title: Clone BT/HerR1.0C rep1

description: Gene expression data from Herceptin-resistant BT/HerR1.0C clone

source_name: Herceptin-resistant clone BT/HerR1.0C

value: Herceptin-resistant clone BT/HerR1.0C


title: Wildtype BT474 rep2

status: Public on Aug 21 2009

type: RNA

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description: Gene expression data from wildtype BT474 cells

hyb_protocol: The GeneChip arrays were hybridized with 20 ug of fragmented cRNA for 16 h at 45 °C and were then washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450 according to Affymetrix specification.

scan_protocol: Affymetrix GeneChip images were scanned at 11 um resolution using a high resolution GeneChip Scanner 3000 (Hewlett-Packard).

data_processing: Quality assessment and statistical analysis of gene expression data were performed using the R/Bioconductor packages.  To ensure the quality of the microarray assay, a set of quality assessment steps implemented in Bioconductor package “AffyExpress” were applied to the data.  Raw intensity measurements of all probe sets were converted into expression measurements using the “RMA” method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Wildtype BT474 cells

label_protocol: Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% penicillin/streptomycin in 5% CO2.

extract_protocol: Total RNA was purified using the RNeasy kit purchased from Qiagen (Valencia, CA).

tag: cell type

value: Wildtype BT474 cells


title: WT_Saline_rep1

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description: 11 arrays were hybridized and represent 3 lung samples for groups WT saline, WT OVA and KO OVA. There are 2 samples for the KO saline group.

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome custom arrays (platform acc# GPL7202). Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.

organism: Mus musculus

source_name: Lung tissues from littermate control mice challenged with saline

label_protocol: 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA  Input Linear Amplification Kit

extract_protocol: Total RNA was extracted using  Qiagen RNEasy columns. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer


title: WT_Saline_rep2


title: SNP500K_188_Nsp

status: Public on Aug 20 2009

type: genomic

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Newly diagnosed patients

hyb_protocol: Following fragmentation, 90 ug of genomic DNA were hybridized for 16 hr at 49C on either the GeneChip® Mapping NspI or StyI chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix GCOS, then dChip software (Cheng Li)

label: Biotin

molecule: genomic DNA

source_name: Bone marrow

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol from 90 ug PCR product (GeneChip® Mapping 500K Assay Manual, 2005, Affymetrix).

extract_protocol:
Mononuclear bone marrow cells were separated using gradient density centrifugation (lymphocyte separation medium, Eurobio, Les Ulis, France), and plasmacytosis was evaluated by morphology in these mononuclear cell suspensions. Plasma cells (PCs) were then positively selected using anti-CD138–coated microbeads (Miltenyi, Paris, France), because CD138 is expressed only on PCs (normal and malignant) within the bone marrow. Purity and viability of the positively selected cell suspension was assessed by morphology and was above 90% in all the cases.
DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA).
DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).

tag: Tumor

value: multiple myeloma. Tissue:bone marrow. Cells:purified CD138+ plasma cells.


title: WT_Saline_rep3


title: Wildtype BT474 rep1


title: SNP500K_186_Nsp

description: Newly diagnosed patients


title: SNP500K_192_Nsp

description: Newly diagnosed patients


title: SNP500K_191_Nsp

description: Newly diagnosed patients


title: SNP500K_185_Nsp

description: Newly diagnosed patients


title: SNP500K_189_Nsp

description: Newly diagnosed patients


title: SNP500K_184_Nsp

description: Newly diagnosed patients


title: SNP500K_187_Nsp

description: Newly diagnosed patients


title: SNP500K_190_Nsp

description: Newly diagnosed patients


title: SNP500K_182_Nsp

description: Newly diagnosed patients


title: SNP500K_181_Nsp

description: Newly diagnosed patients


title: SNP500K_179_Nsp

description: Newly diagnosed patients


title: SNP500K_180_Nsp

description: Newly diagnosed patients


title: SNP500K_176_Nsp

description: Newly diagnosed patients


title: SNP500K_175_Nsp

description: Newly diagnosed patients


title: AG04147

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: AG04147 fibroblast cell line

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: fibroblasts were cultured in DMEM supplemented with 10% fetal calf serum, L-glutamine, penicillin, and streptomycin

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

tag: age

tag: sex

value: M

tag: race

value: cau

value: Skin


title: Clone BT/HerR1.0C rep2


title: SNP500K_177_Nsp

description: Newly diagnosed patients


title: SNP500K_178_Nsp

description: Newly diagnosed patients


title: SNP500K_174_Nsp

description: Newly diagnosed patients


title: SNP500K_183_Nsp

description: Newly diagnosed patients


title: SNP500K_173_Nsp

description: Newly diagnosed patients


title: SNP500K_171_Nsp

description: Newly diagnosed patients


title: SNP500K_169_Nsp

description: Newly diagnosed patients


title: SNP500K_170_Nsp

description: Newly diagnosed patients


title: SNP500K_168_Nsp

description: Newly diagnosed patients


title: SNP500K_166_Nsp

description: Newly diagnosed patients


title: SNP500K_164_Nsp

description: Newly diagnosed patients


title: SNP500K_163_Nsp

description: Newly diagnosed patients


title: SNP500K_165_Nsp

description: Newly diagnosed patients


title: SNP500K_158_Nsp

description: Newly diagnosed patients


title: SNP500K_167_Nsp

description: Newly diagnosed patients


title: SNP500K_155_Nsp

description: Newly diagnosed patients


title: SNP500K_161_Nsp

description: Newly diagnosed patients


title: SNP500K_156_Nsp

description: Newly diagnosed patients


title: SNP500K_157_Nsp

description: Newly diagnosed patients


title: SNP500K_162_Nsp

description: Newly diagnosed patients


title: SNP500K_154_Nsp

description: Newly diagnosed patients


title: SNP500K_153_Nsp

description: Newly diagnosed patients


title: SNP500K_152_Nsp

description: Newly diagnosed patients


title: SNP500K_160_Nsp

description: Newly diagnosed patients


title: SNP500K_172_Nsp

description: Newly diagnosed patients


title: SNP500K_149_Nsp

description: Newly diagnosed patients


title: SNP500K_151_Nsp

description: Newly diagnosed patients


title: SNP500K_148_Nsp

description: Newly diagnosed patients


title: SNP500K_145_Nsp

description: Newly diagnosed patients


title: SNP500K_146_Nsp

description: Newly diagnosed patients


title: SNP500K_140_Nsp

description: Newly diagnosed patients


title: SNP500K_144_Nsp

description: Newly diagnosed patients


title: SNP500K_141_Nsp

description: Newly diagnosed patients


title: SNP500K_139_Nsp

description: Newly diagnosed patients


title: SNP500K_143_Nsp

description: Newly diagnosed patients


title: SNP500K_147_Nsp

description: Newly diagnosed patients


title: SNP500K_142_Nsp

description: Newly diagnosed patients


title: SNP500K_137_Nsp

description: Newly diagnosed patients


title: SNP500K_138_Nsp

description: Newly diagnosed patients


title: SNP500K_150_Nsp

description: Newly diagnosed patients


title: SNP500K_135_Nsp

description: Newly diagnosed patients


title: SNP500K_136_Nsp

description: Newly diagnosed patients


title: Clone BT/HerR1.0E rep1

description: Gene expression data from Herceptin-resistant BT/HerR1.0e clone

source_name: Herceptin-resistant clone BT/HerR1.0E

value: Herceptin-resistant clone BT/HerR1.0E


title: SNP500K_133_Nsp

description: Newly diagnosed patients


title: SNP500K_126_Nsp

description: Newly diagnosed patients


title: SNP500K_131_Nsp

description: Newly diagnosed patients


title: SNP500K_129_Nsp

description: Newly diagnosed patients


title: SNP500K_128_Nsp

description: Newly diagnosed patients


title: SNP500K_127_Nsp

description: Newly diagnosed patients


title: SNP500K_124_Nsp

description: Newly diagnosed patients


title: SNP500K_122_Nsp

description: Newly diagnosed patients


title: SNP500K_121_Nsp

description: Newly diagnosed patients


title: SNP500K_119_Nsp

description: Newly diagnosed patients


title: SNP500K_125_Nsp

description: Newly diagnosed patients


title: SNP500K_117_Nsp

description: Newly diagnosed patients


title: SNP500K_116_Nsp

description: Newly diagnosed patients


title: SNP500K_118_Nsp

description: Newly diagnosed patients


title: SNP500K_123_Nsp

description: Newly diagnosed patients


title: SNP500K_130_Nsp

description: Newly diagnosed patients


title: SNP500K_115_Nsp

description: Newly diagnosed patients


title: SNP500K_120_Nsp

description: Newly diagnosed patients


title: SNP500K_114_Nsp

description: Newly diagnosed patients


title: SNP500K_112_Nsp

description: Newly diagnosed patients


title: SNP500K_107_Nsp

description: Newly diagnosed patients


title: SNP500K_111_Nsp

description: Newly diagnosed patients


title: SNP500K_113_Nsp

description: Newly diagnosed patients


title: SNP500K_110_Nsp

description: Newly diagnosed patients


title: SNP500K_109_Nsp

description: Newly diagnosed patients


title: SNP500K_106_Nsp

description: Newly diagnosed patients


title: SNP500K_099_Nsp

description: Newly diagnosed patients


title: SNP500K_104_Nsp

description: Newly diagnosed patients


title: SNP500K_098_Nsp

description: Newly diagnosed patients


title: SNP500K_101_Nsp

description: Newly diagnosed patients


title: SNP500K_097_Nsp

description: Newly diagnosed patients


title: SNP500K_100_Nsp

description: Newly diagnosed patients


title: SNP500K_103_Nsp

description: Newly diagnosed patients


title: SNP500K_102_Nsp

description: Newly diagnosed patients


title: SNP500K_105_Nsp

description: Newly diagnosed patients


title: SNP500K_159_Nsp

description: Newly diagnosed patients


title: SNP500K_132_Nsp

description: Newly diagnosed patients


title: SNP500K_096_Nsp

description: Newly diagnosed patients


title: SNP500K_094_Nsp

description: Newly diagnosed patients


title: SNP500K_093_Nsp

description: Newly diagnosed patients


title: SNP500K_095_Nsp

description: Newly diagnosed patients


title: SNP500K_086_Nsp

description: Newly diagnosed patients


title: SNP500K_087_Nsp

description: Newly diagnosed patients


title: SNP500K_134_Nsp

description: Newly diagnosed patients


title: SNP500K_092_Nsp

description: Newly diagnosed patients


title: SNP500K_091_Nsp

description: Newly diagnosed patients


title: SNP500K_089_Nsp

description: Newly diagnosed patients


title: SNP500K_088_Nsp

description: Newly diagnosed patients


title: SNP500K_108_Nsp

description: Newly diagnosed patients


title: SNP500K_084_Nsp

description: Newly diagnosed patients


title: SNP500K_082_Nsp

description: Newly diagnosed patients


title: SNP500K_081_Nsp

description: Newly diagnosed patients


title: SNP500K_078_Nsp

description: Newly diagnosed patients


title: SNP500K_080_Nsp

description: Newly diagnosed patients


title: SNP500K_076_Nsp

description: Newly diagnosed patients


title: SNP500K_075_Nsp

description: Newly diagnosed patients


title: SNP500K_085_Nsp

description: Newly diagnosed patients


title: SNP500K_079_Nsp

description: Newly diagnosed patients


title: SNP500K_090_Nsp

description: Newly diagnosed patients


title: SNP500K_074_Nsp

description: Newly diagnosed patients


title: SNP500K_072_Nsp

description: Newly diagnosed patients


title: SNP500K_071_Nsp

description: Newly diagnosed patients


title: Eighth iNOS-/- mouse vs eighth WT mouse after 4 weeks infection (Replicate 8)

city: La Jolla

first: Jeffrey

middle: P.

