title: germ cell tumors (GCT) and normal controls Norm1B4 2

description: Normal Testis Specimen

tag: normal testis


title: germ cell tumors (GCT) and normal controls 472A 2

status: Public on Nov 10 2005

type: RNA

city: New York

first: James

last: Korkola

state: NY

address: 1275 York Ave

department: Cell Biology

country: USA

institute: Memorial Sloan-Kettering

description: Adult Male Germ Cell Tumor

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA (robust multi-array)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: germ cell tumor

label_protocol: Approximately 12 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Frozen tissue from a germ cell tumor was minced and homogenized in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: pure GCT (Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 268A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 473A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Choriocarcinoma, Embryonal Carcinoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 249A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Choriocarcinoma)


title: germ cell tumors (GCT) and normal controls 256A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 248A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 435A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Seminoma)


title: germ cell tumors (GCT) and normal controls 465A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls 429A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 425A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 430A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Seminoma)


title: germ cell tumors (GCT) and normal controls 243A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac, Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 428A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 403A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Teratoma)


title: germ cell tumors (GCT) and normal controls 413A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls 411A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 460A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 231B 1

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (from same patient as 231A)

tag: pure GCT (Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 242A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Seminoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 414A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 231A 1

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (from same patient as 231B)


title: germ cell tumors (GCT) and normal controls 228A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 222A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 234A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 224A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Choriocarcinoma)


title: germ cell tumors (GCT) and normal controls 399A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 221A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 401A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 396A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 435A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 215A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 208B 1

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (same patient as 208A)


title: germ cell tumors (GCT) and normal controls 373A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac)


title: germ cell tumors (GCT) and normal controls 391A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Choriocarcinoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 214A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 210A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 385A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 318D 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 310A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, Yolk Sac Tumor, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 203A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 198A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Choriocarcinoma, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 202A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma, syncytiotrophoblasts)


title: germ cell tumors (GCT) and normal controls 208A 1

description: Adult Male Germ Cell Tumor from testis (same patient as 208B)


title: germ cell tumors (GCT) and normal controls 354B 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 371A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 305A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Yolk Sac)


title: germ cell tumors (GCT) and normal controls 190B 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Seminoma)


title: germ cell tumors (GCT) and normal controls 193A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac Tumor, Teratoma, Seminoma, syncytiotrophoblasts)


title: germ cell tumors (GCT) and normal controls 303B 2

description: Adult Male Germ Cell Tumor from adrenal gland metastasis (same patient as 303B)


title: germ cell tumors (GCT) and normal controls 220A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Teratoma)


title: germ cell tumors (GCT) and normal controls 362A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 186B 1

description: Adult Male Germ Cell Tumor from mediastinum (from same patient as 186A)


title: germ cell tumors (GCT) and normal controls 187A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (anaplastic Seminoma)


title: germ cell tumors (GCT) and normal controls 186A 1

description: Adult Male Germ Cell Tumor from mediastinum (from same patient as 186B)


title: germ cell tumors (GCT) and normal controls 493A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 299A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Yolk Sac, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 184B 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 303A 2

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (same patient as 303A)


title: germ cell tumors (GCT) and normal controls 180A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 289A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 287B 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, Teratoma, Yolk Sac)


title: germ cell tumors (GCT) and normal controls 288A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 177B 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 171A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Teratoma, Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 155C 1

description: Adult Male Germ Cell Tumor liver metastasis (same patient as 155A)

tag: mixed GCT (Embryonal Carcinoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 256A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 268A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 249A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Choriocarcinoma)


title: germ cell tumors (GCT) and normal controls 243A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac, Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 231B 2

tag: pure GCT (Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 242A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Seminoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 234A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 155A 1

description: Adult Male Germ Cell Tumor from testis (same patient as 155C)


title: germ cell tumors (GCT) and normal controls 228A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 248A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 231A 2


title: germ cell tumors (GCT) and normal controls 224A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Choriocarcinoma)


title: germ cell tumors (GCT) and normal controls 220A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 222A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 052B 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Seminoma)


title: germ cell tumors (GCT) and normal controls 214A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 210A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 215A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 203A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 208A 2

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls 208B 2


title: germ cell tumors (GCT) and normal controls 193A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 221A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 202A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma, syncytiotrophoblasts)


title: germ cell tumors (GCT) and normal controls 180A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 192A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Seminoma)


title: germ cell tumors (GCT) and normal controls 187A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (anaplastic Seminoma)


title: germ cell tumors (GCT) and normal controls 186B 2


title: germ cell tumors (GCT) and normal controls 198A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Choriocarcinoma, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 186A 2


title: germ cell tumors (GCT) and normal controls 171A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 184B 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Teratoma)


title: germ cell tumors (GCT) and normal controls 177B 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 155C 2


title: germ cell tumors (GCT) and normal controls 155A 2


title: germ cell tumors (GCT) and normal controls 052B 2

description: Adult Male Germ Cell Tumor


title: 293TsiLL-3

status: Public on Nov 07 2005

city: philadelphia

first: Chris

last: Hoffmann

state: PA

address: 3610 hamilton walk

institute: University of Pennsylvania

description: Cell line was established and described in LLano et al. (2004). J. Virol. 78(17):9524-9537.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: phycoerythrin

source_name: 293T cells with LEDGF transcript knockdown (PSIP1 gene).

tag: 293T cells stably transfected with 2 shRNA constructs (si1340/si1428) against LEDGF transcript (PSIP1 gene).


title: germ cell tumors (GCT) and normal controls 372B 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac Tumor, syncytiotrophoblasts)


title: 293TsiScram-3

label: Phycoerythrin

source_name: 293T cells with scramble shRNA (control cell line).

tag: 293T cells stably transfected with 1 scramble shRNA construct. Control cell line for 293TsiLL cell line (LEDGF transcript knockdown - PSIP1 gene).


title: 293TsiLL-2


title: HRas-v12 transgenic male replicate 3 late timepoint

status: Public on Nov 01 2005

city: Los Angeles

first: Scherise

last: Mitchell

state: CA

address: 650 Charles E Young Dr, BH 569 CHS

department: Anesthesiology

institute: UCLA

description: The mouse strains for all the transgenic lines are C57black background and established after nearly 2 years of cross-breeding between the floxed alleles and the MCM strain. ?MHC-floxed-HRas-v12/MKK3bE/MKK7D transgenic mice were established as reported previously(19, 20, 36, 37, 40). They were bred with ?MHC-Mer-Cre-Mer (MCM) mice (from Dr. J. Molkentin, Cincinnati Children’s Hospital)(32) to generate double transgenic animals harboring both floxed transgenes and Mer-Cre-Mer transgene.  At 12 weeks of age the double transgenic mice and non-transgenic littermate controls were treated via i.p. injection of tamoxifen at a dosage of 20mg/kgBW once a day for 3 consecutive days as reported.  The hearts were harvested at an early (4-7 days post first tamoxifen injection) and a late (2-4 weeks) time point.  Left ventricles were dissected and rapidly frozen in liquid nitrogen and stored at -80?C prior to protein and RNA analysis.

