city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description:
E15.5_Lung_Mek1flox/flox;Mek2-/-;Dermo1+/Cre_rep4.
SAMPLE12

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were log2 transformed and normalised using quantile normalisation with lumi in R

source_name: E15.5  lung

label_protocol: Performed by Genome Quebec (Montreal, Qc, Canada)

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) followed by DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Quantification by Nanodrop.

tag: background strain

tag: developmental stage

value: Lung


title: lung 4 days [L4_32]

status: Public on Sep 02 2014

type: RNA

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description: The signal#1 and signal#2 (i.e. SIGNAL_MEAN*.1 and SIGNAL_MEAN*.2) columns in .ftr files correspond to 'test/Cy3' and 'reference/Cy5' channels, respectively.

hyb_protocol: Each hybridization mixture was made up from 1.1 µg Test (Cy3) and 1.1 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of the appropriate sample tracking control (STC, Roche Nimblegen) was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 95°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto a 12x135k Mus musculus microarray (Catalog no. 05543797001, Design 090901 MM9 EXP HX12) containing 44,170 genes with 3 probes per target gene. Microarrays were hybridized for 20 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen). Afterwards, the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0

scan_protocol: Slides were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

data_processing: Raw microarray signal data were normalised in R (www.r-project.org), using a four step approach: (1) natural log-transformation, (2) quantile normalisation of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate oligo spots. Normalised data for the resulting 44170 oligonucleotides were further analysed in R and Microsoft Excel. As the actual calculations for this experiment are done on ratios infected vs uninfected (t=0), the sample data table contains log2-ratios per sample vs average control. Further calculations were based on logratios compared to uninfected animals.

molecule: total RNA

organism: Mus musculus

source_name: lung 4 days

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: Female BALB/c mice (Harlan, The Netherlands), 8-week-old, were divided in groups of three animals and housed in cages (macrolon III including filter top).

extract_protocol: RNA isolation was performed using a miRNeasy Mini Kit with DNAse treatment (Qiagen). RNA concentrations were determined using UV spectroscopy (Tech3 module, Synergy Mx, BioTek). RNA quality was determined using electrophoresis (RNA nano 6000 kit, 2100 Bioanalyzer, Agilent).

treatment_protocol: Three healthy mice were euthanized at day 0 and considered as naïve group. Other mice were intranasally infected under anesthesia (isoflurane/oxygen), with 2x10^5 cfu Bordetella pertussis B1917 in 40 µl Verweij medium at day 0. Groups of animals (n=3) were euthanized after 2, 4, 6 hours, and after 1, 2, 4, 7, 10, 14, 21 and 28 days of infection, respectively. Please note that some  timepoints were not used for microarray analysis, but were included to compare bacterial counts.

tag: strain

value: BALB/c

tag: gender

value: female

tag: age

value: 8 weeks

tag: infected with

value: 2x10^5 cfu Bordetella pertussis B1917

tag: tissue

value: lung

tag: time after infection

value: 4 days

source_name: lung 4 days (reference pool)


title: lung 2 days [L2_30]

source_name: lung 2 days

value: 2 days

source_name: lung 2 days (reference pool)


title: 4M_41P

city: Trondheim

first: Duan

last: Chen

address: Erling Skjalgssons Gate 1

department: Department of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

description: Gene expression of unvagtomized posterior stomach at 10 months old mice

hyb_protocol: 1.5ug of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58°C to the MouseWG-6 v2.0 BeadChips.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Reader.

data_processing: Data was log2 transformed and quantile normalized using the Lumi package implemented in Bioconductor/R. The data was filtered using a detection p-value <= 0.01 in more than one sample for each probe.

label: biotin

source_name: Posterior abdomen, 4 months post surgery

label_protocol: Biotin labeling was performed using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.)

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA were purified with Trizol reagent

treatment_protocol: Mice were anterior vagotomized at 6 months, and sacrificed at 8, 10, or 12 months.

value: FVB/N

value: Female

tag: genotype

value: INS-GAS

value: 10 months

value: unvagotomized posterior stomach


title: 2M_58A

description: Gene expression of vagtomized anterior stomach at 8 months old mice

source_name: Anterior abdomen, 2 months post surgery

value: 8 months

value: vagotomized anterior stomach


title: 6M_34P

description: Gene expression of unvagtomized posterior stomach at 12 months old mice

source_name: Posterior abdomen, 6 months post surgery

value: Male

value: 12 months


title: lung 4 hours [L0-4_21]

source_name: lung 4 hours

value: 4 hours

source_name: lung 4 hours (reference pool)


description:
E15.5_Lung_Mek1flox/flox;Mek2-/-;Dermo1+/Cre_rep3.
SAMPLE11

scan_protocol: Standard Illumina scanning protocol

value: Lung


title: lung 2 days [L2_29]

value: BALB/c

value: female


title: 4M_36A

description: Gene expression of vagtomized anterior stomach at 10 months old mice

source_name: Anterior abdomen, 4 months post surgery


title: 6M_34A

description: Gene expression of vagtomized anterior stomach at 12 months old mice

source_name: Anterior abdomen, 6 months post surgery


title: lung 2 days [L2_28]

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917


description:
E15.5_Lung_Mek1flox/flox;Mek2-/-;Dermo1+/Cre_rep2.
SAMPLE10


title: 4M_36P


title: 2M_52A


title: lung 4 hours [L0-4_20]

value: lung


description:
E15.5_Lung_Mek1+/flox;Mek2-/-;Dermo1+/Cre_rep3.
SAMPLE7


title: 6M_33A


description:
E15.5_Lung_Mek1+/flox;Mek2-/-;Dermo1+/Cre_rep4.
SAMPLE8


title: 2M_52P

description: Gene expression of unvagtomized posterior stomach at 8 months old mice

source_name: Posterior abdomen, 2 months post surgery


title: lung 10 days [L10_40]

source_name: lung 10 days

value: 10 days

source_name: lung 10 days (reference pool)


title: lung 21 days [L21_50]

source_name: lung 21 days

value: 21 days

source_name: lung 21 days (reference pool)


title: lung 4 hours [L0-4_19]


description:
E15.5_Lung_Mek1+/flox;Mek2-/-;Dermo1+/Cre_rep1.
SAMPLE5

source_name: E15.5  lung


title: 4M_35A

value: FVB/N


title: lung 0 hours [L0-0_1]

source_name: lung 0 hours

value: 0 hours

source_name: lung 0 hours (reference pool)


title: lung 0 hours [L0-0_2]


title: 6M_33P

value: INS-GAS


title: E15.5_Lung_Dermo1+/Cre_rep4.

description:
E15.5_Lung_Dermo1+/Cre_rep4.
SAMPLE4


description:
E15.5_Lung_Mek1flox/flox;Mek2-/-;Dermo1+/Cre_rep1.
SAMPLE9


description:
E15.5_Lung_Mek1+/flox;Mek2-/-;Dermo1+/Cre_rep2.
SAMPLE6


title: 4M_35P

value: 10 months

value: unvagotomized posterior stomach


title: lung 0 hours [L0-0_3]


title: 2M_40A

value: Female

value: 8 months

value: vagotomized anterior stomach


title: E15.5_Lung_Dermo1+/Cre_rep1.

description:
E15.5_Lung_Dermo1+/Cre_rep1.
SAMPLE1


title: 2M_40P


title: 6M_45P

value: 12 months


title: MDT-MB-10

type: genomic

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

description: Methylation data from a glioblastoma tumor sample

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Data analysis has been carried out using the minfi Bioconductor package (version 1.4.0), performing background correction and normalization to internal controls.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary medulloblastoma tumor tissue

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Allprep DNA/RNA/Protein Mini Kit.

value: M

tag: histology

value: classic


title: E15.5_Lung_Dermo1+/Cre_rep3.

description:
E15.5_Lung_Dermo1+/Cre_rep3.
SAMPLE3

value: Lung


title: E-FABP knockout GM-BMMs, biological rep1

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

description: Gene expression data of tumor treated BMM

hyb_protocol: The IVT products were column-purified, fragmented and hybridized at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

