title: Primary patient sample MMRC0445_1

middle: Anthony

last: Chapman

address: 7 Cambridge Center

institute: Broad Institute

description:
Primary patient sample
Untreated cells

hyb_protocol: Labeled DNA was hybridized to Agilent Human Genome 244A CGH Microarrays and arrays were washed as recommended by the manufacturer

scan_protocol: Microarrays were scanned with a Agilent GA2565BA or GA2505C scanner at 5um resolution and 16-bit color depth

data_processing: Data was extracted from the aquired TIFF files using Agilent Feature Extraction v10.5.1.1 using the CGH_105_Dec08 extraction protocol. Data were subsequently corrected for batch-to-batch variation and for wave artifact.

source_name: CD138+ plasma cells

label_protocol: 1.2 ug of DNA was digested with DNase I for 12 minutes.  The digested DNA was labeled using the BioPrime Array CGH Genomic Labeling Module with Amersham cUTP-CY dyes from GE Healthcare (Reference=CY3 and Tumor=CY5).  The labeled DNA was purified using Vivaspin 500 columns

growth_protocol: After informed consent bone marrow aspirates were collected in sodium citrate tubes at MMRC member institutions and shipped by overnight courier to the MMRC Tissue Bank (Scottsdale, Arizona).  White blood cells were collected after red cell lysis using ACK reagent.  Plasma cells were selected using CD138 and the RoboSep (StemCell Technologies) as per the manufacturers protocol.  The purified plasma cells were lysed in 1 ml of TRIzol Reagent (Life Technologies).

extract_protocol: RNA was extracted from the TRIzol suspension using the manufacturers protocol and subsequently DNA was isolated from the remaining fraction as suggested by the manufacturer.  The isolated DNA was treated with RNaseA for 15 minutes and digested with proteinase K overnight.  Subsequently, the DNA was cleaned-up with two phenol-chloroform extractions and one final chlorophorm extraction before the DNA was precipitated with EtOH and NaOAc.  The purified DNA was quantified on a Nanodrop Spectrophotometer

treatment_protocol: No post collection treatment was performed.

tag: cell type

value: CD138+ plasma

tag: disease state

value: tumor

source_name: Promega XX Control DNA

value: reference


title: Primary patient sample MMRC0440_1

status: Public on Jan 26 2011

type: genomic

city: Cambridge

first: Michael

state: MA

country: USA

description:
Primary patient sample
Untreated cells

molecule: genomic DNA

organism: Homo sapiens


title: Primary patient sample MMRC0443_1

description:
Primary patient sample
Untreated cells


title: AnCHM1

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Androgenetic complete hydatidiform mole 1

hyb_protocol: Standard Illumina protocol for DNA methylation.

scan_protocol: Standard Illumina protocol for DNA methylation using the Bead Array Scanner.

data_processing: The data was generated using the BeadStudio 2.0 software provided by Illumina by following their analytical matrix. Average normalization was performed.

label: Cy3, Cy5

source_name: Androgenetic complete hydatidiform mole

growth_protocol: Placenta samples were stored in RNAlater prior to DNA extraction, WBC samples are collected in ACD tubes, AnCHMs and MCT DNA were extracted from snap frozen tissues.

extract_protocol: DNA extraction was performed using standard protocols.

treatment_protocol: All samples were bisulfite modified using kits from Qiagen and Sigma

tag: tissue

value: Androgenetic complete hydatidiform mole


title: Primary patient sample MMRC0438_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0419_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0441_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0422_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0439_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0418_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0417_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0434_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0415_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0414_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0432_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0444_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0420_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0442_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0431_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0436_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0430_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0421_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0435_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0413_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0412_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0433_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0409_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0402_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0410_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0404_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0403_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0399_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0406_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0411_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0400_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0401_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0395_2

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0394_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0386_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0389_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0382_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0390_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0392_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0381_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0379_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0408_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0391_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0396_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0387_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0360_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0362_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0375_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0393_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0384_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0359_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0365_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0372_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0364_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0356_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0355_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0358_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0340_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0357_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0353_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0351_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0352_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0334_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0343_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0324_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0329_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0331_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0330_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0319_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0307_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0303_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0308_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0309_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0312_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0305_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0318_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0304_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0287_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0302_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0291_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0298_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0290_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0332_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0285_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0286_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0283_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0299_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0272_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0281_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0284_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0282_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0277_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0258_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0264_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0280_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0259_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0250_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0261_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0256_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0268_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0260_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0249_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0247_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0252_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0246_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0244_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0245_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0243_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0239_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0227_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0248_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0228_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0240_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0226_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0224_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0238_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0206_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0207_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0198_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0208_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0195_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0233_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0196_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0220_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0197_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0204_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0200_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0191_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0189_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0192_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0203_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0187_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0194_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0201_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0185_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0183_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0186_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0184_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0182_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0180_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0173_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0181_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0179_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0174_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0161_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0175_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0164_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0167_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0171_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0172_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0170_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0165_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0159_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0168_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0177_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0163_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0154_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0158_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0155_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0141_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0144_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0150_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0160_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0147_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0149_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0145_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0156_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0138_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0153_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0139_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0134_1

description:
Primary patient sample
Untreated cells


title: P19, biological rep3 (MOE430B)

type: RNA

city: Setagaya

first: Yoji

last: Sato

state: Tokyo

address: 1-18-1 Kami-yoga

department: Cell. Gene Thpy. Prod.

country: Japan

institute: NIHS

description: Gene expression data from a mouse embryonal carcinoma cell strain

hyb_protocol: Labeled RNA was processed for microarray hybridization to MOE430B GeneChips (Affymetrix). An Affymetrix GeneChip Fluidics Station was used to perform streptavidin/phycoerythrin staining.

scan_protocol: The hybridization signals on microarray were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with GCOS software. Normalization was performed by global scaling with the arrays scaled to a trimmed average intensity of 500 after excluding the 2% of probe sets with the highest and the lowest values.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: P19 mouse embryonal carcinoma cells

label_protocol: Total RNA isolated from undifferentiated EC cell strains (P19 cells, P19CL6 cells, and 4 P19CL6 sublines) was converted to biotinylated cRNA using a Two-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: The mouse embryonal carcinoma cells were maintained in alpha-minimum essential medium (Invitrogen) supplemented with 10% fetal calf serum (FCS, Cell Culture Technologies), 2 mM L-glutamine (Sigma-Aldrich), 100 U/ml penicillin, and 100 µg/ml streptomycin (Invitrogen) at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from cells with an RNeasy Mini kit (QIAGEN)according to the manufacturer’s instruction.

tag: strain

tag: gender

value: male

value: embryo

tag: cell line

value: P19 mouse embryonal carcinoma cells


title: Primary patient sample MMRC0137_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0140_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0135_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0124_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0133_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0125_1

description:
Primary patient sample
Untreated cells


title: P19, biological rep1 (MOE430B)


title: P19, biological rep5 (MOE430B)


title: Primary patient sample MMRC0094_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0131_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0093_1

description:
Primary patient sample
Untreated cells


title: CL6G52, biological rep4 (MOE430B)

source_name: substrain of P19CL6 cells

value: CL6G52, substrain of P19CL6 cells


title: Primary patient sample MMRC0122_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0104_1

description:
Primary patient sample
Untreated cells


title: CL6G45, biological rep4 (MOE430B)

value: CL6G45, substrain of P19CL6 cells


title: CL6G52, biological rep1 (MOE430B)


title: CL6G45, biological rep3 (MOE430B)


title: P19, biological rep2 (MOE430B)


title: P19, biological rep4 (MOE430B)


title: CL6G45, biological rep5 (MOE430B)


title: Primary patient sample MMRC0095_1

description:
Primary patient sample
Untreated cells


title: CL6G52, biological rep2 (MOE430B)


title: Primary patient sample MMRC0128_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0089_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0092_1

description:
Primary patient sample
Untreated cells


title: CL6G52, biological rep3 (MOE430B)


title: Primary patient sample MMRC0090_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0087_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0091_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0083_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0080_1

description:
Primary patient sample
Untreated cells


title: CL6G36, biological rep3 (MOE430B)

value: CL6G36, substrain of P19CL6 cells


title: CL6G36, biological rep4 (MOE430B)


title: CL6G26, biological rep5 (MOE430B)

value: CL6G26, substrain of P19CL6 cells


title: CL6G36, biological rep1 (MOE430B)


title: CL6G45, biological rep2 (MOE430B)


title: CL6G36, biological rep5 (MOE430B)


title: CL6G52, biological rep5 (MOE430B)


title: CL6G45, biological rep1 (MOE430B)


title: CL6G36, biological rep2 (MOE430B)


title: CL6G26, biological rep4 (MOE430B)


title: Primary patient sample MMRC0073_1

description:
Primary patient sample
Untreated cells


title: CL6G26, biological rep2 (MOE430B)


title: Primary patient sample MMRC0079_1

description:
Primary patient sample
Untreated cells


title: CL6G26, biological rep1 (MOE430B)


title: Primary patient sample MMRC0072_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0081_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0078_1

description:
Primary patient sample
Untreated cells


title: CL6G26, biological rep3 (MOE430B)


title: Primary patient sample MMRC0071_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0067_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0069_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0064_1

description:
Primary patient sample
Untreated cells


title: P19CL6, biological rep5 (MOE430B)

value: P19CL6, substrain of P19 mouse embryonal carcinoma cells


title: P19CL6, biological rep4 (MOE430B)

source_name: substrain of P19 mouse embryonal carcinoma cells


title: Primary patient sample MMRC0063_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0065_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0062_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0070_1

description:
Primary patient sample
Untreated cells


title: P19CL6, biological rep2 (MOE430B)


title: P19CL6, biological rep3 (MOE430B)


title: P19, biological rep1 (MOE430A)

hyb_protocol: Labeled RNA was processed for microarray hybridization to MOE430A GeneChips (Affymetrix). An Affymetrix GeneChip Fluidics Station was used to perform streptavidin/phycoerythrin staining.


