title: brain_neurons_rep6

description: individual suffered sudden death, without brain injury

hyb_protocol: Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer.

scan_protocol: The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software

data_processing: Gene probe set expression values were calculated using the Robust Multichip Average for small RNA quantities (srma) algorithm. As probe weights for signal summary statistic calculation we used the inverse of the probe specific coefficient of variation calculated across chips.    Probe sets were defined as expressed if the P-value determined by a signed rank test of perfect match versus mismatch signal distributions was lower or equal 0.065 in at least three chip experiments in a given cell type. Probe sets that showed statistically significant higher expression in neurons or endothelial cells in two-sided t-tests were considered as preferentially neuronal or endothelial expressed genes, respectively.

source_name: neurons from dorsolateral prefrontal cortex

label_protocol: Amplification of mRNA was carried out in three consecutive linear amplifications using the RiboAmpHS kit (Arcturus). During the last amplification, biotin-labeled UTP was incorporated. The quality of the amplified RNA was assessed with a Bioanalyser Nanochip (Agilent).

extract_protocol: Endothelial cells were collected from seven humans and neuronal cells from six humans which partially overlap. Fifteen µm thick cryosections (Bright Technologies) of dorsolateral prefrontal cortex were cut, mounted onto microscope slides, air dried, and acetone fixed. The sections were stained either with a polyclonal antibody to detect neurons (Neurofilament 160/200kDa mouse; Cambridge Bioscience 13-1300) or endothelial cells (von Willebrand factor (VWF) rabbit; Chemicon AB7356) in conjunction with a secondary fluorescently labeled (Cy2  goat-anti-mouse (Jackson Immunoresearch) for the neuron and Cy3 goat anti-rabbit (Jackson Immunoresearch) for the endothelial staining) polyclonal antibody in the presence of RNAse inhibitor (Amersham Biosciences). The stained sections were subsequently washed with phosphate buffered saline (PBS, Ambion) and dehydrated by incubation in increasing ethanol concentrations (30%, 50%, 70%, 90%, and absolute ethanol).  Approximately 1,000 neurons or an equivalent tissue area of endothelium per individual were microdissected using a laser capture microdissection microscope (P.A.L.M.), RNA was extracted using a commercially available RNA extraction kit (P.A.L.M.).

tag: sex

value: m; age (years):34


title: R2 old vs CNS, biol rep 2, DAA

status: Public on May 20 2010

type: RNA

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

country: USA

institute: University of Florida

description:
Biological replicate 2

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

hyb_protocol: The recommended amount of 750 ng of labeled cRNA was fragmented and hybridized to the arrays using recommended procedures described in the In situ Hybridization Kit PlusTM (Agilent Technologies). Controls provided in the In situ Hybridization Kit were spiked in at the time of hybridization. The arrays were washed according to the manufacturer's recommended protocol.

scan_protocol: The arrays were scanned on an Agilent Technologies G2565AA Microarray ScannerTM. Data were extracted after scanning using Agilent’s Feature Extraction 5.1.1TM software.

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8 +/- 1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis. All experiments were performed in triplicates from three independent samples from 3 different animals.

molecule: total RNA

organism: Aplysia californica

source_name: R2 old neuron

label_protocol: cRNA production was performed using Agilent’s Low RNA Input Linear Amplification kitTM (Agilent Technologies). All amplification reactions involved only one round of amplification. Concentration of the cRNA was determined by GeneSpec IIITM and the 2100 Bioanalyzer both described above. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kitTM (PerkinElmer).

growth_protocol: Aplysia californica were obtained from the NIH/University of Miami National Resource for Aplysia and held in 40-400 liter aquaria with circulating fresh seawater at 15-17º C.

extract_protocol: Total RNA was extracted using RNAqueousTM or RNAqueous-MicroTM (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover it provides information about potential DNA contamination and the approximate RNA concentration. Additionally RNA concentration was measured spectrophotometrically by using the GeneSpec III systemTM (Mirai Bio).

treatment_protocol: Aplysia californica weighing 25-30g for the young subgroup and 1000-14000g for the old subgroup were used (see GSE18783_Table1.txt, which is linked to the Series GSE18783 record as a supplementary file). Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanical removed with fine forceps and scissors and cell were isolated as described above. Neurons were then fixed in 75% ethanol for several minutes and RNA isolated immediately.

tag: cell type

value: cholinergic neuron

tag: neuron

tag: age

value: old

source_name: CNS

tag: tissue

value: central nervous system (CNS)


title: brain_neurons_rep4

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max-Planck-Institute of Evolutionary Anthropology

label: biotin

organism: Homo sapiens

value: m; age (years):47


title: cerebellum_3x_amplified_rep1

hyb_protocol: Hybridization, washing and staining to Affymetrix® GeneChip® Mouse Genome arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters. Probe set expression values were calculated using the Robust Multichip Average for small RNA quantities (sRMA) algorithm (Cope et al. 2006). As probe weights for signal summary statistic calculation, we used the inverse of the probe specific coefficient of variation calculated across chips.   Probe sets were defined as expressed if the P-value determined by a signed rank test of perfect match versus mismatch signal distributions was lower or equal 0.05 in at least three chip experiments in a tissue.

organism: Mus musculus

source_name: cerebellum, 3X amplified

label_protocol: The 1X Samples were processed according to the Affymetrix standard protocol which involved one linear amplification. The 3X Samples were amplified through two rounds using the RiboAmp HS kit (Arcturus). Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP. The quality of the amplified RNA was assessed with a Bioanalyzer Nanochip (Agilent). Amplified cRNA samples were chemically fragmented according to instructions in the Affymetrix sample preparation protocol.

extract_protocol: Total RNA was isolated using TRIzol® reagent from the frozen mouse tissue according to manufacturer’s instructions. After isolation, the RNA was column purified with the Qiagen® RNeasy® kit.

tag: strain

tag: developmental stage

value: adult

value: cerebellum

tag: linear amplification


title: liver_1x_amplified

source_name: liver, 1X amplified

value: liver


title: R2 old vs CNS, biol rep 3, DAA

description:
Biological replicate 3

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: R2 old vs CNS, biol rep 1, DAA

description:
Biological replicate 1

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: LPL1 old vs CNS, biol rep 1, DAA

source_name: LPL1 old neuron


title: LPL1 old vs CNS, biol rep 2, DAA


title: brain_endothelial_cells_rep7

source_name: endothelial cells from dorsolateral prefrontal cortex


title: cerebellum_1x_amplified

source_name: cerebellum, 1X amplified


title: LPL1 old vs CNS, biol rep 3, DAA


title: brain_neurons_rep5

value: f; age (years):39


title: brain_neurons_rep2

value: m; age (years):45; this individual had a medical history of schizophrenia


title: brain_neurons_rep3

value: m; age (years):37


title: brain_endothelial_cells_rep6

value: m; age (years):55


title: cortex_3x_amplified_rep1

source_name: cortex, 3X amplified

value: cortex


title: Single cell comparison of R2 Old vs R2 Young, rep 1, DAA

description:
DR2Old R2Young-1
Biological replicate 1 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8 +/- 1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis. All experiments were performed in triplicate from three independent samples from 3 different animals.

extract_protocol: Total RNA was extracted using RNAqueousTM or RNAqueous-MicroTM (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover, it provides information about potential DNA contamination and the approximate RNA concentration. Additionally, RNA concentration was measured spectrophotometrically by using the GeneSpec III systemTM (Mirai Bio).

treatment_protocol: Aplysia californica of appropriate age and weight were used. Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanically removed with fine forceps and scissors and cell were isolated as described above. Neurons were then fixed in 75% ethanol for several minutes and RNA isolated immediately.

source_name: R2 young neuron

value: young


title: Pulmonary artery intimal sarcoma 8

type: genomic

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: Pulmonary artery intime sarcoma

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Scanner protocol for a full slide

data_processing: The Agilent Feature Extraction software (Version 10.5.1.1) was used to process the images obtained from the scanner (Agilent DNA microarray scanner, with up to 2 µm precision) and to generate a text file (FE file). Subsequently, the FE files were analyzed using the Agilent Genomic Workbench Standard Edition 5.0.14 software. It allowed applying different algorithms and statistical methods for reporting copy number aberrations (CNA).  The ADM-2 algorithm was chosen for all the samples. The threshold, the nesting level and the aberration filter values were adjusted case by case due to differen  ces in the standard deviation of the log2 ratios of individual cases.  Regions with a log2 ratio > 2 were considered as amplified, regions with a log2 ratio < -1 were considered as homozygously deleted.

molecule: genomic DNA

source_name: Pulmonary artery intimal sarcoma 8

label_protocol: Agilent lable protocol

extract_protocol: Genomic DNA was isolated from frozen eight tumor tissues using the High Pure PCR Template Preparation Kit (Roche Diagnostics, Basel, Switzerland).

