title: BNY01ROU

description:
IG090820BRE153-2_01.CEL
Gene expression data from round spermatids from young rats


title: BNY02ROU

status: Public on Jan 06 2012

type: RNA

city: Montreal

first: Bernard

last: Robaire

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

description:
IG090820BRE154-2_01.CEL
Gene expression data from round spermatids from young rats

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat 230 2.0 genome array chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Genespring v11.0.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Round spermatids from 4 month old rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit

treatment_protocol: Testicular germ cells were isolated using a collagenase and trypsin digest followed by a STAPUT density gradient to isolate fractions of round spermatids with a purity of greater than 83%

tag: strain

value: Brown Norway (BN)

tag: age

value: young

tag: cell type

value: Round spermatids


title: BNY13ROU

description:
IG090820BRE158-2_01.CEL
Gene expression data from round spermatids from young rats


title: BNA02ROU

description:
IG090820BRE159-2_01.CEL
Gene expression data from round spermatids from aged rats

source_name: Round spermatids from 18 month old rats

value: aged


title: BNA09PACH

description:
IG090820BRE175-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats

hyb_protocol: Following fragmentation

source_name: Pachytene spermatocytes from 18 month old rats

treatment_protocol: Testicular germ cells were isolated using a collagenase and trypsin digest followed by a STAPUT density gradient to isolate fractions of pachytene spermatocytes and round spermatids with a purity of greater than 83%

value: Pachytene spermatocytes


title: H22_Aicy5/Cicy3_rep3

city: Montpellier Cedex 05

first: Stéphanie

last: Barrère

address: 141 rue de la cardonille

country: France

institute: CNRS

hyb_protocol: Prior to hybridization, excess oligonucleotides were removed from the arrays by shaking them twice 1min in 0.2% SDS. Arrays were then washed twice with distilled water.

scan_protocol: Microarrays were immediately scanned in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) at 10 µm resolution with a variable PMT voltage to obtain maximal signal intensities with less than 0.1% probe saturation. ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. Local background noise was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot.

data_processing: No spatial bias in the quality analysis has been detected. A Loess normalisation was performed for all microarrays to correct technical bias and dye effects. No background correction was performed.

organism: Mus musculus

source_name: [control] ischemic region of hearts subjected to IR

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and synthesised using Amino Allyl Message Amp II aRNA amplification kit (Ambion), according the manufacturer’s instructions. One-half of the RNA derived from each condition (IR, Prec, PostC) was labelled with Cy3 and the other half with Cy5 to account for any bias in dye coupling or emission efficiency.

growth_protocol: Anesthetized mice were subjected to a surgical protocol of 40 minutes of ischemia (coronary occlusion) and 60 minutes reperfusion (IR)

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

treatment_protocol: A conditioning comprising 3 cycles of 1 minute ischemia-1minute reperfusion is applied 10 minutes before ischemia (PreC) , 1 minute after reperfusion (PostC) or 30 minutes after reperfusion (Post30).

source_name: Ci - ischemic region of hearts subjected to PostC


title: H23_Aicy5/Dicy3_rep3

source_name: Di - ischemic region of heart subjected to Post30


title: BNA10PACH

description:
IG090820BRE176-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats


title: BNA05PACH

description:
IG090820BRE173-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats


title: NH Osteoblasts sample B3

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86237.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4100A 01

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: stratagene human reference plus doping controls.

label_protocol:
StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)

extract_protocol: MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions

tag: reference

source_name: NH Osteoblasts sample B3  plus doping controls.

label_protocol: Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)

growth_protocol: osteoblast co-culture; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Walkersville, MD) were expanded in mammary epithelial basal medium that was supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Walkersville, MD). MCF-7, T47D, MDA-MB231, SKBR-3, Hs578T, (ATCC, Atlanta, GA) were propagated in DMEM with 4.5% glucose (Gibco, Grand Island, NY) that was supplemented with 10% FBS (HyClone, Logan, UT), glutamine, 100 U/ml penicillin and 100 ??g/ml streptomycin (Gibco, Grand Island, NY). Normal human Osteoblasts (NHOST) (Lonza Walkersville, Walkersville, MD) were expanded in Clonetics Osteoblast Basal Medium (OBM???) (Lonza Walkersville, Walkersville, MD) supplemented with osteoblast growth medium (OGM TM) SingleQuots?? (Lonza Walkersville, Walkersville, MD) with 10 % FBS. For the co-culture experiments, the cells were cultivated for 48 hours at equal density of 30???000 cells/cm2 (15???000 tumor cells /cm2 and 15???000 normal human Osteoblast cells /cm2) in Clonetics Osteoblast Basal Medium (OBM???) supplemented with 0.2% FBS without any further additives. This medium served as a good universal media for all the cells in the study

extract_protocol:
RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions

tag: cells

value: normal human osteoblasts sample B3  plus doping controls.


title: BNY13PACH

description:
IG090820BRE170-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats

source_name: Pachytene spermatocytes from 4 month old rats


title: BNY03ROU

description:
IG090820BRE155-2_01.CEL
Gene expression data from round spermatids from young rats


title: BNA03PACH

description:
IG090820BRE172-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats


title: H24_Aicy5/Ascy3_rep3

source_name: As - non ischemic region of hearts subjected to IR


title: BNA02PACH

description:
IG090820BRE171-2_01.CEL
Gene expression data from pachytene spermatocytes from aged rats


title: H20_Aicy3/Ascy5_rep3


title: H21_Aicy5/Bicy3_rep3

source_name: Bi - ischemic region of hearts subjected to PreC


title: ST486 NT_2

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

country: USA

institute: Columbia University

description: Lentiviral-mediated expression of non-target control shRNA in ST486 Burkitt's lymphoma cells for 60h. 5 ug of total RNA were hybridized in Affymetrix U95Av2 expression arrays.

hyb_protocol: According to Affymetrix 701025 rev 6

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: Normalization and summarization by gcrma implemented in affy package / bioconductor (www.bioconductor.org), and log2 transformation

source_name: ST486 Burkitt's lymphoma cells transduced with NT control shRNA lentivirus-vector for 60h

label_protocol: Affymetrix one cycle cDNA synthesis protocol (Affymetrix 701025 Rev 6)

extract_protocol: TRIZOL followed by RNAeasy (Qiagen) columns cleanup

tag: cell line

tag: transduction

value: non-target control shRNA (Sigma SHC002)

tag: time


title: BNY10PACH

description:
IG090820BRE168-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats


title: ST486 NT_5


title: ST486 NT_3


title: BNY03PACH

description:
IG090820BRE167-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats


title: NH Osteoblasts and HMEC coculture B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86245.gif

value: stratagene human reference plus doping controls.

source_name: NH Osteoblasts and HMEC coculture B plus doping controls.

value: normal human osteoblasts and HMEC coculture B plus doping controls.


title: H19_Aicy3/Dicy5_rep3


title: BNY02PACH

description:
IG090820BRE166-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats


title: BNY11PACH

description:
IG090820BRE169-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats


title: ST486 NT_4


title: H17_Aicy3/Bicy5_rep3


title: ST486 NT_1


title: H16_Aicy5/Ascy3_rep2


title: ST486 B11-5

description: Lentiviral-mediated expression of STK38 shRNA in ST486 Burkitt's lymphoma cells for 60h. 5 ug of total RNA were hybridized in Affymetrix U95Av2 expression arrays.

source_name: ST486 Burkitt's lymphoma cells transduced with STK38 shRNA lentivirus-vector for 60h

value: STK38 shRNA (Sigma TRCN0000010215)


title: H18_Aicy3/Cicy5_rep3


title: BNY01PACH

description:
IG090820BRE165-2_01.CEL
Gene expression data from pachytene spermatocytes from young rats


title: ST486 B11-4


title: ST486 B11-2


title: ST486 B11-3


title: ST486 B11-1


title: HMEC sample B

description:
Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86241.gif

source_name: HMEC sample B plus doping controls.

value: HMEC sample B plus doping controls.


title: H15_Aicy5/Dicy3_rep2


title: H14_Aicy5/Cicy3_rep2


title: H13_Aicy5/Bicy3_rep2


title: FGFR1OP-RET-2

city: TOULOUSE

first: Naïs

last: PRADE

address: Place du Dr. Baylac

institute: CHU Purpan

description:
FGFR1OP-RET-2.rma-gene-default.chp
FGFR1OP-RET-2.cel
RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

