title: Trophoblast rep2

description: H9 human ES cells treated with BMP-4

hyb_protocol: Fragmented targets are added onto a microarray, assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60ºC for 17 hours in a hybridization oven with rotation. Hybridized microarrays are washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned using an Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.1 software.

data_processing: gProcessedSignals from all six samples were quantile normalized using R. The data matrix contains the normalized values.

source_name: H9 human ES cells treated with BMP-4

label_protocol: Sample amplification and labeling procedures were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).  Total RNA was reverse transcribed into first strand and second strand cDNA by MMLV-RT using an oligo dT primer that incorporates a T7 promoter sequence. cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine labeled CTPs. The labeled cRNA is purified using RNeasy micro kit (Qiagen) and followed by quantification on both concentrations of cRNA and dye labeled. RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.  Entire amount of each samples labeled with Cy3 or Cy5 are mixed with control targets (Agilent Technologies). Fragmentation is carried out by incubating at 60C for 30 minutes and stopped by adding equal volume of 2x GE Hi-RPM hybridization buffer (Agilent Technologies).

growth_protocol: H9 human embryonic stem cells were grown in standard culture conditions to maintain them in an undifferentiated state.  Colonies were transferred to matrigel for 2 passages before treatment

extract_protocol: Total RNA was extracted from undifferentiated and BMP-4 treated H9 cells using a Qiagen Rneasy kit.

treatment_protocol: H9 cells, grown on matrigel were treated with BMP-4 for 6 days

value: BMP-4 6 days


title: GM12878 SLBP RIP RNA Rep3

status: Public on Sep 19 2011

type: RNA

city: Albany

first: Frank

last: Doyle

state: NY

address: 257 Fuller Rd

department: Nanobiology

country: USA

institute: UAlbany CNSE

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
SLBP_IP_14_GM12878_08102009.CEL

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix GeneChipScanner 30007G using Affymetrix Gene Chip Command Console v3.1

data_processing: Agilent GeneSpringGX software (version 11.0) Iterative PLIER 16 with quantile normalization applied across replicates within replicate groups

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: GM12878 SLBP RIP RNA

label_protocol: Affymetrix WT standard

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeSunyAlbanyGeneSt#TRACK_HTML
RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation.

tag: rip antibody

value: anti-SLBP


title: GM12878 SLBP RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
SLBP_IP_13_GM12878_08102009.CEL


title: H9 undifferentiated rep3

city: Baltimore

first: Hongkai

last: Ji

state: MD

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

description: H9 human ES cells untreated

source_name: H9 human ES cells untreated

tag: treatment

value: undifferentiated


title: LP1_inactive_8hr_rep2

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

hyb_protocol: The fragmented and labelled ST-cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Following the hybridization for 18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000.  Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: CEL files were processed by the Affymetrix Expression Console software package using the gene-level RMA algorithm on the core set of probesets and the annotation file Huex-1_0-st-v2_na31_hg19 provided by Affmyetrix.

source_name: LP1 cell line, 8hr after treatment with inactive enantiomer

label_protocol: Total RNA was amplified using the NuGEN Applause™ WT Amp Plus ST Amplification System. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity.  A modification step targeting the amplified single-stranded cDNA resulted in the generation of sense target (ST) cDNA product compatible with the Affymetrix  GeneChip® Exon arrays.  The ST-cDNA was purified for accurate quantitation and to ensure optimal performance during the fragmentation and labeling process. The ST- cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer.  The appropriate amount of amplified ST-cDNA was fragmented and labeled using the Encore™ Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented ST-cDNA.

growth_protocol: LP1 cells were cultured in IMDM/10% Fetal Bovine Serum/1% penicillin/streptomycin.  Raji cells were cultured in RPMI/10% Fetal Bovine Serum/1% penicillin/streptomycin.

extract_protocol: Total RNA was prepared using a Qiagen RNEasy Mini Kit with on column DNAse digestion according to the manufacturer's instructions.

treatment_protocol: LP1 or Raji cells were treated with the active or inactive BET inhibitor at 500 nM for 4 or 8 h.

tag: cell line

value: Inactive enantiomer

tag: treatment time (hours)


title: GM12878 CELF1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
CUGBP1_IP_27_GM12878_08052009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 CUGBP1 RIP RNA


title: Trophoblast rep3

description: H9 human ES cells treated with BMP-4


title: Raji_BETi_4hr_rep1

source_name: Raji cell line, 4hr after treatment with BET inhibitor

value: Raji

value: BET inhibitor


title: GM12878 PABPC1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_GM12878_PABP_IP1_01_03112010_(HuGene-1_0-st-v1).CEL

source_name: GM12878 PABPC1 RIP RNA


title: Raji_inactive_4hr_rep1

source_name: Raji cell line, 4hr after treatment with inactive enantiomer


title: Raji_none_0hr_rep1

source_name: Raji cell line, 0hr after treatment with no compound


title: Raji_BETi_4hr_rep2


title: H9 undifferentiated rep2

description: H9 human ES cells untreated


title: GM12878 PABPC1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
PABP_IP_2_07152009_(HuGene-1_0-st-v1).CEL


title: LP1_BETi_4hr_rep1

source_name: LP1 cell line, 4hr after treatment with BET inhibitor


title: GM12878 Negative Control Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
G10_IP_24_GM12878_08052009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 T7 control RIP RNA

value: anti-bacteriophage coat protein T7


title: LP1_BETi_8hr_rep2

source_name: LP1 cell line, 8hr after treatment with BET inhibitor


title: GM12878 ELAVL1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
HuR_IP7_GM12878_03_01122010_(HuGene-1_0-st-v1).CEL

source_name: GM12878 ELAVL1 RIP RNA


title: Raji_none_0hr_rep2


title: wild-type quadriceps, biological rep1

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Gene expression data from WT quadriceps

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with MG430 2.0 arrays, washed and processed in accordance with standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 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.

organism: Mus musculus

source_name: wild-type quadriceps

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

extract_protocol:
Quadriceps muscles were isolated from mice.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: genotype/variation

value: wild-type

tag: strain

tag: age

tag: gender

value: male


title: LP1_inactive_4hr_rep2

source_name: LP1 cell line, 4hr after treatment with inactive enantiomer


title: GM12878 Negative Control Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
G10_IP_34_GM12878_08052009_(HuGene-1_0-st-v1).CEL


title: Trophoblast rep1

description: H9 human ES cells treated with BMP-4


title: wild-type quadriceps, biological rep3

description: Gene expression data from WT quadriceps


title: ERRgamma transgenic quadriceps, biological rep2

description: Gene expression data from ERRg transgenic quadriceps

source_name: ERRgamma transgenic quadriceps

value: hSkeletal Actin -ERRg transgenic


title: BY4741, 240 min after mock treatment vs untreated cells rep3

status: Public on Sep 18 2011

city: Madison

first: Suraiya

middle: Ruma

last: Haroon

state: WI

address: 425 Henry Mall

department: Genetics

institute: University of Wisconsin - Madison

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414.

scan_protocol: Arrays were scanned on an Axon 4000B scanner.

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics. The data was further filtered to retain the information of the genes that had data for at least 60 percent of the 32 arrays done. Analyis of the data was done on the remaining 5615 genes. All values in Matrix file have been adjusted such that a positive log2 value = induced by by treatment (NaCl or H2O2), and a negative log2 value = repressed by treatment (or expressed lower in NaCl or H2O2 treatment).

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: BY4741 grown in log phase for 3 doublings

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414.

growth_protocol: All experiments were done in YPD and cells were grown exponentially in YPD for 3 doublings prior to the beginning of any treatment.

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414.

treatment_protocol: BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.

label: Oyster cyanine 650 dye

source_name: Mock-treated BY4741 grown stress-free for 4 hours


title: H9 undifferentiated rep1

description: H9 human ES cells untreated


title: BY4741, 240 min after mock treatment vs untreated cells rep2


title: Raji_BETi_8hr_rep1

source_name: Raji cell line, 8hr after treatment with BET inhibitor


title: ERRgamma transgenic quadriceps, biological rep1


title: GM12878 ELAVL1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_02_HuR_IP_GM12878_12072009_(HuGene-1_0-st-v1).CEL


title: wild-type quadriceps, biological rep2

description: Gene expression data from WT quadriceps


title: DC-CRA-LPS

city: Toledo

first: Hironori

last: Matsushima

state: OH

address: 3000 Arlington Avenue Mail Stop 1021

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

description: Replicate 1 of 1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were analyzed with Illumina BeadStudio software.

label: Biotin

source_name: Bone marrow dendritic cells, CRA + LPS

label_protocol: Illumina TotalPrep.

growth_protocol: Crude bone marrow cells were cultured with 10 ng/ml of GM-CSF for 5 days to generate dendritic cells.

extract_protocol: RNA was extracted with Trizol reagent with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Bone marrow-derived dendritic cells were cultured for 6 hours with small chemical compounds or vehicle alone (DMSO) in the presence or absence of LPS.

tag: tissue

value: bone marrow

tag: cell type

value: dendritic cells

value: crassin acetate (CRA) + LPS


title: DC-DMSO-LPS

description: Replicate 1 of 1.

source_name: Bone marrow dendritic cells, DMSO + LPS

value: DMSO + LPS


title: ERRgamma transgenic quadriceps, biological rep3


title: DC-CRA

description: Replicate 1 of 1.

source_name: Bone marrow dendritic cells, CRA

value: crassin acetate (CRA)


title: DC-DMSO

description: Replicate 1 of 1.

source_name: Bone marrow dendritic cells, DMSO

value: DMSO


title: GM12878 Total RNA Rep3

description:
total cellular RNA as input into the accompanying RIP samples
SLBP_input_16_GM12878_08102009.CEL

source_name: GM12878 RIP input RNA (total)


title: BY4741, 240 min after mock treatment vs untreated cells rep1


title: BY4741, 240 min after 60 min NaCl vs untreated cells rep2

source_name: BY4741 grown in log phase for 3 doublings, treated with 0.7M NaCl for 60 min, then grown in YPD for 4 hours


title: BY4741, 240 min after 60 min NaCl vs untreated cells rep1


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 40 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings, treated with 0.7M NaCl for 60 min, then grown in YPD for 4 hours, then exposed to 0.4mM H2O2 (40min)


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 40 min vs 0 min rep1


title: BY4741, 240 min after 60 min NaCl vs untreated cells rep3


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 30 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings, treated with 0.7M NaCl for 60 min, then grown in YPD for 4 hours, then exposed to 0.4mM H2O2 (30min)


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 30 min vs 0 min rep1


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 20 min vs 0 min rep3

source_name: BY4741 grown in log phase for 3 doublings, treated with 0.7M NaCl for 60 min, then grown in YPD for 4 hours, then exposed to 0.4mM H2O2 (20min)


title: GM12878 Total RNA Rep2

description:
total cellular RNA as input into the accompanying RIP samples
IMP_Input_07152009_(HuGene-1_0-st-v1).CEL


title: Subject 516, biological rep2

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)

data_processing: Data processed using Robust Multi-Array Average consists of background correction, quantile normalization, and probe summarization using median polish. All statistical analyses were performed in R.

