title: Peripheral blood mononuclear cells of 128-Cy5 pre-treatment and 239-Cy3 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: G250E; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not available; Ph+ metaphases after dasatinib treatment (%):95; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_128.239_Cy5.txt


title: Peripheral blood mononuclear cells of 234-Cy5 post-treatment and 152-Cy3 pre-treatment dasatinib responder patient

status: Public on Jul 31 2013

type: RNA

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 30; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013127_2007-07-12_509-524_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: 825ng of each Cy3 and Cy5 labeled cRNA was hybridized using Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R1_152.234_Cy5.txt

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-5

label_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis protocol: Starting with 200 ng of total RNA, we performed cDNA synthesis and generated fluorescent labeled cRNA targets using Agilent Low RNA Input Fluorescent Linear Amplification Kit and oligo-dT-T7 promoter primer. Each patient sample was separately labeled with Cy3 and Cy5 to perform a dye swap technical replicate.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen), treated with RNase-free DNase I and purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.

tag: dasatinib treatment

value: post-treatment

tag: drug response

value: responder

tag: cell type

value: peripheral blood mononuclear cells

tag: gender

value: F

tag: age (yrs) at dasatinib start

tag: treatments prior to dasatinib

value: HU, IFN, araC, IM

tag: mutations detected in the bcr/abl kinase domain after dasatinib treatment

value: Not detected

tag: ph+ metaphases after dasatinib treatment (%)

tag: additional cytogenetic abnormalities after dasatinib treatment

value: Not detected.

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-3

value: pre-treatment

tag: mutations detected in the bcr/abl kinase domain before dasatinib treatment

tag: ph+ metaphases before dasatinib treatment (%)


title: Testis, DHT50, Rep1

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Fundulus heteroclitus

source_name: Testis, 5α-dihydrotestosterone (DHT)

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Microarray analysis was performed with four biological replicates (4 control and 4 treatment).  Individuals from the high concentration, 50 ug/L DHT, were used for the microarray analysis.

treatment_protocol: DHT waterborne exposure at 5 and 50 ug/L for 21 days

tag: age

value: adult

tag: Sex

value: male

tag: tissue

value: testis


title: Peripheral blood mononuclear cells of 240-Cy5 post-treatment and 150-Cy3 pre-treatment dasatinib responder patient

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):75.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R_150.240_Cy5.txt

value: M

value: HU, IFN, araC, ASCT, IM


title: Peripheral blood mononuclear cells of 240-Cy3 post-treatment and 150-Cy5 pre-treatment dasatinib responder patient

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):75.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R_150.240_Cy3.txt

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-3

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-5


title: MM_113: CD138_selected_plasma_cells_presentation

city: London

first: Gareth

last: Morgan

address: 15 Cotswold Road

department: Division of Molecular Pathology

country: United Kingdom

institute: The Institute of Cancer Research

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

hyb_protocol: The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0 following Affymetrix recommended protocol.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G scanner.

data_processing: The data were extracted using Affymetrix miRNA QC tool software using default analysis settings for normalization and summarization methods.

label: biotin

source_name: pre-treatment bone marrow

label_protocol: small RNA was processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, RNA extracted and small RNA enriched using Qiagen AllPrep DNA/RNA mini kit

value: myeloma cells

tag: extraction

value: AllPrep

tag: storage

value: RLT


title: MM_112: CD138_selected_plasma_cells_presentation


title: Peripheral blood mononuclear cells of 234-Cy3 post-treatment and 152-Cy5 pre-treatment dasatinib responder patient

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 30; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R1_152.234_Cy3.txt


title: Peripheral blood mononuclear cells of 235-Cy3 post-treatment and 155-Cy5 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485012777_2007-08-07_505_495_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_155.235_Cy3.txt

value: non-responder


title: MM_114: CD138_selected_plasma_cells_presentation


title: Peripheral blood mononuclear cells of 235-Cy5 post-treatment and 155-Cy3 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485012777_2007-08-07_505_495_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_155.235_Cy5.txt

value: post-treatment


title: Peripheral blood mononuclear cells of 221-Cy5 post-treatment and 136-Cy3 pre-treatment dasatinib responder patient

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: 8+.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R_136.221_Cy5.txt

value: responder

value: HU, IFN, IM


title: Peripheral blood mononuclear cells of 195-Cy3 post-treatment and 148-Cy5 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):90; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain in before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_148.195_Cy3.txt

value: peripheral blood mononuclear cells

value: F

tag: mutations detected in the bcr/abl kinase domain in before dasatinib treatment


title: MM_111: CD138_selected_plasma_cells_presentation


title: MM_110: CD138_selected_plasma_cells_presentation


title: Peripheral blood mononuclear cells of 221-Cy3 post-treatment and 136-Cy5 pre-treatment dasatinib responder patient

description:
ch1: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: 8+.
ch2: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_R_136.221_Cy3.txt

tag: dasatinib treatment

value: Not detected


title: Peripheral blood mononuclear cells of 195-Cy5 post-treatment and 148-Cy3 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):90; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain in before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_148.195_Cy5.txt

tag: drug response

value: HU, IFN, araC, IM

value: Not detected.


