title: T. forsythia bone 28B

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

institute: University of Florida, College of Dentistry

description: Gene expression data from T. forsythia infected bone.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles.

source_name: T. forsythia infected bone 3

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

growth_protocol: T. forsythia ATCC 43037 was cultured in trypticase soy agar II basal media supplemented with yeast extract, phytone peptone, sheep blood (5%), and N-acetylmuramic acid (NAM) under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.

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

treatment_protocol: Infection protocol: T. forsythia was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 10) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.

value: calvarial bone

value: T. denticola

value: 9 weeks


title: Tumor sample 117T vs RP

status: Public on Feb 07 2011

type: genomic

city: Leiden

first: Eddy

last: van Roon

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: Tumor vs Reference panel LogRatios

hyb_protocol: Hybridisation and washing was performed in a GeneTAC hybstation (microgen, Oklahoma City, OK, USA) using a hybsolution containing 66% formamide, 2.5x SSC and 12.5g/100ml dextran sulphate.

scan_protocol: Image analysis was done using GenePix6.0 (Molecular Devices, Union City, CA, USA)

data_processing: Pre-processing was performed using the GenePix error model in Rosetta Resolver version 5.0 (Rosetta Biosoftware, Seattle, WA, USA). Microarray data for the tumour and normal samples were compared using an error-weighted ANOVA model and corrected for multiple testing in Rosetta resolver

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon tumor

label_protocol: MseI digestion was performed in a 50 ul sample volume containing  2 ug of genomic DNA. Digests were purified and their sticky-ends ligated with 0.5 nmol of unphosphorylated linkers. Ligated DNA was digested with methylation-sensitive endonucleases BstUI and HpaII. Incorporation of aminoallyl dUTP into amplicons (5 ug) was conducted using the BioPrime DNA labeling system (Life Technologies, Inc.). Cy5 and Cy3 fluorescent dyes were coupled to amino-allyl dUTP-labeled tumor and normal amplicons.

extract_protocol: Total genomic DNA has been isolated using a standard phenol/cholorform and alcohol precipitation extraction

tag: sample type

value: Male, 69, coecum, MSS

tag: gender

value: Male

tag: age

tag: tissue

value: Colon tumor

source_name: Reference panel

value: SW48, RKO, SW480, Caco2, SW837, and LS411


title: Normal mucosa 503N vs RP

description: Normal mucosa vs Reference panel LogRatios

source_name: Colon, normal mucosa

value: Female, 63, coecum

value: Female

value: Colon, normal mucosa


title: T. forsythia soft tissue 30

type: RNA

country: USA

description: Gene expression data from T. forsythia infected tissue.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: T. forsythia infected tissue 5

value: soft tissue overlying calvarial bone

tag: infection


title: Tumor sample 118T vs RP

description: Tumor vs Reference panel LogRatios

value: Female, 69, coecum, MSS


title: T. forsythia bone 26B

source_name: T. forsythia infected bone 1


title: MeDIP BMP2 day 6

city: Nijmegen

first: Marlinda

last: Hupkes

address: Heyendaalseweg 135

department: Cell and Applied Biology

institute: Radboud University Nijmegen

description:
MeDIP-on-chip, promoter array
.CEL files contain raw scanned output data; .bar files contain estimates of fold enrichment over input DNA, computed as pseudomedian signal of all ChIP or MeDIP/input ratios (median of pairwise averages) within a 400bp sliding window; .bed files contain locations of intervals and active regions computed using TAS parameters threshold = 1.8; MaxGap = 300; MinRun = 180.

hyb_protocol: Labeled DNA was hybridized to the Affymetrix GeneChip mouse promoter 1.0R array at 45°C overnight.

scan_protocol: Arrays were scanned by GeneChip ® HT Array Plate Scanner according to standard Affymetrix procedures.  Arrays were washed and scanned by GeneChip ® HT Array Plate Scanner according to standard procedures.

data_processing: Scanned output CEL files were analyzed using Affymetrix tiling analysis (TAS) software that computed estimates of fold enrichment over input DNA (referred to as probe signal values) for all probes on the arrays in linear scale. Genomic regions where probe signal values were greater than 1.8 for a total length of at least 180 bp, allowing for gaps of maximally 300 bp, were subsequently defined as ‘intervals’ and represent the locations of signal peaks. To compare peak metrics between the 7 different samples, overlapping intervals were grouped into ‘active regions’. Enrichment values for active regions were calculated by averaging the probe signal values of all probes within the active region. Active regions -6 kb upstream from a transcription start site or within a gene were assigned to that associated gene. Gene annotations were taken from NCBI Build 37 (mm9).

source_name: MeDIP DNA from day 6 BMP2-treated C2C12

label_protocol: Amplified DNA was fragmented and labeled using the DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: C2C12 cells were plated at 25.000cells per cm2 in DMEM 10% Newborn Calf Serum and grown for 24 hrs to sub-confluence.

extract_protocol: For MeDIP studies, genomic DNA from C2C12 cultures was isolated using the ChargeSwitch gDNA Mini Tissue Kit (Invitrogen) and sonicated to an average length of 300-500 bp. Genomic DNA from aliquots was purified for use as input. Methylated DNA fragments were immunoprecipitated using an antibody against 5-methyl-cytosine (P00704; Capralogics) as described elsewhere (Zhang et al. 2006). For RNA polymerase II (Pol-II) ChIP-on-chip, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine for 5min. Lysates were sonicated to an average DNA fragment length of 300-500 bp and Pol-II-bound DNA fragments were immunoprecipitated using sc-9001 antibody (Santa Cruz) as described previously (Wang et al. 2008). MeDIP, Pol-II ChIP and input DNAs were amplified using the GenomePlex whole-genome amplification kit (Sigma). To assess quality of the amplification reactions, specific genomic regions were tested in triplicate by qPCR in both the original immunoprecipitated materials and after amplification.

treatment_protocol: Cells were treated with DMEM 5% Newborn Calf Serum with or without 300ng/ml BMP2 to induce osteogenic and myogenic differentiation, respectively. Samples were extracted 0, 1, 3 and 6 days after induction of differentiation.

tag: cell line

tag: antibody

tag: treatment

value: 300ng/ml BMP2

tag: days after induction of differentiation

tag: antibody manufacturer

value: Capralogics

tag: antibody lot #

tag: antibody catalog #

source_name: C2C12 input DNA

value: input DNA


title: Normal mucosa 117N vs RP

value: Male, 69, coecum


title: Normal mucosa 74N vs RP

value: unknown


title: T. forsythia soft tissue 28

source_name: T. forsythia infected tissue 3


title: Sample 1 / Control 1

city: Rehovot

first: Akhil

last: Rajput

address: 1, Herzl

department: Biological Chemistry

country: Israel

institute: The Weizmann Institute

description: Sample 1 / Control 1

hyb_protocol: Arrays labelled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and hybridised using the In situ Hybridization Kit. All protocols available from www.agilent.com

scan_protocol: Scanner Model: G2565BA DNA Scanner.

data_processing:
Agilent Feature Extraction Software Version: 9.5. Extraction Protocol: GE2-v5_95_Feb07. Data pre-processing involved normalization (linear lowess) and background subtraction. Data table below represents log10(knockdown/control) ratios, [log(REDsignal/GREENsignal) per feature (processed signals used)].
Data Analysis was performed in GeneSpring (Agilent Technologies) with pathway analysis performed using “Pathway Express” from Wayne State University (http://vortex.cs.wayne.edu/research.htm). This is a free web-based programme.

source_name: SV80 Cells, sample

growth_protocol: SV80 cells were grown in DMEM with 10% FBS and antibiotics

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Cat. No. 74104, QIAGEN) according to manufacturers instructions.

treatment_protocol: The cells were treated with Control or caspase-8 siRNA expressing lenti viruses

value: fibroblastoid cell line SV80

tag: protocol

value: siRNA-mediated caspase-8 knockdown

source_name: SV80 Cells, control

value: control


title: T. forsythia soft tissue 29

source_name: T. forsythia infected tissue 4

value: T. denticola

value: 9 weeks


title: Normal mucosa 180N vs RP

value: Female, 86, ascending colon


title: T. forsythia soft tissue 27

source_name: T. forsythia infected tissue 2


title: Sample 2 / Control 2

description: Sample 2 / Control 2

label_protocol: Arrays labelled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and hybridised using the In situ Hybridization Kit. All protocols available from www.agilent.com


title: T. forsythia bone 27B

source_name: T. forsythia infected bone 2

value: calvarial bone


title: MeDIP untreated day 6

source_name: MeDIP DNA from day 6 untreated C2C12

value: untreated


title: Control  bone 2

description: Gene expression data from control bone.

data_processing: The data was normalized  using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles

source_name: Control bone, no infection 2

growth_protocol: P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.

treatment_protocol: P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.

value: uninfected (control)


title: Normal mucosa 118N vs RP

value: Female, 69, coecum

value: Female

value: Colon, normal mucosa

value: SW48, RKO, SW480, Caco2, SW837, and LS411


title: MeDIP BMP2 day 3

source_name: MeDIP DNA from day 3 BMP2-treated C2C12

value: 300ng/ml BMP2

value: Capralogics


title: MeDIP untreated day 3

source_name: MeDIP DNA from day 3 untreated C2C12

value: input DNA


title: ZF4_H3K27me3_Repl1

status: Public on Feb 08 2011

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted

organism: Danio rerio

source_name: H3K27me3 ChIP DNA

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Cell grown under standard condition as per Driever and Rangini, 1993 In vitro Cell Dev Biol.Anim 294, 749

extract_protocol: Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, cells were cross-linked in suspension with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added to ~120 µl and samples incubated for 5 min on ice. Cells were sonicated on ice using a Bioruptor (Diagenode) to produce fragments of ~400 bp. The lysate was centrifuged, the supernatant collected, chromatin diluted to 0.5 A260 units and 100 µl was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h at 4oC. ChIP material was washed as described [46]. Elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated and dissolved in 50 μl TE buffer. 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 16 μl MilliQ water. Input DNA (channel 2) was purified by phenol-chloroform isoamylalcohol extraction and RNAse-treated as above.

