title: Quadriceps from mdx mouse 2

description:
Quad_mdx_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from mdx mouse 2


title: Quadriceps from WT mouse 3

status: Public on Jun 12 2012

type: RNA

city: Oxford

first: Thomas

middle: C

last: Roberts

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description:
Quad_C57_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

hyb_protocol: Total labeled RNA was hybridised to the Affymetrix GeneChip miRNA array 2.0 using the manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with the Affymetrix Expression Console package.

data_processing: The processing and data analyses were performed in Affymetrix miRNA QCTool, as well as in DNA-Chip Analyzer (dChip) and Excel. The analysis was done according to the following workflow; BC-CG background adjustment, Quantile normalisation and Median Polish summarisation. Since the miRNA 2.0 array covers 131 organisms, we sorted out Mus musculus transcripts only.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Quadriceps from C57 mouse 3

label_protocol: 1 ug of total RNA was labeled using the FlashTag Biotin HSR kit (Genisphere).

extract_protocol: The heart, quadriceps femoris, and diaphragm were dissected and flash frozen in liquid nitrogen-cooled isopentane. Samples were homogenised using Precellys 24 (Bertin Technologies, France), and RNA was extracted using TRIzol reagent (Invitrogen) as according to the manufacturer’s instructions. Each RNA sample was analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to assess RNA quality.

tag: background strain

tag: genotype

value: wild-type

tag: gender

value: male

tag: age

value: 8 weeks

tag: tissue

value: quadriceps

tag: mouse identifier

value: WT 3


title: Quadriceps from WT mouse 4

description:
Quad_C57_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from C57 mouse 4

value: WT 4


title: Quadriceps from WT mouse 1

description:
Quad_C57_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from C57 mouse 1

value: WT 1


title: Diaphragm from mdx mouse 4

description:
Dia_mdx_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from mdx mouse 4

value: mdx

value: diaphragm

value: mdx 4


title: ALL patient 3

city: NY

first: Teena

last: Bhatla

state: NY

address: 550 first avenue

country: USA

institute: NYU medical center

hyb_protocol: Biotinylated cRNA (20ng) was fragmented,10 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Array. 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 set to 150.

organism: Homo sapiens

source_name: ALL

label_protocol: Total RNA (50 ng) was used as template in a single-amplification protocol (RiboAmp OA, Mountain View, CA) according to manufacturer's instructions.

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA) and quality was verified by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Leukemic bone marrow samples were used for RNA extraction without further treatment.

tag: disease state

value: bone marrow


title: Quadriceps from mdx mouse 1

description:
Quad_mdx_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from mdx mouse 1

value: mdx 1


title: RS4 1 uM vorinostat

tag: cell line

tag: treatment

value: 1 uM vorinostat


title: MV4 1 uM vorinostat


title: Quadriceps from WT mouse 2

description:
Quad_C57_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from C57 mouse 2

value: WT 2


title: Reh cells 1 uM vorinostat

value: Reh


title: Diaphragm from WT mouse 1

description:
Dia_C57_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from C57 mouse 1


title: Diaphragm from WT mouse 4

description:
Dia_C57_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from C57 mouse 4


title: Diaphragm from WT mouse 2

description:
Dia_C57_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from C57 mouse 2


title: Diaphragm from mdx mouse 1

description:
Dia_mdx_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from mdx mouse 1


title: Diaphragm from mdx mouse 2

description:
Dia_mdx_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from mdx mouse 2

value: mdx 2


title: Diaphragm from WT mouse 3

description:
Dia_C57_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from C57 mouse 3


title: Diaphragm from mdx mouse 3

description:
Dia_mdx_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Diaphragm from mdx mouse 3

value: mdx 3


title: MV4


title: Ewing sarcoma sample microRNA EW248

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

country: France

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

hyb_protocol: standard Illumina protocol

scan_protocol: BeadStudio 1.5

data_processing: Probes were average-normalized to correct for between-sample variation.

source_name: Ewing sarcoma sample EW248

label_protocol: 100ng of RNA is polyadenylated and converted to cDNA according to the standard Illumina protocol

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

treatment_protocol: FrozenTumor biopsy

value: Ewing tumor


title: Ewing sarcoma sample microRNA EW249

source_name: Ewing sarcoma sample EW249


title: Ewing sarcoma sample microRNA EW236

source_name: Ewing sarcoma sample EW236


title: Ewing sarcoma sample microRNA EW247

source_name: Ewing sarcoma sample EW247


title: Ewing sarcoma sample microRNA EW250

source_name: Ewing sarcoma sample EW250


title: Ewing sarcoma sample microRNA EW251

source_name: Ewing sarcoma sample EW251


title: Ewing sarcoma sample microRNA EW252

source_name: Ewing sarcoma sample EW252


title: Ewing sarcoma sample microRNA EW212

source_name: Ewing sarcoma sample EW212


title: Ewing sarcoma sample microRNA EW204

source_name: Ewing sarcoma sample EW204


title: Ewing sarcoma sample microRNA EW207

source_name: Ewing sarcoma sample EW207


title: Ewing sarcoma sample microRNA EW206

source_name: Ewing sarcoma sample EW206


title: GEP data of patient 115

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description:
gene expression profiles
P2456-01-H125-U133Plus-2.CEL

hyb_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813

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 500.

source_name: CD138 plus plasma cells

tag: patient

value: multiple myeloma (MM)

tag: cell type

value: CD138 plus plasma cells

tag: sample type

value: test set


title: Ewing sarcoma sample microRNA EW208

source_name: Ewing sarcoma sample EW208


title: Reh cells 0.5 uM vorinostat

source_name: ALL

value: 0.5 uM vorinostat


title: Reh cells


title: GEP data of patient 112

description:
gene expression profiles
P2363-01-G875-U133Plus-2.CEL

scan_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813


title: GEP data of patient 109

description:
gene expression profiles
P2275-01-G699-U133Plus-2.CEL

label_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813


title: GEP data of patient 114

description:
gene expression profiles
P2421-01-H013-U133Plus-2.CEL

extract_protocol: mRNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Human Genome U133Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described in PMID: 17105813


title: GEP data of patient 102

description:
gene expression profiles
P2205-01-G507-U133Plus-2.CEL


title: GEP data of patient 99

description:
gene expression profiles
P2200-01-G476-U133Plus-2.CEL


title: GEP data of patient 106

description:
gene expression profiles
P2304-01-G620-U133Plus-2.CEL


title: GEP data of patient 104

description:
gene expression profiles
P2243-01-G580-U133Plus-2.CEL


title: GEP data of patient 108

description:
gene expression profiles
P2289-04-G656-U133Plus-2.CEL


title: GEP data of patient 98

description:
gene expression profiles
P2152-01-G402-U133Plus-2.CEL


title: GEP data of patient 111

description:
gene expression profiles
P2346-04-G859-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW124

source_name: Ewing sarcoma sample EW124


title: GEP data of patient 105

description:
gene expression profiles
P2232-02-G562-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW135

source_name: Ewing sarcoma sample EW135


title: RS4


title: Ewing sarcoma sample microRNA EW83

source_name: Ewing sarcoma sample EW83


title: Reh cells 2.5 uM vorinostat

value: 2.5 uM vorinostat


title: GEP data of patient 113

description:
gene expression profiles
P2405-02-H001-U133Plus-2.CEL


title: ALL patient 1

value: B-precursor acute lymphoblastic leukemia


title: Ewing sarcoma sample microRNA EW66

source_name: Ewing sarcoma sample EW66


title: Ewing sarcoma sample microRNA EW98

source_name: Ewing sarcoma sample EW98


title: GEP data of patient 96

description:
gene expression profiles
P2069-01-G167-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW48

source_name: Ewing sarcoma sample EW48


title: Ewing sarcoma sample microRNA EW19

source_name: Ewing sarcoma sample EW19


title: GEP data of patient 101

description:
gene expression profiles
P2213-02-G545-U133Plus-2.CEL


title: GEP data of patient 107

description:
gene expression profiles
P2283-02-G714-U133Plus-2.CEL


title: GEP data of patient 97

description:
gene expression profiles
P2102-01-G290-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW189

source_name: Ewing sarcoma sample EW189


title: Ewing sarcoma sample microRNA EW175

source_name: Ewing sarcoma sample EW175


title: Ewing sarcoma sample microRNA EW168

source_name: Ewing sarcoma sample EW168


title: GEP data of patient 103

description:
gene expression profiles
P2229-00-G558-U133Plus-2.CEL


title: GEP data of patient 95

description:
gene expression profiles
P2366-01-G907-U133Plus-2.CEL


title: GEP data of patient 100

description:
gene expression profiles
P2176-01-G470-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW163

source_name: Ewing sarcoma sample EW163


title: GEP data of patient 93

description:
gene expression profiles
P2057-04-G660-U133Plus-2.CEL


title: GEP data of patient 110

description:
gene expression profiles
P2322-01-G764-U133Plus-2.CEL


title: GEP data of patient 92

description:
gene expression profiles
P0768-01-C363-U133Plus-2.CEL

value: training set


title: GEP data of patient 94

description:
gene expression profiles
P2317-01-G767-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW158

source_name: Ewing sarcoma sample EW158


title: GEP data of patient 89

description:
gene expression profiles
P0973-01-C948-U133Plus-2.CEL


title: GEP data of patient 90

description:
gene expression profiles
P0967-01-C704-U133Plus-2.CEL


title: GEP data of patient 87

description:
gene expression profiles
P0958-00-C922-U133Plus-2.CEL


title: GEP data of patient 86

description:
gene expression profiles
P0978-01-C884-U133Plus-2.CEL


title: GEP data of patient 91

description:
gene expression profiles
P1236-01-D742-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW142

source_name: Ewing sarcoma sample EW142


title: Stage 15-->23 Anterior Endoderm (AE) Set 3

city: Cincinnati

first: Alan

middle: Patrick

last: Kenny

state: OH

address: 3333 Burnet Avenue

department: Neonatology

institute: Cincinnati Children's Hospital Medical Center

description: Stage 15 to 23 Endoderm Cultured without Mesoderm Set 3; Gene expression data from explants without mesoderm

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Xenopus laevis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics protocol FS450-0001.

data_processing: The data were analyzed with Genespring 7.0 with RMA normalization

organism: Xenopus laevis

source_name: Stage 15 Foregut Endoderm Cultured to Stage 23 Set 3

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: St. 15 Foregut Intact and Isolated Endoderm Explants Cultured to St. 23 in 0.5X MBS

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

treatment_protocol: Isolated Endoderm and Endoderm from the Stage 23 Intact Explants were Isolated and frozen in dry ice.

