title: retina, Arc, P9

description: GFP

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: LV_DCM_3

status: Public on Nov 30 2011

type: RNA

city: Bad Oeynhausen

first: Patrick

last: Schwientek

address: Georgstr. 11

department: Klinik f. Thorax- & Kardiovaskularchirurgie

country: Germany

institute: Herz- & Diabeteszentrum NRW

description: Gene expression data from dilated failing hearts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: left ventricle of DCM patient 3

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

growth_protocol: Myocardial tissue was directly taken from non-failing and failing hearts.

extract_protocol: Samples were pruned from the left ventricle near the apex. RNA extraction has been carried out with TRIzol reagent and tissue was homogenized using a rotor-stator homogenizer. Homogenates were transferred to a Phase Lock Gel (PLG) Heavy tube (Eppendorf), chloroform was added, and the mixture was centrifuged. Supernatants were collected, and isopropanol was added to precipitate the RNA. The RNA pellet was washed with 80% ethanol, then air-dried before dissolving in 100 l of RNase-free H2O. RNA was further purified using the RNeasy Mini protocol according to the manufacturer’s directions (Qiagen).

treatment_protocol: The samples were frozen in liquid nitrogen directly after pruning and defrosted only for microarray analysis.

tag: age

tag: indication

value: Dilated cardiomyopathy

tag: gender

value: f

tag: ventricle

value: left


title: MIWI -/-  biological replicate 1

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with RMA from aroma.affy normalization method.

organism: Mus musculus

source_name: purified Round Spermatids total RNA, adult

label_protocol: Affymetrix protocol

growth_protocol: no specific treatment of mice, testes dissection at room temperature, testes kept in cold PBS before cell fractionation

extract_protocol: Trizol extraction of total RNA from round spermatids pooled from the respective gradient fractions

treatment_protocol: removal tunica albuginea, collagenase treatment in PBS, cell extraction from seminiferous tubules by pipetting with pasteur pipette, cell fractionation with BSA gradient 2-4%

tag: genotype/variation

value: MIWI -/-

tag: strain


title: RV_DCM_3

source_name: right ventricle of DCM patient 3

value: right


title: MIWI +/- biological replicate 1

value: MIWI +/-


title: LV_DCM_2

source_name: left ventricle of DCM patient 2


title: MIWI -/KI biological replicate 1

value: MIWI -/KI


title: RV_DCM_2

source_name: right ventricle of DCM patient 2


title: hFOB 1.19 human osteoblasts

city: Neuherberg

first: Jan

last: Smida

address: Ingolstaedter Land 1

department: CCg Osteosarcoma

institute: HelmholtzZentrum

description: Transcriptom determination for correlation with miRNA expression

hyb_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary and normalisation employing the loess smoother

source_name: hFOB 1.19 human osteoblasts

label_protocol: MessageAmp (1. round) and MessageAmp II-Biotin Enhanced (2.round) 2-cycle protocoll (Ambion)

growth_protocol: grown in RPMI 1640 (Invitrogen, Karlsruhe, Germany) supplemented with 2% L-glutamine (Invitrogen) and 10% fetal calf serum (FCS)

extract_protocol: using the mirVana™ miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer´s instructions

tag: cell type

value: possible osteosarcoma progenitor

tag: cell line

value: hFOB 1.19 human osteoblasts


title: retina, Arc, P17

city: Basel

first: Sandra

last: Siegert

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

description: GFP

hyb_protocol: Hybridization was performed with 5 μg biotinylated target, which was incubated with the GeneChip Gene 1.0 ST array (Affymetrix) at 45°C for 16 h. GeneChip Mouse Exon 1.0 ST array was used for the developmental study. Following hybridization, non-specifically bound nucleotides were removed by washing and the specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and CEL files acquired using a GeneChip Command Console Software (Affymetrix).

data_processing:
Data analysis of gene arrays was done in R (version 2.11.1) using bioconductor. For exon arrays, the transcript cluster expression was calculated with the rma function using the command expr <- rma(read.celfiles[filenames, pkgname=pd.moex.1.0.st.v1]). Annotations for transcript clusters were downloaded from Affymetrix (MoEx-1_0-st-v1.na24.mm8.transcript.csv). The Arc-GFP time-course data was created in two batches: batch A contained samples P6-P16; batch B contained two non-contiguous sets of samples, P1-P6 and P17-P43. Correlation analysis revealed extensive batch effects between the samples. Because time-course batch A was surrounded on both sides by batch B, we shifted (in log2 space) the expression values for each transcript in batch A so that the average expression in batch A corresponded to the average expression in batch B. That is why we have in the matrix file only 1 value per Data point for Arc
MoEx-1_0-st-v1.r2_core.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

label_protocol: We used transgenic mouse lines that showed fluorescent-protein expression (RFP or GFP) in distinct cell types within the retina.

growth_protocol: Mice obtained from Mutant Mouse Regional Resource Centers (MMRRC) were FVB/N-Swiss Webster hybrids that are known to harbor a recessive mutation causing photoreceptor degeneration. These were backcrossed into the C57BL/6J background (RCC) and the F2 generation was used for transcriptome analysis. All other mouse lines had already been in the C57BL/6J background for several previous generations.

extract_protocol: Retinal cells were dissociated using a modified Papain-dissociation protocol of Morrow et al. with a process time of only 15 min. Cells from the retina were sorted. Cell sorting was performed using a MoFlo (Cytomation, Fort Collins, USA) with HQ515/30 (GFP) and HQ616/26 (RFP) bandpass filters. After recording several thousand events the fluorescence gate was set using Summit V 4.3.01 Build 2449 software and a population of events selected. Size and granularity of this population were determined using the forward and side scatter values, respectively, and cell debris discarded by setting a second gate. Finally, after determination of the duration of the events (pulse-width), a third gate was selected that served to exclude cell doublets or clumps. Using these three gates, cells were sorted in single-cell drop mode. A total of 200 cells were sorted at room temperature (RT) into a low-binding tube (Eppendorf) containing 60 µl cell lysis buffer (TRI reagent, Sigma-Aldrich).

value: Retinal Arc amacrine cell

tag: batch

value: A and B

tag: age (day)

tag: genetic background

tag: line


title: retina, Arc, P7

description: GFP


title: retina, Arc, P6, #1

description: GFP

value: A and B of 2


title: SJSA osteosarcoma cell line CRL-2098

scan_protocol: According to the Affymetrix expression protocol

source_name: SJSA osteosarcoma cell line CRL-2098

value: osteosarcoma derivate

value: SJSA osteosarcoma cell line CRL-2098


title: RV_ARVC_6

description: Gene expression data from arrhytmogenic failing hearts

source_name: right ventricle of ARVC patient 6

value: Arrhythmogenic right ventricular cardiomyopathy

value: m


title: LV_DCM_1

source_name: left ventricle of DCM patient 1


title: retina, Arc, P6, #2

description: GFP

value: A and B of 1

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: L87/4 human stem cells

source_name: L87/4 human stem cells

value: L87/4 human stem cells


title: RV_DCM_1

source_name: right ventricle of DCM patient 1

value: Dilated cardiomyopathy

value: f


title: Saos osteosarcoma cell line HTB-85

source_name: Saos osteosarcoma cell line HTB-85

value: Saos osteosarcoma cell line HTB-85


title: retina, Arc, P8

description: GFP


title: U2-OS osteosarcoma cell line HTB-96

source_name: U2-OS osteosarcoma cell line HTB-96

value: U2-OS osteosarcoma cell line HTB-96


title: LV_ARVC_6

source_name: left ventricle of ARVC patient 6

value: left


title: MG-63 osteosarcoma cell line CRL-1427

source_name: MG-63 osteosarcoma cell line CRL-1427

value: MG-63 osteosarcoma cell line CRL-1427


title: retina, Arc, P2

description: GFP


title: MNNG/HOS osteosarcoma cell line CRL-1547


title: retina, Arc, P4

description: GFP


title: retina, Arc, P5

description: GFP


title: retina, Arc, P1

description: GFP


title: RV_ARVC_5

source_name: right ventricle of ARVC patient 5

value: w

value: right


title: LV_ARVC_5

source_name: left ventricle of ARVC patient 5


title: retina, Arc, P3

description: GFP

value: Retinal Arc amacrine cell

value: A and B


title: RV_ARVC_3

source_name: right ventricle of ARVC patient 3


title: 231BrM-2a CD24-/CD44+/ESA+ population, biological rep1

city: Springfield

first: Hiroshi

last: Okuda

state: IL

address: 825 N. Rutledge

department: Med. Microbiol. Immunol. & Cell Biol.

country: USA

institute: Southern Illinois University School of Medicine

description: Gene expression data from cancer stem cell population in breast cancer cell line

hyb_protocol: Following fragmentation, approx 2 ug ss cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix Expression Console Software.

source_name: CD24-/CD44+/ESA+ population in breast cancer cell line 231BrM-2a

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix WT protocol from 100 ng total RNA.

