title: Artemis/P53 null, NMYC genomically amplified, Biological rep 6

status: Public on Oct 08 2009

city: Bar Harbor

first: priyam

last: singh

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Mice containing germline, gene targeted knockout alleles of Dclre1c/Art, or Trp53 were rederived by in vitro fertilization (IVF) in a C57BL/6J strain background, and then backcrossed with C57BL/6J mice for at least 4 generations to generate heterozygous animal with a minimum of 95% C57BL/6J genetic content. Trp53 heterozygotes were intercrossed with Dclre1c/Art heterozygotes, and subsequently incrossed to generate double mutant (Art Trp53).

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scan

data_processing: MAS5 normalization

molecule: polyA RNA

source_name: lymph nodes

label_protocol: Standard Affymetrix one-cycle labelling protocol

treatment_protocol: Single-cell suspensions for flow cytometric analysis of pro-B-cells, B-cells, and tumor samples were prepared by dispersion of bone marrow, spleen, or lymph nodes (respectively) using fine, sterile mesh.  Cell suspensions were prepared in RPMI 1640 medium containing with 10%fetal calf serum. Cell preparations were then stained with an antibody cocktail specific for B-lymphocytes, containing antibodies directed against the pan-B cell maker B220, and the developmental stage markers CD19, CD43, and IgM.  Flow cytometry was carried out using a Becton Dickinson FACSCalibur cytometer with CellQuest Pro acquisition software, and analyzed using FlowJo 2.0 software. Cell sorting to obtain purified populations of progenitor or mature B cells was carried out on a FACSvantage SE/DiVa cell sorter after staining of whole bone marrow or splenocyte preparations (respectively) with the same B-cell cocktail used for flow cytometry.  For histopathology, lymph node-derived tumor samples were treated with Bouin’s fixative and embedded in paraffin.  After sectioning, slides were stained with hematoxylin & eosin (H&E) prior to imaging.  At necropsy, lymphoma tissue samples were obtained from cervical lymphnode or thymus lymphoma foci, submerged in RNALater, and stored until processing for total RNA recovery. Normal pro-B-cells were sorted by fluorescence activated cell sorting (FACS) to obtain B220+ CD43+ IgM- cells from bone marrow of normal C57BL/6J mice and B-cells were the B220+ fraction from spleen of normal C57BL/6J mice, sorted by FACS.

value: lymph nodes

tag: tumor stage

value: Best prognosis (better than APC)


title: Human cerebellum individual 5

type: RNA

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

description: No subjects with prolonged agonal state were used. All samples were taken from the middle part of the cerebellar cortex.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on the Human Gene 1.0 ST Array . GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: Prior to expression data analysis, we masked all probes that did not match reference human genomes perfectly (hg18) and did not map to a unique location. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared the signal intensity for each probe to a distribution of signal intensities of the antigenomic probes with the same GC content. Antigenomic probes are specifically designed by Affymetrix to provide an estimate of the non-specific background hybridization. The probe signal was classified as detected above background if its intensity was larger than the 95% percentile of the background probes with the same GC content. If more than 80% of probes and at least ten probes per transcript were detected, the transcript signal was classified as detected for each sample. To further remove any possible systematic experimental differences between the arrays, we performed a PM-GCBG correction and quantile normalization using R package \u201caffy\u201d . Prior to the normalization, all intensities were base-two-logarithm transformed. The intensities of transcripts were summarized by median polish method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human cerebellum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Whole Transcript (WT) Sense Target Labeling protocol, Affymetrix).

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

tag: Age

value: 71 years old

tag: Gender

value: male


title: Artemis/P53 null, NMYC genomically amplified, Biological rep 4

country: USA

label: Biotin

organism: Mus musculus

tag: tissue


title: Lps, 0.5_hours, rep1

status: Public on Oct 09 2009

city: Cambridge

first: Tal

last: Shay

state: MA

institute: Broad Institute

hyb_protocol: Standard Affymetrix protocols for mouse ht arrays

data_processing: RMA - All values lower than 20 were replaced by 20. All probesets whose values in all samples are equal or below 20 were removed.

source_name: Lps, 0.5_hours

growth_protocol: mouse primary BMDCs (Amit et al. 2009)

extract_protocol: miRNEASY  (QIAGEN) as recommended by manufactor

tag: cell type

value: primary bone marrow dendritic cell


title: Artemis/P53 null, NMYC genomically amplified, Biological rep 1


title: Human cerebellum individual 1

value: 39 years old


title: Artemis/P53 null, NMYC genomically amplified, Biological rep 5


title: Human cerebellum individual 4

value: 59 years old


title: Mature Bcells, biological replicate 4

description: mature B-cells (B220+ fraction from spleen of normal C57BL/6J mice, sorted by FACS)

source_name: Spleen

value: Spleen


title: Human cerebellum individual 2

value: 45 years old


title: Artemis/P53 null, NMYC genomically amplified, Biological rep 3


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 11

value: Medium prognosis (better than LPC)


title: Human cerebellum pool 1

source_name: pooled mRNA from 5 adult human individuals


title: Human cerebellum pool 2


title: Human cerebellum individual 3


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 6


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 9


title: Mature Bcells, biological replicate 1


title: WildType versus LuxS01 in MEM replicate 4

city: Dublin

first: Kathryn

last: Holmes

address: Trinity Centre for Health Science, Adelaide and Meath Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

description: Biological replicate 4 of 4

hyb_protocol: Labelled cDNA was purified using a Qiaquick purification kit (Qiagen) and dried before being resuspended in 19.5 µl water, 2.25 µl human Cot1 DNA (Invitrogen), 4.5 µl 20x SSC, 0.72 µl 1 M HEPES, pH 7.0, 0.68 µl 10 % SDS and 3 µl Denhardt solution. Samples were heated for 3 min in a boiling water bath, cooled at room temperature for 5 min and centrifuged at maximum speed in a microfuge for 2 min to remove particulates. The mixture was put onto the microarray slide, sealed with a coverslip in a hybridization chamber and incubated for 18 h at 63 °C. Following hybridization, microarray slides were washed briefly in pre-warmed (60 °C) 1x SSC/0.03 % SDS to remove the coverslip and then washed twice for 5 min in each of the following buffers: a) 1x SSC/0.03 % SDS (pre-warmed to 60 °C), b) 0.2x SSC and finally c) 0.05x SSC. Microarray slides were dried by centrifugation at 300 x g for 15 min before scanning.

scan_protocol: Microarrays were scanned using an Axon 4000A scanner and images were acquired using GenePixPro 3.0 software (Axon).

data_processing: All microarray data were filtered to remove poor-quality data using four sequential cut-off values (Mark Reuter, IFR, personal communication). All data values were from features above 50 µm in diameter, with sum of medians above 50, regression coefficient squared values above 0.2 and with a sum of the signal : noise ratio greater than 3. Data was block median normalized prior to analysis.

organism: Campylobacter jejuni

source_name: Wild-type C.jejuni 11168 cultured in MEM- α medium.

label_protocol: RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences) and made to 12.4 µl total volume with water and supplemented on ice with 3 µl 10x RT buffer (Invitrogen), 0.6 µl 50x dNTPs mixture (25 mM each dATP, dTTP, dGTP and 10 mM dCTP), 3 µl 0.1 M DTT, 2 µl 1mM Cy3 or Cy5 (Perkin Elmer), and 200U Stratascript RT (Stratagene UK). Incubation was  at 37 °C overnight.

growth_protocol: Cultures of Wild-type and mutant LuxS01 C. jejuni NCTC 11168 were grown in 3x 50 ml volumes of MHB and/or MEM- α in 100 ml bottles. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC.

extract_protocol: The cells were harvested during late logarithmic phase of growth (approximately 8h, OD 0.3 and verified by viable counts) by centrifugation at 3000 g for 20 min. Pellets were resuspended in 1ml Tri reagent (Sigma-Aldrich, UK), to which 0.2ml of chloroform was added ( Sigma-Aldrich, UK), mixed by vortexing and equilibrated at room temperature for 10 min. After centrifugation at 12000g for 15 min the aqueous phase was removed and applied to Qiagen’s RNeasy Mini kits for purification of total RNA according to the manufacturer’s protocol. DNA removal was ensured by treatment with DNA-free (Ambion, UK). Samples from 3x50ml cultures were pooled and used as one individual sample.

treatment_protocol: The only treatment was the use of different culture medium for growth.

tag: strain

tag: genotype

value: wildtype

tag: culture medium

value: MEM- α medium (Invitrogen)

source_name: C.jejuni 11168 LuxS01 cultured in MEM- α.

value: LuxS01 mutant


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 10


title: Mature Bcells, biological replicate 2


title: Control Wild Type in MEM replicate 1

description: Biological control replicate 1 of 2

source_name: Wild-type C.jejuni 11168 cultured in MEM- α.


title: Control Wild Type in MEM replicate 2

description: Biological control replicate 2 of 2


title: Mature Bcells, biological replicate 3


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 5


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 8


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 4


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 7


title: Artemis/P53 null, NMYC genomically amplified, Biological rep 2


title: WildType versus LuxS01 in MEM replicate 3

description: Biological replicate 3 of 4


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 3


title: Control Wild Type in MHB replicate 2

description: Biological control replicate 2 of 2

source_name: Wild-type C.jejuni 11168 cultured in Mueller Hinton broth (MHB).

value: Mueller Hinton Broth (MHB)

source_name: Wild-type C.jejuni 11168 cultured in MHB.