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

data_processing: The data were analyzed using R package Affy (version 1.36.1), affycoretools (version 1.34.0), limma (version 3.14.4) and gcrma (version 2.30.0).  The QC of the data was assessed using AffyQCReport (version 1.36.0). RMA function with default setting was used to globally normalize the data. Probes with absent call values in any of the samples using mas5calls function were treated as non-expressed probes and excluded from the downstream analysis. The probe annotation is done using mouse4302.db package (version 2.9.0) from BioConductor.

source_name: Bone marrow from naive C57BL/6 mice

label_protocol: Microarray analysis was conducted according to the manufacture's instructions for Affymetrix 3' IVT Express Kit.  RNA quality was assessed by Agilent Bioanalyzer. Reverse transcription to second strand cDNA was generated from 100 ng of high quality total RNA. Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: Bone marrow cells were collected from naive C57BL/6 and E-FABP knockout mice of 6~8 week old. GM-BMMs were derived using GM-CSF(20ng/ml) in RPMI1640 with 5%FBS for 7 days in 100mm plates before tumor treatment. Fresh media with GM-CSF were added every 2 days to replace about half the old media.

extract_protocol: Total RNA was extracted from tumor-stimulated GM-BMMs of WT and E-FABP-/- mice using RNeasy Mini Kit (Qiagen), following the manufacturer's protocol.

treatment_protocol: BM-GMMs were lifted off the plate and replated in a 12-well tissue culture plate. After cells were re-attached, E0771 tumor cells were added to the well using cell culture insert. After 18hr of GM-BMM, E0771 co-culture, tumor cell inserts were tossed away. Treated GM-BMMs were lysed for total RNA isolation.

value: mouse bone marrow

value: E-FABP knockout

tag: treatment

value: 1x10^6 cells in a 12-well plate co-cultured overnight with 1x10^6 E0771 tumor cells in an sterile insert


title: E15.5_Lung_Dermo1+/Cre_rep2.

description:
E15.5_Lung_Dermo1+/Cre_rep2.
SAMPLE2


title: Muscle biopsies from trained COPD patient #4

status: Public on Sep 01 2014

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description:
TD4
n30
Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.

hyb_protocol: Hybridization to Affymetrix Human Genome Focus oligonucleotide arrays following the manufacturer’s instructions.

scan_protocol: Affymetrix Scanner 3000 7G.

data_processing: The data were quantile normalized using the R package RMA.

source_name: Trained COPD with normal BMI

label_protocol: Amplification and labeling of cRNA was performed with the Affymetrix IVT labeling  kit.

extract_protocol: Muscle samples (~0.1 g) were placed in RNA stabilization reagent (RNAlater, Ambion, Inc., 2130, Woodward street, Austin TX-USA) and stored at -20oC for RNA extraction, which was performed by using the TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: 3 weeks of endurance training.

value: musculus vastus lateralis

tag: disease state

value: chronic obstructive pulmonary disease (COPD)

tag: exercise state

value: trained

tag: bmi

value: normal

tag: individual


title: Muscle biopsies from healthy sedentary individual #1

description:
SH1
n7
Gene expression data from muscle biopsies of a sedentary healthy individual.

source_name: Sedentary healthy

value: healthy

value: sedentary


title: Muscle biopsies from trained healthy individuals #3

description:
TH3
n29
Gene expression data from muscle biopsies of a trained healthy individual.

source_name: Trained healthy


title: Muscle biopsies from trained COPD patient #5

description:
TD5
n39
Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.


title: Muscle biopsies from trained healthy individual #2

description:
TH2
n18
Gene expression data from muscle biopsies of a trained healthy individual.


title: Muscle biopsies from healthy sedentary individual #3

description:
SH3
n21
Gene expression data from muscle biopsies of a sedentary healthy individual.


title: Muscle biopsies from sedentary COPD patient #4

description:
SD4
n22
Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.

source_name: Sedentary COPD with normal BMI


title: Muscle biopsies from trained COPD patient #3

description:
TD3
n32
Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.


title: Muscle biopsies from trained healthy individual #1

description:
TH1
n17
Gene expression data from muscle biopsies of a trained healthy individual.


title: Muscle biopsies from sedentary COPD patient #5

description:
SD5
n37
Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.


title: Muscle biopsies from sedentary COPD patient #1

description:
SD1
n4
Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.


title: Muscle biopsies from trained COPD patient #1

description:
TD1
n31
Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.


title: Muscle biopsies from trained COPD patient #2

description:
TD2
n20
Gene expression data from muscle biopsies of a trained COPD individual with normal BMI.


title: Muscle biopsies from sedentary COPD patient #2

description:
SD2
n10
Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.


title: Hs606T_siRECK_1

city: New York

first: Logan

middle: A

last: Walsh

state: NY

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: RECK siRNA

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The raw CEL files of the 8 samples was imported into Partek without normalization or background correction.

source_name: Breast Cancer Cell line_RECK_siRNA

label_protocol: Expression analysis of RNA samples was performed using the Affymetrix U133 2.0 microarray (Affymetrix). Processing of the arrays was per the manufacturer’s protocol.

extract_protocol: RNeasy Mini Kit (Qiagen)

value: breast

tag: cell line

tag: biomaterial provider

value: ATCC


title: Muscle biopsies from sedentary COPD patient #3

description:
SD3
n23
Gene expression data from muscle biopsies of a sedentary COPD individual with normal BMI.


title: Hs343T_siRECK_1

description: RECK siRNA


title: Hs606T_siSCR_1

description: Scramble siRNA

source_name: Breast Cancer Cell line_scramble_siRNA


title: Hs606T_siRECK_2

description: RECK siRNA


title: Hs606T_siSCR_2

description: Scramble siRNA


title: Hs343T_siRECK_2

description: RECK siRNA


title: LM24175_RECK_1

description: +RECK

source_name: Breast Cancer Cell line_RECK_overexpression


title: Muscle biopsies from healthy sedentary individual #2

description:
SH2
n8
Gene expression data from muscle biopsies of a sedentary healthy individual.


title: LM24175_RECK_2

description: +RECK


title: Hs343T_siSCR_2

description: Scramble siRNA


title: LM24175_EV_1

description: +Empty Vector

source_name: Breast Cancer Cell line_emptyvector


title: MDAMB231_RECK_1

description: +RECK


title: Hs343T_siSCR_1

description: Scramble siRNA


title: MDAMB231_RECK_2

description: +RECK


title: Panicles of OX-Ghd7HJ19-biological rep1

city: Wuhan

first: Xiaoyu

last: Weng

address: HZAU

country: China

institute: NCPGR

description: expression variations in rice flag leaf at heading date

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

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

data_processing: The Robust multi-array average (RMA) was used to backgroud correction and probeset expression value collection.

organism: Oryza sativa

source_name: developing panicles (0.1cm) of OX-Ghd7HJ19-biological rep1

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

growth_protocol: OX-Ghd7HJ19 transgenic and wild-type plants were grown under natural field conditions in the experimental station of Huazhong Agricultural University, Wuhan, China.

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

treatment_protocol: Young leaves in vegetative stage (35-days old) and developing panicles (0.1cm) of OX-Ghd7HJ19 transgenic and wild-type plants were collected at 3 hours after dawn under natural field conditions.

value: panicles

tag: genotype/variation

value: Over-expressing Ghd7 in Hejiang19


title: Young leaves of OX-Ghd7HJ19-biological rep2

source_name: Young leaves in vegetative stage of OX-Ghd7HJ19-biological rep2.CEL

value: young leaves


title: MDAMB231_EV_2

description: +Empty Vector


title: Panicles of OX-Ghd7HJ19-biological rep2

source_name: developing panicles (0.1cm) of OX-Ghd7HJ19-biological rep2


title: BCG-vaccinated-1

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

description: Gene expression data from BCG vaccinated and Mtb-infected mouse lung

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

data_processing: The microarray data was normalized using RMA and processed in the Partek Genomics Suite, version 6.5 as described previously in Koo,MS et.al (PMID: 22280836 and 21364878).

source_name: Mouse lungs-BCG vaccinated and Mtb-infected

label_protocol: Total RNA samples were reverse transcribed and labled with biotin as suggested by the array manufacturer (affymetrix)

growth_protocol: Female C57BL/6 mice were vaccinated subcutaneously with ∆bfrB or BCG (n=3 per group) .  At 8 weeks post-vaccination, mice were aerosol infected with Mtb H37Rv. At 4 weeks post infection, mice  were sacrificed and lungs were removed. Lung total RNA from vaccinated and Mtb-infected mice was extracted, purified  and were processed separately for microarray analysis.