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

data_processing: Raw data were processed with the Expression Console software (Affymetrix) for background correction and RMA normalization at gene-level. Data analysis and statistical evaluations were performed with DNA-Chip Analyzer (dChip) software (Harvard School of Public Health, Boston, MA).

source_name: retrovirally infected and sorted BAF/3 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol Reagent

value: IL-3-dependent hematopoietic cell line BaF3

tag: retrovirus infection


title: FGFR1OP-RET-3

description:
FGFR1OP-RET-3.rma-gene-default.chp
FGFR1OP-RET-3.cel
RMA expression value derived from Expression Console software

growth_protocol: retrovirally infected and sorted BAF/3 cells


title: FGFR1OP-RET-1

description:
FGFR1OP-RET-1.rma-gene-default.chp
FGFR1OP-RET-1.cel
RMA expression value derived from Expression Console software


title: H12_Aicy3/Ascy5_rep2


title: Intestine_KO_day8_2 [exon-level]

status: Public on Jan 07 2012

city: Baltimore

first: Tai-Chung

last: Huang

state: MD

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description: THua-DIC-Cre_TA_1014-2a-mmExon1_(MoEx-1_0-st-v1).CEL

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Johns Hopkins Microarray Core Facility.

data_processing:
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935
program-company = Affymetrix
The statistical analysis was performed using GeneSpring GX 10.

source_name: small intestine (jejunum)

growth_protocol: Conditional knockout of Dicer exon 21 & 22 in C57B/6 mice of 8 weeks of age

extract_protocol: miRNeasy Mini (Qiagen)

treatment_protocol: Tamoxifen gavage to induce conditional knockout

tag: genotype/variation

value: Dicer KO

value: 8 weeks


title: H8_Aicy5/Ascy3_rep1


title: oocyte_DirectLysis_rep2

type: other

city: Philadelphia

first: Don

last: Baldwin

state: PA

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description:
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45 C on Mouse Gene 1.0ST Arrays. GeneChips were    washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G.

data_processing: Affymetrix GCOS, Affymetrix Expression Console, gc-RMA

molecule: other

source_name: single oocyte, crude lysate

label_protocol: NuGEN WT Ovation One-Direct amplification followed by NuGEN Encore Biotin module

growth_protocol: two-month-old female mice (ICR strain) were intraperitoneally injected with 10IU PMSG, followed 46 hours later with 10IU hCG. Non-mated female mice were used for MII oocyte collection and mated females were used for collection of fertilized single-cell embryos. 1 to 3 cells were collected from each of 3 mice per condition.

extract_protocol: Qiagen RNeasyMini, Arcturus PicoPure, or NuGEN direct lysis per manufacturer's instructions

tag: tissue

value: oocyte

value: ICR

tag: sample prep

value: NuGEN direct lysis


title: BCR-RET-1

description:
BCR-RET-1.rma-gene-default.chp
BCR-RET-1.cel
RMA expression value derived from Expression Console software

value: BCR-RET


title: BCR-RET-3

description:
BCR-RET-3.rma-gene-default.chp
BCR-RET-3.cel
RMA expression value derived from Expression Console software


title: oocyte_DirectLysis_rep3


title: H7_Aicy5/Dicy3_rep1


title: BCR-RET-2

description:
BCR-RET-2.rma-gene-default.chp
BCR-RET-2.cel
RMA expression value derived from Expression Console software


title: BCR-ABL-3

description:
BCR-ABL-3.rma-gene-default.chp
BCR-ABL-3.cel
RMA expression value derived from Expression Console software

value: BCR-ABL


title: H11_Aicy3/Dicy5_rep2


title: BCR-ABL-2

description:
BCR-ABL-2.rma-gene-default.chp
BCR-ABL-2.cel
RMA expression value derived from Expression Console software


title: H10_Aicy3/Cicy5_rep2


title: H9_Aicy3/Bicy5_rep2


title: BCR-ABL-1

description:
BCR-ABL-1.rma-gene-default.chp
BCR-ABL-1.cel
RMA expression value derived from Expression Console software


title: oocyte_PicoPure_rep3

source_name: single oocyte, purified RNA

value: Arcturus PicoPure


title: H6_Aicy5/C3cy3_rep1


title: oocyte_DirectLysis_rep1


title: H5_Aicy5/Bicy3_rep1


title: oocyte_PicoPure_rep1


title: oocyte_PicoPure_rep2


title: H3_Aicy3/Dicy5_rep1


title: H1_Aicy3/Bicy5_rep1


title: oocyte_RNeasyMini_rep3

value: Qiagen RNeasyMini


title: H4_Aicy3/Ascy5_rep1


title: H2_Aicy3/Cicy5_rep1


title: oocyte_RNeasyMini_rep2


title: H9 diff. KDR+CD31+sorted. Day8, biological rep2

city: Newcastle upon Tyne

first: Sun

last: Yung

address: Central Parkway

country: United Kingdom

institute: Newcastle University

description: Gene expression data from KDR+CD31+ FACS sorted cells from 8 days of haematopoietic differentiation of human embryonic stem cells

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

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

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

source_name: H9 KDR+CD31+ Day 4

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: The human embryonic stem cell lines H9 and H1 (WiCell. Inc.) were routinely passaged and maintained in human embryonic stem cell media on mitotically inactivated mouse embryonic fibroblast (MEF) feeder layers and differentiation was achieved by forming em

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

treatment_protocol: Differentiation of human embryonic stem cells within optimised haematopoietic media consisting of StemPro34 Serum-free media (Invitrogen), Penicillin-Streptomycin Solution (1mM), Bone Morphogenic Protein 4 (BMP-4), Glutamax (2mM), Monothioglycerol (MTG),

value: FACS sorted KDR+CD31

tag: developmental stage

value: Day 8 of Differentiation


title: H9 diff. KDR+CD31+sorted. Day8, biological rep1


title: H9 diff. KDR+CD31+sorted. Day6, biological rep2

description: Gene expression data from KDR+CD31+ FACS sorted cells from 6 days of haematopoietic differentiation of human embryonic stem cells

value: Day 6 of Differentiation


title: H9 undiff. unsorted. Day0, biological rep2

description: Gene expression data from undifferentied human embryonic stem cells

source_name: H9 Day 0

value: Undifferentiated


title: H9 diff. KDR+CD31+sorted. Day4, biological rep2

description: Gene expression data from KDR+CD31+ FACS sorted cells from 4 days of haematopoietic differentiation of human embryonic stem cells

value: Day 4 of Differentiation


title: H9 diff. KDR+CD31+sorted. Day6, biological rep1

source_name: H9 KDR+CD31+ Day 6


title: H9 undiff. unsorted. Day0, biological rep1


title: Hct8-TcdA-24hr-1

city: Charlottesville

first: Kevin

middle: Michael

last: D'Auria

state: VA

address: 415 Lane Road, Room 2041

department: Biomedical Engineering

institute: University of Virginia

hyb_protocol: RNA was hybridized to Human Genome U133 Plus 2.0 chips, washed, and stained according to the recommended Affymetrix protocols.

scan_protocol: A GeneChip Scanner 3000 7G was used.

data_processing: All arrays were normalized with the Bioconductor gcrma package (version 2.0.0).

label: Biotin

source_name: 24hr after TcdA treatment

label_protocol: RNA was labeled using either the Affymetrix 3’ IVT expression or one-cycle target labeling methods.

growth_protocol: Cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1mM sodium pyruvate.

extract_protocol: RNA was isolated using the Quiagen QIAshredder and RNeasy mini kits according to the manufacturer’s instructions. An RNase inhibitor was added (RNasin, Promega) and samples were stored at -80˚C. RNA integrity was assessed using an Agilent 2100 BioAnalyzer.

treatment_protocol: Confluent HCT-8 cells treated with 100 ng/ml of Toxin A or Toxin B (isolated from C. difficile VPI 10463).


title: Hct8-Control-24hr-3

source_name: Untreated, 24 hr


title: Hct8-TcdB-6hr-3

source_name: 6hr after TcdB treatment


title: Hct8-Control-24hr-1


title: Hct8-TcdB-24hr-3

source_name: 24hr after TcdB treatment


title: Hct8-TcdB-24hr-1


title: ES_ZERT #18 Day4 Tmx++++ rep2

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: ES_ZERT #18 Day4 Tmx++++

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 20 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr (adjust to UMR)
(4) Remove outliers. Each cell/treatment type (CTT) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is logintensities for i-th CTT and replication j, N = number of CTT. Then we estimate z-value for each CTT:  z =  (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4 then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: ES_ZERT #18 Day4 Tmx++++