title: WildType versus LuxS01 in MHB replicate 2

description: Biological replicate 2 of 4

source_name: C.jejuni 11168 LuxS01cultured in MHB.


title: Control Wild Type in MHB replicate 1

description: Biological control replicate 1 of 2


title: WildType versus LuxS01 in MHB replicate 1

description: Biological replicate 1 of 4


title: DC control 4h rep2

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: The arrays were stained and washed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) using the GeneChip Fluidics Station 450

scan_protocol: The arrays were scanned according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 7G.

data_processing: The microarray data was analyzed using R and Bioconductor (Gentleman et al. 2004). Raw probe intensities were normalized using qspline and expression index calculations were performed using rma (Irizarry et al. 2003;Workman et al. 2002). For statistical testing ANOVA was performed using stimulation time as factor where all untreated samples were treated as one group.

source_name: Bone-marrow derived dendritic cells, control, 4h

label_protocol: 1 μg RNA per stimulation condition was converted into cDNA, and biotin-labeled aRNA was synthesized using the MessageAmpTM II-Biotin Enhanced Kit (Ambion, Austin, TX, USA) according to the manufacturers instructions.

growth_protocol: Bone marrow from wild type (WT) C57BL/6 mice was flushed out from the femur and tibia and washed twice in sterile PBS. 3 x 105 bone marrow cells were seeded into Petri dishes in 10 ml RPMI 1640 (Sigma-Aldrich, St. Louis, MO) containing 10% (v/v) heat-inactivated fetal calve serum supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml), glutamine (4 mM), 50 µm 2-mercaptoethanol (all purchased from Cambrex Bio Whittaker) and 15 ng/ml murine GM-CSF (harvested from a GM-CSF transfected Ag8.653 myeloma cell line). The cells were incubated for 8 days at 37 ºC in 5% CO2 humidified atmosphere. On day 3, 10 ml of complete medium containing 15 ng/ml GM-CSF was added. On day 6, 10 ml were removed and replaced by fresh medium. Non-adherent immature DC were harvested on day 8.

extract_protocol: Murine DC, harvested at various stimulation time points, were homogenised by QIAshredder (Qiagen, Ballerup, Denmark), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Immature DC (2 x 10^6 cells/ml) were resuspended in fresh medium supplemented with 10 ng/ml GM-CSF, and 500 µl/well were seeded in 48-well tissue culture plates (Nunc, Roskilde, Denmark). L. acidophilus NCFM were suspended in medium and added (100 µl/well) in a final concentration of 10 μg/ml and the cell cultures were incubated at 37ºC in 5 % CO2 for the duration of the treatment.

tag: treatment

value: Control

tag: time

value: 4 hours


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 2


title: DC control 4h rep1


title: DC ncfm 10h rep3

source_name: Bone-marrow derived dendritic cells, Lactobacillus acidophilus NCFM treated, 10h

value: Lactobacillus acidophilus NCFM

value: 10 hours


title: DC ncfm 18h rep2

source_name: Bone-marrow derived dendritic cells, Lactobacillus acidophilus NCFM treated, 18h

value: 18 hours


title: DC control 18h rep1

source_name: Bone-marrow derived dendritic cells, control, 18h


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 6

description: Mice containing germline, gene targeted knockout alleles of Lig4, or Trp53 were rederived by in vitro fertilization (IVF) in a C57BL/6J strain background, and then backcrossed with C57BL/6J mice for at least 4 generations to generate heterozygous animal with a minimum of 95% C57BL/6J genetic content. Trp53 heterozygotes were intercrossed with Lig4 heterozygotes, and subsequently incrossed to generate double mutant (Lig4 Trp53).

value: lymph nodes

value: Worst prognosis


title: DC ncfm 18h rep3


title: DC ncfm 18h rep1


title: DC control 10h rep2

source_name: Bone-marrow derived dendritic cells, control, 10h


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 2


title: Normal progenitor B-cells from wild type mice rep1

description: Normal pro-B-cells (B220+ CD43+ IgM- cells from bone marrow of normal C57BL/6J mice)

source_name: Bone marrow

value: Bone marrow


title: Normal progenitor B-cells from wild type mice rep 2


title: DC control 10h rep1


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 1

source_name: lymph nodes


title: DC control 18h rep2


title: DC ncfm 10h rep1


title: DC control 4h rep3


title: DC ncfm 10h rep2


title: DC ncfm 4h rep3

source_name: Bone-marrow derived dendritic cells, Lactobacillus acidophilus NCFM treated, 4h


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 5


title: Artemis/P53 null, CMYC genomically amplified, Biological rep 1


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 3


title: Lig4/P53 null, CMYC genomically amplified, Biological rep 4


title: DC ncfm 4h rep2


title: M114-04

city: Aarhus

first: Karsten

middle: Bork

last: Nielsen

address: 4 Wilhelm Meyers Allé, Building 1242

department: Institute of Human Genetics

institute: University of Aarhus

description: Gene expression data from porcine cerebral cortex E80

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

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

data_processing: The data were analyzed with Array Assist 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: Sus scrofa

source_name: Cerebral cortex

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

extract_protocol: Total RNA was extracted using Qiagen RNeasy micro coulmns performed according to the manufacturer's instructions.

tag: embryonic day

value: cortical


title: DC ncfm 4h rep1


title: M114-05


title: M114-06


title: M114-03

description: Gene expression data from porcine cerebral cortex E60


title: M114-01


title: WildType versus LuxS01 in MEM replicate 2

description: Biological replicate 2 of 4


title: WildType versus LuxS01 in MEM replicate 1

description: Biological replicate 1 of 4


title: Control AI-2 Experiment LuxS01 replicate 3

description: Biological control replicate 3 of 3

source_name: C.jejuni 11168 LuxS01 cultured in MEM- α and AI-2 negative buffer.

growth_protocol: Cultures of Wild-type and mutant LuxS01 C. jejuni NCTC 11168 were grown in 3x 50 ml volumes of MEM- α in 100 ml bottles. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % Oxygen, 10 % Carbon dioxide, 80 % Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC.

extract_protocol: The cells were harvested during late logarithmic phase of growth (approximately 8h, OD 0.3 and verified by viable counts) by centrifugation at 3000 g for 20 min. Pellets were resuspended in 1ml Tri reagent (Sigma-Aldrich, UK), to which 0.2ml of chloroform was added ( Sigma-Aldrich, UK), mixed by vortexing and equilibrated at room temperature for 10 min. After centrifugation at 12000g for 15 min the aqueous phase was removed and applied to Qiagen’s RNeasy Mini kits for purification of total RNA according to the manufacturer’s protocol. DNA removal was ensured by treatment with DNA-free (Ambion, UK). Sample from 3x50ml cultures were pooled and used as one sample.

treatment_protocol: After 2.5 hr of culture, buffer containing AI-2 or AI-2 negative buffer was added to the cultures.

value: MEM- α and AI-2 negative buffer


title: M114-02


title: Addition of AI-2 to LuxS01 replicate 3

description: Biological replicate 3 of 3

source_name: C.jejuni 11168 LuxS01 cultured in MEM- α with addition of exogenous AI-2.

value: MEM- α with addition of exogenous AI-2


title: Control AI-2 Experiment LuxS01 replicate 2

description: Biological control replicate 2 of 3


title: Addition of AI-2 to LuxS01 replicate 1

description: Biological replicate 1 of 3


title: WildType versus LuxS01 in MHB replicate 4

description: Biological replicate 4 of 4


title: WildType versus LuxS01 in MHB replicate 3

description: Biological replicate 3 of 4


title: 22_P156548

city: Seattle

first: Lawrence

middle: D

last: Adams

state: WA

address: 1959 NE Pacific Street

department: BNHS

institute: University of Washington

description: CIS #: P156548

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

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.

source_name: CD14+ blood monocytes

label_protocol: Affymetrix standard protocol.

growth_protocol: Not applicable.

extract_protocol: Rneasy Mini column kit from Qiagen.

treatment_protocol: CD14+ monocytes were isolated by aphoresis followed by negative sorting by antibodys to other PBMC fractions.

value: blood

value: CD14+ monocytes

tag: fatigue status

value: high

tag: nrti treatment status

value: Yes

tag: hiv status

value: HIV


title: Addition of AI-2 to LuxS01 replicate 2

description: Biological replicate 2 of 3

value: LuxS01 mutant


title: 13_P155149

description: CIS #: P155149

value: healthy

value: No

value: Neg


title: 11_P155303

description: CIS #: P155303


title: Control AI-2 Experiment Wild Type replicate 2

description: Biological control replicate 2 of 3

source_name: Wild-type C.jejuni 11168 cultured in MEM- α and AI-2 negative buffer.

value: wildtype


title: Control AI-2 Experiment Wild Type replicate 3

description: Biological control replicate 3 of 3


title: Control AI-2 Experiment LuxS01 replicate 1

description: Biological control replicate 1 of 3


title: 16_P155548

description: CIS #: P155548


title: 20_P155883

description: CIS #: P155883

value: low


title: 10_P154853

description: CIS #: P154853


title: Control AI-2 Experiment Wild Type replicate 1

description: Biological control replicate 1 of 3


title: 17_P156310

description: CIS #: P156310


title: 12_P154969

description: CIS #: P154969


title: 18_P155517

description: CIS #: P155517


title: 23_P155896

description: CIS #: P155896


title: Addition of AI-2 to Wild Type replicate 3

description: Biological replicate 3 of 3

source_name: Wild-type C.jejuni 11168 cultured in MEM- α with addition of exogenous AI-2.