hyb_protocol: standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

scan_protocol: standard affymetrix protocol-GeneChip Scanner 3000 using the protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

data_processing: Affymetrix MAS5.0 gene expressions are normalized with median invariant method.  To filter out significant genes, we adapted two approaches. A primary filtering method we used the standard two samples t-test in pair-wise comparisons involving gender (male or female), animal types (control, JNK, RAS, p38) and different time points (0, 1, 3, 4, 5, 9, 14). The selection criteria are as follows: |the fold change >2, |difference|>100, and p-value < 0.05

organism: Mus musculus

source_name: Mouse cardiac left ventricle

extract_protocol: RNA extration was accomplished using TRIzol reagent(http://www.invitrogen.com/content/sfs/manuals/15596026.pdf) and purified using Qiagen Rneasy Mini Kit (http://www1.qiagen.com/literature/protocols/pdf/RY20.pdf)

tag: Adult mouse, C57black background, left ventricle of heart


title: 293TsiLL-1


title: MKK3bE transgenic female replicate 1 early timepoint

label_protocol: standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf


title: MKK3bE transgenic male replicate 3 late timepoint


title: 293TsiScram-2


title: HRas-v12 transgenic female replicate 3 early timepoint


title: HRas-v12 transgenic female replicate 2 late timepoint


title: HRas-v12 transgenic male replicate 4 late timepoint


title: MKK3bE transgenic male replicate 4 late timepoint


title: MKK3bE transgenic female replicate 2 late timepoint


title: MKK3bE transgenic female replicate 3 late timepoint


title: MKK3bE transgenic male replicate 2 late timepoint


title: HRas-v12 transgenic male replicate 2 early timepoint


title: HRas-v12 transgenic female replicate 1 early timepoint


title: 293TsiLL-4


title: HRas-v12 transgenic male replicate 1 late timepoint


title: HRas-v12 transgenic female replicate 3 late timepoint


title: HRas-v12 transgenic male replicate 3 early timepoint


title: MKK3bE transgenic female replicate 2 early timepoint


title: HRas-v12 transgenic female replicate 4 late timepoint


title: 293TsiScram-1


title: 293TsiScram-4


title: HRas-v12 transgenic male replicate 1 early timepoint


title: ES/N2bFGF_3

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

description: ES/N2bFGF normalized log ratio

hyb_protocol: the labeled sample was resuspended with Hybridization buffer(50mM Na-Phosphate, ph8.1, 50% Formamide, 6X SSC, 5X Denhardtdts Solution, 0.5% SDS), then hybridized in humidified chamber at 42℃ for 24 hours.

scan_protocol: Cy3 and Cy5 fluorescent intensities were determined using the GenePix scanner (Axon Instruments), and images were analyzed using the GenePix Pro.

data_processing: Variance stabilizing normalization was applied with the ‘vsn’ package in Bioconductor using the R statistical package. After performing intensity-dependent global LOWESS regression, spatial and intensity dependent effects were managed by pin-group LOWESS normalization.

source_name: Mouse Embryonic Stem Cell

label_protocol: With 5ug of total RNA, Microarray cDNA synthesis kit(Roche) was used for first and second strand cDNA synthesis. Then double strand cDNA was prufied with RNeasy mini kit(Qiagen). For in vitro transcription, T7 MegaScript(Ambion) was used with Cy5-UTP(5mM, Amersham pharmacia) for 16 hours at 37℃.

growth_protocol: Undifferentiated R1 mouse ES cells (stage 1) were grown and maintained on gelatin-coated dishes with leukemia inhibitory factor (ESGRO, Invitrogen, NY) in ES cell medium, KODMEM supplemented with 15% FBS, nonessential amino acids, beta-mercaptoethanol, L-glutamine, and antibiotics

extract_protocol: Total RNA was prepared by using TriZol reagent (Invitrogen)

treatment_protocol: no treatment

tag: control

label_protocol: : With 5ug of total RNA, Microarray cDNA synthesis kit(Roche) was used for first and second strand cDNA synthesis. Then double strand cDNA was prufied with RNeasy mini kit(Qiagen). For in vitro transcription, T7 MegaScript(Ambion) was used with Cy3-UTP(5mM, Amersham pharmacia) for 16 hours at 37℃.

treatment_protocol: EBs were dissociated and plated onto tissue culture dishes in the serum-free medium containing Insulin/Transferrin/Selenium/Fibronectin (ITSF). After 6 days, the cells were expanded and plated onto polyornithine (15 mg ml-1) and laminin-coated plates (Becton Dickinson Labware, Bedford, MA) with the N2 medium (Johe, 1996) supplemented with laminin, bFGF (R&D Systems, Minneapolis, MN), murine N-terminal fragment of SHH and murine FGF8 isoform b (R&D Systems) (stage 4) . Finally the cells were induced to differentiated into DA neurons by removal of bFGF.

tag: treatment


title: ES/N2AA_3

description: ES/N2AA normalized log ratio

treatment_protocol: EBs were dissociated and plated onto tissue culture dishes in the serum-free medium containing Insulin/Transferrin/Selenium/Fibronectin (ITSF). After 6 days, the cells were expanded and plated onto polyornithine (15 mg ml-1) and laminin-coated plates (Becton Dickinson Labware, Bedford, MA) with the N2 medium (Johe, 1996) supplemented with laminin, bFGF (R&D Systems, Minneapolis, MN), murine N-terminal fragment of SHH and murine FGF8 isoform b (R&D Systems) (stage 4) . Finally the cells were induced to differentiated into DA neurons by removal of bFGF. The differentiation medium consisted of N2 medium supplemented with laminin in the presence or absence of cAMP, AA (Sigma, St. Louis, MO). The cells were incubated under differentiation conditions for 6–15 days.


title: ES/N2AA_2

description: ES/N2AA normalized log ratio


title: MKK7D transgenic female replicate 14 late timepoint


title: E. coli K12 BW25113 wildtype

city: Storrs

first: Thomas

middle: K

last: Wood

state: CT

address: 191 Auditorium Rd

department: Chemical Engineering

institute: University of Connecticut

description: RNA extracted from biofilm cells grown 24 hours in LB + 0.2% glucose, at 37 C and 250 rpm

data_processing: Affymetrix protocol

label: E. coli K12 BW25113

organism: Escherichia coli

source_name: Channel 1


title: ES/N2AA_1

description: ES/N2AA normalized log ratio


title: ES/N2bFGF_2

description: ES/N2bFGF normalized log ratio


title: MKK7D control female replicate 8 late timepoint


title: MKK7D transgenic female replicate 13 late timepoint


title: control male replicate 2


title: MKK7D transgenic female replicate 15 late timepoint


title: control female replicate 1


title: MKK7D control female replicate 10 late timepoint


title: MKK7D transgenic female replicate 5 early timepoint


title: MKK7D transgenic female replicate 6 early timepoint


title: control male replicate 5


title: control female replicate 2


title: E. coli K12 delta ydgG

description: RNA extracted from biofilm cells of E. coli K12 wild type after 24 hours of growth in LB supplemented with 0.2% glucose.

label: E. coli delta ydgG


title: MKK7D control female replicate 1 early timepoint


title: ES/N2bFGF_1

description: ES/N2bFGF normalized log ratio


title: ES/ITSF_3

description: ES/ITSF normalized log ratio

source_name: ITSF

treatment_protocol: EBs were dissociated and plated onto tissue culture dishes in the serum-free medium containing Insulin/Transferrin/Selenium/Fibronectin (ITSF)

tag: teatment


title: MKK7D control female replicate 2 early timepoint


title: control female replicate 4


title: MKK7D control female replicate 3 early timepoint


title: MKK7D control female replicate 9 late timepoint


title: Control male replicate1


title: ES/ITSF_1

description: ES/ITSF normalized log raio


title: ES/EB21d_2

description: ES/EB21d normalized log ratio

hyb_protocol: Hybridization solution

label_protocol: With 5ug of total RNA, Microarray cDNA synthesis kit(Roche) was used for first and second strand cDNA synthesis. Then double strand cDNA was prufied with RNeasy mini kit(Qiagen). For in vitro transcription, T7 MegaScript(Ambion) was used with Cy3-UTP(5mM, Amersham pharmacia) for 16 hours at 37℃.

