description: Gene expression data for 1655 delta tnaA exposed to low levels of norfloxacin, t0


title: GermlineContaining_adult_totalRNA_replicate1

status: Public on Sep 02 2010

type: RNA

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

country: USA

institute: University of North Carolina at Chapel Hill

description: Gene expression data from young feminized germline containing (fem-2) adults.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Caenorhabditis elegans

source_name: mixed stage embryos from N2

label_protocol: Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Worms were grown in standard S-basal media liquid culture. DH245 (fem-2 (b245)) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 23C. Adults were collected over 35uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: 1V sample (frozen powdered worm) in 10V Trizol that was stored at -80C was thawed at 37C. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.

tag: strain

tag: developmental stage

value: young adults


title: Expired U133A_B_rep2

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Ambion Human Brain Reference RNA

hyb_protocol: The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the GeneChip® 3’-Amplification Reagent Kit for IVT Labeling (Affymetrix). The A260/A280 ratio and yield of each of the cRNAs were recorded. For each sample, 10 µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a GeneChip® microarray for 16 hours at 45ºC.

scan_protocol: Following hybridization, all microarrays were washed and stained in an Affymetrix GeneChip® Fluidics Station. Stained microarrays were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: Quality checks and data analyses were carried out using Affymetrix GeneChip® Operating Software (GCOS) and Quality Reporter.

label: biotin

organism: Homo sapiens

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)

label_protocol: Biotinylated cRNA samples were prepared according to the standard Affymetrix GeneChip® protocol. One µg of total RNA from each sample, along with poly A spikes (labeling control), were converted to double-stranded cDNA with GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA). After second-strand synthesis, the cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix).

extract_protocol: The two RNA samples had been stored under  80°C at their respective vendor’ freezer since 2005, and were shipped with dry ice from the vendors to the microarray laboratory of Dr. Charles Wang at UCLA. The same batches of the two samples as those used in the MAQC project in 2005 were used in this study. Upon receiving RNA samples in 2009, the microarray laboratory evaluated and confirmed their quality using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. The RNA Integrity Number (RIN) for each sample was around 8.0.

tag: tissue

value: brain reference


title: CO92_Cy5_YP3758_Cy3

type: genomic

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing: log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY from  from default normalized Agilent Feature Extraction settings for 2 channel arrays

molecule: genomic DNA

organism: Yersinia pestis

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: Expired U133A_B_rep3

description: Ambion Human Brain Reference RNA


title: ear_6pm_day1

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

institute: Pioneer Hi-Bred International

description: Gene Expression at ear_6pm_rep1_day1

hyb_protocol: Standard Agilent Hybridization protocol

scan_protocol: After hybridization, the microarray slides were washed and scanned immediately with Agilent’s G2505B DNA Microarray Scanner at two laser power settings (100% and 10%).  The images were inspected visually for image artifacts, and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v 9.5.1).

data_processing: The data were then normalized using quantile normalization (BOLSTAD http://www.ncbi.nlm.nih.gov/pubmed/12538238) and passed forward for periodicity determination.  Further quality control and downstream analysis were performed using data analysis tools in Rosetta’s Resolver Database and in the statistical program R

label: Cy3, Cy5

organism: Zea mays

label_protocol: Each mRNA sample was made into double-stranded DNA, amplified by an in-vitro transcription reaction, and labeled with Cy3 or Cy5 fluorescent dye, all using Agilent’s Low RNA Linear Amp kit.  Biological replicates were labeled alternately using Cy3 or Cy5 to guard against dye-bias.

growth_protocol: Plants of the public inbred line B73 were grown under field conditions in Johnston, Iowa,  U.S.A. to V14-V15 stages, as defined according to the appearance of the leaf collar of the uppermost leaf

extract_protocol: Total RNA was isolated from frozen ground tissue (SQ Tissue Kit, Omega Biotek), followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for the 108 samples.  The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: For Agilent microarray profiling, samples were taken starting at daybreak on day 1 (ZT0), and taken every 4 hours hence for 72 hours.  At each time point, the top-most immature ear, 4-5 cm in length, was collected from two separate plants to create one of three biological field replicates.

value: Immature Ear

tag: cultivar

tag: time

value: 6pm day1


title: CO92_Cy5_YP8790_Cy3


title: ear_2pm_day1

description: Gene Expression at ear_2pm_rep1_day1

value: 2pm day1


title: Expired U133A_B_rep1

description: Ambion Human Brain Reference RNA


title: Expired U133A_A_rep2

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)

value: universal reference


title: CO92_Cy5_YpTB29910_Cy3

organism: Yersinia pseudotuberculosis


title: CO92_Cy5_YpTB32_Cy3


title: Expired U133A_A_rep3

description: Stratagene Universal Human Reference RNA


title: ear_10am_day1

description: Gene Expression at ear_10am_rep1_day1

value: 10am day1


title: ear_2am_day1

description: Gene Expression at ear_2am_rep1_day1

value: 2am day1


title: CO92_Cy5_Pestoides_J_Cy3


title: Naegleria_gruberi_80min_rep2

city: Berkeley

first: Lillian

last: Fritz-Laylin

state: CA

address: 345 LSA, UC Berkeley MCB

department: MCB

institute: UC Berkeley

description: This sample is of Naegleria gruberi, strain NEG, isolated at 80 minutes after initiation of differentiation. It is the second of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.

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

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

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

organism: Naegleria gruberi

source_name: Naegleria gruberi, 80 minutes after initiation of differentiation

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

growth_protocol: Naegleria gruberi strain NEG amoeba were grown on solid medium (NM) in association with Klebsiella pneumoniae.

extract_protocol: RNA was extracted using Trizol Reagent (Invitrogen), followed by RNAeasy columns (Qiagen), treated with Turbo DNAse (Ambion), and re-purified over another RNAeasy column (Qiagen), all according to the manufacturer's instructions.

treatment_protocol: Amoeba were differentiated using standard protocols (see Fulton and Dingle, 1967).

value: NEG

tag: timepoint


title: CO92_Cy5_YP8081_Cy3


title: ear_6am_ day1

description: Gene Expression at ear_6am_rep1_ day1

source_name: ear_6am_rep1_ day1

value: 6am  day1


title: Naegleria_gruberi_60min_rep2

description: This sample is of Naegleria gruberi, strain NEG, isolated at 60 minutes after initiation of differentiation. It is the second of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.

source_name: Naegleria gruberi, 60 minutes after initiation of differentiation


title: ear_6am_ day3

description: Gene Expression at ear_6am_rep1_ day3

source_name: ear_6am_rep1_ day3

value: 6am  day3


title: CO92_Cy5_PestoidesF_Cy3

source_name: PestoidesF

value: PestoidesF


title: Naegleria_gruberi_80min_rep3

description: This sample is of Naegleria gruberi, strain NEG, isolated at 80 minutes after initiation of differentiation. It is the third of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: ear_6am_ day2

description: Gene Expression at ear_6am_rep1_ day2

source_name: ear_6am_rep1_ day2

value: 6am  day2


title: CO92_Cy5_Pestoides_C_Cy3


title: ear_10am_day2

description: Gene Expression at ear_10am_rep1_day2

value: 10am day2


title: Expired U133A_A_rep1


title: Naegleria_gruberi_80min_rep1

description: This sample is of Naegleria gruberi, strain NEG, isolated at 80 minutes after initiation of differentiation. It is the first of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: Naegleria_gruberi_60min_rep3

description: This sample is of Naegleria gruberi, strain NEG, isolated at 60 minutes after initiation of differentiation. It is the third of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: CO92_Cy5_YP1953_Cy3


title: CO92_Cy5_y225_Cy3


title: ear_10pm_day3

description: Gene Expression at ear_10pm_rep1_day3

value: 10pm day3


title: N2_embryo_totalRNA_replicate1

description: Gene expression data from mixed stage embryos isolated from N2 strain.

growth_protocol: Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture.

extract_protocol: 1V sample in 10V Trizol that was stored at -80C was thawed at 37C, vortexed 30 seconds and re-frozen in liquid nitrogen. Freeze-cracking was repeated a total of four times. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.

value: mixed embryos


title: CO92_Cy5_YP6902_Cy3


title: ear_2am_day2

description: Gene Expression at ear_2am_rep1_day2

value: 2am day2


title: ear_2am_day3

description: Gene Expression at ear_2am_rep1_day3

value: 2am day3


title: N2_embryo_totalRNA_replicate2


title: Naegleria_gruberi_40min_rep2

description: This sample is of Naegleria gruberi, strain NEG, isolated at 40 minutes after initiation of differentiation. It is the second of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.

source_name: Naegleria gruberi, 40 minutes after initiation of differentiation


title: Naegleria_gruberi_20min_rep1

description: This sample is of Naegleria gruberi, strain NEG, isolated at 20 minutes after initiation of differentiation. It is the first of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.