tag: growth protocol

value: Stage 15 to 23 Foregut Endoderm Cultured without Mesoderm

tag: tissue type

value: explants without mesoderm


title: Ewing sarcoma sample microRNA EW137

source_name: Ewing sarcoma sample EW137


title: Stage 15 Anterior Mesendoderm Cultured to Stage 23 Isolated Endoderm (AEM) Set 4

description: Stage 15 to 23 Endoderm Cultured with Mesoderm Set 4; Gene expression data from explants with mesoderm

source_name: Stage 15 Foregut Explants Cultured to Stage 23 and Endoderm Isolated Set 4

value: Stage 15 to 23 Foregut Endoderm Cultured with Mesoderm

value: explants with mesoderm


title: GEP data of patient 88

description:
gene expression profiles
P0955-01-C950-U133Plus-2.CEL

source_name: CD138 plus plasma cells


title: Stage 15-->23 Anterior Endoderm (AE) Set 1

description: Stage 15 to 23 Endoderm Cultured without Mesoderm Set 1; Gene expression data from explants without mesoderm

source_name: Stage 15 Foregut Endoderm Cultured to Stage 23 Set 1


title: Stage 15 Anterior Mesendoderm Cultured to Stage 23 Isolated Endoderm (AEM) Set 2

description: Stage 15 to 23 Endoderm Cultured with Mesoderm Set 2; Gene expression data from explants with mesoderm

source_name: Stage 15 Foregut Explants Cultured to Stage 23 and Endoderm Isolated Set 2


title: Stage 15-->23 Anterior Endoderm (AE) Set 2

description: Stage 15 to 23 Endoderm Cultured without Mesoderm Set 2; Gene expression data from explants without mesoderm

source_name: Stage 15 Foregut Endoderm Cultured to Stage 23 Set 2


title: Stage 15 Anterior Mesendoderm Cultured to Stage 23 Isolated Endoderm (AEM) Set 1

description: Stage 15 to 23 Endoderm Cultured with Mesoderm Set 1; Gene expression data from explants with mesoderm

source_name: Stage 15 Foregut Explants Cultured to Stage 23 and Endoderm Isolated Set 1


title: Ewing sarcoma sample microRNA EW128

source_name: Ewing sarcoma sample EW128


title: GEP data of patient 83

description:
gene expression profiles
P0981-01-C890-U133Plus-2.CEL


title: GEP data of patient 84

description:
gene expression profiles
P0972-01-C889-U133Plus-2.CEL


title: Stage 15-->23 Anterior Endoderm (AE) Set 4

description: Stage 15 to 23 Endoderm Cultured without Mesoderm Set 4; Gene expression data from explants without mesoderm

source_name: Stage 15 Foregut Endoderm Cultured to Stage 23 Set 4


title: Stage 15 Anterior Mesendoderm Cultured to Stage 23 Isolated Endoderm (AEM) Set 3

description: Stage 15 to 23 Endoderm Cultured with Mesoderm Set 3; Gene expression data from explants with mesoderm

source_name: Stage 15 Foregut Explants Cultured to Stage 23 and Endoderm Isolated Set 3


title: Ewing sarcoma sample microRNA EW116

source_name: Ewing sarcoma sample EW116


title: GEP data of patient 82

description:
gene expression profiles
P0907-01-C859-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW110

source_name: Ewing sarcoma sample EW110


title: GEP data of patient 81

description:
gene expression profiles
P0965-01-C860-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW41

source_name: Ewing sarcoma sample EW41


title: aCGH data of patient 112

type: genomic

description:
array CGH
US23502303_251469347318_S01_CGH-v4_95_Feb07.txt

hyb_protocol: Tumor- and sex-matched reference genomic DNA (Promega Corp., Madison, WI) was hybridized to the Agilent 244K aCGH array according to the manufacturer’s instructions (Agilent Technologies, Inc., Santa Clara, CA).

scan_protocol: Scanned on an Agilent Microarray Scanner G2565BA with 5-μm resolution.

data_processing: Lowess algorithm was used to normalize aCGH data {Yang, 2002}. Statistically, altered regions were identified with the use of a circular binary segmentation algorithm {Venkatraman, 2007}.

molecule: genomic DNA

source_name: test

label_protocol: DNA were labeled with cyanine (Cy)3-deoxyuridine triphosphate (dUTP) or Cy5-dUTP.

extract_protocol: High-molecular-weight genomic DNA was isolated from aliquots of CD138-enriched plasma cells with the use of the QIAamp DNA mini kit (Qiagen, Valencia, CA).

source_name: reference

tag: reference

value: sex-matched reference genomic DNA (Promega)


title: aCGH data of patient 115

description:
array CGH
US23502303_251469347183_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 111

description:
array CGH
US23502303_251469347189_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 85

description:
gene expression profiles
P0971-01-C885-U133Plus-2.CEL


title: GEP data of patient 78

description:
gene expression profiles
P0939-02-C830-U133Plus-2.CEL


title: GEP data of patient 80

description:
gene expression profiles
P0961-01-C891-U133Plus-2.CEL


title: Ewing sarcoma sample microRNA EW53

source_name: Ewing sarcoma sample EW53


title: Ewing sarcoma sample microRNA EW29

source_name: Ewing sarcoma sample EW29


title: aCGH data of patient 114

description:
array CGH
US23502303_251469347320_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample microRNA EW36

source_name: Ewing sarcoma sample EW36


title: GEP data of patient 79

description:
gene expression profiles
P0976-01-C848-U133Plus-2.CEL


title: GEP data of patient 76

description:
gene expression profiles
P0927-03-C787-U133Plus-2.CEL


title: aCGH data of patient 104

description:
array CGH
US23502303_251469347388_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 113

description:
array CGH
US23502303_251469347530_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 109

description:
array CGH
US23502303_251469347526_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample microRNA EW27

source_name: Ewing sarcoma sample EW27


title: Ewing sarcoma sample microRNA EW24

source_name: Ewing sarcoma sample EW24


title: GEP data of patient 75

description:
gene expression profiles
P0941-02-C782-U133Plus-2.CEL

source_name: CD138 plus plasma cells


title: aCGH data of patient 107

description:
array CGH
US23502303_251469347190_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 77

description:
gene expression profiles
P0937-02-C826-U133Plus-2.CEL


title: aCGH data of patient 110

description:
array CGH
US23502303_251469347527_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 108

description:
array CGH
US23502303_251469347391_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample microRNA EW17

source_name: Ewing sarcoma sample EW17


title: aCGH data of patient 106

description:
array CGH
US23502303_251469347389_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 105

description:
array CGH
US23502303_251469347150_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 102

description:
array CGH
US23502303_251469347387_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 74

description:
gene expression profiles
P0942-02-C791-U133Plus-2.CEL


title: GEP data of patient 73

description:
gene expression profiles
P0986-01-C780-U133Plus-2.CEL


title: aCGH data of patient 97

description:
array CGH
US23502303_251469347372_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 99

description:
array CGH
US23502303_251469346993_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 101

description:
array CGH
US23502303_251469347133_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample microRNA EW02

source_name: Ewing sarcoma sample EW02


title: Ewing sarcoma sample microRNA EW01

source_name: Ewing sarcoma sample EW01


title: Ewing sarcoma sample microRNA EW09

source_name: Ewing sarcoma sample EW09


title: aCGH data of patient 103

description:
array CGH
US23502303_251469347149_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 96

description:
array CGH
US23502303_251469347373_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 94

description:
array CGH
US23502303_251469347241_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 100

description:
array CGH
US23502303_251469347242_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 93

description:
array CGH
US23502303_251469347240_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 98

description:
array CGH
US23502303_251469346994_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 72

description:
gene expression profiles
P0984-01-C763-U133Plus-2.CEL


title: aCGH data of patient 95

description:
array CGH
US23502303_251469347319_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 70

description:
gene expression profiles
P0908-01-C702-U133Plus-2.CEL


title: aCGH data of patient 92

description:
array CGH
US23502387_251469325733_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 71

description:
gene expression profiles
P0911-01-C725-U133Plus-2.CEL


title: GEP data of patient 69

description:
gene expression profiles
P0770-01-C497-U133Plus-2.CEL


title: aCGH data of patient 91

description:
array CGH
US23502387_251469323755_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 90

description:
array CGH
US23502387_251469323754_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 83

description:
array CGH
US23502387_251469323342_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 89

description:
array CGH
US23502387_251469323228_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 86

description:
array CGH
US23502387_251469323223_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 85

description:
array CGH
US23502387_251469323344_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 68

description:
gene expression profiles
P0782-01-C451-U133Plus-2.CEL


title: aCGH data of patient 87

description:
array CGH
US23502387_251469323224_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 67

description:
gene expression profiles
P0797-01-C469-U133Plus-2.CEL


title: aCGH data of patient 88

description:
array CGH
US23502387_251469323226_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 65

description:
gene expression profiles
P0746-01-C401-U133Plus-2.CEL


title: aCGH data of patient 82

description:
array CGH
US23502387_251469323341_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 66

description:
gene expression profiles
P0778-01-C427-U133Plus-2.CEL


title: GEP data of patient 62

description:
gene expression profiles
P0734-01-C311-U133Plus-2.CEL


title: aCGH data of patient 84

description:
array CGH
US23502387_251469323343_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 64

description:
gene expression profiles
P0762-01-C375-U133Plus-2.CEL


title: GEP data of patient 61

description:
gene expression profiles
P0723-01-C277-U133Plus-2.CEL


title: aCGH data of patient 80

description:
array CGH
US23502387_251469323329_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 79

description:
array CGH
US23502387_251469323328_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 72

description:
array CGH
US23502387_251469323747_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 81

description:
array CGH
US23502387_251469323340_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 78

description:
array CGH
US23502387_251469323326_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 74

description:
array CGH
US23502387_251469324196_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 76

description:
array CGH
US23502387_251469324166_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 70

description:
array CGH
US23502387_251469323744_S01_CGH-v4_95_Feb07.txt


title: Nox1m zone 3 of Developmental stage_replicate 14

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

institute: Institut de Génétique et Microbiologie UMR 8621

description: Biological replicate 4 of 4.  Zone 3 of  IDC343 PaNox1

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used in this study are the wild type S of either mat+ or mat- mating type, DPaMpk1 mat+, ∆PaMpk2 mat+ and IDC343 PaNox1. Growth was carried out on a minimal synthetic medium at 27°C (http://podospora.igmors.u-psud.fr/methods.php)

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) placed on square Petri-dishes (10 cm wide). In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 2 Petri-dishes were simultaneously inoculated from each edge. Biological material was scraped from cellophane sheets and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: strain

value: IDC343 PaNox1 S

tag: growth condition

value: harvested of the distal zone of the colony (zone 3) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane

tag: mating type

value: mat+

source_name: Common reference

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name biosource 4


title: aCGH data of patient 71

description:
array CGH
US23502387_251469323746_S01_CGH-v4_95_Feb07.txt

tag: patient

tag: disease state

value: multiple myeloma (MM)

value: CD138 plus plasma cells


title: GEP data of patient 60

description:
gene expression profiles
P0725-01-C278-U133Plus-2.CEL

tag: cell type

tag: sample type


title: aCGH data of patient 77

description:
array CGH
US23502387_251469325748_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 57

description:
gene expression profiles
P0686-01-C122-U133Plus-2.CEL


title: GEP data of patient 58

description:
gene expression profiles
P0673-01-C144-U133Plus-2.CEL


title: Nox1m zone 2 of Developmental stage_replicate 27

description: Biological replicate 4 of 4.  Zone 2 of  IDC343 PaNox1

value: harvested of the intermediate zone of the colony (zone 2) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: Nox1m zone 3 of Developmental stage_replicate 33

description: Biological replicate 1 of 4.  Zone 3 of  IDC343 PaNox1


title: GEP data of patient 59

description:
gene expression profiles
P0724-01-C258-U133Plus-2.CEL


title: Nox1m zone 3 of Developmental stage_replicate 35

description: Biological replicate 2 of 4. Zone 3 of  IDC343 PaNox1


title: Nox1m zone 3 of Developmental stage_replicate 37

description: Biological replicate 3 of 4. Zone 3 of  IDC343 PaNox1


title: aCGH data of patient 69

description:
array CGH
US23502387_251469324245_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 65