last: Murry

address: 10010 N. Torrey Pines Road

department: IMPL-Y

institute: Salk Institute

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 8 of 8

hyb_protocol: The Tecan HS400 hybridization station was used.  Slides were washed with 5x SSC and 0.1% SDS at 42ºC for 30 s and allowed to soak in wash for 30 s.  Prehybridization buffer was added at 42ºC for 30 min with agitation every 7 min for 1.5 min.  Slides were washed twice with water for 30 s and soaked for 30 s each time. Slides were washed with 5x SSC and 0.1% SDS for 30 s and allowed to soak for 30 s at 23ºC.  50 pmol dye of each labeled cDNA suspended in hybridization buffer was injected into the slide chamber at 60ºC.  Slides were heated to 95ºC for 2 min and hybridized at 42ºC for 16 h with 1.5 min agitation every 7 min.  Slides were washed with 5x SSC and 0.1% SDS for 30 s and soaked for 30 s at 23ºC, washed with 0.2x SSC and 0.1% SDS for 30 s and soaked for 30 s at 23ºC, washed five times with 0.05x SSC for 30 s and soaked for 30 s each time at 23ºC, washed with 0.05x SSC for 30 s and soaked for 30 s at 23ºC, and dried at 30ºC for 90 min.

scan_protocol: Scanned on a Genepix4000 scanner.

data_processing: LOWESS normalized, background subtracted data, with values less than 0.01 set to 0.01, obtained from log2 of processed Red signal/processed Green signal or from log2 of processed Green signal/processed Red signal for dye-swaps. Genespring software was used.

organism: Mycobacterium tuberculosis

source_name: Transposon library recovered from eighth iNOS-/- mouse after 4 weeks of infection

label_protocol: Cy3 or Cy5 were used to label aminoallyl-dUTPs within the cDNA.

growth_protocol: A transposon library was made in the strain M. tuberculosis H37Rv using the MycoMarT7 phage. The transposon library was grow to mid-log phase, filtered through a 5 micron syringe filter, sonicated two times for 5 seconds each, diluted to approximately 10^7 colony forming units per ml.

extract_protocol: Genomic DNA was extracted using multiple steps including treatment with chloroform:methanol (2:1), lysozyme, SDS and proteinase K, extraction with phenol:chloroform, and precipitation with isopropanol and ethanol.  Genomic DNA was then partially digested with MspI or HinP1I and ligated to adaptors.  Transposon ends and adjacent genomic DNA were amplified using PCR, then an outward facing T7 promoter within the transposon was used to transcribe RNA.  cDNA was made from the transcription products using aminoallyl-dUTP.

treatment_protocol: 10^6 colony forming units of the transposon library were injected into the tail vein of C57BL/6J or iNOS-/- mice (backcrossed to a C57BL/6J background).  Three or four weeks after infection, mice were sacrificed, spleens were harvested, and bacteria were recovered from spleen homogenates by plating on 7H10 agar medium containing OADC.

tag: strain

tag: source

value: Transposon library

source_name: Transposon library recovered from eighth WT C57BL/6J mouse after 4 weeks of infection


title: SNP500K_070_Nsp

description: Newly diagnosed patients


title: SNP500K_066_Nsp

description: Newly diagnosed patients


title: SNP500K_069_Nsp

description: Newly diagnosed patients


title: SNP500K_064_Nsp

description: Newly diagnosed patients


title: Eighth WT mouse vs eighth iNOS-/- mouse after 4 weeks infection (Replicate 8 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 8 of 8, dye swap


title: SNP500K_063_Nsp

description: Newly diagnosed patients


title: SNP500K_065_Nsp

description: Newly diagnosed patients


title: SNP500K_061_Nsp

description: Newly diagnosed patients


title: SNP500K_067_Nsp

description: Newly diagnosed patients


title: Seventh iNOS-/- mouse vs seventh WT mouse after 4 weeks infection (Replicate 7)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 7 of 8

source_name: Transposon library recovered from seventh iNOS-/- mouse after 4 weeks of infection

source_name: Transposon library recovered from seventh WT C57BL/6J mouse after 4 weeks of infection


title: Seventh WT mouse vs seventh iNOS-/- mouse after 4 weeks infection (Replicate 7 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 7 of 8, dye swap


title: Sixth WT mouse vs sixth iNOS-/- mouse after 4 weeks infection (Replicate 6 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 6 of 8, dye swap

source_name: Transposon library recovered from sixth WT C57BL/6J mouse after 4 weeks of infection

source_name: Transposon library recovered from sixth iNOS-/- mouse after 4 weeks of infection


title: Sixth iNOS-/- mouse vs sixth WT mouse after 4 weeks infection (Replicate 6)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 6 of 8


title: Fifth iNOS-/- mouse vs fifth WT mouse after 4 weeks infection (Replicate 5)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 5 of 8

source_name: Transposon library recovered from fifth iNOS-/- mouse after 4 weeks of infection

source_name: Transposon library recovered from fifth WT C57BL/6J mouse after 4 weeks of infection


title: Fifth WT mouse vs fifth iNOS-/- mouse after 4 weeks infection (Replicate 5 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 5 of 8, dye swap


title: SNP500K_060_Nsp

description: Newly diagnosed patients


title: SNP500K_059_Nsp

description: Newly diagnosed patients


title: Fourth iNOS-/- mouse vs fourth WT mouse after 4 weeks infection (Replicate 4)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 4 of 8

source_name: Transposon library recovered from fourth iNOS-/- mouse after 4 weeks of infection

source_name: Transposon library recovered from fourth WT C57BL/6J mouse after 4 weeks of infection


title: SNP500K_058_Nsp

description: Newly diagnosed patients


title: SNP500K_056_Nsp

description: Newly diagnosed patients


title: Third WT mouse vs third iNOS-/- mouse after 4 weeks infection (Replicate 3 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 3 of 8, dye swap

source_name: Transposon library recovered from third WT C57BL/6J mouse after 4 weeks of infection

source_name: Transposon library recovered from third iNOS-/- mouse after 4 weeks of infection


title: Third iNOS-/- mouse vs third WT mouse after 4 weeks infection (Replicate 3)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 3 of 8


title: Fourth WT mouse vs fourth iNOS-/- mouse after 4 weeks infection (Replicate 4 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 4 of 8, dye swap


title: Second WT mouse vs second iNOS-/- mouse after 4 weeks infection (Replicate 2 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 2 of 8, dye swap

source_name: Transposon library recovered from second WT C57BL/6J mouse after 4 weeks of infection

source_name: Transposon library recovered from second iNOS-/- mouse after 4 weeks of infection


title: SNP500K_057_Nsp

description: Newly diagnosed patients


title: SNP500K_053_Nsp

description: Newly diagnosed patients


title: SNP500K_062_Nsp

description: Newly diagnosed patients


title: SNP500K_054_Nsp

description: Newly diagnosed patients


title: First WT mouse vs first iNOS-/- mouse after 4 weeks infection (Replicate 1 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 1 of 8, dye swap

source_name: Transposon library recovered from first WT C57BL/6J mouse after 4 weeks of infection

source_name: Transposon library recovered from first iNOS-/- mouse after 4 weeks of infection


title: Second iNOS-/- mouse vs second WT mouse after 4 weeks infection (Replicate 2)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 2 of 8


title: SNP500K_052_Nsp

description: Newly diagnosed patients

source_name: Bone marrow


title: SNP500K_077_Nsp

description: Newly diagnosed patients


title: Fifth iNOS-/- mouse vs fifth WT mouse after 3 weeks infection (Replicate 5)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 5 of 5

source_name: Transposon library recovered from fifth iNOS-/- mouse after 3 weeks of infection

source_name: Transposon library recovered from fifth WT C57BL/6J mouse after 3 weeks of infection


title: SNP500K_051_Nsp

description: Newly diagnosed patients


title: SNP500K_068_Nsp

description: Newly diagnosed patients


title: First iNOS-/- mouse vs first WT mouse after 4 weeks infection (Replicate 1)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 1 of 8


title: Fourth WT mouse vs fourth iNOS-/- mouse after 3 weeks infection (Replicate 4 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 4 of 5, dye swap

source_name: Transposon library recovered from fourth WT C57BL/6J mouse after 3 weeks of infection

source_name: Transposon library recovered from fourth iNOS-/- mouse after 3 weeks of infection


title: SNP500K_050_Nsp

description: Newly diagnosed patients


title: SNP500K_047_Nsp

description: Newly diagnosed patients


title: SNP500K_083_Nsp

description: Newly diagnosed patients


title: Fourth iNOS-/- mouse vs fourth WT mouse after 3 weeks infection (Replicate 4)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 4 of 5


title: SNP500K_048_Nsp

description: Newly diagnosed patients


title: SNP500K_049_Nsp

description: Newly diagnosed patients


title: SNP500K_055_Nsp

description: Newly diagnosed patients


title: Third iNOS-/- mouse vs third WT mouse after 3 weeks infection (Replicate 3)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 3 of 5

source_name: Transposon library recovered from third iNOS-/- mouse after 3 weeks of infection

source_name: Transposon library recovered from third WT C57BL/6J mouse after 3 weeks of infection


title: Third WT mouse vs third iNOS-/- mouse after 3 weeks infection (Replicate 3 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 3 of 5, dye swap


title: Fifth WT mouse vs fifth iNOS-/- mouse after 3 weeks infection (Replicate 5 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 5 of 5, dye swap


title: Second WT mouse vs second iNOS-/- mouse after 3 weeks infection (Replicate 2 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 2 of 5, dye swap

source_name: Transposon library recovered from second WT C57BL/6J mouse after 3 weeks of infection

source_name: Transposon library recovered from second iNOS-/- mouse after 3 weeks of infection


title: Second iNOS-/- mouse vs second WT mouse after 3 weeks infection (Replicate 2)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 2 of 5


title: SNP500K_044_Nsp

description: Newly diagnosed patients


title: First iNOS-/- mouse vs first WT mouse after 3 weeks infection (Replicate 1)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 1 of 5

source_name: Transposon library recovered from first iNOS-/- mouse after 3 weeks of infection

source_name: Transposon library recovered from first WT C57BL/6J mouse after 3 weeks of infection


title: SNP500K_040_Nsp

description: Newly diagnosed patients


title: SNP500K_045_Nsp

description: Newly diagnosed patients


title: SNP500K_192_Sty2

description: Newly diagnosed patients

extract_protocol:
Mononuclear bone marrow cells were separated using gradient density centrifugation (lymphocyte separation medium, Eurobio, Les Ulis, France), and plasmacytosis was evaluated by morphology in these mononuclear cell suspensions.
Plasma cells (PCs) were then positively selected using anti-CD138–coated microbeads (Miltenyi, Paris, France), because CD138 is expressed only on PCs (normal and malignant) within the bone marrow.
Purity and viability of the positively selected cell suspension was assessed by morphology and was above 90% in all the cases.
DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA).
DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).