source_name: Naegleria gruberi, 20 minutes after initiation of differentiation


title: CO92_Cy5_WA_Cy3

source_name: WA

value: WA


title: CO92_Cy5_YPT910_Cy3


title: Naegleria_gruberi_20min_rep2

description: This sample is of Naegleria gruberi, strain NEG, isolated at 20 minutes after initiation of differentiation. It is the second of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: Naegleria_gruberi_40min_rep3

description: This sample is of Naegleria gruberi, strain NEG, isolated at 40 minutes after initiation of differentiation. It is the third of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: ear_2pm_day3

description: Gene Expression at ear_2pm_rep1_day3

value: Immature Ear

value: 2pm day3


title: CO92_Cy5_2516-87_Cy3


title: Naegleria_gruberi_20min_rep3

description: This sample is of Naegleria gruberi, strain NEG, isolated at 20 minutes after initiation of differentiation. It is the third of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: Naegleria_gruberi_60min_rep1

description: This sample is of Naegleria gruberi, strain NEG, isolated at 60 minutes after initiation of differentiation. It is the first of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: ear_10pm_day2

description: Gene Expression at ear_10pm_rep1_day2

value: 10pm day2


title: Naegleria_gruberi_40min_rep1

description: This sample is of Naegleria gruberi, strain NEG, isolated at 40 minutes after initiation of differentiation. It is the first of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: Naegleria_gruberi_0min_rep3

description: This sample is of Naegleria gruberi, strain NEG, isolated at 0 minutes after initiation of differentiation. It is the third of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.

source_name: Naegleria gruberi, 0 minutes after initiation of differentiation


title: Naegleria_gruberi_0min_rep2

description: This sample is of Naegleria gruberi, strain NEG, isolated at 0 minutes after initiation of differentiation. It is the second of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: CO92_Cy5_907_Cy3


title: CO92_Cy5_Y231_Cy3

source_name: Genomic DNA purified from wild type bacteria


title: Naegleria_gruberi_0min_rep1

description: This sample is of Naegleria gruberi, strain NEG, isolated at 0 minutes after initiation of differentiation. It is the first of three biological replicates used in this experiment, each from separate cultures, and differentiated at separate times.


title: 1st Sham surgery followed by 2nd sham surgery after 1 week No. 2

status: Public on Sep 01 2010

city: Sydney

first: Rajkumar

last: Cheluvappa

state: NSW

address: Inflammation and Infection Research Centre, School of Medical Sciences, Wallace Wurth Building, University of New South Wales, Gate 9 High Street, Sydney, NSW 2052, Australia.

department: St George Clinical School

country: Australia

institute: University of New South Wales

description:
Sample name:  SS2
CEL file (original name): RC_RJ15_(MoGene-1_0-st-v1).CEL

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using a Affymetrix GCS3000 7G four-colour Gene Array scanner with autoloader (Affymetrix) at the Ramaciotti Centre for Gene Function Analysis, UNSW, Australia

data_processing:
Raw data from 8 CEL files was normalisd in a single batch using RMA in Partek 6.4, with default settings, excluding the control probesets. Batch effects in the normalised data due to date of processing were removed using the batch removal tool in partek (essentially using the residuals from an ANOVA fitted to batch effect). Probesets not detected on any array were excluded. Probeset detection based upon the detected above background procedure from affymetrix power tools, where detected means DABG P=10^-5 in at least one sample
probe group file: MoGene-1_0-st-v1.r3.pgf

organism: Mus musculus

source_name: Most distal colon from 5 -week old Male BALB/c mice

label_protocol: 100 ng of RNA from each sample was labelled using the Whole Transcript Sense Target Labelling Assay, following manufacturers instructions

growth_protocol: 5 -week old Male BALB/c mice maintained at Standard PC2 Animal Storage Facility at the 5th Floor, Wallace Wurth Building, UNSW, Sydney.

extract_protocol: RNA was extracted (TRIzol®) from 4 individual colonic samples per group (AA group vs. SS group) with each sample taken independently through Affymetrix® microarray hybridization.

treatment_protocol: Appendicitis induction followed by appendicectomy after 1 week OR 1st Sham surgery followed by 2nd sham surgery after 1 week.

value: BALB/c

tag: age

value: 5 weeks

value: Most distal colon

tag: protocol

value: Sham-Sham (SS)

tag: batch


title: ear_6pm_day3

description: Gene Expression at ear_6pm_rep1_day3

value: 6pm day3


title: CO92_Cy5_CO92_Cy3


title: Appendicitis induction followed by appendicectomy after 1 week No. 4

description:
Sample name:  AA4
CEL file (original name): RC_MG8_(MoGene-1_0-st-v1).CEL

value: Appendicitis-Appendicectomy (AA)


title: CO92_Cy5_Pestoides_Angola_Cy3


title: ear_6pm_day2

description: Gene Expression at ear_6pm_rep1_day2

value: 6pm day2


title: 1st Sham surgery followed by 2nd sham surgery after 1 week No. 1

description:
Sample name:  SS1
CEL file (original name): RC_RJ13_(MoGene-1_0-st-v1).CEL


title: 1st Sham surgery followed by 2nd sham surgery after 1 week No. 3

description:
Sample name:  SS3
CEL file (original name): RC_MG1_(MoGene-1_0-st-v1).CEL


title: 1st Sham surgery followed by 2nd sham surgery after 1 week No. 4

description:
Sample name:  SS4
CEL file (original name): RC_MG3_(MoGene-1_0-st-v1).CEL


title: TS 7

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS7

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.

source_name: Human B-cell chronic lymphocytic leukemia patient TS7

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: legend

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

tag: Sex

value: M

tag: vh status

value: unmut

tag: disease

value: B-cell chronic lymphocytic leukemia (B-CLL)

tag: Stage

value: Binet A

tag: cell type

value: CD5/CD19/CD23 triple-positive B cells


title: ear_10am_day3

description: Gene Expression at ear_10am_rep1_day3

value: 10am day3


title: Appendicitis induction followed by appendicectomy after 1 week No. 2

description:
Sample name:  AA2
CEL file (original name): RC_RJ17_(MoGene-1_0-st-v1).CEL


title: ear_2pm_day2

description: Gene Expression at ear_2pm_rep1_day2

value: Immature Ear

value: 2pm day2


title: TS 18

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS18

source_name: Human B-cell chronic lymphocytic leukemia patient TS18

value: F

value: mut


title: RC 95

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC95

source_name: Human B-cell chronic lymphocytic leukemia patient RC95


title: TS 21

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS21

source_name: Human B-cell chronic lymphocytic leukemia patient TS21


title: Appendicitis induction followed by appendicectomy after 1 week No. 1

description:
Sample name:  AA1
CEL file (original name): RC_RJ16_(MoGene-1_0-st-v1).CEL

value: BALB/c

value: 5 weeks


title: TS 12

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS12

source_name: Human B-cell chronic lymphocytic leukemia patient TS12


title: RC 94

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC94

source_name: Human B-cell chronic lymphocytic leukemia patient RC94


title: TS 3

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS3

source_name: Human B-cell chronic lymphocytic leukemia patient TS3


title: Appendicitis induction followed by appendicectomy after 1 week No. 3

description:
Sample name:  AA3
CEL file (original name): RC_MG6_(MoGene-1_0-st-v1).CEL