title: Peripheral blood mononuclear cells of 239-Cy5 post-treatment and 128-Cy3 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not available; Ph+ metaphases after dasatinib treatment (%):95; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: G250E; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_128.239_Cy5.txt

tag: cell type

value: Not available

value: pre-treatment


title: Peripheral blood mononuclear cells of 205-Cy5 post-treatment and 131-Cy3 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: F317L; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: F317L; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_131.205_Cy5.txt

tag: gender


title: MCMV Mutant M79 infection

city: Saint Louis

first: travis

last: Chapa

state: MO

address: 4440 Parkview Place

department: Microbiology

institute: Washington University in St. Louis

description: US82600140_252372810011_S01_GE2_107_Sep09_1_2.txt

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Non-specific background fluorescence signal was subtracted from each probe value. Signals from different samples were linearally normalized using spike-in RNA fluorescence levels. Probe signal from Mock-infected samples were subtracted from each MCMV infected sample to correct for host RNA cross-hybridization.

organism: Mus musculus

source_name: MEF10.1 + M79 MCMV

label_protocol: cDNA probes were synthesized, fluorescently labeled by random hexamer-primed polymerization using the SuperScript Plus Indirect cDNA Labeling module (Invitrogen)

growth_protocol: MEF10.1 cells were either mock or infected with wt. MCMV or M79 mutant MCMV at an MOI of 2. RNA was harvested 20 hours post-infection

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

treatment_protocol: Cells were either mock or treated with PAA co-incident with infection.

tag: infection

value: MCMV Mutant M79 infection


title: MCMV WT infection + PAA

source_name: MEF10.1 + WT MCMV + PAA

value: MCMV WT infection + PAA


title: Mock infection

description: US82600140_252372810011_S01_GE2_107_Sep09_1_1.txt

value: Mock infection


title: Peripheral blood mononuclear cells of 205-Cy3 post-treatment and 131-Cy5 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: F317L; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: F317L; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_131.205_Cy3.txt

value: M

tag: age (yrs) at dasatinib start

tag: treatments prior to dasatinib


title: MM_109: CD138_selected_plasma_cells_presentation

value: myeloma cells

value: AllPrep


title: Peripheral blood mononuclear cells of 239-Cy3 post-treatment and 128-Cy5 pre-treatment dasatinib non-responder patient

description:
ch1: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not available; Ph+ metaphases after dasatinib treatment (%):95; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.
ch2: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: G250E; Ph+ metaphases before dasatinib treatment (%):100.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_2.txt

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Scan resolution 5um.

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pos_NR_128.239_Cy3.txt

value: non-responder

tag: mutations detected in the bcr/abl kinase domain after dasatinib treatment

tag: ph+ metaphases after dasatinib treatment (%)


title: MM_108: CD138_selected_plasma_cells_presentation

value: RLT


title: MM_107: CD138_selected_plasma_cells_presentation

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in Trizol, RNA was isolated using Trizol and the Invitrogen Micro-to-Midi total RNA purification kit and then enriched with small RNA

value: Trizol


title: MM_106: CD138_selected_plasma_cells_presentation


title: MM_105: CD138_selected_plasma_cells_presentation


title: Transgenic heart with low FASN-rep1

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data of heart with low level of transgenic FASN expression

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

source_name: Transgenic heart with low FASN expression

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5; and Invitrogen manual for SuperScript One-Cycle cDNA Kit).

growth_protocol: The study was performed with heart tissue isolated from transgenic mouse lines expressing FASN under control of the myocardium-specific alpha-MHC promoter. Two different transgenic lines with high and low level of cardiac FASN expression, respectively, were used. The third group consisted of age-matched B6 control mice.

extract_protocol: Total RNA was isolated from heart tissue with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: For the microarray study, hearts were isolated from three study groups: (i) Transgenic mice with high cardiac FASN expression, (ii) transgenic mice with low cardiac FASN expression, and (iii) age-matched B6 control mice.

value: transgenic heart

tag: strain

tag: phenotype

value: low FASN

value: male


title: 8_DAP_20C_Rep3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Five Medicago truncatula plants were grown at controlled light/temperature conditions: 16h, 19-21°C from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 8 day after pollination (DAP) to Abscission. Dry seeds (DS) was the last analysed stage of development, after abscission seeds were let in the same environmental conditions for one week.