tag: source

value: American Type Culture Collection

tag: developmental stage

value: Embryo

tag: chip antibody

value: anti-H3K27me3 from Millipore (cat# 07-449)

source_name: Input DNA from ZF4 cells


title: ZF4_H3K4me3_Repl2

source_name: H3K4me3 ChIP DNA

value: anti-H3K4me3 from Diagenode (cat# pAb-003-050)


title: Control  bone 4

description: Gene expression data from control bone.

source_name: Control bone, no infection 4


title: MeDIP BMP2 day 1

source_name: MeDIP DNA from day 1 BMP2-treated C2C12


title: T. forsythia soft tissue 26

source_name: T. forsythia infected tissue 1

value: soft tissue overlying calvarial bone

value: T. denticola


title: Control  bone 3

description: Gene expression data from control bone.

source_name: Control bone, no infection 3

value: 9 weeks


title: Control soft tissue 4

description: Gene expression data from control tissue.

source_name: Control tissue, no infection 4


title: Control soft tissue 3

source_name: Control tissue, no infection 3


title: ZF4_H3K27me3_Repl2


title: Tet1-KD_sc_TS_rep3

city: Turku

first: Kian Peng

last: Koh

address: Tykistökatu 5

country: Finland

institute: Btk

description:
Tet1-KD_sc_TS
Tet1-kd/shRNA#2.1-sc3 TS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data: The numerical results were extracted with GenomeStudio v. 2009.1 without any normalization or background subtraction.
Normalized data: Normalized using quantile normalisation with limma in R

source_name: subclones of Tet1 shRNA-transfected ES cells in TS cell culture

label_protocol: For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: Cells were cultured in standard culture media conditions in 37⁰C/5% CO2 incubators

extract_protocol: total RNA was isolated with an Rneasy kit (Qiagen, Chatsworth, CA) with on-column Dnase treatment

tag: strain

value: ES cells

tag: transfection protocol

value: Tet1 shRNA transfected

tag: culture media

value: TS


title: Control soft tissue 2

source_name: Control tissue, no infection 2

value: uninfected (control)

tag: age


title: Control  bone 1

description: Gene expression data from control bone.

source_name: Control bone, no infection 1

tag: tissue

value: calvarial bone


title: TSC_TS_rep3

description:
TSC
TS cells Expt3

source_name: true TS cells

value: TS cells

value: untransfected


title: Tet1-KD_sc_TS_rep2

description:
Tet1-KD_sc_TS
Tet1-kd/shRNA#2.1-sc2 TS


title: TSC_TS_rep1

description:
TSC
TS cells Expt1


title: TSC_TS_rep2

description:
TSC
TS cells Expt2


title: Control soft tissue 5

source_name: Control tissue, no infection 5

tag: infection


title: Tet1-KD_sc_TS_rep1

description:
Tet1-KD_sc_TS
Tet1-kd/shRNA#2.1-sc1 TS


title: Tet1-kd_TS_rep4

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.1 TS Expt2

source_name: Tet1 shRNA-transfected ES cells in TS cell culture


title: Tet1-kd_TS_rep5

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.1 TS Expt3


title: Tet1-kd_TS_rep6

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.2 TS Expt2


title: ZF4_H3K4me3_Repl1

tag: cell line


title: MeDIP undifferentiated day 0

source_name: MeDIP DNA from day 0 undifferentiated C2C12

tag: antibody

value: untreated

source_name: C2C12 input DNA

tag: sample type


title: MeDIP untreated day 1

source_name: MeDIP DNA from day 1 untreated C2C12

tag: treatment

tag: days after induction of differentiation

value: Capralogics


title: Pol-II ChIP untreated day 6

description:
RNA Pol-II ChIP-on-chip, promoter array
.CEL files contain raw scanned output data; .bar files contain estimates of fold enrichment over input DNA, computed as pseudomedian signal of all ChIP or MeDIP/input ratios (median of pairwise averages) within a 400bp sliding window; .bed files contain locations of intervals and active regions computed using TAS parameters threshold = 1.8; MaxGap = 300; MinRun = 180.

source_name: Pol-II ChIP DNA from day 6 untreated C2C12

value: anti-RNA polymerase 2, rabbit polyclonal

tag: antibody manufacturer

value: Santa Cruz

tag: antibody lot #

value: input DNA


title: Pol-II ChIP BMP2 day 6

source_name: Pol-II ChIP DNA from day 6 BMP2-treated C2C12

value: 300ng/ml BMP2

tag: antibody catalog #


title: Pol-II ChIP BMP2 day 3

source_name: Pol-II ChIP DNA from day 3 BMP2-treated C2C12


title: Pol-II ChIP BMP2 day 1

source_name: Pol-II ChIP DNA from day 1 BMP2-treated C2C12


title: Tet1-kd_TS_rep2

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.2 TS Expt1


title: Control soft tissue 1

source_name: Control tissue, no infection 1


title: Tet1-kd_TS_rep3

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.3 TS


title: Pol-II ChIP undifferentiated day 0

source_name: Pol-II ChIP DNA from day 0 undifferentiated C2C12


title: G1_TS_rep3

description:
GFP-kd_TS
GFP-kd G1 TS Expt3

source_name: GFP (control) shRNA-transfected ES cells in TS cell culture

value: GFP shRNA transfected


title: Pol-II ChIP untreated day 3

source_name: Pol-II ChIP DNA from day 3 untreated C2C12


title: Tet1-kd_TS_rep1

description:
Tet1-kd_TS
Tet1-kd/shRNA#2.1 TS Expt1


title: G1_TS_rep2

description:
GFP-kd_TS
GFP-kd G1 TS Expt2


title: G1_TS_rep1

description:
GFP-kd_TS
GFP-kd G1 TS Expt1


title: ESC_TS_rep2

description:
ESC_TS
parental control TS Expt2

source_name: untransfected (parental control) ES cells in TS cell culture


title: Pol-II ChIP untreated day 1

source_name: Pol-II ChIP DNA from day 1 untreated C2C12


title: ESC_TS_rep3

description:
ESC_TS
parental control TS Expt3


title: Tet1-kd_ES_rep3

description:
Tet1-kd_ES
Tet1-kd/shRNA#2.3 ES

source_name: Tet1 shRNA-transfected ES cells in ES cell culture

value: ES


title: Tet1-kd_ES_rep1

description:
Tet1-kd_ES
Tet1-kd/shRNA#2.1 ES


title: GFP-kd_ES_rep2

description:
GFP-kd_ES
GFP-kd G2 ES

source_name: GFP (control) shRNA-transfected ES cells in ES cell culture


title: E11, Tamoxifen Treated, Group_II (Dye Swap)

city: Mumbai

first: Nafisa

middle: H

last: Balasinor

state: Maharashtra

address: J.M.Street, Parel

country: India

institute: National Institute for Research in Reproductive Health

description: T10 (cy3) vs. T9 (cy5)

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint.. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths. Grid and spot alignment is performed by using Scan array microarray analysis software form PerkinElmer.

data_processing:
Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent.
Two color hybridizations were performed by labeling set of samples with cy3 channel and set of samples with cy5 channel. Intensities generated from feature extraction raw data were split based on channel type. Samples were grouped based conditions and were compared across samples to identify significant gene expression pattern. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Significant genes up and down regulated showing one fold and above among the samples was identified. Differentially regulated genes were clustered using hierarchical clustering to identify significant gene expression patterns. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, Significant Functions were identified for the significant genes.
Sample Details:
Group 1: Pool C3 and C5 Control Normal (13 GD)
Group 2: Pool C4 and C6 Control Resorbed (13 GD)
Group 3: Pool T3 and T5 Treated Normal (13 GD)
Group 4: Pool T4 and T6 Treated Resorbed (13 GD)
Group 5: Pool T7 and T9 Treated Normal (11 GD)
Group 6: Pool T8 and T10 Treated Resorbed (11 GD)

organism: Rattus norvegicus

source_name: Resorbed Rat Embryo at embryonic day 11 (E11): TR-E11-2

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA

extract_protocol: Entire Resorbed embryo was homogenized in 1 ml TRIzol. 500 µl of the lysate was used for RNA extraction. The RNA Integrity number (RIN) of the sample was 7.8, as evaluated by Agilent Bioanalyzer 2100. The RNA sample was purified using Qiagen’s RNeasy mini kit.

treatment_protocol: 0.4mg/kg/day tamoxifen for 60 days

value: Holtzman

value: E11 resorbed embryos sired by male rats

source_name: Normal Rat Embryo at embryonic day 11 (E11): TN-E11-2

extract_protocol: Embryo along with placenta was homogenized in 1 ml TRIzol. 500 µl of the lysate was used for RNA extraction. The RNA Integrity number (RIN) of the sample was 8.1, as evaluated by Agilent Bioanalyzer 2100. The RNA sample was purified using Qiagen’s RNeasy mini kit.

value: E11 normal embryos sired by male rats


title: GFP-kd_ES_rep1

description:
GFP-kd_ES
GFP-kd G1 ES

value: ES cells


title: E11, Tamoxifen Treated, Group_I

description: T7 (cy3) vs. T8 (cy5)

source_name: Normal Rat Embryo at embryonic day 11 (E11): TN-E11-1

source_name: Resorbed Rat Embryo at embryonic day 11 (E11): TR-E11-1


title: ESC_ES_rep2

description:
ESC
v6.5 ES cells Expt2

source_name: true ES cells


title: E13, Tamoxifen Treated, Group_II (Dye Swap)

description: T6 (cy3) vs. T5 (cy5)

source_name: Resorbed Rat Embryo at embryonic day 13 (E13): TR-E13-2

value: E13 resorbed embryos sired by male rats

source_name: Normal Rat Embryo at embryonic day 13 (E13): TN-E13-2

value: E13 normal embryos sired by male rats


title: GFP-kd_ES_rep3

description:
GFP-kd_ES
GFP-kd G3 ES


title: E13, Control, Group_I

description: C3 (cy3) vs. C4 (cy5)

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

source_name: Normal Rat Embryo at embryonic day 13 (E13): CN-E13-1

extract_protocol: Embryo along with placenta was homogenized in 1 ml TRIzol. 500 µl of the lysate was used for RNA extraction. The RNA Integrity number (RIN) of the sample was 8.2, as evaluated by Agilent Bioanalyzer 2100. The RNA sample was purified using Qiagen’s RNeasy mini kit.

source_name: Resorbed Rat Embryo at embryonic day 13 (E13): CR-E13-1

extract_protocol: Entire Resorbed embryo was homogenized in 1 ml TRIzol. 500 µl of the lysate was used for RNA extraction. The RNA Integrity number (RIN) of the sample was 7.1, as evaluated by Agilent Bioanalyzer 2100. The RNA sample was purified using Qiagen’s RNeasy mini kit.


title: ESC_TS_rep1

description:
ESC_TS
parental control TS Expt1

value: TS


title: CDC6 samples vs INPUT (genomic DNA)

status: Public on Feb 06 2011

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description:
CDC6 x2 replicates vs INPUT x 3 replicates.

