title: shRNA transduced 2

city: Minneapolis

first: Ashish

last: Kumar

state: MN

address: 425 East River Road

institute: University of Minnesota

description: shRNA transduced 2

hyb_protocol: As per Affymetrix protocols

scan_protocol: As per Affymetrix protocols

data_processing: Expression values were obtained using RMA

source_name: shRNA

label_protocol: Affymetrix one cycle labeling kit

growth_protocol: Culture media: IMDM containing 15% FBS and 2ng/ml IL-3

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen)

treatment_protocol: Cells were transduced with control virus (vector only) or a virus carrying Meis1 shRNA construct as indicated; samples are paired by sample number eg. Control 1 is paired with shRNA 1

tag: Murine Mll-AF9 leukemia cells

tag: Myeloid leukemia cell line


title: shRNA transduced 4

status: Public on Dec 23 2008

type: RNA

country: USA

description: shRNA transduced 4

label: Biotin

molecule: total RNA

organism: Mus musculus


title: shRNA transduced 3

description: shRNA transduced 3


title: H295R _2OHBDE85_rep2

status: Public on Dec 25 2008

city: Leicester

first: George

middle: DD

last: Jones

address: Biocentre, University Road

department: Cancer Studies & Molecular Medicine

country: United Kingdom

institute: University of Leicester

hyb_protocol: Fragmented, labelled cRNA (15 µg) was added to 15 µl of 2× hybridisation buffer (final 1× concentration is 100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20), 3 µl of 10 mg/ml herring sperm DNA (Promega, Southampton, UK), 3 µl of 50 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK) and 30 µl of DMSO. The hybridisation buffer was spiked with 5 µl of 3nM control oligonucleotide B2 and 15 µl of the 20× eukaryotic cRNA controls bioB, bioC, bioD and cre (final concentration is 1.5, 5, 25 and 100 pM, respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix, Santa Clara, California, USA). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA (200 µl) was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human U133 Plus 2.0 array (Affymetrix, Santa Clara, California, USA) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Hybridisation Oven 640 (Affymetrix, Santa Clara, California, USA). Probe array washing and staining were performed according to EukGE-WS2v5 Gene Chip protocol (Affymetrix, Santa Clara, California, USA) in the Fluidics Station 400 (Affymetrix, Santa Clara, California, USA). Briefly, arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20. Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Finally, the probe arrays were re-stained with SAPE as described above.

scan_protocol: Probe arrays were scanned once at 570 nm using an Affymetrix GeneChip scanner (Affymetrix, Santa Clara, California, USA) and the fluorescence intensity of the scanned image registered in CEL intensity files.

data_processing: DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files using the PM/MM values.

label: biotin

organism: Homo sapiens

source_name: H295R adrenocortical carcinoma cells, 2-OH-BDE85-treated

label_protocol:
The One-cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, California, USA) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 6 g of T-RNA, 2 µl of diluted poly-A RNA controls, 2 µl of 50 µM T7-oligo (dT) primer and RNase-free water to a final volume of 12 µl. This mixture was incubated at 70 °C for 10 minutes and chilled at 4 °C for 5 minutes, after which the following reagents were added: 4 µl of first strand reaction mix, 2 µl of 100 mM dithiothreitol (DTT) and 1 µl of 10 mM dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (1µl) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 3 µl of 10mM dNTP, 1 µl of E. coli DNA ligase, 4 µl of E. coli DNA polymerase I, 1 µl of E. coli RNase H, 30 µl of second strand reaction buffer and 91 µl of RNase-free water. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 2 µl of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 10 µl of 0.5 M EDTA. The resulting ds-cDNA was cleaned up using the Sample Cleanup Module (Affymetrix, Santa Clara, California, USA), according to the manufacturer’s instructions.
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the IVT labelling kit (Affymetrix, Santa Clara, California, USA). Briefly, the ds-cDNA synthesised above (12 µl) was used as template, and added to 4 µl of 10× IVT labelling buffer, 12 µl of Labeling NTP mix, 4 µl of IVT Labeling Enzyme mix and 8 µl of RNase-free water. The reaction was incubated at 37 °C for 16 hours. This step was followed by cRNA cleanup with the Affymetrix Sample Cleanup Module, according to the manufacturer’s specifications. Quantification of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (20 µg) was fragmented by adding 8 µl of the fragmentation buffer provided in the Sample Cleanup Module and RNase-free water to a final volume of 40 µl, and incubating at 94 °C for 35 minutes. Fragmentation efficiency was confirmed by analysing the size distribution of the fragmented, labelled transcripts in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA).

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with Ham’s nutrient mixture F-12 with 1% ITS+Premix and 2.5% Nu-Serum at 37°C in a 5% CO2 atmosphere.

extract_protocol: After treatment, T-RNA was extracted using QIAGEN RNeasy Mini kit according to the manufacturer’s instructions. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

treatment_protocol: Cells were exposed to 10 µM of 2-OH-BDE85 dissolved in 0.1% dimethyl sulfoxide (DMSO) for 24 hours.

tag: H295R adrenocortical carcinoma cell line


title: shRNA transduced 5

description: shRNA transduced 5


title: 3 weeks old transgenic plants (empty vector; inducible system), biological rep1, normalized w/ANAC059

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description:
Gene expression data from empty inducible vector
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

hyb_protocol: Affymetrix protocol, performed by Atlas Biolabs

data_processing: The data were analyzed with Robust Multi-array Average (Irizarry et al., 2003). GSM353589 raw files (CEL and CHP) are identical to GSM353584 raw files

organism: Arabidopsis thaliana

source_name: 3 weeks old transgenic plants (empty vector; inducible system), WT_col0

label_protocol: Labling procedure performed using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Seeds were surface sterilized and sown in half-strength MS medium supplemented with 1% sucrose and solidified with 0.7% phytoagar and appropriate antibiotic. After inbibition, the seeds were strafied at 4C° for 3 days. The seeds were germinated at 22 C° under a 16-h day (140µmol m2- s1-) / 8-h night regime. The three weeks old Arabidopsis seedlings were removed carefully and subjected to the treatment. T-DNA insertion lines were grown in soil and germinated under controlled condition in a growth chamber with a 16-h day lenght provided by fluorescent light at 80 or 120 µmol m2- s1- and a days/night temperature of 20/16 C° and relative humidity 60/75%.

extract_protocol: RNA extraction performed using Rneasy Plant MiniKit (Qiagene)

treatment_protocol: Three weeks old Arabidopsis seedlings were treated with 10µM estradiole for 5 hourse and then shoots were carefully harvested.. The leaf no.11 of wt and ANAC059 and ANAC092 T-DNA insertion lines were carefully harvested.

tag: 5hr estradiole treated shoot


title: H295R _2OHBDE85_rep3


title: Control virus transduced 4

description: Control virus transduced 4

source_name: Control


title: H295R _Control_rep2

source_name: H295R adrenocortical carcinoma cells, control

treatment_protocol: Cells were exposed to vehicle (0.1% DMSO) for 24 hours.


title: H295R _2OHBDE47_rep2

source_name: H295R adrenocortical carcinoma cells, 2-OH-BDE47-treated

treatment_protocol: Cells were exposed to 10 µM of 2-OH-BDE47 dissolved in 0.1% dimethyl sulfoxide (DMSO) for 24 hours.


title: H295R _2OHBDE47_rep1


title: H295R _Control_rep3


title: Control virus trandsduced 2

description: Control virus trandsduced 2


title: MOUSE_HZ_01

city: Komaba

first: Shuichi

last: Tsutsumi

country: Japan

institute: The University of Tokyo

description: Hypertrophic Zone of mouse tibias' glowth plate.

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 with target intensity=100

source_name: mouse 1 HZ

label_protocol: RNAs were labeled according to the Affymetrix-provided protocol: Eukaryotic Small Sample Target Labeling Assay Version II.  To improve quality and yield of cRNA, the protocol was modified as described below.  Total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (InvitrogenTM).  The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(dT)24-3’ (Affymetrix).  In vitro transcription (IVT) was performed on cDNA using the MEGAscript T7 kit (Ambion).  The amplified cRNA was purified following the RNeasy Micro Protocol (Qiagen).  Approximately 3ug of purified antisense RNA was obtained from each sample, and 200ng of antisense RNA from each sample was used in the following experiment.  Following IVT, the antisense RNA product was reverse-transcribed, using random primers (Invitrogen) that filled in the T7 ends.  After second strand synthesis with T7-Oligo (dT) promoter primer, double-stranded cDNA was purified using the Qiagen PCR purification kit.   Second round IVT for cRNA amplification was then carried out using the MEGAscript T7 kit (Ambion).  This time, during IVT, a fixed concentration of Biotin-16-UTP and Biotin-11-CTP was incorporated into the cRNA products. The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Each segment of growth plate (RZ, PZ, MZ, and HZ) was harvested separately using the Application Solutions Laser Microdissection System (Leica Microsystems, Bannockburn, IL). Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan).

treatment_protocol: The mice were sacrificed by cervical dislocation under deep anesthesia and both tibias were harvested immediately, embedded in OCT compound, frozen in liquid nitrogen and stored at –80°C.

tag: Mouse tibias


title: Control virus transduced 3

description: Control virus transduced 3


title: H295R _2OHBDE47_rep3


title: retina_nasal_rep2

status: Public on Dec 30 2008

city: Canberra

first: Peter

last: Kozulin

state: ACT

address: Building 46, Sullivan's Creek Road

department: Research School of Biological Sciences

country: Australia

institute: ANU

description: biological replicate: Macula2_human, Nasal2_human, Surround2_human

hyb_protocol: The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.

