title: B5_Frontal_Cortex_HIV infected

description:
35G758.CEL
Gene expression data from the white matter of HIV infected human brain


title: A4_basal_ganglia_Control

status: Public on Aug 01 2012

type: RNA

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

country: USA

institute: University of Nebraska Medical Center

description:
52G759.CEL
Gene expression data from the white matter of control human brain

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Human U133 2.0 plus GeneChips were washed and stained.

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

data_processing: The data were analyzed with Affy package for R programming.

label: biotin

molecule: total RNA

organism: Homo sapiens

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 was performed according to the manufacturer's instructions.

tag: race

value: White

tag: age

tag: gender

value: male

tag: phenotype

value: normal (control)

tag: tissue

value: Basal ganglia


title: A4_Frontal_Cortex_Control

description:
28G758.CEL
Gene expression data from the white matter of control human brain

value: Frontal cortex


title: A5_Frontal_Cortex_Control

description:
29G758.CEL
Gene expression data from the white matter of control human brain


title: A6_Frontal_Cortex_Control

description:
30G758.CEL
Gene expression data from the white matter of control human brain

value: female


title: A2_Frontal_Cortex_Control

description:
26G758.CEL
Gene expression data from the white matter of control human brain


title: A1_Frontal_Cortex_Control

description:
25G758.CEL
Gene expression data from the white matter of control human brain


title: D5_white_matter_HIV infected_w/HAD_w/ HIVE

description:
24G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain

value: Hispanic

value: HIV Infected with HAD and HIV encephalitis (HIVE)

value: White matter


title: B1_Frontal_Cortex_HIV infected

description:
31G758.CEL
Gene expression data from the white matter of HIV infected human brain

value: HIV Infected


title: A3_Frontal_Cortex_Control

description:
27G758.CEL
Gene expression data from the white matter of control human brain


title: C6_white_matter_HIV infected_w/HAD_w/o HIVE

description:
18G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain

value: HIV Infected with neurocognitive impairment (HAD:HIV-associated dementia)


title: D1_white_matter_HIV infected_w/HAD_w/ HIVE

description:
20G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: C2_white_matter_HIV infected_w/HAD_w/o HIVE

description:
14G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: B5_white_matter_HIV infected

description:
11G756.CEL
Gene expression data from the white matter of HIV infected human brain


title: D4_white_matter_HIV infected_w/HAD_w/ HIVE

description:
23G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: B2_white_matter_HIV infected

description:
8G756.CEL
Gene expression data from the white matter of HIV infected human brain


title: B4_white_matter_HIV infected

description:
10G756.CEL
Gene expression data from the white matter of HIV infected human brain


title: A6_white_matter_Control

description:
6G756.CEL
Gene expression data from the white matter of control human brain


title: A1_white_matter_Control

description:
1G756.CEL
Gene expression data from the white matter of control human brain


title: C4_white_matter_HIV infected_w/HAD_w/o HIVE

description:
16G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: A5_white_matter_Control

description:
5G756.CEL
Gene expression data from the white matter of control human brain


title: D3_white_matter_HIV infected_w/HAD_w/ HIVE

description:
22G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: C7_white_matter_HIV infected_w/HAD_w/o HIVE

description:
19G757.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: D2_white_matter_HIV infected_w/HAD_w/ HIVE

description:
21G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain


title: B3_white_matter_HIV infected

description:
9G756.CEL
Gene expression data from the white matter of HIV infected human brain


title: A4_white_matter_Control

description:
4G756.CEL
Gene expression data from the white matter of control human brain


title: A3_white_matter_Control

description:
3G756.CEL
Gene expression data from the white matter of control human brain


title: C5_white_matter_HIV infected_w/HAD_w/o HIVE

description:
17G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: A6_basal_ganglia_Control

description:
54G759.CEL
Gene expression data from the white matter of control human brain


title: B1_white_matter_HIV infected

description:
7G756.CEL
Gene expression data from the white matter of HIV infected human brain


title: C1_white_matter_HIV infected_w/HAD_w/o HIVE

description:
13G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain

value: Black


title: C3_white_matter_HIV infected_w/HAD_w/o HIVE

description:
15G756.CEL
Gene expression data from the white matter of HIV infected HAD human brain


title: SMZL_7q32del_6

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

description: Gene expression data from SMZL patient with 7q32 deletion

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Splenic Marginal Zone Lymphoma patient sample

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Mononuclear cells were isolated from peripheral blood of Splenic Marginal Zone Lymphoma patients

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: disease state

value: splenic marginal zone lymphoma

tag: 7q32 deletion

value: yes


title: SMZL_without_7q32del_1

description: Gene expression data from SMZL patient without 7q32 deletion

value: no


title: A2_white_matter_Control

description:
2G756.CEL
Gene expression data from the white matter of control human brain


title: SMZL_7q32del_5


title: SMZL_7q32del_3


title: SMZL_without_7q32del_3


title: SMZL_7q32del_1


title: DLBCL GEP data N0614

city: Pleasanton

first: Yan

last: Li

state: CA

address: 4300 Hacienda Dr

department: Bioinformatics

institute: Roche Molecular Systems

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample

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

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278.

source_name: DLBCL patient sample

label_protocol: 50 ng of FFPE total RNA was used as input amount for amplification by WT-Ovation FFPE System (NuGEN Cat.# 3400) according to manufacturer’s instructions.  5 μg of the amplified cDNA was fragmentated and biotin labeled by FL-Ovation™ cDNA Biotin Module V2 (NuGEN Cat.# 4200) according to manufacturer’s instructions.

extract_protocol: FFPE RNA was isolated by HighPure Paraffin RNA extraction kit (Roche Applied Science Cat # 03270289001 X) according to manufacturer’s instructions

treatment_protocol: The standard therapy for these patients is rituximab combined with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP).

tag: gene expression profiling subgroup

value: ABC

tag: immunohistochemistry subgroup


title: DLBCL GEP data N0611

value: GCB


title: DLBCL GEP data N0616


title: DLBCL GEP data N0607


title: SMZL_without_7q32del_2


title: SMZL_7q32del_4


title: DLBCL GEP data N0612


title: DLBCL GEP data N0615


title: SMZL_7q32del_2


title: DLBCL GEP data N0618


title: DLBCL GEP data N0603

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278. The signal used was DQN3, i.e., DQN signal normalized with quantiles of the beta distribution with parameters p=1.2 and q=3


title: DLBCL GEP data N0609


title: DLBCL GEP data N0602


title: DLBCL GEP data N0617

value: UC


title: D1_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE

description:
44G757.CEL
Gene expression data from the white matter of HIV infected HAD and HIVE human brain

