title: 4827

city: Gainesville

first: Yajie

address: 2033 Mowry Road Room 118

country: USA

institute: UF

hyb_protocol: The prepared target samples were then hybridized using the Hybridization, Wash and Stain Kit (P/N 900720) following the manufacturer’s protocol for the Fluidics Station 450 with protocol FS450_0001.

scan_protocol: Arrays were scanned using an Affymetrix® 7G scanner.

data_processing:
Signals were extracted from the scans using the apt-cel-extract program of the Affymetrix Powel Tools® (version 1.10.2) suite. GC bin control probes provide an estimate of non-specific hybridization (Affymetrix 2005) and help to assess the overall quality of the hybridization.  A GC bin control is a standard Affymetrix® control based upon the number of G/C bases (from 3 to 24) in the 25 mer probe.  None of the GC bin control probes align to the D. melanogaster or D. simulans reference genomes. Individual probes were classified according to their GC content and matched to the corresponding GC bin controls. A probe was considered detected when signal strength was higher than the median intensity of the corresponding GC band controls. Detection above background (DABG) was calculated at the individual probe level.
To correct for the background noise and to normalize the probe signals, each probe was classified into a GC bin and the 5 percentile signal for that GC bin was subtracted from the probe. The expression of a probe set was estimated by the natural log of the arithmetic mean of individual probe signals.

organism: Drosophila simulans

source_name: fly body

label_protocol: For each sample, target material was prepared for array hybridization using recommended Affymetrix® kits following the GeneChip© WT Double-Stranded Target Assay Manual protocol for single Tiling Arrays (no amplification) Ch3 . Procedures A-D. Briefly, 10 ug of Total RNA was concentrated to 8ul in DEPC H2O and 1st and 2nd strand cDNA were synthesized using the WT Double-Stranded DNA Synthesis Kit (P/N 900813). Following Cleanup  (P/N 900371), 7.5 ug of dsDNA was fragmented and labeled following the standard protocol (WT Double-Stranded DNA Terminal Labeling Kit, P/N 900812).

extract_protocol: Flies were freeze dried at -20° overnight prior to homogenization. Dried flies were ground to a fine powder using a GenoGrinder (Maximum, three minutes, repeated twice). Trizol (1 ml) was added to each homogenized sample and mixed thoroughly in the GenoGrinder (Max, 3 minutes). Samples were transferred to a new tube, 1 ul linear acrylamide was added to each and samples were then incubated at room temperature for 5 minutes. RNA was extracted using a standard Trizol extraction protocol: phase separation using 0.1 vol BCP, RNA precipitation with isopropanol, 70% ethanol wash and resuspension in 80 ul DEPC H2O.  Concentration was measured using a NanoDrop and up to 30 ug RNA per sample was treated with DNase I in 100 ul reaction volumes for 30 minutes at 37° (reaction mix: 4U Cloned DNase I TaKaRa 2220A, 80U Promega Recombinant RNasin N2515, in 1X TaKaRa Cloned DNase I Buffer II). Samples were cleaned prior to concentration using the Qiagen RNeasy Mini Kit (Cat. # 74104) following the manufacturer’s standard protocol with 30 ul DEPC H2O elutions (run through the column twice). RNA quality was examined using BioAnalyzer RNA 6000 Nano chips and all samples were found to be of good quality.  Genomic DNA was isolated from 35-40 flash frozen females using the AllPrep Mini Kit (Qiagen) following standard manufacturer’s protocols.  Samples were concentrated by standard ethanol precipitation and resuspended in 31 ul DEPC H2O.

tag: genotype

value: XS

tag: nucleic acid

value: DNA

tag: autosome

tag: x origin

tag: Sex

value: F

tag: rep


title: HeLa SGR Vs HeLa DMSO Experiment_2

status: Public on Sep 12 2011

type: RNA

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced scientific Research

description: Grid and spot alignment is performed by using Scanarray microarray analysis software form PerkinElmer.

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done. To account for dye swap, the signal channel and control channel measurements for sample(s) 2 were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cell line treated with DMSO

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 40 µg total RNA was used in each of the labeling reactions

extract_protocol: Trizol Method

tag: cell line

value: HeLa

tag: cell type

value: derived from human cervical cancer tissue

tag: treatment

value: DMSO

source_name: HeLa cell line treated with SGR

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 50 µg total RNA was used in each of the labeling reactions.

value: sanguinarine (SGR)


title: SqCC_92_CGH

type: genomic

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Please see Lockwood et al 2007 (PMID: 18391978) and Watson et al 2007 (PMID: 17051368)

data_processing: Normalized using algorithm by Khojasteh et al (PMID: 16297240)

molecule: genomic DNA

source_name: Microdissected lung tumor

label_protocol: Cy3 sample, Cy5 normal male reference

growth_protocol: microdissected lung tumor tissue

extract_protocol: Phenol/Chloroform DNA extraction. For the reference DNA, DNA from blood from an anonymous male reference was used.

tag: tissue

value: Lung tumor

tag: subtype

value: Squamous Cell Carcinoma

source_name: Normal male (blood DNA)

tag: reference

value: Normal male (blood DNA)


title: HeLa_Mock_rep2

city: Tokyo

first: Aiko

last: Sato-Otsubo

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

country: Japan

institute: University of Tokyo

hyb_protocol: Affymetrix starndard

scan_protocol: Affymetrix starndard

data_processing: Raw array signals were processed using Expression Console software (Affymetrix) in which RMA was performed.

label: biotin

source_name: HeLa cells, mock

label_protocol: Affymetrix starndard

growth_protocol: HeLa and TF-1 cells were retrovirally transduced with either mock, wild-type U2AF35 or S34F mutant . The cells were sorted by GFP-marking using a MoFlo® FACS cell sorter (Beckman Coulter) 48 hrs after retoroviral tranduction.

extract_protocol: Total RNA from cultured cells was isolated with the RNeasy Total RNA kit (Qiagen) using RNase-free DNase set (Qiagen) to reduce contamination of genomic DNA according to the manufacturer’s protocol.

tag: transduction

value: mock


title: HeLa_Mock_rep1


title: SqCC_91_CGH

scan_protocol: Please see Lockwood et al 2007 (PMID: 18391978) and Watson et al 2007 (PMID: 17051368)


title: SqCC_90_CGH


title: SqCC_88_CGH


title: SqCC_86_CGH


title: SqCC_87_CGH


title: HeLa_Mock_rep3


title: SqCC_85_CGH


title: SqCC_83_CGH


title: 4826

status: Public on Sep 13 2011

last: Yang

state: FL


title: 4797

description: 4797 CR-3_(dros_snpa520726F).CEL

value: XX


title: SqCC_84_CGH


title: TF1_S34F_rep2

source_name: TF1 cells, S34F U2AF35

value: S34F U2AF35


title: SqCC_82_CGH


title: 4796

description: 4796 CR-2_(dros_snpa520726F).CEL


title: SqCC_80_CGH


title: SqCC_73_CGH


title: SqCC_79_CGH


title: SqCC_74_CGH


title: SqCC_77_CGH


title: SqCC_75_CGH


title: SqCC_78_CGH


title: SqCC_72_CGH


title: 4795

description: 4795 CR-1_(dros_snpa520726F).CEL


title: SqCC_70_CGH


title: 4828


title: SqCC_76_CGH


title: SqCC_81_CGH


title: 4900

value: RNA


title: SqCC_69_CGH


title: SqCC_66_CGH


title: SqCC_68_CGH


title: SqCC_89_CGH


title: SqCC_65_CGH


title: SqCC_71_CGH


title: SqCC_63_CGH


title: SqCC_64_CGH


title: SqCC_62_CGH


title: SqCC_61_CGH


title: 4830

description: 4830_St_e_R2_female_gDNA_(dros_snpa520726F).CEL

value: SS

value: st e


title: SqCC_59_CGH


title: SqCC_58_CGH


title: 4901


title: SqCC_55_CGH


title: SqCC_57_CGH


title: SqCC_56_CGH


title: 4829

description: 4829_St_e_R1_female_gDNA_(dros_snpa520726F).CEL


title: SqCC_60_CGH


title: 4898

value: XY

value: M


title: 4902

value: XS


title: SqCC_54_CGH


title: 4899


title: SqCC_51_CGH


title: SqCC_44_CGH


title: SqCC_49_CGH


title: SqCC_53_CGH


title: SqCC_50_CGH


title: SqCC_47_CGH


title: SqCC_67_CGH


title: SqCC_46_CGH


title: SqCC_52_CGH


title: SqCC_43_CGH


title: SqCC_39_CGH


title: SqCC_45_CGH


title: SqCC_41_CGH


title: SqCC_42_CGH


title: SqCC_48_CGH


title: 4897


title: SqCC_32_CGH


title: 4831

description: 4831_St_e_R3_female_gDNA_(dros_snpa520726F).CEL

value: DNA

value: F


title: SqCC_40_CGH


title: SqCC_37_CGH


title: SqCC_36_CGH


title: SqCC_33_CGH


title: SqCC_35_CGH


title: SqCC_30_CGH


title: SqCC_38_CGH


title: SqCC_26_CGH


title: SqCC_34_CGH


title: SqCC_31_CGH


title: SqCC_27_CGH


title: SqCC_25_CGH


title: SqCC_24_CGH


title: SqCC_15_CGH


title: SqCC_12_CGH


title: SqCC_16_CGH


title: SqCC_11_CGH


title: SqCC_23_CGH


title: SqCC_28_CGH


title: SqCC_21_CGH


title: SqCC_22_CGH


title: SqCC_18_CGH


title: SqCC_19_CGH


title: SqCC_20_CGH


title: SqCC_17_CGH


title: SqCC_13_CGH


title: SqCC_1_CGH


title: SqCC_5_CGH


title: SqCC_6_CGH


title: SqCC_14_CGH


title: AC_179_CGH

value: Adenocarcinoma


title: SqCC_2_CGH


title: SqCC_9_CGH


title: SqCC_3_CGH


title: SqCC_10_CGH


title: SqCC_4_CGH


title: SqCC_8_CGH


title: SqCC_7_CGH


title: AC_174_CGH


title: AC_167_CGH


title: AC_178_CGH


title: AC_177_CGH


title: AC_168_CGH


title: AC_169_CGH


title: AC_173_CGH


title: AC_172_CGH


title: AC_175_CGH


title: AC_166_CGH


title: AC_161_CGH


title: AC_162_CGH


title: AC_164_CGH


title: AC_171_CGH


title: AC_159_CGH


title: AC_154_CGH


title: AC_153_CGH


title: AC_163_CGH


title: AC_155_CGH


title: AC_157_CGH


title: AC_152_CGH


title: AC_158_CGH


title: SqCC_29_CGH


title: AC_160_CGH


title: AC_151_CGH


title: AC_176_CGH


title: AC_165_CGH


title: AC_170_CGH


title: AC_156_CGH


title: AC_143_CGH


title: AC_142_CGH


title: AC_144_CGH


title: AC_141_CGH


title: AC_150_CGH


title: AC_148_CGH


title: AC_147_CGH


title: AC_140_CGH


title: AC_145_CGH


title: AC_136_CGH


title: AC_149_CGH


title: AC_137_CGH


title: AC_138_CGH


title: AC_133_CGH


title: AC_130_CGH


title: AC_134_CGH


title: AC_124_CGH


title: AC_129_CGH


title: AC_139_CGH


title: AC_131_CGH


title: AC_126_CGH


title: AC_146_CGH


title: AC_125_CGH


title: AC_123_CGH


title: AC_128_CGH


title: AC_135_CGH


title: AC_122_CGH


title: AC_132_CGH


title: AC_121_CGH


title: AC_118_CGH


title: AC_116_CGH


title: AC_115_CGH


title: AC_127_CGH


title: AC_117_CGH


title: AC_109_CGH


title: AC_114_CGH


title: AC_119_CGH


title: AC_120_CGH


title: AC_112_CGH


title: AC_97_CGH


title: AC_113_CGH


title: AC_106_CGH


title: AC_111_CGH


title: AC_105_CGH


title: AC_110_CGH


title: AC_100_CGH


title: AC_94_CGH


title: AC_102_CGH


title: AC_101_CGH


title: AC_103_CGH


title: retina_ko/ko_rep2

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description: retina free of retinal pigment epithelium (RPE)

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix 430.2 mouse GeneChips and the arrays were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: RMA

organism: Mus musculus

source_name: retina at age PN40

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2008, Affymetrix)

growth_protocol: Animals were grown until post-natal day 40.

extract_protocol: Retinal tissue was dissected free of retinal pigment epithelium (RPE) and placed in guanidine HCL.  The samples  were subsequently disrupted and homogenized using a rotor–stator  (Polytron PT2100).  Total RNA used for microarray studies was purified  from a caesium chloride gradient produced by high-speed  ultra-centrifugation.

treatment_protocol: Animals were housed under a 12 h light/12 h dark cycle and ad-lib access to food and water. Animals were sacrificed by cervical dislocation.

tag: strain

value: BALB/c AJ

value: retina

value: ko/ko


title: AC_96_CGH

value: Lung tumor


title: AC_108_CGH

value: Normal male (blood DNA)


title: AC_104_CGH


title: AC_95_CGH


title: AC_98_CGH


title: retina_ko/ko_rep3


title: AC_107_CGH


title: AC_99_CGH


title: AC_93_CGH


title: AC_92_CGH


title: AC_91_CGH


title: retina_wt/wt_rep1

value: wt/wt


title: AC_90_CGH


title: AC_89_CGH


title: retina_ko/ko_rep1


title: retina_wt/wt_rep2


title: retina_wt/wt_rep3


title: AC_85_CGH


title: AC_88_CGH


title: AC_81_CGH


title: AC_79_CGH


title: AC_83_CGH


title: AC_80_CGH


title: AC_87_CGH


title: AC_78_CGH


title: AC_84_CGH


title: AC_82_CGH


title: AC_76_CGH


title: AC_75_CGH


title: Tumor bearing mice: 24-hour light cycle (L/L) vs. 12-hour light/dark cycle (L/D)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log2 ratio (KB3L/KB7L/B)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: GenePix Pro version 6.0(Axon Instruments). F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.  Data presented below are normalized log2 ratio (KB3L/KB7L/B).

source_name: KB7L/B; tumor of Hela cells bearing mice; this group was caged in 12-hour light/dark cycle (L/D).