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was extracted by TRizol Reagent (Invitrogen, 15596-018) according to manufacturer   s recommendation. Briefly, cells were disrupted by adding 1 ml of TRizol Reagent to a well of 6-well plate and passing several times through a pipette. The cell lysate was transferred to a nuclease free eppendorf tube and incubated for 5 minutes at room temperature. To separate phases, the lysate was mixed with 0.2 ml of chloroform, incubated at room temperature for 3 minutes and centrifuged at 12,000    g for 15 minutes at 4C.  Following centrifugation, the aqueous phase were transferred to fresh tubes.  The RNA was precipitated from the aqueous phase by mixing with 0.5ml isopropyl alcohol, incubating at room temperature for 10 minutes and centrifuging at 12,000    g for 10 minutes at 4C.  The RNA pellet was washed with 1ml of 75% ethanol and dried for less than 5 minutes.  RNA was dissolved in RNase-free water by passing the solution a few times through a pipette tip and incubating for 10 minutes at 60C. Dissolved RNA was stored at -70C.

treatment_protocol: cells were plated onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium with 200nM tamoxyfen.

value: ES cell

tag: culture condition

value: tamoxifen on day1,day2,day3,day4

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: H9 diff. KDR+CD31+sorted. Day4, biological rep1


title: ES_ZERT #18 Day4 Tmx++++ rep1

description: ES_ZERT #18 Day4 Tmx++++


title: ES_ZERT #18 Day3 Tmx+++ rep2

description: ES_ZERT #18 Day3 Tmx+++

source_name: ES_ZERT #18 Day3 Tmx+++

value: tamoxifen on day1,day2s,day3


title: ES_ZERT #18 Day4 Tmx+--- rep2

description: ES_ZERT #18 Day4 Tmx+---

source_name: ES_ZERT #18 Day4 Tmx+---

treatment_protocol: cells were plated onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium with 200nM tamoxyfen at 1st day. Medium was changed to ES medium from 2nd day to 4th day.

value: tamoxifen on day1, no tamoxifen on day2,day3,day4


title: ES_ZERT #18 Day4 Tmx+--- rep1

description: ES_ZERT #18 Day4 Tmx+---


title: EGFR ACT 3

city: Columbus

first: Amanda

last: Simcox

state: OH

address: 484 W 12th Ave

department: Molecular Genetics

institute: Ohio State University

scan_protocol: GCOS v1

data_processing: GCRMA

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: third instar wing disc

growth_protocol: Flies were raised at 25C

extract_protocol: RNAeasy (Qiagen)

treatment_protocol: Samples were dissected on ice and placed into RLT (Qiagen) at -80

value: wing disc

tag: transgene

value: activated EGFR (TOP)


title: Hct8-TcdA-6hr-3

source_name: 6hr after TcdA treatment


title: EGFR ACT 2


title: Hct8-TcdA-24hr-3


title: BNY10ROU

description:
IG090820BRE156-2_01.CEL
Gene expression data from round spermatids from young rats

source_name: Round spermatids from 4 month old rats

value: Brown Norway (BN)

value: young

value: Round spermatids


title: Hct8-TcdB-6hr-2


title: EGFR ACT 1


title: Hct8-TcdA-6hr-2


title: EGFR DN 3

value: dominant negative EGFR


title: ES_ZERT #18 Day3 Tmx+++ rep1

description: ES_ZERT #18 Day3 Tmx+++

value: tamoxifen on day1,day2,day3


title: oocyte_RNeasyMini_rep1

value: oocyte

value: ICR

value: Qiagen RNeasyMini


title: Hct8-TcdA-6hr-1


title: Hct8-TcdB-6hr-1


title: EGFR DN 1


title: Hct8-Control-6hr-3

source_name: Untreated, 6 hr


title: ES_ZERT #18 Day2 Tmx+- rep1

description: ES_ZERT #18 Day2 Tmx+-

source_name: ES_ZERT #18 Day2 Tmx+-

treatment_protocol: cells were plated onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium with 200nM tamoxyfen at 1st day. Medium was changed to ES medium at 2nd day.

value: tamoxifen on day1, no tamoxifen on day2


title: ES_ZERT #18 Day2 Tmx++ rep2

description: ES_ZERT #18 Day2 Tmx++

source_name: ES_ZERT #18 Day2 Tmx++

value: tamoxifen on day1 and day2


title: ES_ZERT #18 Day2 Tmx+- rep2

description: ES_ZERT #18 Day2 Tmx+-

value: ES cell


title: ES_ZERT #18 Day2 Tmx-- rep1

description: ES_ZERT #18 Day2 Tmx--

source_name: ES_ZERT #18 Day2 Tmx--

treatment_protocol: cells were plated onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium .

value: no tamoxifen on day1,day2


title: Hct8-TcdB-2hr-2

source_name: 2hr after TcdB treatment


title: ES_ZERT #18 Day3 Tmx+-- rep2

description: ES_ZERT #18 Day3 Tmx+--

source_name: ES_ZERT #18 Day3 Tmx+--

treatment_protocol: cells were plated onto gelatin-coated 6-well plate and were cultured as a monolayer in ES medium with 200nM tamoxyfen at 1st day. Medium was changed to ES medium at 2nd day and 3rd day.

value: tamoxifen on day1,no tamoxifen on day2,day3

value: Universale Mouse Reference


title: anti-FGFR1_rep6

city: South San Francisco

first: Li

last: Li

state: CA

address: 1 DNA Way

institute: Genentech, Inc

hyb_protocol: For DNA microarray analysis, labeled RNA (n = 6) prepared from brown adipose tissues was hybridized to Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: Standard Affy scanning

data_processing: Expression intensity for each probe set was calculated using the RMA method available in the rma package from Bioconductor.  Differential expression analysis was conducted using empirical Bayes moderated t statistics available in the limma package from Bioconductor.

label_protocol: Affy with Enzo

growth_protocol: Adult male ob/ob mice on normal chow.

extract_protocol: Tissue RNAs were isolated by using QIAzol reagent.

treatment_protocol: No sample treatment

tag: tissue type

value: brown adipose

tag: gender

value: male

value: ob/ob

tag: harvest time

value: 4 day post injection

value: 3 months


title: anti-FGFR1_rep5

tag: age


title: ES_ZERT #18 Day2 Tmx-- rep2

description: ES_ZERT #18 Day2 Tmx--

tag: cell type


title: anti-FGFR1_rep4


title: ES_ZERT #18 Day2 Tmx++ rep1

description: ES_ZERT #18 Day2 Tmx++


title: Hct8-Control-6hr-2


title: Hct8-TcdA-2hr-2

source_name: 2hr after TcdA treatment


title: EGFR DN 2

value: wing disc


title: Hct8-Control-2hr-2

source_name: Untreated, 2 hr


title: ES_ZERT #18 Day3 Tmx+-- rep1

description: ES_ZERT #18 Day3 Tmx+--


title: Hct8-TcdB-2hr-1


title: anti-FGFR1_rep3


title: ES_ZERT #18 Day1 Tmx+ rep2

description: ES_ZERT #18 Day1 Tmx+

source_name: ES_ZERT #18 Day1 Tmx+

value: tamoxifen on day1


title: Hct8-TcdA-2hr-1


title: control IgG_rep6

source_name: control IgG


title: ES_ZERT #18 Day1 Tmx- rep2

description: ES_ZERT #18 Day1 Tmx-

source_name: ES_ZERT #18 Day1 Tmx-

value: no tamoxifen on day1


title: colorectal cancer sample AUS2_180_p1572

city: Oslo

first: Trude

middle: Holmeide

last: Ågesen

address: Ullernch. 70

department: Department of Cancer Prevention

country: Norway

institute: Oslo University Hospital

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_180_p1572_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_180_p1572_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

data_processing: CEL files were analyzed in the Affymetrix® Expression Console software using the Robust Multichip Analysis (RMA) algorithm for background correction and quantile normalization (Affymetrix Expression Console™ Software Version 1.0 User Guide) and the HuEx-1_0-st-v2.r2 gene-core library file.

source_name: Colorectal cancer patient

extract_protocol: For the colorectal cancer samples, total RNA was isolated from <30 mg tissue biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol. For the normal colon mucosa samples, total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.