value: White

value: male


title: DLBCL GEP data N0608


title: DLBCL GEP data N0605


title: DLBCL GEP data N0601


title: DLBCL GEP data N0600


title: DLBCL GEP data N0598


title: DLBCL GEP data N0597


title: DLBCL GEP data N0610


title: DLBCL GEP data N0606

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensit


title: DLBCL GEP data N0593


title: DLBCL GEP data N0581


title: DLBCL GEP data N0590


title: DLBCL GEP data N0588


title: DLBCL GEP data N0592


title: DLBCL GEP data N0589


title: DLBCL GEP data N0596


title: DLBCL GEP data N0583


title: DLBCL GEP data N0585


title: DLBCL GEP data N0586


title: DLBCL GEP data N0591


title: DLBCL GEP data N0578


title: DLBCL GEP data N0584


title: DLBCL GEP data N0575


title: DLBCL GEP data N0580


title: DLBCL GEP data N0577


title: DLBCL GEP data N0576


title: DLBCL GEP data N0582


title: DLBCL GEP data N0594


title: DLBCL GEP data N0595


title: DLBCL GEP data N0574


title: DLBCL GEP data N0568


title: DLBCL GEP data N0571


title: DLBCL GEP data N0569


title: DLBCL GEP data N0573


title: DLBCL GEP data N0557


title: DLBCL GEP data N0559


title: DLBCL GEP data N0560


title: DLBCL GEP data N0554


title: DLBCL GEP data N0566


title: DLBCL GEP data N0549


title: DLBCL GEP data N0555


title: DLBCL GEP data N0551


title: DLBCL GEP data N0553


title: DLBCL GEP data N0545


title: DLBCL GEP data N0547


title: DLBCL GEP data N0539


title: DLBCL GEP data N0541


title: DLBCL GEP data N0556


title: DLBCL GEP data N0540


title: DLBCL GEP data N0567


title: DLBCL GEP data N0550


title: DLBCL GEP data N0538


title: DLBCL GEP data N0552


title: DLBCL GEP data N0562


title: DLBCL GEP data N0542


title: DLBCL GEP data N0546


title: DLBCL GEP data N0548


title: DLBCL GEP data N0536


title: DLBCL GEP data N0531


title: DLBCL GEP data N0533


title: DLBCL GEP data N0526


title: DLBCL GEP data N0529


title: DLBCL GEP data N0527


title: DLBCL GEP data N0528


title: DLBCL GEP data N0570


title: DLBCL GEP data N0535


title: DLBCL GEP data N0530


title: DLBCL GEP data N0524


title: DLBCL GEP data N0532


title: DLBCL GEP data N0521


title: DLBCL GEP data N0516


title: DLBCL GEP data N0518


title: DLBCL GEP data N0500


title: DLBCL GEP data N0517


title: DLBCL GEP data N0514


title: DLBCL GEP data N0506


title: DLBCL GEP data N0513


title: DLBCL GEP data N0579


title: DLBCL GEP data N0510


title: DLBCL GEP data N0494


title: DLBCL GEP data N0498


title: DLBCL GEP data N0511


title: DLBCL GEP data N0502


title: DLBCL GEP data N0497


title: DLBCL GEP data N0509


title: DLBCL GEP data N0522


title: DLBCL GEP data N0491


title: W4 mES cells from Taconic, P15

city: Singapore

first: Bipasha

last: Bose

address: 60, Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Gene expression of 70% confluent feeder free colonies

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Cultured cells, mouse ES cells, W4, Passage15

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Cell isolation protocol. MDSC were isolated using a well established preplate technique based on cell adhesion properties from entire hindlimb muscles of WT and Myostatin null mice. The cells settle as different fractions called rapidly adhering populations(RAP) in the begining and slowly adhering cell poulations (SAP). RAPs are primarily fibroblasts follwed by myoblasts while SAPs are stem cells called MDSC. This protocol involves 0.2% collagenase 1 digestion of entire hind limb muscles of mice followed by their initial plating for 3 hours onto tissue culture dishes. After three hours, the settling down cell population is called Preplate1(PP1). The supernatant  from PP1 was then transferred to a matrigel coated 10cm tissue culture dish  and was allowed to settle for 24 hours. The adhering cell population is called Preplate2(PP2). Next day, after 24 hours,the supernatant from PP2 which is called PP3 was  transferred to another matrigel coated 10 cm dish for adhesion for another 24 hours. Like this sequential transfer of supernatant was done every 24 hours till preplate 6( PP6). The adhering cell population from PP6 is called MDSC. MDSC at P1 was expanded and used for RNA isolation and current microarray gene expression analysis. In case of mouse ES cells, the W4 mES cell line from Taconic was received as a gift.These cells at P11 was revived on mitomycin C inactivated Mouse Embryonic Fibroblasts( MEF)/Feeders and then passaged till P15 on mitotically inactivated feeders.For RNA isolation of mESC, the W4 mESC growing on MEFs were trypsinized and plated onto gelatin coated dishes for 20 minutes so as to get rid of the MEFs.
MDSC isolated by preplate technique were grown on MDSC media consisting of DMEM, high glucose with 10% fetal bovine serum( Hyclone), 10% Horse serum(Gibco),!%Chicken Embryo Extract(US Biologicals),1% Penstep( Gibco) and 0.1mM cell culture grade β mercaptoethanol( Sigma) under 5% CO2 and humidified environment in a tissue culture incubator. W4 mESC were grown on mitotically inactivated MEFs in media containing DMEM High Glucose, 20% Fetal bovine serum(Hyclone),1% Non Essential Amino Acids(Gibco),1%Sodium pyruvate(Gibco),1%L-Glutamine(Gibco), 1% Penstep(Gibco) and Leukemia inhibitory factor , LIF(Millipore) at a concentration of 10^3 units per ml under 5% CO2 and humidified environment in a tissue culture incubator.

extract_protocol: RNA was prepared using Qiagen RNeasy Mini kit as per manufacturer's instructions.

treatment_protocol: As the cells were plain growing cells and the aim of the experiment was to define the cell potency on the basis of gene expression signature, no treatment were given to MDSC or mESC.

value: Mouse Embryos as source of ESC

value: Male

value: Not applicable


title: DLBCL GEP data N0499


title: DLBCL GEP data N0501


title: DLBCL GEP data N0505


title: DLBCL GEP data N0519


title: DLBCL GEP data N0525


title: DLBCL GEP data N0488


title: DLBCL GEP data N0489


title: DLBCL GEP data N0487


title: DLBCL GEP data N0492


title: DLBCL GEP data N0485


title: W4 mES cells from Taconic, P12

source_name: Cultured cells, mouse ES cells, W4, Passage12


title: MDSC, P1, WT mice, Isolation 2

description: Gene expression of 70% confluent cells in culture

source_name: Cultured cells, WT MDSC, Passage-1, Replicate2

value: Hindlimb muscle as source of MDSC

value: 5 weeks


title: DLBCL GEP data N0486


title: DLBCL GEP data N0477


title: DLBCL GEP data N0483


title: DLBCL GEP data N0480


title: DLBCL GEP data N0484


title: DLBCL GEP data N0481


title: DLBCL GEP data N0474


title: DLBCL GEP data N0476


title: DLBCL GEP data N0479


title: MDSC, P1, Mystn null mice, Isolation 2

source_name: Cultured cells, Mstn null MDSC, Passage-1, Replicate2


title: MDSC, P1, Mystn null mice, Isolation 1

source_name: Cultured cells, Mstn null MDSC, Passage-1, Replicate1


title: CON_2

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression in mouse skin 12 hr post-initiation

hyb_protocol: Samples were hybridized to the Agilent 8X60 K mouse array following manufacturer instructions.

scan_protocol: Agilent Technologies Scanner G2505C 3um 20bit

data_processing: Raw Agilent intensity data were background subtracted and quantile-normalized by RMA summarization as described by (Bolstad et al., 2003). Statistical analysis was performed by one-way ANOVA for unequal variances (Welch’s ANOVA) with Tukey’s posthoc test and 5% FDR.

source_name: Mouse skin exposed to toluene control (CON), biological rep2

label_protocol: The RNA was labeled with Agilent’s 2 color Quickamp kit.

extract_protocol: In order to eliminate RNase degradation, epidermis and dermis layers were kept intact, removed as one piece and snap frozen in liquid nitrogen. A 1-cm2 section of frozen skin was placed in a 15-ml sterile, disposable conical homogenizer, VWR Scientific Inc. (San Francisco, CA.) and homogenized in 2 ml Trizol® reagent. RNA was extracted according to the manufacturer’s instructions followed by a clean-up step using an RNeasy® mini kit, Qiagen Corp.,  Valencia, CA.

treatment_protocol: At 7.5 weeks of age, mice were shaved on their dorsal surface and allowed to rest 48 h to confirm that animals were in the resting phase of the hair growth cycle. The following initiation treatments were applied to groups of  mice (N=4 or 5 biological replicates) by slowly pipetting solutions on the shaved area; toluene vehicle control (200 μl), benzo[a]pyrene (BAP) 400 nmol (100 μg), dibenzo[def,p]chrysene (DBC) 4 nmol (1.2 μg), or 1 of 3 PAH mixtures: Mix 1 (1 mg diesel particulate extract), Mix 2 (1 mg diesel particulate extract + 1 mg coal tar extract), or Mix 3(1 mg diesel particulate extract + 1 mg coal tar extract + 2 mg cigarette smoke condensate).

