title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 3

description: Cerebellar tumor from hGFAP-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:29


title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 6

status: Public on Jun 24 2008

type: RNA

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

country: USA

institute: Boston Children's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Cerebellar tumor from hGFAP-cre:SmoM2 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Trizol extraction of total RNA followed by additional purification using RNeasy (Qiagen) performed according to the manufacturer's instructions.

tag: submitter:DR,  date:2006/12/05,  run#:02


title: Training_Site9_19

city: Pleasanton

first: Rachel

last: Li

state: CA

address: 4300 Hacienda Dr.

institute: Roche

description: Performed by Operator 1 from Site9 at Training stage

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 as recommended by the manufacturer.

data_processing: Data pre-processing included the summarization to generate probe set level signals for each microarray experiment and was performed using DQN algorithm.

label: biotin

organism: Homo sapiens

source_name: AML with t(8;21)

label_protocol:
For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24  T7 primer(Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA).
The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol:
The eight samples that were analysed during the training course were represented by MCF-7 (breast adenocarcinoma) and HepG2 (liver carcinoma) cell line total RNA (Ambion, Austin, TX, USA) with 1.0 µg to 8.0 µg input of total RNA (for labeling described below), and four leukaemia patient sample lysates prepared from mononuclear cells obtained after Ficoll density purification.
The total RNA from the patient lysates was extracted at each centre as part of the training program, making these samples a test of the entire microarray process workflow post sample acquisition (RNeasy kit, Qiagen, Hilden, Germany).

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Training_Site3_02

description: Performed by Operator 1 from Site3 at Training stage

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 79.8; Lot# = 124PO44836A


title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 1

tag: Cerebellar tumor from hGFAP-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:27


title: Training_Site3_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 19.4; Lot# = 124PO44836A


title: Training_Site3_05

source_name: CML in blast crisis

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 5

description: Cerebellar tumor from Olig2-tva-cre:SmoM2 mice

tag: submitter:KL,  date:2007/09/05,  run#:31


title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 2

tag: submitter:DR,  date:2006/10/13,  run#:30


title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 5

tag: submitter:DR,  date:2006/12/05,  run#:01


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 7

source_name: Cerebellar tumor from Olig2-tva-cre:SmoM2 mice

tag: submitter:KL,  date:2007/09/07,  run#:33


title: Non-tumor cerebellar tissue control 2

description: Non-tumor cerebellar tissue from Olig2-tva-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:26


title: hGFAP-cre:SmoM2 cerebellar tumor, biological replicate 4

tag: submitter:DR,  date:2006/12/05,  run#:03


title: Proficiency_Site4_20

description: Performed by Operator 1 from Site4 at Proficiency stage

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 57.1; Lot# = 035PO41658D


title: Proficiency_Site4_21

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 65.4; Lot# = 035PO41658D


title: Proficiency_Site4_16

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 50; Lot# = 055PO30555B


title: Proficiency_Site4_19

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 27.3; Lot# = 035PO41658D


title: Proficiency_Site4_15

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 22.9; Lot# = 055PO30555B


title: Proficiency_Site4_17

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 62.8; Lot# = 055PO30555B


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 4

tag: Cerebellar tumor from Olig2-tva-cre:SmoM2 mice

tag: submitter:DR,  date:2006/12/05,  run#:04


title: Proficiency_Site4_18

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 62.9; Lot# = 055PO30555B


title: Tlx3-cre:SmoM2 cerebellar tumor, biological replicate 3

description: Cerebellar tumor from Tlx3-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:21


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 1

tag: submitter:DR,  date:2006/10/13,  run#:24


title: Proficiency_Site4_14

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 56.4; Lot# = 035PO41658D


title: Proficiency_Site4_13

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 10.21; Lot# = 035PO41658D


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 2

tag: submitter:DR,  date:2006/10/13,  run#:23


title: Proficiency_Site4_22

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 72.7; Lot# = 035PO41658D


title: Tlx3-cre:SmoM2 cerebellar tumor, biological replicate 2

source_name: Cerebellar tumor from Tlx3-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:22


title: Proficiency_Site4_11

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 9.7; Lot# = 055PO30555B


title: Tlx3-cre:SmoM2 cerebellar tumor, biological replicate 1

tag: Cerebellar tumor from Tlx3-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:20


title: Math1-cre:SmoM2 cerebellar tumor, biological replicate 3

description: Cerebellar tumor from Math1-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:19


title: Training_Site4_07

description: Performed by Operator 1 from Site4 at Training stage

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Proficiency_Site4_12

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 35.1; Lot# = 055PO30555B


title: Training_Site4_05

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Training_Site4_06

source_name: CLL

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Math1-cre:SmoM2 cerebellar tumor, biological replicate 2

source_name: Cerebellar tumor from Math1-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:17


title: Training_Site4_08


title: Math1-cre:SmoM2 cerebellar tumor, biological replicate 1

tag: Cerebellar tumor from Math1-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:18


title: Skin: hCycle11 0 hr_le1

status: Public on Jun 23 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: 0 hr after synchronization

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: skin

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: skin, fibroblast


title: Skin: hCycle11 2 hr_le1

description: 2 hr after synchronization


title: Skin: hCycle11 1 hr_le1

description: 1hr after synchronization


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 6

tag: Cerebellar tumor from Olig2-tva-cre:SmoM2 mice

tag: submitter:KL,  date:2007/09/05,  run#:32


title: Skin: hCycle11 3 hr_le1

description: 3 hr after synchronization


title: Skin: hCycle11 7 hr_le2

description: 7 hr after synchronization


title: Skin: hCycle11 6 hr_le1

description: 6 hr after synchronization


title: Skin: hCycle11 10 hr_le2

description: 10 hr after synchronization


title: Skin: hCycle11 5 hr_le1

description: 5 hr after synchronization


title: Skin: hCycle11 8 hr_le2

description: 8 hr after synchronization


title: Skin: hCycle11 4 hr_le1

description: 4 hr after synchronization


title: Skin: hCycle11 9 hr_le2

description: 9 hr after synchronization


title: Skin: hCycle11 11 hr_le2

description: 11 hr after synchronization


title: Olig2-tva-cre:SmoM2 cerebellar tumor, biological replicate 3

tag: submitter:DR,  date:2006/12/05,  run#:05


title: Skin: hCycle11 12 hr_le2

description: 12 hr after synchronization


title: hMSCs 30 days TCM replicate 2

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

description: Samples were processed in CINJ Core Expression Array Facility according to Affymetrix protocol

hyb_protocol: Water, Molecular Biology Grade or DEPC-treated Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL) Herring Sperm DNA GeneChip Eukaryotic Hybridization Control Kit 5M NaCl, RNase-free, DNase-free MES Free Acid Monohydrate MES Sodium Salt EDTA Disodium Salt Miscellaneous Reagents/Supplies Surfact-Amps 20 (Tween-20), 10% Hybridization Oven 640 Sterile, RNase-free, microcentrifuge tubes, 1.5mL Micropipettors Sterile-barrier pipette tips and non-barrier tips Heatblock

scan_protocol: Washing, Staining, and Scanning Water, Molecular Biology Grade Distilled water Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL) R-Phycoerythrin Streptavidin 20X SSPE (3M NaCl, 0.2M NaH2PO4, 0.02M EDTA) Goat IgG, Reagent Grade Anti-streptavidin antibody (goat), biotinylated 10% surfact-Amps 20 (Tween-20)

source_name: bone marrow derived cells

label_protocol:
Synthesis of Biotin-Labeled cRNA/Purification
ENZO BioArray RNA Transcript Labeling Kit
GeneChip Sample Cleanup Module
Miscellaneous Reagents/Supplies
100% ethanol at room temperature
80% ethanol at room temperature
Water, Molecular Biology Grade or DEPC-treated
Ethidium Bromide
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier, RNase-free pipette tips
Mini agarose gel electrophoresis unit with appropriate buffers
UV Spectrophotometer
Cooling water bath

growth_protocol: standard cell culture condition (95% air, 5% CO2, 37C)

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen

treatment_protocol: Cells were exposed to 100 % condition media collected overnight from MDAMB231 cells for 30 days. Condition media was changed every 3 days.

tag: hMSCs exposed to breast tumor condition media


title: hMSC DMEM replicate 1

source_name: bone marrow derived

treatment_protocol: Cells were grown in DMEM media for 30 days as a control. Media was changed every 3 days.

tag: hMSCs control DMEM media


title: hMSCs MEM replicate 1

treatment_protocol: Cells were grown in alpha MEM media for 30 days as a control. Media was changed every 3 days.

tag: hMSCs control alpha MEM media


title: hMSC 30days TCM replicate 3

tag: HMSCs exposed to breast cancer condition media for 30 days


title: hMSC 30 days TCM replicate 1

tag: HMSCs exposed to breast cancer tumor condition media for 30 days


title: 5-Aza hMSCs replicate 3

treatment_protocol: Cells were exposed to 5-Azacytidine and cultured for 21 days. Media was changed every 3 days.

tag: hMSCs exposed to 5-Azacytidine


title: 5-Aza hMSCs replicate 1


title: hMSCs DMEM replicate 2

source_name: bone marrow


title: hMSCs DMEM replicate 3


title: NY79

status: Public on Jun 22 2008

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

description: 91 hepatocellular carcinomas were obtained at the time of surgical resection or orthotopic transplantation.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix

scan_protocol: Affymetrix standard procedure

data_processing: RMA.  Supplementary data file also contains RMA based on AceView probeset remappings (PMID: 15850491, 16925834)

source_name: hepatocellular carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Tumors obtained at time of surgical resection or transplantation, according to institutional review board approved protocols