CDC6 ChIP replicates:
CDC6_3.CEL
CDC6_4.CEL

INPUT replicates:
Wt_1_At35b_MR_v04.CEL
Wt_2_At35b_MR_v04.CEL
Wt_3_At35b_MR_v04.CEL

Arabidopsis thaliana genome tiling array used in this study has 2.8 million probes, spaced 35 bases apart, with one 25 base probe within each window. Start of Probe position on chromosome based on TAIR7 genome build (probe length is 25 nts and positions are 0-based not 1-based). Tiles most of the Arabidopsis genome.

hyb_protocol: Hybridization was performed by the standard Affymetrix protocol.

scan_protocol: Scanning was performed at 0.7μm resolution using a GeneChip Scanner 3000 7G (Affymetrix Inc, Santa Clara, CA).

data_processing:
ChIP data were quantile normalized to genomic DNA (INPUT) using Affymetrix Tiling Analysis Software. Each data set was then normalized so that the mean signal across all probes in the genome was zero.
Results file (found on Series record): Enrichment ratio calculated from normalized intensities and averaged over all replicates. Positive values indicate enrichment of the ChIP fraction versus the INPUT sample.

organism: Arabidopsis thaliana

source_name: ChIP: genomic DNA enriched in CDC6 binding fragments

label_protocol: DNA was amplified using Affymetrix Chromatin Immunoprecipitation Assay protocol. 7.5 μg of amplification product were fragmented and labeled using GeneChip® WT Double-stranded DNA terminal labeling kit (Affymetrix).

growth_protocol: Arabidopsis seedlings (Col-0 ecotype) were grown in MS salts medium supplemented with 1% sucrose and 1% agar in a 16h/8h light/dark regime at 22°C. Plants constitutively expressing the Myc-ORC1a-tagged and the hemagglutinin (HA)-tagged Arabidopsis CDC6a protein have been described elsewhere (Castellano et al., 2001; Sanchez and Gutierrez, 2009).

extract_protocol: After washing, the immunocomplexes were eluted and incubated at 65ºC for 6h to reverse crosslinking. Residual protein was eliminated with 20µg of proteinase K and phenol-chloroform extractions. The DNA obtained (ChIP and input) was cleaned up using Affymetrix cDNA cleanup columns.

treatment_protocol: ChIP assays were carried out using 10-day-old plants except that they were preincubated with 50µM MG132 prior to the fixation step. For immunoprecipitation, 10µl of anti-Myc (SC-40ac; Santa Cruz Biotechnology) or anti-HA (A2095; SIGMA), were incubated with 1mg of chromatin extract, previously sonicated, to obtain DNA fragments of ~500-1000bp.

value: ChIP fraction

value: anti-HA (A2095; SIGMA)

source_name: INPUT: genomic DNAs

value: input


title: H4K5ac_ChIP

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: H4K5ac ChIP

hyb_protocol: Hybridized as previously described (Zhang et al., 2006)

scan_protocol: Scanned as previously described (Zhang et al., 2006)

data_processing: H4K5ac intensities were quantile normalized to H3 intensities using Affymetrix Tiling Analysis Software to produce the bar file.

source_name: H4K5ac ChIP DNA

label_protocol: Labelled as previously described (Zhang et al., 2006)

extract_protocol: ChIP was performed as described (Schubert et al., 2006). Plants were grown under 16 h of light on 1/2 X Murashige and Skoog media, and 1.0–1.5g of whole seedling tissue was harvested and fixed after 10–14 d. α-H4K5ac (Upstate 06-759) and α-H3 (Abcam number ab1791; http://www.abcam.com) antibodies were incubated for 3–5 h at 4 °C with 25 μl of magnetic protein A beads (Invitrogen number 100.01; http://www.invitrogen.com). The IP was performed as described (Schubert et al., 2006), and DNA was resuspended in 50–75 μl H2O.

value: Upstate

tag: antibody catalog

value: seedlings

source_name: H3 ChIP DNA

value: Abcam


title: ORC1 samples vs INPUT (genomic DNA)

description:
ORC1 x3 replicates vs INPUT x3 replicates.

ORC1 ChIP replicates:
ORC1_0.CEL
ORC1_1.CEL
ORC1_2.CEL

INPUT replicates:
Wt_1_At35b_MR_v04.CEL
Wt_2_At35b_MR_v04.CEL
Wt_3_At35b_MR_v04.CEL

Arabidopsis thaliana genome tiling array used in this study has 2.8 million probes, spaced 35 bases apart, with one 25 base probe within each window. Start of Probe position on chromosome based on TAIR7 genome build (probe length is 25 nts and positions are 0-based not 1-based). Tiles most of the Arabidopsis genome.

source_name: ChIP: genomic DNA enriched in ORC1 binding fragments

value: anti-Myc (SC-40ac; Santa Cruz Biotechnology)

source_name: INPUT: genomic DNA


title: Tet1-kd_ES_rep2

description:
Tet1-kd_ES
Tet1-kd/shRNA#2.2 ES

source_name: Tet1 shRNA-transfected ES cells in ES cell culture

value: Tet1 shRNA transfected


title: WT KLS 2

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

country: Japan

institute: Fukushima Medical University

hyb_protocol: The standard Affymetrix protocol.

scan_protocol: The standard Affymetrix protocol.

data_processing: Expression Console were used to generate chp files (program-version = 1.1.2800.19935, algorithm-version = 1.0, algorithm-name = rma-gene-default).

source_name: bone marrow

label_protocol: The standard Affymetrix protocol.

extract_protocol:
Flow sorting of KLS cells and MEP cells.
Trizol RS extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: KLS

tag: genotype/varation

value: wildtype


title: E13, Tamoxifen Treated, Group_I

description: T3 (cy3) vs. T4 (cy5)

source_name: Normal Rat Embryo at embryonic day 13 (E13): TN-E13-1

tag: strain

value: Holtzman

source_name: Resorbed Rat Embryo at embryonic day 13 (E13): TR-E13-1


title: [E-MTAB-115] NRF2_lane2_201EKAAXX_6.um.eland

status: Public on Feb 05 2011

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

library_source: genomic

data_processing:
Solexa pipeline.
The Eland software (Illumina) was used to align reads against the hg18 reference genome. The first 32 bases were aligned allowing a maximum of 2 mismatches. Reads aligning to multiple locations were discarded. The remaining un-aligned reads were shortened by 3 bases at the 3' end and the procedure repeated until the remaining aligned sequences were 23 bases long.

growth_protocol: grow | RPMI 1640 medium supplemented with 10% non-inactivated FBS, l-glutamine and PEST at 37C with 5% CO2.

extract_protocol:
specified_biomaterial_action | Antibodies were from Santa Cruz Biotechnology (sc-6554, sc-6556 and sc-13442) and ChIP was performed using 10e7-10e8 cells per reaction. Briefly, crosslinking of protein and DNA was done in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were scraped and washed in PBS before treatment of cell lysis buffer with protease inhibitors for 10 min on ice. Pelleted nuclei were resuspeded in RIPA buffer and a BioRuptor (Diagenode) was used to sonicate DNA with 2-3 * 15  cycles of 30 seconds on/off at the highest amplitude. For FOXA2 two biological replicates FOXA2 were done using slightly different protocols. For the first replicate, chromatin from a sub-confluent T-175 flask was sonicated to a broad range of fragments, with a median size close to 500 bp, and ChIP was performed in parallel for FOXA2 and IgG with 10 µg antibody. ChIP DNA was gel fractionated and amplified to create two size libraries corresponding to insert sizes of 50-150 bp and 250-450 bp. For the second replicate, chromatin was sonicated to a median size around 200 bp. DNA obtained from two precipitations using 20 µg of the ChIP-grade antibody (sc-6554x) was pooled. For all ChIPs washing was done four times with RIPA, once with LiCl buffer and once with TE-buffer and DNA-protein complexes were eluted from beads twice with 225 ?l 0.1 M NaHCO3 and 1 % SDS and treated with RNAseA at 65C for 6 hours and Proteinase K at 45C over night. For the large IgG library one lane was used for sequencing, for all other libraries two lanes were used. For HNF4a the ChIP DNA obtained from two replicates was pooled and concentrated on silica columns by centrifugation using a Quiagen PCR-purification kit before library construction. For GABP, HNF4a and the second FOXA2 replicate one library with insert sizes between 100 and 300 bp was sequenced using the Illumina 1G instrument according to the manufacturers protocol for 36 bp reads. For ChIP-PCR of GABPa an additional ChIP was performed using a monoclonal antibody (sc-28312).
sequencing | Solexa sequencing of ChIP material from HepG2 cells.