source_name: Mouse Embryoid Body of 21 day

treatment_protocol: Embryoid Bodies were dissociated and plated onto tissue culture dish in DMEM with fetal bovine serum and antibiotics for 21 days


title: ES/EB21d_1

description: ES/EB21d normalized log ratio


title: ES/EB15d_3

description: ES/EB15d normalized log ratio

source_name: Mouse Embryoid Body of 15 day

treatment_protocol: Embryoid Bodies were dissociated and plated onto tissue culture dish in DMEM with fetal bovine serum and antibiotics for 15 days


title: germ cell tumors (GCT) and normal controls 190B 2

description: Adult Male Germ Cell Tumor


title: ES/EB21d_3

description: ES/EB21d normalized log ratio


title: ES/EB15d_2

description: ES/EB15d normalized log ratio


title: ES/EB4d_1

description: ES/EB4d normalized log ratio

source_name: Mouse Embryonic Stem cell

source_name: Mouse Embryoid Body of 4 day

treatment_protocol: Embryoid Bodies were dissociated and plated onto tissue culture dish in DMEM with fetal bovine serum and antibiotics for 4 days

tag: experiment


title: ES/ITSF_2

description: ES/ITSF normalized log ratio


title: ES/EB15d_1

description: ES/EB15d normalized log ratio


title: hypothalamus la hypo

status: Public on Oct 29 2005

city: Jerusalem

first: Michal

last: Horowitz

department: Physiology

country: Israel

institute: Hebrew University

description: Hypothalamus of rats before and during subjection to  long term (30d) heat acclimation and hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).

scan_protocol: For analysis, the membranes were exposed for 15 and 24 h to a phosphor screen and detected using a Bio-imaging Analyzer BAS2000 (Fuji Photo Film Co. Ltd Japan.

data_processing: We used Atlas Image 2.01 software (Clontech) to grid the phosphor image, to record the pixel density of each spot, and to perform background subtraction. The background-subtracted data were then further analyzed.

organism: Rattus norvegicus

source_name: hypothalamus

tag: Sabra strain, males, 3 mo old, hypothalamus


title: hypothalamus hypohydration

description: Hypothalamus of rats following subjection to hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).


title: hypothalamus sa hyp

description: Hypothalamus of rats befrm (2d) heat acclimation and hypohydration (10% loss of b. wgt, water deprivation). RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).


title: ES/EB4d_3

description: ES/EB4d normalized log ratio


title: hypothalamussa

description: Hypothalamus of rats before and during subjection to short (2 days)  term heat acclimation. RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).


title: ES/EB8d_1

description: ES/EB8d normalized log ratio

source_name: embryoid body of 8 day

treatment_protocol: Embryoid Bodies were dissociated and plated onto tissue culture dish in DMEM with fetal bovine serum and antibiotics for 8 days


title: Candida uninfected #13072403

city: Montreal

first: Gundula

last: Min-Oo

state: Quebec

department: Biochemistry

country: Canada

institute: McGill University

description: Animals were sacrificed, ex-sanguinated and hearts were rapidly frozen in liquid nitrogen, and subsequently stored at -80oC. Infected tissues were taken from mice injected with 3x105 C.albicans blastospores into the tail vein.  Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TRIzol; Invitrogen). For cDNA labeling, either 20 mg of total RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42oC for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum.

data_processing: dye swap and intensity dependent (LOWESS) normalization

tag: Strain

value: BcA70, Gender:Male, Tissue:Heart, Time:uninfected, RNA:18

source_name: C57BL/6 heart; uninfected

value: C57Bl/6, Gender:male, Tissue:heart, Time:uninfected, RNA:20


title: Candida uninfected #13072361

source_name: BcA70 heart; uninfected

value: BcA70, Gender:female, Tissue:heart, Time:uninfected, RNA:F1

value: C57BL/6, Gender:female, Tissue:heart, Time:uninfected, RNA:19


title: ES/EB4d_2

description: ES/EB4d normalized log ratio


title: Candida uninfected #13072309

value: BcA70, Gender:male, Tissue:heart, Time:uninfected, RNA:17

value: C57BL/6, Gender:male, Tissue:heart, Time:uninfected, RNA:12


title: ES/EB8d_2

description: ES/EB8d normalized log ratio

source_name: Mouse embroid body of 8day


title: ES/EB8d_3

description: ES/EB8d normalized log ratio

source_name: Mouse Embryoid Body of 8 day


title: Candida infected #13036661

source_name: BcA70 heart; infected

value: BcA70, Gender:male, Tissue:heart, Time:24hr post infection, RNA:9

source_name: C57BL/6 heart; infected

value: C57BL/6, Gender:male, Tissue:heart, Time:24hr post infection, RNA:6


title: Candida infected#13036515

data_processing: Dye swap and intensity dependent (LOWESS)

value: BcA70, Gender:male, Tissue:heart, Time:24hr post infection, RNA:M3

value: BcA70, Gender:male, Tissue:heart, Time:24hr post infection, RNA:M1


title: Candida infected #13036517

description:
Animals were sacrificed, ex-sanguinated and hearts were rapidly frozen in liquid nitrogen, and subsequently stored at -80oC. Infected tissues were taken from mice injected with 3x105 C.albicans blastospores into the tail vein.  Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TRIzol; Invitrogen). For cDNA labeling, either 20 mg of total RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42oC for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum.
The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation.
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpringv.7 (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings.

value: BcA70, Gender:male, Tissue:heart, Time:24hr post infection, RNA:7

value: C57BL/6, Gender:male, Tissue:heart, Time:24hr post infection, RNA:5


title: Candida infected #13025559

value: BcA70, Gender:Male, Tissue:heart, Time:24hr post infection, RNA:M1

source_name: C57Bl/6 heart; infected

value: C57BL/6, Gender:Male, Tissue:heart, Time:24hr post infection, RNA:M2


title: hypothalamus control euhydration

description: Hypothalamus of rat, untreated-euhydrated controls. RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).


title: hypothalamus la

description: Hypothalamus of rats before and during subjection to long (30 days)  term heat acclimatio. RNA extraction was accomplished using Tri Reagent (Molecular Research Center Inc. Ohio, USA). The probes were labeled for 1 h by the reverse transcription of total RNA (3 µg) at 42°C in a primer mix (Clontech) containing [32P]dATP (Amersham Biosciences, Buckinghamshire, UK). The reaction was terminated by adding 0.1M EDTA and 1 mg/ml glycogen (Sigma).The unincorporated 32P-labeled nucleotides were removed by Nucleo-Spin extraction columns (Clontech).


title: control 0 hours

city: Boston

first: Alexander

last: Turchin

state: MA

address: 221 Longwood Avenue

department: Division of Endocrinology

institute: Brigham and Women's Hospital

description: mouse whole heart control group 0 hours (no injection)

data_processing: Affymetrix GCOS 1.2

source_name: heart

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Whole hearts were removed upon the sacrifice of the animal and immediately frozen in liquid nitrogen. RNA was extracted using Trizol reagent.

tag: Male C57BL6, whole heart


title: trm8-dus3

status: Public on Oct 28 2005

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

description: Defects in tRNA modifications were assayed in trm8-dus3 double mutant background.

data_processing: spatial detrending, lowess smoothing

label: direct-covalent

organism: Saccharomyces cerevisiae


title: ZFL T9+

city: Singapore

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description: Zebrafish liver tumor tissue (induced by carcinogens) vs zebrafish normal liver tissue.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were reared at room temperature (27 ± 2°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

tag: Zebrafish liver tumor tissue or normal liver tissue

source_name: Zebrafish normal liver tissue

label_protocol: For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

tag: Reference RNA was obtained by pooling equal amount of male total RNA extracted from liver tissues of wild-type zebrafish.


title: ZFL T6+


title: dus3

description: Defects in tRNA modifications were assayed in dus3 mutant background.


title: ZFL T8+


title: trm8,pus7

description: Defects in tRNA modifications were assayed in trm8-pus7 double mutant background.


title: ZFL T5+


title: ZFL T3+


title: trm8-trm4

description: Defects in tRNA modifications were assayed in trm8-trm4 double mutant background.


title: trm8

description: Defects in tRNA modifications were assayed in trm8 mutant background.


title: ZFL T7+


title: ZFL T2+


title: ZFL T4+


title: ZFL T10+


title: Pus7

description: Defects in tRNA modifications were assayed in pus7 mutant background.

tag: Pus7 mutant vs. wild-type.