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

tag: vascular invasion

tag: code

value: transplant

tag: class

value: Proliferation

tag: tp53 mutation

tag: ctnnb1 mutation

tag: immunohistochemistry

value: pRPS6 :0

value: pIGFR1 :0

value: pAkt :1

value: CTNNB1 :0

tag: used for prognostic prediction

value: yes

tag: used for microrna profiling

value: Yes

tag: uhrf1 study

value: Not used


title: NY96

tag: age

tag: Sex

value: M

value: resection

value: pRPS6 :1

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: NY99

value: C

value: F

tag: afp


title: 5-Aza hMSCs replicate 2


title: NY82

value: pAkt :0

value: CTNNB1 :1

value: no


title: NY44

value: transplant

value: Inflammation


title: hMSCs MEM replicate 2


title: NY70

value: pRPS6 :0


title: NY6


title: NY41


title: NY65

value: A

value: Proliferation

value: pIGFR1 :0


title: NY36

value: Yes

value: CTNNB1 :0


title: NY331

value: No

value: M

value: yes


title: NY7

value: pRPS6 :1

value: Not used


title: NY333

value: resection


title: NY327

value: C

value: F

value: pAkt :0

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: NY34

value: Inflammation

value: no


title: NY323

value: A

value: pIGFR1 :1

value: pAkt :1


title: NY39

value: transplant

value: Proliferation

value: Yes


title: NY317

value: No

value: M

value: pIGFR1 :0

value: CTNNB1 :0


title: NY325

value: resection

value: pRPS6 :1

value: yes


title: NY319

value: Polysomy chr7

value: pRPS6 :0


title: NY329

value: CTNNB1 :1

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: NY26

value: Inflammation

value: pAkt :0

value: no

value: Not used


title: NY311

value: C

value: Proliferation

value: pIGFR1 :1


title: NY216

value: Yes

value: M

value: pAkt :1


title: NY313

value: A

value: F

value: resection

value: pIGFR1 :0

value: CTNNB1 :0


title: NY228

value: pRPS6 :1


title: NY232

value: pRPS6 :0

value: CTNNB1 :1

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: NY206

value: Polysomy chr7

value: yes


title: NY224

value: C


title: NY226

value: B


title: NY18

value: No

value: Inflammation

value: no


title: NY307

value: Yes

value: pAkt :0


title: NY16

value: transplant

value: Not used


title: NY321

value: F

value: resection

value: pIGFR1 :0


title: NY309

value: M

value: pRPS6 :1


title: NY208

value: A

value: pRPS6 :0

value: CTNNB1 :1

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: NY218

value: C

value: yes


title: NY222

value: B

value: CTNNB1 :0


title: NY2

value: No

value: no

value: Yes


title: M94

value: Polysomy chr7

value: pAkt :0


title: M92

value: resection

value: Unannotated

value: pIGFR1 :1


title: M98

value: M

value: pIGFR1 :0

value: pAkt :1


title: M69

value: A

value: F

value: Proliferation

value: pRPS6 :0

value: CTNNB1 :1


title: M71

value: Not used


title: M59

value: No

value: pRPS6 :1

value: yes


title: M90

value: Polysomy chr7

value: CTNNB1 :0

value: Yes

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: M43

value: resection

value: pIGFR1 :1

value: pAkt :0


title: M96

value: pIGFR1 :0


title: M81

value: A


title: M15

value: M

value: Unannotated

value: pAkt :1


title: M67

value: F

value: Proliferation


title: M13

value: No

value: Not used


title: M53

value: B

value: pRPS6 :1

value: yes


title: M17

value: pRPS6 :0

value: CTNNB1 :1

value: Yes


title: M73

value: resection

value: Inflammation

value: CTNNB1 :0

value: no


title: M49

value: M

value: pIGFR1 :1


title: M106

value: A

value: Unannotated

value: pIGFR1 :0

value: pAkt :0

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: M11

value: F

value: Proliferation


title: M35

value: pRPS6 :1

value: pAkt :1

value: yes


title: M31

value: No

value: pRPS6 :0

value: Yes

value: Not used


title: M79

value: resection

value: CTNNB1 :1


title: M88

value: M

value: CTNNB1 :0


title: B98

value: A

value: pIGFR1 :1


title: M102


title: M100

value: Unannotated

value: pIGFR1 :0

value: pAkt :0


title: B94

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: B88


title: M104

value: F

value: pRPS6 :1


title: B96

value: Polysomy chr7

value: yes


title: B86

value: No

value: pRPS6 :0


title: B82

value: Yes

value: pAkt :1

value: no


title: NY204

value: M

value: resection

value: CTNNB1 :1


title: B84

value: A


title: B78

value: CTNNB1 :0


title: B76

value: pIGFR1 :0


title: B80

value: pAkt :0


title: B25

value: Unannotated

value: pIGFR1 :1

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: B68


title: B31

value: B


title: B35

value: Inflammation


title: B70

value: No

value: Polysomy chr7

value: yes


title: B17

value: F

value: pRPS6 :0

value: Yes


title: B90

value: resection


title: B33

value: M


title: B74

value: C

value: Proliferation

value: pRPS6 :1

value: pAkt :1

value: no


title: B39

value: A

value: pIGFR1 :0

value: pAkt :0

value: CTNNB1 :0

value: Not used


title: B13

value: No

value: Inflammation

value: Used in UHRF1 study (Mudbhary, et al., 2013)


title: B19

value: B

value: Polysomy chr7

value: pIGFR1 :1

value: yes


title: B29

value: Yes

value: M

value: resection

value: Unannotated

value: pRPS6 :0


title: B72

value: A

value: pRPS6 :1

value: no


title: B66

value: Proliferation

value: pIGFR1 :0

value: pAkt :0

value: CTNNB1 :0


title: Colonic_mucosa_control_90

status: Public on Jun 20 2008

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: The sample is a part of a series of analyses of colonic gene expression in patients with inflammatory bowel diseases

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

scan_protocol: The Affymetrix system was used and the protocols supplied by Affymetrix followed.

data_processing: Log(2) transformed expression measures were calculated with the RMA procedure using the software from www.Bioconductor.org

label: Phycoerythrin

source_name: Colonic mucosal endoscopic pinch biopsy

label_protocol: First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ul reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ul RNase free water, 30 ul 5 times second strand reaction buffer (Invitrogen), 3 ul 10 mM dNTP, 1 ul Escherichia coli DNA ligase (10 U/ml), 4 ul E. coli DNA polymerase I (10 U/ml), 1 ul E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

extract_protocol: RNA was extracted with Trizol

tag: Biopsy taken from the sigmoideum from a control subject. No macroscopic signs of inflammation


title: Colonic_mucosa_control_70


title: Colonic_mucosa_control_82


title: Colonic_mucosa_control_92


title: Colonic_mucosa_control_36

description: The sample is a part of a series of analyses of colonic gene expression in patients with  inflammatory bowel diseases

tag: Biopsy taken from the sigmoideum from control subject, no macroscopic signs of inflammation.


title: Colonic_mucosa_control_97


title: Colonic_mucosa_control_80


title: Colonic_mucosa_control_45

tag: Biopsy taken from the sigmoideum from a control subject, no macroscopic signs of inflammation.


title: Colonic_mucosa_control_73


title: Colonic_mucosa_control_67


title: Colonic_mucosa_control_79


title: Colonic_mucosa_control_87


title: Colonic_mucosa_control_37

tag: Biopsy taken from the sigmoideum of a control subject, no macroscopic signs of inflammation.


title: HEK293 cell line #4 with induced HNF4a2 wild type

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Analysis of gene expression in human embryonic kidney cells (HEK293) overexpressing the transcription factor HNF4a2 or mutant forms HNF4a2 C106R or R154X, which were introduced by FRT/FLP recombination. The analysis were performed 24 hours following 1 µg/ml doxycyclin treatment to induce the expression of the trans-genes. Results identify HNF4 regulated genes in kidney cells being several of these genes deregulated in renal cell carcinoma.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual v2, Affymetrix).

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

treatment_protocol: Cells were treated for 24 h with 1 µg/ml doxycyclin or solvent.


title: Colonic_mucosa_control_31


title: Colonic_mucosa_control_47


title: HEK293 cell line #6 with noninduced HNF4a2 mutant R154X


title: HEK293 cell line #6 with induced HNF4a2 mutant R154X


title: HEK293 cell line #1 with noninduced HNF4a2 mutant C106R


title: Colonic_mucosa_control_86


title: Colonic_mucosa_control_108


title: HEK293 cell line #4 with noninduced HNF4a2 wild type


title: HEK293 cell line #1 with noninduced HNF4a2 wild type


title: HEK293 cell line #1 with induced HNF4a2 mutant C106R


title: HEK293 cell line #1 with induced HNF4a2 wild type


title: GBM, TMZ/radiotherapy (90)

city: Lausanne

first: Monika

middle: E

last: Hegi

state: Vaud

address: Bugnon 46

department: Neurosurgery

country: Switzerland

institute: CHUV

description: MGMT status: M

hyb_protocol: Affymetrix hybridisation protocol

scan_protocol: GeneChip Operating Software instructions using GeneChip Scanner 3000 High-Resolution Scanning Patch

data_processing: RMA: background substruction, quantile normalization and median polish summarization.

source_name: brain (resected material)

label_protocol: Affymetrix Small sample target labelling assay (double amplification) with ENZO kit, start with 100ng

extract_protocol: Qiagen Rneasy Lipid Tissue mini kit protocol

tag: tissue

value: brain (resected material)

tag: disease status

value: GBM

tag: patient

tag: gender

value: FEMALE

tag: treatment

value: TMZ/radiotherapy

tag: survival status

tag: survival time in months

tag: mgmt status


title: GBM, radiotherapy (97)

description: MGMT status: U

value: radiotherapy

value: U


title: GBM, radiotherapy (574)

description: MGMT status: U


title: GBM, radiotherapy (84)

description: MGMT status: M

value: MALE

value: M


title: GBM, radiotherapy (63)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (ge205)

description: MGMT status: M


title: GBM, radiotherapy (94bis)

description: MGMT status: U


title: Recurrent GBM, TMZ/radiotherapy (65R)

description: MGMT status: M

value: recurrent GBM


title: GBM, TMZ/radiotherapy (93)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (ge197)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (57)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (563)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (558)

description: MGMT status: U


title: Recurrent GBM, TMZ/radiotherapy (57R)

description: MGMT status: M


title: GBM, radiotherapy (70)

description: MGMT status: ?


