title: MU.1.817

description: KDM4A Mutant IP/Input, Array 2/2, Biological Replicate 1.

source_name: dKDM4A mutant whole embryos, ChIP

value: Bloomington Drosophila Stock Center No. 13828

value: dKDM4A mutant

value: whole body

tag: developmental stage

value: 2-4 hour embryos

tag: chip antibody

tag: antibody vendor

value: abcam

tag: antibody catalog #

source_name: dKDM4A mutant whole embryos, input


title: MU.2.817

status: Public on Jul 10 2012

type: genomic

city: Kansas City

first: Ariel

last: Paulson

state: MO

department: Computational Biology

country: USA

institute: Stowers Institute for Medical Research

description: KDM4A Mutant IP/Input, Array 2/2, Biological Replicate 2.

hyb_protocol: A mixture of Cy5-labeled IP DNA and Cy3-labeled input DNA (4.5 µg each for replicates 1, and 9 µg each for replicates 2) was hybridized at 65ºC for 40 hours to Drosophila Whole Genome ChIP-on-Chip Set 244K arrays using Agilent Technologies CGH protocol and reagents (Oligo aCGH Hybridization Kit; Cat. No.: 5188-5220 and Oligo aCGH Wash Buffer Kit; Cat. No.: 5188-5226).

scan_protocol: Slides were scanned with an Agilent High-Resolution DNA Microarray Scanner (G2505C), and image analysis was performed with Agilent Technologies Feature Extraction software (version 10.5.1.1).

data_processing: Arrays were median-normalized in R using the limma package.

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: Immunoprecipitated (IP) samples and input samples (200 ng) were amplified by ligation-mediated PCR (LM-PCR ), and 2 µg each were differentially labeled by random-primed, Klenow-based extension as described in PMID 17406303.

growth_protocol: dKDM4A mutant with P element insertion (y1 w67c23; P{y+mDint2 wBR.E.BR=SUPor-P}Kdm4AKG04636) was obtained from Bloomington Stock Center at Indiana University (stock #13828). P element KG04636 was mobilized by crossing the mutant to y1w*; CyO, H{w[+mc]=PΔ2-3}Hop2.1/Bc1EgfrE1 flies. Males of KG04646 over the transposase gene PΔ2-3 were crossed to a CyO balanced stock. P element excision was screened by eye color and confirmed by PCR.  To generate the dKDM4A genomic rescue, a fragment containing the dKDM4A locus (incl. 1.6 KB upstream / 220 bp downstream) was amplified from genomic DNA of Oregon R flies. Double FLAG tags were added at dKDM4A C-terminus. V423A mutation was generated using Quick Change II XL Site-Directed Mutagenesis Kit (Stratagene); fragment was cloned into pCa4B vector [PMID:18311141]. Site-specific integration at attP40 landing site (2L 25C7) was carried out by Genetic Services. To rescue the mutant, the transgene (FLAG-dKDM4A or dKDM4A-V423A) on the second chromosome was recombined to the chromosome carrying KG04636 insertion.

extract_protocol: Genomic DNA was purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: ChIP was performed from staged 2-4 hours embryos collected in population cages as described in PMID 17406543 and PMID 17322397 with minor modifications. Briefly, embryos were cross-linked in 1.8% formaldehyde and homogenized in Buffer A1 (15 mM Hepes pH 7.5, 15 mM NaCl, 60 mM, KCl, 4 mM MgCl, 0.5% Triton X-100, 0.5 mM DTT and protease inhibitors). Nuclei were resuspended in A2 buffer (15 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS, 0.5% N-lauroylsarcosine and protease inhibitors) and sonicated to obtain chromatin fragments with an average size of ~500 bp. For input controls, 50 μl of chromatin was used. About 700µg to 1mg of chromatin was incubated with 1.5µg anti-H3K36me3 antibody (abcam, ab9050) overnight at 4ºC. 30 µl of sheep anti-rabbit IgG Dynabeads was added to each chromatin/antibody solution and incubated for 2 hr, 4ºC, then beads were washed 5 times with RIPA Buffer (50 mM Hepes pH 7.5, 0.5 M LiCl, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate) and once with 50mM NaCl in TE. Bound complexes were eluted twice with 200 μl of elution buffer (50mM Tris pH 8.0, 10 mM EDTA, 1% SDS) at 65ºC for 30min. The eluate were treated with RNase A (0.2 μg/μl) for 1 hour at 37ºC followed by Proteinase K treatment (0.2 μg/μl) for 1 hour at 55ºC. Crosslinks were reversed by incubating samples at 65ºC overnight.

tag: strain

tag: genotype/variation

tag: tissue


title: Human Whole blood RNA 239

status: Public on Jul 09 2012

type: RNA

city: Los Angeles

first: Simone

last: de Jong

state: California

address: 695 Charles E. Young Drive south

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected in Beadstudio (v. 3.2.3) and transformed (vst) and normalised (rsn) in Lumi (R package)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: schizophrenia (SCZ)_whole blood

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

extract_protocol: Standard Qiagen PAXgene extraction (manual and Qiacube)

tag: age

tag: gender

value: female

tag: status

value: schizophrenia (SCZ)

value: whole blood


title: WT.2.817

description: WT IP/Input, Array 2/2, Biological Replicate 2.

source_name: WT whole embryos, ChIP

value: wild type

source_name: WT whole embryos, input


title: Human Whole blood RNA 235

value: male


title: Human Whole blood RNA 238


title: Human Whole blood RNA 230


title: Human Whole blood RNA 228


title: Human Whole blood RNA 229


title: Human Whole blood RNA 227

source_name: CONTROL_whole blood

value: CONTROL


title: Human Whole blood RNA 231


title: Human Whole blood RNA 236


title: Human Whole blood RNA 226


title: Human Whole blood RNA 232


title: Human Whole blood RNA 219


title: WT.1.817

description: WT IP/Input, Array 2/2, Biological Replicate 1.


title: Human Whole blood RNA 221


title: Human Whole blood RNA 223


title: Human Whole blood RNA 225


title: Human Whole blood RNA 224


title: Human Whole blood RNA 222


title: Human Whole blood RNA 220


title: Human Whole blood RNA 218


title: Human Whole blood RNA 215


title: Human Whole blood RNA 217


title: Human Whole blood RNA 216


title: Human Whole blood RNA 211


title: Human Whole blood RNA 214


title: Human Whole blood RNA 213


title: Human Whole blood RNA 212


title: Human Whole blood RNA 204


title: Human Whole blood RNA 200


title: Human Whole blood RNA 206


title: Human Whole blood RNA 209


title: Human Whole blood RNA 202


title: Human Whole blood RNA 203


title: Human Whole blood RNA 205


title: Human Whole blood RNA 201


title: Human Whole blood RNA 199


title: Human Whole blood RNA 198


title: Human Whole blood RNA 196


title: Human Whole blood RNA 194


title: Human Whole blood RNA 192


title: Human Whole blood RNA 195


title: Human Whole blood RNA 197


title: Human Whole blood RNA 210


title: Human Whole blood RNA 193


title: Human Whole blood RNA 191


title: Human Whole blood RNA 189


title: Human Whole blood RNA 188


title: Human Whole blood RNA 190


title: Human Whole blood RNA 186


title: Human Whole blood RNA 184


title: Human Whole blood RNA 183


title: Human Whole blood RNA 187


title: Human Whole blood RNA 185


title: Human Whole blood RNA 181


title: Human Whole blood RNA 177


title: Human Whole blood RNA 174


title: Human Whole blood RNA 176


title: Human Whole blood RNA 173


title: Human Whole blood RNA 179


title: Human Whole blood RNA 182


title: Human Whole blood RNA 178


title: Human Whole blood RNA 180


title: Human Whole blood RNA 169


title: Human Whole blood RNA 166


title: Human Whole blood RNA 175


title: MG1655Δ6/pCA24N-dinJ Ery 10min

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from cell of E.coli MG1655Δ6/pCA24N-dinJ after exposed to erythromycin for 10 min at 37°C

hyb_protocol: Following affymetrix protocol. cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: MG1655Δ6/pCA24N-dinJ Ery 10min

extract_protocol: The overnight cultures were diluted into OD600 (0.05) with in LB-low salt-Cm30. After incubation for 2 hrs, added to 1 mM IPTG for 2 h, and then dilute culture to be OD ~ 1.0. Then exposed cell to erythromycin (75µg/mL) for 10 min, harvest cell as quickly as possible to avoid mRNA degradation. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat#74104).

tag: molecule

value: total RNA.

value: E.coli MG1655Δ6/pCA24N-dinJ

tag: condition

value: erythromycin exposure

tag: time

value: 10 min

tag: temp


title: MG1655 Δ6/pCA24N erythromycin 10min 37°C

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

value: E.coli MG1655Δ6/pCA24N


title: Human Whole blood RNA 172


title: Human Whole blood RNA 168


title: Human Whole blood RNA 170


title: Human Whole blood RNA 162


title: DNA obtained from the supernatant of SW480 cell cultures [Mapping250K_Sty]

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 7G Plus

data_processing: CEL files were captured using the Affymetrix genotyping console. The files were normalized and compared against a common DNA copy number reference generated with data from the International HapMap project using the copy number pipeline in the Partek Genomics Suite software.

label: Biotin

source_name: SW480 cell culture supernatant

label_protocol: Affymetrix standard protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: When the cell confluence was 80%, the supernatants were collected by pippeting and were prepared for future experiments. Fifty ml of the supernatant of the cell lines SW480 or NIH3T3 were cleared of any remaining cells and cell debris by a centrifugation step at 400 x g for 20 min (Biofuge primo R, Heraeus) and passed through a 0.45mm filter (Sartorius, 16555), to remove potentially contaminating cells. The supernatants were processed as follows: 1) enzymatically digested with DNAse and/or Proteases, or 2) concentrated, first with an ultra filtration system, and then with a speed vacuum device (Vacufuge plus, Eppendorf) up to 10 ml; or 3) it was immediately used for passive transfection. The concentrated supernatant was immediately cryopreserved at -80C until circulating DNA extraction. An aliquot of each processed supernatant was seeded in a culture flask and incubated at 37C for 48 hours, to verify the absence of living cells.

tag: cell line

tag: cell type

value: colon adenocarcinoma


title: Human Whole blood RNA 165


title: Human Whole blood RNA 167


title: Human Whole blood RNA 161


title: Human Whole blood RNA 160


title: Human Whole blood RNA 171


title: Human Whole blood RNA 163


title: Human Whole blood RNA 159


title: Human Whole blood RNA 164


title: DNA from the SW480 cell line [Mapping250K_Sty]

source_name: SW480 cells


title: Human Whole blood RNA 208


title: Human Whole blood RNA 158


title: human pancreatic nontumor tissue, patient sample 39

city: Bethesda

first: Perwez

last: Hussain

address: 37 Convent Drive

institute: NCI/NIH

description: cancer related death

hyb_protocol: Samples were hybridized using Affymetrix GeneChip Hybridization, Wash, and Stain Kit and according to the manufacturer's protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: All arrays were RMA normalized and gene expression summaries were created for each gene by averaging all probe sets for each gene using Partek Genomics Suite 6.5.  All data analysis was performed on gene summarized data.