tag: treatment

value: toluene vehicle control (200 ul)

value: skin

tag: strain

value: FVB/N


title: DLBCL GEP data N0471


title: DLBCL GEP data N0470


title: DLBCL GEP data N0472


title: DLBCL GEP data N0473


title: CON_1

source_name: Mouse skin exposed to toluene control (CON), biological rep1


title: MDSC, P1, WT mice, Isolation 1

source_name: Cultured cells, WT MDSC, Passage-1, Replicate1


title: CON_4

source_name: Mouse skin exposed to toluene control (CON), biological rep4


title: Mix2_2

source_name: Mouse skin exposed to PAH mixture 2 (Mix2), biological rep2

value: 1 mg diesel particulate extract + 1 mg coal tar extract


title: Mix3_3

source_name: Mouse skin exposed to PAH mixture 3 (Mix3), biological rep3

value: 1 mg diesel particulate extract + 1 mg coal tar extract + 2 mg cigarette smoke condensate


title: CON_5

source_name: Mouse skin exposed to toluene control (CON), biological rep5


title: Mix3_1

source_name: Mouse skin exposed to PAH mixture 3 (Mix3), biological rep1


title: DLBCL GEP data N0469


title: DLBCL GEP data N0467


title: CON_3

source_name: Mouse skin exposed to toluene control (CON), biological rep3


title: DLBCL GEP data N0468


title: Mix3_2

source_name: Mouse skin exposed to PAH mixture 3 (Mix3), biological rep2


title: Mix2_3

source_name: Mouse skin exposed to PAH mixture 2 (Mix2), biological rep3


title: Mix2_4

source_name: Mouse skin exposed to PAH mixture 2 (Mix2), biological rep4


title: Mix1_3

source_name: Mouse skin exposed to PAH mixture 1 (Mix1), biological rep3

value: 1 mg diesel particulate extract


title: Mix3_4

source_name: Mouse skin exposed to PAH mixture 3 (Mix3), biological rep4


title: Mix1_4

source_name: Mouse skin exposed to PAH mixture 1 (Mix1), biological rep4


title: Mix2_1

source_name: Mouse skin exposed to PAH mixture 2 (Mix2), biological rep1


title: Mix1_2

source_name: Mouse skin exposed to PAH mixture 1 (Mix1), biological rep2


title: DLBCL GEP data N0459

source_name: DLBCL patient sample


title: DLBCL GEP data N0464


title: DBC_4

source_name: Mouse skin exposed to dibenzo[def,p]chrysene (DBC), biological rep4

value: dibenzo[def,p]chrysene (DBC) 4 nmol (1.2 ug)


title: DLBCL GEP data N0458

value: ABC


title: DLBCL GEP data N0449


title: Mix1_1

source_name: Mouse skin exposed to PAH mixture 1 (Mix1), biological rep1


title: DLBCL GEP data N0466

value: GCB


title: DBC_1

source_name: Mouse skin exposed to dibenzo[def,p]chrysene (DBC), biological rep1


title: DLBCL GEP data N0451


title: DLBCL GEP data N0454

value: UC


title: DLBCL GEP data N0456


title: DLBCL GEP data N0450


title: BAP_4

source_name: Mouse skin exposed to benzo[a]pyrene (BAP), biological rep4

value: benzo[a]pyrene (BAP) 400 nmol (100 ug)


title: DLBCL GEP data N0452


title: DBC_2

source_name: Mouse skin exposed to dibenzo[def,p]chrysene (DBC), biological rep2


title: DBC_3

source_name: Mouse skin exposed to dibenzo[def,p]chrysene (DBC), biological rep3


title: DLBCL GEP data N0460


title: DLBCL GEP data N0455


title: DLBCL GEP data N0448


title: BAP_1

source_name: Mouse skin exposed to benzo[a]pyrene (BAP), biological rep1


title: DLBCL GEP data N0442


title: BAP_3

source_name: Mouse skin exposed to benzo[a]pyrene (BAP), biological rep3


title: DLBCL GEP data N0446


title: DLBCL GEP data N0443


title: UtxKO +/- RA

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 65°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Agilent Wash Buffer 1 at room temperature for 2 minutes, and then AgilentWash Buffer 2 for 2 minutes at 37°C. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature

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

data_processing: Within-array LOESS and Across-array quantile normalization using limma for R

source_name: UtxKO ESC

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s Low Input Quick Amp Sample Labeling Kit. Input was 200ng total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: ES cells were grown on gelatin in an undifferentiated state (ES medium (+LIF)).

extract_protocol: Cells were washed with PBS and RNA was extracted using RNAeasy Kit (Qiagen).

treatment_protocol: ES media was replaced with ES media minus LIF plus 1x10-7M retinoic acid (RA).  Cells were cultured for an additional 48 hours with one media exchange.

tag: cell type

value: ES cells

tag: genotype/variation

value: Utx KO

tag: developmental stage

value: RA for 48 hrs


title: V6.5 +/- RA

source_name: V6.5 ESC

value: WT


title: DLBCL GEP data N0447


title: BAP_2

source_name: Mouse skin exposed to benzo[a]pyrene (BAP), biological rep2


title: DLBCL GEP data N0441


title: DLBCL GEP data N0440


title: DLBCL GEP data N0428


title: DLBCL GEP data N0433


title: DLBCL GEP data N0431


title: DLBCL GEP data N0439


title: T. gammatolerans cells treated 270min with 1mM cadmium sulfate, Replicate 2

city: Orsay

first: Arnaud

last: Lagorce

address: Université Paris-Sud 11

department: Institut de Génétique et de Microbiologie

country: France

institute: University Paris Sud

description: T. gammatolerans cells treated 270min with 1mM cadmium sulfate (slide name: AUT015, barcode: 019487)

hyb_protocol: After a denaturation step for 2 min at 95°C, the concentrated Cy3 and Cy5 cDNA were dropped onto glass slide microarrays and incubated in a hybridization chamber (Corning) for 17h at 50°C. Four post-hybridization washes of 5min were carried out at room temperature by incubating slides under agitation in a 2x SSC/0.1% SDS solution, in a 1x SSC solution, in a 0.2x SSC solution and in a 0.05x SSC solution, respectively. The slides were dried by centrifugation.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

data_processing: Fluorescent signals were detected by a laser microarray scanner (GenePix 4000B from Axon Instruments). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained using Genepix Pro 4.0 software (Axon Instruments). Spots or areas of the array with obvious blemishes, deformation or dust were manually flagged and excluded from subsequent analysis. The result files were imported into MANGO software and a non-linear LOWESS normalization was applied to the raw data. Each gene expression ratio is reported as an average value, and statistical significance was calculated using the Student’s t-test.

organism: Thermococcus gammatolerans

label_protocol: Indirect labeling of cDNA (amino allyl-dUTP) with either cyanine3 (Cy3) or cyanine5 (Cy5) monofunctional NHS-ester (Amersham Bioscience) occurred after the reverse transcription. cDNAs, mono reactive Cy3 or Cy5 dye and 1μl of 0.5M pH9 sodium bicarbonate are mixed together and incubated 1 hour at room temperature in the dark for the coupling reaction. The fluorescently labeled cDNAs were purified using a Nucleospin Extract II kit (Macherey-Nagel) and dye incorporation was measured using Nanodrop BD-1000 spectrophotometer (Nanodrop Technologies).

growth_protocol: Large volumes of exponentially growing cells (600mL in 1L Schott bottles) were treated with Cd (0.1 mM or 1mM) before sampling 30, 120 and 270min after Cd addition. Cells were left 5 min at 4°C without shaking, leading to cystine sedimentation in the bottle, pelleted by centrifugation 20min/2000g/4°C, immediately frozen and stored at -80°C until further processing.

extract_protocol: Total RNAs were extracted with TriReagent solution (Sigma) and contaminating DNA was digested using DNA-free™ (Ambion) following the manufacturer's instructions. RNA quantity and quality were assessed using a Nanodrop BD-1000 spectrophotometer (Nanodrop Technologies) and Experion Automated Electrophoresis System (Bio-Rad Laboratories), respectively. The reverse transcription reactions were performed with 400 units of Superscript II reverse transcriptase (Invitrogen), RNA (20μg), random hexamers (6µg), 1.5 mM dATP, dCTP, and dGTP, 1.2 mM dTTP, and 0.3 mM amino allyl-dUTP (Sigma) for 1.5 hours at 42°C. RNA was then hydrolyzed during 15min at 37°C by 2 units of RNase H. The cDNAs were purified with Microcon-G30 (Millipore), dried and resuspended in 10μL water.