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Hela cells tumor bearing mice were randomly caged (5/cage) and subdivided into L/L (24-hour light cycle) and L/D (12-hour light/dark cycle) groups. 11days after injection, we sacrificed one L/L mouse and one L/D mouse.

extract_protocol: Total RNA from tumors were isolated using QIAshredder and RNeasy-Mini kits (Qiagen).

value: BALBc nu/nu

tag: protocol

value: 12-hour light/dark cycle (L/D)

source_name: KB3L; tumor of Hela cells bearing mice; this group was caged in 24 hour light cycle (L/L).

value: 24 hour light cycle (L/L)


title: AC_86_CGH


title: AC_77_CGH


title: AC_74_CGH


title: AC_73_CGH


title: AC_72_CGH


title: AC_71_CGH


title: AC_68_CGH


title: AC_69_CGH


title: AC_70_CGH


title: AC_67_CGH


title: AC_66_CGH


title: AC_64_CGH


title: AC_65_CGH


title: HeLa_S34F_rep3

data_processing: Raw array signals were processed using the Exon Array Analyzer ( http://EAA.mpi-bn.mpg.de/supp.php) in which RMA was performed.

source_name: HeLa cells, S34F U2AF35

growth_protocol: HeLa cells were retrovirally transduced with either mock, wild-type U2AF35 or S34F mutant . The cells were sorted by GFP-marking using a MoFlo® FACS cell sorter (Beckman Coulter) 48 hrs after retoroviral tranduction.

value: HeLa

value: S34F U2AF35


title: AC_62_CGH


title: AC_63_CGH


title: HeLa_Mock_rep3

value: mock


title: CMML-02_Tumor

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

label: Biotin

source_name: CMML primary specimen

label_protocol: Affymetrix standard protocol

growth_protocol: T cells used as germline control were cultured in the presence of phytohemagglutinin and IL-2 in some cases.

extract_protocol: Tumor DNAs were extracted from patients’ bone marrow or peripheral blood mononuclear cells.  For germline control, DNA was obtained from either buccal mucosa or paired CD3 positive T cells.

tag: disease

value: myelodysplastic syndromes (MDS)

tag: tissue type

value: tumor


title: CMML-04_Normal

description: Hybridized to 250K_Nsp

source_name: Normal primary specimen

value: normal


title: HeLa_S34F_rep2


title: CMML-02_Normal

description: Hybridized to 250K_Nsp


title: HeLa_S34F_rep1


title: HeLa_Mock_rep1

data_processing: Raw array signals were processed using the Exon Array Analyzer( http://EAA.mpi-bn.mpg.de/supp.php) in which RMA was performed.


title: CMML-03_Normal

description: Hybridized to 250K_Nsp


title: AC_60_CGH


title: HeLa_WT_rep2

source_name: HeLa cells, wild-type U2AF35

value: wild-type U2AF35


title: HeLa_Mock_rep2


title: CMML-03_Tumor

description: Hybridized to 250K_Nsp


title: AC_61_CGH

value: Adenocarcinoma


title: CMML-01_Normal

description: Hybridized to 250K_Nsp


title: HeLa_WT_rep1


title: HeLa_WT_rep3


title: CMML-01_Tumor

description: Hybridized to 250K_Nsp


title: tAML-05_Normal

description: Hybridized to 250K_Nsp


title: AC_58_CGH


title: AC_57_CGH


title: tAML-07_Normal

description: Hybridized to 250K_Nsp


title: CMML-04_Tumor

description: Hybridized to 250K_Nsp


title: tAML-06_Tumor

description: Hybridized to 250K_Nsp

source_name: tAML primary specimen


title: AC_56_CGH


title: tAML-06_Normal

description: Hybridized to 250K_Nsp


title: tAML-04_Tumor

description: Hybridized to 250K_Nsp


title: tAML-05_Tumor

description: Hybridized to 250K_Nsp


title: AC_55_CGH


title: AC_54_CGH


title: AC_52_CGH


title: AC_53_CGH


title: tAML-04_Normal

description: Hybridized to 250K_Nsp


title: tAML-07_Tumor

description: Hybridized to 250K_Nsp


title: AC_51_CGH


title: AC_50_CGH


title: AC_46_CGH


title: AC_49_CGH


title: AC_48_CGH


title: AC_45_CGH


title: AC_43_CGH


title: AC_47_CGH


title: tAML-03_Tumor

description: Hybridized to 250K_Nsp


title: tAML-03_Normal

description: Hybridized to 250K_Nsp


title: AC_42_CGH


title: AC_41_CGH


title: tAML-02_Tumor

description: Hybridized to 250K_Nsp


title: tAML-01_Normal

description: Hybridized to 250K_Nsp


title: tAML-01_Tumor

description: Hybridized to 250K_Nsp


title: AC_59_CGH


title: SqCC_83_mRNA

hyb_protocol: Affymetrix hyb protocol

scan_protocol: Affymetrix scanning protocol

data_processing: RMA Normalized using the "affy" package in Bioconductor in R

source_name: RNA from microdissected lung tumor

label_protocol: Affymetrix labeling protocol

extract_protocol: Qiagen RNeasy

treatment_protocol: Microdissected tumor tissue

value: Resected lung tumor

value: Squamous Cell Carcinoma


title: SqCC_84_mRNA


title: AC_40_CGH


title: MDS-21_Normal

description: Hybridized to 250K_Nsp


title: AC_39_CGH


title: AC_44_CGH


title: tAML-02_Normal

description: Hybridized to 250K_Nsp


title: SqCC_27_mRNA


title: SqCC_91_mRNA


title: AC_38_CGH


title: MDS-20_Tumor

description: Hybridized to 250K_Nsp

source_name: MDS primary specimen


title: MDS-18_Normal

description: Hybridized to 250K_Nsp


title: MDS-21_Tumor

description: Hybridized to 250K_Nsp


title: SqCC_12_mRNA


title: MDS-19_Normal

description: Hybridized to 250K_Nsp


title: SqCC_21_mRNA


title: SqCC_3_mRNA


title: AC_37_CGH


title: SqCC_9_mRNA


title: MDS-20_Normal

description: Hybridized to 250K_Nsp


title: SqCC_30_mRNA


title: AC_35_CGH


title: MDS-18_Tumor

description: Hybridized to 250K_Nsp


title: SqCC_88_mRNA


title: SqCC_92_mRNA


title: AC_36_CGH


title: AC_34_CGH


title: MDS-15_Tumor

description: Hybridized to 250K_Nsp


title: MDS-15_Normal

description: Hybridized to 250K_Nsp


title: SqCC_10_mRNA


title: SqCC_81_mRNA


title: MDS-17_Tumor

description: Hybridized to 250K_Nsp


title: MDS-14_Tumor

description: Hybridized to 250K_Nsp


title: MDS-16_Tumor

description: Hybridized to 250K_Nsp


title: MDS-19_Tumor

description: Hybridized to 250K_Nsp


title: SqCC_50_mRNA


title: AC_32_CGH


title: SqCC_49_mRNA


title: MDS-14_Normal

description: Hybridized to 250K_Nsp


title: SqCC_40_mRNA


title: AC_33_CGH


title: SqCC_39_mRNA


title: AC_30_CGH


title: AC_29_CGH


title: AC_31_CGH


title: MDS-17_Normal

description: Hybridized to 250K_Nsp


title: MDS-13_Tumor

description: Hybridized to 250K_Nsp


title: SqCC_45_mRNA


title: SqCC_24_mRNA


title: AC_28_CGH


title: AC_27_CGH


title: MDS-12_Normal

description: Hybridized to 250K_Nsp


title: AC_85_mRNA


title: SqCC_59_mRNA


title: MDS-16_Normal

description: Hybridized to 250K_Nsp


title: MDS-11_Normal

description: Hybridized to 250K_Nsp


title: AC_26_CGH


title: AC_25_CGH


title: AC_139_mRNA


title: AC_150_mRNA


title: AC_22_CGH


title: AC_1_mRNA


title: AC_24_CGH


title: MDS-13_Normal

description: Hybridized to 250K_Nsp


title: AC_21_CGH


title: MDS-11_Tumor

description: Hybridized to 250K_Nsp


title: AC_151_mRNA


title: AC_147_mRNA


title: MDS-12_Tumor

description: Hybridized to 250K_Nsp


title: AC_23_CGH


title: AC_149_mRNA


title: Patient 22 (aCGH)

city: Leiden

first: Marloes

last: van Kester

address: Einthovenweg 20

department: Dermatology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

scan_protocol: Scanned on an Genepix 4100A scanner. Images were quantified using Genepix Pro 4.1 software.

data_processing: Within this software, spots in which the reference DNA intensity was either below five times the average of the background or presented more than 3% saturated pixels were excluded from further analyses. The test/reference ratios were normalized for the median of the ratios of all features. The triplicates of the features were averaged in a homemade routine developed in Microsoft Excel 2000, and spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. Unbalances of the targets were determined based on log2 ratios of the average of their replicates, and we considered sequences as amplified or deleted when outside the ±0.3 range.

source_name: MF tumor biopsy

label_protocol: overnight random prime labelling reaction (BioPrime Random Prime labelling Kit, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA was isolated from 25 x 20 uM frozen sections using the Genomic-tips 20/G kit (Qiagen, Hilden, Germany), yielding 10-60 ug genomic DNA.

value: skin

tag: Stage

value: transformed

source_name: reference DNA

tag: sample type

value: gender mismatched pooled reference DNA


title: AC_36_mRNA


title: Patient 21 (aCGH)


title: AC_20_CGH

value: Lung tumor

value: Normal male (blood DNA)


title: AC_161_mRNA


title: MDS-10_Normal

description: Hybridized to 250K_Nsp


title: MDS-09_Tumor

description: Hybridized to 250K_Nsp


title: Patient 19 (aCGH)


title: Patient 18 (aCGH)


title: Patient 17 (aCGH)


title: AC_131_mRNA


title: AC_19_CGH


title: AC_46_mRNA


title: AC_17_CGH


title: AC_18_CGH


title: AC_16_CGH


title: AC_160_mRNA


title: AC_138_mRNA


title: AC_15_CGH


title: Patient 16 (aCGH)


title: MDS-10_Tumor

description: Hybridized to 250K_Nsp


title: AC_12_mRNA


title: MDS-09_Normal

description: Hybridized to 250K_Nsp


title: MDS-08_Normal

description: Hybridized to 250K_Nsp


title: MDS-06_Normal

description: Hybridized to 250K_Nsp


title: Patient 15 (aCGH)


title: Patient 20 (aCGH)


title: MDS-07_Tumor

description: Hybridized to 250K_Nsp


title: AC_170_mRNA


title: AC_14_CGH


title: MDS-07_Normal

description: Hybridized to 250K_Nsp


title: MDS-08_Tumor

description: Hybridized to 250K_Nsp


title: 5q- syndrome treated lenalidomide (at the time of first erytroid response) 1

city: Prague 2

first: Monika

last: Belickova

address: U nemocnice 1

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: CD14+ monocytes were isolated from peripheral blood. Mononuclear cells were purified by Ficoll-Hipaque density centrifugation (GE Health Care) and CD14+ cells were isolated using magnetic separation kit with specific antibodies according to manufacturer recommendations (MACS; Miltenyi Biotec). For total RNA extraction, we applied the acid guanidin-thiocyanat-phenol-chloroform method . The samples were incubated with DNase I (following manufacturer's instructions) (Qiagen). To evaluate the final integrity of total RNA, the Bioanalyzer 2100 instrument with Eukaryote Total RNA Pico Chip (both produced by Agilent Technologies) was used.

value: CD14+ monocytes from peripheral blood

tag: gender

value: M

tag: age in years

tag: disease state

tag: karyotype

tag: i-fish del(5)(q31)

tag: transfusions

value: yes

value: lenalidomide


title: Patient 14 (aCGH)


title: Patient 13 (aCGH)


title: Patient 12 (aCGH)


title: MDS-06_Tumor

description: Hybridized to 250K_Nsp


title: AC_12_CGH


title: 5q- syndrome treated lenalidomide (at the time of first erytroid response) 4

tag: cell type

value: no

tag: treatment


title: MDS-04_Tumor

description: Hybridized to 250K_Nsp

value: myelodysplastic syndromes (MDS)


title: 5q- syndrome before treatment 6

source_name: 5q- syndrome before treatment

value: F

value: 5q- syndrome before treatment

value: baseline


title: 5q- syndrome treated lenalidomide (at the time of first erytroid response) 3

value: not done


title: 5q- syndrome treated lenalidomide (at the time of first erytroid response) 5


title: Patient 11 (aCGH)

tag: tissue


title: AC_26_mRNA

value: Resected lung tumor

tag: subtype

value: Adenocarcinoma


title: 5q- syndrome treated lenalidomide (at the time of first erytroid response) 2


title: 5q- syndrome before treatment 4


title: 5q- syndrome before treatment 5


title: AC_108_mRNA


title: AC_9_CGH

source_name: Microdissected lung tumor

tag: reference


title: MDS-03_Tumor

description: Hybridized to 250K_Nsp

value: tumor


title: AC_10_CGH

source_name: Normal male (blood DNA)


title: AC_13_CGH


title: Patient 10 (aCGH)

value: skin

value: transformed


title: AC_94_mRNA


title: MDS-04_Normal

description: Hybridized to 250K_Nsp

value: normal


title: AC_11_CGH

value: Lung tumor

value: Normal male (blood DNA)


title: AC_8_CGH


title: 5q- syndrome before treatment 3

value: CD14+ monocytes from peripheral blood


title: Patient 9 (aCGH)

value: gender mismatched pooled reference DNA


title: MDS-03_Normal

description: Hybridized to 250K_Nsp


title: Patient 8 (aCGH)


title: Patient 7 (aCGH)


title: AC_72_mRNA


title: Patient 6 (aCGH)


title: 5q- syndrome before treatment 2

value: yes


title: AC_6_CGH


title: AC_70_mRNA


title: 5q- syndrome before treatment 1

value: M


title: AC_5_CGH


title: Patient 5 (aCGH)


title: AC_7_CGH


title: Patient 4 (aCGH)


title: Healthy donor 6

source_name: Healthy donor

value: Healthy donor

value: no


title: AC_69_mRNA


title: Healthy donor 5

value: F


title: Patient 3 (aCGH)


title: AC_3_CGH


title: AC_4_CGH


title: AC_2_CGH


title: Healthy donor 4


title: AC_113_mRNA


title: AC_81_mRNA


title: AC_58_mRNA


title: Healthy donor 3


title: AC_73_mRNA


title: AC_57_mRNA


title: Healthy donor 2


title: Patient 2 (aCGH)


title: AC_74_mRNA


title: RA1045_control_-3549 [ANALYTE: CK]

status: Public on Sep 10 2011

type: protein

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

description: Region of assignment and time of serum sampling were used to pull appropriated controls for each case sample, but this identifying information was not disclosed to us by the Department of Defense.

hyb_protocol: Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. The bead mix was added to a 96-well flat-bottom plate (1x concentration, 25 uL/well). The plate was washed twice with provided wash buffer using a Bio-Plex Pro II magnetic wash station (100 uL/well per wash). Serum was diluted 1:4 in provided universal sample diluent. Standard or diluted sample was added to the plate (25 uL/well), incubated at room temperature for one hour on a microtiter plate shaker, and removed by washing the plate three times on the wash station.