growth_protocol: Cells were grown in RPMI-1640 media with 10% FBS and antibiotics in 4% CO2 incubator.

extract_protocol: Total RNA was extracted by using Qiagen RNeasy kit followed by DNase treatment and repulified by using Qiagen RNA cleanup kit.

treatment_protocol: Stem cell population (CD24-/CD44+/ESA+) was isolated by MACS system (Miltenyi) using CD24, CD44 and ESA antibodies.


title: RV_ARVC_4

source_name: right ventricle of ARVC patient 4


title: HOS osteosarcoma cell line CRL-1543

source_name: HOS osteosarcoma cell line CRL-1543

value: osteosarcoma derivate

value: HOS osteosarcoma cell line CRL-1543


title: LV_ARVC_4

source_name: left ventricle of ARVC patient 4

value: Arrhythmogenic right ventricular cardiomyopathy


title: RV_ARVC_2

source_name: right ventricle of ARVC patient 2

value: m


title: HOS-58 osteosarcoma cell line

source_name: HOS-58 osteosarcoma cell line

value: HOS-58 osteosarcoma cell line


title: LV_ARVC_3

source_name: left ventricle of ARVC patient 3


title: HU (PG0121) mutant relative to P. gingivalis WT mid-exponential

city: Cambridge

first: Mary

middle: Ellen

last: Davey

state: MA

address: 245 First Street

department: Molecular Genetics

institute: The Forsyth Institute

description: Comparative expression profile of P. gingivalis HU protein (PG0121) mutant to parent strain W83 during exponential growth in rich medium.

hyb_protocol: The Cy-coupled cDNA samples from the wild-type and mutant strain (opposite labeling) were combined in a microfuge tube along with 20 g of denatured salmon testes DNA (facilitates precipitation) and precipitated with ethanol.   After the ethanol has evaporated, the labeled cDNA from the wild-type and the mutant were each suspended in 25 l of hybridization buffer (50% formamide, 5X SSC, 0.5% SDS, in ultra pure water) and then combined into one tube.  To denature the cDNA, the target mixture was boiled for 10 minutes, and then placed on ice.  The target was then applied to the already prepared microarray slide, and allowed to incubate overnight at 42 °C.  Microarray slides were  pre-hybridized and washed.

scan_protocol: Microarrays will be scanned using the GenePix 4000B scanner (Axon).

data_processing:
Data analysis was performed using GenePix Pro 6.1 (Axon), as well as analysis software SAOPMD (http://www.brop.org/saopmd/) supplied by The Bioinformatic Resources for Oral Pathogens (BROP).
Normalized data generated by SAOPMD (http://www.brop.org/saopmd/) using the Limma software; within-array normalization method: Loess; between-array normalization method: Aquantile

organism: Porphyromonas gingivalis

source_name: HU (PG0121) mutant

label_protocol: For each Cy-labeling reaction, total RNA (15 ug) was reverse transcribed to cDNA using random hexamer primers and Superscript II (Invitrogen, CA), amino allyl-dUTP was incorporated for labeling with Cy-5 or Cy-3.  For the coupling reaction, the cDNA was dissolved in 2X coupling buffer (0.2 M NaHCO3 pH9.0) and mixed with 5 l FluoroLink Cy-5 or Cy-3 monofunctional dye (Amersham) dissolved in DMSO.  The reaction was incubated for 1 hr at room temperature, in the dark, and then purified with Qiagen PCR purification kit.

growth_protocol: P. gingivalis strains were grown anaerobically in a COY anaerobic chamber to mid-exponential growth phase (OD600 of 0.5) in trypicase soy broth supplemented with haemin (1µg/ml) and menadione (1µg/ml).

extract_protocol: RNA was isolated using the MasterPure RNA purification kit (Epicentre) according to manufacturer’s instructions.

treatment_protocol: Comparative expression profiles of WT and mutant when grown in rich medium to mid-exponential growth.  No treatment.

tag: genotype

value: wild type

source_name: P. gingivalis WT

value: HU (PG0121) mutant


title: 231BrM-2a CD24-/CD44+/ESA+ population, biological rep2


title: 231BoM-1833 CD24-/CD44+/ESA+ population, biological rep1

source_name: CD24-/CD44+/ESA+ population in breast cancer cell line 231BoM-1833


title: RV_ARVC_1

source_name: right ventricle of ARVC patient 1


title: LV_ARVC_2

source_name: left ventricle of ARVC patient 2


title: LV_ARVC_1

source_name: left ventricle of ARVC patient 1


title: 231BoM-1833 CD24-/CD44+/ESA+ population, biological rep2


title: MDA-MB-231 CD24-/CD44+/ESA+ population, biological rep2

source_name: CD24-/CD44+/ESA+ population in breast cancer cell line MDA-MB-231


title: MDA-MB-231 CD24-/CD44+/ESA+ population, biological rep1


title: CncC induced replicate 2

status: Public on Nov 29 2011

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description:
7950E10_251897210382_S01_GE2-v5.2_10_Apr08_2_1_2.txt
Replicate 2 of 4.CncC inducible genes.

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer. Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers. Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm. Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each. Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution. The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide. Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 9.5.1.1. The software automatically positions a grid and finds the centroid positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a tab-delimited text file. The data were Lowess-normalized using R and are presented in log base 2

organism: Drosophila melanogaster

source_name: Heat treated w1118

label_protocol: The Agilent Twoe-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations. Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng). The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT. Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP. Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit. The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: Flies were raised on standard cornmeal/molasses/agar food at 20-25°C.

extract_protocol: Total RNA was extracted with Tripure (Roche) following manufacturer's instructions and purified RNAeasy columns (Qiagen)

treatment_protocol: Mature adult w1118 males were treated witheither 5% sucrose alone or 5% sucrose supplemented with 0.3% phenobarbital for six hours, following which RNA was extracted and subjected to micraoarray analysis.Similarly,mature adult w1118 flies or HS-CncC flies were subjected to heat treatment at 37oC for 30 minutes and recovered at room temperature for two hours,after which RNA was exctracted and subjected to microarray analysis.

tag: treatment

value: Heat treated

source_name: Heat treated HS-CncC

value: HS-CncC


title: CncC induced replicate 4

description:
79501E2_251897210382_S01_GE2-v5.2_10_Apr08_2_1_4.txt
Replicate 4 of 4.CncC inducible genes.


title: CncC induced replicate 3

description:
7950E11_251897210382_S01_GE2-v5.2_10_Apr08_2_1_3.txt
Replicate 3 of 4.CncC inducible genes.


title: PB induced replicate 4

description:
7950E5E8_251897210381_S01_GE2-v5.2_10_Apr08_2_1_4.txt
Replicate 4 of 4.PB inducible genes.

source_name: Vehicle treated w1118

value: Vehicle treated

source_name: PB treated w1118

value: PB treated


title: PB induced replicate 3

description:
7950E5E8_251897210381_S01_GE2-v5.2_10_Apr08_2_1_3.txt
Replicate 3 of 4.PB inducible genes.


title: PB induced replicate 2

description:
7950E5E8_251897210381_S01_GE2-v5.2_10_Apr08_2_1_2.txt
Replicate 2 of 4.PB inducible genes.


title: PB induced replicate 1

description:
7950E5E8_251897210381_S01_GE2-v5.2_10_Apr08_2_1_1.txt
Replicate 1 of 4.PB inducible genes.

source_name: Vehiclel treated w1118


title: CncC induced replicate 1

description:
7950E9_251897210382_S01_GE2-v5.2_10_Apr08_2_1_1.txt
Replicate 1 of 4.CncC inducible genes.


title: senescent WI-38 AGO_1of2

type: genomic

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

country: France

institute: Institut Pasteur

description: Chip-chip input/AGO ChIP DNA

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: Input DNA from senescent WI-38 AGO_1of2

label_protocol: 1 µg Input DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (Input DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Culturing of cells of primary human diploid fibroblasts strain WI38 were performed at physiological oxygen concentration of 3%

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: transformed by Retroviral vector pBABE-RASV12

value: primary human fibroblast WI-38

value: senescent fibroblast

tag: chip antibody

value: none, input DNA

source_name: AGO ChIP DNA from WI-38 pre-senescent human fibroblast

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

value: pan AGO antibody


title: pre-senescent WI-38 AGO_1of2

description: Chip-chip input/AGO ChIP DNA

source_name: Input DNA from pre-senescent WI-38 AGO_1of2

treatment_protocol: no treatment

value: pre-senescent fibroblast


title: retina, Arc, P11

description: GFP

value: Retinal Arc amacrine cell

value: A and B

value: mixed FVB/N-Swiss Webster hybrid and C57BL/6J


title: primary human: blood; FACS-sorted CD3+ cells (CLL264N_CD3_062410)

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each DNA sample were analyzed using Affymetrix's Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to determine final call rates and quality. Call rates for the entire group of CD19+ samples included in this report were between 95.06% and 99.63%, with a mean call rate of 98.53%. Corresponding call rates for CD3+ or buccal DNA were between 93.14% and 99.66%, with a mean call rate of 98.49%. Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.
dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using the software's median-smoothing algorithm.