tag: As a control RNA, T. gammatolerans cells treated 270min with 0mM cadmium sulfate was used


title: T. gammatolerans cells treated 270min with 1mM cadmium sulfate, Replicate 4

description: T. gammatolerans cells treated 270min with 1mM cadmium sulfate (slide name: AUW016, barcode: 019813)

source_name: T. gammatolerans cells treated 270min with 0mM cadmium sulfate


title: T. gammatolerans cells treated 270min with 1mM cadmium sulfate, Replicate 3

description: T. gammatolerans cells treated 270min with 1mM cadmium sulfate (slide name: AUW008, barcode: 019811)

tag: T. gammatolerans cells treated 270min with 0mM cadmium sulfate


title: DLBCL GEP data N0437


title: DLBCL GEP data N0435


title: T. gammatolerans cells treated 270min with 1mM cadmium sulfate, Replicate 1

description: T. gammatolerans cells treated 270min with 1mM cadmium sulfate (slide name AUT014, barcode 019488)

tag: T. gammatolerans cells treated 270min with 0µM cadmium sulfate


title: DLBCL GEP data N0434


title: DLBCL GEP data N0426


title: DLBCL GEP data N0422


title: DLBCL GEP data N0425


title: DLBCL GEP data N0419


title: DLBCL GEP data N0424


title: DLBCL GEP data N0415


title: T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate, Replicate 2

description:
T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate
(slide name: AUT017, barcode: 019489)

source_name: T. gammatolerans cells treated 270min with 0,1mM cadmium sulfate

tag: As a control RNA, T. gammatolerans cells treated 270min with 0 mM cadmium sulfate was used


title: DLBCL GEP data N0421


title: DLBCL GEP data N0420


title: T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate, Replicate 3

description:
T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate
(slide name: AUW009, barcode: 019760)


title: DLBCL GEP data N0418


title: T. gammatolerans cells treated 120min with 1mM cadmium sulfate, Replicate 4

description:
T. gammatolerans cells treated 120min with 1mM cadmium sulfate
(slide name: AUW013, barcode: 019816)

tag: As a control RNA, T. gammatolerans cells treated 120min with 0mM cadmium sulfate was used


title: T. gammatolerans cells treated 270min with 0,1mM cadmium sulfate, Replicate 1

description: T. gammatolerans cells treated 270min with 0,1mM cadmium sulfate (slide name AUT016, barcode 019527)

tag: T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate


title: T. gammatolerans cells treated 270min with 0,1mM cadmium sulfate, Replicate 4

description:
T. gammatolerans cells treated 270min with 0,1 mM cadmium sulfate
(slide name: AUW017, barcode 019752)


title: T. gammatolerans cells treated 120min with 1mM cadmium sulfate, Replicate 3

description:
T. gammatolerans cells treated 120min with 1mM cadmium sulfate
(slide name: AUW005, barcode 019753)

source_name: T. gammatolerans cells treated 120min with 0mM cadmium sulfate


title: DLBCL GEP data N0417


title: T. gammatolerans cells treated 120min with 1mM cadmium sulfate, Replicate 2

description:
T. gammatolerans cells treated 120min with 1mM cadmium sulfate
(slide name: AUT007, barcode: 019616)

tag: T. gammatolerans cells treated 120min with 0mM cadmium sulfate


title: T. gammatolerans cells treated 120min with 1mM cadmium sulfate, Replicate 1

description:
T. gammatolerans cells treated 120min with 1mM cadmium sulfate
(slide name: AUT006, barcode 019614)


title: T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate, Replicate 4

description:
T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate
(slide name: AUW014, barcode 019815)

source_name: T. gammatolerans cells treated 120min with 0,1mM cadmium sulfate


title: DLBCL GEP data N0416

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample


title: DLBCL GEP data N0412


title: DLBCL GEP data N0414


title: DLBCL GEP data N0413


title: T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate, Replicate 3

description:
T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate
(slide name: AUW006, barcode: 019751)

tag: T. gammatolerans cells treated 120 min with 0,1mM cadmium sulfate

tag: As a control RNA, T. gammatolerans cells treated 120 min with 0mM cadmium sulfate was used


title: DLBCL GEP data N0405


title: T. gammatolerans cells treated 30min with 1mM cadmium sulfate, Replicate 4

description:
T. gammatolerans cells treated 30 min with 1 mM cadmium sulfate
(slide name: AUW003, barcode: 019756)

source_name: T. gammatolerans cells treated 30 min with 1mM cadmium sulfate

growth_protocol: Larges volumes of exponentially growing cells (600mL in 1L Schott bottles) were treated with Cd (0.1 mM or 1mM) before sampling 30, 120 and 270min after Cd addition. Cells were left 5 min at 4°C without shaking, leading to cystine sedimentation in the bottle, pelleted by centrifugation 20min/2000g/4°C, immediately frozen and stored at -80°C until further processing.

tag: As a control RNA, T. gammatolerans cells treated 30 min with 0 mM cadmium sulfate was used

source_name: T. gammatolerans cells treated 30 min with 0mM cadmium sulfate


title: T. gammatolerans cells treated 120min with 0,1mM cadmium sulfate, Replicate 2

description:
T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate
(slide name: AUT009, barcode 019698)


title: DLBCL GEP data N0407

source_name: DLBCL patient sample

tag: gene expression profiling subgroup


title: T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate, Replicate 1

description:
T. gammatolerans cells treated 120min with 0,1 mM cadmium sulfate
(slide name: AUT008, barcode: 019697)

tag: T. gammatolerans cells treated 120 min with 0,1 mM cadmium sulfate

tag: As a control RNA, T. gammatolerans cells treated 120 min with 0 mM cadmium sulfate was used

tag: T. gammatolerans cells treated 120min with 0µM cadmium sulfate

tag: Growth protocol


title: T. gammatolerans cells treated 30min with 1mM cadmium sulfate, Replicate 3

description:
T. gammatolerans cells treated 30 min with 1 mM cadmium sulfate
(slide name: AUT003, barcode: 019615)

tag: T. gammatolerans cells treated 30 min with 1mM cadmium sulfate

tag: As a control RNA, T. gammatolerans cells treated 30 min with 0mM cadmium sulfate was used

tag: T. gammatolerans cells treated 30 min with 0µM cadmium sulfate


title: DLBCL GEP data N0410

tag: immunohistochemistry subgroup


title: DLBCL GEP data N0406


title: DLBCL GEP data N0408


title: T. gammatolerans cells treated 30min with 1mM cadmium sulfate, Replicate 1

description: T. gammatolerans cells treated 30 min with 1 mM cadmium sulfate (slide name AUT002, barcode 019611)

hyb_protocol: After a denaturation step for 2 min at 95°C, the concentrated Cy3 and Cy5 cDNA were dropped onto glass slide microarrays and incubated in a hybridization chamber (Corning) for 17h at 50°C. Four post-hybridization washes of 5min were carried out at room temperature by incubating slides under agitation in a 2x SSC/0.1% SDS solution, in a 1x SSC solution, in a 0.2x SSC solution and in a 0.05x SSC solution, respectively. The slides were dried by centrifugation. Scan protocol

treatment_protocol: Larges volumes of exponentially growing cells (600mL in 1L Schott bottles) were treated with Cd (0.1 mM or 1mM) before sampling 30, 120 and 270min after Cd addition. Cells were left 5 min at 4°C without shaking, leading to cystine sedimentation in the bottle, pelleted by centrifugation 20min/2000g/4°C, immediately frozen and stored at -80°C until further processing.

tag: T. gammatolerans cells treated 30 min with 0 µM cadmium sulfate


title: DLBCL GEP data N0403


title: T. gammatolerans cells treated 30min with 1mM cadmium sulfate, Replicate 2

description: T. gammatolerans cells treated 30 min with 1 mM cadmium sulfate (slide name AUW011, barcode 019758)

source_name: T. gammatolerans cells treated 30 min with 0 mM cadmium sulfate


title: DLBCL GEP data N0411


title: DLBCL GEP data N0400


title: T. gammatolerans cells treated 30min with 0,1 mM cadmium sulfate, Replicate 3

description:
T. gammatolerans cells treated 30 min with 0,1 mM cadmium sulfate
(slide name: AUT004, barcode: 019612)


title: T. gammatolerans cells treated 30min with 0,1 mM cadmium sulfate, Replicate 2

description:
T. gammatolerans cells treated 30 min with 0,1 mM cadmium sulfate
(slide name: AUW010, barcode: 019759)


title: DLBCL GEP data N0404


title: DLBCL GEP data N0401


title: T. gammatolerans cells treated 30min with 0,1 mM cadmium sulfate, Replicate 4

description:
T. gammatolerans cells treated 30 min with 0,1 mM cadmium sulfate
(slide name: AUT005, barcode: 019613)


title: Strain 2221ΔFasX after 60 min exposure to plasma sample B

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

hyb_protocol: Labeled cDNA was hybridized to out custom array for 16h at 40 degrees C.  GeneChips were washed and stained using  the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Streptococcus pyogenes

source_name: 60 min exposure

label_protocol: RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin

growth_protocol: GAS strains were grown in THY broth to O.D. 600 of 0.5, pelleted, and resuspended in human plasma.  Samples were taken after 0, 15, and 60 mins.