title: P19CL6, biological rep1 (MOE430B)


title: Primary patient sample MMRC0061_1

description:
Primary patient sample
Untreated cells


title: P19, biological rep5 (MOE430A)


title: Primary patient sample MMRC0059_1

description:
Primary patient sample
Untreated cells


title: P19, biological rep4 (MOE430A)


title: P19, biological rep2 (MOE430A)


title: P19, biological rep3 (MOE430A)


title: CL6G52, biological rep5 (MOE430A)


title: Primary patient sample MMRC0058_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0052_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0056_1

description:
Primary patient sample
Untreated cells


title: CL6G52, biological rep3 (MOE430A)


title: Primary patient sample MMRC0055_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0051_1

description:
Primary patient sample
Untreated cells


title: CL6G52, biological rep4 (MOE430A)


title: skeletal muscle side population cells from fetal human subject 9

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Standard Affymetrix hybridization protocol for the Affymetrix human HG-U133A GeneChip for 20 µg of cRNA.

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: CEL files were inputted into Bioconductor/R to derive Affymetrix Microarray Suite version 5.0 (MAS 5.0) normalized output.

label_protocol: Fragmented cRNA was biotin-labeled via standard Affymetrix labeling protocol.

growth_protocol: Human samples were thawed and plated overnight in DMEM 20% FBS. SP and MP cells were isolated by FACS purification the next day.

extract_protocol: Total RNA was extracted from sorted human fetal muscle side population (SP) and main population (MP) cells using the RNeasy kit (QIAGEN). Total RNA (100 ng) from 22 SP and 10 MP samples were subjected to two rounds of linear amplification using a MessageAmp kit (Ambion).

tag: tissue of origin

value: skeletal muscle

tag: gestational age of subject in weeks

value: 14 weeks

tag: percentage (%) of sp cells

tag: percentage (%) of mp cells

tag: microarray hybridization date

tag: microarray data quality

value: good


title: Primary patient sample MMRC0050_1

description:
Primary patient sample
Untreated cells


title: skeletal muscle side population cells from fetal human subject 11

value: 17 weeks


title: skeletal muscle side population cells from fetal human subject 10


title: skeletal muscle side population cells from fetal human subject 8

value: poor


title: CL6G52, biological rep2 (MOE430A)


title: skeletal muscle side population cells from fetal human subject 13

value: 15 weeks


title: skeletal muscle side population cells from fetal human subject 7


title: Primary patient sample MMRC0046_1

description:
Primary patient sample
Untreated cells

value: CD138+ plasma

value: tumor


title: skeletal muscle side population cells from fetal human subject 6


title: skeletal muscle side population cells from fetal human subject 4


title: Primary patient sample MMRC0048_1

description:
Primary patient sample
Untreated cells

value: reference


title: Primary patient sample MMRC0053_1

description:
Primary patient sample
Untreated cells


title: skeletal muscle side population cells from fetal human subject 5


title: Primary patient sample MMRC0043_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0045_1

description:
Primary patient sample
Untreated cells


title: CL6G45, biological rep5 (MOE430A)

value: male


title: skeletal muscle side population cells from fetal human subject 3


title: skeletal muscle main population cells from fetal human subject 15

value: 18 weeks


title: CL6G52, biological rep1 (MOE430A)

value: embryo


title: skeletal muscle side population cells from fetal human subject 1


title: skeletal muscle main population cells from fetal human subject 12


title: Primary patient sample MMRC0044_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0042_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0040_1

description:
Primary patient sample
Untreated cells


title: CL6G45, biological rep3 (MOE430A)


title: CL6G45, biological rep2 (MOE430A)


title: Primary patient sample MMRC0049_1

description:
Primary patient sample
Untreated cells


title: CL6G45, biological rep1 (MOE430A)


title: skeletal muscle main population cells from fetal human subject 7


title: Primary patient sample MMRC0039_1

description:
Primary patient sample
Untreated cells


title: skeletal muscle side population cells from fetal human subject 2


title: skeletal muscle main population cells from fetal human subject 14


title: skeletal muscle main population cells from fetal human subject 3


title: CL6G36, biological rep5 (MOE430A)


title: skeletal muscle main population cells from fetal human subject 13


title: skeletal muscle main population cells from fetal human subject 2


title: skeletal muscle main population cells from fetal human subject 9


title: CL6G36, biological rep4 (MOE430A)


title: skeletal muscle main population cells from fetal human subject 5


title: CL6G36, biological rep3 (MOE430A)


title: Primary patient sample MMRC0036_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0037_1

description:
Primary patient sample
Untreated cells


title: CL6G36, biological rep2 (MOE430A)


title: Primary patient sample MMRC0035_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0034_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0038_1

description:
Primary patient sample
Untreated cells


title: a9034 vs A9033 [Veg]

city: Uppsala

first: Nicklas

last: Samils

address: Norbyägen 18D

department: Evolutionary Biology

country: Sweden

institute: Uppsala University

description: dye-swap

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53¡C water bath). After hybridization, slides were washed sequentially

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora tetrasperma

source_name: Mycelia

label_protocol: 2 µg of mRNA were primed with .5 µg of Oligo-d(T) primer at 70¡C for 10min, then reversed transcribed at 42¡C for 2h in the presence of 40 U SuperScript II RTase (Invitrogen), and .8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Vegetative Nutrient Medium (Vogel's Medium)

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

treatment_protocol: Constant Darkness

tag: mating type

value: Mat-a FGSC#9034

tag: growth medium

value: Mat-A FGSC#9033


title: CL6G36, biological rep1 (MOE430A)

value: CL6G36, substrain of P19CL6 cells


title: a1271 vs a4200 [Veg]

description: dye-swap

value: Mat-a FGSC#1271

value: Vegetative Nutrient Medium (Vogel's Medium)

organism: Neurospora crassa

value: Mat-a FGSC#4200


title: CL6G26, biological rep5 (MOE430A)

value: CL6G26, substrain of P19CL6 cells


title: a9034 vs a4200 [Veg]

description: dye-swap


title: a4200 vs a9034 [Veg]

description: dye-swap


title: a4200 vs a1271 [Veg]

description: dye-swap


title: A9033 vs a9034 [Veg]

description: dye-swap


title: a1271 vs a9034 [Veg]

description: dye-swap


title: CL6G26, biological rep4 (MOE430A)


title: a4200 vs A2489 [Veg]

description: dye-swap

value: Mat-A FGSC#2489


title: Primary patient sample MMRC0033_1

description:
Primary patient sample
Untreated cells


title: a9034 vs a1271 [Veg]

description: dye-swap


title: skeletal muscle main population cells from fetal human subject 4

value: skeletal muscle

value: 17 weeks

value: good


title: A2489 vs A1270 [Veg]

description: dye-swap

value: Mat-A FGSC#1270


title: A2489 vs a4200 [Veg]

description: dye-swap


title: A1270 vs A2489 [Veg]

description: dye-swap


title: Primary patient sample MMRC0030_1

description:
Primary patient sample
Untreated cells

value: CD138+ plasma

value: tumor


title: Primary patient sample MMRC0032_1

description:
Primary patient sample
Untreated cells

value: reference


title: Primary patient sample MMRC0031_1

description:
Primary patient sample
Untreated cells


title: A9033 vs A2489 [Veg]

description: dye-swap


title: A9033 vs A1270 [Veg]

description: dye-swap


title: CL6G26, biological rep3 (MOE430A)

value: male


title: CL6G26, biological rep1 (MOE430A)

value: embryo


title: A1270 vs A9033 [Veg]

description: dye-swap


title: CL6G26, biological rep2 (MOE430A)


title: a1271 vs A1270 [Veg]

description: dye-swap


title: Primary patient sample MMRC0028_1

description:
Primary patient sample
Untreated cells


title: A1270 va a1271 [Veg]

description: dye-swap


title: a9034 vs A9033 [SC]

description: dye-swap

growth_protocol: Synthetic Crossing Medium

value: Mat-a FGSC#9034

value: SC Medium


title: a1271 vs a9034 [SC]

description: dye-swap


title: P19CL6, biological rep4 (MOE430A)

value: P19CL6, substrain of P19 mouse embryonal carcinoma cells


title: P19CL6, biological rep5 (MOE430A)


title: A9033 vs a9034 [SC]