value: Most distal colon


title: RC 87

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC87

source_name: Human B-cell chronic lymphocytic leukemia patient RC87


title: RC 84

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC84

source_name: Human B-cell chronic lymphocytic leukemia patient RC84


title: RC 93

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC93

source_name: Human B-cell chronic lymphocytic leukemia patient RC93


title: RC 81

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC81

source_name: Human B-cell chronic lymphocytic leukemia patient RC81


title: RC 92

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC92

source_name: Human B-cell chronic lymphocytic leukemia patient RC92


title: RC 89

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC89

source_name: Human B-cell chronic lymphocytic leukemia patient RC89


title: RC 75

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC75

source_name: Human B-cell chronic lymphocytic leukemia patient RC75


title: RC 33

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC33

source_name: Human B-cell chronic lymphocytic leukemia patient RC33


title: RC 20

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC20

source_name: Human B-cell chronic lymphocytic leukemia patient RC20


title: RC 88

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC88

source_name: Human B-cell chronic lymphocytic leukemia patient RC88


title: RC 11

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC11

source_name: Human B-cell chronic lymphocytic leukemia patient RC11


title: RC 14

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC14

source_name: Human B-cell chronic lymphocytic leukemia patient RC14


title: RC 7

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC7

source_name: Human B-cell chronic lymphocytic leukemia patient RC7


title: RC 21

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC21

source_name: Human B-cell chronic lymphocytic leukemia patient RC21


title: RC 19

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC19

source_name: Human B-cell chronic lymphocytic leukemia patient RC19


title: RC 24

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC24

source_name: Human B-cell chronic lymphocytic leukemia patient RC24


title: RC 22

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC22

source_name: Human B-cell chronic lymphocytic leukemia patient RC22


title: GE 225

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE225

source_name: Human B-cell chronic lymphocytic leukemia patient GE225


title: GE 126

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE126

source_name: Human B-cell chronic lymphocytic leukemia patient GE126


title: RC 17

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC17

source_name: Human B-cell chronic lymphocytic leukemia patient RC17


title: GE 130

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE130

source_name: Human B-cell chronic lymphocytic leukemia patient GE130


title: RC 18

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC18

source_name: Human B-cell chronic lymphocytic leukemia patient RC18


title: RC 5

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC5

source_name: Human B-cell chronic lymphocytic leukemia patient RC5


title: GE 87

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE87

source_name: Human B-cell chronic lymphocytic leukemia patient GE87


title: GE 98

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE98

source_name: Human B-cell chronic lymphocytic leukemia patient GE98


title: GE 99

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE99

source_name: Human B-cell chronic lymphocytic leukemia patient GE99


title: RC 1

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC1

source_name: Human B-cell chronic lymphocytic leukemia patient RC1


title: GE 93

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE93

source_name: Human B-cell chronic lymphocytic leukemia patient GE93


title: GE 163

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE163

source_name: Human B-cell chronic lymphocytic leukemia patient GE163


title: RC 12

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient RC12

source_name: Human B-cell chronic lymphocytic leukemia patient RC12


title: GE 173

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE173

source_name: Human B-cell chronic lymphocytic leukemia patient GE173


title: GE 88

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE88

source_name: Human B-cell chronic lymphocytic leukemia patient GE88


title: GE 107

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE107

source_name: Human B-cell chronic lymphocytic leukemia patient GE107


title: GE 115

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE115

source_name: Human B-cell chronic lymphocytic leukemia patient GE115


title: CZ 78

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ78

source_name: Human B-cell chronic lymphocytic leukemia patient CZ78


title: GE 117

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE117

source_name: Human B-cell chronic lymphocytic leukemia patient GE117


title: GE 111

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE111

source_name: Human B-cell chronic lymphocytic leukemia patient GE111


title: GE 114

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE114

source_name: Human B-cell chronic lymphocytic leukemia patient GE114


title: GE 110

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE110

source_name: Human B-cell chronic lymphocytic leukemia patient GE110


title: GE 101

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE101

source_name: Human B-cell chronic lymphocytic leukemia patient GE101


title: CZ 42

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ42

source_name: Human B-cell chronic lymphocytic leukemia patient CZ42


title: CZ 41

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ41

source_name: Human B-cell chronic lymphocytic leukemia patient CZ41


title: CZ 7

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ7

source_name: Human B-cell chronic lymphocytic leukemia patient CZ7


title: CS 38

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS38

source_name: Human B-cell chronic lymphocytic leukemia patient CS38


title: CZ 4

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ4

source_name: Human B-cell chronic lymphocytic leukemia patient CZ4


title: CS 3

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS3

source_name: Human B-cell chronic lymphocytic leukemia patient CS3


title: CZ 28

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ28

source_name: Human B-cell chronic lymphocytic leukemia patient CZ28


title: CZ 47

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ47

source_name: Human B-cell chronic lymphocytic leukemia patient CZ47


title: CZ 36

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ36

source_name: Human B-cell chronic lymphocytic leukemia patient CZ36


title: 6 h LPS-stimulated cells, biological rep3

status: Public on Aug 29 2010

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

country: Germany

institute: Hannover Medical School

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 6 h_3
Gene expression data from cells stimulated for 6 h with LPS 100 ng/mL (acute response).

hyb_protocol: Hybridization was performed according to standard protocols recommended by Affymetrix.

scan_protocol: Scanning was performed using an Affymetrix GeneChip 3000 7G Scanner in combination with GCOS (Affymetrix) software according to standard protocols recommended by Affymetrix. Affymetrix GeneChip v3.2 software was used to create the CEL files.

data_processing: The data were normalized using GC-RMA using the ArrayAssist Lite (Affymetrix) software package.

source_name: mouse small intestinal epithelial m-ICcl2 cells, 6 h LPS

label_protocol: Probe labelling was performed according to standard protocols recommended by Affymetrix.

growth_protocol: m-ICcl2 cells were grown in supplemented medium on collagen-coated tissue flasks for days as described in Bens et al., Am J Physiol, 1996, 270(6 Pt 1):C1666-74.

extract_protocol: TRIzol RNA isolation reagent (Life Technologies) was used for total RNA preparation following the manufacturer's instructions. RNA quality was confirmed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Cell were left untreated (control), stimulated for 6 h with 100 ng/mL LPS (E. coli D31m4, List Biochemicals Inc.), or stimulated for 6 h with LPS 100 ng/mL with subsequent incubation in LPS-free medium for another 90 h.

tag: cell line

tag: transgene

value: SV40 large T antigen

value: small intestinal epithelial

tag: treatment

value: lipopolysaccharide (LPS) for 6 h


title: CS 12

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS12

source_name: Human B-cell chronic lymphocytic leukemia patient CS12

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)


title: 6 h LPS-stimulated cells, biological rep2

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 6 h_2
Gene expression data from cells stimulated for 6 h with LPS 100 ng/mL (acute response).

tag: strain


title: 6 h LPS followed by 90 h in LPS-free medium, biological rep1

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 96 h_1
Gene expression data from cells stimulated for 6 h with LPS (100 ng/mL) and subsequently incubated with LPS-free medium for 90 h (tolerant response).

source_name: mouse small intestinal epithelial m-ICcl2 cells, 6 h LPS followed by 90 h LPS-free medium

value: lipopolysaccharide (LPS) for 6 h followed by LPS-free medium for 90 h


title: 6 h LPS followed by 90 h in LPS-free medium, biological rep2

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 96 h_2
Gene expression data from cells stimulated for 6 h with LPS (100 ng/mL) and subsequently incubated with LPS-free medium for 90 h (tolerant response).


title: CS 17

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CS17

source_name: Human B-cell chronic lymphocytic leukemia patient CS17

value: unmut


title: MS_M5

status: Public on Aug 20 2010

city: Mumbai

first: Madhurima

last: Benekareddy

state: Maharashtra

address: 1, Homibhabha Road, Colaba

department: Department of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT. Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The labeled aRNA samples were hybridized on to a Custom Rat Array 8X15K (AMADID: 21617). 600 ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled RNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution. Laser detection of Cyanine 3 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing:
Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data
1. Transformation: Set measurements less than 0.01 to 0.01,
2. Per Chip: Normalize to 50th percentile,
3. Per Gene: Normalize to Specific Samples (Control).
Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.66 for Down Regulation were obtained. The p-value cutoff used was 0.05.

organism: Rattus norvegicus

source_name: prefrontal cortex, MS group, saline

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. aRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled aRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: 30mg of tissue was used for RNA isolation by   using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: group

value: MS

value: saline


title: CZ 26

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient CZ26

source_name: Human B-cell chronic lymphocytic leukemia patient CZ26

value: B-cell chronic lymphocytic leukemia (B-CLL)

value: Binet A

value: CD5/CD19/CD23 triple-positive B cells


title: unstimulated cells, biological rep3

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
unstimulated control_3
Gene expression data from unstimulated cells (control).

source_name: mouse small intestinal epithelial m-ICcl2 cells, unstimulated

value: unstimulated


title: 6 h LPS followed by 90 h in LPS-free medium, biological rep3

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 96 h_3
Gene expression data from cells stimulated for 6 h with LPS (100 ng/mL) and subsequently incubated with LPS-free medium for 90 h (tolerant response).


title: unstimulated cells, biological rep1

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
unstimulated control_1
Gene expression data from unstimulated cells (control).


title: 6 h LPS-stimulated cells, biological rep1

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
LPS 6 h_1
Gene expression data from cells stimulated for 6 h with LPS 100 ng/mL (acute response).


title: Control_C2

source_name: prefrontal cortex, control group, saline

value: control


title: TS 45

description: Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient TS45

source_name: Human B-cell chronic lymphocytic leukemia patient TS45

value: M

value: mut


title: MS_M2


title: Control_DOI_D4

source_name: prefrontal cortex, control group, DOI

value: DOI


title: Control_DOI_D3


title: MS_M3


title: unstimulated cells, biological rep2

description:
m-ICcl2 cells derived from C-section-derived fetal small intestinal tissue.
unstimulated control_2
Gene expression data from unstimulated cells (control).

value: SV40 large T antigen

value: small intestinal epithelial


title: Quercetin 1000mg/kg treated rep2 (cy3)

status: Public on Aug 11 2010

city: Lucknow

first: Prabhat

last: Singh

state: Uttar Pradesh

address: MG Marg

department: Toxicology

institute: Central Drug Research Institute

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Mouse 8x60k (AMADID No: 26986).  800ng of cy3 labeled and 800 ng of cy5 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing:
Data extraction done using Agilent Feature extraction software v10.5.
Please note that the supplementary raw data files for the replicate Samples are duplicated.

source_name: Liver tissue

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) and Cy5 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: The animals were housed in plastic cages and acclimated to controlled conditions of light and dark (12 h each), and temperature (23±2ºC) for next 24 hrs. after drug administration. Access to food and water was ‘ad libitum’ before and after drug treatment.

extract_protocol: Approximately 50 mg of frozen liver tissue was crushed manually in liquid nitrogen and immediately homogenized (cole parmer) in 1 ml, TRIzol (Invitrogen). The homogenized tissue was incubated for 10 min at room temperature followed by the addition of 200 μl chloroform (Sigma) per ml of TRIzol used and mixed vigorously for 10-15 sec. The sample was allowed to stand undisturbed for 15 min at room temperature and then centrifuged at 12,500 g for 20 min at 4C. The aqueous phase was carefully transferred to a fresh tube and RNA was precipitated with 500 μl isopropyl alcohol (Merck). Further centrifugation at 12,000 g for 15 min at 4C and washing (twice) with 1 ml, 75% ethanol was done to recover pure RNA pellet. Finally, the RNA pellet was air dried and resuspended in molecular grade water (Sigma). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at -80 °C until use.