extract_protocol: Total RNA was extracted via mechanical disruption and purified using the Qiagen Rneasy kit.

treatment_protocol: Two volumes of RNAprotect was added to each strain, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.

tag: strain

value: fasX mutant


title: Strain 2221ΔFasX after 0 min exposure to plasma sample B

source_name: 0 min exposure


title: Strain 2221ΔFasX after 15 min exposure to plasma sample B

source_name: 15 min exposure


title: DLBCL GEP data N0398


title: T. gammatolerans cells treated 30min with 0,1 mM cadmium sulfate, Replicate 1

description:
T. gammatolerans cells treated 30 min with 0,1 mM cadmium sulfate
(slide name: AUW002, barcode: 019757)

treatment_protocol: cadmium treatment

treatment_protocol: NON TREATED


title: DLBCL GEP data N0397


title: DLBCL GEP data N0427


title: DLBCL GEP data N0399


title: Strain MGAS2221 after 15 min exposure to plasma sample B


title: DLBCL GEP data N0393


title: DLBCL GEP data N0396


title: Strain MGAS2221 after 60 min exposure to plasma sample B


title: DLBCL GEP data N0395


title: Strain 2221ΔFasX after 60 min exposure to plasma sample A


title: Strain MGAS2221 after 0 min exposure to plasma sample B


title: Strain 2221ΔFasX after 0 min exposure to plasma sample A


title: DLBCL GEP data N0391


title: DLBCL GEP data N0389


title: DLBCL GEP data N0392


title: DLBCL GEP data N0390


title: Strain 2221ΔFasX after 15 min exposure to plasma sample A


title: Strain MGAS2221 after 15 min exposure to plasma sample A


title: Strain MGAS2221 after 60 min exposure to plasma sample A


title: Splenic Marginal Zone Lymphoma P57

type: genomic

hyb_protocol: Hybridization methods and analytical procedures have been described elsewhere: Snijder AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.

scan_protocol: Images of the arrays were captured using a custom-built CCD camera

data_processing: UCSF SPOT software was used to analyze the images

molecule: genomic DNA

source_name: Splenic Marginal Zone Lymphoma P57

label_protocol: genomic DNA from SMZL samples and reference genomic DNA were labeled by random priming using Cy3 and Cy5, respectively

extract_protocol: genomic DNA were extracted from mononuclear cells of Splenic Mariginal Zone Lymphoma patients obtained from spleen, peripheral blood or bone marrow using standard methods

tag: disease state

value: Splenic Marginal Zone Lymphoma

source_name: reference genomic DNA

tag: sample type

value: reference


title: Splenic Marginal Zone Lymphoma P76

source_name: Splenic Marginal Zone Lymphoma P76


title: Strain MGAS2221 after 0 min exposure to plasma sample A


title: DLBCL GEP data N0388


title: Splenic Marginal Zone Lymphoma P70

source_name: Splenic Marginal Zone Lymphoma P70


title: Splenic Marginal Zone Lymphoma P42

source_name: Splenic Marginal Zone Lymphoma P42


title: DLBCL GEP data N0386


title: DLBCL GEP data N0379


title: DLBCL GEP data N0385


title: DLBCL GEP data N0387


title: DLBCL GEP data N0383


title: normal (grade 1) articular cartilage, superficial zone, rep 1

city: La Jolla

first: Shawn

middle: Patrick

last: Grogan

address: 10550 N. Torrey Pines Road, MEM161

department: MEM

institute: TSRI

description:
062211_Bov1SZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

hyb_protocol: The post fragmentation and labeling product (5ug) was used for the hybridization cocktail and hybridized overnight to the Affymetrix GeneChip Bovine Genome Array (Affymetrix P/N 900562) following the NuGEN Encore Biotin Module protocol.  Hybridization and scanning of samples to arrays was performed using the standard NuGEN Hybridization, Cocktail Assembly, and Fluidics Protocols  using Affymetrix’s GeneChip Hybridization, Wash, and Stain Kit (Affymetrix P/N 900720), according to Appendix V1 of the NuGEN Encore Biotin Module protocol.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G with default settings and a target intensity of 250 for scaling.

data_processing:
Data was normalized using both RMA and dCHIP.
Log2 RMA signals are presented in the data table below.
Log2 dCHIP signals can be found in a supplementary file linked to the Series record.
The normalized data have filtered out the Affymetrix Control probes and the 30% lowest variant probesets.

organism: Bos taurus

source_name: bov1, cartilage, superficial zone

label_protocol: Five nanograms (5 ng) of total RNA was taken through the NuGEN Ovation Pico WTA System version 1.0.  Post amplification, 5ug of the purified cDNA product was fragmented and labeled using NuGEN Encore Biotin Module.

growth_protocol: skeletally mature animals (14-30 months of age)

extract_protocol: Total RNA was isolated from cartilage zones using the Qiagen Rneasy kit with Dnase digestion following the manufacturer's instructions.  Total RNA was quantified using NanoDrop (ND-1000).  Sample quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Pico LabChip (Agilent Cat. # 5065-4473).

treatment_protocol: Osteochondral cores were obtained from weight bearing area of the distal femoral condyles of bovine knees.  The bone portion of each osteochondral core was embedded in paraffin in a standard plastic cassette to allow fixation of the plug in the microtome. The entire cartilage was sliced into 50 μm thick sections from the cartilage surface downwards to the calcified cartilage using a microtome (Microm HM 325, Thermo Scientific, Walldorf, Germany).  Each section was transferred to one well of a 96-well plate filled with RNAlater (Qiagen). The sections were segregated into zones for RNA isolation as follows: The upper 10% of zonal slices were allocated to the SZ, the middle 40% were allocated to the MZ and the lower 30% were allocated to the DZ. To avoid overlap between zones, regions of approximately 200 μm between the SZ and MZ and between the MZ and DZ were discarded.

tag: bovine id

tag: age

value: mature (14-30 months)

tag: tissue

value: cartilage, superficial zone


title: DLBCL GEP data N0382


title: DLBCL GEP data N0381


title: DLBCL GEP data N0377


title: DLBCL GEP data N0380


title: DLBCL GEP data N0384


title: DLBCL GEP data N0378


title: normal (grade 1) articular cartilage, deep zone, rep 2

description:
110111_Bov4DZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

source_name: bov4, cartilage, deep zone

value: cartilage, deep zone


title: normal (grade 1) articular cartilage, mid zone, rep 2

description:
062211_Bov4MZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

source_name: bov4, cartilage, middle zone

value: cartilage, middle zone


title: normal (grade 1) articular cartilage, superficial zone, rep 2

description:
062211_Bov4SZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

source_name: bov4, cartilage, superficial zone


title: DLBCL GEP data N0376


title: normal (grade 1) articular cartilage, mid zone, rep 1

description:
062211_Bov1MZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

source_name: bov1, cartilage, middle zone


title: normal (grade 1) articular cartilage, deep zone, rep 1

description:
110111_Bov1DZ
normal mature (14-30 months) bovine articular cartilage from medial and lateral condyles of knee joints

source_name: bov1, cartilage, deep zone


title: DLBCL GEP data N0374

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample


title: DLBCL GEP data N0373


title: DLBCL GEP data N0371


title: Splenic Marginal Zone Lymphoma P64

source_name: Splenic Marginal Zone Lymphoma P64


title: DLBCL GEP data N0370

source_name: DLBCL patient sample


title: PB-025

city: Stanford

first: Stanley

middle: G.

last: Rockson

address: 300 Pasteur Dr.

