title: Splenic Marginal Zone Lymphoma P7 250KNSP

description: Hybridized to 250K_Nsp

source_name: Splenic Marginal Zone Lymphoma P7


title: top1Δtop2ts, biological rep2

status: Public on Aug 01 2012

type: RNA

city: Aarhus

first: Jakob

middle: Madsen

last: Pedersen

state: Aarhus

address: CF Mollers Alle 3

department: Molecular Biology

country: Denmark

institute: Aarhus University

description: Gene expression data from top1Δtop2ts replicate 2, arrested in G1, 90 min at 37ºC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 18 hr at 45 Celcius on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the 450 Fluidics Station.

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

data_processing: Signal intensities were generated with Microarray Suite version 5.0 (MAS 5.0) in Affymetrix GeneChip Operating Software Version 1.4.0.036 using default analysis settings. External normalization was used subsequently as normalization method. The trimmed mean target intensity of selected probe sets corresponding to External Affymetrix RNA controls (ERCs) in mutant arrays was adjusted to the trimmed mean signal of the ERCs in the respective baseline wildtype array. Next, the signal intensity of each probe set on the mutant array was multiplied with this normalization value.

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: top1Δtop2ts rep2, arrested in G1, 90 min at 37ºC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast strains were exponentially grown in YPD media supplemented with alpha-factor for cell cycle arrest

extract_protocol: Total RNA was prepared by acid phenol extraction and further purified on Rneasy columns (Qiagen) according to manufacturers prescriptions.

treatment_protocol: Yeast strains were grown to exponential phase at 25ºC in YPD and further grown for 90 min at 25ºC in YPD with alpha-factor to synchronize cells in G1. Cultures were then placed at 37ºC with alpha-factor for another 90 min to abolish Top2p function.

tag: strain

value: W303 top1::natr top2-1


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.2 [central nucleus of amygdala]

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

country: USA

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 ANA 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: NPr


title: top1Δtop2ts, biological rep3

description: Gene expression data from top1Δtop2ts replicate 3, arrested in G1, 90 min at 37ºC

source_name: top1Δtop2ts rep3, arrested in G1, 90 min at 37ºC


title: DLBCL GEP data N0302

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. The signal used was DQN3, i.e., DQN signal normalized with quantiles of the beta distribution with parameters p=1.2 and q=3

organism: Homo sapiens

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: Line Pair AA.ANA - Alc Pref NPr - animal ANA.4 [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P10  [central nucleus of amygdala]

source_name: central nucleus of amygdala from P rat

value: Pr


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP9  [central nucleus of amygdala]

source_name: central nucleus of amygdala from NP rat


title: top1Δtop2ts, biological rep1

description: Gene expression data from top1Δtop2ts replicate 1, arrested in G1, 90 min at 37ºC

source_name: top1Δtop2ts rep1, arrested in G1, 90 min at 37ºC


title: DLBCL GEP data N0301


title: top2ts, biological rep3

description: Gene expression data from top2ts replicate 3, arrested in G1, 90 min at 37ºC

source_name: top2ts rep3, arrested in G1, 90 min at 37ºC


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP7  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P8  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP8  [central nucleus of amygdala]


title: DLBCL GEP data N0300

value: GCB


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.3 [central nucleus of amygdala]

source_name: central nucleus of amygdala from AA rat


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP6  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P7  [central nucleus of amygdala]


title: DLBCL GEP data N0299


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP5  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P6  [central nucleus of amygdala]


title: DLBCL GEP data N0297

value: UC


title: Line Pair P.NP - Alc Pref Pr - animal P.P4  [central nucleus of amygdala]


title: DLBCL GEP data N0298


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP3 [central nucleus of amygdala]


title: DLBCL GEP data N0295


title: DLBCL GEP data N0296


title: top1Δ, biological rep2

description: Gene expression data from top1Δ replicate 2, arrested in G1, 90 min at 37ºC

source_name: top1Δ rep2, arrested in G1, 90 min at 37ºC

value: W303 top1::natr


title: Line Pair P.NP - Alc Pref Pr - animal P.P3  [central nucleus of amygdala]


title: top2ts, biological rep1

description: Gene expression data from top2ts replicate 1, arrested in G1, 90 min at 37ºC

source_name: top2ts rep1, arrested in G1, 90 min at 37ºC


title: DLBCL GEP data N0294


title: top2ts, biological rep2

description: Gene expression data from top2ts replicate 2, arrested in G1, 90 min at 37ºC

source_name: top2ts rep2, arrested in G1, 90 min at 37ºC


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP4  [central nucleus of amygdala]


title: top1Δ, biological rep3

description: Gene expression data from top1Δ replicate 3, arrested in G1, 90 min at 37ºC

source_name: top1Δ rep3, arrested in G1, 90 min at 37ºC


title: Line Pair P.NP - Alc Pref Pr - animal P.P2  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P5  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP2  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP1  [central nucleus of amygdala]


title: Line Pair P.NP - Alc Pref Pr - animal P.P1  [central nucleus of amygdala]


title: DLBCL GEP data N0291


title: DLBCL GEP data N0293


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.40 [central nucleus of amygdala]

source_name: central nucleus of amygdala from LAD1 rat


title: wildtype, biological rep3

description: Gene expression data from wildtype replicate 3, arrested in G1, 90 min at 37ºC

source_name: wildtype rep3, arrested in G1, 90 min at 37ºC


title: wildtype, biological rep2

description: Gene expression data from wildtype replicate 2, arrested in G1, 90 min at 37ºC

source_name: wildtype rep2, arrested in G1, 90 min at 37ºC


title: top1Δ, biological rep1

description: Gene expression data from top1Δ replicate 1, arrested in G1, 90 min at 37ºC

source_name: top1Δ rep1, arrested in G1, 90 min at 37ºC


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.39 [central nucleus of amygdala]


title: DLBCL GEP data N0290


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.30 [central nucleus of amygdala]

source_name: central nucleus of amygdala from HAD1 rat


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.37 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.35 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.29 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.28 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.38 [central nucleus of amygdala]


title: Het_LF_3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251486820070_1_2
Gene expression from Het low-fat diet mouse liver.

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Mus musculus

source_name: Liver from low-fat diet Het mouse

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol.

growth_protocol: SIRT1 WT and Het mice were fed with either a low-fat diet (LF) or a high-fat diet (HF) for 34 weeks.

extract_protocol: Livers from these mice were dissected and RNA were isolated with a Qiagen RNeasy Mini Kit with on-column DNase I treatment. RNA quality is validated by a denaturing RNA gel and by the Agilent 2100 Bioanalyzer.

tag: gender

value: male

tag: tissue

value: liver

tag: treatment

value: low-fat diet


title: DLBCL GEP data N0289


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.36 [central nucleus of amygdala]


title: DLBCL GEP data N0288


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.34 [central nucleus of amygdala]


title: DLBCL GEP data N0287


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.26 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.24 [central nucleus of amygdala]


title: wildtype, biological rep1

description: Gene expression data from wildtype replicate 1, arrested in G1, 90 min at 37ºC

source_name: wildtype rep1, arrested in G1, 90 min at 37ºC


title: DLBCL GEP data N0283

source_name: DLBCL patient sample


title: DLBCL GEP data N0284


title: DLBCL GEP data N0285


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.25 [central nucleus of amygdala]


title: WT_LF_1

description:
251486820069_1_1
Gene expression from WT low-fat diet mouse liver.

source_name: Liver from low-fat diet WT mouse


title: WT_LF_3

description:
251486820069_1_3
Gene expression from WT low-fat diet mouse liver.


title: Het_LF_1

description:
251486820069_1_4
Gene expression from Het low-fat diet mouse liver.


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.33 [central nucleus of amygdala]

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


title: WT_LF_2

description:
251486820069_1_2
Gene expression from WT low-fat diet mouse liver.


title: Het_LF_2

description:
251486820070_1_1
Gene expression from Het low-fat diet mouse liver.