source_name: non-tumor tissue, patient 39

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol. RNA quality was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies) before the microarray gene expression profiling

value: N


title: human pancreatic nontumor tissue, patient sample 40

description: cancer related death

source_name: non-tumor tissue, patient 40


title: Human Whole blood RNA 207


title: human pancreatic tumor tissue, patient sample 41

description: cancer related death

source_name: tumor tissue, patient 41

value: T


title: human pancreatic tumor tissue, patient sample 40

description: cancer related death

source_name: tumor tissue, patient 40


title: Human Whole blood RNA 156


title: Human Whole blood RNA 155


title: Human Whole blood RNA 152


title: human pancreatic nontumor tissue, patient sample 44

description: cancer related death

source_name: non-tumor tissue, patient 44


title: Human Whole blood RNA 153


title: Human Whole blood RNA 157


title: human pancreatic tumor tissue, patient sample 39

description: cancer related death

source_name: tumor tissue, patient 39


title: human pancreatic tumor tissue, patient sample 44

description: cancer related death

source_name: tumor tissue, patient 44


title: human pancreatic nontumor tissue, patient sample 43

description: cancer related death

source_name: non-tumor tissue, patient 43


title: Human Whole blood RNA 151


title: human pancreatic tumor tissue, patient sample 45

description: censored

source_name: tumor tissue, patient 45


title: Human Whole blood RNA 150


title: Human Whole blood RNA 149


title: Human Whole blood RNA 148


title: Human Whole blood RNA 154


title: Human Whole blood RNA 146


title: Human Whole blood RNA 147


title: human pancreatic tumor tissue, patient sample 43

description: cancer related death

source_name: tumor tissue, patient 43


title: PAO1_TSB_8h_008

city: Lubbock

first: Jane

middle: A.

last: Colmer-Hamood

state: Texas

address: 3601 4th Street  STOP 6591

department: Microbiology & Immunology

institute: Texas Tech University Health Sciences Center

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT8h_008

hyb_protocol: Equal quantities (1 ug/of each) of labeled cDNA were hybridized in prepared hybridization solution (a final concentration of 8.3X SSC, 50% formamide, 0.16%SDS, 0.1 ug/ul sheared salmon sperm DNA in water). The arrays were incubated for 16 h at 42°C, and then washed once at 42°C in 2X SSC/0.2% SDS, once in 0.5X at room temperature, and then four times in 0.1X SSC and once with 0.05X SSC with a final rinse in water, all at room temperature.

scan_protocol: Incorporation of fluorophore was analyzed by using the absorbance at 647 nm or 555 nm for Alexa Fluor 647 and Alexa Fluor 555, respectively. Acquisition and quantification of array images from the JCVI PFGRC microarray chips was performed in an GenePix 4200A array scanner with its accompanying software GenePix Pro acquisition and analysis software (Molecular Devices).  The 650/550 nm ratio was used to optimize PMT gain.  All images were captured on optimum PMT gain, laser power, resolution, and scan rate settings determined by analysis of self-hybridization samples.

data_processing:
Microarray data analysis was performed according to the following parameters (mitchell.wachtel@ttuhsc.edu).
Determination of genes of interest: Background subtracted values were affine transformed by adding 110 to each value. For all experiments, a Red-Green correlation of 0.90 on transformed data was required. Log gamma regression analyzed the data. Affine transformed values were the outcome variable. Predictor variables were a set of orthogonal contrasts: 1) green versus red; 2) eight hours versus four hours; 3) the interaction of color and time.  Genes were discarded if the absolute value of a studentized residual was greater than 4.29, corresponding to a Bonferroni-corrected P < 0.05/5552 = 9.01 x 10-6. Genes were discarded if linear regression of the fitted values upon either the standardized residuals or the squares of the standardized residuals yielded  a value of an F test of R2 with an associated P < 0.05/5552 =  9.01 x 10-6. Genes were discarded if a t test of the standardized residuals showed the mean was not zero with P < 0.05/5552 =  9.01 x 10-6.  Results of log gamma regression were considered for further analysis if a chi-square test of the deviance yielded a result associated with P < 0.001/5552 =  1.80 x 10-7. Point estimates of coefficients were said to differ from zero if the z ratio had an associated P < 0.001/5552 = 1.80 x 10-7.
Determination of effect size: Non-affine transformed expression values > 0 were used. For each color and each array, the mean of the natural logarithms of AT gene expression values was calculated; this mean was exponentiated to yield adjustment factors for each color and each array.  Expression values of PA genes deemed important were divided by the corresponding adjustment factors to yield array and color adjusted expression values.  For those genes that were deemed to have differences in red - green expression that changed with respect to time, median adjusted expression values were calculated for each color and each time period, yielding two results: 1) the ratio of the median red expression and the median green expression at four hours and 2) the ratio of the median red expression and the median green expression at eight hours. For those genes that were deemed to have differences in red - green expression that did not change with time, median adjusted expression values were calculated for each color to yield one result: the ratio of the median red expression and the median green expression.
Genes were considered differentially regulated if the relative change (n-fold) was 2.0 between PAO1 grown in TSB-DC/ABS and TSB-DC at the same time point (either 4 h or 8 h) and the P-value was, 0.05.

label: AlexaFluor 555

organism: Pseudomonas aeruginosa

source_name: Prokaryote,Bacteria

label_protocol: 10-15 mg of total RNA were used for cDNA synthesis, incorporating aminoallyl dUTP/dNTP (Invitrogen) using SuperScript III (Invitrogen) in the presence of RNasin (Invitrogen) for 2 h at 45°C.  Alkaline hydrolysis of the RNA strand followed the incubation. The cDNA from PAO1 grown in TSB-DC/ABS was then labeled with Alexa Fluor® 647 and that from PAO1 grown in TSB-DC alone was labeled with Alexa Fluor® 555.

growth_protocol: PAO1 was grown overnight in Luria-Bertani broth at 37°C.  An aliquot of the overnight culture was pelleted, washed and resuspended in TSB-DC (trypticase soy broth dialysate, chelexed to remove iron).  The resuspended culture was used to inoculate fresh TSB-DC with or without 10% (v/v) adult bovine serum (ABS) to an optical density at 600 nm of 0.02-0.03. Triplicate cultures of PAO1 were grown at 37 °C with shaking in either TSB-DC or TSB-DC/ABS to an OD600 of 1.11 and 0.69 (early exponential phase of growth, 4-h time point) and 4.7 and 2.5 (early stationary phase, 8-h time point), respectively.

extract_protocol: Cultures were incubated in RNA Protect (Qiagen) according to manufacturer’s instructions and pelleted. Total RNA were isolated from the cells using RNA Mini Kit (Qiagen) per manufacturer’s instructions.  DNA was degraded by DNase I (RNase free) (Invitrogen).

treatment_protocol: As growth levels in TSB-DC/ABS were reduced compared to growth in TSB-DC, the TSB-DC cultures were adjusted to the sameOD600 as their companion cultures in TSB-DC/ABS by dilution with fresh TSB-DC prior to RNA extraction.

tag: medium

value: TSBDC only

tag: growth phase

value: Early stationary, 8h


title: human pancreatic nontumor tissue, patient sample 42

description: censored

source_name: non-tumor tissue, patient 42


title: human pancreatic nontumor tissue, patient sample 45

description: censored

source_name: non-tumor tissue, patient 45


title: PAO1_TSBABS_8h_008

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAS8h_008

label: AlexaFluor 647

value: TSBDC with 10% ABS


title: human pancreatic tumor tissue, patient sample 42

description: censored

source_name: tumor tissue, patient 42


title: human pancreatic nontumor tissue, patient sample 38

description: cancer related death

source_name: non-tumor tissue, patient 38


title: human pancreatic tumor tissue, patient sample 38

description: cancer related death

source_name: tumor tissue, patient 38


title: Human Whole blood RNA 144

source_name: CONTROL_whole blood


title: PAO1_TSB_8h_007

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT8h_007


title: Human Whole blood RNA 145


title: Human Whole blood RNA 142

value: female


title: human pancreatic nontumor tissue, patient sample 37

description: censored

source_name: non-tumor tissue, patient 37


title: human pancreatic tumor tissue, patient sample 37

description: censored

source_name: tumor tissue, patient 37


title: Human Whole blood RNA 140

source_name: schizophrenia (SCZ)_whole blood

value: schizophrenia (SCZ)


title: PAO1_TSBABS_8h_007

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAS8h_007


title: Human Whole blood RNA 138

value: whole blood


title: PAO1_TSBABS_8h_006

description:
Technical replicate
500 Arabidopsis thaliana 70mers included as controls
PAS8h_006


title: PAO1_TSB_8h_006

description:
Technical replicate
500 Arabidopsis thaliana 70mers included as controls
PAT8h_006


title: human pancreatic tumor tissue, patient sample 36

description: cancer related death

source_name: tumor tissue, patient 36


title: Human Whole blood RNA 141


title: Human Whole blood RNA 136


title: Human Whole blood RNA 143


title: Human Whole blood RNA 137


title: Human Whole blood RNA 139


title: human pancreatic nontumor tissue, patient sample 35

description: censored

source_name: non-tumor tissue, patient 35


title: human pancreatic nontumor tissue, patient sample 36

description: cancer related death

source_name: non-tumor tissue, patient 36


title: human pancreatic tumor tissue, patient sample 35

description: censored

source_name: tumor tissue, patient 35


title: PAO1_TSBABS_8h_005

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAS8h_005


title: Human Whole blood RNA 135


title: Human Whole blood RNA 134


title: Human Whole blood RNA 131


title: Human Whole blood RNA 132


title: human pancreatic nontumor tissue, patient sample 34

description: cancer related death

source_name: non-tumor tissue, patient 34


title: Human Whole blood RNA 133


title: Human Whole blood RNA 130


title: Human Whole blood RNA 129


title: Human Whole blood RNA 128


title: PAO1_TSB_4h_004

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT4h_004

value: Early exponential, 4h


title: human pancreatic tumor tissue, patient sample 34

description: cancer related death

source_name: tumor tissue, patient 34


title: PAO1_TSB_4h_003

description:
Technical replicate
500 Arabidopsis thaliana 70mers included as controls
PAT4h_003