description:
array CGH
US23502387_251469323762_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 68

description:
array CGH
US23502387_251469324244_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 67

description:
array CGH
US23502387_251469324243_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 56

description:
gene expression profiles
P0681-01-C86-U133Plus-2.CEL


title: aCGH data of patient 60

description:
array CGH
US23502387_251469323752_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 66

description:
array CGH
US23502387_251469324242_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 53

description:
gene expression profiles
P0584-01-B895-U133Plus-2.CEL


title: GEP data of patient 63

description:
gene expression profiles
P0740-01-C343-U133Plus-2.CEL


title: aCGH data of patient 64

description:
array CGH
US23502387_251469323761_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 62

description:
array CGH
US23502387_251469323759_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 63

description:
array CGH
US23502387_251469323760_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 59

description:
array CGH
US23502387_251469323751_S01_CGH-v4_95_Feb07.txt


title: Nox1m zone 2 of Developmental stage_replicate 24

description: Biological replicate 2 of 4.  Zone 2 of  IDC343 PaNox1


title: aCGH data of patient 61

description:
array CGH
US23502387_251469323758_S01_CGH-v4_95_Feb07.txt


title: Nox1m zone 2 of Developmental stage_replicate 25

description: Biological replicate 3 of 4.  Zone 2 of  IDC343 PaNox1


title: GEP data of patient 52

description:
gene expression profiles
P0577-01-B877-U133Plus-2.CEL


title: GEP data of patient 54

description:
gene expression profiles
P0604-01-B933-U133Plus-2.CEL


title: Nox1m zone 2 of Developmental stage_replicate 23

description: Biological replicate 1 of 4.  Zone 2 of  IDC343 PaNox1


title: GEP data of patient 55

description:
gene expression profiles
P0669-01-C95-U133Plus-2.CEL


title: Nox1m zone 1 of Developmental stage_replicate 17

description: Biological replicate 4 of 4. Zone 1 of  IDC343 PaNox1

value: harvested of the growing edge of the colony (zone 1) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: aCGH data of patient 58

description:
array CGH
US23502387_251469323749_S01_CGH-v4_95_Feb07.txt

value: training set


title: aCGH data of patient 57

description:
array CGH
US23502387_251469325732_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 56

description:
array CGH
US23502387_251469323618_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 73

description:
array CGH
US23502387_251469324195_S01_CGH-v4_95_Feb07.txt


title: Nox1m zone 1 of Developmental stage_replicate 34

description: Biological replicate 3 of 4. Zone 1 of  IDC343 PaNox1


title: GEP data of patient 50

description:
gene expression profiles
P0561-01-B827-U133Plus-2.CEL


title: Nox1m zone 1 of Developmental stage_replicate 15

description: Biological replicate 2 of 4. Zone 1 of  IDC343 PaNox1


title: aCGH data of patient 52

description:
array CGH
US23502387_251469323623_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 75

description:
array CGH
US23502387_251469324197_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 49

description:
array CGH
US23502387_251469323620_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 51

description:
gene expression profiles
P0559-01-B814-U133Plus-2.CEL


title: aCGH data of patient 50

description:
array CGH
US23502387_251469323621_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 54

description:
array CGH
US23502387_251469323615_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 49

description:
gene expression profiles
P0556-01-B807-U133Plus-2.CEL


title: aCGH data of patient 51

description:
array CGH
US23502387_251469323622_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 55

description:
array CGH
US23502387_251469323616_S01_CGH-v4_95_Feb07.txt


title: Nox1m zone 1 of Developmental stage_replicate 13

description: Biological replicate 1 of 4. Zone 1 of  IDC343 PaNox1


title: aCGH data of patient 48

description:
array CGH
US23502387_251469323619_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 47

description:
gene expression profiles
P0511-01-B707-U133Plus-2.CEL


title: aCGH data of patient 53

description:
array CGH
US23502387_251469323614_S01_CGH-v4_95_Feb07.txt


title: ∆Mpk2 zone 3 of Developmental stage_replicate 39

description: Biological replicate 3 of 4. Zone 3 of  ∆PaMpk2

value: DPaMpk2 S


title: GEP data of patient 46

description:
gene expression profiles
P0508-01-B697-U133Plus-2.CEL


title: ∆Mpk2 zone 3 of Developmental stage_replicate 310

description: Biological replicate 4 of 4.  Zone 3 of ∆PaMpk2


title: testicular somatic cell

city: Minato-ku

first: Makoto

last: Hayashi

state: Tokyo

address: Konan 4-5-7

department: Department of Marine Biosciences

country: Japan

institute: Tokyo University of Marine Science and Technology

description: Gene expression in testicular somatic cell in rainbow trout immature testis

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 µl of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hr at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107 and Grid: 034067_D_F_20110503) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Oncorhynchus mykiss

source_name: testicular somatic cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng RNA using the One-Color Low Imput Quick Amp Labeling Kit (Agilent Technologies, Santa Clara) following the manufacture's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacture's instructions. The protocol includes an on-column DNase digestion.

treatment_protocol: Type A spermatogonia or testicular somatic cells were isolated from the fishes carrying the transgene, pvasa-GFP, which expresses GFP in spermatogonia, by using fluorescence-activated cell sorting (FACS)

tag: gender

value: male

value: testicular somatic cell


title: type A spermatogonia

description: Gene expression in type A spermatogonia in rainbow trout immature testis

source_name: type A spermatogonia

value: type A spermatogonia


title: aCGH data of patient 47

description:
array CGH
US23502387_251469322573_S01_CGH-v4_95_Feb07.txt

tag: reference

value: sex-matched reference genomic DNA (Promega)


title: aCGH data of patient 46

description:
array CGH
US23502387_251469322571_S01_CGH-v4_95_Feb07.txt


title: ∆Mpk2 zone 3 of Developmental stage_replicate 38

description: Biological replicate 2 of 4. Zone 3 of ∆PaMpk2

tag: strain


title: GEP data of patient 48

description:
gene expression profiles
P0510-01-B703-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW189

hyb_protocol: As according to the manufacturer's instructions

scan_protocol: GCOS 1.4

data_processing: Data were normalized and combined using R 2.13.0 environment. We used the combineAffyBatch function in the matchprobes library to merge data from HG-U133A and HG-U133Plus2 GeneChips and we applied RMA normalization to the merged dataset

source_name: Ewing sarcoma sample EW189

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2µg total RNA

tag: tissue

value: Ewing tumor


title: aCGH data of patient 43

description:
array CGH
US23502387_251469322568_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 44

description:
array CGH
US23502387_251469322569_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 44

description:
gene expression profiles
P0501-01-B675-U133Plus-2.CEL


title: aCGH data of patient 42

description:
array CGH
US23502387_251469322580_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 45

description:
array CGH
US23502387_251469322570_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 43

description:
gene expression profiles
P0495-01-B659-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW175

source_name: Ewing sarcoma sample EW175


title: ∆Mpk2 zone 3 of Developmental stage_replicate 37

description: Biological replicate 1 of 4.  Zone 3 of ∆PaMpk2

tag: growth condition

value: harvested of the distal zone of the colony (zone 3) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane

tag: mating type


title: Ewing sarcoma sample mRNA EW158

source_name: Ewing sarcoma sample EW158


title: GEP data of patient 45

description:
gene expression profiles
P0503-01-B683-U133Plus-2.CEL


title: aCGH data of patient 41

description:
array CGH
US23502387_251469322577_S01_CGH-v4_95_Feb07.txt

source_name: test

source_name: reference


title: ∆Mpk2 zone 2 of Developmental stage_replicate 210

description: Biological replicate 4 of 4.  Zone 2 of ∆PaMpk2

value: mat+

tag: biosource 1

tag: name biosource 1


title: GEP data of patient 42

description:
gene expression profiles
P0451-01-B549-U133Plus-2.CEL


title: ∆Mpk2 zone 2 of Developmental stage_replicate 29

description: Biological replicate 3 of 4.  Zone 2 of ∆PaMpk2

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 2

tag: name biosource 2


title: GEP data of patient 41

description:
gene expression profiles
P0447-01-B544-U133Plus-2.CEL


title: aCGH data of patient 40

description:
array CGH
US23502387_251469322576_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample mRNA EW142

source_name: Ewing sarcoma sample EW142


title: Ewing sarcoma sample mRNA EW168

source_name: Ewing sarcoma sample EW168


title: ∆Mpk2 zone 2 of Developmental stage_replicate 28

description: Biological replicate 2 of 4.  Zone 2 of ∆PaMpk2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 3

tag: name biosource 3


title: GEP data of patient 40

description:
gene expression profiles
P0434-01-B522-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW137

source_name: Ewing sarcoma sample EW137


title: Ewing sarcoma sample mRNA EW163

source_name: Ewing sarcoma sample EW163


title: ∆Mpk2 zone 1 of Developmental stage_replicate 19

description: Biological replicate 3 of 4. Zone 1 of ∆PaMpk2

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: biosource 4

tag: name biosource 4


title: GEP data of patient 38

description:
gene expression profiles
P0924-01-C899-U133Plus-2.CEL

source_name: CD138 plus plasma cells

tag: patient

tag: disease state


title: GEP data of patient 39

description:
gene expression profiles
P0446-01-B540-U133Plus-2.CEL

tag: cell type

tag: sample type


title: Ewing sarcoma sample mRNA EW110

source_name: Ewing sarcoma sample EW110


title: ∆Mpk2 zone 1 of Developmental stage_replicate 110

description: Biological replicate 4 of 4. Zone 1 of ∆PaMpk2

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: ∆Mpk2 zone 1 of Developmental stage_replicate 18

description: Biological replicate 2 of 4. Zone 1 of ∆PaMpk2


title: Ewing sarcoma sample mRNA EW116

source_name: Ewing sarcoma sample EW116


title: aCGH data of patient 39

description:
array CGH
US23502387_251469323219_S01_CGH-v4_95_Feb07.txt

value: multiple myeloma (MM)

tag: reference


title: aCGH data of patient 38

description:
array CGH
US23502387_251469323218_S01_CGH-v4_95_Feb07.txt

value: CD138 plus plasma cells


title: ∆Mpk2 zone 2 of Developmental stage_replicate 27

description: Biological replicate 1 of 4.  Zone 2 of  ∆PaMpk2

tag: strain

value: harvested of the intermediate zone of the colony (zone 2) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: GEP data of patient 36

description:
gene expression profiles
P0421-01-B491-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW53

source_name: Ewing sarcoma sample EW53

tag: tissue


title: aCGH data of patient 33

description:
array CGH
US23502387_251469323345_S01_CGH-v4_95_Feb07.txt


title: ∆Mpk1 zone 3 of Developmental stage_replicate 310

description: Biological replicate 4 of 4.  Zone 3 of ∆PaMpk1

value: DPaMpk1 S

tag: growth condition


title: ∆Mpk2 zone 1 of Developmental stage_replicate 17

description: Biological replicate 1 of 4. Zone 1 of ∆PaMpk2

value: harvested of the growing edge of the colony (zone 1) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane

tag: mating type


title: ∆Mpk1 zone 3 of Developmental stage_replicate 39

description: Biological replicate 3 of 4. Zone 3 of ∆PaMpk1

tag: biosource 1


title: GEP data of patient 37

description:
gene expression profiles
P0418-01-B487-U133Plus-2.CEL

value: training set


title: Ewing sarcoma sample mRNA EW128

source_name: Ewing sarcoma sample EW128


title: aCGH data of patient 36

description:
array CGH
US23502387_251469323348_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 34