title: SNP500K_046_Nsp

description: Newly diagnosed patients


title: SNP500K_041_Nsp

description: Newly diagnosed patients


title: SNP500K_043_Nsp

description: Newly diagnosed patients


title: SNP500K_039_Nsp

description: Newly diagnosed patients


title: SNP500K_038_Nsp

description: Newly diagnosed patients


title: HTLV-1 positive, in vitro transformed cell line MT-2, biological rep2

city: Erlangen

first: Ralph

last: Grassmann

address: Schlossgarten 4

department: Institute of Clinical and Molecular Virology

country: Germany

institute: Universität Erlangen Nürnberg

description: Gene expression data from HTLV-1 positive, in vitro transformed cell line MT-2.

hyb_protocol: Standard Affymterix protocol

scan_protocol: Standard Affymterix protocol

data_processing: GeneChip Operating Software (GCOS) and MAS5.0

source_name: CD4 positive, HTLV-1 positive T cell line, in vitro transformed by HTLV-2

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

growth_protocol: Primary CD4 T cells were kept in RPMI 1640M with 10% FCS, 0.35g/l glutamine, streptomycin, 20U/ml IL-2 after initial stimulation with PHA-P (2µg/ml, 24hours); StEd were kept in RPMI 1640M with 50% Panserin, 20% FCS, 0.35g/l glutamine, streptomycin, 40U/ml IL-2; MT-2 were kept in RPMI 1640M with 10% FCS, 0.35g/l glutamine, streptomycin.

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy Kit and QIAshredder columns according to the manufacturer's instructions.

value: CD4 T cell line (in vitro transformed)

tag: htlv infection

value: positive


title: First WT mouse vs first iNOS-/- mouse after 3 weeks infection (Replicate 1 dye-swap)

description:
cDNA amplified from genomic DNA adjacent to transposon insertion sites
Biological replicate 1 of 5, dye swap


title: SNP500K_190_Sty2

description: Newly diagnosed patients


title: SNP500K_191_Sty2

description: Newly diagnosed patients


title: SNP500K_189_Sty2

description: Newly diagnosed patients


title: SNP500K_188_Sty2

description: Newly diagnosed patients


title: SNP500K_037_Nsp

description: Newly diagnosed patients


title: SNP500K_187_Sty2

description: Newly diagnosed patients


title: SNP500K_036_Nsp

description: Newly diagnosed patients


title: HTLV-1 positive, in vitro transformed cell line MT-2, biological rep1

source_name: CD4 positive, HTLV-1 positive T cell line, in vitro transformed by HTLV-1


title: SNP500K_042_Nsp

description: Newly diagnosed patients


title: SNP500K_182_Sty2

description: Newly diagnosed patients


title: SNP500K_186_Sty2

description: Newly diagnosed patients


title: SNP500K_181_Sty2

description: Newly diagnosed patients


title: SNP500K_184_Sty2

description: Newly diagnosed patients


title: HTLV-1 positive, ATL-derived cell line StEd, biological rep1

description: Gene expression data from HTLV-1 positive, ATL-derived cell line StEd.

source_name: CD4 positive, HTLV-1 positive T cell line, established from adult T cell leukemia (ATL) patient material

value: CD4 T cell line (ATLL-derived)


title: HTLV-1 positive, ATL-derived cell line StEd, biological rep2


title: postmitotic CD4 T cells, biological rep2

description: Gene expression data from postmitotic CD4 T cells.

source_name: CD4 T cells, magnetic bead-separated, postmitotic

value: primary CD4 T cells

value: negative


title: postmitotic CD4 T cells, biological rep1


title: SNP500K_033_Nsp

description: Newly diagnosed patients


title: SNP500K_032_Nsp

description: Newly diagnosed patients


title: SNP500K_035_Nsp

description: Newly diagnosed patients


title: SNP500K_185_Sty2

description: Newly diagnosed patients


title: SNP500K_180_Sty2

description: Newly diagnosed patients


title: SNP500K_034_Nsp

description: Newly diagnosed patients


title: SNP500K_179_Sty2

description: Newly diagnosed patients


title: SNP500K_178_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 72 h, experiment #3

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method (PMID: 15705192).

source_name: Human A549 lung adenocarcinoma cell line, obtained from the American type Culture Collection (Manassas, VA).

label_protocol: Biotinylated cRNA was prepare from 3-5 ug total RNA using standard Affymetrix protocol

growth_protocol: A549 cells were maintained in RPMI-1640 medium with glutamine, supplemented with 10% FBS, penicillin, and streptomycin and tested for mycoplasma contamination. All tissue culture media and media supplements were purchased from Life Technologies (Gaithersburg, MD).

extract_protocol: Total RNA was isolated from the harvested cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

treatment_protocol: Cells were serum-starved for 24 h and then treated with 5 ng/mL porcine transforming growth factor beta 1 (TGF-beta, R&D Systems, Minneapolis, MN) for indicated times.

tag: cell line


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 72 h, experiment #2


title: SNP500K_031_Nsp

description: Newly diagnosed patients


title: SNP500K_183_Sty2

description: Newly diagnosed patients


title: SNP500K_175_Sty2

description: Newly diagnosed patients


title: SNP500K_177_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 24 h, experiment #2


title: SNP500K_030_Nsp

description: Newly diagnosed patients


title: SNP500K_176_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 72 h, experiment #1


title: SNP500K_174_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 24 h, experiment #3


title: SNP500K_173_Sty2

description: Newly diagnosed patients


title: SNP500K_172_Sty2

description: Newly diagnosed patients


title: SNP500K_170_Sty2

description: Newly diagnosed patients


title: SNP500K_028_Nsp

description: Newly diagnosed patients


title: SNP500K_027_Nsp

description: Newly diagnosed patients


title: SNP500K_171_Sty2

description: Newly diagnosed patients


title: SNP500K_169_Sty2

description: Newly diagnosed patients


title: SNP500K_167_Sty2

description: Newly diagnosed patients


title: SNP500K_166_Sty2

description: Newly diagnosed patients


title: SNP500K_026_Nsp

description: Newly diagnosed patients


title: SNP500K_168_Sty2

description: Newly diagnosed patients


title: SNP500K_164_Sty2

description: Newly diagnosed patients


title: SNP500K_025_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 24 h, experiment #1


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 16 h, experiment #3


title: SNP500K_024_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 16 h, experiment #2


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 16 h, experiment #1


title: SNP500K_165_Sty2

description: Newly diagnosed patients


title: SNP500K_163_Sty2

description: Newly diagnosed patients


title: SNP500K_161_Sty2

description: Newly diagnosed patients


title: SNP500K_160_Sty2

description: Newly diagnosed patients


title: SNP500K_022_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 8 h, experiment #3


title: SNP500K_023_Nsp

description: Newly diagnosed patients


title: SNP500K_162_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 8 h, experiment #1


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 8 h, experiment #2


title: SNP500K_159_Sty2

description: Newly diagnosed patients


title: SNP500K_155_Sty2

description: Newly diagnosed patients


title: SNP500K_154_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 4 h, experiment #3


title: SNP500K_020_Nsp

description: Newly diagnosed patients


title: SNP500K_019_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 4 h, experiment #2


title: SNP500K_156_Sty2

description: Newly diagnosed patients


title: SNP500K_157_Sty2

description: Newly diagnosed patients


title: SNP500K_029_Nsp

description: Newly diagnosed patients


title: SNP500K_152_Sty2

description: Newly diagnosed patients


title: SNP500K_151_Sty2

description: Newly diagnosed patients


title: SNP500K_158_Sty2

description: Newly diagnosed patients


title: SNP500K_153_Sty2

description: Newly diagnosed patients


title: SNP500K_150_Sty2

description: Newly diagnosed patients


title: SNP500K_018_Nsp

description: Newly diagnosed patients


title: SNP500K_017_Nsp

description: Newly diagnosed patients


title: SNP500K_021_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 4 h, experiment #1


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 1 h, experiment #2


title: SNP500K_149_Sty2

description: Newly diagnosed patients


title: SNP500K_016_Nsp

description: Newly diagnosed patients


title: SNP500K_145_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 1 h, experiment #3


title: SNP500K_146_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 2 h, experiment #1


title: SNP500K_013_Nsp

description: Newly diagnosed patients


title: SNP500K_014_Nsp

description: Newly diagnosed patients


title: SNP500K_142_Sty2

description: Newly diagnosed patients


title: SNP500K_015_Nsp

description: Newly diagnosed patients


title: SNP500K_148_Sty2

description: Newly diagnosed patients


title: SNP500K_144_Sty2

description: Newly diagnosed patients


title: SNP500K_147_Sty2

description: Newly diagnosed patients


title: SNP500K_143_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 1 h, experiment #1


title: SNP500K_140_Sty2

description: Newly diagnosed patients


title: SNP500K_139_Sty2

description: Newly diagnosed patients


title: SNP500K_138_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 0.5 h, experiment #3


title: SNP500K_137_Sty2

description: Newly diagnosed patients


title: SNP500K_011_Nsp

description: Newly diagnosed patients


title: SNP500K_136_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 0.5 h, experiment #2


title: SNP500K_134_Sty2

description: Newly diagnosed patients


title: SNP500K_012_Nsp

description: Newly diagnosed patients


title: SNP500K_010_Nsp

description: Newly diagnosed patients


title: SNP500K_009_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line, untreated, experiment #3