extract_protocol: For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations

treatment_protocol: Medicago truncatula seeds developed at 16h, 19-21°C from 1 DAP to DS stage

value: seed

tag: genetic background

tag: developmental stage

value: 8_DAP maturation

value: Wild-type

tag: treatment

value: Seeds developed at 21-19°C 16h

tag: age

value: 8 days after flowering

tag: harvest date


title: Transgenic heart with high FASN-rep2

description: Gene expression data of heart with high level of transgenic FASN expression

source_name: Transgenic heart with high FASN expression

tag: tissue

value: high FASN


title: MCMV WT infection

source_name: MEF10.1 + WT MCMV

value: MCMV WT infection


title: 8_DAP_20C_Rep4


title: B6 control heart rep2

description: Gene expression data of B6 control heart

source_name: B6 control heart

value: control heart


title: Transgenic heart with low FASN-rep2


title: MM_103: CD138_selected_plasma_cells_presentation

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

tag: extraction

tag: storage


title: MM_104: CD138_selected_plasma_cells_presentation


title: DS_DAP_20C_Rep1

value: Dry Seed

value: DS


title: B6 control heart rep1


title: Abs_DAP_20C_Rep1

value: Abscission


title: DS_DAP_20C_Rep2


title: Transgenic heart with high FASN-rep1


title: MM_102: CD138_selected_plasma_cells_presentation

value: myeloma cells

value: AllPrep


title: Abs_DAP_20C_Rep2


title: MM_101: CD138_selected_plasma_cells_presentation

value: RLT


title: MM_116: CD138_selected_plasma_cells_presentation


title: MM_100: CD138_selected_plasma_cells_presentation


title: MM_099: CD138_selected_plasma_cells_presentation


title: MEF_WT3

city: Wako-shi

first: ayako

last: kurimoto

state: Saitama

address: Hirosawa

country: Japan

institute: RIKEN

description: replicate 1

hyb_protocol: Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

scan_protocol: GeneChips were scanned using  GeneChip Scaner 3000 7G.

data_processing: The data were analyzed with Gene Chip operation software (GCOS) Ver. 1.4 using Affymetrix default analysis settings.

source_name: Mouse cell lines

label_protocol:
The total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted template for transcription into a double-stranded DNA synthesize first-strand cDNA.
This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: MEFs were cultured in Dulbecco’s minimal essential medium containing 10% fetal calf serum and 1% (w/v) penicillin/streptomycin at 37˚C and 5% CO2.

extract_protocol: Total RNA was isolated from the cells using RNeasy Mini Kit (QIAGEN). The quality of RNA was measured using 2100 Bioanalyzer (Agilent).

tag: cell line

value: MEF

tag: genotype


title: MEF_KO3

description: replicate 1


title: 44_DAP_20C_Rep1

value: 44_DAP maturation

value: 44 days after flowering


title: MM_098: CD138_selected_plasma_cells_presentation


title: 41_DAP_20C_Rep1

value: seed

value: 41_DAP maturation

value: 41 days after flowering


title: 44_DAP_20C_Rep2

value: Wild-type

value: Seeds developed at 21-19°C 16h


title: MM_117: CD138_selected_plasma_cells_presentation


title: BMT-mock-1

city: Tokyo

first: Daichi

last: Inoue

address: 4-6-1 Shirokanedai, Minato-ku

institute: Division of Cellular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm.

source_name: CD3-B220-Ter119- Myeloid BM cells derived from mock-transplanted mice (normal control)

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

tag: cell type

value: myeloid BM cells


title: 41_DAP_20C_Rep2


title: BMT-mock-2


title: 38_DAP_20C_Rep2

value: 38_DAP maturation

value: 38 days after flowering


title: DNA methylation in 8 week sperm (replicate#2)

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
MIRA_Sperm_R
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

hyb_protocol: According to the NimbleGen Kit.

scan_protocol: Follow NimbleScan's default using the Agilent Scanner.

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: Methylated-CpG island recovery assay (MIRA) DNA from 8-week-old male sperm

label_protocol: According to the standard NimbleGen protocol.

extract_protocol: GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryos and fetus gonads using a MoFlo or Aria II flow cytometer. For chromatin immunoprecipitation, cells were crosslinked before sorting. Chromatin from 400,000 cells was used for one ChIP using various antibodies. For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify ChIP- and MIRA-enriched DNA.

tag: strain/background

value: CF1 x TgOG2

value: sperm

tag: gender

value: male

value: 8 weeks

tag: mira

value: MBD3L1 and MBD2b

tag: epigenetic feature

value: DNA methylation

source_name: Input DNA from 8 week sperm


title: DNA methylation in 8 week sperm (replicate#3)

description:
MIRA_Sperm_R2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).


title: BMT-ASXL1Mt-3

source_name: Myeloid BM cells derived from ASXL1-MT-transplanted mice (myelodysplastic symdrome-like disease)


title: MM_097: CD138_selected_plasma_cells_presentation

data_processing: The data were extracted using Affymetrix miRNA QC tool software using default analysis settings for normalization and summarization methods.

value: myeloma cells

value: AllPrep

value: RLT


title: 38_DAP_20C_Rep1

value: seed


title: MM_096: CD138_selected_plasma_cells_presentation


title: DNA methylation in 8 week sperm (replicate#1)

description:
MIRA_Sperm
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).


title: DNA methylation in the male germ cells at 17.5dpc (replicate#2)

description:
MIRA_MGC_17_R
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 17.5dpc

value: germ cells

source_name: Input DNA from 17.5 dpc male germ cells at 17.5 dpc


title: MM_095: CD138_selected_plasma_cells_presentation


title: DNA methylation in the male germ cells at 17.5dpc (replicate#3)

description:
MIRA_MGC_17_R2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).