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.32 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.22 [central nucleus of amygdala]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.23 [central nucleus of amygdala]


title: DLBCL GEP data N0282

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


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.31 [central nucleus of amygdala]


title: DLBCL GEP data N0280


title: DLBCL GEP data N0281


title: Het_HF_3

description:
251486820048_1_4
Gene expression from Het high-fat diet mouse liver.

source_name: Liver from high-fat diet Het mouse

value: high-fat diet


title: Line Pair P.NP - Alc Pref Pr - animal P.P9  [central nucleus of amygdala]

source_name: central nucleus of amygdala from P rat


title: Het_HF_2

description:
251486820048_1_3
Gene expression from Het high-fat diet mouse liver.


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.21 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.20 [central nucleus of amygdala]

source_name: central nucleus of amygdala from LAD2 rat


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.18 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.19 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.10 [central nucleus of amygdala]

source_name: central nucleus of amygdala from HAD2 rat


title: WT_HF_3

description:
251486820048_1_1
Gene expression from WT high-fat diet mouse liver.

source_name: Liver from high-fat diet WT mouse


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.9 [central nucleus of amygdala]


title: DLBCL GEP data N0279


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.17 [central nucleus of amygdala]


title: Het_HF_1

description:
251486820048_1_2
Gene expression from Het high-fat diet mouse liver.


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.8 [central nucleus of amygdala]


title: WT_HF_2

description:
251486820047_1_4
Gene expression from WT high-fat diet mouse liver.


title: DLBCL GEP data N0278


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.7 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.15 [central nucleus of amygdala]


title: DLBCL GEP data N0277


title: DLBCL GEP data N0276


title: WT_HF_1

description:
251486820047_1_3
Gene expression from WT high-fat diet mouse liver.


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.5 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.6 [central nucleus of amygdala]


title: siUbr5 replicate2

city: New York

first: Shannon

last: Buckley

state: NY

address: 550 First Ave MSB 504

institute: NYU School of Medicine

description: 48hrs post siRNA transfection

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: Embryonic stem cells were reverse transfected with siRNA, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays

tag: cell line

tag: cell type

value: embryonic stem cells

tag: transfection


title: DLBCL GEP data N0275


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.4 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.3 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.13 [central nucleus of amygdala]


title: siUbr5 replicate1

description: 48hrs post siRNA transfection


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.11 [central nucleus of amygdala]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.2 [central nucleus of amygdala]


title: DLBCL GEP data N0273


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.12 [central nucleus of amygdala]


title: siDdb1 replicate1

description: 48hrs post siRNA transfection


title: DLBCL GEP data N0271


title: siPsmd14 replicate2

description: 48hrs post siRNA transfection


title: siDdb1 replicate2

description: 48hrs post siRNA transfection


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP9  [nucleus accumbens shell]

description: Gene expression data from brain nucleus accumbens shell

source_name: Nucleus accumbens shell from sP rat


title: DLBCL GEP data N0274


title: DLBCL GEP data N0272


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP8  [nucleus accumbens shell]

source_name: Nucleus accumbens shell from sNP rat


title: siSox2 replicate2

description: 48hrs post siRNA transfection


title: siPsmd14 replicate1

description: 48hrs post siRNA transfection


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP9  [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP8  [nucleus accumbens shell]


title: DLBCL GEP data N0270


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP7  [nucleus accumbens shell]


title: DLBCL GEP data N0269


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.1 [central nucleus of amygdala]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP5  [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP4  [nucleus accumbens shell]


title: DLBCL GEP data N0265


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP7  [nucleus accumbens shell]


title: siNonTarget replicate1

description: 48hrs post siRNA transfection

source_name: siNonTarget

value: siNonTarget


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP6 [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP6  [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP2 [nucleus accumbens shell]


title: DLBCL GEP data N0267


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP5  [nucleus accumbens shell]


title: DLBCL GEP data N0263


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP2 [nucleus accumbens shell]


title: siSocs3 replicate2

description: 48hrs post siRNA transfection

treatment_protocol: Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays


title: siSox2 replicate1

description: 48hrs post siRNA transfection


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP4  [nucleus accumbens shell]


title: siNonTarget replicate2

description: 48hrs post siRNA transfection


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP3 [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP3 [nucleus accumbens shell]


title: siRnf31 replicate1

description: 48hrs post siRNA transfection


title: DLBCL GEP data N0264


title: siSocs3 replicate1

description: 48hrs post siRNA transfection


title: DLBCL GEP data N0266


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP1 [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP1 [nucleus accumbens shell]


title: DLBCL GEP data N0262


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.19 [nucleus accumbens shell]

source_name: Nucleus accumbens shell from AA rat


title: siRnf31 replicate2

description: 48hrs post siRNA transfection


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.17 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.16 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.18 [nucleus accumbens shell]

source_name: Nucleus accumbens shell from ANA rat


title: siFbxw7 replicate1

description: 48hrs post siRNA transfection


title: DLBCL GEP data N0260


title: DLBCL GEP data N0258


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.11 [nucleus accumbens shell]


title: siSox17 replicate1

description: 48hrs post siRNA transfection


title: DLBCL GEP data N0259


title: DLBCL GEP data N0261


title: DLBCL GEP data N0256


title: DLBCL GEP data N0251


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.20 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.15 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.12 [nucleus accumbens shell]


title: siSox17 replicate2

description: 48hrs post siRNA transfection


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.16 [nucleus accumbens shell]


title: siFbxw7 replicate2

description: 48hrs post siRNA transfection


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.14 [nucleus accumbens shell]


title: siNonTarget replicate2

description: 48hrs post siRNA transfection


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.10 [nucleus accumbens shell]


title: DLBCL GEP data N0250


title: siNonTarget replicate1

description: 48hrs post siRNA transfection


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.7 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.13 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.8 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.14 [central nucleus of amygdala]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.6 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.3 [nucleus accumbens shell]


title: Sdc4-/- SC 48h, replicate 2

city: Boulder

first: Bradley

middle: B

last: Olwin

state: CO

address: 347 UCB

department: MCD-Biology

institute: University of Colorado

description:
Sdc4-48-2
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

hyb_protocol: Following fragmentation, 5000 cell equivalents of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430v2 Array. GeneChips were washed and stained.

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

data_processing: Spot intensities were recovered using the Affymetrix GeneChip Operating System (GCOS).  The data were processed using Spotfire™ DecisionSite v.2 for Microarray Analysis with GCRMA normalization for further analysis.

source_name: Sdc4-/-_satellite cells_muscle 48h post-injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5000 cell equivalents of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tibialis anterior muscle was either harvested from untreated animals or injected with 1.2% barium chloride to induce muscle injury 12h or 48h prior to harvest.

extract_protocol: Total RNA was isolated using the Arcturus PicoPure RNA Isolation Kit followed by two rounds of T7-based linear amplification using the Arcturus RiboAmp HA kit according to the manufacturer's instructions.

treatment_protocol: Satellite cells were digested from minced tibialis anterior muscles with 400U/mL collagenase and isolated via flourescence activated cell sorting based on immunoreactivity to syndecan-3 on a Dako Cytomation MoFlo Legacy cell sorter.

tag: genotype

value: female

tag: age

value: 3-6 months

value: tibialis anterior muscle

tag: tissue condition

value: 48h after barium chloride-induced muscle injury

value: FACS isolated satellite cells


title: Line Pair P.NP - Alc Pref Pr - animal P.P10  [nucleus accumbens shell]

source_name: Nucleus accumbens shell from P rat


title: Sdc4-/- SC 48h, replicate 3

description:
Sdc4-48-3
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Sdc4-/- SC 48h, replicate 1

description:
Sdc4-48-1
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: DLBCL GEP data N0248