department: Cardiovascular Medicine

institute: Stanford University

description:
Stanford HIMC numbering: Sample 75
Clinical Specimen ID: PB-025
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.

hyb_protocol: Labeled cRNA (850 mcg) was hybridized overnight to the Agilent Whole Human Genome 4 × 44 K slide (Cat. #G4845A) that contains 44,000 probes, including 19,596 Entrez Gene RNAs.

scan_protocol: The arrays were then washed, blocked, stained and scanned on the Agilent microarray scanner following the manufacturer’s protocols.

data_processing: Data were extracted using Agilent Feature Extraction Software. The log10 ratios were taken directly from the 'LogRatio' column of the Agilent Feature Extraction files, then imported into the statistical program R for analysis.  Microarray normalization was performed by library marray in the statistical program R 2.12.2.  The method is "within-print-tip-group intensity dependent location normalization using the loess function." The first output of data we receive from the program is a single value for each identifier that represents an aggregate log2(lymphedema/normal) value.  The aggregate log2(lymphedema/normal) matrix is linked as a supplementary file on the Series record.

source_name: Lymphedema Limb Skin Biopsy

label_protocol: Cy3 and/or Cy5 florescent dye-labeled, amplified antisense complementary RNA (cRNA) targets were prepared from 20 to 500 ng of the total RNA using the Agilent QuickAmp labeling kit (5190-0444) or the Low Input Quick Amp Labeling Kit (Cat.# 5190-2305).

extract_protocol: Skin biopsies were collected in 1ml TRIzol (Invitrogen, Cat.# 10296-010), homogenized, and stored at -80c until use. Total RNA was isolated according to the manufacturer’s Instructions by using TRIzol protocol (Invitrogen) or Qiagen RNeasy Mini Kit (QIAGEN, Cat.# 74104).For using the Qiagen RNeasy Mini Kit, the entire procedure was carried out at room temperature with the QIAcube automated method (QIAGEN, Cat.#9001292) . The total RNA yield was assessed using the Thermo Scientific NanoDrop  1000 micro-volume spectrophotometer (absorbance at 260 nm and the ration of 260/280 and 260/230). The total RNA integrity was assessed using the Agilent’s Bioanalyzer NANO Lab-on-a-Chip instrument (Agilent, Cat.# G2940CA).

value: Lymphedema Positive

value: Lymphedema Limb Skin

source_name: Normal Limb Skin Biopsy

value: Normal Limb Skin


title: PB-026

description:
Stanford HIMC numbering: Sample 78
Clinical Specimen ID: PB-026
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: Splenic Marginal Zone Lymphoma P23

source_name: Splenic Marginal Zone Lymphoma P23


title: Splenic Marginal Zone Lymphoma P27

source_name: Splenic Marginal Zone Lymphoma P27


title: DLBCL GEP data N0369

value: ABC

value: GCB


title: DLBCL GEP data N0366


title: PB-027

description:
Stanford HIMC numbering: Sample 81
Clinical Specimen ID: PB-027
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: 22A

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description:
P68 22A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 4.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. MicroRNA oligos are represented as duplicate, quadruplicate, or sextuplet spots.  Duplicate and sextuplet spots were averaged while quadruplicate spots, represented by quadruplicate spots as two distant pairs of two adjacent spots, may have been flagged according to the following.  If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged.

source_name: Colon tissue from patient with surgically removed adenoma

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

value: colon adenoma

tag: case id


title: 22N

description:
P67 22N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.

value: adjecent non-adenoma


title: 18A

description:
P64 18A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: DLBCL GEP data N0364

tag: gene expression profiling subgroup


title: 19A

description:
P66 19A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-023

description:
Stanford HIMC numbering: Sample 69
Clinical Specimen ID: PB-023
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0363


title: DLBCL GEP data N0367

value: UC


title: 18N

description:
P63 18N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 19N

description:
P65 19N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-022

description:
Stanford HIMC numbering: Sample 66
Clinical Specimen ID: PB-022
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-024

description:
Stanford HIMC numbering: Sample 72
Clinical Specimen ID: PB-024
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-020

description:
Stanford HIMC numbering: Sample 60
Clinical Specimen ID: PB-020
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: 17A

description:
P62 17A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-021

description:
Stanford HIMC numbering: Sample 63
Clinical Specimen ID: PB-021
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: 17N

description:
P61 17N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-019

description:
Stanford HIMC numbering: Sample 57
Clinical Specimen ID: PB-019
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0368

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample


title: PB-018

description:
Stanford HIMC numbering: Sample 54
Clinical Specimen ID: PB-018
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0362


title: 16A

description:
P60 16A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: DLBCL GEP data N0361


title: 15A

description:
P58 15A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 14A

description:
P56 14A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 15N

description:
P57 15N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 16N

description:
P59 16N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 13A

description:
P54 13A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 13N

description:
P53 13N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 12A

description:
P52 12A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 14N

description:
P55 14N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 10N

description:
P49 10N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-016

description:
Stanford HIMC numbering: Sample 48
Clinical Specimen ID: PB-016
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: 10A

description:
P50 10A pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 12N

description:
P51 12N pmt800  07242007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-011

description:
Stanford HIMC numbering: Sample 39
Clinical Specimen ID: PB-011
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0358


title: DLBCL GEP data N0360


title: 8A

description:
P48 8A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 7A

description:
P46 7A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 7N

description:
P45 7N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 6A

description:
P44 6A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 8N

description:
P47 8N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: DLBCL GEP data N0356

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample


title: DLBCL GEP data N0357


title: PB-007

description:
Stanford HIMC numbering: Sample 36
Clinical Specimen ID: PB-007
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0359


title: PB-013

description:
Stanford HIMC numbering: Sample 32
Clinical Specimen ID: PB-013
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-014

description:
Stanford HIMC numbering: Sample 42
Clinical Specimen ID: PB-014
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-015

description:
Stanford HIMC numbering: Sample 45
Clinical Specimen ID: PB-015
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-017

description:
Stanford HIMC numbering: Sample 51
Clinical Specimen ID: PB-017
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0353


title: DLBCL GEP data N0355


title: PB-012

description:
Stanford HIMC numbering: Sample 29
Clinical Specimen ID: PB-012
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: 6N

description:
P43 6N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 5A

description:
P42 5A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 5N

description:
P41 5N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 4A

description:
P40 4A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 4N

description:
P39 4N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 3N

description:
P37 3N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 3A

description:
P38 3A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 2N

description:
P35 2N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 2A

description:
P36 2A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: DLBCL GEP data N0352


title: 1A

description:
P34 1A pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: 1N

description:
P33 1N pmt800  07182007.gpr
Tissues were defined as colon adenoma or adjecent non-adenoma tissue.


title: PB-008

description:
Stanford HIMC numbering: Sample 20
Clinical Specimen ID: PB-008
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PhoridParasitizedBee_15

city: San Francisco

first: Charles

last: Runckel

department: Biochemistry

institute: UCSF

hyb_protocol: Samples were hybridized overnight at 65C in an SSC/SDS/HEPES buffer

scan_protocol: Samples were scanned at 5 um resolution in the 532 and 635 channels by an Axon 4000A scanner

data_processing: The software analysis used is E-predict (E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns and http://derisilab.ucsf.edu/software/epredict/index.html). The data was analyzed using e-predict V1.0 and V2.02 (they use identical algorithms, but different user interfaces). The default sum normalization parameter was used.  Samples were analyzed manually and scored as positive for a pathogen if at least three unique oligonucleotides hybridized with at least five times background intensity. Arrays were further analyzed by a second unbiased method using the E-Predict algorithm (version 2.02), wherein all virus genomes were computationally hybridized to the array oligos and array results are compared to expected binding profiles. The top 5 unique oligos were removed and the algorithm reiterated twice in order to improve detection of low titer target(s) during a co-infection. Known honey bee pathogens were called positive if they exceeded a similarity score of 0.001 and were the highest ranked call in any iteration. In the event of a disagreement between the two analysis methods, a specific PCR reaction was performed, using material from the first PCR step, to resolve the call.