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA). Data were acquired with the following advanced settings: 125 beads per region, 50 uL sample size, and DD gate values of 5,000 to 25,000.

data_processing: Serum concentrations were interpolated from standard curves for each respective cytokine in Bio-Plex manager software. These concentrations were then normalized by calculating a Z-score using the formula: ((observed value)-(mean value of control patients))/(standard deviation).

label: PE

molecule: protein

source_name: serum

label_protocol: Biotinylated detection antibodies were added (1x concentration, 25 uL/well), allowed to incubate at room temperature for 30 minutes, and removed by washing the plate three times. Streptavidin-PE was added (1x concentration, 50 uL/well), incubated at room temperature for 10 minutes, and promptly removed by washing the plate three times. Provided assay buffer was added to re-suspend the beads (90 uL/well) and the plate was placed on the shaker for 30 seconds before reading.

extract_protocol: Serum was isolated and provided by a clinical laboratory.

tag: subject id

tag: group

value: control

tag: relative days to diagnosis

tag: Sex

value: Male

tag: race

value: Caucasian

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: RA1044_control_-146 [ANALYTE: CK]

value: Female

value: African American


title: AC_1_CGH

value: Adenocarcinoma


title: AC_2_mRNA

value: Resected lung tumor


title: RA1044_control_-1371 [ANALYTE: CK]


title: RA1045_control_-1050 [ANALYTE: CK]


title: RA1045_control_-356 [ANALYTE: CK]


title: RA1045_control_-2225 [ANALYTE: CK]


title: RA1043_control_-2969 [ANALYTE: CK]


title: RA1043_control_99 [ANALYTE: CK]


title: RA1043_control_-2424 [ANALYTE: CK]


title: RA1043_control_-597 [ANALYTE: CK]


title: RA1043_control_-1332 [ANALYTE: CK]


title: Patient 1 (aCGH)

value: skin

tag: Stage

value: transformed

tag: sample type


title: RA1042_control_-1559 [ANALYTE: CK]


title: RA1042_control_-847 [ANALYTE: CK]


title: RA1040_control_2783 [ANALYTE: CK]


title: RA1042_control_-3722 [ANALYTE: CK]


title: RA1041_control_-1839 [ANALYTE: CK]


title: Healthy donor 1

tag: gender

tag: age in years

tag: disease state

tag: karyotype


title: RA1041_control_-4225 [ANALYTE: CK]


title: RA1041_control_-4078 [ANALYTE: CK]


title: RA1040_control_-850 [ANALYTE: CK]


title: AC_98_mRNA


title: RA1040_control_-2272 [ANALYTE: CK]


title: RA1045_control_1588 [ANALYTE: CK]


title: RA1039_control_-13 [ANALYTE: CK]


title: RA1041_control_-2671 [ANALYTE: CK]


title: RA1040_control_-2462 [ANALYTE: CK]


title: RA1038_control_169 [ANALYTE: CK]

value: Other


title: RA1038_control_-1154 [ANALYTE: CK]


title: RA1038_control_-3493 [ANALYTE: CK]


title: RA1036_control_-163 [ANALYTE: CK]


title: RA1036_control_783 [ANALYTE: CK]


title: RA1038_control_-1787 [ANALYTE: CK]


title: RA1037_control_-2847 [ANALYTE: CK]


title: RA1035_control_-1672 [ANALYTE: CK]


title: RA1038_control_-26 [ANALYTE: CK]


title: RA1035_control_-881 [ANALYTE: CK]


title: RA1034_control_150 [ANALYTE: CK]


title: RA1035_control_758 [ANALYTE: CK]


title: RA1036_control_-2571 [ANALYTE: CK]


title: RA1033_control_249 [ANALYTE: CK]


title: RA1033_control_-376 [ANALYTE: CK]


title: RA1034_control_-2489 [ANALYTE: CK]


title: RA1034_control_-144 [ANALYTE: CK]


title: RA1034_control_-4809 [ANALYTE: CK]


title: RA1032_control_479 [ANALYTE: CK]


title: RA1033_control_-514 [ANALYTE: CK]


title: RA1034_control_-2515 [ANALYTE: CK]


title: RA1032_control_-347 [ANALYTE: CK]


title: RA1036_control_-3993 [ANALYTE: CK]


title: RA1032_control_-914 [ANALYTE: CK]


title: RA1032_control_-544 [ANALYTE: CK]


title: RA1031_control_-384 [ANALYTE: CK]


title: RA1036_control_-2451 [ANALYTE: CK]


title: RA1031_control_-1603 [ANALYTE: CK]


title: RA1030_control_143 [ANALYTE: CK]


title: RA1030_control_-2830 [ANALYTE: CK]


title: RA1030_control_-200 [ANALYTE: CK]


title: RA1028_control_-1180 [ANALYTE: CK]


title: RA1029_control_-2035 [ANALYTE: CK]


title: RA1028_control_-1966 [ANALYTE: CK]


title: RA1028_control_28 [ANALYTE: CK]


title: RA1028_control_-111 [ANALYTE: CK]


title: RA1027_control_1197 [ANALYTE: CK]


title: RA1026_control_3259 [ANALYTE: CK]


title: RA1025_control_-3702 [ANALYTE: CK]


title: RA1027_control_-1511 [ANALYTE: CK]


title: RA1025_control_-2763 [ANALYTE: CK]


title: RA1026_control_-633 [ANALYTE: CK]


title: RA1024_control_-2492 [ANALYTE: CK]


title: RA1024_control_-2199 [ANALYTE: CK]


title: RA1027_control_-1892 [ANALYTE: CK]


title: RA1026_control_-808 [ANALYTE: CK]


title: RA1025_control_306 [ANALYTE: CK]


title: RA1025_control_-475 [ANALYTE: CK]


title: RA1025_control_-3167 [ANALYTE: CK]


title: RA1023_control_-314 [ANALYTE: CK]


title: RA1023_control_-1413 [ANALYTE: CK]


title: RA1023_control_-688 [ANALYTE: CK]


title: RA1022_control_-334 [ANALYTE: CK]


title: RA1028_control_-2370 [ANALYTE: CK]


title: RA1022_control_-1744 [ANALYTE: CK]


title: RA1022_control_-639 [ANALYTE: CK]


title: RA1021_control_2371 [ANALYTE: CK]


title: RA1024_control_-723 [ANALYTE: CK]


title: RA1018_control_1915 [ANALYTE: CK]


title: RA1023_control_246 [ANALYTE: CK]


title: RA1018_control_-1868 [ANALYTE: CK]


title: RA1019_control_-626 [ANALYTE: CK]


title: RA1019_control_-1437 [ANALYTE: CK]


title: RA1018_control_-2115 [ANALYTE: CK]


title: RA1017_control_858 [ANALYTE: CK]


title: RA1017_control_-1620 [ANALYTE: CK]


title: RA1015_control_-2257 [ANALYTE: CK]


title: RA1015_control_562 [ANALYTE: CK]


title: RA1015_control_-3306 [ANALYTE: CK]


title: RA1020_control_-3160 [ANALYTE: CK]


title: RA1020_control_-1707 [ANALYTE: CK]


title: RA1020_control_-454 [ANALYTE: CK]


title: RA1014_control_379 [ANALYTE: CK]


title: RA1015_control_-3677 [ANALYTE: CK]


title: RA1013_control_-787 [ANALYTE: CK]


title: RA1017_control_-4333 [ANALYTE: CK]


title: RA1017_control_-3466 [ANALYTE: CK]


title: RA1017_control_-2421 [ANALYTE: CK]


title: RA1012_control_15 [ANALYTE: CK]


title: RA1021_control_-528 [ANALYTE: CK]


title: RA1013_control_-4169 [ANALYTE: CK]


title: RA1011_control_-1235 [ANALYTE: CK]


title: RA1011_control_-478 [ANALYTE: CK]


title: RA1010_control_-835 [ANALYTE: CK]


title: RA1013_control_-2460 [ANALYTE: CK]


title: RA1015_control_-1525 [ANALYTE: CK]


title: RA1011_control_221 [ANALYTE: CK]


title: RA1013_control_-449 [ANALYTE: CK]


title: RA1009_control_-988 [ANALYTE: CK]


title: RA1009_control_-2448 [ANALYTE: CK]


title: RA1009_control_-2079 [ANALYTE: CK]


title: RA1009_control_-1352 [ANALYTE: CK]


title: RA1010_control_-1399 [ANALYTE: CK]


title: RA1008_control_-880 [ANALYTE: CK]


title: RA1005_control_-575 [ANALYTE: CK]


title: RA1006_control_-1984 [ANALYTE: CK]


title: RA1006_control_-2231 [ANALYTE: CK]


title: RA1005_control_-3632 [ANALYTE: CK]


title: RA1005_control_-1352 [ANALYTE: CK]


title: RA1005_control_-945 [ANALYTE: CK]


title: RA1012_control_-357 [ANALYTE: CK]


title: RA1008_control_-1104 [ANALYTE: CK]


title: RA1006_control_-173 [ANALYTE: CK]


title: RA1008_control_-1431 [ANALYTE: CK]


title: RA1006_control_-1339 [ANALYTE: CK]


title: RA1007_control_-208 [ANALYTE: CK]


title: RA1004_control_-481 [ANALYTE: CK]


title: RA1008_control_66 [ANALYTE: CK]


title: RA1006_control_233 [ANALYTE: CK]


title: RA1004_control_-4004 [ANALYTE: CK]


title: RA1004_control_-3545 [ANALYTE: CK]


title: RA1003_control_-1590 [ANALYTE: CK]


title: RA1003_control_-1026 [ANALYTE: CK]


title: RA1002_control_-1209 [ANALYTE: CK]


title: RA1002_control_-556 [ANALYTE: CK]


title: RA1003_control_-2370 [ANALYTE: CK]


title: RA1003_control_-2862 [ANALYTE: CK]


title: RA1002_control_120 [ANALYTE: CK]


title: RA1002_control_-82 [ANALYTE: CK]


title: RA1001_control_351 [ANALYTE: CK]


title: RA1001_control_-482 [ANALYTE: CK]


title: RA1001_control_-2225 [ANALYTE: CK]


title: RA1002_control_-1608 [ANALYTE: CK]


title: RA1001_control_-798 [ANALYTE: CK]


title: RA1083_case_-105 [ANALYTE: CK]

value: case


title: RA1081_case_1497 [ANALYTE: CK]


title: RA1081_case_-32 [ANALYTE: CK]


title: RA1081_case_-848 [ANALYTE: CK]


title: RA1001_control_-4884 [ANALYTE: CK]


title: RA1081_case_-2882 [ANALYTE: CK]


title: RA1079_case_-983 [ANALYTE: CK]


title: RA1080_case_-1668 [ANALYTE: CK]


title: RA1079_case_-1404 [ANALYTE: CK]


title: RA1079_case_-1500 [ANALYTE: CK]


title: RA1083_case_2624 [ANALYTE: CK]


title: RA1078_case_-1014 [ANALYTE: CK]


title: RA1078_case_-1342 [ANALYTE: CK]


title: RA1078_case_-2100 [ANALYTE: CK]


title: RA1079_case_-2892 [ANALYTE: CK]


title: RA1078_case_-3289 [ANALYTE: CK]


title: RA1082_case_-733 [ANALYTE: CK]


title: RA1081_case_-1559 [ANALYTE: CK]


title: RA1076_case_1605 [ANALYTE: CK]


title: RA1077_case_-4176 [ANALYTE: CK]


title: RA1076_case_-1453 [ANALYTE: CK]


title: RA1077_case_-2334 [ANALYTE: CK]


title: RA1080_case_-453 [ANALYTE: CK]


title: RA1076_case_-264 [ANALYTE: CK]


title: RA1077_case_-3071 [ANALYTE: CK]


title: RA1075_case_-1244 [ANALYTE: CK]


title: RA1075_case_-532 [ANALYTE: CK]


title: RA1075_case_-903 [ANALYTE: CK]


title: RA1076_case_-1852 [ANALYTE: CK]


title: RA1074_case_-2005 [ANALYTE: CK]


title: RA1074_case_-834 [ANALYTE: CK]