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol: Purification_protocol: Cryopreserved CLL cells were washed and stained with phycoerythrin (PE)–conjugated anti-CD19 and fluorescein isothiocyanate (FITC)–conjugated anti-CD3 antibodies (eBioscience, San Diego, CA). Propidium iodide was added to a concentration of 1 μg/mL to discriminate dead cells, and viable CD19+ and CD3+ single-positive cells were sorted on a high-speed FACSAria cell sorter (Becton Dickinson, Mountain View, CA).  Buccal swabs were used as normal controls in eleven cases.

treatment_protocol: Not applicable

tag: normal vs tumor

value: normal


title: primary human: blood; FACS-sorted CD19+ cells (CLL262T)

value: tumor


title: primary human: blood; FACS-sorted CD3+ cells (CLL265N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL263N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL266N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL263T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL265T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL266T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL264T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL261N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL259T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL259N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL258N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL260N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL255N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL260T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL261T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL253N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL257T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL262N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL254N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL256T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL254T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL252N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL258T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL257N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL253T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL255T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL256N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL252T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL249N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL251N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL249T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL250T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL248N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL250N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL248T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL251T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL243N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL247N_CD3)


title: primary human: buccal swab (CLL245N_BU)

source_name: primary human: buccal swab


title: primary human: blood; FACS-sorted CD19+ cells (CLL243T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL246T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL246N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL245T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL241T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL239T)


title: primary human: buccal swab (CLL244N_BU)


title: primary human: buccal swab (CLL242N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL234T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL244T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL238T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL235T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL240T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL237T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL241N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL236T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL233T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL242T_062410)


title: primary human: blood; FACS-sorted CD19+ cells (CLL247T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL233N_CD3_020309)


title: primary human: blood; FACS-sorted CD3+ cells (CLL232N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL230T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL232T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL230N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL229T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL228T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL234N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL231N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL227N_CD3_062410)


title: primary human: blood; FACS-sorted CD3+ cells (CLL229N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL226T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL228N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL225N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL225T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL224T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL222T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL231T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL222N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL223T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL221N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL224N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL221T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL219T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL227T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL220N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL219N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL223N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL226N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL220T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL218N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL217T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL217N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL214N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL216T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL211T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL213N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL213T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL218T)


title: primary human: buccal swab (CLL211N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL212T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL210N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL216N_CD3)


title: primary human: buccal swab (CLL212N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL210T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL214T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL209T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL208N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL208T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL205T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL206T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL207T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL207N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL204N_CD3)


title: primary human: buccal swab (CLL209N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL204T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL203T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL206N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL202T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL203N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL201N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL199N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL201T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL198T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL196T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL194T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL195N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL200T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL193T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL194N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL192N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL193N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL197N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL197T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL195T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL202N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL198N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL200N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL196N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL191N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL191T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL190T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL189T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL190N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL192T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL189N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL188N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL188T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL186N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL185T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL186T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL185N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL187N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL205N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL184T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL184N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL187T_022309)


title: primary human: blood; FACS-sorted CD19+ cells (CLL182T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL199T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL183T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL180N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL181T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL179N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL183N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL177N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL180T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL179T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL181N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL178T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL174T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL176T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL177T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL178N_CD3)


title: primary human: buccal swab (CLL172N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL173T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL182N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL175T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL172T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL171T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL168T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL164T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL161N_CD3)


title: primary human: buccal swab (CLL171N_BU)


title: primary human: blood; FACS-sorted CD3+ cells (CLL167N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL165T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL164N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL160T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL170T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL166N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL167T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL161T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL158T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL156T_092809)


title: primary human: blood; FACS-sorted CD19+ cells (CLL159T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL160N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL157T_062410)


title: primary human: blood; FACS-sorted CD19+ cells (CLL154T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL166T_013108)


title: primary human: blood; FACS-sorted CD3+ cells (CLL154N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL152T_062410)


title: primary human: blood; FACS-sorted CD19+ cells (CLL151T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL149T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL150T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL155T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL153T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL143T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL148N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL141T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL143N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL148T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL145T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL141N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL138T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL144T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL146T_062410)


title: primary human: blood; FACS-sorted CD19+ cells (CLL147T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL136T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL138N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL135T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL151N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL137T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL137N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL132T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL133T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL140T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL142T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL127T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL127N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL130T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL131T)


title: primary human: buccal swab (CLL133N_BU)


title: primary human: blood; FACS-sorted CD19+ cells (CLL139T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL129T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL128T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL134T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL124N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL125T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL124T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL123T_032009)


title: primary human: blood; FACS-sorted CD3+ cells (CLL122N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL120N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL122T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL121T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL117T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL126T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL119T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL116T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL118T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL115T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL113T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL114T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL110T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL103N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL120T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL112T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL102T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL106T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL111T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL109T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL105T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL103T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL108T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL101T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL098T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL107T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL097T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL104T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL097N)


title: primary human: blood; FACS-sorted CD3+ cells (CLL104N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL108N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL099T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL101N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL096T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL116N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL095T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL096N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL091T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL094T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL089T_013108)


title: primary human: blood; FACS-sorted CD3+ cells (CLL095N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL092T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL093T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL091N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL081T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL088T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL084T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL084N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL085T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL082T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL082N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL079T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL078T_062410)


title: primary human: blood; FACS-sorted CD19+ cells (CLL083T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL086T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL081N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL078N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL075T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL074T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL090T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL087T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL077T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL080T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL073T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL074N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL072N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL072T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL071T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL073N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL070T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL071N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL069T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL068T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL066T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL063N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL064T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL067T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL064N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL062T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL058T_013108)


title: primary human: blood; FACS-sorted CD19+ cells (CLL061T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL059T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL058N_CD3)


title: primary human: blood; FACS-sorted CD3+ cells (CLL056N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL055T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL056T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL060T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL063T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL054T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL052T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL051N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL053T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL049T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL051T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL054N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL050T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL044T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL057T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL045T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL046T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL047T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL048T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL041T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL044N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL043T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL042T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL049N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL033T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL030T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL040T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL034T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL036T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL037N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL039T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL025T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL038T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL029T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL035T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL026T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL021T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL017T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL037T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL024T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL021NT_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL032T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL016T)


title: Propolis 5 min x ethanol 5 min Replicate 1 (dye swap)

city: Ribeirão Preto

first: Patricia

middle: Alves

last: de Castro

state: São Paulo

address: Av. do Café

department: Pharmaceuticals Sciences

country: Brazil

institute: USP

description: Dye Swap of biological replicate 1.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test). Data in the matrices are log2 LOWESS normalized Cy5/Cy3 ratios.

organism: Saccharomyces cerevisiae

source_name: total RNA from BY4742 treated with propolis for 5 min

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 or Cyanine-5 for 2 hours at 40 oC.

growth_protocol: The yeast cells were growth in YPD liquid medium until the Exponential (9 h) growth phase. After this, the BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm).

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

treatment_protocol: The BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm).    The samples were immediately frozen in liquid nitrogen and stored at ultra low temperature (-70oC) for further analysis of transcriptome.

source_name: total RNA from BY4742 treated with ethanol for 5 min


title: Propolis 10 min x ethanol 10 min Replicate 2

description: Biological replicate 2 of 2.

source_name: total RNA from BY4742 treated with propolis for 10 min

source_name: total RNA from BY4742 treated with ethanol for 10 min


title: Propolis 10 min x ethanol 10 min Replicate 1 (dye swap)

description: Dye Swap of biological replicate 1.


title: Propolis 5 min x ethanol 5 min Replicate 2 (dye swap)

description: Dye Swap of biological replicate 2.


title: Propolis 5 min x ethanol 5 min Replicate 2

description: Biological replicate 2 of 2.


title: primary human: blood; FACS-sorted CD19+ cells (CLL019T)


title: Propolis 10 min x ethanol 10 min Replicate 1

description: Biological replicate 1 of 2.


title: Propolis 10 min x ethanol 10 min Replicate 2 (dye swap)

description: Dye Swap of biological replicate 2.


title: primary human: blood; FACS-sorted CD19+ cells (CLL027T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL014N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL014T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL022T)


title: Propolis 5 min x ethanol 5 min Replicate 1

description: Biological replicate 1 of 2.


title: primary human: blood; FACS-sorted CD19+ cells (CLL013T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL007T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL004T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL005T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL020T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL009T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL012T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL003N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL006T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL003T_013108)


title: primary human: blood; FACS-sorted CD19+ cells (CLL001T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL001N_CD3)


title: primary human: blood; FACS-sorted CD19+ cells (CLL010T)


title: primary human: blood; FACS-sorted CD19+ cells (CLL008T)


title: primary human: blood; FACS-sorted CD3+ cells (CLL012N)


title: primary human: blood; FACS-sorted CD19+ cells (CLL002T)


title: Apex TCDD 7 dpa 2

city: Madison

first: Peter

middle: Jacobs

last: Hofsteen

state: WI

address: 777 Highland Ave

department: Pharmacy

institute: University of Wisconsin - Madison

description: Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Inhibition of Adult Zebrafish Heart Regeneration

hyb_protocol: 15 ug of cRNA was hybridized to a zebrafish Affymetrix array for 16 h at 45ºC with rotation (53 rpm).  Arrays were washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400 using protocol EukGE-W32v4.