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.2 [nucleus accumbens shell]

value: NPr


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.4 [nucleus accumbens shell]


title: Sdc4-/- SC 12h, replicate 2

description:
Sdc4-12-2
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

source_name: Sdc4-/-_satellite cells_muscle 12h post-injury

value: 12h after barium chloride-induced muscle injury


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.9 [nucleus accumbens shell]

value: Pr


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.1 [nucleus accumbens shell]


title: DLBCL GEP data N0240

value: GCB


title: DLBCL GEP data N0245


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP10  [nucleus accumbens shell]

source_name: Nucleus accumbens shell from NP rat


title: Sdc4-/- SC 12h, replicate 1

description:
Sdc4-12-1
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP8  [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP9  [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP7  [nucleus accumbens shell]


title: DLBCL GEP data N0244


title: DLBCL GEP data N0243

value: UC


title: Sdc4-/- SC 0h, replicate 3

description:
Sdc4-UI-3
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

value: resting (uninjured) muscle


title: Line Pair P.NP - Alc Pref Pr - animal P.P9  [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref Pr - animal P.P8  [nucleus accumbens shell]


title: Sdc4-/- SC 0h, replicate 2

description:
Sdc4-UI-2
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.5 [nucleus accumbens shell]


title: Sdc4-/- SC 12h, replicate 3

description:
Sdc4-12-3
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: DLBCL GEP data N0246

value: ABC


title: DLBCL GEP data N0239


title: Line Pair P.NP - Alc Pref Pr - animal P.P7  [nucleus accumbens shell]


title: DLBCL GEP data N0237


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP6  [nucleus accumbens shell]


title: Sdc4-/- SC 0h, replicate 1

description:
Sdc4-UI-1
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair P.NP - Alc Pref Pr - animal P.P5  [nucleus accumbens shell]


title: DLBCL GEP data N0234

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


title: WT SC 48h, replicate 2

description:
WT-48-2
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

source_name: WT_satellite cells_muscle 48h post-injury

value: C57Bl/6 x DBA2

value: Wild Type


title: DLBCL GEP data N0231

source_name: DLBCL patient sample


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP3 [nucleus accumbens shell]


title: WT SC 48h, replicate 3

description:
WT-48-3
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP2  [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref Pr - animal P.P2  [nucleus accumbens shell]


title: WT SC 48h, replicate 1

description:
WT-48-1
Gene expression data from satellite cells isolated 48h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair P.NP - Alc Pref Pr - animal P.P3  [nucleus accumbens shell]


title: DLBCL GEP data N0233


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP4  [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.39 [nucleus accumbens shell]

source_name: Nucleus accumbens shell from LAD1 rat


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP1  [nucleus accumbens shell]


title: WT SC 12h, replicate 3

description:
WT-12-3
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

source_name: WT_satellite cells_muscle 12h post-injury


title: DLBCL GEP data N0235


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.37 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.38 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.40 [nucleus accumbens shell]


title: DLBCL GEP data N0229


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP5  [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref Pr - animal P.P1  [nucleus accumbens shell]


title: WT SC 0h, replicate 3

description:
WT-UI-3
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)

source_name: WT_satellite cells_uninjured muscle


title: WT SC 12h, replicate 1

description:
WT-12-1
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: WT SC 12h, replicate 2

description:
WT-12-2
Gene expression data from satellite cells isolated 12h post-injury as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: DLBCL GEP data N0228


title: DLBCL GEP data N0230


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.29 [nucleus accumbens shell]

description: Gene expression data from brain nucleus accumbens shell

source_name: Nucleus accumbens shell from HAD1 rat


title: DLBCL GEP data N0227


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.28 [nucleus accumbens shell]


title: WT SC 0h, replicate 2

description:
WT-UI-2
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.27 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.30 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.34 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.35 [nucleus accumbens shell]


title: WT SC 0h, replicate 1

description:
WT-UI-1
Gene expression data from freshly isolated satellite cells as described in Tanaka et al. Cell Stem Cell 4:3 217-25 (2009)


title: DLBCL GEP data N0226


title: DLBCL GEP data N0225


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.25 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.22 [nucleus accumbens shell]


title: Uninfected

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description:
uninfected
Gene expression data from mouse cecal tissue uninfected

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 2 GeneChip arrays, the arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000

data_processing: Data were analyzed with dChip, version 2005

source_name: Uninfected

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

growth_protocol: All mice were maintained in standard caging conditions by the UC Davis Center for Laboratory Animal Science, receiving standard rodent chow and sterile drinking water ad libitum.

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

treatment_protocol: Cecal tissue was harvested 4 days following infection or mock infection and snap frozen in liquid nitrogen

value: CBA/J

value: 6-8 weeks

value: cecum


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.26 [nucleus accumbens shell]


title: DLBCL GEP data N0224


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.32 [nucleus accumbens shell]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.23 [nucleus accumbens shell]


title: Salmonella-Plasmodium co-infected

description:
S_typh_P_yoelii
Gene expression data from mouse cecal tissue infected with Salmonella and Plasmodium

source_name: Salmonella-Plasmodium co-infected

value: female


title: Plasmodium yoelii infected

description:
P_yoelii
Gene expression data from mouse cecal tissue infected with P. yoelii

source_name: Plasmodium yoelii infected


title: DLBCL GEP data N0221


title: DLBCL GEP data N0223


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.31 [nucleus accumbens shell]


title: HFD fed TIS7 SKMc15 double knock out mouse 3

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: Expression profile of high fat diet fed TIS7 (Ifrd1) SKMc15 (Ifrd2) double knock out mouse.

hyb_protocol: Following RNA purification, 20 μg of cRNA were fragmented at 95° using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to the GeneChips (Mouse Genome 430 2.0).

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: Data preprocessing was performed in R using Bioconductor's (version 2.6) GCRMA package (version 2.18.0).

label_protocol: 500 ng total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Age-matched (7-10 week old) male wild type and TIS7 SKMc15 double knock out mice were caged individually and maintained from 3 weeks up to 8 weeks on a synthetic high saturated fat (HFD) diet (Ssniff)

extract_protocol: Tissues from animals fed for 3 weeks with high fat diet were snap frozen and stored at –80°C. Total RNA was isolated using the TRIzol reagent (Invitrogen) and purified using Rneasy columns (Quiagene).

treatment_protocol: high saturated fat (HFD) diet (Ssniff); 42% kcal from milk fat, 0.2% kcal from cholesterol).

value: TIS7 SKMc15 double knock out

value: jejunum

tag: diet

value: high fat

tag: genetic background


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.33 [nucleus accumbens shell]


title: DLBCL GEP data N0222


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.24 [nucleus accumbens shell]


title: DLBCL GEP data N0219


title: Salmonella Typhimurium infected

description:
S_typh
Gene expression data from mouse cecal tissue infected with S. Typhimurium

source_name: Salmonella Typhimurium infected


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.21 [nucleus accumbens shell]


title: DLBCL GEP data N0218


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.18 [nucleus accumbens shell]

source_name: Nucleus accumbens shell from LAD2 rat


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.19 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.17 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.20 [nucleus accumbens shell]


title: HFD fed TIS7 SKMc15 double knock out mouse 1


title: HFD fed TIS7 SKMc15 double knock out mouse 2


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.10 [nucleus accumbens shell]

source_name: Nucleus accumbens shell from HAD2 rat


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.8 [nucleus accumbens shell]


title: DLBCL GEP data N0217


title: HFD fed wild type mouse 4

description: Expression profile of high fat diet fed wild type mouse.