tag: tissue type

value: Pulmonary artery intime sarcoma

source_name: control 8

extract_protocol: Not applicable, normal DNA sample purchased from Agilent

tag: reference

value: Normal DNA sample from Agilent


title: brain_neurons_rep1

value: m; age (years):46


title: brain_endothelial_cells_rep5


title: R2 young vs CNS, biol rep 2, DAA


title: cortex_1x_amplified

source_name: cortex, 1X amplified


title: Pulmonary artery intimal sarcoma 7

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 7

source_name: control 7


title: brain_endothelial_cells_rep4


title: 99F_C

status: Public on May 19 2010

city: Beijing

first: Jin

last: Xu

address: Beijing Institute of Genomics, Chinese Academy of Sciences No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

country: China

institute: BIG,CAS

description: Gene expression data from abdomen of fertile line

hyb_protocol: Target hybridization for GeneChips were performed according to the standard protocol in Affymetrix GeneChip expression Analysis Technical Manual

scan_protocol: Target scanning for GeneChips were performed according to the standard protocol in Affymetrix GeneChip expression Analysis Technical Manual

data_processing: GeneChip images were quantified and gene expression values(signal intensity) were calculated by Affymetrix Microarry Sute Version 5.0(MAS 5.0).

organism: Drosophila simulans

source_name: Drosophila simulans fertile males

label_protocol: Label for GeneChips were performed according to the standard protocol outline in th Affymetrix GeneChip expression Analysis Technical Manual and the protocals are avaliable at http://fgf.bsd.uchicago.edu/facility/microarray.htm

growth_protocol: The fertile and sterile introgression lines were constructed and maintained as described in Ting et al.(1998)

extract_protocol: The testes were dissected on ice in RNALater and transferred into TRIzol® Reagent (Invitrogen). The abdomens were separated from whole body in dry ice and immediately homogenized in TRIzol®. Total RNA was isolated according to the manufacture's instruction, further purified with phenol-choroform extraction,and precipitated with isopropanol.

treatment_protocol: We collected on average 150 adult male files aged 3-4 days from each line for testis dissection,and 50 files for abdomen dissection

value: male

value: abdomen

tag: genotype/variation

value: X chromosome (OdsH locus) F variant from D. mauritiana

tag: fertility status

value: fertile

value: 3-4 days


title: Pulmonary artery intimal sarcoma 5

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 5

source_name: control 5


title: brain_endothelial_cells_rep3

value: m; age (years):44


title: R2 young vs CNS, biol rep 3, DAA

value: cholinergic neuron

value: central nervous system (CNS)


title: LPL1 young vs CNS, biol rep 2, DAA

source_name: LPL1 young neuron


title: LPL1 young vs CNS, biol rep 3, DAA

source_name: CNS


title: 99F_B


title: 99F_A


title: brain_endothelial_cells_rep2

value: m; age (years):32


title: LPL1 young vs CNS, biol rep 1, DAA


title: brain_endothelial_cells_rep1

value: m; age (years):45; this individual had a medical history of schizophrenia


title: R2 young vs CNS, biol rep 1, DAA


title: Pulmonary artery intimal sarcoma 6

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 6

source_name: control 6


title: Pulmonary artery intimal sarcoma 4

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 4

source_name: control 4


title: Pulmonary artery intimal sarcoma 1

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 1

source_name: control 1


title: Pulmonary artery intimal sarcoma 2

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 2

source_name: control 2


title: 193s_A

description: Gene expression data from abdomen of sterile line

source_name: Drosophila simulans sterile males

value: X chromosome (OdsH locus) S variant from D. mauritiana

value: sterile


title: 193s_C


title: Pulmonary artery intimal sarcoma 3

description: Pulmonary artery intime sarcoma

source_name: Pulmonary artery intimal sarcoma 3

source_name: control 3


title: 193s_B


title: Embryo 13, blastomere 2

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual).

source_name: blastomere, biopsied cleavage embryo

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied blastomere samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).  Whole genome amplification was performed as previously described (Treff et al., 2010, Fertil. Steril., In Press).

tag: cleavage stage snp

value: blastomere

value: blastomere cell


title: Embryo 13, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 12, blastomere 2

description: Hybridized to 250K_Nsp

value: complex aneuploid


title: Embryo 13, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 13, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 13, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 12, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 12, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 7

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 7

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 8

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 12, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 11, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 12, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 7

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 6, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 6, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 6, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 5, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 8

description: Hybridized to 250K_Nsp


title: Embryo 6, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 10, blastomere 7

description: Hybridized to 250K_Nsp


title: Embryo 8, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 6, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 9, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 7, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 5, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 5, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 7

description: Hybridized to 250K_Nsp


title: Embryo 5, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 5, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 8

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 2, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 3, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 5

description: Hybridized to 250K_Nsp


title: Embryo 2, blastomere 1

description: Hybridized to 250K_Nsp


title: Embryo 2, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 4, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 2

description: Hybridized to 250K_Nsp


title: Embryo 2, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 4

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 1

description: Hybridized to 250K_Nsp


title: mixture 25%GM00323_75%GM00321

description: Hybridized to 250K_Nsp

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set of 61 normal females from the HapMap database (www.hapmap.org).

source_name: mixed male and female samples: 25% GM00323 and 75% GM00321

extract_protocol: mixture samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

tag: cleavage stage fish result

tag: blastocyt ma-pgd result

tag: cell line karyotype

tag: corielle catalog id


title: mixture 0%GM00323_100%GM00321

description: Hybridized to 250K_Nsp

source_name: mixed male and female samples: 0% GM00323 and 100% GM00321


title: mixture 40%GM00323_60%GM00321

description: Hybridized to 250K_Nsp

source_name: mixed male and female samples: 40% GM00323 and 60% GM00321


title: mixture 60%GM00323_40%GM00321

description: Hybridized to 250K_Nsp

source_name: mixed male and female samples: 60% GM00323 and 40% GM00321


title: Embryo 2, blastomere 3

description: Hybridized to 250K_Nsp


title: Embryo 1, blastomere 6

description: Hybridized to 250K_Nsp


title: Embryo 2, blastomere 2

description: Hybridized to 250K_Nsp


title: Cell line GM15603, lymphocyte, sample 4

description:
Hybridized to 250K_Nsp
CEL and CHP files

source_name: Lymphocyte, cultured

extract_protocol: Biopsied trophectoderm and ICM samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

value: cultured lymphocyte

tag: karyotype

value: 46,XY (UPID chr8)


title: mixture 75%GM00323_25%GM00321

description: Hybridized to 250K_Nsp

source_name: mixed male and female samples: 75% GM00323 and 25% GM00321


title: Cell line GM15603, lymphocyte, sample 3

tag: cell type


title: Cell line GM15603, lymphocyte, sample 2


title: Cell line GM11496, lymphocyte, sample 4

value: 46,XX (UPID chr7)


title: Embryo 50, sample C, trophectoderm

source_name: Trophectoderm, biopsied, blastocyst stage

value: Trophectoderm

value: blastocyst


title: Cell line GM15603, lymphocyte, sample 1


title: mixture 100%GM00323_0%GM00321

description: Hybridized to 250K_Nsp

source_name: mixed male and female samples: 100% GM00323 and 0% GM00321


title: Embryo 49, sample D, inner cell mass

source_name: Inner cell mass, biopsied, blastocyst stage

value: Inner cell mass


title: Embryo 50, sample B, trophectoderm


title: Cell line GM11496, lymphocyte, sample 2


title: Embryo 48, sample D, inner cell mass


title: Embryo 50, sample D, inner cell mass


title: Embryo 49, sample C, trophectoderm


title: Embryo 49, sample B, trophectoderm


title: Embryo 49, sample A, trophectoderm


title: Cell line GM11496, lymphocyte, sample 3


title: Embryo 48, sample B, trophectoderm


title: Cell line GM11496, lymphocyte, sample 1


title: Embryo 46, sample B, trophectoderm


title: Embryo 48, sample A, trophectoderm


title: Embryo 48, sample C, trophectoderm


title: Embryo 46, sample D, inner cell mass


title: Embryo 46, sample C, trophectoderm


title: Embryo 47, sample B, trophectoderm


title: Embryo 47, sample A, trophectoderm


title: Embryo 47, sample D, inner cell mass


title: Embryo 45, sample C, trophectoderm


title: Embryo 45, sample D, inner cell mass


title: Embryo 45, sample A, trophectoderm


title: Embryo 44, sample D, inner cell mass


title: Embryo 45, sample B, trophectoderm


title: Embryo 43, sample B, trophectoderm


title: Embryo 47, sample C, trophectoderm


title: Embryo 46, sample A, trophectoderm


title: Embryo 43, sample C, trophectoderm


title: Embryo 44, sample A, trophectoderm


title: Embryo 44, sample C, trophectoderm


title: Embryo 43, sample A, trophectoderm


title: Embryo 40, sample C, trophectoderm


title: Embryo 43, sample D, inner cell mass


title: Embryo 50, sample A, trophectoderm


title: Embryo 42, sample B, trophectoderm


title: Embryo 41, sample D, inner cell mass


title: Embryo 38, sample D, inner cell mass


title: Embryo 42, sample D, inner cell mass


title: Embryo 42, sample A, trophectoderm


title: Embryo 41, sample B, trophectoderm


title: Embryo 39, sample A, trophectoderm


title: Embryo 39, sample B, trophectoderm


title: Embryo 42, sample C, trophectoderm


title: Embryo 44, sample B, trophectoderm


title: Embryo 38, sample B, trophectoderm


title: Embryo 41, sample A, trophectoderm


title: Embryo 37, sample B, trophectoderm


title: Embryo 41, sample C, trophectoderm


title: Embryo 37, sample C, trophectoderm


title: Embryo 37, sample D, inner cell mass


title: Embryo 38, sample A, trophectoderm


title: Embryo 36, sample A, trophectoderm


title: Embryo 40, sample A, trophectoderm


title: Embryo 37, sample A, trophectoderm


title: Embryo 35, sample A, trophectoderm


title: Embryo 40, sample B, trophectoderm


title: Embryo 34, sample D, inner cell mass


title: Embryo 36, sample B, trophectoderm


title: Bmi1-shRNA 0 hrs (2)