description: dye-swap

value: Mat-A FGSC#9033


title: a9034 vs a1271 [SC]

description: dye-swap

value: Mat-a FGSC#1271


title: a4200 vs a1271 [SC]

description: dye-swap

value: Mat-a FGSC#4200


title: A2489 vs A9033 [Veg]

description: dye-swap

value: Vegetative Nutrient Medium (Vogel's Medium)


title: Primary patient sample MMRC0029_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0027_1

description:
Primary patient sample
Untreated cells


title: P19CL6, biological rep3 (MOE430A)


title: a1271 vs a4200 [SC]

description: dye-swap


title: a4200 vs a9034 [SC]

description: dye-swap


title: P19CL6, biological rep2 (MOE430A)


title: a9034 vs a4200 [SC]

description: dye-swap


title: Primary patient sample MMRC0024_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0021_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0019_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0018_1

description:
Primary patient sample
Untreated cells


title: A2489 vs A1270 [SC]

description: dye-swap

value: Mat-A FGSC#2489


title: P19CL6, biological rep1 (MOE430A)


title: A1270 vs A2489 [SC]

description: dye-swap


title: a4200 vs A2489 [SC]

description: dye-swap


title: A2489 vs a4200 [SC]

description: dye-swap


title: A9033 vs A2489 [SC]

description: dye-swap


title: A2489 vs A9033 [SC]

description: dye-swap


title: CL6G45, biological rep4 (MOE430A)

value: CL6G45, substrain of P19CL6 cells


title: a1271 vs A1270 [SC]

description: dye-swap


title: PH1_tebuconazole treated_rep2

city: Halle/Saale

first: Rayko

last: Becher

address: Betty-Heimann-Str. 3

department: Department of Phytopathology and Plant Protection

country: Germany

institute: Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences

description: Gene expression after 12 h - treatment with 5mg/l tebuconazole

hyb_protocol: For hybridizations, 600 ng of Cy3-labelled cRNA was used. Hybridization was set up in an Agilent Microarray Hybridization Chamber (G2534A) and incubated in an Agilent Hybridization Oven (G2545A) at 65°C and 10 rpm for 17 h. Thereafter, suggested washing steps were performed.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15K array slides (scan resolution: 5 µm resolution).

data_processing: The microarray scan data were analyzed by Agilent's Feature Extraction software_v10.5 obtaining background subtracted and spatially detrended signal intensities. These 'gProcessedSignal' data were converted to gene signals by a median polish algorithm as implemented in the RMA algorithm. Gene signals were normalized between experiments by quantile normalization.

organism: Fusarium graminearum

source_name: PH1_complete medium_5 mg/l tebuconazole_12h

label_protocol: For sample preparation and array processing the Agilent protocol “One-color microarray-based gene expression analysis (Quick Amp Labelling)” was used (http://www.chem.agilent.com).Briefly, the recommended volume of control RNAs (Agilent One-Color RNA Spike-In Kit) was added to 200 ng of total RNA. Thereafter, cyanine 3´- labelled cRNA was produced, using the Agilent Quick Amp Kit (one-color) according to the manufacturer’s protocol. Labelled cRNA was purified with the RNeasy mini kit (Qiagen). Yield and Cy3 incorporation rates were analyzed using a NanoDrop ND-1000 UV-VIS spectrophotometer. In addition, size distribution of cRNAs was assessed by a BioAnalyzer 2100.

growth_protocol: 106 conidia were inoculated into 300 ml flasks each containing 100 ml complete medium (Leslie & Summerell, The Fusarium Laboratory Manual, Blackwell Publishing) and cultivated at 23°C with shaking at 150 rpm.

extract_protocol: Total RNA was isolated from mycelia grown in vitro with the Qiagen RNeasy Plant Mini Kit following the manufacturer’s protocol. The optional on-column DNase digestion step was performed using RNase-free DNase (Qiagen).

treatment_protocol: After 24 h, CM medium of the treatment cultures was adjusted to 5 mg/l tebuconazole and incubation of all cultures continued for further 12 h.

value: PH1 (syn. NRRL31084)


title: A1270 vs A9033 [SC]

description: dye-swap


title: PH1_untreated_rep3

description: Gene expression in untreated control culture

source_name: PH1_complete medium_non-treated control


title: A9033 vs A1270 [SC]

description: dye-swap


title: PH1_untreated_rep2


title: A1270 va a1271 [SC]

description: dye-swap


title: PH1_tebuconazole treated_rep3


title: PH1_tebuconazole treated_rep1


title: Primary patient sample MMRC0020_1

description:
Primary patient sample
Untreated cells


title: PH1_untreated_rep1


title: Primary patient sample MMRC0014_1

description:
Primary patient sample
Untreated cells


title: A small RNA controls expression of the chitinase ChiA  in Listeria monocytogenes

city: Ithaca

first: Teresa

middle: M

last: Bergholz

state: NY

address: 405 Stocking Hall

department: Food Science

institute: Cornell University

hyb_protocol: Spotted microarray slides were first incubated for 1 h in a 1% bovine serum albumin-5X SSC-0.1% sodium dodecyl sulfate solution pre-warmed to 42ºC. Subsequently, slides were washed twice in 0.1X SSC and twice in filtered water and then dried. The combined cDNA targets were reconstituted in 55 µl hybridization buffer and denatured at 95ºC for 5 minutes. Targets were applied to microarray slides and overlaid with mSeries LifterSlips (Erie Scientific) followed by overnight hybridization at 42ºC. Slides were then washed 5 minutes in 42ºC pre-warmed 2X SSC plus 0.1% SDS, 5 minutes in 2X SCC, and 2.5 min in 0.2X SSC.

scan_protocol: After a final wash in filtered water, slides were dried and scanned with a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The median fluorescence intensity data for all probes on the array were analyzed using LIMMA (linear models for microarray analysis). We first normalized the data on each array using print-tip Lowess, followed by log2 conversion of the normalized data. A correlation was determined for the signal from duplicate spots of each probe. Significant differences were determined by calculating a moderated t-statistic which is similar to an ordinary t-statistic except that the standard errors have been shrunk towards a common value using a Bayesian model. P-values were calculated for each gene based on the moderated t-statistics and adjusted with the Benjamini-Hochberg false discovery rate correction for multiple tests. Differences in transcripts levels were considered meaningful only when adjusted P < 0.05 and fold change > 1.5.

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659585/suppl/GSM659585_slide 33_630_500_062708 - Early stationary phase Cy3-EGD.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659585/suppl/GSM659585_slide 34_610_480_062708 - Early stationary phase Cy3-EGD.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659585/suppl/GSM659585_slide 35_600_520_062708 - Early stationary phase Cy5-EGD.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659585/suppl/GSM659585_slide 36_600_520_062708 - Early stationary phase Cy5-EGD.gpr.gz

label: Cy3 or Cy5

organism: Listeria monocytogenes

source_name: Listeria monocytogenes EGD

label_protocol: cDNA from each strain was labeled twice with Cy3 and twice with Cy5 to minimize any bias. cDNA synthesis and labeling of total RNA were performed using the SuperScript Plus indirect cDNA labeling system for DNA microarrays (Invitrogen). 10 µg total RNA was mixed with 5 µg random hexamers and incubated for 10 minutes at 70ºC, with a subsequent chill on ice for at least 5 minutes. Superscript III RT, amino-modified deoxynucleoside triphophates, dithiothreitol, RNaseOUT, and buffer was then added and the reaction mix incubated at 42ºC for 17 hours. RNA was hydrolyzed by the addition of 10 µl 1M NaOH and 10 µl 0.5 M EDTA, followed by incubation at 65ºC for 15 minutes. The mixture was neutralized with 10 µl 1M HCl and cDNA purified using the Qiagen PCR purification kit. Labeling reactions with Alexa Fluor 555 or Alexa Fluor 647 fluorescent dyes were performed for 2 h at room temperature. Differentially labeled cDNAs from the two strains to be cohybridized were combined, dried in a Savant SVC100 Speed-Vac (Farmingdale) and stored at -80ºC until hybridization.

growth_protocol: Strains were grown to early stationary phase in BHI broth at 37C, defined as OD 1 + 3h.

extract_protocol: RNA was purified using the RNeasy mini or midi kit from Qiagen as described by the manufacturer. Cells grown to early-stationary phase were first treated with RNA protect as instructed by the manufacturer (Qiagen) and subsequently disrupted by sonication on ice (3 X 30 seconds, each round followed by a 30 second pause). RNA was then extracted using the Qiagen RNeasy kit. The integrity of the RNA was confirmed by agarose gel electrophoresis and the concentration and purity was determined on a NanoDrop 2000.