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 0.5 h, experiment #1


title: SNP500K_135_Sty2

description: Newly diagnosed patients


title: SNP500K_133_Sty2

description: Newly diagnosed patients


title: SNP500K_132_Sty2

description: Newly diagnosed patients


title: SNP500K_008_Nsp

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line, untreated, experiment #2


title: SNP500K_131_Sty2

description: Newly diagnosed patients


title: SNP500K_130_Sty2

description: Newly diagnosed patients


title: SNP500K_129_Sty2

description: Newly diagnosed patients


title: SNP500K_128_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line, untreated, experiment #1


title: SNP500K_007_Nsp

description: Newly diagnosed patients


title: SNP500K_006_Nsp

description: Newly diagnosed patients


title: SNP500K_126_Sty2

description: Newly diagnosed patients


title: A549 lung adenocarcinoma cell line treated with TGFB1 protein for 2 h, experiment #2


title: SNP500K_127_Sty2

description: Newly diagnosed patients


title: SNP500K_005_Nsp

description: Newly diagnosed patients


title: CD4-HDACi-12h_3

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: Gene expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: Human CD4+ T cell with HDAC inhibitor treatment after 12 hours

label_protocol: standard Affymetrix protocol

extract_protocol: as described in Wang et al., 2009

value: CD4+ T cell

tag: agent

value: HDAC inhibitor treatment after 12 hours


title: CD4-HDACi-12h_1

description: Gene expression


title: SNP500K_125_Sty2

description: Newly diagnosed patients

source_name: Bone marrow


title: SNP500K_124_Sty2

description: Newly diagnosed patients


title: SNP500K_003_Nsp

description: Newly diagnosed patients


title: SNP500K_121_Sty2

description: Newly diagnosed patients


title: SNP500K_004_Nsp

description: Newly diagnosed patients


title: SNP500K_122_Sty2

description: Newly diagnosed patients


title: SNP500K_123_Sty2

description: Newly diagnosed patients


title: SNP500K_002_Nsp

description: Newly diagnosed patients


title: CD4-HDACi-2h_3

description: Gene expression

source_name: Human CD4+ T cell with HDAC inhibitor treatment after 2 hours

value: HDAC inhibitor treatment after 2 hours


title: N-lim anaerobic chemostat of msn2msn4 double mutant -3

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
N-lim, ANAE
LH62b

hyb_protocol: According to manufacturer's procedures

scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

data_processing: GCOS

organism: Saccharomyces cerevisiae

label_protocol:
Microarrays, data acquisition and statistical analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described (2). Results for each growth condition were derived from three independent culture replicates. Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software version 1.2. To eliminate insignificant variations, genes with expression values below 12 were set to 12 as previously described (6).
Reference List
1. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
2. De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
3. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
5. Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
6. Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274

growth_protocol:
Media for chemostat cultivation. The synthetic medium composition was based on that described by Verduyn (1). The modifications introduced for carbon, nitrogen, sulphur, phosphorus and zinc limited growth were determined previously (1-3) and are listed in Table 2. In all chemostats except for those limited by carbon, the residual glucose concentration was targeted to 17 g/l (95 mM) in order to have the same degree of glucose repression. The reservoir medium was supplemented with vitamins and the anaerobic growth factors Tween-80 and ergosterol as previously described (1).
Chemostat cultivation. Chemostat cultures were fed with synthetic medium that limited growth by carbon, nitrogen, sulphur, phosphorus or zinc with all other growth requirements in excess and at constant residual concentration. The dilution rate was set at 0.10 h-1, the pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH as previously described (3). Cultures were assumed to be in steady-state when, after at least 5 volume changes, culture dry-weight, glucose concentration, carbon-dioxide production rate and oxygen consumption rate varied by less than 2 % during one additional volume change (4). Steady-state samples were taken after 10 generations at the latest to avoid strain adaptation due to long-term cultivation (5). Each cultivation condition was performed in triplicate.
Reference List
1.Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
2.De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
3.Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
4.Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
5.Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
6.Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274

treatment_protocol: Quenching in liquid nitrogen

tag: genotype

value: cen.pk113-7d prototropic strain mata mal2-8c suc2 ura3 msn2::loxP msn4::loxP-kanMX-loxP p426(URA3)


title: SNP500K_119_Sty2

description: Newly diagnosed patients


title: CD4-HDACi-2h_2

description: Gene expression


title: SNP500K_118_Sty2

description: Newly diagnosed patients


title: CD4-HDACi-2h_1

description: Gene expression


title: SNP500K_141_Sty2

description: Newly diagnosed patients


title: SNP500K_116_Sty2

description: Newly diagnosed patients


title: SNP500K_117_Sty2

description: Newly diagnosed patients


title: N-lim anaerobic chemostat of msn2msn4 double mutant -2

description:
N-lim, ANAE
LH57

extract_protocol:
Microarrays, data acquisition and statistical analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described (2). Results for each growth condition were derived from three independent culture replicates. Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software version 1.2. To eliminate insignificant variations, genes with expression values below 12 were set to 12 as previously described (6).
Reference List
1. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) J. Gen. Microbiol. 136, 405-412
2. De Nicola, R., Hazelwood, L. A., De Hulster, E. A., Walsh, M. C., Knijnenburg, T. A., Reinders, M. J., Walker, G. M., Pronk, J. T., Daran, J. M., and Daran-Lapujade, P. (2007) Appl. Environ. Microbiol. 73, 7680-7692
3. Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J. M., and Pronk, J. T. (2005) J. Biol. Chem. 280, 437-447
4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A 96, 9721-9726
5. Jansen, M. L., Daran-Lapujade, P., de Winde, J. H., Piper, M. D., and Pronk, J. T. (2004) Appl. Environ. Microbiol. 70, 1956-1963
6. Boer, V. M., de Winde, J. H., Pronk, J. T., and Piper, M. D. (2003) J. Biol. Chem. 278, 3265-3274


title: SNP500K_001_Nsp

description: Newly diagnosed patients


title: SNP500K_120_Sty2

description: Newly diagnosed patients


title: SNP500K_114_Sty2

description: Newly diagnosed patients


title: SNP500K_115_Sty2

description: Newly diagnosed patients


title: CD4-HDACi-12h_2

description: Gene expression


title: SNP500K_113_Sty2

description: Newly diagnosed patients


title: C-lim anaerobic chemostat of msn2msn4 double mutant -3

description:
C-lim, ANAE
LH61


title: N-lim anaerobic chemostat of msn2msn4 double mutant -1

description:
N-lim, ANAE
LH55


title: CD4-HDACi-0h_2

description: Gene expression

source_name: Human CD4+ T cell without HDAC inhibitor treatment


title: C-lim anaerobic chemostat of msn2msn4 double mutant -1

description:
C-lim, ANAE
LH54b


title: C-lim anaerobic chemostat of msn2msn4 double mutant -2

description:
C-lim, ANAE
LH56


title: CD4-HDACi-0h_3

description: Gene expression


title: SNP500K_111_Sty2

description: Newly diagnosed patients


title: CD4-HDACi-0h_1

description: Gene expression


title: Human_Myometrium_Donor 23_Replicate_1

city: Cambridge

first: Scott

last: Jelinsky

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

description: Replicate 1 of 1

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

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

data_processing: The data were analyzed with GCOS1.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Myometrium tissue from a human donor undergoing hysterectomy for Leiomyoma

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

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNAeasy purification was performed according to the manufacturer's instructions.

tag: Donor 23


title: Human_Myometrium_Donor 22_Replicate_1

description: Replicate 1 of 1

tag: Donor 22


title: SNP500K_110_Sty2

description: Newly diagnosed patients


title: SNP500K_112_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 21_Replicate_1

description: Replicate 1 of 1

tag: Donor 21


title: SNP500K_105_Sty2

description: Newly diagnosed patients


title: SNP500K_109_Sty2

description: Newly diagnosed patients


title: SNP500K_108_Sty2

description: Newly diagnosed patients


title: SNP500K_107_Sty2

description: Newly diagnosed patients


title: SNP500K_106_Sty2

description: Newly diagnosed patients


title: SNP500K_104_Sty2

description: Newly diagnosed patients


title: P-lim anaerobic chemostat, dilution rate 0.1 h-1 -3

description:
P-lim, ANAE
LH64b

value: CEN.PK113-7D prototropic strain (MATa MAL2-8c SUC2)


title: P-lim anaerobic chemostat, dilution rate 0.1 h-1 -1

description:
P-lim, ANAE
LH53


title: P-lim anaerobic chemostat, dilution rate 0.1 h-1 -2

description:
P-lim, ANAE
LH59


title: S-lim anaerobic chemostat, dilution rate 0.1 h-1 -3

description:
S-lim, ANAE
LH63


title: SNP500K_101_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 20_Replicate_1

description: Replicate 1 of 1

tag: Donor 20


title: S-lim anaerobic chemostat, dilution rate 0.1 h-1 -2

description:
S-lim, ANAE
LH58b

source_name: S-lim anaerobic chemostat dilution rate 0.1 h-1


title: S-lim anaerobic chemostat, dilution rate 0.1 h-1 -1

description:
S-lim, ANAE
LH52b

value: CEN.PK113-7D prototrophic strain (MATa MAL2-8c SUC2)


title: SNP500K_099_Sty2

description: Newly diagnosed patients

value: multiple myeloma. Tissue:bone marrow. Cells:purified CD138+ plasma cells.


title: SNP500K_103_Sty2

description: Newly diagnosed patients


title: SNP500K_100_Sty2

description: Newly diagnosed patients


title: SNP500K_102_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 16_Replicate_1

description: Replicate 1 of 1

tag: Donor 16


title: Human_Myometrium_Donor 17_Replicate_1

description: Replicate 1 of 1

tag: Donor 17


title: SNP500K_096_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 18_Replicate_1

description: Replicate 1 of 1

tag: Donor 18


title: SNP500K_098_Sty2

description: Newly diagnosed patients

tag: Tumor


title: SNP500K_095_Sty2

description: Newly diagnosed patients


title: SNP500K_097_Sty2

description: Newly diagnosed patients


title: SPD_4

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Yeast culture.