title: ZFL C10-


title: MKK7D transgenic female replicate 7 early timepoint

description: The mouse strains for all the transgenic lines are C57black background and established after nearly 2 years of cross-breeding between the floxed alleles and the MCM strain. ?MHC-floxed-HRas-v12/MKK3bE/MKK7D transgenic mice were established as reported previously(19, 20, 36, 37, 40). They were bred with ?MHC-Mer-Cre-Mer (MCM) mice (from Dr. J. Molkentin, Cincinnati Children’s Hospital)(32) to generate double transgenic animals harboring both floxed transgenes and Mer-Cre-Mer transgene.  At 12 weeks of age the double transgenic mice and non-transgenic littermate controls were treated via i.p. injection of tamoxifen at a dosage of 20mg/kgBW once a day for 3 consecutive days as reported.  The hearts were harvested at an early (4-7 days post first tamoxifen injection) and a late (2-4 weeks) time point.  Left ventricles were dissected and rapidly frozen in liquid nitrogen and stored at -80?C prior to protein and RNA analysis.

source_name: Mouse cardiac left ventricle


title: ZFL C8-


title: ZFL C7-


title: E12.5 Embryo2, 5 pooled(16011321000044)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: E12.5 Placentas, 5 pooled

hyb_protocol: Slides were hybridized according to manufacturers protocol (Agilent in situ Microarray Hybridization Protocol, Product # G2559A or P/N G2556-66003, September 10, 2001)

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

source_name: E12.5 Embryos, 5 pooled

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

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

tag: C57BL/6 mixed sex embryo

source_name: E12.5 Placentas, 5 pooled


title: E12.5 Placenta2, 5 pooled(16011321000045)

description: E12.5 Embryos, 5 pooled


title: ZFL C9-


title: E12.5 Placenta1, 5 pooled(16011321000039)

description: E12.5 Placentas, 5 pooled

tag: mixed C57BL/6 mixed sex embryo


title: ZFL C5-


title: ZFL C6-


title: ZFL T1+


title: fasted liver fish oil diet 2

city: Regensburg

first: Roland

last: Buettner

address: Franz-Josef-Strauss-Allee 11

department: Internal Medicine I

country: Germany

institute: University of Regensburg

description: liver sample of Wistar rat fed for 12 weeks with fish oil diet, after overnight fast

data_processing: Affymetrix Microarray Suite version 5.0

source_name: liver

label_protocol: Approximately 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Wistar rats were fasted overnight and killed by CO2. A piece of the reight venreal liver lobe was removed and clamp frozen. Total RNA was isolated from the clamp-frozen liver pieces using RNeasyR mini spin columns (Qiagen). The purified RNA was routinely checked for visible signs of degradation in a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, USA), and only high quality RNA was processed.


title: fasted liver standard chow diet 1

description: liver sample of Wistar rat fed for 12 weeks with standard chow diet, after overnight fast


title: ZFL C4-


title: E12.5 Embryo1, 5 pooled(16011321000040)

description: E12.5 Placentas, 5 pooled


title: fasted liver fish oil diet 1

tag: liver sample of Wistar rat fed for 12 weeks with fish oil diet, after overnight fast


title: fasted liver coconut fat diet 1

description: liver sample of Wistar rat fed for 12 weeks with coconut fat diet, after overnight fast


title: ZFL C3-


title: fasted liver coconut fat diet 2

tag: liver sample of Wistar rat fed for 12 weeks with coconut fat diet, after overnight fast


title: E12.5 Placenta3, 3 pooled(16011321000017)

description: E12.5 Placenta, 3 pooled

source_name: E12.5 Placenta, 3 pooled


title: ZFL C2-


title: fasted liver standard chow diet 2

description: liver sample of Wistar rat fed for 12 weeks with standard chow diet, after overnight fasts


title: fasted liver olive oil diet 2

description: liver sample of Wistar rat fed for 12 weeks with olive oil diet, after overnight fast


title: E12.5 Placenta1, 5 pooled(16011321000041)

description: E12.5 Embryos, 5 pooled


title: fasted liver lard diet 1

description: liver sample of Wistar rat fed for 12 weeks with lard diet, after overnight fast


title: fasted liver olive oil diet 1

tag: liver sample of Wistar rat fed for 12 weeks with olive oil diet, after overnight fast


title: E12.5 Embryo1, 5 pooled(16011321000038)

description: E12.5 Embryos, 5 pooled


title: ZFL C1-


title: E12.5 Placenta3, 3 pooled(16011321000019)

description: E12.5 Embryo, 3 pooled

source_name: E12.5 Embryo, 3 pooled


title: T36

status: Public on Oct 27 2005

city: Dallas

first: Benjamin

middle: P

last: Tu

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: time interval 36, cycle 3

data_processing: affy

label: affy

source_name: continuous culture

tag: time interval 36


title: E12.5 Placenta2, 5 pooled(16011321000043)

description: E12.5 Placentas, 5 pooled


title: E12.5 Embryo3, 3 pooled(16011321000016)

description: E12.5 Embryo, 3 pooled


title: E12.5 Embryo2, 5 pooled(16011321000042)

description: E12.5 Embryos, 5 pooled


title: fasted liver lard diet 2

tag: liver sample of Wistar rat fed for 12 weeks with lard diet, after overnight fast


title: E12.5 Embryo3, 3 pooled(16011321000018)

description: E12.5 Placenta, 3 pooled


title: T31

description: time interval 31, cycle 3

tag: time interval 31


title: T32

description: time interval 32, cycle 3

tag: time interval 32


title: T28

description: time interval 28, cycle 3

tag: time interval 28


title: T33

description: time interval 33, cycle 3

tag: time interval 33


title: T24

description: time interval 24, cycle 2

tag: time interval 24


title: T30

description: time interval 30, cycle 3

tag: time interval 30


title: T29

description: time interval 29, cycle 3

tag: time interval 29


title: T26

description: time interval 26, cycle 3

tag: time interval 26


title: T21

description: time interval 21, cycle 2

tag: time interval 21


title: T25

description: time interval 25, cycle 3

tag: time interval 25


title: T27

description: time interval 27, cycle 3

tag: time interval 27


title: T34

description: time interval 34, cycle 3

tag: time interval 34


title: T23

description: time interval 23, cycle 2

tag: time interval 23


title: T19

description: time interval 19, cycle 2

tag: time interval 19


title: T22

description: time interval 22, cycle 2

tag: time interval 22


title: T17

description: time interval 17, cycle 2

tag: time interval 17


title: T35

description: time interval 35, cycle 3

tag: time interval 35


title: T18

description: time interval 18, cycle 2

tag: time interval 18


title: T20

description: time interval 20, cycle 2

tag: time interval 20


title: T15

description: time interval 15, cycle 2

tag: time interval 15


title: T10

description: time interval 10, cycle 1

tag: time interval 10


title: T16

description: time interval 16, cycle 2

tag: time interval 16


title: T13

description: time interval 13, cycle 2

tag: time interval 13


title: T9

description: time interval 9, cycle 1

tag: time interval 9


title: T14

description: time interval 14, cycle 2

tag: time interval 14


title: T11

description: time interval 11, cycle 1

tag: time interval 11


title: T12

description: time interval 12, cycle 1

tag: time interval 12


title: T8

description: time interval 8, cycle 1

tag: time interval 8


title: T6

description: time interval 6, cycle 1

tag: time interval 6


title: T3

description: time interval 3, cycle 1

tag: time interval 3


title: T7

description: time interval 7, cycle 1

tag: time interval 7


title: T2

description: time interval 2, cycle 1

tag: time interval 2


title: T4

description: time interval 4, cycle 1

source_name: continous culture

tag: time interval 4


title: 20531, GATA2 overexpresed, FLT3 mutated

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description: Expression profiling of the leukemia patient number 20531, presenting GATA overexpression and FLT3 mutation.

data_processing: Data were imported to the Array Norm 1.7.2 software (Institute for Genomics and Bioinformatics, Graz University of Technology, Austria) for data processing and normalization. The intensity value associated to each spot was calculated subtracting the local background noise from the foreground values. Then, the Lowess normalization method was applied to normalize the data. Finally, the scale across slides function was used and the data were base 2 logarithm transformed and imported to the Genesis software (Institute for Genomics and Bioinformatics, Graz University of Technology, Austria) for statistical analysis. Only genes without missing values were included in the analysis. All different comparisons between groups were performed by using ANOVA with a p value threshold of 0.01 and a fold ratio threshold of 2 between the two groups of patients tested in each comparison.