value: EGD

tag: genotype/variation

value: wild type

source_name: Listeria monocytogenes EGD delta LhrA

value: delta LhrA


title: Primary patient sample MMRC0013_1

description:
Primary patient sample
Untreated cells

value: CD138+ plasma

value: tumor


title: Primary patient sample MMRC0010_1

description:
Primary patient sample
Untreated cells

value: reference


title: Primary patient sample MMRC0016_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0009_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0011_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0012_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0015_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0002_1

description:
Primary patient sample
Untreated cells


title: Primary patient sample MMRC0001_1

description:
Primary patient sample
Untreated cells


title: EryP_E11.5_rep3

status: Public on Jan 25 2011

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: replicate 3

hyb_protocol: Hybridization was performed at the Yale Microarray Facility. After quality control assessment, 1.5 µg of cRNA was mixed with the hybridization controls and hybridized to the array. The array was hybridized for 16 hours in a hybridization oven with a rocking platform at 58°C. The array chip then was subjected to a series of washes before it was stained with streptavidin-Cy3. After the staining, it went through a final wash and drying.

scan_protocol: The standard Illumina scanning protocol was performed using an iScan system at the Yale Microarray Facility.

data_processing: Data were background corrected, variance stabilizing transformed and quantile normalized using the lumi software package (version 1.10.1) for the R programming environment (version 2.9.0). Amplified and unamplified samples were background corrected, VST transformed and quantile normalized separately.

source_name: primitive erythroid (EryP) cells

label_protocol: For one-cycle amplification, biotinylated cDNA was prepared with the Illumina TotalPrep RNA Amplification Kit.  Biotin-labeled cRNA was produced from the double stranded cDNA via an in vitro transcription (IVT) reaction overnight in the presence of biotinylated UTP.  For two cycle amplification, amplified and biotin-labeled using the TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre Biotechnologies, Madison, WI).  This technique uses Eberwine-type linear RNA amplification methodology (Van Gelder et al., 1990). Superscript III reverse transcriptase (Invitrogen, Carlsbad, California) was used for the first round of cDNA synthesis. Superscript II reverse transcriptase (Invitrogen, Carlsbad, California) was used for the second round of cDNA synthesis.

extract_protocol: Total RNA was extracted FACS-sorted GFP(+) cells from epsilon-globin::H2B-EGFP embryos at the indicated stages (E7.5 to E12.5).  Samples from E7.5-E9.5 were sorted from collagenase-digested whole embryos.  Samples from E10.5-E12.5 were sorted from embryonic blood collected by exsanguination.  Each replicate from E7.5-E10.5 was a pool from mutliple embryos.  Each replicate from E11.5 and E12.5 was prepared from individual embryos.  RNA was extracted using an RNeasy mini kit (Qiagen) according to the manufacturer's instructions.  Samples sorted from E7.5 and E8.5 embryos were collected directly into RLT buffer (Qiagen) and processed using an RNeasy micro kit (Qiagen).  All RNA samples were treated with RNase-free DNase I (Qiagen).  Quality control was performed using an Agilent Bioanalyser.

tag: developmental stage

tag: genotype

value: human epsilon globin::H2B-EGFP

tag: cell population

value: GFP(+) sorted

tag: amplification type

value: One-cycle

tag: array #

value: primitive erythroid (EryP) cells


title: EryP_E11.5_rep1

description: replicate 1

tag: cell type


title: EryP_E12.5_rep3

description: replicate 3


title: Primary patient sample MMRC0003_1

description:
Primary patient sample
Untreated cells

tag: disease state


title: Male_Parent_86828

city: Salt Lake City

first: Scott

last: Watkins

state: UT

department: Human Genetics

institute: University of Utah

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Array was washed using the Affymetrix fluidics stations and scanned on Affymetrix 3000-7G scanner.

data_processing:
Data was collected and processed using the Genotyping console software.  Genotypes were called with Birdseed v2.
primary data description (complete table provided as a supplementary file on the Series record): Chromosome 6 (126000054-140001863) copy number analysis results for 86828.  Sample called with a European reference file. ENPP1 position is 132,170,849-132,257,988 (hg18).  Datafields for the table are ProbeSet, Chromosome, Chromosomal Position, CNState, Log2Ratio, SmoothSignal, LOH, Allele Difference, dbSNP RSID

label_protocol: Standard Affymetrix 6.0 labeling protocol

extract_protocol: Standard salting out dna extraction protocol using PureGene reagents

value: lymphocytes

tag: sex

value: male

tag: disease status

value: unaffected

tag: inheritance

value: recessive


title: EryP_E12.5_rep2

description: replicate 2


title: EryP_E10.5_rep2

description: replicate 2


title: EryP_E9.5_rep3

description: replicate 3


title: EryP_E12.5_rep1

description: replicate 1


title: EryP_E11.5_rep2

description: replicate 2


title: EryP_E9.5_rep1

description: replicate 2


title: EryP_E8.5_rep2

description: replicate 2


title: EryP_E8.5_rep6

description: replicate 3


title: EryP_E10.5_rep3

description: replicate 3


title: EryP_E10.5_rep1

description: replicate 1


title: EryP_E8.5_rep4

description: replicate 1


title: EryP_E8.5A_rep2

description: replicate 2

value: Two-cycle


title: EryP_E9.5_rep2

description: replicate 2


title: EryP_E8.5_rep3

description: replicate 3


title: EryP_E8.5_rep1

description: replicate 1


title: EryP_E7.5A_rep3

description: replicate 3


title: EryP_E7.5A_rep1

description: replicate 1


title: EryP_E8.5_rep5

description: replicate 2


title: EryP_E8.5A_rep1

description: replicate 1


title: Primary patient sample MMRC0006_1

description:
Primary patient sample
Untreated cells


title: EryP_E7.5A_rep2

description: replicate 2


title: EryP_E8.5A_rep3

description: replicate 3


title: lin-35, mes-4(RNAi) replicant 4

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description: Biological replicate 4 of 4.  lin-35 and lin-35, mes-4RNAi first larval stage grown at 26 degrees.

hyb_protocol: Hybridization buffer (Genisphere 2X fromamide hyb buffer) and KREAblock were added, and samples were applied to microarrays enclosed in Die-Tech hyb chambers. After hybridization, slides were washed sequential with 2X SSC/0.2% SDS, 2X SSC and 0.2X SSC.

scan_protocol: Scanned on an Axon 4000A scanner.

data_processing: Signal from each channel was background subtracted and log2 of test sample signal over reference sample signal was obtained. log 2 ratios were print-tip LOWESS normalized, then global scale normalized using median absolut deviation. Bioconductor package marray was used for all processing.

organism: Caenorhabditis elegans

source_name: lin-35 mutant first larval stage at 26 degrees fed mes-4 RNAi

label_protocol: aRNA was labeled using Kreatech ULS-Cy 3/5 aRNA Labeling Kit (Open Biosystems) and then fragmented using  Ambion Fragmentation Reagents

growth_protocol: Fourth larval stage worms were shifted from 20 degrees to 26 degrees and grown until adult stage when embryos were harvested using hyperchloride treatment.  First larval stage worms were collected at 26 degrees after being hatched from these embryos in the absense of food.

extract_protocol: Total RNA was extracted using Trizol reagent, then amplified poly-A RNA was maid using the MessageAmp II aRNA Amplification Kit (Ambion)

treatment_protocol: Starting in the parental generation, worms were either fed bacteria containing empty vector(L4440) or mes-4 RNAi vector from Ahringer feeding library.

tag: strain

tag: Stage

tag: temperature

value: 26 degrees

tag: RNAi treatment

source_name: lin-35 mutant first larval stage at 26 degrees fed empty vector RNAi

value: empty vector


title: lin-35, mes-4(RNAi) replicant 3

description: Biological replicate 3 of 4.  lin-35 and lin-35, mes-4RNAi first larval stage grown at 26 degrees.


title: lin-35 mutant replicant 4

description: Biological replicate 4 of 4.  Mutant and wild type first larval stage grown at 26 degrees.

data_processing: Signal from each channel was background subtracted and log2 of test (mt) sample signal over reference (wt) sample signal was obtained. log 2 ratios were print-tip LOWESS normalized, then global scale normalized using median absolut deviation. Bioconductor package marray was used for all processing.

source_name: lin-35 mutant first larval stage at 26 degrees

source_name: wild type first larval stage at 26 degrees


title: lin-35 mutant replicant 2

description: Biological replicate 2 of 4.  Mutant and wild type first larval stage grown at 26 degrees.


title: lin-15B mutant replicant 4

data_processing: Signal from each channel was background subtracted and log2 of test sample (mt) signal over reference sample (wt) signal was obtained. log 2 ratios were print-tip LOWESS normalized, then global scale normalized using median absolut deviation. Bioconductor package marray was used for all processing.

source_name: lin-15B mutant first larval stage at 26 degrees


title: lin-35, mes-4(RNAi) replicant 2

description: Biological replicate 2 of 4.  lin-35 and lin-35, mes-4RNAi first larval stage grown at 26 degrees.


title: lin-35 mutant replicant 1

description: Biological replicate 1 of 4.  Mutant and wild type first larval stage grown at 26 degrees.


title: lin-35, mes-4(RNAi) replicant 1

description: Biological replicate 1 of 4.  lin-35 and lin-35, mes-4RNAi first larval stage grown at 26 degrees.


title: Plus.4hr

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

description: Gene expression of P53 +/+ thymocytes after 4 hours of 5 Gy treatment