title: GBM, radiotherapy (566)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (80)

description: MGMT status: M


title: GBM, radiotherapy (83)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (528bis)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (444)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (458)

description: MGMT status: U


title: GBM, radiotherapy (527)

description: MGMT status: M


title: GBM, radiotherapy (55)

description: MGMT status: M


title: GBM, radiotherapy (534)

description: MGMT status: M


title: GBM, radiotherapy (428)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (396)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (461)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (547)

description: MGMT status: U


title: GBM, radiotherapy (390)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (506)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (344)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (356bis)

description: MGMT status: U


title: GBM, radiotherapy (323)

description: MGMT status: M


title: GBM, radiotherapy (328)

description: MGMT status: U


title: GBM, radiotherapy (284)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (300)

description: MGMT status: ?


title: GBM, TMZ/radiotherapy (274)

description: MGMT status: U


title: GBM, radiotherapy (283)

description: MGMT status: M


title: GBM, radiotherapy (254)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (30)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (222)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (288)

description: MGMT status: M


title: GBM, radiotherapy (246)

description: MGMT status: M


title: GBM, radiotherapy (345)

description: MGMT status: M


title: Re-recurrent GBM, TMZ/radiotherapy (1869RR)

description: MGMT status: M

value: re-recurrent GBM


title: GBM, TMZ/radiotherapy (236)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (1621)

description: MGMT status: M


title: Recurrent GBM, TMZ/radiotherapy (1622R)

description: MGMT status: M


title: GBM, radiotherapy (349)

description: MGMT status: M


title: Recurrent GBM, radiotherapy (212R)

description: MGMT status: U


title: GBM, radiotherapy (218)

description: MGMT status: M


title: GBM, radiotherapy (242)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (269)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (360)

description: MGMT status: M


title: Non-tumoral,  (1780)

description: MGMT status:

value: non-tumoral

tag: mgmt status:


title: GBM, TMZ/radiotherapy (161)

description: MGMT status: U


title: Recurrent GBM, TMZ/radiotherapy (1795R)

description: MGMT status: M


title: Recurrent GBM, TMZ/radiotherapy (1854R)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (190)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (157)

description: MGMT status: U


title: GBM, radiotherapy (159)

description: MGMT status: U


title: GBM, radiotherapy (15)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (1357)

description: MGMT status: M


title: Recurrent GBM, TMZ/radiotherapy (1497R)

description: MGMT status: M


title: Non-tumoral,  (148)

description: MGMT status:


title: Non-tumoral,  (1553)

description: MGMT status:


title: GBM, TMZ/radiotherapy (1317)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (1360)

description: MGMT status: M


title: GBM, radiotherapy (211)

description: MGMT status: M


title: Recurrent GBM, TMZ/radiotherapy (155R)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (1437)

description: MGMT status: U


title: GBM, radiotherapy (147)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (1453)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (1297)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (1430)

description: MGMT status: M


title: Non-tumoral,  (1076)

description: patient: 1076; age: NA; gender: NA; treatment: NA; survival status: NA; survival time in months: NA


title: GBM, TMZ/radiotherapy (1308)

description: MGMT status: M


title: Recurrent GBM, TMZ/radiotherapy (100R)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (12)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (1399)

description: MGMT status: M


title: GBM, TMZ/radiotherapy (129)

description: MGMT status: U


title: GBM, TMZ/radiotherapy (104)

description: MGMT status: M


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het)_B

city: San Francisco

first: Xuyu

last: Zhou

address: 513 Parnassus Ave

department: Diabetes Center

institute: UCSF

description: GCRMA Normalized data

hyb_protocol: Affymetrix standard hydridization protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 and Affymetrix Expression Console software

data_processing: Data were analyzed by GeneSpring GX7.3.1 (Agilent Technologies).

source_name: CD4+YFP+ T cells from FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het) mice

label_protocol: MessageAmp™ II aRNA Amplification Kit

extract_protocol: TRIzol (Invitrogen, Carlsbad, CA)

tag: Lymph node CD4+YFP+ T cells (> 95% pure) from FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het) mice were isolated by flow cytometry.


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO)_B

description: GCRMA Normalized data

source_name: CD4+YFP+ T cells from FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO) mice

tag: Lymph node CD4+YFP+ T cells (> 95% pure) from FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO) mice were isolated by flow cytometry.


title: GBM, TMZ/radiotherapy (106)

description: MGMT status: U

tag: age


title: Col_mock_rep3

city: Seattle

first: Jennifer

last: Nemhauser

state: WA

institute: Univ. of Washington

description: Total RNA was extracted from 4-day-old, etiolated arf2 and Col Arabidopsis seedlings grown on 0.5 µM BRZ or mock treatments.

hyb_protocol: Hybridization and washing were were carried out according to the protocols provided by the gene chip manufacturer Affymetrix (Santa Clara, California, United States).

scan_protocol: Scan protocols were were carried out according to the protocols provided by the gene chip manufacturer Affymetrix (Santa Clara, California, United States).

data_processing: Expression was normalized and estimated using the gcRMA package of BioConductor.

organism: Arabidopsis thaliana

source_name: Col on mock

label_protocol: Total RNA from the treated seedlings was used for preparing probes for the microarray experiments, which were carried out according to the protocols provided by the gene chip manufacturer Affymetrix (Santa Clara, California, United States).

extract_protocol: Total RNA was extracted with Spectrum™ Plant Total RNA Kit from Sigma-Aldrich according to manufacturer’s protocols.

tag: 4-day-old, etiolated Col seedlings grown on mock treatments


title: arf2_mock_rep3

source_name: arf2 on mock

tag: 4-day-old, etiolated arf2 seedlings grown on mock treatments


title: arf2_brz_1

description: Total RNA was extracted from 4-day-old, etiolated arf2 Arabidopsis seedlings grown on 0.5 µM BRZ.

source_name: arf2 on BRZ

label_protocol:
Total RNA from the treated seedlings was used for preparing probes
for the microarray experiments, which were carried out according to
the protocols provided by the gene chip manufacturer Affymetrix
(Santa Clara, California, United States).

tag: 4-day-old, etiolated arf2 seedlings grown on 0.5 µM BRZ


title: Col_BRZ_rep1

source_name: Col on BRZ

tag: 4-day-old, etiolated Col seedlings grown on 0.5 µM BRZ


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het)_C

description: GCRMA Normalized data


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO)_C

description: GCRMA Normalized data


title: GBM, TMZ/radiotherapy (1284)

description: MGMT status: M


title: Nodal DLBCL 21N

status: Public on Jun 19 2008

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

description: Gene expression data of nodal DLBCL

hyb_protocol: The samples were hybridized, stained and washed following the protocol for eukaryotic target hybridization, washing ans staining in the Expression analysis technical manual from Affymetrix (available at www.affymetrix.com). In detail, after 16 h of hybridization at 45°C the arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned following the protocol for eukaryotic array scanning in the Expression analysis technical manual from Affymetrix (available at www.affymetrix.com) using the Affymetrix GC scanner 3000.

data_processing: Probe signals were extracted from .CEL files using the MAS5.0 algorithm and the GeneChip operating software (GCOS). The average probe array signals were scaled to a target signal of 500.

source_name: Nodal DLBCL

label_protocol: The samples were processed following the protocol for eukaryotic samples in the Expression analysis technical manual from Affymetrix (available at www.affymetrix.com). In detail, cDNA synthesis was performed with a starting amount of 2µg total RNA using the One-cycle cDNA synthesis kit (Affymetrix) following the Affymetrix standard protocol. Double stranded cDNA and cRNA was purified with the GeneChip Sample Cleanup module. Synthesis of Biotin-labeled cRNA was performed using the IVT Labeling Kit from Affymetrix, followed by cleanup and fragmentation.

extract_protocol: Total RNA was isolated from frozen tumor specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA) according to the manufacturers’ instructions.

tag: Tissue

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:RNA, Gender:Female


title: Col_mock_rep1


title: arf2_mock_rep2


title: arf2_brz_2


title: Nodal DLBCL 23N

description: Gene expression data of nodal DLBCL


title: Col_BRZ_rep2


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO)_A

description: GCRMA Normalized data


title: arf2_mock_rep1

description: Total RNA was extracted from 4-day-old, etiolated arf2 Arabidopsis seedlings grown on mock treatments.

tag: 4-day-old, etiolated arf2 seedlings grown on mock treatment


title: Nodal DLBCL 20N

description: Gene expression data of nodal DLBCL

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:RNA, Gender:Male


title: T cells_FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het)_A

description: GCRMA Normalized data


title: Nodal DLBCL 19N

description: Gene expression data of nodal DLBCL


title: Nodal DLBCL 22N

description: Gene expression data of nodal DLBCL


title: Nodal DLBCL 17N

description: Gene expression data of nodal DLBCL


title: Col_mock_rep2


title: Col_BRZ_rep3


title: Nodal DLBCL 13N

description: Gene expression data of nodal DLBCL


title: Nodal DLBCL 11N

description: Gene expression data of nodal DLBCL


title: Nodal DLBCL 15N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 22T

description: Gene expression data of testicular DLBCL

source_name: Testicular DLBCL

value: Testicular diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:RNA, Gender:Male


title: Nodal DLBCL 1N

description: Gene expression data of nodal DLBCL


title: Nodal DLBCL 14N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 11T


title: Testicular DLBCL 20T


title: Nodal DLBCL 18N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 19T


title: Nodal DLBCL 16N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 18T


title: Testicular DLBCL 7T


title: Testicular DLBCL 8T


title: Testicular DLBCL 15T


title: Nodal DLBCL 12N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 17T


title: Nodal DLBCL 6N

description: Gene expression data of nodal DLBCL


title: Testicular DLBCL 6T


title: Testicular DLBCL 16T


title: Testicular DLBCL 9T


title: Testicular DLBCL 4T


title: Testicular DLBCL 1T


title: Testicular DLBCL 12T


title: CNS DLBCL 12C

description: Gene expression data of CNS DLBCL

source_name: Central nervous system DLBCL

value: Central nervous system diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:RNA, Gender:Female


title: CNS DLBCL 13C

description: Gene expression data of CNS DLBCL


title: Testicular DLBCL 3T


title: CNS DLBCL 3C

description: Gene expression data of CNS DLBCL

value: Central nervous system diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:RNA, Gender:Male


title: CNS DLBCL 2C

description: Gene expression data of CNS DLBCL


title: CNS DLBCL 11C

description: Gene expression data of CNS DLBCL


title: CNS DLBCL 10C

description: Gene expression data of CNS DLBCL


title: CNS DLBCL 1C

description: Gene expression data of CNS DLBCL


title: CNS DLBCL 8C

description: Gene expression data of CNS DLBCL


title: GW 3 (set 2)

status: Public on Jun 18 2008

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Treated with GW1516 for 6 days