city: Cambridge

first: Michael

last: Morrissey

state: MA

address: 250 Massachusetts Ave

department: Oncology

institute: Novartis Institutes for Biomedical Research

description: RPMI-8226 multiple myeloma cell line with inducible control shRNA

hyb_protocol: Following fragmentation cRNA was hybridized at 45ºC for approximately 18 hours, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

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 150.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 to 5 µg of total RNA

growth_protocol: Cell lines were maintained in Advanced RPMI-8226 medium (Invitrogen) with 1% FBS, and 1% LGlutamine.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

treatment_protocol: If dox induction, then shRNAs induced using 100ng/ml doxycline.

tag: cell line

value: RPMI-8226 multiple myeloma cell line

tag: stable infection

tag: dox induction

value: dox

tag: time post-induction

value: 0 hours

tag: replicate


title: Embryo 35, sample C, trophectoderm

tag: developmental stage


title: Embryo 36, sample C, trophectoderm


title: Embryo 34, sample C, trophectoderm


title: Embryo 33, sample D, inner cell mass


title: Embryo 38, sample C, trophectoderm


title: Embryo 36, sample D, inner cell mass


title: Bmi1-shRNA 0 hrs (1)

source_name: RPMI-8226 multiple myeloma cell line with inducible control shRNA


title: Embryo 33, sample B, trophectoderm


title: Embryo 35, sample D, inner cell mass


title: Bmi1-shRNA 0 hrs (3)


title: Embryo 34, sample A, trophectoderm


title: Ctl-shRNA 0 hrs (3)

value: control

value: no dox


title: Embryo 35, sample B, trophectoderm


title: Ctl-shRNA 0 hrs (1)


title: Ctl-shRNA 0 hrs (2)


title: Bmi1-shRNA + dox 48 hrs (2)

description: RPMI-8226 multiple myeloma cell line with inducible BMI1 shRNA

value: 48 hours


title: Bmi1-shRNA + dox 48 hrs (3)

source_name: RPMI-8226 multiple myeloma cell line with inducible BMI1 shRNA


title: Bmi1-shRNA + dox 48 hrs (1)


title: Embryo 32, sample D, inner cell mass


title: Embryo 33, sample A, trophectoderm


title: Embryo 34, sample B, trophectoderm


title: Bmi1-shRNA 48 hrs (3)


title: Embryo 31, sample D, inner cell mass


title: Bmi1-shRNA 48 hrs (1)


title: Ctl-shRNA + dox 48 hrs (3)


title: Embryo 31, sample A, trophectoderm


title: Embryo 30, sample C, trophectoderm


title: Bmi1-shRNA 48 hrs (2)


title: Ctl-shRNA + dox 48 hrs (2)


title: Ctl-shRNA + dox 48 hrs (1)


title: Embryo 32, sample B, trophectoderm


title: Embryo 32, sample C, trophectoderm


title: Embryo 32, sample A, trophectoderm


title: Ctl-shRNA 48 hrs (2)


title: Ctl-shRNA 48 hrs (1)


title: Embryo 30, sample D, inner cell mass


title: Bmi1-shRNA + dox 32 hrs (3)

value: 32 hours


title: Bmi1-shRNA + dox 32 hrs (2)


title: Embryo 28, sample C, trophectoderm


title: Embryo 30, sample A, trophectoderm


title: Embryo 30, sample B, trophectoderm


title: Embryo 29, sample D, inner cell mass


title: Embryo 29, sample B, trophectoderm


title: Embryo 28, sample D, inner cell mass


title: Bmi1-shRNA 32 hrs (3)


title: Embryo 31, sample B, trophectoderm


title: Embryo 28, sample B, trophectoderm


title: Bmi1-shRNA 32 hrs (1)


title: Bmi1-shRNA 32 hrs (2)


title: Embryo 27, sample D, inner cell mass


title: Embryo 26, sample C, trophectoderm


title: Embryo 28, sample A, trophectoderm


title: Ctl-shRNA + dox 32 hrs (1)


title: Ctl-shRNA 32 hrs (3)


title: Ctl-shRNA 48 hrs (3)


title: Ctl-shRNA + dox 32 hrs (3)


title: Ctl-shRNA + dox 32 hrs (2)


title: Ctl-shRNA 32 hrs (2)


title: Embryo 26, sample B, trophectoderm


title: Embryo 27, sample A, trophectoderm


title: Ctl-shRNA 32 hrs (1)


title: Bmi1-shRNA + dox 24 hrs (3)

value: 24 hours


title: Embryo 27, sample C, trophectoderm


title: Embryo 26, sample D, inner cell mass


title: Bmi1-shRNA + dox 32 hrs (1)


title: Bmi1-shRNA + dox 24 hrs (2)


title: Embryo 25, sample C, trophectoderm


title: Bmi1-shRNA + dox 24 hrs (1)


title: Embryo 25, sample D, inner cell mass


title: Embryo 26, sample A, trophectoderm


title: Bmi1-shRNA 24 hrs (3)


title: Bmi1-shRNA 24 hrs (2)


title: Ctl-shRNA + dox 24 hrs (3)


title: Embryo 24, sample D, inner cell mass


title: Embryo 27, sample B, trophectoderm


title: Ctl-shRNA + dox 24 hrs (1)


title: Ctl-shRNA + dox 24 hrs (2)


title: Embryo 24, sample B, trophectoderm


title: Ctl-shRNA 24 hrs (3)


title: Embryo 24, sample C, trophectoderm


title: Embryo 25, sample A, trophectoderm


title: Ctl-shRNA 24 hrs (2)


title: Embryo 22, sample C, trophectoderm


title: Embryo 23, sample C, trophectoderm


title: Embryo 24, sample A, trophectoderm


title: Embryo 23, sample D, inner cell mass


title: Ctl-shRNA 24 hrs (1)


title: Embryo 22, sample D, inner cell mass


title: Embryo 33, sample C, trophectoderm


title: KUCaP2_CR_3

city: Kyoto

first: Naoki

last: Terada

address: 54, Shogoinkawahara-cho, Sakyo-ku

department: Department of Urology

country: Japan

institute: Naoki Terada

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: We used 'RMA' processing algorithm on 'R/Bioconductor'.

source_name: Xenograft tissue

label_protocol: According to Affymetrix protocol

extract_protocol: Xenograft tissues of KUCaP-2 were collected during various stages and total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen)

tag: tissue type

value: Human prostate cancer xenograft

tag: stage

value: castration-resistant regrowth


title: Embryo 22, sample A, trophectoderm


title: Embryo 21, sample D, inner cell mass


title: KUCaP2_CR_4


title: Embryo 20, sample D, inner cell mass


title: Embryo 23, sample A, trophectoderm


title: Embryo 22, sample B, trophectoderm


title: KUCaP2_ND_4

value: castration-induced regression nadir


title: KUCaP2_ND_3


title: KUCaP2_AD_4

value: androgen-dependent growth


title: KUCaP2_CR_1


title: KUCaP2_ND_2


title: Embryo 21, sample C, trophectoderm


title: Embryo 19, sample D, inner cell mass


title: KUCaP2_AD_3


title: Embryo 20, sample A, trophectoderm


title: Embryo 21, sample A, trophectoderm


title: Embryo 19, sample B, trophectoderm


title: KUCaP2_ND_1


title: Bmi1-shRNA 24 hrs (1)


title: KUCaP2_AD_1


title: Embryo 20, sample C, trophectoderm


title: Embryo 19, sample C, trophectoderm


title: NP6 LP

city: Manassas

first: Margaret

middle: Claire

last: Emblom-Callahan

state: VA

address: 10900 University Blvd.