data_processing: Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.

source_name: 19-20 weeks' gestation human retina, nasal biopsy

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).

extract_protocol: Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.

treatment_protocol: Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.

tag: Gestational age

value: 19-20 weeks' gestation

tag: Tissue

value: retina


title: MOUSE_HZ_02

source_name: mouse 2 HZ


title: H295R _Control_rep1

treatment_protocol: Cells were exposed to (0.1% DMSO) for 24 hours.


title: shRNA transduced 1

description: shRNA transduced 1


title: Control virus trandsduced 1

description: Control virus trandsduced 1


title: MOUSE_MZ_01

description: Maturing Zone of mouse tibias' glowth plate.

source_name: mouse 1 MZ


title: MOUSE_PZ_02

description: Proliferating Zone of mouse tibias' glowth plate.

source_name: mouse 2 PZ


title: MOUSE_MZ_02

source_name: mouse 2 MZ


title: MOUSE_PZ_01

source_name: mouse 1 PZ


title: MOUSE_RZ_01

description: Resting Zone of mouse tibias' glowth plate.

source_name: mouse 1 RZ


title: CLDN1 overexpressed CL1-5, biological rep2

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from vector control transfectants and CLDN1 overexpressed transfectants were quantitatively determined.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring software version 7.2 GC-RMA preprocessor to use on the CEL files

source_name: Human lung adenocarcinoma cell line CL1-5 CLDN1-transfected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human lung adenocarcinoma cell lines of CL1-5 CLDN1-transfected and CL1-5 vector control were grown in RPMI 1640 with 10% fetal bovine serum at 37°C, 20% O2, 5% CO2 and 400 μg/ml G418.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

treatment_protocol: Gentamycin (G418) 400 μg/ml

tag: Gender

value: male


title: CLDN1 overexpressed CL1-5, biological rep1


title: Control virus transduced 5

description: Control virus transduced 5


title: CL1-5, biological rep1

source_name: Human lung adenocarcinoma cell line CL1-5 vector control


title: Synchronous liver metastasis colorectal CA 05

status: Public on Dec 22 2008

city: Bologna

first: Maria

middle: Abbondanza

last: Pantaleo

state: BO

address: via Massarenti 9

department: Institute of Hematology and Medical Oncology "L.A.Seragnoli"

country: Italy

institute: Policlinico S. Orsola-Malpighi, University of Bologna

hyb_protocol: According to Affymetrix Expression_analysis_technical_manual

scan_protocol: Affymetrix scanner 7G. GCOS 1.4 acquisition software

data_processing: MAS5.0 Signal and Detection algorithm. Scaling to 500.

source_name: Synchronous liver metastasis from colorectal cancer_sample S05

label_protocol: Affymetrix one-cycle labeling protocol (Expression_analysis_technical_manual)

extract_protocol: Trizol reagent on frozen, pulverized tissue specimen

value: liver metastasis; Tumor:colorectal carcinoma. Status:Synchronous metastasis


title: Synchronous liver metastasis colorectal CA 12

source_name: Synchronous liver metastasis from colorectal cancer_sample S12


title: Synchronous liver metastasis colorectal CA 13

source_name: Synchronous liver metastasis from colorectal cancer_sample S13


title: MOUSE_RZ_02

source_name: mouse 2 RZ


title: Synchronous liver metastasis colorectal CA 06

source_name: Synchronous liver metastasis from colorectal cancer_sample S06


title: Metachronous liver metastasis colorectal CA 23

source_name: Metachronous liver metastasis from colorectal cancer_sample M23

value: liver metastasis; Tumor:colorectal carcinoma. Status:Metachronous metastasis


title: Synchronous liver metastasis colorectal CA 18

source_name: Synchronous liver metastasis from colorectal cancer_sample S18


title: Metachronous liver metastasis colorectal CA 28

source_name: Metachronous liver metastasis from colorectal cancer_sample M28


title: Synchronous liver metastasis colorectal CA 17

source_name: Synchronous liver metastasis from colorectal cancer_sample S17


title: Metachronous liver metastasis colorectal CA 22

source_name: Metachronous liver metastasis from colorectal cancer_sample M22


title: CL1-5, biological rep2


title: Synchronous liver metastasis colorectal CA 19

source_name: Synchronous liver metastasis from colorectal cancer_sample S19


title: Metachronous liver metastasis colorectal CA 24

source_name: Metachronous liver metastasis from colorectal cancer_sample M24


title: Synchronous liver metastasis colorectal CA 15

source_name: Synchronous liver metastasis from colorectal cancer_sample S15


title: Synchronous liver metastasis colorectal CA 14

source_name: Synchronous liver metastasis from colorectal cancer_sample S14


title: Metachronous liver metastasis colorectal CA 02

source_name: Metachronous liver metastasis from colorectal cancer_sample M02


title: Synchronous liver metastasis colorectal CA 07

source_name: Synchronous liver metastasis from colorectal cancer_sample S07


title: Metachronous liver metastasis colorectal CA 09

source_name: Metachronous liver metastasis from colorectal cancer_sample M09


title: Metachronous liver metastasis colorectal CA 08

source_name: Metachronous liver metastasis from colorectal cancer_sample M08


title: Metachronous liver metastasis colorectal CA 03

source_name: Metachronous liver metastasis from colorectal cancer_sample M03


title: Gingival tissue sample 4 from patient 42, Affected site

city: New York

first: Ryan

middle: T

last: Demmer

state: NY

department: Epidemiology

institute: Columbia University

description: A total of 90 subjects with moderate to severe periodontitis (63 with chronic and 27 with aggressive periodontitis) were recruited among the patients referred for periodontal therapy to the Clinic for Post-doctoral Periodontics, Columbia University College of Dental Medicine. Eligible patients were (i) at least 13 yr old; (ii) had a minimum of 24 teeth present; (iii) had no past history of systematic periodontal therapy other than occasional prophylaxis provided by the referring general dentist, (iv) had received no systemic antibiotics or anti-inflammatory drugs for at least 6 months, (v) harbored a minimum of 4 teeth with radiographic bone loss, (vi) did not suffer from diabetes mellitus, (vii) did not suffer from any of the systemic conditions or genetic disorders that entail a diagnosis of 'Periodontitis as a manifestation of systemic diseases', (viii) were not pregnant, and (ix) were not current users of tobacco products or of nicotine replacement medication. Signed informed consent was obtained prior to enrollment. All participants underwent a full-mouth examination of the periodontal tissues at six sites per tooth, using a manual probe. The examination included assessments of presence/absence of dental plaque and bleeding on probing (BoP), and linear measurements of probing pocket depth (PPD) and clinical attachment level (CAL).  'Diseased' sites showed BoP, had an interproximal PPD of>3 mm, and a concomitant CAL of>2 mm. 'Healthy' sites showed no BoP, had PPD of<5 mm and CAL of<3 mm. A software program identified (i) maxillary 'diseased' and 'healthy' interdental papillae, based on the above criteria and (ii) pairs of diseased interdental papillae with similar clinical presentation, i.e., with PPD and CAL within 2 mm of each other. A posterior maxillary sextant encompassing a pair of qualifying 'diseased' interdental papillae was identified.  Periodontal surgery was performed at the identified sextant without any prior supra- or subgingival instrumentation. After infiltration with an appropriate local anesthetic, submarginal incisions were performed, mucoperiosteal flaps were reflected, and the portion of each interproximal gingival papilla that adhered to the root surface was carefully dissected. This section comprised the ulcerated epithelial lining of the interproximal periodontal pockets and a portion of the underlying connective tissue.

hyb_protocol: According to the manufacturer's instructions.

data_processing: All CEL files in the series were processed using RMA in R using justRMA with default parameters.

source_name: Patient 42 gingival tissue sample collected as Affected

label_protocol: Synthesis of Biotin-Labeled cRNA was performed using the GeneChip Expression 3'-Amplification Reagents for IVT labeling kit (Affymetrix). The cRNA yield was determined spectrophotometrically at 260 nm. Finally, the cRNA was fragmented by incubation in fragmentation buffer  at 94 0C for 35 min and stored at –80 0C until hybridizations.

extract_protocol: Gingival tissue specimens were homogenized in Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA collected in the upper aqueous phase was precipitated by mixing with isopropyl alcohol and additional centrifugation and washed in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The purified RNA was quantitated spectrophotometrically, and 7.5 micrograms of total RNA was reverse transcribed using GeneChip Expression 3' amplification one-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions.

treatment_protocol: After collection gingival tissue specimens were thoroughly rinsed with sterile normal saline solution and transferred into Eppendorf tubes containing 5 volumes of a RNA stabilization reagent (RNAlater, Ambion, Austin, TX, USA).  Specimens were stored in RNAlater overnight at 4.0 C and thereafter snap-frozen and stored in liquid nitrogen. All further processing occurred simultaneously for gingival biopsies originating from the same donor.

tag: Gingival tissue phenotype

value: Diseased (BoP + interproximal PPD of>3 mm + concomitant CAL of>2 mm)

value: Gingival


title: Parotid-Male, 62 years

status: Public on Dec 21 2008

city: Rochester

first: Alaka

last: Srivastava

address: 601 Elmwood Avenue

department: Oral Biology

institute: University of Rochester Medical Center

description: Human parotid gland gene expression analysis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized using standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: Human Parotid Gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 13 ug total RNA

