title: Parental cell line

city: Ottawa

first: Wing

middle: Y

last: Chang

state: Ontario

address: 501 Smyth

institute: Ottawa Hospital Research Institute

description: Endothelial Progenitor Cell

hyb_protocol: Samples were hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix) in a GeneChip Hyb Oven 640 (Affymetrix) according to standard protocol. Arrays were washed and stained using the GeneChip Hyb, Wash and Stain kit (Affymetrix) with a GeneChip Fluidics Station 450 (Affymetrix) according to standard protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix), and image processing was performed using AGCC version 3.1.

data_processing: The arrays were RMA normalized using the rma function of the R-Bioconductor affy package.

source_name: endothelial progenitor cells derived from leukapheresis product

label_protocol: Microarray target preparation from total RNA was performed with the Ambion WT Expression kit (Life Technologies) according to the Affymetrix standard protocol. Sense-strand cDNA was then fragmented and biotin-labeled using the Genechip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Endothelial progenitor cells were cultured in Endothelial Growth Medium (Lonza), and human embryonic stem cells (WiCell) and induced-pluripotent stem cells were cultured in E8 medium.

extract_protocol: Total RNA was isolated using the Macherey-Nagel total RNA isolation kit.

tag: cell type

value: endothelial progenitor cells


title: Human embryonic stem cell line

status: Public on Dec 16 2012

type: RNA

country: Canada

description: H9 hESC

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: human embryonic stem cell line

tag: cell line

value: embryonic stem cells


title: Liver_WT_Chow_Biolrep1

city: Portland

first: Harini

last: Sampath

state: OR

address: 3181 SW Sam Jackson Park Rd

department: CROET

country: USA

institute: OHSU

hyb_protocol: 1.8 ug of target was hybridized with the GeneChip Mouse Gene ST Array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Affymetrix), signal amplification with biotinylated anti-streptavidin antibody (Affymetrix), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip 3000 laser scanner (Affymetrix) with the 7G upgrade.

data_processing: Data visualization and exploratory analysis were conducted using GeneSifter web-based software, release 59.0 (GeoSpiza Inc., Seattle, WA). Affymetrix .cel files were uploaded to the GeneSifter web site with GC robust multiarray average (RMA) normalization

label: biotin

organism: Mus musculus

source_name: Chow-fed wild-type liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with 125 ng input RNA

growth_protocol: 10 week old male mice were individually housed for 10 weeks

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

treatment_protocol: Mice were given ad libitum access to chow or HFD for 10 weeks

tag: gender

value: male

tag: strain

tag: tissue

value: liver

tag: diet

value: Chow-fed

tag: genotype/variation

value: wild-type


title: Liver_Ogg1-/-_HFD_Biolrep4

source_name: HFD-fed Ogg1-/- liver

value: HFD-fed


title: Mammoplastic reduction (control) N. 90

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: Frozen mammoplastic reduction sample was provided from the NCCR Molecular Oncology (Prof. Cathrin Brisken), Lausanne, Switzerland.

label_protocol: We performed miRNA expression profiling from 100 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad).

extract_protocol: After surgical removal, sample was macro-dissected by pathologists, quickly frozen and stored at –80°C. Total RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissue, according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity and content of microRNAs (%) in each sample was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA sample with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 30% were used for microarray analysis.

tag: - sex

value: female

tag: - date of birth

tag: - date of surgery


title: Induced pluripotent stem cell clone B

description: EPC 106 iPS1B

source_name: induced-pluripotent stem cell line derived from endothelial progenitor cells

value: induced-pluripotent stem cells


title: Mammoplastic reduction (control) N. 93


title: Induced pluripotent stem cell clone C

description: EPC 106 iPS1C


title: Induced pluripotent stem cell clone A

description: EPC 106 iPS1A


title: Mammoplastic reduction (control) N. 87

extract_protocol: After surgical removal, sample was macro-dissected by pathologists, quickly frozen and stored at –80°C. Total RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissue, according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity and content of microRNAs (%) in each sample was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA sample with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 30% were used for microarray analysis


title: Mammoplastic reduction (control) N. 88


title: Induced pluripotent stem cell clone D

description: EPC 106 iPS1D


title: Mammoplastic reduction (control) N. 83


title: Uterine leoimyoma tumor_642_Secretory

city: Botucatu

first: Priscila

middle: Daniele Ramos

last: Cirilo

state: SP

address: Distrito de Rubião Junior S/N

department: Genética

country: Brazil

institute: Instituto de Biociências de Botucatu

description:
642
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.

hyb_protocol: After clean-up (RNeasy mini-kit - QIAGEN), labeling efficiency was calculated and 850 ng from each Cy3 and Cy5 samples were mixed and add 10x blocking agent, 25X fragmentation buffer and 2X GE hybridization buffer RPM (Agilent Kit). Solutions were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: Agilent Feature Extraction Software version (v.10.1.1.1) was used for background subtraction and LOWESS normalization.

source_name: Uterine leoimyoma tumor sample, secretory phase

label_protocol: 0.5 to 1 µg of total RNA were reversed transcribed at 40°C for 2h and 65ºC for 15min in the presence of MMLV-RT enzyme (Agilent), 10mM dNTP mix. cDNA tumor samples were labeled with Cy3 and cDNA reference samples with Cy5 in the presence of T7 RNA Polymerase, RNase OUT, NTPmix, 50% PEG and 0,1M DTT for 40°C for 2h.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from frozen tissues (ULs and normal myometrium) using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.

value: uterine leoimyoma tumor

tag: menstrual cycle phase

value: secretory

source_name: Adjacent normal myometrium, secretory phase

value: normal uterine tissue (myometrium)


title: Uterine leoimyoma tumor_670_Secretory

description:
670
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Mammoplastic reduction (control) N. 78


title: Uterine leoimyoma tumor_631_Proliferative

description:
631
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.

source_name: Uterine leoimyoma tumor sample, proliferative phase

value: proliferative

source_name: Adjacent normal myometrium, proliferative phase


title: Uterine leoimyoma tumor_630_Proliferative

description:
630
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Mammoplastic reduction (control) N. 81


title: Uterine leoimyoma tumor_625_Secretory

description:
625
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Mammoplastic reduction (control) N. 74


title: Uterine leoimyoma tumor_708_Secretory

description:
708
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Mammoplastic reduction (control) N. 73


title: Liver_WT_HFD_Biolrep6

source_name: HFD-fed wild-type liver


title: Mammoplastic reduction (control) N. 9M


title: Mammoplastic reduction (control) N. 4Mdx


title: Mammoplastic reduction (control) N. 68


title: Ssalar_0daypostSBMfeed_rep3_tank2

status: Public on Dec 17 2012

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

hyb_protocol: Each experimental sample and reference pool (825 ng each) was fragmented for 30 minutes at 60°C, mixed with an equal amount of 2x GEx Hybridization buffer HI-RPM (Agilent Gene Expression Hybridization Kit, No. 5188-5242) and loaded onto a cGRASP 44k Salmonid oligonucleotide microarray (Agilent Technologies, [21]). The hybridization was incubated for 17 hrs (10 rpm at 65°C) in a hybridization oven (Agilent). Slides were washed immediately after hybridization using wash buffers, acetonitrile and Stabilization and Drying Solution, as per manufacturer’s instructions to prevent ozone-related problems. Slides were then kept in the dark at low ozone (<9 ppb) and scanned as soon as possible.

scan_protocol: All slides were scanned using a ScanArray® Express scanner (PerkinElmer®; 5μm resolution; PMTs: Cy5: 60, Cy3: 65) in a low-ozone environment (<9 ppb).