title: PAO1_TSBABS_4h_004

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAS4h_004


title: PAO1_TSB_8h_005

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT8h_005


title: human pancreatic nontumor tissue, patient sample 41

description: cancer related death

source_name: non-tumor tissue, patient 41


title: human pancreatic tumor tissue, patient sample 32

description: censored

source_name: tumor tissue, patient 32


title: PAO1_TSBABS_4h_003

description:
Technical replicate
500 Arabidopsis thaliana 70mers included as controls
PAS4h_003

source_name: Prokaryote,Bacteria


title: human pancreatic tumor tissue, patient sample 33

description: censored

source_name: tumor tissue, patient 33


title: PAO1_TSBABS_4h_002

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAS4h_002


title: human pancreatic nontumor tissue, patient sample 31

description: censored

source_name: non-tumor tissue, patient 31


title: human pancreatic nontumor tissue, patient sample 32

description: censored

source_name: non-tumor tissue, patient 32


title: PAO1_TSB_4h_002

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT4h_002


title: Human Whole blood RNA 122


title: Human Whole blood RNA 124


title: Human Whole blood RNA 126


title: Human Whole blood RNA 120

value: male


title: Human Whole blood RNA 118


title: Human Whole blood RNA 121


title: Human Whole blood RNA 125

value: CONTROL


title: Human Whole blood RNA 119


title: PAO1_TSB_4h_001

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls
PAT4h_001


title: human pancreatic nontumor tissue, patient sample 33

description: censored

source_name: non-tumor tissue, patient 33


title: Human Whole blood RNA 123

source_name: CONTROL_whole blood


title: Human Whole blood RNA 127


title: Human Whole blood RNA 117


title: PAO1_TSBABS_4h_001

description:
Biological replicate
500 Arabidopsis thaliana 70mers included as controls; empty spots included as background controls
PAS4h_001


title: Human Whole blood RNA 116


title: Human Whole blood RNA 115


title: Human Whole blood RNA 114


title: human pancreatic nontumor tissue, patient sample 30

description: cancer related death

source_name: non-tumor tissue, patient 30


title: human pancreatic tumor tissue, patient sample 30

description: cancer related death

source_name: tumor tissue, patient 30


title: Human Whole blood RNA 112

source_name: schizophrenia (SCZ)_whole blood


title: 947-TM1

city: East Lansing

first: Daniel

middle: Patrick

last: Hollern

state: MI

address: 2194 Biomedical Physical Sciences

institute: Michigan State University

description: Gene expression data from mouse mammary tumor tissue.

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse 430A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara,

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

data_processing: The data were analyzed using Stratagene's ArrayAssist Enterprise using Affymetrix default analysis settings.

organism: Mus musculus

source_name: Mammary Tumor

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

growth_protocol: Animal use and husbandry was in accordance with institutional and federal guidelines.

extract_protocol: Total RNA from mouse mammary tumors was extracted using the Qiagen RNeasy Midi kit.

value: FVB

tag: tissue type

value: Mammary Tumor

tag: histology

value: T58A Low Expressing, EMT


title: Human Whole blood RNA 113


title: Human Whole blood RNA 110


title: human pancreatic tumor tissue, patient sample 31

description: censored

source_name: tumor tissue, patient 31


title: Human Whole blood RNA 108


title: Human Whole blood RNA 111


title: Human Whole blood RNA 109


title: human pancreatic nontumor tissue, patient sample 29

description: censored

source_name: non-tumor tissue, patient 29


title: 1260-TM1

value: T58A Low Expressing, Squamous


title: human pancreatic tumor tissue, patient sample 29

description: censored

source_name: tumor tissue, patient 29


title: Human Whole blood RNA 106


title: Human Whole blood RNA 105


title: 2527_6511_31092_1407-2


title: Human Whole blood RNA 107


title: 1226-TM1


title: 2527_6511_31093_1658-1


title: human pancreatic tumor tissue, patient sample 28

description: censored

source_name: tumor tissue, patient 28


title: Human Whole blood RNA 103


title: 2527_6511_31091_1407-1


title: Human Whole blood RNA 100


title: Human Whole blood RNA 102


title: 2527_6511_31090_1309-1


title: Human Whole blood RNA 98


title: Human Whole blood RNA 101


title: Human Whole blood RNA 104


title: human pancreatic nontumor tissue, patient sample 27

description: censored

source_name: non-tumor tissue, patient 27


title: Human Whole blood RNA 99


title: human pancreatic nontumor tissue, patient sample 25

description: cancer related death

source_name: non-tumor tissue, patient 25


title: 2527_6511_31089_1308-2

value: T58A Low Expressing, Microacinar


title: Human Whole blood RNA 97


title: Human Whole blood RNA 95


title: human pancreatic nontumor tissue, patient sample 26

description: cancer related death

source_name: non-tumor tissue, patient 26


title: 2527_6511_31088_1308-1


title: Human Whole blood RNA 96


title: human pancreatic tumor tissue, patient sample 27

description: censored

source_name: tumor tissue, patient 27


title: Human Whole blood RNA 94


title: human pancreatic tumor tissue, patient sample 26

description: cancer related death

source_name: tumor tissue, patient 26


title: 2527_6511_31086_1183-1


title: Human Whole blood RNA 92


title: human pancreatic tumor tissue, patient sample 25

description: cancer related death

source_name: tumor tissue, patient 25


title: 2527_6511_31087_1227-1

value: T58A Low Expressing, Papillary


title: Human Whole blood RNA 90


title: Human Whole blood RNA 91


title: Human Whole blood RNA 93


title: human pancreatic nontumor tissue, patient sample 28

description: censored

source_name: non-tumor tissue, patient 28

value: N


title: human pancreatic nontumor tissue, patient sample 24

description: censored

source_name: non-tumor tissue, patient 24


title: Human Whole blood RNA 87

source_name: CONTROL_whole blood


title: Human Whole blood RNA 88


title: Human Whole blood RNA 86


title: Human Whole blood RNA 89


title: human pancreatic nontumor tissue, patient sample 23

description: cancer related death

source_name: non-tumor tissue, patient 23


title: 2527_6511_31083_927-1


title: Human Whole blood RNA 85


title: 2527_6511_31085_938-1


title: 2527_6511_31080_482-1


title: Human Whole blood RNA 83


title: human pancreatic tumor tissue, patient sample 23

description: cancer related death

source_name: tumor tissue, patient 23

value: T


title: human pancreatic tumor tissue, patient sample 24

description: censored

source_name: tumor tissue, patient 24


title: human pancreatic nontumor tissue, patient sample 22

description: cancer related death

source_name: non-tumor tissue, patient 22


title: Human Whole blood RNA 79


title: human pancreatic tumor tissue, patient sample 22

description: cancer related death

source_name: tumor tissue, patient 22


title: Human Whole blood RNA 78


title: Human Whole blood RNA 82


title: Human Whole blood RNA 84


title: Human Whole blood RNA 80


title: Human Whole blood RNA 77


title: Human Whole blood RNA 81


title: 2527_6511_31082_925-1

source_name: Mammary Tumor


title: 2527_6511_31081_486-1


title: human pancreatic nontumor tissue, patient sample 21

description: cancer related death

source_name: non-tumor tissue, patient 21


title: 2527_6511_31084_928-1


title: adult-midbrain-1 vs. E13.5c

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)* Priming: 5xSSC, 0.1%SDS* Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul* Hybridization: 45 min at 42C.* Wash 2x: milliQ* Wash: 5xSSC, 0.1%SDS* Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)* Hybridization: 16 hours at 42C.* Wash 2x: 1xSSC, 0.2%SDS at 23C* Wash 2x: 0.1xSSC, 0.2%SDS at 23C* Wash 2x: 0.1xSSC at 23C* Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol:
robot amplification and labeling v1.0
All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  mRNA amplification protocol description:* all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.* mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.* plate is incubated @ 70C for 10 mins, cooled to 48C.* mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.* plate is incubated @ 48C for 2 hours and cooled to room temperature.* 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well.* plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .* 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).* Plate is incubated @37C for 4 hours.* cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol. * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.* Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script :* 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).* 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.* 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.* 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.* Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.* RNA concentration and labeling incorporation are measured (SpectraMax 190).* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.* Samples are stored at -20C until hybridization.

extract_protocol:
RNA isolation using Trizol v1.0 (tissue sections)
Trizol RNA isolation of tissue sections:  1. After sectioning, store sections in ice-cold RNAlater (~10 ml RNAlater per 20-mm section). Make sure that the sections do not thaw before they are in ice-cold RNAlater. 50 ml RNAlater.2. Add X ml Trizol (10x volume of RNAlater) and mix by inverting the tube several times. 500 ml Trizol.3. Incubate 5 min at room temperature.4. Pre-incubate Proteinase K (10 mg/ml) at 37 C for at least 10 minutes.5. Add 10 ml of the pre-heated Proteinase K solution to Trizol mixture. 10 ml Prot-K.6. Incubate 30 min at 55 C.7. Add X ml chloroform (20 ml per 100 ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 100 ml chloroform.8. Centrifuge 20 min at 14000 rpm without brake at 4 C. After centrifugation, transfer the water-phase to a new 1.5 ml micro centrifuge tube (~300 ml).9. Continue with RNeasy columns (Qiagen) for clean-up of RNA.10. Adjust each sample to a volume of 300 ml with sterile MilliQ water. Add 160 ml buffer RLT to the samples, and mix (= lysis buffer).11. Add 240 ml ethanol (100% stored at -20 C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipette and work as quickly as possible). Next lysate, and so on.12. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flow-through and collection tube.13. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ml buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in step 5.14. Pipette 500 ml buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.15. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).16. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipette 100 ml milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.17. Pipette the eluate of step 7 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.