extract_protocol: Total RNA from the mouse lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using RNA mini prep columns (Qiagen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: no treatment involved

value: female

tag: vaccinated with

value: BCG

value: Mtb H37Rv

tag: time point

value: 4 weeks post infection

value: lung


title: Panicles of HJ19-biological rep2

source_name: developing panicles (0.1cm) of HJ19-biological rep2


title: MDAMB231_EV_1

description: +Empty Vector


title: ΔbfrB-vaccinated-3

description: Gene expression data from ΔbfrB vaccinated and Mtb-infected mouse lung

scan_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

source_name: Mouse lungs-ΔbfrB-vaccinated and Mtb-infected

tag: strain

tag: gender

value: ∆bfrB


title: Young leaves of HJ19-biological rep2

source_name: Young leaves in vegetative stage of HJ19-biological rep2.CEL


title: Panicles of HJ19-biological rep1

source_name: developing panicles (0.1cm) of HJ19-biological rep1


title: Young leaves of HJ19-biological rep1

source_name: Young leaves in vegetative stage of HJ19-biological rep1.CEL


title: BCG-vaccinated-3

tag: infected with


title: N1 24h

city: Tokorozawa

first: Motoshi

last: Nagao

state: Saitama

address: 4-1 Namiki

department: Department of Rehabilitation for the Movement Functions

country: Japan

institute: Research Institute, National Rehabilitation Center for Persons with Disabilities

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: HMGN1 virus-infected mouse E11.5 NPCs, cultured in the absence of FGF2 and EGF

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: NPCs derived from E11.5 mouse forebrains were maintained in the presence of FGF2 and EGF. After infection, the virus-infected NPCs were dissociated and seeded on poly-D-lysine -coated dishes, and then the cells were cultured for 1 day without  FGF2 and EGF.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: developmental stage

tag: tissue

value: brain

tag: cell type

value: neural precursor cells

tag: infection

value: HMGN1 retrovirus


title: BCG-vaccinated-2


title: Young leaves of OX-Ghd7HJ19-biological rep1

source_name: Young leaves in vegetative stage of OX-Ghd7HJ19-biological rep1.CEL


title: ΔbfrB-vaccinated-1


title: LM24175_EV_2

description: +Empty Vector


title: P85 3

city: Frankfurt am Main

first: Anahita

last: Rafiei

address: Theodor Stern Kai 7

country: Germany

institute: University Clinic Frankfurt

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) were hybridized with 2.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Mouse Gene 1.0 ST Array CDF Files
meta-probeset file: MoGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (7.8 MB, 10/7/11)

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with construct harboring p185BCR/ABL protein

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Sca1+/lin- cells were isolated from the bone marrow of C57BL6/J mice, transduced with the desired constructs after one day keeping in culture in the presence of mIL-3, mIL-6 and mSCF, and kept nine days in culture until the transplantation time point

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

treatment_protocol: No treatment


title: P96 P85 2

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with construct harboring p96ABL/BCR and p185BCR/ABL proteins


title: P85 1


title: P96 3

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with construct harboring p96ABL/BCR protein


title: P85 2


title: P96 2


title: P96 P85 1


title: P96 1


title: P40 3

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with construct harboring p40ABL/BCR protein


title: ΔbfrB-vaccinated-2


title: P96 P85 3


title: P40 P85 2

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with construct harboring p40ABL/BCR and p185BCR/ABL proteins


title: P40 P85 1


title: P2

source_name: RNA from spleens of mice transplanted with Sca1+/lin- murine stem cells transduced retrovirally with empty vector control


title: P40 P85 3


title: P40 1


title: Progesterone +RU-486 at 12h, biological rep2

city: Mexico City

first: Ivan

last: Salido-Guadarrama

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

description: Gene expression data from U373 cells after 12h of combined Progesterone and RU-484 treatment

hyb_protocol: Labeled DNA was hybridized to the Affymetrix Gene Chip Human Gene ST 1.0 Arrayin a hybridization cocktail . Washing and staining steps were carried out using GeneChip Fluidics Station 450.

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara CA)

data_processing: Raw intensity data were pre-processed and quantile normalized using the robust multi-array average (RMA) expression measure  function implemented within the oligo package of bioconductor. Log2 transformed expression values, obtained after RMA, were used to analyze the differential expressions between different groups was analyzed using empirical Bayes method implemented in the LIMMA package and P values were computed.

source_name: U373 cells collected after 12h of combined Progesterone and RU-484 treatment

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Whole-Transcript Sense Target Labeling Protocol

growth_protocol: U373 cells were grown to ∼70% confluence in DMEM without antibiotic, washed with serum-free media, and changed into media containing 5% of free-hormone fetal bovine serum for 24 h

treatment_protocol: Cells were then treated with 10 nM of P4, 1µM RU 486 or both  for 12 h.

value: astrocytoma cell line U37


title: P3


title: P40 2


title: Progesterone +RU-486 at 12h, biological rep1


title: P1


title: RU-486 at 12h, biological rep2

description: Gene expression data from U373 cells after 12h of RU-484 treatment

source_name: U373 cells collected after 12h of RU-484 treatment


title: Progesterone at 12h, biological rep1

description: Gene expression data from U373 cells after 12h of Progesterone treatment

source_name: U373 cells collected after 12h of Progesterone treatment


title: RU-486 at 12h, biological rep1


title: Progesterone at 12h, biological rep2


title: Luteolin added high-fat diet_adipose rep3

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing:
The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).
All probe signal value was transformed by logarithm and normalized by quantile method. The 1-way anova test, tukey HSD test and fold change were applied. Statistical significance was adjusted by the Benjamini-Hocbherg multiple-testing correction with false discovery rate(FDR). All data analysis was conducted using R statistical language v. 2.4.1.

source_name: Luteolin added high-fat diet_epididymal adipose

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Thirty-six male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet for a one-week acclimation period after arrival

extract_protocol: Total RNA was extracted from the adipose tissue and liver using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a normal diet (ND, n=10), high-fat diet consisting of 20% fat and 1% cholesterol (HFD, n=13) or HFD with 0.005% (w/w) luteolin (Sigma Chemical, MO) (LU, n=13) for 16 weeks

tag: age

value: 4 weeks

value: male

tag: diet

value: HFD with 0.005% (w/w) luteolin (LU) for 16 wks

value: epididymal adipose tissue


title: Luteolin added high-fat diet_adipose rep1


title: Vehicle at 12h, biological rep2

description: Gene expression data from U373 cells after 12h of vehicle treatment

source_name: U373 cells collected after 12h of vehicle treatment


title: Vehicle at 12h, biological rep1


title: High-fat diet_adipose rep3

source_name: High-fat diet_epididymal adipose

value: high-fat (20% fat and 1% cholesterol; HFD) for 16 wks


title: High-fat diet_adipose rep2


title: Luteolin added high-fat diet_liver rep3

source_name: Luteolin added high-fat diet_liver

value: liver


title: High-fat diet_liver rep2

source_name: High-fat diet_liver


title: High-fat diet_adipose rep1


title: Normal diet_adipose rep3

source_name: Normal diet_epididymal adipose

value: normal diet (ND) for 16 wks


title: Normal diet_adipose rep2


title: Luteolin added high-fat diet_adipose rep2


title: Normal diet_adipose rep1


title: High-fat diet_liver rep3


title: Luteolin added high-fat diet_liver rep2


title: High-fat diet_liver rep1


title: Normal diet_liver rep1

source_name: Normal diet_liver


title: Normal diet_liver rep2


title: PVH_WT_1

city: Maebashi

first: Daisuke

last: Kohno

state: Gunma

institute: Gunma University

description:
male, hypothalamus, PVH
Sample names: 7909591045_A, WT-1

hyb_protocol: Hybridization was done by UTSW Microarray Core (http://microarray.swmed.edu/).

scan_protocol: Scanning was done by UTSW Microarray Core (http://microarray.swmed.edu/).

data_processing:
To generate normalized data, quantile normalization was performed using GeneSpring GX (Agilent Technologies, Santa Clara, CA).
Microsoft Excel was used to sort FC (KO/WT) values in  descending order.  'Final processed normalized data.xls' is linked as a supplementary file on the Series record.

source_name: PVH

label_protocol: Labeling was done by UTSW Microarray Core (http://microarray.swmed.edu/).

growth_protocol: Food and water were given ad libitum

extract_protocol: Total RNA was extracted from PVH of WT and Sim1-Cre specific DNMT3a deletion mice using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen) and Phase Lock Gel (5 Prime Inc., Gaitherburg, MD).

treatment_protocol: Mice at 6 weeks old were used.

value: WT

value: paraventricular nucleus in the hypothalamus (PVH)


title: vmix_rep2

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description: HUVECs transfected with KSHV miRNAs replicate 2 of 2.