value: wild type


title: HFD fed wild type mouse 3


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.7 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.13 [nucleus accumbens shell]

value: NPr


title: DLBCL GEP data N0214

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


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.15 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.16 [nucleus accumbens shell]


title: HFD fed wild type mouse 1


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.14 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.4 [nucleus accumbens shell]


title: Line Pair P.NP - Alc Pref Pr - animal P.P6  [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.9 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.3 [nucleus accumbens shell]


title: DLBCL GEP data N0216


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.5 [nucleus accumbens shell]


title: DLBCL GEP data N0212


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.12 [nucleus accumbens shell]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.11 [nucleus accumbens shell]


title: DLBCL GEP data N0209


title: DLBCL GEP data N0213


title: DLBCL GEP data N0211


title: Line Pair P.NP - Alc Pref Pr - animal P.P4  [nucleus accumbens shell]


title: DLBCL GEP data N0208


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.1 [nucleus accumbens shell]


title: DLBCL GEP data N0210


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.2 [nucleus accumbens shell]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP9 [ventral tegmental area]

description: Gene expression data from brain ventral tegmental area (VTA)

source_name: ventral tegmental area from sNP rat


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP8 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP9 [ventral tegmental area]

source_name: ventral tegmental area from sP rat


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP8 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP7 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP5 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP5 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP3 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP2 [ventral tegmental area]


title: DLBCL GEP data N0206


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP6 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP1 [ventral tegmental area]


title: DLBCL GEP data N0204


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP6 [ventral tegmental area]


title: DLBCL GEP data N0200


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP7 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP4 [ventral tegmental area]


title: DLBCL GEP data N0199


title: DLBCL GEP data N0205


title: Line Pair SP.SNP - Alc Pref Pr - animal sP.sP4 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP2 [ventral tegmental area]


title: Line Pair SP.SNP - Alc Pref NPr - animal sNP.sNP3 [ventral tegmental area]


title: DLBCL GEP data N0197


title: DLBCL GEP data N0202


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.20 [ventral tegmental area]

source_name: ventral tegmental area from ANA rat


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.19 [ventral tegmental area]

source_name: ventral tegmental area from AA rat


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.17 [ventral tegmental area]


title: DLBCL GEP data N0195


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.16 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.15 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.12 [ventral tegmental area]


title: DLBCL GEP data N0198


title: DLBCL GEP data N0196


title: DLBCL GEP data N0194


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.11 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.8 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.13 [ventral tegmental area]


title: DLBCL GEP data N0191


title: DLBCL GEP data N0193


title: DLBCL GEP data N0189


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.3 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.6 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.14 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.9 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.10 [ventral tegmental area]


title: DLBCL GEP data N0192


title: DLBCL GEP data N0187


title: DLBCL GEP data N0190


title: DLBCL GEP data N0188


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.5 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.6 [nucleus accumbens shell]


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.1 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P10 [ventral tegmental area]

source_name: ventral tegmental area from P rat


title: DLBCL GEP data N0186


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.4 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P9 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP10 [ventral tegmental area]

source_name: ventral tegmental area from NP rat


title: Line Pair AA.ANA - Alc Pref Pr - animal AA.7 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP8 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.2 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP7 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP9 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP6 [ventral tegmental area]


title: DLBCL GEP data N0184

source_name: DLBCL patient sample


title: DLBCL GEP data N0185


title: DLBCL GEP data N0182


title: Line Pair P.NP - Alc Pref Pr - animal P.P8 [ventral tegmental area]


title: DLBCL GEP data N0180


title: DLBCL GEP data N0183


title: Line Pair P.NP - Alc Pref Pr - animal P.P7 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P5 [ventral tegmental area]


title: DLBCL GEP data N0179


title: Line Pair P.NP - Alc Pref Pr - animal P.P3 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP2 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP1 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.39 [ventral tegmental area]

source_name: ventral tegmental area from LAD1 rat


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP5 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.38 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.27 [ventral tegmental area]

source_name: ventral tegmental area from HAD1 rat


title: DLBCL GEP data N0175


title: DLBCL GEP data N0178


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.36 [ventral tegmental area]


title: DLBCL GEP data N0181


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP4 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.35 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref NPr - animal NP.NP3 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P4 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.26 [ventral tegmental area]


title: Line Pair AA.ANA - Alc Pref NPr - animal ANA.18 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.25 [ventral tegmental area]


title: DLBCL GEP data N0171


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.23 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.33 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.34 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.32 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.22 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P1 [ventral tegmental area]


title: Line Pair P.NP - Alc Pref Pr - animal P.P2 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.21 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.40 [ventral tegmental area]


title: DLBCL GEP data N0177


title: DLBCL GEP data N0176


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.37 [ventral tegmental area]


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.30 [ventral tegmental area]


title: DLBCL GEP data N0174


title: Line Pair HAD1.LAD1 - Alc Pref Pr - animal HAD1.29 [ventral tegmental area]


title: DLBCL GEP data N0163


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.17 [ventral tegmental area]

source_name: ventral tegmental area from LAD2 rat


title: DLBCL GEP data N0173


title: DLBCL GEP data N0161


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.15 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.14 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.5 [ventral tegmental area]

source_name: ventral tegmental area from HAD2 rat


title: DLBCL GEP data N0167


title: DLBCL GEP data N0165


title: DLBCL GEP data N0170


title: Line Pair HAD1.LAD1 - Alc Pref NPr - animal LAD1.31 [ventral tegmental area]


title: DLBCL GEP data N0153


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.20 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.11 [ventral tegmental area]


title: DLBCL GEP data N0150


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.19 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.10 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.12 [ventral tegmental area]


title: DLBCL GEP data N0143


title: DLBCL GEP data N0159


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.9 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.7 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.18 [ventral tegmental area]


title: DLBCL GEP data N0158


title: heart_dtg_rep4

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

hyb_protocol: The fragmentated Cy3 labeled cRNA were hybridised on Agilent Mouse GE 4x44K v2 arrays in Hi-RPM Hybridization Buffer (Agilent) at 65°Cand  65 rpm for 17h.

scan_protocol: Scannning of the arrays were performed by the Agilent High Resolution  Scanner G2505C.

data_processing: The fluorescence intensities were calculated with the Feature Extraction Software Version 10.7.3.1. For further data analysis the FE files were imported to GeneSpring GX Version 11.

source_name: heart

label_protocol: 100 ng of total RNA were reverse transcribed, linear amplified and labeled using the One Color Low Input Qick Amp Labeling Kit (Agilent).

growth_protocol: Mice were bred at the Tierversuchsanlage of the Heinrich-Heine-Universitaet, Duesseldorf, Germany. Animal experiments were performed in accordance with the national guidelines on animal care and approved by the Bezirksregierung Duesseldorf. Animals received standard rodent chow diet and tap water ad libitum and were kept on a dark/light cycle of 12/12 h.

extract_protocol: The total RNA was isolated using the Trizol reagent (Invitrogen) following manufactures instructions. After ispropanol precipitation a clean up step using RNeasy Mini columns (Qiagen) were performed.

treatment_protocol: At the age of 8 month the animals were treated with 4OH-Tamoxifen (500 µg dissolved in 100 µl peanut oil) on 10 consecutive days to excise Exon 3 of the IGF-1R. Six weeks after the treatment hearts were removed for further analysis.

value: male

tag: genotype/variation

value: merCremer/+ IGFloxP/IGFloxP


title: Set_DuppDeddeda_vs_Ref_Dupp_9

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Preparation of the slides was performed in 50 ml Falcon tubes. All reagents were from the OpArray system from Eurofins MWG Operon. Slides were incubated at 42°C in Pre-Hyb solution for 1 h, then the slides were transferred to Wash 1 solution (1.25 ml Wash B and 48.75 ml H2O) and incubated for 5 min at 37°C. Slides were washed with H2O and dried in a centrifuge (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Hybridization was carried out for 16–18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: For post-hybridization, slides were washed at 37°C in Wash 2 solution (5 ml Wash A, 2.5 ml Wash B and 42.5 ml H2O) and Wash 3 solution (5 ml Wash A and 45 ml H2O) for 10 minutes each. Slides were rotated in Wash 4 solution (1 ml Wash A and 49 ml H2O) for 5 min at room temperature. Finally, the slides were dried by centrifugation (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Fluorescence of the hybridized DNA microarrays was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) at 10 µm resolution with a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The transcriptome comparisons of Δupp Δgnd zwf* vs. Δupp and of Δupp Δedd-eda vs. Δupp, and of Δupp Δgnd versus Δupp, were repeated independently three times in biological replicates. Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (http://www.bioconductor.org). For further analysis, the processed and loess-normalized data as well as detailed experimental information according to MIAME (Brazma et al., 2001) were stored in the in-house microarray database (Polen and Wendisch, 2004). To filter for differentially expressed genes, the following criteria had to be fulfilled: (i) flags 0 (GenePix Pro 6.0), (ii) signal/noise 5 for Cy5 (F635Median/B635Median, GenePix Pro 6.0) or Cy3 (F532Median/B532Median, GenePix Pro 6.0), (iii) mRNA ratio 2.0 (lower ones allowed in the case of operons) or 0.5 (higher ones allowed in the case of operons), (iv) in a paired Students t test, relative RNA levels had to be significantly different from all spots (p < 0.05).