department: Molecular and Microbiology

institute: George Mason University

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 6

hyb_protocol: Using Ambion 10x Frag Buffer, Cy Dye aRNA probe was fragmented according to manufaturers directions. Hybridization was carried out using the Maui protocol with Maui hybridization buffer: 500 ul Formamide, 240 uls water, 250 ul 20X SSC, 10 ul 10% SDS, over night at 42 C follwed by washing using the TIGR protocols.

scan_protocol: Scans were carried out by the Duke Institute for Genomic Sciences and Policy using an Axon Genepix Scanner (Genepix 4000B) according to protocols for that scanner.

data_processing: Raw genepix data files (.GPR) derived from the HO36K human chip (Operon Human Oligo set V4) were downloaded from the Duke Website. All further analysis was carried out using the TM4 software suite (ExpressConverter V1.0, MIDAS, MEV) (63). Each genepix file was converted to multi-experiment viewer (.MEV) format using ExpressConverter V1.0 implementing background subtraction and using median intensity. All files were normalized by Microarray Data Analysis System (MIDAS) using a one bad channel tolerance “stringent” flags A and B, channel A and B background checking and signal/Noise threshold at 2.0.  Further normalization employing locally weighted linear regression (lowess) was then carried out utilizing the block mode and smoothing parameter of 0.33. Normalized, filtered (percent filter cut-off 60%) data was viewed and statistically analyzed using MultiExperiment (MeV) Statistical Analysis of Microarray (SAM) analysis and the stringent Tusher method. A final list of 1813 transcripts was derived setting the False Discovery Rate (FDR) to 0% and the δ score to 2.26.  Significant transcripts were then clustered by Euclidean distance hierarchical clustering using average linkage.

source_name: lower peripheral lung zone of normal lung from brain-dead donor

label_protocol: Starting with about 1 micro gram total RNA at a concentration of about 100 ng/microliter, RNA was reverse transcriebed using the MessageAmp II™ aRNA Kit (Ambion Catalog # 1751).  Second strand cDNA synthesis and cDNA purification were also carried out using the same kit.  Using the same kit, in vitro transcription step was used to amino-allylate RNA with a reacion mixture that included: 3 uL (50 mM) aaUTP, 4 uL (75 mM) T7 ATP solution, 4 uL (75 mM) T7 CTP solution, 4 uL (75 mM) T7 GTP, 2 uL (75 mM) T7 UTP solution, 4 uL T7 10X Reaction Buffer, 4 uL T7 Enzyme mix (total 25 uL per sample). Samples were incubated at 37 C for 14 hours and then maintained at 4 C prior to purification of amino-allylated amplified RNA using the same Message Amp II Kit in 100 uL of nuclease free water. Yield was verified by Nano-drop.  10 micrograms of amino-allylated amplified RNA were then coupled with Cy5 for experiemental and control samples, and Cy3 for Stratagene Human reference aaaRNA by incubation in dark for 1 hour after addition of 1 ul of 1M sodium bicarbonate pH9.0  according to the TIGR protocol used by Duke Institute for Genomic Science and Policy. MEGAclear Kit (Cat#1908) was used to remove unincorporated Cy Dye

extract_protocol: Lung obtained in the operating room within 1 minute of explantation and briefly dissected into 4 regions representing the upper and lower regions of the lung and within these both the peripheral regions and the central regions were dissected apart.  Lung tissue was kept in ice cold (4 C) PBS for transportation to the lab.  In the lab, tissue was briefly and rapidly dissected into 1 mm cubed pieces and placed in 4% collagenase P (Roche) in DMEM media with 20% FBS, 2X Penicillin, Streptomycin, Amphotericin B in 37 C humidified incubator with a magnetic stir bar oscillating at a medium rate to dissociate the tissues for 2 hours.  Tissue was strained through sterile strainer and centrifuged for 5 minutes at 1,000 RPM.  The supernatant was removed, and the cell pellet was plated on standard cell culture dish for 45 minutes with DMEM, 20% FBS, 1%P/S/F.  After 45 minutes the plates were vigorously washed with 1X PBS to remove unattached cells.  The attached cells (fibroblasts) were flash frozen, and the total RNA extracted using Qiagen RNeasy Kit and QIAShredder columns to remove DNA contaminants.  Fibroblast identity confirmed using immunocytochemistry on cells isolated onto microscope slides.  Cells stained for alpha smooth muscle actin (ACTA2) and the absence of von willebrand's factor (endothelial cell marker), cytokeratin 18 (epithelial cell marker) and cd11b (macrophage/monocyte cell marker).  RNA QA/QC done on Agilent bio-analyzer to confirm purity and integrity.  RNA quantitated on Thermo-Fisher Nano drop.

tag: isolate

value: brain-dead donor 6

value: non-cultured fibroblast

tag: tissue

value: lower peripheral lung zone

source_name: Stratagene Human Reference RNA

tag: reference

value: Stratagene Human Reference RNA


title: KUCaP2_AD_2


title: N5 UP

description: Human pulmonary non-cultured fibroblast Upper Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 5

source_name: upper peripheral lung zone of normal lung from brain-dead donor

value: brain-dead donor 5

value: upper peripheral lung zone


title: N4 UC

description: Human pulmonary non-cultured fibroblast Upper Central lung zone Normal Brain Dead Donor Normal Control Lung 4

source_name: upper central lung zone of normal lung from brain-dead donor

value: brain-dead donor 4

value: upper central lung zone


title: Embryo 25, sample B, trophectoderm

value: Trophectoderm

value: blastocyst

tag: cleavage stage fish result


title: N4 UP

description: Human pulmonary non-cultured fibroblast Upper Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 4


title: Embryo 23, sample B, trophectoderm

tag: blastocyt ma-pgd result


title: Embryo 18, sample D, inner cell mass

value: Inner cell mass


title: N5 LP

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 5


title: Embryo 18, sample C, trophectoderm


title: Embryo 17, sample C, trophectoderm


title: N5 LC

description: Human pulmonary non-cultured fibroblast Lower Central lung zone Normal Brain Dead Donor Normal Control Lung 5

source_name: lower central lung zone of normal lung from brain-dead donor

value: lower central lung zone


title: Embryo 18, sample A, trophectoderm


title: N4 LP

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 4


title: Embryo 21, sample B, trophectoderm


title: KUCaP2_CR_2


title: Embryo 17, sample D, inner cell mass


title: N4 LC

description: Human pulmonary non-cultured fibroblast Lower Central lung zone Normal Brain Dead Donor Normal Control Lung 4


title: N3 UC

description: Human pulmonary non-cultured fibroblast Upper Central lung zone Normal Brain Dead Donor Normal Control Lung 3

value: brain-dead donor 3


title: N3 UP

description: Human pulmonary non-cultured fibroblast Upper Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 3


title: Embryo 17, sample A, trophectoderm


title: N2 UP

description: Human pulmonary non-cultured fibroblast Upper Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 2

value: brain-dead donor 2


title: N3 LP

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 3


title: N2 UC

description: Human pulmonary non-cultured fibroblast Upper Central lung zone Normal Brain Dead Donor Normal Control Lung 2


title: Embryo 16, sample C, trophectoderm


title: Embryo 16, sample B, trophectoderm


title: Embryo 16, sample A, trophectoderm


title: Embryo 15, sample D, inner cell mass


title: N1 UP

description: Human pulmonary non-cultured fibroblast Upper Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 1

value: brain-dead donor 1


title: N1 UC

description: Human pulmonary non-cultured fibroblast Upper Central lung zone Normal Brain Dead Donor Normal Control Lung 1


title: Embryo 16, sample D, inner cell mass

description:
Hybridized to 250K_Nsp
CEL and CHP files


title: N2 LP

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 2


title: N1 LP

description: Human pulmonary non-cultured fibroblast Lower Peripheral lung zone Normal Brain Dead Donor Normal Control Lung 1


title: Embryo 14, sample D, inner cell mass


title: N2 LC

description: Human pulmonary non-cultured fibroblast Lower Central lung zone Normal Brain Dead Donor Normal Control Lung 2


title: Embryo 15, sample C, trophectoderm


title: Embryo 14, sample B, trophectoderm


title: Embryo 15, sample A, trophectoderm


title: IPF9 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 9

source_name: lower peripheral lung zone of patient with idiopathic pulmonary fibrosis

value: idiopathic pulmonary fibrosis patient 9


title: IPF9 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 9

source_name: lower central lung zone of patient with idiopathic pulmonary fibrosis


title: IPF9 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 9

source_name: upper central lung zone of patient with idiopathic pulmonary fibrosis


title: Embryo 15, sample B, trophectoderm


title: IPF8 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 8

value: idiopathic pulmonary fibrosis patient 8


title: Embryo 13, sample D, inner cell mass


title: IPF8 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 8


title: Embryo 12, sample C, trophectoderm


title: Embryo 13, sample C, trophectoderm


title: Embryo 12, sample D, inner cell mass


title: IPF8 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 8


title: IPF8 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 8


title: IPF7 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 7

value: idiopathic pulmonary fibrosis patient 7


title: IPF9 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 9

value: non-cultured fibroblast


title: N5 UC

description: Human pulmonary non-cultured fibroblast Upper Central lung zone Normal Brain Dead Donor Normal Control Lung 5