title: 9_P154529

description: CIS #: P154529


title: 4_P154164

description: CIS #: P154164


title: Addition of AI-2 to Wild Type replicate 2

description: Biological replicate 2 of 3


title: 5_P154104

description: CIS #: P154104


title: 2_P154204

description: CIS #: P154204


title: Addition of AI-2 to Wild Type replicate 1

description: Biological replicate 1 of 3


title: GFP oxLDL 6hr 282295623

status: Public on Oct 07 2009

first: Andrew

last: Hill

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from HAECT cells

tag: Quality

value: Gradient Severity:0.03

value: Distortion Severity:0.03

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:1.02

value: Absent (%) Dev.:0.18

value: Scaling Factor:0.73

value: Scaling Factor Dev.:1.06

tag: Pretreatment [C]:GFP

tag: Time point [C]:6 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:121301

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_oxLDL_6hr

tag: RNA extraction source key [A]:282295623


title: LOX1 Untreated 24hr 282295913

value: Gradient Severity:0.04

value: Distortion Severity:0.08

value: Defective Area (%):0.03

value: Outlier Area (%):0.02

value: Background Mean Dev.:2.24

value: Absent (%) Dev.:2.34

value: Scaling Factor:1.66

value: Scaling Factor Dev.:9.07

tag: Pretreatment [C]:LOX1

tag: Time point [C]:24 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213503

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:LOX1_Untreated_24hr

tag: RNA extraction source key [A]:282295913


title: 8_P154597

description: CIS #: P154597

tag: tissue

value: blood

tag: cell type

value: CD14+ monocytes

tag: fatigue status

value: healthy

tag: nrti treatment status

value: No

tag: hiv status

value: Neg


title: GFP oxLDL 6hr 282295633

tag: Quality

value: Gradient Severity:0.06

value: Distortion Severity:0.05

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.4

value: Absent (%) Dev.:0.43

value: Scaling Factor:0.71

value: Scaling Factor Dev.:0.89

tag: Pretreatment [C]:GFP

tag: Time point [C]:6 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:121302

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: RNA extraction source key [A]:282295633


title: LOX1 oxLDL 24hr 282295923

value: Gradient Severity:0.05

value: Distortion Severity:0.03

value: Defective Area (%):0.02

value: Background Mean Dev.:4.68

value: Absent (%) Dev.:0.69

value: Scaling Factor:0.33

value: Scaling Factor Dev.:2.44

tag: Pretreatment [C]:LOX1

tag: Time point [C]:24 hours

tag: Genomic ID [C]:221501

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:LOX1_oxLDL_24hr

tag: RNA extraction source key [A]:282295923


title: LOX1 oxLDL 6hr 282295683

value: Gradient Severity:0.01

value: Distortion Severity:0.04

value: Background Mean Dev.:0.45

value: Absent (%) Dev.:0.38

value: Scaling Factor:0.62

value: Scaling Factor Dev.:0.1

tag: Genomic ID [C]:221301

tag: Cohort name [C]:LOX1_oxLDL_6hr

tag: RNA extraction source key [A]:282295683


title: LOX1 Untreated 24hr 282295903

tag: Quality

value: Gradient Severity:0.07

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:1.06

value: Absent (%) Dev.:0.76

value: Scaling Factor:0.47

value: Scaling Factor Dev.:1.26

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213502

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:LOX1_Untreated_24hr

tag: RNA extraction source key [A]:282295903


title: LOX1 Untreated 6hr 282295653

value: Gradient Severity:0.03

value: Distortion Severity:0.09

value: Outlier Area (%):0.02

value: Background Mean Dev.:0.52

value: Absent (%) Dev.:0.88

value: Scaling Factor:0.53

value: Scaling Factor Dev.:0.69

tag: Time point [C]:6 hours

tag: Genomic ID [C]:213301

tag: Cell name [C]:HAECT

tag: Cohort name [C]:LOX1_Untreated_6hr

tag: RNA extraction source key [A]:282295653


title: LOX1 Untreated 24hr 282295893

value: Distortion Severity:0.02

value: Background Mean Dev.:0.43

value: Absent (%) Dev.:0.91

value: Scaling Factor:0.75

value: Scaling Factor Dev.:1.18

tag: Pretreatment [C]:LOX1

tag: Time point [C]:24 hours

tag: Genomic ID [C]:213501

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: RNA extraction source key [A]:282295893


title: LOX1 0hr 282295453

tag: Extract Description:LOX1_0hr:213102

tag: Quality

value: Gradient Severity:0.04

value: Distortion Severity:0.07

value: Defective Area (%):0.01

value: Outlier Area (%):0

value: Background Mean Dev.:1.4

value: Absent (%) Dev.:0.65

value: Scaling Factor:0.6

value: Scaling Factor Dev.:0.13

tag: Time point [C]:0 hours

tag: Genomic ID [C]:213102

tag: Cohort name [C]:LOX1_0hr

tag: RNA extraction source key [A]:282295453


title: LOX1 oxLDL 24hr 282295933

value: Gradient Severity:0.06

value: Distortion Severity:0.03

value: Defective Area (%):0.07

value: Outlier Area (%):0.01

value: Background Mean Dev.:3.63

value: Absent (%) Dev.:0.02

value: Scaling Factor:0.39

value: Scaling Factor Dev.:1.93

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221502

tag: Treatment amount [C]:50 ug/ml

tag: Cohort name [C]:LOX1_oxLDL_24hr

tag: RNA extraction source key [A]:282295933


title: GFP Untreated 6hr 282295603

value: Gradient Severity:0.03

value: Distortion Severity:0.02

value: Defective Area (%):0

value: Background Mean Dev.:1.03

value: Absent (%) Dev.:0.77

value: Scaling Factor:0.87

value: Scaling Factor Dev.:2.23

tag: Pretreatment [C]:GFP

tag: Time point [C]:6 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113302

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:GFP_Untreated_6hr

tag: RNA extraction source key [A]:282295603


title: GFP oxLDL 2hr 282295523

tag: Quality

value: Defective Area (%):0.01

value: Background Mean Dev.:0.54

value: Absent (%) Dev.:0.62

value: Scaling Factor:0.57

value: Scaling Factor Dev.:0.38

tag: Time point [C]:2 hours

tag: Genomic ID [C]:121203

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_oxLDL_2hr

tag: RNA extraction source key [A]:282295523


title: GFP Untreated 6hr 282295613

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.13

value: Absent (%) Dev.:0.13

value: Scaling Factor:0.63

value: Scaling Factor Dev.:0.14

tag: Genomic ID [C]:113303

tag: RNA extraction source key [A]:282295613


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-1

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68082.gif

hyb_protocol: not provided

scan_protocol: Scanner Model = GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis

label_protocol: not provided

extract_protocol: not provided

tag: strain/genotype

source_name: MTB1254 WT

label_protocol: AMPLIFICATION AND LABELING OPP STUDY; 1. Bring 0.5-5??g RNA (Typically 2-3 ??g) to 11??l and add 2.0 ??l (2 mg/ml) N6 primers. 2. Heat 2min at 98??C, Snap cool on ice in PCR rack kept in ice. 3. Add 12 ??l (keep on ice) of the next mixture:                                                   2.5??l 10X Stratascript Buffer        3.5??l RNase free H20        2.5??l dNTP (5mM A,G,C and 0.2mM T)        1.5??l Cy3 or Cy5 (Cy5 for experimental sample)        2.0??l Stratascript Reverse Transcriptase.   4. Incubate 10 min at 25??C (room temperature) followed by 90 min at 42??C in PCR machine. Can freeze or leave at 4??C o/n.  5. Add both reactions to a microcon10 (Amicon) with 400??l TE. Centrifuge at 13000 rpm until ~25??l remaining (~20min). Add 200??l more TE and spin until almost dry (~12min) (< 5??l). (make sure that the cup is really dry and the color should be purple) (START THE PRE HYB OF SLIDES FOR 1 HR). 7. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1min (8000 rpm/1 min). 8. Bring sample to 5??l with TE and transfer to a 0.5 ml PCR tube.; Protocol Type = Labeling; Performer: Mario Alberto,,Flores-Valdez

growth_protocol: GROWTH CONDITIONS OPP STUDY; Culture were made using Middlebrook 7H9 media (BD, Franklin Lakes, NJ, USA), containing 10% Middlebrook oleic-acid-dextrose-catalase (OADC) enrichment (BD, Franklin Lakes, NJ, USA), 0.5% glycerol (Fisher Scientific, Pittsburgh, PA, USA) and 0.05% Tween 80 (Sigma Aldrich, St. Louis, MO, USA), or 7H10 agar (BD, Franklin Lakes, NJ, USA) containing 10% OADC and 0.5% glycerol.Mtb strain 1254 wild type (WT) and its isogenic ??opp KO and complemented strains were cultured in liquid media, in a 150 mL volume, contained in roller bottles, and incubated at 37??C. When cells reached OD600 nm of 0.3, 1.0, and 2.0, an aliquot of 30, 10, and 10 mL, respectively, was taken, centrifuged 3 min at 3000 g, at room temperature, and the supernatant was discarded, with cell pellets being immediately frozen by inclusion into dry ice. Frozen cell pellets were stored at -80??C for later RNA isolation.; Protocol Type = Growth Conditions; Performer: Mario Alberto,,Flores-Valdez