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Fresh parotid tissue were frozen in liquid nitrogen

tag: Male Female genotyping

tag: Aging and genotyping


title: Parotid-Male, 42 years


title: Parotid-Male, 71 years


title: Gingival tissue sample 1 from patient 43, Affected site

scan_protocol: According to the manufacturer's instructions.

source_name: Patient 43 gingival tissue sample collected as Affected


title: Parotid-Male, 70 years


title: Parotid-Female, 38 years (Human-5)


title: Parotid-Female, 69 years


title: Parotid-Female, 65 years (Human-3)

source_name: Human Parotig Gland


title: Parotid-Male, 59 years


title: Gingival tissue sample 3 from patient 82, Unaffected site

source_name: Patient 82 gingival tissue sample collected as Unaffected

value: Healthy (no BoP + PPD of<5 mm + CAL of<3 2 mm


title: Parotid-Female, 65 years (Human-9)


title: Parotid-Female, 38 years (Human-8)


title: Parotid-Female, 19 years


title: Patient after treatment-Replicate 1

status: Public on Dec 20 2008

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

country: Canada

institute: Toronto General Hospital

description: RNA was extracted from whole blood before and after 2 months of established Nocturnal home hemodialysis

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 Chips were examined for any defects and removed if any defect detected

data_processing: Signals were scaled to 150

source_name: Blood sample from patient after NHD treatment

label_protocol: Affymetrix standard labeling protocol

extract_protocol: Total RNA (TRNA) was isolated from blood samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol.  The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies).  Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

treatment_protocol: Medically stable Anemia secondary to end-stage renal disease patients (age between 18 – 85 years) who have received a minimum of 3 months of the conversion from conventional hemodialysis and were training for nocturnal home hemodialysis were invited to participate in this study

tag: RNA was extracted from whole blood after a minimum 3 months of Nocturnal home hemodialysis (NHD)


title: Patient after treatment-Replicate 8

description: RNA was extracted from whole blood before and after a minimum 3 months of established Nocturnal home hemodialysis


title: Patient after treatment-Replicate 5


title: Parotid-Female, 41years


title: Patient after treatment-Replicate 6


title: Patient after treatment-Replicate 2


title: Patient after treatment-Replicate 7


title: Patient after treatment-Replicate 3


title: Parotid-Female, 49 years


title: Patient before treatment-Replicate 8

source_name: Blood sample from patient before NHD treatment

tag: RNA was extracted from whole blood before Nocturnal home hemodialysis (NHD)


title: Patient after treatment-Replicate 4


title: Patient before treatment-Replicate 3


title: Patient before treatment-Replicate 5


title: Patient before treatment-Replicate 4


title: Patient before treatment-Replicate 7


title: Patient before treatment-Replicate 6


title: Patient before treatment-Replicate 2


title: SG-108B_phenotype of EPC colony assay

status: Public on Dec 19 2008

city: Bethesda

first: Richard

last: Cannon

state: MD

address: 10 Center Drive

institute: NIH

description: EPC sampled from blood and cultured

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation

source_name: cultured EPC, after 3 months of exercise

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: Blood was collected into CPT tubes with Ficoll and sodium heparin for isolation of mononuclear cells, washed twice in PBS with 5% fetal bovine serum and re-suspended in media for endothelial progenitor-colony-forming assay.

extract_protocol: Total RNA was extracted from cultured EPC with an RNAqueous micro RNA isolation kit (Ambion, Austin, TX).  Cells were lysed in buffer containing guanidinium thiocyanate.

treatment_protocol: cells were harvested after 5 days.

tag: after 3 months of exercise


title: SG-107A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured

source_name: cultured EPC, baseline

tag: baseline


title: SG-95B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-103A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-107B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-95A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-92B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-94A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-91B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-108A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-103B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-90A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: Patient before treatment-Replicate 1


title: SG-90B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-94B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-91A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-83A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-109A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-86B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-84A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-83B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-92A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-84B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: SG-86A_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: small airways, smoker 097

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: white

tag: Smoking status

value: smoker, 70 pack-years


title: SG-109B_phenotype of EPC colony assay

description: EPC sampled from blood and cultured


title: small airways, smoker 094

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

tag: age

tag: sex

value: M

tag: ethnic group

value: black

tag: smoking status

value: smoker, 45 pack-years


title: small airways, smoker 093

value: smoker, 29 pack-years


title: small airways, smoker 069


title: small airways, early-COPD 145

value: early-COPD, 20 pack-years


title: small airways, early-COPD 114

value: early-COPD, 50 pack-years


title: small airways, smoker 040

value: smoker, 24 pack-years


title: small airways, early-COPD 132

value: early-COPD, 32 pack-years


title: small airways, smoker 057


title: small airways, COPD 015

value: COPD, GOLD-II, 20 pack-years


title: small airways, early-COPD 001

value: early-COPD, 23 pack-years


title: small airways, COPD 008

value: COPD, GOLD-I, 50 pack-years


title: large airways, smoker 098

value: smoker, 36 pack-years


title: large airways, smoker 103

value: smoker, 15 pack-years


title: small airways, COPD 074

value: asian

value: COPD, GOLD-III, 110 pack-years


title: small airways, early-COPD 053

value: early-COPD, 30 pack-years


title: large airways, smoker 102

value: F

value: white


title: large airways, smoker 074

value: M

value: black

value: smoker, 20 pack-years


title: small airways, COPD 094

value: COPD, GOLD-III, 53 pack-years


title: large airways, smoker 119

value: smoker, 33 pack-years


title: large airways, smoker 114

value: smoker, 22 pack-years


title: large airways, smoker 063

value: smoker, 60 pack-years


title: large airways, smoker 112

value: smoker, 23 pack-years


title: large airways, smoker 069

value: smoker, 70 pack-years


title: large airways, smoker 093

value: smoker, 29 pack-years


title: large airways, smoker 095

value: smoker, 32 pack-years


title: large airways, smoker 097


title: large airways, smoker 094

value: smoker, 45 pack-years


title: large airways, smoker 057

value: smoker, 24 pack-years


title: large airways, smoker 049


title: large airways, smoker 023


title: large airways, smoker 058

value: smoker, 80 pack-years


title: large airways, smoker 025

value: smoker, 30 pack-years


title: large airways, non-smoker 035

value: non-smoker


title: large airways, non-smoker 008

value: white


title: large airways, non-smoker 005

value: M


title: ac_2_WT_m1_2h

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

description: Affymetrix GeneChip 3000 7G Scanner using GeneChip Operating Software (GCOS) with default paramaters for scanning Mouse 430 2.0 arrays.

hyb_protocol: Standard protocol for GeneChip Expression Analysis from Affymetrix Technical Manual.

data_processing: MAS5 detection call, gcRMA

label_protocol: 4 µg of total RNA was analysed for integrity and labeled for microarray analysis using the Affymetrix Mouse Genome 430 2.0 array. cDNA generated using Alternative Protocol for One-Cycle cDNA synthesis from Total RNA.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen) and further purified with QIAGEN RNAeasy kit

tag: Strain

value: WT, time:2hours, replicate:m1


title: ac_6_WT_m2_8h

scan_protocol: Affymetrix GeneChip 3000 7G Scanner using GeneChip Operating Software (GCOS) with default paramaters for scanning Mouse 430 2.0 arrays.

value: WT, time:8hours, replicate:m2


title: large airways, non-smoker 030


title: ac_9_WT_m3_8h

value: WT, time:8hours, replicate:m3


title: large airways, non-smoker 044


title: ac_17_KO_m3_2h

value: Knockout, time:2hours, replicate:m3


title: ac_7_WT_m3_unt

value: WT, untreated, replicate:m3


title: ac_18_KO_m3_8h

value: Knockout, time:8hours, replicate:m3


title: large airways, non-smoker 011


title: large airways, smoker 002

value: smoker, 21 pack-years


title: large airways, non-smoker 002


title: ac_11_KO_m1_2h

value: knockout, time:2hours, replicate:m1


title: large airways, non-smoker 004

value: black


title: large airways, smoker 003

value: F

value: smoker, 25 pack-years


title: ac_10_KO_m1_unt

value: knockout, untreated, replicate:m1


title: ac_12_KO_m1_8h

value: knockout, time:8hours, replicate:m1


title: ac_15_KO_m2_8h

value: knockout, time:8hours, replicate:m2


title: ac_8_WT_m3_2h

value: WT, time:2hours, replicate:m3


title: ac_16_KO_m3_unt

value: Knockout, untreated, Replicate:m3


title: ac_14_KO_m2_2h

value: knockout, time:2hours, replicate:m2


title: ac_13_KO_m2_unt

value: knockout, untreated, replicate:m2


title: ac_1_WT_m1_unt

value: WT, untreated, replicate:m1


title: large airways, non-smoker 042

value: M

value: non-smoker


title: ac_5_WT_m2_2h

value: WT, time:2hours, replicate:m2


title: ac_3_WT_m1_8h

value: WT, time:8hours, replicate:m1


title: ac_4_WT_m2_unt

value: WT, untreated, replicate:m2


title: small airways, COPD 044

value: white

value: COPD, GOLD-I, 35 pack-years


title: FHC - control 21

status: Public on Dec 18 2008

city: Ljubljana

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: A study in patients with familial hypercholesterolemia

hyb_protocol: Sample was hybridized to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA), and washed using GeneChip® Fluidics Station 450 and user prepared solutions according to manufacturer’s recommendations.

scan_protocol: Slide was scanned using GeneChip® Scanner 3000 7G and images were analyzed using GCOS (GeneChip® Operating Software).

data_processing: Data was normalized using Robust Multichip Average (RMA) as implemented in Expression Console and transformed to non-logarithmic data.