tag: reference

value: pooled RNA from adult VMs

value: ventral midbrain

tag: developmental stage


title: human pancreatic tumor tissue, patient sample 21

description: cancer related death

source_name: tumor tissue, patient 21


title: E13.5c vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 19

description: cancer related death

source_name: tumor tissue, patient 19


title: human pancreatic nontumor tissue, patient sample 20

description: cancer related death

source_name: non-tumor tissue, patient 20


title: Human Whole blood RNA 76

source_name: schizophrenia (SCZ)_whole blood


title: Human Whole blood RNA 74


title: Human Whole blood RNA 75


title: human pancreatic nontumor tissue, patient sample 17

description: censored

source_name: non-tumor tissue, patient 17


title: Human Whole blood RNA 73


title: Human Whole blood RNA 71


title: adult-midbrain-1 vs. E12.5b


title: Human Whole blood RNA 69


title: Human Whole blood RNA 70


title: adult-midbrain-1 vs. E13.5b


title: E13.5a vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 18

description: censored

source_name: tumor tissue, patient 18


title: Human Whole blood RNA 72


title: human pancreatic nontumor tissue, patient sample 18

description: censored

source_name: non-tumor tissue, patient 18


title: human pancreatic nontumor tissue, patient sample 19

description: cancer related death

source_name: non-tumor tissue, patient 19


title: E13.5b vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 20

description: cancer related death

source_name: tumor tissue, patient 20


title: adult-midbrain-1 vs. E12.5c


title: E12.5b vs. adult-midbrain-1


title: Human Whole blood RNA 68


title: adult-midbrain-1 vs. E13.5a


title: adult-midbrain-1 vs. E12.5a


title: E12.5c vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 17

description: censored

source_name: tumor tissue, patient 17


title: Human Whole blood RNA 67


title: Human Whole blood RNA 65


title: E11.5c vs. adult-midbrain-1


title: human pancreatic nontumor tissue, patient sample 15

description: cancer related death

source_name: non-tumor tissue, patient 15


title: human pancreatic tumor tissue, patient sample 15

description: cancer related death

source_name: tumor tissue, patient 15


title: Human Whole blood RNA 66


title: adult-midbrain-1 vs. E11.5c


title: human pancreatic tumor tissue, patient sample 14

description: cancer related death

source_name: tumor tissue, patient 14


title: Human Whole blood RNA 62


title: adult-midbrain-1 vs. E11.5b


title: human pancreatic tumor tissue, patient sample 16

description: cancer related death

source_name: tumor tissue, patient 16


title: human pancreatic nontumor tissue, patient sample 13

description: cancer related death

source_name: non-tumor tissue, patient 13


title: Human Whole blood RNA 63


title: E11.5b vs. adult-midbrain-1


title: Human Whole blood RNA 61


title: human pancreatic nontumor tissue, patient sample 14

description: cancer related death

source_name: non-tumor tissue, patient 14


title: E12.5a vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 13

description: cancer related death

source_name: tumor tissue, patient 13


title: human pancreatic nontumor tissue, patient sample 16

description: cancer related death

source_name: non-tumor tissue, patient 16


title: adult-midbrain-1 vs. E11.5a


title: adult-midbrain-1 vs. E10.5c


title: Human Whole blood RNA 60


title: E11.5a vs. adult-midbrain-1


title: human pancreatic tumor tissue, patient sample 12

description: cancer related death

source_name: tumor tissue, patient 12


title: Human Whole blood RNA 59


title: E10.5c vs. adult-midbrain-1


title: Human Whole blood RNA 57

source_name: CONTROL_whole blood


title: human pancreatic nontumor tissue, patient sample 12

description: cancer related death

source_name: non-tumor tissue, patient 12


title: Human Whole blood RNA 58


title: human pancreatic nontumor tissue, patient sample 11

description: cancer related death

source_name: non-tumor tissue, patient 11


title: Yolksac endoderm_Day4_1

city: Kobe

first: Fumie

last: Nakazawa

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

country: Japan

institute: Center for Developmental Biology, RIKEN

description: Pooled samples collected at every 4 hours over 1 day

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Gallus gallus

source_name: Day4 Yolksac endoderm

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

growth_protocol: Fertilized hens’ eggs were incubated at 38°C in a humid incubator to the desired stages.

extract_protocol: Total RNA from endodermal tissues were isolated with using Qiagen RNAeasy Mini-Kit. RNA concentrations were measured and equalized, and RNA quality was checked on gel. 5 ug of total RNA were used for each array.

treatment_protocol: The yolksac tissue from Day 1, 2, 3, and 4 was dissected with 27G needle. After treatment with dispase in Pannett-Compton saline for 5 minutes at room temperature, endoderm tissues were separated from the mesoderm layer and used for further experiments. Collected tissues were stored at -80 ˚C.

value: Yolksac Endoderm

tag: Stage

value: Embryonic Day 4


title: Human Whole blood RNA 56

value: female

tag: tissue


title: human pancreatic tumor tissue, patient sample 11

description: cancer related death

source_name: tumor tissue, patient 11


title: adult-midbrain-1 vs. E10.5b


title: E10.5b vs. adult-midbrain-1


title: Human Whole blood RNA 54

tag: age

value: whole blood


title: human pancreatic nontumor tissue, patient sample 10

description: cancer related death

source_name: non-tumor tissue, patient 10


title: adult-midbrain-1 vs. E10.5a


title: E10.5a vs. adult-midbrain-1


title: Human Whole blood RNA 55

tag: gender


title: human pancreatic tumor tissue, patient sample 10

description: cancer related death

source_name: tumor tissue, patient 10


title: Yolksac endoderm_Day4_2


title: human pancreatic nontumor tissue, patient sample 9

description: no survival information, removed from cox regression analysis

source_name: non-tumor tissue, patient 9


title: Yolksac endoderm_Day2_2

source_name: Day2 Yolksac endoderm

value: Embryonic Day 2


title: Yolksac endoderm_Day3_2

source_name: Day3 Yolksac endoderm

value: Embryonic Day 3


title: BMDC, Asc-/-, replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 5 micrograms of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Probe level normalization and signal summarization was performed using the Robust Multi-chip Algorithm (RMA) as implemented in the Affymetrix Expression Console software version 1.1

source_name: BMDC, Asc-/-

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Bone marrow cells were isolated from the femurs of mice and in vitro cultured for seven days. Cell were induced to differentiate into BMDCs using 20ng/ml of GM-CSF for seven days.

extract_protocol: RNA was extracted using the Trizol method (Invitrogen)

treatment_protocol: Bone marrow cells were cultured in RPMI growth media containing 10% Fetal bovine serum and in the presence of GM-CSF (20 ng/ml). Cell culture medium was replenished with fresh medium every two days. On day 7 cells were used for isolation of RNA using the Trizol method.

tag: strain

tag: genotype/variation

value: Asc -/-

value: bone marrow derived dendritic cells


title: Yolksac endoderm_Day2_1


title: DNA obtained from the supernatant of SW480 cell cultures [Mapping250K_Nsp]

source_name: SW480 cell culture supernatant

value: colon adenocarcinoma


title: DNA from the SW480 cell line [Mapping250K_Nsp]

source_name: SW480 cells


title: BMDC, Asc-/-, replicate 2


title: human pancreatic tumor tissue, patient sample 9

source_name: tumor tissue, patient 9


title: human pancreatic nontumor tissue, patient sample 8

source_name: non-tumor tissue, patient 8


title: Human Whole blood RNA 53

source_name: schizophrenia (SCZ)_whole blood

value: male

tag: status

value: schizophrenia (SCZ)


title: Yolksac endoderm_Day3_1


title: human pancreatic tumor tissue, patient sample 8

source_name: tumor tissue, patient 8


title: human pancreatic tumor tissue, patient sample 7

description: cancer related death

source_name: tumor tissue, patient 7


title: Yolksac endoderm_Day1_1

source_name: Day1 Yolksac

value: Embryonic Day 1


title: BMDC, wt, replicate 3

source_name: BMDC, wt

value: wild type


title: Human Whole blood RNA 50

source_name: CONTROL_whole blood

value: CONTROL


title: BMDC, wt, replicate 2


title: Human Whole blood RNA 51


title: Yolksac endoderm_Day1_2


title: Human Whole blood RNA 49


title: human pancreatic nontumor tissue, patient sample 7

description: cancer related death

source_name: non-tumor tissue, patient 7

value: N


title: BMDC, Asc-/-, replicate 1


title: BMDC, wt, replicate 1


title: human pancreatic tumor tissue, patient sample 6

description: cancer related death

source_name: tumor tissue, patient 6

value: T


title: human pancreatic nontumor tissue, patient sample 6

description: cancer related death

source_name: non-tumor tissue, patient 6


title: human pancreatic nontumor tissue, patient sample 5

source_name: non-tumor tissue, patient 5


title: Human Whole blood RNA 48


title: Human Whole blood RNA 46


title: human pancreatic tumor tissue, patient sample 5

source_name: tumor tissue, patient 5


title: Human Whole blood RNA 47


title: Human Whole blood RNA 37

data_processing: Data were backgroundcorrected in Beadstudio (v.3.2.3) and transformed (vst) and normalised (rsn) in Lumi (R package)

source_name: CONTROL_Whole blood

value: Whole blood


title: Human Whole blood RNA 45


title: Human Whole blood RNA 36


title: Human Whole blood RNA 34


title: Human Whole blood RNA 35


title: Human Whole blood RNA 33

source_name: schizophrenia (SCZ)_Whole blood


title: Human Whole blood RNA 44


title: human pancreatic nontumor tissue, patient sample 4

description: cancer related death

source_name: non-tumor tissue, patient 4


title: Human Whole blood RNA 32


title: Human Whole blood RNA 64


title: human pancreatic tumor tissue, patient sample 4

description: cancer related death

source_name: tumor tissue, patient 4


title: Human Whole blood RNA 31


title: human pancreatic nontumor tissue, patient sample 3

description: cancer related death

source_name: non-tumor tissue, patient 3


title: human pancreatic nontumor tissue, patient sample 2

description: cancer related death

source_name: non-tumor tissue, patient 2


title: Human Whole blood RNA 42

source_name: schizophrenia (SCZ)_whole blood


title: Human Whole blood RNA 28


title: Human Whole blood RNA 41


title: Human Whole blood RNA 29


title: Human Whole blood RNA 27


title: Human Whole blood RNA 39


title: Human Whole blood RNA 30


title: human pancreatic tumor tissue, patient sample 1

description: cancer related death

source_name: tumor tissue, patient 1


title: Human Whole blood RNA 25


title: Human Whole blood RNA 40


title: human pancreatic tumor tissue, patient sample 3

description: cancer related death

source_name: tumor tissue, patient 3


title: ER:Ras-IMR90 cells 4OHT day 6 replicate 4

city: Cambridge

first: Rafik

last: Salama

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor.

source_name: IMR90 human diploid fibroblasts, 100nM 4OHT for 6d

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: DMEM supplemented with 10% FBS and antibiotics in 5% oxygen