source_name: AML-M1 leukemia patient 20531, GATA2 overexpresed, FLT3 mutated

tag: Bone marrow of patient with AML-M1, history number 20531. With GATA2 overexpression and FLT3 ITD mutation

source_name: Pool 9 healthy bone marrows

tag: Pool of 9 healthy bone marrows


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-3 using Msp I enzyme on spot array

status: Public on Oct 26 2005

type: genomic

city: Seattle

first: Robert

last: Tran

state: WA

address: 1100 Fairview Ave N; A1-111

institute: Fred Hutchinson cancer research center

description: No additional information

data_processing: Median-centered normalization of log2 ratios

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: whole plant (5 weeks old)

tag: Ecotype

value: LER

tag: Age

value: 5 weeks old

tag: Tissue

value: whole plant of LER wild type

value: whole plant of DRM1/2-CMT3 mutant


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-3R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-2R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-2 using Msp I enzyme on spot array

description: No additional information


title: T5

description: time interval 5, cycle 1

tag: time interval 5


description: Expression profiling of the leukemia patient number 26611, not presenting GATA overexpression nor FLT3 mutation.

source_name: AML-M1 leukemia patient 26611, GATA2 non-overexpresed, FLT3 non-mutated

tag: Bone marrow of patient with AML-M1, history number 26611. Without GATA2 overexpression nor FLT3 ITD mutation


description: Expression profiling of the leukemia patient number 18861, not presenting GATA overexpression nor FLT3 mutation.

source_name: AML-M1 leukemia patient 18861, GATA2 non-overexpresed, FLT3 non-mutated

tag: Bone marrow of patient with AML-M1, history number 18861. Without GATA2 overexpression nor FLT3 ITD mutation


title: T1

description: time interval 1, cycle 1

source_name: Continuous culture

tag: Time interval 1


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-3 using Msp I enzyme

description:
Channel 1 - Reference (LEX.R)
Channel 2 - Experimental (LEX.E)

data_processing: log2[(LEX.E - BG)/LEX.R Norm*]  *-LEX.R Norm = background subtracted, LEX.R intensity which has been block level LOWESS normalized, excluding 'flagged' spots

source_name: Whole plants (5 weeks old)

value: whole plant of AGO4 mutant


title: 16583, GATA2 overexpresed, FLT3 mutated

description: Expression profiling of the leukemia patient number 16583, presenting GATA overexpression and FLT3 mutation.

source_name: AML-M1 leukemia patient 16583, GATA2 overexpresed, FLT3 mutated

tag: Bone marrow of patient with AML-M1, history number 16583. With GATA2 overexpression and FLT3 ITD mutation


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-2 using Msp I enzyme


title: 20505, GATA2 overexpresed, FLT3 non-mutated

description: Expression profiling of the leukemia patient number 20505, presenting GATA overexpression and absence of FLT3 mutation.

tag: Bone marrow of patient with AML-M1, history number 20505. Endogenous GATA2 overexpression and absence of FLT3 ITD mutation


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-1R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-1R using Msp I enzyme


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-3R using Msp I enzyme


description: Expression profiling of the leukemia patient number 16320, not presenting GATA overexpression nor FLT3 mutation.

source_name: AML-M1 leukemia patient 16320, GATA2 non-overexpresed, FLT3 non-mutated

tag: Bone marrow of patient with AML-M1, history number 16320. Without GATA2 overexpression nor FLT3 ITD mutation


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-1 using Msp I enzyme


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-2R using Msp I enzyme


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-1 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-3R using Msp I enzyme on spot array

description: No additional information


title: 18788, GATA2 overexpresed, FLT3 mutated

description: Expression profiling of the leukemia patient number 18788, presenting GATA overexpression and FLT3 mutation.

source_name: AML-M1 leukemia patient 18788, GATA2 overexpresed, FLT3 mutated

tag: Bone marrow of patient with AML-M1, history number 18788. With GATA2 overexpression and FLT3 ITD mutation


description: Expression profiling of the leukemia patient number 23353, presenting GATA overexpression and absence of FLT3 mutation.

source_name: AML-M1 leukemia patient 23353, GATA2 overexpresed, FLT3 non-mutated

tag: Bone marrow of patient with AML-M1, history number 23353. Endogenous GATA2 overexpression and absence of FLT3 ITD mutation


description: Expression profiling of the leukemia patient number 14413, presenting GATA overexpression and absence of FLT3 mutation.

source_name: AML-M1 leukemia patient 14413, GATA2 overexpresed, FLT3 non-mutated

tag: Bone marrow of patient with AML-M1, history number 14413. Endogenous GATA2 overexpression and absence of FLT3 ITD mutation


title: Methylation profiling of KRYPTONITE mutant (KYP)-3R using Msp I enzyme

source_name: whole plants (5 weeks old)

value: whole plant of KYP mutant


title: Methylation profiling of KRYPTONITE mutant (KYP)-3 using Msp I enzyme


title: Methylation profiling of KRYPTONITE mutant (KYP)-2R using Msp I enzyme


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-1R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-2R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of KRYPTONITE mutant (KYP)-2 using Msp I enzyme


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-3 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-2 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of KRYPTONITE mutant (KYP)-1R using Msp I enzyme


title: Methylation profiling of KRYPTONITE mutant (KYP)-1 using Msp I enzyme


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-3R using Msp I enzyme


title: Methylation profiling of KRYPTONITE mutant (KYP)-3R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of AGONAUTE4 mutant (AGO4)-1 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of KRYPTONITE mutant (KYP)-3 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of KRYPTONITE mutant (KYP)-2R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-2R using Msp I enzyme


title: Methylation profiling of KRYPTONITE mutant (KYP)-1R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-3 using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-2R using Msp I enzyme on spot array

description: No additional information

value: WS

value: whole plant of WS wild type

value: whole plant of DRM1/2 mutant


title: Methylation profiling of KRYPTONITE mutant (KYP)-2 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-1R using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-3R using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-3 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-3R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-1 using Msp I enzyme


title: Methylation profiling of triple mutant (DRM1/2-CMT3)-2 using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-3 using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-2R using Msp I enzyme


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-1 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-1R using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of chromomethylase 3 (CMT3)-3R using Msp I enzyme  on spot array

description: No additional information

value: whole plant of CMT3 mutant


title: Methylation profiling of chromomethylase 3 (CMT3)-2R using Msp I enzyme  on spot array

description: No additional information


title: Methylation profiling of chromomethylase 3 (CMT3)-3R using Msp I enzyme


title: 2,4,6-trinitrotoluene (TNT)-contaminated soil_rep3

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

description: Dissociation curves were generated by increasing the temperature of the microarray (1°C/min) from 20°C to 68°C and recording signal intensities every 1°C or 2°C (Urakawa et al. 2003, Appl. Environ. Microbiol. 68:235-244).

hyb_protocol: 5 µg of fragmented and labeled RNA was hybridised and washed as previously described (El Fantroussi et al. 2003, Appl. Environ. Microbiol. 69:2377-2382), except that hybridisation time was 1 h. Each hybridisation experiment was done in triplicate.

scan_protocol: Fluorescence signal intensities were recorded for each probe on the microarray with a custom epifluorescence microscope and software (Guschin et al. 1997, Anal. Biochem. 250:203-211).

data_processing: The hybridisation signals were corrected by subtracting the local background signal and normalising the corrected hybridisation signal to the background (Fotin et al. 1998, Nucleic Acids Res. 26:1515-1521).