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

source_name: yeast, SPD-treated

label_protocol: Affymetrix standard protocol.

growth_protocol: Yeast were grown in the standard protocol.

extract_protocol: Kit from Qiagen:RNeasy Protect MiniKits.

treatment_protocol: Treated with spermine or spermidine.

value: delta-spe3 delta-fms1

tag: treatment

value: spermidine


title: SNP500K_094_Sty2

description: Newly diagnosed patients


title: SPD_3

description: Yeast culture.


title: SPD_5

description: Yeast culture.


title: Human_Myometrium_Donor 15_Replicate_1

description: Replicate 1 of 1

tag: Donor 15


title: SNP500K_092_Sty2

description: Newly diagnosed patients


title: SNP500K_093_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 13_Replicate_1

description: Replicate 1 of 1

tag: Donor 13


title: SNP500K_091_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 12_Replicate_1

description: Replicate 1 of 1

tag: Donor 12


title: SNP500K_090_Sty2

description: Newly diagnosed patients


title: SPD_2

description: Yeast culture.


title: Human_Myometrium_Donor 14_Replicate_1

description: Replicate 1 of 1

tag: Donor 14


title: SPD_1

description: Yeast culture.


title: SNP500K_088_Sty2

description: Newly diagnosed patients


title: SNP500K_086_Sty2

description: Newly diagnosed patients


title: SNP500K_089_Sty2

description: Newly diagnosed patients


title: SNP500K_085_Sty2

description: Newly diagnosed patients


title: SNP500K_087_Sty2

description: Newly diagnosed patients


title: SP_3

description: Yeast culture.

source_name: yeast, SP-treated

value: spermine


title: Human_Myometrium_Donor 10_Replicate_1

description: Replicate 1 of 1

tag: Donor 10


title: SNP500K_083_Sty2

description: Newly diagnosed patients


title: SNP500K_084_Sty2

description: Newly diagnosed patients


title: SP_2

description: Yeast culture.


title: SP_1

description: Yeast culture.


title: Control_5

description: Yeast culture.

source_name: yeast, control

value: control


title: SNP500K_080_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 8_Replicate_1

description: Replicate 1 of 3

tag: Donor 8


title: Human_Myometrium_Donor 8_Replicate_3

description: Replicate 3 of 3


title: Human_Myometrium_Donor 8_Replicate_2

description: Replicate 2 of 3


title: Human_Myometrium_Donor 9_Replicate_1

description: Replicate 1 of 1

tag: Donor 9


title: SNP500K_082_Sty2

description: Newly diagnosed patients


title: SNP500K_077_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 11_Replicate_1

description: Replicate 1 of 1

tag: Donor 11


title: SNP500K_078_Sty2

description: Newly diagnosed patients


title: SNP500K_079_Sty2

description: Newly diagnosed patients


title: SNP500K_076_Sty2

description: Newly diagnosed patients


title: SNP500K_075_Sty2

description: Newly diagnosed patients


title: SNP500K_081_Sty2

description: Newly diagnosed patients


title: Control_2

description: Yeast culture.


title: Control_1

description: Yeast culture.


title: Human_Myometrium_Donor 7_Replicate_2

description: Replicate 2 of 3

tag: Donor 7


title: Control_3

description: Yeast culture.


title: Control_4

description: Yeast culture.


title: SNP500K_072_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 6_Replicate_1

description: Replicate 1 of 1

tag: Donor 6


title: SNP500K_071_Sty2

description: Newly diagnosed patients


title: SNP500K_074_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 7_Replicate_3

description: Replicate 3 of 3


title: SNP500K_069_Sty2

description: Newly diagnosed patients


title: SNP500K_067_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 5_Replicate_1

description: Replicate 1 of 1

tag: Donor 5


title: SNP500K_070_Sty2

description: Newly diagnosed patients


title: SNP500K_073_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d13_4

city: Frederick

first: Brian

middle: D.

last: Peyser

address: 1425 Porter St

department: Bacteriology

institute: USAMRIID

description: CD45 62% (C57BL/6) mouse splenocytes 13 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

hyb_protocol: The biotin labeled RNA was hybridized 16-24 hours at 45 degrees Celsius at 60RPM to Affymetrix Mouse Genome 430 2.0 according to manufacturer’s instruction. Following hybridization, the GeneChip® Fluidics Station 450 was used for the wash and stain operation of Affymetrix Mouse GeneChip® arrays.  Fluidic protocol EukGE-Ws2v5_450 was used.

scan_protocol: The processed Affymetrix Mouse GeneChip® array was scanned on the GeneChip® Scanner 3000 7G according to manufacturer’s instruction.

data_processing: Data were preprocessed and summarized in R/Bioconductor using GC-RMA.

source_name: 62% CD45 splenocytes 13 days post- EBOV-infection

label_protocol: 2 ug of DNA was labeled with biotin using the Affymetrix GeneChip® IVT kit according to manufacturer’s instruction.

extract_protocol: Cells were homogenized in 3mL of TRIzol.  The homogenate was extracted with 1.2 mL of Chloroform.  Eppendorf PLG tubes were used to aid in phase separation.  The aqueous phase was removed and processed for RNA using the Qiagen RNease Mini kit according to manufacturer’s instruction (DNase Treatment protocol).  RNA was eluted in 40 uL of RNase-free water.  RNA concentrations were determined using A260 values obtained from the SpectraMax Plus plate reader spectrophotometer.  RNA RIN values were determined by analysis on the Agilent Bioanalyzer (RNA 6000 Nano kit).

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 13 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.

tag: mice strain

tag: tissue

value: Splenocytes

tag: pathogen

value: Mouse adapted Ebola Zaire

tag: route of pathogen infection

value: Intraperitoneal

tag: pathogen load


title: Human_Myometrium_Donor 7_Replicate_1

description: Replicate 1 of 3


title: SNP500K_065_Sty2

description: Newly diagnosed patients

tag: Tumor


title: SNP500K_066_Sty2

description: Newly diagnosed patients


title: SNP500K_068_Sty2

description: Newly diagnosed patients


title: SNP500K_064_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 4_Replicate_2

description: Replicate 2 of 2

tag: Donor 4


title: SNP500K_063_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 4_Replicate_1

description: Replicate 1 of 2


title: SNP500K_062_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d9_4

description: CD45 62% (C57BL/6) mouse splenocytes 9 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 9 days post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 9 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: splenocytes_62%_d5_8

description: CD45 62% (C57BL/6) mouse splenocytes 5 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 5 days post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 5 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: SNP500K_059_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d11_4

description: CD45 62% (C57BL/6) mouse splenocytes 11 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 11 days post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 11 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: SNP500K_060_Sty2

description: Newly diagnosed patients


title: Human_Myometrium_Donor 3_Replicate_1

description: Replicate 1 of 1

tag: Donor 3


title: splenocytes_62%_d7_3

description: CD45 62% (C57BL/6) mouse splenocytes 7 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 7 days post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 7 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: splenocytes_100%_d7_4

description: Wild-type (C57BL/6) mouse splenocytes 7 days post- EBOV-infection

source_name: WT (100% CD45) splenocytes 7 days post- EBOV-infection


title: Human_Myometrium_Donor 2_Replicate_1

description: Replicate 1 of 1

tag: Donor 2


title: Human_Myometrium_Donor 1_Replicate_1

description: Replicate 1 of 1

tag: Donor 1


title: SNP500K_061_Sty2

description: Newly diagnosed patients


title: SNP500K_057_Sty2

description: Newly diagnosed patients


title: SNP500K_056_Sty2

description: Newly diagnosed patients


title: SNP500K_058_Sty2

description: Newly diagnosed patients


title: SNP500K_055_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 23_Replicate_3

description: Replicate 3 of 3

source_name: Leiomyoma tissue from a human donor undergoing hysterectomy for Leiomyoma

tag: Donor 23


title: splenocytes_100%_d5_7

description: Wild-type (C57BL/6) mouse splenocytes 5 days post- EBOV-infection

source_name: WT (100% CD45) splenocytes 5 days post- EBOV-infection


title: splenocytes_62%_d13_3


title: splenocytes_62%_d11_3


title: SNP500K_054_Sty2

description: Newly diagnosed patients


title: SNP500K_053_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d9_3


title: SNP500K_047_Sty2

description: Newly diagnosed patients


title: SNP500K_050_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d5_7


title: Human_Leiomyoma_Donor 23_Replicate_1

description: Replicate 1 of 3


title: splenocytes_62%_d7_2


title: Human_Leiomyoma_Donor 22_Replicate_2

description: Replicate 2 of 2

tag: Donor 22


title: Human_Leiomyoma_Donor 23_Replicate_2

description: Replicate 2 of 3


title: SNP500K_049_Sty2

description: Newly diagnosed patients


title: SNP500K_051_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 22_Replicate_1

description: Replicate 1 of 2


title: SNP500K_046_Sty2

description: Newly diagnosed patients


title: SNP500K_045_Sty2

description: Newly diagnosed patients


title: SNP500K_048_Sty2

description: Newly diagnosed patients


title: SNP500K_052_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 21_Replicate_1

description: Replicate 1 of 1

tag: Donor 21


title: Human_Leiomyoma_Donor 20_Replicate_1

description: Replicate 1 of 1

tag: Donor 20


title: Human_Leiomyoma_Donor 19_Replicate_1

description: Replicate 1 of 2

tag: Donor 19


title: SNP500K_044_Sty2

description: Newly diagnosed patients


title: splenocytes_100%_d5_6


title: splenocytes_62%_d13_2


title: SNP500K_043_Sty2

description: Newly diagnosed patients


title: SNP500K_039_Sty2

description: Newly diagnosed patients


title: splenocytes_100%_d7_3


title: Human_Leiomyoma_Donor 18_Replicate_1

description: Replicate 1 of 1

tag: Donor 18


title: SNP500K_042_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 19_Replicate_2

description: Replicate 2 of 2


title: SNP500K_038_Sty2

description: Newly diagnosed patients


title: SNP500K_041_Sty2

description: Newly diagnosed patients


title: SNP500K_036_Sty2

description: Newly diagnosed patients


title: SNP500K_037_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d11_2


title: SNP500K_035_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 17_Replicate_1

description: Replicate 1 of 3

tag: Donor 17


title: Human_Leiomyoma_Donor 17_Replicate_3

description: Replicate 3 of 3


title: splenocytes_62%_d7_1

tag: mice strain


title: splenocytes_62%_d5_6

tag: tissue


title: splenocytes_100%_d7_2

description: C57BL/6 mouse splenocytes 7 days post- EBOV-infection.

tag: pathogen


title: SNP500K_032_Sty2

description: Newly diagnosed patients


title: SNP500K_034_Sty2

description: Newly diagnosed patients


title: SNP500K_031_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 17_Replicate_2

description: Replicate 2 of 3


title: splenocytes_62%_d9_2

tag: route of pathogen infection


title: SNP500K_029_Sty2

description: Newly diagnosed patients


title: SNP500K_033_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 16_Replicate_1

description: Replicate 1 of 1

tag: Donor 16


title: SNP500K_030_Sty2

description: Newly diagnosed patients

tag: Tumor


title: SNP500K_028_Sty2

description: Newly diagnosed patients


title: SNP500K_027_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 15_Replicate_3

description: Replicate 3 of 3

tag: Donor 15


title: Human_Leiomyoma_Donor 15_Replicate_2

description: Replicate 2 of 3


title: splenocytes_100%_d5_5

description: C57BL/6 mouse splenocytes 5 days post- EBOV-infection.