scan_protocol: Arrays were scanned using the Agilent gene array scanner (Aligent Technologies, Santa Clara, CA).

data_processing: Analysis of microarray data was adapted from Gould et al., 2006.  The raw data (.CEL files) were normalized by RMA algorithm using the ExpressionFileCreator module of the Genepattern software.  Differences in gene expression by amputation or TCDD exposure were determined using the comparative selection marker module of GenePattern.  Cutoffs for statistical significance were a Benjamini- Hochberg corrected False Discovery Rate (FDR) <0.1 and a minimum fold change >2. To compare the change in gene expression induced by amputation in PC or TCDD exposed groups, the log2 values were calculated

label: Biotin

organism: Danio rerio

source_name: amputated TCDD 7 dpa rep 2

label_protocol: cRNA amplification and hybridization was conducted using an Affymetrix GeneChip IVT Express Kit and protocol.  500 ng of total RNA was used to generated cRNA sample.

growth_protocol: Adult zebrafish (danio rerio) were injected (i.p) to vehicle control or TCDD (70 ng/g) one day prior to heart ventricle amputation.  A set of fish were not amputated to understand which genes were altered without amputation.  Amputated hearts were collected at 6 hours post amputation and 7 days post amputation.

extract_protocol: RNA was isolated using QIAGEN Rneasy Micro Kit.  A total of n=10 hearts were pooled per sample.

treatment_protocol: Ventricles were removed and separated into two sections: upper (anterior to regenerate; ventricle top) and apex (regenerate and amputation plane; ventricle bottom)

value: Adult AB

tag: amputated

value: yes

value: TCDD

tag: dpa


title: Apex TCDD 6 hpa 1

source_name: amputated TCDD 6 hpa rep 1

tag: age

tag: hpa


title: Apex TCDD 6 hpa 2

source_name: amputated TCDD 6 hpa rep 2


title: primary human: blood; FACS-sorted CD19+ cells (CLL018T)


title: Apex TCDD 7 dpa 1

source_name: amputated TCDD 7dpa rep 1


title: Apex TCDD 0 hpa 2

source_name: unamputated TCDD rep 2

value: no


title: Apex TCDD 0 hpa 1

source_name: unamputated TCDD rep 1


title: Apex Control 7 dpa 2

source_name: amputated control 7 dpa rep 2


title: Keratinocyte-5_KN5 input, depleted

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

source_name: Input fraction from Keratinocyte-5_KN5

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: keratinocyte

source_name: Methyl-depleted fraction from Keratinocyte-5_KN5


title: Apex Control 6 hpa 1

source_name: amputated control 6 hpa rep 1


title: Cord_Blood-28M_CB28M input, depleted

source_name: Input fraction from Cord_Blood-28M_CB28M

value: cord blood

source_name: Methyl-depleted fraction from Cord_Blood-28M_CB28M


title: Apex Control 6 hpa 2

source_name: amputated control 6 hpa rep 2


title: CB-iPSC-10_C10 input, depleted

source_name: Input fraction from CB-iPSC-10_C10

value: cord blood-derived iPS cells

source_name: Methyl-depleted fraction from CB-iPSC-10_C10


title: Apex Control 0 hpa 1

source_name: unamputated control rep 1


title: CB-iPSC-12_C12 input, depleted

source_name: Input fraction from CB-iPSC-12_C12

source_name: Methyl-depleted fraction from CB-iPSC-12_C12


title: CB-iPSC-6_C6 input, depleted

source_name: Input fraction from CB-iPSC-6_C6

source_name: Methyl-depleted fraction from CB-iPSC-6_C6


title: Keratinocyte-8_KN8 input, depleted

source_name: Input fraction from Keratinocyte-8_KN8

source_name: Methyl-depleted fraction from Keratinocyte-8_KN8


title: K-iPSC-4_G4 input, depleted

source_name: Input fraction from K-iPSC-4_G4

value: keratinocyte-derived iPS cells

source_name: Methyl-depleted fraction from K-iPSC-4_G4


title: K-iPSC-12_N1 input, depleted

source_name: Input fraction from K-iPSC-12_N1

source_name: Methyl-depleted fraction from K-iPSC-12_N1


title: CB-iPSC-13_C13 input, depleted

source_name: Input fraction from CB-iPSC-13_C13

source_name: Methyl-depleted fraction from CB-iPSC-13_C13


title: Keratinocyte-58_KG58 input, depleted

source_name: Input fraction from Keratinocyte-58_KG58

source_name: Methyl-depleted fraction from Keratinocyte-58_KG58


title: Apex Control 0 hpa 2

source_name: unamputated control rep 2


title: msh1, albino, biological rep 3

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

hyb_protocol: RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions

scan_protocol: According to Affymetrix instructions

data_processing: Expression data from Affymetrix Genechips were normalized using the Robust Multichip Average (RMA) method using Bioconductor’s affy package in the R language

organism: Arabidopsis thaliana

source_name: msh1 albino mutant

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

growth_protocol: plants were grown on MS media with 1.5% supplement of sucrose in percival growth chamber with 12h-light/12-dark period at 24ºC.

extract_protocol: total RNA was extracted from each plant using TRIzol (Invitrogen) extraction procedure followed by purification on RNeasy columns (Qiagen).

value: msh1 albino mutant

tag: tissue

value: aerial part

value: 4-week-old old plant


title: msh1, albino, biological rep 2


title: wild type, biological rep 2

source_name: wild type

value: wild type


title: K-iPSC-11_N11 input, depleted

source_name: Input fraction from K-iPSC-11_N11

source_name: Methyl-depleted fraction from K-iPSC-11_N11


title: msh1, albino, biological rep 1


title: K-iPSC-1_G1 input, depleted

source_name: Input fraction from K-iPSC-1_G1

source_name: Methyl-depleted fraction from K-iPSC-1_G1


title: K-iPSC-9_N9 input, depleted

source_name: Input fraction from K-iPSC-9_N9

source_name: Methyl-depleted fraction from K-iPSC-9_N9


title: CB-iPSC-8_C8 input, depleted

source_name: Input fraction from CB-iPSC-8_C8

source_name: Methyl-depleted fraction from CB-iPSC-8_C8


title: TNFa_treated_HUVEC_6hr-3

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

hyb_protocol: 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed and placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.

scan_protocol: The arrays were scanned with Agilnet DNA Microarray Scanner model G2565BA.

data_processing: The scanned images were quantified with CodeLink Expression Array Software (Applied Microarrays, formally supplied by GE Healthcare), where the intensity of each spot was divided by the spot’s signal median.

source_name: HUVEC

label_protocol: Biotin-labelled complex cRNAs were prepared to according to the manufacturer's protocols (Applied Microarrays, formally supplied by GE Healthcare)

growth_protocol: HUVECs were isolated from umbilical cords by collagenase digestion and cultured at 37ºC/5%CO2 in basal culture medium supplemented with a proprietary mixture of heparin, hydrocortisone, epidermal growth factor, 2% foetal calf serum (FCS; EGM-2, Cambrex, Workingham, UK).

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.

treatment_protocol: HUVEC pools consisting of 10 biological isolates were treated with TNFa (10ng/mL). Cells were incubated at37ºC/5%CO2 for the time points in transcriptional profiling.

value: HUVEC

tag: tnfa treatment time point


title: wild type, biological rep 1


title: TNFa_treated_HUVEC_6hr-1


title: TNFa_treated_HUVEC_5hr-3


title: ESC-CHB8 input, depleted

source_name: Input fraction from ESC-CHB8

value: ES cells

source_name: Methyl-depleted fraction from ESC-CHB8


title: TNFa_treated_HUVEC_6hr-2


title: wild type, biological rep 3


title: Apex Control 7 dpa 1

source_name: amputated control 7 dpa rep 1


title: ESC-Hue2 input, depleted

source_name: Input fraction from ESC-Hue2

source_name: Methyl-depleted fraction from ESC-Hue2


title: TNFa_treated_HUVEC_4hr-1


title: ESC-H9 input, depleted

source_name: Input fraction from ESC-H9

source_name: Methyl-depleted fraction from ESC-H9


title: TNFa_treated_HUVEC_3hr-2


title: TNFa_treated_HUVEC_3hr-3


title: TNFa_treated_HUVEC_4hr-2


title: TNFa_treated_HUVEC_3hr-1


title: TNFa_treated_HUVEC_5hr-1


title: TNFa_treated_HUVEC_4hr-3


title: CB-iPSC-3_C3 input, depleted

source_name: Input fraction from CB-iPSC-3_C3

source_name: Methyl-depleted fraction from CB-iPSC-3_C3


title: TNFa_treated_HUVEC_2hr-3


title: TNFa_treated_HUVEC_1.5hr-2


title: TNFa_treated_HUVEC_1.5hr-1


title: TNFa_treated_HUVEC_1hr-2


title: TNFa_treated_HUVEC_1.5hr-3


title: ESC-BG01 input, depleted

source_name: Input fraction from ESC-BG01

source_name: Methyl-depleted fraction from ESC-BG01


title: ZNF143_KD

treatment_protocol: HUVEC pools consisting of 10 biological isolates were transfected with siRNA smartpools from Dharmacon Inc. (Lafayette, Colorado, USA) using the siFectamine transfection reagent (ICVEC, London, UK) used according to the manufacturer’s instructions. Transfection was carried out when HUVEC pools were 60-80% confluent, with siRNA smartpools at a final concentration of 100nm per treatment and RNA was extracted 24hrs after transfection.