data_processing: Scanned images were processed in the ImaGene® software (V 8.0; Biodiscovery, El Segundo, CA, USA) using the 44K salmonid GAL file (11/09) (http://web.uvic.ca/grasp/microarray/array.html). The raw data was imported into GeneSpring GX11.5 (Agilent). Annotation files and specifications of the microarray can be found at the cGRASP microarray page (http://web.uvic.ca/grasp/microarray/array.html). All spots were thresholded to 1.0, samples were normalized using an intensity-dependent LOWESS normalization and a per gene baseline to median normalization. Control spots were removed and all entities were filtered to retain only those entities in which 80% of the biological replicates had raw values ≥500 in any one of the six conditions (i.e. time points). Entities were then filtered to retain the entities in which at least 80% were flagged as ‘present’ in six of six conditions. The remaining entities were tested for significant differential expression by comparing each of the time points (day one, two, three, five, seven) to day zero using the Mann-Whitney test (p<0.05) without multiple test correction. Only genes that changed more than 1.5 fold were considered for further analysis.

organism: Salmo salar

source_name: Distal intestine

label_protocol: Reverse transcription and labeling of the RNA was done according to Agilent’s two color Low Input Quick Amp labeling protocol (Version 6.5, May 2010).cRNA was quantified using spectrophotometry (NanoDrop1000™, Thermo Fisher Scientific). All samples had specific activity >6 pmol dye per µg cRNA. Labeled cRNA was stored at -80°C in the dark until hybridization.

growth_protocol: Atlantic salmon (Salmo salar L.) of the Sunndalsøra breed held in 1 m3 fiberglass tanks with running seawater (25-30 fish per tank) at the research facilities of Nofima Marin, Sunndalsøra, Norway. Initial body weight of 500-600 g. Two diets, the reference (FM) diet contained 563 g kg-1 fishmeal meal as the sole protein source while the test diet contained 200 g kg-1 hexane-extracted (defatted) soybean meal, partially replacing the fishmeal in the FM diet. Both diets were approximately iso-nitrogenous and iso-energetic on a crude protein and gross energy basis, containing 28% lipid and 43% crude protein. All fish were adapted to the FM diet for seven days.

extract_protocol: For RNA extraction, sections of distal intestinal tissue (distal-most region of the post-gastric intestinal tract defined by appearance of annular mucosal folds and widening of intestinal diameter) were taken and placed in RNAlater at 4°C for 24h and then stored at -80°C. To ensure exposure to SBM, only fish that had content throughout the intestinal tract were sampled. From ten fish per time point (five from each tank duplicate) approximately 20 mg of sample tissue was immersed in 1 ml TRIzol® (Invitrogen), homogenized with a mixermill (Retsch MM301) and total RNA was extracted as per manufacturers protocol. Total RNA was purified using RNeasy columns as per manufacturer’s instructions (Qiagen), including an optional on-column DNase I digestion step. Samples were quantified by spectrophotometry (NanoDrop1000™, Thermo Fisher Scientific) and quality checked by agarose gel electrophoresis. Samples confirmed free of genomic DNA by PCR with and without reverse transcriptase. Samples were stored at -80°C until further use.

treatment_protocol: Day zero in this experiment marks the sampling of FM fed fish. Duplicate tanks of the remaining fish received the SBM test diet from day zero and were sampled after one, two, three, five and seven days of exposure.

source_name: Pooled 3 indiv intestine samples from each condition (n=18)

tag: reference

value: Reference pool


title: Uterine leoimyoma tumor_759_Secretory

description:
759
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 4d

source_name: Frozen breast tumor sample was selected from the Tumor Bank of the Department of Obstetrics and Gynecology, University of Turin.

tag: age (years)

tag: t stage

tag: grade

tag: lymph node (ln) status

value: negative

tag: estrogen receptor (er)

tag: progesterone receptor (pgr)

value: positive

tag: relapse

value: no


title: Uterine leoimyoma tumor_719_Secretory

description:
719
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.

tag: gender


title: Breast cancer patient N. 40d

value: yes


title: Breast cancer patient N. 71T


title: Uterine leoimyoma tumor_761_Secretory

description:
761
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_844_Proliferative

description:
844
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_853_Secretory

description:
853
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 46d


title: Breast cancer patient N. 6dbis


title: Breast cancer patient N. 54d


title: Breast cancer patient N. 44d


title: Uterine leoimyoma tumor_634_Secretory

description:
634
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 42d


title: Uterine leoimyoma tumor_1002_Secretory

description:
1002
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 7d


title: Uterine leoimyoma tumor_857_Secretory

description:
857
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 39d


title: Uterine leoimyoma tumor_855_Secretory

description:
855
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_644_Proliferative

description:
644
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_615_Proliferative

description:
615
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_1005_Proliferative

description:
1005
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_901_Proliferative

description:
901
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_947_Proliferative

description:
947
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_614_Proliferative

description:
614
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_729_Secretory

description:
729
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 38Tbis

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.


title: Uterine leoimyoma tumor_681_Proliferative

description:
681
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_629TA_Secretory

description:
629TA
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 31d


title: Breast cancer patient N. 33T

value: not available


title: Breast cancer patient N. 31T


title: Breast cancer patient N. 37d


title: Breast cancer patient N. 2d


title: Breast cancer patient N. 37T


title: Breast cancer patient N. 38d


title: Breast cancer patient N. 29d


title: Breast cancer patient N. 28T


title: Breast cancer patient N. 36T


title: Breast cancer patient N. 27bis


title: Breast cancer patient N. 28d


title: Breast cancer patient N. 27d


title: Breast cancer patient N. 26dbis


title: Breast cancer patient N. 25dbis


title: Breast cancer patient N. 24d


title: Breast cancer patient N. 16T

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings


title: Breast cancer patient N. 18d


title: Breast cancer patient N. 21bis


title: Breast cancer patient N. 16d


title: Breast cancer patient N. 19bis


title: Uterine leoimyoma tumor_631TA_Proliferative

description:
631TA
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_629TB_Secretory

description:
629TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_301T_1_Proliferative

description:
301T_1
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_301T_2_Proliferative

description:
301T_2
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_300TB_Secretory

description:
300TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 19d


title: Uterine leoimyoma tumor_301T_3_Proliferative

description:
301T_3
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 13T


title: Breast cancer patient N. 18T


title: Breast cancer patient N. 14d


title: Uterine leoimyoma tumor_630T_1_Proliferative

description:
630T_1
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_300TA_Secretory

description:
300TA
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_307T_1_Proliferative

description:
307T_1
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 22d


title: Breast cancer patient N. 13d


title: Breast cancer patient N. 13bis


title: Breast cancer patient N. 123T


title: Uterine leoimyoma tumor_303T_Secretory

description:
303T
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_304T_Proliferative

description:
304T
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_307T_2_Proliferative

description:
307T_2
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_317T_3_Secretory

description:
317T_3
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 120T


title: Uterine leoimyoma tumor_631TC_Proliferative

description:
631TC
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_317T_1_Secretory

description:
317T_1
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_642TB_Secretory

description:
642TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 6593

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis


title: Breast cancer patient N. 109T


title: Breast cancer patient N. 118T


title: Breast cancer patient N. 10d


title: Breast cancer patient N. 6624


title: Breast cancer patient N. 6592


title: Breast cancer patient N. 6587


title: Breast cancer patient N. 6609


title: Breast cancer patient N. 117T


title: Breast cancer patient N. 101T


title: Breast cancer patient N. 107T


title: Breast cancer patient N. 6571


title: Breast cancer patient N. 103T


title: Breast cancer patient N. 61


title: Breast cancer patient N. 6568


title: Breast cancer patient N. 58


title: Breast cancer patient N. 114T


title: Breast cancer patient N. 57


title: Uterine leoimyoma tumor_683TA_Secretory

description:
683TA
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_683TB_Secretory

description:
683TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_722TA_Secretory

description:
722TA
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_729TB_Secretory

description:
729TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 56


title: Breast cancer patient N. 53


title: Uterine leoimyoma tumor_722TB_Secretory

description:
722TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_722TC_Secretory

description:
722TC
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_844TB_Proliferative

description:
844TB
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Uterine leoimyoma tumor_954T_Secretory

description:
954T
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 52


title: Uterine leoimyoma tumor_317T_2_Secretory

description:
317T_2
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 49


title: Breast cancer patient N. 45


title: Breast cancer patient N. 48


title: Breast cancer patient N. 37


title: Breast cancer patient N. 36


title: Uterine leoimyoma tumor_684T_Secretory

description:
684T
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.