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated from 2.5mL of whole blood according to manufacturer protocols and purified using the RNeasy mini kit (Qiagen, Chatsworth, CA)

tag: methacholine inhalation challenge

value: Post

value: Male

tag: race

value: W

tag: severity class

tag: fev1 %predicted

tag: pc20 (mg/ml)

tag: steriod usage

value: No

value: whole blood


title: Subject 516, biological rep1

value: Pre


title: Subject 515, biological rep2

value: Yes


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 10 min vs 0 min rep3

source_name: BY4741 grown in log phase for 3 doublings, treated with 0.7M NaCl for 60 min, then grown in YPD for 4 hours, then exposed to 0.4mM H2O2 (10min)


title: Subject 514, biological rep1


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 20 min vs 0 min rep2


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 10 min vs 0 min rep2


title: Subject 515, biological rep1


title: Subject 514, biological rep2


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 20 min vs 0 min rep1


title: Subject 512, biological rep1


title: Subject 511, biological rep2

value: O


title: BY4741 +  H2O2 40 min vs 0 min rep1

source_name: BY4741 grown in log phase for 3 doublings, then exposed to 0.4mM H2O2 (40min)


title: NaCl-pretreated BY4741 + 0.4 mM H2O2 10 min vs 0 min rep1


title: BY4741 +  H2O2 40 min vs 0 min rep2


title: Subject 512, biological rep2


title: Subject 513, biological rep1


title: Subject 513, biological rep2


title: Subject 511, biological rep1


title: Subject 510, biological rep1


title: BY4741 +  H2O2 20 min vs 0 min rep3

source_name: BY4741 grown in log phase for 3 doublings, then exposed to 0.4mM H2O2 (20min)


title: BY4741 +  H2O2 30 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings, then exposed to 0.4mM H2O2 (30min)


title: BY4741 +  H2O2 30 min vs 0 min rep1


title: Subject 509, biological rep2


title: Subject 510, biological rep2


title: BY4741 +  H2O2 20 min vs 0 min rep1


title: Subject 509, biological rep1


title: Subject 508, biological rep1


title: Subject 506, biological rep2


title: Subject 508, biological rep2


title: Subject 506, biological rep1


title: Subject 504, biological rep2


title: Subject 505, biological rep2


title: BY4741 +  H2O2 10 min vs 0 min rep1

source_name: BY4741 grown in log phase for 3 doublings, then exposed to 0.4mM H2O2 (10min)


title: BY4741 +  H2O2 10 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings


title: Subject 505, biological rep1


title: BY4741 + 0.7M NaCl 45 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings, then grown in 0.7M NaCl (45 min)


title: BY4741 + 0.7M NaCl 60 min vs 0 min

source_name: BY4741 grown in log phase for 3 doublings, then grown in 0.7M NaCl (60 min)


title: BY4741 + 0.7M NaCl 45 min vs 0 min rep1


title: BY4741 +  H2O2 10 min vs 0 min rep3


title: BY4741 +  0.7M NaCl 30 min vs 0 min rep2

source_name: BY4741 grown in log phase for 3 doublings, then grown in 0.7M NaCl (30 min)


title: BY4741 +  H2O2 20 min vs 0 min rep2


title: Subject 504, biological rep1


title: BY4741 + 0.7M NaCl 15 min vs 0 min

source_name: BY4741 grown in log phase for 3 doublings, then grown in 0.7M NaCl (15 min)


title: Subject 503, biological rep1


title: BY4741 + 0.7M NaCl 30 min vs 0 min rep1


title: Subject 059, biological rep1


title: Subject 059, biological rep2


title: Periodontal plaque diseased_521

status: Public on Sep 17 2011

type: genomic

first: Jorge

last: Frias-Lopez

address: 245 First street

institute: Forsyth Institute

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

hyb_protocol: Prior to hybridization, slides were blocked with sodium borohydride (NaBH4, 1X PBS, 99% ethanol) in order to reduce unreactive aldehyde groups, thus minimizing the fluorescent background.  Fourteen microliter of each labeled and purified PCR sample were mixed with 6 µl of hybridization buffer containing 2X SSC, 0.2 µg/µl yeast tRNA, 0.1% SDS, and heated for 5 minutes at 100oC. After that, 10 µl of each solution were loaded slowly at one corner and under the cover slip, allowing capillary action to pull the solution over the array. Slides were then placed on incubation racks in a humidified chamber, and hybridization was then performed at 55oC for 16 h in a microarray incubator. Slides were removed from the hybridization chamber and sunk into a water bath containing a washing solution (2X SSC, 10%SDS, at 55oC) to remove the cover slips. The slides were washed using an automated microarray robotic instrument. A washing program was set up as follow: one washing in buffer (2X SSC, 10%SDS) at 55oC for 2 minutes, a second washing in 2X SSC buffer at room temperature for 2 minutes, and a final washing in 0.1X SSC buffer at room temperature for 2 minutes. Once the slides are finished spinning in the centrifuge, they were removed and placed in a light-proof container until scanning.

scan_protocol: The microarray slides are scanned using an Axon 4000B scanner and crude data is extracted using GenePix Pro software. Data are normalized by comparing individual signal intensities to the average of signals from universal probes.

data_processing: Non-oral organisms were removed from analysis. Individual probe spot net intensity was calculated by subtracting the median foreground intensity (F532) with background intensity (B532).  The "HOMIM Online Tools" and the documentation of this software can be found on the following web site: http://bioinformatics.forsyth.org/homim/

molecule: genomic DNA

source_name: Subgingival plaque

label_protocol: Two separate PCR reactions were set up with, respectively, forward primer 5´-CCA GAG TTT GAT YMT GGC-3´ with reverse primer  5´-GAA GGA GGT GWT CCA RCC GCA -3´, and forward primer 5´-GAC TAG AGT TTG ATY MTG GC-3´ with reverse primer 5´-GYT ACC TTG TTA CGA CTT-3´.  Two µl of genomic DNA template were added to the reaction mixture (final volume 25 µl) containing 20 pmol of each primer, 40 nmol  of deoxytriphosphates, 1.5 mM Mg2+ and 1 U of Platinum  High Fidelity Taq polymerase (Invitrogen, San Diego, CA). The samples were preheated at 94°C for 2 min, followed by 32 cycles of amplification under the following conditions: 94°C for 30 s, 55°C for 30 s, and 68°C for 1.5 min, with an additional 1 s for each cycle. A final 10 min elongation step at 68°C was added. The results of the PCR amplification were examined by electrophoresis in a 1% agarose gel. The two parallel PCR reactions were combined and the products purified with QIAquick PCR Purification Kit (Qiagen).Purified PCR products were labeled via the incorporation of Cy3-dCTP during a second reaction. Briefly, 7 μL of each product were added into a 25 μL reaction mixture containing 15 pmol of the forward primer 9F (5`-GAGTTTGATYMTGGCTCAG-3`) , 5 pmol of the 1492R primer , 2.5 μL 10•X high fidelity PCR buffer, 2 mM MgSO4, 2.5 μL of deoxynucleotide triphosphate mixture without deoxycytidine triphosphate (10 mM, 0.2 mM final concentration of each deoxynucleotide), 2.5 μL of deoxycytidine triphosphate mixture (1 μL of 1 mM Cy3-dCTP + 4 μL of 2 mM dCTP, 0.2 mM final concentration), 0.25 μL 10% Triton X, and 1.25 U Taq polymerase. The PCR program included an initial denaturation step at 94oC for 2 minutes, followed by 40 cycles of denaturation at 94oC for 30s, annealing at 55oC for 30s, elongation at 68C for 1.5 minute with an additional 1 s for each cycle, and a final elongation step at 68oC for 10 minutes.

growth_protocol: none, DNA was extracted directly from clinical samples

extract_protocol: Bacterial DNA was eluted from subgingival samples taken with a Gracey currette and suspended in 150 ul of TE. Genomic DNA was then extracted using a MasterPure DNA Purification Kit from Epicentre (# MCD85201)