title: RA1074_case_-55 [ANALYTE: CK]


title: RA1073_case_-1043 [ANALYTE: CK]


title: RA1072_case_-278 [ANALYTE: CK]


title: RA1077_case_-1618 [ANALYTE: CK]


title: RA1076_case_-628 [ANALYTE: CK]


title: RA1072_case_-710 [ANALYTE: CK]


title: RA1074_case_127 [ANALYTE: CK]


title: RA1071_case_-176 [ANALYTE: CK]


title: RA1071_case_-2433 [ANALYTE: CK]


title: RA1071_case_-1450 [ANALYTE: CK]


title: RA1070_case_-808 [ANALYTE: CK]


title: RA1071_case_-3409 [ANALYTE: CK]


title: RA1070_case_-1809 [ANALYTE: CK]


title: RA1070_case_-1221 [ANALYTE: CK]


title: RA1070_case_-2104 [ANALYTE: CK]


title: RA1073_case_2704 [ANALYTE: CK]


title: RA1072_case_-1280 [ANALYTE: CK]


title: RA1069_case_-1400 [ANALYTE: CK]


title: RA1069_case_1785 [ANALYTE: CK]


title: RA1069_case_-1485 [ANALYTE: CK]


title: RA1072_case_4141 [ANALYTE: CK]


title: RA1071_case_723 [ANALYTE: CK]


title: RA1069_case_-574 [ANALYTE: CK]


title: RA1069_case_-2025 [ANALYTE: CK]


title: RA1068_case_-1041 [ANALYTE: CK]


title: RA1066_case_-4132 [ANALYTE: CK]


title: RA1067_case_-705 [ANALYTE: CK]


title: RA1067_case_3841 [ANALYTE: CK]


title: RA1066_case_-1930 [ANALYTE: CK]


title: RA1066_case_-345 [ANALYTE: CK]


title: RA1065_case_-876 [ANALYTE: CK]


title: RA1064_case_4275 [ANALYTE: CK]


title: RA1065_case_-1593 [ANALYTE: CK]


title: RA1065_case_-1389 [ANALYTE: CK]


title: RA1064_case_-294 [ANALYTE: CK]


title: RA1066_case_-1366 [ANALYTE: CK]


title: RA1063_case_-1196 [ANALYTE: CK]


title: RA1062_case_-2061 [ANALYTE: CK]


title: RA1062_case_-298 [ANALYTE: CK]


title: RA1063_case_1001 [ANALYTE: CK]


title: RA1065_case_1412 [ANALYTE: CK]


title: RA1062_case_-3571 [ANALYTE: CK]


title: RA1064_case_-464 [ANALYTE: CK]


title: RA1061_case_-2399 [ANALYTE: CK]


title: RA1061_case_-376 [ANALYTE: CK]


title: RA1061_case_-4743 [ANALYTE: CK]


title: RA1061_case_-2611 [ANALYTE: CK]


title: RA1060_case_-1856 [ANALYTE: CK]


title: RA1062_case_1219 [ANALYTE: CK]


title: RA1062_case_-2105 [ANALYTE: CK]


title: RA1058_case_2304 [ANALYTE: CK]


title: RA1057_case_238 [ANALYTE: CK]


title: RA1057_case_-2462 [ANALYTE: CK]


title: RA1058_case_-1542 [ANALYTE: CK]


title: RA1060_case_270 [ANALYTE: CK]


title: RA1060_case_-3062 [ANALYTE: CK]


title: RA1060_case_-3636 [ANALYTE: CK]


title: RA1059_case_-217 [ANALYTE: CK]


title: RA1059_case_2418 [ANALYTE: CK]


title: RA1056_case_-666 [ANALYTE: CK]


title: RA1056_case_-4967 [ANALYTE: CK]


title: RA1056_case_-3102 [ANALYTE: CK]


title: RA1056_case_-2477 [ANALYTE: CK]


title: RA1060_case_-4624 [ANALYTE: CK]


title: RA1055_case_2675 [ANALYTE: CK]


title: RA1055_case_-103 [ANALYTE: CK]


title: RA1055_case_-2311 [ANALYTE: CK]


title: RA1053_case_-1072 [ANALYTE: CK]


title: RA1055_case_-2563 [ANALYTE: CK]


title: RA1053_case_-82 [ANALYTE: CK]


title: RA1052_case_-900 [ANALYTE: CK]


title: RA1053_case_-2751 [ANALYTE: CK]


title: RA1052_case_699 [ANALYTE: CK]


title: RA1053_case_-1358 [ANALYTE: CK]


title: RA1052_case_-63 [ANALYTE: CK]


title: RA1052_case_-1348 [ANALYTE: CK]


title: RA1051_case_-354 [ANALYTE: CK]


title: RA1051_case_414 [ANALYTE: CK]


title: RA1052_case_-1578 [ANALYTE: CK]


title: RA1050_case_-1642 [ANALYTE: CK]


title: RA1050_case_1100 [ANALYTE: CK]


title: RA1050_case_-136 [ANALYTE: CK]


title: RA1050_case_-2890 [ANALYTE: CK]


title: RA1048_case_914 [ANALYTE: CK]


title: RA1049_case_-1302 [ANALYTE: CK]


title: RA1049_case_-3174 [ANALYTE: CK]


title: RA1049_case_-735 [ANALYTE: CK]


title: RA1048_case_-306 [ANALYTE: CK]


title: RA1047_case_-510 [ANALYTE: CK]


title: RA1047_case_-1746 [ANALYTE: CK]


title: RA1047_case_-964 [ANALYTE: CK]


title: RA1047_case_-2730 [ANALYTE: CK]


title: RA1046_case_-2389 [ANALYTE: CK]


title: RA1049_case_-3181 [ANALYTE: CK]


title: RA1050_case_-1720 [ANALYTE: CK]


title: RA1046_case_-4558 [ANALYTE: CK]


title: RA1046_case_-3474 [ANALYTE: CK]


title: RA1046_case_-3029 [ANALYTE: CK]


title: RA1045_case_-371 [ANALYTE: CK]


title: RA1045_case_-2061 [ANALYTE: CK]


title: RA1045_case_-720 [ANALYTE: CK]


title: RA1045_case_1601 [ANALYTE: CK]


title: RA1045_case_-3527 [ANALYTE: CK]


title: RA1044_case_-169 [ANALYTE: CK]


title: RA1043_case_-580 [ANALYTE: CK]


title: RA1044_case_-1353 [ANALYTE: CK]


title: RA1043_case_-1395 [ANALYTE: CK]


title: RA1043_case_114 [ANALYTE: CK]


title: RA1043_case_-2982 [ANALYTE: CK]


title: RA1043_case_-2604 [ANALYTE: CK]


title: RA1042_case_-876 [ANALYTE: CK]


title: RA1042_case_-1547 [ANALYTE: CK]


title: RA1041_case_-1858 [ANALYTE: CK]


title: RA1042_case_-2210 [ANALYTE: CK]


title: RA1041_case_-4238 [ANALYTE: CK]


title: RA1041_case_-2642 [ANALYTE: CK]


title: RA1041_case_-2748 [ANALYTE: CK]


title: RA1042_case_-3711 [ANALYTE: CK]


title: RA1040_case_2805 [ANALYTE: CK]


title: RA1040_case_-842 [ANALYTE: CK]


title: RA1040_case_-2482 [ANALYTE: CK]


title: RA1040_case_-2410 [ANALYTE: CK]


title: RA1038_case_142 [ANALYTE: CK]


title: RA1038_case_-25 [ANALYTE: CK]


title: RA1038_case_-1157 [ANALYTE: CK]


title: RA1036_case_789 [ANALYTE: CK]


title: RA1036_case_-162 [ANALYTE: CK]


title: RA1037_case_-2869 [ANALYTE: CK]


title: RA1036_case_-2255 [ANALYTE: CK]


title: RA1038_case_-3484 [ANALYTE: CK]


title: RA1036_case_-2395 [ANALYTE: CK]


title: RA1036_case_-3976 [ANALYTE: CK]


title: RA1035_case_773 [ANALYTE: CK]


title: RA1035_case_-867 [ANALYTE: CK]


title: RA1035_case_-1691 [ANALYTE: CK]


title: RA1034_case_170 [ANALYTE: CK]


title: RA1039_case_-23 [ANALYTE: CK]


title: RA1033_case_234 [ANALYTE: CK]


title: RA1034_case_-4803 [ANALYTE: CK]


title: RA1033_case_-380 [ANALYTE: CK]


title: RA1034_case_-2109 [ANALYTE: CK]


title: RA1034_case_-2004 [ANALYTE: CK]


title: RA1032_case_-669 [ANALYTE: CK]


title: RA1031_case_-16 [ANALYTE: CK]


title: RA1031_case_-385 [ANALYTE: CK]


title: RA1032_case_-317 [ANALYTE: CK]


title: RA1032_case_473 [ANALYTE: CK]


title: RA1030_case_154 [ANALYTE: CK]


title: RA1030_case_-228 [ANALYTE: CK]


title: RA1031_case_-1603 [ANALYTE: CK]


title: RA1029_case_-2035 [ANALYTE: CK]


title: RA1034_case_-120 [ANALYTE: CK]


title: RA1030_case_-2834 [ANALYTE: CK]


title: RA1028_case_23 [ANALYTE: CK]


title: RA1032_case_-905 [ANALYTE: CK]


title: RA1028_case_-1596 [ANALYTE: CK]


title: RA1028_case_-1198 [ANALYTE: CK]


title: RA1027_case_1185 [ANALYTE: CK]


title: RA1026_case_3260 [ANALYTE: CK]


title: RA1026_case_-615 [ANALYTE: CK]


title: RA1026_case_-1276 [ANALYTE: CK]


title: RA1027_case_-1896 [ANALYTE: CK]


title: RA1027_case_-1534 [ANALYTE: CK]


title: RA1033_case_-508 [ANALYTE: CK]


title: RA1025_case_329 [ANALYTE: CK]


title: RA1025_case_-477 [ANALYTE: CK]


title: RA1028_case_-111 [ANALYTE: CK]


title: RA1025_case_-2689 [ANALYTE: CK]


title: RA1025_case_-3713 [ANALYTE: CK]


title: RA1024_case_-2261 [ANALYTE: CK]


title: RA1024_case_-750 [ANALYTE: CK]


title: RA1024_case_-2506 [ANALYTE: CK]


title: RA1023_case_-329 [ANALYTE: CK]


title: RA1028_case_-2370 [ANALYTE: CK]


title: RA1023_case_-483 [ANALYTE: CK]


title: RA1023_case_231 [ANALYTE: CK]


title: RA1022_case_-328 [ANALYTE: CK]


title: RA1023_case_-1438 [ANALYTE: CK]


title: RA1022_case_-428 [ANALYTE: CK]


title: RA1022_case_-1720 [ANALYTE: CK]


title: RA1021_case_2396 [ANALYTE: CK]


title: RA1021_case_-515 [ANALYTE: CK]


title: RA1020_case_-424 [ANALYTE: CK]


title: RA1025_case_-2714 [ANALYTE: CK]


title: RA1020_case_-1122 [ANALYTE: CK]


title: RA1020_case_-1393 [ANALYTE: CK]


title: RA1018_case_-1857 [ANALYTE: CK]


title: RA1017_case_845 [ANALYTE: CK]


title: RA1020_case_-3561 [ANALYTE: CK]


title: RA1019_case_-1461 [ANALYTE: CK]


title: RA1018_case_-2109 [ANALYTE: CK]


title: RA1019_case_-617 [ANALYTE: CK]


title: RA1017_case_-1638 [ANALYTE: CK]


title: RA1018_case_1890 [ANALYTE: CK]


title: RA1017_case_-4335 [ANALYTE: CK]


title: RA1017_case_-2764 [ANALYTE: CK]


title: RA1017_case_-2488 [ANALYTE: CK]


title: RA1015_case_-1497 [ANALYTE: CK]


title: RA1015_case_589 [ANALYTE: CK]


title: RA1015_case_-3467 [ANALYTE: CK]


title: RA1014_case_366 [ANALYTE: CK]


title: RA1013_case_-2485 [ANALYTE: CK]


title: RA1015_case_-3648 [ANALYTE: CK]


title: RA1014_case_-686 [ANALYTE: CK]


title: RA1013_case_-2474 [ANALYTE: CK]


title: RA1013_case_-4163 [ANALYTE: CK]


title: RA1011_case_250 [ANALYTE: CK]


title: RA1012_case_-5 [ANALYTE: CK]


title: RA1012_case_-336 [ANALYTE: CK]


title: RA1011_case_-471 [ANALYTE: CK]


title: RA1010_case_-1398 [ANALYTE: CK]


title: RA1009_case_-984 [ANALYTE: CK]


title: RA1009_case_-1500 [ANALYTE: CK]


title: RA1010_case_-845 [ANALYTE: CK]


title: RA1015_case_-2557 [ANALYTE: CK]


title: RA1006_case_250 [ANALYTE: CK]


title: RA1007_case_-188 [ANALYTE: CK]


title: RA1013_case_-469 [ANALYTE: CK]


title: RA1007_case_-740 [ANALYTE: CK]


title: RA1009_case_-2442 [ANALYTE: CK]


title: RA1008_case_-852 [ANALYTE: CK]


title: RA1008_case_-896 [ANALYTE: CK]


title: RA1008_case_-1445 [ANALYTE: CK]


title: RA1009_case_-2365 [ANALYTE: CK]


title: RA1008_case_37 [ANALYTE: CK]


title: RA1006_case_-169 [ANALYTE: CK]


title: RA1006_case_-1374 [ANALYTE: CK]


title: RA1011_case_-1235 [ANALYTE: CK]


title: RA1006_case_-2258 [ANALYTE: CK]


title: RA1006_case_-1922 [ANALYTE: CK]


title: RA1005_case_-547 [ANALYTE: CK]


title: RA1004_case_-470 [ANALYTE: CK]


title: RA1005_case_-1634 [ANALYTE: CK]


title: RA1005_case_-1612 [ANALYTE: CK]


title: RA1003_case_-1047 [ANALYTE: CK]


title: RA1004_case_-3978 [ANALYTE: CK]


title: RA1003_case_-1814 [ANALYTE: CK]


title: RA1003_case_-2132 [ANALYTE: CK]


title: RA1003_case_-2882 [ANALYTE: CK]


title: RA1002_case_93 [ANALYTE: CK]


title: RA1004_case_-3347 [ANALYTE: CK]


title: RA1007_case_-1536 [ANALYTE: CK]


title: RA1002_case_-68 [ANALYTE: CK]


title: RA1002_case_-557 [ANALYTE: CK]


title: RA1002_case_-1139 [ANALYTE: CK]


title: RA1002_case_-1585 [ANALYTE: CK]


title: RA1001_case_-4908 [ANALYTE: CK]


title: RA1001_case_358 [ANALYTE: CK]


title: RA1001_case_-463 [ANALYTE: CK]


title: RA1082_control_-747 [ANALYTE: AG]

hyb_protocol: Spectrally-distinct polystyrene beads with magnetic cores were conjugated with native and/or citrullinated proteins and peptides. Controls and samples were diluted (1:30) in sample diluent and added to a 96-well flat-bottom plate (75 uL/well). Bead mix was then added to the plate (25 uL/well) and incubated for 30 minutes on a microtiter plate shaker at room temperature. The plate was washed three times with wash buffer using a Bio-Plex Pro II magnetic wash station (200 uL/well per wash).