tag: sirna knocked down

value: ZNF143 siRNA knocked down


title: ZEB1_KD

value: ZEB1 siRNA knocked down


title: ZNF274_KD

value: ZNF274 siRNA knocked down


title: K-iPSC-6_G6 input, depleted

source_name: Input fraction from K-iPSC-6_G6

tag: cell type

source_name: Methyl-depleted fraction from K-iPSC-6_G6


title: TNFa_treated_HUVEC_1hr-1


title: TNFa_untreated_HUVEC_3

value: untreatment


title: TNFa_untreated_HUVEC_2


title: TNFa_untreated_HUVEC_1


title: YWHAZ_KD

value: YWHAZ siRNA knocked down


title: VAV1_KD

value: VAV1 siRNA knocked down


title: TTRAP_KD

value: TTRAP siRNA knocked down


title: UBE2J1_KD

value: UBE2J1 siRNA knocked down


title: USF2_KD

value: USF2 siRNA knocked down


title: VASH1_KD

value: VASH1 siRNA knocked down


title: ESC-BG03 input, depleted

source_name: Input fraction from ESC-BG03

source_name: Methyl-depleted fraction from ESC-BG03


title: TRAF1_KD

value: TRAF1 siRNA knocked down


title: TTF2_KD

value: TTF2 siRNA knocked down


title: TP73_KD

value: TP73 siRNA knocked down


title: TNFa_treated_HUVEC_5hr-2


title: primary human: blood; FACS-sorted CD19+ cells (CLL011T)