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array.

scan_protocol: Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000

data_processing: Data was processed using Affymetrix Microarray Suite 5.0 software.  The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.

source_name: Rodent quadricep muscles

label_protocol: Double straned DNA was prepared from 10ug of total RNA, which in turn was biotinylated using standard protocol.

extract_protocol: Total RNA from the frozen samples was extracted using Trizol method.  For each sample, total RNA from 3 mice within the group was pooled.

treatment_protocol: Mice were treated with vehicle, AICAR (250mg/kg/day), GW1516 (5mg/kg/day) or the combination for 6 days.  At the end of treatment, mice in each group were euthanized, quadricep muscle were immediately disceted and flash frozen in liquid nitrogen.

tag: 10 wks old male C57Bl/6J mice


title: GW 2 (set 2)

description: Treated with GW1516 for 6 days


title: Vehicle 2 (set 2)

description: Treated with vehicle for 6 days


title: GW 1 (set 2)

description: Treated with GW1516 for 6 days


title: GW + AICAR 3 (set 2)

description: Treated with AICAR and GW for 6 days


title: CNS DLBCL 9C

description: Gene expression data of CNS DLBCL


title: Vehicle 3 (set 2)

description: Treated with vehicle for 6 days


title: AICAR 1 (set 2)

description: Treated with AICAR for 6 days


title: GW + AICAR 2 (set 2)

description: Treated with AICAR and GW for 6 days


title: Vehicle 1 (set 2)

description: Treated with vehicle for 6 days


title: AICAR 3 (set 2)

description: Treated with AICAR for 6 days


title: GW + AICAR 1 (set 2)

description: Treated with AICAR and GW for 6 days


title: AICAR 2 (set 2)

description: Treated with AICAR for 6 days


title: FLK1_2

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9440

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 5ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: endothelial layer of renal vein & endothelial layer of renal artery

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 5-10 E15.5 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization & FACS
Tie2 transgenic mice are time-mated.  Pregnant Tie2 transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Embryonic kidneys are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC. Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS. The dissociated cells from the kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes. The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.   Filter cells through 70 micron mesh filter and proceed with FACS.

tag: gene reported

value: Tg(TIE2GFP)287Sato / MGI:3056937

tag: strain

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: FLK1_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:9439


title: small airways, COPD 134

status: Public on Jun 17 2008

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: small airways, COPD 134

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: ethnic group

value: white

tag: smoking status

value: COPD, GOLD-I, 24 pack-years


title: small airways, COPD 114

description: small airways, COPD 114

tag: age

value: black

value: COPD, GOLD-II, 29 pack-years


title: small airways, COPD 122

description: small airways, COPD 122

value: COPD, GOLD-I, 14 pack-years


title: small airways, COPD 110

description: small airways, COPD 110

value: F

value: COPD, GOLD-II, 15 pack-years


title: small airways, smoker 095

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

value: M

value: smoker, 32 pack-years


title: small airways, COPD 108

description: small airways, COPD 108

tag: Age

tag: Sex

tag: Ethnic group

tag: Smoking status

value: COPD, GOLD-I, 57 pack-years


title: small airways, COPD 024

description: small airways, COPD 024

value: hispanic

value: COPD, GOLD-II, 27.5 pack-years


title: small airways, smoker 169

description: small airways, smoker 169

value: smoker, 47 pack-years


title: small airways, smoker 103

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD

value: smoker, 15 pack-years


title: small airways, smoker 114

description: small airways, smoker 114

value: smoker, 22 pack-years


title: small airways, COPD 103

value: COPD, GOLD-I, 23 pack-years


title: small airways, COPD 080

value: COPD, GOLD-I, 22 pack-years


title: small airways, smoker 152

description: small airways, smoker 152

value: white

value: smoker, 16 pack-years


title: small airways, COPD 046

value: black

value: COPD, GOLD-II, 75 pack-years


title: small airways, smoker 098

value: smoker, 36 pack-years


title: small airways, smoker 074

value: smoker, 20 pack-years


title: small airways, COPD 093

description: small airways, COPD 093

value: F

value: COPD, GOLD-II, 34 pack-years


title: small airways, smoker 119

description: small airways, smoker 119

value: smoker, 33 pack-years


title: small airways, COPD 068

value: M

value: COPD, GOLD-II, 60 pack-years


title: small airways, non-smoker 035

value: non-smoker


title: small airways, COPD 119

description: small airways, COPD 119

value: hispanic

value: COPD, GOLD-I, 32.5 pack-years


title: small airways, non-smoker 059

description: small airways, non-smoker 059


title: small airways, COPD 014

value: COPD, GOLD-II, 35 pack-years


title: small airways, non-smoker 078

description: small airways, non-smoker 078


title: small airways, smoker 112

description: small airways, smoker 112

value: smoker, 23 pack-years


title: small airways, non-smoker 071

description: small airways, non-smoker 071


title: Small airways, non-smoker 036

description: small airways, non-smoker


title: small airways, non-smoker 034

description: small airways, non-smoker


title: small airways, COPD 036

value: COPD, GOLD-I, 48 pack-years


title: small airways, COPD 059

value: COPD, GOLD-II, 27 pack-years


title: Thymus, technical replicate 3

status: Public on Jun 15 2008

city: Providence

first: Fenghai

last: Duan

state: RI

address: 121 S. Main Street

department: Biostatistics

institute: Brown University

description: Gene expression data from thymus

hyb_protocol: Following fragmentation, the biotinylated cRNA were hybridized for 16 hr at 45C on Rhesus Macaque Genome Array or Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned on Affymetrix scanner 3000

data_processing: The data were preprossed with GC-Robust Multichip Analysis (RMA).

organism: Macaca mulatta

source_name: rhesus macaques thymus

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

tag: Tissue

value: thymus


title: small airways, non-smoker 045

description: small airways, non-smoker 045

value: black


title: Pancreas, technical replicate 4

description: Gene expression data from pancreas

source_name: rhesus macaques pancreas

value: pancreas


title: Testis, technical replicate 3

description: Gene expression data from testis

source_name: rhesus macaques testis

value: testis


title: Fibroblasts, technical replicate 4

description: Gene expression data from immortalized fibroblasts

source_name: rhesus macaques fibroblasts

tag: Cell Line

value: immortalized fibroblasts


title: Testis, technical replicate 4

description: Gene expression data from testis


title: Pancreas, technical replicate 3

description: Gene expression data from pancreas


title: Cerebral cortex, technical replicate 3

description: Gene expression data from cerebral cortex

source_name: rhesus macaques cerebral cortex

value: cerebral cortex


title: Cerebral cortex, technical replicate 4


title: AML12+RA (3h)

city: Jackson

first: Tereza

last: Ventura-Holman

state: MS

address: 2500 North State St.

institute: University of Mississippi Medical Center

description: AML12 cells exposed to 1 micromolar RA for 3h

hyb_protocol: following Affymetrix GeneChip Expression Analysis Manual

data_processing: Expression data were analyzed by the software DNA-Chip Analyzer (dCHIP) available at www.dchip.org

source_name: AML12+RA (3h)

extract_protocol: Total RNA was isolated with Trizol and processed using the RNeasy kit from Qiagen

treatment_protocol: AML12 cells were exposed to 1 micromolar retinoic acid (RA) for 3h

tag: cultured hepatocytes


title: AML12 control (24h)

description: AML12 cells- no treatment control

scan_protocol: following Affymetrix GeneChip Expression Analysis Manual

source_name: AML12 control (24h)

tag: cell type

value: cultured hepatocytes

tag: cell line


title: RA-treated, v-erbA-transfected AML12 (24h)

description: v-erbA-transfected AML12 cells exposed to RA for 3h

label_protocol: following Affymetrix GeneChip Expression Analysis Manual

tag: murine hepatocytes in culture, transfected with v-erbA and exposed to 1 micromolar retinoic acid for 24h


title: v-erbA-transfected AML12 control (24h)

description: v-erbA-transfected AML12 cells, 3h control

source_name: v-erbA-transfected AML12 control (24h)

value: v-erbA-transfected cultured hepatocytes


title: Thymus, technical replicate 4

description: Gene expression data from thymus


title: AML12+RA (24h)

treatment_protocol: AML12 cells were exposed to 1 micromolar retinoic acid (RA) for 24h


title: OPflR#66 cell line

first: Carl

last: Walkley

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: determine the expression profile of mouse osteosarcoma

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. (http://chip.dfci.harvard.edu/lab/services.php)

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. (http://chip.dfci.harvard.edu/lab/services.php)

data_processing: dChip normalization

source_name: tumour tissue derived from OS cell line

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.  (http://chip.dfci.harvard.edu/lab/services.php)

growth_protocol: mouse model

extract_protocol: Trizol/QIAGEN columns

tag: primary tumor tissue, grown in Rag2-/- recipient


title: RA-treated, v-erbA-transfected AML12 (3h)

tag: murine hepatocytes in culture transfected with v-erbA and exposed to 1 micromolar retinoic acid for 3h


title: v-erbA-transfected AML12 control (3h)

source_name: v-erbA-transfected AML12 control (3h)


title: AML12 control (3h)

description: AML12 no treatment control

data_processing: Expression data were analyzed by the software DNA-Chip Analyzer (dCHIP) available at www.dchip.org.

source_name: AML12 control (3h)

treatment_protocol: AML12 cells were exposed to 1 micromolar RA for 3h.


title: OPflR#64 secondary

source_name: secondary transplant osteosarcoma


title: Small intestinal GIST 8

city: Chuo

first: Umio

last: Yamaguchi

state: Tokyo

address: 5-1-1, Tsukiji

department: Chemotherapy

country: Japan

institute: NCCRI

description: Frozen tumour specimens from untreated GIST of the stomach or small intestine.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix human genome HG-U133A genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanned on a GeneArray scanner. Images were quantified using Microarray Analysis Suite version 4.0 software (Affymetrix).

data_processing: The data were analyzed and normalized using MAS5 algorithm with the ArrayAssist 4.X. software.

source_name: Total RNA from human small intestinal GIST.