extract_protocol: EXTRACT PREPARATION OPP STUDY; M. tb. RNA isolation.   1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.15-0.2) 5m at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ???80C.  2. Add 1 ml Trizol (Invitrogen) to each of 4-8 pellets, suspend first pellet by vortexing, while other pellets are still frozen. Add suspension to 0.5 mL glass beads in a 2 mL screw cap tube. If cells are either from OD 0.8 or above, or from experiments for ST-CF, use 2 mL of Trizol. Dispense only1 mL of the suspension into the 2 mL tubes with glass beads. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample. Continue to periodically invert samples for at least 5min in Trizol.  4. Centrifuge samples 1 min at max speed, remove Trizol solution to a 2 mL Phase Lock Gel Heavy tube (Eppendorf). Make sure that the volume is 1 mL; if not, complete the volume using fresh Trizol, up to 1mL. Add 300??l Chloroform, and invert rapidly for 15s. Continue inverting periodically for 2 min.a  5. Centrifuge 5-10 min, remove aqueous layer (540??l) and add to a 1.5 ml tube containing 270??l isopropanol. Then add 265??l high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically precipitated at 4??C overnight (or can be precipitated in -20c for 2-3 hrs). Note: Using 270 ??L of ammonium acetate 5 M pH 5.2, and 270 ??L of isopropanol, with incubation overnight at 4??C, as well as making sure the Trizol volume combined with chloroform was 1 mL, RNA practically genomic DNA-free was obtained. 6. Centrifuge 10m at 4??C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5min.  7. Remove ethanol by drying under vacuum 2m [Do not over dry] (this take around 20 min or so). 8. Suspend RNA in 90 ul RNase free water (don???t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration). 9. Add 10??l 10X DNaseI buffer to RNA (use no more than 80 ??g RNA) and add 2??l DNaseI. Incubate 30min at 37??C.  Qiagen RNeasy purification.   1. Add 350??l RLT buffer (add 10??l ??-mercaptoethanol to 1 ml RLT before using), vortex, and add 265??l 95% EtOH to each sample, vortex.  2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500??l RPE, centrifuge 15s, discard flow-through, add 500??l additional RPE and centrifuge 2 min. If column still wet on sides, remove wash solution from tube and spin 1min to dry.  3. Transfer to a 1.5 ml collection tube, elute with 40??l RNase free water, centrifuge 1m.  4. Determine RNA concentration with A260/A280 readings. Dilute 1??l in 199??l TE. [200(dilution factor)x 40  x A260 = ng/??l].  5. Run 1??l RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts.  aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200??l. The yield will be less. Be careful not to remove any of the interface layer  bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce.  cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used.  Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Mario Alberto,,Flores-Valdez

value: MTB1254 WT


title: GFP oxLDL 2hr 282295503

value: Gradient Severity:0.04

value: Distortion Severity:0.05

value: Outlier Area (%):0

value: Background Mean Dev.:1.33

value: Absent (%) Dev.:0.48

value: Scaling Factor:0.43

value: Scaling Factor Dev.:1.59

tag: Pretreatment [C]:GFP

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:121201

tag: Treatment amount [C]:50 ug/ml

tag: RNA extraction source key [A]:282295503


title: GFP oxLDL 24hr 282295883

value: Gradient Severity:0.03

value: Distortion Severity:0.04

value: Defective Area (%):0

value: Background Mean Dev.:0.42

value: Absent (%) Dev.:0.57

value: Scaling Factor:0.73

value: Scaling Factor Dev.:0.99

tag: Time point [C]:24 hours

tag: Genomic ID [C]:121503

tag: Cell name [C]:HAECT

tag: Cohort name [C]:GFP_oxLDL_24hr

tag: RNA extraction source key [A]:282295883


title: LOX1 oxLDL 12hr 282295803

tag: Quality

value: Defective Area (%):0.03

value: Background Mean Dev.:1.41

value: Absent (%) Dev.:1.19

value: Scaling Factor:0.62

value: Scaling Factor Dev.:0.08

tag: Pretreatment [C]:LOX1

tag: Time point [C]:12 hours

tag: Genomic ID [C]:221401

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:LOX1_oxLDL_12hr

tag: RNA extraction source key [A]:282295803


title: SBA_48

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.

hyb_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: The raw signal intensities were obtained with Bluefuse. The unreliable and morphologically corrupted measurement spots were removed from the data. We used the global mode normalization.

molecule: genomic DNA

source_name: small intestinal adenocarcinoma

extract_protocol: DNA extraction was performed using the the QIAmp DNA Micro Kit (Qiagen).

tag: age

tag: sex

value: female

tag: site tumor

value: Jejunum

tag: celiac disease

value: Yes

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: reference

value: Pooled DNA from the blood of 10 normal male individuals


title: GFP Untreated 12hr 282295723

value: Distortion Severity:0.02

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.18

value: Absent (%) Dev.:0.95

value: Scaling Factor:0.7

value: Scaling Factor Dev.:0.72

tag: Pretreatment [C]:GFP

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113402

tag: Treatment amount [C]:(Not applicable)

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_Untreated_12hr

tag: RNA extraction source key [A]:282295723


title: GFP Untreated 24hr 282295853

tag: Quality

value: Gradient Severity:0.04

value: Distortion Severity:0.04

value: Defective Area (%):0.01

value: Outlier Area (%):0.04

value: Background Mean Dev.:0.36

value: Absent (%) Dev.:0.02

value: Scaling Factor:0.65

value: Scaling Factor Dev.:0.34

tag: Time point [C]:24 hours

tag: Genomic ID [C]:113503

tag: Cell name [C]:HAECT

tag: Cohort name [C]:GFP_Untreated_24hr

tag: RNA extraction source key [A]:282295853


title: SBA_47

label_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: age

tag: sex

value: female

value: Jejunum


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68091.gif

tag: strain/genotype

value: MTB1254 WT


title: GFP Untreated 12hr 282295713

value: Gradient Severity:0.03

value: Distortion Severity:0.02

value: Defective Area (%):0

value: Background Mean Dev.:0.03

value: Absent (%) Dev.:0.5

value: Scaling Factor:0.61

value: Scaling Factor Dev.:0

tag: Time point [C]:12 hours

tag: Genomic ID [C]:113401

tag: Cell type [C]:Endothelial

tag: RNA extraction source key [A]:282295713


title: SBA_46

value: male

tag: site tumor

tag: celiac disease

value: Yes

source_name: female reference DNA

tag: reference

value: Pooled DNA from the blood of 10 normal female individuals


title: LOX1 Untreated 2hr 282295543

value: Gradient Severity:0.04

value: Distortion Severity:0.03

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.27

value: Absent (%) Dev.:0.52

value: Scaling Factor:0.62

value: Scaling Factor Dev.:0.05

tag: Pretreatment [C]:LOX1

tag: Time point [C]:2 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213202

tag: Treatment amount [C]:(Not applicable)

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:LOX1_Untreated_2hr

tag: RNA extraction source key [A]:282295543


title: MTB1254 Opp KO complemented vs Opp KO in 7H9OADC, OD  1.0-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68155.gif

source_name: MTB 1254 Rv3662c-3665c  (Opp) KO::complemented


title: LOX1 Untreated 6hr 282295663

tag: Quality

value: Gradient Severity:0.08

value: Distortion Severity:0.08

value: Background Mean Dev.:0.99

value: Absent (%) Dev.:1.92

value: Scaling Factor:1.1

value: Scaling Factor Dev.:4.2

tag: Time point [C]:6 hours

tag: Genomic ID [C]:213302

tag: Cell name [C]:HAECT

tag: Cohort name [C]:LOX1_Untreated_6hr

tag: RNA extraction source key [A]:282295663


title: MTB1254 Opp KO complemented vs Opp KO in 7H9OADC, OD  1.0-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68154.gif

tag: strain/genotype

value: MTB 1254 Rv3662c-3665c  (Opp) KO::complemented


title: GFP Untreated 2hr 282295473

value: Gradient Severity:0.05

value: Distortion Severity:0.1

value: Defective Area (%):0

value: Outlier Area (%):0

value: Background Mean Dev.:1.93

value: Absent (%) Dev.:0.71

value: Scaling Factor:0.64

value: Scaling Factor Dev.:0.22

tag: Pretreatment [C]:GFP

tag: Genomic ID [C]:113201

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:GFP_Untreated_2hr

tag: RNA extraction source key [A]:282295473


title: LOX1 oxLDL 12hr 282295813

value: Gradient Severity:0.04

value: Distortion Severity:0.02

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.89

value: Absent (%) Dev.:1.34

value: Scaling Factor:0.54

value: Scaling Factor Dev.:0.58

tag: Pretreatment [C]:LOX1

tag: Time point [C]:12 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221402

tag: Treatment amount [C]:50 ug/ml

tag: Cohort name [C]:LOX1_oxLDL_12hr

tag: RNA extraction source key [A]:282295813


title: GFP Untreated 2hr 282295483

tag: Quality

value: Gradient Severity:0.06

value: Distortion Severity:0.07

value: Defective Area (%):0.01

value: Background Mean Dev.:2.27

value: Absent (%) Dev.:0.67

value: Scaling Factor:0.55

value: Scaling Factor Dev.:0.5

tag: Time point [C]:2 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113202

tag: Treatment amount [C]:(Not applicable)

tag: Organism species [C]:Human:Homo sapiens

tag: RNA extraction source key [A]:282295483


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68083.gif

tag: strain/genotype

value: MTB1254 WT


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 0.3-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68081.gif