tag: pathogen load


title: SNP500K_026_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d11_1


title: SNP500K_024_Sty2

description: Newly diagnosed patients


title: SNP500K_025_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 14_Replicate_1

description: Replicate 1 of 1

tag: Donor 14


title: splenocytes_62%_d13_1


title: SNP500K_022_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 15_Replicate_1

description: Replicate 1 of 3


title: SNP500K_019_Sty2

description: Newly diagnosed patients


title: SNP500K_023_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d9_1


title: SNP500K_020_Sty2

description: Newly diagnosed patients


title: SNP500K_021_Sty2

description: Newly diagnosed patients


title: SNP500K_018_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d5_5


title: SNP500K_040_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 13_Replicate_1

description: Replicate 1 of 2

tag: Donor 13


title: splenocytes_100%_d7_1


title: SNP500K_017_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 12_Replicate_3

description: Replicate 3 of 3

tag: Donor 12


title: splenocytes_100%_d5_4


title: Human_Leiomyoma_Donor 13_Replicate_2

description: Replicate 2 of 2


title: SNP500K_016_Sty2

description: Newly diagnosed patients


title: SNP500K_012_Sty2

description: Newly diagnosed patients


title: SNP500K_014_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 12_Replicate_2

description: Replicate 2 of 3


title: SNP500K_013_Sty2

description: Newly diagnosed patients


title: SNP500K_015_Sty2

description: Newly diagnosed patients


title: SNP500K_011_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d5_4


title: splenocytes_62%_d5_3


title: Human_Leiomyoma_Donor 12_Replicate_1

description: Replicate 1 of 3


title: Human_Leiomyoma_Donor 11_Replicate_3

description: Replicate 3 of 3

tag: Donor 11


title: SNP500K_008_Sty2

description: Newly diagnosed patients


title: SNP500K_010_Sty2

description: Newly diagnosed patients


title: splenocytes_62%_d5_2


title: Human_Leiomyoma_Donor 11_Replicate_2

description: Replicate 2 of 3


title: splenocytes_62%_d5_1


title: SNP500K_006_Sty2

description: Newly diagnosed patients


title: SNP500K_009_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 11_Replicate_1

description: Replicate 1 of 3


title: splenocytes_62%_d3_4

description: CD45 62% (C57BL/6) mouse splenocytes 3 days post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 3 days post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 3 days post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: Human_Leiomyoma_Donor 10_Replicate_2

description: Replicate 2 of 3

tag: Donor 10


title: splenocytes_62%_d3_2


title: SNP500K_005_Sty2

description: Newly diagnosed patients

source_name: Bone marrow


title: SNP500K_007_Sty2

description: Newly diagnosed patients


title: SNP500K_004_Sty2

description: Newly diagnosed patients


title: Rat_Myometrium_Donor_2901

description: The Eker rat is a preclinical model of leiomyoma.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RAE230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Rattus norvegicus

source_name: Normal myometrium tissue from an Eker rat

tag: Rat model of uterine fibroids.


title: Rat_Myometrium_Donor_3201


title: Rat_Myometrium_Donor_3401


title: Rat_Myometrium_Donor_3301


title: splenocytes_62%_d3_3


title: Human_Leiomyoma_Donor 10_Replicate_3

description: Replicate 3 of 3


title: splenocytes_62%_d3_1


title: Rat_Myometrium_Donor_2801


title: SNP500K_003_Sty2

description: Newly diagnosed patients


title: Human_Leiomyoma_Donor 10_Replicate_1

description: Replicate 1 of 3


title: splenocytes_62%_d1_4

description: CD45 62% (C57BL/6) mouse splenocytes 1 day post- EBOV-infection. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes 1 day post- EBOV-infection

treatment_protocol:
Pathogen: Mouse adapted Ebola Zaire
Route of pathogen infection: Intraperitoneal
Pathogen load: 1000 pfu
Mouse was euthanized at 1 day post-infection and spleen tissue was harvested. Splenocytes were isolated, RBCs were lysed and cell pellet resuspended in Trizol solution.


title: SNP500K_002_Sty2

description: Newly diagnosed patients


title: SNP500K_001_Sty2

description: Newly diagnosed patients


title: Rat_Myometrium_Donor_2001


title: Rat_Myometrium_Donor_2501


title: Rat_Myometrium_Donor_2201


title: splenocytes_62%_d1_1


title: Rat_Myometrium_Donor_1601


title: splenocytes_62%_d1_2


title: Rat_Myometrium_Donor_2601


title: Human_Leiomyoma_Donor 9_Replicate_1

description: Replicate 1 of 3

tag: Donor 9


title: Rat_Myometrium_Donor_1801


title: Rat_Myometrium_Donor_1201


title: Rat_Myometrium_Donor_1401


title: splenocytes_62%_d1_3


title: Human_Leiomyoma_Donor 8_Replicate_2

description: Replicate 2 of 2

tag: Donor 8


title: Human_Leiomyoma_Donor 9_Replicate_2

description: Replicate 2 of 3


title: splenocytes_62%_d0_4

description: Uninfected CD45 62% (C57BL/6) mouse splenocytes. Mice are heterozygous for CD45 (PTPRC) and express 62% as much protein as wild-type.

source_name: 62% CD45 splenocytes pre-infection

treatment_protocol: No infection


title: Human_Leiomyoma_Donor 8_Replicate_1

description: Replicate 1 of 2


title: Rat_Myometrium_Donor_0401


title: Rat_Leiomyoma_Donor_3501

source_name: Leiomyoma tissue from an Eker rat


title: Rat_Leiomyoma_Donor_2701


title: Rat_Leiomyoma_Donor_1901


title: Rat_Leiomyoma_Donor_2301


title: Rat_Leiomyoma_Donor_3101


title: Rat_Leiomyoma_Donor_1701


title: Human_Leiomyoma_Donor 7_Replicate_1

description: Replicate 1 of 2

tag: Donor 7


title: splenocytes_100%_d5_3

tag: mice strain


title: splenocytes_62%_d0_3

tag: tissue


title: splenocytes_62%_d0_1


title: Rat_Leiomyoma_Donor_2101


title: Rat_Leiomyoma_Donor_1501


title: Human_Leiomyoma_Donor 6_Replicate_2

description: Replicate 2 of 2

tag: Donor 6


title: Human_Leiomyoma_Donor 7_Replicate_2

description: Replicate 2 of 2


title: splenocytes_62%_d0_2


title: Human_Leiomyoma_Donor 6_Replicate_1

description: Replicate 1 of 2


title: Human_Leiomyoma_Donor 5_Replicate_1

description: Replicate 1 of 1

tag: Donor 5


title: Rat_Leiomyoma_Donor_1301


title: splenocytes_100%_d5_2

tag: pathogen

tag: route of pathogen infection


title: Rat_Leiomyoma_Donor_0701


title: splenocytes_100%_d5_1


title: Rat_Leiomyoma_Donor_0101


title: Rat_Leiomyoma_Donor_1101


title: Rat_Leiomyoma_Donor_0301


title: Human_Leiomyoma_Donor 4_Replicate_2

description: Replicate 2 of 2

tag: Donor 4


title: Rat_Leiomyoma_Donor_0501


title: Human_Leiomyoma_Donor 3_Replicate_1

description: Replicate 1 of 3

tag: Donor 3


title: Human_Leiomyoma_Donor 4_Replicate_1

description: Replicate 1 of 2


title: splenocytes_100%_d3_1

description: Wild-type (C57BL/6) mouse splenocytes 3 days post- EBOV-infection

source_name: WT (100% CD45) splenocytes 3 days post- EBOV-infection

tag: pathogen load


title: Human_Leiomyoma_Donor 3_Replicate_3

description: Replicate 3 of 3


title: splenocytes_100%_d3_3


title: splenocytes_100%_d3_4


title: Human_Leiomyoma_Donor 3_Replicate_2

description: Replicate 2 of 3


title: splenocytes_100%_d3_2


title: splenocytes_100%_d1_4

description: Wild-type (C57BL/6) mouse splenocytes 1 day post- EBOV-infection

source_name: WT (100% CD45) splenocytes 1 day post- EBOV-infection


title: splenocytes_100%_d1_3


title: Human_Leiomyoma_Donor 2_Replicate_2

description: Replicate 2 of 3

tag: Donor 2


title: Human_Leiomyoma_Donor 2_Replicate_3

description: Replicate 3 of 3


title: Rat_Myometrium_Donor_2401


title: Human_Leiomyoma_Donor 1_Replicate_3

description: Replicate 3 of 3

tag: Donor 1


title: HMLER, salinomycin, rep1

first: Piyush

middle: B.

last: Gupta

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research/MIT

description: Global gene expression signature upon salinomycin treatment

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

source_name: HMLER breast cancer cells after 1uM salinomycin treatment

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in a 1:1 mixture of DMEM+10%FBS, insulin, hydrocortisone and MEGM.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Cells were treated for one week with paclitaxel (10nM) or salinomycin (1uM); after one week of treatment, the cells were cultured in the absence of compound for 3 weeks. Medium changes with performed every 2 days.

tag: strain

value: HMLER

value: breast

tag: genotype

value: SV40ER, hTERT, HrasV12

tag: agent

value: salinomycin


title: Human_Leiomyoma_Donor 1_Replicate_2

description: Replicate 2 of 3


title: splenocytes_100%_d1_2


title: Human_Leiomyoma_Donor 2_Replicate_1

description: Replicate 1 of 3


title: splenocytes_100%_d0_3

description: Uninfected wild-type (C57BL/6) mouse splenocytes

source_name: WT (100% CD45) splenocytes pre-infection


title: Human_Leiomyoma_Donor 9_Replicate_3

description: Replicate 3 of 3

tag: Donor 9


title: Human_Leiomyoma_Donor 1_Replicate_1

description: Replicate 1 of 3


title: HMLER, paclitaxel, rep3

description: Global gene expression signature upon paclitaxel treatment

source_name: HMLER breast cancer cells after 10nM paclitaxel treatment

value: paclitaxel


title: HMLER, salinomycin, rep3


title: splenocytes_100%_d0_2


title: splenocytes_100%_d0_1


title: HMLER, paclitaxel, rep2


title: HMLER, paclitaxel, rep1


title: splenocytes_100%_d1_1


title: HMLER, salinomycin, rep2


title: Triclosan exposure 1

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: An investigation in the transcriptomic effects upon exposure of Escherichia coli K12 MG1655 to the MIC (0.12 mg/L) of the biocide, triclosan.

