source_name: aerial tissues of Terese non-acclimated 2 days


title: Leaves: Terese acclimated 20 days

source_name: aerial tissues of Terese acclimated 20 days

treatment_protocol: acclimated plants, corresponding to 20 days


title: HCR_rep5

description:
replicate 5
RAT 11


title: LCR_rep7

description:
replicate 7
RAT 13


title: LCR_rep5

description:
replicate 5
RAT 9


title: Leaves: Champagne non-acclimated 10 days

source_name: aerial tissues of Champagne non-acclimated 10 days

source_name: aerial tissues of Champagne without treatment (d0)


title: LCR_rep4

description:
replicate 4
RAT 6


title: HCR_rep6

description:
replicate 6
RAT 12


title: Leaves: Champagne non-acclimated 20 days

source_name: aerial tissues of Champagne non-acclimated 20 days


title: LCR_rep6

description:
replicate 6
RAT 10


title: HCR_rep3

description:
replicate 3
RAT 7


title: Leaves: Champagne acclimated 10 days

data_processing:
Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles.
Three biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of six hybridizations per condition.

source_name: aerial tissues of Champagne acclimated 10 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery), following of 10 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).


title: Leaves: Champagne non-acclimated 5 days

source_name: aerial tissues of Champagne non-acclimated 5 days

treatment_protocol: non-acclimated plants, corresponding to 5 days


title: Leaves: Champagne non-acclimated 2 days

source_name: aerial tissues of Champagne non-acclimated 2 days

treatment_protocol: Without temperature treatment (d0)


title: LCR_rep8

description:
replicate 8
RAT 14


title: HCR_rep4

description:
replicate 4
RAT 8


title: LCR_rep3

description:
replicate 3
RAT 5


title: Leaves: Champagne acclimated 20 days

source_name: aerial tissues of Champagne acclimated 20 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery), following of 20 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).


title: LCR_rep1

description:
replicate 1
RAT 3


title: Leaves: Champagne acclimated 5 days

source_name: aerial tissues of Champagne acclimated 5 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery), following of 5 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).


title: Leaves: Champagne d0 vs Terese d0

scan_protocol: Images were acquired with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations. For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. To identify genes displaying a change in expression over repetitions, a script utilizing libraries functions in R with a false discovery rate (FDR) less than 5% was used for all experimental conditions. Only genes with smooth expression profiles were retained. The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions and log2(ratio) ≥1 and ≤ -1 were used for filtering gene expression profiles.
VALUE data represents the average of 5 hybridizations.

source_name: Leaves Champagne d0

label_protocol:
Twenty-five μg of total RNA were used for each experiment. Reverse transcription and fluorochrome incorporation were performed in a MJ PTC-200 Peltier Thermal Cycler, using oligo-dT (Roche), the Superscript II Kit (Invitrogen) and CY3- and CY5-labelled d-CTP (Amersham). The QIAquick PCR Purification Kit (Qiagen) was used for target purification.
Three biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of six hybridizations per condition.

growth_protocol: 11 days of culture to 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery)

extract_protocol: Total RNA was extracted from d0, d2, d5, d10 and d20 cold treated for acclimation (A) and control (N) plants using a Tri reagent kit (Euromedex). Aerial tissues (shoots and leaves) were treated separately from root tissues. RNA quantification was done by capillary electrophoresis (Experion, Biorad).

source_name: Leaves Terese d0


title: LCR_rep2

description:
replicate 2
RAT 4

source_name: Rat gastrocnemius muscle


title: Leaves: Champagne acclimated 2 days

source_name: aerial tissues of Champagne acclimated 2 days

growth_protocol: Plants were grown under greenhouse conditions 19°C day/12°C night, 10h light/day and 300µmol/m²s (phase of nursery), following of 2 days of culture to 10°C day/2°C night 10h light/day and 250µmol/m²s (phase of acclimation).


title: HCR_rep1

description:
replicate 1
RAT 1


title: MEGAKARYOBLASTS

status: Public on Mar 31 2010

city: Modena

first: Elena

last: Tenedini

state: MO

address: Via Campi, 287

department: Biomedical Sciences

institute: University of Modena and Reggio Emilia

description: In vitro differentiated normal human megakaryoblasts

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Statistical analyses were obtained using the 2- Delta-delta-CTs method and the Threshold was determined automatically by means of SDS Enterprise Edition software (Applied Biosystems). Delta-delta-CTs and Relative Quantities (RQ) were calculated for each detector using the CD34 HPCs sample as calibrator and mir-hsa-let-7a as endogenous control. The raw data files are encoded in a proprietary file format of Applied  Biosystems (.SDS data files) that can be analyzed with Applied Biosystems SDS software.