label: lissamine rhodamine

organism: unidentified

source_name: In vitro transcribed product of 16S rDNA amplified from an TNT-contaminated soil sample

label_protocol: RNA was simultaneously fragmented and end-labeled following Bavykin et al. (2001, Appl. Environ. Microbiol. 67:922-928) except that RNA was fragmented in solution rather than on-column. Fragmentation and labeling of RNA samples of uncontaminated and TNT-contaminated soils was done in parallel at the same time with the same freshly prepared reactants. In brief, RNA (30 µg) was suspended in 20 µl of diethyl pyrocarbonate (DEPC)-treated water and incubated at 95°C for 4 min. The RNA solution was mixed with 122 µl of preheated (95ÂºC for 30 s), filtered (0.22 µm) fragmentation and labeling solution that contained 700 µl of 25 mM sodium phosphate buffer (pH 7.0), 30 µl of 150 mM 1,10-phenanthroline, 3 µl of 150 mM CuSO4, and 6 µl of 100 mg/ml lissamine rhodamine B ethylenediamine (Molecular Probes, Inc., Eugene, OR). Three microliters of 200 mM H2O2 and 5 µl of 600 mM NaCNBH3 were added, and the mixture was incubated at 95°C for 10 min. The reaction was stopped with 540 µl of cold 100% ethanol and 20 µl of stop solution (2.6 M sodium acetate and 68 mM EDTA, pH 8.0). Following precipitation at -80°C for 10 min, RNA was centrifuged and washed three times with 100% ethanol. The RNA pellet was suspended in 20 µl of DEPC-treated water.

extract_protocol: DNA was extracted from soil samples with the UltraClean Soil DNA kit from Mo Bio (Carlsbad, CA) following the manufacturer's instructions. PCR was done with primers BACT 11 F (Kane et al. 1993, Appl. Environ. Microbiol. 59:682-686) containing the T7 promoter sequence and S-D-Bact-1512-a-A-16 (Fry et al. 1997, Appl. Environ. Microbiol. 63:1498-1504) in a thermal cycler (Thermo Hybaid US, Franklin, MA) in 100 µl reactions under the following conditions (reagents were from Invitrogen (Carlsbad, CA)): 1 X PCR buffer, 2 µl of deoxynucleoside triphosphate mixture (2.5 mM each), 2.5 µM of each primer, 5 U of Taq DNA polymerase, and 100 ng of template DNA. An initial denaturation step of 3 min at 94°C was followed by 30 cycles of 30 s at 94°C, 30 s at 55°C, and 1 min at 72°C. A final extension at 72°C for 7 min was also done. PCR products were purified with the Qiaquick PCR purification kit (Qiagen, Inc.) following the manufacturer's instructions. In vitro transcription was used to produce 16S rRNA according to the manufacturer's protocol (Invitrogen, Inc.). RNA samples were purified with the Qiagen RNeasy mini kit.

tag: Top 5-cm layer of soil, homogenised. Contains 23g TNT/g soil


title: 2,4,6-trinitrotoluene (TNT)-contaminated soil_rep2


title: Uncontaminated soil_rep2

source_name: In vitro transcribed product of 16S rDNA amplified from an uncontaminated soil sample

tag: Top 5-cm layer of soil, homogenised. Sampled a few meters from a 2,4,6-trinitrotoluene contaminated soil sample.


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-2 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of chromomethylase 3 (CMT3)-2 using Msp I enzyme  on spot array

description: No additional information


title: Methylation profiling of chromomethylase 3 (CMT3)-3 using Msp I enzyme  on spot array

description: No additional information


title: Methylation profiling of KRYPTONITE mutant (KYP)-1 using Msp I enzyme on spot array

description: No additional information


title: Methylation profiling of chromomethylase 3 (CMT3)-1 using Msp I enzyme  on spot array

description: No additional information


title: 2,4,6-trinitrotoluene (TNT)-contaminated soil_rep1


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-1R using Msp I enzyme

source_name: Whole plants (5 weeks old)Ecotype: WS


title: Uncontaminated soil_rep1

tag: Top 5-cm layer of soil, homogenised.

tag: Sampled a few meters from a 2,4,6-trinitrotoluene contaminated soil sample.


title: Methylation profiling of chromomethylase 3 (CMT3)-1R using Msp I enzyme  on spot array

description: No additional information

tag: Ecotype


title: Methylation profiling of  Domain Rearrange Methylase (DRM1/2)-1 using Msp I enzyme

tag: Age


title: Uncontaminated soil_rep3


title: Methylation profiling of chromomethylase 3 (CMT3)-2 using Msp I enzyme

tag: Tissue


title: Methylation profiling of chromomethylase 3 (CMT3)-2R using Msp I enzyme


title: Methylation profiling of chromomethylase 3 (CMT3)-3 using Msp I enzyme

source_name: Whole plants (5 weeks old)Ecotype: LER


title: Methylation profiling of chromomethylase 3 (CMT3)-1 using Msp I enzyme


title: Methylation profiling of chromomethylase 3 (CMT3)-1R using Msp I enzyme


title: Water Restricted Mouse 3 vs Control Mouse 3

status: Public on Oct 25 2005

city: Tucson

first: Kevin

last: Greer

state: AZ

department: Biomedical Engineering

institute: University of Arizona

description: Two channel hybridization of amplified (from total) RNA.

data_processing: Ratio of CH1/CH2 (after linlog [base 2] transformation and location/intensity lowess normalization of local background subtracted data)

label: Alexa Fluor 546

source_name: Water Restricted Mouse 3

tag: Kidney inner-medullae

label: Alexa Fluor 647

source_name: Control Mouse 3


title: Water Restricted Mouse 2 vs Control Mouse 2

source_name: Water Restricted Mouse 2

source_name: Control Mouse 2


title: Control Mouse 3 vs Water Restricted Mouse 2


title: Control Mouse 2 vs Water Restricted Mouse 1

source_name: Water Restricted Mouse 1


title: Water Restricted Mouse 1 vs Control Mouse 1

source_name: Control Mouse 1


title: Control Mouse 1 vs Water Restricted Mouse 3


title: Water Restricted Mouse 3 vs Control Mouse 2


title: HS-5 stromal cells+monocytes #1

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: Purpose is to determine the effect of monocytes on gene expression of bone marrow stromal cells

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.

source_name: HS-5+monocyte co-culture

label_protocol: The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA was covalently coupled with Cy5 monoreactive fluor in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine.

growth_protocol: HS-27a cells were plated in T75 flasks at 3,000,000 cells/flask in RPMI/10% FBS. They were cultured for 3 days with 500,000 CD14+ cells. Non-adherent cells were removed and adherent cells were harvested by trypsinization.

extract_protocol: All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

tag: CD14+ cells were isolated from peripheral blood mononuclear cells from a normal donor by antibody staining and magnetic bead (AutoMacs) selection.

source_name: Universal Reference RNA

label_protocol: The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA was covalently coupled with Cy3 monoreactive fluor in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine.

tag: A mixture of RNA from 10 human cell lines approximating the expression profile of the majority of human genes


title: Radium Human 22k v2.0, NOWAC86

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

country: Norway

institute: "The Norwegian Women and Cancer project"

description: Whole blood samples collectedin PAXgene tubes

hyb_protocol: use of stabilization and drying solution, Agilent, Palo Alto, CA

data_processing: Agilent Feature Extraction software version A.7.5.1 (default settings)

source_name: Stratagen reference

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit (Product Number 5184-3523).300 ng of total RNA were amplified and labeled

tag: Stratagen reference

tag: no HRT use 9.7 pmol/ug cRNA


title: HS-27a stromal cells+monocytes #1

source_name: HS-27a+monocytes 3 days

tag: CD14+ cells were isolated from peripheral blood mononuclear cells from a normal donor by antibody staining and magnetc bead (AutoMacs) selection.

source_name: Universal human reference RNA

tag: A mixture of RNA from 10 human cell lines approximating the expression profile of the majority of human genes.