title: 35_DAP_20C_Rep2

value: 35_DAP maturation

value: 35 days after flowering


title: DI_32Dcl3_mock_G24h

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using RMA algorithm with target intensity=100.

source_name: 32Dcl3 cells transduced with mock, treated with G-CSF for 24 hours

tag: transfection

value: pMYs-IG (mock)

value: treated with G-CSF for 24 hours


title: 35_DAP_20C_Rep1

tag: phenotype

value: Wild-type

value: Seeds developed at 21-19°C 16h


title: MM_094: CD138_selected_plasma_cells_presentation


title: BMT-ASXL1Mt-1

value: myeloid BM cells


title: DI_32Dcl3_mock_G6h

source_name: 32Dcl3 cells transduced with mock, treated with G-CSF for 6 hours

value: treated with G-CSF for 6 hours


title: BMT-ASXL1Mt-2


title: 32_DAP_20C_Rep2

tag: genetic background

value: 32_DAP maturation

value: 32 days after flowering


title: 32_DAP_20C_Rep1

tag: developmental stage


title: MM_093: CD138_selected_plasma_cells_presentation


title: DNA methylation in the male germ cells at 15.5dpc (replicate#1)

description:
MIRA_MGC_15
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 15.5dpc

value: CF1 x TgOG2

value: male

value: MBD3L1 and MBD2b

source_name: Input DNA from 15.5 dpc male germ cells at 15.5 dpc


title: DI_32Dcl3_mock_IL-3

source_name: 32Dcl3 cells transduced with mock, treated with IL-3

tag: treatment

value: treated with IL-3


title: DNA methylation in the female germ cells at 15.5dpc

description:
MIRA_FGC_15
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from female germ cells at 15.5dpc

value: female

tag: age

value: DNA methylation

source_name: Input DNA from 15.5 dpc female germ cells at 15.5 dpc


title: MM_091: CD138_selected_plasma_cells_presentation

source_name: pre-treatment bone marrow

value: myeloma cells

value: AllPrep

value: RLT


title: BMT-mock-3


title: DNA methylation in the female germ cells at 17.5dpc

description:
MIRA_FGC_17
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from female germ cells at 17.5dpc

value: germ cells

source_name: Input DNA from 17.5 dpc female germ cells at 17.5 dpc


title: 29_DAP_20C_Rep2

value: seed

value: 29_DAP maturation

value: 29 days after flowering

tag: harvest date


title: DNA methylation in the male germ cells at 15.5dpc (replicate#3)

description:
MIRA_MGC_15_R2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).


title: DI_32Dcl3_ASXL1_G24h

source_name: 32Dcl3 cells transduced with ASXL1-MT, treated with G-CSF for 24 hours

value: treated with G-CSF for 24 hours


title: DI_32Dcl3_mock_G2h

source_name: 32Dcl3 cells transduced with mock, treated with G-CSF for 2 hours

value: pMYs-IG (mock)

value: treated with G-CSF for 2 hours


title: 29_DAP_20C_Rep1

tag: tissue

value: Wild-type

value: Seeds developed at 21-19°C 16h


title: MM_092: CD138_selected_plasma_cells_presentation

tag: extraction


title: MM_090: CD138_selected_plasma_cells_presentation

tag: storage


title: MM_089: CD138_selected_plasma_cells_presentation


title: DNA methylation in the female germ cells at 13.5dpc

description:
MIRA_FGC_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from female germ cells at 13.5dpc

value: CF1 x TgOG2

source_name: Input DNA from 13.5 dpc female germ cells at 13.5 dpc


title: 26_DAP_20C_Rep2

value: 26_DAP maturation

value: 26 days after flowering


title: DNA methylation in the male germ cells at 15.5dpc (replicate#2)

description:
MIRA_MGC_15_R
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

value: male

value: MBD3L1 and MBD2b


title: 26_DAP_20C_Rep1


title: MM_087: CD138_selected_plasma_cells_presentation

value: myeloma cells


title: DNA methylation in the female germ cells at 12.5dpc

description:
MIRA_FGC_12
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from female germ cells at 12.5dpc

value: female

value: DNA methylation

source_name: Input DNA from 12.5 dpc female germ cells at 12.5 dpc


title: DNA methylation in the female germ cells at 11.5dpc

description:
MIRA_FGC_11
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from female germ cells at 11.5dpc

value: germ cells

source_name: Input DNA from 11.5 dpc female germ cells at 11.5 dpc


title: DI_32Dcl3_ASXL1_IL-3

source_name: 32Dcl3 cells transduced with ASXL1-MT, treated with IL-3

tag: cell line

value: treated with IL-3


title: MM_086: CD138_selected_plasma_cells_presentation

value: AllPrep

value: RLT


title: DI_32Dcl3_ASXL1_G6h

source_name: 32Dcl3 cells transduced with ASXL1-MT, treated with G-CSF for 6 hours

value: treated with G-CSF for 6 hours


title: MM_088: CD138_selected_plasma_cells_presentation


title: 23_DAP_20C_Rep2

value: seed

value: 23_DAP maturation

value: 23 days after flowering


title: 23_DAP_20C_Rep1

value: Wild-type

value: Seeds developed at 21-19°C 16h


title: DI_32Dcl3_ASXL1_G2h

source_name: 32Dcl3 cells transduced with ASXL1-MT, treated with G-CSF for 2 hours