tag: material type

value: cell

tag: cellline

tag: Sex

value: male

tag: diseasestate

value: hepatocellular carcinoma

value: GABP

tag: library fragment size


title: TG MEP 1

value: MEP


title: WT MEP 2


title: [E-MTAB-115] NRF2_lane1_FC14065_1.um.eland


title: ESC_ES_rep1

description:
ESC
v6.5 ES cells Expt1

value: ES cells

tag: transfection protocol

value: untransfected

tag: culture media

value: ES


title: ESC_ES_rep3

description:
ESC
v6.5 ES cells Expt3


title: E13, Control, Group_II (Dye Swap)

description: C6 (cy3) vs. C5 (cy5)

source_name: Resorbed Rat Embryo at embryonic day 13 (E13): CR-E13-2

tag: tissue

value: E13 resorbed embryos sired by male rats

source_name: Normal Rat Embryo at embryonic day 13 (E13): CN-E13-2

value: E13 normal embryos sired by male rats


title: [E-MTAB-115] HNF4a_first_lane_FC14065_2.um.eland

tag: antibody


title: [E-MTAB-115] HNF4a_second_lane_200D9AAXX_7.um.eland


title: WT KLS 1


title: TG KLS 2


title: TG MEP 2


title: [E-MTAB-115] FOXA2_rep2b_lane_6.um.eland_rep2b


title: [E-MTAB-115] FOXA2_rep1long_lane_7.um.eland


title: [E-MTAB-115] NRF2_lane1_FC14065_1.nm.eland


title: [E-MTAB-115] FOXA2_rep1short_lane_3.um.eland


title: [E-MTAB-115] FOXA2_rep1long_lane_6.um.eland_rep1


title: [E-MTAB-115] FOXA2_rep1short_lane_4.um.eland


title: [E-MTAB-115] lane_6.um.eland_rep2a


title: WT MEP 1


title: [E-MTAB-131] MCF-7_+E2 IP 2

data_processing:
Solexa pipeline standard workflow for sequence extraction and quality control.
The Eland software (Illumina) was used to align reads against the hg18 reference genome. The first 32 bases were aligned allowing a maximum of 2 mismatches. Reads aligning to multiple locations were discarded.

source_name: MCF-7_+E2 IP 2

growth_protocol: grow | Human breast cancer MCF-7 cells were propagated as monolayer cultures in DMEM medium supplemented with 10% fetal bovine serum (both from Invitrogen Spa, San Giuliano Milanese, Italy), 100 U/ml penicillin, 100 microg/ml streptomycin and 250 ng/ml Amfotericin-B. For G0-G1 synchronization cells were plated at  20-40% confluence in steroid free medium (phenol reed-free DMEM medium, with 5% fetal bovine serum pre-treated with dextran-coated charcoal and antibiotics) and maintained for 4 days with replacement of same fresh medium.

extract_protocol:
specified_biomaterial_action | A total of 5*106 cells were fixed with 1% of formaldeyde for 10 min at room temperature, and the reaction was stopped by adding glycine at final concentration of 0.125 M. Fixed cells were washed twice with ice-cold PBS, harvested by scraping, pelleted and resuspended in SDS lysis buffer. Samples were sonicated with Diagenode Bioruptor, for 12 x 30 s cycles at high level, centrifuged at 13,200 rmp for 15 min, and diluited 8-fold in ChIP dilution buffer. After removing a input aliquot (whole-cell extract), sample was incubate at 4 C overnight with antibodies against C-terminal ERalpha (HC-20 Santa Cruz) and N-terminal ERalpha (18-32 Sigma). Complexes were precipitated with protein A Agarose/Salmon Sperm DNA beads. Beads were washed sequentially with low-salt immune complex wash buffer, high salt immune complex wash buffer, LiCl immune complex wash buffer, and TE buffer for twice. Immunoprecipitated chromatin was eluted in elution buffer, incubated at 65 C overnight, and treated with proteinase K. DNA was purified by extracting with phenol\chloroform\isoamyl alcohol (25\24\1) and precipitating in ethanol. DNA pellets were resuspended in a nuclease free water.
sequencing | Solexa sequencing of ChIP material from MCF-7 cells.

treatment_protocol: specified_biomaterial_action | Cells were treated with 10nM of 17 beta-estradiol and harvested 45 minutes after treatment.

value: breast cancer

value: ER-alpha

tag: compound

tag: time

value: 45 minutes


title: [E-MTAB-131] MCF-7_+E2_noAb IP

source_name: MCF-7_+E2_noAb IP

value: no antibody


title: [E-TABM-482] SP3

data_processing: Sequence reads were aligned to the reference genome assembly, and the read depth was sampled at intervals along the genome.  The raw read-density information was processed using the Batman method (Down et al, 2008) to correct for the effects of varying CpG density across the genome and generate quantitative estimates of DNA methylation levels.

extract_protocol:
nucleic_acid_extraction | 10 mg sperm DNA was nebulized with compressed nitrogen for 6 min at 32 p.s.i., giving fragments of <800 bp. These fragments were end repaired, phosphorylated and A-tailed the fragmented DNA and ligated Illumina paired end adapters to fragments.
immunoprecipitate | Approximately 1µg of the sample prepared by DNA_prep was subjected to MeDIP as described previously (Weber et al. 2005; PMID: 16007088). The immunoprecipitated (IP) sample was purified using Zymo-5 kit (using 700 µl binding buffer) according to the manufacturers instructions.
PCR_amplification | The sample isolated by meDIP was amplified using Illumina paired-end PCR primers before gel electrophoresis and size-selecting libraries. We excised bands from the gel to produce libraries with insert sizes of 85-160 bp, and quantified these libraries using an Agilent Bioanalyzer 2100.
high_throughput_sequencing | Following sequencing_prep, Paired-end flowcells were prepared with 3.2 pM DNA (using two-primer chemistry) using the manufacturer's recommended protocol and sequenced for 36 cycles on an Illumina genome analyzer fitted with a paired-end module.

tag: celltype

value: spermatozoon

tag: developmentalstage

value: adult

tag: individual


title: [E-MTAB-131] MCF-7_+E2 IP

source_name: MCF-7_+E2 IP


title: [E-MTAB-131] MCF-7_-E2 IP

source_name: MCF-7_-E2 IP

value: ethanol


title: TG KLS 1

tag: cell type

value: KLS


title: [E-MTAB-345] TAP-ER-beta_-E2_ER-beta IP sequence Performer: Illumina_Hayward

description: Performer: Illumina_Hayward

data_processing: bioassay_data_transformation | Solexa pipeline standard workflow for sequence extraction and quality control. The Eland software (Illumina) was used to align reads against the hg18 reference genome. The first 32 bases were aligned allowing a maximum of 2 mismatches. Reads aligning to multiple locations were discarded.

source_name: TAP-ER-beta_-E2_ER-beta IP sequence

growth_protocol:
transfect | Human breast cancer MCF-7 (6-7×105/60 mm dish) were plated and transfected with 3.5 mg of DNA using Lipofectamine 2000 reagent (Invitrogen), according to the manufacturer’s instructions.
pooling | Ct-ER-beta and Nt-ER-beta DNAs from cells with or without E2, were pooled together, to generate TAP-ER-beta +E2 and TAP-ER-beta -E2 samples, respectively.
grow | Human breast cancer MCF-7 wt were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (Ct-ER-beta and Nt-ER-beta) as previously described. All were grown in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS) (both from Invitrogen SpA, San Giuliano, Milanese, Italy), 100 U/ml penicillin, 100 mg/ml streptomycin, 250 ng/ml Amfotericin-B, 50 µg/ml G418 (normal growing condition) For G0-G1 synchronization cells were plated at 40% confluence in steroid-free medium (phenol red-free DMEM medium, with 5% fetal bovine serum pre-treated with dextran-coated charcoal and antibiotics) and maintained for 5 days with replacement of same fresh medium before stimulation with 10 nM 17beta-estradiol (E2).

extract_protocol:
specified_biomaterial_action | Total of 5x10^6 cells were fixed with 1% of formaldeyde for 10 min at room temperature, and the reaction was stopped by adding glycine at final concentration of 0.125 M. Fixed cells were washed twice with ice-cold PBS, harvested by scraping, centrifuged and the cell pellets were re-suspended in SDS lysis buffer. Samples were sonicated with a Diagenode Bioruptor (Diagenode SA, Belgium) for 12 cycles of 30sec at high power, centrifuged at 13,200rpm for 15 minutes and diluted 8-fold in ChIP dilution buffer. After removing an aliquot (whole-cell extract input), the chromatin sample was incubated at 4°C overnight with antibodies against the C-terminus (HC-20, from Santa Cruz Biotechnology, Europe) or the N-terminus (anti-Estrogen Receptor 18-32, from SigmaAldrich, Italy) of human ER alpha. As control aliquotes of the same chromatins were processed in the same way but the Abs were omitted form the reaction. The samples  were then precipitated by binding to protein A-Agarose/Salmon Sperm DNA beads (Millipore, Billerica, USA), or to IgG Sepharose 6 fast Flow (GE Healthcare Bio-Science AB, Uppsala, Sweden).The beads were washed sequentially with ‘low-salt immune complex wash buffer’, ‘high salt immune complex wash buffer’, ‘LiCl immune complex wash buffer’ and TE buffer, before elution in Elution buffer by ON incubation at 65°C  and treatment with Proteinase K. DNA was purified from IPP chromatin by extraction with phenol:chloroform:isoamyl alcohol (25:24:1) and ethanol precipitation according to  standard procedures. DNA pellets were dissolved in nuclease-free water and kept frozen before further use.
sequencing | Solexa sequencing of ChIP material from MCF-7 cells. Sequencing centre: Illumina, Inc., Hayward; Genomics Core Faility, EMBL.

value: cell

tag: genotype

value: pooled Ct-ER-beta and Nt-ER-beta

value: ER-beta

tag: compound dose

value: 10 nM


title: [E-MTAB-345] TAP-ER-beta_+E2_ER-beta IP sequence Performer: EMBL_Heidelberg

description: Performer: EMBL_Heidelberg

source_name: TAP-ER-beta_+E2_ER-beta IP sequence

tag: material type


title: [E-MTAB-345] TAP-ER-beta_-E2_ER-beta IP sequence Performer: EMBL_Heidelberg

description: Performer: EMBL_Heidelberg

tag: cellline


title: K18R_3

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Affymetrix data were analyzed by R/Bioconductor software (CBMi, The Children’s Hospital of Philadelphia).