source_name: Control 21

label_protocol: Sample was labeled using 1 µg of total RNA and GeneChip® Expression 3’-Amplification One-Cycle Target Labeling and Control Reagents Kit (Affymetrix, Santa Clara, CA, USA) according to manufacturer’s recommendations.

extract_protocol: Blood was collected in PaxGeneTM Blood RNA Tubes (PreAnalytiX GmbH, A Qiagen/BD Company, Switzerland). Total RNA from white blood cells was isolated using PaxGeneTM RNA Kit (PreAnalytiX GmbH, A Qiagen/BD Company, Switzerland) according to manufacturer’s protocol. DNAse I treatment was done on columns using RNase-Free DNase Set (Qiagen GmbH, Hilden, Germany) according to manufacturer’s recommendations.

treatment_protocol: No treatment.

tag: Gender

value: male

value: 37 years

tag: Disease

tag: Drugs

tag: Tissue

value: blood


title: FHC - control 2

source_name: Control 2

value: 33 years


title: CD4+CD25- Tconv, B6.H2g7, rep3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: CEL File: jos3504.CEL

hyb_protocol: Per Joslin Diabetes Center microarray core facility.

data_processing: RMA algorithm, through GenePattern module ExpressionFileCreator from the Broad Institute.

source_name: CD4+CD25- Tconv cells from B6.H2g7 mouse spleens

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Genetic background

value: B6 congenic for MHC Class II Ag7 (H2g7)

value: 6 wks

tag: Number of mice per chip

value: Spleen

tag: Sorting

value: MACS for CD25- cells, then double-sorted for CD8a-CD11b-CD69-B220- CD4+CD25- cells


title: CD4+CD25- Tconv, B6.H2g7, rep2

description: CEL File: jos3496.CEL

scan_protocol: Per Joslin Diabetes Center microarray core facility.


title: FHC - control 13

source_name: Control 13

value: 35 years


title: FHC - control 1

source_name: Control 1

value: 45 years


title: FHC - control 22

source_name: Control 22

value: 22 years


title: CD4+CD25+ Treg, B6.H2g7, rep1

description: CEL File: jos3499.CEL

source_name: CD4+CD25+ Treg cells from B6.H2g7 mouse spleens

value: MACS for CD25+ cells, then double-sorted for CD8a-CD11b-CD69-B220- CD4+CD25hi cells

tag: %Foxp3+ after restaining


title: H929 myeloma cells-treated_pristimerin_500nM_4h

city: Scottsdale

first: rodger

last: tiedemann

state: AZ

address: 13400 E Sahuaro Dr

department: Division of Hematology Oncology

institute: Mayo Clinic

description: H929 myeloma cells were treated with prisitimerin 500nM and DMSO 0.1% for 4h at 37oC and total RNA was prepared using Trizol

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16h at 45 degrees Celsius onto Affymetrix GeneChip arrays with rotisserie mixing at 60rpm. GeneChips were washed and stained with streptavidin-phycoerythrin.

scan_protocol: GeneChips were scanned using the GeneChip system confocal scanner.

data_processing: The data were PLIER16 transformed using Affymetrix Expression Console and Excel and paired with detection calls generated from Affymetrix Expression ConsoleMAS5 analysis using default analysis settings

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

growth_protocol: Myeloma cell lines were cultured in RPMI 10% FBS at 37oC in 5%CO2

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

treatment_protocol: Cells were treated with DMSO 0.1% (+/- pristimerin 500nM dissolved in DMSO) for 4h at 37oC

tag: tissue

value: multiple myeloma cell line


title: FHC - patient 14

source_name: Patient 14

tag: Age

value: familial hypercholesterolemia

value: Altrain (lovastatin), 20 mg


title: CD4+CD25- Tconv, B6.H2g7, rep1

description: CEL File: jos3500.cel

data_processing: RMA algorithm, through GenePattern module "ExpressionFileCreator" from the Broad Institute.


title: FHC - patient 19

source_name: Patient 19


title: CD4+CD25+ Treg, NOD, rep3

description: CEL File: jos3501.CEL

source_name: CD4+CD25+ Treg cells from NOD mouse spleens

value: NOD


title: U266 myeloma cells-treated_pristimerin_500nM_4h

description: U266 myeloma cells were treated with prisitimerin 500nM and DMSO 0.1% for 4h at 37oC and total RNA was prepared using Trizol


title: CD4+CD25- Tconv, NOD, rep2

description: CEL File: jos3494.CEL

source_name: CD4+CD25- Tconv cells from NOD mouse spleens


title: CD4+CD25- Tconv, NOD, rep1

description: CEL File: jos3498.CEL


title: CD4+CD25+ Treg, B6.H2g7, rep3

description: CEL File: jos3503.CEL


title: FHC - patient 17

source_name: Patient 17

value: 46 years

value: Silvacor (simvastatin), 20 mg


title: CD4+CD25+ Treg, B6.H2g7, rep2

description: CEL File: jos3495.CEL


title: CD4+CD25+ Treg, NOD, rep1

description: CEL File: jos3497.CEL


title: FHC - patient 18

source_name: Patient 18

value: male

value: Sortis (atorvastatin), 40 mg, Ezetrol (ezetimib)


title: H929 myeloma cells-treated_DMSO_4h

description: H929 myeloma cells were treated with DMSO 0.1% for 4h at 37oC and total RNA was prepared using Trizol

source_name: H929 myeloma cells-treated_DMSO_4h


title: sample91MHG - normal

city: Pomezia(Rome)

first: Emanuele

last: de Rinaldis

address: Via Pontina

institute: IRBM (MERCK)

description: Expression data from primary gastric tumors and adjacent normal samples

hyb_protocol: Biotinylated cRNA targets were synthesised from each sample and hybridised to Affymetrix oligonucleotide chips (GeneChip HG-U133 plus 2.0)

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

data_processing: DAT files were analysed by MAS 5.0 to generate background-normalized image data (CEL files).The full data set was normalized according to the global normalization method.

source_name: adjacent normal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: RNA isolation was performed using the Rneasy Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA, USA). Following the isolation of RNA, the integrity of each RNA sample was verified by Bioanalyser (Agilent Technologies) using RNA nanochips according to manufacturer's instructions. Only those RNAs that passed this quality control were subjected to array analysis

treatment_protocol: The tissues were homogenised, and a maximum of 250 mg of the sample was subjected to RNA isolation

tag: NORMAL


title: FHC - patient 15

source_name: Patient 15

value: 33 years

value: blood


title: CD4+CD25- Tconv, NOD, rep3

description: CEL File: jos3502.CEL

value: 6 wks


title: CD4+CD25+ Treg, NOD, rep2

description: CEL File: jos3493.CEL

value: Spleen


title: sample96MHG - normal

tag: MSS


title: U266 myeloma cells-treted_DMSO_4h

description: U266 myeloma cells were treated with DMSO 0.1% for 4h at 37oC and total RNA was prepared using Trizol

source_name: U266 myeloma cells-treted_DMSO_4h


title: sample96KHG - tumor

source_name: tumor biopsy

tag: TUMOR


title: sample91KHG - tumor


title: sample63MHG - normal


title: sample63KHG - tumor


title: sample60MHG - normal


title: sample61KHG - tumor

tag: MSI


title: sample58KHG - tumor


title: sample60KHG - tumor


title: sample46MHG - normal


title: sample53KHG - tumor


title: sample196MHG - normal


title: sample53MHG - normal


title: sample202KHG - tumor


title: sample196KHG - tumor


title: sample46KHG - tumor


title: sample195KHG - tumor


title: sample43KHG - tumor


title: sample192MHG - normal


title: sample39KHG - tumor


title: sample203KHG - tumor


title: sample39MHG - normal


title: sample192KHG - tumor


title: sample189KHG - tumor


title: sample186MHG - normal


title: sample177KHG - tumor


title: sample17MHG - normal


title: sample183MHG - normal


title: sample186KHG - tumor


title: sample183KHG - tumor


title: sample202MHG - normal


title: sample17KHG - tumor


title: sample203MHG - normal


title: sample174MHG - normal


title: sample22MHG - normal


title: sample174KHG - tumor


title: sample195MHG - normal


title: sample189MHG - normal


title: sample22KHG - tumor


title: sample159MHG - normal


title: sample159KHG - tumor


title: sample148KHG - tumor


title: sample158MHG - normal


title: sample158KHG - tumor


title: sample130MHG - normal


title: sample154KHG - tumor


title: sample149MHG - normal


title: sample154MHG - normal


title: sample129KHG - tumor


title: sample149KHG - tumor


title: sample146KHG - tumor


title: sample146MHG - normal


title: sample129MHG - normal


title: sample130KHG - tumor


title: sample124KHG - tumor


title: sample127KHG - tumor


title: sample123KHG - tumor


title: sample114MHG - normal


title: sample117KHG - tumor


title: sample127MHG - normal


title: sample105MHG - normal


title: sample114KHG - tumor


title: sample118KHG - tumor


title: sample115KHG - tumor


title: sample118MHG - normal


title: sample117MHG - normal


title: sample105KHG - tumor


title: sample123MHG - normal


title: neuron_rep12

city: Cambridge

first: Laura

middle: Wiseman

last: Harris

address: Tennis Court Road

department: Insitute of Chemical Engineering and Biotechnology

institute: University of Cambridge

description: amplified RNA

hyb_protocol: Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..

scan_protocol: The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software

data_processing: Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.

source_name: human neurons isolated from postmortem dorsolateral prefrontal cortex

label_protocol: RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).