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

extract_protocol: Total RNA extracted using IsoGen lysis buffer following manufacturer's instructions.

tag: Gender

value: female

tag: Tumor size

tag: KIT mutation

value: Exon 11


title: primary OS #353

city: Boston

source_name: osteosarcoma

tag: primary tumor tissue


title: Gastric GIST 20

source_name: Total RNA from human gastric GIST.

value: male

value: Wild type


title: Gastric GIST 23


title: OPflR#94 secondary


title: OPflR#29 secondary


title: Small intestinal GIST 9


title: Gastric GIST 21


title: Gastric GIST 17


title: Gastric GIST 18


title: Gastric GIST 19


title: Gastric GIST 22


title: Small intestinal GIST 7

value: Exon 9


title: Gastric GIST 16


title: Small intestinal GIST 6


title: primary OS #330


title: Fibroblasts, technical replicate 3


title: primary OS #331


title: primary OS #188


title: Gastric GIST 15


title: primary OS #183


title: Small intestinal GIST 5


title: primary OS #182


title: primary OS #179


title: primary OS #176


title: Gastric GIST 13


title: Gastric GIST 14


title: primary OS#87


title: Gastric GIST 9


title: Gastric GIST 11


title: Gastric GIST 10


title: primary OS#64


title: primary OS#29


title: primary OS#94


title: primary OS#66


title: primary OS#12


title: Gastric GIST 12


title: Small intestinal GIST 4


title: primary OS#119


title: Gastric GIST 8


title: Gastric GIST 7


title: Gastric GIST 6


title: #213 cell line

source_name: osteosarcoma cell line


title: #182 cell line


title: #176 cell line


title: Small intestinal GIST 3


title: #179 cell line


title: Gastric GIST 5


title: primary OB #2

source_name: osteoblasts (in vitro differentiated)

tag: WT


title: Gastric GIST 4

tag: Age


title: Gastric GIST 2


title: Gastric GIST 3


title: primary OB #3


title: Small intestinal GIST 1


title: Gastric GIST 1


title: Small intestinal GIST 2


title: Granulosa cell tumor from Smad1/5/8 mutant mouse Sample 2

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: All labeling, hybridization, and scanning performed from standard Affymetrix protocols at the Baylor College of Medicine Microarray Facility

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix

data_processing: GCOS

label: Affymetrix Standard

source_name: granulosa cell tumor

label_protocol: Affymetrix Standard

growth_protocol: No growth protocol

extract_protocol: Tumor collected and stored in RNA later overnight at 4 degrees, then frozen at -80.  RNA from Qiagen Rneasy kit.

treatment_protocol: No treatment

tag: Granulosa cell tumor isolated from a Smad1flox/flox;Smad5flox/flox;Smad8+/-;Amhr2cre/+ female mouse age 32 weeks. Background is C57BL/6J;129S5/SvEvBrd


title: 070_Ca_Mon

status: Public on Jun 14 2008

city: Rotterdam

first: Marieke

last: Emonts

address: Dr Molewaterplein 50, room Ee15-02

institute: Erasmus MC

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

data_processing: Micro-array analysis. Background was removed using robust multichip analysis (RMA) and probe intensity levels were quantile normalized. Array groups were compared based on the perfect match (PM) probe intensity levels only, by performing a per-probeset two-way analysis of variance (ANOVA, with factors “probe” and “group”). This results in average expression levels for each probeset in each group, as well as raw p-values for the significance of the difference between the groups. The latter were adjusted for multiple testing using ¬Šidák step-up adjustment to control the family-wise error rate (FWER), i.e. the probability of incorrectly calling at least one probeset differentially expressed. All differences with adjusted p-values < 0.05 were considered significant. The Ingenuity program was used to analyse what pathophysiological pathways were differentially expressed between patients at t=0 and controls (Ingenuity Pathway Analysis; 5.5.1-1002).

source_name: Control-a/Monocyte

label_protocol: standard Affymetrix

extract_protocol:
RNA isolation from leukocyte subsets. One ml of whole blood was used for
immediate RNA isolation (internal validation step) using QIAamp RNA Blood Kit (Qiagen, Hilden, Germany). The remaining 10 ml whole blood was used to perform a ficoll density separation using Lymphoprep (Nycomed Pharma, Oslo, Norway). Granulocytes and peripheral blood mononuclear cells (PBMCs) were isolated and immediately frozen at -80°C. From the PBMCs, CD14-positive cells (here referred to as monocytes) and CD14-negative cells, hence enriched for B- and T-cells (and therefore here referred to as lymphocytes) were separated using autoMACS (Miltenyi Biotec). RNA was isolated using RNeasy columns according to the standard protocol provided by the manufacturer (Qiagen, Hilden, Germany). The integrity of the RNA was assessed using the RNA 6000 Nano assay kit on a Bioanalyzer (Agilent Technologies).

tag: Controle a


title: primary OB #1


title: 092_P6_Lym_T24

tag: T24 patient 6


title: 064_Cc_Blo

source_name: Control-c/Blood

tag: controle c


title: 066_Cd_Mon

source_name: Control-d/Monocyte

tag: Controle d


title: Granulosa cell tumor from Smad1/5/8 mutant mouse Sample 3

tag: Granulosa cell tumor disssected from a Smad1flox/flox;Smad5flox/flox;Smad8-/-;Amhr2cre/+ female mouse age 32 weeks


title: 069_Ca_Lym

source_name: Control-a/Lymphocyte


title: 072_Ca_Blo

source_name: Control-a/Blood


title: Granulosa cell tumor from Smad1/5/8 mutant mouse Sample 1

extract_protocol: Tumor collected and stored in RNA later overnight at 4degrees, then frozen at -80.  RNA from Qiagen Rneasy kit.

tag: Granulosa cell tumor from  Smad1/5 conditional knockout Smad1flox/floxSmad5floxfloxSmad8+/-Amhr2cre+.  Background is C57BL/6J;129S5/SvEvBrd.  35 week-old female mouse


title: 061_Cc_Lym

source_name: Control-c/Lymphocyte

tag: Controle c


title: 093_P6_Mon_T0

tag: T0 patient 6


title: 057_Cb_Lym

source_name: Control-b/Lymphocyte

tag: controle b


title: 065_Cd_Lym

source_name: Control-d/Lymphocyte


title: 060_Cb_Blo

source_name: Control-b/Blood

tag: Controle b


title: 058_Cb_Mon

source_name: Control-b/Monocyte


title: 047_P4_Lym_T24

tag: T24 patient 4


title: 048_P4_Mon_T0

tag: T0 patient 4


title: 046_P4_Lym_T8


title: 032_P2_Blo_T72

tag: T72 patient 2


title: 034_P3_Lym_T8

tag: T8 patient 3


title: 044_P3_Blo_T24

tag: T24 patient 3


title: 042_P3_Blo_T0

tag: T0 patient 3


title: 029_P2_Blo_T0

tag: T0 patient 2


title: 036_P3_Mon_T0


title: 035_P3_Lym_T24


title: 031_P2_Blo_T24

tag: T24 patient 2


title: 037_P3_Mon_T8


title: 033_P3_Lym_T0


title: 019_P2_Lym_T24

tag: T24 Patient 2


title: 023_P2_Mon_T24


title: 030_P2_Blo_T8

tag: T8 patient 2


title: 015_P1_Blo_T24

tag: T24 Patient 1


title: 020_P2_Lym_T72


title: 017_P2_Lym_T0

tag: T0 Patient 2


title: 005_P1_Mon_T0

tag: T0 patient 1


title: 008_P1_Mon_T72

tag: T72 patient 1


title: 007_P1_Mon_T24


title: 022_P2_Mon_T8


title: 004_P1_Lym_T72

tag: T72 patient1


title: 006_P1_Mon_T8

tag: T8 Patient 1


title: 003_P1_Lym_T24

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

label_protocol: Standard Affymetrix

tag: T24 patient 1


title: 002_P1_Lym_T8

tag: T8 patient 1


title: 016_P1_Blo_T72


title: KO biol. Repeat3

status: Public on Jun 13 2008

city: Bethesda

first: Bing Mei

last: Zhu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: Gene expression data from E14.5 fetal liver Ter119 + cells

hyb_protocol: Genechip hybridization oven 640. Incubate 16hrs with 60 cycles/minute rotation at 45 degrees celsius

scan_protocol: Affymetrix 7G autoloader genechip scanner

data_processing: Microarray analyses were performed using Affymetrix Mouse Genome 430 2.0 array GeneChips (Affymetrix).  Microarray signals were analyzed using the Affymetrix RMA algorithm.  Up- and down-regulated genes were selected based on P values of <0.05 and fold changes of >1.5 or -1.5 as assessed by ANOVA using Partek Pro software (Partek).  To determine specific pathways, gene pathway analysis (http://trials.genego.com/cgi/index.cgi) was obtained using the statistically significant gene list (P<0.05) represented on the chip.