description:
array CGH
US23502387_251469323346_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 32

description:
array CGH
US23502387_251469322585_S01_CGH-v4_95_Feb07.txt


title: ∆Mpk1 zone 3 of Developmental stage_replicate 38

description: Biological replicate 2 of 4. Zone 3 of ∆PaMpk1

source_name: Common reference

tag: name biosource 1


title: Ewing sarcoma sample mRNA EW29

source_name: Ewing sarcoma sample EW29


title: ∆Mpk1 zone 2 of Developmental stage_replicate 210

description: Biological replicate 4 of 4.  Zone 2 of ∆PaMpk1

tag: biosource 2


title: aCGH data of patient 35

description:
array CGH
US23502387_251469323347_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 33

description:
gene expression profiles
P0408-01-B457-U133Plus-2.CEL


title: GEP data of patient 34

description:
gene expression profiles
P0397-01-B440-U133Plus-2.CEL


title: aCGH data of patient 37

description:
array CGH
US23502387_251469323349_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample mRNA EW41

source_name: Ewing sarcoma sample EW41


title: ∆Mpk1 zone 2 of Developmental stage_replicate 29

description: Biological replicate 3 of 4.  Zone 2 of ∆PaMpk1

tag: name biosource 2


title: GEP data of patient 35

description:
gene expression profiles
P0433-01-B517-U133Plus-2.CEL


title: GEP data of patient 32

description:
gene expression profiles
P0401-01-B444-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW24

source_name: Ewing sarcoma sample EW24


title: ∆Mpk1 zone 3 of Developmental stage_replicate 37

description: Biological replicate 1 of 4.  Zone 3 of ∆PaMpk1

tag: biosource 3


title: Ewing sarcoma sample mRNA EW36

source_name: Ewing sarcoma sample EW36


title: aCGH data of patient 31

description:
array CGH
US23502387_251469322584_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample mRNA EW17

source_name: Ewing sarcoma sample EW17


title: GEP data of patient 30

description:
gene expression profiles
P0390-01-B423-U133Plus-2.CEL


title: GEP data of patient 31

description:
gene expression profiles
P0393-01-B433-U133Plus-2.CEL


title: aCGH data of patient 30

description:
array CGH
US23502387_251469322582_S01_CGH-v4_95_Feb07.txt

source_name: test


title: aCGH data of patient 28

description:
array CGH
US23502387_251469323771_S01_CGH-v4_95_Feb07.txt

source_name: reference


title: Ewing sarcoma sample mRNA EW27

source_name: Ewing sarcoma sample EW27


title: aCGH data of patient 29

description:
array CGH
US23502387_251469322581_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 27

description:
array CGH
US23502387_251469323770_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 25

description:
array CGH
US23502387_251469323768_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 26

description:
array CGH
US23502387_251469323769_S01_CGH-v4_95_Feb07.txt


title: Ewing sarcoma sample mRNA EW01

source_name: Ewing sarcoma sample EW01


title: GEP data of patient 28

description:
gene expression profiles
P0365-01-B379-U133Plus-2.CEL


title: ∆Mpk1 zone 2 of Developmental stage_replicate 27

description: Biological replicate 1 of 4.  Zone 2 of ∆PaMpk1

tag: name biosource 3


title: GEP data of patient 29

description:
gene expression profiles
P0391-01-B424-U133Plus-2.CEL


title: ∆Mpk1 zone 1 of Developmental stage_replicate 112

description: Biological replicate 4 of 4. Zone 1 of ∆PaMpk1

tag: biosource 4


title: GEP data of patient 27

description:
gene expression profiles
P0357-01-B359-U133Plus-2.CEL


title: Ewing sarcoma sample mRNA EW09

source_name: Ewing sarcoma sample EW09


title: GEP data of patient 24

description:
gene expression profiles
P0335-01-B312-U133Plus-2.CEL


title: GEP data of patient 25

description:
gene expression profiles
P0343-01-B333-U133Plus-2.CEL


title: ∆Mpk1 zone 1 of Developmental stage_replicate 19

description: Biological replicate 3 of 4. Zone 1 of ∆PaMpk1

tag: name biosource 4


title: GEP data of patient 26

description:
gene expression profiles
P0347-01-B346-U133Plus-2.CEL

tag: patient


title: ∆Mpk1 zone 2 of Developmental stage_replicate 28

description: Biological replicate 2 of 4.  Zone 2 of ∆PaMpk1


title: ∆Mpk1 zone 1 of Developmental stage_replicate 18

description: Biological replicate 2 of 4. Zone 1 of ∆PaMpk1


title: ∆Mpk1 zone 1 of Developmental stage_replicate 17

description: Biological replicate 1 of 4. Zone 1 of ∆PaMpk1


title: G4, biological repl. 5

city: Odense

first: Rikke

last: Leth-Larsen

address: JB Winsloewsvej 25

department: Institute of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

hyb_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000175

scan_protocol: Affymetrix Gene ChIP Scanner 3000 Dx. Standard Affymetrix Cel file scan protocol.

data_processing:
Microarray data were normalized and processed by Partek® Genomics Suite (FDR 0.01) using RMA normalization methods
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174

extract_protocol: mRNA was purified by TRIzol followed by EtOH precipitation

value: CD44+/CD24- Basal B (G4) cells

tag: disease state

value: breast cancer


title: Ewing sarcoma sample mRNA EW02

source_name: Ewing sarcoma sample EW02


title: G4, biological repl. 3

tag: cell type


title: Wild Type zone 3 of Developmental stage_replicate 311

description: Biological replicate 4 of 4.  Zone 3 of WT

value: Wild type S


title: aCGH data of patient 23

description:
array CGH
US23502387_251469324237_S01_CGH-v4_95_Feb07.txt

tag: sample type

value: sex-matched reference genomic DNA (Promega)


title: GEP data of patient 23

description:
gene expression profiles
P0332-01-B302-U133Plus-2.CEL

source_name: CD138 plus plasma cells


title: aCGH data of patient 21

description:
array CGH
US23502387_251469324234_S01_CGH-v4_95_Feb07.txt

tag: reference


title: aCGH data of patient 22

description:
array CGH
US23502387_251469324235_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 20

description:
array CGH
US23502387_251469324251_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 24

description:
array CGH
US23502387_251469324238_S01_CGH-v4_95_Feb07.txt


title: G4, biological repl. 4


title: Wild Type zone 3 of Developmental stage_replicate 310

description: Biological replicate 3 of 4. Zone 3 of WT

tag: strain


title: A4, biological repl. 5

value: CD44+/CD24low epithelioid Basal A (A4) cells


title: GEP data of patient 22

description:
gene expression profiles
P0308-01-B235-U133Plus-2.CEL


title: G4, biological repl. 1


title: Wild Type zone 3 of Developmental stage_replicate 39

description: Biological replicate 2 of 4. Zone 3 of WT

value: harvested of the distal zone of the colony (zone 3) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: Wild Type zone 2 of Developmental stage_replicate 211

description: Biological replicate 4 of 4.  Zone 2 of WT

value: mat+


title: Wild Type zone 3 of Developmental stage_replicate 32

description: Biological replicate 1 of 4.  Zone 3 of WT

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.


title: A4, biological repl. 4


title: aCGH data of patient 19

description:
array CGH
US23502387_251469324250_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 21

description:
gene expression profiles
P0381-01-B409-U133Plus-2.CEL


title: A4, biological repl. 3


title: GEP data of patient 19

description:
gene expression profiles
P0291-01-B172-U133Plus-2.CEL


title: G4, biological repl. 2


title: GEP data of patient 17

description:
gene expression profiles
P0280-01-B135-U133Plus-2.CEL


title: GEP data of patient 18

description:
gene expression profiles
P0278-01-B133-U133Plus-2.CEL


title: aCGH data of patient 18

description:
array CGH
US23502387_251469324249_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 20

description:
gene expression profiles
P0301-01-B211-U133Plus-2.CEL


title: A4, biological repl. 1


title: Wild Type zone 1 of Developmental stage_replicate 110

description: Biological replicate 3 of 4. Zone 1 of WT

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: A4, biological repl. 2


title: aCGH data of patient 15

description:
array CGH
US23502387_251469323776_S01_CGH-v4_95_Feb07.txt


title: Suspension_8days_rep3

city: Padova

first: Barbara

last: Di Camillo

address: via Gradenigo 6B

department: Information Engineering Department

country: Italy

institute: University of Padova

description: Whole genome expression in embryoid bodies from hESCs, cultured in suspension for 8 days

hyb_protocol: Whole Human Genome Oligo Microarray Kit, 4x44K (Agilent) was used according to the manufacturer’s protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using Scan Control software (Version A.8.1.3) for 4x44k array slides, with profile AgilentHD_GX_1Color, and scan resolution 5um

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using grid: 014850_D_20070207 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Embryoid Bodies, suspension culture, 8 days, replicate 3

label_protocol: Labelled Cy3 cDNAs were synthesized by reverse transcription from the total RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from pelleted embryoid bodies using TRIZOL reagent (Invitrogen) coupled to RNeasy Kit (Qiagen) according to the manufacturer’s instructions.

value: Developing embryoid bodies from hESCs


title: aCGH data of patient 13

description:
array CGH
US23502387_251469323774_S01_CGH-v4_95_Feb07.txt


title: Wild Type zone 1 of Developmental stage_replicate 111

description: Biological replicate 4 of 4. Zone 1 of WT

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: GEP data of patient 16

description:
gene expression profiles
P0281-01-B136-U133Plus-2.CEL

value: multiple myeloma (MM)

value: CD138 plus plasma cells


title: aCGH data of patient 17

description:
array CGH
US23502387_251469324248_S01_CGH-v4_95_Feb07.txt


title: Wild Type zone 2 of Developmental stage_replicate 210

description: Biological replicate 3 of 4.  Zone 2 of WT

value: harvested of the intermediate zone of the colony (zone 2) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: Wild Type zone 2 of Developmental stage_replicate 29

description: Biological replicate 2 of 4.  Zone 2 of WT


title: aCGH data of patient 14

description:
array CGH
US23502387_251469323775_S01_CGH-v4_95_Feb07.txt


title: Suspension_8days_rep2

source_name: Embryoid Bodies, suspension culture, 8 days, replicate 2


title: GEP data of patient 15

description:
gene expression profiles
P0271-01-B95-U133Plus-2.CEL


title: GEP data of patient 13

description:
gene expression profiles
P0260-01-B33-U133Plus-2.CEL


title: aCGH data of patient 11

description:
array CGH
US23502387_251469323664_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 12

description:
array CGH
US23502387_251469322624_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 16

description:
array CGH
US23502387_251469324247_S01_CGH-v4_95_Feb07.txt


title: Hydrogel_1:1ratio(width/depth)_8days_rep3

description: Whole genome expression in embryoid bodies from hESCs, cultured in 1:1 microwells for 8 days

source_name: Embryoid Bodies, 1:1 microwell culture, 8 days, replicate 3


title: GEP data of patient 12

description:
gene expression profiles
P0208-01-A823-U133Plus-2.CEL


title: Wild Type zone 2 of Developmental stage_replicate 22

description: Biological replicate 1 of 4.  Zone 2 of WT


title: Wild Type zone 1 of Developmental stage_replicate 19

description: Biological replicate 2 of 4. Zone 1 of WT

value: harvested of the growing edge of the colony (zone 1) after 72 hours of growth in light, on M2 media covered with a sheet of cellophane