value: treated with G-CSF for 2 hours


title: MM_085: CD138_selected_plasma_cells_presentation


title: MM_122: CD138_selected_plasma_cells_presentation


title: DNA methylation in the male germ cells at 17.5dpc (replicate#1)

description:
MIRA_MGC_17
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 17.5dpc

value: CF1 x TgOG2

source_name: Input DNA from 17.5 dpc male germ cells at 17.5 dpc


title: ICR renal cortex_8w_rep3

city: Osaka

first: Kotaro

last: Tamura

address: 2-1-6, Kashima, Yodogawa-ku

institute: Astellas Pharma Inc.

description: Gene expression data from renal cortex of 8-week-old ICR mouse (rep 3)

hyb_protocol: Fragmented cRNA (20 µg) was hybridized to a Mouse Genome 430 2.0 Array for 18 hr at 45˚C at 60 rpm, after which the array was washed and stained by streptavidin-phycoerythrin (Fluidics Station 400, Affymetrix).

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Renal cortex from 8-week-old ICR mice

label_protocol: Microarray analysis was conducted by using the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix). The procedure was conducted according to the manufacturer's instructions. The cDNA synthesis and purification was performed with the Superscript Choice System (Invitrogen), the T7-(dT)24-oligonucleotide primer (Affymetrix), and the cDNA Cleanup Module (Affymetrix). The biotinylated cRNA synthesis and purification was performed using the GeneChip Expression 3-Amplification Reagents for IVT Labeling (Affymetrix) and the cRNA Cleanup Module (Affymetrix).

extract_protocol: RNA was harvested from the renal cortex of 4- and 8-week-old ICGN and ICR mice. The samples of renal cortex were separated from the slices fixed in RNAlater (Invitrogen) and homogenized using the Mill Mixer (Qiagen) with zirconium beads. Total RNA was isolated from the kidney homogenate using the RNeasy kit (Qiagen).

tag: strain

value: ICR

value: normal

value: renal cortex

value: 8 weeks


title: ICR renal cortex_8w_rep1

description: Gene expression data from renal cortex of 8-week-old ICR mouse (rep 1)


title: MM_084: CD138_selected_plasma_cells_presentation

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

source_name: pre-treatment bone marrow

value: myeloma cells


title: 20_DAP_20C_Rep2

value: 20_DAP maturation

value: 20 days after flowering


title: 20_DAP_20C_Rep1


title: MM_083: CD138_selected_plasma_cells_presentation

value: AllPrep


title: 17_DAP_20C_Rep2

value: 17_DAP maturation

value: 17 days after flowering


title: ICGN renal cortex_8w_rep3

description: Gene expression data from renal cortex of 8-week-old ICGN mouse (rep 3)

source_name: Renal cortex from 8-week-old ICGN mice

value: ICGN

value: nephrotic syndrome


title: DNA methylation in the male germ cells at 12.5dpc

description:
MIRA_MGC_12
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 12.5dpc

tag: cell type

value: germ cells

value: male

value: MBD3L1 and MBD2b

value: DNA methylation

source_name: Input DNA from 12.5 dpc male germ cells at 12.5 dpc


title: DNA methylation in the male germ cells at 11.5dpc

description:
MIRA_MGC_11
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 11.5dpc

tag: strain/background

value: CF1 x TgOG2

source_name: Input DNA from 11.5 dpc male germ cells at


title: ICGN renal cortex_8w_rep2

description: Gene expression data from renal cortex of 8-week-old ICGN mouse (rep 2)


title: 17_DAP_20C_Rep1

value: seed

value: Wild-type

value: Seeds developed at 21-19°C 16h


title: MM_082: CD138_selected_plasma_cells_presentation

value: RLT


title: ICGN renal cortex_8w_rep1

description: Gene expression data from renal cortex of 8-week-old ICGN mouse (rep 1)

value: renal cortex

value: 8 weeks


title: MM_081: CD138_selected_plasma_cells_presentation

value: myeloma cells


title: MM_080: CD138_selected_plasma_cells_presentation

value: AllPrep


title: ICR renal cortex_4w_rep2

description: Gene expression data from renal cortex of 4-week-old ICR mouse (rep 2)

source_name: Renal cortex from 4-week-old ICR mice

value: ICR

value: normal

value: 4 weeks


title: ICR renal cortex_4w_rep3

description: Gene expression data from renal cortex of 4-week-old ICR mouse (rep 3)


title: 14_DAP_20C_Rep2

value: 14_DAP maturation

value: 14 days after flowering


title: MM_079: CD138_selected_plasma_cells_presentation


title: ICR renal cortex_8w_rep2

description: Gene expression data from renal cortex of 8-week-old ICR mouse (rep 2)


title: 14_DAP_20C_Rep1


title: 8_DAP_20C_Rep2

value: 8_DAP maturation

value: 8 days after flowering


title: DNA methylation in the male germ cells at 13.5dpc

description:
MIRA_MGC_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: Methylated-CpG island recovery assay (MIRA) DNA from male germ cells at 13.5dpc