value: tumor


title: TP63_KD

value: TP63 siRNA knocked down


title: TOX4_KD

value: HUVEC

value: TOX4 siRNA knocked down


title: TNFa_treated_HUVEC_2hr-1


title: TOP2A_KD

value: TOP2A siRNA knocked down


title: TNIP2_KD

value: TNIP2 siRNA knocked down


title: TNFRSF1A_KD

value: TNFRSF1A siRNA knocked down


title: TOP2B_KD

value: TOP2B siRNA knocked down


title: TNFAIP1_KD

value: TNFAIP1 siRNA knocked down


title: TGIF1_KD

value: TGIF1 siRNA knocked down


title: TMED2_KD

value: TMED2 siRNA knocked down


title: TP53_KD

value: TP53 siRNA knocked down


title: TMF1_KD

value: TMF1 siRNA knocked down


title: TGFBR1_KD

value: TGFBR1 siRNA knocked down


title: TFPT_KD

value: TFPT siRNA knocked down


title: TM7SF2_KD

value: TM7SF2 siRNA knocked down


title: TIE1_KD

value: TIE1 siRNA knocked down


title: TFDP2_KD

value: TFDP2 siRNA knocked down


title: TFDP1_KD

value: TFDP1 siRNA knocked down


title: TEK_KD

value: HUVEC

value: TEK siRNA knocked down


title: TGFB1_KD

value: TGFB1 siRNA knocked down


title: TFEC_KD

value: TFEC siRNA knocked down


title: TCERG1_KD

value: TCERG1 siRNA knocked down


title: TCEB3_KD

value: TCEB3 siRNA knocked down


title: TCEAL4_KD

value: TCEAL4 siRNA knocked down


title: TCEB1_KD

value: TCEB1 siRNA knocked down


title: TCEA1_KD

value: TCEA1 siRNA knocked down


title: TNFa_treated_HUVEC_1hr-3


title: TCEA2_KD

value: TCEA2 siRNA knocked down


title: TBP_KD

value: TBP siRNA knocked down


title: TAF5L_KD

value: TAF5L siRNA knocked down


title: TAF4_KD

value: TAF4 siRNA knocked down


title: TCEAL1_KD

value: TCEAL1 siRNA knocked down


title: TNFa_treated_HUVEC_2hr-2


title: TAF1B_KD

value: TAF1B siRNA knocked down


title: WT1_KD

value: WT1 siRNA knocked down


title: TAF9_KD

value: TAF9 siRNA knocked down


title: TAF2_KD

value: HUVEC

value: TAF2 siRNA knocked down


title: TAF10_KD

value: TAF10 siRNA knocked down


title: TAF6_KD

value: TAF6 siRNA knocked down


title: TAF1C_KD

value: TAF1C siRNA knocked down


title: TAF7_KD

value: TAF7 siRNA knocked down


title: TAF11_KD

value: TAF11 siRNA knocked down


title: TAF5_KD

value: TAF5 siRNA knocked down


title: TAF15_KD

value: TAF15 siRNA knocked down


title: STAT4_KD

value: STAT4 siRNA knocked down


title: STAT2_KD

value: STAT2 siRNA knocked down


title: TAF12_KD

value: TAF12 siRNA knocked down


title: ESC-H1OGN input, depleted

source_name: Input fraction from ESC-H1OGN

value: ES cells

source_name: Methyl-depleted fraction from ESC-H1OGN


title: Cord_Blood-28A_CB28A input, depleted

source_name: Input fraction from Cord_Blood-28A_CB28A

value: cord blood

source_name: Methyl-depleted fraction from Cord_Blood-28A_CB28A


title: STAT5A_KD

source_name: HUVEC

value: STAT5A siRNA knocked down


title: TAF6L_KD

value: TAF6L siRNA knocked down


title: SRF_KD

value: SRF siRNA knocked down


title: STAT5B_KD

value: HUVEC

value: STAT5B siRNA knocked down


title: STAT1_KD

value: STAT1 siRNA knocked down


title: STAT3_KD

value: STAT3 siRNA knocked down


title: SP2_KD

value: SP2 siRNA knocked down


title: STAT6_KD

value: STAT6 siRNA knocked down


title: SP100_KD

value: SP100 siRNA knocked down


title: Cord_Blood-10A_CB10A input, depleted

source_name: Input fraction from Cord_Blood-10A_CB10A

source_name: Methyl-depleted fraction from Cord_Blood-10A_CB10A


title: SOX18_KD

value: SOX18 siRNA knocked down


title: SMAD4_KD

value: SMAD4 siRNA knocked down


title: SMAD7_KD

value: SMAD7 siRNA knocked down


title: RXRA_KD

value: RXRA siRNA knocked down


title: SMAD1_KD

value: SMAD1 siRNA knocked down


title: RRM1_KD

value: RRM1 siRNA knocked down


title: RUNX1_KD

value: RUNX1 siRNA knocked down


title: RBP1_KD

value: RBP1 siRNA knocked down


title: RELA_KD

value: RELA siRNA knocked down


title: SKP1_KD

value: SKP1 siRNA knocked down


title: RPL11_KD

value: HUVEC

value: RPL11 siRNA knocked down


title: SLC15A3_KD

value: SLC15A3 siRNA knocked down


title: SKP2_KD

value: SKP2 siRNA knocked down


title: RB1_KD

value: RB1 siRNA knocked down


title: RREB1_KD

value: RREB1 siRNA knocked down


title: RELB_KD

value: RELB siRNA knocked down


title: SDHB_KD

value: SDHB siRNA knocked down


title: RBL1_KD

value: RBL1 siRNA knocked down


title: SIX3_KD

value: SIX3 siRNA knocked down


title: RBL2_KD

value: RBL2 siRNA knocked down


title: RARB_KD

value: RARB siRNA knocked down


title: RPA3_KD

value: RPA3 siRNA knocked down


title: RAC1_KD

value: RAC1 siRNA knocked down


title: RAD17_KD

value: RAD17 siRNA knocked down


title: RAD1_KD

value: RAD1 siRNA knocked down


title: PTX3_KD

value: PTX3 siRNA knocked down


title: REL_KD

value: HUVEC

value: REL siRNA knocked down


title: PTMA_KD

value: PTMA siRNA knocked down


title: PRKACB_KD

value: PRKACB siRNA knocked down


title: RARG_KD

value: RARG siRNA knocked down


title: PRKAR1A_KD

value: PRKAR1A siRNA knocked down


title: PPARD_KD

value: PPARD siRNA knocked down


title: PTGS2_KD

value: PTGS2 siRNA knocked down


title: PPP3CB_KD

value: PPP3CB siRNA knocked down


title: PRKCA_KD

value: PRKCA siRNA knocked down


title: POU2F1_KD

value: POU2F1 siRNA knocked down


title: PRMT1_KD

value: PRMT1 siRNA knocked down


title: POU6F1_KD

value: POU6F1 siRNA knocked down


title: POLR2I_KD

value: POLR2I siRNA knocked down


title: POLR2C_KD

value: POLR2C siRNA knocked down


title: PRKRIR_KD

value: PRKRIR siRNA knocked down


title: POLR2D_KD

value: POLR2D siRNA knocked down


title: RAD9A_KD

value: HUVEC

value: RAD9A siRNA knocked down


title: PLK2_KD

value: PLK2 siRNA knocked down


title: PPARA_KD

value: PPARA siRNA knocked down


title: SNAPC4_KD

value: SNAPC4 siRNA knocked down


title: PIN1P1_KD

value: PIN1P1 siRNA knocked down


title: POLR2A_KD

value: POLR2A siRNA knocked down


title: PIN1_KD

value: PIN1 siRNA knocked down


title: PML_KD

value: PML siRNA knocked down


title: PLK3_KD

value: PLK3 siRNA knocked down


title: PLK1_KD

value: PLK1 siRNA knocked down


title: PCNA_KD

value: PCNA siRNA knocked down


title: PIK3R3_KD

value: PIK3R3 siRNA knocked down


title: PKNOX2_KD

value: PKNOX2 siRNA knocked down


title: PDGFRA_KD

value: PDGFRA siRNA knocked down


title: PDGFRB_KD

value: PDGFRB siRNA knocked down


title: PIAS3_KD

value: PIAS3 siRNA knocked down


title: ORC1L_KD

value: HUVEC

value: ORC1L siRNA knocked down


title: ORC4L_KD

value: ORC4L siRNA knocked down


title: NUDT5_KD

value: NUDT5 siRNA knocked down


title: NRP1_KD

value: NRP1 siRNA knocked down


title: ORC3L_KD

value: ORC3L siRNA knocked down


title: PIK3CB_KD

value: PIK3CB siRNA knocked down


title: NMI_KD

value: NMI siRNA knocked down


title: ORC2L_KD

value: ORC2L siRNA knocked down


title: PIAS1_KD

value: PIAS1 siRNA knocked down


title: SP1_KD

value: SP1 siRNA knocked down


title: POLR2E_KD

value: POLR2E siRNA knocked down


title: NKX3-1_KD

value: NKX3-1 siRNA knocked down


title: NFKBIL2_KD

value: NFKBIL2 siRNA knocked down


title: NFKB2_KD

value: NFKB2 siRNA knocked down


title: NFKB1_KD

value: NFKB1 siRNA knocked down


title: PIK3R2_KD

value: PIK3R2 siRNA knocked down


title: PIK3R1_KD

value: HUVEC

value: PIK3R1 siRNA knocked down


title: PIK3CG_KD

value: PIK3CG siRNA knocked down


title: PPP5C_KD

value: PPP5C siRNA knocked down


title: NCOR2_KD

value: NCOR2 siRNA knocked down


title: NFKBIE_KD

value: NFKBIE siRNA knocked down


title: ORC5L_KD

value: ORC5L siRNA knocked down


title: MNT_KD

value: MNT siRNA knocked down


title: MYCBP_KD

value: MYCBP siRNA knocked down


title: NFKBIA_KD

value: NFKBIA siRNA knocked down


title: MSC_KD

value: MSC siRNA knocked down


title: PIK3CD_KD

value: PIK3CD siRNA knocked down


title: NFKBIL1_KD

value: NFKBIL1 siRNA knocked down


title: MYOG_KD

value: MYOG siRNA knocked down


title: MYC_KD

value: MYC siRNA knocked down


title: NR2F2_KD

value: NR2F2 siRNA knocked down


title: MNAT1_KD

value: MNAT1 siRNA knocked down


title: ORC6L_KD

value: HUVEC

value: ORC6L siRNA knocked down


title: MYBL2_KD

value: MYBL2 siRNA knocked down


title: NCOR1_KD

value: NCOR1 siRNA knocked down


title: MLL_KD

value: MLL siRNA knocked down


title: MLL2_KD

value: MLL2 siRNA knocked down


title: MSX1_KD

value: MSX1 siRNA knocked down


title: MKI67_KD

value: MKI67 siRNA knocked down


title: MED7_KD

value: MED7 siRNA knocked down


title: MEOX2_KD

value: MEOX2 siRNA knocked down


title: MECP2_KD

value: MECP2 siRNA knocked down


title: MDM2_KD

value: MDM2 siRNA knocked down


title: MED1_KD

value: MED1 siRNA knocked down


title: MCM6_KD

value: MCM6 siRNA knocked down


title: MCM3_KD

value: MCM3 siRNA knocked down


title: MCM5_KD

value: MCM5 siRNA knocked down


title: MCM4_KD

value: MCM4 siRNA knocked down


title: MAPK14_KD

value: HUVEC

value: MAPK14 siRNA knocked down


title: MCM7_KD

value: MCM7 siRNA knocked down


title: MAX_KD

value: MAX siRNA knocked down


title: MARCH7_KD

value: MARCH7 siRNA knocked down


title: MAZ_KD

value: MAZ siRNA knocked down


title: MAPK1_KD

value: MAPK1 siRNA knocked down


title: MCM2_KD

value: MCM2 siRNA knocked down


title: LTA4H_KD

value: LTA4H siRNA knocked down


title: KDM5A_KD

value: KDM5A siRNA knocked down


title: ISL1_KD

value: ISL1 siRNA knocked down


title: JunD_KD

value: JunD siRNA knocked down


title: MAD2L1_KD

value: MAD2L1 siRNA knocked down


title: MAP2K1_KD

value: MAP2K1 siRNA knocked down


title: IRF7_KD

value: IRF7 siRNA knocked down


title: MAFF_KD

value: MAFF siRNA knocked down


title: MAD2L2_KD

value: MAD2L2 siRNA knocked down


title: IRF1_KD

value: HUVEC

value: IRF1 siRNA knocked down


title: KDR_KD

value: KDR siRNA knocked down


title: JUNB_KD

value: JUNB siRNA knocked down


title: ILF3_KD