title: GEP data of patient 14

description:
gene expression profiles
P0266-01-B79-U133Plus-2.CEL

value: training set


title: Hydrogel_1:1ratio(width/depth)_8days_rep2

source_name: Embryoid Bodies, 1:1 microwell culture, 8 days, replicate 2


title: Wild Type zone 1 of Developmental stage_replicate 12

description: Biological replicate 1 of 4. Zone 1 of WT

source_name: Common reference


title: Suspension_8days_rep1

description: Whole genome expression in embryoid bodies from hESCs, cultured in suspension for 8 days

source_name: Embryoid Bodies, suspension culture, 8 days, replicate 1


title: Hydrogel_1:2ratio(width/depth)_8days_rep3

description: Whole genome expression in embryoid bodies from hESCs, cultured in 1:2 microwells for 8 days

source_name: Embryoid Bodies, 1:2 microwell culture, 8 days, replicate 3


title: GEP data of patient 11

description:
gene expression profiles
P0165-01-A596-U133Plus-2.CEL


title: GEP data of patient 8

description:
gene expression profiles
P0095-01-A355-U133Plus-2.CEL


title: aCGH data of patient 10

description:
array CGH
US23502387_251469323663_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 9

description:
gene expression profiles
P0077-01-A357-U133Plus-2.CEL


title: aCGH data of patient 9

description:
array CGH
US23502387_251469323662_S01_CGH-v4_95_Feb07.txt


title: aCGH data of patient 8

description:
array CGH
US23502387_251469323661_S01_CGH-v4_95_Feb07.txt


title: Hydrogel_1:2ratio(width/depth)_8days_rep2

source_name: Embryoid Bodies, 1:2 microwell culture, 8 days, replicate 2


title: K562+HUVEC_extracellular_miRNA

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The qPCR data were processed by SDS 2.3 software (Applied Biosystems, Foster City, CA) and importing files to RQ manager 2.0 and DataAssist 3.0 software (Applied Biosystems); the undetermined data were set to the Ct value of 35. The Ct values were normalized by miR-159a (ath-miR159a).

label: FAM

source_name: Supernatant of K562 cell line with HUVEC

label_protocol: not applicable

extract_protocol: Total RNA extracted using the mirVana PARIS kit (Ambion, Austin, TX, USA) according to manufacturer’s instructions. An RT reaction step was set up according to manufacturer’s recommendations. MiRNAs were reverse transcribed using 30ng of total RNA, the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Applied Biosystems, Bedford, MA, USA).

tag: cell lines

value: human myeloid leukemia cell line K562 and human umbillical vein endothelial cell HUVEC


title: Hydrogel_1:2ratio(width/depth)_8days_rep1

source_name: Embryoid Bodies, 1:2 microwell culture, 8 days, replicate 1


title: GEP data of patient 10

description:
gene expression profiles
P0111-01-A403-U133Plus-2.CEL


title: HUVEC extracellular miRNAs

source_name: Supernatant of HUVEC

tag: cell line

value: human umbillical vein endothelial cell HUVEC


title: Glu5_Suc3_2

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Biological replicate 2 of 2. Dye swap 2

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer. Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner.  Images were processed using GenePix Pro software (version 4.1)  and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

data_processing: Data normalization between and within array using LOWESS using R/Bioconductor Statistical software.

organism: Limosilactobacillus reuteri

source_name: Bacteria

label_protocol: 2 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes. Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP. After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned. cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Bacterial cells were grown for 24h in MRS at 37C in anaerobic conditions

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol. Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin. After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

tag: carbon source

value: glucose

value: ATCC PTA 6475

value: sucrose


title: Glu5_Suc3_1

description: Biological replicate 1 of 2. Dye swap 2


title: aCGH data of patient 6

description:
array CGH
US23502387_251469325731_S01_CGH-v4_95_Feb07.txt

source_name: test

source_name: reference

value: sex-matched reference genomic DNA (Promega)


title: K562_extracellular_miRNAs

source_name: Supernatant of K562 cell line

value: human myeloid leukemia cell line K562


title: Glu3_Suc5_1

description: Biological replicate 1 of 2. Dye swap 1


title: Glu3_Suc5_2

description: Biological replicate 2 of 2. Dye swap 1


title: aCGH data of patient 4

description:
array CGH
US23502387_251469323262_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 7

description:
gene expression profiles
P0168-01-A602-U133Plus-2.CEL


title: GEP data of patient 5

description:
gene expression profiles
P0063-01-A248-U133Plus-2.CEL


title: HUVEC intercellular miRNAs

data_processing: The qPCR data were processed by SDS 2.3 software (Applied Biosystems, Foster City, CA) and importing files to RQ manager 2.0 and DataAssist 3.0 software (Applied Biosystems); the undetermined data were set to the Ct value of 35. The Ct values were normalized by RNU6B (mammU6).

source_name: HUVEC


title: mouse fibroblasts ColI Cre x RBP loxp-loxp in vivo

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

description:
in vivo deletion of RBP-Jk in mouse fibroblasts
ColI Cre x RBP loxp-loxp

hyb_protocol: Biotin-labeled cRNA (10ug/sample) was hybridized on Mouse Genome 430 2.0 Array Chips according to the manufacturer’s recommendation.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Raw microarray values were quantified using GeneChip Operating Software (Affymetrix).

data_processing: Raw data files were loaded into the Resolver SE System (Rosetta Biosoftware) for data processing and normalization, using platform-specific error models. Intensity profiles were then compared to form ratio experiments where each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the “treated” versus the control sample.

molecule: polyA RNA

label_protocol: The resulting cDNAs were used for preparation of biotin-labeled antisense cRNA

extract_protocol: Poly(A)+ mRNAs (2–5 μg) from cells under various conditions were used as template for double-stranded cDNA preparations with T7-(dT)24 oligonucleotide primers for the first-strand reaction.

value: fibroblasts

tag: genotype

tag: genetic background


title: mouse fibroblasts RBP loxp-loxp in vivo

description:
control for in vivo deletion of RBP-Jk in mouse fibroblasts
RBP loxp-loxp


title: GEP data of patient 6

description:
gene expression profiles
P0098-01-A308-U133Plus-2.CEL

source_name: CD138 plus plasma cells


title: K562_intercellular_miRNAs

source_name: K562 cell line


title: Hydrogel_1:1ratio(width/depth)_8days_rep1

description: Whole genome expression in embryoid bodies from hESCs, cultured in 1:1 microwells for 8 days

source_name: Embryoid Bodies, 1:1 microwell culture, 8 days, replicate 1


title: aCGH data of patient 5

description:
array CGH
US23502387_251469323263_S01_CGH-v4_95_Feb07.txt


title: GEP data of patient 4

description:
gene expression profiles
P0569-01-B853-U133Plus-2.CEL


title: GEP data of patient 3

description:
gene expression profiles
P0598-01-B924-U133Plus-2.CEL


title: aCGH data of patient 7

description:
array CGH
US23502387_251469323660_S01_CGH-v4_95_Feb07.txt


title: mouse fibroblasts Adeno GFP in vitro

description:
control for in vitro deletion of RBP-Jk in mouse fibroblasts
Adeno GFP


title: aCGH data of patient 2

description:
array CGH
US23502387_251469323658_S01_CGH-v4_95_Feb07.txt


title: mouse fibroblasts Adeno Cre in vitro

description:
in vitro deletion of RBP-Jk in mouse fibroblasts
Adeno Cre


title: fibroblast

status: Public on Jun 11 2012

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description: fibroblasts from CINCA syndrome patient (CiRA188Ai)

hyb_protocol: Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.

scan_protocol: Images were acquired by DNA Microarray Scanner (Agilent Technologies)

data_processing: Raw data were processed with FeatureExtraction version 10.7. Background signal was subtracted.

label_protocol: 20 µg of total RNA was first amplified with WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).

growth_protocol: We expanded the fibroblasts in DMEM (Nacalai tesque) containing 10% FBS (Invitrogen) and 0.5% penicillin and streptomycin (Invitrogen).  To generate iPS cells, we introduced OCT3/4, SOX2, KLF4 and c-MYC by using ecotropic retroviral transduction into fibroblasts expressing the mouse Slc7a1 gene.  Six days after transduction, the cells were harvested and re-plated onto mitotically inactivated SNL feeder cells. The next day, we replaced the medium with Primate ES cell medium (ReproCELL) supplemented with 4 ng/ml bFGF (Wako).  Three weeks after this period, individual colonies were isolated and expanded. Cell culture was performed under 37°C , with 5% CO2 and 21% O2.

extract_protocol: Total RNA was column-purified with the RNeasy kit (Qiagen) and treated with RNase-free DNase (Qiagen).

treatment_protocol: Undifferentiated human ESC and iPSC lines were cultured on mitotically-inactivated SNL feeder cells with Primate ES cell medium supplemented with 4 ng/ml bFGF. During the differentiation of the cells into macrophages, cells were cultured under 37°C , with 5% CO2 and 5% O2. On day 0, the iPSCs were plated at a ratio of 1:15 onto a mitotically-inactivated OP9 feeder layer on 100 mm cell culture plates in αMEM (Invitrogen) containing 10% FBS and 1% Antibiotic-Antimycotic (Invitrogen) supplemented with 50 ng/ml VEGFα (R&D Systems). On day 5, the medium was changed. On day 10, the differentiating iPSCs were collected by trypsinization, and Tra-1-85+ CD34+ and KDR+ hematopoietic progenitors were sorted on a FACS Aria II instrument (BD Biosciences). The progenitors were plated at 2 x 104 cells on another mitotically inactivated OP9 feeder layer on 100 mm cell culture plates or at 3 x 103 cells/well in 6 well cell culture plates in αMEM containing 10% FBS and 1% Antibiotic-Antimycotic supplemented with 50 ng/ml IL-3, 50 ng/ml SCF, 10 ng/ml TPO, 50 ng/ml FL and 50 ng/ml M-CSF (all R&D Systems). On day 18, the medium was changed. On day 26, differentiating cells were collected with Accumax (Innovative Cell Technologies), and CD14+ iPS-MPs were purified on an autoMACSpro instrument (Miltenyi Biotec).

value: fibroblast


title: Macrophage_from_iPSC+NLRP3mut

description: iPS cells carrying mutant NLRP3 derived from fibroblasts (FIBRO), clone 1

source_name: iPSC

value: iPS cells


title: Macrophage_from_iPSC+NLRP3wt

description: iPS cells carrying wild type NLRP3 derived from fibroblasts (FIBRO), clone 1


title: GEP data of patient 2

description:
gene expression profiles
P0565-01-B840-U133Plus-2.CEL


title: aCGH data of patient 1

description:
array CGH
US23502387_251469323655_S01_CGH-v4_95_Feb07.txt


title: ESC

description: ES cells which was previously established

source_name: ESC

value: ES cells


title: CINCA_WildType-Macrophage-3

description: macrophages obtained from wild type iPS cells (W3)

value: macrophage


title: Macrophage_from_ESC

description: macrophages obtained from ES cells (khES3)


title: Macrophage_from_iPSC

description: macrophages obtained from previously established iPS cells (B7)


title: CINCA_NLRP3mut-Macrophage-3

description: macrophages obtained from NLRP3-mutant iPS cells (M3)


title: Normal-Macrophage-1

description: macrophages obtained from blood of healthy volunteer 1


title: CINCA_NLRP3mut-Macrophage-1

description: macrophages obtained from NLRP3-mutant iPS cells (M1)


title: GEP data of patient 1

description:
gene expression profiles
P0789-01-C458-U133Plus-2.CEL

value: multiple myeloma (MM)


title: Normal-Macrophage-3

description: macrophages obtained from blood of healthy volunteer 3


title: CINCA_WildType-Macrophage-1

description: macrophages obtained from wild type iPS cells (W1)


title: CINCA_WildType-Macrophage-2

description: macrophages obtained from wild type iPS cells (W2)


title: Normal-Macrophage-2

description: macrophages obtained from blood of healthy volunteer 2


title: CINCA_NLRP3mut-Macrophage-2

description: macrophages obtained from NLRP3-mutant iPS cells (M2)


title: aCGH data of patient 3

description:
array CGH
US23502387_251469323659_S01_CGH-v4_95_Feb07.txt

value: CD138 plus plasma cells


title: hLung_GRNG_443

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

hyb_protocol: The amplified cDNAs were hybridized to Affymetrix gene expression chips (Human Rosetta Custom Affymetrix 2.0, Affymetrix, Santa Clara, CA) using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G. The images were analyzed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Expression values were extracted using the Robust Multichip Average method (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-64) as implemented in the Affymetrix Power Tools software (available at: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).