value: colorectal cancer biopsy

tag: tumor stage

value: IV

tag: msi-status


title: Hct8-Control-2hr-1

tag: cell line


title: ES_ZERT #18 Day0 rep2

description: ES_ZERT #18 Day0

source_name: ES_ZERT #18 Day0

source_name: Universal Mouse Reference 129ES Cell


title: ES_ZERT #18 Day1 Tmx+ rep1

description: ES_ZERT #18 Day1 Tmx+


title: colorectal cancer sample AUS2_040_p308

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_040_p308_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_040_p308_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: MSS


title: control IgG_rep5


title: colorectal cancer sample AUS2_033_p481

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_033_p481_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_033_p481_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: I

value: MSI-H


title: control IgG_rep2


title: control IgG_rep4


title: ES_ZERT #18 Day1 Tmx- rep1

description: ES_ZERT #18 Day1 Tmx-

value: ES cell


title: control IgG_rep1


title: anti-FGFR1_rep1


title: colorectal cancer sample AUS2_035_p324

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_035_p324_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_035_p324_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day3 Rep1

description: Transgenic MEF

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 36 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr (adjust to UMR)
(4) Remove outliers. Each growth factor (GF) is characterized by 2 replications, all are log-transformed (log10). Here we check if any of these values is an outlier.
First we estimate the average square difference (ASD) between replication pairs:
ASD = SUM[(x(i,1)-x(i,2))^2]/N/2
where x(i,j) is logintensities for i-th GF and replication j, N = number of GFs. Then we estimate z-value for each TF:  z =  (x(i,1)-x(i,2))/sqrt(ASD). If abs(z) > 4 then one of the replications is an outlier. The value that is farther away from the median expression value is considered an outlier and it is replaced with the value from another replication.
The result is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and Dox (1.5ug/ml) and Tamoxifen (200nM)

tag: genetic background

value: hybrid from C57Bl/6 x 129

tag: development stage

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day3 Rep1; 251508710912A3

tag: treatment

value: Dox+Tmx+

value: MEF

tag: time

value: day 3

tag: sample type

value: Stratagene Universal Mouse Reference


title: colorectal cancer sample AUS2_046_p1109_norm

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_046_norm_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_046_norm_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

source_name: Normal colonic mucosa from colorectal cancer patient

tag: tissue

value: normal colonic mucosa biopsy


title: ES_ZERT #18 Day0 rep1

description: ES_ZERT #18 Day0

value: Universale Mouse Reference


title: colorectal cancer sample AUS2_020_p352

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_020_p352_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_020_p352_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day3 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and Dox (1.5ug/ml)

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day3 Rep2; 251508710912A2

value: Dox+Tmx-


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day3 Rep2

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day3 Rep2; 251508710912A4


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day3 Rep1

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day3 Rep1; 251508710912A1


title: colorectal cancer sample AUS2_021_p284

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_021_p284_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_021_p284_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy

value: MSS


title: colorectal cancer sample AUS2_023_p1083_norm

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_023_norm_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_023_norm_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: WT liver 3

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: WT liver

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Merelbeke, Belgium). All subsequent steps were performed in accordance with the manufacturer's specifications.

value: liver

value: 10 weeks

tag: genotype

value: WT

value: mixed, Alb-Cre Tac:[Sw]fBR

value: male


title: L-Pex5 Knockout liver 2

source_name: KO liver

value: L Pex5 -/-


title: L-Pex5 Knockout liver 3


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day3 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and tamoxifen (200nM)

value: hybrid from C57Bl/6 x 129

value: 2nd Generation MEF

tag: individual identifier

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day3 Rep2; 251508710911A4

value: Dox-Tmx+

value: MEF


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day3 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day3 Rep2; 251508710911A2

value: Dox-Tmx-

tag: transgene

value: day 3

value: Stratagene Universal Mouse Reference


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day3 Rep1

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day3 Rep1; 251508710911A3


title: colorectal cancer sample AUS2_001_p385

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_001_p385_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_001_p385_(HuEx-1_0-st-v2).CEL
.
Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy

value: I

value: MSS


title: control IgG_rep3

tag: tissue type

value: brown adipose

tag: genotype/variation

value: ob/ob

value: 4 day post injection

value: 3 months


title: WT liver 2

value: liver

value: 10 weeks

value: WT

value: mixed, Alb-Cre Tac:[Sw]fBR

tag: gender

value: male


title: colorectal cancer sample AUS2_150_p1614

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_150_p1614_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_150_p1614_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: III


title: colorectal cancer sample AUS2_124_p922

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_124_p922_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_124_p922_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: L-Pex5 Knockout liver 1

tag: age

value: L Pex5 -/-


title: colorectal cancer sample AUS2_131_p956

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_131_p956_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_131_p956_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: IV


title: colorectal cancer sample AUS2_121_p929

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_121_p929_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_121_p929_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: Mouse four-cell stage embryos_HP treated_rep1

city: Godollo

first: Istvan

last: Bock

address: Aulich Lajos utca 26.

country: Hungary

institute: BioTalentum Ltd.

hyb_protocol: 825 ng of Cy5 and Cy3 labelled-cRNA were incubated with 10X Blocking Agent and 25X Fragmentation Buffer (Agilent Technologies, Palo Alto, USA) at 60 °C for 30 min, according to the Two-Color Microarray-Based Gene Expression Analysis protocol. After the addition of 2x GEx Hybridization HI-RPM Buffer the samples were loaded to the arrays and were hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Oven. After hybridization, slides were washed following manufacturer's protocol.

scan_protocol: The slides were scanned with an Agilent Technologies Scanner G2505B, according to the Two-Color Microarray-Based Gene Expression Analysis protocol.

data_processing: The data was extracted using Agilent Feature Extraction Software (version 9.5.1.1) with GE2-v5_95_Feb07 protocol and was normalized with LOWESS normalization.

source_name: Pool of 44 four-cell stage mouse embryos. Oocytes were treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C. After HP treatment the oocytes were fertilized by ICSI and cultured till four-cell stage.

label_protocol: TrueLabeling-PicoAMP kit (SABiosciences, Frederick, USA) was used to amplify appropriate quantity of cRNA form 240 pg total RNA at each sample, following the manufacturer's protocol. This kit utilizes an advanced two-round RNA amplification procedure. CyDye Post-Labeling Reactive Dye Pack (GE Healthcare, Waukesha, USA) was applied to generate labelled cRNA target.

extract_protocol: Total RNA was extracted from the replicate pools using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany).

tag: cell type

value: four-cell stage embryo

source_name: Pool of 36 four-cell stage mouse embryos. Oocytes were kept under identical conditions as pressure treated ones, except HP treatment. Thereafter the oocytes were fertilized by ICSI and cultured till four-cell stage.


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day3 Rep1

description: Transgenic MEF

value: hybrid from C57Bl/6 x 129

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day3 Rep1; 251508710911A1

value: Dox-Tmx-

value: MEF

value: day 3

value: Stratagene Universal Mouse Reference


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day1 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and DOX (1.5ug/ml)and Tamoxifen (200nM).

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day1 Rep2; 251508710910A4

value: Dox+Tmx+

value: day 1


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day1 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF.

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day1 Rep2; 251508710909A2


title: colorectal cancer sample AUS2_085_p623

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_085_p623_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_085_p623_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy

tag: tumor stage

value: I

value: MSI-H


title: WT liver 1

value: liver

value: 10 weeks

value: WT

value: mixed, Alb-Cre Tac:[Sw]fBR

value: male


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day1 Rep1

description: Transgenic MEF

treatment_protocol: ES cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and TAMOXIFEN(200nM).

value: hybrid from C57Bl/6 x 129

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day1 Rep1; 251508710909A3

value: Dox-Tmx+


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day1 Rep2

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and DOX (1.5ug/ml)

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day1 Rep2; 251508710910A2

value: Dox+Tmx-

value: MEF

value: Stratagene Universal Mouse Reference


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day1 Rep2

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day1 Rep2; 251508710909A4

value: day 1


title: colorectal cancer sample AUS2_108_p880

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_108_p880_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_108_p880_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy

value: I

tag: msi-status

value: MSS


title: colorectal cancer sample AUS2_099_p666

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_099_p666_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_099_p666_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: IV


title: colorectal cancer sample AUS2_083_p206

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_083_p206_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_083_p206_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day1 Rep1

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and DOX (1.5ug/ml)tamoxifen (200nM)

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day1 Rep1; 251508710910A3

value: Dox+Tmx+


title: colorectal cancer sample AUS2_115_p894

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_115_p894_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_115_p894_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: MSI-H


title: colorectal cancer sample AUS2_088_p644

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_088_p644_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_088_p644_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: II


title: colorectal cancer sample AUS2_082_p619

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_082_p619_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_082_p619_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: Mouse oocytes_HP treated_rep1

source_name: Pool of 50 oocytes treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C.