title: Embryo 13, sample B, trophectoderm


title: Embryo 13, sample A, trophectoderm


title: Embryo 12, sample A, trophectoderm


title: Embryo 11, sample B, trophectoderm


title: Embryo 11, sample A, trophectoderm


title: IPF7 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 7

value: lower peripheral lung zone


title: IPF6 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 6

value: idiopathic pulmonary fibrosis patient 6

value: Stratagene Human Reference RNA


title: IPF6 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 6


title: Embryo 11, sample D, inner cell mass

description:
Hybridized to 250K_Nsp
CEL and CHP files


title: Embryo 20, sample B, trophectoderm


title: N1 LC

description: Human pulmonary non-cultured fibroblast Lower Central lung zone Normal Brain Dead Donor Normal Control Lung 1


title: Embryo 12, sample B, trophectoderm


title: IPF6 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 6


title: IPF6 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 6


title: IPF7 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 7


title: Embryo 10, sample C, trophectoderm


title: IPF5 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 5

value: idiopathic pulmonary fibrosis patient 5


title: Embryo 10 sample D, inner cell mass


title: IPF5 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 5


title: IPF5 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 5


title: Embryo 11, sample C, trophectoderm


title: IPF4 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 4

value: idiopathic pulmonary fibrosis patient 4


title: IPF5 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 5


title: Embryo 10, sample A, trophectoderm


title: Embryo 10, sample B, trophectoderm


title: Embryo 9, sample C, trophectoderm


title: IPF4 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 4


title: Embryo 14, sample C, trophectoderm


title: IPF4 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 4

value: upper central lung zone


title: IPF4 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 4


title: Embryo 9, sample A, trophectoderm

value: Trophectoderm


title: Embryo 9, sample D, inner cell mass

value: blastocyst


title: Embryo 9, sample B, trophectoderm


title: IPF2 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 2

value: idiopathic pulmonary fibrosis patient 2


title: Embryo 18, sample B, trophectoderm


title: IPF3 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 3

value: idiopathic pulmonary fibrosis patient 3


title: Embryo 8, sample A, trophectoderm


title: Embryo 8, sample C, trophectoderm


title: Embryo 17, sample B, trophectoderm


title: IPF2 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 2


title: Embryo 7, sample A, trophectoderm


title: Embryo 6, sample C, trophectoderm


title: IPF2 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 2


title: SPL_20w_3

city: Stanford

first: Keiichi

last: Kodama

state: CA

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

description: SPL_20w_3; VALUE=LOG10(NOD/NOD.B10)

hyb_protocol: as described in In situ Hybridization kit-plus

scan_protocol: Agilent scanner, manufacturer's protocol

data_processing: Agilent Feature Extraction software 8.5

source_name: NOD

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Qiagen RNeasy

tag: strain

value: NOD

value: spleen

tag: age

value: 20 weeks

tag: disease state

value: diabetic

value: Control


title: Embryo 6, sample A, trophectoderm

description:
Hybridized to 250K_Nsp
CEL and CHP files

tag: cell type


title: Embryo 7, sample B, trophectoderm


title: Embryo 7, sample D, inner cell mass

value: Inner cell mass


title: IPF3 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 3

value: non-cultured fibroblast

value: lower central lung zone


title: SPL_20w_2

description: SPL_20w_2; VALUE=LOG10(NOD/NOD.B10)


title: SPL_20w_1

description: SPL_20w_1; VALUE=LOG10(NOD/NOD.B10)


title: SPL_16w_4

description: SPL_16w_4; VALUE=LOG10(NOD/NOD.B10)

value: 16 weeks


title: Embryo 8 sample D, inner cell mass


title: Embryo 8, sample B, trophectoderm


title: SPL_20w_5

description: SPL_20w_5; VALUE=LOG10(NOD/NOD.B10)


title: Embryo 5, sample D, inner cell mass


title: IPF11 UC

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 10

value: idiopathic pulmonary fibrosis patient 11

value: lower peripheral lung zone

value: Stratagene Human Reference RNA


title: SPL_16w_2

description: SPL_16w_2; VALUE=LOG10(NOD/NOD.B10)


title: SPL_16w_1

description: SPL_16w_1; VALUE=LOG10(NOD/NOD.B10)


title: SPL_12w_5

description: SPL_12w_5; VALUE=LOG10(NOD/NOD.B10)

value: 12 weeks


title: IPF12 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 12


title: SPL_12w_4

description: SPL_12w_4; VALUE=LOG10(NOD/NOD.B10)


title: IPF10 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 10

value: upper central lung zone


title: Embryo 5, sample C, trophectoderm

value: Trophectoderm

value: blastocyst


title: IPF10 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 10


title: SPL_12w_2

description: SPL_12w_2; VALUE=LOG10(NOD/NOD.B10)


title: IPF10 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 10


title: SPL_12w_3

description: SPL_12w_3; VALUE=LOG10(NOD/NOD.B10)


title: IPF2 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 2

value: idiopathic pulmonary fibrosis patient 2


title: SPL_20w_4

description: SPL_20w_4; VALUE=LOG10(NOD/NOD.B10)

value: NOD


title: Embryo 5, sample A, trophectoderm


title: SPL_8w_3

description: SPL_8w_3; VALUE=LOG10(NOD/NOD.B10)

value: spleen

value: 8 weeks


title: IPF1 UP

description: Human pulmonary non-cultured fibroblast upper peripheral lung zone idiopathic pulmonary fibrosis patient 1

value: idiopathic pulmonary fibrosis patient 1


title: Embryo 6, sample B, trophectoderm


title: Embryo 5, sample B, trophectoderm


title: Embryo 4, sample A, trophectoderm


title: SPL_4w_5

description: SPL_4w_5; VALUE=LOG10(NOD/NOD.B10)

value: diabetic

value: Control


title: SPL_8w_2

description: SPL_8w_2; VALUE=LOG10(NOD/NOD.B10)


title: SPL_4w_4

description: SPL_4w_4; VALUE=LOG10(NOD/NOD.B10)


title: IPF1 UC

description: Human pulmonary non-cultured fibroblast upper central lung zone idiopathic pulmonary fibrosis patient 1

value: non-cultured fibroblast


title: Embryo 4, sample C, trophectoderm


title: SPL_8w_1

description: SPL_8w_1; VALUE=LOG10(NOD/NOD.B10)


title: Embryo 4, sample B, trophectoderm


title: SPL_4w_3

description: SPL_4w_3; VALUE=LOG10(NOD/NOD.B10)


title: SPL_4w_2

description: SPL_4w_2; VALUE=LOG10(NOD/NOD.B10)


title: SPL_4w_1

description: SPL_4w_1; VALUE=LOG10(NOD/NOD.B10)

value: 4 weeks


title: IPF1 LP

description: Human pulmonary non-cultured fibroblast lower peripheral lung zone idiopathic pulmonary fibrosis patient 1


title: Embryo 3, sample D, inner cell mass

value: Inner cell mass


title: Embryo 7, sample C, trophectoderm


title: IPF1 LC

description: Human pulmonary non-cultured fibroblast lower central lung zone idiopathic pulmonary fibrosis patient 1

value: lower central lung zone


title: SPL_12w_1

description: SPL_12w_1; VALUE=LOG10(NOD/NOD.B10)


title: SPL_10d_5

description: SPL_10d_5; VALUE=LOG10(NOD/NOD.B10)

value: 10 days


title: SPL_10d_2

description: SPL_10d_2; VALUE=LOG10(NOD/NOD.B10)


title: SPL_10d_4

description: SPL_10d_4; VALUE=LOG10(NOD/NOD.B10)


title: Mesenchymal Stroma Cells Pool 2

status: Public on May 18 2010

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

description: Staining with Streptavidin-Conjugate

hyb_protocol: 10 µg of cRNA were applied to the Array chambers and these hybridized in a shaker-incubator at 46°C for 20 h and subsequently washed. Staining with Cy5-Streptavidin and re-washing was done according to the standard Codelink protocol.

scan_protocol: Arrays were scanned on an Affymetrix 428 Array Scanner (Affymetrix) at PMT=70 sensitivity and signal intensities calculated with the Codelink 4.0 Expression software (GE Healthcare).

data_processing: Raw expression data was quantile normalized using the Bioconductor 'preprocessCore' package for the R environment.

source_name: Mesenchymal Stroma Cells Pool

label_protocol: 2 µg of total RNA was amplified to cRNA and labeled with biotin-UTP according to the CodeLink UniSet Human 20K I Bioarray protocol (GE Healthcare, Germany).

extract_protocol: total RNA was extracted with the Invisor Spin Cell RNA Mini Kit (Invitek, Germany) according to manufacturer's instructions.