value: ILF3 siRNA knocked down


title: IL8_KD

value: IL8 siRNA knocked down


title: ILF2_KD

value: ILF2 siRNA knocked down


title: JUN_KD

value: JUN siRNA knocked down


title: KLF2_KD

value: KLF2 siRNA knocked down


title: IRAK1_KD

value: IRAK1 siRNA knocked down


title: IL8RB_KD

value: IL8RB siRNA knocked down


title: IL8RA_KD

value: IL8RA siRNA knocked down


title: IL4I1_KD

value: IL4I1 siRNA knocked down


title: IL1A_KD

value: IL1A siRNA knocked down


title: IL1R1_KD

value: IL1R1 siRNA knocked down


title: IL6_KD

value: IL6 siRNA knocked down


title: IL15_KD

value: IL15 siRNA knocked down


title: IFIT3_KD

value: HUVEC

value: IFIT3 siRNA knocked down


title: IKBKB_KD

value: IKBKB siRNA knocked down


title: IL2RG_KD

value: IL2RG siRNA knocked down


title: IL15RA_KD

value: IL15RA siRNA knocked down


title: IKBKE_KD

value: IKBKE siRNA knocked down


title: IFIH1_KD

value: IFIH1 siRNA knocked down


title: IL1B_KD

value: IL1B siRNA knocked down


title: IL1R2_KD

value: IL1R2 siRNA knocked down


title: IL2RB_KD

value: IL2RB siRNA knocked down


title: IKBKG_KD

value: IKBKG siRNA knocked down


title: ID1_KD

value: ID1 siRNA knocked down


title: HSPA4_KD

value: HSPA4 siRNA knocked down


title: HSF2_KD

value: HSF2 siRNA knocked down


title: HSF4_KD

value: HSF4 siRNA knocked down


title: NFATC1_KD

value: NFATC1 siRNA knocked down


title: HUS1_KD

value: HUS1 siRNA knocked down


title: HHEX_KD

value: HUVEC

value: HHEX siRNA knocked down


title: HES1_KD

value: HES1 siRNA knocked down


title: HOXA11_KD

value: HOXA11 siRNA knocked down


title: HIRA_KD

value: HIRA siRNA knocked down


title: HDAC3_KD

value: HDAC3 siRNA knocked down


title: HIVEP2_KD

value: HIVEP2 siRNA knocked down


title: HIPK2_KD

value: HIPK2 siRNA knocked down


title: HDAC1_KD

value: HDAC1 siRNA knocked down


title: HDAC2_KD

value: HDAC2 siRNA knocked down


title: HDAC5_KD

value: HDAC5 siRNA knocked down


title: GTF2H4_KD

value: GTF2H4 siRNA knocked down


title: GTF2H1_KD

value: GTF2H1 siRNA knocked down


title: GTF2F1_KD

value: GTF2F1 siRNA knocked down


title: GTF3C2_KD

value: GTF3C2 siRNA knocked down


title: GTF2B_KD

value: GTF2B siRNA knocked down


title: GTF2A2_KD

value: GTF2A2 siRNA knocked down


title: GATA6_KD

value: HUVEC

value: GATA6 siRNA knocked down


title: GTF2E2_KD

value: GTF2E2 siRNA knocked down


title: FOXO1A_KD

value: FOXO1A siRNA knocked down


title: GTF2F2_KD

value: GTF2F2 siRNA knocked down


title: GATA1_KD

value: GATA1 siRNA knocked down


title: GTF2E1_KD

value: GTF2E1 siRNA knocked down


title: FOXM1_KD

value: FOXM1 siRNA knocked down


title: FOXD2_KD

value: FOXD2 siRNA knocked down


title: GMNN_KD

value: GMNN siRNA knocked down


title: GATA4_KD

value: GATA4 siRNA knocked down


title: GABPB2_KD

value: GABPB2 siRNA knocked down


title: FOXO3A_KD

value: FOXO3A siRNA knocked down


title: FOXF1_KD

value: FOXF1 siRNA knocked down


title: GABPA_KD

value: GABPA siRNA knocked down


title: GTF2I_KD

value: GTF2I siRNA knocked down


title: GPR4_KD

value: GPR4 siRNA knocked down


title: GABARAP_KD

value: HUVEC

value: GABARAP siRNA knocked down


title: FOSL2_KD

value: FOSL2 siRNA knocked down


title: FOXJ2_KD

value: FOXJ2 siRNA knocked down


title: FOSL1_KD

value: FOSL1 siRNA knocked down


title: GATA3_KD

value: GATA3 siRNA knocked down


title: FLT3_KD

value: FLT3 siRNA knocked down


title: FOXC1_KD

value: FOXC1 siRNA knocked down


title: FLT1_KD

value: FLT1 siRNA knocked down


title: FLT4_KD

value: FLT4 siRNA knocked down


title: FOS_KD

value: FOS siRNA knocked down


title: FGFR1_KD

value: FGFR1 siRNA knocked down


title: FAM78A_KD

value: FAM78A siRNA knocked down


title: FBXO32_KD

value: FBXO32 siRNA knocked down


title: FAIM3_KD

value: FAIM3 siRNA knocked down


title: ETV4_KD

value: ETV4 siRNA knocked down


title: ETV5_KD

value: ETV5 siRNA knocked down


title: FABP4_KD

value: HUVEC

value: FABP4 siRNA knocked down


title: EFNB2_KD

value: EFNB2 siRNA knocked down


title: ESRRA_KD

value: ESRRA siRNA knocked down


title: ETV6_KD

value: ETV6 siRNA knocked down


title: ERF_KD

value: ERF siRNA knocked down


title: EFNB1_KD

value: EFNB1 siRNA knocked down


title: EGR1_KD

value: EGR1 siRNA knocked down


title: ENG_KD

value: ENG siRNA knocked down


title: EAF1_KD

value: EAF1 siRNA knocked down


title: ELP2_KD

value: ELP2 siRNA knocked down


title: ETV7_KD

value: ETV7 siRNA knocked down


title: ETS2_KD

value: ETS2 siRNA knocked down


title: EDF1_KD

value: EDF1 siRNA knocked down


title: EFNA1_KD

value: EFNA1 siRNA knocked down


title: E2F1_KD

value: E2F1 siRNA knocked down


title: E2F5_KD

value: E2F5 siRNA knocked down


title: E2F6_KD

value: HUVEC

value: E2F6 siRNA knocked down


title: E2F2_KD

value: E2F2 siRNA knocked down


title: E2F4_KD

value: E2F4 siRNA knocked down


title: DLX4_KD

value: DLX4 siRNA knocked down


title: DUT_KD

value: DUT siRNA knocked down


title: CXCL1_KD

value: CXCL1 siRNA knocked down


title: DUSP1_KD

value: DUSP1 siRNA knocked down


title: E2F3_KD

value: E2F3 siRNA knocked down


title: DEK_KD

value: DEK siRNA knocked down


title: DDX58_KD

value: DDX58 siRNA knocked down


title: CXCR3_KD

value: CXCR3 siRNA knocked down


title: CXCL10_KD

value: CXCL10 siRNA knocked down


title: CTNNB1_KD

value: CTNNB1 siRNA knocked down


title: CXCL3_KD

value: CXCL3 siRNA knocked down


title: CX3CL1_KD

value: CX3CL1 siRNA knocked down


title: CTCF_KD

value: CTCF siRNA knocked down


title: CX3CR1_KD

value: HUVEC

value: CX3CR1 siRNA knocked down


title: CWC15_KD

value: CWC15 siRNA knocked down


title: CRK_KD

value: CRK siRNA knocked down


title: DHX15_KD

value: DHX15 siRNA knocked down


title: CREM_KD

value: CREM siRNA knocked down


title: CXCL11_KD

value: CXCL11 siRNA knocked down


title: CXCL2_KD

value: CXCL2 siRNA knocked down


title: CRI1_KD

value: CRI1 siRNA knocked down


title: CRX_KD

value: CRX siRNA knocked down


title: CREBBP_KD

value: CREBBP siRNA knocked down


title: CHEK2_KD

value: CHEK2 siRNA knocked down


title: CFB_KD

value: CFB siRNA knocked down


title: CREB1_KD

value: CREB1 siRNA knocked down


title: CHUK_KD

value: CHUK siRNA knocked down


title: CHEK1_KD

value: CHEK1 siRNA knocked down


title: CENPC1_KD

value: CENPC1 siRNA knocked down


title: CENPF_KD

value: HUVEC

value: CENPF siRNA knocked down


title: CENPE_KD

value: CENPE siRNA knocked down


title: CENPH_KD

value: CENPH siRNA knocked down


title: CEBPZ_KD

value: CEBPZ siRNA knocked down


title: Cervical cancer cell line HeLa_rep3

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: RMA default expression value derived from Affymetrix Expression Console software

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing:
Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Cervical cancer cell line

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: Cell lines were grown according to standard conditions.

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

tag: gender

value: Female

tag: cell line

value: Hela


title: Mouse_Peripheral_18M_03

city: Palo Alto

first: Li Fen

last: Liu

state: CA

address: 3801 Miranda AVE

institute: Stanford University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit.  Affymetrix GeneChip Hybridization Oven 640  Three heating blocks are required: one at 65°C, one at 99°C, and the third one at 45°C.  1. Prepare the Hybridization Cocktail in a 1.5 mL RNase-free microfuge tube as shown  in Table 5.1.  2. Flick or gently vortex the tubes and spin down.  3. Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes,  and centrifuge at maximum speed for 1 minute.  4. Equilibrate the GeneChip ST Array to room temperature immediately before use.  Label the array with the name of the sample that will be hybridized.  5. Inject the appropriate amount (see Table 5.2) of the specific sample into the array  through one of the septa (see Figure 5.1 for location of the septa on the array).  6. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 17 hours ± 1 hour.  During the latter part of the array hybridization, commence preparation of the  reagents required immediately after completion of hybridization.

scan_protocol: the GeneChip Expression Wash, Stain and Scan User Manual (P/N702731) for the washing and staining steps required immediately after completion of hybridization. Please refer to Appendix C for fluidics protocols and fluidics script information for GeneChip ST Arrays. Scan model are Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip Scanner 3000 7G.

data_processing: The raw data from microarrays were analyzed using Partek Genome Suite software, version 6.3 Copyright  2008 (Partek Inc., St. Louis, MO, USA).  Briefly, Affymetrix .CEL files were processed to generate gcRMA (robust multi-array average) values.  This step was followed by quantile normalization and log2 transformation to represent gene expression levels.

source_name: Peripheral

label_protocol: Whole Transcript Sense Target Labeling Assay using AmbionWT expression Kit P/N 702808.

growth_protocol: Bone marrow adipocytes and peripheral white adipocytes (n=6-10 animals per group) were isolated from obese mice Obob, male C57BL/6J mice (6-months, 14-months and 18-months of age) fed either with standard chow or high fat diet.  All mice were housed in temperature-controlled conditions on a 12-h light, 12-h dark cycle.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies, Grand Island, NY, USA) and chloroform followed by purification on an RNeasy MinElute column (QIAGEN, Valencia, CA. USA).  Three pooled RNA preparations were generated from 6-10 animals due to the low yield of bone marrow adipocytes during isolation.