value: oocyte

source_name: Pool of 50 oocytes kept under identical conditions as pressure treated ones, except HHP treatment.


title: anti-FGFR1_rep2

value: brown adipose

value: male

value: ob/ob

tag: harvest time

value: 4 day post injection

value: 3 months


title: colorectal cancer sample AUS2_107_p899

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_107_p899_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_107_p899_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day1 Rep1

description: Transgenic MEF

tag: genetic background

value: hybrid from C57Bl/6 x 129

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day1 Rep1; 251508710910A1

value: Dox+Tmx-

value: MEF

value: Stratagene Universal Mouse Reference


title: Mouse four-cell stage embryos_HP treated_rep3

source_name: Pool of 37 four-cell stage mouse embryos. Oocytes were treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C. After HP treatment the oocytes were fertilized by ICSI and cultured till four-cell stage.

value: four-cell stage embryo

source_name: Pool of 24 four-cell stage mouse embryos. Oocytes were kept under identical conditions as pressure treated ones, except HP treatment. Thereafter the oocytes were fertilized by ICSI and cultured till four-cell stage.


title: v6.5 (ES Cell) Rep1

description: v6.5 ES Cell

source_name: v6.5 ES Cell

treatment_protocol: ES cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF.

value: ES


title: iPS(KOS-ZERT2) Rep2

description: iPS

source_name: iPS

tag: development stage

value: iPS


title: Mouse four-cell stage embryos_HP treated_rep2

source_name: Pool of 30 four-cell stage mouse embryos. Oocytes were treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C. After HP treatment the oocytes were fertilized by ICSI and cultured till four-cell stage.

tag: treatment

source_name: Pool of 33 four-cell stage mouse embryos. Oocytes were kept under identical conditions as pressure treated ones, except HP treatment. Thereafter the oocytes were fertilized by ICSI and cultured till four-cell stage.


title: v6.5 (ES Cell) Rep2

description: v6.5 ES Cell


title: colorectal cancer sample AUS2_101_p664

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_101_p664_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_101_p664_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

source_name: Colorectal cancer patient

value: colorectal cancer biopsy

value: IV

value: MSS


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day1 Rep1

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day1 Rep1; 251508710909A1

value: Dox-Tmx-

tag: time

value: day 1


title: Mouse oocytes_HP treated_rep4

value: 20 MPa hydrostatic pressure for 60 minutes at 37 °C.

value: oocyte

value: kept under identical conditions as pressure treated ones, except HHP treatment.


title: Mouse oocytes_HP treated_rep3


title: Mouse oocytes_HP treated_rep2


title: iPS(KOS-ZERT2) Rep1

description: iPS

value: hybrid from C57Bl/6 x 129

tag: sample type


title: colorectal cancer sample AUS2_079_p617

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_079_p617_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_079_p617_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

tag: tissue

value: I


title: colorectal cancer sample AUS2_071_p568

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_071_p568_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_071_p568_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: colorectal cancer sample AUS2_077_p598

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_077_p598_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_077_p598_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: colorectal cancer sample AUS2_069_p565

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_069_p565_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_069_p565_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: colorectal cancer sample AUS2_066_p562

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_066_p562_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_066_p562_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: II

value: MSI-H


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day6 Rep2

description: Transgenic MEF

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day6 Rep2; 251508710896A2

value: MEF

value: day 6

value: Stratagene Universal Mouse Reference


title: 2ndMEF-KOS-ZERT2  Dox-Tmx- day6 Rep1

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx- day6 Rep1; 251508710896A1


title: MEF3 Tmx- Rep1

description: wild MEF

source_name: wild MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in MEF medium.

value: F1 hybrid from V6.5

value: Tmx-


title: colorectal cancer sample AUS2_080_p608

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_080_p608_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_080_p608_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day6 Rep1

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF, Dox (1.5ug/ml) and Tamoxifen (200nM)

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day6 Rep1; 251508710897A3

value: Dox+Tmx+

source_name: Universal Mouse Reference 129ES Cell


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day6 Rep2

description: Transgenic MEF

source_name: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day6 Rep2; 251508710897A2

value: Dox+Tmx-


title: colorectal cancer sample AUS2_073_p592

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_073_p592_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_073_p592_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: IV

value: MSI-L


title: 2ndMEF-KOS-ZERT2  Dox+Tmx+ day6 Rep2

description: Transgenic MEF

value: hybrid from C57Bl/6 x 129

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx+ day6 Rep2; 251508710897A4


title: MEF3 Tmx- Rep2

description: wild MEF


title: colorectal cancer sample AUS2_076_p594

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_076_p594_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_076_p594_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: I


title: colorectal cancer sample AUS2_057_p537

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_057_p537_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_057_p537_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: MSS


title: 2ndMEF-KOS-ZERT2  Dox+Tmx- day6 Rep1

description: Transgenic MEF

value: 2nd Generation MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox+Tmx- day6 Rep1; 251508710897A1

value: MEF


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day6 Rep1

description: Transgenic MEF

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in ES standard medium with LIF and Tamoxifen (200nM)

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day6 Rep1; 251508710896A3

value: Dox-Tmx+

value: day 6

value: Stratagene Universal Mouse Reference


title: colorectal cancer sample AUS2_060_p529

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_060_p529_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_060_p529_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy


title: 2ndMEF-KOS-ZERT2  Dox-Tmx+ day6 Rep2

description: Transgenic MEF

value: clone #1; 2ndMEF-KOS-ZERT2  Dox-Tmx+ day6 Rep2; 251508710896A4


title: colorectal cancer sample AUS2_074_p594

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_074_p594_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_074_p594_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: MEF3 Tmx+ Rep2

description: wild MEF

value: F1 hybrid from V6.5

value: Tmx+


title: colorectal cancer sample AUS2_067_p563

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_067_p563_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_067_p563_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: II


title: MEF3 Tmx+ Rep1

description: wild MEF


title: colorectal cancer sample AUS2_063_p559

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_063_p559_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_063_p559_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: IV


title: ESlncRNA over-expression vs. control erythroid progenitor cells rep1

city: Cambridge

first: Wenqian

last: Hu

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Agilent 8X66K expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of cy-dye labeled cRNA, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

data_processing: Data were analyzed using the limma package from Bioconductor. Loess method was used to make intensities consistent within each array, and aquantile method was applied to achieve consistency between arrays.

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

extract_protocol: Total RNA was extracted from vector and ESlncRNA transduced erythroid progenitor cells (sorted as GFP positive cells), respectively. The quality of the RNA sample was determined by a 2100 Bioanalyzer (Agilent Technologies).

tag: strain

tag: developmental stage

value: erythroid progenitor cells from fetal livers

tag: overexpression

value: control

source_name: ESIncRNA transduced erythoid progenitor cells rep1

value: ESlncRNA


title: ESlncRNA over-expression vs. control erythroid progenitor cells rep2

hyb_protocol: Agilent 8X66K expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of cy-dye labeled cRNA, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 100 ng total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

extract_protocol: Total RNA was extracted from FACS sorted vector transduced erythroid progenitor cells (GFP+). The quality of the RNA sample was determined by a 2100 Bioanalyzer (Agilent Technologies).

source_name: ESIncRNA transduced erythoid progenitor cells_rep2

extract_protocol: Total RNA was extracted from FACS sorted ESlncRNA transduced erythroid progenitor cells (GFP+). The quality of the RNA sample was determined by a 2100 Bioanalyzer (Agilent Technologies).


title: colorectal cancer sample AUS2_049_p532

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_049_p532_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_049_p532_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: MSS


title: colorectal cancer sample AUS2_047_p512

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_047_p512_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_047_p512_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: I


title: colorectal cancer sample AUS2_025_p454

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_025_p454_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_025_p454_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: MEF2 ZERT2 Tmx+ Rep2

description: transgenic MEF (Zscan4ERT2)

source_name: transgenic MEF (Zscan4ERT2)

treatment_protocol: cells were plated at 1 x105 cells/well onto gelatin-coated 6-well plate and were cultured as a monolayer in MEF medium with Tamoxifen (200nM).