treatment_protocol: Quercetin  was procured from Sigma. All animal procedures were carried out in compliance to institutional animal ethics committee (IAEC) guidelines. Animals belonging to different treatment groups were administered different doses of Quercetin (500mg/kg, 1500mg/kg, 2000mg/kg) were administered as intraperitoneal (ip) injection in DMSO. The animals of respective control group were administered with DMSO. Blood was withdrawn before sacrificing the animals through heart puncture using 1 ml disposable syringe (Dispo Van) and allowed to stand undisturbed for 30 min in 1.5 ml micro centrifuge tube (Axygen). Left lobe of liver was immediately fixed in 10% formalin for histological investigations. Remaining part of liver tissue was washed with normal saline and rapidly snap frozen in liquid nitrogen and subsequently stored at -80°C (Thermo) until further use.

value: liver

tag: gender

value: male

value: Quercetin  1000mg/kg


title: MS_M4

value: brain


title: Quercetin 1000mg/kg treated rep1 (cy5)


title: Control_DOI_D2

value: prefrontal cortex


title: Control_DOI_D1


title: Quercetin 1500mg/kg treated rep1 (cy5)

value: Quercetin  1500mg/kg


title: Control_C3

value: saline


title: Genistein 250mg/kg treated rep2 (cy3)

value: Genistein 250mg/kg


title: Genistein 500mg/kg treated rep1 (cy5)

value: Genistein 500mg/kg


title: Quercetin 1500mg/kg treated rep2 (cy3)


title: Quercetin 500mg/kg treated rep2 (cy3)

value: Quercetin  500mg/kg


title: Control_C1


title: Genistein 250mg/kg treated rep1 (cy5)


title: Quercetin 500mg/kg treated rep1 (cy5)


title: Genistein 125mg/kg treated rep2 (cy3)

value: Genistein 125mg/kg


title: Control-Vehicle treated rep2 (cy3)

value: Control-Vehicle


title: Control-Vehicle treated rep1 (cy5)


title: Genistein 125mg/kg treated rep1 (cy5)


title: Genistein 500mg/kg treated rep2 (cy3)


title: High-fat+ resveratrol fed group, Time 9 months, male pig number 5

status: Public on Aug 09 2010

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description:
H-F+R9.5.M
Gene expression data from PBMNCs isolated from male pig; group of animals fed a high-fat diet supplemented with resveratrol for 9 months.

hyb_protocol: Following fragmentation, 15 cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Using CEL files obtained from GCOS software (Affymetrix), the data were analyzed with Robust Multichip Average (RMA) using Affymetrix Expression Console (v.1.1) software.

organism: Sus scrofa

source_name: PBMNCs, male pig, high-fat diet supplemented with resveratrol, time 9 months

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 4 μg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Pigs' heparinised blood was processed within two hours after extraction and used to isolate PBMNCs. Isolation was carried out under sterile conditions to avoid the activation of monocytes. Blood was diluted 1:1 with RPMI 1640 cell culture medium and processed by density gradient centrifugation with Histopaque-1077 (Sigma Aldrich) according to the manufacturer instructions. After washing the cells (x2) with phosphate buffer solution (PBS), the PBMNCs were lysed using RLT Buffer (Qiagen) and stored at –80 ºC for RNA extraction.

extract_protocol: Total RNA was isolated using an RNeasy ® Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80ºC.

treatment_protocol:
PBMNCs were isolated from the following groups: i) CT (control group), time 0, n=10 arrays (5 females, 5 males; basal expression levels); ii) CT group, time 9 months, n=4 arrays (2 females, 2 males); iii) High-fat fed animals (H-F group), time 9 months, n=4 arrays (2 females, 2 males); iv) High-fat fed animals supplemented with resveratrol (H-F+RES group), time 9 months, n=4 arrays (2 females, 2 males).

CT diet: 5% beef tallow; H-F diet: 20% beef tallow; H-F+RES diet: 20% beef tallow plus 8 mg/Kg body weight per day resveratrol.

tag: breed

value: Mini Pig

value: blood

value: peripheral blood mononuclear cells (PBMNCs)

tag: diet

value: high-fat + resveratrol

tag: time

value: 9 months

tag: pig


title: High-fat+ resveratrol fed group, Time 9 months, male pig number 4

description:
H-F+R9.4.M
Gene expression data from PBMNCs isolated from male pig; group of animals fed a high-fat diet supplemented with resveratrol for 9 months.


title: High-fat+ resveratrol fed group, Time 9 months, female pig number 21

description:
H-F+R9.21.F
Gene expression data from PBMNCs isolated from female pig; group of animals fed a high-fat diet supplemented with resveratrol for 9 months.

source_name: PBMNCs, female pig, high-fat diet supplemented with resveratrol, time 9 months

value: female


title: High-fat fed group, Time 9 months, male pig number 26

description:
H-F9.26.M
Gene expression data from PBMNCs isolated from male pig; group of animals fed a high-fat diet for 9 months.

source_name: PBMNCs, male pig, high-fat diet, time 9 months

value: male

value: high-fat


title: High-fat fed group, Time 9 months, female pig number 27

description:
H-F9.27.F
Gene expression data from PBMNCs isolated from female pig; group of animals fed a high-fat diet for 9 months.

source_name: PBMNCs, female pig, high-fat diet, time 9 months


title: High-fat fed group, Time 9 months, male pig number 23

description:
H-F9.23.M
Gene expression data from PBMNCs isolated from male pig; group of animals fed a high-fat diet for 9 months.


title: Control group, Time 9 months, male pig number 25

description:
CT9.25.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 9 months.

source_name: PBMNCs, male pig, control group fed a normal chow, time 9 months

value: normal


title: High-fat+ resveratrol fed group, Time 9 months, female pig number 22

description:
H-F+R9.22.F
Gene expression data from PBMNCs isolated from female pig; group of animals fed a high-fat diet supplemented with resveratrol for 9 months.


title: Control group, Time 9 months, female pig number 18

description:
CT9.18.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 9 months.

source_name: PBMNCs, female pig, control group fed a normal chow, time 9 months


title: Control group, Time 0 (basal), male pig number 25

description:
CT0.25.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 0 (basal levels of expression).

source_name: PBMNCs, male pig, control group fed a normal chow, time 0 (basal expression levels)


title: Control group, Time 9 months, male pig number 16

description:
CT9.16.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 9 months.


title: Control group, Time 0 (basal), male pig number 11

description:
CT0.11.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 0 (basal), male pig number 24

description:
CT0.24.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 9 months, female pig number 8

description:
CT9.8.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 9 months.


title: Control group, Time 0 (basal), female pig number 20

description:
CT0.20.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 0 (basal levels of expression).

source_name: PBMNCs, female pig, control group fed a normal chow, time 0 (basal expression levels)


title: Control group, Time 0 (basal), female pig number 6

description:
CT0.6.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 0 (basal), female pig number 17

description:
CT0.17.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 0 (basal levels of expression).


title: High-fat fed group, Time 9 months, female pig number 30

description:
H-F9.30.F
Gene expression data from PBMNCs isolated from female pig; group of animals fed a high-fat diet for 9 months.


title: Control group, Time 0 (basal), female pig number 8

description:
CT0.8.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 0 (basal), male pig number 15

description:
CT0.15.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 0 (basal), male pig number 12

description:
CT0.12.M
Gene expression data from PBMNCs isolated from male pig; control animal, time 0 (basal levels of expression).


title: Control group, Time 0 (basal), female pig number 10

description:
CT0.10.F
Gene expression data from PBMNCs isolated from female pig; control animal, time 0 (basal levels of expression).


title: hiPS_PDB2lox_21_rep2_090811_10

city: Cambridge

first: Garrett

middle: M

last: Frampton

state: MA

address: 9 Cambridge Center

institute: Whitehead Instute - MIT

description: Gene expression data from hiPS_PDB2lox_21

hyb_protocol: Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).  GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees 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 using default settings.

data_processing: Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.

molecule: polyA RNA

label_protocol: 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.

growth_protocol:
All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ).  Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20,  iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).  hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.

extract_protocol: RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).