source_name: CD4+CD25- T-effector cells transduced with Mutant Foxp3 K18R

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

value: CD4+CD25- T-effector cells

tag: transducer

value: :Mutant Foxp3 K18R


title: serum sample from random anonymous human donor at BSRI #18

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description: amplified cDNA / DNA

hyb_protocol: microarrays were hybridized overnight according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit

scan_protocol: microarrays were scanned at 3 um resolution on an Agilent DNA Microarray Scanner

data_processing:
Background normalized output intensities from Agilent's Feature Extraction Software corresponding to 19,058 70-mer viral probes (VALUE) were used for E-Predict (Urisman, et al., 2006), cluster (Eisen, et al., 1998), and Z-score (Chiu, et al., 2006) analysis.
PROCESSING STRATEGY FOR Z-SCORE ANALYSIS     Based on previous Virochip microarray data from many different sample types and disease states, we have generated a empirical list of poorly performing viral oligonucleotide probes (GSE26898_bad_oligos.txt.gz) that are masked to improve the accuracy of the analysis.  The current list consists of 1,460 out of 19,058 probes (7.7%) and is included here.  For all microarrays, these 1,460 bad oligos are removed.       Using the 18 Virochip background microarrays, a median (MEDIAN) and standard deviation (SD) is calculated for each of the 17,598 remaining 70-mer viral probes in the processed data file.  Next, for each experimental microarray, a Z-score is calculated for each viral probe according to the equation:     Z = (X - MEDIAN) / SD, where X = signal intensity      Finally, the Z-scores for each experimental array are ranked from the largest to the smallest.  Probes with the highest Z-scores are considered significant.     For the paper, we report the results of a Z-score analysis on the Virochip microarray corresponding to a lung swab from an affected titi monkey (CMO36992-T28-lung swab).

source_name: serum

label_protocol: randomly amplified cDNA was labelled using a Cy3 or Cy5 fluorescent dye via aa-dNTP incorporation (Wang, et al, 2002; Chiu, et al, 2006; Chiu, et al, 2008)

extract_protocol: Total nucleic acid was extracted from serum using the QIAamp Ultrasens RNA/DNA Virus Kit (Qiagen, Valencia, CA).  Briefly, 200 µL of sample were passed through a 0.22 µm filter (Millipore, Temecula, CA) to remove bacteria and cellular debris and then treated with Turbo DNase (Ambion, Culver City, CA) to degrade host genomic DNA prior to extraction with the kit per the manufacturer's protocols.  Extracted nucleic acid was amplified using a random PCR method to generate cDNA libraries for Virochip as previously described (Wang, et al., PNAS, 2002; Chiu, et al., Clin Inf Dis, 2006).

tag: human donor


title: serum sample from random anonymous human donor at BSRI #15

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #16

description: amplified cDNA / DNA


title: WT2

source_name: CD4+CD25- T-effector cells transduced with Wild Type Foxp3

value: :Wild Type Foxp3


title: serum sample from random anonymous human donor at BSRI #7

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #8

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #12

description: amplified cDNA / DNA


title: K17R_2

source_name: CD4+CD25- T-effector cells transduced with Mutant Foxp3 K17R

value: :Mutant Foxp3 K17R


title: serum sample from random anonymous human donor at BSRI #11

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #9

description: amplified cDNA / DNA


title: EV2

source_name: CD4+CD25- T-effector cells transduced with Empty Vector

value: :Empty Vector


title: WT1


title: serum sample from random anonymous human donor at BSRI #6

description: amplified cDNA / DNA


title: K18R_1


title: serum sample from random anonymous human donor at BSRI #5

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #14

description: amplified cDNA / DNA


title: EV3


title: K18R_2


title: [E-MTAB-345] TAP-ER-beta_+E2_ER-beta IP sequence Performer: Illumina_Hayward

description: Performer: Illumina_Hayward

tag: diseasestate

value: breast cancer


title: EV1


title: serum sample from random anonymous human donor at BSRI #13

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #10

description: amplified cDNA / DNA


title: K17R_1


title: K17R_3


title: [E-MTAB-345] TAP-ER-beta_-E2_ER-alpha IP sequence Performer: EMBL_Heidelberg

description: Performer: EMBL_Heidelberg

source_name: TAP-ER-beta_-E2_ER-alpha IP sequence

value: ER-alpha


title: serum sample from random anonymous human donor at BSRI #17

description: amplified cDNA / DNA


title: serum sample from random anonymous human donor at BSRI #4

description: amplified cDNA / DNA


title: WT3


title: [E-MTAB-345] TAP-ER-beta_+E2_ER-alpha IP sequence Performer: EMBL_Heidelberg

description: Performer: EMBL_Heidelberg

source_name: TAP-ER-beta_+E2_ER-alpha IP sequence


title: serum sample from random anonymous human donor at BSRI #3

description: amplified cDNA / DNA


title: [E-MTAB-345] TAP-ER-beta_+E2_ER-alpha IP sequence Performer: Illumina_Hayward

description: Performer: Illumina_Hayward


title: serum sample from random anonymous human donor at BSRI #1

description: amplified cDNA / DNA


title: mammary tissue_Wt control_untreated

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

description: Gene expression data from FVB wild type mice

hyb_protocol: Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.

scan_protocol: The GeneChip® was scanned using an Agilent Gene Array scanner.

data_processing: Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene.  Genes with a signal of <300 in all experimental groups were excluded from analysis.

source_name: Wild-type group maintained on standard rodent chow

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

growth_protocol: All animal studies were conducted under protocols 07-017 and 09-061.  Female nulliparious FVB/MMTV-PDK1 mice and age-matched FVB/wild-type littermates used in this study.  Numbers of animals per groups were as follows: WT, n=10, WT+GW, n=8, MMTV-PDK1, n=8, MTV-PDK1, n=6.

extract_protocol: Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent).  Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).

treatment_protocol: Mice were maintained on standard rodent chow or a diet supplemented with 0.005% GW501516 for 7 days. GW501516 was provided by the Chemoprevention Branch, National Cancer Institute.

value: mammary gland

tag: genetic background

value: FVB

value: wild type

tag: treatment

value: untreated


title: [E-MTAB-345] TAP-ER-beta_-E2_ER-alpha IP sequence Performer: Illumina_Hayward

description: Performer: Illumina_Hayward

value: ethanol


title: mammary tissue_Wt treated with GW501516_7 days

description: Gene expression data from FVB wild type mice maintained on a GW501516 supplemented diet for 7 days

source_name: Wild-type group, maintained on GW501516 supplemented diet

tag: tissue


title: mammary tissue_MMTV-PDK1_untreated

description: Gene expression data from  MMTV-PDK1 transgenic mice

source_name: Transgenic group, maintained on standard rodent chow

value: MMTV-PDK1 transgenic


title: mammary tissue_ MMTV-PDK1 treated with GW501516_7days

description: Gene expression data from MMTV-PDK1 transgenic mice maintained on a GW501516 supplemented diet for 7 days

source_name: Transgenic group, maintained on GW501516 supplemented diet


title: serum sample from random anonymous human donor at BSRI #2

description: amplified cDNA / DNA


title: lung tissue from affected titi monkey CMO39546

description: amplified cDNA / DNA

organism: Plecturocebus cupreus

source_name: lung tissue

extract_protocol: for swabs, samples were extracted using the QIAamp UltraSens Virus Kit (Qiagen, Valencia, CA); for tissues, samples were extracted using Trizol (Invitrogen, Carlsbad, CA) followed by isopropanol precipitation and two washes in 70% ethanol.

treatment_protocol: for swabs, 200 uL of sample in viral transport media (VTM) were passed through a 0.22 um filter (Millipore, Temecula, CA) and then treated with Turbo DNAse (Ambion, Culver City, CA); tissue samples were homogenized in a 15 mL Eppendorf tube using a disposable microtube pestle and scapel

value: lung tissue


title: lung swab from affected titi monkey CMO36992

description: amplified cDNA / DNA

source_name: lung swab

tag: swab

value: lung swab


title: liver tissue from affected titi monkey CMO39546

description: amplified cDNA / DNA

source_name: liver tissue

value: liver tissue


title: DF19_9_7T

status: Public on Feb 04 2011

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

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

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: We used the bioconductor package (affy package) to generate the RMA data.

label: Biotin

source_name: iPSC line DF19-9-7T generated from human fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: iPS cells were tranferred from MEF to feeder-free culture system to avoid murine RNA contamination

extract_protocol: Tri reagent (Ambioin) extraction of total RNA was performed according to the manufacturer's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer

treatment_protocol: DNA was removed by RNase-free DNase treatment using standard procedure.

value: transgene-free iPSC


title: nasal swab from affected titi monkey CMO36992

description: amplified cDNA / DNA

source_name: nasal swab

value: nasal swab


title: CML15

source_name: iPSC line 15 generated from human CML bone marrow MNC


title: DF6_9

source_name: iPSC line DF6-9 generated from human fibroblast


title: CBT4

source_name: iPSC line T4 generated from human cord blood MNC in the presence of thiazovivin


title: Foreskin

source_name: human foreskin fibroblast

value: somatic cells Fibroblast


title: DF19_9_11T

source_name: iPSC line DF19-9-11T generated from human fibroblast


title: SSC_Not aged_rep1

city: houston

first: Zhiyv

last: Niu

state: tx

address: One baylor plaza, 506E

department: Animal Biology

institute: University of Pennsylvania

description: Gene expression data from 8d donor SSCs, cultured 7-10 weeks

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Mouse Gene 1.0ST Arrays. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using a confocal scanner after excitation at 570 nm.

data_processing: The data were analyzed with Partek Genomics Suite v 6.4 where RMA was applied to normalize and summarize data to yield log2-transformed signal intensities for each probe set.

source_name: Young donor SSCs cultured for 7-10 weeks

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

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

value: Spermatogonial Stem Cell

tag: age

value: 8d donor, cultured 7-10 weeks


title: SSC_Not aged_rep2


title: BM9

source_name: iPS cell line 9 generated from human bone marrow MNC


title: H13B_ESC

source_name: human embryonic stem cell line H13B

value: hESC


title: DF19_9

source_name: iPSC line DF19-9 generated from human fibroblast


title: H7_ESC

source_name: human embryonic stem cell line H7


title: H9_ESC

source_name: human embryonic stem cell line H9


title: BM1L

source_name: iPS cell line 1L generated from human bone marrow MNC


title: BM

source_name: human bone marrow MNC after one day expansion in sera-free media

value: somatic cells bone marrow


title: SSC_Not aged_rep3


title: H1ESC

source_name: human embryonic stem cell line H1


title: DF6_9_9T

source_name: iPSC line DF6-9-9T generatedf from human fibroblast


title: BM1M

source_name: iPS cell line 1M generated from human bone marrow MNC


title: CB6

source_name: iPSC line 6 generated from human cord blood MNC


title: H14A_ESC

source_name: human embryonic stem cell line H13A


title: SSC_Aged in vitro_rep3

description: Gene expression data from 8d donor SSCs, cultured 14-18 months

source_name: Young donor SSCs cultured for 14-18 months

value: 8d donor, cultured 14-18 months


title: BM1i

source_name: iPS cell line 1i generated from human bone marrow MNC


title: SSC_Aged in vitro_rep2


title: 13

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Primary breast tumors sample balanced for lymph node involvement. Each tumor was diagnosed as a poorly differentiated, estrogen positive, her2-neu negative invasive ductal cancer.