title: Breast cancer patient N. 32

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.


title: Breast cancer patient N. 31


title: Breast cancer patient N. 14


title: Breast cancer patient N. 12


title: Breast cancer patient N. 10


title: Breast cancer patient N. 11


title: Breast cancer patient N. 24


title: Breast cancer patient N. 6


title: miR-148b-B (miR-148b-1+, biological replicate 2)

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 73% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed. Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology. 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

source_name: MDA-MB-231 cells transfected with precursor of miR-148b were analyzed 48h after transfection

label_protocol: Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

growth_protocol: MDA-MB-231 cells were from American Type Culture Collection and maintained in standard conditions: Dulbecco's Modified Eagle's Medium containing 10 mM Glutamax and 4.5 g/mLglucose (DMEM Glutamax™, GIBCO Invitrogen Life Technologies, Carlsbad, CA), supplemented with 10% heat-inactivated FCS (Seromed, GmbH), 1 mM sodium pyruvate, 25 mM HEPES pH 7.4 and 100 μg/mL gentamicin (all from GIBCO Invitrogen Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was isolated from 106 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

treatment_protocol: To obtain transient pre-miR-148b (PM10264, Ambion) expression, cells were plated in 6-well plates at 30-50% confluency and transfected 24h later using RNAiFect (QIAGEN, Stanford, CA) reagent, according to manufacturer’s instructions, with 75 nM pre-miR-148b. Cells were tested for miR overexpression 48h later.

tag: cell line


title: Breast cancer patient N. 5


title: Uterine leoimyoma tumor_729TC_Secretory

description:
729TC
Tumor sample Cy3-labeled mixed with reference (adjacent normal myometrium) sample Cy5-labeled.

tag: tissue


title: miR-148b-C (miR-148b-2+, biological replicate 3)


title: miR-148b-D (miR-148b-3, biological replicate 4)


title: miR-148b-A (miR-148b-1, biological replicate 1)


title: CTR-D (CTR-3, biological replicate 4)

source_name: MDA-MB-231 cells transfected with negative control


title: CTR-A (CTR-1, biological replicate 1)


title: Breast cancer patient N. 34


title: CTR-C (CTR-2+, biological replicate 3)


title: Post_transplant patient 4

status: Public on Dec 15 2012

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

description: Post_transplant patient

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

scan_protocol: We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software.

data_processing: GeneSpring for normalization, normalization methods: per spot: devide by control channel, per chip: normalize to 50th percentile, all values are natural log ratio

label: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were used.

label_protocol: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions.

extract_protocol: The blood was drawn in the presence of sodium heparin.  PBMC were isolated by density separation over Ficoll solution. Mononuclear cells at the interface were washed twice with phosphate buffered saline (PBS). Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: patient sample

value: Post_transplant patient 4

source_name: negative control

value: negative control


title: CTR-B (CTR-2, biological replicate 2)


title: Pre_transplant patient 7

description: Pre_transplant patient

value: Pre_transplant patient 7


title: Post_transplant patient 7

description: Post_transplant patient

value: Post_transplant patient 7


title: Post_transplant patient 6

description: Post_transplant patient

value: Post_transplant patient 6


title: Pre_transplant patient 8

description: Pre_transplant patient

value: Pre_transplant patient 8


title: Post_transplant patient 5

description: Post_transplant patient

value: Post_transplant patient 5


title: Pre_transplant patient 6

description: Pre_transplant patient

value: Pre_transplant patient 6


title: Pre_transplant patient 4

description: Pre_transplant patient

value: Pre_transplant patient 4


title: operational tolerance sample 16

description: operational tolerance sample

value: operational tolerance sample 16


title: Cdk4-/-:Eµ-Myc B-lymphoma

city: Columbus

first: Xianghong

last: Zou

state: OH

address: 1645 Neil Ave

department: Pathology

institute: Ohoi State University

description:
mice lymph nodes
Gene expression data from Cdk4-/-:Eµ-Myc B-lymphoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Cdk4-/-:Eµ-Myc B-lymphoma

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

growth_protocol: Cell lines and  isolating the B-lymphoma cells form the cdk4+/+ Eµ-myc and cdk4-/-Eµ-myc mice culture in 45% Iscove’s modified Eagle medium, 45% Dulbecco’s minimal essential medium, 10% fetal bovine serum, 100 U/ml penicillin and streptomycin, 4 mM L-glutamine, and 50 μM 2-mercaptoethanol.

treatment_protocol: rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: cell type

value: B-lymphoma cell

tag: genotype


title: Post_transplant patient 8

description: Post_transplant patient

value: Post_transplant patient 8


title: Cdk4+/+:Eµ-Myc B-lymphoma

description:
mice lymph nodes
Gene expression data from Cdk4+/+:Eµ-Myc B-lymphoma

source_name: Cdk4+/+:Eµ-Myc B-lymphoma


title: Post_transplant patient 1

description: Post_transplant patient

value: Post_transplant patient 1


title: Pre_transplant patient 5

description: Pre_transplant patient

value: Pre_transplant patient 5


title: Post_transplant patient 2

description: Post_transplant patient

value: Post_transplant patient 2


title: operational tolerance sample 15

description: operational tolerance sample

value: operational tolerance sample 15


title: operational tolerance sample 12

description: operational tolerance sample

value: operational tolerance sample 12


title: operational tolerance sample 13

description: operational tolerance sample

value: operational tolerance sample 13


title: Pre_transplant patient 2

description: Pre_transplant patient

value: Pre_transplant patient 2

value: negative control


title: operational tolerance sample 10

description: operational tolerance sample

value: operational tolerance sample 10


title: operational tolerance sample 8

description: operational tolerance sample

value: operational tolerance sample 8


title: operational tolerance sample 11

description: operational tolerance sample

value: operational tolerance sample 11


title: operational tolerance sample 14

description: operational tolerance sample

value: operational tolerance sample 14


title: operational tolerance sample 9

description: operational tolerance sample

value: operational tolerance sample 9


title: Pre_transplant patient 1

description: Pre_transplant patient

value: Pre_transplant patient 1


title: operational tolerance sample 7

description: operational tolerance sample

value: operational tolerance sample 7


title: operational tolerance sample 5

description: operational tolerance sample

value: operational tolerance sample 5


title: operational tolerance sample 6

description: operational tolerance sample

value: operational tolerance sample 6


title: operational tolerance sample 4

description: operational tolerance sample

value: operational tolerance sample 4


title: operational tolerance sample 2

description: operational tolerance sample

value: operational tolerance sample 2


title: healthy control 5

description: healthy control sample

value: healthy control 5


title: operational tolerance sample 1

description: operational tolerance sample

value: operational tolerance sample 1


title: healthy control 4

description: healthy control sample

value: healthy control 4


title: healthy control 3

description: healthy control sample

value: healthy control 3


title: healthy control 1

description: healthy control sample

value: healthy control 1


title: operational tolerance sample 3

description: operational tolerance sample

value: operational tolerance sample 3

value: negative control


title: healthy control 2

description: healthy control sample

value: healthy control 2


title: Godfrey_UR_4938_GenomeWideSNP6

type: genomic

city: Rochester

first: Santhoshi

last: Bandla

state: NY

address: 601 Elmwood Ave. Wilmot Cancer Center (3-0771)

department: Surgery

institute: University of Rochester Medical Center

description: Hybridized to SNP 6.0 arrays

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

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Nexus 6.0 (BioDiscovery, CA)

molecule: genomic DNA

source_name: Esophageal biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from biopsies using the QiaAmp DNA Mini Kit (Qiagen, CA).  DNA concentration and purity was assessed by Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: tissue type

value: Intestinal metaplasia

tag: patient id

value: M

tag: advanced disease state

value: EAC


title: Godfrey_UR_4936_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: chronic rejection sample 9

description: chronic rejection sample

value: chronic rejection sample 9

tag: reference


title: Godfrey_UR_881_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

source_name: Gastroesophageal junction biopsy

value: HGD


title: Godfrey_UR_1137_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: LGD