title: hiPS_PDB2lox_5_rep1_120208_19

description: Gene expression data from hiPS_PDB2lox_5


title: hiPS_PDB2lox_17_rep1_120208_5

description: Gene expression data from hiPS_PDB2lox_17


title: hiPS_PDB2lox_22_rep1_120208_25

description: Gene expression data from hiPS_PDB2lox_22


title: hiPS_PDB1lox_17puro_5_rep1_120208_8

description: Gene expression data from hiPS_PDB1lox_17puro_5


title: hiPS_PDB1lox_21puro_26_rep1_120208_12

description: Gene expression data from hiPS_PDB1lox_21puro_26


title: hiPS_PDB1lox_21puro_20_rep1_120208_11

description: Gene expression data from hiPS_PDB1lox_21puro_20


title: hiPS_PDB1lox_21puro_26_rep2_090811_14


title: hiPS_PDB2lox_17_rep2_090811_9


title: hiPS_C1_rep2_081006_12

description: Gene expression data from hiPS line C1

source_name: hiPS line C1

value: hiPS line C1


title: hiPS_PDB1lox_17puro_33_rep1_120208_10

description: Gene expression data from hiPS_PDB1lox_17puro_33


title: hiPS_PDB1lox_21puro_28_rep1_120208_13

description: Gene expression data from hiPS_PDB1lox_21puro_28


title: hiPS_4_rep1_081006_5

description: Gene expression data from hiPS line 4

source_name: hiPS line 4

value: hiPS line 4


title: hiPS_4_rep2_081006_6

description: Gene expression data from hiPS line 4


title: hiPS_A1_rep1_081006_1

description: Gene expression data from hiPS line A1

source_name: hiPS line A1

value: hiPS line A1


title: hiPS_A1_rep2_081006_2

description: Gene expression data from hiPS line A1


title: hES_WIBR3_rep1_090811_1

description: Gene expression data from hES line WIBR3

source_name: hES line WIBR3

value: hES line WIBR3


title: hiPS_C1_rep1_081006_11

description: Gene expression data from hiPS line C1


title: hES_WIBR7_rep2_090811_4

description: Gene expression data from hES line WIBR7

source_name: hES line WIBR7

value: hES line WIBR7


title: hES_WIBR3_rep2_090811_2


title: hiPS_PDB1lox_17puro_5_rep2_090811_13


title: hES_WIBR2_rep1_090811_8

description: Gene expression data from hES line WIBR2

source_name: hES line WIBR2

value: hES line WIBR2


title: hES_WIBR7_rep1_090811_3


title: hES_WIBR1_rep2_090811_11

description: Gene expression data from hES line WIBR1

source_name: hES line WIBR1

value: hES line WIBR1


title: hiPS_PDB1lox_17puro_10_rep1_120208_9

description: Gene expression data from hiPS_PDB1lox_17puro_10


title: hES_H9_rep2_120208_15

description: Gene expression data from hES line H9

source_name: hES line H9

value: hES line H9


title: hES_WIBR2_rep2_090811_12


title: hiPS_PDB2lox_21_rep1_120208_23


title: hiPS_A6_rep2_081006_4

description: Gene expression data from hiPS line A6

source_name: hiPS line A6

value: hiPS line A6


title: hES_BG01_rep4_081006_14

description: Gene expression data from hES line BG01

source_name: hES line BG01

value: hES line BG01


title: hES_WIBR1_rep1_090811_7


title: hES_BG01_rep3_081006_13

description: Gene expression data from hES line BG01


title: hES_BG01_rep1_081006_9

description: Gene expression data from hES line BG01


title: hES_BG03_rep2_090811_6

description: Gene expression data from hES line BG03

source_name: hES line BG03

value: hES line BG03


title: hES_BG03_rep1_090811_5

description: Gene expression data from hES line BG03


title: hES_BG01_rep2_081006_10

description: Gene expression data from hES line BG01


title: FIBROBLAST_GM_rep1_081006_7

description: Gene expression data from human fibroblast line GM

source_name: human fibroblast line GM

value: human fibroblast line GM


title: hES_H9_rep1_081006_15

description: Gene expression data from hES line H9


title: hES_BG01_rep5_120208_1

description: Gene expression data from hES line BG01


title: FIBROBLAST_PDB_rep1_120208_3

description: Gene expression data from human fibroblast line PDB

source_name: human fibroblast line PDB

value: human fibroblast line PDB


title: FIBROBLAST_GM_rep2_081006_8


title: GM17850

status: Public on Jul 24 2010

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

description: Basal gene expression level of lymphoblastoid cell line GM17850.

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as the normalization method.

source_name: Lymphoblastoid cell line GM17850

label_protocol: Labeling was performed according to the Affymetrix Gene Chip technical manual.

growth_protocol: LCLs were cultured in RPMI 1640 medium supplemented with 15% heat-inactivated Fetal Bovine Serum (FBS). According to the protocol from the Coriell website (http://ccr.coriell.org/sections/support/global/lymphoblastoid.aspx?pgid=213), LCLs were maintained at a density of 2-8 × 10^5 cells/ml, and were split or re-fed with fresh medium every three days, depending on the growth status of each cell line.

extract_protocol: Total RNA was extracted from each of the cell lines using Qiagen RNeasy Mini kits (QIAGEN, Inc.).  RNA quality was tested using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was used.

tag: ethnic group

value: HCA Han Chinese-American

tag: cell line (coriell id)

tag: wei id

value: EBV-transformed lymphoblastoid cells


title: GM17844

description: Basal gene expression level of lymphoblastoid cell line GM17844.

source_name: Lymphoblastoid cell line GM17844


title: GM17837

description: Basal gene expression level of lymphoblastoid cell line GM17837.

source_name: Lymphoblastoid cell line GM17837


title: GM17841

description: Basal gene expression level of lymphoblastoid cell line GM17841.

source_name: Lymphoblastoid cell line GM17841


title: GM17813

description: Basal gene expression level of lymphoblastoid cell line GM17813.

source_name: Lymphoblastoid cell line GM17813


title: GM17852

description: Basal gene expression level of lymphoblastoid cell line GM17852.

source_name: Lymphoblastoid cell line GM17852


title: GM17292

description: Basal gene expression level of lymphoblastoid cell line GM17292.

source_name: Lymphoblastoid cell line GM17292

value: CA Caucasian-American


title: GM17293

description: Basal gene expression level of lymphoblastoid cell line GM17293.

source_name: Lymphoblastoid cell line GM17293


title: GM17839

description: Basal gene expression level of lymphoblastoid cell line GM17839.

source_name: Lymphoblastoid cell line GM17839


title: GM17840

description: Basal gene expression level of lymphoblastoid cell line GM17840.

source_name: Lymphoblastoid cell line GM17840


title: GM17846

description: Basal gene expression level of lymphoblastoid cell line GM17846.

source_name: Lymphoblastoid cell line GM17846


title: GM17842

description: Basal gene expression level of lymphoblastoid cell line GM17842.

source_name: Lymphoblastoid cell line GM17842


title: GM17845

description: Basal gene expression level of lymphoblastoid cell line GM17845.

source_name: Lymphoblastoid cell line GM17845


title: GM17847

description: Basal gene expression level of lymphoblastoid cell line GM17847.

source_name: Lymphoblastoid cell line GM17847


title: GM17273

description: Basal gene expression level of lymphoblastoid cell line GM17273.

source_name: Lymphoblastoid cell line GM17273


title: GM17280

description: Basal gene expression level of lymphoblastoid cell line GM17280.

source_name: Lymphoblastoid cell line GM17280


title: GM17824

description: Basal gene expression level of lymphoblastoid cell line GM17824.

source_name: Lymphoblastoid cell line GM17824


title: GM17289

description: Basal gene expression level of lymphoblastoid cell line GM17289.

source_name: Lymphoblastoid cell line GM17289


title: GM17831

description: Basal gene expression level of lymphoblastoid cell line GM17831.

source_name: Lymphoblastoid cell line GM17831


title: hiPS_A6_rep1_081006_3

description: Gene expression data from hiPS line A6

source_name: hiPS line A6


title: GM17827

description: Basal gene expression level of lymphoblastoid cell line GM17827.

source_name: Lymphoblastoid cell line GM17827


title: GM17843

description: Basal gene expression level of lymphoblastoid cell line GM17843.

source_name: Lymphoblastoid cell line GM17843


title: GM17287

description: Basal gene expression level of lymphoblastoid cell line GM17287.

source_name: Lymphoblastoid cell line GM17287


title: GM17294

description: Basal gene expression level of lymphoblastoid cell line GM17294.

source_name: Lymphoblastoid cell line GM17294


title: GM17279

description: Basal gene expression level of lymphoblastoid cell line GM17279.

source_name: Lymphoblastoid cell line GM17279


title: GM17271

description: Basal gene expression level of lymphoblastoid cell line GM17271.

source_name: Lymphoblastoid cell line GM17271


title: GM17193/GM14679

description: Basal gene expression level of lymphoblastoid cell line GM17193/GM14679.

source_name: Lymphoblastoid cell line GM17193/GM14679

value: AA African-American


title: GM17200

description: Basal gene expression level of lymphoblastoid cell line GM17200.

source_name: Lymphoblastoid cell line GM17200


title: GM17191

description: Basal gene expression level of lymphoblastoid cell line GM17191.

source_name: Lymphoblastoid cell line GM17191


title: GM17178

description: Basal gene expression level of lymphoblastoid cell line GM17178.

source_name: Lymphoblastoid cell line GM17178


title: GM17277

description: Basal gene expression level of lymphoblastoid cell line GM17277.

source_name: Lymphoblastoid cell line GM17277


title: GM17296

description: Basal gene expression level of lymphoblastoid cell line GM17296.

source_name: Lymphoblastoid cell line GM17296


title: GM17173

description: Basal gene expression level of lymphoblastoid cell line GM17173.

source_name: Lymphoblastoid cell line GM17173


title: GM17295

description: Basal gene expression level of lymphoblastoid cell line GM17295.

source_name: Lymphoblastoid cell line GM17295


title: GM17281

description: Basal gene expression level of lymphoblastoid cell line GM17281.

source_name: Lymphoblastoid cell line GM17281


title: GM17290

description: Basal gene expression level of lymphoblastoid cell line GM17290.

source_name: Lymphoblastoid cell line GM17290


title: GM17174

description: Basal gene expression level of lymphoblastoid cell line GM17174.

source_name: Lymphoblastoid cell line GM17174


title: GM17268

description: Basal gene expression level of lymphoblastoid cell line GM17268.

source_name: Lymphoblastoid cell line GM17268


title: GM17283

description: Basal gene expression level of lymphoblastoid cell line GM17283.

source_name: Lymphoblastoid cell line GM17283


title: GM17285

description: Basal gene expression level of lymphoblastoid cell line GM17285.