source_name: STAT5 KO

label_protocol: Total RNA one cycle target labeling assay with streptavidin phycoerythrin (SAPE) labeling

growth_protocol: In vivo fetal liver cells at embryonic day 14.5

treatment_protocol: Isolate Ter119+ fetal liver cells from wild type and STAT5 KO embryos

tag: STAT5 KO


title: KO biol. Repeat2


title: WT biol. Repeat2

source_name: wild type

tag: wild type


title: WT biol. Repeat3


title: WT biol. Repeat1


title: MigRI_Δ_(177-191)_C/EBPα-ER_9hr_1

city: Cambridge

first: Robert

middle: Vincent

last: Martinez

address: 35 Cambridgepark Drive

department: Biological Technologies

institute: Wyeth Research

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 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G System

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

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

growth_protocol: 32-BCR/ABL and derivative cell lines were cultured in Iscove modified Dulbecco medium (IMDM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and penicillin/streptomycin (100 μg/ml each)

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

treatment_protocol: 4-HT-treated 32D-BCR/ABL cells transduced with the MigRI empty vector, MigRI WT C/EBPα-ER , MigRI K298E C/EBPα-ER  (a DNA binding-deficient mutant) or MigRI Δ (177-191) C/EBPα-ER  (a mutant deficient in CDK2/CDK4 interaction).  Total RNA was extracted at 6, 9 and 12h post-4-HT treatment in three separate experiments and hybridized onto the Affymetrix MOE430 _2 array

tag: Mouse Myeloid 32D-BCR/ABL cell line


title: MigRI_Δ_(177-191)_C/EBPα-ER_9hr_2


title: MigRI_Δ_(177-191)_C/EBPα-ER_6hr_1


title: MigRI_Δ_(177-191)_C/EBPα-ER_6hr_3


title: MigRI_Δ_(177-191)_C/EBPα-ER_9hr_3


title: MigRI_Δ_(177-191)_C/EBPα-ER_12hr_2


title: MigRI_Δ_(177-191)_C/EBPα-ER_12hr_3


title: MigRI_Δ_(177-191)_C/EBPα-ER_6hr_2


title: MigRI_K298E_C/EBPα-ER_9hr_3


title: MigRI_Δ_(177-191)_C/EBPα-ER_0hr_3


title: MigRI_K298E_C/EBPα-ER_0hr_1


title: MigRI_K298E_C/EBPα-ER_0hr_2


title: MigRI_WT_C/EBPα-ER__9hr_3


title: MigRI_K298E_C/EBPα-ER_12hr_3


title: MigRI_K298E_C/EBPα-ER_12hr_1


title: MigRI_Δ_(177-191)_C/EBPα-ER_0hr_1


title: MigRI_K298E_C/EBPα-ER_12hr_2


title: MigRI_K298E_C/EBPα-ER_9hr_1


title: MigRI_K298E_C/EBPα-ER_6hr_1


title: MigRI_WT_C/EBPα-ER__12hr_1


title: MigRI_K298E_C/EBPα-ER_6hr_3


title: MigRI_K298E_C/EBPα-ER_9hr_2


title: MigRI_Δ_(177-191)_C/EBPα-ER_0hr_2


title: MigRI_WT_C/EBPα-ER__12hr_3


title: MigRI_WT_C/EBPα-ER__9hr_2


title: MigRI_K298E_C/EBPα-ER_0hr_3


title: MigRI_WT_C/EBPα-ER__12hr_2


title: MigRI_K298E_C/EBPα-ER_6hr_2


title: MigRI_WT_C/EBPα-ER__0hr_3


title: 038_P3_Mon_T24

tag: T24 patient 3


title: MigRI_WT_C/EBPα-ER__6hr_3


title: MigRI_WT_C/EBPα-ER__9hr_1


title: MigRI_WT_C/EBPα-ER__6hr_2


title: MigRI_WT_C/EBPα-ER__0hr_2


title: MigRI_WT_C/EBPα-ER__0hr_1


title: MigRI_WT_C/EBPα-ER__6hr_1


title: KO biol. Repeat1

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


title: MigRI_empty_vector_12hr_3


title: MigRI_empty_vector_9hr_2


title: MigRI_empty_vector_12hr_2


title: MigRI_empty_vector_12hr_1


title: MigRI_empty_vector_0hr_3


title: MigRI_empty_vector_6hr_3


title: MigRI_empty_vector_6hr_2


title: MigRI_empty_vector_9hr_1


title: MigRI_empty_vector_6hr_1


title: MigRI_empty_vector_0hr_1


title: MigRI_empty_vector_9hr_3


title: MigRI_empty_vector_0hr_2


title: HDM_72HRS_rep02

city: Baltimore

first: Joshua

middle: J

last: Reece

address: 615 N. Wolfe Street

department: MMI

institute: Johns Hopkins University BSPH

description: Intensity of hybridization for each probe pair was computed by GCOS 1.2 software (Affymetrix). (For more detailed methods, please refer to the website of the Malaria Research Institute Gene Array Core Facility (MRI-GACF) at the Johns Hopkins Bloomberg School of Public Health http://jhmmi.jhsph.edu)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using affy GCS3000

data_processing: Affymetrix Microarray Suite version 5.0

source_name: hdm challenge 72hrs

label_protocol: standard Affymetrix procedures

extract_protocol: trizol extraction followed by qiagen RNeasy total RNA cleanup protocol

tag: 'strain:BALB/c WT', 'gender:male', 'age:8wks', 'tissue

value: whole lung', 'condition:hdm challenge 72hrs'


title: NbHDM_24HRS_rep01

source_name: Nb infected hdm challenge 24hrs

value: whole lung', 'condition:Nb infected hdm challenge 24hrs'


title: PBS_72HRS_rep03

source_name: pbs challenge 72hrs

value: whole lung', 'condition:pbs challenge 72hrs'


title: PBS_72HRS_rep02


title: NbPBS_24HRS_rep03

source_name: Nb infected pbs challenge 24hrs

value: whole lung', 'condition:Nb infected pbs challenge 24hrs'


title: NbPBS_72HRS_rep03

source_name: Nb infected pbs challenge 72hrs

value: whole lung', 'condition:Nb infected pbs challenge 72hrs'


title: HDM_72HRS_rep03


title: PBS_72HRS_rep01


title: NbPBS_24HRS_rep02


title: NbHDM_72HRS_rep01

source_name: Nb infected hdm challenge 72hrs

value: whole lung', 'condition:Nb infected hdm challenge 72hrs'


title: NbHDM_24HRS_rep02


title: NbPBS_24HRS_rep01


title: NbHDM_72HRS_rep03


title: NbPBS_72HRS_rep02


title: NbHDM_24HRS_rep03


title: NbPBS_72HRS_rep01


title: HDM_72HRS_rep01


title: NbHDM_72HRS_rep02


title: HDM_24HRS_rep02

source_name: hdm challenge 24hrs

value: whole lung', 'condition:hdm challenge 24hrs'


title: MigRI_Δ_(177-191)_C/EBPα-ER_12hr_1


title: PBS_24HRS_rep03

source_name: pbs challenge 24hrs

value: whole lung', 'condition:pbs challenge 24hrs'


title: HDM_24HRS_rep01


title: PBS_24HRS_rep01


title: HDM_24HRS_rep03


title: NbPBS_6HRS_rep02

source_name: Nb infected pbs challenge 6hrs

value: whole lung', 'condition:Nb infected pbs challenge 6hrs'


title: PBS_6HRS_rep01

source_name: pbs challenge 6hrs

value: whole lung', 'condition:pbs challenge 6hrs'


title: NbHDM_6HRS_rep02

source_name: Nb infected hdm challenge 6hrs

value: whole lung', 'condition:Nb infected hdm challenge 6hrs'


title: NbHDM_6HRS_rep03


title: CON_rep03

source_name: uninfected control

value: whole lung', 'condition:uninfected control'


title: NbPBS_6HRS_rep01


title: NbCON_rep02

source_name: Nb infected control

value: whole lung', 'condition:Nb infected control'


title: PBS_24HRS_rep02


title: PBS_6HRS_rep03


title: CON_rep02


title: NbHDM_6HRS_rep01


title: HDM_6HRS_rep02

source_name: hdm challenge 6hrs

value: whole lung', 'condition:hdm challenge 6hrs'


title: NbPBS_6HRS_rep03


title: At.StarchSD.WTSS3.WTR2L4

status: Public on Jun 12 2008

city: Ames

first: Ling

last: Li

state: IA

address: 443 Bessey Hall

department: Department of Genetics, Development, and Cell Biology

institute: Iowa State University

description: The Atss3 mutant and WT plants were arranged according to a Randomized Complete Block Design. The plants were planted in rows with seven rows in each flat; two plants of the same genotype/pot. Plants were grown under a SD photoperiod (8 h light/16 h dark) in a growth chamber as described. Eight randomly selected rows were harvested for each time point from different flats. Plant material was harvested at five time points in the diurnal cycle (1, 4, 8.5, 12, and 16 h; Time 0 is the beginning of the light period); harvesting was conducted under a green safety light. Each sample consisted of rosette leaves (leaves 5 to 8, photosynthetically active) from sixteen six-week-old plants. Leaf samples were frozen in liquid nitrogen immediately after harvest and stored at -80oC for RNA extraction. The experiment was done twice and independent randomizations for plant growth and harvest were used for the two replicates.

hyb_protocol: 20 ug cRNA was used. ATH1 GeneChip was used.

scan_protocol: according to the manufacturer’s recommendation

data_processing: MAS 5.0 signal. Mean per chip is 500.

source_name: leave of different genotype, harvest over diurnal cycle, Short Day (8 h light/16 h dark).

label_protocol: biotin labeled.