title: GFP Untreated 24hr 282295843

value: Gradient Severity:0.12

value: Distortion Severity:0.08

value: Background Mean Dev.:0.06

value: Absent (%) Dev.:1.38

value: Scaling Factor:0.87

value: Scaling Factor Dev.:2.22

tag: Pretreatment [C]:GFP

tag: Time point [C]:24 hours

tag: Genomic ID [C]:113502

tag: Cell name [C]:HAECT

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:GFP_Untreated_24hr

tag: RNA extraction source key [A]:282295843


title: GFP Untreated 12hr 282295733

value: Gradient Severity:0.05

value: Distortion Severity:0.04

value: Defective Area (%):0.04

value: Outlier Area (%):0

value: Background Mean Dev.:1.04

value: Absent (%) Dev.:0.2

value: Scaling Factor:0.48

value: Scaling Factor Dev.:1.14

tag: Time point [C]:12 hours

tag: Genomic ID [C]:113403

tag: Cohort name [C]:GFP_Untreated_12hr

tag: RNA extraction source key [A]:282295733


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.5-6

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68157.gif

value: MTB 1254 Rv3662c-3665c  (Opp) KO::complemented


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68497.gif


title: SBA_43

tag: age

tag: sex

value: male

tag: site tumor

value: Jejunum

tag: celiac disease

value: Yes

tag: reference

value: Pooled DNA from the blood of 10 normal female individuals


title: SBA_40

value: Duodenum


title: GFP Untreated 24hr 282295833

tag: Quality

value: Gradient Severity:0.04

value: Distortion Severity:0.09

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.38

value: Absent (%) Dev.:1.07

value: Scaling Factor:0.52

value: Scaling Factor Dev.:0.75

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113501

tag: Treatment amount [C]:(Not applicable)

tag: Organism species [C]:Human:Homo sapiens

tag: RNA extraction source key [A]:282295833


title: LOX1 Untreated 12hr 282295773

value: Gradient Severity:0.12

value: Distortion Severity:0.05

value: Defective Area (%):0.27

value: Background Mean Dev.:0.52

value: Absent (%) Dev.:0.98

value: Scaling Factor:0.6

value: Scaling Factor Dev.:0.12

tag: Pretreatment [C]:LOX1

tag: Genomic ID [C]:213401

tag: Cell name [C]:HAECT

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:LOX1_Untreated_12hr

tag: RNA extraction source key [A]:282295773


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 0.3-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68089.gif

tag: strain/genotype

value: MTB1254 WT


title: GFP 0hr 282295413

tag: Extract Description:GFP_0hr:113101

value: Gradient Severity:0.05

value: Distortion Severity:0.12

value: Defective Area (%):0.08

value: Outlier Area (%):0

value: Background Mean Dev.:6.14

value: Absent (%) Dev.:2.29

value: Scaling Factor:0.45

value: Scaling Factor Dev.:1.4

tag: Pretreatment [C]:GFP

tag: Time point [C]:0 hours

tag: Genomic ID [C]:113101

tag: Cohort name [C]:GFP_0hr

tag: RNA extraction source key [A]:282295413


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68090.gif


title: LOX1 Untreated 12hr 282295793

tag: Quality

value: Gradient Severity:0.1

value: Distortion Severity:0.04

value: Background Mean Dev.:0.74

value: Absent (%) Dev.:0.86

value: Scaling Factor:0.66

value: Scaling Factor Dev.:0.42

tag: Time point [C]:12 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213403

tag: RNA extraction source key [A]:282295793


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD 0.3-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68494.gif


title: GFP Untreated 6hr 282295593

value: Gradient Severity:0.04

value: Distortion Severity:0.09

value: Defective Area (%):0.01

value: Background Mean Dev.:1.13

value: Absent (%) Dev.:2.56

value: Scaling Factor:0.77

value: Scaling Factor Dev.:1.36

tag: Time point [C]:6 hours

tag: Genomic ID [C]:113301

tag: Treatment amount [C]:(Not applicable)

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_Untreated_6hr

tag: RNA extraction source key [A]:282295593


title: LOX1 oxLDL 2hr 282295573

value: Gradient Severity:0.02

value: Distortion Severity:0.01

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:2.61

value: Absent (%) Dev.:0.45

value: Scaling Factor:0.4

value: Scaling Factor Dev.:1.8

tag: Pretreatment [C]:LOX1

tag: Time point [C]:2 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221202

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:LOX1_oxLDL_2hr

tag: RNA extraction source key [A]:282295573


title: SBA_38

tag: age

tag: sex

value: male

tag: site tumor

value: Jejunum

tag: celiac disease

value: Yes

tag: reference

value: Pooled DNA from the blood of 10 normal female individuals


title: LOX1 oxLDL 24hr 282295943

tag: Quality

value: Gradient Severity:0.04

value: Distortion Severity:0.09

value: Defective Area (%):0.01

value: Background Mean Dev.:0.02

value: Absent (%) Dev.:1.4

value: Scaling Factor:0.45

tag: Time point [C]:24 hours

tag: Genomic ID [C]:221503

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:LOX1_oxLDL_24hr

tag: RNA extraction source key [A]:282295943


title: LOX1 0hr 282295463

tag: Extract Description:LOX1_0hr:213103

value: Distortion Severity:0.03

value: Background Mean Dev.:1.32

value: Absent (%) Dev.:0.46

value: Scaling Factor:0.54

value: Scaling Factor Dev.:0.6

tag: Pretreatment [C]:LOX1

tag: Time point [C]:0 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213103

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:LOX1_0hr

tag: RNA extraction source key [A]:282295463


title: LOX1 oxLDL 6hr 282295693

value: Gradient Severity:0.06

value: Distortion Severity:0.14

value: Outlier Area (%):0.04

value: Background Mean Dev.:2.84

value: Absent (%) Dev.:3.03

value: Scaling Factor:0.63

value: Scaling Factor Dev.:0.12

tag: Time point [C]:6 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221302

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cell type [C]:Endothelial

tag: Cohort name [C]:LOX1_oxLDL_6hr

tag: RNA extraction source key [A]:282295693


title: LOX1 Untreated 2hr 282295533

tag: Quality

value: Gradient Severity:0.04

value: Distortion Severity:0.07

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.2

value: Absent (%) Dev.:0.75

value: Scaling Factor Dev.:0.59

tag: Time point [C]:2 hours

tag: Genomic ID [C]:213201

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:LOX1_Untreated_2hr

tag: RNA extraction source key [A]:282295533


title: SBA_35

tag: age

tag: sex

value: male

tag: site tumor

value: Jejunum

tag: celiac disease

value: Yes

tag: reference

value: Pooled DNA from the blood of 10 normal female individuals


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1.5-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68499.gif

tag: strain/genotype

value: MTB1254 WT


title: GFP 0hr 282295423

tag: Extract Description:GFP_0hr:113102

value: Distortion Severity:0.08

value: Outlier Area (%):0

value: Background Mean Dev.:0.83

value: Absent (%) Dev.:1.65

value: Scaling Factor:0.75

value: Scaling Factor Dev.:1.2

tag: Pretreatment [C]:GFP

tag: Time point [C]:0 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113102

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:GFP_0hr

tag: RNA extraction source key [A]:282295423


title: LOX1 Untreated 12hr 282295783

tag: Quality

value: Gradient Severity:0.05

value: Distortion Severity:0.02

value: Background Mean Dev.:0.39

value: Absent (%) Dev.:0.49

value: Scaling Factor:0.55

value: Scaling Factor Dev.:0.52

tag: Pretreatment [C]:LOX1

tag: Time point [C]:12 hours

tag: Genomic ID [C]:213402

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:LOX1_Untreated_12hr

tag: RNA extraction source key [A]:282295783


title: LOX1 0hr 282295443

tag: Extract Description:LOX1_0hr:213101

value: Gradient Severity:0.04

value: Defective Area (%):0.02

value: Outlier Area (%):0.01

value: Background Mean Dev.:1.12

value: Absent (%) Dev.:0.07

value: Scaling Factor:0.51

value: Scaling Factor Dev.:0.89

tag: Genomic ID [C]:213101

tag: Cohort name [C]:LOX1_0hr

tag: RNA extraction source key [A]:282295443


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD 0.3-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68495.gif

tag: strain/genotype

value: MTB1254 WT


title: SBA_34

tag: age

tag: sex

value: female

tag: site tumor

value: Jejunum

tag: celiac disease

value: Yes

tag: reference

value: Pooled DNA from the blood of 10 normal female individuals


title: LOX1 oxLDL 2hr 282295563

tag: Quality

value: Gradient Severity:0.03

value: Distortion Severity:0.06

value: Defective Area (%):0.01

value: Outlier Area (%):0

value: Background Mean Dev.:1.61

value: Absent (%) Dev.:0.2

value: Scaling Factor:0.58

value: Scaling Factor Dev.:0.28

tag: Pretreatment [C]:LOX1

tag: Time point [C]:2 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221201

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cohort name [C]:LOX1_oxLDL_2hr

tag: RNA extraction source key [A]:282295563


title: GFP Untreated 2hr 282295493

value: Gradient Severity:0.04

value: Distortion Severity:0.02

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.23

value: Absent (%) Dev.:0.66

value: Scaling Factor:0.68

value: Scaling Factor Dev.:0.6

tag: Pretreatment [C]:GFP

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113203

tag: Treatment amount [C]:(Not applicable)