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras

tag: treatment

tag: transgene


title: Human Whole blood RNA 26


title: Human Whole blood RNA 38


title: Human Whole blood RNA 24


title: human pancreatic nontumor tissue, patient sample 1

description: cancer related death

source_name: non-tumor tissue, patient 1


title: human pancreatic tumor tissue, patient sample 2

description: cancer related death

source_name: tumor tissue, patient 2


title: Human Whole blood RNA 21


title: ER:Ras-IMR90 cells 4OHT day 6 replicate 1

tag: cell line


title: ER:Ras-IMR90 cells 4OHT day 6 replicate 2


title: Human Whole blood RNA 20


title: ER:Ras-IMR90 cells 4OHT day 6 replicate 5


title: Human Whole blood RNA 23


title: Human Whole blood RNA 16


title: ER:Ras-IMR90 cells no 4OHT replicate 2

source_name: IMR90 human diploid fibroblasts, no 4OHT

value: no 4OHT


title: Human Whole blood RNA 19


title: ER:Ras-IMR90 cells no 4OHT replicate 1


title: ER:Ras-IMR90 cells 4OHT day 6 replicate 3


title: Human Whole blood RNA 18


title: Human Whole blood RNA 43


title: ER:Ras-IMR90 cells no 4OHT replicate 5


title: Human Whole blood RNA 17


title: Human Whole blood RNA 15


title: Human Whole blood RNA 14


title: Human Whole blood RNA 12


title: ER:Ras-IMR90 cells no 4OHT replicate 3


title: hMABs0203

city: Modena

first: Enrico

last: Tagliafico

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

description: Wild Type human mesoangioblasts from vastus lateralis muscle

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix Standard

data_processing: The data were analyzed using several R (Bioconductor) packages and with Partek GS

source_name: WT adult skeletal muscle derived mesoangioblasts (control)

label_protocol: Affymetrix 3' IVT

growth_protocol: Cells were grown in ISCOVE's modified DMEM, 10% Foetal bovine serum, 1% L-glutammine, 1% non essential amminoacids, 5ng/ul Basic FGF, 0,1mM 2-Mercaptoethanol, 1% ITS, 0,5uM Oleic acid, 0,5uM Linoleic acid, 1,5uM Fe++, 0,12uM Fe+++

extract_protocol: Total cellular RNA was isolated from HIDEMs and MABs using RNeasy RNA isolation kit (Qiagen, USA) following manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer. cDNA synthesis, biotin-labeled target synthesis, HG-U133 plus 2.0 GeneChip (Affymetrix, USA) arrays hybridization, staining and scanning were performed according to the standard protocol supplied by Affymetrix.

treatment_protocol: Cells were trypsinized for 5 minutes, then centrifuged for 5 minutes at 232g to obtain a pellet. Pellet were dryed and stored at -80°C before processing.

tag: cell type

value: human mesoangioblasts

tag: cell origin

value: Wild Type human mesoangioblasts from rectus femoralis muscle


title: hMABs0202

value: Wild Type human mesoangioblasts from left vastus lateralis muscle


title: hMABs0201


title: HIDEMs Pt.1

description: LGMD2D HIDEMs Pt.1

source_name: Limb-girdle muscular dystrophy 2D (LGMD2D) HIDEMs

value: human iPS cell-derived mesoangioblasts (HIDEMs)

value: HIDEMs derived from iPSCs generated from LGMD2D skeletal muscle (vastus lateralis)-derived cells


title: Human Whole blood RNA 13


title: ER:Ras-IMR90 cells no 4OHT replicate 4

value: female


title: Human Whole blood RNA 11


title: HDAC3 -/-, LPS 4h, replicate 1

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used to prepare the Hybridization Cocktail. The kit contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. These control oligos serve as positive controls for hybridization. Biotin-labeled sense targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 C for 5 minutes. Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to loading into the GeneChip array cartridge. Hybridizations were performed for 16 h at 45C in a rotisserie oven at 60 RPM. Upon hybridization, GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol. The cartridge is then loaded into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are scanned using default parameters. Affymetrix GeneChip Command Console software (AGCC) was used to acquire GeneChip images and generate .DAT and .CEL files.

data_processing: CELs files were imported into R, RMA normalized and annotated using the Affy package.

source_name: HDAC3 -/-, LPS 4h

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA. Double stranded cDNA synthesis and related cRNA amplification was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the protocol were performed according to manufacturer’s specifications. Efficacy of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: RNeasy from Qiagen with DNAse I treatment

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 100 ng/ml)

value: knockout (HDAC3 -/-)

value: Primary bone marrow-derived macrophages (BMDM) cells (7th day of differentiation)

value: LPS (100 ng/ml) for 4hrs


title: HIDEMs #1

description: WT HIDEMs Donor no.1

source_name: WT HIDEMs

value: HIDEMs derived from iPSCs generated from WT IMR90 fibroblasts


title: HDAC3 -/-, LPS 4h, replicate 3


title: Human Whole blood RNA 52

value: schizophrenia (SCZ)

value: whole blood


title: HDAC3 -/-, LPS 4h, replicate 2


title: HIDEMs #4

description: WT HIDEMs Donor no.4

value: HIDEMs derived from iPSCs generated from WT skeletal muscle-derived cells

value: male


title: HDAC3 -/-, untreated, replicate 3

source_name: HDAC3 -/-, untreated

value: No treatment


title: HIDEMs Pt.4

description: LGMD2D HIDEMs Pt.4

value: HIDEMs derived from iPSCs generated from LGMD2D skeletal muscle (tibialis anterior)-derived cells


title: Human Whole blood RNA 8

source_name: CONTROL_Whole blood

value: CONTROL

value: Whole blood


title: HIDEMs VIF

description: WT viral integration free HIDEMs

value: HIDEMs derived from commercial WT Viral Integration-Free episomal human iPSCs (Gibco; A1377)


title: Human Whole blood RNA 10

source_name: schizophrenia (SCZ)_Whole blood


title: Human Whole blood RNA 7


title: HDAC3 -/-, untreated, replicate 2


title: HDAC3 -/-, untreated, replicate 1


title: Human Whole blood RNA 4


title: Single embryo_Day3_6_E7

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

country: France

institute: INSERM

hyb_protocol: Following fragmentation and turbo labeling (Arcturus), cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Human embryo_Day 3_6

label_protocol: Complementary RNA (cRNA) was prepared through three rounds of linear amplification according to the manufacturer’s protocol (Arcturus), starting from 450 pg to 855 pg total RNA obtained from a single embryo.

extract_protocol: Total RNA was isolated using Picopure RNA isolation kit (Arcturus Reagents/Molecular Devices, KIT0204, USA) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

value: Day 3 embryo


title: HDAC3 +/-, LPS 4h, replicate 1

source_name: HDAC3 +/-, LPS 4h

value: wild type (HDAC3 +/-)


title: Human Whole blood RNA 5


title: Human Whole blood RNA 6


title: HDAC3 +/-, LPS 4h, replicate 2


title: Single embryo_Day3_4_E3

source_name: Human embryo_Day 3_4


title: P. putida DIMBOA exposure replicate 3

city: Harpenden

first: Andrew

middle: L

last: Neal

state: Herts

address: West Common

institute: Rothamsted Research

description: Biological replicate 3 of 3. Technical (dye swap) replicates have been merged (the original data prior to merging was not available for submission to GEO).

hyb_protocol: Microarrays were pre-treated with BlockIt™ Plus blocking buffer (Arrayit Corporation, Sunnyvale, CA).  Dried cDNA was rehydrated in buffer and hybridised to arrays (Progenika Biopharma S.A, Vizcaya, Spain) for 18 hours at 42 °C, according to the manufacturer’s instructions.

scan_protocol: Scanned on a GenePix® 4000B scanner (Molecular Devices, Sunnyvale, CA). Collected images assessed with GenePix Pro software

data_processing: LOWESS normalised, background subtracted data obtained from log2 of processed Red signal/processed Green signal. TM4 software was used. Data evaluated using Statistical Analysis for Microarrays routine using a false discovery rate of 0.85% (Δ = 1.2)

label: Cy3, HyPer5

organism: Pseudomonas putida KT2440

source_name: control

label_protocol: Synthesised cDNA paired samples (control or DIMBOA) were labelled with Cy3 or HyPer5 (Amersham, Little Chalfont, UK) fluorophores. To remove dye bias, the experimental design included dye-swap normalisation procedures.  Dye incorporation was verified to be more than 150 pmol dye per sample.  Equal amounts of Cy3-cDNA and HyPer5-cDNA, each representing a replicate comparison between control and DIMBOA-treated cells, were combined and dried in a speedvac before proceeding with array hybridisation.

growth_protocol: Cells grown to mid-exponential phase in M9 medium at 21 °C before being exposed to 5 μg/mL DIMBOA for 1 hour before harvesting.

extract_protocol: Cells were harvested by centrifugation at 4 °C. Cell pellets were treated with RNAprotect™ (Qiagen, Valencia CA) immediately following centrifugation.  Cell membrane lysis was achieved with 1 mg/mL lysozyme in TE buffer at pH8 using Qiagen RNeasy® reagent kits following the manufacturer’s instructions.  RNA purified with TURBO DNA-free™ kits (Ambion, Applied Biosystems, Foster City, CA) and quantified on a NanoDrop 1000 spectrophotometer.

treatment_protocol: Exposure to 5 μg/mL DIMBOA in M9 growth medium for 1 hour

label: HyPer5, Cy3

source_name: DIMBOA exposure


title: HDAC3 +/-, LPS 4h, replicate 3


title: P. putida DIMBOA exposure replicate 2

description: Biological replicate 2 of 3. Technical (dye swap) replicates have been merged (the original data prior to merging was not available for submission to GEO).


title: HDAC3 +/-, untreated, replicate 2

source_name: HDAC3 +/-, untreated


title: Human Whole blood RNA 3


title: Single embryo_Day3_5_E5

source_name: Human embryo_Day 3_5


title: HDAC3 +/-, untreated, replicate 3


title: HDAC3 +/-, untreated, replicate 1


title: Single embryo_Day3_2_D1E2

source_name: Human embryo_Day 3_2


title: P. putida DIMBOA exposure replicate 1

description: Biological replicate 1 of 3. Technical (dye swap) replicates have been merged (the original data prior to merging was not available for submission to GEO).


title: Human Whole blood RNA 1


title: Human Whole blood RNA 2


title: Single embryo_Day3_1_D1E1

source_name: Human embryo_Day 3_1


title: Single embryo_Day3_3_E2

source_name: Human embryo_Day 3_3


title: Primary breast tumor_16_Reps 1and2

status: Public on Jul 07 2012

city: Stanford

first: Peter

middle: P.

last: Lee

state: CA

address: CCSR room 1155, 269 Campus Drive

department: Department of Medicine

institute: Stanford University

description:
Dyeswap pair: P16_Rep1 and P16_Rep2
raw data file: 251485025890_1.txt
raw data file: 251485025890_2.txt

hyb_protocol: 825ng labeled sample aRNA and 825ng reverse color-labeled Stratagene universal human reference aRNA were mixed, and fragmented using the Agilent Fragmentation buffer for 30 mins at 60°C. Agilent hybridization buffer was added, and a total of 100ul target solution was hybridized onto Agilent Whole Human Genome Microarray 4x44k using the SureHyb (Agilent) assembly and incubated at 60°C at 10rpm for 17 hours. The arrays were washed and dried according to the Agilent SSPE wash protocol.