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip fluidics station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix).

data_processing: The dataset was preprocessed with MAS 5.0, the GeneChip Microarray Analysis Suite 5.0 software (Affymetrix).

source_name: Primary untreated breast cancer tissue containing at least 70% viable tumor by area (hematoxylin / eosin staining)

label_protocol: Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix). All amplification and labeling reactions were performed on a Biomek 3000 ArrayPlex Workstation (Beckman Coulter).

growth_protocol: Each tumor is snap-frozen in liquid nitrogen within 30 minutes after surgical extirpation and stored at  -80°C

extract_protocol: 8-10 sections from frozen blocks, 10 µm thick, were homogenized and total bulk RNA extracted by the trizol method was further purified using RNAeasy columns (Qiagen, Valencia, CA, USA). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technolgies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).

tag: patient type

value: training set

tag: disease state

value: Primary breast tumor

tag: ln

value: pos

tag: lnratio

tag: er

value: neg

tag: grade

value: III

tag: menopause

value: postmenopausal

tag: histology

value: ID


title: SSC_Aged in vitro_rep1

tag: cell type


title: 10


title: 5304/a


title: SSC_Aged in vivo and in vitro_rep1

description: Gene expression data from Serial transplant SSCs aged 1500 day donor, cultured 14-18 months.

source_name: Serial transplanted SSCs cultured 14-18 months

value: Serial transplant aged 1500 day donor, cultured 14-18 months


title: 4032


title: 4408


title: 3194/b


title: 5458/b


title: SSC_Aged in vivo and in vitro_rep2


title: GGF_aFLAG_2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

hyb_protocol: 15 μg of labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans 3' Gene Expression chip according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Microarrays were scanned with a GeneChip Scanner 3000 according to the manufacturer’s instructions.

data_processing: All the CEL files were processed in R (http://www.r-project.org) using bioconductor. The data were background corrected with gcRMA but not quantile normalized.

organism: Caenorhabditis elegans

source_name: Whole worm lysate at young adult stage

label_protocol: The samples (5µg of each input and 1/3rd of each IP) were amplified once and subsequently labeled according to the GeneChip Expression Analysis Technical Manual (Affymetrix)

extract_protocol: RNA was eluted from beads using TRIzol (Invitrogen) following the manufacturer’s instructions. Precipitation efficiency was enhanced by addition of 10 µg total RNA from mouse brain (Stratagene) to each IP sample.

tag: strain

value: gld-1(q485); ozIs2 [gld-1::gfp::flag]

tag: antibody

value: FLAG

value: whole worm


title: 5201


title: 5303


title: 5310


title: 5218


title: 4523


title: 5377


title: GGF_aFLAG_1


title: 5078


title: N2_aFLAG_1


title: N2_aFLAG_3


title: 4359


title: N2_aFLAG_2


title: 5169


title: aFLAG_3


title: 4371


title: 4704


title: 4128


title: 4741


title: aFLAG_2


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment2, biological rep5

city: Boston

first: Fedik

last: Rahimov

state: MA

address: 3 Blackfan Circle, CLS 15030.4

department: Genetics

institute: Boston Children's Hospital

description: Gene expression data from mouse treated with one dose of ActRIIB-Fc.

hyb_protocol: Affymetrix GeneChip Mouse Gene 1.0 ST arrays were hybridized with the labeled cDNA overnight.

scan_protocol: Arrays were processed and scanned using Fluidics Station 450 and GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Array data were preprocessed using RMA  (apt-1.12.0 and MoGene-1_0-st-v1.r4.analysis-lib-files) and analyzed using the limma package (version 3.4.4, R version 2.11.1, and mogene10sttranscriptcluster.db version 5.0.1) . When multiple probesets mapped to the same gene, the probeset with the highest inter-quantile range across all arrays was retained. Note that in the manuscript, the original and validation studies were analyzed independently, including separate RMA preprocessing; the RMA scores in the Sample tables are also computed separately for the two studies. If analyzing fold-changes from both studies together, explicitly including a factor to correct for the batch variation between the two experiments is advised.

source_name: mouse treated with one dose of ActRIIB-Fc, independent second experiment

label_protocol: Total RNA was labeled with biotin using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay following the manufacturer’s instructions.

extract_protocol: Quadriceps muscles were dissected and immediately snap frozen in liquid nitrogen. Total RNA was isolated from the frozen muscle tissues using TRIzol reagent (Invitrogen).

value: quadriceps muscle

tag: gender

value: female

value: 2 months

value: one dose of ActRIIB-Fc

tag: experiment

value: independent second experiment


title: 4498/b


title: 4255


title: aMYC_3

value: MYC


title: aFLAG_1


title: 4416

value: training set


title: 4567/a

value: Primary breast tumor


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment2, biological rep4

tag: treatment


title: 4522/a

value: pos


title: 4472/b

value: neg


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment2, biological rep3

tag: tissue


title: 4191

value: III


title: aMYC_1


title: aMYC_2


title: Input_3


title: quadriceps, mstn-null mouse, experiment2, biological rep7

description: Gene expression data from mstn-null mouse.

source_name: mstn-null mouse, independent second experiment

tag: genotype

value: mstn-null


title: 4222

value: postmenopausal

value: ID


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment2, biological rep2

tag: age


title: quadriceps, mstn-null mouse, experiment2, biological rep8


title: 4096

tag: patient type


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment2, biological rep1


title: Input_1

value: gld-1(q485); ozIs2 [gld-1::gfp::flag]


title: 4348/b

tag: disease state


title: 3949/b

tag: ln


title: 4005/a

tag: lnratio


title: 3928/a

tag: er


title: 4137/b

tag: grade


title: 4042/b

tag: menopause


title: GGF_aFLAG_3

value: FLAG


title: 3558/b

tag: histology


title: quadriceps, mstn-null mouse, experiment2, biological rep5


title: 4206


title: 3748/2


title: Normal_3

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: trabecular meshwork cells grown in culture from normal human eyes

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

tag: cell type

value: trabecular meshwork cells

tag: Sex

value: unknown

value: healthy


title: 4517


title: 3381


title: Normal_4


title: 3905/a


title: Normal_2


title: Normal_1


title: quadriceps, mstn-null mouse, experiment2, biological rep6

value: quadriceps muscle

value: female

value: 2 months


title: Glaucoma_5

source_name: trabecular meshwork cells grown in culture from glaucoma-stricken human eyes

value: glaucoma


title: Pamoebo_1µg

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

description: Hybridization of 1µg of labeled genomic DNA from P. amoebophila.

hyb_protocol: Labeled targets were hybridized in 400 μl of hybridization buffer [5x SSC, 0.1% SDS, 0.1% n-lauryl sarcosine, 0.1% blocking reagent, 50 μg ml-1 salmon sperm DNA 35% deionized formamide]. After denaturation at 95°C for 10 min, the hybridization solution was immediately applied to the spotted slides using sealed coverslips. Following 16 hours of incubation at 42°C, the slides were washed by three serial washes at 42°C, first in 2xSSC, 0.1% SDS, then in 0.1xSSC, 0.1% SDS and finally in 0.1xSSC. Then, the slides were rinsed in ice-cold double-distilled water, quickly air-dried and stored in the dark until scanning.

scan_protocol: Fluorescence images were recorded by scanning the slides at 10-μm resolution with a GenePix Personal 4100A array scanner (Axon Instruments, Molecular Devices Corporation, Sunnyvale, CA, USA). Each pixel line of the selected area was scanned three times and the obtained signals were averaged to generate the fluorescence image. Scanned images were saved as multilayer tiff images and analyzed with the GenePix Pro 6.0 software (Axon Instruments).

data_processing: Scanned images were analyzed with GenePix Pro 6.0 software (Axon Instruments) and signal intensity surface plots of microarrays were generated using ImageJ with the Interactive 3D Surface Plot plug-in.

organism: Candidatus Protochlamydia amoebophila UWE25

source_name: genomic DNA of P. amoebophila

label_protocol: Genomic DNA was random primed and labelled using the DecaLabel DNA Labelling Kit (Fermentas) according to the manufacturer´s instructions with some modifications. Briefly, per reaction  2 μg fragmented DNA and 10 μl decanucleotides in reaction buffer were mixed, incubated at 95°C for 10 min and immediately placed on ice. After addition of 1 μl dNTP mix, 2 μl 1 mM Cy-dCTP, and 0.8 μl Klenow fragment, the labelling reaction mixture was incubated at 37°C for 90 min. To complete the labelling reaction, another 4 μl of dNTP mix were added to the reaction mix and incubated at 37°C for 60 min. Unincorporated desoxynucleotides and decanucleotides were removed using the QIAquick Nucleotide Removal Kit (Qiagen) and purified genomic DNA was eluted by using double-distilled water.

extract_protocol: DNA was isolated according to the protocol described in (Zhou et al., 1996). Briefly, the pellet was resuspended in 250 μl TE buffer , mixed with 675 μl DNA extraction buffer including Proteinase K and incubated for 30 min at 37°C. After addition of 75 μl 20% SDS the suspension was incubated at 65°C for 2 h with gentle inversions every 20 min. Then, an equal volume of chloroform/isoamylalcohol (24:1, vol/vol) was added and after centrifugation, the aqueous phase was transferred into a new microcentrifuge tube. Nucleic acids were allowed to precipitate after addition of 0.6 vol isopropanol at RT for 1 h. Subsequently DNA was pelleted by centrifugation , washed with ice-cold 70% ethanol and centrifuged again. Finally, nucleic acids were resuspended in double-distilled water and subsequently the DNA was fragmented by sonication.