extract_protocol: Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions

treatment_protocol: 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2).  Pyramidal neurons were selected based on staining and morphology.

tag: Cell type

value: neuronal, age:42, gender:male, diagnostic group:bipolar disorder, PMI:32h


title: neuron_rep5

description: amplified RNA

value: neuronal, age:44, gender:female, diagnostic group:schizophrenia, PMI:26h


title: neuron_rep7

description: amplified RNA

value: neuronal, age:48, gender:male, diagnostic group:bipolar disorder, PMI:23h


title: neuron_rep14

description: amplified RNA

value: neuronal, age:47, gender:female, diagnostic group:schizophrenia, PMI:35h


title: neuron_rep11

description: amplified RNA

value: neuronal, age:32, gender:male, diagnostic group:control, PMI:13h


title: neuron_rep16

description: amplified RNA

value: neuronal, age:49, gender:female, diagnostic group:control, PMI:45h


title: neuron_rep13

description: amplified RNA

value: neuronal, age:52, gender:male, diagnostic group:schizophrenia, PMI:16h


title: neuron_rep4

description: amplified RNA

value: neuronal, age:39, gender:female, diagnostic group:control, PMI:58h


title: endothelial_rep16

description: amplified RNA

source_name: human endothelial cells isolated from postmortem dorsolateral prefrontal cortex

value: endothelial, age:34, gender:male, diagnostic group:control, PMI:22h


title: endothelial_rep14

description: amplified RNA

value: endothelial, age:47, gender:male, diagnostic group:control, PMI:11h


title: endothelial_rep9

description: amplified RNA

value: endothelial, age:19, gender:male, diagnostic group:schizophrenia, PMI:28h


title: neuron_rep6

description: amplified RNA

value: neuronal, age:41, gender:female, diagnostic group:bipolar disorder, PMI:28h


title: neuron_rep9

description: amplified RNA

value: neuronal, age:35, gender:male, diagnostic group:bipolar disorder, PMI:35h


title: neuron_rep3

description: amplified RNA

value: neuronal, age:47, gender:male, diagnostic group:control, PMI:11h


title: neuron_rep15

description: amplified RNA

value: neuronal, age:34, gender:male, diagnostic group:control, PMI:22h


title: neuron_rep8

description: amplified RNA

value: neuronal, age:46, gender:male, diagnostic group:control, PMI:31h


title: endothelial_rep11

description: amplified RNA

value: endothelial, age:54, gender:female, diagnostic group:schizophrenia, PMI:42h


title: endothelial_rep12

description: amplified RNA

value: endothelial, age:47, gender:female, diagnostic group:schizophrenia, PMI:30h


title: endothelial_rep8

description: amplified RNA

value: endothelial, age:44, gender:female, diagnostic group:control, PMI:10h


title: endothelial_rep13

description: amplified RNA

value: endothelial, age:42, gender:male, diagnostic group:schizophrenia, PMI:19h


title: neuron_rep1

description: amplified RNA

value: neuronal, age:45, gender:male, diagnostic group:schizophrenia, PMI:35h


title: endothelial_rep10

description: amplified RNA

value: endothelial, age:47, gender:female, diagnostic group:schizophrenia, PMI:35h


title: endothelial_rep5

description: amplified RNA

value: endothelial, age:44, gender:male, diagnostic group:schizophrenia, PMI:9h


title: endothelial_rep15

description: amplified RNA

value: endothelial, age:55, gender:male, diagnostic group:control, PMI:31h


title: endothelial_rep4

description: amplified RNA

value: endothelial, age:32, gender:male, diagnostic group:control, PMI:13h


title: endothelial_rep7

description: amplified RNA

value: endothelial, age:45, gender:male, diagnostic group:schizophrenia, PMI:18h


title: endothelial_rep6

description: amplified RNA

value: endothelial, age:54, gender:male, diagnostic group:schizophrenia, PMI:38h


title: neuron_rep2

description: amplified RNA

value: neuronal, age:37, gender:male, diagnostic group:schizophrenia, PMI:30h


title: endothelial_rep3

description: amplified RNA

value: endothelial, age:42, gender:male, diagnostic group:schizophrenia, PMI:37h


title: endothelial_rep2

description: amplified RNA

value: endothelial, age:37, gender:male, diagnostic group:schizophrenia, PMI:30h


title: endothelial_rep1

description: amplified RNA

value: endothelial, age:45, gender:male, diagnostic group:schizophrenia, PMI:35h


title: HMEC Acidosis 5

city: Durham

first: Julia

middle: Ling-Yu

state: NC

address: CIEMAS Rm.2141, 101 Science Dr.

institute: Duke university

description: gene expression data from HMEC cells

scan_protocol: Affymetrix standard protocol

data_processing: Data was normalized with RMA and MAS5 and further analyzed with hierarchical clustering as well as binary regression.

source_name: Human Mammary Epithelial Cell

label_protocol: Affymetrix standard protocol

growth_protocol: Human mammary epithelial cells were induced into replicative arrest by growth factor/serum withdrawl for 24 hrs and then exposed to different cultural environments.

extract_protocol: RNAs were extracted with miRVana kit from Ambion

treatment_protocol: The first set of experiments were done in triplicate by exposing cells to control, 25mM lactic acidosis of pH6.7, 2%hypoxia, and the combination of lactic acidosis and hypoxia. The second set of experiments were done in replica of six replicates and cells were exposed to control, acidosis with the addition of HCl to reach pH 6.7 and 25mM sodium lactate.

tag: HMEC in acidosis media under normoxia


title: HMEC Ctrl 2

description: gene expression data from HMEC cells

tag: HMEC in control media under normoxia


title: HMEC Ctrl 3

description: gene expression data from HMEC cells


title: HMEC Lactosis 2

description: gene expression data from HMEC cells

tag: HMEC in media with 25mM sodium lactate under normoxia


title: HMEC Lactosis 3

description: gene expression data from HMEC cells


title: HMEC Ctrl 4

description: gene expression data from HMEC cells


title: HMEC Acidosis 6

description: gene expression data from HMEC cells


title: HMEC Hypoxia 1

description: gene expression data from HMEC cells

tag: HMEC in control media under hypoxia


title: HMEC Acidosis 1

description: gene expression data from HMEC cells


title: HMEC Acidosis 2

description: gene expression data from HMEC cells


title: DSS-treated conventional 1

city: Dallas

first: Lora

middle: V

last: Hooper

state: TX

address: 5323 Harry Hines Blvd.

department: Immunology

institute: The University of Texas Southwestern Medical Center at Dallas

description: comparison of gamma delta intraepithelial lymphocytes from untreated and DSS-treated mouse colons

hyb_protocol: Standard Affymetrix Hybridization Protocol

scan_protocol: Standard Affymetrix Scan protocol

data_processing: Array was scaled to a target intensity of 500, and the CHP file was generated using Affymetrix GCOS software

source_name: gamma delta intraepithelial lymphocytes, DSS-treated conventional mouse colon

label_protocol: Arcturus HS RiboAmp RNA amplification kit protocol

extract_protocol: Arcturus PicoPure RNA isolation kit protocol

treatment_protocol: mice were treated with 2% DSS for 5 days followed by 3 days' recovery on normal drinking water

tag: Strain

value: C57b/6, conventionally-raised, sorted gammadelta intraepithelial lymphocytes from DSS-treated colon


title: HMEC Lactic Acidosis plus hypoxia 3

description: gene expression data from HMEC cells

tag: HMEC in media with 25mM lactic acidosis under hypoxia


title: HMEC Lactosis 1

description: gene expression data from HMEC cells


title: HMEC Ctrl 1

description: gene expression data from HMEC cells


title: DSS-treated conventional 2


title: HMEC Ctrl 6

description: gene expression data from HMEC cells


title: HMEC Hypoxia 3

description: gene expression data from HMEC cells


title: HMEC Lactosis 5

description: gene expression data from HMEC cells


title: HMEC Acidosis 4

description: gene expression data from HMEC cells


title: HMEC Lactic Acidosis plus hypoxia 1

description: gene expression data from HMEC cells


title: conventional 2

source_name: gamma delta intraepithelial lymphocytes, untreated conventional mouse colon

treatment_protocol: no treatment

tag: strain

value: C57b/6, conventionally-raised, sorted gammadelta intraepithelial lymphocytes from untreated colon


title: HMEC Hypoxia 2

description: gene expression data from HMEC cells


title: HMEC Lactosis 4

description: gene expression data from HMEC cells


title: HMEC Acidosis 3

description: gene expression data from HMEC cells


title: HMEC Ctrl 5

description: gene expression data from HMEC cells


title: neuron_rep10

description: amplified RNA

value: neuronal, age:51, gender:male, diagnostic group:bipolar disorder, PMI:23h


title: HMEC Lactic Acidosis 3

description: gene expression data from HMEC cells

tag: HMEC in media with 25mM lactic acidosis under normoxia


title: HMEC Lactic Acidosis plus hypoxia 2

description: gene expression data from HMEC cells


title: HMEC Lactic Acidosis 2

description: gene expression data from HMEC cells


title: HMEC Control 2

description: gene expression data from HMEC cells


title: HMEC Control 3

description: gene expression data from HMEC cells


title: p0617_treated_day_9_rep1

status: Public on Dec 16 2008

city: Hørsholm

first: Morten

last: Lindow

address: Bøge Alle 3

department: microRNA

country: Denmark

institute: Santaris Pharma A/S

hyb_protocol: Fifteen micrograms of biotin-labelled cRNA was fragmented and 10 mg were hybridized onto Affymetrix Mouse Genome 430 2.0 arrays overnight in the GeneChip Hybridisation oven 6400 using standard procedures, The arrays were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: Scanning was carried out using the GeneChip Scanner 3000 and image analysis was performed using GeneChip Operating Software.