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.

scan_protocol: Scanned on an Agilent scanner. Images were processed with Agilent Feature Extraction Software v10.1.1.1.

data_processing: Linear LOWESS normalization was used. Default Agilent normalization was employed within Genespring GX. In detail, Each gene's measured intensity was divided by its control channel value in each sample; if the control channel was below 0 then 0 was used instead. If the control channel and the signal channel were both below 0 then no data was reported.  Each measurement was divided by the 50.0th percentile of all measurements in that sample.   The percentile was calculated using only genes marked present.    Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 0 then each measurement for that gene was divided by 0 if the numerator was above 0, otherwise the measurement was thrown out.

source_name: Stratagene Universal Reference RNA

label_protocol: 500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).

extract_protocol: Universal Reference RNA purchased from Stratagene.

tag: sample type

value: Stratagene Universal Reference RNA (Pooled cell line RNA)

source_name: transfected HUVECs

growth_protocol: HUVECs were grown in T75 flasks overnight and transfected around 70% confluency.

extract_protocol: RNA was purified using Tri reagent (Ambion) and RNA quality was determined using a Bioanalyzer 2100 (Agilent).

treatment_protocol: HUVECs were transfected (total miRNA concentration was 10 nM) in T75 flasks for 6 hr. and then split into new flask, and harvested 30 hr. after transfection.

value: HUVEC

tag: transfection

value: KSHV miRNA mimics (vMix)

tag: time

value: 30 hr. post transfection


title: vmix_rep1

description: HUVECs transfected with KSHV miRNAs replicate 1 of 2.

tag: cell line


title: PVH_DNMT3a/Sim1-Cre_2

description:
male, hypothalamus, PVH
Sample names: 7909591045_E, KO-2

value: Sim1-Cre specific DNMT3a deletion


title: PVH_WT_2

description:
male, hypothalamus, PVH
Sample names: 7909591045_B, WT-2


title: PVH_DNMT3a/Sim1-Cre_1

description:
male, hypothalamus, PVH
Sample names: 7909591045_D, KO-1


title: PVH_DNMT3a/Sim1-Cre_3

description:
male, hypothalamus, PVH
Sample names: 7909591045_F, KO-3


title: Pool x ∆2173_5 stat

city: Greifswald

first: Jan

last: Pané-Farré

address: F.-L.-Jahn-Str. 15

department: Department of Microbial Physiology

hyb_protocol: 300 ng of Cy5-labeled cDNA and 300 ng of Cy3-labeled cDNA were hybridized together to the microarray following Agilent's hybridization, washing, and scanning protocol (Two-Color Microarray-Based Gene Expression Analysis, version 5.5)

scan_protocol: Intensity values were extracted and processed (background subtraction and LOWESS normalization) by means of the Feature Extraction software (version 10.5, Agilent Technologies, Santa Clara, CA, USA).

data_processing: Data analysis was performed using the Cyber-T program (Baldi and Long, 2001). The parameters for the Bayesian standard deviation estimation were: sliding-window size of 301 and a confidence value for the Bayesian variance estimate of 10. Genes with a Benjamini & Hochberg corrected P value of <0.05 and at least a 2-fold change in the mean fluorescence value of the three hybridization experiments were considered biologically significant expression changes.

organism: Staphylococcus aureus

source_name: S. aureus reference pool

label_protocol: Total RNA was prepared from three independent experiments. Synthesis and purification of fluorescently labeled cDNA were carried out according to Charbonnier et al. (2005) with minor modifications. In detail, 10 µg of total RNA were mixed with random primers (Promega, Madison, WI, USA) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies, Santa Clara, CA, USA). The RNA/primer mixture was incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen, Karlsruhe, Germany), 5 µl of 0.1 M DTT (Invitrogen, Karlsruhe, Germany), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare, Little Chalfont, UK) and 2 µl of SuperScript II reverse transcriptase (Invitrogen, Karlsruhe, Germany). The reaction mixture was incubated at 42°C for 60 min and then heated to 70°C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen, Karlsruhe, Germany) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare, Little Chalfont, UK). The individual samples were labeled with Cy5, whereas the reference pool was labeled with Cy3.

growth_protocol: S. aureus was cultured in a defined synthetic medium. Synthetic medium was used as described by Gertz et al. (1999) but without MOPS and glycine and with a final glucose concentration of 0.75 µM.

extract_protocol: For total RNA isolation, S. aureus cells were cultivated in synthetic medium.  For Northern blot analyses, RNA was isolated as described previously using the acid-phenol method (Majumdar et al., 1991) with modifications as described by Fuchs et al. (2007). For DNA microarray analyses the RNA was further purified to eliminate traces of remaining DNA (Reiß et al., 2012). For every strain RNA was extracted from three independent cultivations.

treatment_protocol: An overnight culture (HG001 wild type or isogenic asp23 mutant) was used to inoculate 120 ml medium to an OD500 of 0.075. Samples were taken during exponential growth phase (OD500=0.5) and one hour after entering stationary growth phase.

tag: strains

value: HG001 wild type and HG001 asp23 mutant

tag: growth phase

value: exponential growth and stationary phase

source_name: asp23 mutant, stationary phase

value: HG001 asp23

value: stationary phase


title: Pool x RN6 stat

source_name: wild type, stationary phase

value: HG001 wild type


title: Normal diet_liver rep3

value: 4 weeks

value: male


title: neg_rep1

description: HUVECs transfected with neg. control miRNA replicate 1 of 2.

value: control


title: Pool x ∆2173_6 stat


title: PVH_WT_3

description:
male, hypothalamus, PVH
Sample names: 7909591045_C, WT-3

tag: genotype/variation


title: Pool x RN6 exp

source_name: wild type, exponential growth

value: exponential growth


title: Pool x ∆2173_4 stat


title: Luteolin added high-fat diet_liver rep1

value: HFD with 0.005% (w/w) luteolin (LU) for 16 wks

value: liver


title: Pool x RN2 stat


title: Pool x ∆2173_5 exp

source_name: asp23 mutant, exponential growth


title: Pool x ∆2173_4 exp


title: Pool x ∆2173_6 exp


title: Pool x RN2 exp


title: Pool x RN3 stat


title: AC_chd and wnt3a injected_rep1

city: Shatin

first: Hui

last: Zhao

address: The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Sample name: 3_chd_wnt3a
Gene expression data from animal caps injected with Chordin and Wnt3a mRNAs

hyb_protocol: Following fragmentation, 10 μg of aRNA were hybridized for 16 hr at 45°C on GeneChip® Xenopus laevis 2.0 Genome Array (64 Format). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Xenopus laevis

label_protocol: Biotinylated aRNA was synthesized through in vitro transcription according to the standard Affymetrix protocol (GeneChip® 3' IVT Express Kit user manual).

growth_protocol: Xenopus embryos were incubated in 0.2×MMR at 13°C and staged according to Nieuwkoop and Faber. The dissected animal caps were cultured in L-15 medium (67% L-15, 7.5 mM Tris-HCl pH7.5, 1 mg/ml BSA).

extract_protocol: Total RNA was extracted using the TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: Xenopus embryos were injected with mRNAs or MO in the animal pole at two-cell stage. The animal caps were dissected at stage 9 using forceps in 1×MMR on 1% agar plate.