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA targets is hybridized onto Agilent 4x44k whole genome arrays for 17 hours at 65º C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5µm resolution on Agilent scanner (Agilent)  G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Thymus, P53 +/+, 4hr, 5 Gy

label_protocol: 500 ng total RNA was amplified and labeled using Agilent QuickAmp labeling kit following the manufacturer protocol.

extract_protocol: Total RNA was isolated from purified mouse thymocytes using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by the RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Mouse thymocytes were isolated from the thymuses of mice that were untreated (0 hour) or following 2 or 4 hours of exposure to 5 Gray of gamma radiation (Cesium 137 Irradiator Shepherd model 81-14R).

tag: time point

tag: treatment

tag: tissue

value: thymus

tag: gender

value: 1 male 1 female (2 mouse/time point)

tag: age

value: 6 weeks


title: lin-15B mutant replicant 3

description: Biological replicate 3 of 4.  Mutant and wild type first larval stage grown at 26 degrees.


title: Minus.2hr

description: Gene expression of P53 -/- thymocytes after 2 hours of 5 Gy treatment

source_name: Thymus, P53 -/-, 2hr, 5 Gy

tag: genotype/variation


title: lin-35 mutant replicant 3


title: R.2hr.4

description: Gene expression of R72 in thymocytes after 2 hours of 5 Gy treatment

source_name: Thymus, R72, 2hr, 5 Gy


title: lin-15B mutant replicant 2


title: R.4hr.3

description: Gene expression of R72 in thymocytes after 4 hours of 5 Gy treatment

source_name: Thymus, R72, 4hr, 5 Gy


title: P.4hr.4

description: Gene expression of P72 in thymocytes after 4 hours of 5 Gy treatment

source_name: Thymus, P72, 4hr, 5 Gy


title: Plus.Unt.2

description: Gene expression of P53 +/+ in untreated thymocytes

source_name: Thymus, P53 +/+, 0hr, untrated


title: Minus.Unt.1

description: Gene expression of P53 -/- in untreated thymocytes

source_name: Thymus, P53 -/-, 0hr, untrated


title: R.4hr.4


title: Plus.2hr

description: Gene expression of P53 +/+ thymocytes after 2 hours of 5 Gy treatment

source_name: Thymus, P53 +/+, 2hr, 5 Gy


title: Minus.4hr

description: Gene expression of P53 -/- thymocytes after 4 hours of 5 Gy treatment

source_name: Thymus, P53 -/-, 4hr, 5 Gy


title: Minus.Unt.2


title: Plus.Unt.1


title: lin-15B mutant replicant 1


title: R.Unt.3

description: Gene expression of R72 in untreated thymocytes

source_name: Thymus, R72, 0hr, untreated


title: R.Unt.4


title: R.2hr.3


title: P.Unt.4

description: Gene expression of P72 in untreated thymocytes

source_name: Thymus, P72, 0hr, untreated


title: UROtsa_Cd_4

city: Grand Forks

first: Donald

last: Sens

state: ND

address: 1301 North Columbia Road

department: Pathology

institute: University of North Dakota

description: Gene expression data from cadmium-transformed UROtsa cells

hyb_protocol: 15 ug of fragmented labeled RNA was hybridized for 16 hr at 45 degree C to an Affymetrix U133 Plus 2.0 array.   Arrays were wased and stained using a Fluidics Station 450 according to the manufacturer's instructions.  Arrays were stained with phycoerythrein-conjugated streptavidin.

scan_protocol: The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner from Affymetrix.

data_processing: Images were analyzed using programs resident in GeneChip Operating System v1.4 (GCOS; Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0. The probes whose MAS5 Detection Call=Absent for all 9 samples were filtered out prior to statistical analysis, and thus were not included in the data table.

source_name: UROtsa cell, Cadmium-transformed

label_protocol: Total RNA was biotinylated using the Bioarray cDNA Synthesis kit (ENZO Diagnostics, Farmingdale,  NY)

growth_protocol: Cells grown in Dulbeco's modified Eagles medium supplemented with 5% FCS.  Split ratio was 1-4 weekly.

extract_protocol: Cells were harvested in normal medium without cadmium and the RNA purified using the Rneasy Kit from Qiagen.

treatment_protocol: 1 micromolar cadmium as cadmium chloride was added to the growth medium and the cells were passaged weekly until the cells attained the ability to form colonies in soft agar.

tag: cell line

value: UROtsa

tag: agent

value: Cadmium


title: UROtsa_Cd_6


title: UROtsa_Cd_7


title: P.4hr.3


title: P.2hr.4

description: Gene expression of P72 in thymocytes after 2 hours of 5 Gy treatment

source_name: Thymus, P72, 2hr, 5 Gy


title: P.2hr.3


title: R.4hr.2


title: P.Unt.3


title: UROtsa_Cd_3


title: R.Unt.2


title: P.4hr.1


title: P.4hr.2


title: Control_1

description: Gene expression data from UROtsa cells

source_name: UROtsa cell, control

value: Control


title: R.4hr.1


title: R.Unt.1


title: R.2hr.2


title: P.Unt.2


title: UROtsa_Cd_2


title: Control_3

description: Gene expression data from UROtsa cells


title: P.2hr.2


title: Control_2

description: Gene expression data from UROtsa cells


title: UROtsa_Cd_5


title: R.2hr.1


title: EJ-G4-12011 HCV/AFB1

city: Chapel Hill

first: Ivan

last: Rusyn

state: NC

address: 0031 MHRC

institute: University of North Carolina

description: Biological replicate 4 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.

hyb_protocol: Labeled cRNA was then processed, hybridized to Agilent Mouse Toxicology Arrays (catalog# 4121A, 22,575 features), washed and scanned according to the manufacturer’s protocol.

scan_protocol: The images were analyzed by determining the fluorescence intensity of all gene spots (features) on each array using the Agilent Scaner (model #G2505A).

data_processing:
Agilent Feature Extraction Software (Version 9.5) was used.
Data for analysis was extracted as follows: All genes/clones were extracted; replicate probe names were collapsed by averaging; Log(base2) of R/G Lowess Normalized ratio (Mean) was retrieved; spots were excluded if not found in either channel, saturated in either channel, a non-uniform outlier, background is a non-uniform outlier, not a positive and significant signal in either channel, is not above background in either channel; value is <10 for either channel Lowess Normalized Net (Mean) value; the gene has >70% of good data across all 20 samples. This filtering resulted in 11205 transcripts with data.

source_name: HCV-Tg mouse treated with AFB1, 12 months, liver

label_protocol: RNA amplifications and labeling were performed using Low RNA Input Linear Amplification kits (Agilent Technologies). For hybridization, 750 ng of total RNA from each mouse liver was amplified and labeled with a fluorescent dye Cy5. In parallel, 750 ng of a common mouse liver reference RNA was labeled with a fluorescent dye Cy3.

extract_protocol: Total RNA was isolated from frozen liver samples using the RNeasy (Qiagen, Valencia, CA) kit according to the manufacturer’s instructions. RNA concentration and quality were assessed using ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: Neonatal (7 days old) mice were administered a single dose of AFB1 (6 ug/g bw) or tricaprylin vehicle (15 ul/g bw) by intra-peritoneal injection. Male mice were maintained on the regular animal chow with free access to food and water for up to 12 months.

value: HCV-Tg (SL-139 strain, pAlbSVPA-HCV-S, containing the structural genes core, E1, E2, and p7, nucleotides 342-2771 of HCV genotype 1b, strain N, under the control of the murine albumin promoter/enhancer)

value: 12 months

value: liver

source_name: Total RNA from pooled mouse (C57BL/6J) liver samples, labeled with Cyanine-3 (green).

value: 3 months


title: EJ-G4-12030 HCV/AFB1

description: Biological replicate 6 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.


title: EJ-G4-12006 HCV/AFB1

description: Biological replicate 2 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.


title: P.Unt.1


title: EJ-G4-12007 HCV/AFB1

description: Biological replicate 3 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.


title: EJ-G4-12029 HCV/AFB1

description: Biological replicate 5 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.


title: Red region of liver tissues from 3 uPA/SCID mice

city: Tokyo

first: Fuyuki

last: Miya

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

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

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

data_processing: The data were normalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).

source_name: Pooled red region of liver tissues from 3 uPA/SCID mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

growth_protocol: uPA/SCID mice were transplanted with human hepatocytes derived from a Caucasian 9-month-old male infant and an African American 6-year-old girl. Around 60 days after transplantation the mouse livers were replated with human hepatocytes.

extract_protocol:
Total RNA was extracted from cells or liver tissues with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
The purified total RNAs of white and red regions from 3 uPA/SCID mouse livers were pooled and used for the analysis.

treatment_protocol:
A half of the chimeric mice were continuously infused with  2.5 mg/kg b.w./day h-growth hormone through an s.c.-implanted Alzet micro-osmotic pump for 2 weeks berore sactifice. h-Hepatocytes were isolated from h-GH-treated and untreated chimeric mice by collagenase perfusion method.  h-Hepatocyte-repopulated regions were dissected from liver tissue of h-GH-treated and untreated chimeric mice.
White and red regions were dissected from liver tissue of 3 uPA/SCID mice to investigate cross-reactivity of the mouse genes to the microarrays. White regions are originated from an uPA-derived diseased liver, and red regions are uPA gene-deleted recovered ares of the liver.