scan_protocol: Scanned on Agilent Microarray Scanner G2505B.

data_processing: The data was extracted from the images using the Agilent Feature Extraction Software (version 9.5.1). Quantile normalization and LOESS normalization were used to normalize the raw data. Dye swap pairs have been averaged during the normalization process. All arrays were calibrated to the same scale and variance stabilizing transformation was applied to the data. After normalization, the generalized log2 ratio values for each gene were taken to obtain a relative expression level in samples over the Stratagene universal human reference.

source_name: primary tumor cells  from patient #16

label_protocol: Total RNA was amplified using TrueLabeling-PicoAMPTM kit (QIAGEN). aRNA was labeled with 20,000pmol Cy Dye Post Labeling Reactive Dyes  (GE Healthcare) at room temperature for 30 mins followed by addition of hydroxylamine to 0.18M to quench unreacted dye, for 15 mins at room temperature protected from light. Labeled aRNA was purified using the RNeasy MinElute Cleanup kit (Qiagen).

extract_protocol: Total RNA was extracted using the TRIzoL method according to the manufacturer's protocol. RNA quantity and quality were checked using the Nanodrop ND1000A spectrophotometer (Nanodrop Technologies, DE, USA) and the RNA 6000 Pico LabChip assay using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: Fresh breast tumors and tumor positive lymph nodes were minced and enzymatically dissociated with 200units/ml type III Collagenase (Worthington Biochemical Corp.) and 10Kunitz units/ml DNase I (Sigma) for 30 minutes to 1 hour at 37°C. The digestion process was stopped by addition of M199 media containing 10% FBS. Single cell suspensions were generated by filtering cells through a 70 micron cell strainer followed by a 40 micron cell strainer (BD Biosciences). Cells were stained with pan-leukocyte marker CD45 PE-Cy7, fibroblast marker CD140β PE (both BD Biosciences), epithelial specific antigen ESA FITC (Biolegend), and a dead cell exclusion marker ViViD (Invitrogen). ESA+CD45-CD140β- cells were sorted using FACSAria (BD Bioscience) and homogenized in 1.3mL TRIzol reagent (Invitrogen).

tag: patient

value: breast tumor tissue

value: tumor cells

source_name: Stratagene universal human reference

tag: sample type

value: reference


title: Human Whole blood RNA 22


title: Primary breast tumor_15_Reps 1and2

description:
Dyeswap pair: P15_Rep1 and P15_Rep2
raw data file: 251485020028_3.txt
raw data file: 251485020028_4.txt

source_name: primary tumor cells  from patient #15


title: Primary breast tumor_09_Reps 1and2

description:
Dyeswap pair: P09_Rep1 and P09_Rep2
raw data file: 251485025872_3.txt
raw data file: 251485025872_4.txt

source_name: primary tumor cells  from patient #09


title: Primary breast tumor cell_03_Reps 1and2

description:
Dyeswap pair: P03_Rep1 and P03_Rep2
raw data file: 251485025842_1.txt
raw data file: 251485025842_2.txt

source_name: primary tumor cells from patient #03


title: lymphocytic cell line B958

city: Guangzhou

first: bijun

last: huang

address: 651#Dongfeng East Road

department: State Key Laboratory of Oncology in Southern China

country: China

institute: Cancer Center, Sun Yat-Sen University, Guangzhou, China

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: EBV positive lymphocytic cell line

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

value: lymphocytic cell line


title: lymphocytic cell line Akata

value: Akata(+)


title: lymphocytic cell line Daudi

value: Daudi


title: lymphocytic cell line Namalwa

value: Namalwa


title: LN metastatic tumor cell 4.1_Reps 1and2

description:
Dyeswap pair: M4.1_Rep1 and M4.1_Rep2
raw data file: 251485020244_3.txt
raw data file: 251485020244_4.txt

source_name: lymph node metastatic tumor cells from patient #04

value: lymph node metastasis


title: LN metastatic tumor cell_03_Reps 1and2

description:
Dyeswap pair: M03_Rep1 and M03_Rep2
raw data file: 251485025843_1.txt
raw data file: 251485025843_2.txt

source_name: lymph node metastatic tumor cells from patient #03


title: Primary breast tumor_13_Reps 1and2

description:
Dyeswap pair: P13_Rep1 and P13_Rep2
raw data file: 251485020793_3.txt
raw data file: 251485020793_4.txt

source_name: primary tumor cells  from patient #13


title: Primary breast tumor_14_Reps 1and2

description:
Dyeswap pair: P14_Rep1 and P14_Rep2
raw data file: 251485020666_3.txt
raw data file: 251485020666_4.txt

source_name: primary tumor cells  from patient #14


title: corresponding adjacent normal tissue of patient No.49

city: Shanghai

first: qinsong

last: zeng

address: 168 Changhai Road

institute: Changhai Hospital

description: Gene expression data from corresponding adjacent normal tissue

hyb_protocol: The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.

scan_protocol: Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.

data_processing: The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant and median summarized.

source_name: MIBC

label_protocol: A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).

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

value: Male

tag: bc tumor stage

tag: ethnic group

value: Chinese Han

value: bladder

value: corresponding adjacent normal tissue

tag: patient no


title: Primary breast tumor_17_Reps 1and2

description:
Dyeswap pair: P17_Rep1 and P17_Rep2
raw data file: 251485033319_1.txt
raw data file: 251485033319_2.txt

source_name: primary tumor cells  from patient #17


title: LN metastatic tumor cell 4.2_Reps 1and2

description:
Dyeswap pair: M4.2_Rep1 and M4.2_Rep2
raw data file: 251485020245_3.txt
raw data file: 251485020245_4.txt


title: corresponding adjacent normal tissue of patient No.21

value: Chinese Han people


title: LN metastatic tumor cell_02_Reps 1and2

description:
Dyeswap pair: M02_Rep1 and M02_Rep2
raw data file: 251485033402_1.txt
raw data file: 251485033402_2.txt

source_name: lymph node metastatic tumor cells from patient #02


title: Primary breast tumor_10_Reps 1and2

description:
Dyeswap pair: P10_Rep1 and P10_Rep2
raw data file: 251485025870_3.txt
raw data file: 251485025870_4.txt

source_name: primary tumor cells  from patient #10


title: corresponding adjacent normal tissue of patient No.34


title: Primary breast tumor_01_Reps 1and2

description:
Dyeswap pair: P01_Rep1 and P01_Rep2
raw data file: 251485020665_3.txt
raw data file: 251485020665_4.txt

source_name: primary tumor cells from patient #01


title: LN metastatic tumor cell_06_Reps 1and2

description:
Dyeswap pair: M06_Rep1 and M06_Rep2
raw data file: 251485033385_1.txt
raw data file: 251485033385_2.txt

source_name: lymph node metastatic tumor cells from patient #06


title: Primary breast tumor_12_Reps 1and2

description:
Dyeswap pair: P12_Rep1 and P12_Rep2
raw data file: 251485025845_3.txt
raw data file: 251485025845_4.txt

source_name: primary tumor cells  from patient #12


title: lymphocytic cell line Raji

value: Raji


title: Primary breast tumor_07_Reps 1and2

description:
Dyeswap pair: P07_Rep1 and P07_Rep2
raw data file: 251485020791_1.txt
raw data file: 251485020791_2.txt

source_name: primary tumor cells  from patient #07


title: LN metastatic tumor cell_01_Reps 1and2

description:
Dyeswap pair: M01_Rep1 and M01_Rep2
raw data file: 251485020254_3.txt
raw data file: 251485020254_4.txt

source_name: lymph node metastatic tumor cells from patient #01

source_name: Stratagene universal human reference


title: Primary breast tumor_02_Reps 1and2

description:
Dyeswap pair: P02_Rep1 and P02_Rep2
raw data file: 251485033401_1.txt
raw data file: 251485033401_2.txt

source_name: primary tumor cells  from patient #02


title: corresponding adjacent normal tissue of patient No.20


title: corresponding adjacent normal tissue of patient No.10


title: NPC cell line CNE2

source_name: EBV negetive NPC cell line

value: NPC cell line


title: NPC cell line C666-1

source_name: EBV positive NPC cell line


title: Primary breast tumor_11_Reps 1and2

description:
Dyeswap pair: P11_Rep1 and P11_Rep2
raw data file: 251485020027_3.txt
raw data file: 251485020027_4.txt

source_name: primary tumor cells  from patient #11


title: NPC case NPC11

source_name: Nasopharyngeal carcinoma

value: NPC tumor


title: NPC case NPC28


title: Primary breast tumor_08_Reps 1and2

description:
Dyeswap pair: P08_Rep1 and P08_Rep2
raw data file: 251485020795_3.txt
raw data file: 251485020795_4.txt

source_name: primary tumor cells  from patient #08


title: nup42-delta 0.7M NaCl t30

city: Madison

first: Suraiya

middle: Ruma

last: Haroon

state: WI

address: 425 Henry Mall

department: Genetics

institute: University of Wisconsin - Madison

description:
Sample name: nup42-delta 0.7M NaCl t30 vs BY4741 memory t0
Compare the gene expression of cells exposed to 30min of 0.7M NaCl to basal levels in nup42-delta

hyb_protocol: cDNA labeled with Oyster cyanine 650 dye and cDNA from second sample labelled with Oyster cyanine 650 dye  were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner

data_processing:
Data were extracted using NimblegenScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots. The remaining data was quantile normalized using Bioconductor.
normalized, log2 expression ratios (Oyster cyanine 650 dye/Oyster 550 cyanine dye).  All values have been adjusted such that a positive log2 value = induced by by treatment (NaCl or H2O2), and a negative log2 value = repressed by treatment (or expressed lower in NaCl or H2O2 treatment)

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: BY4741 grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

value: BY4741 strain

label: Oyster cyanine 650 dye

source_name: nup42-delta grown in log phase for at least 7 generations, treated with 30min of 0.7M NaCl

treatment_protocol: treated with 30min of 0.7M NaCl

value: nup42-delta in BY4741 strain


title: BY4741 0.7M NaCl t30

description:
Sample name: BY4741 0.7M NaCl t30 vs BY4741T0
Compare the gene expression of cells exposed to 30min of 0.7M NaCl to basal levels in BY4741

source_name: BY4741 grown in log phase for at least 7 generations, treated with 30min of 0.7M NaCl


title: MIBC tissue of patient No.34

description: Gene expression data from MIBC tissue

source_name: MIBC

value: MIBC


title: corresponding adjacent normal tissue of patient No.63

source_name: NMIBC

value: Ta


title: MIBC tissue of patient No.21

description: Gene expression data from MIBC tissue


title: MIBC tissue of patient No.10

description: Gene expression data from MIBC tissue


title: HIDEMs Pt.3

description: LGMD2D HIDEMs Pt.3

source_name: Limb-girdle muscular dystrophy 2D (LGMD2D) HIDEMs

value: human iPS cell-derived mesoangioblasts (HIDEMs)

value: HIDEMs derived from iPSCs generated from LGMD2D skeletal muscle (vastus lateralis)-derived cells

value: female


title: Poplar_Whole Stem-rep1

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

country: South Korea

institute: Kyung Hee University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus trichocarpa

source_name: Whole Stem from poplar-rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Poplar (Populus trichocarpa) were grown on field (nursery bed).