tag: injected with

value: Chordin and Wnt3a mRNAs

value: animal caps


title: PyMT/S14-null Tumor C

city: Oklahoma City

first: Elizabeth

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

hyb_protocol: Samples were hybridized using the Gene Atlas Microarray System (Affymetrix) hybridization chamber; 20 hours at 48 C

scan_protocol: Samples were scanned and imaged using the Gene Atlas Microarray System Fludics and Imaging equipment (Affymetrix)

data_processing: CEL files were processed in Partek Genomic Suite using RMA Quantile normalization; intensity values were scaled by log2 transformation

source_name: mouse mammary tumor

label_protocol: Fragmented ssDNA was labeled with the Affymetrix WT Terminal Labeling and Hybridization kit according to the instructions, using Affymetrix proprietary biotinylated labeling reagent.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and the RNEasy mini kit (Qiagen) with on-column DNAse digestion was used following Trizol extraction.  100ng total RNA per sample was used for array analysis.

tag: strain

value: FVB/N

tag: genotype


title: PyMT/S14-null Tumor A


title: neg_rep2

description: HUVECs transfected with neg. control miRNA replicate 2 of 2.

value: Stratagene Universal Reference RNA (Pooled cell line RNA)

value: HUVEC


title: PyMT Tumor B

value: PyMT


title: EMT, rep3 (EMT3)

city: Stockholm

first: Jonas

last: Fuxe

address: Scheeles v. 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Single stranded cDNA was probed on a MoGene-1_1-st-v1 array (Affymetrix) using an Affymterix Gene Titan instrument.

data_processing:
Analysis Software = Expression Console, Method = med-polish
rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true,target=0, doavg=false

source_name: EpRas cells_TGF-b1 (2 ng/ml) for 14 d

label_protocol: 150 ng of total RNA per sample was used to synthesize cDNA using a cDNA synthesis kit (Ambion WT). A GeneChip Sense Target Labeling kit (Affymetrix) was used to fragment and biotin label single stranded cDNA

growth_protocol: Mouse mammary EpRas tumor cells were cultured in DMEM/F12 medium supplemented with 10% fetal calf serum, 1% penicillin/streptomycin and 1% L-glutamine in a humified incubator (37C, 5% CO2).

extract_protocol: Total RNA was isoltaed and purified using RNeasy Mini Kit (Qiagen), supplemented with RNase-Free DNase (Qiagen).

treatment_protocol: Cells were either left untreated or treated with 2ng/ml TGF-b1 (Peprotech) for 14 days.

tag: strain background

value: BALB/c

value: EpRas

value: mammary tumor cell line

tag: treated with

value: 2ng/ml TGF-b1 for 14 days


title: AC_chd, wnt3a and lrig3MO injected_rep2

description:
Sample name: 8_chd_wnt3a_L3MO
Gene expression data from animal caps injected with Chordin, Wnt3a mRNAs and Lrig3MO

value: Chordin, Wnt3a mRNAs and Lrig3MO

tag: tissue


title: PyMT Tumor A


title: AC_chd injected_rep2

description:
Sample name: 6_chd
Gene expression data from animal caps injected with Chordin mRNA

source_name: animal caps injected with Chordin mRNA

value: Chordin mRNA


title: AC_chd and wnt3a injected_rep2

description:
Sample name: 7_chd_wnt3a
Gene expression data from animal caps injected with Chordin and Wnt3a mRNAs


title: PyMT Tumor D


title: PyMT/S14-null Tumor B


title: EMT, rep1 (EMT1)

tag: cell type


title: AC_chd injected_rep1

description:
Sample name: 2_chd
Gene expression data from animal caps injected with Chordin mRNA


title: AC_uninjected_rep2

description:
Sample name: 5_control_AC
Gene expression data from uninjected animal caps

source_name: uninjected control animal caps

value: control (uninjected)


title: Ly49C/I+ NK cells_rep3

city: Frederick

first: Stephen

middle: Kent

last: Anderson

address: Building 560, room 31-33

department: CCR

institute: NCI-Frederick

description: IL2 cultured splenocytes sorted for Ly49C/I expression

hyb_protocol: Three  replicates of each group were hybridized to Affymetrix mouse Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

scan_protocol: Wash  and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000.

data_processing:
Data were collected using Affymetrix AGCC software.   Statistical and clustering analysis was performed with Partek Genomics Suite software using the RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that were up- or down-regulated more than 1.5 fold and with a p<0.001 were considered significant.  Significant genes were analyzed for enrichment for pathways using DAVID bioinformatics database (http://david.abcc.ncifcrf.gov/) and Ingenuity Pathway Analysis software.
Quantile normalized gene level expression values from GeneBASE

label: Biotin

source_name: IL2 cultured splenocytes_Ly49C/I+

label_protocol: Sense strand cDNA  was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Splenocytes were removed from C57BL/6 mice and were then incubated with antibodies against Thy1.2 and rabbit complement to eliminate T cells and were then cultured in media and 1000 IU IL-2 for 7 days.

extract_protocol: Flow cytometric cell sorting was performed by gating on CD3-CD122+Ly49G2+Ly49C/I- versus CD3-CD122+Ly49G2-Ly49C/I+. Total mRNA was extracted using the Qiagen RNeasy kit. RNA quality was checked on an Agilent Bioanalyzer.  All samples used for microarray analysis had a high quality score (RIN >9).  100 ng of RNA was reverse transcribed and amplified using the Ambion WT expression kit following manufacturer’s suggested protocol.

value: Spleen

value: natural killer


title: Control, rep1 (Ctrl1)

source_name: Non-treated EpRas cells

value: none (untreated control) for 14 days


title: PyMT/S14-null Tumor D


title: Ly49G+ NK cells_rep3

description: IL2 cultured splenocytes sorted for Ly49G expression

source_name: IL2 cultured splenocytes_Ly49G+


title: EMT, rep2 (EMT2)


title: Ly49C/I+ NK cells_rep2


title: PyMT Tumor C


title: Control, rep2 (Ctrl2)


title: AC_chd, wnt3a and lrig3MO injected_rep1

description:
Sample name: 4_chd_wnt3a_L3MO
Gene expression data from animal caps injected with Chordin, Wnt3a mRNAs and Lrig3MO


title: AC_uninjected_rep1

description:
Sample name: 1_control_AC
Gene expression data from uninjected animal caps


title: Ly49G+ NK cells_rep2


title: Ly49G+ NK cells_rep1


title: Control, rep3 (Ctrl3)


title: Pool x RN3 exp

value: HG001 wild type and HG001 asp23 mutant

value: exponential growth and stationary phase

value: HG001 wild type

value: exponential growth


title: 10h Smu WT rep2 vs. 6h Smu WT rep2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: The hybridisation was carried out according to Agilent manufacturer's protocol. Fragmented RNA (25 µl) was mixed with 25 µl of 2xGEx hybridisation buffer HIRPM and after brief centrifugation (13000 rpm, 1 min), 40 µl was slowly dispensed onto the gasket well. Afterwards, the SureHyb chamber was assembled and vertically rotated (10 rpm) in the hybridisation oven at 65°C for 17 h.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent Feature Extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channel were processed in the R environment using the limma package. Background correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantile-normalization was used for separate microarrays.

organism: Streptococcus mutans UA159

source_name: 10h biofilm, single

label_protocol: The RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labeling kit (Kreatech, Germany). To the 2 µg of RNA, 2 µl of labeling solution Cy3 or Cy5-ULS was added and filled up to 20 µl with RNase-free water. Unbound dye was removed by KREApure columns according to the manufacturer's instruction. The final flow through was purified labelled RNA. The quality of labeling was estimated by calculating the degree of labelling (DoL). For this purpose, purified and labeled RNA was measured at OD260 and OD550 for determining the DoL of Cy3-ULS labelled RNA and at OD650 for Cy5-ULS labeled RNA. For good quality RNA, the DoL value should be 1.0-3.6%. The RNA samples revealed DoL between 1.8-3.2%.