organism: Gluconobacter oxydans 621H

label_protocol: cDNA synthesis for DNA microarray analysis was performed as described (Polen et al., 2007). 25 µg RNA was used for random hexamer-primed synthesis of fluorescently-labeled cDNA with the fluorescent nucleotide analogues Cy3-dUTP and Cy5-dUTP (GE Healthcare, Freiburg, Germany). The mixture contained 3 µl 1 mM Cy3-dUTP or Cy5-dUTP, 3 µl 0.1 M DTT, 6 µl 5x first strand buffer (Invitrogen, Karlsruhe, Germany), 0.6 µl dNTP-mix (25 mM each of dATP, dCTP, and dGTP and 10 mM dTTP) and 2 µl Superscript II reverse transcriptase (Invitrogen, Darmstadt, Germany). The mixture was incubated for 10 min at room temperature and 110 min at 42 °C, stopped by addition of 10 μl 0.1 N NaOH, incubated for 10 min at 70 °C, and then neutralized by addition of 10 μl 0.1 N HCl. The sensors were purified by washing three times with water on a Microcon column (Millipore, YM-30).

growth_protocol: Gluconobacter oxydans ATCC 621H Δupp (ATCC 621H is identical to DSM2343), which lacks the upp gene for uracil phosphoribosyltransferase, was obtained from Armin Ehrenreich (Technical University of Munich, Germany). The strain was cultivated on mannitol medium containing 220 mM (4% w/v) mannitol, 5 g l-1 yeast extract, 2.5 g l-1 MgSO4 x 7 H20, 1 g l-1 (NH4)2SO4, 1 g l-1 KH2PO4 and 10 μM thymidine. The initial pH value of the medium was 6.0. G. oxydans possesses a natural resistance towards cefoxitin; as a precaution to prevent bacterial contaminations, cefoxitin was added to the media at a concentration of 50 μg ml-1. When required, kanamycin (50 ug ml-1) was added. Precultures were grown in baffled shaking flasks at 30°C and 140 rpm. For determination of growth parameters, DNA microarray analyses and enzyme activity measurements, cells were cultivated in 250 ml of the same medium in a bioreactor system (DASGIP, Jülich, Germany) composed of four 400-ml vessels, each equipped with electrodes for measuring the dissolved oxygen concentration (DO) and the pH. The system allows to constantly controlling these two parameters. The carbon dioxide concentration in the exhaust gas was measured continuously by an infrared spectrometer. The pH was kept at pH 6.0 by automatic titration of 2 M NaOH. The oxygen availability was kept constant at 15% DO by mixing air, O2 and N2. Calibration was performed by gassing with air (100% DO) and N2 (0% DO). The agitation speed was kept constant at 900 rpm. Control and recording of all data was carried out by the software “Fedbatch Pro” (DASGIP, Jülich, Germany).

extract_protocol: 25 ml of a G. oxydans culture was added to 25 g of crushed ice in a Falcon tube which had been pre-cooled in liquid nitrogen. The cells were sedimented by centrifugation for 3 min at 4 °C and 10,397 x g and after removal of the supernatant the tube with the cell pellet was immersed in liquid nitrogen and then stored at -70°C. For total RNA preparation, the RNeasy system (Qiagen, Hilden, Germany) was used. The cell pellet was resuspended in 700 µl of RLT buffer containing 7 µl ß-mercaptoethanol and transferred to two vials each containing 0.5 g of 0.1-mm diameter zirconium silica beads (Roth, Karlsruhe, Germany). Cells were disrupted by 4 x 30 s bead beating using a Silamat S5 (Ivoclar Vivadent, Ellwangen, Germany). The lysate was centrifuged at 8,000 x g for 2 min and the supernatant was mixed with 250 µl ethanol (-20 °C). RNA was extracted with two RNeasy mini-columns following the manufacturer’s instructions. DNA digestion was performed for 20 min on column by adding 30 Kuniz U RNase-free DNase. RNA concentration and quality were checked photometrically and on formaldehyde gels according to standard procedures (Sambrook and Russell, 2001).

treatment_protocol: see growth protocol

value: Δupp

tag: growth medium

value: Mannitol

source_name: DuppDeddDeda

value: Δupp Δedd Δeda


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.6 [ventral tegmental area]

tag: line pair

value: Pr


title: DLBCL GEP data N0157

value: ABC


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.8 [ventral tegmental area]

tag: alcohol preference


title: SNU638 LAP2beta-3

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: SNU638 cells overexpressiong LAP2beta

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Quantile-quantile normalization

source_name: SNU638 LAP2beta

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% FBS, 25 mM HEPES and 100 ug/ml of penicillin/streptomycin

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit

value: overexpressing LAP2beta


title: DLBCL GEP data N0151

tag: gene expression profiling subgroup


title: DLBCL GEP data N0164

tag: immunohistochemistry subgroup


title: heart_dtg_rep2

tag: strain

tag: gender


title: SNU638 LAP2beta-2

description: SNU638 cells overexpressiong LAP2beta

tag: treatment


title: Line Pair HAD2.LAD2 - Alc Pref NPr - animal L2.13 [ventral tegmental area]


title: SNU638 LAP2beta-1

description: SNU638 cells overexpressiong LAP2beta

tag: cell line


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.3 [ventral tegmental area]


title: Line Pair HAD2.LAD2 - Alc Pref Pr - animal H2.2 [ventral tegmental area]


title: DLBCL GEP data N0147

value: GCB


title: SNU638 MOCK-3

description: SNU638 cells overexpressing the empty vector

source_name: SNU638 MOCK

value: empty vector


title: DLBCL GEP data N0148


title: Set_DuppDgnd_vs_Ref_Dupp_4

source_name: DuppDgnd

value: Δupp Δgnd


title: DLBCL GEP data N0139

value: UC


title: Splenic Marginal Zone Lymphoma P113 250KSty

type: genomic

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: Hybridized to 250K_Sty

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).

label: Biotin

molecule: genomic DNA

source_name: Splenic Marginal Zone Lymphoma P113

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

tag: tissue

value: Splenic Marginal Zone Lymphoma


title: Splenic Marginal Zone Lymphoma P112 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P112


title: DLBCL GEP data N0146


title: heart_dtg_rep1


title: SNU638 MOCK-2


title: heart_control_rep3

tag: sample type

value: positive for Cre recombinase, but negative for the floxed IGF-1R


title: SNU638 MOCK-1


title: Splenic Marginal Zone Lymphoma P109 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P107


title: Set_DuppDeddeda_vs_Ref_Dupp_8


title: Set_DuppDgnd_vs_Ref_Dupp_6


title: Set_DuppDeddeda_vs_Ref_Dupp_7


title: DLBCL GEP data N0142


title: DLBCL GEP data N0141


title: heart_dtg_rep3


title: Splenic Marginal Zone Lymphoma P114 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P114


title: DLBCL GEP data N0136


title: DLBCL GEP data N0140


title: heart_control_rep1


title: DLBCL GEP data N0133


title: Set_DuppDgnd_vs_Ref_Dupp_5


title: MEF

city: Taichung

first: Shih-Ping

last: Liu

address: No.6, Hsueh-Shih Road

country: Taiwan

institute: China medical university

description: Gene expression of MEF

hyb_protocol: 0.6 g of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE 8×60K microarray (Agilent Technologies, USA) at 65°C for 17 h.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: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3. Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA),

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: MEF

label_protocol: 0.2 g of total RNA was amplified by a Low Input Quick-Amp Labeling kit(Agilent Technologies, USA) and labeled with Cy3 (CyDye, PerkinElmer, USA) during the in vitro transcription process.