title: Godfrey_UR_946_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: chronic rejection sample 8

description: chronic rejection sample

value: chronic rejection sample 8


title: chronic rejection sample 10

description: chronic rejection sample

value: chronic rejection sample 10


title: Godfrey_UR_830_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Non-goblet metaplasia


title: Godfrey_UR_1881_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_242_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_937_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_4937_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_653_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_727_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: chronic rejection sample 6

description: chronic rejection sample

value: chronic rejection sample 6


title: Godfrey_UR_637_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_776_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_931_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_762_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_840_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: IM


title: Godfrey_UR_582_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: F


title: chronic rejection sample 7

description: chronic rejection sample

value: chronic rejection sample 7


title: chronic rejection sample 5

description: chronic rejection sample

value: chronic rejection sample 5


title: chronic rejection sample 4

description: chronic rejection sample

value: chronic rejection sample 4


title: Godfrey_UR_771_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: chronic rejection sample 3

description: chronic rejection sample

value: chronic rejection sample 3

value: negative control


title: Godfrey_UR_402_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Intestinal metaplasia


title: Godfrey_UR_369_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: M


title: Godfrey_UR_291_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: chronic rejection sample 1

description: Chronic Rejection sample

value: chronic rejection sample 1

label_protocol: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer?s instructions.


title: Godfrey_UR_482_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: B-cell lymphoma [RB16]

city: Grand Rapids

first: Marie

last: Mooney

state: MI

address: 333 Bostwick

institute: VanAndel Institute

description:
B-cell lymphoma
gene expression data from canine lymphoma

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized using the GeneChip Eukaryotic Hybridization Control Kit  for 16 hr at 45C on the Canine Genome V2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GeneChip data was normalized to a 95% trimmed mean intensity of 500 using the MAS 5.0 algorithm within the Affymetrix Gene Console.

organism: Canis lupus familiaris

source_name: Companion canine lymph node fine needle aspirate

label_protocol: Biotinylated cRNA were prepared using NuGen Encore Biotin Module from 5 ug total RNA.

growth_protocol: Samples were acquired from naturally occuring canine tissue

extract_protocol: RNA was extracted and purified with the RNeasy Micro kit (Qiagen) at Clinical Research Laboratory (CRL)

treatment_protocol: No controlled treatments were applied to these samples

tag: breed

value: Chesapeake Bay Retriever

value: B-cell lymphoma


title: chronic rejection sample 2

description: Chronic Rejection sample

value: chronic rejection sample 2


title: B-cell lymphoma [FS21]

value: Pitt Bull Terrier/Lab. Retriever Mix


title: normal lymph node [2970]

description:
normal lymph node
gene expression data from canine lymph nodes

source_name: Canine colony normal lymph node tissue

value: Beagle

value: normal lymph node


title: normal lymph node, biological replicate 2 [3024r]

description:
normal lymph node, biological replicate 2
gene expression data from canine lymph nodes


title: Godfrey_UR_773_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: HGD


title: Godfrey_UR_284_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Non-goblet metaplasia


title: B-cell lymphoma [RB03]

value: Pointer


title: B-cell lymphoma [RB10]

value: Boxer


title: B-cell lymphoma [NE42]

value: Labrador Retriever


title: Godfrey_UR_649_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: normal lymph node [63]


title: Godfrey_UR_627_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Composite


title: T-cell lymphoma [FS22]

description:
T-cell lymphoma
gene expression data from canine lymphoma

value: T-cell lymphoma


title: normal lymph node, biological replicate 1 [3024l]

description:
normal lymph node, biological replicate 1
gene expression data from canine lymph nodes


title: T-cell lymphoma [FS25]


title: Godfrey_UR_274_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: T-cell lymphoma [NE45]

value: Golden Retriever


title: THP1_TiO2_100_24hr-2

city: Corvallis

first: Susan

middle: C.

last: Tilton

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from THP-1 cells exposed to 100 ug/ml TiO2-NB for 24hr

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep2

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: THP-1 cells, obtained from ATCC, were suspended in RPMI media supplemented with 10% fetal bovine serum, beta-mercapto ethanol, sodium pyruvate, supplemented with an antimycotic and antibiotics.  For experimental conditions, the cells in suspension were differentiated into a macrophage-like cell by adding phorbol 12-myristate 13-acetate (82 nM PMA, Sigma) for 24 h wherein the cells became adherent.  The cells were then washed with PBS, scraped, centrifuged at 400 x g for 5 min, and counted on a Z2 Coulter Counter (Beckman Coulter).  The cells were suspended at 1 x 106 cells/ml and further cultured as described below.  All cultures were maintained in 37°C water-jacketed CO2 incubators (ThermoForma).

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: For transcriptomics analysis, the suspended cells were plated in 25 cm2 flasks at 5 x 106 cells/flask.  Multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB) were added directly to the wells at specified concentrations (0, 10 or 100 µg/ml) in media.  The cells were cultured for either 1 or 24 h.  At the end of the culture period the adherent cells were washed once in PBS and the RNA was isolated as described below.

value: human acute monocytic leukemia

tag: treatment

tag: dose

value: 100 ug/ml

tag: time

value: 24 hr


title: THP1_TiO2_100_24hr-3

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep3


title: B-cell lymphoma [NE41]

value: Boxer/Pitt Bull Terr. Mix


title: Godfrey_UR_286_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: M

value: IM


title: Godfrey_UR_289_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Intestinal metaplasia


title: THP1_TiO2_10_24hr-3

description: Gene expression data from THP-1 cells exposed to 10 ug/ml TiO2-NB for 24hr

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep3

value: 10 ug/ml


title: THP1_TiO2_100_24hr-1

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep1


title: Godfrey_UR_221_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_269_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: F


title: Godfrey_UR_199_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: EAC


title: Godfrey_UR_222_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Non-goblet metaplasia


title: B-cell lymphoma [RB07]

value: B-cell lymphoma


title: THP1_TiO2_10_24hr-1

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep1


title: THP1_TiO2_10_24hr-2

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep2


title: Godfrey_UR_223_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: THP1_MWCNT_100_24hr-3

description: Gene expression data from THP-1 cells exposed to 100 ug/ml MWCNT for 24hr

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 24hr, biological rep3

value: MWCNT


title: Godfrey_UR_342_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: THP1_MWCNT_100_24hr-2

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 24hr, biological rep2


title: S-MSCs derived from WT mice

city: shanghai

first: fang

last: ke

address: road chongqing 280

country: China

institute: shanghai jiao tong tong university

description: This sample is of wild type S-MSCs

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: mouse C57BL/6J wild-type

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: S-MSCs were cultureed in low glucose DMEM, supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml pencillin and 100 μg/ml streptomycin

extract_protocol: Total RNA was extracted from cultured cells with TRIzol Reagent (Invitrogen). Reverse transcription with by invitrogen Superscript ds-cDNA synthesis kit

tag: strain

value: early postnatal, skin

tag: genotype/variation

value: wild type


title: Godfrey_UR_165_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_301_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: LGD


title: THP1_MWCNT_100_24hr-1

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 24hr, biological rep1


title: THP1_MWCNT_10_24hr-3

description: Gene expression data from THP-1 cells exposed to 10 ug/ml MWCNT for 24hr

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 24hr, biological rep3


title: Godfrey_UR_162_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_158_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_152_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: Godfrey_UR_159_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Composite


title: THP1_MWCNT_10_24hr-1

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 24hr, biological rep1

value: human acute monocytic leukemia


title: Godfrey_UR_218_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: S-MSCs derived from IL6KO mice

description: This sample is of interleukin-6 knockout S-MSCs

source_name: mouse C57BL/6J interleukin-6 knockout

value: interleukin-6 knockout


title: JXCEAR_2 with array type poplar from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Populus x canadensis