value: Whole Stem from poplar

tag: genotype

value: Populus trichocarpa

value: one-year-old field grown poplar


title: MIBC tissue of patient No.20

description: Gene expression data from MIBC tissue

value: Male

value: Chinese Han

tag: tissue


title: MIBC tissue of patient No.49

description: Gene expression data from MIBC tissue

tag: age

value: bladder


title: nup42-delta memory 0.4mM H2O2 t20

description:
Sample name: nup42-delta memory t20 vs nup42-delta memory t0
Compare the gene expression of pretreated cells exposed to 20 min of 0.4 mM H2O2 compared to basal gene expression in nup42-delta

source_name: nup42-delta grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours, then exposed to 0.4mM H2O2 for 20min


title: SCG tissue, biological rep4

city: Athens

first: William

last: Kisaalita

state: GA

address: Dritmier Engineering Center

institute: University of Georgia

description: Gene expression data from SCG tissue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned on Affymetrix scanner 3000 with 7G upgrade

data_processing: The data were analyzed with Affymetrix expression console using Robust Multichip Average (RMA) method with Affymetrix default analysis settings and global scaling as normalization method.

source_name: SCG cells from freshly dissected tissue

label_protocol: Labelled 2 ug Total RNA according to Eberwine protocol using Target Amp kit, Epicentre(Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from all samples using Qiagen RNeasy Kits (Qiagen,Valencia, CA) according to the manufacturer’s standard protocol.

value: 21 days

value: superior cervical ganglion


title: Poplar_Mature Xylem-rep1

source_name: Mature Xylem from poplar stem-rep1

value: Mature Xylem from poplar stem


title: Poplar_Whole Stem-rep2

source_name: Whole Stem from poplar-rep2


title: SCG tissue, biological rep3

description: Gene expression data from SCG tissue


title: Human Whole blood RNA 9

city: Los Angeles

first: Simone

last: de Jong

address: 695 Charles E. Young Drive south

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: CONTROL_Whole blood

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

extract_protocol: Standard Qiagen PAXgene extraction (manual and Qiacube)

tag: gender

value: CONTROL

value: Whole blood


title: Poplar_Shoot and Leaf primordia-rep2

source_name: Shoot and Leaf primordia from poplar-rep2

value: Shoot and Leaf primordia from poplar


title: Poplar_Mature Leaf-rep1

source_name: Mature Leaf without major vein from poplar-rep1


title: Poplar_Mature Xylem-rep2

source_name: Mature Xylem from poplar stem-rep2


title: Poplar_Shoot and Leaf primordia-rep1

source_name: Shoot and Leaf primordia from poplar-rep1


title: Poplar_Mature Leaf-rep2

source_name: Mature Leaf without major vein from poplar-rep2


title: corresponding adjacent normal tissue of patient No.24

value: corresponding adjacent normal tissue


title: nup42-delta memory 0.4mM H2O2 t10

description:
Sample name: nup42-delta memory t10 vs nup42-delta memory t0
Compare the gene expression of pretreated cells exposed to 10 min of 0.4 mM H2O2 compared to basal gene expression in nup42-delta

tag: strain

value: nup42-delta in BY4741 strain

source_name: nup42-delta grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours, then exposed to 0.4mM H2O2 for 10 min


title: nup42-delta 0.4mM H2O2 t20

description:
Sample name: nup42-delta naïve t20 vs nup42-delta memory t0
Compare the gene expression of cells exposed to 20 min of 0.4 mM H2O2 compared to basal gene expression in nup42-delta

source_name: nup42-delta grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours

source_name: nup42-delta grown in log phase for at least 7 generations, then exposed to 0.4mM H2O2 for 20min

treatment_protocol: exposed to 0.4mM H2O2 for 20min


title: SCG tissue, biological rep1

description: Gene expression data from SCG tissue


title: BY4741 memory 0.4mM H2O2 t20

description:
Sample name: BY4741 memory t20 vs BY4741T0
Compare the gene expression of pretreated cells exposed to 20 min of 0.4 mM H2O2 compared to basal gene expression in BY4741

value: BY4741 strain

source_name: BY4741 grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours, then exposed to 0.4mM H2O2 for 20min


title: nup42-delta 0.4mM H2O2 t10

description:
Sample name: nup42-delta naïve t10 vs nup42-delta memory t0
Compare the gene expression of cells exposed to 10 min of 0.4 mM H2O2 compared to basal gene expression in nup42-delta

treatment_protocol: treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours

source_name: nup42-delta grown in log phase for at least 7 generations, then exposed to 0.4mM H2O2 for 10min

treatment_protocol: exposed to 0.4mM H2O2 for 10min


title: BY4741 memory 0.4mM H2O2 t10

description:
Sample name: BY4741 memory t10 vs BY4741T0
Compare the gene expression of pretreated cells exposed to 10 min of 0.4 mM H2O2 compared to basal gene expression in BY4741

source_name: BY4741 grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours, then exposed to 0.4mM H2O2 for 10 min


title: corresponding adjacent normal tissue of patient No.23

description: Gene expression data from corresponding adjacent normal tissue

source_name: NMIBC

value: Ta


title: NMIBC tissue of patient No.63

description: Gene expression data from NMIBC tissue

value: NMIBC


title: 3D SCG cells, biological rep4

description: Gene expression data from 3D cultured SCG cells

source_name: SCG cells cultured in 3D polystyrene scaffolds


title: BY4741 0.4mM H2O2 t20

description:
Sample name: BY4741 naive t20 vs BY4741T0
Compare the gene expression of cells exposed to 20 min of 0.4 mM H2O2 compared to basal gene expression in BY4741

source_name: BY4741 grown in log phase for at least 7 generations, then exposed to 0.4mM H2O2 for 20min


title: Poplar_Developing Xylem-rep2

source_name: Developing Xylem from poplar stem-rep2

value: Developing Xylem from poplar stem


title: 3D SCG cells, biological rep2


title: 2D SCG cells, biological rep4

description: Gene expression data from 2D cultured SCG cells

source_name: SCG cells cultured on 2D substrate (polystyrene Petri dish)


title: 3D SCG cells, biological rep1


title: SCG tissue, biological rep2

description: Gene expression data from SCG tissue

source_name: SCG cells from freshly dissected tissue


title: corresponding adjacent normal tissue of patient No.19


title: 3D SCG cells, biological rep3


title: NMIBC tissue of patient No.23

description: Gene expression data from NMIBC tissue


title: NMIBC tissue of patient No.24

description: Gene expression data from NMIBC tissue


title: corresponding adjacent normal tissue of patient No.7


title: Poplar_Developing Phloem-rep2

source_name: Developing Phloem from poplar stem-rep2

value: Developing Phloem from poplar stem

value: Populus trichocarpa


title: Poplar_Cambium-rep2

source_name: Cambium from poplar stem-rep2

value: Cambium from poplar stem

value: one-year-old field grown poplar


title: Poplar_Developing Phloem-rep1

source_name: Developing Phloem from poplar stem-rep1


title: Poplar_Developing Xylem-rep1

source_name: Developing Xylem from poplar stem-rep1


title: nup42-delta basal

description:
Sample name: BY4741 T0 vs nup42-delta T0
Compare the expression of basal gene expression in nup42-delta cells compared to BY4741 cells

source_name: BY4741 grown in log phase for at least 7 generations

source_name: nup42-delta grown in log phase for at least 7 generations


title: 2D SCG cells, biological rep2


title: NMIBC tissue of patient No.7

description: Gene expression data from NMIBC tissue

value: Male

value: Chinese Han

value: bladder


title: Poplar_Cambium-rep1

source_name: Cambium from poplar stem-rep1


title: Poplar_Bark and mature phloem-rep2

source_name: Bark and mature phloem from poplar stem-rep2

value: Bark and mature phloem from poplar stem


title: Poplar_Bark and mature phloem-rep1

source_name: Bark and mature phloem from poplar stem-rep1


title: BY4741 0.4mM H2O2 t10

description:
Sample name: BY4741 naive t10 vs BY4741T0
Compare the gene expression of cells exposed to 10 min of 0.4 mM H2O2 compared to basal gene expression in BY4741

source_name: BY4741 grown in log phase for at least 7 generations, then exposed to 0.4mM H2O2 for 10min


title: serum Non-TB SD6278

status: Public on Jul 06 2012

type: protein

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

hyb_protocol: Sera were pre-absorbed with E. coli-lysate for 30 minutes.  Prior to incubating with serum, slides were blocked for 30 minutes with Blocking Solution (Candor Bioscience, Germany).  Slides were incubated with sera diluted with LowCross Buffer (Candor Bioscience, Germany) at 4 degree C overnight with gentle shaking.  After washing the slides, the arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.  The slides were washed and dried by centrifugation before scanning.

scan_protocol: The slides were scanned with a Genepix 4200AL microarray scanner (Molecular Devices, USA). The scanner’s laser power and PMT gain were calibrated for each array in such a way that the saturated pixels constitute 0.2% of the total pixels in that array.  Fluorescence intensities were quantified by using Genepix Pro 6.0 (Molecular Devices, USA).

data_processing: log transformed raw data were used for analysis without normalization.

label: biotin-streptavidin

molecule: protein

extract_protocol: fresh serum

tag: final diagnosis

value: NonTB

tag: age in years

tag: country of serum collection

value: PHILIPPINES

tag: m. tuberculosis culture

value: NEG

tag: acid fast bacilli (afb) smear microscopy

tag: previous history of active tb

value: NO

tag: bcg scar or history

tag: tuberculin skin test

value: UNK

value: serum

tag: disease state

value: Non-tuberculosis


title: NMIBC tissue of patient No.19

description: Gene expression data from NMIBC tissue

tag: bc tumor stage

value: Ta

tag: sample type

value: NMIBC


title: serum Non-TB SD6263

label_protocol: arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.