title: Radium Human 22k v2.0, NOWAC88

tag: no HRT use 10.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC89

tag: no HRT use 22.0 pmol/ug cRNA


title: Methylation profiling of Domain Rearrange Methylase (DRM1/2)-2 using Msp I enzyme

source_name: Whole plants (5 weeks old)


title: Radium Human 22k v2.0, NOWAC72

tag: no HRT use 20.2 pmol/ug cRNA


title: Control Mouse 2 vs Water Restricted Mouse 3


title: Radium Human 22k v2.0, NOWAC95

tag: no HRT use 13.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC83

tag: no HRT use 7.2 pmol/ug cRNA


title: Water Restricted Mouse 2 vs Control Mouse 1


title: Radium Human 22k v2.0, NOWAC92

tag: no HRT use 8.8 pmol/ug cRNA


title: Water Restricted Mouse 1 vs Control Mouse 3


title: Radium Human 22k v2.0, NOWAC84

tag: no HRT use 11.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC85

tag: no HRT use 8.1 pmol/ug cRNA


title: Control Mouse 1 vs Water Restricted Mouse 2


title: Radium Human 22k v2.0, NOWAC99

tag: no HRT use 7.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC68

tag: no HRT use 16.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC75


title: Radium Human 22k v2.0, NOWAC79

tag: no HRT use 8.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC67

tag: no HRT use 15.0 pmol/ug cRNA


title: Control Mouse 3 vs Water Restricted Mouse 1

tag: Kidney inner-medullae


title: Radium Human 22k v2.0, NOWAC64

tag: Stratagen reference

tag: no HRT use 14.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC66

tag: no HRT use 10.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC65

tag: no HRT use 13.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC50

tag: no HRT use 9.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC49


title: Radium Human 22k v2.0, NOWAC59

tag: no HRT use 15.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC62

tag: no HRT use 8.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC47

tag: no HRT use 7.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC51

tag: no HRT use 15.6 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 14 (A)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: We compared the transcription profiles of ARMS sample by microarray competitive hybridization against an arbitrary total RNA reference prepared from a pool of 5 human fetal skeletal muscles.

hyb_protocol: Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer).

scan_protocol: Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities

source_name: Human fetal skeletal muscle (Reference)

label_protocol: Total RNA was retro-transcribed and labeled using a MICROMAX TSA Labeling Kit (PerkinElmer). Two ug of total RNA were used in each reaction but only half of the labeled cDNA was actually hybridized to the microarrays.

tag: -Tissue

value: pool of five human fetal skeletal muscles

tag: - Sex

value: male

tag: - Gestation

value: 18-21 weeks

source_name: ARMS biopsy of patient No. 14 (Test)

extract_protocol: Each tumor biopsy was selected by the local pathologist and shipped in dry ice to our laboratory within 24 hours from surgery. Upon arrival samples were minced and subsequently mechanically homogenized for RNA extraction. Total RNA was isolated using the RNA-zol reagent (Tel-Test, Friendswood, USA), following the manufacturer’s instructions.

tag: - Age (years)

tag: - PAX3-FKHR

value: positive

tag: - Primary site

value: retroperitoneum

tag: - Stage (IRS)

value: IV

tag: - Outcome

value: dead of disease


title: Gene expression profiling of ARMS No. 14 (B)


title: Radium Human 22k v2.0, NOWAC39

tag: Stratagen reference

tag: no HRT use 15.7 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC55

tag: no HRT use 17.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC60

tag: no HRT use 9.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC44

tag: no HRT use 10.9 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 12 (B)

source_name: ARMS biopsy of patient No. 12 (Test)

value: female

value: genitor-urinary not bladder-prostate

value: II

value: on first line therapy


title: Gene expression profiling of ARMS No. 12 (A)


title: Gene expression profiling of ARMS No. 13 (A)

source_name: ARMS biopsy of patient No. 13 (Test)

value: negative

value: III

value: first continuous complete remission (8 months)


title: Gene expression profiling of ARMS No. 13 (B)


title: Radium Human 22k v2.0, NOWAC40

tag: no HRT use 9.7 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 11 (B)

source_name: ARMS biopsy of patient No. 11 (Test)

value: pelvis

value: first continuous complete remission (21 months)


title: Radium Human 22k v2.0, NOWAC35

tag: no HRT use 16.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC26

tag: no HRT use 17.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC28

tag: no HRT use 11.1 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC30

tag: no HRT use 9.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC19

tag: no HRT use 7.7 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 11 (A)

tag: -Tissue

tag: - Sex

tag: - Gestation


title: Radium Human 22k v2.0, NOWAC37

tag: no HRT use 12.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC23

tag: no HRT use 11.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC27

tag: no HRT use 10.6 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 9 (B)

source_name: ARMS biopsy of patient No. 9 (Test)

tag: - Age (years)

tag: - PAX3-FKHR

tag: - Primary site

value: paratesticular

tag: - Stage (IRS)

value: I

tag: - Outcome

value: first continuous complete remission (60 months)


title: Radium Human 22k v2.0, NOWAC17

tag: Stratagen reference

tag: no HRT use 11.2 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 10 (A)

value: pool of five human fetal skeletal muscles

value: male

value: 18-21 weeks

source_name: ARMS biopsy of patient No. 10 (Test)

value: head/neck


title: Gene expression profiling of ARMS No. 10 (B)

value: dead of disease


title: Gene expression profiling of ARMS No. 7 (B)

source_name: ARMS biopsy of patient No. 7 (Test)

value: first continuous complete remission (23 months)


title: Gene expression profiling of ARMS No. 8 (B)

source_name: ARMS biopsy of patient No. 8 (Test)

value: IV


title: Gene expression profiling of ARMS No. 8 (A)


title: Gene expression profiling of ARMS No. 4 (B)

source_name: ARMS biopsy of patient No. 4 (Test)

value: female

value: positive

value: limbs

value: first continuous complete remission (18 months)


title: Gene expression profiling of ARMS No. 6 (B)

source_name: ARMS biopsy of patient No. 6 (Test)

value: negative

value: retroperitoneum

value: III

value: first continuous complete remission (28 months)


title: Gene expression profiling of ARMS No. 4 (A)

hyb_protocol: Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 ?l of 3 x SSC. Labeled cDNA was dissolved in 40 ?l of hybridisation buffer, denatured at 90?C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65?C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer).

extract_protocol: Each tumor biopsy was selected by the local pathologist and shipped in dry ice to our laboratory within 24 hours from surgery. Upon arrival samples were minced and subsequently mechanically homogenized for RNA extraction. Total RNA was isolated using the RNA-zol reagent (Tel-Test, Friendswood, USA), following the manufacturer?s instructions.


title: Gene expression profiling of ARMS No. 3 (B)

source_name: ARMS biopsy of patient No. 3 (Test)


title: Gene expression profiling of ARMS No. 5 (B)

source_name: ARMS biopsy of patient No. 5 (Test)

value: alive


title: Radium Human 22k v2.0, NOWAC09

source_name: Stratagen reference

tag: no HRT use 12.2 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 9 (A)

value: paratesticular

value: I

value: first continuous complete remission (60 months)


title: Gene expression profiling of ARMS No. 7 (A)

value: pool of five human fetal skeletal muscles

value: male

value: 18-21 weeks


title: Gene expression profiling of ARMS No. 6 (A)


title: Gene expression profiling of ARMS No. 5 (A)


title: Radium Human 22k v2.0, NOWAC13

tag: no HRT use 13.2 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC06

tag: no HRT use 12.0 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC07

tag: no HRT use 12.7 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC03

tag: no HRT use 9.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC02

tag: no HRT use 15.6 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 3 (A)

tag: -Tissue

tag: - Sex

tag: - Gestation

value: dead of disease


title: Radium Human 22k v2.0, NOWAC05

tag: no HRT use 9.0 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 2 (B)

source_name: ARMS biopsy of patient No. 2 (Test)

tag: - Age (years)

value: first continuous complete remission (24 months)


title: Radium Human 22k v2.0, NOWAC10

tag: no HRT use 14.2 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC08

tag: no HRT use 8.1 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC100

tag: HRT use 9.3 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 2 (A)

value: female

tag: - PAX3-FKHR

tag: - Primary site

tag: - Stage (IRS)

tag: - Outcome


title: Gene expression profiling of ARMS No. 1 (A)

source_name: ARMS biopsy of patient No. 1 (Test)

value: positive

value: head/neck

value: II


title: Radium Human 22k v2.0, NOWAC93

tag: Stratagen reference

tag: HRT use 17.4 pmol/ug cRNA


title: Gene expression profiling of ARMS No. 1 (B)