data_processing: RMA

source_name: p0617 liver, antimiR-122 (SPC3372) treated, day 9

label_protocol: Total RNA was processed following the GeneChip Expression 30-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-labelled cRNA following manufacturer’s specifications.

extract_protocol: The dissected mice livers were immediately stored in RNA  later (Ambion). Total RNA was extracted with Trizol  reagent according to the manufacturer’s instructions  (Invitrogen), except that the precipitated RNA pellet  was washed in 80% ethanol and not vortexed.

tag: NMRI, females


title: p0617_control_day_3_rep1

source_name: p0617 liver, control, day 3


title: p0621_control_day_23_rep1

source_name: p0621 liver, control, day 23


title: p0617_control_day_9_rep1

source_name: p0617 liver, control, day 9


title: p0621_control_day_23_rep3


title: p0617_control_day_3_rep3


title: p0617_treated_day_3_rep3

source_name: p0617 liver, antimiR-122 (SPC3372) treated, day 3


title: p0617_treated_day_23_rep1

source_name: p0617 liver, antimiR-122 (SPC3372) treated, day 23


title: p0617_control_day_9_rep2


title: p0617_treated_day_3_rep1


title: p0617_treated_day_9_rep3


title: p0617_treated_day_23_rep3


title: p0617_control_day_9_rep3


title: p0617_control_day_3_rep2


title: HMEC Lactic Acidosis 1

description: gene expression data from HMEC cells


title: p0617_treated_day_9_rep2


title: p0617_treated_day_23_rep2


title: p0617_treated_day_3_rep2


title: p0621_treated_day_23_rep1

source_name: p0621 liver, antimiR-122 (SPC3372) treated, day 23


title: p0621_control_day_23_rep2


title: p0621_treated_day_23_rep2


title: HMEC Control 1

description: gene expression data from HMEC cells


title: p0621_treated_day_23_rep3


title: conventional 1

scan_protocol: Standard Affymetrix Scan Protocol


title: apoE-Aorta-78-weeks-2

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4

hyb_protocol: 60rpm, 18h, 45 centigrade in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: total aorta

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 24h IVT

growth_protocol: Maintained under normal mouse chow / SPF conditions (12h light-dark cycle)

extract_protocol: Qiagen RNEasy Lipid Tissue Mini Kit, Standardprotocol

treatment_protocol: excised, rinsed with cold PBS (2mM EDTA), removed adipose and connective tissue

tag: gender

value: male

tag: age

value: 78 weeks

value: aorta


title: wt-Aorta-78-weeks-3

tag: tissue


title: apoE-Aorta-6-weeks-2

value: 6 weeks


title: wt-Aorta-78-weeks-1


title: apoE-Aorta-78-weeks-3


title: wt-Aorta-78-weeks-2


title: apoE-Aorta-78-weeks-1


title: wt-Aorta-6-weeks-2


title: wt-Aorta-6-weeks-1


title: apoE-Aorta-6-weeks-3


title: wt-Aorta-6-weeks-3


title: small airways, non-smoker 044

description: small airways, non-smoker

source_name: airway epithelial cells obtained by bronchoscopy and brushing

tag: sex

value: M

tag: ethnic group

value: white

tag: smoking status

value: non-smoker


title: Small airways, non-smoker 040

description: small airways, non-smoker

value: F

value: black/hispanic


title: apoE-Aorta-6-weeks-1


title: Small airways, non-smoker 011

description: small airways, non-smoker


title: Small airways, non-smoker 042

description: small airways, non-smoker

value: black


title: FACS-sorted non-side population neural stem cell, biological replicate #3

status: Public on Dec 15 2008

city: Bar Harbor

first: Kyuson

last: Yun

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: Strandard Affymetrix procedures with modifications according to NuGEN protocol

scan_protocol: Standard Affymetrix procedures

data_processing: MAS5 in Expression Console

label_protocol: Ovation Pico kit from NuGEN

extract_protocol: Total RNA was isolated from FAC-sorted cells using the RNeasy Micro Kit (Qiagen, Inc.) according to the manufacturer’s instructions.

tag: RNA prepared from FACS-sorted non-side population neural stem cells from NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice.  These mice were injected with cultured untransformed neurospheres cells isolated from S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  Cells were sorted directly into lysis buffer.


title: Small airways, non-smoker 029

description: small airways, non-smoker


title: FACS-sorted side population cell sample 4346, biological replicate #2

tag: RNA prepared from FACS-sorted side population cells from cultured brain tumor cells from NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice.  These tumors were induced by subcutaneously injecting cultured tumorsphere 4346 cells isolated from brain tumors in S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  Cells were sorted directly into lysis buffer.


title: FACS-sorted side population cell sample 3447, biological replicate #2

tag: RNA prepared from FACS-sorted side population cells from cultured brain tumor cells from NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice.  These tumors were induced by subcutaneously injecting cultured tumorsphere 3447 cells isolated from brain tumors in S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  Cells were sorted directly into lysis buffer.


title: FACS-sorted side population cell sample 3447, biological replicate #1

extract_protocol: Total RNA was isolated from FAC-sorted cells using the RNeasy Micro Kit (Qiagen, Inc.) according to the manufacturers instructions.


title: FACS-sorted non-side population cell sample 3447, biological replicate #2

tag: RNA prepared from FACS-sorted non-side population cells from cultured brain tumor cells from NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice.  These tumors were induced by subcutaneously injecting cultured tumorsphere 3447 cells isolated from brain tumors in S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  Cells were sorted directly into lysis buffer.


title: FACS-sorted side population cell sample 3447, biological replicate #3


title: FACS-sorted side population neural stem cell, biological replicate #3

tag: RNA prepared from FACS-sorted side population neural stem cells from NOD.Cg-Prkdc<scid>Il2rg<tm1Wjl>/SzJ mice.  These mice were injected with cultured untransformed neurospheres cells isolated from S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice.  Cells were sorted directly into lysis buffer.


title: FACS-sorted non-side population neural stem cell, biological replicate #2


title: FACS-sorted side population cell sample 4346, biological replicate #3


title: FACS-sorted non-side population cell sample 3447, biological replicate #3


title: FACS-sorted non-side population neural stem cell, biological replicate #1


title: FACS-sorted side population neural stem cell, biological replicate #1


title: FACS-sorted side population neural stem cell, biological replicate #2


title: FACS-sorted non-side population cell sample 3447, biological replicate #1


title: SEM_replicate_2

first: Garrett

middle: M

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

description: Gene expression data from SEM leukmeia cell line

hyb_protocol: Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.  GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was performed using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4 (GCOS)

data_processing: The data were analyzed by using Affymetrix Gene Chip Operating Software using default settings.

source_name: SEM leukemia cell line

label_protocol: 1ug of total RNA was labeled according to standard Affymetrix protocols.

growth_protocol: Human SEM cells with the t(4;11) translocation and REH control cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. All cell lines were maintained in RPMI medium 1640 supplemented with 10% FBS.

extract_protocol: Total RNA was isolated from 5 x 106 REH or SEM cells by TRIzol extraction.

tag: SEM leukemia cell line


title: 17-0001B_Septic Shock_day3_217

status: Public on Dec 12 2008

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: 1) Controls: 2) Septic shock; 3) Sepsis; 4) SIRS; 5) SIRS resolved

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

source_name: Septic Shock_day3

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene protocol.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were not manipulated.

tag: Whole blood from normal children and children with SIRS, sepsis, or septic shock.


title: SEM_replicate_1


title: cDNA_(H33_Control_Affymetrix)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Expression in S2 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Drosophila Genome 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data processing was performed using Affymetrix GCOS 1.4 software. After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002).

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).

extract_protocol: S2 cells were harvested and RNA was extracted using the Trizol (Invitrogen) method following the manufacturer's instructions.