tag: disease state

value: periodontitis


title: Periodontal plaque diseased_519

treatment_protocol: none, DNA was extracted directly from clinical samples


title: Periodontal plaque diseased_29_30


title: Periodontal plaque diseased_522


title: Periodontal plaque diseased_513


title: Periodontal plaque diseased_514


title: Periodontal plaque diseased_518


title: Periodontal plaque diseased_515


title: Periodontal plaque diseased_517


title: Periodontal plaque diseased_512


title: Subject 503, biological rep2


title: Periodontal plaque diseased_520


title: Periodontal plaque diseased_511


title: Periodontal plaque diseased_510


title: Periodontal plaque diseased_509


title: Periodontal plaque diseased_508


title: Periodontal plaque diseased_507


title: Periodontal plaque diseased_516


title: Periodontal plaque diseased_506


title: Periodontal plaque diseased_505


title: Periodontal plaque diseased_504


title: Periodontal plaque diseased_503


title: Periodontal plaque diseased_502


title: Periodontal plaque diseased_500


title: Periodontal plaque diseased_501


title: Periodontal plaque diseased_499


title: Periodontal plaque diseased_496


title: Periodontal plaque diseased_498


title: Periodontal plaque diseased_497


title: Periodontal plaque diseased_494


title: Periodontal plaque diseased_492


title: Periodontal plaque diseased_491


title: Periodontal plaque diseased_490


title: Periodontal plaque diseased_489


title: Periodontal plaque diseased_484


title: Periodontal plaque diseased_485


title: Periodontal plaque diseased_486


title: Periodontal plaque diseased_480


title: Periodontal plaque diseased_481


title: Periodontal plaque diseased_479


title: Periodontal plaque diseased_476


title: Periodontal plaque diseased_477


title: Periodontal plaque diseased_475


title: Periodontal plaque diseased_474


title: Periodontal plaque diseased_473


title: Periodontal plaque diseased_469


title: Periodontal plaque diseased_495


title: Periodontal plaque diseased_468


title: Periodontal plaque diseased_471


title: Periodontal plaque diseased_493


title: Periodontal plaque diseased_470


title: Periodontal plaque diseased_467


title: Periodontal plaque diseased_483


title: Periodontal plaque diseased_472


title: Periodontal plaque diseased_466


title: Periodontal plaque diseased_488


title: Periodontal plaque diseased_487


title: Periodontal plaque diseased_482


title: Periodontal plaque diseased_478


title: Periodontal plaque diseased_463


title: Periodontal plaque diseased_462


title: Periodontal plaque diseased_464


title: Periodontal plaque diseased_455


title: Periodontal plaque diseased_458


title: Periodontal plaque diseased_457


title: Periodontal plaque diseased_459


title: Periodontal plaque diseased_456


title: Periodontal plaque diseased_461


title: Periodontal plaque diseased_460


title: Periodontal plaque diseased_454


title: Periodontal plaque diseased_453


title: Periodontal plaque diseased_450


title: Periodontal plaque diseased_448


title: Periodontal plaque diseased_465


title: Periodontal plaque diseased_445


title: Periodontal plaque diseased_447


title: Periodontal plaque diseased_443


title: Periodontal plaque diseased_446


title: Periodontal plaque diseased_442


title: Periodontal plaque diseased_451


title: Periodontal plaque diseased_437


title: Periodontal plaque diseased_439


title: Periodontal plaque diseased_440


title: Periodontal plaque diseased_452


title: Periodontal plaque diseased_449


title: Periodontal plaque diseased_435


title: Periodontal plaque diseased_436


title: Periodontal plaque diseased_434


title: Periodontal plaque diseased_444


title: Periodontal plaque diseased_438


title: Periodontal plaque diseased_425


title: Periodontal plaque diseased_423


title: Periodontal plaque diseased_429


title: Periodontal plaque diseased_427


title: Periodontal plaque diseased_431


title: Periodontal plaque diseased_433


title: Periodontal plaque diseased_424


title: Periodontal plaque diseased_430


title: Periodontal plaque diseased_432


title: Periodontal plaque diseased_426


title: Periodontal plaque diseased_422


title: Periodontal plaque diseased_428


title: Periodontal plaque diseased_421


title: Periodontal plaque diseased_420


title: Periodontal plaque diseased_414


title: Periodontal plaque diseased_416


title: Periodontal plaque diseased_417


title: Periodontal plaque diseased_415


title: Periodontal plaque diseased_418


title: Periodontal plaque diseased_419


title: Periodontal plaque diseased_413


title: Periodontal plaque diseased_411


title: Periodontal plaque diseased_410


title: Periodontal plaque diseased_408


title: Periodontal plaque diseased_407


title: Periodontal plaque diseased_409


title: Periodontal plaque diseased_403


title: Periodontal plaque diseased_406


title: Periodontal plaque diseased_401


title: Periodontal plaque diseased_405


title: Periodontal plaque diseased_404


title: Periodontal plaque diseased_399


title: Periodontal plaque diseased_412


title: Periodontal plaque diseased_400


title: Periodontal plaque diseased_394


title: Periodontal plaque diseased_397


title: Periodontal plaque diseased_398


title: Periodontal plaque diseased_395


title: Periodontal plaque diseased_396


title: Periodontal plaque diseased_392


title: Periodontal plaque diseased_391


title: Periodontal plaque diseased_393


title: Periodontal plaque diseased_388


title: Periodontal plaque diseased_389


title: Periodontal plaque diseased_390


title: Periodontal plaque diseased_384


title: Periodontal plaque diseased_385


title: Periodontal plaque diseased_383


title: Periodontal plaque diseased_382


title: Periodontal plaque diseased_402


title: Periodontal plaque diseased_380


title: Periodontal plaque diseased_381


title: Periodontal plaque diseased_386


title: Periodontal plaque diseased_377


title: Periodontal plaque diseased_379


title: Periodontal plaque diseased_387


title: Periodontal plaque diseased_378


title: Periodontal plaque diseased_372


title: Periodontal plaque diseased_374


title: Periodontal plaque diseased_375


title: Periodontal plaque diseased_376


title: Periodontal plaque diseased_373


title: Periodontal plaque diseased_371


title: Periodontal plaque diseased_365


title: Periodontal plaque diseased_363


title: Periodontal plaque diseased_364


title: Periodontal plaque diseased_370


title: Periodontal plaque diseased_369


title: Periodontal plaque diseased_368


title: Periodontal plaque diseased_366


title: Periodontal plaque diseased_367


title: Periodontal plaque diseased_362


title: Periodontal plaque diseased_361


title: Periodontal plaque diseased_360


title: Periodontal plaque diseased_359


title: Periodontal plaque diseased_358


title: Periodontal plaque diseased_357


title: Periodontal plaque diseased_356


title: Periodontal plaque diseased_355


title: Periodontal plaque diseased_354


title: Periodontal plaque diseased_352


title: Periodontal plaque diseased_351


title: Periodontal plaque diseased_349


title: Periodontal plaque diseased_346


title: Periodontal plaque diseased_348


title: Periodontal plaque diseased_350


title: Periodontal plaque diseased_344


title: Periodontal plaque diseased_345


title: Periodontal plaque diseased_347


title: Periodontal plaque diseased_340


title: Periodontal plaque diseased_342


title: Periodontal plaque diseased_343


title: Periodontal plaque diseased_339


title: Periodontal plaque diseased_341


title: Periodontal plaque diseased_336


title: Periodontal plaque diseased_337


title: Periodontal plaque diseased_333


title: Periodontal plaque diseased_330


title: Periodontal plaque diseased_332


title: Periodontal plaque diseased_338


title: Periodontal plaque diseased_329


title: Periodontal plaque diseased_335


title: Periodontal plaque diseased_334


title: Periodontal plaque diseased_328


title: Periodontal plaque diseased_327


title: Periodontal plaque diseased_331


title: Periodontal plaque diseased_324


title: Periodontal plaque diseased_326


title: Periodontal plaque diseased_323


title: Periodontal plaque diseased_322


title: Periodontal plaque diseased_325


title: Periodontal plaque diseased_321


title: Periodontal plaque diseased_319


title: Periodontal plaque diseased_318


title: Periodontal plaque diseased_320


title: Periodontal plaque diseased_315


title: Periodontal plaque diseased_317


title: Periodontal plaque diseased_314


title: Periodontal plaque diseased_313


title: Periodontal plaque diseased_308


title: Periodontal plaque diseased_310


title: Periodontal plaque diseased_312


title: Periodontal plaque diseased_311


title: Periodontal plaque diseased_307


title: Periodontal plaque diseased_304


title: Periodontal plaque diseased_309


title: Periodontal plaque diseased_306


title: Periodontal plaque diseased_303


title: Periodontal plaque diseased_302


title: Periodontal plaque diseased_305


title: Periodontal plaque diseased_301


title: Periodontal plaque diseased_300


title: Periodontal plaque diseased_298


title: Periodontal plaque diseased_299


title: Periodontal plaque diseased_316


title: Periodontal plaque diseased_297


title: Periodontal plaque diseased_294


title: Periodontal plaque diseased_295


title: Periodontal plaque diseased_296


title: Periodontal plaque diseased_293


title: Periodontal plaque diseased_290


title: Periodontal plaque diseased_291


title: Periodontal plaque diseased_289


title: Periodontal plaque diseased_288


title: Periodontal plaque diseased_286


title: Periodontal plaque diseased_287


title: Periodontal plaque diseased_285


title: Periodontal plaque diseased_284


title: Periodontal plaque diseased_277


title: Periodontal plaque diseased_279


title: Periodontal plaque diseased_282


title: Periodontal plaque diseased_276


title: Periodontal plaque diseased_280


title: Periodontal plaque diseased_292


title: Periodontal plaque diseased_275


title: Periodontal plaque diseased_274


title: Periodontal plaque diseased_271


title: Periodontal plaque diseased_272


title: Periodontal plaque diseased_270


title: Periodontal plaque diseased_269


title: Periodontal plaque diseased_267


title: Periodontal plaque diseased_266


title: Periodontal plaque diseased_265


title: Periodontal plaque diseased_283


title: Periodontal plaque diseased_281


title: Periodontal plaque diseased_278


title: Periodontal plaque diseased_273


title: Periodontal plaque diseased_264


title: Periodontal plaque diseased_263


title: Periodontal plaque diseased_262


title: Periodontal plaque diseased_261


title: Periodontal plaque diseased_259


title: Periodontal plaque diseased_260


title: Periodontal plaque diseased_268


title: Periodontal plaque diseased_258


title: Periodontal plaque diseased_256


title: Periodontal plaque diseased_255


title: Periodontal plaque diseased_254


title: Periodontal plaque diseased_252


title: Periodontal plaque diseased_251


title: Periodontal plaque diseased_250


title: Periodontal plaque diseased_249


title: Periodontal plaque diseased_245


title: Periodontal plaque diseased_244


title: Periodontal plaque diseased_247


title: Periodontal plaque diseased_243


title: Periodontal plaque diseased_242


title: Periodontal plaque diseased_241


title: Periodontal plaque diseased_257


title: Periodontal plaque diseased_240


title: Periodontal plaque diseased_253


title: Periodontal plaque diseased_239


title: Periodontal plaque diseased_238


title: Periodontal plaque diseased_248


title: Periodontal plaque diseased_237


title: Periodontal plaque diseased_236


title: Periodontal plaque diseased_246


title: Periodontal plaque diseased_235


title: Periodontal plaque diseased_234


title: Periodontal plaque diseased_233


title: Periodontal plaque diseased_232


title: Periodontal plaque diseased_230


title: Periodontal plaque diseased_227