treatment_protocol: Lethally irradiated mice (9.5 Gy) were tranplanted with 10E6 bone marrow cells (including HSCs) or 10E6 MSCs.

tag: gender

value: female

value: 6-10 weeks

value: Bone marrow

tag: irradiation

value: lethally irradiated with 9.5 Gy

tag: pool setup

value: 3 pooled samples


title: SPL_10d_1

description: SPL_10d_1; VALUE=LOG10(NOD/NOD.B10)


title: SPL_10d_3

description: SPL_10d_3; VALUE=LOG10(NOD/NOD.B10)


title: Embryo 4, sample D, inner cell mass

value: blastocyst


title: SPL_16w_3

description: SPL_16w_3; VALUE=LOG10(NOD/NOD.B10)

value: NOD

value: 16 weeks


title: Embryo 6, sample D, inner cell mass


title: Embryo 3, sample C, trophectoderm

value: Trophectoderm


title: Mesenchymal Stroma Cells Pool 1

description: Staining with Streptavidin-Conjugate


title: Hematopoietic Stem Cells Pool 1

description: Staining with Streptavidin-Conjugate

source_name: Hematopoietic Stem Cells Pool (Whole Bone Marrow Transplantation)

value: 2 pooled samples


title: Bone Marrow Pool 1

description: Staining with Streptavidin-Conjugate

source_name: Bone Marrow Pool

value: no radiation


title: Hematopoietic Stem Cells Pool 2

description: Staining with Streptavidin-Conjugate


title: Embryo 2, sample D, inner cell mass


title: GRF5, biological rep2 (expt 3)

city: Gent

first: Nathalie

last: Gonzalez

address: Technologiepark 927

department: Plant System Biology

institute: VIB

description: 35S::GRF5, vegetative part of seedlings at stage 1.03

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

label: Standard affymetrix protocol

organism: Arabidopsis thaliana

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

tag: ecotype

value: vegetative part

value: stage 1.03

tag: genotype


title: GRF5, biological rep1 (expt 3)


title: wild type, biological rep2 (expt 3)

description: Wild type, vegetative part of seedlings at stage 1.03

source_name: Wild type

value: WT


title: Embryo 3, sample A, trophectoderm

source_name: Trophectoderm, biopsied, blastocyst stage

tag: developmental stage


title: Embryo 3, sample B, trophectoderm


title: wild type, biological rep3 (expt 2)


title: JAW, biological rep2 (expt 2)

description: 35S::JAW, vegetative part of seedlings at stage 1.03


title: GA20OX, biological rep1 (expt 2)

description: 35S::GA20OX, vegetative part of seedlings at stage 1.03


title: wild type, biological rep1 (expt 3)


title: GA20OX, biological rep2 (expt 2)


title: BRI1, biological rep3 (expt 1)

description: pBRI1::BRI1, vegetative part of seedlings at stage 1.03


title: Embryo 2, sample C, trophectoderm

description:
Hybridized to 250K_Nsp
CEL and CHP files


title: wild type, biological rep1 (expt 2)


title: BRI1, biological rep2 (expt 1)


title: BRI1, biological rep1 (expt 1)


title: GRF5, biological rep3 (expt 3)


title: AVP1, biological rep2 (expt 1)

description: 35S::AVP1, vegetative part of seedlings at stage 1.03


title: AVP1, biological rep3 (expt 1)


title: Embryo 2, sample B, trophectoderm


title: wild type, biological rep3 (expt 1)


title: wild type, biological rep2 (expt 2)


title: wild type, biological rep2 (expt 1)


title: S. mutans UA159 1% sucrose + 1% starch biofilm 48h replicate 1

city: Rochester

first: Marlise

middle: I

last: Klein

state: NY

address: 601 Elmwood Ave.

department: Dentistry - Center for Oral Biology

institute: University of Rochester

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems). Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments).

scan_protocol: Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website. Single-channel images of the slides were loaded into Spotfinder and overlaid. A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots. The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and standard deviation regularization with default setting. MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide. Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Streptococcus mutans UA159

source_name: S. mutans UA159 biofilm RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields. Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Biofilm preparation. Hydroxyapatite discs (2.93 cm2) were coated with amylase-active sterile clarified human saliva (sHA). Biofilms of S. mutans UA159 were formed on sHA discs placed in a vertical position in batch cultures at 37oC in 5% CO2. The biofilms were grown in buffered tryptone yeast-extract broth, pH 7.0, containing specific concentrations of sucrose and/or starch (soluble starch – 80% amylopectin and 20% amylose; Sigma Chemical Company, St Louis, MO). The concentrations of 0.5% sucrose (suc), 0.5% sucrose + 1% starch (st) and 1% sucrose were used.

extract_protocol: At 48h, the biofilms were removed from HA disc in sufficient volume of RNALater, according to manufacture instructions, and stored at 4oC, overnight. Next day, the biofilm samples were washed with cold 1X PBS and sonicated at 7 watts for 30 sec (2 sonication-washings). The supernatant was discarded and biofilm pellets were homogenized and RNA extracted by repeated acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight. RNA pellets were resuspended in 50 μL nuclease-free H2O, and treated with DNase I to remove contaminant genomic DNA. Two types of commercially available DNase I treatments were used: (i) on-column DNase I (Qiagen RNeasy Mini Kit, Qiagen Sciences, Germantown, MD, USA) and (ii) protein-engineered DNase I in solution (Turbo DNase, Ambion). An aliquot of the extracted RNA was treated first using Qiagen’s RNeasy on-column DNase I (Q, 2.7 U DNase I/10 μg RNA) and then with Ambion’s Turbo DNase I (T, 2 U Turbo DNase I/10 μg RNA), followed by Qiagen RNeasy MinElute (for DNase I removal) according to the manufacturer’s protocols with the exception of Qiagen’s on-column DNase I. The RNeasy on-column DNase I protocol was modified by adding a washing step with 350 μl of RLT buffer containing 36% ethanol prior to column washing with RW1 buffer (RLT and RW1 buffers are proprietary solutions of Qiagen Sciences). RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA).The quality of the purified RNA was examined by an Agilent 2100 electrophoresis bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to verify RNA integrity.

tag: biofilm age

value: 21 hours

tag: growth condition

value: 1% sucrose + 1% starch

source_name: wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 in a 5% CO2 incubator at 37°C.

tag: growth phase

value: mid-log


title: GA20OX, biological rep3 (expt 2)

tag: tissue


title: wild type, biological rep3 (expt 3)


title: S. mutans UA159 1% sucrose biofilm 48h replicate 4

value: 1% sucrose


title: Embryo 1, sample B, trophectoderm


title: WT3

city: Oxford

first: Catherine

last: Porcher

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: Oxford University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were transformed to log (base 2) and normalised using quantile normalisation. Differentially expressed genes were identified using LIMMA for R.

source_name: wild-type

label_protocol: Amplification and labeling of the RNA was performed using the Illumina TotalPrep RNA amplification kit (Ambion).

growth_protocol: Fetal liver cells from day E12.5 embryos were expanded for 3 days and Ter119- erythroid progenitors purified as described (Schuh et al, 2005, Mol Cell Biol, 25:10235-50).

extract_protocol: RNA was extracted using RNAqueous (Ambion) and assessed for integrity using the Agilent Bioanalyser 2100 (Agilent Technologies).

value: embryonic day E12.5

value: Ter119 fetal liver erythroid progenitors

tag: genotype/variation

value: wild-type


title: wild type, biological rep1 (expt 1)


title: S. mutans UA159 1% sucrose + 1% starch biofilm 48h replicate 4


title: S. mutans UA159 1% sucrose + 1% starch biofilm 48h replicate 3


title: S. mutans UA159 1% sucrose biofilm 48h replicate 1

growth_protocol: Biofilm preparation. Hydroxyapatite discs (2.93 cm2) were coated with amylase-active sterile clarified human saliva (sHA). Biofilms of S. mutans UA159 were formed on sHA discs placed in a vertical position in batch cultures at 37oC in 5% CO2. The biofilms were grown in buffered tryptone yeast-extract broth, pH 7.0, containing specific concentrations of sucrose and/or starch (soluble starch – 80% amylopectin and 20% amylose; Sigma Chemical Company, St Louis, MO). The concentrations of 1% sucrose (suc) and 1% sucrose + 1% starch were used.


title: WT1

description: replicate 1


title: JAW, biological rep1 (expt 2)


title: S. mutans UA159 1% sucrose biofilm 48h replicate 2


title: Bone Marrow Pool 2

description: Staining with Streptavidin-Conjugate

value: female

value: 6-10 weeks

value: Bone marrow


title: HeLa_siSMILE_PMA_s12

city: Nantes

first: RACAPE

last: MAUD

address: 30 Bd Jean Monnet

country: France

institute: INSERM UMR 643

description: gene expression analysis in SMILE siRNA transfected cells

hyb_protocol: The labeled cRNA samples were then fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Each sample was hybridized to a whole human genome 4x44K Agilent microarrays during 14 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned by Agilent Technologies Microarray Scanner.