treatment_protocol: Briefly, both femurs and tibias were collected after mice were sacrificed.  Bones were cleaned and rinsed with 75% ethanol and DEPC water to eliminate surrounding fat and muscle cells.  Fresh bone marrows were flushed out with PBS containing 1% fatty acid-free BSA and 1% RNAase and DNAase-free water using a 25-gauge needle from femurs and tibias.  Red blood cells were lysed using red cell lysis buffer.  After centrifugation at 3000 RPM for 5 min, floating adipocytes were collected from bone marrow stromal cells and then were washed with PBS buffer three times.

tag: sample type

value: C57BL/6J Male, 18 month old

value: wild type

value: 18 month old

value: male

value: Peripheral white adipocyte

tag: diet

value: control


title: Mouse_Peripheral_Obob_6M_01

value: Obob Male, 6 month old

tag: genetic background

value: ob/ob

value: 6 month old


title: Cervical cancer cell line SiHa_rep3

value: Siha


title: CENPB_KD

value: HUVEC

value: CENPB siRNA knocked down


title: CFLAR_KD

value: CFLAR siRNA knocked down


title: CEBPG_KD

value: CEBPG siRNA knocked down


title: Mouse_BM_Obob_6M_01

source_name: Bone marrow

tag: genotype

value: Bone marrow adipocyte


title: Mouse_BM_Obob_6M_02


title: Mouse_Peripheral_Obob_6M_02


title: CENPA_KD

value: CENPA siRNA knocked down


title: Mouse_Peripheral_Obob_6M_03


title: Cervical cancer cell line CaLo_rep3

value: Female

value: Calo


title: CEBPD_KD

value: CEBPD siRNA knocked down


title: Mouse_Peripheral_18M_02

value: C57BL/6J Male, 18 month old

value: wild type

value: 18 month old


title: Mouse_BM_18M_01

value: male

value: control


title: Mouse_BM_18M_03


title: Mouse_Peripheral_14M_HF diet_03

value: C57BL/6J Male, 14 month old

value: 14 month old

value: Peripheral white adipocyte

value: high fat


title: Mouse_Peripheral_14M_HF diet_01


title: Mouse_BM_Obob_6M_03

value: Obob Male, 6 month old

value: ob/ob

value: 6 month old


title: CDKN2C_KD

value: HUVEC

value: CDKN2C siRNA knocked down


title: CDKN2B_KD

value: CDKN2B siRNA knocked down


title: Mouse_Peripheral_18M_01


title: Mouse_BM_18M_02

value: Bone marrow adipocyte


title: Mouse_Peripheral_14M_HF diet_02


title: CDKN2D_KD

value: CDKN2D siRNA knocked down


title: Cervical cancer cell line CaSki_rep3

value: Female

value: Caski


title: CDKN1C_KD

value: CDKN1C siRNA knocked down


title: CDK9_KD

value: CDK9 siRNA knocked down


title: CDT1_KD

value: CDT1 siRNA knocked down


title: P. aeruginosa pure culture rep1

city: San Marcos

first: Robert

middle: JC

last: McLean

state: TX

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

description: Gene expression data from pure culture

hyb_protocol: Following fragmentation, 4-6ug cDNA was hybridized to E coli or P aeruginosa gene chips

scan_protocol: Gene chips were scanned using an Affymetrix Model 3000 GeneArray scanner

data_processing: Microarray .cel files were analyzed by multiarray analysis method using the Affy package (version 1.18.2, Affymetrix) using default options.

organism: Pseudomonas aeruginosa PAO1

source_name: P. aer. Pure culture

label_protocol: Enzo Bioarray Terminal Labeling Kit (Affymetrix cat # 900181) according to manufacturer's instructions

growth_protocol: E coli and P aeruginosa cells were grown aerobically at 37C in pure and mixed culture in a MOPS-buffered medium containing N-acetyl glucosamine

extract_protocol: Qiagen RNA extraction following manufacturer's protocol

treatment_protocol: Following incubation samples were stabilized with RNA later (Ambion) and stored at 4C prior to RNA extraction

tag: culture

value: P. aeruginosa pure culture


title: Mouse_BM_14M_HF diet_01

value: C57BL/6J Male, 14 month old

value: wild type

value: 14 month old

value: male


title: CEBPA_KD

value: CEBPA siRNA knocked down


title: Mouse_BM_14M_HF diet_03

value: high fat


title: CEBPB_KD

value: HUVEC

value: CEBPB siRNA knocked down


title: Mouse_BM_14M_HF diet_02


title: CDK8_KD

value: CDK8 siRNA knocked down


title: P. aeruginosa and E. coli MG1655 culture rep1

description: Gene expression data from mixed culture

source_name: E. coli and P. aer. Mixed culture

value: P. aeruginosa and E. coli culture


title: CDK7_KD

value: CDK7 siRNA knocked down


title: P. aeruginosa and E. coli MG1655 culture rep2

description: Gene expression data from mixed culture


title: Mouse_Peripheral_14M_03

value: Peripheral white adipocyte

value: control


title: kera_som_NEP

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

description: Gene expression data from keratinocyte NEP

hyb_protocol: According to manufacturer's instructions.

scan_protocol: scanner model: GCS3000

data_processing: RMA quantile summarization and normalization by R/BioConductor

source_name: keratinocyte

label_protocol: GeneChip One- Cycle labeling kit (Affymetrix)

extract_protocol: RNA was purified by an RNeasy kit (Qiagen, Cat# 74106)

value: keratinocyte


title: CDK5_KD

value: CDK5 siRNA knocked down


title: kera_som_GFP

description: Gene expression data from keratinocyte GFP


title: kera_ips_G5_No6

description: Gene expression data from k iPSC G5

source_name: k iPSC

value: iPSC


title: cb_som_CB090_209B

description: Gene expression data from cord blood 209B

source_name: cord blood

value: cord blood


title: Mouse_BM_14M_02

value: C57BL/6J Male, 14 month old

value: Bone marrow adipocyte


title: CDK6_KD

value: CDK6 siRNA knocked down


title: cb_ips_HCB_6

description: Gene expression data from CB iPSC HCB 6

source_name: CB iPSC


title: kera_ips_N9

description: Gene expression data from k iPSC N9


title: CDK3_KD

value: CDK3 siRNA knocked down


title: cb_som_CB090_210A

description: Gene expression data from cord blood 210A


title: EAHY HSHV-infected

city: Bethesda

first: ombretta

last: salvucci

address: 37 Convent Drive

department: LCO

institute: NCI

description: Gene expression data from 12-day KSHV- infected EAHY cells

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

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

source_name: EAHY KSHV-infected

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

growth_protocol: EAHY cells were grown in DMEM with 10% FCS with or without KSHV infection for 12 days.

treatment_protocol: EAHY cells were infected with rKSHV.219 and the infected cells were selected with puromycin (1ug/ml)

value: human endothelial cell line

value: EAHY

tag: infection

value: KSHV


title: Mouse_Peripheral_14M_02

value: wild type

value: 14 month old

value: male


title: EAHY non-infected control

description: Gene expression data from unifected EAHY cells

source_name: EAHY non-infected control


title: CDK2_KD

value: HUVEC

value: CDK2 siRNA knocked down


title: CDK10_KD

value: CDK10 siRNA knocked down


title: Mouse_Peripheral_6M_HF diet_03

value: C57BL/6J Male, 6 month old

value: 6 month old

value: Peripheral white adipocyte

value: high fat


title: Mouse_BM_14M_03

value: C57BL/6J Male, 14 month old

value: control


title: Mouse_BM_14M_01

value: Bone marrow adipocyte


title: Mouse_Peripheral_6M_HF diet_02


title: CDK4_KD

value: CDK4 siRNA knocked down


title: Ventricularis_Oscillatory_6_miRNA

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

institute: Emory University

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Because of low background, no normalization was used for data analysis. GenomeStudio V2010.1 was used to generate values.

source_name: Ventricularis HAVEC, Oscillatory Shear, 24h

label_protocol: Using suggested labelling protocol by Illumina.

growth_protocol: Side-specific human aortic valvular endothelial cells (fHAVEC and vHAVEC) were grown in MCDB 131 supplemented with FBS, ECGS, IGF, EGF, FGF, VEGF, ascorbic acid, and hydrocortisone

extract_protocol: Total RNA was extracted using Qiazol and Qiagen's miRNeasy kit.

treatment_protocol: fHAVEC and vHAVEC were sheared under oscillatory and laminar shear for 24h.

value: Aortic Valve, Endothelial Cells, Shear

tag: group


title: Mouse_Peripheral_14M_01


title: CDH5_KD

value: CDH5 siRNA knocked down


title: Ls174T-pTER-β-catenin dox3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

hyb_protocol: 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: Ls174T, β-catenin siRNA, induced

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.

value: intestinal colorectal carcinoma cells

tag: induction

value: shRNA against β-catenin

tag: time


title: CDH2_KD

value: CDH2 siRNA knocked down


title: Ventricularis_Oscillatory_5_miRNA

description: replicate 5


title: Ls174T-pTER-β-catenin con3

source_name: Ls174T, β-catenin siRNA, uninduced