source_name: Lung

label_protocol: Samples were amplified and labeled using the Ovation WB protocol (NuGEN Technologies, San Carlos, CA), according to the manufacturer’s instructions. In brief, 50 ng of total RNA was amplified using the Ribo-SPIA technology (NuGEN Technologies). After quantification, 4.4 ug cDNA was fragmented and labeled with biotin using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

extract_protocol: Total RNA was extracted and purified from the clinical lung specimens using the SV96 Total RNA Isolation System (Promega) according to a custom automated protocol. The extracted RNA was quantified using RiboGreen RNA Quantitation Reagent (Invitrogen) and its quality was assessed using Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in an Agilent 2100 Bioanalyzer (Agilent).

tag: tissue

value: lung

tag: tumor status

value: non-tumorous


title: hLung_GRNG_441


title: hLung_GRNG_439


title: hLung_GRNG_435


title: hLung_GRNG_437


title: hLung_GRNG_445


title: hLung_GRNG_434


title: hLung_GRNG_427


title: hLung_GRNG_425


title: hLung_GRNG_444


title: hLung_GRNG_431


title: hLung_GRNG_430


title: hLung_GRNG_429


title: hLung_GRNG_428


title: hLung_GRNG_423


title: hLung_GRNG_442


title: hLung_GRNG_424


title: hLung_GRNG_440


title: hLung_GRNG_438


title: hLung_GRNG_419


title: hLung_GRNG_436


title: hLung_GRNG_426


title: hLung_GRNG_418


title: hLung_GRNG_433


title: hLung_GRNG_416


title: hLung_GRNG_421


title: hLung_GRNG_432


title: hLung_GRNG_422


title: hLung_GRNG_415


title: hLung_GRNG_411


title: hLung_GRNG_409


title: hLung_GRNG_412


title: hLung_GRNG_406


title: hLung_GRNG_403


title: hLung_GRNG_398


title: hLung_GRNG_407


title: hLung_GRNG_404


title: hLung_GRNG_399


title: hLung_GRNG_410


title: hLung_GRNG_400


title: hLung_GRNG_417


title: hLung_GRNG_414


title: hLung_GRNG_405


title: hLung_GRNG_402


title: hLung_GRNG_401


title: hLung_GRNG_408


title: hLung_GRNG_397


title: hLung_GRNG_420


title: hLung_GRNG_413


title: hLung_GRNG_396


title: hLung_GRNG_392


title: hLung_GRNG_389


title: hLung_GRNG_395


title: hLung_GRNG_394


title: hLung_GRNG_390


title: hLung_GRNG_393


title: hLung_GRNG_384


title: hLung_GRNG_387


title: hLung_GRNG_380


title: hLung_GRNG_383


title: hLung_GRNG_388


title: hLung_GRNG_386


title: hLung_GRNG_391


title: hLung_GRNG_381


title: hLung_GRNG_382


title: hLung_GRNG_370


title: hLung_GRNG_385


title: hLung_GRNG_378


title: hLung_GRNG_377


title: hLung_GRNG_375


title: hLung_GRNG_379


title: hLung_GRNG_374


title: hLung_GRNG_372


title: hLung_GRNG_368


title: hLung_GRNG_376


title: hLung_GRNG_373


title: hLung_GRNG_371


title: hLung_GRNG_367


title: hLung_GRNG_369


title: hLung_GRNG_361


title: hLung_GRNG_342


title: hLung_GRNG_347


title: hLung_GRNG_356


title: hLung_GRNG_348


title: hLung_GRNG_351


title: hLung_GRNG_350


title: hLung_GRNG_353


title: hLung_GRNG_343


title: hLung_GRNG_358


title: hLung_GRNG_344


title: hLung_GRNG_355


title: hLung_GRNG_362


title: hLung_GRNG_349


title: hLung_GRNG_365


title: hLung_GRNG_352


title: hLung_GRNG_360


title: hLung_GRNG_340


title: hLung_GRNG_338


title: hLung_GRNG_364


title: hLung_GRNG_357


title: hLung_GRNG_339


title: hLung_GRNG_354


title: hLung_GRNG_359


title: hLung_GRNG_345


title: hLung_GRNG_341


title: hLung_GRNG_336


title: hLung_GRNG_366


title: hLung_GRNG_337


title: hLung_GRNG_363


title: hLung_GRNG_346


title: hLung_GRNG_333


title: hLung_GRNG_331


title: hLung_GRNG_335


title: hLung_GRNG_332


title: hLung_GRNG_329


title: hLung_GRNG_327


title: hLung_GRNG_328


title: hLung_GRNG_325


title: hLung_GRNG_324


title: hLung_GRNG_308


title: hLung_GRNG_316


title: hLung_GRNG_309


title: hLung_GRNG_334


title: hLung_GRNG_302


title: hLung_GRNG_322


title: hLung_GRNG_306


title: hLung_GRNG_326


title: hLung_GRNG_301


title: hLung_GRNG_317


title: hLung_GRNG_307


title: hLung_GRNG_319


title: hLung_GRNG_323


title: hLung_GRNG_314


title: hLung_GRNG_311


title: hLung_GRNG_318


title: hLung_GRNG_321


title: hLung_GRNG_330


title: hLung_GRNG_315


title: hLung_GRNG_313


title: hLung_GRNG_304


title: hLung_GRNG_310


title: hLung_GRNG_303


title: hLung_GRNG_320


title: hLung_GRNG_299


title: hLung_GRNG_305


title: hLung_GRNG_312


title: hLung_GRNG_300


title: hLung_GRNG_297


title: hLung_GRNG_286


title: hLung_GRNG_298


title: hLung_GRNG_279


title: hLung_GRNG_272


title: hLung_GRNG_294


title: hLung_GRNG_293


title: hLung_GRNG_290


title: hLung_GRNG_295


title: hLung_GRNG_274


title: hLung_GRNG_280


title: hLung_GRNG_292


title: hLung_GRNG_278


title: hLung_GRNG_276


title: hLung_GRNG_270


title: hLung_GRNG_288


title: hLung_GRNG_284


title: hLung_GRNG_285


title: hLung_GRNG_277


title: hLung_GRNG_296


title: hLung_GRNG_287


title: hLung_GRNG_271


title: hLung_GRNG_282


title: hLung_GRNG_273


title: hLung_GRNG_275


title: hLung_GRNG_291


title: hLung_GRNG_289


title: hLung_GRNG_269


title: hLung_GRNG_283


title: hLung_GRNG_268


title: hLung_GRNG_259


title: hLung_GRNG_264


title: hLung_GRNG_255


title: hLung_GRNG_260


title: hLung_GRNG_262


title: hLung_GRNG_257


title: hLung_GRNG_253


title: hLung_GRNG_267


title: hLung_GRNG_266


title: hLung_GRNG_250


title: hLung_GRNG_243


title: hLung_GRNG_244


title: hLung_GRNG_246


title: hLung_GRNG_251


title: hLung_GRNG_258


title: hLung_GRNG_245


title: hLung_GRNG_265


title: hLung_GRNG_242


title: hLung_GRNG_261


title: hLung_GRNG_252


title: hLung_GRNG_256


title: hLung_GRNG_254


title: hLung_GRNG_249


title: hLung_GRNG_263


title: hLung_GRNG_240


title: hLung_GRNG_236


title: hLung_GRNG_237


title: hLung_GRNG_241


title: hLung_GRNG_248


title: hLung_GRNG_247


title: hLung_GRNG_281


title: hLung_GRNG_239


title: hLung_GRNG_233


title: hLung_GRNG_234


title: hLung_GRNG_232


title: hLung_GRNG_238


title: hLung_GRNG_230


title: hLung_GRNG_228


title: hLung_GRNG_235


title: hLung_GRNG_224


title: hLung_GRNG_231


title: hLung_GRNG_223


title: hLung_GRNG_222


title: hLung_GRNG_229


title: hLung_GRNG_221


title: hLung_GRNG_226


title: hLung_GRNG_219


title: hLung_GRNG_227


title: hLung_GRNG_225


title: hLung_GRNG_220


title: hLung_GRNG_217


title: hLung_GRNG_215


title: hLung_GRNG_213


title: hLung_GRNG_218


title: hLung_GRNG_212


title: hLung_GRNG_216


title: hLung_GRNG_211


title: hLung_GRNG_206


title: hLung_GRNG_208


title: hLung_GRNG_209


title: hLung_GRNG_210


title: hLung_GRNG_214


title: hLung_GRNG_201


title: hLung_GRNG_205


title: hLung_GRNG_207


title: hLung_GRNG_204


title: hLung_GRNG_198


title: hLung_GRNG_203


title: hLung_GRNG_200


title: hLung_GRNG_197


title: hLung_GRNG_195


title: hLung_GRNG_196


title: hLung_GRNG_191


title: hLung_GRNG_194


title: hLung_GRNG_192


title: hLung_GRNG_199


title: hLung_GRNG_189


title: hLung_GRNG_193


title: hLung_GRNG_185


title: hLung_GRNG_187


title: hLung_GRNG_186


title: hLung_GRNG_190


title: hLung_GRNG_178


title: hLung_GRNG_176


title: hLung_GRNG_188


title: hLung_GRNG_183


title: hLung_GRNG_175


title: hLung_GRNG_182


title: hLung_GRNG_184


title: hLung_GRNG_180


title: hLung_GRNG_173


title: hLung_GRNG_181


title: hLung_GRNG_177


title: hLung_GRNG_169


title: hLung_GRNG_170


title: hLung_GRNG_174


title: hLung_GRNG_171


title: hLung_GRNG_162


title: hLung_GRNG_172


title: hLung_GRNG_168


title: hLung_GRNG_179


title: hLung_GRNG_160


title: hLung_GRNG_158


title: hLung_GRNG_166


title: hLung_GRNG_167


title: hLung_GRNG_165


title: hLung_GRNG_163


title: hLung_GRNG_156


title: hLung_GRNG_151


title: hLung_GRNG_164


title: hLung_GRNG_157


title: hLung_GRNG_161


title: hLung_GRNG_149


title: hLung_GRNG_137


title: hLung_GRNG_144


title: hLung_GRNG_140


title: hLung_GRNG_135


title: hLung_GRNG_159


title: hLung_GRNG_155


title: hLung_GRNG_145


title: hLung_GRNG_133


title: hLung_GRNG_147


title: hLung_GRNG_138


title: hLung_GRNG_152


title: hLung_GRNG_131


title: hLung_GRNG_130


title: hLung_GRNG_154


title: hLung_GRNG_202


title: hLung_GRNG_142


title: hLung_GRNG_128


title: hLung_GRNG_126


title: hLung_GRNG_129


title: hLung_GRNG_136


title: hLung_GRNG_134


title: hLung_GRNG_143


title: hLung_GRNG_141


title: hLung_GRNG_148


title: hLung_GRNG_124


title: hLung_GRNG_127


title: hLung_GRNG_146


title: hLung_GRNG_150


title: hLung_GRNG_117


title: hLung_GRNG_139


title: hLung_GRNG_122


title: hLung_GRNG_115


title: hLung_GRNG_132


title: hLung_GRNG_119


title: hLung_GRNG_120


title: hLung_GRNG_153