tag: individual identifier

tag: transgene


title: MEF2 ZERT2 Tmx- Rep1

description: transgenic MEF (Zscan4ERT2)

value: Tmx-


title: colorectal cancer sample AUS2_007_p389

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_007_p389_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_007_p389_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: MSI-H


title: EB9 control biological replicate 3

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: embyoid bodies

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: embroid bodies


title: EB9 control biological replicate 4


title: colorectal cancer sample AUS2_016_p449

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_016_p449_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_016_p449_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: MEF2 ZERT2 Tmx+ Rep1

description: transgenic MEF (Zscan4ERT2)

value: MEF


title: colorectal cancer sample AUS2_015_p447

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_015_p447_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_015_p447_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: colorectal cancer sample AUS2_032_p480

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_032_p480_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_032_p480_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: colorectal cancer sample AUS2_045_p509

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_045_p509_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_045_p509_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: MEF2 ZERT2 Tmx- Rep2

description: transgenic MEF (Zscan4ERT2)


title: EB9 KD33 biological replicate 1

value: Cbx7 depleted KD33


title: EB9 control biological replicate 1


title: ES control biological replicate 3

source_name: embryonic stem cells

value: embryonic stem cells


title: colorectal cancer sample AUS2_039_p495

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_039_p495_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_039_p495_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

value: colorectal cancer biopsy


title: EB9 KD33 biological replicate 2


title: EB9 control biological replicate 2


title: EB9 KD33 biological replicate 3


title: ES control biological replicate 4


title: EB9 KD33 biological replicate 4


title: colorectal cancer sample AUS2_008_p418

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_008_p418_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_008_p418_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: ES KD33 biological replicate 4


title: 252665511345-4

status: Public on Jan 05 2012

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile interslide normalization.

source_name: Burkitt lymphoma

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski, total RNA extraction

value: Lymph node

tag: amount in (µg)

tag: origin

value: Burkitt lymphoma

tag: genotype

value: Black 6

value: Mature B cell

tag: disease

value: Lymphoma

tag: rin number


title: 252665511345-3


title: colorectal cancer sample AUS2_006_p417

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_006_p417_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_006_p417_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable

tag: tumor stage

tag: msi-status


title: ES KD33 biological replicate 2


title: ES control biological replicate 2


title: 252665511345-2


title: colorectal cancer sample AUS2_002_p393

description:
RMA expression value derived from Expression Console software; gene-core analysis:
AUS2_002_p393_(HuEx-1_0-st-v2).GEOfiles.rma-gene-core.chp
AUS2_002_p393_(HuEx-1_0-st-v2).CEL

Definitions of the microsatellite instability phenotypes:
MSI-H: microsatellite instability high
MSI-L: microsatellite instability low
MSS: microsatellite stable


title: ES KD33 biological replicate 3


title: 252665511345-1


title: 252665511343-3

source_name: Plasma cell lymphoma

value: Plasma cell lymphoma


title: 252665511343-1


title: 252665511344-1

source_name: Mantle cell lymphoma

value: Mantle cell lymphoma


title: ES KD33 biological replicate 1


title: HL60 leukemic cells, MycA+RA, replicate 3

hyb_protocol: The labeled cRNA was hybridized to the Agilent Whole Human Genome 4x44k 60-mer oligo microarray (G4112F) according to the manufacturer's protocol. After hibridization, the microarrays were washed.

scan_protocol: Slides were scanned on an Agilent G2565BA microarray scanner at Green channel XDR Hi 100% and XDR Lo 100% green PMT and 5 um resolution.

data_processing: Intensity data was extracted using the Feature Extraction software (Agilent).

source_name: HL60 leukemic cells, MycA+RA

label_protocol: 500 ng of total RNA was labeled using Agilent's QuickAmp Labeling Kit following manufacturer instructions. Briefly: mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA.

growth_protocol: HL60 cells were cultured at 37ºC and 5% of CO2 in RPMI medium supplemented with 10% of fetal bovine serum.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit including DNAse I digestion to avoid potential contaminations of DNA  following the manufacturer's recommendations.

treatment_protocol: HL60 cells infected with MSCV-based retroviral vectors containing ER-tagged empty vector (CTL), MycA or MycD were seeded at a density of 0.5M/mL in RPMI medium containing 200nM of 4-OHT. After 16 hours, 100nM of retinoic acid or EtOH (vehicle) were added to the medium for 4 hours. Cells were then harvested and RNA was extracted.

tag: cell line

tag: cell type

value: leukemic

value: MycA+RA


title: 252665511343-2


title: 252665511344-2


title: 252665511344-3


title: HL60 leukemic cells, MycA+RA, replicate 2

tag: treatment


title: HL60 leukemic cells, RA, replicate 2

source_name: HL60 leukemic cells, RA

value: RA


title: HL60 leukemic cells, RA, replicate 1


title: HL60 leukemic cells, MycD, replicate 3

source_name: HL60 leukemic cells, MycD

value: MycD


title: 014502

description:
CONTROL vs P796
Date:2006/06/26

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: CONTROL

label_protocol: Ambion

extract_protocol: Chomzynski

tag: label

value: CONTROL

tag: extract

tag: sample

tag: subject

value: Liver

value: Pooled control liver (n=10)

value: Cirrhosis

value: alcohol abuse


title: HL60 leukemic cells, MycA+RA, replicate 1


title: HL60 leukemic cells, MycD, replicate 2


title: HL60 leukemic cells, MycD+RA, replicate 1

source_name: HL60 leukemic cells, MycD+RA

value: MycD+RA


title: HL60 leukemic cells, RA, replicate 3


title: HL60 leukemic cells, empty vector, replicate 2

source_name: HL60 leukemic cells, empty vector

value: empty vector


title: HL60 leukemic cells, MycD+RA, replicate 4


title: 014501

description:
P6C vs CONTROL
Date:2006/06/26

tag: tissue

value: Hepatitis C Virus (HCV) Infection


title: HL60 leukemic cells, MycD+RA, replicate 3


title: HL60 leukemic cells, empty vector, replicate 4


title: 014521

description:
CONTROL vs P3C
Date:2006/06/20


title: HL60 leukemic cells, MycD, replicate 1


title: HL60 leukemic cells, MycD+RA, replicate 2


title: HL60 leukemic cells, RA, replicate 4


title: 014482

description:
P16C vs CONTROL
Date:2006/06/20


title: HL60 leukemic cells, empty vector, replicate 3


title: 014540

description:
P21C vs CONTROL
Date:2006/06/20


title: 014534

description:
P820 vs CONTROL
Date:2006/06/20


title: 014500

description:
CONTROL vs P14C
Date:2006/06/20


title: 014536

description:
CONTROL vs P201
Date:2006/06/20


title: T. neapolitana polysaccharide mix vs. glucose

city: Raleigh

first: Andrew

last: Frock

state: NC

address: 840 Main Campus Drive, Partners II, Room 3304

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

hyb_protocol: Microarray slides were pre-hybridized at 42°C for 45 min in 5X SSC, 0.1% SDS, 0.1% BSA, dipped five times in sterile dH2O, dipped twice in isopropanol, and dried in a slide spinner. cDNA was concentrated, resuspended in sterile dH2O, and heated to 95°C for 2 min. 2X hybridization buffer (5X SSC, 5X Denhardt's solution, 30% (v/v) formamide, 0.1% SDS) was added to equal part cDNA. This mixture was applied to the slide and covered with a 20x60 mm polyethylene hydrophobic coverslip. The slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18-20 hours. Slides were washed for 4 min in buffer 1 (2X SSC, 0.2% SDS), 4 min in buffer 2 (0.5X SSC, 0.2% SDS), and 4 min in buffer 3 (0.5X SSC). Then slides were dried using a slide spinner.

scan_protocol: Slides for T. neapolitana and T. sp. RQ2 were scanned with an Perkin Elmer ScanArray Lite scanner and ScanArray 2.1 software, while T. maritima and T. petrophila slides were scanned with an Axon GenePix 4000b scanner and GenePix Pro 6.0 software.

data_processing: Spots were identified, quantified, and background intensity was subtracted using ScanArray 2.1 or GenePix Pro 6.0. Data processing was performed using JMP Genomics (SAS) and included log2 transformation, lowess normalization, ANOVA normalization, and row-by-row ANOVA modeling.

organism: Thermotoga neapolitana

source_name: Glucose-grown

label_protocol: Superscript III (Invitrogen) was used to reverse transcribe RNA and incorporate 5-(3-aminoallyl)-dUTP (Ambion). cDNA was labeled with Cy5 or Cy3 dye (GE Healthcare).