extract_protocol: To isolate the RNA from S. mutans, the LM buffer (TE buffer containing 15 mg/ml of lysozyme and 500 U/ml of mutanolysin from S. globisporus ATCC 21553) was added to the biofilm pellets thawed on ice and following full resuspension the pellets were incubated on a shaking incubator (90 min, 25°C, 350 rpm). Afterwards, 700 µl of buffer RLTß? were added, and after vortexing, samples were transferred to 2 ml tubes containing 50 µg sterile acid-washed glass beads (diameter 106 µm, SIGMA). The cells were disrupted by vortexing for 10 x 30 sec. Following centrifugation at 13 000 rpm, 2 min, room temperature, the supernatants were transferred into new tubes. RNA extraction was performed using the RNA extraction mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Traces of genomic DNA were removed by RNase-free DNaseI (Qiagen, Hilden, Germany) applying the on-column digestion protocol. The absence of genomic DNA in the RNA solutions was confirmed by PCR targeting the 16S rDNA. If necessary, the DNA digestion protocol in solution was additionally applied. The concentration of RNA was measured with a Nanodrop 1000 spectrophotometer (Peqlab, Germany). The quality and integrity of RNA were determined with the Bioanalyser (Agilent, Germany).

treatment_protocol: The dual- and single-species biofilms were formed in 24-well microtitre plates. After 6, 10 and 24 h incubation time in YNBB medium, the biofilm supernatants were removed and 300 µl of RNA protect (Qiagen, Hilden, Germany) was added. Following 5 min incubation at room temperature, the biofilms were collected with the sterile cell scraper. Collected biofilms were transferred to sterile tubes and centrifuged at 13 000 rpm, 5 min. The supernatants were removed and the pellets were stored at -70°C until RNA extraction.

value: WT

tag: single/coculture

value: single

tag: timepoint

tag: replicate

source_name: 6h biofilm, single


title: 24h Smu WT rep3 vs. Smu WT+Ca rep3

source_name: 24h biofilm, single

organism:
Candida albicans
Streptococcus mutans UA159

source_name: 24h biofilm, coculture

value: coculture


title: 24h Smu WT+Ca rep3 vs. Smu WT rep3


title: 24h Smu WT rep2 vs. 6h Smu WT+Ca rep2

source_name: 6h biofilm, coculture


title: 10h Smu WT+Ca rep2 vs. 24h Smu WT+Ca rep2

source_name: 10h biofilm, coculture


title: 6h Smu WT+Ca rep3 vs. Smu WT rep3


title: 10h Smu WT rep3 vs. Smu WT+Ca rep3


title: 6h Smu WT rep3 vs. Smu WT+Ca rep3


title: 10h Smu WT+Ca rep3 vs. Smu WT rep3


title: Ly49C/I+ NK cells_rep1


title: 6h Smu WT+Ca rep1 vs. Smu WT rep1


title: 6h Smu WT rep1 vs. Smu WT+Ca rep1


title: 6h Smu WT rep2 vs. 10h Smu WT rep2


title: 10h Smu WT rep1 vs. Smu WT+Ca rep1


title: 24h Smu WT rep1 vs. Smu WT+Ca rep1


title: Subject 441 baseline

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262386.CEL

hyb_protocol: Samples were hybridized to Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarrays (GEO accession number GPL10379).

scan_protocol: Scanning was performed according to Affymetrix recommendations.

data_processing: Data were normalized and expression intensities derived using the RMA algorithm in R/Bioconductor.

source_name: pre-treatment whole blood

label_protocol: RNA was amplified and labeled using the NuGEN Ovation WB protocol

extract_protocol: RNA was isolated from PAXgene blood samples (2.5ml) according to the manufacturer’s instructions. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

treatment_protocol: whole blood was collected in 2.5ml PAXgene tubes according to the manufacturer's instructions.

tag: das28 week 0

tag: das28 week 14

tag: log ktrans week 0

tag: log ktrans week 14

tag: treatment

value: Infliximab

tag: eular response

value: moderate


title: 10h Smu WT+Ca rep1 vs. Smu WT rep1

tag: genotype/variation


title: Subject 444 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262393.CEL


title: Subject 440 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262387.CEL

value: Placebo


title: Subject 438 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262381.CEL


title: Subject 446 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262377.CEL

value: nonresponder


title: Subject 442 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262237.CEL


title: Subject 439 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262353.CEL


title: Subject 437 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262240.CEL


title: Subject 443 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262383.CEL


title: Subject 447 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262379.CEL


title: Subject 445 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918592101513415118262315.CEL


title: Subject 433 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290057.CEL


title: Subject 436 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262347.CEL


title: Subject 435 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262260.CEL


title: Subject 430 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262200.CEL


title: Subject 426 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262216.CEL


title: Subject 431 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290060.CEL


title: Subject 428 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290080.CEL


title: Subject 434 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918592101513415118262310.CEL


title: Subject 422 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923315041914416882290035.CEL


title: Subject 424 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262354.CEL


title: Subject 425 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262231.CEL


title: Subject 418 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290059.CEL


title: Subject 429 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262203.CEL


title: Subject 427 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262258.CEL


title: Subject 414 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290078.CEL


title: Subject 416 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290101.CEL


title: Subject 423 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262362.CEL


title: Subject 421 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262366.CEL


title: Subject 419 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262192.CEL


title: Subject 417 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290069.CEL


title: Subject 412 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290088.CEL


title: Subject 411 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290093.CEL


title: Subject 408 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923315041914416882289996.CEL


title: Subject 410 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290090.CEL


title: Subject 406 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290055.CEL


title: Subject 413 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290066.CEL


title: Subject 409 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290086.CEL


title: Subject 407 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290068.CEL


title: Subject 404 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290076.CEL

value: responder


title: Subject 415 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290102.CEL


title: 24h Smu WT+Ca rep1 Smu WT rep1


title: Subject 420 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923316041914416882290056.CEL


title: Subject 405 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923315041914416882289997.CEL


title: Subject 403 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923315041914416882290044.CEL


title: Subject 402 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923315041914416882290041.CEL


title: Subject 306 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262249.CEL


title: Subject 308 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918592101513415118262334.CEL


title: Subject 304 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262359.CEL


title: Subject 302 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900923314041914416882289938.CEL


title: Subject 305 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262376.CEL


title: Subject 307 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262360.CEL


title: Subject 301 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262391.CEL


title: Subject 201 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262168.CEL


title: scr-mye

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Only Gene probes with Detection P value below 0.05 in at least one samples were kept for further processing including normalization. Signals were normalized against the median in each sample.

source_name: mobilized CD34+ cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: CD34+ cells were cultured in IMDM (Invitrogen, New York) containing 20% BIT 9500 (STEMCELL Technologies, Vancouver, Canada, Cat# 09500) freshly supplemented with stem cell factor (SCF; 100 ng/ml), Fms-like tyrosine kinase 3 (FLT-3; 10 ng/ml), thrombopoietin (TPO; 100 ng/ml), interleukin-6 (IL-6; 20 ng/ml), and low density lipoprotein (LDL 40 ng/ml).

extract_protocol: Total RNAs were extracted using the RNeasy kit (Qiagen).

treatment_protocol: Cells stably infected with viruses expressing indicated shRNAs were cultured (for 0 or 9 days) in medium that supports myelomonocytic lineage differentiation (IMDM, 20% BIT 9500, SCF 100 ng/ml, FLT-3 ligand 10 ng/ml, IL-3 20 ng/ml, IL-6 20 ng/ml, GM-CSF 20 ng/ml, G-CSF 20 ng/ml).

value: mobilized CD34+ cells

value: control

tag: time point

value: 9 days after culturing under myelomonocytic differentiation condition


title: scr

description: SAMPLE 1

value: before culturing under myelomonocytic differentiation condition


title: Subject 309 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918593101513415118262374.CEL


title: Subject 204 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262229.CEL


title: Subject 202 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900917894101513415118262201.CEL


title: hD2-mye

description: SAMPLE 5

value: DPY30 KD (sh#2)


title: Subject 203 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262253.CEL


title: hD5

description: SAMPLE 3

value: DPY30 KD (sh#5)


title: MDA-MB-231 - MTDH-isoform-KD-1

city: Hyderabad

first: Srigiridhar

last: Kotamraju

state: Andhrapradesh

address: Uppal road

department: Centre for Chemical Biology

country: India

institute: CSIR-Indian Institute of Chemical Technology

description:
SAMPLE 7
replicate 1

data_processing: Probe level data were quantile normalized using 'normalize.quantiles' function available in preprocessCore package (v. 1.26.1) of R (v. 3.1.0) and log2 transformed.

source_name: MDA-MB-231 - MTDH_isoform_KD

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: MDA-MB-231 cells were grown in DMEM  supplemented with 10 % Foetal Bovine Serum, 2mM glutamine and Pen-Strep