source_name: Lymphoblastoid cell line GM17285


title: GM17262

description: Basal gene expression level of lymphoblastoid cell line GM17262.

source_name: Lymphoblastoid cell line GM17262


title: GM17272

description: Basal gene expression level of lymphoblastoid cell line GM17272.

source_name: Lymphoblastoid cell line GM17272


title: GM17288

description: Basal gene expression level of lymphoblastoid cell line GM17288.

source_name: Lymphoblastoid cell line GM17288


title: GM17282

description: Basal gene expression level of lymphoblastoid cell line GM17282.

source_name: Lymphoblastoid cell line GM17282


title: GM17286

description: Basal gene expression level of lymphoblastoid cell line GM17286.

source_name: Lymphoblastoid cell line GM17286


title: GM17270

description: Basal gene expression level of lymphoblastoid cell line GM17270.

source_name: Lymphoblastoid cell line GM17270


title: GM17175/GM13649

description: Basal gene expression level of lymphoblastoid cell line GM17175/GM13649.

source_name: Lymphoblastoid cell line GM17175/GM13649


title: GM17269

description: Basal gene expression level of lymphoblastoid cell line GM17269.

source_name: Lymphoblastoid cell line GM17269


title: GM17275

description: Basal gene expression level of lymphoblastoid cell line GM17275.

source_name: Lymphoblastoid cell line GM17275


title: GM17274

description: Basal gene expression level of lymphoblastoid cell line GM17274.

source_name: Lymphoblastoid cell line GM17274


title: GM17276

description: Basal gene expression level of lymphoblastoid cell line GM17276.

source_name: Lymphoblastoid cell line GM17276


title: GM17284

description: Basal gene expression level of lymphoblastoid cell line GM17284.

source_name: Lymphoblastoid cell line GM17284


title: GM17278

description: Basal gene expression level of lymphoblastoid cell line GM17278.

source_name: Lymphoblastoid cell line GM17278


title: GM17267

description: Basal gene expression level of lymphoblastoid cell line GM17267.

source_name: Lymphoblastoid cell line GM17267


title: GM17265

description: Basal gene expression level of lymphoblastoid cell line GM17265.

source_name: Lymphoblastoid cell line GM17265


title: GM17266

description: Basal gene expression level of lymphoblastoid cell line GM17266.

source_name: Lymphoblastoid cell line GM17266


title: GM17291

description: Basal gene expression level of lymphoblastoid cell line GM17291.

source_name: Lymphoblastoid cell line GM17291


title: GM17264

description: Basal gene expression level of lymphoblastoid cell line GM17264.

source_name: Lymphoblastoid cell line GM17264


title: GM17263

description: Basal gene expression level of lymphoblastoid cell line GM17263.

source_name: Lymphoblastoid cell line GM17263


title: GM17261

description: Basal gene expression level of lymphoblastoid cell line GM17261.

source_name: Lymphoblastoid cell line GM17261


title: GM17195

description: Basal gene expression level of lymphoblastoid cell line GM17195.

source_name: Lymphoblastoid cell line GM17195


title: GM17199

description: Basal gene expression level of lymphoblastoid cell line GM17199.

source_name: Lymphoblastoid cell line GM17199


title: GM17197

description: Basal gene expression level of lymphoblastoid cell line GM17197.

source_name: Lymphoblastoid cell line GM17197


title: GM17196

description: Basal gene expression level of lymphoblastoid cell line GM17196.

source_name: Lymphoblastoid cell line GM17196


title: GM17198

description: Basal gene expression level of lymphoblastoid cell line GM17198.

source_name: Lymphoblastoid cell line GM17198


title: GM17185

description: Basal gene expression level of lymphoblastoid cell line GM17185.

source_name: Lymphoblastoid cell line GM17185


title: GM17194

description: Basal gene expression level of lymphoblastoid cell line GM17194.

source_name: Lymphoblastoid cell line GM17194


title: GM17190

description: Basal gene expression level of lymphoblastoid cell line GM17190.

source_name: Lymphoblastoid cell line GM17190


title: GM17181

description: Basal gene expression level of lymphoblastoid cell line GM17181.

source_name: Lymphoblastoid cell line GM17181


title: GM17187

description: Basal gene expression level of lymphoblastoid cell line GM17187.

source_name: Lymphoblastoid cell line GM17187


title: GM17184

description: Basal gene expression level of lymphoblastoid cell line GM17184.

source_name: Lymphoblastoid cell line GM17184


title: GM17177

description: Basal gene expression level of lymphoblastoid cell line GM17177.

source_name: Lymphoblastoid cell line GM17177


title: GM17180

description: Basal gene expression level of lymphoblastoid cell line GM17180.

source_name: Lymphoblastoid cell line GM17180


title: GM17189

description: Basal gene expression level of lymphoblastoid cell line GM17189.

source_name: Lymphoblastoid cell line GM17189


title: GM17171

description: Basal gene expression level of lymphoblastoid cell line GM17171.

source_name: Lymphoblastoid cell line GM17171


title: GM17172

description: Basal gene expression level of lymphoblastoid cell line GM17172.

source_name: Lymphoblastoid cell line GM17172


title: GM17168

description: Basal gene expression level of lymphoblastoid cell line GM17168.

source_name: Lymphoblastoid cell line GM17168


title: GM17179

description: Basal gene expression level of lymphoblastoid cell line GM17179.

source_name: Lymphoblastoid cell line GM17179


title: GM17170

description: Basal gene expression level of lymphoblastoid cell line GM17170.

source_name: Lymphoblastoid cell line GM17170


title: GM17186

description: Basal gene expression level of lymphoblastoid cell line GM17186.

source_name: Lymphoblastoid cell line GM17186


title: GM17182

description: Basal gene expression level of lymphoblastoid cell line GM17182.

source_name: Lymphoblastoid cell line GM17182


title: GM17183

description: Basal gene expression level of lymphoblastoid cell line GM17183.

source_name: Lymphoblastoid cell line GM17183


title: GM17176

description: Basal gene expression level of lymphoblastoid cell line GM17176.

source_name: Lymphoblastoid cell line GM17176


title: GM17165

description: Basal gene expression level of lymphoblastoid cell line GM17165.

source_name: Lymphoblastoid cell line GM17165


title: GM17826

description: Basal gene expression level of lymphoblastoid cell line GM17826.

source_name: Lymphoblastoid cell line GM17826


title: GM17161

description: Basal gene expression level of lymphoblastoid cell line GM17161.

source_name: Lymphoblastoid cell line GM17161


title: GM17833

description: Basal gene expression level of lymphoblastoid cell line GM17833.

source_name: Lymphoblastoid cell line GM17833


title: GM17167

description: Basal gene expression level of lymphoblastoid cell line GM17167.

source_name: Lymphoblastoid cell line GM17167


title: GM17816

description: Basal gene expression level of lymphoblastoid cell line GM17816.

source_name: Lymphoblastoid cell line GM17816


title: GM17162

description: Basal gene expression level of lymphoblastoid cell line GM17162.

source_name: Lymphoblastoid cell line GM17162


title: GM17808

description: Basal gene expression level of lymphoblastoid cell line GM17808.

source_name: Lymphoblastoid cell line GM17808


title: GM17825

description: Basal gene expression level of lymphoblastoid cell line GM17825.

source_name: Lymphoblastoid cell line GM17825


title: GM17163

description: Basal gene expression level of lymphoblastoid cell line GM17163.

source_name: Lymphoblastoid cell line GM17163


title: GM17164

description: Basal gene expression level of lymphoblastoid cell line GM17164.

source_name: Lymphoblastoid cell line GM17164


title: GM17809

description: Basal gene expression level of lymphoblastoid cell line GM17809.

source_name: Lymphoblastoid cell line GM17809


title: GM17818

description: Basal gene expression level of lymphoblastoid cell line GM17818.

source_name: Lymphoblastoid cell line GM17818


title: GM17838

description: Basal gene expression level of lymphoblastoid cell line GM17838.

source_name: Lymphoblastoid cell line GM17838


title: GM17823

description: Basal gene expression level of lymphoblastoid cell line GM17823.

source_name: Lymphoblastoid cell line GM17823


title: GM17817

description: Basal gene expression level of lymphoblastoid cell line GM17817.

source_name: Lymphoblastoid cell line GM17817


title: GM17835

description: Basal gene expression level of lymphoblastoid cell line GM17835.

source_name: Lymphoblastoid cell line GM17835


title: GM17811

description: Basal gene expression level of lymphoblastoid cell line GM17811.

source_name: Lymphoblastoid cell line GM17811


title: GM17166

description: Basal gene expression level of lymphoblastoid cell line GM17166.

source_name: Lymphoblastoid cell line GM17166


title: GM17828

description: Basal gene expression level of lymphoblastoid cell line GM17828.

source_name: Lymphoblastoid cell line GM17828


title: GM17814

description: Basal gene expression level of lymphoblastoid cell line GM17814.

source_name: Lymphoblastoid cell line GM17814


title: GM17812

description: Basal gene expression level of lymphoblastoid cell line GM17812.

source_name: Lymphoblastoid cell line GM17812


title: GM17810

description: Basal gene expression level of lymphoblastoid cell line GM17810.

source_name: Lymphoblastoid cell line GM17810


title: GM17805

description: Basal gene expression level of lymphoblastoid cell line GM17805.