growth_protocol: Thermotoga species were grown at 80°C in an orbital shaking bath on artificial sea water media supplemented with either 2.5 g/L glucose or a polysaccharide mixture consisting of 0.12 g/L of each of the following: galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose. Cultures were sub-cultured at least six times with the appropriate carbon source in 50 mL cultures before being inoculated into 350 mL cultures for RNA extraction.

extract_protocol: At harvest, cultures were cooled in a dry ice-ethanol bath before centrifugation. Total RNA was extracted using TRIzol (Invitrogen) and purified using an RNeasy kit (Qiagen) with on-column DNase treatment.

value: glucose

source_name: Polysaccharide-mix grown


title: T. sp. RQ2 polysaccharide mix vs. glucose

organism: Thermotoga sp. RQ2

value: galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose


title: T. petrophila polysaccharide mix vs. glucose

organism: Thermotoga petrophila


title: 014498

description:
CONTROL vs P24C
Date:2006/06/20


title: HL60 leukemic cells, empty vector, replicate 1


title: 014484

description:
CONTROL vs P1C
Date:2006/06/20


title: 014539

description:
CONTROL vs P704
Date:2006/06/20


title: T. maritima polysaccharide mix vs. glucose

scan_protocol: Slides were scanned with an Axon GenePix 4000b scanner and GenePix Pro 6.0 software.

data_processing: Spots were identified, quantified, and background intensity was subtracted using GenePix Pro 6.0. Data processing was performed using JMP Genomics (SAS) and included log2 transformation, lowess normalization, ANOVA normalization, and row-by-row ANOVA modeling.

organism: Thermotoga maritima

source_name: Polysaccharide mix-grown


title: 014522

description:
P4C vs CONTROL
Date:2006/06/20


title: 014538

description:
P491 vs CONTROL
Date:2006/06/20

label_protocol: Agilent low RNA - BC


title: 014532

description:
CONTROL vs P764
Date:2006/06/29


title: 014531

description:
P894 vs CONTROL
Date:2006/06/29


title: 014499

description:
P12C vs CONTROL
Date:2006/06/20


title: 014530

description:
CONTROL vs P867
Date:2006/06/29


title: 014491

description:
CONTROL vs P939
Date:2006/06/29

value: Alcohol abuse


title: 014529

description:
P983 vs CONTROL
Date:2006/06/29


title: 014579

description:
P693 vs CONTROL
Date:2006/06/29


title: 014469

description:
P970 vs CONTROL
Date:2006/06/29


title: Rhinitis R9

description: Gene expression data from dust mite allergic child nasal brushing with isolated rhinitis

hyb_protocol: Following fragmentation and labeling, 3ug of DNA were hybridized for 17 hr at 45C on Huge gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and Gene Level-RMA sketch  as normalization method.

source_name: Nasal airway epithelium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

extract_protocol: Absolutely RNA® Microprep Kit  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Nasal airway epithelial cells were brushed from children and immediately lysed with 100 µl of Absolutely RNA® Microprep Kit lysis buffer mixed with 0,7 µl of ?-Mercaptoethanol 14,2M then stored at -70°C.

tag: disease state

value: Rhinitis

value: Nasal airway epithelium

tag: gender

value: Male

tag: age


title: 014492

description:
P789 vs CONTROL
Date:2006/06/29

tag: origin


title: Rhinitis R14


title: 014632

description:
P635 vs CONTROL
Date:2006/06/26


title: Rhinitis R13

value: Female


title: Uncontrolled asthma UA5

description: Gene expression data from dust mite allergic child nasal brushing with rhinitis + asthma

value: Uncontrolled asthma


title: 014628

description:
CONTROL vs P944
Date:2006/06/26


title: Uncontrolled asthma UA6


title: 014633

description:
CONTROL vs P780
Date:2006/06/26

value: Fibrosis


title: Uncontrolled asthma UA4


title: Rhinitis R8


title: Healthy C7

description: Gene expression data from control child nasal brushing

value: Healthy


title: 014496

description:
CONTROL vs P639
Date:2006/06/29

value: CONTROL

value: Liver


title: Rhinitis R7


title: Healthy C10


title: Healthy C9


title: 014627

description:
P1028 vs CONTROL
Date:2006/06/26

value: Cirrhosis

value: Pooled control liver (n=10)


title: 014470

description:
CONTROL vs P538
Date:2006/06/26

value: fibrosis


title: Controlled asthma CA6

value: Rhinitis with controlled asthma


title: 014625

description:
CONTROL vs P608
Date:2006/06/26

value: alcohol abuse


title: Rhinitis R3


title: Uncontrolled asthma UA3


title: 014467

description:
CONTROL vs P995
Date:2006/06/29


title: 014626

description:
P617 vs CONTROL
Date:2006/06/26


title: 014629

description:
P719 vs CONTROL
Date:2006/06/26

value: Hepatitis C Virus (HCV) Infection


title: Controlled asthma CA5


title: Healthy C11


title: Female-Soy-formula-fed-pool3

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

description: hepatic gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3
RMA normalization was utilized to generated values using GeneSpring v 7.3

organism: Sus scrofa

source_name: postnatal day 21-pig liver

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Sow fed pigs compared piglets weaned onto commercial infant formulas (soy and dairy) on PND2 through PND21

extract_protocol: Total hepatic RNA was isolated from the sow, milk and soy-formula fed piglets using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Liver tissues was collected from neonatal pigs at sacrifice and flash frozen in liquid nitrogen

tag: diet

value: Soy-formula

value: female

value: liver


title: Controlled asthma CA7

value: Nasal airway epithelium


title: Female-Soy-formula-fed-pool2

description: hepatic gene expression


title: Rhinitis R6

value: Rhinitis

value: Male


title: Healthy C6


title: colorectal cancer sample  C1398III [gene-level]

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

institute: Institute for Cancer Research, Oslo University Hospital

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1398III_(HuEx-1_0-st-v2).rma-gene-core.chp
C1398III_(HuEx-1_0-st-v2).CEL

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

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using Expression Console (Affymetrix).

source_name: Colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from <30 mg colorectal cancer biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol.

value: colorectal cancer biopsy

value: MSI-L


title: Healthy C8

value: Healthy

value: Female


title: colorectal cancer sample  C1355III [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1355III_(HuEx-1_0-st-v2).rma-gene-core.chp
C1355III_(HuEx-1_0-st-v2).CEL

value: MSS


title: Female-Milk formula-fed-pool3

description: hepatic gene expression

value: dairy (milk) formula


title: Controlled asthma CA4


title: Female-Soy-formula-fed-pool1

description: hepatic gene expression


title: Rhinitis R2


title: colorectal cancer sample  C1165III [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1165III_(HuEx-1_0-st-v2).rma-gene-core.chp
C1165III_(HuEx-1_0-st-v2).CEL


title: Rhinitis R1


title: Female-Milk formula-fed-pool1

description: hepatic gene expression


title: colorectal cancer sample  C1338III [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1338III_(HuEx-1_0-st-v2).rma-gene-core.chp
C1338III_(HuEx-1_0-st-v2).CEL


title: Controlled asthma CA3


title: Rhinitis R11


title: colorectal cancer sample  C1350II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1350II_(HuEx-1_0-st-v2).rma-gene-core.chp
C1350II_(HuEx-1_0-st-v2).CEL


title: Female-Sow-fed-pool3

description: hepatic gene expression

value: breast fed


title: Uncontrolled asthma UA2

value: Uncontrolled asthma


title: Healthy C5


title: Controlled asthma CA2

value: Rhinitis with controlled asthma


title: Female-Sow-fed-pool2

description: hepatic gene expression


title: Rhinitis R10


title: Female-Milk formula-fed-pool2

description: hepatic gene expression


title: Rhinitis R12


title: Rhinitis R5


title: Healthy C4


title: colorectal cancer sample  C1158II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1158II_(HuEx-1_0-st-v2).rma-gene-core.chp
C1158II_(HuEx-1_0-st-v2).CEL


title: Healthy C3


title: colorectal cancer sample  C1122II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1122II_(HuEx-1_0-st-v2).rma-gene-core.chp
C1122II_(HuEx-1_0-st-v2).CEL


title: Healthy C1


title: Rhinitis R4


title: Controlled asthma CA1


title: Male-Soy-formula-fed-pool2

description: hepatic gene expression

value: male


title: Uncontrolled asthma UA1


title: Male-Soy-formula-fed-pool1

description: hepatic gene expression


title: Healthy C2


title: Male-Soy-formula-fed-pool3

description: hepatic gene expression


title: Female-Sow-fed-pool1

description: hepatic gene expression


title: colorectal cancer sample  C903II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C903II_(HuEx-1_0-st-v2)_2.rma-gene-core.chp
C903II_(HuEx-1_0-st-v2)_2.CEL