title: Periodontal plaque diseased_228


title: Periodontal plaque diseased_229


title: Periodontal plaque diseased_225


title: Periodontal plaque diseased_226


title: Periodontal plaque diseased_224


title: Periodontal plaque diseased_223


title: Periodontal plaque diseased_222


title: Periodontal plaque diseased_221


title: Periodontal plaque diseased_220


title: Periodontal plaque diseased_219


title: Periodontal plaque diseased_218


title: Periodontal plaque diseased_217


title: Periodontal plaque diseased_216


title: Periodontal plaque diseased_214


title: Periodontal plaque diseased_215


title: Periodontal plaque diseased_231


title: Periodontal plaque diseased_211


title: Periodontal plaque diseased_213


title: Periodontal plaque diseased_210


title: Periodontal plaque diseased_209


title: Periodontal plaque diseased_212


title: Periodontal plaque diseased_205


title: Periodontal plaque diseased_204


title: Periodontal plaque diseased_207


title: Periodontal plaque diseased_208


title: Periodontal plaque diseased_203


title: Periodontal plaque diseased_202


title: Periodontal plaque diseased_201


title: Periodontal plaque diseased_198


title: Periodontal plaque diseased_199


title: Periodontal plaque diseased_200


title: Periodontal plaque diseased_197


title: Periodontal plaque diseased_195


title: Periodontal plaque diseased_193


title: Periodontal plaque diseased_191


title: Periodontal plaque diseased_192


title: Periodontal plaque diseased_190


title: Periodontal plaque diseased_189


title: Periodontal plaque diseased_188


title: Periodontal plaque diseased_206


title: Periodontal plaque diseased_186


title: Periodontal plaque diseased_187


title: Periodontal plaque diseased_185


title: Periodontal plaque diseased_184


title: Periodontal plaque diseased_183


title: Periodontal plaque diseased_182


title: Periodontal plaque diseased_181


title: Periodontal plaque diseased_196


title: Periodontal plaque diseased_180


title: Periodontal plaque diseased_179


title: Periodontal plaque diseased_178


title: Periodontal plaque diseased_177


title: Periodontal plaque diseased_194


title: Periodontal plaque diseased_174


title: Periodontal plaque diseased_176


title: Periodontal plaque diseased_175


title: Periodontal plaque diseased_171


title: Periodontal plaque diseased_168


title: Periodontal plaque diseased_167


title: Periodontal plaque diseased_165


title: Periodontal plaque diseased_164


title: Periodontal plaque diseased_162


title: Periodontal plaque diseased_161


title: Periodontal plaque diseased_160


title: Periodontal plaque diseased_173


title: Periodontal plaque diseased_172


title: Periodontal plaque diseased_170


title: Periodontal plaque diseased_159


title: Periodontal plaque diseased_157


title: Periodontal plaque diseased_158


title: Periodontal plaque diseased_169


title: Periodontal plaque diseased_156


title: Periodontal plaque diseased_154


title: Periodontal plaque diseased_155


title: Periodontal plaque diseased_151


title: Periodontal plaque diseased_153


title: Periodontal plaque diseased_152


title: Periodontal plaque diseased_150


title: Periodontal plaque diseased_149


title: Periodontal plaque diseased_148


title: Periodontal plaque diseased_147


title: Periodontal plaque diseased_166


title: Periodontal plaque diseased_163


title: Periodontal plaque diseased_146


title: Periodontal plaque diseased_145


title: Periodontal plaque diseased_141


title: Periodontal plaque diseased_143


title: Periodontal plaque diseased_138


title: Periodontal plaque diseased_137


title: Periodontal plaque diseased_140


title: Periodontal plaque diseased_132


title: Periodontal plaque diseased_130


title: Periodontal plaque diseased_135


title: Periodontal plaque diseased_129


title: Periodontal plaque diseased_144


title: Periodontal plaque diseased_131


title: Periodontal plaque diseased_125


title: Periodontal plaque diseased_124


title: Periodontal plaque diseased_126


title: Periodontal plaque diseased_136


title: Periodontal plaque diseased_128


title: Periodontal plaque diseased_134


title: Periodontal plaque diseased_133


title: Periodontal plaque diseased_120


title: Periodontal plaque diseased_123


title: Periodontal plaque diseased_118


title: Periodontal plaque diseased_127


title: Periodontal plaque diseased_122


title: Periodontal plaque diseased_121


title: Periodontal plaque diseased_117


title: Periodontal plaque diseased_119


title: Periodontal plaque diseased_142


title: Periodontal plaque diseased_139


title: Periodontal plaque diseased_112


title: Periodontal plaque diseased_115


title: Periodontal plaque diseased_111


title: Periodontal plaque diseased_106


title: Periodontal plaque diseased_105


title: Periodontal plaque diseased_107


title: Periodontal plaque diseased_104


title: Periodontal plaque diseased_114


title: Periodontal plaque diseased_116


title: Periodontal plaque diseased_113


title: Periodontal plaque diseased_102


title: Periodontal plaque diseased_101


title: Periodontal plaque diseased_94


title: Periodontal plaque diseased_110


title: Periodontal plaque diseased_108


title: Periodontal plaque diseased_109


title: Periodontal plaque diseased_90


title: Periodontal plaque diseased_89


title: Periodontal plaque diseased_88


title: Periodontal plaque diseased_99


title: Periodontal plaque diseased_98


title: Periodontal plaque diseased_97


title: Periodontal plaque diseased_100


title: Periodontal plaque diseased_95


title: Periodontal plaque diseased_93


title: Periodontal plaque diseased_86


title: Periodontal plaque diseased_103


title: Periodontal plaque diseased_92


title: Periodontal plaque diseased_96


title: Periodontal plaque diseased_77


title: Periodontal plaque diseased_91


title: Periodontal plaque diseased_82


title: Periodontal plaque diseased_87


title: Periodontal plaque diseased_73


title: Periodontal plaque diseased_72


title: Periodontal plaque diseased_70


title: Periodontal plaque diseased_79


title: Periodontal plaque diseased_81


title: Periodontal plaque diseased_83


title: Periodontal plaque diseased_67


title: Periodontal plaque diseased_76


title: Periodontal plaque diseased_74


title: Periodontal plaque diseased_71


title: Periodontal plaque diseased_84


title: Periodontal plaque diseased_69


title: Periodontal plaque diseased_68


title: Periodontal plaque diseased_65


title: Periodontal plaque diseased_62


title: Periodontal plaque diseased_63


title: Periodontal plaque diseased_61


title: Periodontal plaque diseased_59


title: Periodontal plaque diseased_85


title: Periodontal plaque diseased_58


title: Periodontal plaque diseased_66


title: Periodontal plaque diseased_54


title: Periodontal plaque diseased_75


title: Periodontal plaque diseased_60


title: Periodontal plaque diseased_56


title: Periodontal plaque diseased_57


title: Periodontal plaque diseased_52


title: Periodontal plaque diseased_64


title: Periodontal plaque diseased_53


title: Periodontal plaque diseased_49


title: Periodontal plaque diseased_48


title: Periodontal plaque diseased_46


title: Periodontal plaque diseased_51


title: Periodontal plaque diseased_41


title: Periodontal plaque diseased_45


title: Periodontal plaque diseased_42


title: Periodontal plaque diseased_47


title: Periodontal plaque diseased_441


title: Periodontal plaque diseased_43


title: Periodontal plaque diseased_44


title: Periodontal plaque diseased_39


title: Periodontal plaque diseased_50


title: Periodontal plaque diseased_38


title: Periodontal plaque diseased_35


title: Periodontal plaque diseased_37


title: Periodontal plaque diseased_40


title: Periodontal plaque diseased_34


title: Periodontal plaque diseased_55


title: Periodontal plaque diseased_36


title: Periodontal plaque diseased_32


title: Periodontal plaque diseased_33


title: Periodontal plaque diseased_27


title: Periodontal plaque diseased_28


title: Periodontal plaque diseased_26


title: Periodontal plaque diseased_25


title: Periodontal plaque diseased_31


title: Periodontal plaque diseased_22


title: Periodontal plaque diseased_23


title: Periodontal plaque diseased_21


title: Periodontal plaque diseased_20


title: Periodontal plaque diseased_18


title: Periodontal plaque diseased_12


title: Periodontal plaque diseased_16


title: Periodontal plaque diseased_15


title: Periodontal plaque diseased_14


title: Periodontal plaque diseased_24


title: Periodontal plaque diseased_13


title: Periodontal plaque diseased_17


title: Periodontal plaque diseased_8


title: Periodontal plaque diseased_11


title: Periodontal plaque diseased_6


title: Periodontal plaque diseased_10


title: Periodontal plaque diseased_3


title: Periodontal plaque healthy_9C

value: healthy


title: Periodontal plaque healthy_99C


title: Periodontal plaque healthy_98C


title: Periodontal plaque diseased_2


title: Periodontal plaque diseased_4


title: Periodontal plaque healthy_97C


title: Periodontal plaque healthy_94C


title: Periodontal plaque diseased_1


title: Periodontal plaque healthy_92C


title: Periodontal plaque healthy_90C


title: Periodontal plaque healthy_91C


title: Periodontal plaque healthy_88C


title: Periodontal plaque healthy_85C


title: Periodontal plaque healthy_86C


title: Periodontal plaque healthy_87C


title: Periodontal plaque healthy_83C


title: Periodontal plaque healthy_84C


title: Periodontal plaque healthy_82C


title: Periodontal plaque healthy_78C


title: Periodontal plaque healthy_81C


title: Periodontal plaque healthy_79C


title: Periodontal plaque healthy_72C


title: Periodontal plaque healthy_77C


title: Periodontal plaque healthy_76C


title: Periodontal plaque healthy_74C


title: Periodontal plaque healthy_6C


title: Periodontal plaque healthy_75C


title: Periodontal plaque healthy_67C


title: Periodontal plaque healthy_63C


title: Periodontal plaque healthy_73C


title: Periodontal plaque healthy_68C


title: Periodontal plaque healthy_70C


title: Periodontal plaque healthy_64C


title: Periodontal plaque healthy_71C


title: Periodontal plaque healthy_69C


title: Periodontal plaque healthy_93C


title: Periodontal plaque healthy_62C


title: Periodontal plaque healthy_65C


title: Periodontal plaque healthy_66C


title: Periodontal plaque healthy_60C


title: Periodontal plaque healthy_61C


title: Periodontal plaque healthy_5C


title: Periodontal plaque healthy_58C


title: Periodontal plaque healthy_57C


title: Periodontal plaque healthy_56C


title: Periodontal plaque healthy_53C


title: Periodontal plaque healthy_54C


title: Periodontal plaque healthy_55C


title: Periodontal plaque healthy_49C


title: Periodontal plaque healthy_52C


title: Periodontal plaque healthy_50C


title: Periodontal plaque healthy_4C


title: Periodontal plaque healthy_51C


title: Periodontal plaque healthy_43C


title: Periodontal plaque healthy_42C


title: Periodontal plaque healthy_40C


title: Periodontal plaque healthy_3C


title: Periodontal plaque healthy_39C


title: Periodontal plaque healthy_44C


title: Periodontal plaque healthy_38C


title: Periodontal plaque healthy_59C


title: Periodontal plaque healthy_35C


title: Periodontal plaque healthy_34C


title: Periodontal plaque healthy_47C


title: Periodontal plaque healthy_36C


title: Periodontal plaque healthy_37C


title: Periodontal plaque healthy_46C


title: Periodontal plaque healthy_48C


title: Periodontal plaque healthy_45C


title: Periodontal plaque healthy_41C


title: Periodontal plaque healthy_31C


title: Periodontal plaque healthy_2C


title: Periodontal plaque healthy_30C


title: Periodontal plaque healthy_28C


title: Periodontal plaque healthy_27C


title: Periodontal plaque healthy_25C


title: VPA 2, 4hrs

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra campus

country: Israel

institute: The Hebrew University of Jerusalem

description: Replicate 2 of 2.