title: Radium Human 22k v2.0, NOWAC87

tag: HRT use 8.5 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC98

tag: HRT use 10.1 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC97

tag: HRT use 9.5 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC90

tag: HRT use 14.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC94

tag: HRT use 15.0 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC91

tag: HRT use 12.5 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC77

tag: HRT use 14.5 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC76

tag: HRT use 11.7 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC78


title: Radium Human 22k v2.0, NOWAC81

tag: HRT use 12.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC80

tag: HRT use 9.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC54

tag: HRT use 10.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC82

tag: HRT use 9.2 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC96

tag: HRT use 12.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC61


title: Radium Human 22k v2.0, NOWAC74

tag: HRT use 10.5 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC45

tag: HRT use 16.2 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC46

tag: Stratagen reference

tag: HRT use 9.1 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC73


title: Radium Human 22k v2.0, NOWAC41


title: Radium Human 22k v2.0, NOWAC63

tag: HRT use 15.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC69

tag: HRT use 15.2 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC42

tag: HRT use 8.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC53

tag: HRT use 11.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC38

tag: HRT use 19.0 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC16

tag: no HRT use 17.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC01


title: Radium Human 22k v2.0, NOWAC21

tag: HRT use 8.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC24

tag: HRT use 8.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC11

tag: HRT use 15.3 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC25

tag: HRT use 14 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC29

tag: HRT use 9.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC04

tag: HRT use 10.4 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC14

tag: HRT use 11.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC15

tag: HRT use 13.8 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC33

tag: HRT use 15.6 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC32

tag: Stratagen reference

tag: HRT use 9.9 pmol/ug cRNA


title: Radium Human 22k v2.0, NOWAC12


title: Radium Human 22k v2.0, NOWAC34

tag: HRT use 14.0 pmol/ug cRNA


title: 51 (R) Hsab-08-93

status: Public on Oct 24 2005

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike, Building 4, room 111

department: NIAID

description:
aRNA:	51
Array ID:	Hsab-08-93
Patient&sample ID:	G108
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	108
Histology (ISHLT grade):	3A
Clinical history notes:	anti-rejection pulse
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08

source_name: reference pool, Cy5

source_name: endomyocardial biopsy, Cy3


title: 73 (N) Hsab-08-99

description:
aRNA:	73
Array ID:	Hsab-08-99
Patient&sample ID:	AD28
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	28
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 74 (N) Hsab-08-87

description:
aRNA:	74
Array ID:	Hsab-08-87
Patient&sample ID:	AD92
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	92
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 82 (Ch) Hsab-08-92

description:
aRNA:	82
Array ID:	Hsab-08-92
Patient&sample ID:	I93
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	93
Histology (ISHLT grade):	Ch
Clinical history notes:	continue anti-chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 79 (Ch) Hsab-08-90

description:
aRNA:	79
Array ID:	Hsab-08-90
Patient&sample ID:	E143
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	143
Histology (ISHLT grade):	Ch
Clinical history notes:	changing anti-chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 78 (Ch) Hsab-08-89

description:
aRNA:	78
Array ID:	Hsab-08-89
Patient&sample ID:	E78
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	78
Histology (ISHLT grade):	Ch
Clinical history notes:	starting anti-chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: Radium Human 22k v2.0, NOWAC20


title: 81 (Ch) Hsab-08-91

description:
aRNA:	81
Array ID:	Hsab-08-91
Patient&sample ID:	I72
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	72
Histology (ISHLT grade):	Ch
Clinical history notes:	starting anti-Chagas treatment
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 65 (N) Hsab-08-97

description:
aRNA:	65
Array ID:	Hsab-08-97
Patient&sample ID:	AC30
Sex:	male
Basic disease:	ischemic cardiomyopathy
Days after Tx:	30
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 63 (N) Hsab-08-96

description:
aRNA:	63
Array ID:	Hsab-08-96
Patient&sample ID:	R13
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	13
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 61 (N) Hsab-08-94

description:
aRNA:	61
Array ID:	Hsab-08-94
Patient&sample ID:	M218
Sex:	male
Basic disease:	ischemic cardiomyopathy
Days after Tx:	218
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 77 (Ch) Hsab-08-84

description:
aRNA:	77
Array ID:	Hsab-08-84
Patient&sample ID:	B92
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	92
Histology (ISHLT grade):	3A
Clinical history notes:	anti-rejection treatment; positive imunohistochemistry for T.cruzi
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 75 (N) Hsab-08-88

description:
aRNA:	75
Array ID:	Hsab-08-88
Patient&sample ID:	O18
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	18
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 72 (pre-Ch) Hsab-08-83

description:
aRNA:	72
Array ID:	Hsab-08-83
Patient&sample ID:	F45
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	45
Histology (ISHLT grade):	0
Clinical history notes:	37 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 66 (pre-R) Hsab-08-82

description:
aRNA:	66
Array ID:	Hsab-08-82
Patient&sample ID:	G18
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	18
Histology (ISHLT grade):	0
Clinical history notes:	15 day before acute rejection
Final Clinical diagnosis:	Pre-R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 69 (N) Hsab-08-73

description:
aRNA:	69
Array ID:	Hsab-08-73
Patient&sample ID:	S25
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	25
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 63 (N) Hsab-08-72

description:
aRNA:	63
Array ID:	Hsab-08-72
Patient&sample ID:	R13
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	13
Histology (ISHLT grade):	0
Clinical history notes:	no
Final Clinical diagnosis:	N
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 83 (Ch) Hsab-08-48

description:
aRNA:	83
Array ID:	Hsab-08-48
Patient&sample ID:	D56
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	56
Histology (ISHLT grade):	3A
Clinical history notes:	at this time patient had cutaneous Chagas that was successfully treated
Final Clinical diagnosis:	Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: Radium Human 22k v2.0, NOWAC36

description: Whole blood samples collectedin PAXgene tubes

tag: HRT use 15.8 pmol/ug cRNA


title: 50 (R) Hsab-08-58

description:
aRNA:	50
Array ID:	Hsab-08-58
Patient&sample ID:	J111
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	111
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08

source_name: endomyocardial biopsy, Cy5

source_name: reference pool, Cy3


title: 85 (pre-Ch) Hsab-08-44

description:
aRNA:	85
Array ID:	Hsab-08-44
Patient&sample ID:	E24
Sex:	male
Basic disease:	Chagas cardiomyopathy
Days after Tx:	24
Histology (ISHLT grade):	0
Clinical history notes:	54 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 50 (R) Hsab-08-41

description:
aRNA:	50
Array ID:	Hsab-08-41
Patient&sample ID:	J111
Sex:	male
Basic disease:	dilated cardiomyopathy
Days after Tx:	111
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 56 (R) Hsab-08-71

description:
aRNA:	56
Array ID:	Hsab-08-71
Patient&sample ID:	AC55
Sex:	male
Basic disease:	ischemic cardiomyopathy
Days after Tx:	55
Histology (ISHLT grade):	3A
Clinical history notes:	no
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: 64 (pre-Ch) Hsab-08-81

description:
aRNA:	64
Array ID:	Hsab-08-81
Patient&sample ID:	D29
Sex:	female
Basic disease:	Chagas cardiomyopathy
Days after Tx:	29
Histology (ISHLT grade):	0
Clinical history notes:	27 days before Chagas disease reactivation
Final Clinical diagnosis:	Pre-Ch
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08


title: US1 (R) Hsab-08-47

description:
aRNA:	US1
Array ID:	Hsab-08-47
Patient&sample ID:	US11
Sex:	female
Basic disease:	ischemic cardiomyopathy
Days after Tx:	11y
Histology (ISHLT grade):	3A
Clinical history notes:	transplanted more than 11 years ago, patient stopped to take immunosuppression for about 1 year before this rejection
Final Clinical diagnosis:	R
Symbols and abbreviations: Patient&Sample ID: letter=patient ID,  number=days after Tx. Tx=transplantation; ISHLT=International Society for heart and Lung Transplantation; R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas.

Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Lot batch = Hsab-08