source_name: Lymphoblastoid cell line GM17805


title: GM17815

description: Basal gene expression level of lymphoblastoid cell line GM17815.

source_name: Lymphoblastoid cell line GM17815


title: GM17806

description: Basal gene expression level of lymphoblastoid cell line GM17806.

source_name: Lymphoblastoid cell line GM17806


title: GM17807

description: Basal gene expression level of lymphoblastoid cell line GM17807.

source_name: Lymphoblastoid cell line GM17807


title: GM17256

description: Basal gene expression level of lymphoblastoid cell line GM17256.

source_name: Lymphoblastoid cell line GM17256


title: GM17785

description: Basal gene expression level of lymphoblastoid cell line GM17785.

source_name: Lymphoblastoid cell line GM17785


title: GM17157

description: Basal gene expression level of lymphoblastoid cell line GM17157.

source_name: Lymphoblastoid cell line GM17157


title: GM17789

description: Basal gene expression level of lymphoblastoid cell line GM17789.

source_name: Lymphoblastoid cell line GM17789


title: GM17774

description: Basal gene expression level of lymphoblastoid cell line GM17774.

source_name: Lymphoblastoid cell line GM17774


title: GM17787

description: Basal gene expression level of lymphoblastoid cell line GM17787.

source_name: Lymphoblastoid cell line GM17787


title: GM17783

description: Basal gene expression level of lymphoblastoid cell line GM17783.

source_name: Lymphoblastoid cell line GM17783


title: GM17800

description: Basal gene expression level of lymphoblastoid cell line GM17800.

source_name: Lymphoblastoid cell line GM17800


title: GM17782

description: Basal gene expression level of lymphoblastoid cell line GM17782.

source_name: Lymphoblastoid cell line GM17782


title: GM17259

description: Basal gene expression level of lymphoblastoid cell line GM17259.

source_name: Lymphoblastoid cell line GM17259


title: GM17802

description: Basal gene expression level of lymphoblastoid cell line GM17802.

source_name: Lymphoblastoid cell line GM17802


title: GM17145

description: Basal gene expression level of lymphoblastoid cell line GM17145.

source_name: Lymphoblastoid cell line GM17145


title: GM17158

description: Basal gene expression level of lymphoblastoid cell line GM17158.

source_name: Lymphoblastoid cell line GM17158


title: GM17258

description: Basal gene expression level of lymphoblastoid cell line GM17258.

source_name: Lymphoblastoid cell line GM17258


title: GM17803

description: Basal gene expression level of lymphoblastoid cell line GM17803.

source_name: Lymphoblastoid cell line GM17803


title: GM17246

description: Basal gene expression level of lymphoblastoid cell line GM17246.

source_name: Lymphoblastoid cell line GM17246


title: GM17159

description: Basal gene expression level of lymphoblastoid cell line GM17159.

source_name: Lymphoblastoid cell line GM17159


title: GM17804

description: Basal gene expression level of lymphoblastoid cell line GM17804.

source_name: Lymphoblastoid cell line GM17804


title: GM17801

description: Basal gene expression level of lymphoblastoid cell line GM17801.

source_name: Lymphoblastoid cell line GM17801


title: GM17160

description: Basal gene expression level of lymphoblastoid cell line GM17160.

source_name: Lymphoblastoid cell line GM17160


title: GM17155

description: Basal gene expression level of lymphoblastoid cell line GM17155.

source_name: Lymphoblastoid cell line GM17155


title: GM17260

description: Basal gene expression level of lymphoblastoid cell line GM17260.

source_name: Lymphoblastoid cell line GM17260


title: GM17257

description: Basal gene expression level of lymphoblastoid cell line GM17257.

source_name: Lymphoblastoid cell line GM17257


title: GM17156

description: Basal gene expression level of lymphoblastoid cell line GM17156.

source_name: Lymphoblastoid cell line GM17156


title: GM17798

description: Basal gene expression level of lymphoblastoid cell line GM17798.

source_name: Lymphoblastoid cell line GM17798


title: GM17252

description: Basal gene expression level of lymphoblastoid cell line GM17252.

source_name: Lymphoblastoid cell line GM17252


title: GM17799

description: Basal gene expression level of lymphoblastoid cell line GM17799.

source_name: Lymphoblastoid cell line GM17799


title: GM17150

description: Basal gene expression level of lymphoblastoid cell line GM17150.

source_name: Lymphoblastoid cell line GM17150


title: GM17255

description: Basal gene expression level of lymphoblastoid cell line GM17255.

source_name: Lymphoblastoid cell line GM17255


title: GM17215

description: Basal gene expression level of lymphoblastoid cell line GM17215.

source_name: Lymphoblastoid cell line GM17215


title: GM17154

description: Basal gene expression level of lymphoblastoid cell line GM17154.

source_name: Lymphoblastoid cell line GM17154


title: GM17253

description: Basal gene expression level of lymphoblastoid cell line GM17253.

source_name: Lymphoblastoid cell line GM17253


title: GM17797

description: Basal gene expression level of lymphoblastoid cell line GM17797.

source_name: Lymphoblastoid cell line GM17797


title: GM17251

description: Basal gene expression level of lymphoblastoid cell line GM17251.

source_name: Lymphoblastoid cell line GM17251


title: GM17796

description: Basal gene expression level of lymphoblastoid cell line GM17796.

source_name: Lymphoblastoid cell line GM17796


title: GM17792

description: Basal gene expression level of lymphoblastoid cell line GM17792.

source_name: Lymphoblastoid cell line GM17792


title: GM17254

description: Basal gene expression level of lymphoblastoid cell line GM17254.

source_name: Lymphoblastoid cell line GM17254


title: GM17192

description: Basal gene expression level of lymphoblastoid cell line GM17192.

source_name: Lymphoblastoid cell line GM17192


title: GM17147

description: Basal gene expression level of lymphoblastoid cell line GM17147.

source_name: Lymphoblastoid cell line GM17147


title: GM17188

description: Basal gene expression level of lymphoblastoid cell line GM17188.

source_name: Lymphoblastoid cell line GM17188


title: GM17204

description: Basal gene expression level of lymphoblastoid cell line GM17204.

source_name: Lymphoblastoid cell line GM17204


title: GM17249

description: Basal gene expression level of lymphoblastoid cell line GM17249.

source_name: Lymphoblastoid cell line GM17249


title: GM17233

description: Basal gene expression level of lymphoblastoid cell line GM17233.

source_name: Lymphoblastoid cell line GM17233


title: GM17793

description: Basal gene expression level of lymphoblastoid cell line GM17793.

source_name: Lymphoblastoid cell line GM17793


title: GM17795

description: Basal gene expression level of lymphoblastoid cell line GM17795.

source_name: Lymphoblastoid cell line GM17795


title: GM17250

description: Basal gene expression level of lymphoblastoid cell line GM17250.

source_name: Lymphoblastoid cell line GM17250


title: GM17247

description: Basal gene expression level of lymphoblastoid cell line GM17247.

source_name: Lymphoblastoid cell line GM17247


title: GM17791

description: Basal gene expression level of lymphoblastoid cell line GM17791.

source_name: Lymphoblastoid cell line GM17791


title: GM17149

description: Basal gene expression level of lymphoblastoid cell line GM17149.

source_name: Lymphoblastoid cell line GM17149


title: GM17146

description: Basal gene expression level of lymphoblastoid cell line GM17146.

source_name: Lymphoblastoid cell line GM17146


title: GM17790

description: Basal gene expression level of lymphoblastoid cell line GM17790.

source_name: Lymphoblastoid cell line GM17790


title: GM17209

description: Basal gene expression level of lymphoblastoid cell line GM17209.

source_name: Lymphoblastoid cell line GM17209


title: GM17768

description: Basal gene expression level of lymphoblastoid cell line GM17768.

source_name: Lymphoblastoid cell line GM17768


title: GM17794

description: Basal gene expression level of lymphoblastoid cell line GM17794.

source_name: Lymphoblastoid cell line GM17794


title: GM17234

description: Basal gene expression level of lymphoblastoid cell line GM17234.

source_name: Lymphoblastoid cell line GM17234


title: GM17231

description: Basal gene expression level of lymphoblastoid cell line GM17231.

source_name: Lymphoblastoid cell line GM17231


title: GM17132

description: Basal gene expression level of lymphoblastoid cell line GM17132.

source_name: Lymphoblastoid cell line GM17132


title: GM17235

description: Basal gene expression level of lymphoblastoid cell line GM17235.

source_name: Lymphoblastoid cell line GM17235


title: GM17133

description: Basal gene expression level of lymphoblastoid cell line GM17133.

source_name: Lymphoblastoid cell line GM17133


title: GM17134

description: Basal gene expression level of lymphoblastoid cell line GM17134.

source_name: Lymphoblastoid cell line GM17134


title: GM17148

description: Basal gene expression level of lymphoblastoid cell line GM17148.

source_name: Lymphoblastoid cell line GM17148


title: GM17232

description: Basal gene expression level of lymphoblastoid cell line GM17232.

source_name: Lymphoblastoid cell line GM17232


title: GM17121

description: Basal gene expression level of lymphoblastoid cell line GM17121.

source_name: Lymphoblastoid cell line GM17121


title: GM17131

description: Basal gene expression level of lymphoblastoid cell line GM17131.

source_name: Lymphoblastoid cell line GM17131


title: GM17223

description: Basal gene expression level of lymphoblastoid cell line GM17223.