hyb_protocol: According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

scan_protocol: GeneChip Scanner 3000 7G according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

data_processing: RMA signal intensity calculation using Affymetrix Expression Console, version 1.1.

source_name: E14 embryonic stem cells, VPA

growth_protocol: Cells were grown on mitomycin-C-treated primary embryonic fibroblasts, with ES cell medium with 15% FBS and leukemia inhibitory factor.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: 0.5mM VPA was added to the cell medium in the indicated samples for 4 hrs.

value: embryonic stem cells (ESCs)

value: valproic acid (VPA)

tag: treatment time

value: 4 hours


title: Periodontal plaque healthy_24C


title: Periodontal plaque healthy_33C


title: Periodontal plaque healthy_26C


title: Periodontal plaque healthy_32C


title: Control 2, 4hrs

description: Replicate 2 of 2.

source_name: E14 embryonic stem cells, untreated

label_protocol: According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

tag: treatment

value: untreated


title: Periodontal plaque healthy_23C


title: Control 1, 4hrs

description: Replicate 1 of 2.

tag: cell line


title: NaBu 2, 16hrs

description: Replicate 2 of 2.

source_name: E14 embryonic stem cells, NaBu

treatment_protocol: 0.5mM VPA or 0.2mM NaBu were added to the cell medium in the indicated samples for 16 hrs.

value: sodium butyrate (NaBu)

value: 16 hours


title: NaBu 1, 16hrs

description: Replicate 1 of 2.


title: Control 2, 16hrs

description: Replicate 2 of 2.


title: Periodontal plaque healthy_29C


title: VPA 1, 4hrs

description: Replicate 1 of 2.


title: Periodontal plaque healthy_22C


title: Control 1, 16hrs

description: Replicate 1 of 2.


title: VPA 2, 16hrs

description: Replicate 2 of 2.


title: H7_BMP4_day12_rep2

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

hyb_protocol: Microarrays were hybridized, washed and stained according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

scan_protocol: Te scan protocol was according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: Bioinformatic statistical analysis was performed using Bioconductor functions (http://www.bioconductor.org/) in R software (http://www.r-project.org/). To remove all possible sources of variation of nonbiological origin between arrays, data were normalized using the RMA normalization function implemented in the Bioconductor affylmGUI package (http://www.bioconductor.org/packages/2.0/bioc/html/affylmGUI.html). Then, we selected those probes with known gene symbol identities, and the values corresponding to redundant symbols were averaged. Statistically significant differences between groups were identified using the nonparametric test implemented in the RankProd software (http://www.bioconductor.org/packages/2.2/bioc/html/RankProd.html). Functional annotations were carried out using Ingenuity (http://www.ingenuity.com/) software, where gene symbols and fold change of the up- and down-regulated genes were imported.

source_name: cell line H7 with BMP4 in day 12

label_protocol: Briefly, for each sample, 100 ng of total RNA was retrotranscripted to cDNA by using 500 ng of T7-(N6) primers and SuperScript II. A second strand of DNA was generated by using the DNA polymerase enzyme, followed by an overnight in vitro transcription to generate cRNA. After samples were processed using cRNA cleanup spin columns, 10 lg of cRNA was retrotranscripted using random primers and SuperScript II. Mixtures were digested with RNase H, and the cDNA was purified using cDNA cleanup spin columns. Finally, 5.5 lg of sense cDNA was fragmented and labeled using the GeneChip WT terminal labeling kit (Affymetrix).

extract_protocol:
Total RNA was extracted from cells by using the TRIzol method according to the protocol recommended by the manufacturer (Life Technologies, Inc.).
The purified total RNA was stored at -80ºC until cells from all time points were collected. RNA was quantified by spectrophotometry, and its quality was assessed using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Only samples with an RNA integrity number of .8.0 were used for microarray analysis.

value: hESCs

tag: feeder

value: on irradiated mouse embryonic fibroblast (MEF) feeders


title: Periodontal plaque healthy_21C


title: Periodontal plaque healthy_20C


title: Periodontal plaque healthy_1C


title: Periodontal plaque healthy_18C


title: Periodontal plaque healthy_17C


title: H7_BMP4_day12_rep3


title: H7_BMP4_day10_rep3

source_name: cell line H7 with BMP4 in day 10


title: Periodontal plaque healthy_12C


title: Periodontal plaque healthy_13C


title: H7_BMP4_day12_rep1


title: H7_BMP4_day10_rep1


title: Normal Progress 3

city: Dublin

first: Donal

last: Brennan

address: Holles Street

department: UCD School of Medicine, National Maternity Hospital

country: Ireland

institute: University College Dublin

description: Gene expression data from non-dystocic myometrium

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The affy package in R/Bioconductor was used. These data are normalised used RMA

source_name: Normal Progress 3

label_protocol: standard Affymetrix procedures

extract_protocol: Surgically isolated myometrial were immediately placed in RNALater and subseqently frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

value: myometrial biopsies

tag: Sex

value: female


title: H7_BMP4_day8_rep3

source_name: cell line H7 with BMP4 in day 8


title: Periodontal plaque healthy_11C


title: H7_BMP4_day8_rep2


title: H7_BMP4_day6_rep1

source_name: cell line H7 with BMP4 in day 6


title: Normal Progress 2

source_name: Normal Progress 2


title: Normal Progress 4

source_name: Normal Progress 4


title: H7_BMP4_day8_rep1


title: H7_BMP4_day6_rep2


title: Normal Progress 1

source_name: Normal Progress 1


title: H7_BMP4_day10_rep2


title: H7_BMP4_day4_rep2

source_name: cell line H7 with BMP4 in day 4


title: VPA 1, 16hrs

description: Replicate 1 of 2.


title: Periodontal plaque healthy_10C


title: H7_BMP4_day4_rep1


title: H7_BMP4_day2_rep1

source_name: cell line H7 with BMP4 in day 2


title: Dystocia 3

description: Gene expression data from dystocic myometrium

source_name: Dystocia 3


title: Periodontal plaque healthy_100C


title: Dystocia 2

source_name: Dystocia 2


title: H7_BMP4_day4_rep3


title: H7_BMP4_day6_rep3


title: Dystocia 4

source_name: Dystocia 4


title: H7_BMP4_day2_rep3


title: H7_BMP4_day2_rep2


title: Dystocia 1

source_name: Dystocia 1


title: H7_BMP4_day0_rep3

source_name: cell line H7 with BMP4 in day 0


title: H7_BMP4_day0_rep1


title: H7_BMP4_day0_rep2


title: U-2 OS cell line

status: Public on Sep 16 2011

city: Xiamen

first: Long

middle: Ji

last: Liu

address: 59# Daxue Road

country: China

institute: NEAU

hyb_protocol: The final synthesized biotinylated cDNAs were hybridized to Affymetrix GeneChip® U133A 2.0 arrays following the protocol strictly.

scan_protocol: Arrays were scanned with the Affymetrix scanner 3000.

data_processing: Data analysis was performed by Microarray Suite 5.0 after pre-standard procedure.

molecule: polyA RNA

source_name: U-2 OS cell line

label_protocol: Per manufacturer's instructions.

growth_protocol: All cells used were kept in exponential phase of growth.

extract_protocol: Total RNA was extracted using the RNeasy Total RNA Isolation kit (QIAGEN). The quality and purity of the products were controlled by Agilent 2100.

value: U-2 OS

value: osteosarcoma cells


title: N2 vs. mir-243_Replicate1_dye swap

city: Utrecht

first: Rene

last: Ketting

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Biological replicate 1 of 3 - dye-swap.

hyb_protocol: Samples were hybridized to Agilent C. elegans whole genome arrays at 65ºC overnight.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Txt files were then analyzed by the GeneSpring software.

organism: Caenorhabditis elegans

label_protocol: 500 ng of RNA samples from wild-type and mir-243 young-adult worms were reverse-transcribed with random primers. Each cDNA sample was split and labeled with both Cy3 and Cy5.

growth_protocol: Nematodes were cultured according to standard procedures. The Bristol strain N2 was used as the standard wild-type strain.

extract_protocol: RNA from nematodes were isolated using Trizol LS (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: The mir-243 allele used in this study was n4759.

tag: strain

tag: genotype

value: wild-type

tag: developmental stage

value: young adult

source_name: mir-243 mutant

value: mir-243 mutant


title: N2 vs. mir-243_Replicate2_dye swap

description: Biological replicate 2 of 3 - dye-swap.


title: N2 vs. mir-243_Replicate3

description: Biological replicate 3 of 3.


title: MG-63 cell line

source_name: MG-63 cell line


title: SaoS-2 cell line

source_name: SaoS-2 cell line


title: HFOB1 cell line

source_name: osteoblastic control cell line HFOB1

value: osteoblastic cells


title: N2 vs. mir-243_Replicate3_dye swap

description: Biological replicate 3 of 3 - dye-swap.


title: N2 vs. mir-243_Replicate2

description: Biological replicate 2 of 3.


title: ASD LCL_HI3144_Propanol-treated

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

hyb_protocol: For two-color cDNA microarray analyses, each sample and the reference RNA were co-hybridized onto a TIGR 40K cDNA microarray.

scan_protocol: After hybridization, each microarray was washed and scanned for fluorescence signals using a GenePix 4000B laser scanner (Molecular Devices).

data_processing: The raw intensity data were obtained using TIGR Spotfinder software, then normalized and filtered using the Lowess normalization and standard deviation (variance) regularization programs contained within TIGR MIDAS software. Prior to and following normalization and filtering of microarray data, LOWESS plots were visually inspected for skewness and artifacts.

source_name: LCL from individual with ASD, treated with propanol

label_protocol: Fluorescently labeled cDNA was obtained by incorporation of amino-allyl dUTP during first-strand synthesis, followed by coupling to the ester of Cyanine (Cy)-3 as previously described by Hu and colleagues (2006). Strategene Universal human reference RNA was used as a common reference RNA sample for all hybridizations where the reference cDNA was labeled with Cy-5 dye, allowing for comparisons of gene expression profiles across all samples.

growth_protocol: Lymphoblastoid cell lines (LCLs) derived from peripheral lymphocytes of 10 males (5 individuals with autism and 5 unaffected siblings) were obtained from the Autism Genetic Resource Exchange (AGRE, Los Angeles, CA) and kept in liquid nitrogen until used. All LCLs were established and maintained by the Cell Repository of the Department of Genetics at Rutgers University under contract from AGRE. The frozen cells were subcultured in RPMI 1640 (Mediatech Inc., Herndon, VA) supplemented with 15% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA) and 1% penicillin-streptomycin (Mediatech).