title: colorectal cancer sample C844II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C844II_(HuEx-1_0-st-v2).rma-gene-core.chp
C844II_(HuEx-1_0-st-v2).CEL


title: colorectal cancer sample  C1103III [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1103III_(HuEx-1_0-st-v2)_2.rma-gene-core.chp
C1103III_(HuEx-1_0-st-v2)_2.CEL


title: colorectal cancer sample  C938III [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C938III_(HuEx-1_0-st-v2).rma-gene-core.chp
C938III_(HuEx-1_0-st-v2).CEL


title: Male-Milk formula-fed-pool2

description: hepatic gene expression


title: Male-Milk formula-fed-pool1

description: hepatic gene expression


title: colorectal cancer sample  C1079II [gene-level]

description:
RMA expression value derived from Expression Console software; gene-core analysis
C1079II_(HuEx-1_0-st-v2).rma-gene-core.chp
C1079II_(HuEx-1_0-st-v2).CEL


title: 21-D25-C

description: Gene expression data from control HNECs

source_name: Gene expression data from control HNECs

treatment_protocol: Control HNECs

tag: sample type

value: Differentiated HNECs cultured in ALI between D15-D21

value: HNECs


title: 20-D25-IFNgamma

description: Gene expression data from HNECs treated with IFNgamma

treatment_protocol: HNECs were treated with 100 ng/mL IFNgamma for 6 h


title: 19-D25-IFNbeta

description: Gene expression data from HNECs treated with IFNbeta

treatment_protocol: HNECs were treated with 1000 UI/mL IFNbeta for 6 h


title: Male-Milk formula-fed-pool3

description: hepatic gene expression


title: Male-Sow-fed-pool2

description: hepatic gene expression


title: 15-D24-IFNbeta

source_name: Gene expression data from HNECs treated with IFNbeta


title: 14-D24-IFNalpha

description: Gene expression data from HNECs treated with IFNalpha

treatment_protocol: HNECs were treated with 1000 UI/mL IFNalpha for 6 h


title: 18-D25-IFNalpha

source_name: Gene expression data from HNECs treated with IFNalpha


title: Male-Sow-fed-pool3

description: hepatic gene expression


title: 13-D21-C

description: Gene expression data from control HNECs


title: 09-D26-C

description: Gene expression data from control HNECs


title: 16-D24-IFNgamma

source_name: Gene expression data from HNECs treated with IFNgamma


title: 17-D24-C

description: Gene expression data from control HNECs


title: 07-D26-IL4

description: Gene expression data from HNECs treated with IL4

treatment_protocol: HNECs were treated with 10 ng/mL IL4 for 24 h


title: 11-D21-IFNbeta


title: 10-D21-IFNalpha


title: 08-D26-IL13

description: Gene expression data from HNECs treated with IL13

treatment_protocol: HNECs were treated with 10 ng/mL IL13 for 24 h


title: 05-D25-IL13

source_name: Gene expression data from HNECs treated with IL13


title: 03-D24-C

description: Gene expression data from control HNECs


title: 04-D25-IL4

source_name: Gene expression data from HNECs treated with IL4


title: Male-Sow-fed-pool1

description: hepatic gene expression


title: 06-D25-C

description: Gene expression data from control HNECs


title: osteogenic differentiation day 14

city: seoul

first: Mi Kyung

last: Choi

address: daehyundong

country: South Korea

institute: Ewha womans university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: adipose derived mesenchymal stem cell

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

growth_protocol: Isolated adipose derived stem cells from mouse were normally cultured in DMEM/F12 Medium with 10% FBS/1% streptomycin/penicillin. And for osteogenic differentiation, cells were plated in 24 well-culture dishes. After overnight culture, the osteogenic medium (DMEM-F12, 50 μM L-ascorbic acid, 10 mM β-glycerophosphate, 0.1 μM dexamethasone, 0.4% DMSO, 15% FBS, 1% streptomycin/penicillin) was applied, and sample was extracted after 0,1,3,6,10 and 14 days.

extract_protocol: RNA was extracted and 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.

tag: strain

value: dorsal and inguinal fat tissue

value: adipose derived mesenchymal stem cell


title: 02-D24-IL13


title: 01-D24-IL4

extract_protocol: Trizol® extraction of total RNA


title: osteogenic differentiation day 1


title: osteogenic differentiation day 0


title: osteogenic differentiation day 10


title: osteogenic differentiation day 6


title: osteogenic differentiation day 3


title: Control_IFNγ_replicate1

city: Saint Louis

first: Nicole

last: Maloney

state: MO

address: 660 South Euclid

department: Pathology/Immunology

institute: Washington University in St Louis School of Medicine

description: Bone marrow derived macrophages

hyb_protocol: Following fragmentation, 12.5μg of cRNA were hybridized for 16 hr at 45°C on Mouse 430 2.0 Genome Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

data_processing: Probe set summarization (CHP) files were derived from feature intensity (CEL) files using Affymetrix® Expression Console™ software (v.1.1). Default analysis settings were used for background adjustment and quantile normalization.

source_name: IFNγ treated Atg5 flox/flox macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: Bone marrow derived macrophages were generated by isolating and culturing mouse marrows in media containing DMEM, FBS, horse serum, CMG14-12 (Takeshita et al., 2000), MEM nonessential amino acids, sodium pyruvate, L-glutamine.

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

treatment_protocol: Macrophages were incubated with media alone or 100U/ml IFNγ for 14 hrs before RNA was extracted

tag: genotype/variation

value: Atg5 flox/flox

value: 100U/ml of IFN-gamma for 14 hrs


title: Atg5 deficient_Untreated_replicate2

description: Bone marrow derived macrophages

source_name: Untreated Atg5 flox/flox + LysM cre macrophages

value: Atg5 flox/flox + LysM cre


title: Control_Untreated_replicate2

description: Bone marrow derived macrophages

source_name: Untreated Atg5 flox/flox control macrophages


title: Atg5 deficient_Untreated_replicate1

description: Bone marrow derived macrophages


title: Control_Untreated_replicate1

description: Bone marrow derived macrophages


title: A549_exposed_to_CuO-nano particles

city: Tsukuba

first: Taro

last: Takemura

state: Ibaraki

address: 1-2-1 Sengen

department: Nanotechnology Innovation Station

country: Japan

institute: National Institute for Materials Science

description:
Three scanning (gain changed) for each hybridization
CuO-NPs

hyb_protocol: Labelled samples were mixed with hybridization buffer (Agilent GE Hybridization Kit) and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on an Axon GenePix 4000B scanner.

data_processing:
GenePix Pro Software (v 6.1) was used.
Three profiles (gain changed) were combined and processed by LOWESS.
Reproducible values were obtained from two hybridization.

source_name: Lung epithelial cells_CuO-NPs

label_protocol: 1 µg of total RNA were amplified and labelled with Cy5 or Cy3 using Ambion Amino Ally MessageAmp II aRNA Amplification Kit.

growth_protocol: Human lung epithelial cells A549 were seeded in DMEM and cultured for 48 hours.

extract_protocol: Total RNA extracted using ISOGEN following manufacturer's instructions.

treatment_protocol: Exposured to CuO-nano particles for 24 hours.

value: Lung epithelial cells

tag: exposed to

value: 25 ug/mL CuO-nano particles for 24hr

source_name: Lung epithelial cells A549

value: reference (not_exposed)


title: NB4 leukemic cells, ARAC+RA, replicate 1

source_name: ARAC+RA

growth_protocol: NB4 cells were cultured at 37C and 5% of CO2 in RPMI medium supplemented with 10% of fetal bovine serum.

treatment_protocol: NB4 cells infected with MSCV-based retroviral vectors containing ER-tagged empty vector (CTL), MycA or MycD were seeded at a density of 0.5M/mL in RPMI medium containing 200nM of 4-OHT and 25uM of AraC if indicated. After 16 hours, 10 nM of RA or EtOH (vehicle) were added to the medium for 4 hours. Cells were then harvested and RNA was extracted.

tag: cell line

value: leukemic


title: NB4 leukemic cells, MycA+RA, replicate 4

source_name: MycA+RA

tag: cell type


title: NB4 leukemic cells, MycA+RA, replicate 3


title: Control_IFNγ_replicate2

description: Bone marrow derived macrophages

tag: treatment