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_Untreated_2hr

tag: RNA extraction source key [A]:282295493


title: LOX1 Untreated 6hr 282295673

tag: Quality

value: Gradient Severity:0.05

value: Distortion Severity:0.1

value: Background Mean Dev.:0.14

value: Absent (%) Dev.:0.53

value: Scaling Factor:0.44

value: Scaling Factor Dev.:1.44

tag: Time point [C]:6 hours

tag: Genomic ID [C]:213303

tag: Cohort name [C]:LOX1_Untreated_6hr

tag: RNA extraction source key [A]:282295673


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1.5-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68498.gif

tag: strain/genotype

value: MTB1254 WT


title: SBA_31

tag: age

tag: sex

value: female

tag: site tumor

value: Jejunum

tag: celiac disease

value: No

tag: reference

value: Pooled DNA from the blood of 10 normal male individuals


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 0.3-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68088.gif


title: LOX1 oxLDL 2hr 282295583

value: Gradient Severity:0.11

value: Distortion Severity:0.06

value: Defective Area (%):0.01

value: Outlier Area (%):0

value: Background Mean Dev.:0.64

value: Absent (%) Dev.:1.36

value: Scaling Factor:0.72

value: Scaling Factor Dev.:0.89

tag: Pretreatment [C]:LOX1

tag: Time point [C]:2 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221203

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cohort name [C]:LOX1_oxLDL_2hr

tag: RNA extraction source key [A]:282295583


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68491.gif


title: GFP oxLDL 12hr 282295763

tag: Quality

value: Gradient Severity:0.07

value: Distortion Severity:0.05

value: Defective Area (%):0

value: Background Mean Dev.:1.1

value: Absent (%) Dev.:0.81

value: Scaling Factor:0.64

value: Scaling Factor Dev.:0.23

tag: Pretreatment [C]:GFP

tag: Time point [C]:12 hours

tag: Genomic ID [C]:121403

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_oxLDL_12hr

tag: RNA extraction source key [A]:282295763


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68490.gif

tag: strain/genotype

value: MTB1254 WT


title: SBA_29

description: 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.

tag: age

tag: sex

value: female

tag: site tumor

value: Duodenum

tag: celiac disease

value: No

tag: reference

value: Pooled DNA from the blood of 10 normal male individuals


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.5-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68087.gif


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD 0.3-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68489.gif


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.5-4

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68093.gif


title: SBA_28

value: 71 Sex=female

value: duodenum


title: GFP oxLDL 24hr 282295863

value: Gradient Severity:0.09

value: Distortion Severity:0.07

value: Outlier Area (%):0

value: Background Mean Dev.:2.02

value: Absent (%) Dev.:1.17

value: Scaling Factor:0.61

value: Scaling Factor Dev.:0.04

tag: Time point [C]:24 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:121501

tag: Cell name [C]:HAECT

tag: Treatment amount [C]:50 ug/ml

tag: Cohort name [C]:GFP_oxLDL_24hr

tag: RNA extraction source key [A]:282295863


title: GFP oxLDL 12hr 282295743

tag: Quality

value: Gradient Severity:0.03

value: Distortion Severity:0.03

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.54

value: Absent (%) Dev.:0.89

value: Scaling Factor:0.53

value: Scaling Factor Dev.:0.69

tag: Pretreatment [C]:GFP

tag: Time point [C]:12 hours

tag: Genomic ID [C]:121401

tag: Cell type [C]:Endothelial

tag: RNA extraction source key [A]:282295743


title: GFP oxLDL 12hr 282295753

value: Gradient Severity:0.02

value: Distortion Severity:0.01

value: Background Mean Dev.:0.11

value: Absent (%) Dev.:0.09

value: Scaling Factor:0.69

value: Scaling Factor Dev.:0.66

tag: Genomic ID [C]:121402

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_oxLDL_12hr

tag: RNA extraction source key [A]:282295753


title: GFP oxLDL 24hr 282295873

value: Gradient Severity:0.07

value: Defective Area (%):0.04

value: Background Mean Dev.:0.79

value: Absent (%) Dev.:0.14

value: Scaling Factor:0.52

value: Scaling Factor Dev.:0.75

tag: Time point [C]:24 hours

tag: Genomic ID [C]:121502

tag: RNA extraction source key [A]:282295873


title: LOX1 oxLDL 12hr 282295823

value: Gradient Severity:0.03

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.18

value: Absent (%) Dev.:0.24

value: Scaling Factor:0.68

value: Scaling Factor Dev.:0.56

tag: Pretreatment [C]:LOX1

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221403

tag: Cell name [C]:HAECT

tag: Cohort name [C]:LOX1_oxLDL_12hr

tag: RNA extraction source key [A]:282295823


title: LOX1 Untreated 2hr 282295553

tag: Quality

value: Gradient Severity:0.05

value: Distortion Severity:0.02

value: Outlier Area (%):0

value: Background Mean Dev.:0.44

value: Absent (%) Dev.:0.3

value: Scaling Factor:0.58

value: Scaling Factor Dev.:0.29

tag: Time point [C]:2 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:213203

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:LOX1_Untreated_2hr

tag: RNA extraction source key [A]:282295553


title: GFP oxLDL 2hr 282295513

value: Gradient Severity:0.04

value: Background Mean Dev.:0.6

value: Absent (%) Dev.:0.2

value: Scaling Factor:0.72

value: Scaling Factor Dev.:0.95

tag: Pretreatment [C]:GFP

tag: Genomic ID [C]:121202

tag: Treatment amount [C]:50 ug/ml

tag: Cell type [C]:Endothelial

tag: Organism species [C]:Human:Homo sapiens

tag: Cohort name [C]:GFP_oxLDL_2hr

tag: RNA extraction source key [A]:282295513


title: LOX1 oxLDL 6hr 282295703

value: Gradient Severity:0.06

value: Distortion Severity:0.03

value: Defective Area (%):0

value: Outlier Area (%):0.01

value: Background Mean Dev.:0.77

value: Absent (%) Dev.:0.98

value: Scaling Factor:0.87

value: Scaling Factor Dev.:2.24

tag: Pretreatment [C]:LOX1

tag: Time point [C]:6 hours

tag: Treatment [C]:Oxidized LDL

tag: Genomic ID [C]:221303

tag: Cell name [C]:HAECT

tag: Cohort name [C]:LOX1_oxLDL_6hr

tag: RNA extraction source key [A]:282295703


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-5

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68150.gif

tag: strain/genotype

value: MTB1254 WT


title: GFP oxLDL 6hr 282295643

tag: Quality

value: Gradient Severity:0.02

value: Distortion Severity:0.04

value: Defective Area (%):0.01

value: Background Mean Dev.:1.42

value: Absent (%) Dev.:0.38

value: Scaling Factor:0.45

value: Scaling Factor Dev.:1.43

tag: Genomic ID [C]:121303

tag: Cohort name [C]:GFP_oxLDL_6hr

tag: RNA extraction source key [A]:282295643


title: GFP 0hr 282295433

tag: Extract Description:GFP_0hr:113103

value: Gradient Severity:0.04

value: Background Mean Dev.:0.49

value: Absent (%) Dev.:0.17

value: Scaling Factor:0.63

value: Scaling Factor Dev.:0.13

tag: Pretreatment [C]:GFP

tag: Time point [C]:0 hours

tag: Treatment [C]:(Not applicable)

tag: Genomic ID [C]:113103

tag: Treatment amount [C]:(Not applicable)

tag: Cohort name [C]:GFP_0hr

tag: RNA extraction source key [A]:282295433


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.0-6

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68151.gif


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1.5-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68493.gif


title: Slide 70 LpMB452_A_High

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: This data relates to an experiment studying the effect of Lactobacillus plantarum MB452 on the gene expression of the intestinal epithelial cell line Caco-2. Experiment was carried out by Dr Rachel Anderson at AgResearch Grasslands, Palmerston North, New Zealand.

hyb_protocol: The amplified and fluorescently-labeled cRNA were hybridized using the Agilent oligonucleotide microarray in situ hybridization kit (5184-3568). Experimental and reference cRNA (750 ng of each) was mixed with the control target, fragmented for 30 minutes at 60C in the dark and hybridized onto Agilent Technologies 44k whole human genome oligonucleotide arrays (G4112A) in a rotation oven at 60C, at 4 rpm for 17 hours. Following hybridization the chambers were dissembled and the microarray slides were washed in Agilent Wash Solutions I, II and III, and air dried.

scan_protocol: The slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA). Each slide was scanned at two photomultiplier tube (PMT) voltages intensities - a high scan of approximately 600 PMT, and a low scan of approximately 450 PMT.

data_processing:
The values from these two scans were then combined to give a single set of data based on the method of Lyng et al (2004; BMC Genomics). The high intensity scan values were used for all spots except those nearing saturation (this level was optimized for each slide by determining the approximate point at which there was no longer a constant ratio between the high and low scans). Then for higher intensity spots, the low intensity scan values were substituted into the equation describing the linear relationship between the low and high scans and the resultant reading used. Spot identification and quantification was performed with GenePix 6.0 software (Molecular Devices). The images were also manually checked and any poor quality spots hand-flagged and these values removed before statistical analysis.
The Limma package in Bioconductor was used to analyze the microarray data. No background correction was used as image analysis of the foreground and background fluorescence intensity measurements did not detect any relationship. The data were normalized using a loess smoothing procedure to remove systematic spatial effects, and internal Agilent control spot values (Pro25G and EQC) were removed before further analysis. For each spot, a modified t-test was calculated using an empirical Bayes approach. Genes with a fold change greater than 1.2 and a modified p-value less than 0.05 were considered differentially expressed.