title: hLung_GRNG_125


title: hLung_GRNG_109


title: hLung_GRNG_114


title: hLung_GRNG_113


title: hLung_GRNG_106


title: hLung_GRNG_111


title: hLung_GRNG_107


title: hLung_GRNG_110


title: hLung_GRNG_112


title: hLung_GRNG_103


title: hLung_GRNG_104


title: hLung_GRNG_108


title: hLung_GRNG_098


title: hLung_GRNG_099


title: hLung_GRNG_097


title: hLung_GRNG_116


title: hLung_GRNG_118


title: hLung_GRNG_096


title: hLung_GRNG_094


title: hLung_GRNG_105


title: hLung_GRNG_123


title: hLung_GRNG_102


title: hLung_GRNG_101


title: hLung_GRNG_095


title: hLung_GRNG_100


title: hLung_GRNG_090


title: hLung_GRNG_093


title: hLung_GRNG_121


title: hLung_GRNG_089


title: hLung_GRNG_085


title: hLung_GRNG_087


title: hLung_GRNG_092


title: hLung_GRNG_080


title: hLung_GRNG_091


title: hLung_GRNG_082


title: hLung_GRNG_088


title: hLung_GRNG_076


title: hLung_GRNG_075


title: hLung_GRNG_077


title: hLung_GRNG_069


title: hLung_GRNG_070


title: hLung_GRNG_071


title: hLung_GRNG_068


title: hLung_GRNG_081


title: hLung_GRNG_083


title: hLung_GRNG_079


title: hLung_GRNG_086


title: hLung_GRNG_067


title: hLung_GRNG_066


title: hLung_GRNG_072


title: hLung_GRNG_073


title: hLung_GRNG_078


title: hLung_GRNG_064


title: hLung_GRNG_063


title: hLung_GRNG_057


title: hLung_GRNG_060


title: hLung_GRNG_059


title: hLung_GRNG_053


title: hLung_GRNG_055


title: hLung_GRNG_052


title: hLung_GRNG_049


title: hLung_GRNG_058


title: hLung_GRNG_044


title: hLung_GRNG_051


title: hLung_GRNG_062


title: hLung_GRNG_056


title: hLung_GRNG_045


title: hLung_GRNG_054


title: hLung_GRNG_065


title: hLung_GRNG_061


title: hLung_GRNG_048


title: hLung_GRNG_046


title: hLung_GRNG_042


title: hLung_GRNG_050


title: hLung_GRNG_040


title: hLung_GRNG_047


title: hLung_GRNG_043


title: hLung_GRNG_038


title: hLung_GRNG_041


title: hLung_GRNG_037


title: hLung_GRNG_035


title: hLung_GRNG_039


title: hLung_GRNG_036


title: hLung_GRNG_031


title: hLung_GRNG_030


title: hLung_GRNG_034


title: hLung_GRNG_022


title: hLung_GRNG_074


title: hLung_GRNG_032


title: hLung_GRNG_033


title: hLung_GRNG_028


title: hLung_GRNG_018


title: hLung_GRNG_026


title: hLung_GRNG_025


title: hLung_GRNG_024


title: hLung_GRNG_027


title: hLung_GRNG_017


title: hLung_GRNG_029


title: hLung_GRNG_020


title: hLung_GRNG_021


title: hLung_GRNG_084


title: hLung_GRNG_016


title: hLung_GRNG_013


title: hLung_GRNG_014


title: hLung_GRNG_023


title: hLung_GRNG_012


title: hLung_GRNG_019


title: hLung_GRNG_011


title: hLung_GRNG_015


title: hLung_GRNG_008


title: hLung_GRNG_005


title: hLung_GRNG_009


title: hLung_GRNG_007


title: hLung_UBC_402


title: hLung_GRNG_006


title: hLung_GRNG_003


title: hLung_UBC_405


title: hLung_GRNG_010


title: hLung_UBC_403


title: hLung_UBC_400


title: hLung_GRNG_002


title: hLung_UBC_404


title: hLung_GRNG_001


title: hLung_UBC_401


title: hLung_GRNG_004


title: hLung_UBC_388


title: hLung_UBC_393


title: hLung_UBC_386


title: hLung_UBC_389


title: hLung_UBC_399


title: hLung_UBC_397


title: hLung_UBC_394


title: hLung_UBC_398


title: hLung_UBC_395


title: hLung_UBC_383


title: hLung_UBC_392


title: hLung_UBC_390


title: hLung_UBC_391


title: hLung_UBC_385


title: hLung_UBC_396


title: hLung_UBC_387


title: hLung_UBC_382


title: hLung_UBC_380


title: hLung_UBC_381


title: hLung_UBC_378


title: hLung_UBC_369


title: hLung_UBC_376


title: hLung_UBC_371


title: hLung_UBC_374


title: hLung_UBC_372


title: hLung_UBC_367


title: hLung_UBC_364


title: hLung_UBC_362


title: hLung_UBC_375


title: hLung_UBC_365


title: hLung_UBC_377


title: hLung_UBC_370


title: hLung_UBC_363


title: hLung_UBC_368


title: hLung_UBC_361


title: hLung_UBC_366


title: hLung_UBC_359


title: hLung_UBC_360


title: hLung_UBC_373


title: hLung_UBC_355


title: hLung_UBC_357


title: hLung_UBC_354


title: hLung_UBC_353


title: hLung_UBC_345


title: hLung_UBC_348


title: hLung_UBC_352


title: hLung_UBC_350


title: hLung_UBC_343


title: hLung_UBC_341


title: hLung_UBC_340


title: hLung_UBC_344


title: hLung_UBC_358


title: hLung_UBC_347


title: hLung_UBC_349


title: hLung_UBC_346


title: hLung_UBC_356


title: hLung_UBC_351


title: hLung_UBC_338


title: hLung_UBC_339


title: hLung_UBC_336


title: hLung_UBC_334


title: hLung_UBC_337


title: hLung_UBC_335


title: hLung_UBC_332


title: hLung_UBC_330


title: hLung_UBC_328


title: hLung_UBC_325


title: hLung_UBC_342


title: hLung_UBC_384


title: hLung_UBC_333


title: hLung_UBC_326


title: hLung_UBC_331


title: hLung_UBC_324


title: hLung_UBC_329


title: hLung_UBC_318


title: hLung_UBC_323


title: hLung_UBC_311


title: hLung_UBC_315


title: hLung_UBC_379


title: hLung_UBC_312


title: hLung_UBC_316


title: hLung_UBC_309


title: hLung_UBC_313


title: hLung_UBC_306


title: hLung_UBC_305


title: hLung_UBC_327


title: hLung_UBC_320


title: hLung_UBC_304


title: hLung_UBC_308


title: hLung_UBC_314


title: hLung_UBC_307


title: hLung_UBC_319


title: hLung_UBC_303


title: hLung_UBC_322


title: hLung_UBC_298


title: hLung_UBC_302


title: hLung_UBC_310


title: hLung_UBC_317


title: hLung_UBC_300


title: hLung_UBC_299


title: hLung_UBC_301


title: hLung_UBC_292


title: hLung_UBC_295


title: hLung_UBC_294


title: hLung_UBC_321


title: hLung_UBC_293


title: hLung_UBC_296


title: hLung_UBC_291


title: hLung_UBC_297


title: hLung_UBC_290


title: hLung_UBC_289


title: hLung_UBC_286


title: hLung_UBC_285


title: hLung_UBC_284


title: hLung_UBC_288


title: hLung_UBC_283


title: hLung_UBC_287


title: hLung_UBC_281


title: hLung_UBC_282


title: hLung_UBC_276


title: hLung_UBC_274


title: hLung_UBC_279


title: hLung_UBC_270


title: hLung_UBC_278


title: hLung_UBC_271


title: hLung_UBC_273


title: hLung_UBC_280


title: hLung_UBC_275


title: hLung_UBC_272


title: hLung_UBC_269


title: hLung_UBC_277


title: hLung_UBC_263


title: hLung_UBC_260


title: hLung_UBC_267


title: hLung_UBC_268


title: hLung_UBC_264


title: hLung_UBC_255


title: hLung_UBC_266


title: hLung_UBC_265


title: hLung_UBC_257


title: hLung_UBC_261


title: hLung_UBC_262


title: hLung_UBC_258


title: hLung_UBC_254


title: hLung_UBC_248


title: hLung_UBC_253


title: hLung_UBC_259


title: hLung_UBC_252


title: hLung_UBC_256


title: hLung_UBC_251


title: hLung_UBC_249


title: hLung_UBC_247


title: hLung_UBC_250


title: hLung_UBC_244


title: hLung_UBC_245


title: hLung_UBC_246


title: hLung_UBC_243


title: hLung_UBC_241


title: hLung_UBC_239


title: hLung_UBC_232


title: hLung_UBC_237


title: hLung_UBC_240


title: hLung_UBC_236


title: hLung_UBC_230


title: hLung_UBC_242


title: hLung_UBC_229


title: hLung_UBC_234


title: hLung_UBC_238


title: hLung_UBC_231


title: hLung_UBC_228


title: hLung_UBC_225


title: hLung_UBC_224


title: hLung_UBC_233


title: hLung_UBC_235


title: hLung_UBC_223


title: hLung_UBC_227


title: hLung_UBC_226


title: hLung_UBC_218


title: hLung_UBC_220


title: hLung_UBC_212


title: hLung_UBC_219


title: hLung_UBC_217


title: hLung_UBC_202


title: hLung_UBC_209


title: hLung_UBC_205


title: hLung_UBC_221


title: hLung_UBC_215


title: hLung_UBC_222


title: hLung_UBC_210


title: hLung_UBC_207


title: hLung_UBC_208


title: hLung_UBC_211


title: hLung_UBC_213


title: hLung_UBC_203


title: hLung_UBC_196


title: hLung_UBC_199


title: hLung_UBC_216


title: hLung_UBC_204


title: hLung_UBC_206


title: hLung_UBC_200


title: hLung_UBC_193


title: hLung_UBC_214


title: hLung_UBC_198


title: hLung_UBC_197


title: hLung_UBC_201


title: hLung_UBC_194


title: hLung_UBC_192


title: hLung_UBC_195


title: hLung_UBC_178


title: hLung_UBC_185


title: hLung_UBC_176


title: hLung_UBC_183


title: hLung_UBC_188


title: hLung_UBC_179


title: hLung_UBC_182


title: hLung_UBC_186


title: hLung_UBC_177


title: hLung_UBC_172


title: hLung_UBC_173


title: hLung_UBC_175


title: hLung_UBC_174


title: hLung_UBC_180


title: hLung_UBC_181


title: hLung_UBC_190


title: hLung_UBC_184


title: hLung_UBC_191


title: hLung_UBC_187


title: hLung_UBC_171


title: hLung_UBC_164


title: hLung_UBC_170


title: hLung_UBC_189


title: hLung_UBC_168


title: hLung_UBC_167


title: hLung_UBC_169


title: hLung_UBC_163


title: hLung_UBC_161


title: hLung_UBC_147


title: hLung_UBC_154


title: hLung_UBC_160


title: hLung_UBC_166


title: hLung_UBC_162


title: hLung_UBC_165


title: hLung_UBC_153


title: hLung_UBC_140


title: hLung_UBC_145


title: hLung_UBC_144


title: hLung_UBC_158


title: hLung_UBC_159