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: stem - Plants were grown in a greenhouse, in 10 liter pots filled with peat/sand mix(50/50 v/v amended with 60g/60l CaMg(CO2)3 and fertilised with Nutricote T100(13-13-13-2,N-P-K-Mg+trace elements). In the greehouse, temperature oscillated with rayonnement but kept in the range 15-27 °C, and air humidity in the range 50-70%. Light dependend on natural and varied in the range. During the 3 days preceeding harvest, temperature was, humidity was and light was

extract_protocol: Pool of extract, 130-C-JX-EAR:1ug, 131-C-JX-EAR:1ug, 133-C-JX-EAR:1ug.

treatment_protocol: Name:EAR - environmental treatment - hygrometry,drought:time 36hour . short time at REW 20-30 percent

tag: hybrid

value: populus deltoides x populus nigra

tag: harvest date

tag: clone

value: Carpaccio

value: xylem


title: Godfrey_UR_151_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

tag: gender

value: M


title: JXCEAR_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 81-C-JX-EAR:1ug, 96-C-JX-EAR:1ug, 97-C-JX-EAR:1ug.

tag: tissue


title: THP1_MWCNT_10_24hr-2

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 24hr, biological rep2

tag: cell line

tag: cell type

value: 24 hr


title: JXSEAR_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 100-S-JX-EAR:1ug, 83-S-JX-EAR:1ug, 98-S-JX-EAR:1ug.

value: Soligo


title: JXSAMO_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 108-C-JX-AMO:1ug, 119-C-JX-AMO:1ug, 141-C-JX-AMO:1ug, 92-S-JX-AMO:10.3ug.

treatment_protocol: Name:AMO - environmental treatment - hygrometry,drought:time 12day . REW 10-20 percent


title: THP1_CON_0_24hr-3

description: Gene expression data from THP-1 cells exposed to 0 ug/ml control for 24hr

source_name: THP-1 cells exposed to 0 ug/ml control for 24hr, biological rep3

value: control

value: 0 ug/ml


title: Godfrey_UR_128_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

source_name: Esophageal biopsy

tag: tissue type

value: Non-goblet metaplasia

value: F

value: NGM


title: THP1_CON_0_24hr-2

source_name: THP-1 cells exposed to 0 ug/ml control for 24hr, biological rep2


title: Godfrey_UR_194_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

tag: patient id

value: HGD


title: THP1_TiO2_100_1hr-3

description: Gene expression data from THP-1 cells exposed to 100 ug/ml TiO2-NB for 1hr

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep3

value: 100 ug/ml

value: 1 hr


title: Godfrey_UR_182_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

source_name: Gastroesophageal junction biopsy

tag: advanced disease state

value: EAC


title: JXSCTL_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 111-S-JX-CTL:1ug, 118-S-JX-CTL:1ug, 128-S-JX-CTL:1ug.

treatment_protocol: no treatment


title: THP1_CON_0_24hr-1

source_name: THP-1 cells exposed to 0 ug/ml control for 24hr, biological rep1

value: human acute monocytic leukemia


title: JXCCTL_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 117-C-JX-CTL:1ug, 134-C-JX-CTL:1ug, 139-C-JX-CTL:1ug.


title: THP1_TiO2_100_1hr-2

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep2


title: THP1_TiO2_10_1hr-2

description: Gene expression data from THP-1 cells exposed to 10 ug/ml TiO2-NB for 1hr

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep2

value: 10 ug/ml


title: THP1_TiO2_100_1hr-1

source_name: THP-1 cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep1


title: JXCAMI_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 129-C-JX-AMI:1ug, 85-C-JX-AMI:1ug, 90-C-JX-AMI:1ug.

treatment_protocol: Name:AMI - environmental treatment - abiotic stress,water deficit:time 12day . AMI : Acclimated response to mild water deficit : soil relative extractable water (REW) was reduced and maintained in the range 20-30 % of field capacity for 12 days.

value: populus deltoides x populus nigra


title: JXCCTL_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 105-C-JX-CTL:1ug, 87-C-JX-CTL:1ug.

value: Carpaccio


title: Godfrey_UR_117_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays


title: THP1_TiO2_10_1hr-1

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep1


title: XSCTL_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 111-S-X-CTL:1ug, 118-S-X-CTL:1ug.

value: xylem


title: XCCTL_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 105-C-X-CTL:1ug, 87-C-X-CTL:1ug.


title: THP1_MWCNT_100_1hr-2

description: Gene expression data from THP-1 cells exposed to 100 ug/ml MWCNT for 1hr

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 1hr, biological rep2

value: MWCNT


title: Godfrey_UR_99_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: M


title: THP1_TiO2_10_1hr-3

source_name: THP-1 cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep3


title: THP1_MWCNT_100_1hr-1

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 1hr, biological rep1


title: Godfrey_UR_122_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Intestinal metaplasia

value: LGD


title: THP1_MWCNT_100_1hr-3

source_name: THP-1 cells exposed to 100 ug/ml MWCNT for 1hr, biological rep3


title: XSEAR_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 121-S-X-EAR:1ug, 142-S-X-EAR:1ug, 143-S-X-EAR:1ug.

value: Soligo


title: THP1_MWCNT_10_1hr-3

description: Gene expression data from THP-1 cells exposed to 10 ug/ml MWCNT for 1hr

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 1hr, biological rep3


title: XCCTL_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 117-C-X-CTL:1ug, 134-C-X-CTL:1ug.


title: XCEAR_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 130-C-X-EAR:1ug, 131-C-X-EAR:1ug, 133-C-X-EAR:1ug.


title: THP1_CON_0_1hr-3

description: Gene expression data from THP-1 cells exposed to 0 ug/ml control for 1hr

source_name: THP-1 cells exposed to 0 ug/ml control for 1hr, biological rep3

value: control

value: 0 ug/ml


title: Godfrey_UR_309_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

extract_protocol: Genomic DNA was extracted from biopsies using the QiaAmp DNA Mini Kit (Qiagen, CA).  DNA concentration and purity was assessed by Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Non-goblet metaplasia

value: F

value: IM


title: THP1_MWCNT_10_1hr-1

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 1hr, biological rep1

value: 1 hr


title: THP1_MWCNT_10_1hr-2

source_name: THP-1 cells exposed to 10 ug/ml MWCNT for 1hr, biological rep2


title: THP1_CON_0_1hr-1

source_name: THP-1 cells exposed to 0 ug/ml control for 1hr, biological rep1


title: XSCTL_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 103-S-X-CTL:1ug, 104-S-X-CTL:1ug.


title: THP1_CON_0_1hr-2

source_name: THP-1 cells exposed to 0 ug/ml control for 1hr, biological rep2

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).


title: XSAMI_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 122-S-X-AMI:1ug, 136-S-X-AMI:1ug, 99-S-X-AMI:1ug.


title: XCEAR_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 81-C-X-EAR:1ug, 96-C-X-EAR:1ug, 97-C-X-EAR:1ug.


title: XSEAR_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 100-S-X-EAR:1ug, 83-S-X-EAR:1ug, 98-S-X-EAR:1ug.


title: Godfrey_UR_28_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: Composite


title: XCAMI_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 129-C-X-AMI:1ug, 85-C-X-AMI:1ug, 90-C-X-AMI:1ug.


title: Godfrey_UR_103_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

source_name: Esophageal biopsy


title: SAE_TiO2_100_24hr-3

description: Gene expression data from SAE cells exposed to 100 ug/ml TiO2-NB for 24hr

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep3

growth_protocol: Small airway epithelial (SAE) cells were obtained from Lonza Walkersville Inc.  Cells were maintained in Lonza Clonetics SABM media (cat # cc-3119) supplemented with Lonza Clonetics SAGM single quots (cat# cc-4124).  For experimental conditions, adherent SAEC cells were washed with HBSS (cat# cc-5022) and trypsin (cat# cc-5012) was then used to dislodge the cells.  A trypsin neutralizing solution (cat# cc-5002) was then added and the cells were centrifuged at 250 x g for 5 min.  The supernatant was discarded and the cells were resuspended and counted as stated above.  All cultures were maintained in 37°C water-jacketed CO2 incubators (ThermoForma).