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA). Data were acquired with the following advanced settings: 200 beads per region, 50 uL sample size, high RP1, and DD gate values of 7,500 to 25,000.

data_processing: Observed fluorescence intensities were normalized by calculating a Z-score using the formula: ((observed value)-(mean value of control patients))/(standard deviation).

label_protocol: Anti-human IgG-PE secondary antibody was added (25 uL/well), allowed to incubate at room temperature for 15 minutes on a microtiter plate shaker at room temperature, and removed by washing the plate three times. Beads were re-suspended in wash buffer (100 uL) and the plate was placed on the shaker for 30 seconds before reading.


title: RA1083_control_2597 [ANALYTE: AG]


title: RA1081_control_-1265 [ANALYTE: AG]


title: RA1081_control_-1611 [ANALYTE: AG]


title: RA1081_control_-2884 [ANALYTE: AG]


title: RA1079_control_-982 [ANALYTE: AG]


title: RA1079_control_-2894 [ANALYTE: AG]


title: RA1078_control_-1381 [ANALYTE: AG]


title: RA1078_control_-986 [ANALYTE: AG]


title: RA1079_control_-1606 [ANALYTE: AG]


title: RA1078_control_-3319 [ANALYTE: AG]


title: RA1083_control_-101 [ANALYTE: AG]


title: RA1077_control_-1631 [ANALYTE: AG]


title: RA1077_control_-2843 [ANALYTE: AG]


title: RA1076_control_1630 [ANALYTE: AG]


title: RA1077_control_-4193 [ANALYTE: AG]


title: RA1081_control_-39 [ANALYTE: AG]


title: RA1077_control_-3261 [ANALYTE: AG]


title: RA1081_control_1470 [ANALYTE: AG]


title: RA1076_control_-263 [ANALYTE: AG]


title: RA1080_control_-1650 [ANALYTE: AG]


title: RA1001_case_-700 [ANALYTE: CK]


title: RA1080_control_-444 [ANALYTE: AG]


title: RA1076_control_-600 [ANALYTE: AG]


title: RA1079_control_-1298 [ANALYTE: AG]


title: RA1076_control_-992 [ANALYTE: AG]


title: RA1076_control_-1859 [ANALYTE: AG]


title: RA1078_control_-2043 [ANALYTE: AG]


title: RA1075_control_-502 [ANALYTE: AG]


title: RA1075_control_-1086 [ANALYTE: AG]


title: RA1075_control_-1232 [ANALYTE: AG]


title: RA1074_control_-77 [ANALYTE: AG]


title: RA1074_control_133 [ANALYTE: AG]


title: RA1072_control_-1305 [ANALYTE: AG]


title: RA1071_control_711 [ANALYTE: AG]


title: RA1073_control_2698 [ANALYTE: AG]


title: RA1073_control_-1061 [ANALYTE: AG]


title: RA1074_control_-2030 [ANALYTE: AG]


title: RA1074_control_-744 [ANALYTE: AG]


title: RA1072_control_-300 [ANALYTE: AG]


title: RA1072_control_-1110 [ANALYTE: AG]


title: RA1071_control_-190 [ANALYTE: AG]


title: RA1071_control_-859 [ANALYTE: AG]


title: RA1071_control_-2618 [ANALYTE: AG]


title: RA1071_control_-3438 [ANALYTE: AG]


title: RA1070_control_-1185 [ANALYTE: AG]


title: RA1070_control_-1744 [ANALYTE: AG]


title: RA1070_control_-813 [ANALYTE: AG]


title: RA1070_control_-2103 [ANALYTE: AG]


title: RA1069_control_1774 [ANALYTE: AG]


title: RA1069_control_-572 [ANALYTE: AG]


title: RA1069_control_-1287 [ANALYTE: AG]


title: RA1069_control_-1979 [ANALYTE: AG]


title: RA1069_control_-2018 [ANALYTE: AG]


title: RA1068_control_-1044 [ANALYTE: AG]


title: RA1067_control_3832 [ANALYTE: AG]


title: RA1067_control_-691 [ANALYTE: AG]


title: RA1066_control_-366 [ANALYTE: AG]


title: RA1066_control_-4158 [ANALYTE: AG]


title: RA1066_control_-1762 [ANALYTE: AG]


title: RA1063_control_-1175 [ANALYTE: AG]


title: RA1065_control_-1296 [ANALYTE: AG]


title: RA1065_control_-879 [ANALYTE: AG]


title: RA1064_control_-277 [ANALYTE: AG]


title: RA1065_control_-2196 [ANALYTE: AG]


title: RA1065_control_-1730 [ANALYTE: AG]


title: RA1062_control_1224 [ANALYTE: AG]


title: RA1063_control_1013 [ANALYTE: AG]


title: RA1062_control_-319 [ANALYTE: AG]


title: RA1061_control_-2691 [ANALYTE: AG]


title: RA1061_control_-4750 [ANALYTE: AG]


title: RA1066_control_-1405 [ANALYTE: AG]


title: RA1060_control_278 [ANALYTE: AG]


title: RA1060_control_-1827 [ANALYTE: AG]


title: RA1060_control_-3677 [ANALYTE: AG]


title: RA1061_control_-2404 [ANALYTE: AG]


title: RA1060_control_-4629 [ANALYTE: AG]


title: RA1060_control_-2815 [ANALYTE: AG]


title: RA1065_control_1427 [ANALYTE: AG]


title: RA1064_control_4246 [ANALYTE: AG]


title: RA1064_control_-438 [ANALYTE: AG]


title: RA1059_control_-234 [ANALYTE: AG]


title: RA1058_control_2293 [ANALYTE: AG]


title: RA1062_control_-3560 [ANALYTE: AG]


title: RA1061_control_-402 [ANALYTE: AG]


title: RA1062_control_-2580 [ANALYTE: AG]


title: RA1058_control_-1551 [ANALYTE: AG]


title: RA1057_control_241 [ANALYTE: AG]


title: RA1062_control_-2216 [ANALYTE: AG]


title: RA1057_control_-2449 [ANALYTE: AG]


title: RA1055_control_2695 [ANALYTE: AG]


title: RA1055_control_-118 [ANALYTE: AG]


title: RA1056_control_-4977 [ANALYTE: AG]


title: RA1055_control_-1784 [ANALYTE: AG]


title: RA1056_control_-1940 [ANALYTE: AG]


title: RA1056_control_-652 [ANALYTE: AG]


title: RA1056_control_-3678 [ANALYTE: AG]


title: RA1053_control_-102 [ANALYTE: AG]


title: RA1052_control_-812 [ANALYTE: AG]


title: RA1053_control_-1658 [ANALYTE: AG]


title: RA1052_control_-1552 [ANALYTE: AG]


title: RA1051_control_391 [ANALYTE: AG]


title: RA1059_control_2436 [ANALYTE: AG]


title: RA1051_control_-360 [ANALYTE: AG]


title: RA1052_control_-77 [ANALYTE: AG]


title: RA1053_control_-1174 [ANALYTE: AG]


title: RA1050_control_-143 [ANALYTE: AG]


title: RA1049_control_-741 [ANALYTE: AG]


title: RA1050_control_-1532 [ANALYTE: AG]


title: RA1050_control_-2889 [ANALYTE: AG]


title: RA1053_control_-2753 [ANALYTE: AG]


title: RA1055_control_-2546 [ANALYTE: AG]


title: RA1052_control_-1167 [ANALYTE: AG]


title: RA1049_control_-3167 [ANALYTE: AG]


title: RA1048_control_912 [ANALYTE: AG]


title: RA1049_control_-1471 [ANALYTE: AG]


title: RA1049_control_-2542 [ANALYTE: AG]


title: RA1047_control_-506 [ANALYTE: AG]


title: RA1047_control_-1757 [ANALYTE: AG]


title: RA1047_control_-895 [ANALYTE: AG]


title: RA1050_control_1120 [ANALYTE: AG]


title: RA1047_control_-2755 [ANALYTE: AG]


title: RA1046_control_-2767 [ANALYTE: AG]


title: RA1046_control_-3243 [ANALYTE: AG]


title: RA1050_control_-1233 [ANALYTE: AG]


title: RA1045_control_-2225 [ANALYTE: AG]


title: RA1045_control_-356 [ANALYTE: AG]


title: RA1048_control_-288 [ANALYTE: AG]


title: RA1045_control_-1050 [ANALYTE: AG]


title: RA1046_control_-2413 [ANALYTE: AG]


title: RA1046_control_-4554 [ANALYTE: AG]


title: RA1043_control_-597 [ANALYTE: AG]


title: RA1044_control_-146 [ANALYTE: AG]


title: RA1044_control_-1371 [ANALYTE: AG]


title: RA1045_control_-3549 [ANALYTE: AG]


title: RA1043_control_-2424 [ANALYTE: AG]


title: RA1043_control_-2969 [ANALYTE: AG]


title: RA1043_control_-1332 [ANALYTE: AG]


title: RA1042_control_-2275 [ANALYTE: AG]


title: RA1043_control_99 [ANALYTE: AG]


title: RA1042_control_-847 [ANALYTE: AG]


title: RA1042_control_-1559 [ANALYTE: AG]


title: RA1042_control_-3722 [ANALYTE: AG]


title: RA1041_control_-2671 [ANALYTE: AG]


title: RA1041_control_-4078 [ANALYTE: AG]


title: RA1041_control_-1839 [ANALYTE: AG]


title: RA1041_control_-4225 [ANALYTE: AG]


title: RA1040_control_-2272 [ANALYTE: AG]


title: RA1038_control_169 [ANALYTE: AG]


title: RA1038_control_-26 [ANALYTE: AG]


title: RA1039_control_-13 [ANALYTE: AG]


title: RA1040_control_-2462 [ANALYTE: AG]


title: RA1038_control_-1154 [ANALYTE: AG]


title: RA1038_control_-1787 [ANALYTE: AG]


title: RA1038_control_-3493 [ANALYTE: AG]


title: RA1037_control_-2847 [ANALYTE: AG]


title: RA1040_control_2783 [ANALYTE: AG]


title: RA1040_control_-850 [ANALYTE: AG]


title: RA1036_control_-3993 [ANALYTE: AG]


title: RA1035_control_-881 [ANALYTE: AG]


title: RA1036_control_783 [ANALYTE: AG]


title: RA1035_control_758 [ANALYTE: AG]


title: RA1036_control_-2571 [ANALYTE: AG]


title: RA1036_control_-2451 [ANALYTE: AG]


title: RA1034_control_-144 [ANALYTE: AG]


title: RA1036_control_-163 [ANALYTE: AG]


title: RA1035_control_-1672 [ANALYTE: AG]


title: RA1033_control_249 [ANALYTE: AG]


title: RA1034_control_-2489 [ANALYTE: AG]


title: RA1033_control_-376 [ANALYTE: AG]


title: RA1034_control_-2515 [ANALYTE: AG]


title: RA1034_control_150 [ANALYTE: AG]


title: RA1034_control_-4809 [ANALYTE: AG]


title: RA1031_control_-42 [ANALYTE: AG]


title: RA1032_control_-544 [ANALYTE: AG]


title: RA1032_control_-347 [ANALYTE: AG]


title: RA1032_control_-914 [ANALYTE: AG]


title: RA1033_control_-514 [ANALYTE: AG]


title: RA1031_control_-1603 [ANALYTE: AG]


title: RA1030_control_143 [ANALYTE: AG]


title: RA1031_control_-384 [ANALYTE: AG]


title: RA1032_control_479 [ANALYTE: AG]


title: RA1030_control_-200 [ANALYTE: AG]


title: RA1030_control_-2830 [ANALYTE: AG]


title: RA1028_control_-1180 [ANALYTE: AG]


title: RA1028_control_-2370 [ANALYTE: AG]


title: RA1028_control_28 [ANALYTE: AG]


title: RA1028_control_-111 [ANALYTE: AG]


title: RA1027_control_-1892 [ANALYTE: AG]


title: RA1027_control_1197 [ANALYTE: AG]


title: RA1029_control_-2035 [ANALYTE: AG]


title: RA1027_control_-1511 [ANALYTE: AG]


title: RA1024_control_-723 [ANALYTE: AG]


title: RA1028_control_-1966 [ANALYTE: AG]


title: RA1023_control_246 [ANALYTE: AG]


title: RA1025_control_-3167 [ANALYTE: AG]


title: RA1026_control_-808 [ANALYTE: AG]