source_name: L. plantarum MB452-treated Caco-2 cells

label_protocol: An equal amount of RNA from three wells of the same treatment was pooled together to yield enough RNA for the gene expression analysis. Equal amounts of RNA from all wells were pooled together to make the reference RNA sample. The RNA samples (experimental and reference) were labeled using the Agilent Low RNA Input Linear Amplification Kit (5183-3523). The total RNA (500 ng) was amplified and reverse transcribed to cDNA using T7-polymerase. The cDNA was labeled with either cyanine3 (reference sample) or cyaninine5 (experimental samples) labeled CTP dye (Perkin-Elmer/NEN Life Sciences, Boston, MA, USA). Dye incorporation was analyzed using a Nanodrop ND-1000 spectrophotometer. All samples had a yield of > 825 ng of cRNA and specific activity of > 8 pmol dye/µg cRNA.

growth_protocol: Caco-2 cells were seeded into all wells in 6-well plates at a density of 3 x 105 cells/well. Cells were grown in M199 tissue culture medium with 10% fetal bovine serum (GIBCO, Invitrogen Corporation, Auckland, NZ), 1% non-essential amino acids (MEM non-essential amino acids 100x solution, Sigma-Aldrich, St Louis, USA) and 1% penicillin-streptomycin (10000 units penicillin G sodium salt and 10000 g streptomycin sulfate in 0.85% saline, GIBCO, Invitrogen Corporation, Auckland, NZ) at 37C in 5% CO2. The media was replaced every 3-4 days and the Caco-2 monolayers were grown for 18 days to allow them to differentiate prior to the experiment.

extract_protocol: The total RNA was extracted from the Caco-2 cells using TRIzol (Invitrogen, Auckland, New Zealand) according to the manufacturer’s instructions. The RNA was precipitated by the addition of 1 L glycogen (5 mg/mL), 0.1 volumes 3M sodium acetate and 2.5 volumes 100% ethanol and incubated at -85C for 30 minutes prior to centrifugation (12000g for 30 minutes). The pellet was washed with 100% ethanol and recollected (12000g for 20 minutes) three times. This ensured that all contaminating salts were removed from the sample prior to further purification. The RNA quantity and purity was determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmingtom, DE, USA), and all samples had an OD260nm/OD230nm ratio > 1.8. The extracted RNA was purified using RNeasy mini columns (QIAGEN, San Diego, CA, USA) and RNA quality was assessed using an RNA 6000 NanoLabChip kit with the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). All samples had an OD260nm/OD280nm ratio, a Bioanalyser 28s/18s peak ratio > 1.5 and a RNA integrity number (RIN) > 8.

treatment_protocol: L. plantarum MB 452 was cultured overnight in MRS broth at 37C with 5% CO2. Bacterial cells were collected by centrifugation (12000 rpm for 5 minutes in a micro centrifuge) and suspended in M199 with 1% non-essential amino acids to an optical density at 600 nm of 0.9. The media was removed from the top of the Caco-2 monolayers and replaced with the treatment solution. Six wells were treated with L. plantarum MB 452 (OD 600 nm of 0.9) suspended in cell culture media (M199 and 1% non-essential amino acids) and six wells were treated with control media. After 10 hours of exposure (37C, 5% CO2) the treatment solutions were removed and the monolayers were rinsed with PBS.

tag: cell line

tag: cell type

value: human colorectal adenocarcinoma

source_name: L. plantarum MB452-treated Caco-2 cells Reference Sample


title: Slide 71 LpMB452_B_Low

treatment_protocol: L. plantarum MB 452 was cultured overnight in MRS broth at 37C with 5% CO2. Bacterial cells were collected by centrifugation (12000 rpm for 5 minutes in a micro centrifuge) and suspended in M199 with 1% non-essential amino acids to an optical density at 600 nm of 0.9.


title: MTB1254 Opp KO complemented vs Opp KO in 7H9OADC, OD  1.0-2

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68153.gif

value: MTB 1254 Rv3662c-3665c  (Opp) KO::complemented


title: Slide 68 Control_A_High

source_name: Control Caco-2 cells

source_name: Control Caco-2 cells Reference Sample


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD 0.3-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68488.gif


title: Slide 69 Control_B_Low


title: Slide 68 Control_A_Low


title: Slide 70 LpMB452_A_Low


title: Slide 71 LpMB452_B_High


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 0.3-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68080.gif


title: MTB1254 Opp KO complemented vs Opp KO in 7H9OADC, OD  1.0-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68152.gif


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.5-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68092.gif


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC, OD 1.5-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68084.gif


title: pCs98scpr20060512_melM3simF5_65

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description: Cy3= male_melanogaster genomic DNA Cy5= male_simulans genomic DNA hybed by SCP Renn on 2004

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  65 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=800_720 ScanPower=100_100

data_processing: After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized in R/Bioconductor with within-arrays loess (using a set of 1000 conserved genes) and intensity ratios were calculated.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster

label_protocol: dCTP incorporation with Klenow

growth_protocol: Grown in fly nutrient media

extract_protocol: ProteinaseK/Phenol Extraction

tag: gender

value: male

tag: species

value: melanogaster

organism: Drosophila simulans

source_name: Drosophila simulans

value: simulans


title: pEs59scpr20060512_simM3melM5_65

description: Cy3= male_simulans genomic DNA Cy5= male_melanogaster genomic DNA hybed by SCP Renn on 2004

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_720 ScanPower=100_100


title: SBA_21

tag: age

tag: sex

value: female

tag: site tumor

value: ILeum

tag: celiac disease

value: No

tag: reference

value: Pooled DNA from the blood of 10 normal male individuals


title: pCs28scpr20060520_melM3secM5_65

description: Cy3= male_melanogaster genomic DNA Cy5= male_sechellia genomic DNA hybed by SCP Renn on 2004

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=780_720 ScanPower=100_100

organism: Drosophila sechellia

source_name: Drosophila sechellia

value: sechellia


title: pCs29scpr20060520_secM3melM5_65

description: Cy3= male_sechellia genomic DNA Cy5= male_melanogaster genomic DNA hybed by SCP Renn on 2004

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_720 ScanPower=100_100


title: SBA_16

description: 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.

value: Jejunum


title: SBA_18

value: duodenum


title: SBA_15


title: SBA_19

value: Pooled DNA from the blood of 10 normal female individuals


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1-3

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68496.gif

tag: strain/genotype

value: MTB1254 WT


title: MTB1254 WT vs Rv3662c-3665c KO in 7H9OADC-Exp2, OD1.5-1

description:
biological sample opp study; the clinical mtb isolate 1254 was used as the parental, wild type (wt) for construction of the permease knock-out and complemented strains.; protocol type = biological sample; performer: Mario Alberto,,Flores-Valdez
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68492.gif


title: pCs31scpr20060520_yakM3melM5_65

description: Cy3= male_yakuba genomic DNA Cy5= male_melanogaster genomic DNA hybed by SCP Renn on 2004

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=750_760 ScanPower=100_100

organism: Drosophila yakuba

source_name: Drosophila yakuba

value: yakuba


title: pCs56scpr20060510_yakM3melM5_65_eq

description: Cy3= female_yakuba genomic DNA Cy5= male_melanogaster genomic DNA hybed by SCP Renn on 2004

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=720_720 ScanPower=100_100


title: pCs34scpr20060510_melM3yakM5_70_opt

description: Cy3= male_melanogaster genomic DNA Cy5= male_yakuba genomic DNA hybed by SCP Renn on 2004

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  70 degrees 12-16 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=840_720 ScanPower=100_100


title: pCs41scpr20060510_melM3yakM5_67_opt

description: Cy3= male_melanogaster genomic DNA Cy5= female_yakuba genomic DNA hybed by SCP Renn on 2004

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at  67 degrees 12-16 hours


title: growth-arrested cells (7b HCE2CT+BIO)

city: Dallas

first: Andres

middle: I

last: Roig

state: TX

address: 5323 Harry Hines Blvd

department: Cell Biology

institute: UT Southwestern

hyb_protocol: Hybridization is done according to manufacturer's (Illumina) instruction using their reagents

scan_protocol: scanned using beadstation 500 beadarray reader, aquisition with BeadStudio

data_processing: normalized using MBCB described in, Enhanced identification and biological validation of differential gene expression via Illumia whole-genome expression arrays through the use of the model-based background correction methodology. Nucleic Acids Research. 2008, Vol 36, No.10.

label: biotinylated UTP

source_name: Human Colonic Epithelial Cells

label_protocol: Illumina Total Prep Kit from Ambion

growth_protocol: Cells were routinely grown in 2% calf serum, insulin, transferring, selenium, hydrocortisone, and 25ng/ml of EGF in Primaria tissue culture dishes and in 2% oxygen. Log-growth phase non-immortalized and immortalized cells were submitted through the extraction procedure when 75% confluent.  The slow-growing and growth- arrested cells were 85% confluent when submitted through the extraction procedure

extract_protocol: RNA was extreacted using the TRIZOL-Kit Hybrid Protocol

treatment_protocol: Slow growing cells: exposed to reduce serum (0.1%) and reduced EGF (1.25 ng/ml) for two days prior to extraction procedure. Growth arrested cells: exposed to reduce serum (0.1%), reduced EGF (1.25 ng/ml), and BIO (5 micrograms/ml) for two days prior to extraction procedure.