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MDA-MB-231 cells were transfected with siRNA of either  MTDH-WT or MTDH-isoform (200 pmols) for 24 h.

tag: cell line

tag: disease state

value: Breast adenocarcinoma, estrogen receptor-negative


title: MDA-MB-231 - MTDH-isoform-KD-3

description:
SAMPLE 9
replicate 3


title: MDA-MB-231 - MTDH-isoform-KD-2

description:
SAMPLE 8
replicate 2


title: Subject 432 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918590101513415118262244.CEL


title: MDA-MB-231 - MTDH-WT-KD-3

description:
SAMPLE 6
replicate 3

source_name: MDA-MB-231 - MTDH_WT_KD


title: hD2

description: SAMPLE 2


title: MDA-MB-231 - Control-2

description:
SAMPLE 2
replicate 2

source_name: MDA-MB-231 - Control

value: Control


title: MCF7 - MTDH_isoform_KD_3

description:
SAMPLE 9
replicate 3

source_name: MCF7 - MTDH_isoform_KD

growth_protocol: MCF-7 cells were grown in DMEM  supplemented with 10 % Foetal Bovine Serum, 2mM glutamine and Pen-Strep

treatment_protocol: MCF-7 cells were transfected with siRNA of either  MTDH-WT or MTDH-isoform (200 pmols) for 24 h.

value: Breast adenocarcinoma, estrogen receptor-positive

value: MTDH isoform KD


title: MDA-MB-231 - MTDH-WT-KD-2

description:
SAMPLE 5
replicate 2


title: MCF7 - MTDH_WT_KD_3

description:
SAMPLE 6
replicate 3

source_name: MCF7 - MTDH_WT_KD

value: MTDH WT KD


title: MDA-MB-231 - MTDH-WT-KD-1

description:
SAMPLE 4
replicate 1


title: MCF7 - MTDH_isoform_KD_1

description:
SAMPLE 7
replicate 1


title: MDA-MB-231 - Control-3

description:
SAMPLE 3
replicate 3


title: MDA-MB-231 - Control-1

description:
SAMPLE 1
replicate 1


title: MCF7 - Control_3

description:
SAMPLE 3
replicate 3

source_name: MCF7 - Control


title: MCF7 - MTDH_isoform_KD_2

description:
SAMPLE 8
replicate 2


title: MCF7 - MTDH_WT_KD_2

description:
SAMPLE 5
replicate 2


title: MDA-MB-231 - Control_2

description: SAMPLE 2

extract_protocol: At the end of the treatment, cells were extracted using TRI reagent for RNA isolation and cDNA was synthesized using 500ng of total RNA

treatment_protocol: MDA-MB-231 cells were treated with sterile water for a period of 24h as a mock control

value: ER-ve basal breast cancer cells

value: water for 24hrs (mock-control)


title: MCF7 - MTDH_WT_KD_1

description:
SAMPLE 4
replicate 1


title: MDA-MB-231- Fluvastatin 10µM_24h_2

description: SAMPLE 5

source_name: MDA-MB-231_Fluvastatin 10µM_24h

value: 10µM fluvastatin for 24hrs


title: MCF-7- Fluvastatin 24h_1

description: SAMPLE  4

treatment_protocol: MCF-7 cells were treated with sterile water for a period of 24h as a mock control

value: ER+ve luminal breast cancer cells

value: fluvastatin for 24hrs


title: MCF7 - Control_1

description:
SAMPLE 1
replicate 1


title: MDA-MB-231 - Control_1

description: SAMPLE 1


title: MCF-7- Control_3

description: SAMPLE 3


title: MCF-7- Fluvastatin 24h_2

description: SAMPLE  5


title: MCF-7- Control_1

description: SAMPLE 1


title: MCF7 - Control_2

description:
SAMPLE 2
replicate 2


title: MCF-7- Control_2

description: SAMPLE 2


title: Subject 303 baseline

description:
pre-treatment whole blood gene expression data from rheumatoid arthritis patient participating in a placebo-controlled clincal trial of infliximab
@52070900918592101513415118262313.CEL

value: Placebo

value: moderate


title: MDA-MB-231 - Control_3

description: SAMPLE 3


title: MDA-MB-231- Fluvastatin 10µM_24h_1

description: SAMPLE 4


title: D3_Mesp1pos replicate 3

city: Leiden

first: Sabine

last: Den Hartogh

state: Zuid-Holland

address: Einthovenweg 20

department: Anatomy and Embryology

institute: LUMC

description: SAMPLE 8

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridizized onto the illumina human HT-12-v4 (illumina).

scan_protocol: scanning was perofmred on the illumina iscan (illumina). Image analysis and extraction of raw expression data was performed with illumina genome studio v2011.1 gene expression software with default settings (no background subtraction and no normalization)

data_processing:
Data was normalized using Genespring Version 12.6 (Agilent Technologies)
Normalization: shift to 75 percentile. Baseline transformation: median of all samples.

label_protocol: RNA Quality and integrity was determined using Lab-on-chip analysis on the agilent 2100 Bioanalyzer (agilent technologies). Biotinylated cRNA was prepared using the Illumina Totalprep RNA amplification kit (ambion, according to manufactureres specifications with an input of 200 ng total RNA.

extract_protocol: At day 3 of differentiaiton, MESP1-mCherry expressing cells were sorted and directly lysated in lysation buffer enclosed in the RNA isolation kit: Nucleospin RNA XS kit from Macherey Nagel, RNA was isolated according to manufactures protocol, and treated with RNAse-free DNAse. Micro analysis was performed on three biologically independent replicates using Illumina human HT-12v4 arrays (Service XS).

value: human embryonic stem cell (hESCs)

tag: cell subtype

tag: reporter phenotype

value: mCherry pos


title: D3_Mesp1pos replicate 2

description: SAMPLE 5


title: D3_Mesp1neg replicate 3

description: SAMPLE 9

value: mCherry neg


title: D3_Mesp1neg replicate 2

description: SAMPLE 6


title: D3_Mesp1neg replicate 1

description: SAMPLE 3


title: untargeted control H9ESC-derived NSCs

first: Jizhong

last: Zou

address: 50 South Drive, Room 1146

institute: NIAMS/NIH

description:
H9NSC
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

source_name: NSC

value: H9ESC-derived NSC

tag: gene-targeted

tag: targeted integration

value: control


title: Undifferentiated replicate 2

description: SAMPLE 4

tag: cell type

value: undifferentiated hESCs


title: untargeted control NCRM1 iPSC-derived NSCs

description:
NCRM1NSC
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: NCRM1 iPSC-derived NSC


title: Undifferentiated replicate 3

description: SAMPLE 7


title: AAVS1 targeted tdTomato-expressing H9NSC polyclonal population

description:
H9NSC-AS1-iCAGTom
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: AAVS1 safe-harbor

value: tdTomato


title: AAVS1 targeted Nanoluc-HaloTag-expressing NCRM1NSC polyclonal population

description:
NCRM1NSC-AS1-iCLHN
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: Nanoluc-HaloTag


title: AAVS1 targeted Nanoluc-HaloTag-expressing iPSC clone 11

description:
NCRM5-AS1-iCLHN c11
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

source_name: iPSC

value: NCRM5 iPSC


title: C13 safe-harbor targeted Nanoluc-HaloTag-expressing iPSC clone 7

description:
NCRM5-C13-iCLHN c7
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: C13 safe-harbor


title: AAVS1 targeted copGFP-expressing iPSC clone 9

description:
NCRM5-AS1-iCAGcGFP c9
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: copGFP


title: AAVS1 and C13 dual safe-harbor targeted iPSC clone 14, expressing tdTomato and copGFP

description:
NCRM5-AS1Tom-C13GFP c14
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.

value: AAVS1 and C13 safe-harbor

value: tdTomato and copGFP


title: Undifferentiated  replicate 1

description: SAMPLE 1


title: AAVS1 and C13 dual safe-harbor targeted iPSC clone 1, expressing tdTomato and copGFP

description:
NCRM5-AS1Tom-C13GFP c1
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.


title: C13 safe-harbor targeted Nanoluc-HaloTag-expressing iPSC clone 6

description:
NCRM5-C13-iCLHN c6
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.