extract_protocol: Total RNA was isolated from LCLs using TRIzol reagent (Invitrogen, CA) and purified using RNeasy Mini Kit (Qiagen) according to the manufacturers' protocols. The concentration and purity of total RNA were measured with a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer was used to determine RNA integrity.

treatment_protocol: Propionic acid (PPA) and 1-propanol (Fisher Scientific) were each diluted with appropriate complete growth medium to 10mM. An equal volume of PBS was diluted in the same manner as PPA. Non-ASD LCLs were treated with PBS, propanol, or PPA. LCLs from individuals with ASD were treated with PBS or propanol.

value: lymphoblastoid cell

value: ASD

tag: agent

value: propanol

tag: gender

value: Male

tag: agre blood id

source_name: Universal human RNA

tag: supplier

value: Stratagene, USA


title: ASD LCL_HI2769_Propanol-treated

tag: cell type


title: ASD LCL_HI3144_PBS-treated

source_name: LCL from individual with ASD, treated with PBS

value: PBS


title: ASD LCL_HI2044_Propanol-treated


title: N2 vs. mir-243_Replicate1

description: Biological replicate 1 of 3.


title: LjMyb14 overexpressing line 3

city: Fredriksberg

first: Dale

last: Shelton

address: Thorvaldsensvej 40

department: Dept. Plant Biology and Biotechnology

country: Denmark

institute: University of Copenhagen

description: Transgenic Lotus japonicus MG20 leaf

hyb_protocol: The fragmentation mixture and hybridized to Agilent custom oligo array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then 10 sec in acetonitrile and allowed to air dry.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8 x 15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.7.3.1 (Agilent) using default parameters (protocol GE1_107_sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Lotus japonicus

source_name: LjMyb14 overexpressing line

label_protocol: 200ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

growth_protocol: Lotus japonicus (MG20) plants were grown in vitro on 1/2 MS media.

extract_protocol: RNA was extract from material frozen in liquid nitrogen using the Qiagen Rneasy plant kit and including the optional on-column Dnase treatment as per the manufacturer's instruction.

tag: germplasm

value: LjMyb14 overexpressing

tag: tissue

value: leaf


title: LjMyb14 overexpressing line 2

description: Transgenic Lotus japonicus MG20 leaf


title: ASD LCL_HI4360_PBS-treated


title: ASD LCL_HI0777_Propanol-treated


title: ASD LCL_HI2769_PBS-treated


title: ASD LCL_HI4360_Propanol-treated


title: Wild type leaf_3

description: Wild-type Lotus japonicus MG20 leaf

source_name: Wild type leaf

value: wild type


title: LjMyb14 overexpressing line 1

description: Transgenic Lotus japonicus MG20 leaf


title: ASD LCL_HI2044_PBS-treated


title: non-ASD LCL_HI0779_PPA-treated

source_name: LCL from non-ASD individual, treated with PPA

value: non-ASD

value: PPA


title: Wild type leaf_2

description: Wild-type Lotus japonicus MG20 leaf


title: non-ASD LCL_HI3914_PPA-treated


title: non-ASD LCL_HI2022_PPA-treated


title: non-ASD LCL_HI2772_PPA-treated


title: Wild type leaf_1

description: Wild-type Lotus japonicus MG20 leaf


title: non-ASD LCL_HI3143_PPA-treated


title: non-ASD LCL_HI2022_Propanol-treated

source_name: LCL from non-ASD individual, treated with propanol


title: LotusLeaf_6hr_rep3

description: Gene induction after elicitation with 10mM glutathione

source_name: Lotus MG20 Leaf, GSH elicited, 6hrs

label_protocol: 200ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. .

growth_protocol: Lotus japonicus (MG20) plants were grown under glasshouse conditions.

extract_protocol: RNA was extract from material frozen in liquid nitrogen using the Qiagen Rneasy plant kit and including the optional on-column Dnase treatment as per the manufacturer's instruction

treatment_protocol: Mature leaves of MG20 where removed from the plant and submerged in a solution of 10mM GSH and shaken (200rpm) at 28 degrees celcius for the stated elicitation period.

value: Leaf

tag: response

value: GSH elicited

tag: time


title: MCF-7 cell_tRA-H_12hr_biological rep1

city: Columbus

first: Sissy

last: Jhiang

address: 1645 Neil Ave

department: Physiology and Cell Biology

institute: The Ohio State University

hyb_protocol: 15ug of labeled and fragmented cRNA was hybridized at 45 C for 16 hours at 60rpm. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 according to Affymetrix protocol.

scan_protocol: Raw data was generated with Affymetrix GeneChip Operating Software on a Human Genome U133 plus 2.0 Affymetrix platform.  Briefly, gene chips were scanned with the Affymetrix GeneChip Scanner 3000 7G for data generation and Affymetrix AGCC software and Expression Console was used for data processing.

data_processing: Background correction and normalization was performed and gene expression level was summarized over probes using the RMA method. A filtering method based on the percentage of samples with expression value above noise level was applied to filter out probe-sets with little or no expression. Generalized linear models were used to detect differentially expressed genes between DMSO-, tRA- or tRA/H-treated MCF-7 cells.  In order to improve the estimates of variability and statistical tests for differential expression, a variance shrinkage method was employed. The differentially expressed genes were claimed based on the p-values by controlling the average number of false positives at 1 over all the tested probe sets. Fold changes of at least 1.5 were used to further reduce the list of significant probe-sets after controlling the number of false positives.

label_protocol: Biotinylated-cRNA was generated from 2 ug of RNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual.

growth_protocol: MCF-7 human breast cancer cells were maintained in a 1:1 ratio of DMEM and Ham’s F-12 media (Gibco), 10% FBS (Invitrogen) and 1% penicillin/streptomycin.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen) and chloroform (Sigma).  RNA integrity and quantity were determined by the Agilent Bioanalyzer 2100 by the MicroArray Shared Resource (MASR) for the OSU Comprehensive Cancer Center (OSUCCC).

treatment_protocol: MCF-7 cells were treated with DMSO vehicle, tRA, or tRA/H for 12 hours

value: Breast Cancer Cells


title: MCF-7 cell_tRA-H_12hr_biological rep2


title: non-ASD LCL_HI0779_Propanol-treated

tag: disease state


title: MCF-7 cell_DMSO_12hr_biological rep2


title: LotusLeaf_6hr_rep2


title: non-ASD LCL_HI3143_Propanol-treated


title: non-ASD LCL_HI2772_Propanol-treated


title: LotusLeaf_3hr_rep3

source_name: Lotus MG20 Leaf, GSH elicited, 3 hrs


title: non-ASD LCL_HI3914_PBS-treated

source_name: LCL from non-ASD individual, treated with PBS


title: LotusLeaf_6hr_rep1


title: MCF-7 cell_tRA_12hr_biological rep1

source_name: MCF-7_trans-retinoic acid_12hr


title: non-ASD LCL_HI3143_PBS-treated


title: MCF-7 cell_tRA_12hr_biological rep2


title: non-ASD LCL_HI2772_PBS-treated


title: 10^-6M BPA treatment, rep 2 (expression)

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2. 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: RMA normalization using the Bioconductor 'affy' package.

source_name: normal breast epithelium, 10^-6M BPA

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: Standard conditions (37°C and 5% CO2 until confluent).

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

treatment_protocol: 10^-6M BPA continuously for two weeks.

tag: treatment

value: bisphenol A (BPA)

tag: treatment dosage


title: 10^-5M BPA treatment, rep 4 (expression)

source_name: normal breast epithelium, 10^-5M BPA

treatment_protocol: 10^-5M BPA continuously for two weeks.

tag: cell line


title: 10^-5M BPA treatment, rep 3 (expression)


title: 10^-5M BPA treatment, rep 2 (expression)


title: LotusLeaf_3hr_rep1


title: MCF-7 cell_DMSO_12hr_biological rep1


title: non-ASD LCL_HI2022_PBS-treated


title: 10^-6M BPA treatment, rep 1 (expression)


title: Control, rep 2 (expression)

source_name: normal breast epithelium, control

treatment_protocol: DMSO

value: DMSO


title: LotusLeaf_3hr_rep2


title: 5-chloro-8-hydroxyquinoline treated rep2

city: Changchun

first: Lu

address: Xi'an Road 5333

institute: Jilin university

description: Biological replicate 2 of 2. DMSO or 5-chloro-8-hydroxyquinoline treated, harvested after several passages.

hyb_protocol: The samples were hybridized with Agilent whole genome oligo microarray,performed by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) in Agilent’s SureHyb Hybridization Chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mycobacterium tuberculosis

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, 5-chloro-8-hydroxyquinoline stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

source_name: M. tuberculosis_DMSO


title: Control, rep 1 (expression)


title: 10^-5M BPA treatment, rep 1 (expression)


title: LotusLeaf_0hr_rep2

source_name: Lotus MG20 Leaf, Unelicited

value: unelicited


title: LotusLeaf_0hr_rep3


title: non-ASD LCL_HI0779_PBS-treated

value: lymphoblastoid cell


title: 04_FSBS_MLL-RA

city: Riverside

first: Frank

last: Sauer

state: California

address: 2202A Genomics Building

department: Biochemistry

institute: University of California Riverside

description:
MLL1 RNA-chip vs mock RNA chip, arrayF
test: 03_FSBS_MLLRA-2.CEL
ctrl: 04_FSBS_MLLRA-C2.CEL

hyb_protocol: Approximately 2 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The  arrays were hybridized for 16 hours at 45° at 60rpm by using an Affymetrix hybridization oven. Hybridization, washing, and staining,  were performed using the Affymetrix GeneChip Workstation according to the manufacturer’s instructions (GeneChip®Expression Analysis; Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 with upgrade for tiling arrays.

data_processing:
Data normalization, background subtraction, and peak detection of the arrays was conducted using Model-based Analysis of Tiling-array (MAT) software (Johnson et al., 2006) and mouse genome version 8 (February, 2006) as a reference sequence (NCBI36/mm8). Peaks with a p-value of ≥10-4 were considered to be significant. Processed peak data was extracted using a custom Perl script.
esc_plusRAvsMock_undif_RAmin.bed,esc_undifvsmock_minRA_plusRA.Mm35b_P06R_v02-1_NCBIv36.NR.bpmap_matscore.bar
bed and bar file shows the association of Mira with MLL1 in +RA CJ7 cells, the analysis was ln(01_FSBS_MLLRA+2.CEL - (02_FSBS_MLLRA+C2.CEL +05_FSBS_MLLU2.CEL +03_FSBS_MLLRA-2.CEL)) the relevant peaks are described in the paper.