tag: target concentration

value: 1 µg


title: 3350

value: training set

value: Primary breast tumor


title: 3815

value: pos

value: neg


title: quadriceps, mstn-null mouse, experiment2, biological rep2

tag: gender

value: mstn-null

value: independent second experiment


title: Glaucoma_4


title: quadriceps, mstn-null mouse, experiment2, biological rep3

tag: experiment


title: 3965

value: III

value: postmenopausal

value: ID


title: 3839


title: 4173


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment2, biological rep5

description: Gene expression data from mouse treated with four doses of ActRIIB-Fc.

source_name: mouse treated with four doses of ActRIIB-Fc, independent second experiment

tag: treatment

value: four doses of ActRIIB-Fc


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment2, biological rep4

tag: tissue


title: quadriceps, mstn-null mouse, experiment2, biological rep4

tag: genotype


title: 3107


title: quadriceps, mstn-null mouse, experiment2, biological rep1

tag: age


title: 3443

tag: patient type


title: Glaucoma_3

value: trabecular meshwork cells

value: unknown

tag: disease state


title: Glaucoma_2


title: Glaucoma_1


title: 3207

tag: ln


title: Glaucoma_5

source_name: glaucoma trabecular meshwork cells samples harvested from cadavers

value: Glaucoma


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment2, biological rep3

value: quadriceps muscle

value: female


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment2, biological rep1

value: 2 months


title: 4561

tag: lnratio


title: 2361

tag: er


title: 2424

tag: grade


title: quadriceps, control mouse, experiment2, biological rep3

description: Gene expression data from control mouse.

source_name: control mouse, independent second experiment

value: control


title: 4208

value: training set

tag: menopause


title: quadriceps, control mouse, experiment2, biological rep2


title: 1832

value: Primary breast tumor

tag: histology


title: 3392

value: pos


title: 3025

value: neg


title: 3016


title: 4249


title: 1905


title: 1847


title: Glaucoma_2

tag: cell type


title: quadriceps, control mouse, experiment2, biological rep5


title: Glaucoma_4

tag: Sex


title: quadriceps, control mouse, experiment2, biological rep4


title: 55


title: Glaucoma_3


title: 3995


title: Input_2

tag: strain

value: gld-1(q485); ozIs2 [gld-1::gfp::flag]

value: whole worm


title: 4130

value: III


title: quadriceps, control mouse, experiment2, biological rep1

tag: gender

value: independent second experiment


title: Glaucoma_1


title: Normal_5

source_name: normal trabecular meshwork cells samples harvested from cadavers

value: Healthy


title: Normal_4


title: WT_3

source_name: Lymph Node; Wild Type

value: Female

tag: genotype/variation

value: wild type

value: lymph node


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment1, biological rep3

source_name: mouse treated with one dose of ActRIIB-Fc, original experiment

tag: treatment

value: one dose of ActRIIB-Fc

tag: experiment

value: original experiment


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment1, biological rep2

tag: tissue

value: quadriceps muscle

value: female


title: Normal_1

value: trabecular meshwork cells

value: unknown


title: Normal_3


title: quadriceps, mstn-null mouse, experiment1, biological rep2

source_name: mstn-null mouse, original experiment

tag: age

value: 2 months

tag: genotype

value: mstn-null


title: Normal_2

tag: disease state


title: 54

tag: patient type

value: training set

value: Primary breast tumor

tag: ln

value: neg

value: pos

value: postmenopausal

value: ID


title: WT_2

value: Female

value: Healthy


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment2, biological rep2

value: four doses of ActRIIB-Fc

value: independent second experiment


title: quadriceps, mouse treated with one dose of ActRIIB-Fc, experiment1, biological rep1

value: one dose of ActRIIB-Fc

value: original experiment


title: 50

tag: lnratio

tag: er

value: III


title: 40

tag: grade

tag: menopause


title: 8

tag: histology


title: 38


title: 47


title: 12


title: 45


title: quadriceps, mstn-null mouse, experiment1, biological rep1

value: quadriceps muscle

value: female


title: 9


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment1, biological rep3

source_name: mouse treated with four doses of ActRIIB-Fc, original experiment

value: 2 months


title: 46


title: 48


title: 3114


title: 37


title: 51


title: 43


title: quadriceps, mstn-null mouse, experiment1, biological rep3

value: mstn-null


title: WT_1

tag: Sex

value: wild type

value: lymph node


title: GST3 KO_2

source_name: Lymph Node; HEC-GIcNAc6ST KO

tag: strain

value: HEC-GIcNAc6ST KO


title: GST3 KO_3


title: 36

source_name: Primary untreated breast cancer tissue containing at least 70% viable tumor by area (hematoxylin / eosin staining)

value: training set

value: Primary breast tumor

value: neg

value: pos


title: GST2 KO_2

source_name: Lymph Node; GIcNAc6ST 1 KO

value: Female

value: GIcNAc6ST 1 KO

value: Healthy


title: 32

value: postmenopausal

value: ID


title: Double KO_3

source_name: Lymph Node; Double Knockout HEC-GICNAc6ST and GICNAc6ST-1


title: 29

value: III


title: 33


title: quadriceps, control mouse, experiment1, biological rep3

source_name: control mouse, original experiment

value: quadriceps muscle

tag: gender

value: control

value: original experiment


title: 7


title: 28


title: quadriceps, control mouse, experiment1, biological rep1

value: female

value: 2 months


title: GST2 KO_3

tag: genotype/variation

value: lymph node


title: 5


title: 2


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment1, biological rep2

tag: treatment

value: four doses of ActRIIB-Fc


title: quadriceps, mouse treated with four doses of ActRIIB-Fc, experiment1, biological rep1

tag: experiment


title: 6

value: training set


title: quadriceps, control mouse, experiment1, biological rep2

tag: tissue


title: 30

value: Primary breast tumor


title: 26

value: neg


title: 34

value: pos


title: GST2 KO_1

value: Female


title: 24


title: GST3 KO_1

value: HEC-GIcNAc6ST KO


title: 4


title: 1


title: Double KO_2

value: Double Knockout HEC-GICNAc6ST and GICNAc6ST-1

value: Healthy


title: 27

value: postmenopausal

value: ID


title: Double KO_1


title: SOD_KO3

source_name: TER-119 CD71 erythroid cells Sod 2 Knock Out

value: KO SOD -/-

value: Anemic

tag: cell type

value: TER-119 CD71 erythroid progenitor cells


title: SOD_KO4

value: female


title: SOD_KO2


title: 22

value: III


title: SOD_WT4

source_name: TER-119 CD71 erythroid progenitor cells from wild type cells

value: wild type SOD+/+


title: 3590

value: internal dataset balanced for lymph node involvement


title: 3179


title: 2249


title: SOD_KO1


title: 3253


title: 21

value: training set


title: 3472

value: Primary breast tumor


title: 3126

value: neg


title: 2366

value: pos


title: 3573


title: 2369


title: 2159


title: 2270


title: 3073


title: 2291


title: 2056


title: SOD_WT1


title: 2288


title: 2364


title: 3109


title: 2090


title: MGAT3 WT3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Brain of E10.5 embryos from wild type

tag: developmental stage

value: E10.5 embryo

value: brain

value: unknown

value: MGAT3 +/+ (WT)

value: healthy


title: SOD_WT3

tag: disease state

value: Healthy


title: MGAT3 WT2


title: SOD_WT2


title: MGAT3 WT1


title: MGAT3 KO3

source_name: Brain of E10.5 embryos from Mgat3 knockout

value: MGAT3 -/-


title: 2026

growth_protocol: Each tumor is snap-frozen in liquid nitrogen within 30 minutes after surgical extirpation and stored at -80°C

tag: patient type

value: postmenopausal

value: ID


title: 2028

tag: ln


title: MGAT3 KO2


title: MGAT3 KO1


title: Male Thymus A

source_name: Male mouse thymus

value: Male

tag: age

value: 60 days

value: thymus


title: Female Thymus C

source_name: Female mouse thymus

value: Female


title: Male Thymus B


title: Male Thymus C


title: Female Thymus B


title: BRCA1mut/+ epithelium, patient 3

first: Charlotte

last: Kuperwasser

address: 750 Washington St. Box 5609

institute: Tufts University School of Medicine

description: Global gene expression signature of BRCA1mut/+ epithelium

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

source_name: BRCA1mut/+ epithelium

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in a 1:1 mixture of DMEM+10%FBS, insulin, hydrocortisone and MEGM.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Following retroviral transduction, cells were treated for 5 days with blasticidin (5ng/ml); after drug selection, cells were grown for at least one week prior to RNA extraction.

value: uncultured epithelium

value: breast

tag: genotype


title: BRCA1mut/+ epithelium, patient 2


title: BRCA1mut/+ Tumor 3

description: Global gene expression signature of tumor tissues derived from BRCA1mut/+ cells

source_name: BRCA1mut/+ Tumor

value: Tumor tissue

value: BRCA1mut/+, mut p53, K-ras, myrPI3K,cyclinD1


title: Female Thymus A


title: BRCA1mut/+ Tumor 4


title: BRCA1mut/+ epithelium, patient 1


title: BRCA1mut/+ epithelium, patient 4


title: BRCA1+/+ epithelium, patient 4

description: Global gene expression signature of BRCA1+/+ epithelium

source_name: BRCA1+/+ epithelium


title: BRCA1+/+ epithelium, patient 2


title: BRCA1+/+ epithelium, patient 1


title: BRCA1+/+ Tumor 3

description: Global gene expression signature of tumor tissues derived from BRCA1+/+ cells

source_name: BRCA1+/+ Tumor

value: BRCA1+/+, mut p53, K-ras, myrPI3K,cyclinD1


title: BRCA1+/+ Tumor 1


title: BRCA1+/+ Tumor 4


title: BRCA1mut/+ Tumor 2


title: BRCA1+/+ epithelium, patient 3


title: BRCA1+/+ Tumor 2


title: BRCA1mut/+ Tumor 1


title: hEB16d H1

status: Public on Feb 03 2011

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Cultured under normal growth conditions

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

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

data_processing: The data were normalized using GCRMA and Bioconductor 2.4 with default parameters.

source_name: Human embryoid body derived from H1 passage 38

label_protocol: Total RNA from the samples was normalized to 50 ng/ul and the GeneChip 3’ IVT Express Protocol was used for amplification in a semi automated process. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization on the microarray.

growth_protocol: The pluripotent cell lines were grown in human ES media consisting of KO-DMEM (Invitrogen), 10% KOSR (Invitrogen), 10% plasmanate (Talecris), 1% glutamax or L-glutamin, non-essential amino acids, penicillin/streptomycin, 0.1% 2-mercaptoethanol and 10-20ng/ml bFGF. All pluripotent cells were grown on a monolayer of irradiated CF1-MEFs (GlobalStem) and passaged using trypsin (0.05%) or dispase (Invitrogen). Before collection of RNA for analysis, ES and iPS cells were either isolated using trypsin (0.05%) or dispase, or plated on matrigel (BD Biosciences) for one passage and fed with human ES cell media conditioned in CF1-MEFs for 24h.