source_name: Lymphoblastoid cell line GM17223


title: GM17135

description: Basal gene expression level of lymphoblastoid cell line GM17135.

source_name: Lymphoblastoid cell line GM17135


title: GM17765

description: Basal gene expression level of lymphoblastoid cell line GM17765.

source_name: Lymphoblastoid cell line GM17765


title: GM17767

description: Basal gene expression level of lymphoblastoid cell line GM17767.

source_name: Lymphoblastoid cell line GM17767


title: GM17764

description: Basal gene expression level of lymphoblastoid cell line GM17764.

source_name: Lymphoblastoid cell line GM17764


title: GM17129

description: Basal gene expression level of lymphoblastoid cell line GM17129.

source_name: Lymphoblastoid cell line GM17129


title: GM17130

description: Basal gene expression level of lymphoblastoid cell line GM17130.

source_name: Lymphoblastoid cell line GM17130


title: GM17128

description: Basal gene expression level of lymphoblastoid cell line GM17128.

source_name: Lymphoblastoid cell line GM17128


title: GM17127

description: Basal gene expression level of lymphoblastoid cell line GM17127.

source_name: Lymphoblastoid cell line GM17127


title: GM17126

description: Basal gene expression level of lymphoblastoid cell line GM17126.

source_name: Lymphoblastoid cell line GM17126


title: GM17230

description: Basal gene expression level of lymphoblastoid cell line GM17230.

source_name: Lymphoblastoid cell line GM17230


title: GM17226

description: Basal gene expression level of lymphoblastoid cell line GM17226.

source_name: Lymphoblastoid cell line GM17226


title: GM17143

description: Basal gene expression level of lymphoblastoid cell line GM17143.

source_name: Lymphoblastoid cell line GM17143


title: GM17144

description: Basal gene expression level of lymphoblastoid cell line GM17144.

source_name: Lymphoblastoid cell line GM17144


title: GM17245

description: Basal gene expression level of lymphoblastoid cell line GM17245.

source_name: Lymphoblastoid cell line GM17245


title: GM17141

description: Basal gene expression level of lymphoblastoid cell line GM17141.

source_name: Lymphoblastoid cell line GM17141


title: GM17762

description: Basal gene expression level of lymphoblastoid cell line GM17762.

source_name: Lymphoblastoid cell line GM17762


title: GM17243

description: Basal gene expression level of lymphoblastoid cell line GM17243.

source_name: Lymphoblastoid cell line GM17243


title: GM17242

description: Basal gene expression level of lymphoblastoid cell line GM17242.

source_name: Lymphoblastoid cell line GM17242


title: GM17142

description: Basal gene expression level of lymphoblastoid cell line GM17142.

source_name: Lymphoblastoid cell line GM17142


title: GM17773

description: Basal gene expression level of lymphoblastoid cell line GM17773.

source_name: Lymphoblastoid cell line GM17773


title: GM17766

description: Basal gene expression level of lymphoblastoid cell line GM17766.

source_name: Lymphoblastoid cell line GM17766


title: GM17244

description: Basal gene expression level of lymphoblastoid cell line GM17244.

source_name: Lymphoblastoid cell line GM17244


title: GM17228

description: Basal gene expression level of lymphoblastoid cell line GM17228.

source_name: Lymphoblastoid cell line GM17228


title: GM17770

description: Basal gene expression level of lymphoblastoid cell line GM17770.

source_name: Lymphoblastoid cell line GM17770


title: GM17779

description: Basal gene expression level of lymphoblastoid cell line GM17779.

source_name: Lymphoblastoid cell line GM17779


title: GM17769

description: Basal gene expression level of lymphoblastoid cell line GM17769.

source_name: Lymphoblastoid cell line GM17769


title: GM17771

description: Basal gene expression level of lymphoblastoid cell line GM17771.

source_name: Lymphoblastoid cell line GM17771


title: GM17241

description: Basal gene expression level of lymphoblastoid cell line GM17241.

source_name: Lymphoblastoid cell line GM17241


title: GM17140

description: Basal gene expression level of lymphoblastoid cell line GM17140.

source_name: Lymphoblastoid cell line GM17140


title: GM17136

description: Basal gene expression level of lymphoblastoid cell line GM17136.

source_name: Lymphoblastoid cell line GM17136


title: GM17775

description: Basal gene expression level of lymphoblastoid cell line GM17775.

source_name: Lymphoblastoid cell line GM17775


title: GM17138

description: Basal gene expression level of lymphoblastoid cell line GM17138.

source_name: Lymphoblastoid cell line GM17138


title: GM17229

description: Basal gene expression level of lymphoblastoid cell line GM17229.

source_name: Lymphoblastoid cell line GM17229


title: GM17239

description: Basal gene expression level of lymphoblastoid cell line GM17239.

source_name: Lymphoblastoid cell line GM17239


title: GM17236

description: Basal gene expression level of lymphoblastoid cell line GM17236.

source_name: Lymphoblastoid cell line GM17236


title: GM17139

description: Basal gene expression level of lymphoblastoid cell line GM17139.

source_name: Lymphoblastoid cell line GM17139


title: GM17780

description: Basal gene expression level of lymphoblastoid cell line GM17780.

source_name: Lymphoblastoid cell line GM17780


title: GM17240

description: Basal gene expression level of lymphoblastoid cell line GM17240.

source_name: Lymphoblastoid cell line GM17240


title: GM17758

description: Basal gene expression level of lymphoblastoid cell line GM17758.

source_name: Lymphoblastoid cell line GM17758


title: GM17238

description: Basal gene expression level of lymphoblastoid cell line GM17238.

source_name: Lymphoblastoid cell line GM17238


title: GM17759

description: Basal gene expression level of lymphoblastoid cell line GM17759.

source_name: Lymphoblastoid cell line GM17759


title: GM17776

description: Basal gene expression level of lymphoblastoid cell line GM17776.

source_name: Lymphoblastoid cell line GM17776


title: GM17137

description: Basal gene expression level of lymphoblastoid cell line GM17137.

source_name: Lymphoblastoid cell line GM17137


title: GM17756

description: Basal gene expression level of lymphoblastoid cell line GM17756.

source_name: Lymphoblastoid cell line GM17756


title: GM17237

description: Basal gene expression level of lymphoblastoid cell line GM17237.

source_name: Lymphoblastoid cell line GM17237


title: GM17757

description: Basal gene expression level of lymphoblastoid cell line GM17757.

source_name: Lymphoblastoid cell line GM17757


title: GM17761

description: Basal gene expression level of lymphoblastoid cell line GM17761.

source_name: Lymphoblastoid cell line GM17761


title: GM17125

description: Basal gene expression level of lymphoblastoid cell line GM17125.

source_name: Lymphoblastoid cell line GM17125


title: GM17752

description: Basal gene expression level of lymphoblastoid cell line GM17752.

source_name: Lymphoblastoid cell line GM17752


title: GM17213

description: Basal gene expression level of lymphoblastoid cell line GM17213.

source_name: Lymphoblastoid cell line GM17213


title: GM17123

description: Basal gene expression level of lymphoblastoid cell line GM17123.

source_name: Lymphoblastoid cell line GM17123


title: GM17122

description: Basal gene expression level of lymphoblastoid cell line GM17122.

source_name: Lymphoblastoid cell line GM17122


title: GM17248

description: Basal gene expression level of lymphoblastoid cell line GM17248.

source_name: Lymphoblastoid cell line GM17248


title: GM17124

description: Basal gene expression level of lymphoblastoid cell line GM17124.

source_name: Lymphoblastoid cell line GM17124


title: GM17749

description: Basal gene expression level of lymphoblastoid cell line GM17749.

source_name: Lymphoblastoid cell line GM17749


title: GM17221

description: Basal gene expression level of lymphoblastoid cell line GM17221.

source_name: Lymphoblastoid cell line GM17221


title: GM17110

description: Basal gene expression level of lymphoblastoid cell line GM17110.

source_name: Lymphoblastoid cell line GM17110


title: GM17746

description: Basal gene expression level of lymphoblastoid cell line GM17746.

source_name: Lymphoblastoid cell line GM17746


title: GM17755

description: Basal gene expression level of lymphoblastoid cell line GM17755.

source_name: Lymphoblastoid cell line GM17755


title: GM17754

description: Basal gene expression level of lymphoblastoid cell line GM17754.

source_name: Lymphoblastoid cell line GM17754


title: GM17225

description: Basal gene expression level of lymphoblastoid cell line GM17225.

source_name: Lymphoblastoid cell line GM17225


title: GM17753

description: Basal gene expression level of lymphoblastoid cell line GM17753.

source_name: Lymphoblastoid cell line GM17753


title: GM17224

description: Basal gene expression level of lymphoblastoid cell line GM17224.

source_name: Lymphoblastoid cell line GM17224


title: GM17118

description: Basal gene expression level of lymphoblastoid cell line GM17118.

source_name: Lymphoblastoid cell line GM17118


title: GM17218

description: Basal gene expression level of lymphoblastoid cell line GM17218.

source_name: Lymphoblastoid cell line GM17218


title: GM17119

description: Basal gene expression level of lymphoblastoid cell line GM17119.

source_name: Lymphoblastoid cell line GM17119


title: GM17116

description: Basal gene expression level of lymphoblastoid cell line GM17116.

source_name: Lymphoblastoid cell line GM17116