label: FAM dye

label_protocol: FAM TaqMan Assay

growth_protocol: Megakaryoblasts were obtained by in vitro differentiation of CD34+ cells. Briefly, megakaryocytes were obtained from CD34+ cells cultured in serum-free medium supplemented with 50 ng/mL SCF and 100ng/mL thrombopoietin (TPO) for 14-16 days and subsequently selected by means of a magnetic beads sorting procedure using monoclonal antibody directed against CD41a antigen.

extract_protocol: Cells were collected and mirVana kit (Ambion) was used for total cellular RNA extraction according to the manufacturer's instructions.

value: in vitro differentiated cells derived from CD34+ stem/progenitor cells from healthy donors


title: MYELOBLASTS

description: In vitro differentiated normal human myeloblasts

growth_protocol: Monoblasts (CD14+ precursors) and myeloblasts (CD14- precursors) were obtained by in vitro differentiation of cord blood (CB) derived CD34+ cells. Briefly, CB CD34+ cells were cultured in IMDM added with 20% FCS, in the presence of human hematopoietic cytokines: SCF (50 ng/ml), Flt3-ligand (Flt3-L) (50 ng/ml), IL-11 (50 ng/ml), IL-6 (10 ng/ml), IL-3 (10 ng/ml) and G-CSF (10 ng/ml). After 7 days of culture, hematopoietic cells were analyzed, by flow cytometry, for CD14 antigen expression, estimated at about 25-30% of the entire cell population. Then monoblasts (CD14+) and myeloblasts (CD14-) cell fractions were obtained by immunomagnetic separation using the MACS technology. Differentiation of CD34+ cells was monitored by morphological analysis of MGG-stained cytospins and by flow-cytometric analysis of CD34, CD38 and CD14 surface antigen expression.


title: CD34_HPCs

description: Stem/progenitor hematopoietic cells CD34+ from cord blood (CB)

growth_protocol: Human CD34+ cells were purified from umbilical cord blood samples: mononuclear cells were isolated by Ficoll-Hypaque gradient separation, washed twice with PBS, and then CD34+ cells separated using a magnetic cell sorting procedure (EasySep Human CD34 Positive Selection Kit, StemCell Technologies).

value: primary cells from healthy donors


title: ERYTROBLASTS

description: In vitro differentiated normal human erythroblasts

growth_protocol: Normal human erythroblasts were obtained from cord blood CD34+ hematopoietic progenitors cultured in IMDM supplemented with 20% BIT, 50 ng/ml SCF and 4 U/ml Erythropoietin for 8-10 days. Differentiation of CD34+ cells was monitored daily by morphological analysis of May and Grunwald - Giemsa stained cytospins and by flow-cytometric analysis of glycophorin A (GPA) surface antigen expression, using the phycoerythrin (PE)-conjugated mouse anti-human GPA monoclonal antibody.


title: HCR_rep2

description:
replicate 2
RAT 2


title: MONOBLASTS

description: In vitro differentiated normal human monoblasts

growth_protocol: Monoblasts (CD14+ precursors) and myeloblasts (CD14- precursors) were obtained by in vitro differentiation of cord blood (CB) derived CD34+ cells. Briefly, CB CD34+ cells were cultured in IMDM added with 20% FCS, in the presence of human hematopoietic cytokines: SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-11 (50 ng/ml), IL-6 (10 ng/ml), IL-3 (10 ng/ml) and G-CSF (10 ng/ml). After 7 days of culture, hematopoietic cells were analyzed, by flow cytometry, for CD14 antigen expression, estimated at about 25-30% of the entire cell population. Then monoblasts (CD14+) and myeloblasts (CD14-) cell fractions were obtained by immunomagnetic separation using the MACS technology. Differentiation of CD34+ cells was monitored by morphological analysis of MGG-stained cytospins and by flow-cytometric analysis of CD34, CD38 and CD14 surface antigen expression.