growth_protocol:
MEF cells were cultured in DMEM with 10% heat-inactivated FBS (both GIBCO BRL), penicillin (100 U per ml), streptomycin (100 µg/ml), non-essential amino acids (0.1 mM), and L-glutamine (2 mM) in a humidified incubator with 5% CO2 (37°C)
iPS-OSH, iPS-J, ESC cultured in DMEM with 15% heat-inactivated FBS (both GIBCO BRL), non-essential amino acids (0.1 mM), L-glutamine (2 mM), 2-Me (0.1 mM), and LIF (103 unit/ml)

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

tag: cell type

value: MEF


title: Splenic Marginal Zone Lymphoma P111 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P111


title: heart_control_rep4


title: heart_control_rep2


title: DLBCL GEP data N0138


title: Splenic Marginal Zone Lymphoma P110 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P110


title: Splenic Marginal Zone Lymphoma P107 250KSty

description: Hybridized to 250K_Sty


title: Splenic Marginal Zone Lymphoma P104 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P104


title: Splenic Marginal Zone Lymphoma P103 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P103


title: Set_DuppDgnd_zwf_vs_Ref_Dupp_2

value: Δupp Δgnd zwf


title: Set_DuppDgnd_zwf_vs_Ref_Dupp_3


title: Set_DuppDgnd_zwf_vs_Ref_Dupp_1


title: DLBCL GEP data N0134

source_name: DLBCL patient sample


title: PBMC_68hr_Rep4b

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

hyb_protocol: Microarray experiments were carried out using the swine protein annotated oligonucleotide microarray (www.pigoligoarray.org). This array is comprised of 20,400 oligo probes designed by comparison of porcine expressed sequence tags (ESTs) to annotated vertebrate proteins. Each hybridization used 160 pmol of Cy3 and Cy5 labeled probes in hybridization buffer containing 2X SSC, 0.08% SDS, and 0.5X Western Blocking Reagent (Roche). Probes were denatured at 65°C for 5 min prior to loading onto the microarray under a Lifterslip (Thomas Scientific). Hybridizations were carried out in ArrayIT Hybridization cassettes (Telechem) in a hybridization oven at 55°C for 15 hr. Microarrays were washed consecutively in solutions of 2X SSC; 0.5% SDS at 55°C for 5 min, 0.5X SSC at room termperature for 5 min, and 0.1X SSC at room temperature for 5 min, and dried by centrifugation.

scan_protocol: Hybridization signal intensity data were obtained using a GenePix AL4200 scanner and GenePix Pro v6.1 software (Molecular Devices).

data_processing: Background-subtracted median intensity values for each spot were used for subsequent analyses. Probes for which the combined signal from both channels was < 50 were classified as 'not expressed' and removed from each slide in the comparison of interest. Data were imported into R v2.11.1 and subsequently analyzed using the 'Limma' (linear models for microarray analysis) software package to identify differentially expressed genes. Normalization of microarray data was carried out both within arrays (using a global loess procedure) and between arrays (using a quantile normalization). A linear model was fitted to the log2 transformed data to estimate variability, and an empirical Bayes method used to calculate moderated T statistics for each oligo. The associated p values were adjusted for multiple testing using the False Discovery Rate (FDR) method of Benjani and Hochberg.

organism: Sus scrofa

label_protocol: Labeled target RNA for microarray hybridizations were generated using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion) with minor modifications to the manufacturer's protocol. A 20 ng amount of total RNA underwent two rounds of linear amplification by in vitro transcription for 14 hr. The second round of in vitro transcription used a1:3 ratio of UTP: amino allyl UTP. A 6 μg amount of amino allyl aRNA was labeled with 10,000 pmol of either Cy3 or Cy5 dye (GE Healthcare). Dye incorporation was measured using the Nanodrop 2000 (Thermo Scientific).

growth_protocol: Animals were the offspring of PIC Camborough plus  sows and 337 boars, and were raised on a 300 sow commercial farm in Saskatchewan. At 15 weeks of age, 5 ml samples were collected into heparin-coated Vacutainer tubes (BD). PBMC were isolated by density gradient centrifugation using Lymphoprep (Axis-Shield) using a modified protocol. Briefly, samples were centrifuged at 1730 x g for 10 min. Buffy coats were transferred to a new tube, mixed with an equal volume of Hank's Balanced Salt Solution (HBSS) containing 1% (w/v) bovine serum albumin (BSA), and layered over an equal volume of Lymphoprep. After centrifugation at 620 x g for 30 min, the PBMC layer was transferred to a new tube and the cells were washed once in HBSS + BSA by centrifugation at 430 x g for 10 min. Cell pellets were then incubated for 5 min at 37 °C in a lysis buffer (155mM NH4Cl; 20 mM NaHCO3; 1mM EDTA, pH 8) to lyse erythrocytes. Cells were washed twice more in HBSS + BSA, then resuspended in RPMI medium containing 10% (w/v) fetal bovine serum, 1% (v/v) pen-strep solution, and 1mM sodium pyruvate. Cells were enumerated using a hemocytometer and viability was confirmed by exclusion of the vital dye Trypan blue.

extract_protocol: Total RNA was isolated using the AllPrep DNA/RNA mini kit (Qiagen) according to the manufacturer’s instructions. RNA integrity and yield were assessed on RNA 6000 Nano and Pico chips on an Agilent Bioanalyzer 2100 (Agilent Technologies). All RNA samples had an RNA integrity number (RIN) score of ≥ 7.

treatment_protocol: For each animal, 1 x 10^5 cells were transferred in triplicate to 96 well culture plates (Costar) and treated with concanavalin A in RPMI medium (final concentration 1.25 μg/ml) or RPMI medium only (unstimulated control). Five replicate plates were prepared in this manner and incubated at 37 °C at 5% CO2. Cells from four of the plates were collected by centrifugation at 0, 3, 20, and 68 hr post-stimulation time-points, and snap-frozen for the subsequent isolation RNA (next section). At 68 hr, cells from the fifth plate were pulsed with 0.5 μCi [3H] thymidine for 18 hr. Cells were harvested onto filter plates and radioactivity was measured in counts per minute (cpm) using a TopCount microplate scintillation counter (Perkin Elmer). For each individual, proliferation was quantified as the mean value for the stimulated cells minus that of the unstimulated cells.

value: Female

tag: age

value: 15 weeks

value: Peripheral Blood Mononuclear Cell (PBMC) fraction of blood


title: DLBCL GEP data N0125


title: ESC

description: Gene expression of ESC

source_name: ESC

value: ESC


title: DLBCL GEP data N0132


title: Splenic Marginal Zone Lymphoma P105 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P105


title: iPS-J

description: Gene expression of iPS-J

source_name: iPS-J

value: iPS


title: P2_Cy5 vs.P2_Cy3 (Kidney)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: GX 75th percentile shift-normalized values of individual channels available on series record

hyb_protocol: 300ng of cy3 labeled samples and 300ng of cy5 labeled samples were fragmented and hybridized on the slides .  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

scan_protocol: Scanned using the Agilent Technologies Scanner G2505C at 5 micron resolution. Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1 )

data_processing: Data was analyzed in GeneSpring GX software from Agilent using 75th percentile shift normalization. Probe intensities generated from feature extraction raw data were split based on channel type. All the cy3 and cy5 labeled test samples were compared to control cy3 and cy5 samples to generate ratios. Genes showing >One fold change in the test sample compared to the reference were compiled as differentially regulated genes. ( Note: Analysis performed for Liver and kidney separately)

source_name: murine kidney with intermediate level of parasitamia

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the cy3 and cy5  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Mice were kept in standard laboratory conditions and water and food were provided ad libitum.

extract_protocol: Total RNA was extracted from each group of mice using standard procedure utilising Trizol reagent.

treatment_protocol: Mice were infected with Plasmodium vinckei strain of murine paraiste to induce malaria like symptoms in mice. Different levels of percetage  parasitemic mice were generated following varying the incubation period of parasite within the target organs in mice.