value: colonic epithelial progenitor cells

tag: phentoype

value: growth-arrested cells


title: pCs30scpr20060520_melM3yakM5_65


title: slow-growing cells (8b HCE2CT-BIO)

value: slow-growing cells


title: pCs43scpr20060510_yakM3melM5_70_eq

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_770 ScanPower=100_100


title: non-immortalized cells  (6b HCEC2CT)

value: non-immortalized cells


title: growth-arrested cells (7a HCE2CT+BIO)

value: male


title: pCs44scpr20060510_yakM3melM5_67_eq

value: melanogaster


title: pCs42scpr20060510_melM3yakM5_65_opt


title: slow-growing cells (8a HCE2CT-BIO)


title: SBA_12


title: SBA_11


title: Slide 69 Control_B_High

description: This data relates to an experiment studying the effect of Lactobacillus plantarum MB452 on the gene expression of the intestinal epithelial cell line Caco-2. Experiment was carried out by Dr Rachel Anderson at AgResearch Grasslands, Palmerston North, New Zealand.

value: human colorectal adenocarcinoma


title: non-immortalized cells  (6a HCEC2CT)


title: immortalized cells (5a HCEC2)

value: immortalized cells


title: slow-growing cells (4b HCE1CT-BIO)


title: immortalized cells (5b HCEC2)


title: SBA_07

value: female


title: slow-growing cells (4a HCE1CT-BIO)


title: SBA_06

value: No


title: growth-arrested cells (3b HCE1CT+BIO)


title: Biopsy 4712

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76454.gif

scan_protocol: Scanner Model: GenePix 4000B

organism: Macaca mulatta

source_name: 1.0 ug amplified normal monkey stomach cDNA

value: normal monkey stomach cDNA

source_name: 1.0 ug amplified Biopsy 4712 cDNA

tag: tissue

value: stomach biopsy

tag: biopsy number

tag: infection

tag: compound based treatment


title: growth-arrested cells (3a HCE1CT+BIO)


title: Biopsy 4694

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76448.gif

source_name: 1.0 ug amplified Biopsy 4694 cDNA


title: non-immortalized cells  (2a HCEC1CT)


title: Biopsy 4718

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76457.gif

source_name: 1.0 ug amplified Biopsy 4718 cDNA


title: Biopsy 4724

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76460.gif

source_name: 1.0 ug amplified Biopsy 4724 cDNA


title: Biopsy 4676

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76430.gif

source_name: 1.0 ug amplified Biopsy 4676 cDNA


title: Biopsy 4690

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76444.gif

source_name: 1.0 ug amplified Biopsy 4690 cDNA


title: Biopsy 4674

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76429.gif

source_name: 1.0 ug amplified Biopsy 4674 cDNA


title: Biopsy 4678

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76432.gif

source_name: 1.0 ug amplified Biopsy 4678 cDNA


title: Biopsy 4710

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76452.gif

source_name: 1.0 ug amplified Biopsy 4710 cDNA


title: SBA_02

description: 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.

source_name: small intestinal adenocarcinoma

value: Duodenum

source_name: female reference DNA


title: Biopsy 4722

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76459.gif

source_name: 1.0 ug amplified Biopsy 4722 cDNA


title: immortalized cells (1a HCEC1)


title: immortalized cells (1b HCEC1)


title: Biopsy 4714

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76455.gif

source_name: 1.0 ug amplified Biopsy 4714 cDNA


title: Biopsy 4726

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76461.gif

source_name: 1.0 ug amplified Biopsy 4726 cDNA


title: Biopsy 4680

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76434.gif

source_name: 1.0 ug amplified Biopsy 4680 cDNA


title: Biopsy 4682

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76436.gif

source_name: 1.0 ug amplified Biopsy 4682 cDNA


title: Biopsy 4692

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76446.gif

source_name: 1.0 ug amplified normal monkey stomach cDNA

source_name: 1.0 ug amplified Biopsy 4692 cDNA


title: Biopsy 4716

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76456.gif

source_name: 1.0 ug amplified Biopsy 4716 cDNA


title: non-immortalized cells  (2b HCEC1CT)

source_name: Human Colonic Epithelial Cells


title: Biopsy 4686

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76440.gif

source_name: 1.0 ug amplified Biopsy 4686 cDNA


title: Biopsy 4720

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76458.gif

source_name: 1.0 ug amplified Biopsy 4720 cDNA


title: Biopsy 4688

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76442.gif

source_name: 1.0 ug amplified Biopsy 4688 cDNA


title: 1971 vs 1970

status: Public on Oct 06 2009

city: PAMPLONA

first: David

last: Blanco

address: Avda Pio XII, 55

department: Area Oncology

country: Spain

institute: CIMA

description: The general reproducibility of the hybridization platform (labeling procedure, hybridization and detection) was assessed by means of self to self hybridization.

hyb_protocol: Arrays were hybridized during 17h at 60ºC employing Agilent gaskets and hybridization chambers in an Agilent Hybridization Oven (G2545A).

scan_protocol: Raw data were acquired using an Agilent DNA Microarray Scanner and Agilent Feature Extraction Software (v.9.1).

data_processing: For data processing, a novel algorithm that distinguished between changes in gene expression and splicing variation was developed.

source_name: Paired normal tissue

label_protocol: First-strand cDNA synthesis employing a chimeric primer including the T7 promoter sequences and a stretch of 6 random bases. Second-strand cDNA synthesis and in vitro transcription using the T7 RNA polymerase in the presence of a labeled ribonucleotide (Cy3- or Cy5-CTP).

extract_protocol: PolyA+ RNA was extracted using Dynabead magnetic particles.

value: normal lung

tag: patient

value: diagnostic NSCLC

source_name: Paired tumor tissue

value: lung tumor


title: Tumour High Hypoxia H5

city: Manchester

first: Carla

middle: Sofia

last: Moller-Levet

address: Wilmslow Road

department: Paterson Insitute for Cancer Research

country: United Kingdom

institute: The University of Manchester

description: Tumour High Hypoxia H5

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChip scanner 3000 7G

data_processing:
Exon array analysis was performed using the Bioconductor package Exonmap and Matlab. Data were  first summarised using RMA (affy package in Bioconductor)  and then filltered to include only exon targeting probesets, predicted to hybridize to a single locus within the genome.
probe group file: HuEx-1_0-st-v2.pgf

source_name: HNSCC high HS

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

extract_protocol: Samples were treated with the RiboMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: hypoxia score

value: High


title: 1887 vs 1886


title: 1965 vs 1964


title: 1899 vs 1989


title: Biopsy 4684

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76438.gif

source_name: 1.0 ug amplified Biopsy 4684 cDNA


title: 1977 vs 1976


title: Biopsy 4696

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76450.gif

source_name: 1.0 ug amplified Biopsy 4696 cDNA


title: 1803 vs 1802


title: Tumour High Hypoxia H2

description: Tumour High Hypoxia H2


title: 1869 vs 1868


title: 1839 vs 1838


title: 1857 vs 1856


title: 1875 vs 1874


title: Tumour High Hypoxia H3

description: Tumour High Hypoxia H3


title: NB4_cell_ATRA_72hours

city: Nijmegen

first: Joop

middle: H.

last: Jansen

address: Geert Grooteplein Zuid 8

department: Laboratory for Hematology

institute: Radboud University Nijmegen Medical Centre

description:
t=72
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: IterPlier alogrithm from Affymetrix Expression Console

source_name: Blood

label_protocol: GeneChip WT Terminal Labeling Kit

extract_protocol: Total mRNA was extracted using RNAbee according to the manufacturer's instructions.


title: NB4_cell_ATRA_48hours

description:
t=48
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: Tumour High Hypoxia H4

description: Tumour High Hypoxia H4


title: 1833 vs 1832


title: NB4_cell_ATRA_96hours

description:
t=96
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: 1947 vs 1946


title: 1821 vs 1820


title: 1815 vs 1814


title: Tumour Low Hypoxia L4

description: Tumour Low Hypoxia L4

source_name: HNSCC low HS

value: Low


title: Tumour Low Hypoxia L5

description: Tumour Low Hypoxia L5


title: 4352_Stom_Tum_U133A

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 31 primary gastric tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

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 500.

source_name: primary gastric tumor, 4352

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

value: gastric tumor


title: Tumour High Hypoxia H1

description: Tumour High Hypoxia H1


title: 1779 vs 1778


title: 4350_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 4350


title: 4349_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 4349


title: 3865_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3865


title: 4351_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 4351


title: 1845 vs 1844


title: 3862_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3862


title: Tumour Low Hypoxia L2

description: Tumour Low Hypoxia L2


title: 304 vs 303


title: 3864_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3864


title: 3861_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3861


title: 0202 vs 0201


title: 3857_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3857


title: 3860_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3860


title: NB4_cell_no_ATRA

description:
t=0
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: 3819_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3819


title: Tumour Low Hypoxia L3

description: Tumour Low Hypoxia L3


title: 3858_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3858


title: 1785 vs 1754

source_name: Paired normal tissue

source_name: Paired tumor tissue


title: 3818_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3818


title: 3863_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3863


title: 3820_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3820


title: 3817_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3817


title: 3814_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3814


title: 3816_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3816


title: 3813_Stom_Tum_U133A

description: Series of 31 primary gastric tumors

source_name: primary gastric tumor, 3813