extract_protocol: Total RNA was extracted from leaves with GibcoBRL TRIzol reagent (Life Technologies) according to the protocol provided with the reagent and purified using a RNease Cleanup Kit (Qiagen).

tag: Columbia 0 wild type and Atss3 mutant, leave samples over diurnal cycle (1, 4 h in the light; 0.5, 4, 8 h in the dark).


title: HDM_6HRS_rep03


title: NbCON_rep03


title: At.StarchSD.WTSS3.WTR2D4


title: NbCON_rep01


title: CON_rep01


title: At.StarchSD.WTSS3.WTR2L1


title: PBS_6HRS_rep02


title: Murine Runx3, biological rep 2

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

description: Comparative study of gene targets regulated by overexpression of the different Runx family members

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array in the GeneChip Hybridization Oven 640. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility. Differential expression was calculated using RankProducts method.

source_name: NIH3T3 retrovirally transduced with constitutive Mouse Runx3 construct in pBabe-puro

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: All cultures were grown to confluence (7 days) in DMEM under standard conditions. The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility

extract_protocol: RNA was extracted using Rneasy Mini kit (Qiagen) according to the manufacturers' protocol

treatment_protocol: All samples were treated with ethanol alone (0.2%) or 4-OHT tamoxifen (0.1mM) in ethanol for 24 hours prior to RNA extraction.

tag: NIH3T3 (p16/p19arf null) confluent cell cultures, harvested after 24hrs treatment


title: HDM_6HRS_rep01


title: At.StarchSD.WTSS3.WTR1D8


title: Murine Runx1, biological rep 2

source_name: NIH3T3 retrovirally transduced with constitutive Mouse Runx1 construct in pBabe-puro


title: At.StarchSD.WTSS3.WTR2D8


title: Murine Runx3, biological rep 1


title: Murine Runx1, biological rep 1


title: Murine Runx2, biological rep 1

source_name: NIH3T3 retrovirally transduced with constitutive Mouse Runx2 construct in pBabe-puro


title: At.StarchSD.WTSS3.WTR2D0.5


title: Human RUNX1, single sample

source_name: NIH3T3 retrovirally transduced with constitutive Human RUNX1 construct in pBabe-puro


title: At.StarchSD.WTSS3.WTR1L1


title: Murine Runx2, biological rep 2


title: Vector control, biological rep 1

source_name: NIH3T3 retrovirally transduced with pBabe-puro control vector


title: Tamoxifen treated vector control, biological rep 2


title: At.StarchSD.WTSS3.SS3R2L4


title: Tamoxifen treated vector control, biological rep 1


title: Vector control, biological rep 2


title: At.StarchSD.WTSS3.WTR1L4


title: At.StarchSD.WTSS3.WTR1D4


title: At.StarchSD.WTSS3.WTR1D0.5


title: At.StarchSD.WTSS3.SS3R2L1


title: At.StarchSD.WTSS3.SS3R2D8


title: At.StarchSD.WTSS3.SS3R1D8


title: Tamoxifen treated (induced) RUNX1-ER, biological rep 1

source_name: NIH3T3 retrovirally transduced with inducible Human RUNX1 construct in pBabe-puro


title: Tamoxifen treated (induced) RUNX1-ER, biological rep 2


title: Uninduced RUNX1-ER, biological rep 1


title: Uninduced RUNX1-ER, biological rep 2


title: At.StarchSD.WTSS3.SS3R2D4


title: At.StarchSD.WTSS3.SS3R1L4


title: At.StarchSD.WTSS3.SS3R1L1


title: At.StarchSD.WTSS3.SS3R1D4


title: At.StarchSD.WTSS3.SS3R1D0.5

tag: Columbia wild type and Atss3 mutant, leave samples over diurnal cycle (1, 4 h in the light; 0.5, 4, 8 h in the dark).


title: Argyrin A treated 24h_2

status: Public on Jun 11 2008

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: MCF7 Argyrin A treated 24h

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: MCF7 Argyrin A treated 24h

growth_protocol: DMEM, FCS Pen/Strep, 37° , 5% CO2

extract_protocol: RNAeasy

tag: genetic modification:

tag: tissue

value: breast adenocarcinoma


title: Argyrin A treated 12h_2

description: MCF7 Argyrin A treated 12h

source_name: MCF7 Argyrin A treated 12h


title: siRNA 24h_2

description: MCF7 siRNA 24h

source_name: MCF7 siRNA 24h


title: T/C-28.a

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

institute: University Göttingen

description: Affymetrix

hyb_protocol: Affymetrix standard protocol

data_processing: MAS5 signal

source_name: T/C-28 cells (fetal human sternal chondrocytes, immortalized, M.Goldring)

label_protocol: Affymetrix standard protocol

extract_protocol: Qiagen protocol


title: Ostecytes/-blasts 2

description: Affymetrix

source_name: Osteocytes/-blasts in P2 from human bone chips of patients with OA


title: siRNA 12h_2

description: MCF7 siRNA 12h

source_name: MCF7 siRNA 12h


title: Argyrin A treated 24h_1

description: MCF7 Argyrin A treated 24h


title: untreated_2

description: MCF7 untreated

source_name: MCF7 untreated


title: Ostecytes/-blasts 1

description: Affymetrix

tag: Osteocytes/-blasts in P2 from human bone chips of patients with OA


title: T/C-28.b

description: Affymetrix

tag: T/C-28 cells (fetal human sternal chondrocytes, immortalized, M.Goldring)


title: Argyrin A treated 12h_1

description: MCF7 Argyrin A treated 12h


title: neocortex-30 months of age-CR diet-biological replicate2

status: Public on Jun 10 2008

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

description: Gene expression of old calorie-restricted mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating System 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: neocortex, 30 months of age, CR diet

growth_protocol: B6C3F1 hybrid mice were individually housed and fed on of the following three diets from 14 to 30 months of age: control AIN93M diet, 40% calorie restricted diet, or a control diet supplemented with resveratrol to achieve a dose of 4.9 mg resveratrol per kg bodyweight

treatment_protocol: At 30 months of age mice were euthanized via cervical dislocation; organs were dissected, flash-forzen in liquid nitrogen and stored at -80C for future analysis

tag: B6C3F1 male


title: neocortex-30 months of age-CR diet-biological replicate1


title: neocortex-30 months of age-resveratrol diet-biological replicate3

description: Gene expression of old mice treated with a low dose of resveratrol

source_name: neocortex, 30 months of age, resveratrol diet


title: neocortex-30 months of age-CR diet-biological replicate5


title: neocortex-30 months of age-control diet-biological replicate5

description: Gene expression of old control mice

source_name: neocortex, 30 months of age, control diet


title: neocortex-30 months of age-control diet-biological replicate1

description: Gene expression of old control mice


title: neocortex-30 months of age-control diet-biological replicate3

description: Gene expression of old control mice


title: neocortex-30 months of age-CR diet-biological replicate3


title: neocortex-5 months of age-control diet-biological replicate4

description: Gene expression of young control mice

source_name: neocortex, 5 months of age, control diet


title: neocortex-30 months of age-resveratrol diet-biological replicate4


title: neocortex-30 months of age, resveratrol diet-biological replicate5


title: neocortex-5 months of age-control diet-biological replicate2

description: Gene expression of young control mice


title: neocortex-30 months of age-control diet-biological replicate4

description: Gene expression of old control mice


title: neocortex-30 months of age-resveratrol diet-biological replicate1


title: neocortex-30 months of age-control diet-biological replicate2

description: Gene expression of old control mice


title: neocortex-30 months of age-resveratrol diet-biological replicate2


title: neocortex-30 months of age-CR diet-biological replicate4


title: neocortex-5 months of age-control diet-biological replicate3

description: Gene expression of young control mice


title: gastrocnemius-30 months of age-resveratrol diet-biological replicate4

source_name: gastrocnemius, 30 months of age, resveratrol diet


title: neocortex-5 months of age-control diet-biological replicate1

description: Gene expression of young control mice


title: gastrocnemius-30 months of age-CR diet-biological replicate5

source_name: gastrocnemius, 30 months of age, CR diet


title: gastrocnemius-30 months of age-CR diet-biological replicate2


title: gastrocnemius-30 months of age-CR diet-biological replicate4


title: gastrocnemius-30 months of age, resveratrol diet-biological replicate5


title: gastrocnemius-30 months of age-resveratrol diet-biological replicate2


title: gastrocnemius-30 months of age-CR diet-biological replicate3


title: gastrocnemius-30 months of age-resveratrol diet-biological replicate3


title: gastrocnemius-30 months of age-resveratrol diet-biological replicate1


title: gastrocnemius-30 months of age-control diet-biological replicate4

description: Gene expression of old control mice

source_name: gastrocnemius, 30 months of age, control diet


title: gastrocnemius-30 months of age-control diet-biological replicate1

description: Gene expression of old control mice


title: gastrocnemius-5 months of age-control diet-biological replicate4

description: Gene expression of young control mice

source_name: gastrocnemius, 5 months of age, control diet


title: gastrocnemius-5 months of age-control diet-biological replicate3

description: Gene expression of young control mice


title: heart-30 months of age-resveratrol diet-biological replicate2

source_name: heart, 30 months of age, resveratrol diet


title: gastrocnemius-30 months of age-control diet-biological replicate3

description: Gene expression of old control mice


title: gastrocnemius-5 months of age-control diet-biological replicate5

description: Gene expression of young control mice


title: heart-30 months of age-resveratrol diet-biological replicate4


title: gastrocnemius-5 months of age-control diet-biological replicate2

description: Gene expression of young control mice


title: gastrocnemius-30 months of age-control diet-biological replicate2

description: Gene expression of old control mice


title: heart-30 months of age-CR diet-biological replicate5

source_name: heart, 30 months of age, CR diet


title: gastrocnemius-30 months of age-control diet-biological replicate5

description: Gene expression of old control mice


title: heart-30 months of age, resveratrol diet-biological replicate5


title: gastrocnemius-30 months of age-CR diet-biological replicate1


title: heart-30 months of age-resveratrol diet-biological replicate1


title: gastrocnemius-5 months of age-control diet-biological replicate1

description: Gene expression of young control mice


title: heart-30 months of age-CR diet-biological replicate4


title: heart-30 months of age-resveratrol diet-biological replicate3


title: heart-30 months of age-CR diet-biological replicate1


title: heart-30 months of age-control diet-biological replicate4

description: Gene expression of old control mice

source_name: heart, 30 months of age, control diet


title: heart-30 months of age-CR diet-biological replicate3


title: heart-30 months of age-control diet-biological replicate1

description: Gene expression of old control mice


title: heart-30 months of age-control diet-biological replicate5

description: Gene expression of old control mice


title: heart-30 months of age-control diet-biological replicate3

description: Gene expression of old control mice


title: heart-30 months of age-CR diet-biological replicate2


title: At.StarchSD.WTSS3.SS3R2D0.5

source_name: leave of different genotype, harvest over diurnal cycle, Short Day (8 h light/16 h dark).