tag: donor of hepatocytes

tag: gender of mice

tag: age of mice (wk)

tag: days post-transplantation

tag: human albumin level in mouse blood (mg/ml)

value: Red region of liver tissues

tag: host genetic background

value: uPA/SCID


title: EJ-G3-12009 HCV/Control

description: Biological replicate 3 of 4. HCV-Tg/Control mouse, vehicle treated.

source_name: HCV-Tg mouse treated with vehicle, 12 months, liver

tag: strain


title: P.2hr.1


title: EJ-G2-12040 WT/AFB1

description: Biological replicate 6 of 6. WT/AFB1 mouse, AFB1 treated.

source_name: WT mouse treated with AFB1, 12 months, liver


title: EJ-G3-12010 HCV/Control

description: Biological replicate 4 of 4. HCV-Tg/Control mouse, vehicle treated.


title: EJ-G2-12014 WT/AFB1

description: Biological replicate 5 of 6. WT/AFB1 mouse, AFB1 treated.


title: EJ-G2-12007 WT/AFB1

description: Biological replicate 4 of 6. WT/AFB1 mouse, AFB1 treated.


title: White region of liver tissues from 3 uPA/SCID mice

source_name: Pooled white region of liver tissues from 3 uPA/SCID mice

value: male

value: White region of liver tissues


title: EJ-G4-12003 HCV/AFB1

description: Biological replicate 1 of 6. HCV-Tg/AFB1 mouse, AFB1 treated.


title: EJ-G3-12007 HCV/Control

description: Biological replicate 1 of 4. HCV-Tg/Control mouse, vehicle treated.


title: EJ-G2-12005 WT/AFB1

description: Biological replicate 2 of 6. WT/AFB1 mouse, AFB1 treated.


title: EJ-G2-12006 WT/AFB1

description: Biological replicate 3 of 6. WT/AFB1 mouse, AFB1 treated.


title: Hepatocytes from h-GH-treated chimeric mouse 3

value: Caucasian 9-month-old male infant

value: female

tag: cell type

value: Hepatocytes


title: EJ-G1-12008 WT/Control

description: Biological replicate 2 of 4. WT/Control mouse, vehicle treated.

source_name: WT mouse treated with vehicle, 12 months, liver


title: Hepatocytes from h-GH-treated chimeric mouse 2


title: EJ-G1-12007 WT/Control

description: Biological replicate 1 of 4. WT/Control mouse, vehicle treated.


title: EJ-G2-12002 WT/AFB1

description: Biological replicate 1 of 6. WT/AFB1 mouse, AFB1 treated.


title: EJ-G3-12008 HCV/Control

description: Biological replicate 2 of 4. HCV-Tg/Control mouse, vehicle treated.


title: Hepatocytes from chimeric mouse 2

source_name: Hepatocytes from untreated chimeric mouse 2


title: EJ-G1-12009 WT/Control

description: Biological replicate 3 of 4. WT/Control mouse, vehicle treated.


title: Hepatocytes from chimeric mouse 3

source_name: Hepatocytes from untreated chimeric mouse 3


title: E35_EpiSC

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: Gene expression of EpiSCs (E3.5)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E3.5 EpiSCs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were grown in Knockout DMEM +20% KSR

extract_protocol: Total RNA was prepared using TRIzol (Invitrogen) and samples were treated with DNase (turbo DNA-free, Applied Biosystems)

treatment_protocol: Treated samples were provided SB431542 (20uM) each day for 4 days

value: E3.5 EpiSCs

tag: developmental stage


title: Hepatocytes from h-GH-treated chimeric mouse 1


title: E55_EpiSC_SB

description: Gene expression of EpiSCs (E5.5) treated with 20um SB431542 for 4 days

value: E5.5 EpiSCs


title: EJ-G1-12010 WT/Control

description: Biological replicate 4 of 4. WT/Control mouse, vehicle treated.


title: E35_mES_SB

description: Gene expression of mouse ES cells treated with 20um SB431542 for 4 days

source_name: mouse ES cells, +SB431542

value: mouse ES cells


title: E35_EpiSC_SB

description: Gene expression of EpiSCs (E3.5) treated with 20um SB431542 for 4 days


title: P815 +IMATINIB

city: Baltimore

first: Cliff

last: Takemoto

state: MD

address: 720 Rutland Ave/Ross 1125

department: Pediatric Hematology

institute: The Johns Hopkins University

description: total RNA from P815 mast cell line  treated with imatinib

hyb_protocol: Arrays were prehybridized at 37C degrees for 1 hour in 3X SSC, 0.1% SDS, 0.2% BSA.   Cy3 labeled RNA was hybridized to arrays at 37C degrees overnight in 400 m Na2HPo4 (pH 7.0), 0.8% BSA, 5% SDS, and 12% formamide.  Arrays were washed once at room temperature in 2X SSC, 0.25% SDS, three times at room temperature in 1.6X SSC and twic in ice-cold 0.8X SSC.

scan_protocol: Hybridized arrays were scanned with a GenePix 4000B microarray scanner (Axon) and signal intensities were extracted using the Combimatrix Microarray Imager software.

data_processing: The background value was determined by calculating the median signal from the mismatch (MM) probes, and this value was subtracted from all perfect match (PM) probes.  Signals that were less than 1.5 times background were removed and the data sets were median centered pror to calculating fold change values.

label_protocol: 10 mcg of total RNA was labeled with Cy3 with RNA ligase.

growth_protocol: BMMC grown in SCF and IL3.  P815 grown in cytokine free media

extract_protocol: RNA extracted with trizol protocol

treatment_protocol: BMMC treated with 100 ng/cc of SCF for 24 hours; P815 treated with 10 nM imatinib for 24 hours

value: D814V KIT mutant cell line


title: E35_mES

description: Gene expresison of mouse ES cells

source_name: mouse ES cells


title: BMMC +SCF

description: total RNA from murine primary bone marrow derived mast cells treated with SCF

value: primary bone marrow derived mast cell


title: BMMC -SCF

description: total RNA from murine primary bone marrow derived mast cells starved of SCF


title: P815 -IMATINIB

description: total RNA from P815 mast cell line not treated with imatinib


title: E55_EpiSC

description: Gene expression of EpiSCs (E5.5)

source_name: E5.5 EpiSCs


title: foregut_NF44_RFX6MM_biologicalrep3

status: Public on Jan 24 2011

city: Montreal

first: Esther

middle: J

last: Pearl

state: Quebec

address: 110 Pine Avenue West

institute: Clinical Research Institute of Montreal

description: Gene expression data from MM injected embryo foreguts dissected at NF44

hyb_protocol: 10 μg of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Xenopus Genome array.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000 7G. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: The data were analyzed with Affymetrix expression control using PLIER algorithm and quantile normalization, no scaling was used during the primary analysis.

organism: Xenopus laevis

source_name: Xenopus laevis tadpoles injected with MM at 8-cell stage, dissected at NF44

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit. 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: Embryos were grown in 0.1XMMR

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

treatment_protocol: Tadpoles were anaesthetized in MS-222

value: foregut

value: MM


title: foregut_NF44_RFX6MO1_biologicalrep1

description: Gene expression data from MO1 injected embryo foreguts dissected at NF44

source_name: Xenopus laevis tadpoles injected with MO1 at 8-cell stage, dissected at NF44


title: Stage II 6294 Vs 16114

city: Thuwal

first: Eduardo

middle: Andres

last: Gorron Gomez

address: KAUST, Thuwal, Saudi Arabia

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: Comparison between gene expression in ovaries of apomictic and sexual accesions of the same species in the same stage of reproductive development

hyb_protocol: The sample pair (sample with Cy5 and sample with Cy3) was diluted to 25 μl, and 25 μl of 2X fresh hybridization buffer (formamide 50%, SSC 10X, SDS 2%), and the sample was incubated at 95ºC for 3 minutes to denature DNA, followed by incubation on ice during other 3 minutes. The sample and 1X hybridization buffer (diluted 2X buffer) was added to the hybridization chamber, followed by incubation at 42ºC for 16 hours. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using a VersArrayTM Chip Reader (BIO-RAD) scanner and VersArrayTM Analyzer Software (BIO-RAD),.

data_processing:
Local normalization by LOWESS was performed with the VersArrayTM Analyzer Software (BIO-RAD), using the spots of the non – subtractive libraries as a reference. The resulting data were regularized according to their variance in the TIGR MIDAS software version 2.19 (Liang and Quackenbush, 2004, www.tigr.org/software/tm4/). This regularization was done for all microarray data of one specific stage (I or II). In the saturated scan data, all the values superior to 60000 (saturated data) were replaced with their corresponding counterparts from the non – saturated scan file. In this way, the data of low expression genes were kept, and the data of high expression transcripts corresponds to the non – saturated scan.
Lowess normalized log2 (experiment/control) ratios were calculated. This information was processed with the SAM software version 3.0 (Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/). One analysis for all data of stage I was performed, as well as for stage II. The threshold value ∆ was adjusted in order to obtain a FDR value of 10%.