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s recommendation.

treatment_protocol: Embryoid body (EB) differentiation was performed as follows: Undifferentiated cells were harvested using dispase or trypsin and plated in suspension in low-adherence plates in the presence of human ES cell culture media without bFGF and plasmanate. Cell aggregates (EBs) were allowed to grow for a total of 16 days, refreshing media every 48h.

tag: cell line

value: hEB16d H1

value: male

tag: passage number


title: hFib 20

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 20, harvested at passage 7

value: hFib 20


title: hFib 18

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 18, harvested at passage 7

value: hFib 18

value: female


title: hFib 17

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 17, harvested at passage 7

value: hFib 17


title: hiPS 15b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 15b, harvested at passage 16

value: hiPS 15b


title: hiPS 20b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 20b, harvested at passage 43

value: hiPS 20b


title: hEB16d HUES6

description: Cultured under normal growth conditions

source_name: Human embryoid body derived from HUES6 passage 30

value: hEB16d HUES6


title: hiPS 18b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 18b, harvested at passage 27

value: hiPS 18b


title: hFib 27

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 27, harvested at passage 7

value: hFib 27


title: hFib 11

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 11, harvested at passage 8

value: hFib 11


title: hEB16d HUES1

description: Cultured under normal growth conditions

source_name: Human embryoid body derived from HUES1 passage 29

value: hEB16d HUES1


title: hFib 15

description: Cultured under normal growth conditions

source_name: Human fibroblast cell line 15, harvested at passage 7

value: hFib 15


title: hiPS 17a

description: Cultured under normal growth conditions

source_name: Human iPS cell line 17a, harvested at passage 12

value: hiPS 17a


title: hiPS 17b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 17b, harvested at passage 32

value: hiPS 17b


title: H9

description: Cultured under normal growth conditions

source_name: Human ES cell line H9, harvested at passage 65


title: hiPS 18c

description: Cultured under normal growth conditions

source_name: Human iPS cell line 18c, harvested at passage 27

value: hiPS 18c


title: hEB16d HUES45

description: Cultured under normal growth conditions

source_name: Human embryoid body derived from HUES45 passage 21

value: hEB16d HUES45


title: H1

description: Cultured under normal growth conditions

source_name: Human ES cell line H1, harvested at passage 37

value: male


title: H7

description: Cultured under normal growth conditions

source_name: Human ES cell line H7, harvested at passage 48


title: HUES66

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES66, harvested at passage 20


title: hiPS 11b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 11b, harvested at passage 13

value: hiPS 11b


title: hiPS 18a

description: Cultured under normal growth conditions

source_name: Human iPS cell line 18a, harvested at passage 30

value: hiPS 18a


title: hiPS 11a

description: Cultured under normal growth conditions

source_name: Human iPS cell line 11a, harvested at passage 22

value: hiPS 11a


title: hiPS 27b

description: Cultured under normal growth conditions

source_name: Human iPS cell line 27b, harvested at passage 31

value: hiPS 27b

value: female


title: hiPS 27e

description: Cultured under normal growth conditions

source_name: Human iPS cell line 27e, harvested at passage 30

value: hiPS 27e


title: HUES65

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES65, harvested at passage 19


title: HUES64

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES64, harvested at passage 19


title: HUES63

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES63, harvested at passage 14


title: HUES62

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES62, harvested at passage 17


title: HUES53

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES53, harvested at passage 18


title: hiPS 11c

description: Cultured under normal growth conditions

source_name: Human iPS cell line 11c, harvested at passage 18

value: hiPS 11c


title: HUES48

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES48, harvested at passage 19


title: HUES8

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES8, harvested at passage 30


title: PRO_24h_24h_PRO-1

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Data were resolved from microarray images using Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA).

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.

organism: Pimephales promelas

source_name: Ovary from prochloraz-exposed fathead minnow at 24h

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA).

growth_protocol: At the time of sample collection, fish were humanely killed in a buffered (200 mg Na2HCO3/L) solution tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond WA, USA). Ovaries were removed and weighed. Tissue was transferred to a labeled microcentrifuge tube and snap-frozen in liquid nitrogen, then stored at -80o C until extracted.

extract_protocol: Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA).  RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).  Total RNA was stored at -80oC until analyzed.

treatment_protocol: Fathead minnow ovary from the prochloraz treatment at 24h exposure

value: prochloraz

tag: time

value: ovary


title: PRO_24h_24h_PRO-3


title: PRO_24h_24h_PRO-2


title: HUES9

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES9, harvested at passage 24

tag: Sex


title: HUES28

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES28, harvested at passage 17


title: PRO_24h_24h_CON-3

source_name: Ovary from control fathead minnow at 24h

treatment_protocol: Fathead minnow ovary from the control treatment at 24h exposure

value: control


title: HUES13

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES13, harvested at passage 46


title: PRO_24h_24h_CON-4


title: HUES44

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES44, harvested at passage 18


title: HUES45

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES45, harvested at passage 20


title: HUES3

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES3, harvested at passage 27


title: HUES6

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES6, harvested at passage 23


title: PRO_24h_12h_PRO-4

source_name: Ovary from prochloraz-exposed fathead minnow at 12h

treatment_protocol: Fathead minnow ovary from the prochloraz treatment at 12h exposure


title: HUES1

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES1, harvested at passage 28


title: Smokers 13

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 GeneChip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), and signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade.

data_processing:
Data were collected using the GeneChip Operating Software (GCOS) v1.4. Data were normalized by RMA using PartekGS v 6.5.

Genome build: hg18
Exons used in analysis: core
Probe group file: HuEx-1_-st-v2.r2pgf
Meta-probeset file: HuEx-1_0-st-v2.rx.dt1.hg18.core.mps

source_name: Bronchoalveolar lavage, smoker

label_protocol: Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: After informed consent was obtained, subjects underwent standard flexible bronchoscopy.  After the application of local anesthesia, bronchoalveolar lavage was performed by instilling 20 ml of normal saline into a tertiary bronchus up to five times in three different lung segments.  The first collection out of five was discarded for possible contamination from upper airway secretions or by lidocaine, which is used to locally anesthetize the subject during the procedure.  The remaining lavage was transported to the laboratory where fluid was filtered through sterile gauze and centrifuged at 200 x g for 5 min to pellet cellular material. The resulting pellet was suspended in phosphate-buffered saline and centrifuged at 16,000 x g for one minute.  The macrophages were suspended in medium, labeled with Wright stain and microscopically examined to ensure that greater than 95% of the cells were macrophages.  Following validation, 5x10^6 cell aliquots were frozen at -80°C for later DNA and RNA isolation.

value: alveolar macrophages

tag: sample type

value: smoker


title: PRO_24h_12h_PRO-3


title: PRO_24h_12h_PRO-2


title: PRO_24h_12h_PRO-1


title: Smokers 11


title: HUES49

description: Cultured under normal growth conditions

source_name: Human ES cell line HUES49, harvested at passage 17


title: PRO_24h_12h_CON-3

source_name: Ovary from control fathead minnow at 12h

treatment_protocol: Fathead minnow ovary from the control treatment at 12h exposure


title: Smokers 12


title: Smokers 7


title: PRO_24h_6h_CON-4

source_name: Ovary from control fathead minnow at 6h

treatment_protocol: Fathead minnow ovary from the control treatment at 6h exposure


title: PRO_24h_6h_PRO-3

source_name: Ovary from prochloraz-treated fathead minnow at 6h

treatment_protocol: Fathead minnow ovary from the prochloraz treatment at 6h exposure


title: PRO_24h_6h_PRO-2


title: PRO_24h_24h_CON-1

source_name: Ovary from fathead minnow at 24h

treatment_protocol: Fathead minnow ovary from control treatment at 24h exposure


title: PRO_24h_6h_PRO-1


title: Smokers 10


title: hEB16d HUES3

description: Cultured under normal growth conditions

source_name: Human embryoid body derived from HUES3 passage 22

value: hEB16d HUES3


title: Smokers 9


title: PRO_24h_12h_CON-4


title: Smokers 8


title: PRO_24h_24h_CON-2


title: PRO_24h_12h_CON-2


title: PRO_24h_12h_CON-1


title: PRO_24h_6h_PRO-4


title: PRO_24h_6h_CON-3


title: Non-smokers 7

source_name: Bronchoalveolar lavage, non-smoker

value: non-smoker


title: Smokers 5


title: Smokers 6


title: Non-smokers 3


title: PRO_24h_6h_CON-1


title: Non-smokers 1


title: Smokers 1


title: PRO_24h_6h_CON-2


title: Non-smokers 6


title: Smokers 3


title: Smokers 4


title: Smokers 2


title: HeLa_control_3

city: Prague

first: David

last: Stanek

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

hyb_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay (P/N 701880 Rev. 5)

scan_protocol: Affymetrix GeneChip Expression Wash, Stain, and Scan User Manual (P/N 702731)

data_processing: Data were analysed using Partek Genomics Suite 6.4 software (RMA, quantile normalization). Only  ‘core’ meta-probe sets were used to identify alternative splicing events.

source_name: HeLa control

growth_protocol: HeLa cells cultured in DMEM supplemented with 10% fetal calf serum, penicillin, and streptomycin.

extract_protocol: Total RNA isolated with TRIzol

treatment_protocol: 15 hrs treatment with 5mM sodium butyrate

value: HeLa

tag: agent