treatment_protocol: For transcriptomics analysis, cells were suspended at 1 x 106 cells per ml and plated in 25 cm2 flasks at 5 x 106 cells/flask.  The multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB) were added directly to the wells at specified concentrations (0, 10 or 100 µg/ml) in media.  The cells were cultured for either 1 or 24 h.  At the end of the culture period the adherent cells were washed once in PBS and the RNA was isolated as described below.

value: SAE

value: small airway epithelial

value: 100 ug/ml

value: 24 hr


title: JXSCTL_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 104-S-JX-CTL:1ug, 107-S-JX-CTL:1ug, 103-S-JX-CTL:1ug.

value: populus deltoides x populus nigra

value: xylem


title: XSAMI_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 101-S-X-AMI:1ug, 94-S-X-AMI:1ug.


title: Godfrey_UR_84_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: M


title: XCAMI_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 76-C-X-AMI:1ug, 84-C-X-AMI:1ug.

value: Carpaccio


title: SAE_TiO2_100_24hr-2

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep2


title: Godfrey_UR_58_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: LGD


title: Godfrey_UR_550_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

value: EAC


title: Godfrey_UR_109_GenomeWideSNP6

description: Hybridized to SNP 6.0 arrays

source_name: Gastroesophageal junction biopsy


title: XSAMO_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 77-S-X-AMO:1ug, 92-S-X-AMO:1ug.

value: Soligo


title: SAE_TiO2_100_24hr-1

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep1


title: SAE_TiO2_10_24hr-1

description: Gene expression data from SAE cells exposed to 10 ug/ml TiO2-NB for 24hr

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep1

value: 10 ug/ml


title: SAE_TiO2_10_24hr-2

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep2


title: XCAMO_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 108-C-X-AMO:1ug, 119-C-X-AMO:1ug, 141-C-X-AMO:1ug.


title: JXCAMI_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 76-C-JX-AMI:1ug, 84-C-JX-AMI:1ug.


title: SAE_TiO2_10_24hr-3

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep3


title: SAE_MWCNT_10_24hr-2

description: Gene expression data from SAE cells exposed to 10 ug/ml MWCNT for 24hr

source_name: SAE cells exposed to 10 ug/ml MWCNT for 24hr, biological rep2

value: MWCNT


title: SAE_MWCNT_100_24hr-2

description: Gene expression data from SAE cells exposed to 100 ug/ml MWCNT for 24hr

source_name: SAE cells exposed to 100 ug/ml MWCNT for 24hr, biological rep2


title: XCAMO_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 125-C-X-AMO:1ug, 73-C-X-AMO:1ug, 74-C-X-AMO:1ug.


title: XSAMO_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 126-S-X-AMO:1ug, 132-S-X-AMO:1ug, 95-S-X-AMO:1ug.


title: JXCAMO_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 108-C-JX-AMO:1ug, 119-C-JX-AMO:1ug, 141-C-JX-AMO:1ug, 92-S-JX-AMO:10.3ug.


title: SAE_MWCNT_10_24hr-3

source_name: SAE cells exposed to 10 ug/ml MWCNT for 24hr, biological rep3


title: JXSAMI_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 101-S-JX-AMI:1ug, 94-S-JX-AMI:1ug.


title: SAE_MWCNT_10_24hr-1

source_name: SAE cells exposed to 10 ug/ml MWCNT for 24hr, biological rep1


title: JXCAMO_1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 125-C-JX-AMO:1ug, 73-C-JX-AMO:1ug, 74-C-JX-AMO:1ug.


title: SAE_CON_0_24hr-3

description: Gene expression data from SAE cells exposed to 0 ug/ml control for 24hr

source_name: SAE cells exposed to 0 ug/ml control for 24hr, biological rep3

value: control

value: 0 ug/ml


title: SAE_MWCNT_100_24hr-3

source_name: SAE cells exposed to 100 ug/ml MWCNT for 24hr, biological rep3


title: SAE_CON_0_24hr-2

source_name: SAE cells exposed to 0 ug/ml control for 24hr, biological rep2


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR3A]

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

description: Differential expression of genes during growth on insoluble vs soluble electron acceptor

hyb_protocol: Combimatrix 100 ul volume cap

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing: The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.   1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.   2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.   3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: Mn(IV) oxide provided as electron acceptor

label_protocol: amplified RNA was labeled with cy5 (Mn(IV) oxide) or cy3 (Fe(III) citrate)

growth_protocol: G. sulfurreducens cells were incubated at 30°C in the dark under 80:20 N2:CO2 atmosphere

extract_protocol: RNA was extracted with phenol chloroform and amplified with MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) prior to labeling

treatment_protocol: Cells were grown in the presence of an insoluble vs soluble electron acceptor

tag: growth condition

value: DL1 was grown in medium containing acetate as the electron donor and Mn(IV) oxide as the electron acceptor.

source_name: Fe(III) citrate provided as electron acceptor

value: DL1 was grown in medium containing acetate as the electron donor and Fe(III) citrate as the electron acceptor.


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR1B]


title: SAE_MWCNT_100_24hr-1

source_name: SAE cells exposed to 100 ug/ml MWCNT for 24hr, biological rep1

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

value: SAE


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR2B]


title: SAE_CON_0_24hr-1

source_name: SAE cells exposed to 0 ug/ml control for 24hr, biological rep1

value: small airway epithelial


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR3B]


title: JXSAMI_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 122-S-JX-AMI:1ug, 136-S-JX-AMI:1ug, 99-S-JX-AMI:1ug.


title: JXSEAR_2 with array type poplar from Affymetrix


title: JXSAMO_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 126-S-JX-AMO:1ug, 132-S-JX-AMO:1ug, 95-S-JX-AMO:1ug.


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR2A]


title: Mn(IV) oxide grown vs Fe(III) citrate grown cells [BR1A]


title: SAE_TiO2_100_1hr-1

description: Gene expression data from SAE cells exposed to 100 ug/ml TiO2-NB for 1hr

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep1

value: 100 ug/ml

value: 1 hr


title: SAE_TiO2_100_1hr-3

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep3


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR3B]

source_name: Fe(III) oxide provided as electron acceptor

label_protocol: amplified RNA was labeled with cy5 (Fe(III) oxide) or cy3 (Fe(III) citrate)

treatment_protocol: Cells were grown in the presence of an insoluble vs soluble iron source

value: DL1 was grown in medium containing acetate as the electron donor and Fe(III) oxide as the electron acceptor.


title: SAE_TiO2_100_1hr-2

source_name: SAE cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep2


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR3A]


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR1B]


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR1A]


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR2A]


title: SAE_TiO2_10_1hr-3

description: Gene expression data from SAE cells exposed to 10 ug/ml TiO2-NB for 1hr

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep3


title: SAE_TiO2_10_1hr-2

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep2


title: SAE_TiO2_10_1hr-1

source_name: SAE cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep1


title: SAE_MWCNT_100_1hr-3

description: Gene expression data from SAE cells exposed to 100 ug/ml MWCNT for 1hr

source_name: SAE cells exposed to 100 ug/ml MWCNT for 1hr, biological rep3


title: SAE_MWCNT_100_1hr-2

source_name: SAE cells exposed to 100 ug/ml MWCNT for 1hr, biological rep2


title: SAE_MWCNT_10_1hr-3

description: Gene expression data from SAE cells exposed to 10 ug/ml MWCNT for 1hr

source_name: SAE cells exposed to 10 ug/ml MWCNT for 1hr, biological rep3


title: SAE_MWCNT_10_1hr-2

source_name: SAE cells exposed to 10 ug/ml MWCNT for 1hr, biological rep2


title: Fe(III) oxide vs Fe(III) citrate grown cells [BR2B]


title: SAE_CON_0_1hr-3

description: Gene expression data from SAE cells exposed to 0 ug/ml control for 1hr

source_name: SAE cells exposed to 0 ug/ml control for 1hr, biological rep3


title: SAE_MWCNT_100_1hr-1

source_name: SAE cells exposed to 100 ug/ml MWCNT for 1hr, biological rep1


title: SAE_CON_0_1hr-2

source_name: SAE cells exposed to 0 ug/ml control for 1hr, biological rep2


title: SAE_MWCNT_10_1hr-1

source_name: SAE cells exposed to 10 ug/ml MWCNT for 1hr, biological rep1


title: SAE_CON_0_1hr-1

source_name: SAE cells exposed to 0 ug/ml control for 1hr, biological rep1


title: Caco2_TiO2_100_24hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 24hr