value: germ cells

tag: gender

value: male

value: MBD3L1 and MBD2b

value: DNA methylation

source_name: Input DNA from 13.5 dpc male germ cells at 13.5 dpc


title: 11_DAP_20C_Rep2

value: seed

value: 11_DAP maturation

value: Wild-type

value: Seeds developed at 21-19°C 16h

value: 11 days after flowering


title: H3K9me3 (antibody#2) in the female somatic cells at 15.5 dpc

description:
FSC.H3K9me3.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 (antibody#2) ChIP DNA from 15.5 dpc female somatic cells

value: CF1 x TgOG2

value: gonadal somatic cells

value: female

tag: chip antibody

value: anti-H3K9me3.ab2 (Abcam ab8898, lot# GR70497-1)

source_name: Input DNA from 15.5 dpc female gonadal somatic cells


title: H3K9me3 in the male somatic cells at 15.5 dpc

description:
MSC.H3K9me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 ChIP DNA from 15.5 dpc male somatic cells

value: anti-H3K9me3 (Abcam ab8898, lot# 484099)

tag: epigenetic feature

source_name: Input DNA from 15.5 dpc male gonadal somatic cells


title: 11_DAP_20C_Rep1


title: ICR renal cortex_4w_rep1

description: Gene expression data from renal cortex of 4-week-old ICR mouse (rep 1)

value: ICR

value: normal

value: renal cortex

value: 4 weeks


title: MM_078: CD138_selected_plasma_cells_presentation

value: myeloma cells

value: AllPrep

value: RLT


title: H3K9me3 (antibody#2) in the male somatic cells at 15.5 dpc

description:
MSC.H3K9me3.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 (antibody#2) ChIP DNA from 15.5 dpc male somatic cells

value: male


title: MM_076: CD138_selected_plasma_cells_presentation


title: MM_077: CD138_selected_plasma_cells_presentation


title: MM_075: CD138_selected_plasma_cells_presentation


title: H3K9me2 (antibody#2) in the male somatic cells at 15.5 dpc

description:
MSC.H3K9me2.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me2 (antibody#2) ChIP DNA from 15.5 dpc male somatic cells

value: anti-H3K9me2.ab2 (Abcam ab1220, lot# GR77144-1)


title: H3K79me3 in the male somatic cells at 15.5 dpc

description:
MSC.H3K79me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me3 ChIP DNA from 15.5 dpc male somatic cells


title: MM_074: CD138_selected_plasma_cells_presentation


title: H3K9ac in the female somatic cells at 15.5 dpc

description:
FSC.H3K9ac
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 15.5 dpc female somatic cells

value: anti-H3K9ac (Millipore 07-352, lot# DAM1658697)


title: ICGN renal cortex_4w_rep2

description: Gene expression data from renal cortex of 4-week-old ICGN mouse (rep 2)

source_name: Renal cortex from 4-week-old ICGN mice

value: ICGN

value: nephrotic syndrome


title: ICGN renal cortex_4w_rep1

description: Gene expression data from renal cortex of 4-week-old ICGN mouse (rep 1)


title: H3K9me2 (antibody#2) in the female somatic cells at 15.5 dpc

description:
FSC.H3K9me2.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me2 (antibody#2) ChIP DNA from 15.5 dpc female somatic cells

value: CF1 x TgOG2


title: ICGN renal cortex_4w_rep3

description: Gene expression data from renal cortex of 4-week-old ICGN mouse (rep 3)


title: H3K9ac in the male somatic cells at 15.5 dpc

description:
MSC.H3K9ac
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 15.5 dpc male somatic cells

value: gonadal somatic cells

source_name: Input DNA from 15.5 dpcmale gonadal somatic cells


title: H3K79me3 in the female somatic cells at 15.5 dpc

description:
FSC.H3K79me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me3 ChIP DNA from 15.5 dpc female somatic cells

value: female


title: 8_DAP_20C_Rep1

value: seed

value: 8_DAP maturation

value: Wild-type

value: Seeds developed at 21-19°C 16h

value: 8 days after flowering


title: 32dap-Xcc contaminated seeds Replicate 2

growth_protocol: Medicago truncatula ssp. tricycla R108 were grown in growth chambers under 16 h of light at 22°C and 8 h of darkness at 19°C. At the flower stage, plants were transferred to a confied claimte cell at 21°C/19°C, 16h light and high (95%) relative humidity

extract_protocol: Total RNAs were extracted from the frozen grinded seeds lots using the NucleoSpin Extract II, Total RNA Purification kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions

treatment_protocol: Flowers were tagged on plants at the ﬂower bud stage, then spray inoculated until runoff with bacterial suspensions at 1×107 CFU ml-1