organism: Apis mellifera

source_name: Whole Bee Homogenate

label_protocol: Total nucleic acid was randomly amplified by random priming and single primer PCR, and labeled with a Cy3-labelled primer prior to hybridization

growth_protocol: Samples were collected as adults

extract_protocol: Samples were extracted by Trizol and isopropanol precipitation

treatment_protocol: Samples were stored on dry ice prior to extraction

tag: number of bees


title: PhoridParasitizedBee_16


title: DLBCL GEP data N0347

description:
DLBCL GEP data
Gene expression data from DLBCL lymphoma FFPET sample


title: DLBCL GEP data N0349


title: DLBCL GEP data N0351


title: DLBCL GEP data N0348


title: DLBCL GEP data N0346


title: DLBCL GEP data N0350


title: PhoridParasitizedBee_14


title: PB-009

description:
Stanford HIMC numbering: Sample 23
Clinical Specimen ID: PB-009
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-005

description:
Stanford HIMC numbering: Sample 14
Clinical Specimen ID: PB-005
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-010

description:
Stanford HIMC numbering: Sample 26
Clinical Specimen ID: PB-010
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PB-006

description:
Stanford HIMC numbering: Sample 17
Clinical Specimen ID: PB-006
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0345


title: DLBCL GEP data N0343


title: PhoridParasitizedBee_11


title: PhoridParasitizedBee_13


title: PB-002

description:
Stanford HIMC numbering: Sample 5
Clinical Specimen ID: PB-002
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: DLBCL GEP data N0342


title: PhoridParasitizedBee_8


title: PhoridParasitizedBee_12


title: DLBCL GEP data N0341


title: PB-001

description:
Stanford HIMC numbering: Sample 2
Clinical Specimen ID: PB-001
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: PhoridParasitizedBee_6


title: PhoridParasitizedBee_7


title: PB-003

description:
Stanford HIMC numbering: Sample 8
Clinical Specimen ID: PB-003
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.


title: Whole blood_LCAP_rep7

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: normalized log2 ratio (7B/7A)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: Using peripheral whole blood from Rheumatoid arthritis patients who have received Leukocytapheresis therapy

extract_protocol: Total RNA extracted using  RNeasy mini kit following manufacturer's instructions

treatment_protocol: Leukocytepheresis (blood throughput come up to 5000ml) using Cellsorba CS-180S filled with purified water with nafamostat mesilate as anticoagulant agents.

value: whole blood

tag: lcap

value: before Leukocytapheresis

value: after Leukocytapheresis


title: PhoridParasitizedBee_10


title: PhoridParasitizedBee_5


title: Whole blood_LCAP_rep10

description: normalized log2 ratio (10B/10A)


title: PhoridParasitizedBee_9


title: PhoridParasitizedBee_4


title: PhoridParasitizedBee_3


title: Whole blood_LCAP_rep14

description: normalized log2 ratio (14B/14A)


title: Whole blood_LCAP_rep3

description: normalized log2 ratio (3B/3A)


title: DLBCL GEP data N0340


title: DLBCL GEP data N0337


title: DLBCL GEP data N0336


title: Whole blood_LCAP_rep13

description: normalized log2 ratio (13B/13A)


title: PhoridParasitizedBee_2


title: PhoridParasitizedBee_1


title: Lung, influenza infection, 72 h, biol rep2

city: seattle

first: madhumati

last: gundapuneni

address: 401 Terry avenue North

institute: Institute for systems biology

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and a manual threshold of 0.1 were applied to each data set.

label: FAM

source_name: Lung, influenza infection, 72 h

extract_protocol: Trizol, according to the manufacturer's instructions. Total RNA (1 microgram) from 2 independent biological replicates was reverse transcribed using microRNA-specific Megaplex primers without pre-amplification and loaded on TLDA Taqman real time assay card A. Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

treatment_protocol: Mice were infected intranasally with 700 pfu Influenza A/PR/8/34 for 72 hours

value: lung


title: Lung, influenza infection, 72 h, biol rep1


title: DLBCL GEP data N0335


title: DLBCL GEP data N0339


title: Whole blood_LCAP_rep6

description: normalized log2 ratio (6B/6A)


title: DLBCL GEP data N0334


title: Whole blood_LCAP_rep12

description: normalized log2 ratio (12B/12A)


title: Whole blood_LCAP_rep11

description: normalized log2 ratio (11B/11A)


title: DLBCL GEP data N0333


title: DLBCL GEP data N0326


title: DLBCL GEP data N0324


title: DLBCL GEP data N0327


title: DLBCL GEP data N0330


title: DLBCL GEP data N0321


title: DLBCL GEP data N0325


title: DLBCL GEP data N0323


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP9  [central nucleus of amygdala]

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain central nucleus of amygdala (CeA)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with RMA.

organism: Rattus norvegicus

source_name: central nucleus of amygdala from sP rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 2-cycle protocol from 25 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA was extracted using Trizol followed by Qiagen RNeasy mini kit.

tag: line pair

tag: alcohol preference

value: Pr


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP8  [central nucleus of amygdala]

source_name: central nucleus of amygdala from sNP rat

value: NPr


title: BB12_WithCaco2versusWithout_4hours

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

description: Note that on this array the culture without Caco-2 cells (the reference) was labelled with Cy5, where the culture with Caco-2 cells (the test) was labelled with Cy3. This is oppositely of most common protocols and in the processed data the log2(ratio) values have been negated to to reflect this.

hyb_protocol: According to the Amersham protocol the Cy3 and Cy5 labelled cDNA were combined and lyophilized. Hereafter they were resuspended in 3uL of nuclease free water and, 5uL of hybdridization buffer (4x), and 12uL of formamide was added. This 20uL solution was applied to the array under a 24x24mm LifterSlip (Erie Scientific Company, Portsmouth, NH) and put in an airtight box containing paper towels soaked with NaCl-saturated water. Arrays were hybridized for 16-20h at 42ºC, and then washed using the UltraGAPS protocol (Corning B.V.).

scan_protocol: Arrays were scanned using the GenePix 4100A Personal Scanner with GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA). The photo multiplier tube (PMT) sensitivity was set to "Auto-PMT" with a "saturation tolerance" of 0.1%.

data_processing:
A grid with 110um spots was laid over the array and was manually adjusted to fit small irregularities in spotting. Spots clearly covered by for example dust particles were flagged “Bad”. The intensity of all spots was then calculated using the “Analyze” function. Spots with very weak signals in both channels were also flagged “Bad”. These were spots where the signal-to-noise ratio [SNR] < 1 in both channels, or where [% > B + 2SD] < 20 in both channels. All other spots were considered “Found” and had a “Flag” value of >= 0. All data was exported from GenePix Pro in tab-delimited format.
In the further analysis the variables of feature (spot) intensity minus the background intensity around the spot was used, i.e. [F635 median – B635]=Cy5 and [F532 median – B532]=Cy3. The log2(ratio) of this was calculated as log2(Cy5/Cy3). Some spots may have a significant signal in one channel but no signal in the other channel. The latter may result in a negative value due to noise and thus and illegal log2(ratio). To avoid this a macro in Excel 2000 (Microsoft Corporation, Redmond, WA) was used to change [F635 median – B635] and [F532 median – B532] values of <10 to 10 for “Found” spots (the signal scale goes from 0, no signal, to 65535, saturated signal). For these spots the log2(ratio) was re-calculated. The corrected data was exported from Excel and imported into Acuity 4.0 (Axon) where they were ratio-normalized based on the “Found” spots.
In Acuity a dataset was created. For each array only genes were included where 1) at least 3 of the 4 replicate spots were “Found”, 2) the standard deviation was <0.5 among “Found” spots, and 3) <30% of the pixels in “Found” spots, in both channels, were saturated.

organism: Bifidobacterium animalis subsp. lactis BB-12

source_name: BB12 grown in the absence of Caco-2 cells for 4 hours

label_protocol: 10ug of total RNA was lyophilized in a speed-vac. The copying into cDNA and labeling with either Cy3 or Cy5 was done using the CyScribe Post-Labelling Kit using manufacturer’s protocol (Amersham Biosciences, Hillerød, Denmark). 1uL of random nonamer was used for priming.