source_name: MLL1 RNA-ChIP RNA from differentiating CJ7 mESCs

label_protocol: Samples (7.5 μg of double-stranded DNA) were fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

growth_protocol: CJ7 mouse embryonic stem cells (mESCs) were maintained under feeder-free cell conditions as described (Sato et al., 2004) using KnockoutTM Dulbecco's Modified Eagle's Medium (KnockoutTM DMEM) supplemented with 15% fetal bovine serum (FBS), 2 mM L-Glutamine, 0.1 mM MEM non-essential amino acids, 0.1 U/ml penicillin, 0.1 μg/ml streptomycin, 0.55 mM β-mercaptoethanol, and 1,000 U/ml of ESGRO® Leukemia Inhibitory Factor (LIF). Cells were maintained in culture plates coated with 0.1% of gelatin from porcine skin, type A (Sigma).

extract_protocol: ChIP using native chromatin was performed as described (Sanchez-Elsner et al., 2006; Bertani et al., 2008), except that native chromatin was isolated from 1x108 -RA, control, and +RA CJ7 mESCs and all buffers were supplemented with RNase inhibitor (1,000 U/ml). Chromatin was immunoprecipitated with 10 µg antibody to Mll1 or 10 µg rabbit serum (mock). Immunoprecipitated RNA was purified with Trizol and reverse transcribed with Superscript II and random hexamers. The cDNA libraries were amplified using the GenomePLex Whole Genome Amplification kit with 10X Amp Mix (Sigma; WGA1), according the manufacturer’s instructions.

treatment_protocol: For differentiation assays, 2x107 mESCs were cultivated in 8.5 cm plastic dishes in differentiation medium [KnockoutTM DMEM containing 15% FBS, 2 mM of L-glutamine, 0.1 mM MEM non-essential amino acids, 0.1 U/ml penicillin, and 0.1 μg/ml streptomycin], which lacked (differentiating mESCs) or contained (+RA mESCs) 10-6 M (final concentration) RA.

value: CJ7 embryonic stem cells

value: embryo

tag: antibody

value: MLL1 polyclonal antibody

tag: antibody vendor

value: Bethyl Laboratories

tag: antibody catalog number

tag: antibody lot/batch number

source_name: RNA-ChIP RNA from -RA-Control CJ7 mESCs

value: rabbit serum


title: 05_FSBS_MLLU

description:
MLL1 RNA-chip vs mock RNA chip, arrayF
test: 05_FSBS_MLLU2.CEL
ctrl: 06_FSBS_MLLUC2.CEL

source_name: MLL1 RNA-ChIP RNA from -RA CJ7 mESCs

tag: strain

tag: developmental stage

source_name: RNA-ChIP RNA from U-Control CJ7 mESCs


title: LotusLeaf_0hr_rep1


title: LotusLeaf_0hr_rep4


title: 01_FSBS_MLL+RA

description:
MLL1 RNA-chip vs mock RNA chip, arrayF
test: 01_FSBS_MLLRA+2.CEL
ctrl: 02_FSBS_MLLRA+C2.CEL

source_name: MLL1 RNA-ChIP RNA from +RA CJ7 mESCs

source_name: RNA-ChIP RNA from +RA-Control CJ7 mESCs

value: rabbit whole serum


title: 5-chloro-8-hydroxyquinoline treated rep1

description: Biological replicate 1 of 2. DMSO or 5-chloro-8-hydroxyquinoline treated, harvested after several passages.


title: Allopolyploid_0min_120min_rep2-1

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description: Arabidopsis Allotetraploid is a synthetic allotetraploid. It was generated by crossing between Arabidopsis thaliana tetraploid and Arabidopsis arenosa tetraploid

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled targets were combined, dried by speed-vac centrifugation and dissolved in 75 µl of hybridization buffer (3.2 X SSC, 0.27% SDS, and 1% BSA). Hybridization solution was pipetted onto the microarray slide. A cover slip was gently applied to make solution spread evenly over the entire spot matrix. The hybridization assembly was sealed in a humidified hybridization chamber (company name) and submerged in 65oC for 18 to 20 hours. Following hybridization, the slide was washed at room temperature sequentially with 2x SSC plus 0.2% SDS (4 min), 0.2x SSC (2 min), 0.2x SSC (2 min), and 0.05x SSC (4 min).

scan_protocol: Microarrays were scanned at 635nm and 532nm using the Genepix 4000B scanner. Scan image was acquired and processed by the GenePix Pro 4.1.

data_processing: Acuity 4.0 software (Molecular Devices, http://www.moleculardevices.com).Quantified values in each dataset were analyzed by t-test. If at least one of the comparisons showed a statistical significance level of α=0.001, the dataset was selected.

organism: Arabidopsis

source_name: Allo 0 min Cy5

label_protocol: Isolated mRNA was reverse-transcribed to synthesize cDNA using Cy5- labled dCTPs (Amersham Biosciences)

extract_protocol: Total RNA was isolated using Plant RNA reagent (Invitrogen). Each RNA sample was quantified by measuring the 260/280 ratio using Nano drop and by agarose-formaldehyde gel electrophoresis. Quantified total RNA was subjected to mRNA isolation by Micro-fast Track 2.0 mRNA isolation kit (Invitrogen).

tag: genotype/variation

value: Arabidopsis Allotetraploid

tag: age

value: 2 weeks

value: seedling

value: transcription inhibitor (Cordycepin)

tag: harvest time

value: 0 min after treatment treatment

source_name: Allo 120 min Cy3

label_protocol: Isolated mRNA was reverse-transcribed to synthesize cDNA using Cy3- labled dCTPs (Amersham Biosciences)

value: 120 min after treatment treatment


title: Allopolyploid_0min_120min_rep2-4

source_name: Allo 0 min Cy3

source_name: Allo 120 min Cy5


title: Allopolyploid_0min_120min_rep1-3


title: Allopolyploid_0min_120min_rep2-2


title: Allopolyploid_0min_120min_rep2-3


title: Allopolyploid_0min_120min_rep1-2


title: Allopolyploid_0min_120min_rep1-4


title: Allopolyploid_0min_120min_rep1-1


title: CHOP6449

status: Public on Sep 15 2011

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

label: C-Bio and A-DNP

source_name: Tumor DNA

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP6393

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: CHOP2963

data_processing: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: CHOP6448

label_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: CHOP2971


title: CHOP2967


title: CHOP2973


title: CHOP6450


title: CHOP2968


title: CHOP2960


title: CHOP2972


title: CHOP2936


title: CHOP2966


title: CHOP2969


title: CHOP2970


title: EN13 iPSC Line (B2) [SNP]

city: London

first: Jonathan

middle: H

last: Teichroeb

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

institute: University of Western Ontario

description: C and G nucleotides biotin-labeled; A and T nucleotides dinitrophenyl labeled

hyb_protocol: Standard protocols (Infinium® HD Assay Super Protocol Guide Part # 11322427 Rev. B)  (hybridization to beadchip, washing, extension, and staining)

scan_protocol: Standard protocol for Illumina iScan system

data_processing: SNP genotype calls were made using the default parameters in Genome Studio and CNV calls were made using the default parameters of the CNV partition plugin in Genome Studio.

source_name: reprogrammed from EN13, Isogenic with H9

label_protocol: Standard protocols (Infinium® HD Assay Super Protocol Guide Part # 11322427 Rev. B) (whole genome amplification, fragmentation, precipitation and re-suspension of DNA)

growth_protocol: See Spontaneous reversal of the developmental aging of normal human cells following transcriptional reprogramming, H Vaziri, KB Chapman, A Guigova, J Teichroeb, et al., Regenerative Medicine 2010 5:3, 345-363. Also see:  Suppression of the imprinted gene NNAT and X-chromosome gene activation in isogenic human iPS cells, J.H. Teichroeb, D.H. Betts, H. Vaziri., Plos ONE

extract_protocol: DNA extracted using SDS lysis buffer with phenol-chloroform extraction

tag: passage

value: isogenic hiPSC


title: CHOP6447


title: CHOP2952


title: CHOP2937


title: CHOP2959


title: CHOP2962


title: CHOP2961


title: CHOP2957


title: EN13 iPSC Line (EH3) [SNP]

tag: cell line


title: CHOP2953


title: Human Embryonic Stem Cell Line (H9) [SNP]

source_name: Human Embryo ICM

value: hESC


title: CHOP2958


title: EN13 iPSC Line (EH1) [SNP]


title: EN13 iPSC Line (EH6A) [SNP]


title: CHOP2955


title: CHOP2949


title: CHOP2947


title: CHOP2941


title: CHOP2950


title: CHOP2951


title: CHOP3728


title: CHOP2948


title: CHOP2942


title: Mortal Splanchnopleuric Mesoderm (EN13) [SNP]