value: Xanthomonas campestris pv. campestris contamination

value: 32 days after pollination


title: 32dap-Xcc contaminated seeds Replicate 3


title: MM_072: CD138_selected_plasma_cells_presentation

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

source_name: pre-treatment bone marrow

value: myeloma cells

value: AllPrep


title: MM_071: CD138_selected_plasma_cells_presentation

value: RLT


title: 32dap-Xcc contaminated seeds Replicate 1


title: MM_073: CD138_selected_plasma_cells_presentation


title: 32dap-Mock treated seeds Replicate 3b

value: Mock


title: MM_070: CD138_selected_plasma_cells_presentation


title: MM_069: CD138_selected_plasma_cells_presentation


title: 32dap-Mock treated seeds Replicate 1b


title: MM_068: CD138_selected_plasma_cells_presentation


title: 32dap-Mock treated seeds Replicate 2b


title: 32dap-Xaa contaminated seeds Replicate 3

value: Xanthomonas alfalfae pv. alfalfae contamination


title: MM_066: CD138_selected_plasma_cells_presentation


title: MM_065: CD138_selected_plasma_cells_presentation


title: 32dap-Xaa contaminated seeds Replicate 2


title: 32dap-Xaa contaminated seeds Replicate 1


title: 32dap-Mock treated seeds Replicate 3a


title: 32dap-Mock treated seeds Replicate 1a


title: 32dap-Mock treated seeds Replicate 2a


title: MM_064: CD138_selected_plasma_cells_presentation


title: MM_067: CD138_selected_plasma_cells_presentation


title: 16dap-Xcc contaminated seeds Replicate 3

value: 16 days after pollination


title: MM_062: CD138_selected_plasma_cells_presentation


title: H3K79me2 in the male somatic cells at 15.5 dpc

description:
MSC.H3K79me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me2 ChIP DNA from 15.5 dpc male somatic cells

value: male

value: anti-H3K79me2 (Open Biosystem, custom preparation)


title: MM_063: CD138_selected_plasma_cells_presentation


title: H3K4me2 in the male somatic cells at 15.5 dpc

description:
MSC.H3K4me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 15.5 dpc male somatic cells

value: CF1 x TgOG2

value: gonadal somatic cells

value: anti-H3K4me2 (Millipore 07-030, lot# DAM1570816)


title: MM_061: CD138_selected_plasma_cells_presentation


title: H3K4me2 in the female somatic cells at 15.5 dpc

description:
FSC.H3K4me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 15.5 dpc female somatic cells

value: female


title: 16dap-Xcc contaminated seeds Replicate 1

value: seed


title: 16dap-Xcc contaminated seeds Replicate 2


title: 16dap-Mock treated seeds Replicate 2b


title: H3K27me3 in the female somatic cells at 15.5 dpc

description:
FSC.H3K27me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K27me3 ChIP DNA from 15.5 dpc female somatic cells

value: anti-H3K27me3 (Millipore 07-449, lot# DAM1387952)


title: MM_058: CD138_selected_plasma_cells_presentation


title: H3K9me3 in the male germ cells at 15.5 dpc

description:
MGC.H3K9me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 ChIP DNA from 15.5 dpc male germ cells

value: germ cells

value: anti-H3K9me3 (Abcam ab8898, lot# 484099)

source_name: Input DNA from 15.5 dpc male germ cells


title: MM_057: CD138_selected_plasma_cells_presentation


title: H3K27me3 in the male somatic cells at 15.5 dpc

description:
MSC.H3K27me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K27me3 ChIP DNA from 15.5 dpc male somatic cells

source_name: Input DNA from 15.5 dpc male gonadal somatic cells


title: H3K9me3 in the female germ cells at 15.5 dpc

description:
FGC.H3K9me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 ChIP DNA from 15.5 dpc female germ cells

source_name: Input DNA from 15.5 dpc female germ cells


title: MM_060: CD138_selected_plasma_cells_presentation


title: H3K9me2 in the female germ cells at 15.5 dpc

description:
FGC.H3K9me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me2 ChIP DNA from 15.5 dpc female germ cells

value: anti-H3K9me2 (Millipore 07-441, lot# DAM1463717)


title: H3K9me3 (antibody#2) in the male germ cells at 15.5 dpc

description:
MGC.H3K9me3.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me3 (antibody#2) ChIP DNA from 15.5 dpc male germ cells

value: anti-H3K9me3.ab2 (Abcam ab8898, lot# GR70497-1)


title: 16dap-Mock treated seeds Replicate 1b


title: 16dap-Xaa contaminated seeds Replicate 2


title: MM_056: CD138_selected_plasma_cells_presentation

value: myeloma cells

value: AllPrep


title: 16dap-Xaa contaminated seeds Replicate 3


title: H3K9ac in the female germ cells at 15.5 dpc

description:
FGC.H3K9ac
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 15.5 dpc female germ cells

value: anti-H3K9ac (Millipore 07-352, lot# DAM1658697)


title: 16dap-Mock treated seeds Replicate 3b

value: Mock


title: H3K9me2 (antibody#2) in the female germ cells at 15.5 dpc

description:
MGC.H3K9me2.ab2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me2 (antibody#2) ChIP DNA from 15.5 dpc female germ cells

value: anti-H3K9me2.ab2 (Abcam ab1220, lot# GR77144-1)