scan_protocol: Scan with Agilent Technologies Microarray Scanner using default parameters.

data_processing: Data extraction of median feature intensity without background subtraction was realized with Feature Extraction software v9.1.3.1 (Agilent Technologies). Median feature intensity were normalized with the function lowess in Bioconductor in R and then, background signal , defined as signal below the median of mean signal of all slides, and negative spots were removed.

source_name: SMILE siRNA transfected HeLa cells_24h_PMA_s12

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 µg using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the one-colour manufacturer’s protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HeLa cells were cultured in RMPI 1640 medium supplemented with 10% fetal calf serum, 1% penicillin-streptomycin, 1% Glutamine, 1% Sodium pyruvate, 1% Hepes, 1% non essential amino-acids. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: After treatment cells were washed 3 times with PBS and lysed with 1mL TRIzol (Invitrogen, Cergy Pontoise, France). RNA extraction was then made as previously described. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: At a density of 30-50% in a 6-well plate, cells were incubated during 3 hours at 37°C with 5µL control or SMILE siRNA 20µM and 5µL lipofectamine RNAiMAX  (Invitrogen, Cergy-Pontoise, France). Then medium+transfection mix was removed and cells were incubated 24 hours with medium alone. After 24 hours of transfection cells were treated or not with PMA 20µM during 6 hours.

tag: protocol

value: SMILE knockout

tag: agent

value: phorbol-12-myristate-13-acetate (PMA)

tag: cell line

value: HeLa epithelial cells from human cervix carcinoma


title: WT2

description: replicate 2

tag: strain

tag: age


title: SclRER/RER1

description: replicate 1

source_name: SclRER/RER

tag: cell type

value: SclRER/RER


title: SclRER/RER2

description: replicate 2


title: HeLa_siSMILE_PMA_s11

source_name: SMILE siRNA transfected HeLa cells_24h_PMA_s11

tag: gender


title: Embryo 1, sample C, trophectoderm

value: Trophectoderm

value: blastocyst

tag: cleavage stage fish result

tag: blastocyt ma-pgd result


title: Embryo 1, sample A, trophectoderm


title: SclRER/RER3

description: replicate 3


title: S. mutans UA159 1% sucrose biofilm 48h replicate 3


title: HeLa_siSMILE_PMA_s10

source_name: SMILE siRNA transfected HeLa cells_24h_PMA_s10


title: HeLa_siCtrl_PMA_s09

source_name: control siRNA transfected HeLa cells_24h_PMA_s09

value: control


title: HeLa_siCtrl_PMA_s08

source_name: control siRNA transfected HeLa cells_24h_PMA_s08


title: HeLa_siSMILE_s06

source_name: SMILE siRNA transfected HeLa cells_24h_s06


title: HeLa_siSMILE_s05

source_name: SMILE siRNA transfected HeLa cells_24h_s05


title: Embryo 1, sample D, inner cell mass

source_name: Inner cell mass, biopsied, blastocyst stage

value: Inner cell mass


title: VCaP cells treated with R1881, dye swap

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881 (dye swap)

hyb_protocol: Agilent hyb protocol

scan_protocol: Agilent scanner Images were quantified using Genepix6.0

data_processing: Feature Extraction, Agilent

source_name: ethanol treated cells

label_protocol: Agilent labeling protocol

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

tag: VCaP cells

source_name: cells treated with R1881


title: HeLa_siCtrl_s01

description: gene expression analysis in control siRNA transfected cells

source_name: control siRNA transfected HeLa cells_24h_s01


title: VCaP cells treated with ethanol and infected with ERG, dye swap

description:
analysis of ERG overexpression and androgen effect in VCaP cells
eth_erg (dye swap)


title: VCaP cells treated with R1881 and infected with ERG

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881_ERG


title: HeLa_siCtrl_s03

source_name: control siRNA transfected HeLa cells_24h_s03


title: VCaP cells treated with R1881 and infected with LacZ, dye swap

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881_lacZ (dye swap)


title: HeLa_siCtrl_PMA_s07

source_name: control siRNA transfected HeLa cells_24h_PMA_s07


title: VCaP cells treated with ethanol and infected with LacZ, dye swap

description:
analysis of ERG overexpression and androgen effect in VCaP cells
eth_LacZ (dye swap)


title: VCaP cells treated with R1881

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881


title: HeLa_siCtrl_s02

source_name: control siRNA transfected HeLa cells_24h_s02


title: VCaP cells treated with ethanol and infected with LacZ

description:
analysis of ERG overexpression and androgen effect in VCaP cells
eth_LacZ


title: JAW, biological rep3 (expt 2)

tag: ecotype

value: vegetative part

value: stage 1.03

tag: genotype


title: VCaP cells treated with R1881 and infected with ERG, dye swap

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881_ERG (dye swap)


title: VCaP cells treated with ethanol and infected with ERG

description:
analysis of ERG overexpression and androgen effect in VCaP cells
eth_erg


title: LnCaP cells treated with R1881 for 6 hours

description:
time-course analysis of androgen treatment in LNCaP cells
time-course 2 of 5 of R1881 expression

source_name: R1881 treated cells - 6hr

tag: LnCaP cells

source_name: untreated cells


title: VCaP cells treated with R1881 and infected with LacZ

description:
analysis of ERG overexpression and androgen effect in VCaP cells
R1881_lacZ


title: LnCaP cells treated with R1881 for 3 hours

description:
time-course analysis of androgen treatment in LNCaP cells
time-course 1 of 5 of R1881 expression

source_name: R1881 treated cells - 3hr


title: LnCaP cells treated with R1881 for 24 hours

description:
time-course analysis of androgen treatment in LNCaP cells
time-course 4 of 5 of R1881 expression

source_name: R1881 treated cells - 24hr


title: LnCaP cells treated with R1881 for 48 hours

description:
time-course analysis of androgen treatment in LNCaP cells
time-course 5 of 5 of R1881 expression

source_name: R1881 treated cells - 48hr


title: Embryo 2, sample A, trophectoderm

description:
Hybridized to 250K_Nsp
CEL and CHP files

source_name: Trophectoderm, biopsied, blastocyst stage

tag: developmental stage


title: LnCaP cells treated with R1881 for 12 hours

description:
time-course analysis of androgen treatment in LNCaP cells
time-course 3 of 5 of R1881 expression

source_name: R1881 treated cells - 12hr


title: muscle_postTZD_postClamp_NRd_s72

status: Public on May 17 2010

city: La Jolla

first: Gene

last: Hsiao

address: 9500 Gilman Dr

institute: UCSD

description: no additional information

hyb_protocol: 15 ug of biotin-tagged cRNA was fragmented following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). 10 ug of fragmented target cRNA was hybridized (45°C with rotation for 16 hr, Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix Human Genome U133 Plus 2.0 array.  The GeneChip® arrays were washed and stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Data analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method

source_name: skeletal muscle (vastus lateralis)

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® IVT Labeling Kit

extract_protocol: Total RNA samples were isolated and processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip® Expression Analysis Technical Manual) using TRIzol Reagent (Invitrogen Corp., Carlsbad, CA)

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 72

value: muscle

tag: tzd treatment

value: postTZD

tag: clamp status

value: postClamp

tag: insulin resistance

value: NRd (insulin sensitive)

tag: subject


title: muscle_postTZD_preClamp_NRd_s72

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 72

tag: tissue

value: preClamp


title: AVP1, biological rep1 (expt 1)

description: 35S::AVP1, vegetative part of seedlings at stage 1.03


title: muscle_postTZD_postClamp_NRd_s71

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 71


title: muscle_preTZD_preClamp_NRd_s72

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 72

value: preTZD


title: muscle_preTZD_preClamp_NRd_s71

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 71


title: muscle_postTZD_preClamp_NRd_s71

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 71


title: muscle_preTZD_postClamp_NRd_s71

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 71


title: muscle_postTZD_preClamp_NRd_s69

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 69


title: muscle_preTZD_preClamp_NRd_s69

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 69


title: muscle_postTZD_postClamp_NRd_s68

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 68


title: muscle_preTZD_preClamp_NRd_s70

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 70


title: S. mutans UA159 1% sucrose + 1% starch biofilm 48h replicate 2

source_name: S. mutans UA159 biofilm RNA

tag: biofilm age

value: 21 hours

tag: growth condition

value: 1% sucrose + 1% starch

source_name: wild-type mid-log RNA

tag: growth phase

value: mid-log


title: muscle_postTZD_postClamp_NRd_s70

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 70


title: muscle_preTZD_preClamp_NRd_s67

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 67


title: muscle_postTZD_postClamp_NRd_s69

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 69


title: muscle_postTZD_preClamp_NRd_s70

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 70


title: muscle_preTZD_postClamp_NRd_s69

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 69


title: muscle_preTZD_postClamp_NRd_s70

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 70


title: muscle_postTZD_postClamp_NRd_s67

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 67


title: muscle_preTZD_preClamp_NRd_s66

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 66


title: muscle_postTZD_postClamp_NRd_s66

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 66


title: muscle_preTZD_preClamp_NRd_s68

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 68


title: muscle_preTZD_postClamp_NRd_s68

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 68


title: muscle_preTZD_postClamp_NRd_s66

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 66


title: muscle_preTZD_postClamp_NRd_s67

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 67


title: muscle_preTZD_postClamp_NRd_s72

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 72


title: muscle_postTZD_preClamp_NRd_s66

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 66


title: muscle_postTZD_postClamp_NRd_s65

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 65


title: muscle_postTZD_preClamp_NRd_s68

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 68


title: muscle_postTZD_preClamp_NRd_s65

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 65


title: muscle_preTZD_postClamp_NRd_s64

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 64


title: muscle_preTZD_postClamp_IRd_s62

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 62

value: IRd (insulin resistant)