value: YES


title: serum Non-TB SD6270


title: serum Smear + Culture+ TB SD6271

source_name: serum_Smear+ Culture+ TB

value: Smear+ Culture+ TB

value: POS

value: tuberculosis


title: serum Non-TB SD6276


title: serum Non-TB SD6311


title: serum Smear- Culture+ TB SD6265

source_name: serum_Smear- Culture+ TB

value: Smear- Culture+ TB


title: 2D SCG cells, biological rep3

value: 21 days

value: superior cervical ganglion


title: serum Non-TB SD6256


title: serum Non-TB SD6240


title: serum Smear- Culture+ TB SD6249


title: serum Non-TB SD6248


title: serum Non-TB SD6254


title: serum Non-TB SD6262


title: serum Smear- Culture+ TB SD6260


title: serum Smear + Culture+ TB SD6244


title: serum Non-TB SD6247


title: serum Smear- Culture+ TB SD6241


title: serum Non-TB SD6246


title: serum Non-TB SD6250


title: serum Non-TB SD6239


title: serum Non-TB SD6223


title: serum Smear- Culture+ TB SD6218


title: serum Non-TB SD6216


title: serum Non-TB SD6235


title: serum Non-TB SD6224


title: serum Non-TB SD6233


title: serum Non-TB SD6231


title: serum Non-TB SD6230


title: serum Non-TB SD6227


title: serum Smear + Culture+ TB SD6226


title: serum Smear- Culture+ TB SD6225


title: serum Non-TB SD6213


title: serum Smear + Culture+ TB SD6215


title: serum Smear- Culture+ TB SD6208


title: 2D SCG cells, biological rep1


title: serum Smear + Culture+ TB SD6210


title: serum Smear- Culture+ TB SD6209


title: serum Smear- Culture+ TB SD6203


title: serum Smear + Culture+ TB SD6206


title: serum Non-TB SD6201


title: serum Smear- Culture+ TB SD6199


title: serum Non-TB SD6198


title: serum Smear + Culture+ TB SD6191


title: serum Smear- Culture+ TB SD6195


title: serum Smear- Culture+ TB SD6207


title: serum Smear- Culture+ TB SD6189


title: serum Smear + Culture+ TB SD6180


title: serum Smear- Culture+ TB SD6202


title: serum Non-TB SD6192


title: serum Smear- Culture+ TB SD6221


title: serum Smear- Culture+ TB SD6175


title: serum Smear- Culture+ TB SD6181


title: serum Non-TB SD6170


title: serum Non-TB SD6167


title: serum Non-TB SD6187


title: serum Smear- Culture+ TB SD6188


title: serum Non-TB SD6186


title: serum Smear + Culture+ TB SD6190


title: serum Smear- Culture+ TB SD6179


title: serum Non-TB SD6178


title: serum Non-TB SD6173


title: serum Smear- Culture+ TB SD6155


title: serum Non-TB SD6166


title: serum Non-TB SD6151


title: serum Non-TB SD6158


title: serum Non-TB SD6157


title: serum Non-TB SD6156


title: serum Non-TB SD6144


title: serum Non-TB SD6165


title: serum Non-TB SD6139


title: serum Smear- Culture+ TB SD6145


title: serum Non-TB SD6162


title: serum Non-TB SD6163


title: serum Smear + Culture+ TB SD6143


title: serum Smear- Culture+ TB SD6149


title: serum Non-TB SD6147


title: serum Non-TB SD6140


title: serum Non-TB SD6160


title: serum Non-TB SD6137


title: serum Non-TB SD6138


title: serum Non-TB SD6135


title: serum Non-TB SD6132


title: serum Non-TB SD6128


title: serum Non-TB SD6118


title: serum Non-TB SD6122


title: serum Non-TB SD6120


title: serum Non-TB SD6115


title: serum Non-TB SD6127


title: serum Non-TB SD6109


title: serum Smear- Culture+ TB SD6117


title: serum Non-TB SD6130


title: serum Non-TB SD6103


title: serum Non-TB SD6104


title: serum Non-TB SD6107


title: serum Non-TB SD6108


title: serum Non-TB SD6102


title: serum Smear + Culture+ TB SD6092


title: serum Smear- Culture+ TB SD6087


title: serum Smear + Culture+ TB SD6089


title: serum Non-TB SD6100


title: serum Non-TB SD6099


title: serum Non-TB SD6101


title: serum Non-TB SD6094


title: serum Non-TB SD6097


title: serum Smear + Culture+ TB SD6086


title: serum Non-TB SD6091


title: serum Smear + Culture+ TB SD6095


title: serum Smear + Culture+ TB SD6090


title: serum Non-TB SD6076


title: serum Non-TB SD6079


title: serum Non-TB SD6082


title: serum Smear- Culture+ TB SD6080


title: serum Non-TB SD6070


title: serum Non-TB SD6073


title: serum Non-TB SD6093


title: serum Non-TB SD6069


title: serum Non-TB SD6084


title: serum Non-TB SD6096


title: serum Smear- Culture+ TB SD6060


title: serum Non-TB SD6066


title: serum Non-TB SD6058


title: serum Non-TB SD6062


title: serum Non-TB SD6061


title: serum Smear + Culture+ TB SD6065


title: serum Non-TB SD6064


title: serum Non-TB SD6054


title: serum Smear- Culture+ TB SD6048


title: serum Smear- Culture+ TB SD6045


title: serum Non-TB SD6040


title: serum Non-TB SD6044


title: serum Smear- Culture+ TB SD6037


title: serum Non-TB SD6074


title: serum Smear- Culture+ TB SD6042


title: serum Smear- Culture+ TB SD6023


title: serum Non-TB SD6031


title: serum Smear + Culture+ TB SD6033


title: serum Smear- Culture+ TB SD6041


title: serum Non-TB SD6038


title: serum Smear- Culture+ TB SD6036


title: serum Non-TB SD6027


title: serum Smear + Culture+ TB SD6018


title: serum Non-TB SD6014


title: serum Smear- Culture+ TB SD6013


title: serum Non-TB SD6035


title: serum Smear- Culture+ TB SD6043


title: serum Smear- Culture+ TB SD6006


title: serum Smear- Culture+ TB SD6010


title: serum Non-TB SD6012


title: serum Smear + Culture+ TB SD6008


title: serum Smear + Culture+ TB SD6004


title: serum Smear- Culture+ TB SD6002


title: serum Smear + Culture+ TB SD5070


title: serum Non-TB SD5069


title: serum Non-TB SD5051


title: serum Non-TB SD5067


title: serum Non-TB SD5040


title: serum Smear + Culture+ TB SD6015


title: serum Non-TB SD5056


title: serum Non-TB SD5068


title: serum Smear + Culture+ TB SD5049


title: serum Smear + Culture+ TB SD5065


title: serum Non-TB SD5063


title: serum Smear + Culture+ TB SD5046


title: serum Non-TB SD5039


title: serum Smear + Culture+ TB SD5050


title: serum Smear + Culture+ TB SD6003


title: serum Smear + Culture+ TB SD5035


title: serum Smear + Culture+ TB SD5038


title: serum Smear + Culture+ TB SD5034


title: serum Smear + Culture+ TB SD5033


title: serum Non-TB SD5037


title: serum Smear + Culture+ TB SD5031


title: serum Non-TB SD5007


title: serum Non-TB SD5030


title: serum Non-TB SD5032


title: serum Smear + Culture+ TB SD5012


title: serum Smear + Culture+ TB SD5011


title: serum Non-TB SD5027


title: serum Non-TB SD5004


title: serum Non-TB SD4050

value: USA


title: serum Non-TB SD5001

value: NonTB


title: serum Non-TB SD5003

value: PHILIPPINES


title: serum Non-TB SD4049

value: NEG


title: serum Non-TB SD4039

value: NO


title: serum Smear + Culture+ TB SD4037

value: UNK


title: serum Non-TB SD4036

value: serum


title: serum Non-TB SD4042

value: Non-tuberculosis


title: serum Smear + Culture+ TB SD4047


title: serum Non-TB SD4033


title: serum Smear + Culture+ TB SD5029


title: serum Non-TB SD4029


title: serum Non-TB SD4026


title: serum Non-TB SD4034


title: serum Non-TB SD4024


title: serum Non-TB SD4031


title: serum Non-TB SD4025


title: serum Smear + Culture+ TB SD4027


title: serum Smear + Culture+ TB SD5006


title: serum Non-TB SD5054


title: serum Non-TB SD4035


title: serum Non-TB SD4040


title: serum Non-TB SD4022


title: serum Non-TB SD4021


title: serum Non-TB SD4016


title: serum Smear- Culture+ TB SD4019


title: serum Non-TB SD4011


title: serum Non-TB SD4030


title: serum Non-TB SD4005


title: serum Non-TB SD4004


title: serum Smear- Culture+ TB SD4008


title: serum Non-TB SD4002


title: serum Non-TB SD4007


title: serum Non-TB SD4003


title: serum Non-TB SD4010


title: serum Smear + Culture+ TB SD4001


title: serum Smear + Culture+ TB SD4009


title: serum Smear- Culture+ TB SD3058

value: Mexico


title: serum Smear + Culture+ TB SD3043


title: serum Smear + Culture+ TB SD3047


title: serum Non-TB SD3057


title: serum Smear + Culture+ TB SD3049


title: serum Non-TB SD3056


title: serum Smear + Culture+ TB SD3046


title: serum Smear + Culture+ TB SD3051


title: serum Smear + Culture+ TB SD3055


title: serum Smear + Culture+ TB SD3053


title: serum Non-TB SD4012


title: serum Smear + Culture+ TB SD3041


title: serum Smear + Culture+ TB SD3040


title: serum Smear + Culture+ TB SD3038


title: serum Smear + Culture+ TB SD3035


title: serum Smear + Culture+ TB SD3037


title: serum Smear + Culture+ TB SD3027


title: serum Non-TB SD3029


title: serum Smear + Culture+ TB SD3028


title: serum Smear + Culture+ TB SD3044


title: serum Smear + Culture+ TB SD3030


title: serum Smear + Culture+ TB SD3021


title: serum Smear + Culture+ TB SD3020


title: serum Smear + Culture+ TB SD3012


title: serum Non-TB SD3022


title: serum Smear + Culture+ TB SD3011


title: serum Smear + Culture+ TB SD3018


title: serum Smear + Culture+ TB SD3009


title: serum Smear + Culture+ TB SD3010


title: serum Non-TB SD3008


title: serum Smear + Culture+ TB SD3007


title: serum Smear- Culture+ TB SD2101


title: serum Smear- Culture+ TB SD2083


title: serum Smear + Culture+ TB SD2105


title: serum Smear + Culture+ TB SD3003


title: serum Smear + Culture+ TB SD2103


title: serum Smear- Culture+ TB SD2104


title: serum Smear + Culture+ TB SD2096


title: serum Smear- Culture+ TB SD2077


title: serum Smear + Culture+ TB SD3004


title: serum Smear + Culture+ TB SD2075


title: serum Smear + Culture+ TB SD2112


title: serum Smear + Culture+ TB SD3001