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep3

growth_protocol: Caco-2, human colorectal adenocarcinoma cells (ATCC HTB-37, Lot 57863838) were maintained in EMEM media supplemented with 10% FBS (ATCC cat# 30-2003 & 30-2020) and incubated at 37°C – 5% CO2. HT29-MTX, human colon adenocarcinoma cells treated with methotrexate (Lesuffleur et al. 1993) were obtained from Dr. Thécla Lesuffleur (INSERM, Paris, France) and were maintained in DMEM with Glutamax and 10% Hi-FBS (Invitrogen) at 37°C - 5% CO2. Both cell lines were subcultured at 80-90% confluence.  Caco-2 (passage 49 and 63) and HT29-MTX cells (passage 29 and 33) were cultured to obtain several Corning T75 flasks. At 80-90% confluence, the cells were trypsinized and flasks were pooled. Cells were counted using a hemocytometer and then mixed together at a 75:25 Caco-2:HT29-MTX ratio and placed in the HT29-MTX medium with 1% penicillin-streptomycin. Combined cells were mechanically mixed and 1 mL was added to 6-transwell plates to obtain 0.4 x 106 cells per well (8.9 x 104 cells/cm2) (Hilgendorf et al. 2000). Prior to NP exposure, cells were incubated at 37°C - 5% CO2 for 14 days, replacing the medium every other day, to achieve post-confluent differentiation, polarization, and tight-junction formation.

treatment_protocol: For NP exposures, 1.5 ml multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB)  suspensions at 10 or 100 µg/ml media were placed in the top compartment (apical) of the 6 Transwell™ plate containing the 14 days co-cultured cells. The bottom compartment (basolateral) contained 2.5 ml of fresh medium. Control groups received only fresh medium in both compartments. The treated cells were incubated at 37°C – 5% CO2 for 3 and 24 h for proteomics analysis, and for 1 and 24 h for transcriptomics analysis, as described below.

value: human colorectal/colon adenocarcinoma

value: 24 hr


title: THP-1_LPS+TGF_6

city: Utrecht

first: Karlijn

last: van Keulen

address: Heidelberglaan 100, G02.523

department: division heart and lungs

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Gene expression values of the chips were normalized in BeadStudio (version 3.2 Illumina)

source_name: THP-1 monocytes, LPS+TGF, 24hrs

label_protocol: Illumina TotalPrep RNA Amplification Kits were used for cDNA and cRNA synthesis (Ambion) according the manufacturer’s protocol

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium containing 50mM 2-mercaptoethanol, 100 U/ml penicillin, 100 μg/ml streptomycin, and 5% FBS. Monocytes, in a density of 2*10^6 cells/4 mL were starved O/N prior to stimulation in medium containing 0.1% FCS.

extract_protocol: RNA of stimulated monocytes was isolated using Tripure reagent (Roche) according the manufacturer’s protocol. High quality RNA was obtained with NucleoSpin RNA II kits (Machery-Nagel) inclusive DNase treatment

treatment_protocol: THP-1 cells were stimulated with LPS (100ng/mL) or TGFβ1 (1ng/mL) or LPS and TGFβ1 for 24 hrs and kept in an CO2 injecting incubator. As a control PBS was added to the cells.

value: THP-1 monocytic cell line

tag: agent (stimulus)

value: LPS+TGF


title: THP-1_LPS+TGF_1

scan_protocol: According to beadchip array manufacturer's protocol


title: THP-1_LPS+TGF_5


title: THP-1_TGF_8

source_name: THP-1 monocytes, TGF, 24hrs

value: TGF


title: Caco2_TiO2_100_24hr-1

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep1

tag: treatment


title: Caco2_TiO2_100_24hr-2

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 24hr, biological rep2

tag: dose


title: THP-1_LPS+TGF_7


title: THP-1_LPS+TGF_3


title: THP-1_LPS+TGF_4


title: THP-1_LPS+TGF_8


title: THP-1_TGF_7


title: THP-1_LPS+TGF_2


title: Caco2_MWCNT_100_24hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 24hr

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 24hr, biological rep3

tag: time


title: Caco2_TiO2_10_24hr-1

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 24hr

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep1


title: Caco2_TiO2_10_24hr-3

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep3


title: THP-1_TGF_5


title: Caco2_TiO2_10_24hr-2

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep2


title: THP-1_TGF_4


title: THP-1_TGF_3


title: Caco2_MWCNT_100_24hr-2

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 24hr, biological rep2


title: Caco2_MWCNT_100_24hr-1

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 24hr, biological rep1


title: THP-1_LPS_8

source_name: THP-1 monocytes, LPS, 24hrs

value: LPS


title: THP-1_TGF_2


title: THP-1_LPS_7


title: Caco2_MWCNT_10_24hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 24hr

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 24hr, biological rep3

value: 10 ug/ml


title: THP-1_TGF_1


title: tetO-YPI1 + Dox_6h_Exp_2

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description:
the strain mmr09-4 (cml476 background), that contains a kanmx4-teto7 cassette inserted immediately before the ypi1 coding region, has been described in pedelini l. et al. j. biol. chem. 282: 3282-3292(2007).
Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 micro m. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cnio.es) was used to preprocess the data: merge replicates. The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: tetO7_YPI1 conditional mutant strain treated with doxycycline

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Log phase cultures grown in YPD medium was diluted at OD660 0.10 in YPD supplemented with the doxycycline. Cell samples containing the equivalent to 15 OD of cells were collected by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: Treated with doxycycline (100 microg/ml) in an ethanol:water mix (1:1) for 6h.

tag: strain

value: mmr09-4 (cml476 background)

source_name: tetO7_YPI1 conditional mutant strain not treated with doxycycline

label_protocol: Fluorescent labeled cDNA was prepared from 8 micro g of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Log phase cultures grown in YPD medium was diluted at OD660 0.10 in YPD supplemented with ethanol:water mix (1:1). Cell samples containing the equivalent to 15 OD of cells were collected by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: Treated with 1/100 vol of ethanol:water mix (1:1) for 6h.


title: tetO-YPI1 + Dox_4h_Exp_1

treatment_protocol: Treated with doxycycline (100 microg/ml) in an ethanol:water mix (1:1) for 4h.

treatment_protocol: Treated with 1/100 vol of ethanol:water mix (1:1) for 4h.


title: tetO-YPI1 + Dox_4h_Exp_2


title: Caco2_MWCNT_10_24hr-2

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 24hr, biological rep2

value: MWCNT


title: tetO-YPI1 + Dox_6h_Exp_1


title: Caco2_MWCNT_10_24hr-1

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 24hr, biological rep1


title: THP-1_LPS_6


title: tetO-YPI1 + Dox_2h_Exp_2

treatment_protocol: Treated with doxycycline (100 microg/ml) in an ethanol:water mix (1:1) for 2h.

treatment_protocol: Treated with 1/100 vol of ethanol:water mix (1:1) for 2h.


title: Caco2_CON_0_24hr-2

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 24hr

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 24hr, biological rep2

value: control

value: 0 ug/ml


title: THP-1_LPS_4


title: tetO-YPI1 + Dox_2h_Exp_1


title: Caco2_CON_0_24hr-3

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 24hr, biological rep3


title: THP-1_LPS_5


title: THP-1_LPS_3


title: Caco2_CON_0_24hr-1

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 24hr, biological rep1


title: Caco2_TiO2_100_1hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 1hr

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep3


title: THP-1_LPS_2


title: APOE4, replicate 1

city: Rostock

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

country: Germany

institute: University of Rostock

description: E4 2

hyb_protocol: 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.