organism: Urochloa brizantha

source_name: Apomictic accesion, stage II

label_protocol: Labeling using Cy3 and Cy5 from total RNA was done as described by Schena (1999). Samples purified using Promega Wizard SV Gel and PCR Clean-Up System kit before hybridization

growth_protocol: Eight accessions of Brachiaria, 4 apomictic (CIAT codes 3025, 6012, 606, 6294) and 4 sexual (CIAT codes 16114, 16493, 16494, 44-2) were employed in this study. The reproductive mode of all of them was previously characterized. These accessions were kept in the CIAT station of Popayan, Colombia, as mature flowering plants

extract_protocol: Total RNA from each 200 pistils group was extracted using Picopure Kit (Picopure RNA Isolation Kit, Arcturus, Version D, Molecular Devices, Sunnyvale, CA). Extracted RNA was quantified using RiboGreen (Invitrogen, Carslbad, CA).

treatment_protocol: From each accession, 200 pistils of two reproductive stages were taken: Stage I: the aposporic initial cell, which gives place to the diploid embryo sac, is arising from ovary tissues; and stage II: the tetrad derived from megaspore mother cell by meiosis degenerates, and diploid embryo sac reaches the four cell stage. The pistil sizes corresponding to each of these stages were collected based on reproductive calendars reported by Dusi and Willemse (1999) and Araujo et al. (2000) for Brachiaria. Every group of 200 pistils was maintained in 1ml of RNAlater (Ambion Inc, Austin, Texas) at -20ºC until RNA extraction.

value: ovary

value: apomictic

tag: ciat code

value: II

source_name: Sexual accesion, stage II

value: Sexual


title: foregut_NF44_RFX6MO1_biologicalrep2

tag: treatment


title: foregut_NF44_RFX6MM_biologicalrep1

tag: tissue


title: Embryonic Drosophila cells, Kc167 cells, replicate 2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Hybridization of technical replicates of RNA from the same cell culture.
wildtype_2

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel at 10 um resolution using a suitable scan area.

data_processing: Images of the expression arrays were analyzed using Agilent Feature Extraction Software version 9.5.1.1. Mean spot intensities without background subtraction were used to normalize with subarray loess and calculate weighted average ratios per reporter by a NKI platform adjusted Rosetta error model (Weng L. et al., Bioinformatics (2006)), tuned by self-self hybridizations. These mean, normalized data without spike-in control oligos are represented in the Series supplementary data file 'GSE20312_Expression_norm.txt' together with associated A values. The matrix data table contains normalized  values before weighed averaging of duplicate REPORTER_IDs and replicate samples.

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells

label_protocol: 1 µg of RNA was labeled with 0.3 µl of ULS-Cy5 or 1 µl of ULS-Cy3 label using the ULS labeling system from Kreatech. Details can be found at the website of the NKI Central Microarray Facility (http://cmfdb.nki.nl/process/protocolView).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Contaminating gDNA was degraded using DNaseI (1 unit/µg RNA, 15 min. at room temperature).

treatment_protocol: Cells were stored in Trizol at -80°C.

value: embryo


title: Hepatocytes from chimeric mouse 1

source_name: Hepatocytes from untreated chimeric mouse 1

value: uPA/SCID


title: foregut_NF44_RFX6MM_biologicalrep2


title: foregut_NF40_RFX6MO1_biologicalrep3

description: Gene expression data from MO1 injected embryo foreguts dissected at NF40

source_name: Xenopus laevis tadpoles injected with MO1 at 8-cell stage, dissected at NF40


title: Embryonic Drosophila cells, Kc167 cells, replicate 3

description:
Hybridization of technical replicates of RNA from the same cell culture.
wildtype_3


title: foregut_NF44_RFX6MO1_biologicalrep3


title: Stage I 6012 Vs 16493

organism: Urochloa decumbens

source_name: Apomictic accesion, stage I

value: I

source_name: Sexual accesion, stage I


title: foregut_NF40_RFX6MO1_biologicalrep1


title: Stage I 6294 Vs 16114


title: Stage II 3025 Vs 4402

organism: Urochloa ruziziensis


title: foregut_NF40_RFX6MO1_biologicalrep2


title: foregut_NF40_RFX6MM_biologicalrep3

description: Gene expression data from MM injected embryo foreguts dissected at NF40

source_name: Xenopus laevis tadpoles injected with MM at 8-cell stage, dissected at NF40


title: Stage II 6012 Vs 16493


title: Stage I 606 Vs 16494


title: Embryonic Drosophila cells, Kc167 cells, replicate 1

description:
Hybridization of technical replicates of RNA from the same cell culture.
wildtype_1


title: foregut_NF40_RFX6MM_biologicalrep1


title: Stage I 3025 Vs 4402


title: foregut_NF30_RFX6MO1_biologicalrep3

description: Gene expression data from MO1 injected embryo foreguts dissected at NF30

source_name: Xenopus laevis tadpoles injected with MO1 at 8-cell stage, dissected at NF30


title: foregut_NF40_RFX6MM_biologicalrep2


title: foregut_NF30_RFX6MO1_biologicalrep2


title: foregut_NF30_RFX6MO1_biologicalrep1


title: foregut_NF30_RFX6MM_biologicalrep3

description: Gene expression data from MM injected embryo foreguts dissected at NF30

source_name: Xenopus laevis tadpoles injected with MM at 8-cell stage, dissected at NF30


title: foregut_NF30_RFX6MM_biologicalrep1


title: Liver_HS/T+1.0R_rep3

city: Pittsburgh

first: Joyeeta

last: Dutta-Moscato

address: 450 Technology Drive, Suite 300

department: Surgery

institute: University of Pittsburgh

description: Gene expression data from liver

hyb_protocol: High quality cRNA with yield of more than 10 ug was fragmented and hybridized to arrays for 18 hours. After hybridization, arrays were washed at 46oC for a hour, then stained with CyTM5-Streptavidin conjugate for 30 minutes at room temperature, followed by several non-stringent washing steps to remove unbound conjugate.

scan_protocol: After the final rinse, arrays were spun dry and scanned using ScanArray 5000, using 5 um scan resolution and at preset Cy5 parameters which were 85% Laser power and 55% PMT.

data_processing: Scanned images were processed in batches using Codelink Expression Analysis version 4.1

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma followed by 1 hour resuscitation

label_protocol: 1 ug of total RNA was used for reverse transcription to produce single stranded cDNA (oligo dT primers) followed by second strand synthesis to form double stranded cDNA.  Biotin-labeled cRNA target was produced by in vitro transcription using the cDNA template.

extract_protocol: RNA was isolated from whole liver using TRIzol reagent according to manufacturer's protocol

tag: gender

value: male

value: 8-12 weeks

value: liver


title: Liver_HS/T+4.5R_rep4

description: Gene expression data from liver

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma followed by 4.5 hour resuscitation

tag: age


title: Liver_HS/T+4.5R_rep2

description: Gene expression data from liver


title: Muscle-Beef 2

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: Muscle-Beef 2

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

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G

data_processing: Probe Logarithmic Intensity Error (PLIER)

source_name: Ldlr-/- beef

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

extract_protocol: RNA was isolated using the RNeasy mini kit or the RNeasy Lipid tissue mini kit (QIAGEN), according to the manufacturer's instructions.

tag: genotype

value: Ldlr-/-

value: Muscle

tag: diet

value: Beef-fed


title: Liver_HS/T+1.0R_rep2

description: Gene expression data from liver


title: Muscle-Beef 1

description: Muscle-Beef 1


title: Liver_HS/T_rep4

description: Gene expression data from liver

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma


title: Liver_HS/T+1.0R_rep4

description: Gene expression data from liver


title: Liver_HS/T+4.5R_rep3

description: Gene expression data from liver


title: Liver_HS/T+1.0R_rep1

description: Gene expression data from liver


title: Muscle-Herring 1

description: Muscle-Herring 1

source_name: Ldlr-/- herring

value: Herring-fed


title: Liver_HS/T_rep2

description: Gene expression data from liver


title: foregut_NF30_RFX6MM_biologicalrep2


title: Liver_HS/T_rep3

description: Gene expression data from liver


title: Muscle-Herring 3

description: Muscle-Herring 3


title: Liver_HS/T+4.5R_rep1

description: Gene expression data from liver


title: Liver-Beef 2

description: Liver-Beef 2

value: Liver


title: Muscle-Beef 3

description: Muscle-Beef 3


title: Liver-Beef 3

description: Liver-Beef 3


title: Liver_HS/T_rep1

description: Gene expression data from liver


title: Liver-Herring 3

description: Liver-Herring 3


title: Liver-Beef 1

description: Liver-Beef 1


title: Muscle-Herring 2

description: Muscle-Herring 2


title: Liver_MT_rep1

description: Gene expression data from liver

source_name: Liver, minor trauma


title: Liver_C_rep5

description: Gene expression data from liver

source_name: Liver, control


title: Liver_MT_rep2

description: Gene expression data from liver


title: Liver_MT_rep3

description: Gene expression data from liver


title: Liver-Herring 2

description: Liver-Herring 2


title: Liver_C_rep4

description: Gene expression data from liver


title: Adipose-Beef 1

description: Adipose-Beef 1

value: Adipose


title: Adipose-Beef 3

description: Adipose-Beef 3


title: dGPM1_3

hyb_protocol: 60 degree C for 16 hours

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

organism: Saccharomyces cerevisiae

source_name: cells from gpm1 mutant

label_protocol: 250 ng of the total RNA was used to synthesize cDNA using Affymetrix 3’ IVT Express kit and successively aRNA was synthesized (Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: Batch cultivation in ethanol and glycerol