tag: cell type

value: S2 cells


title: 01-0055B_Septic Shock_day3_58


title: 11-0054B_Septic Shock_day3_183


title: REH_replicate_1

description: Gene expression data from REH leukmeia cell line

source_name: REH leukemia cell line

tag: REH leukemia cell line


title: 02-0002B_Septic Shock_day3_62


title: REH_replicate_2


title: 01-0022_Septic Shock_day3_218


title: 17-0003B_Septic Shock_day3_215


title: 05-0014B_Septic Shock_day3_82


title: 10-0013_Septic Shock_day3_122


title: FACS-sorted side population cell sample 4346, biological replicate #1


title: 06-0009B_Septic Shock_day3_84


title: 01-0045B_Septic Shock_day3_44


title: 01-0053B_Septic Shock_day3_56


title: 01-0049B_Septic Shock_day3_47


title: 01-0036B_Septic Shock_day3_40


title: 01-0066B_Septic Shock_day3_22


title: 01-0062B_Septic Shock_day3_18


title: 01-0051B_Septic Shock_day3_53


title: 01-0058B_Septic Shock_day3_11


title: 01-0061B_Septic Shock_day3_16


title: 07-0001_Septic Shock_day3_94


title: 10-0028B_Sepsis_day3_128


title: 04-0002_Sepsis_day3_67


title: 11-0044B_Sepsis_day3_175


title: 01-0062A_Septic Shock_day1_17


title: 10-0011_Sepsis_day3_119


title: 11-0057B_Sepsis_day3_139


title: 05-0011_Septic Shock_day1_81


title: 11-0055B_Sepsis_day3_138


title: 07-0005_Sepsis_day3_98


title: 11-0015_Sepsis_day3_154


title: 03-0001B_Sepsis_day3_63


title: 01-0038B_Sepsis_day3_42


title: 01-0018_Sepsis_day3_25


title: 05-0003_Septic Shock_day1_74


title: 26-260611_Septic Shock_day1_222


title: 04-0005_Septic Shock_day1_70


title: 13-0005B_Sepsis_day3_190


title: 11-0010_Septic Shock_day1_148


title: 01-0034A_Septic Shock_day1_1


title: 01-0050B_Sepsis_day3_50


title: 10-0001_Sepsis_day3_189


title: 11-0050B_Sepsis_day3_181


title: 11-0021_Sepsis_day3_163


title: 14-0002B_Sepsis_day3_196


title: 01-0013_Septic Shock_day1_23


title: 12-0001_Sepsis_day1_228


title: 01-0021_Septic Shock_day1_28


title: 11-0006_Sepsis_day1_192


title: 15-0009A_Sepsis_day1_214


title: 15-0013A_Sepsis_day1_203


title: 11-0022_Sepsis_day1_164


title: 11-0021_Sepsis_day1_162


title: 10-0001_Septic Shock_day1_110


title: 10-0002_Sepsis_day1_224


title: 11-0055A_Sepsis_day1_137


title: 11-0023_Sepsis_day1_165


title: 11-0024_Sepsis_day1_166


title: 11-0044A_Sepsis_day1_174


title: 11-0053A_Sepsis_day1_136


title: 01-0014_Septic Shock_day1_24


title: 11-0004_Sepsis_day1_145


title: 11-0050A_Sepsis_day1_180


title: 10-0015_Sepsis_day1_123


title: 11-0041A_Sepsis_day1_130


title: 11-0047A_Sepsis_day1_131


title: 11-0003_Sepsis_day1_144


title: 10-0010_Sepsis_day1_118


title: Eed-null ES cells at day 6 of LIF withdrawal, biological rep 1

first: Xiaohua

last: Shen

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data

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 dChip.

growth_protocol: standard culture conditions were used to culture MEFs, NSc and ES cells.

treatment_protocol: ES cell differentiation was induced by LIF withdrawal and cells were collected at various time points. wild-type and the two mutant cell lines, grown on feeders, were harvested and allowed to sit in tissue plates for 20-30 min to deplete feeders. Feeder-d

tag: Eed-null ES cells

tag: day 6 of LIF withdrawal


title: Ezh2-null ES cells at day 8 of LIF withdrawal, biological rep 1

description: Gene expression data

tag: Ezh2-null ES cells

tag: day 8 of LIF withdrawal


title: 10-0007_Sepsis_day1_116


title: Eed-null ES cells at day 2 of LIF withdrawal, biological rep 2

description: Gene expression data

tag: day 2 of LIF withdrawal


title: Eed-null ES cells at day 2 of LIF withdrawal, biological rep 1

description: Gene expression data


title: Eed-null ES cells at day 6 of LIF withdrawal, biological rep 2

description: Gene expression data


title: Ezh2-null ES cells at day 6 of LIF withdrawal, biological rep 5

description: Gene expression data


title: Ezh2-null ES cells at day 8 of LIF withdrawal, biological rep 2

description: Gene expression data


title: 10-0005_Sepsis_day1_113


title: Ezh2-null ES cells at day 6 of LIF withdrawal, biological rep 1

description: Gene expression data


title: 05-0002_Sepsis_day1_73


title: 04-0007A_Sepsis_day1_65


title: Ezh2-null ES cells at day 2 of LIF withdrawal, biological rep 2

description: Gene expression data


title: Ezh2-null ES cells at day 6 of LIF withdrawal, biological rep 2

description: Gene expression data


title: Ezh2-null ES cells at day 2 of LIF withdrawal, biological rep 1

description: Gene expression data


title: CJ7 wild-type ES cells at day 8 of LIF withdrawal, biological rep 1

description: Gene expression data

tag: CJ7 wild-type ES cells


title: Ezh2-null ES cells at day 6 of LIF withdrawal, biological rep 3

description: Gene expression data


title: 03-0001A_Sepsis_day1_64


title: 01-0027_Sepsis_day1_35


title: 01-0046A_Sepsis_day1_45


title: CJ7 wild-type ES cells at day 6 of LIF withdrawal, biological rep 5

description: Gene expression data


title: Ezh2-null ES cells at day 2 of LIF withdrawal, biological rep 3

description: Gene expression data


title: 07-0005_Sepsis_day1_97


title: 10-0027A_Sepsis_day1_107


title: 01-0055A_Sepsis_day1_57


title: 01-0038A_Sepsis_day1_4


title: Ezh2-null ES cells at day 6 of LIF withdrawal, biological rep 4

description: Gene expression data


title: Ezh2-null ES cells at day 2 of LIF withdrawal, biological rep 4

description: Gene expression data


title: CJ7 wild-type ES cells at day 8 of LIF withdrawal, biological rep 2

description: Gene expression data


title: 11-0006_SIRS resolved_day3_198

source_name: SIRS resolved_day3


title: CJ7 wild-type ES cells at day 6 of LIF withdrawal, biological rep 4

description: Gene expression data


title: 10-0002_SIRS resolved_day3_225


title: J1 wild-type ES cells at day 6 of LIF withdrawal, biological rep 3

description: Gene expression data

tag: J1 wild-type ES cells


title: CJ7 wild-type ES cells at day 2 of LIF withdrawal, biological rep 4

description: Gene expression data


title: J1 wild-type ES cells at day 6 of LIF withdrawal, biological rep 2

description: Gene expression data


title: J1 wild-type ES cells at day 6 of LIF withdrawal, biological rep 1

description: Gene expression data


title: 11-0059B_SIRS resolved_day3_186


title: 11-0049B_SIRS resolved_day3_179


title: 14-0001B_SIRS resolved_day3_194


title: CJ7 wild-type ES cells at day 2 of LIF withdrawal, biological rep 3

description: Gene expression data


title: 11-0045B_SIRS resolved_day3_177


title: 01-0034B_Septic Shock_day3_2


title: J1 wild-type ES cells at day 2 of LIF withdrawal, biological rep 2

description: Gene expression data


title: J1 wild-type ES cells at day 2 of LIF withdrawal, biological rep 1

description: Gene expression data


title: Eed-null ES cells at day 0 (undifferentiated), biological rep 5

description: Gene expression data

tag: day 0 (undifferentiated)


title: 11-0016_SIRS resolved_day3_156


title: 11-0060B_SIRS resolved_day3_141


title: Eed-null ES cells at day 0 (undifferentiated), biological rep 4

description: Gene expression data


title: Eed-null ES cells at day 0 (undifferentiated), biological rep 3

description: Gene expression data


title: 11-0058B_SIRS resolved_day3_140


title: 11-0051B_SIRS resolved_day3_134


title: Eed-null ES cells at day 0 (undifferentiated), biological rep 1

description: Gene expression data


title: Eed-null ES cells at day 0 (undifferentiated), biological rep 2

description: Gene expression data


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 6

description: Gene expression data


title: 10-0007_SIRS resolved_day3_117


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 1

description: Gene expression data


title: 01-0048B_SIRS resolved_day3_46


title: E14tg1 wild-type ES cells at day 0 (undifferentiated), biological rep 7

description: Gene expression data

tag: E14tg1 wild-type ES cells


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 5

description: Gene expression data


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 4

description: Gene expression data


title: 01-0027_SIRS resolved_day3_36


title: CJ7 wild-type ES cells at day 0 (undifferentiated), biological rep 3

description: Gene expression data


title: 01-0063B_SIRS resolved_day3_20


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 3

description: Gene expression data


title: Ezh2-null ES cells at day 0 (undifferentiated), biological rep 2

description: Gene expression data


title: 01-0039B_SIRS resolved_day3_6


title: E14tg1 wild-type ES cells at day 0 (undifferentiated), biological rep 6

description: Gene expression data


title: CJ7 wild-type ES cells at day 0 (undifferentiated), biological rep 4

description: Gene expression data


title: 01-0059B_SIRS resolved_day3_13


title: J1 wild-type ES cells at day 0 (undifferentiated), biological rep 2

description: Gene expression data


title: 15-0010B_SIRS_day3_200


title: Neuronal stem cells derived from NPc, biological rep 2

description: Gene expression data

source_name: Neuronal stem cells derived from NPc

tag: Neuronal stem cells derived from NPc


title: E14tg1 wild-type ES cells at day 0 (undifferentiated), biological rep 5

description: Gene expression data


title: J1 wild-type ES cells at day 0 (undifferentiated), biological rep 1

description: Gene expression data


title: 01-0043B_SIRS resolved_day3_8


title: Neuronal progenitor cells marked by Sox1-GFP, biological rep 2

description: Gene expression data


title: Neuronal progenitor cells marked by Sox1-GFP, biological rep 3

description: Gene expression data


title: Neuronal stem cells derived from NPc, biological rep 1

description: Gene expression data


title: 15-0010A_SIRS_day1_199


title: 10-0029B_SIRS_day3_109


title: 14-0001A_SIRS_day1_193


title: 11-0036_SIRS_day3_172


title: Neuronal progenitor cells marked by Sox1-GFP, biological rep 1

description: Gene expression data


title: Mesoendodermal cells marked by T-GFP, biological rep 2

description: Gene expression data

source_name: Mesoendodermal cells marked by GFPpositive cells in which GFP expression is driven by brachyury (T) promoter.