scan_protocol: GeneChip® Scanner 3000 using the GCOS software.

data_processing: Quality control and normalisation of CEL data based on the Affymetrix chip deﬁnition ﬁle were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).

source_name: liver, APOE4

label_protocol: Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.

growth_protocol: Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.

extract_protocol: Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.

tag: strain/background

tag: genotype/variation

value: APOE4 targeted gene replacement

value: female

tag: age

value: 3 months

value: liver


title: Caco2_TiO2_100_1hr-2

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep2

value: 100 ug/ml

value: 1 hr


title: APOE4, replicate 2

description: E4 27


title: THP-1_PBS_8

source_name: THP-1 monocytes, PBS, 24hrs

value: PBS


title: APOE3, replicate 5

description: E3 75

source_name: liver, APOE3

value: APOE3 targeted gene replacement


title: APOE3, replicate 4

description: E3 66


title: THP-1_LPS_1

value: THP-1 monocytic cell line


title: cells transfected with GFP vector only, biological rep3

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

description: Exon expression data from HeLa cells, transfected with GFP vector only

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Human Exon 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) in the R application (version 2.11.1). A two-stage statistical analysis was used. The first stage was to identify differentially expressed transcripts between the ZRANB2 and control GFP sets of samples. For a typical transcript g (log-likelihood ratio) we averaged expression values among all exons within transcript g and computed the fold-change and moderated t-statistics between groups.  Then we generated a candidate list of differentially-expressed genes with an absolute moderated t-statistics of 2 and above, and greater than 1.5-fold change between groups. These procedures use functions in the limma library of the Bioconductor software package.

source_name: HeLa cells

label_protocol: 1 μg of total RNA was prepared for hybridisation according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

growth_protocol: The cervical cancer cells HeLa  were obtained from the American Type Culture Collection and cultured at 37°C under 5% CO2 in DMEM (Invitrogen), supplemented with 0.1 mM non-essential amino acids and 1.0 mM sodium pyruvate. Ten percent FCS (Invitrogen) and penicillin/streptomycin (5000 u/mL; Invitrogen) were added to the medium.

extract_protocol: HeLa cells were harvested after 40 h of incubation. RNeasy kit (Qiagen) was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with constructs using Lipofectamine 2000 according to the manufacturer’s instructions (Invitrogen)

value: HeLa

value: transfected with GFP vector only


title: Caco2_TiO2_100_1hr-1

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml TiO2-NB for 1hr, biological rep1

value: human colorectal/colon adenocarcinoma


title: APOE4, replicate 5

description: E4 65


title: APOE3, replicate 3

description: E3 48


title: APOE3, replicate 2

description: E3 39


title: THP-1_PBS_7


title: APOE4, replicate 4

description: E4 56


title: cells transfected with GFP vector only, biological rep5


title: Caco2_TiO2_10_1hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 1hr

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep3

value: 10 ug/ml


title: APOE3, replicate 1

description: E3 12


title: THP-1_PBS_6


title: cells transfected with GFP-ZRANB2 vector, biological rep5

description: Exon expression data from HeLa cells, transfected with GFP-ZRANB2 vector

value: transfected with GFP-ZRANB2 vector


title: cells transfected with GFP vector only, biological rep2


title: NEB_RA-Ag1.3_rep1

city: Los Angeles

first: Kevin

last: Peterson

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

description: Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid and 50nM of Smo agonist (Ag1.3) for additional 3 days before harvested for total RNA extraction.

hyb_protocol: 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays  were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with dChip

source_name: Neuralized embryoid bodies, all trans retinoic acid (500nM) and Smo agonist (Ag1.3), 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard protocol  (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA

growth_protocol: Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.

extract_protocol: Total RNA was isolated with mirVana kit from Ambion

treatment_protocol: Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).

value: Gli1-FLAG ESC-derived neural progenitors


title: NEB_RA-Ag1.3_rep3

value: all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM)


title: NEB_RA-Ag1.3_rep2


title: Caco2_TiO2_10_1hr-2

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep2


title: cells transfected with GFP vector only, biological rep1


title: APOE4, replicate 3

description: E4 47


title: NEB_RA_rep3

description: Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid for additional 3 days before harvested for total RNA extraction.

source_name: Neuralized embryoid bodies, all trans retinoic acid (500nM), 3 days

value: all trans retinoic acid (500nM)


title: cells transfected with GFP-ZRANB2 vector, biological rep3


title: THP-1_PBS_4


title: cells transfected with GFP-ZRANB2 vector, biological rep2


title: Caco2_MWCNT_100_1hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 1hr

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 1hr, biological rep3

value: MWCNT


title: cells transfected with GFP-ZRANB2 vector, biological rep4


title: cells transfected with GFP vector only, biological rep4


title: THP-1_TGF_6

source_name: THP-1 monocytes, TGF, 24hrs

value: TGF


title: THP-1_PBS_5


title: THP-1_PBS_3


title: untransfected cells, biological rep3

description: Exon expression data from HeLa cells, untransfected

value: untransfected


title: cells transfected with GFP-ZRANB2 vector, biological rep1


title: untransfected cells, biological rep5


title: Caco2_MWCNT_100_1hr-2

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 1hr, biological rep2


title: untransfected cells, biological rep4


title: Caco2_MWCNT_10_1hr-1

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 1hr

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 1hr, biological rep1


title: Caco2_MWCNT_100_1hr-1

source_name: Caco-2/HT29-MTX cells exposed to 100 ug/ml MWCNT for 1hr, biological rep1


title: THP-1_PBS_1


title: Caco2_MWCNT_10_1hr-3

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 1hr, biological rep3


title: Caco2_MWCNT_10_1hr-2

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml MWCNT for 1hr, biological rep2


title: untransfected cells, biological rep1


title: Caco2_CON_0_1hr-3

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 1hr

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 1hr, biological rep3

value: control

value: 0 ug/ml


title: Caco2_CON_0_1hr-2

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 1hr, biological rep2

value: 1 hr


title: untransfected cells, biological rep2


title: Caco2_TiO2_10_1hr-1

source_name: Caco-2/HT29-MTX cells exposed to 10 ug/ml TiO2-NB for 1hr, biological rep1


title: 12hr_DMSO_Cyto_3

status: Public on Dec 14 2012

city: CAMBRIDGE

first: Danny

last: Chou

address: 500 Main St

institute: MIT

description: Gene expression data from rat INS-1E cells in the presence and absence of cytokines and/or BRD0476

hyb_protocol: Biotinlyated cRNA targets were normalized, fragmented and hybridized to Affymetrix Rat 230 2.0 arrays (GPL16251) using Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)

data_processing: The data were analyzed with GenePattern (modules ExpressionFileCreator, PreProcessDataset, and GSEA) using robust multi-array (RMA) analysis for background correction, thresholding and normalization.

organism: Rattus norvegicus

source_name: Rat INS-1E cells with cytokines and DMSO for 12 hours

label_protocol: 500 ng of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).

growth_protocol: Rat INS-1E cells were grown in RPMI medium with 10% FBS, pen/strep, HEPES, sodium pyruvate and beta-mercaptoethanol.

extract_protocol: Extraction of total RNA was performed using the RNEasy kit according to the manufacturer's instructions.

treatment_protocol: Rat INS-1E cells were treated with 10ng/ml IL-1b, 50ng/ml IFN-g and 25 ng/ml TNF-a for 6 or 12 hours in the presence or absence of 10uM BRD0476.

value: insulinoma cell

tag: agent

value: cytokines and DMSO

tag: time point

value: 12 hours

value: pancreatc islets


title: 12hr_DMSO_Cyto_1

tag: tissue


title: 12hr_BRD0476_NoCyto_2

source_name: Rat INS-1E cells with no cytokines and BRD0476 for 12 hours

tag: cell line


title: 12hr_BRD0476_Cyto_1

source_name: Rat INS-1E cells with cytokines and BRD0476 for 12 hours

tag: cell type

value: cytokines and BRD0476


title: 12hr_DMSO_Cyto_2


title: 12hr_BRD0476_Cyto_2