extract_protocol: total RNA was extracted from cells through mechanical disruption with glass beads, digested with DNAse and purified using the RNeasy kit (Qiagen, Hilden, Germany)

treatment_protocol: The sample was centrifuged at 2°C and 5000 rpm for 5 min, the supernatant discarded and the biomass immediately frozen in liquid nitrogen

value: gpm1 mutant


title: Adipose-Beef 2

description: Adipose-Beef 2


title: Adipose-Herring 3

description: Adipose-Herring 3


title: Adipose-Herring 2

description: Adipose-Herring 2


title: dGPM1_2


title: Liver-Herring 1

description: Liver-Herring 1


title: Liver_C_rep3

description: Gene expression data from liver


title: Adipose-Herring 1

description: Adipose-Herring 1


title: WT3

source_name: cells from wild type yeast

value: wild type


title: WT1


title: WT2


title: dGPM1_1


title: Liver_C_rep2

description: Gene expression data from liver


title: Liver_HS/T+4.5R_rep4

description: Gene expression data from liver

data_processing: Scanned images were processed in batches using Affymetrix MAS 5.0 using default settings


title: Liver_C_rep1

description: Gene expression data from liver


title: Liver_HS/T+4.5R_rep3

description: Gene expression data from liver


title: Ptf1a E10.5 HT dp rep1

city: Copenhagen N

first: Anne

last: Grapin-Botton

address: Blegdamsvej3 B

department: DanStem

country: Denmark

institute: University of Copenhagen

description: 3 dp pooled for RNA and 2X linear amplification

hyb_protocol: 12.5 ug of cRNA was fragmented, checked for size on a Bioanalyzer RNA Nanochip. For each sample 11ug were hybridized for 16 hours at 45°C on the Affymetrix Mouse 430_2 . GeneChips were washed and stained in the Afmetrix Fluidics Station.

scan_protocol: Affymetrix's GeneChip Scanner 3000 7G System

data_processing: Probe set summarization was done with GCOS ( GeneChip Operating Software) to enable CEL files to create CHP files. We also used RACE based on RMA to analyze our CEL files for normalization, quality control and expression levels for genes.

label: Biotin

source_name: Ptf1a mutant mice MGI 1328312

label_protocol: Biotinylated cRNAs were prepared from the amplified cDNA using the IVT Affymetrix Kit and purified with Rneasy Mini Kit and quantified (Nanodrop) and the quality was checked on a Bioanalyer RNA Nanochip

growth_protocol: Adult Ptf1a heterozygote mice were timed mated and embyos were collected at E10.5;midday on the day of vaginal plug appearance was considered E0.5. DNA for genotyping was isolated from the unused embryonic tissue.

extract_protocol: 3 pools of 3 dosal E10.5 pancreatic buds (about 2000 to 3000 cells total) were pooled and total RNA was extracted with the Qiagen Rneasy Mini Kit and DNAsed on the column. After cDNA synthesis with a T7-oligo(dT) primer the material was twice amplified using the AmpTec,Express Art mRNA  Amplification Kit.

treatment_protocol: Dorsal pancreatic buds were dissected and the mesenchyme was removed by mechancal dissection. Individual buds were frozen in 5ul of RNA lysis buffer until the genotype was determined.

value: dorsal pancreas

tag: genotype/variation

value: heterozygote


title: Ptf1a E10.5 KO dp rep3

value: null mutant


title: Ptf1a E10.5 KO dp rep1


title: Mo growth minimal medium w/o nitrogen rep2

city: Newark

first: Nicole

last: Donofrio

state: DE

address: 531 S. College Ave

department: Plant and Soil Sciences

institute: University of Delaware

hyb_protocol: Dye swap hybridizations of the labeled cRNA samples were performed using 0.5 μg of each sample per hybridization, following Agilent protocol. Each treatment was hybridized with the control (C) sample for 17 h at 60 ºC in the dark. Washes were performed at 25 °C as follows: 10 min in wash #1 (6X SSC) two times; 5 min in wash #2 (0.1X SSC) two times. Slides were immediately dried using a nitrogen gun (Fisher, Pittsburgh, PA) and scanning was immediately followed.

scan_protocol: Scanned on an Agilent Technologies Scanner System (G2565AA) with SureScan technology. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data pre-processed by the Agilent Feature Extraction Software (version 10.5.1.1) was loaded in R and processed with the Bioconductor package Limma. Microarray spots with background intensity > 100 were not used. Applied background correction with the method “subtract”. Normalization within slides and between channels using the method “loess”. Normalization between slides using the method “Aquantile.

organism: Pyricularia oryzae

source_name: mycelia grown in minimal medium without the nitrogen source

label_protocol: The isolated RNA was labeled with Cy3 and Cy5 fluorescent dyes using Low RNA Input Fluorescent Linear Amp Kit (Agilent Technologies, Wilmington, DE) following manufacturer’s instructions.

growth_protocol: M. oryzae was grown on oatmeal-agar medium (50 g/L oatmeal, 15 g/L agar) for 10 days, under continuous light at 25ºC. Fungal plugs (5mm) were transferred to flasks containing liquid complete medium (LCM; 10g/L sucrose, 6 g/L casamin acids, 6 g/L yeast extract, 0.1% (v/v) trace elements) and incubated in a shaker at 27ºC and 150 rpm on dark for 4 days. The mycelia were collected using Wattmann filter paper and washed with distilled autoclaved water. The collected mycelia was divided in parts and used as a control (C) and as the start material for all in vitro experiments (heat shock, oxidative, and nutritional limitation).

extract_protocol: Total RNA was extracted using Trizol (Sigma Chemical, St. Louis, MO) following manufacturer's instructions.

treatment_protocol: M. oryzae mycelia grown in liquid complete medium (LCM) on a dark shaker (150 rpm) for four days (set as the control); 72 hours post-incoulated rice (cv. Maratelli) leaves; 72 hours post-incoulated barley (cv. ) leaves; fungal mycelia in LCM on a dark shaker (150 rpm) at 42°C during 45 min; fungal mycelia in LCM plus methyl viologen (Paraquat, 5mM) on a dark shaker (150 rpm) at 27ºC for 24 h; mycelia grown in minimal media (MM; 6g/L NaNO3, 0.5g/L KCl, 0.5g/L MgSO4, 1.5g/L KH2PO4, 0.1% (v/v) trace elements, 10g/L D-glucose), in a dark shaker (150 rpm) for 16 h at 27ºC; fungal mycelia under nitrogen starvation in MM without the nitrogen source (NaNO3; MM-N); fungal mycelia under carbon starvation in MM without the carbon source (D-glucose; MM-C).

tag: sample type

value: mycelia

source_name: mycelia grown in liquid complete medium 4 days


title: Mo growth minimal medium w/o carbon rep1

value: mycelia grown in liquid complete medium 4 days

source_name: mycelia grown in minimal medium without the carbon source


title: Ptf1a E10.5 KO dp rep2


title: Liver_HS/T+1.0R_rep4

description: Gene expression data from liver


title: Control_Patient_10

city: Dresden

first: Susanne

last: Mende

address: Fetscherstrasse 74

department: Neurology

institute: University Clinic Dresden

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched healthy control pool for MELAS patient 10

hyb_protocol: Following fragmentation, samples of each patients two age- and sex-specific controls were pooled in equal amounts (5 microgramm each). 10 microgramm of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Chip intensity data were retrieved in cel-files and further proceeded with RMA-Express (www.rmaexpress.bmbolstad.com). Results were exported in log2-scale. In order to reduce inter-experimental variation, all chips scanned on the same day were put into a group. The chips were fitted to a common reference profile by using the median polish procedure. For further analysis, the matched control-chips were subtracted from the individual patient-chips, resulting in age- and sex-corrected profiles.

source_name: Human blood from healthy individuals

label_protocol: Biotinylated cRNA was prepared from 3 microgramm of globin-depleted RNA using the GeneChip Expression 3`-Amplification reagents (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated with the PAXgene Blood RNA kit combined with the RNase-free DNase set (both from Qiagen, Hilden, Germany). RNA samples were concentrated with the RNeasy MinElute Cleanup Kit (Qiagen) prior to globin-mRNA depletion using the GLOBINClear Kit from Ambion (Austin, TX).

treatment_protocol: Whole blood samples (7.5ml) were directly collected into PAXgene Blood RNA Tubes of the PAXgene Blood RNA System (Qiagen, Hilden, Germany) to stabilize RNA for gene expression profiling. Blood samples were incubated at room temperature in their PAXgene Blood RNA tubes for at least 2h to ensure complete cell lysis.

value: whole blood


title: Mo growth minimal medium w/o carbon rep2

value: mycelia grown in minimal medium without the carbon source