title: heart-30 months of age-control diet-biological replicate2

description: Gene expression of old control mice


title: heart-5 months of age-control diet-biological replicate5

description: Gene expression of young control mice

source_name: heart, 5 months of age, control diet


title: heart-5 months of age-control diet-biological replicate4

description: Gene expression of young control mice


title: neocortex-5 months of age-control diet-biological replicate5

description: Gene expression of young control mice


title: heart-5 months of age-control diet-biological replicate2

description: Gene expression of young control mice


title: heart-5 months of age-control diet-biological replicate3

description: Gene expression of young control mice


title: heart-5 months of age-control diet-biological replicate1

description: Gene expression of young control mice


title: blastocyst cultured by Ca free medium, replicate 3

status: Public on Jun 07 2008

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

description: Gene expression data from mouse blastocyst cultured in Ca free medium

hyb_protocol: cRNA was fragmented following the Affymetrix protocol, and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 arrays

scan_protocol: standard Affymetrix procedures

source_name: blastocyst cultured in Ca2+ free medium

label_protocol: total RNA was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

extract_protocol: Total RNA was extracted and purified using an Picopure kit (Arcturus).

tag: gene expression of blastocyst cultured by Ca free medium


title: blastocyst treated by 20 pulses, replicate 4

description: Gene expression data from mouse blastocyst treated by 20 pulses

source_name: blastocyst treated by 20 Ca2+ pulses

tag: blastocyst treated by 20 pulses


title: blastocyst cultured by Ca free medium, replicate 2


title: blastocyst treated by 20 pulses, replicate 2


title: blastocyst treated by 20 pulses, replicate 1


title: blastocyst cultured by Ca free medium, replicate 1


title: blastocyst treated by 20 pulses, replicate 3


title: gene expression in GV oocyte from young mice, replicate 4

description: Gene expression of GV oocyte from 6 weeks old B6D2 mice

source_name: GV oocyte from young mice (6 weeks)

tag: fully-grown GV oocyte from 6 weeks old mice.


title: blastocyst cultured by Ca free medium, replicate 4


title: gene expression in MII oocyte from aged mice, replicate 1

description: Gene expression of MII oocyte from 66 weeks old B6D2 mice

source_name: MII oocyte from old mice (66 weeks)

tag: MII oocyte from 66 weeks old mice.


title: gene expression in MII oocyte from young mice, replicate 3

description: Gene expression of MII oocyte from 6 weeks old B6D2 mice

source_name: MII oocyte from young mice (6 weeks)

tag: MII oocyte from 6 weeks old mice.


title: gene expression in MII oocyte from young mice, replicate 1


title: gene expression in MII oocyte from aged mice, replicate 3


title: gene expression in GV oocyte from young mice, replicate 2


title: control blastocyst, replicate 1

description: Gene expression data from normal mouse blastocyst

source_name: control blastocyst

tag: normal mouse blastocyst


title: gene expression in MII oocyte from young mice, replicate 2


title: gene expression in MII oocyte from young mice, replicate 4


title: control blastocyst, replicate 4

tag: control blastocyst


title: control blastocyst, replicate 3

tag: control mouse blastocyst


title: gene expression in GV oocyte from young mice, replicate 3


title: gene expression in MII oocyte from aged mice, replicate 4


title: gene expression in GV oocyte from young mice, replicate 1


title: gene expression in GV oocyte from aged mice, replicate 2

description: Gene expression of GV oocyte from 66 weeks old B6D2 mice

source_name: GV oocyte from old mice (66 weeks)

tag: fully-grown GV oocyte from 66 weeks old mice


title: control blastocyst, replicate 2


title: gene expression in MII oocyte from aged mice, replicate 2


title: gene expression in GV oocyte from aged mice, replicate 3


title: gene expression in GV oocyte from aged mice, replicate 1

tag: fully-grown GV oocyte from 66 weeks old mice.


title: gene expression in GV oocyte from aged mice, replicate 4


title: mesenchymal stem cells, lot#5F0138, 9th passage

status: Public on Jun 06 2008

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#5F0138, passage number 9

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for aprx. 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using GCOS Affymetrix standard analysis settings and mask-file (Affymetrix, hgu133_plus_2norm) scaling as normalization methods. The trimmed mean target intensity of each array was arbitrarily set to 10000.

label_protocol: Biotinylated cRNA were prepared according to Two-cycle Affymetrix protocol from 100 ng (Two-cycle) of total RNA (Expression Analysis Technical Manual, 701024 Rev.3, Affymetrix).

growth_protocol: Mesenchymal stem cells were cultured according to manufacturer's protocol (Lonza).

extract_protocol: Total RNA extraction was performed using silica-gel-based membrane according to manufacturer's protocol (QIAGEN, RNeasy)

treatment_protocol: Cells were lysed in 600 ul of buffer RLT (QIAGEN).

tag: bone marrow mesenchymal stem cells


title: mesenchymal stem cells, lot#4F1127, 22nd passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1127, passage number 22


title: mesenchymal stem cells, lot#4F1127, 9th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1127, passage number 9


title: mesenchymal stem cells, lot#4F0591, 7th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0591, passage number 7


title: mesenchymal stem cells, lot#4F1560, 7th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1560, passage number 7


title: mesenchymal stem cells, lot#5F0138, 24th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#5F0138, passage number 24


title: mesenchymal stem cells, lot#4F0312, 9th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0312, passage number 9


title: mesenchymal stem cells, lot#4F0591, 28th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0591, passage number 28


title: mesenchymal stem cells, lot#4F0591, 9th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0591, passage number 9


title: mesenchymal stem cells, lot#4F0312, 4th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0312, passage number 4


title: mesenchymal stem cells, lot#4F1560, 9th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1560, passage number 9


title: mesenchymal stem cells, lot#4F0760, 9th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0760, passage number 9


title: mesenchymal stem cells, lot#4F0760, 4th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0760, passage number 4


title: mesenchymal stem cells, lot#4F0312, 7th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0312, passage number 7


title: mesenchymal stem cells, lot#4F1127, 7th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1127, passage number 7


title: mesenchymal stem cells, lot#5F0138, 4th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#5F0138, passage number 4


title: mesenchymal stem cells, lot#4F0760, 28th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0760, passage number 28


title: mesenchymal stem cells, lot#5F0138, 7th passage

description:
GCOS1.2
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#5F0138, passage number 7


title: mesenchymal stem cells, lot#4F0312, 28th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0312, passage number 28


title: mesenchymal stem cells, lot#4F0591, 4th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F0591, passage number 4


title: mesenchymal stem cells, lot#4F1560, 5th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1560, passage number 5


title: mesenchymal stem cells, lot#4F1560, 28th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1560, passage number 28


title: mesenchymal stem cells, lot#4F1127, 4th passage

description:
GCOS1.4
Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), lot#4F1127, passage number 4


title: MSC #9, technical rep-label-rep6

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 9

source_name: mesenchymal stem cells, 9th passage

label_protocol: Biotinylated cRNA were prepared according to Two-cycle or One-cycle Affymetrix protocol from 100 ng (Two-cycle) or 1ug (One-cycle) total RNA (Expression Analysis Technical Manual, 701024 Rev.3, Affymetrix).

tag: started from 2nd cycle (step6) in two-cycle protocol


title: MSC #28, technical rep-extract-rep1

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 28

source_name: mesenchymal stem cells, 28th passage

tag: two-cycle


title: MSC #28, technical rep-extract-rep2


title: MSC #21, technical rep-extract-rep1

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 21

source_name: mesenchymal stem cells, 21st passage


title: MSC #7, technical rep-label-rep6

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 7

source_name: mesenchymal stem cells, 7th passage


title: MSC #7, technical rep-label-rep5


title: MSC #9, technical rep-label-rep3


title: MSC #7, technical rep-label-rep3


title: MSC #21, technical rep-extract-rep2


title: MSC #9, technical rep-label-rep1


title: MSC #13, technical rep-extract-rep3

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 13

source_name: mesenchymal stem cells, 13th passage

tag: one-cycle


title: MSC #7, technical rep-label-rep2


title: MSC #7, technical rep-label-rep4


title: MSC #7, technical rep-extract-rep2


title: MSC #13, technical rep-extract-rep2


title: MSC #13, technical rep-extract-rep1


title: MSC #9, technical rep-label-rep4


title: MSC #9, technical rep-extract-rep2


title: MSC #9, technical rep-label-rep2


title: MSC #28, technical rep-extract-rep3


title: MSC #14

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 14

source_name: mesenchymal stem cells, 14th passage


title: MSC #7, technical rep-extract-rep3


title: MSC #7, technical rep-extract-rep1


title: MSC #7, technical rep-label-rep1


title: MSC #9, technical rep-extract-rep3


title: MSC #9, technical rep-extract-rep1


title: MSC #5, technical rep-amplification- rep3

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 5

source_name: mesenchymal stem cells, 5th passage