title: muscle_postTZD_postClamp_IRd_s63

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 63


title: muscle_postTZD_preClamp_IRd-_s61

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 61

tag: response to tzd treatment

value: - (non responder)


title: muscle_preTZD_postClamp_NRd_s65

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 65


title: muscle_postTZD_postClamp_IRd-_s61

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 61


title: muscle_postTZD_preClamp_NRd_s64

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 64


title: muscle_postTZD_preClamp_IRd_s63

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 63


title: muscle_preTZD_preClamp_NRd_s65

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 65


title: muscle_preTZD_postClamp_IRd-_s61

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 61


title: muscle_postTZD_postClamp_NRd_s64

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 64


title: muscle_postTZD_postClamp_IRd_s62

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 62


title: muscle_postTZD_preClamp_IRd_s58

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 58


title: HeLa_siSMILE_s04

description: gene expression analysis in SMILE siRNA transfected cells

source_name: SMILE siRNA transfected HeLa cells_24h_s04

treatment_protocol: At a density of 30-50% in a 6-well plate, cells were incubated during 3 hours at 37°C with 5µL control or SMILE siRNA 20µM and 5µL lipofectamine RNAiMAX  (Invitrogen, Cergy-Pontoise, France). Then medium+transfection mix was removed and cells were incubated 24 hours with medium alone. After 24 hours of transfection cells were treated or not with PMA 20µM during 6 hours.

tag: protocol

value: SMILE knockout

tag: cell line

value: HeLa epithelial cells from human cervix carcinoma

tag: gender

value: female


title: muscle_preTZD_postClamp_IRd_s63

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 63


title: muscle_preTZD_preClamp_IRd_s63

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 63


title: muscle_postTZD_preClamp_NRd_s60

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 60


title: muscle_preTZD_postClamp_NRd_s60

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 60


title: muscle_preTZD_preClamp_NRd_s60

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 60


title: muscle_postTZD_preClamp_IRd_s59

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 59


title: muscle_preTZD_preClamp_IRd_s59

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 59


title: muscle_preTZD_preClamp_IRd-_s61

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 61


title: muscle_preTZD_postClamp_IRd_s59

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 59


title: muscle_postTZD_postClamp_NRd_s60

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 60


title: muscle_postTZD_postClamp_IRd_s58

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 58


title: muscle_preTZD_preClamp_IRd_s62

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 62


title: muscle_postTZD_postClamp_IRd_s59

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 59


title: muscle_preTZD_postClamp_IRd_s58

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 58


title: muscle_preTZD_preClamp_IRd_s58

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 58


title: muscle_preTZD_postClamp_IRd_s57

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 57


title: muscle_preTZD_preClamp_NRd_s55

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin sensitive, , subject 55


title: muscle_preTZD_preClamp_IRd-_s56

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 56


title: muscle_postTZD_preClamp_IRd_s57

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 57


title: muscle_preTZD_postClamp_IRd-_s56

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 56


title: muscle_postTZD_postClamp_IRd_s54

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 54


title: muscle_preTZD_postClamp_IRd_s54

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 54


title: muscle_postTZD_postClamp_IRd_s57

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 57


title: muscle_postTZD_postClamp_IRd_s52

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 52


title: muscle_postTZD_preClamp_IRd_s52

description: CEL file not provided for this Sample.

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 52


title: muscle_postTZD_postClamp_IRd-_s56

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 56


title: muscle_postTZD_postClamp_IRd_s53

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 53


title: muscle_postTZD_postClamp_IRd_s51

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 51


title: muscle_postTZD_preClamp_IRd_s53

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 53


title: muscle_preTZD_preClamp_IRd_s54

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 54


title: muscle_postTZD_preClamp_IRd_s51

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 51


title: muscle_postTZD_postClamp_NRd_s55

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin sensitive, , subject 55


title: muscle_postTZD_preClamp_IRd_s54

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 54


title: muscle_preTZD_preClamp_IRd_s57

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 57


title: muscle_postTZD_preClamp_IRd-_s56

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 56


title: muscle_preTZD_postClamp_NRd_s55

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin sensitive, , subject 55


title: muscle_preTZD_postClamp_IRd_s52

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 52


title: muscle_preTZD_postClamp_IRd_s51

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 51


title: muscle_preTZD_postClamp_IRd_s53

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 53


title: muscle_postTZD_postClamp_IRd-_s50

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 50


title: muscle_preTZD_preClamp_IRd_s51

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 51


title: muscle_preTZD_preClamp_IRd_s52

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 52


title: muscle_postTZD_preClamp_NRd_s55

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin sensitive, , subject 55


title: muscle_postTZD_preClamp_IRd-_s50

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 50


title: muscle_postTZD_preClamp_IRd+_s49

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 49

value: + (responder)


title: muscle_postTZD_postClamp_IRd+_s49

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 49


title: muscle_preTZD_postClamp_IRd+_s49

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 49


title: muscle_preTZD_preClamp_IRd+_s48

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 48


title: muscle_preTZD_preClamp_IRd+_s49

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 49


title: muscle_postTZD_postClamp_IRd_s47

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 47


title: muscle_postTZD_postClamp_IRd+_s48

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 48


title: muscle_preTZD_postClamp_IRd+_s48

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 48


title: muscle_postTZD_preClamp_IRd_s47

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 47


title: muscle_postTZD_preClamp_IRd+_s48

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 48


title: muscle_preTZD_postClamp_IRd-_s45

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, post-clamp, insulin resistant, non responder, subject 45


title: muscle_preTZD_postClamp_IRd_s47

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 47


title: muscle_preTZD_preClamp_IRd_s47

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 47


title: muscle_postTZD_postClamp_IRd_s46

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 46


title: muscle_preTZD_preClamp_IRd-_s45

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, non responder, subject 45


title: muscle_postTZD_postClamp_IRd-_s45

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, non responder, subject 45


title: muscle_preTZD_postClamp_IRd_s46

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 46


title: muscle_postTZD_preClamp_IRd_s46

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 46


title: adipose_preTZD_IRd_s44

description: no additional information

source_name: adipose tissue (abdominal subcutaneous)

treatment_protocol: pre-TZD, insulin resistant, , subject 44

value: adipose


title: muscle_preTZD_preClamp_IRd_s46

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 46


title: muscle_postTZD_preClamp_IRd_s44

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 44


title: muscle_postTZD_postClamp_IRd+_s43

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, responder, subject 43


title: adipose_postTZD_IRd+_s43

description: no additional information

treatment_protocol: post-TZD, insulin resistant, responder, subject 43


title: muscle_preTZD_postClamp_IRd_s44

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, , subject 44


title: adipose_preTZD_IRd+_s43

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, responder, subject 43


title: muscle_preTZD_preClamp_IRd_s44

description: CEL file not provided for this Sample.

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, , subject 44


title: muscle_postTZD_preClamp_IRd-_s45

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, non responder, subject 45


title: muscle_postTZD_preClamp_IRd+_s43

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, responder, subject 43


title: adipose_postTZD_IRd_s44

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 44


title: muscle_postTZD_postClamp_IRd_s44

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 44


title: adipose_postTZD_IRd_s42

description: no additional information

treatment_protocol: post-TZD, insulin resistant, , subject 42


title: muscle_postTZD_postClamp_IRd_s42

description: no additional information

treatment_protocol: post-TZD, post-clamp, insulin resistant, , subject 42


title: muscle_postTZD_preClamp_IRd_s42

description: no additional information

treatment_protocol: post-TZD, pre-clamp, insulin resistant, , subject 42


title: muscle_preTZD_preClamp_IRd+_s43

description: no additional information

treatment_protocol: pre-TZD, pre-clamp, insulin resistant, responder, subject 43


title: adipose_preTZD_IRd_s42

description: no additional information

treatment_protocol: pre-TZD, insulin resistant, , subject 42


title: muscle_preTZD_postClamp_IRd+_s43

description: no additional information

treatment_protocol: pre-TZD, post-clamp, insulin resistant, responder, subject 43