hyb_protocol: Prehybridization of the array slides was performed for 4 h in filtered prehybridization solution [25 % formamide, 5x SSC, 10 mg l–1 BSA (fraction V), 0·1 % SDS] at 42 °C. Slides were briefly washed in ethanol and dried by centrifugation at 1000 g for 5 min. Hybridization of the probe was performed using hybridization solution (25 % formamide, 5x SSC, 0·1 % SDS, 0·1 µg poly(A) ml–1, 1x Denhardt's solution and 80 pmol Cy3 and Cy5 combined probe). The hybridization solution containing the Cy-Dye-labelled cDNA was heated to 95 °C for 3 min, Lifter slips (Erie Scientific) were placed on the array slides and the hybridization solution was applied between the Lifter slip and the array slide. The slides were incubated overnight at 42 °C in the dark in a Corning hybridization chamber (Corning Scientific). After hybridization, slides were washed in wash buffer I (2x SSC/0·1 % SDS) for 2 min at 42 °C, in wash buffer II (0·2x SSC) for 2 min at room temperature and then twice in wash buffer III (0·05x SSC) for 2 min at room temperature. All washes were done with vigorous shaking of the microarray slides. The slides were dried by centrifugation at 1000 g for 5 min.

scan_protocol: Slides were analysed using an Axon Genepix 4000B microarray scanner, and Genepix 5.1 software (Axon Scientific).

data_processing: Data were normalised by background subtraction using Kooperberg, then normalization using printtip loess (within arrays). Both functions were performed using the limma package (Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420).

organism: Escherichia coli

source_name: E. coli K12 MG1655, MOPS minimal media + 0.12 mg/L triclosan

label_protocol: 20 µg total RNA was converted to Cy5-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer's instructions. Amino-allyl-labelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy3 and Cy5 NHS-dye esters to the amino-allyl-labelled cDNAs.

growth_protocol: Grown to mid-logarithmic phase (OD600 ~ 0.7 +/- 0.02) at 37 C, then incubated for an additional 30 min in the presence of 0.12 mg/L triclosan at 37 C.

extract_protocol: RNA isolation was performed using the Qiagen RNAprotectTM, RNeasy Mini Kit and RNase-free DNase sets according to the manufacturers’ instructions (Qiagen Ltd, Surrey, UK). The total RNA isolated from the cultures was quantified using an Agilent Bioanalyser 2100 RNA NanoLabchip, where, the quality of the RNA was indicated from the ratio of absorbance of 23S to 16S ribosomal RNA which was between 1.6 and 2.

treatment_protocol: Upon the culture reaching mid-logarithmic growth phase (OD600 ~ 0.7 +/- 0.02), 0.12 mg/L triclosan was added and the culture incubated for an additional 30 min.

tag: media

value: MOPS minimal medium + 0.12 mg/L triclosan

source_name: E. coli K12 MG1655, MOPS minimal media

growth_protocol: Grown to mid-logarithmic phase (OD600 ~ 0.7 +/- 0.02) at 37 C, then incubated for an additional 30 min at 37 C.

treatment_protocol: No treatment

value: MOPS minimal medium


title: Triclosan exposure 2

hyb_protocol: l 	Prehybridization of the array slides was performed for 4 h in filtered prehybridization solution [25 % formamide, 5x SSC, 10 mg l–1 BSA (fraction V), 0·1 % SDS] at 42 °C. Slides were briefly washed in ethanol and dried by centrifugation at 1000 g for 5 min. Hybridization of the probe was performed using hybridization solution (25 % formamide, 5x SSC, 0·1 % SDS, 0·1 µg poly(A) ml–1, 1x Denhardt's solution and 80 pmol Cy3 and Cy5 combined probe). The hybridization solution containing the Cy-Dye-labelled cDNA was heated to 95 °C for 3 min, Lifter slips (Erie Scientific) were placed on the array slides and the hybridization solution was applied between the Lifter slip and the array slide. The slides were incubated overnight at 42 °C in the dark in a Corning hybridization chamber (Corning Scientific). After hybridization, slides were washed in wash buffer I (2x SSC/0·1 % SDS) for 2 min at 42 °C, in wash buffer II (0·2x SSC) for 2 min at room temperature and then twice in wash buffer III (0·05x SSC) for 2 min at room temperature. All washes were done with vigorous shaking of the microarray slides. The slides were dried by centrifugation at 1000 g for 5 min.


title: Triclosan exposure 3


title: Lt2 phoP mutant

status: Public on Aug 19 2009

first: Richelle

middle: C.

last: Charles

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

description: Expression profiling of Salmonella enterica serovar Typhimurium LT2 phoPQ-

hyb_protocol: After blocking in 5x SSC, 0.1% SDS, 1% BSA overnight, samples (resuspended in 50% formamide, 5x SSC, 0.1% SDS, 0.6 μg/µL Salmon Sperm DNA) were added to slide and allowed to hybridize for 20 hours at 42ºC in Corning hybridization chambers.  After hybridization the slides were washed twice with the following increasingly stringent solutions for 5 minutes each: low (2x SSC, 0.1% SDS heated to 55°C), medium (0.1x SSC, 0.1% SDS),  high (0.1x SSC).  Then a final wash with water.

scan_protocol: Scanned on a ScanArray Ecpress Instrument (PerkinElmer Life Sciences) and signals quantified using Scan Arrau Express software, version 4 (Perkin Elmer).

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
Since the samples were hybridized to two-channel arrays, the data from different slides were not normalized to have the same median intensities. Instead we used a standard method of analysis described by Kerr et al. (2001; PMID: 11355567) which included a slide effect in the analysis of variance model.Thus, for each gene when comparing High and Low levels, the slide effect was adjusted for in the model fit, and there was no need to normalize data to have same median intensities across the slides.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella grown in PhoP-inducing (Low Mg) or  PhoP non-inducing conditions (High Mg)

label_protocol: 2 µg of total RNA were primed with 2 ul random hexamers, RNaseOUT, and DepC water for 10 minutes at 70°C and then reversed transcribed at 42°C for 18 hrs in the presence of  SuperScript III RTase (Invitrogen), dNTP/aa-UTP labeling mix, DTT, First strand buffer and RNA/primer mix.  RNA was hydrolyzed with 1M NaOH and 0.5M EDTA and unincorporated aa-dUTP was removed using Qiagen Min Elute PCR purification kit protocol except phosphate wash and phosphate elution buffer was substituted for those provided in the kit.  Samples were  lyphophilized and then resuspended samples (in 4.5 ul of 0.1M sodium bicarbonate buffer) were labeled with Cy3 or Cy5 by incubating sample after resuspension in with the appropriate label for 1 hour.

growth_protocol: Bacteria strains were grown in M9 minimal media containing either 10 mM MgCl2 (high Mg) or 10 uM MgCl2 (low Mg/Pho-inducing conditions) to mid log phase

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

tag: genotype/variation

value: phoP-/Q- mutant

tag: growth condition

value: Minimial media with High Mg

value: Minimial media with Low Mg


title: Ty800_ Dye reversal

description: Expression profiling of Salmonella enterica serovar Typhi Ty800

organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

value: Ty800 (phoP-/Q- mutant)


title: Ty2_Dye reversal

description: Expression profiling of Salmonella enterica serovar Typhi Ty2


title: Ty800


title: Lt2 phoP mutant_Dye reversal


title: CT18_Dye reversal

description: Expression profiling of Salmonella enterica serovar Typhi CT18

organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18


title: LT2_replicate 3

description: Expression profiling of Salmonella enterica serovar Typhimurium LT2


title: CT18


title: LT2_dye reversal


title: LT2_replicate 2


title: 05-109

city: Beijing

last: Qiao

address: Datun Road

department: System Biology

country: China

institute: Institute of Genetics and Developmental Biology

description:
Chinese ALL sample.
Sample ID: 05-109

hyb_protocol: The labeled RNA was then fragmented and hybridized to HG-U133A 2.0 oligonucleotide arrays (Affymetrix Incorporated, Santa Clara, CA) according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Data were processed by using the robust multi-array analysis (RMA) from the Bioconductor package.

label_protocol: Biotinylated cRNA were synthesized with One-Cycle Target Labeling and Control Reagents (Affymetrix).

extract_protocol: Total RNA was extracted from cryopreserved mononuclear cell suspensions from BM samples using Trizol (Invitrogen) and purified with the RNeasy Kit (Qiagen).

tag: tissue

value: Bone marrow

tag: ethnicity

value: Chinese

tag: disease

value: pediatric acute lymphoblastic leukemia

tag: chinese pediatric all subtype


title: 05-094

description:
Chinese ALL sample.
Sample ID: 05-094

source_name: No fusion B-ALL

value: No fusion B-ALL


title: 05-110

description:
Chinese ALL sample.
Sample ID: 05-110


title: 05-096

description:
Chinese ALL sample.
Sample ID: 05-096


title: control

description:
Pool of 5 Chinese non-ALL BM samples.
Control

hyb_protocol: The labeled RNA was then fragmented and hybridized to HG-U133A 2.0 oligonucleotide arrays (Affymetrix Incorporated, Santa Clara, CA) according to Affymetrix protocols. A total of 10 ug of the pooled RNA was used for a single microarray hybridization.

source_name: control

extract_protocol: Total RNA was extracted from cryopreserved mononuclear cell suspensions from five non-ALL BM samples using Trizol (Invitrogen) and purified with the RNeasy Kit (Qiagen). The purified total RNA samples were pooled together using equal amounts from each sample.