source_name: Differentiated from H9, Isogenic with H9

value: isogenic mortal H9


title: CHOP3944


title: CHOP2354


title: CHOP3753


title: CHOP1261


title: CHOP2199


title: CHOP2945


title: CHOP2198


title: CHOP1155


title: CHOP3538


title: CHOP3382


title: CHOP2205


title: CHOP3440


title: CHOP1849


title: CHOP2350


title: CHOP2943


title: CHOP2940


title: CHOP1042


title: CHOP0501


title: CHOP2003


title: CHOP1938


title: CHOP1940


title: CHOP1913


title: CHOP1933


title: CHOP1931


title: CHOP1907


title: CHOP1891


title: CHOP1858


title: CHOP1847


title: CHOP1867


title: CHOP1930


title: CHOP1920


title: CHOP1744


title: CHOP1844


title: CHOP1798


title: CHOP1823


title: CHOP1878


title: CHOP1749


title: CHOP1838


title: CHOP1851


title: CHOP1848


title: CHOP1864


title: CHOP1906


title: CHOP1894


title: CHOP1736


title: CHOP1716


title: CHOP1881


title: CHOP1904


title: CHOP1796


title: CHOP1853


title: CHOP1729


title: CHOP1720


title: CHOP1691


title: CHOP1702


title: CHOP1701


title: CHOP1713


title: CHOP1698


title: CHOP1645


title: CHOP1705


title: CHOP1695


title: CHOP1647


title: CHOP1683


title: CHOP1661


title: CHOP1640


title: CHOP1734


title: CHOP1673


title: CHOP1642


title: CHOP1672


title: CHOP1678


title: CHOP1659


title: CHOP1667


title: CHOP1643


title: CHOP1638


title: CHOP1633


title: CHOP1613


title: CHOP1639


title: CHOP1603


title: CHOP1669


title: CHOP1719


title: CHOP1634


title: CHOP1598


title: CHOP1596


title: CHOP1595


title: CHOP1555


title: CHOP1592


title: CHOP1557


title: CHOP1510


title: CHOP1636


title: CHOP1562


title: CHOP1589


title: CHOP1506


title: CHOP1512


title: CHOP1499


title: CHOP1551


title: CHOP1513


title: CHOP1497


title: CHOP1501


title: CHOP1552


title: CHOP1492


title: CHOP1491


title: CHOP1601


title: CHOP1577


title: CHOP1468


title: CHOP1599


title: CHOP1480


title: CHOP1456


title: CHOP1591


title: CHOP1446


title: CHOP1467


title: CHOP1488


title: CHOP1463


title: CHOP1433


title: CHOP1415


title: CHOP1437


title: CHOP1393


title: CHOP1439


title: CHOP1386


title: CHOP1413


title: CHOP1395


title: CHOP1382


title: CHOP1417


title: CHOP1366


title: CHOP1379


title: CHOP1396


title: CHOP1378


title: CHOP1384


title: CHOP1368


title: CHOP1369


title: CHOP1414


title: CHOP1388


title: CHOP1365


title: CHOP1360


title: CHOP1353


title: CHOP1354


title: CHOP1347


title: CHOP1349


title: CHOP1375


title: CHOP1344


title: CHOP1322


title: CHOP1340


title: CHOP1460


title: CHOP1326


title: CHOP1337


title: CHOP1323


title: CHOP1318


title: CHOP1302


title: CHOP1317


title: CHOP1341


title: CHOP1319


title: CHOP1315


title: CHOP1310


title: CHOP1351


title: CHOP1301


title: CHOP1303


title: CHOP1316


title: CHOP1292


title: CHOP1364


title: CHOP1362


title: CHOP1293


title: CHOP1296


title: CHOP1291


title: CHOP1290


title: CHOP1288


title: CHOP1327


title: CHOP1343


title: CHOP1320


title: CHOP1294


title: CHOP1285


title: CHOP1263


title: CHOP1264


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title: CHOP1173


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title: CHOP1064


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title: CHOP1003


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title: CHOP0450


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title: CHOP0462


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title: CHOP0415


title: PHO84c 500microM t23h

city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

institute: Weizmann Institute of Science

description:
PHO84c_PMT10.srr (block 5, Cy3)
PHO84c_PMT100.srr (block 5, Cy3)

hyb_protocol: Agilent yeast dual color expression microarrays  (8x15K, G2509F)

scan_protocol: Agilent microarray scanner

data_processing: The scanned images were analyzed using SpotReader software (Niles Scientific). Problematic probes (flagged by SpotReader, or highly variable, with no signal, or at regions of spatial bias) were declared 'missing values'. Dye-dependent (Cy3 vs. Cy5) and array-dependent (same color in different arrays) biases were corrected by Lowess normalization. Data was anaylzed from the PMT100 raw data files, except of saturated probes that were analyzed from the PMT10 file (the same microarray that was scanned in low intensity).

source_name: PHO84c, t=23h

label_protocol: The samples were amplified, labeled with Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Cells were grown to logarithmic phase in SC medium (OD=0.5), washed and then incubated in SC medium with intermediate phosphate level (0.5mM, initial OD=0.05). During the experiment (0, 1, 5, 8 and 23 hours) cells were harvested, pelleted and frozen for further analysis.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

tag: phenotype

value: abundant PHO84c

tag: time (h)

tag: control

value: No

tag: treatment

value: 0.5 M phosphate


title: CHOP0417


title: CHOP0367


title: CHOP0406


title: CHOP0422


title: CHOP0395


title: PHO84c 500microM t8h

description:
PHO84c_PMT10.srr (block 6, Cy3)
PHO84c_PMT100.srr (block 6, Cy3)

source_name: PHO84c, t=8h


title: CHOP0412


title: CHOP0353


title: CHOP0360


title: CHOP0341


title: CHOP0358


title: PHO84c 500microM t5h

description:
PHO84c_PMT10.srr (block 3, Cy3)
PHO84c_PMT100.srr (block 3, Cy3)

source_name: PHO84c, t=5h


title: CHOP0426


title: CHOP0342


title: CHOP0427


title: PHO84c 500microM t0 rep3

description:
One of 4 control arrays
PHO84c_PMT10.srr (block 1, Cy5)
PHO84c_PMT100.srr (block 1, Cy5)

source_name: PHO84c, t=0

value: Yes


title: PHO84c 500microM t0 rep2

description:
One of 4 control arrays
PHO84c_PMT10.srr (block 2, Cy3)
PHO84c_PMT100.srr (block 2, Cy3)


title: CHOP0333


title: CHOP0338


title: PHO84c 500microM t0 rep4

description:
One of 4 control arrays
PHO84c_PMT10.srr (block 2, Cy5)
PHO84c_PMT100.srr (block 2, Cy5)


title: CHOP0376


title: CHOP0401


title: CHOP0355


title: WT 500microM t8h

description:
WT_PMT10.srr (block 6, Cy3)
WT_PMT100.srr (block 6, Cy3)

source_name: wild type, t=8h

value: Wild-type


title: WT 500microM t23h

description:
WT_PMT10.srr (block 5, Cy3)
WT_PMT100.srr (block 5, Cy3)

source_name: wild type, t=23h


title: CHOP0340


title: WT 500microM t5h

description:
WT_PMT10.srr (block 3, Cy3)
WT_PMT100.srr (block 3, Cy3)

source_name: wild type, t=5h


title: CHOP0321


title: WT 500microM t0 rep4

description:
One of 4 control arrays
WT_PMT10.srr (block 2, Cy5)
WT_PMT100.srr (block 2, Cy5)

source_name: wild type, t=0


title: WT 500microM t0 rep3

description:
One of 4 control arrays
WT_PMT10.srr (block 1, Cy5)
WT_PMT100.srr (block 1, Cy5)


title: PHO84c 500microM t1h

description:
PHO84c_PMT10.srr (block 4, Cy3)
PHO84c_PMT100.srr (block 4, Cy3)

source_name: PHO84c, t=1h


title: WT 500microM t0 rep2

description:
One of 4 control arrays
WT_PMT10.srr (block 2, Cy3)
WT_PMT100.srr (block 2, Cy3)


title: CHOP0308


title: WT 500microM t0 rep1

description:
One of 4 control arrays
WT_PMT10.srr (block 1, Cy3)
WT_PMT100.srr (block 1, Cy3)


title: WT 500microM t1h

description:
WT_PMT10.srr (block 4, Cy3)
WT_PMT100.srr (block 4, Cy3)

source_name: wild type, t=1h


title: CHOP0317

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.


title: CHOP0292


title: CHOP0295


title: CHOP0307


title: Photorhabdus M-form gene expression compared to P-form Rep 2

city: East Lansing

first: Todd

last: Ciche

state: MI

address: 2215 MMG, BPS Building, MSU

institute: Michigan State University

description: Biological replicate 2 of 3

hyb_protocol: Hybridization of the labeled cDNA was carried out using Agilent gene expression hybridization and wash reagents and the slides scanned on an Agilent G2505B array scanner.

scan_protocol: Intensity data was generated using the GenePix 3.0 software (Molecular Devices, Sunnyvale, CA)

data_processing: GeneSpring 11.0 software (Agilent Technologies, Santa Clara, CA) was used. All arrays were subjected to Lowess normalization. The array features which had intensities in the lower 20th percentile in all channels and all arrays features were filtered out.

organism: Photorhabdus laumondii subsp. laumondii TTO1

source_name: Locked M-form cells M2

label_protocol: Reverse transcription of the total RNA population was done to make aminoallyl cDNA followed by attachment of the fluorescent dye using the Fairplay III Microarray Labeling Kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: genetically locked P-form and M-form cells of Photorhabdus were grown in LB media supplemented with 1 g/liter sodium pyruvate at 28 degree celcius for 16 hours.

extract_protocol: RNA was extracted using Qiagen RNeasy Protect Bacteria Mini Kit (Qiagen Inc., Valencia CA) following manufacturer's instructions, with an additional step of on-column DNAseI treatment.

treatment_protocol: Three strains each of M-form and P-form were grown and M-form gene expression was compared to P-form.

tag: cell type

value: M-form

source_name: Locked P-form cells P2

value: P-form


title: Photorhabdus M-form gene expression compared to P-form Rep 1

description: Biological replicate 1 of 3

source_name: Locked M-form cells M1

source_name: Locked P-form cells P1


title: Day 10 neural precursor cells (NPCs) differentiated from H9 hESCs

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

hyb_protocol: Microarrays were hybridized in duplicate with fluor reversal and washed using an HS 4800 hybridization station (Tecan)

scan_protocol: Scanned with an Agilent microarray scanner and images were processed by the Agilent Feature Extraction software (version 9.5)

data_processing:
Variance stabilizing normalization (vsn) was performed using the vsn package within Bioconductor (version 2.1).
Raw, unprocessed input data are reported under the gVSNSignal and gVSNSignal columns of supplementary file.
Normalized intensity values from the microarray scans are reported under the gProcessedSignal and rProcessedSignal columns of supplementary file.
Normalized intensity values were input into the PATA algorithm (Mavadadi et al. In preparation) to generate final, processed data, i.e., estimates for percent exon inclusion levels (PATA output linked as supplementary file on Series record).

source_name: H9-derived NPCs (Day 10)

label_protocol: cDNAs were labelled using the ULS labeling kit (Kreatech Biotechnology) according to manufacturer's recommendations.

growth_protocol: H9 hESCs were cultured with mouse feeder cells to promote self-renewal. H9 ESCs were also cultured in micropatterned chambers of 200μm2, 400μm2 and 800μm2 to control colony size, which previously has been shown induce differentiation along endoderm, mesoderm and neural-specified lineages, respectively (Lee et al., 2009; Peerani et al., 2007).

extract_protocol: Total RNA was extracted from ESCs using TRI reagent (Sigma-Aldrich) as per the manufacturer recommendations. PolyA+ mRNA was purified using Nucleotrap Midiprep kits (Clonetech). cDNA was synthesized using the WT-Ovation RNA Amplification System (Nugen) and was hybridized to custom AS microarrays as described previously (Pan et al., 2004).

value: H9-derived NPC

value: blastocyte-derivative

value: day 10


title: PHO84c 500microM t0 rep1

description:
One of 4 control arrays
PHO84c_PMT10.srr (block 1, Cy3)
PHO84c_PMT100.srr (block 1, Cy3)


title: CHOP0249

source_name: Tumor DNA


title: CHOP0288


title: H9 human embryonic stem cell replicate #2

source_name: H9 hESCs

value: H9 hESC

value: blastocytes


title: Photorhabdus M-form gene expression compared to P-form Rep 3

description: Biological replicate 3 of 3

source_name: Locked M-form cells M3

source_name: Locked P-form cells P3


title: CHOP0278


title: CHOP0287


title: H9 human embryonic stem cell replicate #1


title: CHOP0265