value: Swiss albino

value: kidney


title: DLBCL GEP data N0135


title: iPS-OSH

description: Gene expression of iPS-OSH

source_name: iPS-OSH


title: DLBCL GEP data N0137

value: ABC


title: P3_Cy5 vs.P3_Cy3 (Kidney)

source_name: murine kidney with high level of parasitamia


title: DLBCL GEP data N0127


title: Splenic Marginal Zone Lymphoma P108 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P108


title: PBMC_68hr_Rep4a


title: PBMC_68hr_Rep3b

value: Male


title: DLBCL GEP data N0126


title: Splenic Marginal Zone Lymphoma P78 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P78


title: DLBCL GEP data N0128

value: GCB


title: PBMC_68hr_Rep3a


title: C_Cy5 vs.C_Cy3 (Kidney)

source_name: Control murine kidney


title: Splenic Marginal Zone Lymphoma P80 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P80


title: P1_Cy5 vs.P1_Cy3 (Kidney)

source_name: murine kidney with low parasitamia


title: DLBCL GEP data N0123


title: PBMC_68hr_Rep1a


title: PBMC_68hr_Rep1b


title: DLBCL GEP data N0122


title: Splenic Marginal Zone Lymphoma P102 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P102


title: PBMC_68hr_Rep2b


title: PBMC_68hr_Rep2a


title: Splenic Marginal Zone Lymphoma P72 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P72


title: DLBCL GEP data N0124


title: DLBCL GEP data N0120


title: Wide type I-S plants, biological rep3

city: Hangzhou

first: Xuming

last: Wang

state: Zhejiang

address: Shiqiao Road 198#

department: Institute of Virology and Biotechnology

country: China

institute: Zhejiang Academy of Agricultural Sciences

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

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

data_processing: The data were analyzed with Agilent GeneSpring 11 using default analysis settings and global scaling as normalization method.

organism: Oryza sativa Japonica Group

source_name: leaf from WT, japonica rice (I-S)

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

growth_protocol: Rice seeds were germinated at 37 ºC for 1 d. After germination, the plants were grown in a growth room under a photosynthetic photon flux density of approximately 200 μmol photons m-2s-1 with a 12 h light (32 ºC)/12 h dark (28 ºC) photoperiod. Humidity was controlled at 60%.

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

treatment_protocol: For the evaluation of the function of OsPR1L1, rice plants overexpressing OsRP1L1 were developed. Plants overexpressing OsRP1L1 were used for RNA extraction from three independent treatments.

tag: cultivar

value: Ishikari-shiroge (I-S)

value: wild type

value: leaf

tag: developmental stage

value: max tilling


title: Splenic Marginal Zone Lymphoma P79 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P79

value: Splenic Marginal Zone Lymphoma


title: DLBCL GEP data N0119


title: Splenic Marginal Zone Lymphoma P60 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P60


title: Splenic Marginal Zone Lymphoma P39 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P39


title: P2_Cy5 vs.P2_Cy3 (Liver)

source_name: murine liver with intermediate parasitamia

value: liver


title: DLBCL GEP data N0121

source_name: DLBCL patient sample


title: DLBCL GEP data N0118


title: OsRP1L1-overexpressing plants, biological rep3

source_name: leaf from OsRP1L1-overexpressing plants

value: OsRP1L1 overexpressing


title: Wide type I-S plants, biological rep2


title: Wide type I-S plants, biological rep1


title: PBMC_20hr_Rep4b


title: PBMC_20hr_Rep4a


title: C_Cy5 vs.C_Cy3 (Liver)

source_name: Control murine liver


title: DLBCL GEP data N0117


title: Splenic Marginal Zone Lymphoma P38 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P38


title: P1_Cy5 vs.P1_Cy3 (Liver)

source_name: murine liver with low parasitamia


title: PBMC_20hr_Rep2b

value: Female


title: OsRP1L1-overexpressing plants, biological rep1


title: Splenic Marginal Zone Lymphoma P25 250KSty

description: Hybridized to 250K_Sty

source_name: Splenic Marginal Zone Lymphoma P25


title: PBMC_20hr_Rep3b

value: 15 weeks


title: PBMC_20hr_Rep2a

value: Peripheral Blood Mononuclear Cell (PBMC) fraction of blood


title: PBMC_20hr_Rep1b


title: PBMC_20hr_Rep1a


title: PBMC_20hr_Rep3a


title: Peripheral T cell lymphoma 37

city: Madrid

first: Esperanza

last: Martín-Sánchez

address: Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

description:
PTCL 37
Biological replicate 37 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Technologies, Inc.) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were sequentially washed.

scan_protocol: Microarray slides were scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Bioconductor's limma package was employed for preprocessing and normalization. Thus, background was corrected using the normexp method and data were normalized using the loess and quantiles method for within-array and inter-array normalization, respectively.

source_name: Human lymph node from a peripheral T cell lymphoma patient

label_protocol: 500 ng of total RNA were primed with the T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ºC (all reagents were obtained from Agilent Technologies, Inc.).

growth_protocol: Lymph nodes were frozen to preserve the RNA properties.

extract_protocol: Total RNA was extracted using Trizol, precipitated with isopropanol and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

value: lymph node

tag: disease status

value: peripheral T cell lymphoma (PTCL)

source_name: Universal Human Reference RNA

value: 10 human tumor cell lines

value: reference


title: PBMC_3hr_Rep4b


title: DLBCL GEP data N0114


title: DLBCL GEP data N0116

value: ABC


title: Peripheral T cell lymphoma 38

description:
PTCL 38
Biological replicate 38 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0112


title: DLBCL GEP data N0113


title: Peripheral T cell lymphoma 35

description:
PTCL 35
Biological replicate 35 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 36

description:
PTCL 36
Biological replicate 36 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0115


title: OsRP1L1-overexpressing plants, biological rep2

tag: genotype/variation


title: Peripheral T cell lymphoma 32

description:
PTCL 32
Biological replicate 32 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0107


title: DLBCL GEP data N0106


title: PBMC_3hr_Rep3b


title: PBMC_3hr_Rep4a

value: Male


title: PBMC_3hr_Rep3a


title: DLBCL GEP data N0104

value: GCB


title: DLBCL GEP data N0105


title: DLBCL GEP data N0102


title: Peripheral T cell lymphoma 33

description:
PTCL 33
Biological replicate 33 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 30

description:
PTCL 30
Biological replicate 30 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0101


title: PBMC_3hr_Rep2a


title: PBMC_3hr_Rep2b


title: Splenic Marginal Zone Lymphoma P106 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P106


title: Peripheral T cell lymphoma 34

description:
PTCL 34
Biological replicate 34 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 31

description:
PTCL 31
Biological replicate 31 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0096


title: DLBCL GEP data N0095


title: PBMC_3hr_Rep1a


title: DLBCL GEP data N0111

value: UC


title: Peripheral T cell lymphoma 29

description:
PTCL 29
Biological replicate 29 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P93 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P93


title: PBMC_3hr_Rep1b


title: P3_Cy5 vs.P3_Cy3 (Liver)

source_name: murine liver with high parasitamia

value: Swiss albino


title: Peripheral T cell lymphoma 28

description:
PTCL 28
Biological replicate 28 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 27

description:
PTCL 27
Biological replicate 27 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P89 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P89


title: DLBCL GEP data N0099


title: Sugarcane transcriptome - ch1: Drought_72h_Exp_2; ch2: control_72h_2

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

description: Plants under drought conditions (72h) x control plants, experiment 2

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data. The used software was the Feature Extraction version 9.5.3.1 (Agilent Technologies).

organism: Saccharum hybrid cultivar (mixed)

label_protocol: Agilent's Quick Amp Labeling Kit Protocol

growth_protocol: Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Plants were maintained under greenhouse conditions.

extract_protocol: Total RNA was extracted using TriZol reagent

treatment_protocol: Sugarcane plantlets with 105 days were maintained without irrigation for 72h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.

value: Aerial parts of sugarcane

value: hybrid SP90-1638

tag: pool

value: 6 individuals

tag: time point

tag: condition

value: exposure to drought conditions

treatment_protocol: Sugarcane plantlets with 105 days were maintained with irrigation for 72h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.