title: RA1026_control_-1270 [ANALYTE: AG]


title: RA1025_control_-2763 [ANALYTE: AG]


title: RA1026_control_-633 [ANALYTE: AG]


title: RA1025_control_-475 [ANALYTE: AG]


title: RA1024_control_-2492 [ANALYTE: AG]


title: RA1023_control_-314 [ANALYTE: AG]


title: RA1025_control_-3702 [ANALYTE: AG]


title: RA1022_control_-334 [ANALYTE: AG]


title: RA1025_control_306 [ANALYTE: AG]


title: RA1026_control_3259 [ANALYTE: AG]


title: RA1023_control_-688 [ANALYTE: AG]


title: RA1024_control_-2199 [ANALYTE: AG]


title: RA1022_control_-639 [ANALYTE: AG]


title: RA1021_control_2371 [ANALYTE: AG]


title: RA1022_control_-1744 [ANALYTE: AG]


title: RA1021_control_-528 [ANALYTE: AG]


title: RA1023_control_-1413 [ANALYTE: AG]


title: RA1020_control_-454 [ANALYTE: AG]


title: RA1020_control_-3160 [ANALYTE: AG]


title: RA1020_control_-1707 [ANALYTE: AG]


title: RA1019_control_-626 [ANALYTE: AG]


title: RA1019_control_-1437 [ANALYTE: AG]


title: RA1020_control_-3541 [ANALYTE: AG]


title: RA1018_control_1915 [ANALYTE: AG]


title: RA1018_control_-1868 [ANALYTE: AG]


title: RA1017_control_858 [ANALYTE: AG]


title: RA1018_control_-2115 [ANALYTE: AG]


title: RA1014_control_-666 [ANALYTE: AG]


title: RA1013_control_-787 [ANALYTE: AG]


title: RA1015_control_-3677 [ANALYTE: AG]


title: RA1013_control_-449 [ANALYTE: AG]


title: RA1014_control_379 [ANALYTE: AG]


title: RA1013_control_-2460 [ANALYTE: AG]


title: RA1017_control_-1620 [ANALYTE: AG]


title: RA1017_control_-2421 [ANALYTE: AG]


title: RA1017_control_-3466 [ANALYTE: AG]


title: RA1015_control_562 [ANALYTE: AG]


title: RA1017_control_-4333 [ANALYTE: AG]


title: RA1012_control_15 [ANALYTE: AG]


title: RA1015_control_-1525 [ANALYTE: AG]


title: RA1012_control_-357 [ANALYTE: AG]


title: RA1011_control_221 [ANALYTE: AG]


title: RA1011_control_-478 [ANALYTE: AG]


title: RA1010_control_-835 [ANALYTE: AG]


title: RA1015_control_-2257 [ANALYTE: AG]


title: RA1015_control_-3306 [ANALYTE: AG]


title: RA1009_control_-988 [ANALYTE: AG]


title: RA1011_control_-1235 [ANALYTE: AG]


title: RA1010_control_-1399 [ANALYTE: AG]


title: RA1013_control_-4169 [ANALYTE: AG]


title: RA1009_control_-2079 [ANALYTE: AG]


title: RA1008_control_66 [ANALYTE: AG]


title: RA1009_control_-2448 [ANALYTE: AG]


title: RA1008_control_-880 [ANALYTE: AG]


title: RA1008_control_-1431 [ANALYTE: AG]


title: RA1006_control_233 [ANALYTE: AG]


title: RA1007_control_-208 [ANALYTE: AG]


title: RA1008_control_-1104 [ANALYTE: AG]


title: RA1006_control_-1984 [ANALYTE: AG]


title: RA1006_control_-1339 [ANALYTE: AG]


title: RA1006_control_-173 [ANALYTE: AG]


title: RA1005_control_-1352 [ANALYTE: AG]


title: RA1006_control_-2231 [ANALYTE: AG]


title: RA1005_control_-575 [ANALYTE: AG]


title: RA1003_control_-1026 [ANALYTE: AG]


title: RA1005_control_-945 [ANALYTE: AG]


title: RA1005_control_-3632 [ANALYTE: AG]


title: RA1004_control_-481 [ANALYTE: AG]


title: RA1004_control_-4004 [ANALYTE: AG]


title: RA1004_control_-3545 [ANALYTE: AG]


title: RA1003_control_-1590 [ANALYTE: AG]


title: RA1009_control_-1352 [ANALYTE: AG]


title: RA1003_control_-2370 [ANALYTE: AG]


title: RA1002_control_-1209 [ANALYTE: AG]


title: RA1003_control_-2862 [ANALYTE: AG]


title: RA1002_control_-1608 [ANALYTE: AG]


title: RA1002_control_-556 [ANALYTE: AG]


title: RA1001_control_351 [ANALYTE: AG]


title: RA1002_control_-82 [ANALYTE: AG]


title: RA1002_control_120 [ANALYTE: AG]


title: RA1001_control_-2225 [ANALYTE: AG]


title: RA1083_case_-105 [ANALYTE: AG]


title: RA1083_case_2624 [ANALYTE: AG]


title: RA1001_control_-482 [ANALYTE: AG]


title: RA1082_case_-733 [ANALYTE: AG]


title: RA1001_control_-4884 [ANALYTE: AG]


title: RA1081_case_1497 [ANALYTE: AG]


title: RA1081_case_-1559 [ANALYTE: AG]


title: RA1081_case_-32 [ANALYTE: AG]


title: RA1081_case_-848 [ANALYTE: AG]


title: RA1081_case_-2882 [ANALYTE: AG]


title: RA1080_case_-453 [ANALYTE: AG]


title: RA1079_case_-1500 [ANALYTE: AG]


title: RA1079_case_-2892 [ANALYTE: AG]


title: RA1079_case_-1404 [ANALYTE: AG]


title: RA1079_case_-983 [ANALYTE: AG]


title: RA1078_case_-1014 [ANALYTE: AG]


title: RA1078_case_-3289 [ANALYTE: AG]


title: RA1078_case_-2100 [ANALYTE: AG]


title: RA1077_case_-1618 [ANALYTE: AG]


title: RA1001_control_-798 [ANALYTE: AG]


title: RA1077_case_-2334 [ANALYTE: AG]


title: RA1076_case_1605 [ANALYTE: AG]


title: RA1076_case_-1453 [ANALYTE: AG]


title: RA1076_case_-628 [ANALYTE: AG]


title: RA1077_case_-4176 [ANALYTE: AG]


title: RA1076_case_-264 [ANALYTE: AG]


title: RA1077_case_-3071 [ANALYTE: AG]


title: RA1078_case_-1342 [ANALYTE: AG]


title: RA1080_case_-1668 [ANALYTE: AG]


title: RA1074_case_-834 [ANALYTE: AG]


title: RA1074_case_-2005 [ANALYTE: AG]


title: RA1074_case_-55 [ANALYTE: AG]


title: RA1075_case_-903 [ANALYTE: AG]


title: RA1076_case_-1852 [ANALYTE: AG]


title: RA1074_case_127 [ANALYTE: AG]


title: RA1075_case_-1244 [ANALYTE: AG]


title: RA1072_case_4141 [ANALYTE: AG]


title: RA1073_case_-1043 [ANALYTE: AG]


title: RA1072_case_-278 [ANALYTE: AG]


title: RA1072_case_-710 [ANALYTE: AG]


title: RA1071_case_-176 [ANALYTE: AG]


title: RA1070_case_-808 [ANALYTE: AG]


title: RA1071_case_-1450 [ANALYTE: AG]


title: RA1071_case_723 [ANALYTE: AG]


title: RA1071_case_-3409 [ANALYTE: AG]


title: RA1071_case_-2433 [ANALYTE: AG]


title: RA1070_case_-1809 [ANALYTE: AG]


title: RA1069_case_1785 [ANALYTE: AG]


title: RA1073_case_2704 [ANALYTE: AG]


title: RA1069_case_-1400 [ANALYTE: AG]


title: RA1072_case_-1280 [ANALYTE: AG]


title: RA1065_case_-876 [ANALYTE: AG]


title: RA1066_case_-1930 [ANALYTE: AG]


title: RA1067_case_-705 [ANALYTE: AG]


title: RA1065_case_-1593 [ANALYTE: AG]


title: RA1065_case_-1389 [ANALYTE: AG]


title: RA1066_case_-345 [ANALYTE: AG]


title: RA1069_case_-1485 [ANALYTE: AG]


title: RA1069_case_-2025 [ANALYTE: AG]


title: RA1064_case_-464 [ANALYTE: AG]


title: RA1068_case_-1041 [ANALYTE: AG]


title: RA1066_case_-4132 [ANALYTE: AG]


title: RA1067_case_3841 [ANALYTE: AG]


title: RA1066_case_-1366 [ANALYTE: AG]


title: RA1063_case_1001 [ANALYTE: AG]


title: RA1070_case_-1221 [ANALYTE: AG]


title: RA1062_case_1219 [ANALYTE: AG]


title: RA1069_case_-574 [ANALYTE: AG]


title: RA1062_case_-2105 [ANALYTE: AG]


title: RA1062_case_-2061 [ANALYTE: AG]


title: RA1062_case_-298 [ANALYTE: AG]


title: RA1062_case_-3571 [ANALYTE: AG]


title: RA1061_case_-376 [ANALYTE: AG]


title: RA1061_case_-2399 [ANALYTE: AG]


title: RA1061_case_-2611 [ANALYTE: AG]


title: RA1064_case_4275 [ANALYTE: AG]


title: RA1065_case_1412 [ANALYTE: AG]


title: RA1064_case_-294 [ANALYTE: AG]


title: RA1060_case_-1856 [ANALYTE: AG]


title: RA1061_case_-4743 [ANALYTE: AG]


title: RA1060_case_-3636 [ANALYTE: AG]


title: RA1063_case_-1196 [ANALYTE: AG]


title: RA1059_case_-217 [ANALYTE: AG]


title: RA1060_case_-3062 [ANALYTE: AG]


title: RA1058_case_2304 [ANALYTE: AG]


title: RA1056_case_-4967 [ANALYTE: AG]


title: RA1058_case_-1542 [ANALYTE: AG]


title: RA1057_case_238 [ANALYTE: AG]


title: RA1059_case_2418 [ANALYTE: AG]


title: RA1056_case_-2477 [ANALYTE: AG]


title: RA1056_case_-666 [ANALYTE: AG]


title: RA1057_case_-2462 [ANALYTE: AG]


title: RA1060_case_-4624 [ANALYTE: AG]


title: RA1060_case_270 [ANALYTE: AG]


title: RA1055_case_2675 [ANALYTE: AG]


title: RA1056_case_-3102 [ANALYTE: AG]


title: RA1053_case_-1358 [ANALYTE: AG]


title: RA1055_case_-2311 [ANALYTE: AG]


title: RA1055_case_-103 [ANALYTE: AG]


title: RA1053_case_-82 [ANALYTE: AG]


title: RA1053_case_-1072 [ANALYTE: AG]


title: RA1052_case_699 [ANALYTE: AG]


title: RA1052_case_-63 [ANALYTE: AG]


title: RA1055_case_-2563 [ANALYTE: AG]


title: RA1052_case_-900 [ANALYTE: AG]


title: RA1052_case_-1578 [ANALYTE: AG]


title: RA1052_case_-1348 [ANALYTE: AG]


title: RA1053_case_-2751 [ANALYTE: AG]


title: RA1051_case_414 [ANALYTE: AG]


title: RA1050_case_-136 [ANALYTE: AG]


title: RA1050_case_1100 [ANALYTE: AG]


title: RA1051_case_-354 [ANALYTE: AG]


title: RA1050_case_-1642 [ANALYTE: AG]


title: RA1049_case_-1302 [ANALYTE: AG]


title: RA1050_case_-2890 [ANALYTE: AG]


title: RA1049_case_-3174 [ANALYTE: AG]


title: RA1047_case_-2730 [ANALYTE: AG]


title: RA1048_case_914 [ANALYTE: AG]


title: RA1047_case_-510 [ANALYTE: AG]


title: RA1050_case_-1720 [ANALYTE: AG]


title: RA1047_case_-1746 [ANALYTE: AG]


title: RA1045_case_-371 [ANALYTE: AG]


title: RA1046_case_-3474 [ANALYTE: AG]


title: RA1045_case_-720 [ANALYTE: AG]


title: RA1044_case_-169 [ANALYTE: AG]


title: RA1045_case_-2061 [ANALYTE: AG]


title: RA1045_case_-3527 [ANALYTE: AG]


title: RA1044_case_-1353 [ANALYTE: AG]


title: RA1049_case_-3181 [ANALYTE: AG]


title: RA1043_case_114 [ANALYTE: AG]


title: RA1049_case_-735 [ANALYTE: AG]


title: RA1043_case_-580 [ANALYTE: AG]


title: RA1048_case_-306 [ANALYTE: AG]


title: RA1047_case_-964 [ANALYTE: AG]


title: RA1043_case_-1395 [ANALYTE: AG]


title: RA1046_case_-2389 [ANALYTE: AG]


title: RA1043_case_-2604 [ANALYTE: AG]


title: RA1042_case_-1547 [ANALYTE: AG]


title: RA1045_case_1601 [ANALYTE: AG]


title: RA1042_case_-876 [ANALYTE: AG]


title: RA1043_case_-2982 [ANALYTE: AG]


title: RA1046_case_-3029 [ANALYTE: AG]


title: RA1042_case_-3711 [ANALYTE: AG]


title: RA1046_case_-4558 [ANALYTE: AG]


title: RA1042_case_-2210 [ANALYTE: AG]


title: RA1041_case_-2748 [ANALYTE: AG]


title: RA1041_case_-1858 [ANALYTE: AG]


title: RA1041_case_-2642 [ANALYTE: AG]


title: RA1041_case_-4238 [ANALYTE: AG]


title: RA1040_case_-842 [ANALYTE: AG]


title: RA1040_case_-2482 [ANALYTE: AG]