title: D3_Mesp1pos replicate 1

description: SAMPLE 2


title: AAVS1 targeted copGFP-expressing iPSC clone 10

description:
NCRM5-AS1-iCAGcGFP c10
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.


title: untargeted control NCRM5 iPSCs

description:
NCRM5
replicate 1
Approximately one million pelleted cells were sent to Expression Analysis (Durham, NC USA) for extraction, amplification, labeling and hybridization of RNA to an Illumina (San Diego, CA USA) HT-12 v4 BeadChip array (Illumina, #BD-103-0204). The Gene Expression module of the Illumina GenomeStudio software package was used to process the array image files, normalize data with background subtraction.


title: norm-VUB-1002-FDMSO-72H-R-2-4_(HG-U133_Plus_2).CEL

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Control F

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. As the number of controls were less than the number of treatments, the same controls were used several to normalize data from several treatments.

source_name: HepaRG cell line

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: The human hepatoma-derived HepaRG cells (Biopredic International, France) were cultivated as previously described  by A. Guillouzo et al. 168 (2007) 66-73.  and P. Gripon et al 99 (2002) 15655-15660. At day 13 of cultivation, dimethylsulfoxide (DMSO)-containing medium (2%) was added for 7 days . At day 19 exposure with the selected compounds was initiated.

extract_protocol: Samples for RNA isolation were collected after 24 and 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: The cells were individually exposed to 15 prototypical compounds for 24h and 72 hours at IC10 concentrations, i.e. 5 GTX (N-nitrosomorpholine, NMP, IC10=0.216mM; Hydroquinone, HQO, IC10=0.15mM; Hydrazine dihydrochloride, HHC, IC10=0.86mM; 2-acetylaminofluorene, TAF, IC10=0.0408mM; 2-amino-3-methylimidazo(4,5-f)quinoline, AMQ, IC10=0.003mM), 5 NGTX (Fumonisin B1, FMB, IC10=2.4mM; Cyclosporine A, CsA, IC10=0.0026mM; Acetamide, ACE, IC10=5.9; Diethylhexyl Phthalate, DHP, IC10=10mM; Ethanol, ETH, IC10=10mM), 5 NC (4-acetylaminofluorene, FAF, IC10=0.22; D,L-Menthol, DLM, IC10=1.2mM; Benzoin, BEN, IC10=0.345mM; Benzyl Alcohol, BEA, IC10=6.5mM; Triclosan, TRI, IC10=0.022mM).

value: HepaRG cell line

value: Control F


title: norm-VUB-1002-F-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with F

value: Treatment with F


title: norm-VUB-1003-F-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1003-FDMSO-72H-R-3-4_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1003-FDMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1003-FDMSO-24H-R-3-4_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1001-FDMSO-24H-R-1-4_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1003-F-24H-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1006-FDMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1002-FDMSO-24H-R-2-4_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1004-FDMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1003-EDMSO-72H-R-3-4_(HG-U133_Plus_2).CEL

description: Control E

value: Control E


title: norm-VUB-1001-F-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1005-FDMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1002-F-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1001-FDMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1003-FDMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1004-FDMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1001-FDMSO-72H-R-1-4_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1006-FDMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1005-FDMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1002-FDMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1002-FDMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1005-EDMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1001-FDMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1004-EDMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1006-EDMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1002-EDMSO-72H-R-2-4_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1003-EDMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1002-EDMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1001-EDMSO-72H-R-1-4_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1006-EDMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1005-E-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with E

value: Treatment with E


title: norm-VUB-1002-EDMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1001-EDMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1003-EDMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1006-E-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-VUB-1005-DMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control D

value: Control D


title: norm-VUB-1004-EDMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1001-EDMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1004-E-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-VUB-1006-DMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1005-EDMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1004-DMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1005-E-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-VUB-1006-E-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-VUB-1004-E-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-VUB-1002-EDMSO-24H-R-2-4_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1001-EDMSO-24H-R-1-4_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1003-D-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Treatment with D

value: Treatment with D


title: norm-VUB-1001-DMSO-72H-R-1-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1003-EDMSO-24H-R-3-4_(HG-U133_Plus_2).CEL

description: Control E


title: norm-VUB-1003-DMSO-72H-R-3-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1003-DMSO-72H-R-3-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1001-DMSO-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1001-F-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1002-DMSO-72H-R-2-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1002-DMSO-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1003-DMSO-24H-R-3-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1001-D-72H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-VUB-1004-DMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1002-DMSO-24H-R-2-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1002-D-72H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-VUB-1003-DMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1006-DMSO-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1003-D-24H-R-3-2_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-VUB-1001-D-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-VUB-1002-DMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1002-D-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-HUL-PRE-CPFDMO-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPFDMO-72H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPF-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-VUB-1005-DMSO-24H-R-2-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-VUB-1001-DMSO-24H-R-1-4_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-CPFDMO-72H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPFDMO-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-VUB-1001-DMSO-24H-R-1-2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-CPFDMO-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPF-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-HUL-PRE-CPF-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-HUL-PRE-CPFDMO-72H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPF-24H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-HUL-PRE-CPFDMO-24H-R-2-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPFDMO-24H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPEDMO-72H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPFDMO-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPEDMO-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPFDMO-24H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPEDMO-72H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPFDMO-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPE-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-HUL-PRE-CPE-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-HUL-PRE-CPFDMO-24H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control F


title: norm-HUL-PRE-CPEDMO-24H-R-2-CD_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPE-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-HUL-PRE-CPEDMO-24H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPEDMO-24H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPF-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-HUL-PRE-CPEDMO-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPEDMO-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Control E


title: TKO2-2

city: Chicago

first: Relja

last: Popovic

address: 303 East Superior Street

institute: Northwestern University

description: Replicate 2 of 3.

hyb_protocol: cRNA was hybridized to the Illumina HumanWG-6 v3.0 Expression BeadChip using standard protocols (provided by Illumina).

scan_protocol: The arrays were scanned on an Illumina BeadArray Reader.

data_processing: The data was processed using GenomeStudio.

source_name: TKO cells

label_protocol: Biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.

tag: parental cell line

value: multiple myeloma cell line

value: overexpressed MMSET allele inactivated


title: norm-HUL-PRE-CPEDMO-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control E

tag: replicate


title: norm-HUL-PRE-CPEDMO-72H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPEDMO-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPF-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with F


title: TKO2-1

description: Replicate 1 of 3.


title: norm-HUL-PRE-CPE-24H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: TKO2-3

description: Replicate 3 of 3.


title: norm-HUL-PRE-CPE-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-HUL-PRE-CPEDMO-24H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control E


title: norm-HUL-PRE-CPE-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with E


title: TKO1-2

description: Replicate 2 of 3.


title: norm-HUL-PRE-DMO-72H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: TKO1-1

description: Replicate 1 of 3.


title: norm-HUL-PRE-DMO-72H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-DMO-72H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: NTKO2

description: Replicate 2 of 3.

source_name: NTKO cells

value: wild type MMSET allele inactivated


title: norm-HUL-PRE-DMO-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Control D


title: TKO1-3

description: Replicate 3 of 3.


title: norm-HUL-PRE-DMO-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-DMO-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control D


title: NTKO1

description: Replicate 1 of 3.


title: norm-HUL-PRE-DMO-24H-R-3-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: WT3

description: Replicate 3 of 3.

source_name: KMS11 cells

value: WT


title: norm-HUL-PRE-DMO-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-CPD-72H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with D


title: femur_AEA001_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: replicate 3

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina GenomeStudio 2011.1

source_name: femur

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: genotype

value: AEA001 - Ednra mutant

tag: tissue

value: femur

tag: age

value: 17 weeks

tag: mouse id


title: norm-HUL-PRE-CPD-72H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with D

tag: treatment


title: femur_AEA001_rep2

description: replicate 2


title: femur_AEA001_rep4

description: replicate 4


title: norm-HUL-PRE-DMO-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Control D


title: femur_wt_rep2

description: replicate 2

value: wild type


title: norm-HUL-PRE-DMO-24H-R-2-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-HUL-PRE-CPD-72H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with D


title: white adipose tissue_AEA001_rep4

description: replicate 4

source_name: white adipose tissue

value: white adipose tissue


title: femur_wt_rep3

description: replicate 3


title: femur_AEA001_rep1

description: replicate 1