value: 6 control plants

value: irrigation


title: DLBCL GEP data N0094

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

tag: gene expression profiling subgroup


title: Splenic Marginal Zone Lymphoma P87 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P87

value: Splenic Marginal Zone Lymphoma


title: Peripheral T cell lymphoma 26

description:
PTCL 26
Biological replicate 26 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0089

tag: immunohistochemistry subgroup


title: Sugarcane transcriptome - ch2: Drought_24h_Exp_1; ch1: control_24h_1

description: Plants under drought conditions (24h) x control plants, experiment 1

treatment_protocol: Sugarcane plantlets with 105 days were maintained with irrigation for 24h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.

treatment_protocol: Sugarcane plantlets with 105 days were maintained without irrigation for 24h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.


title: Splenic Marginal Zone Lymphoma P84 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P84


title: Peripheral T cell lymphoma 24

description:
PTCL 24
Biological replicate 24 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Sugarcane transcriptome - ch1: Drought_120h_Exp_2; ch2: control_120h_2

description: Plants under drought conditions (120h) x control plants, experiment 2

treatment_protocol: Sugarcane plantlets with 105 days were maintained without irrigation for 120h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.

treatment_protocol: Sugarcane plantlets with 105 days were maintained with irrigation for 120h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.


title: Splenic Marginal Zone Lymphoma P85 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P85


title: Sugarcane transcriptome - ch2: Drought_72h_Exp_1; ch1: control_72h_1

description: Plants under drought conditions (72h) x control plants, experiment 1


title: Peripheral T cell lymphoma 21

description:
PTCL 21
Biological replicate 21 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P83 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P83


title: DLBCL GEP data N0093

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


title: Sugarcane transcriptome - ch2: Drought_120h_Exp_1; ch1: control_120h_1

description: Plants under drought conditions (120h) x control plants, experiment 1


title: Splenic Marginal Zone Lymphoma P82 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P82


title: Splenic Marginal Zone Lymphoma P86 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P86


title: DLBCL GEP data N0090

source_name: DLBCL patient sample


title: DLBCL GEP data N0088


title: Splenic Marginal Zone Lymphoma P81 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P81


title: Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2

description: Plants under drought conditions (24h) x control plants, experiment 2


title: Peripheral T cell lymphoma 25

description:
PTCL 25
Biological replicate 25 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 20

description:
PTCL 20
Biological replicate 20 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 23

description:
PTCL 23
Biological replicate 23 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 22

description:
PTCL 22
Biological replicate 22 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0087


title: Peripheral T cell lymphoma 19

description:
PTCL 19
Biological replicate 19 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0083


title: Splenic Marginal Zone Lymphoma P68 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P68


title: DLBCL GEP data N0082


title: DLBCL GEP data N0081


title: Splenic Marginal Zone Lymphoma P66 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P66


title: Peripheral T cell lymphoma 18

description:
PTCL 18
Biological replicate 18 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0076


title: DLBCL GEP data N0085


title: DLBCL GEP data N0080


title: Splenic Marginal Zone Lymphoma P64 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P64


title: Peripheral T cell lymphoma 17

description:
PTCL 17
Biological replicate 17 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

source_name: Human lymph node from a peripheral T cell lymphoma patient


title: Peripheral T cell lymphoma 14

description:
PTCL 14
Biological replicate 14 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

source_name: Universal Human Reference RNA


title: Splenic Marginal Zone Lymphoma P73 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P73


title: Peripheral T cell lymphoma 16

description:
PTCL 16
Biological replicate 16 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P69 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P69


title: DLBCL GEP data N0077

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


title: Peripheral T cell lymphoma 13

description:
PTCL 13
Biological replicate 13 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 15

description:
PTCL 15
Biological replicate 15 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P56 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P56


title: Splenic Marginal Zone Lymphoma P58 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P58


title: Peripheral T cell lymphoma 11

description:
PTCL 11
Biological replicate 11 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Splenic Marginal Zone Lymphoma P42 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P42


title: DLBCL GEP data N0075


title: Splenic Marginal Zone Lymphoma P53 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P53


title: Splenic Marginal Zone Lymphoma P26 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P26


title: DLBCL GEP data N0073


title: Peripheral T cell lymphoma 10

description:
PTCL 10
Biological replicate 10 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 12

description:
PTCL 12
Biological replicate 12 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 9

description:
PTCL 9
Biological replicate 9 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0071


title: DLBCL GEP data N0069


title: Peripheral T cell lymphoma 7

description:
PTCL 7
Biological replicate 7 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: Peripheral T cell lymphoma 8

description:
PTCL 8
Biological replicate 8 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.


title: DLBCL GEP data N0070


title: DLBCL GEP data N0074


title: Splenic Marginal Zone Lymphoma P21 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P21


title: Mm303-97

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

hyb_protocol: Agilent recommended protocol

scan_protocol: scan at 3 uM resolution

data_processing: Agilent Feature Extraction software. Dye bias correction was performed using default settings in Agilent Feature Extraction. The Log2 ratios were calculated using the ratio of rProcessedSignal to gProcessedSignal from the Feature Extraction files.

organism: Macaca mulatta

source_name: rhesus macaque_B cell line

label_protocol: Agilent recommended protocol

growth_protocol: standard for B cell lines

extract_protocol: standard DNA extraction from B cell lines using cell lysis

tag: commercial source of sample

value: Yerkes-not available for purchase

source_name: human_reference_B cell line

tag: reference


title: Splenic Marginal Zone Lymphoma P24 50XbaI

description: Hybridized to 50K_Xba

source_name: Splenic Marginal Zone Lymphoma P24


title: PR00648_Coriell

data_processing: Agilent Feature Extraction software. Dye bias correction was peformed using a subset of probes with 100% sequence identity across human, chimpanzee, gorilla, orangutan, and rhesus macaque reference genomes. The Log2 ratios were calculated using the ratio of rProcessedSignal to gProcessedSignal from the Feature Extraction files.

organism: Pongo abelii

source_name: orangutan_B cell line

value: Coriell


title: Peripheral T cell lymphoma 6

description:
PTCL 6
Biological replicate 6 of 38. Lymph node from a PTCL patient.
Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell lines.

value: lymph node

value: peripheral T cell lymphoma (PTCL)


title: Normal 4

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: Hybridisation of labelled RNA was done on miRNAChip_human_V2 at 42ºC for 16h. The normal gastric pooled reference sample was labelled and hybridised four times to check arrays’ reproducibility.

scan_protocol: Slides were scanned using an Agilent G2565AA microarray scanner

data_processing: Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer). Manually flagged bad spots were eliminated and the Cy3 median pixel intensity values were  background subtracted, followed by the averaging of quadruplicate features on the array. Data points were removed when intensity values were below 100 (2 times the background signal). A global median normalization of human gastric cancer microarray data was applied using BRB-ArrayTools v3.4.0 software. Log-transformed (base 2) cy3 intensities were obtained. Differentially expressed miRNAs from each sample were identified using the Multiple Experiment Viewer Mev software version 4.6.2. A nonparametric Wilcoxon rank sum (Mann-Whitney) test at a critical value of P=0.05 and FDR=0.05 was performed to identify miRNAs that demonstrated statistically significant difference in expression between normal gastric mucosa and tumour tissue.

source_name: 10 Normal Gastric Mucosas

label_protocol: Two μg of total RNA from primary gastric tumors and normal gastric reference sample were labelled with Cy3-ULS using the ULSTM miRNA labelling kit (Kreatech) followed by purification and monitoring of dye incorporation by UV-visible spectroscopy.

extract_protocol: Total RNA was isolated from tumours and normal gastric mucosas using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion Inc, Austin, TX) according to manufacturer’s protocol. RNA quantity and integrity were assessed using the Nanodrop and Agilent 2100 bioanalyzer systems, respectively.  The 10 normal gastric mucosa RNA samples were pooled to obtain the normal gastric reference sample. All tumour samples were histologically verified to contain a minimum of 70% of neoplastic cells.

value: Normal Gastric Mucosa

tag: lauren histology

value: Normal