title: 05-080

description:
Chinese ALL sample.
Sample ID: 05-080


title: 05-081

description:
Chinese ALL sample.
Sample ID: 05-081


title: Ty2


title: LT2_replicate 1


title: 05-090

description:
Chinese ALL sample.
Sample ID: 05-090


title: 05-078

description:
Chinese ALL sample.
Sample ID: 05-078


title: 05-072

description:
Chinese ALL sample.
Sample ID: 05-072


title: *05-074

description:
Chinese ALL sample.
Sample ID: 05-074

tag: relapsed

value: yes


title: 05-054

description:
Chinese ALL sample.
Sample ID: 05-054


title: *05-075

description:
Chinese ALL sample.
Sample ID: 05-075


title: 05-044

description:
Chinese ALL sample.
Sample ID: 05-044


title: 05-055

description:
Chinese ALL sample.
Sample ID: 05-055


title: 05-046

description:
Chinese ALL sample.
Sample ID: 05-046


title: 05-041

description:
Chinese ALL sample.
Sample ID: 05-041


title: 05-017

description:
Chinese ALL sample.
Sample ID: 05-017


title: 05-021

description:
Chinese ALL sample.
Sample ID: 05-021


title: 05-043

description:
Chinese ALL sample.
Sample ID: 05-043


title: 05-028

description:
Chinese ALL sample.
Sample ID: 05-028

source_name: T-ALL

value: T-ALL


title: 05-020

description:
Chinese ALL sample.
Sample ID: 05-020


title: 04-175

description:
Chinese ALL sample.
Sample ID: 04-175


title: 05-005

description:
Chinese ALL sample.
Sample ID: 05-005


title: 05-040

description:
Chinese ALL sample.
Sample ID: 05-040


title: 04-174

description:
Chinese ALL sample.
Sample ID: 04-174


title: 04-171

description:
Chinese ALL sample.
Sample ID: 04-171


title: 05-059

description:
Chinese ALL sample.
Sample ID: 05-059


title: 04-169

description:
Chinese ALL sample.
Sample ID: 04-169


title: 04-162

description:
Chinese ALL sample.
Sample ID: 04-162


title: 04-165

description:
Chinese ALL sample.
Sample ID: 04-165


title: 04-164

description:
Chinese ALL sample.
Sample ID: 04-164


title: 04-161

description:
Chinese ALL sample.
Sample ID: 04-161


title: 04-155

description:
Chinese ALL sample.
Sample ID: 04-155


title: 04-156

description:
Chinese ALL sample.
Sample ID: 04-156


title: *04-153

description:
Chinese ALL sample.
Sample ID: 04-153


title: 04-144

description:
Chinese ALL sample.
Sample ID: 04-144


title: 04-157

description:
Chinese ALL sample.
Sample ID: 04-157


title: 04-141

description:
Chinese ALL sample.
Sample ID: 04-141


title: 04-151

description:
Chinese ALL sample.
Sample ID: 04-151


title: 04-150

description:
Chinese ALL sample.
Sample ID: 04-150


title: 04-139

description:
Chinese ALL sample.
Sample ID: 04-139


title: 04-154

description:
Chinese ALL sample.
Sample ID: 04-154


title: 04-136

description:
Chinese ALL sample.
Sample ID: 04-136


title: 04-152

description:
Chinese ALL sample.
Sample ID: 04-152


title: 04-140

description:
Chinese ALL sample.
Sample ID: 04-140


title: 04-149

description:
Chinese ALL sample.
Sample ID: 04-149


title: 04-132

description:
Chinese ALL sample.
Sample ID: 04-132


title: 04-129

description:
Chinese ALL sample.
Sample ID: 04-129


title: 04-134

description:
Chinese ALL sample.
Sample ID: 04-134


title: 04-130

description:
Chinese ALL sample.
Sample ID: 04-130


title: 04-131

description:
Chinese ALL sample.
Sample ID: 04-131


title: 04-128

description:
Chinese ALL sample.
Sample ID: 04-128


title: 04-126

description:
Chinese ALL sample.
Sample ID: 04-126


title: 04-127

description:
Chinese ALL sample.
Sample ID: 04-127


title: *04-123

description:
Chinese ALL sample.
Sample ID: 04-123


title: *04-122

description:
Chinese ALL sample.
Sample ID: 04-122


title: 05-029

description:
Chinese ALL sample.
Sample ID: 05-029


title: 04-112

description:
Chinese ALL sample.
Sample ID: 04-112


title: 04-116

description:
Chinese ALL sample.
Sample ID: 04-116


title: 04-108

description:
Chinese ALL sample.
Sample ID: 04-108


title: 04-107

description:
Chinese ALL sample.
Sample ID: 04-107


title: 04-114

description:
Chinese ALL sample.
Sample ID: 04-114


title: 04-103

description:
Chinese ALL sample.
Sample ID: 04-103


title: *04-106

description:
Chinese ALL sample.
Sample ID: 04-106


title: 04-119

description:
Chinese ALL sample.
Sample ID: 04-119


title: *04-090

description:
Chinese ALL sample.
Sample ID: 04-090


title: 04-099

description:
Chinese ALL sample.
Sample ID: 04-099


title: 04-089

description:
Chinese ALL sample.
Sample ID: 04-089


title: 04-092

description:
Chinese ALL sample.
Sample ID: 04-092


title: 04-111

description:
Chinese ALL sample.
Sample ID: 04-111


title: *04-088

description:
Chinese ALL sample.
Sample ID: 04-088


title: 04-086

description:
Chinese ALL sample.
Sample ID: 04-086


title: *04-081

description:
Chinese ALL sample.
Sample ID: 04-081


title: 04-082

description:
Chinese ALL sample.
Sample ID: 04-082


title: 04-091

description:
Chinese ALL sample.
Sample ID: 04-091


title: 04-080

description:
Chinese ALL sample.
Sample ID: 04-080


title: 04-078

description:
Chinese ALL sample.
Sample ID: 04-078


title: 04-077

description:
Chinese ALL sample.
Sample ID: 04-077


title: 04-076

description:
Chinese ALL sample.
Sample ID: 04-076


title: 04-075

description:
Chinese ALL sample.
Sample ID: 04-075


title: 04-073

description:
Chinese ALL sample.
Sample ID: 04-073


title: 04-072

description:
Chinese ALL sample.
Sample ID: 04-072


title: 04-069

description:
Chinese ALL sample.
Sample ID: 04-069


title: 04-066

description:
Chinese ALL sample.
Sample ID: 04-066


title: 04-057

description:
Chinese ALL sample.
Sample ID: 04-057


title: 04-058

description:
Chinese ALL sample.
Sample ID: 04-058


title: 04-053

description:
Chinese ALL sample.
Sample ID: 04-053


title: *04-047

description:
Chinese ALL sample.
Sample ID: 04-047


title: 04-055

description:
Chinese ALL sample.
Sample ID: 04-055


title: 04-050

description:
Chinese ALL sample.
Sample ID: 04-050


title: 04-059

description:
Chinese ALL sample.
Sample ID: 04-059


title: 04-045

description:
Chinese ALL sample.
Sample ID: 04-045


title: 04-062

description:
Chinese ALL sample.
Sample ID: 04-062


title: *04-046

description:
Chinese ALL sample.
Sample ID: 04-046


title: 04-051

description:
Chinese ALL sample.
Sample ID: 04-051


title: 04-052

description:
Chinese ALL sample.
Sample ID: 04-052


title: 04-044

description:
Chinese ALL sample.
Sample ID: 04-044


title: 04-042

description:
Chinese ALL sample.
Sample ID: 04-042


title: 04-043

description:
Chinese ALL sample.
Sample ID: 04-043


title: Rat2_PCB126_5

city: Niskayuna

first: Erik

middle: A

last: Carlson

state: NY

address: 1 Research Circle

institute: General Electric

description: Rat Pool 2, -5logM PCB 126

hyb_protocol: GeneChips were hybridized according to the standard Affymetrix protocol

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol

data_processing: All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.

source_name: Rat Pool 2, -5logM PCB 126

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

growth_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519

tag: Organism

value: Sprague Dawley Rats

tag: Strain

value: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA

tag: Tissue

value: Liver

tag: Gender

value: Female

tag: Chemical

value: PCB 126

tag: Dose


title: Rat2_PCB126_6

description: Rat Pool 2, -6logM PCB 126

source_name: Rat Pool 2, -6logM PCB 126

extract_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519


title: Rat2_PCB126_8

description: Rat Pool 2, -8logM PCB 126

source_name: Rat Pool 2, -8logM PCB 126

treatment_protocol: See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519


title: 05-011

description:
Chinese ALL sample.
Sample ID: 05-011


title: Rat2_TCDD_6.5

description: Rat Pool 2, -6.5logM TCDD

source_name: Rat Pool 2, -6.5logM TCDD

value: TCDD


title: Rat1_PCB126_8

description: Rat Pool 1, -8logM PCB 126

source_name: Rat Pool 1, -8logM PCB 126


title: Rat1_PCB126_10

description: Rat Pool 1, -10logM PCB 126

source_name: Rat Pool 1, -10logM PCB 126


title: Rat2_PCB126_12

description: Rat Pool 2, -12logM PCB 126

source_name: Rat Pool 2, -12logM PCB 126


title: Rat2_PCB126_10

description: Rat Pool 2, -10logM PCB 126

source_name: Rat Pool 2, -10logM PCB 126


title: Rat2_TCDD_9

description: Rat Pool 2, -9logM TCDD

source_name: Rat Pool 2, -9logM TCDD


title: Rat1_PCB126_5

description: Rat Pool 1, -5logM PCB 126

source_name: Rat Pool 1, -5logM PCB 126


title: Rat1_PCB126_6

description: Rat Pool 1, -6logM PCB 126

source_name: Rat Pool 1, -6logM PCB 126


title: Rat1_TCDD_8

description: Rat Pool 1, -8logM TCDD

source_name: Rat Pool 1, -8logM TCDD


title: Rat2_PCB126_11

description: Rat Pool 2, -11logM PCB 126

source_name: Rat Pool 2, -11logM PCB 126


title: Rat1_TCDD_10

description: Rat Pool 1, -10logM TCDD

source_name: Rat Pool 1, -10logM TCDD


title: Rat1_PCB126_12

description: Rat Pool 1, -12logM PCB 126

source_name: Rat Pool 1, -12logM PCB 126


title: Rat2_TCDD_10

description: Rat Pool 2, -10logM TCDD

source_name: Rat Pool 2, -10logM TCDD


title: Rat2_TCDD_8

description: Rat Pool 2, -8logM TCDD

source_name: Rat Pool 2, -8logM TCDD


title: Rat2_TCDD_12

description: Rat Pool 2, -12logM TCDD

source_name: Rat Pool 2, -12logM TCDD


title: Rat1_TCDD_6.5

description: Rat Pool 1, -6.5logM TCDD

source_name: Rat Pool 1, -6.5logM TCDD


title: Rat1_Control_0

description: Rat Pool 1, vehicle control

source_name: Rat Pool 1, vehicle control

value: Vehicle Control (0.5% DMSO)


title: Rat2_Control_0

description: Rat Pool 2, vehicle control

source_name: Rat Pool 2, vehicle control


title: Rat1_TCDD_12

description: Rat Pool 1, -12logM TCDD

source_name: Rat Pool 1, -12logM TCDD


title: Rat2_TCDD_14

description: Rat Pool 2, -14logM TCDD

source_name: Rat Pool 2, -14logM TCDD


title: Rat1_TCDD_14

description: Rat Pool 1, -14logM TCDD

source_name: Rat Pool 1, -14logM TCDD


title: Human3_PCB126_10

description: Human donor 3, (ZYZ), IVT Lot MHU-L-0730044, was a 46 year-old African-American male who died from anoxia (http://www.celsis.com/characterisation.html).

source_name: Human Donor 3, -10logM PCB126

value: Human

value: Male

tag: Age


title: Human3_PCB126_11

source_name: Human Donor 3, -11logM PCB126


title: Human3_PCB126_12

source_name: Human Donor 3, -12logM PCB126


title: Human3_PCB126_8

source_name: Human Donor 3, -8logM PCB126