title: RA1039_case_-23 [ANALYTE: AG]


title: RA1038_case_142 [ANALYTE: AG]


title: RA1038_case_-25 [ANALYTE: AG]


title: RA1038_case_-1157 [ANALYTE: AG]


title: RA1036_case_-2255 [ANALYTE: AG]


title: RA1037_case_-2869 [ANALYTE: AG]


title: RA1038_case_-3484 [ANALYTE: AG]


title: RA1036_case_789 [ANALYTE: AG]


title: RA1036_case_-2395 [ANALYTE: AG]


title: RA1036_case_-162 [ANALYTE: AG]


title: RA1040_case_2805 [ANALYTE: AG]


title: RA1034_case_170 [ANALYTE: AG]


title: RA1036_case_-3976 [ANALYTE: AG]


title: RA1035_case_-867 [ANALYTE: AG]


title: RA1035_case_-1691 [ANALYTE: AG]


title: RA1035_case_773 [ANALYTE: AG]


title: RA1034_case_-120 [ANALYTE: AG]


title: RA1034_case_-4803 [ANALYTE: AG]


title: RA1040_case_-2410 [ANALYTE: AG]


title: RA1034_case_-2004 [ANALYTE: AG]


title: RA1033_case_-380 [ANALYTE: AG]


title: RA1032_case_473 [ANALYTE: AG]


title: RA1033_case_234 [ANALYTE: AG]


title: RA1034_case_-2109 [ANALYTE: AG]


title: RA1031_case_-385 [ANALYTE: AG]


title: RA1031_case_-16 [ANALYTE: AG]


title: RA1032_case_-669 [ANALYTE: AG]


title: RA1032_case_-905 [ANALYTE: AG]


title: RA1031_case_-1603 [ANALYTE: AG]


title: RA1030_case_154 [ANALYTE: AG]


title: RA1030_case_-228 [ANALYTE: AG]


title: RA1030_case_-2834 [ANALYTE: AG]


title: RA1029_case_-2035 [ANALYTE: AG]


title: RA1028_case_-1596 [ANALYTE: AG]


title: RA1028_case_-2370 [ANALYTE: AG]


title: RA1033_case_-508 [ANALYTE: AG]


title: RA1032_case_-317 [ANALYTE: AG]


title: RA1028_case_-111 [ANALYTE: AG]


title: RA1028_case_23 [ANALYTE: AG]


title: RA1028_case_-1198 [ANALYTE: AG]


title: RA1027_case_1185 [ANALYTE: AG]


title: RA1027_case_-1896 [ANALYTE: AG]


title: RA1027_case_-1534 [ANALYTE: AG]


title: RA1025_case_-477 [ANALYTE: AG]


title: RA1026_case_-615 [ANALYTE: AG]


title: RA1026_case_3260 [ANALYTE: AG]


title: RA1025_case_-3713 [ANALYTE: AG]


title: RA1025_case_329 [ANALYTE: AG]


title: RA1025_case_-2714 [ANALYTE: AG]


title: RA1025_case_-2689 [ANALYTE: AG]


title: RA1024_case_-2506 [ANALYTE: AG]


title: RA1023_case_231 [ANALYTE: AG]


title: RA1023_case_-483 [ANALYTE: AG]


title: RA1022_case_-328 [ANALYTE: AG]


title: RA1024_case_-2261 [ANALYTE: AG]


title: RA1023_case_-329 [ANALYTE: AG]


title: RA1023_case_-1438 [ANALYTE: AG]


title: RA1022_case_-1720 [ANALYTE: AG]


title: RA1022_case_-428 [ANALYTE: AG]


title: RA1021_case_-515 [ANALYTE: AG]


title: RA1026_case_-1276 [ANALYTE: AG]


title: RA1020_case_-3561 [ANALYTE: AG]


title: RA1021_case_2396 [ANALYTE: AG]


title: RA1019_case_-617 [ANALYTE: AG]


title: RA1024_case_-750 [ANALYTE: AG]


title: RA1020_case_-1122 [ANALYTE: AG]


title: RA1020_case_-424 [ANALYTE: AG]


title: RA1018_case_1890 [ANALYTE: AG]


title: RA1020_case_-1393 [ANALYTE: AG]


title: RA1018_case_-2109 [ANALYTE: AG]


title: RA1015_case_-1497 [ANALYTE: AG]


title: RA1018_case_-1857 [ANALYTE: AG]


title: RA1019_case_-1461 [ANALYTE: AG]


title: RA1017_case_845 [ANALYTE: AG]


title: RA1017_case_-1638 [ANALYTE: AG]


title: RA1015_case_-2557 [ANALYTE: AG]


title: RA1015_case_589 [ANALYTE: AG]


title: RA1017_case_-4335 [ANALYTE: AG]


title: RA1017_case_-2764 [ANALYTE: AG]


title: RA1017_case_-2488 [ANALYTE: AG]


title: RA1013_case_-469 [ANALYTE: AG]


title: RA1013_case_-2474 [ANALYTE: AG]


title: RA1015_case_-3648 [ANALYTE: AG]


title: RA1013_case_-4163 [ANALYTE: AG]


title: RA1013_case_-2485 [ANALYTE: AG]


title: RA1015_case_-3467 [ANALYTE: AG]


title: RA1012_case_-5 [ANALYTE: AG]


title: RA1012_case_-336 [ANALYTE: AG]


title: RA1011_case_250 [ANALYTE: AG]


title: RA1011_case_-471 [ANALYTE: AG]


title: RA1014_case_366 [ANALYTE: AG]


title: RA1011_case_-1235 [ANALYTE: AG]


title: RA1010_case_-845 [ANALYTE: AG]


title: RA1009_case_-984 [ANALYTE: AG]


title: RA1009_case_-1500 [ANALYTE: AG]


title: RA1009_case_-2365 [ANALYTE: AG]


title: RA1010_case_-1398 [ANALYTE: AG]


title: RA1009_case_-2442 [ANALYTE: AG]


title: RA1008_case_-852 [ANALYTE: AG]


title: RA1008_case_-1445 [ANALYTE: AG]


title: RA1008_case_37 [ANALYTE: AG]


title: RA1008_case_-896 [ANALYTE: AG]


title: RA1007_case_-188 [ANALYTE: AG]


title: RA1007_case_-740 [ANALYTE: AG]


title: RA1007_case_-1536 [ANALYTE: AG]


title: RA1006_case_-1922 [ANALYTE: AG]


title: RA1006_case_-169 [ANALYTE: AG]


title: RA1006_case_-1374 [ANALYTE: AG]


title: RA1006_case_250 [ANALYTE: AG]


title: RA1005_case_-547 [ANALYTE: AG]


title: RA1006_case_-2258 [ANALYTE: AG]


title: RA1005_case_-1612 [ANALYTE: AG]


title: RA1004_case_-3347 [ANALYTE: AG]


title: RA1005_case_-1634 [ANALYTE: AG]


title: RA1004_case_-470 [ANALYTE: AG]


title: RA1004_case_-3978 [ANALYTE: AG]


title: RA1003_case_-1047 [ANALYTE: AG]


title: RA1003_case_-1814 [ANALYTE: AG]


title: RA1003_case_-2132 [ANALYTE: AG]


title: RA1003_case_-2882 [ANALYTE: AG]


title: RA1002_case_-68 [ANALYTE: AG]


title: RA1002_case_93 [ANALYTE: AG]


title: RA1002_case_-557 [ANALYTE: AG]


title: RA1002_case_-1139 [ANALYTE: AG]


title: RA1002_case_-1585 [ANALYTE: AG]


title: RA1001_case_-463 [ANALYTE: AG]


title: RA1001_case_-700 [ANALYTE: AG]


title: RA1001_case_358 [ANALYTE: AG]


title: RA1001_case_-2213 [ANALYTE: AG]


title: RA1001_case_-4908 [ANALYTE: AG]


title: mammary tumor  WT

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

description: Gene expression data from MP-DMBA induced mammary tumor in WT mice

hyb_protocol: Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.

scan_protocol: The GeneChip® was scanned using an Agilent Gene Array scanner.

data_processing: Raw data generation was performed with the Affymetrix GeneChip®ware 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal <300 in all experimental groups were excluded from subsequent analysis.

source_name: Wild-type group, treated with MP-DMBA maintained on standard rodent chow

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

growth_protocol: All animal studies were conducted under GUACUC protocol 09-061. Female nulliparious Sca-1-knockout mice and age-matched C57/wild-type littermates were used in this study.

extract_protocol: Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).

treatment_protocol: Mice were maintained on standard rodent chow and injected s.c. with  15 mg MP suspension (Depo-Provera™), followed by four weekly doses of 1 mg DMBA/0.1 ml cottonseed oil  administered by gavage

value: mammary tumor

tag: genetic background

tag: genotype

value: wild type

tag: treatment

value: MP-DMBA


title: A1

city: Berlin

first: Qing

last: Wang

state: Berlin

address: Robert Rössle Str. 10

department: Surgical Oncology

country: Germany

institute: Charite-Berlin

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 110µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 100 µl of fragmentation mixture were hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).

data_processing: Extract tif images using the Feature Extraction software FE9.1 by GE1-v5_91 protocols. TXT data files were improted in GeneSpring GX10.0.2 software (Agilent Technologies, Santa Clara, USA) and pre-processed using the agilent algorithm. Baseline transformation to median of all samples

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cryo-conserved primary tumour tissue were collected immediately after surgical removal snap-frozen in liquid nitrogen.

extract_protocol: Qiagen Rneasy extraction of total RNA was performed according to the manufactures instructions.

treatment_protocol: Primary tumor tissue and adjacent normal tissues were collected at the time of surgery and were snap-frozen in liquid nitrogen within 30 min. Histopathological examination following hematoxilin/ eosin staining of tissue sections ensured that only tumor samples containing at least 60% of non necrotic tumor epithelium were used for further analysis.

tag: tumor stage

tag: rec.

value: x

tag: tissue type

value: Adenoma


title: mammary tumor  Sca-1-KO

description: Gene expression data from MP-DMBA induced mammary tumor in KO mice

source_name: Knockout group, treated with MP-DMBA maintained on standard rodent chow

tag: tissue

value: Sca-1 KO


title: mammary gland  Sca-1-KO

description: Gene expression data from 6 weeks KO mammary gland

source_name: Knockout group, maintained on standard rodent chow

value: mammary gland


title: mammary gland  WT

description: Gene expression data from 6 weeks WT mammary gland

source_name: Wild-type group maintained on standard rodent chow


title: A4

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 110µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 100 µl of fragmentation mixture were hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.


title: N26

value: Normal


title: HUVEC VEGF Rg3R rep2

city: Hong Kong

first: Patrick

middle: YK

last: Yue

address: Waterloo Road

department: Biology

country: Hong Kong

institute: Hong Kong Baptist University

description:
Control cells were induced with VEGF (20 ng/ml) for 24 hrs in medium 199 supplemented with 10% heat-inactivated FBS, 20 μg/ml ECGS, 90 μg/ml heparin and 1% PS.
Experiimental cells were co-treated with VEGF (20 ng/ml) and Rg3-R (100 nM) for 24 hrs in medium 199 supplemented with 10% heat-inactivated FBS, 20 μg/ml ECGS, 90 μg/ml heparin and 1% PS.
VEGF-induced HUVEC were treated with 100 nM Rg3-R in medium 199 supplemented with 10 % heat-inactivated fetal bovine serum for 24 hrs. Control experiment was set up at the same time by culturing VEGF-induced HUVEC without Rg3-R.

hyb_protocol: The Alexa Fluor® 3-tagged and Alexa Fluor® 5-tagged miRNAs were co-hybridized onto miRNA microarray chips provided in the NCodeTM Multi-Species miRNA Microarray Kit V2 (Invitrogen) at 52ºC for 16 hours. Then the miRNAs hybridized on the chip were labelled with Alexa Fluor® 3 or Alexa Fluor® 5 Capture Reagents in dark at 62ºC for 4 hours.

scan_protocol: The microarrays were scanned using a ScanArray 5000 confocal laser scanner (Parkard Biochip Technologies / GSI Lumonics)

data_processing: The signal intensities for both Alexa Fluor® 3 and 5 from each spot were quantified and analyzed by QuantArray® Quantitative Microarray Analysis Software (GSI Lumonics) and GeneSpring GX software (Version 10.0; Agilent Technologies).

label: Alexa Fluor 5

source_name: VEGF-induced HUVEC

label_protocol: The purified miRNAs from two different treatment groups were polyadenylated, and then labelled with Alexa Fluor® 3 or Alexa Fluor® 5 Ligatin Mix seperately using NCodeTM miRNA Labeling System.(Invitrogen).

growth_protocol: HUVEC were cultured in medium 199 supplemented with 20% heat-inactivated fetal bovine serum (FBS), 1% penicillin-streptomycin (PS), 20 μg/ml endothelial cell growth supplement (ECGS) and 90 μg/ml heparin. The cells were grown on 0.1% gelatin-coated culture flask and incubated in a humidified incubator at 37 ºC with 5 % CO2.

extract_protocol: Total RNA was extracted using TRIzol® Reagent (Invitrogen) according to the manufacturer’s protocol. Small RNA was purified and enriched through a column-based procedure using the PureLinkTM miRNA Isolation Kit (Invitrogen) as manufacturer's instruction.

tag: cell type

value: HUVEC

value: Treatment with VEGF, 24 hours

label: Alexa Fluor 3

source_name: VEGF-induced HUVEC treated with Rg3-R

value: Co-treatment with VEGF and Rg3-R, 24 hours


title: HUVEC VEGF Rg3R rep3


title: 36

value: IV

value: CIV


title: 6

value: III

value: CR


title: 28


title: N19


title: N24


title: A2


title: 39

value: II

value: CC


title: 13


title: 31

value: I


title: 34


title: HUVEC VEGF Rg3R rep1


title: A3


title: 38


title: Sall3 wild-type P0/7 days in vitro explant, sample 2

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45°C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer's specifications.