title: hLung_UBC_151


title: hLung_UBC_155


title: hLung_UBC_150


title: hLung_UBC_146


title: hLung_UBC_143


title: hLung_UBC_148


title: hLung_UBC_141


title: hLung_UBC_156


title: hLung_UBC_138


title: hLung_UBC_152


title: hLung_UBC_142


title: hLung_UBC_149


title: hLung_UBC_139


title: hLung_UBC_135


title: hLung_UBC_137


title: hLung_UBC_129


title: hLung_UBC_123


title: hLung_UBC_133


title: hLung_UBC_126


title: hLung_UBC_121


title: hLung_UBC_136


title: hLung_UBC_124


title: hLung_UBC_128


title: hLung_UBC_130


title: hLung_UBC_134


title: hLung_UBC_120


title: hLung_UBC_157


title: hLung_UBC_109


title: hLung_UBC_111


title: hLung_UBC_112


title: hLung_UBC_114


title: hLung_UBC_116


title: hLung_UBC_118


title: hLung_UBC_122


title: hLung_UBC_113


title: hLung_UBC_119


title: hLung_UBC_115


title: hLung_UBC_125


title: hLung_UBC_132


title: hLung_UBC_108


title: hLung_UBC_105


title: hLung_UBC_102


title: hLung_UBC_099


title: hLung_UBC_106


title: hLung_UBC_098


title: hLung_UBC_101


title: hLung_UBC_094


title: hLung_UBC_096


title: hLung_UBC_100


title: hLung_UBC_103


title: hLung_UBC_092


title: hLung_UBC_095


title: hLung_UBC_104


title: hLung_UBC_093


title: hLung_UBC_087


title: hLung_UBC_089


title: hLung_UBC_110


title: hLung_UBC_085


title: hLung_UBC_084


title: hLung_UBC_091


title: hLung_UBC_086


title: hLung_UBC_127


title: hLung_UBC_082


title: hLung_UBC_097


title: hLung_UBC_088


title: hLung_UBC_090


title: hLung_UBC_081


title: hLung_UBC_079


title: hLung_UBC_080


title: hLung_UBC_075


title: hLung_UBC_083


title: hLung_UBC_077


title: hLung_UBC_074


title: hLung_UBC_073


title: hLung_UBC_076


title: hLung_UBC_068


title: hLung_UBC_066


title: hLung_UBC_064


title: hLung_UBC_131


title: hLung_UBC_072


title: hLung_UBC_070


title: hLung_UBC_071


title: hLung_UBC_062


title: hLung_UBC_065


title: hLung_UBC_078


title: hLung_UBC_069


title: hLung_UBC_061


title: hLung_UBC_063


title: hLung_UBC_067


title: hLung_UBC_059


title: hLung_UBC_060


title: hLung_UBC_058


title: hLung_UBC_056


title: hLung_UBC_055


title: hLung_UBC_050


title: hLung_UBC_044


title: hLung_UBC_057


title: hLung_UBC_039


title: hLung_UBC_043


title: hLung_UBC_052


title: hLung_UBC_053


title: hLung_UBC_047


title: hLung_UBC_045


title: hLung_UBC_048


title: hLung_UBC_051


title: hLung_UBC_036


title: hLung_UBC_034


title: hLung_UBC_054


title: hLung_UBC_037


title: hLung_UBC_117


title: hLung_UBC_046


title: hLung_UBC_049


title: hLung_UBC_038


title: hLung_UBC_035


title: hLung_UBC_042


title: hLung_UBC_041


title: hLung_UBC_032


title: hLung_UBC_033


title: hLung_UBC_031


title: hLung_UBC_030


title: hLung_UBC_040


title: hLung_UBC_024


title: hLung_UBC_021


title: hLung_UBC_029


title: hLung_UBC_017


title: hLung_UBC_020


title: hLung_UBC_028


title: hLung_UBC_018


title: hLung_UBC_010


title: hLung_UBC_008


title: hLung_UBC_026


title: hLung_UBC_027


title: hLung_UBC_015


title: hLung_UBC_022


title: hLung_UBC_025


title: hLung_UBC_011


title: hLung_UBC_016


title: hLung_UBC_004


title: hLung_UBC_013


title: hLung_UBC_107


title: hLung_UBC_007


title: hLung_UBC_023


title: hLung_UBC_002


title: hLung_UBC_003


title: hLung_UBC_006


title: hLung_UBC_005


title: hLung_UBC_019


title: hLung_UBC_012


title: hLung_Laval_495

description: Lung specimen was obtained from a patient undergoing lung cancer surgery.


title: hLung_Laval_499


title: hLung_Laval_496


title: hLung_Laval_489


title: hLung_Laval_497


title: hLung_Laval_494


title: hLung_UBC_001


title: hLung_Laval_493


title: hLung_Laval_488


title: hLung_Laval_485


title: hLung_Laval_490


title: hLung_Laval_498


title: hLung_Laval_487


title: hLung_Laval_478


title: hLung_Laval_475


title: hLung_Laval_482


title: hLung_Laval_486


title: hLung_Laval_476


title: hLung_Laval_477


title: hLung_Laval_491


title: hLung_Laval_481


title: hLung_Laval_483


title: hLung_Laval_484


title: hLung_Laval_474


title: hLung_Laval_470


title: hLung_Laval_473


title: hLung_Laval_472


title: hLung_Laval_471


title: hLung_Laval_454


title: hLung_Laval_464


title: hLung_Laval_469


title: hLung_Laval_467


title: hLung_Laval_457


title: hLung_Laval_466


title: hLung_Laval_461


title: hLung_Laval_468


title: hLung_Laval_455


title: hLung_Laval_460


title: hLung_Laval_452


title: hLung_Laval_450


title: hLung_Laval_451


title: hLung_Laval_459


title: hLung_UBC_009


title: hLung_Laval_492


title: hLung_Laval_449


title: hLung_Laval_456


title: hLung_Laval_462


title: hLung_Laval_465


title: hLung_Laval_458


title: hLung_Laval_463


title: hLung_Laval_479


title: hLung_UBC_014


title: hLung_Laval_480


title: hLung_Laval_453


title: hLung_Laval_447


title: hLung_Laval_442


title: hLung_Laval_435


title: hLung_Laval_444


title: hLung_Laval_436


title: hLung_Laval_448


title: hLung_Laval_440


title: hLung_Laval_439


title: hLung_Laval_431


title: hLung_Laval_437


title: hLung_Laval_429


title: hLung_Laval_445


title: hLung_Laval_441


title: hLung_Laval_446


title: hLung_Laval_438


title: hLung_Laval_433


title: hLung_Laval_443


title: hLung_Laval_427


title: hLung_Laval_428


title: hLung_Laval_426


title: hLung_Laval_422


title: hLung_Laval_432


title: hLung_Laval_434


title: hLung_Laval_423


title: hLung_Laval_420


title: hLung_Laval_421


title: hLung_Laval_424


title: hLung_Laval_419


title: hLung_Laval_425


title: hLung_Laval_430


title: hLung_Laval_416


title: hLung_Laval_417


title: hLung_Laval_410


title: hLung_Laval_414


title: hLung_Laval_405


title: hLung_Laval_408


title: hLung_Laval_418


title: hLung_Laval_415


title: hLung_Laval_407


title: hLung_Laval_411


title: hLung_Laval_404


title: hLung_Laval_413


title: hLung_Laval_412


title: hLung_Laval_400


title: hLung_Laval_409


title: hLung_Laval_397


title: hLung_Laval_406


title: hLung_Laval_399


title: hLung_Laval_395


title: hLung_Laval_402


title: hLung_Laval_401


title: hLung_Laval_393


title: hLung_Laval_403


title: hLung_Laval_390


title: hLung_Laval_398


title: hLung_Laval_394


title: hLung_Laval_396


title: hLung_Laval_392


title: hLung_Laval_386


title: hLung_Laval_387


title: hLung_Laval_388


title: hLung_Laval_385


title: hLung_Laval_371


title: hLung_Laval_384


title: hLung_Laval_372


title: hLung_Laval_382


title: hLung_Laval_376


title: hLung_Laval_380


title: hLung_Laval_379


title: hLung_Laval_368


title: hLung_Laval_374


title: hLung_Laval_369


title: hLung_Laval_373


title: hLung_Laval_383


title: hLung_Laval_370


title: hLung_Laval_381


title: hLung_Laval_366


title: hLung_Laval_363


title: hLung_Laval_377


title: hLung_Laval_367


title: hLung_Laval_365


title: hLung_Laval_389


title: hLung_Laval_364


title: hLung_Laval_359


title: hLung_Laval_361


title: hLung_Laval_360


title: hLung_Laval_358


title: hLung_Laval_375


title: hLung_Laval_353


title: hLung_Laval_348


title: hLung_Laval_351


title: hLung_Laval_352


title: hLung_Laval_349


title: hLung_Laval_346


title: hLung_Laval_356


title: hLung_Laval_355


title: hLung_Laval_345


title: hLung_Laval_347


title: hLung_Laval_354


title: hLung_Laval_340


title: hLung_Laval_338


title: hLung_Laval_350


title: hLung_Laval_339


title: hLung_Laval_343


title: hLung_Laval_342


title: hLung_Laval_357


title: hLung_Laval_362


title: hLung_Laval_336


title: hLung_Laval_344


title: hLung_Laval_341


title: hLung_Laval_332


title: hLung_Laval_326


title: hLung_Laval_333


title: hLung_Laval_330


title: hLung_Laval_391


title: hLung_Laval_328


title: hLung_Laval_327


title: hLung_Laval_320


title: hLung_Laval_325


title: hLung_Laval_335


title: hLung_Laval_318


title: hLung_Laval_315


title: hLung_Laval_312


title: hLung_Laval_322


title: hLung_Laval_331


title: hLung_Laval_316


title: hLung_Laval_317


title: hLung_Laval_321


title: hLung_Laval_313


title: hLung_Laval_323


title: hLung_Laval_311


title: hLung_Laval_319


title: hLung_Laval_324


title: hLung_Laval_378


title: hLung_Laval_334


title: hLung_Laval_307


title: hLung_Laval_306


title: hLung_Laval_299


title: hLung_Laval_309


title: hLung_Laval_308


title: hLung_Laval_329


title: hLung_Laval_296


title: hLung_Laval_294


title: hLung_Laval_289


title: hLung_Laval_286


title: hLung_Laval_310


title: hLung_Laval_301


title: hLung_Laval_295


title: hLung_Laval_298


title: hLung_Laval_305


title: hLung_Laval_304


title: hLung_Laval_314


title: hLung_Laval_288


title: hLung_Laval_293