tag: Mesoendodermal cells marked by T-GFP


title: 11-0059A_SIRS_day1_185


title: 11-0060A_SIRS_day1_187


title: MEF, biological rep 2

description: Gene expression data

source_name: MEF

tag: MEF


title: 10-0006_SIRS_day3_115


title: MEF, biological rep 1

description: Gene expression data


title: 11-0036_SIRS_day1_171


title: 11-0045A_SIRS_day1_176


title: Mesoendodermal cells marked by T-GFP, biological rep 1

description: Gene expression data


title: 11-0016_SIRS_day1_155


title: 11-0046A_SIRS_day1_178


title: 11-0049A_SIRS_day1_132


title: 11-0015_SIRS_day1_153


title: 10-0006_SIRS_day1_114


title: 11-0031_SIRS_day1_170


title: 11-0040A_SIRS_day1_129


title: 11-0051A_SIRS_day1_133


title: 10-0022A_SIRS_day1_105


title: 04-0008A_SIRS_day1_71


title: 01-0039A_SIRS_day1_5


title: 10-0023A_SIRS_day1_106


title: 04-0010C_Control_day1_72


title: 06-0002_SIRS_day1_87


title: 11-0052C_Control_day1_135


title: 01-0037A_SIRS_day1_41


title: 04-0011C_Control_day1_66


title: proline_rep3

status: Public on Dec 11 2008

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

description: Five weeks old Arabidopsis mature leaves were infiltrated with 10 mM of AZC and harvested 3 houts later.

hyb_protocol: For each sample, 10ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Arabidopsis microarray for 16 hours at 45ºC.Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000.  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

data_processing: RMA algorithm was used for raw chip data normalization and summary.

source_name: Arabidopsis mature leaves infiltrated with 10mM AZC

label_protocol: Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences).  After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences).  The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).

growth_protocol: Arabidopsis thaliana Columbia-0 were grown in a growth cabinet at 20 °C with a photoperiod of 8 h light/ 16 h dark.

extract_protocol: RNA was extracted by TRIreagent (SIGMA) and purified by using QIAGEN RNeasy kit.

treatment_protocol: Five weeks old Arabidopsis mature leaves were infiltrated with 10 mM of AZC or L-Proline (control of AZC) or 2 mg/l of tunicamycin (tunicamycin stock was prepared as 1mg/ml in DMF and diluted to 2mg/l by water) or DMF(solvent control of tunicamycin, 2ul/ml in water). Six infiltrated leaves were harvested three hours after the infiltration of chemicals. For the heat shock treatment, six mature leaves were detached from plant and placed in 50 ml plastic tube. The tubes were incubated at 37 °C or 20°C (as a control) for a period of 1h.


title: tunicamycin_rep5

description: Five weeks old Arabidopsis mature leaves were infiltrated with 2mg/l of tunicamycin and harvested 3 houts later.

source_name: Arabidopsis mature leaves infiltrated with 2mg/l tunicamycin


title: proline_rep2


title: tunicamycin_rep3


title: DMF_rep4

description: Five weeks old Arabidopsis mature leaves were infiltrated with 1mg/ml of DMF and harvested 3 houts later.

source_name: Arabidopsis mature leaves infiltrated with 2ul/ml of DMF


title: AZC_rep2

description: Five weeks old Arabidopsis mature leaves were infiltrated with 10 mM of proline and harvested 3 houts later.

source_name: Arabidopsis mature leaves infiltrated with 10mM proline


title: tunicamycin_rep2


title: DMF_rep2


title: DMF_rep1


title: noneHS_rep3

description: Five weeks old Arabidopsis six mature leaves were detached from plant and placed in 50 ml plastic tube. The tubes were incubated at 20°C for a period of 1h.

source_name: Arabidopsis mature leaves incubated at 20 °C for 1h


title: AZC_rep1


title: DMF_rep3


title: AZC_rep3


title: tunicamycin_rep1


title: HS_rep2

description: Five weeks old Arabidopsis six mature leaves were detached from plant and placed in 50 ml plastic tube. The tubes were incubated at 37°C for a period of 1h.

source_name: Arabidopsis mature leaves incubated at 37 °C for 1h


title: HS_rep3


title: proline_rep1


title: DMF_rep5


title: tunicamycin_rep4


title: noneHS_rep2


title: HS_rep1


title: noneHS_rep1


title: CLL_7_14dNLC

city: Wuerzburg

last: Rosenwald

address: Josef-Schneider-Strasse 2

department: Institute of Pathology

institute: University of Wuerzburg

description: purified CLL cells from peripheral blood after 14 days co-culture with Nurse-like cells (NLC)

hyb_protocol: Affymetrix Hybridization Protocol. Following fragmentation, 20 microgr of cRNA were hybridized for 16 hours at 45°C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Scanning Protocol. Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The average probe array signals were scaled to a target signal of 500.

source_name: purified CLL cells, patient 7 after 14d co-culture with Nurse like cells (NLC)

label_protocol:
Affymetrix Labeling Protocol.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microgr total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Using TRIzol from Invitrogen, purified B cells were lysed according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). Total RNA extraction then was performed with the PureLink Micro-to-Midi Total RNA Purification System as described by the manufacturer (Invitrogen).


title: CLL_9_14dNLC

source_name: purified CLL cells, patient 9 after 14d co-culture with Nurse like cells (NLC)


title: CLL_5_fresh

description: purified CLL cells from peripheral blood

source_name: purified CLL cells, patient 5, fresh

tag: purified CLL cells, patient 5, fresh


title: CLL_4_fresh

source_name: purified CLL cells, patient 4, fresh

tag: purified CLL cells, patient 4, fresh


title: CLL_4_14dNLC

source_name: purified CLL cells, patient 4 after 14d co-culture with Nurse like cells (NLC)


title: CLL_7_fresh

source_name: purified CLL cells, patient 7, fresh

tag: purified CLL cells, patient 7, fresh


title: CLL_8_14dNLC

source_name: purified CLL cells, patient 8 after 14d co-culture with Nurse like cells (NLC)


title: CLL_9_fresh

source_name: purified CLL cells, patient 9, fresh

tag: purified CLL cells, patient 9, fresh


title: CLL_5_14dNLC

source_name: purified CLL cells, patient 5 after 14d co-culture with Nurse like cells (NLC)


title: CLL_6_fresh

source_name: purified CLL cells, patient 6, fresh

tag: purified CLL cells, patient 6, fresh


title: CLL_8_fresh

source_name: purified CLL cells, patient 8, fresh

tag: purified CLL cells, patient 8, fresh


title: CLL_2_14d_NLC

source_name: purified CLL cells, patient 2 after 14 days co-culture with Nurse-like cells (NLC)


title: CLL_1_14dNLC

source_name: purified CLL cells, patient 1 after 14 days co-culture with Nurse-like cells (NLC)


title: CLL_3_14dNLC

source_name: purified CLL cells, patient 3 after 14days co-culture with Nurse like cells (NLC)


title: StrainSM_M_HF_Rep1

status: Public on Dec 10 2008

first: Keith

last: Shockley

department: Computational and Systems Biology

description: One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet.  Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.

hyb_protocol: Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto MOE430v2.0 GeneChip® arrays for 16 hours at 45°C. Post-hybridization staining and washing were performed according to the manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner. Images were quantified using GeneChip Operating Software (GCOS) v1.2 (Affymetrix).

data_processing: RMA values are in the VALUE column here. Briefly, the RMA method was used to adjust the background of perfect match (PM) probes, apply a quantile normalization of the corrected PM values and calculate final expression measures using the Tukey median polish algorithm.

source_name: Strain SM, Males, HF Diet

label_protocol: The cDNA was linearly amplified with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY) through an in vitro transcription reaction with T7 RNA polymerase.

extract_protocol: Liver samples were extracted from each mouse as described previously (Shockley and Churchill, 2006). Total RNA was reverse transcribed with oligo(dT)-T7 primers. before double-stranded cDNA was generated with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen).

tag: Strain

value: SM

tag: Sex

value: Male

tag: Diet

value: 30% fat

tag: Biological Replicate


title: CLL_6_14dNLC

source_name: purified CLL cells, patient 6 after 14d co-culture with Nurse like cells (NLC)


title: StrainSM_M_6C_Rep3

source_name: Strain SM, Males, 6C Diet

value: 6% fat (regular chow)


title: StrainSM_F_HF_Rep3

source_name: Strain SM, Females, HF Diet

value: Female


title: CLL_2_fresh

source_name: purified CLL cells, patient 2, fresh

tag: purified CLL cells, patient 2, fresh


title: StrainSM_F_6C_Rep2

source_name: Strain SM, Females, 6C Diet


title: CLL_3_fresh

source_name: purified CLL cells, patient 3, fresh

tag: purified CLL cells, patient 3, fresh


title: StrainPERA_M_HF_Rep1

source_name: Strain PERA, Males, HF Diet

value: PERA


title: StrainSM_F_HF_Rep1


title: StrainPERA_M_HF_Rep2


title: CLL_1_fresh

source_name: purified CLL cells, patient 1, fresh

tag: purified CLL cells, patient 1, fresh


title: StrainSM_M_6C_Rep2


title: StrainPERA_M_6C_Rep1

source_name: Strain PERA, Males, 6C Diet


title: StrainPERA_M_HF_Rep3


title: StrainSM_M_6C_Rep1


title: StrainSM_F_6C_Rep1


title: StrainPERA_M_6C_Rep3