Exons included in the analysis: extended
Mouse genome build: UCSC mm8

source_name: P0 Sall3 wild-type retina, cultured 7 days in vitro as an explant

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: Mice were housed in the Johns Hopkins BRB animal facility.  Animals were kept in a 10 hours dark:14 hours light cycle environment.  Animals were fed Harlan 20-18 SX chow and reverse osmosis hyperchlorinated water (3-5 PPM chlorine).

extract_protocol: RNeasy Kit (Qiagen)

treatment_protocol: Retinas used for explant cultures were extracted by microdissection at P0 in sterile PBS.  Four cuts were made using micro-dissection scissors and the retinas were transferred to Nucleopore Track-Etch membrane filters (Whatman) and the tissue flattened out evenly.  Filters were then floated on DMEM/F12, 10% FBS, 1X penicillin/streptomycin in 12 well plates and incubated at 37oC, 5% CO2 for 7 days.

tag: strain

value: wild-type

tag: Sex

value: mixed

tag: age

value: postnatal day 0; 7 days in vitro culture (P0/7DIV)

value: retina


title: 37


title: 1


title: 24


title: Sall3 wild-type P0/7 days in vitro explant, sample 1


title: Sall3 wild-type P0/7 days in vitro explant, sample 3


title: Sall3 knockout P0/7 days in vitro explant, sample 3

source_name: P0 Sall3-knockout retina, cultured 7 days in vitro as an explant

value: Sall3 knockout


title: RA1081_control_1470 [ANALYTE: CK]

tag: subject id

tag: group

value: control

tag: relative days to diagnosis

value: Male

tag: race

value: Caucasian

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: RA1082_control_-747 [ANALYTE: CK]


title: RA1083_control_-101 [ANALYTE: CK]


title: RA1083_control_2597 [ANALYTE: CK]


title: RA1081_control_-39 [ANALYTE: CK]


title: RA1081_control_-1611 [ANALYTE: CK]


title: RA1081_control_-1265 [ANALYTE: CK]


title: RA1081_control_-2884 [ANALYTE: CK]


title: RA1080_control_-444 [ANALYTE: CK]


title: 35


title: RA1079_control_-982 [ANALYTE: CK]

value: African American


title: 27


title: Sall3 knockout P0/7 days in vitro explant, sample 1


title: RA1079_control_-1298 [ANALYTE: CK]


title: Sall3 knockout P0/7 days in vitro explant, sample 2


title: 32


title: 106


title: N2

value: x

value: Normal


title: N9


title: 127

value: IV

value: CIV


title: RA1079_control_-1606 [ANALYTE: CK]


title: RA1079_control_-2894 [ANALYTE: CK]


title: RA1078_control_-986 [ANALYTE: CK]

value: Female


title: 29

value: III


title: RA1080_control_-1650 [ANALYTE: CK]


title: RA1078_control_-1381 [ANALYTE: CK]


title: 128

value: II

value: CC


title: 120


title: 101


title: N5


title: 109


title: RA1078_control_-3319 [ANALYTE: CK]


title: 108


title: 14

value: I

value: CR


title: RA1077_control_-1631 [ANALYTE: CK]


title: 2


title: 19


title: 102


title: RA1077_control_-3261 [ANALYTE: CK]


title: 33


title: RA1077_control_-2843 [ANALYTE: CK]


title: RA1077_control_-4193 [ANALYTE: CK]


title: RA1078_control_-2043 [ANALYTE: CK]


title: RA1076_control_1630 [ANALYTE: CK]


title: RA1076_control_-600 [ANALYTE: CK]


title: RA1076_control_-263 [ANALYTE: CK]


title: RA1076_control_-992 [ANALYTE: CK]


title: RA1076_control_-1859 [ANALYTE: CK]


title: 118


title: RA1075_control_-502 [ANALYTE: CK]


title: 122


title: 124


title: 112


title: 132


title: 129


title: 105


title: 114


title: 111


title: 125


title: RA1075_control_-1086 [ANALYTE: CK]


title: RA1074_control_133 [ANALYTE: CK]


title: RA1074_control_-744 [ANALYTE: CK]


title: RA1074_control_-2030 [ANALYTE: CK]


title: 30


title: 110


title: RA1073_control_-1061 [ANALYTE: CK]


title: RA1073_control_2698 [ANALYTE: CK]


title: 25


title: 23


title: RA1075_control_-1232 [ANALYTE: CK]


title: RA1074_control_-77 [ANALYTE: CK]


title: RA1072_control_-1110 [ANALYTE: CK]


title: RA1014_case_-686 [ANALYTE: AG]

value: case


title: RA1072_control_-1305 [ANALYTE: CK]


title: RA1071_control_711 [ANALYTE: CK]


title: RA1071_control_-190 [ANALYTE: CK]


title: RA1071_control_-859 [ANALYTE: CK]


title: RA1071_control_-2618 [ANALYTE: CK]


title: 26


title: 10


title: 17


title: 20


title: RA1072_control_-300 [ANALYTE: CK]


title: 5


title: 18


title: RA1071_control_-3438 [ANALYTE: CK]


title: RA1070_control_-813 [ANALYTE: CK]


title: 15


title: 22


title: 21


title: 9


title: 4


title: RA1070_control_-1185 [ANALYTE: CK]


title: RA1070_control_-1744 [ANALYTE: CK]


title: RA1070_control_-2103 [ANALYTE: CK]


title: 12


title: A5

value: Adenoma


title: RA1069_control_-572 [ANALYTE: CK]


title: 3


title: 11


title: RA1069_control_1774 [ANALYTE: CK]


title: muscle_lake-type_rep12

city: King Salmon

first: Scott

middle: A

last: Pavey

state: Alaska

address: PO Box 7

department: Natural Resources

institute: Katmai National Park

hyb_protocol: We followed an established hybridization protocol for the 16k cDNA array {von Schalburg, 2005 #1175}. In brief, both 250 ng of reference aRNA and 500 ng of sample cDNA were collected in a single tube and kept dark. The mixture was concentrated with a speed vacuum and brought up to 23 μl with RNase free water (Gibco). Hybridization buffer #3 (Ambion) was heated to 65oC while occasionally mixing for one hour. The heated buffer and LNAdt blocker (Genesphere) was then added to the collected sample, as per manufacturer’s instructions. We used the Tecan HS 4800 Pro, an automated hybridization machine to hybridize sample cDNA to the arrays (Tecan). Before the sample injection, the programmed Tecan washed with several solutions containing first 1xSSC, then 0.1xSSC 0.014% SDS, then 5x SSC, 0.01% SDS, and 0.2% BSA. Samples were heated to 80oC for 5 minutes, and then kept at 65oC until injected onto the pre-washed arrays in a Tecan HS 4800 Pro, as per manufacturers’ instructions. Microarrays were hybridized for 16 hours, and the full protocol for the hybridization can be viewed in Additional File 2.   Post-hybridization, arrays were rinsed in the Tecan modules with increasingly stringent SSC and SDS solutions, starting with 2xSSC, 0.014%SDS for four washes incrementally decreasing temperature, then one final wash of 0.2xSSC at 23 ºC. Finally, slides were dried with 37 psi nitrogen gas and kept dark until scanned.

scan_protocol: All microarrays were scanned immediately after hybridization was complete using a ScanArray Express (Perkin-Elmer). The microarray images were quantified manually with ImaGene 5.6.1 (BioDiscovery). Spots with unusual morphology, offset, or other poor quality parameters were flagged as marginal and excluded these from downstream analyses.

data_processing: We performed all analyses in GeneSpring GX 7.3 (Agilent). The arrays were normalized as per typical two-color experiments by performing an array-wide intensity-dependent Lowess normalization, followed by a per gene normalization, which normalized each spot to the median value. The average base/proportionate value was calculated to be an intensity of 72, so we filtered data to retain only entities with average raw signal expression values greater than 72 in at least one of the populations. This became our base expression data for analysis. Our GeneSpring analysis was performed in two ways. First, the dataset was filtered to retain only the genes where the average differential expression was ≥ 1.5 fold. This list was significance tested with a t-test without equal variances assumption (P ≤ 0.05) with a Benjamini and Hochberg False Discovery Rate multiple test correction (MTC; {Benjamini, 2001 #879}. The spot ID’s from the cGRASP 16k annotation file (current annotation files available at: http://web.uvic.ca/grasp/microarray/array.html; {Koop, 2008 #1176}) were used to associate ESTs (expressed sequence tags) on the array with gene descriptions. To confirm current annotation of the differential gene list, a Megablast was performed on associated EST sequences, or used tBLASTx on the associated EST, or contiguous sequence (contig). The default parameters were used for these database queries.

organism: Oncorhynchus nerka

source_name: lake-type muscle

label_protocol: cDNA was synthesized with Invitrogen SuperScriptTM III Indirect cDNA labeling system kits per manufacturer’s instructions. In brief, 10 µg of total RNA was combined with a master mix including reverse-transcriptase and oligo (dT)20 primers. This reaction was incubated for three hours at 46ºC to synthesize single-stranded cDNA. The samples were cleaned with the S.N.A.P TM column purification procedure (Invitrogen).   A reference pool was prepared with representative total RNA samples of juvenile sockeye muscle and liver, and adult sockeye brain, muscle and liver. Multiple tissues were used to ensure hybridization of the reference channel to all spots that may have been hybridized by the sample channel cDNA, and therefore able to be quantified as a ratio. The total RNA was amplified using an Amino Allyl MessageAmp™ II aRNA amplification Kit (Ambion) as per manufacturers instructions. Briefly, RNA from several individuals from both populations of a single tissue type were combined. Then, single-stranded cDNA was synthesized from the RNA whereupon the second strand was synthesized with DNA polymerase. This product was purified through columns, and then amino allyl-modified aRNA was transcribed from the cDNA. The aRNA from divergent tissue types was combined in equal amounts at this point and this common reference pool was run with each sample on the microarray.   Sample and reference material was coupled with mono-reactive CyDyeTM packs (GE Healthcare). In short, the reference aRNA was coupled with Cy3 and the sample cDNA with Cy5 dyes for one hour at 4ºC. The samples were then purified to remove all uncoupled dye using S.N.A.P.TM columns as per manufacturer’s instructions (Invitrogen). The dye coupled sample and reference were stored at 4ºC in the dark until hybridization.

growth_protocol: Sampled in nature

extract_protocol: Total RNA was extracted with a modified protocol of the Invitrogen TRIzol® Plus RNA purification kit using PureLinkTM Micro-to-MidiTM columns. Disruption and homogenization were achieved with a MixerMill MM301 (Retsch). The manufacturer’s protocol was followed with the exception of using 150 µl of chloroform and 150 µl of low pH phenol for tissue dissociate protein and isolate RNA.

treatment_protocol: Sampled in nature from either riverine or lake habitat

value: muscle

tag: isolation source

value: lake-type

source_name: aRNA pool from muscle, brain, liver

value: pool from muscle, brain, liver


title: RA1068_control_-1044 [ANALYTE: CK]

value: control

value: Caucasian


title: RA1069_control_-1979 [ANALYTE: CK]

value: Male


title: RA1069_control_-2018 [ANALYTE: CK]


title: muscle_riverine_rep10

source_name: riverine, muscle

value: riverine


title: muscle_lake-type_rep1


title: RA1069_control_-1287 [ANALYTE: CK]


title: RA1066_control_-366 [ANALYTE: CK]

value: Other


title: RA1067_control_-691 [ANALYTE: CK]


title: RA1067_control_3832 [ANALYTE: CK]


title: RA1066_control_-1762 [ANALYTE: CK]


title: muscle_riverine_rep6


title: RA1066_control_-4158 [ANALYTE: CK]


title: RA1066_control_-1405 [ANALYTE: CK]


title: muscle_riverine_rep4


title: RA1065_control_-1296 [ANALYTE: CK]

value: African American


title: muscle_riverine_rep17


title: muscle_lake-type_rep8


title: RA1065_control_1427 [ANALYTE: CK]


title: muscle_lake-type_rep13


title: muscle_riverine_rep15


title: muscle_lake-type_rep4


title: N39

value: x

value: Normal


title: RA1065_control_-1730 [ANALYTE: CK]


title: muscle_lake-type_rep5


title: muscle_riverine_rep12


title: muscle_lake-type_rep11


title: muscle_riverine_rep2


title: RA1065_control_-2196 [ANALYTE: CK]


title: muscle_riverine_rep8


title: muscle_lake-type_rep2


title: muscle_riverine_rep13


title: RA1064_control_4246 [ANALYTE: CK]


title: muscle_riverine_rep7


title: muscle_riverine_rep11


title: muscle_riverine_rep1


title: RA1063_control_1013 [ANALYTE: CK]

value: Female


title: RA1064_control_-277 [ANALYTE: CK]


title: RA1065_control_-879 [ANALYTE: CK]


title: RA1063_control_-1175 [ANALYTE: CK]


title: muscle_lake-type_rep3


title: RA1062_control_-319 [ANALYTE: CK]


title: RA1062_control_1224 [ANALYTE: CK]


title: muscle_lake-type_rep10


title: RA1062_control_-2216 [ANALYTE: CK]


title: RA1062_control_-2580 [ANALYTE: CK]


title: muscle_lake-type_rep9


title: RA1064_control_-438 [ANALYTE: CK]


title: RA1061_control_-402 [ANALYTE: CK]


title: RA1062_control_-3560 [ANALYTE: CK]


title: RA1061_control_-2404 [ANALYTE: CK]


title: RA1061_control_-2691 [ANALYTE: CK]


title: muscle_riverine_rep3


title: muscle_lake-type_rep7


title: muscle_riverine_rep16


title: RA1060_control_278 [ANALYTE: CK]


title: RA1061_control_-4750 [ANALYTE: CK]


title: muscle_riverine_rep5


title: RA1060_control_-2815 [ANALYTE: CK]


title: muscle_riverine_rep9