growth_protocol:
Caco-2 intestinal enterocyte cells (ACC 169, Deutsche Sammlung von  Mikroorganismen und Zellkulturen, Germany) were routinely grown in Dulbecco modified Eagle minimal (DMEM) medium Glutamax (Invitrogen, Carlsbad, CA) supplemented with 20% fetal bovine serum (FBS) (HyClone, Cramlington, UK) and 1% nonessential amino acids (NEAA) (Invitrogen, Carlsbad, CA) and 0.2% antibiotics gentamicin/amphotericin (Cascade Biologics, Portland, OR). Cells were cultured at 37°C in a 5% CO2 - 95% air atmosphere. The culture medium was changed every 2 days. Differentiated cells were used after 21 days of culturing for expression experiments and LTA phenotypic experiments done in 0.4 um polyester transwell permeable insert chambers (Corning B.V., Schiphol-Rijk, The Netherlands); trans epithelial electrical resistance measurement (TEER) was used as a measure of cell differentiation – TEER between 500-700 Ohm/cm2 - after 14 days of culturing (for adhesion assays done in cell culture plates Nunclon (Nunc, Roskilde, Denmark)).
BB12 was grown under anaerobic conditions for 16-20 hours at 37°C to stationary phase in De Man-Rogosa-Sharpe (MRS) broth (Difco, Franklin Lakes, NJ) supplemented with 0.05% Cys-HCl from an autoclaved 10% solution (VWR, Herlev, Denmark) to stationary phase. Then the bacterial culture was spun down at 5000 × g for 5 min supernatant discarded, bacterial pellet washed with Hanks Balanced Salt Solution HBSS (Invitrogen, Carlsbad, CA). Then the pellet was re-suspended in fresh DMEM cell culture media without antibiotics to OD600 = 1.0. Such a suspension of BB12 was co-cultured in the cell culture media together with differentiated 21 days Caco-2 cells in transwell inserts. The same experimental set-up without the Caco-2 was used as a control for the transcriptomics experiments. The bacterial cells were harvested from the transwell inserts after 4 hours of co-cultivation.

extract_protocol:
500 ul of the suspension was mixed with 1 ml of RNA protect (Qiagen, Hilden, Germany), vortexed and incubated for 5 min at 22°C. Then the solution was centrifuged for 10 min at 5000 × g and pellet stored at -80°C until isolation of RNA.
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) except for the following: the 200uL TE buffer contained 15mg/mL of lysozyme, 15uL of proteinase K at 20mg/mL, and 2uL of mutanolysin at 25U/uL with vortexing every 10s at 37ºC for the 2min. The quality and concentration of RNA was determined using the RNA 6000 Nano Kit on the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Routinely, 20-50ug of total RNA was obtained. Only high quality total RNA, as indicated by two sharp rRNA peaks, was used.

tag: growth condition

value: absence of Caco-2 cells for 4 hours

source_name: BB12 grown in the presence of Caco-2 cells for 4 hours

value: presence of Caco-2 cells for 4 hours


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP7  [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP7  [central nucleus of amygdala]


title: DLBCL GEP data N0320


title: DLBCL GEP data N0319


title: Splenic Marginal Zone Lymphoma P97 250KNSP

description: Hybridized to 250K_Nsp

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The CEL files were analyzed using the aroma.affymetrix package of R/Bioconductor (CRLMM-algorithm to produce genotype calls and SNPRMA to produce the summarized signal).

source_name: Splenic Marginal Zone Lymphoma P97

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS

extract_protocol: Genomic DNA was extracted from mononuclear cells and cell lines using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: Not treatment

value: Splenic Marginal Zone Lymphoma


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP6 [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP5  [central nucleus of amygdala]


title: PB-004

description:
Stanford HIMC numbering: Sample 11
Clinical Specimen ID: PB-004
Study subjects with lymphedema (n=27) were recruited from the patient population of the Stanford Center for Lymphatic and Venous Disorders. Two contiguous 6 mm full-thickness punch biopsy specimens were obtained from the medial aspect of the forearm or calf, respectively, of the affected extremity with an Acu-Punch (Ft. Lauderdale, FL) disposable device. Comparable specimens were obtained from the contralateral normal limb. In bilateral lymphedema patients, normal skin was obtained from a biopsy site from one of the unaffected extremities.

value: Lymphedema Positive


title: Splenic Marginal Zone Lymphoma P101 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P101


title: Marginal zone lymphoma cell line-K1718

description: Hybridized to 250K_Nsp

source_name: Marginal zone lymphoma cell line-K1718

value: Marginal zone lymphoma


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP6  [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP9  [central nucleus of amygdala]


title: DLBCL GEP data N0318

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278. The signal used was DQN3, i.e., DQN signal normalized with quantiles of the beta distribution with parameters p=1.2 and q=3


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP4  [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP4  [central nucleus of amygdala]


title: DLBCL GEP data N0317


title: Marginal zone lymphoma cell line-SL-15

description: Hybridized to 250K_Nsp

source_name: Marginal zone lymphoma cell line-SL-15


title: Marginal zone lymphoma cell line-VL51

description: Hybridized to 250K_Nsp

source_name: Marginal zone lymphoma cell line-VL51


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP3 [central nucleus of amygdala]


title: Splenic Marginal Zone Lymphoma P98 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P98


title: Splenic Marginal Zone Lymphoma P99 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P99


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP2 [central nucleus of amygdala]


title: DLBCL GEP data N0316

source_name: DLBCL patient sample


title: Splenic Marginal Zone Lymphoma P100 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P100


title: Marginal zone lymphoma cell line-SSK41

description: Hybridized to 250K_Nsp

source_name: Marginal zone lymphoma cell line-SSK41


title: DLBCL GEP data N0315


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP3 [central nucleus of amygdala]


title: Splenic Marginal Zone Lymphoma P96 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P96


title: Splenic Marginal Zone Lymphoma P94 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P94


title: Splenic Marginal Zone Lymphoma P95 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P95


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP5  [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP1 [central nucleus of amygdala]

source_name: central nucleus of amygdala from sP rat


title: Splenic Marginal Zone Lymphoma P92 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P92


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP2 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.20 [central nucleus of amygdala]

source_name: central nucleus of amygdala from ANA rat


title: DLBCL GEP data N0314


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP1 [central nucleus of amygdala]

source_name: central nucleus of amygdala from sNP rat


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.16 [central nucleus of amygdala]


title: DLBCL GEP data N0311


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.19 [central nucleus of amygdala]

source_name: central nucleus of amygdala from AA rat


title: DLBCL GEP data N0312


title: DLBCL GEP data N0313


title: Splenic Marginal Zone Lymphoma P91 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P91


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.17 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.18 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.15 [central nucleus of amygdala]


title: DLBCL GEP data N0310


title: Splenic Marginal Zone Lymphoma P88 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P88


title: Splenic Marginal Zone Lymphoma P90 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P90


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.14 [central nucleus of amygdala]


title: Glc-R2

city: Gothenburg

first: Kuk-Ki

last: Hong

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Sample 6

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.13.2. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae grown on glucose medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: strain background

tag: genotype/variation

value: wild type

tag: growth medium

value: Minimal glucose-based medium

value: Controlled fermenter kept at pH 5.0

tag: sampling time

value: mid exponential phase

tag: replicate no.


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.13 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.7 [central nucleus of amygdala]


title: Glc-R1

description: Sample 5


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.9 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.11 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.6 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.10 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.12 [central nucleus of amygdala]


title: DLBCL GEP data N0308

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

extract_protocol: FFPE RNA was isolated by HighPure Paraffin RNA extraction kit (Roche Applied Science Cat # 03270289001 X) according to manufacturer’s instructions

value: GCB

tag: immunohistochemistry subgroup


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.8 [central nucleus of amygdala]


title: Splenic Marginal Zone Lymphoma P77 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P77


title: DLBCL GEP data N0304


title: DLBCL GEP data N0307

value: UC

value: ABC


title: Splenic Marginal Zone Lymphoma P41 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P41


title: Splenic Marginal Zone Lymphoma P37 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P37


title: DLBCL GEP data N0306

source_name: DLBCL patient sample


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.5 [central nucleus of amygdala]


title: Glc-62A

description: Sample 1

value: adaptively evolved yeast mutants on galactose


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.1 [central nucleus of amygdala]


title: Glc-62C

description: Sample 4


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP10  [central nucleus of amygdala]

source_name: central nucleus of amygdala from NP rat


title: Glc-62B2

description: Sample 3


title: Glc-62B1

description: Sample 2


title: DLBCL GEP data N0303


title: DLBCL GEP data N0305


title: DLBCL GEP data N0309