title: H3K9ac in the male germ cells at 15.5 dpc

description:
MGC.H3K9ac
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 15.5 dpc male germ cells

value: male


title: MM_055: CD138_selected_plasma_cells_presentation

value: RLT


title: MM_059: CD138_selected_plasma_cells_presentation


title: 16dap-Xaa contaminated seeds Replicate 1

value: Xanthomonas alfalfae pv. alfalfae contamination

value: 16 days after pollination


title: 16dap-Mock treated seeds Replicate 3a


title: MM_054: CD138_selected_plasma_cells_presentation


title: H3K9ac in the female germ cells at 13.5 dpc

description:
FGC.H3K9ac_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 13.5 dpc female germ cells

value: CF1 x TgOG2

source_name: Input DNA from 13.5 dpc female germ cells


title: H3K79me3 in the female germ cells at 15.5 dpc

description:
FGC.H3K79me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me3 ChIP DNA 15.5 dpc from female germ cells

value: female


title: 16dap-Mock treated seeds Replicate 2a

value: seed


title: H3K79me3 in the male germ cells at 15.5 dpc

description:
MGC.H3K79me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me3 ChIP DNA 15.5 dpc from male germ cells


title: H3K79me2 in the female somatic cells at 15.5 dpc

description:
FSC.H3K79me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me2 ChIP DNA from 15.5 dpc female somatic cells

value: gonadal somatic cells

value: anti-H3K79me2 (Open Biosystem, custom preparation)

source_name: Input DNA from 15.5 dpc female gonadal somatic cells


title: MM_053: CD138_selected_plasma_cells_presentation

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

source_name: pre-treatment bone marrow


title: MM_052: CD138_selected_plasma_cells_presentation


title: 16dap-Mock treated seeds Replicate 1a


title: MM_051: CD138_selected_plasma_cells_presentation


title: H3K9me2 in the male germ cells at 15.5 dpc

description:
MGC.H3K9me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9me2 ChIP DNA from 15.5 dpc male germ cells

value: germ cells

source_name: Input DNA from 15.5 dpc male germ cells


title: MM_050: CD138_selected_plasma_cells_presentation


title: MM_049: CD138_selected_plasma_cells_presentation


title: MM_048: CD138_selected_plasma_cells_presentation


title: Mouse universal RNA__R1

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description: Gene expression data from Mouse Universal RNA

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com)

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner

data_processing: Affymetrix Expression console v1.3

label: Biotin

source_name: Mouse Universal RNA

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com)

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all human cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Cells (1 x 107 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice. When tumors reached approximately 500 mg (10x10 mm), they were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments.

extract_protocol: Total RNA isolated using RNeasy (Qiagen)

tag: tissue origin

value: Mouse Universal RNA

value: pool


title: Human universal RNA__R2

description: Gene expression data from Human Universal RNA

source_name: Human Universal RNA

value: Human Universal RNA


title: H3K9ac in the male germ cells at 13.5 dpc

description:
MGC.H3K9ac_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K9ac ChIP DNA from 13.5 dpc male germ cells

source_name: Input DNA from 13.5 dpc male germ cells


title: H3K4me3 in the male germ cells at 15.5 dpc

description:
MGC.H3K4me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me3 ChIP DNA from 15.5 dpc male germ cells

value: anti-H3K4me3 (Millipore 07-473, lot# DAM1661080)


title: H3K4me3 in the female germ cells at 15.5 dpc

description:
FGC.H3K4me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me3 ChIP DNA from 15.5 dpc female germ cells

source_name: Input DNA from 15.5 dpc female germ cells


title: H3K4me2 in the male germ cells at 16.5 dpc

description:
MGC.H3K4me2_16
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 16.5 dpc male germ cells

value: anti-H3K4me2 (Millipore 07-030, lot# DAM1570816)

source_name: Input DNA from 16.5 dpc male germ cells


title: MM_047: CD138_selected_plasma_cells_presentation

value: myeloma cells

value: AllPrep


title: COLON-26_Skin_R3

description: Gene expression data from skin adjacent to COLON-26 Mouse colon cancer xenograft

value: Skin


title: H3K79me2 in the male germ cells at 15.5 dpc

description:
MGC.H3K79me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me2 ChIP DNA 15.5 dpc from male germ cells

value: male


title: Human universal RNA__R1


title: Mouse universal RNA__R2


title: H3K79me2 in the female germ cells at 15.5 dpc

description:
FGC.H3K79me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K79me2 ChIP DNA from 15.5 dpc female germ cells


title: COLON-26_Skin_R1

value: skin adjacent to COLON-26 Mouse colon cancer xenograft


title: MM_045: CD138_selected_plasma_cells_presentation

value: RLT


title: MM_046: CD138_selected_plasma_cells_presentation


title: COLON-26_Skin_R2


title: B16-F10_Skin_R3

description: Gene expression data from skin adjacent to B16-F10 Mouse Melanoma xenograft


title: H3K4me2 in the male germ cells at 15.5 dpc

description:
MGC.H3K4me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 15.5 dpc male germ cells

value: CF1 x TgOG2


title: B16-F10_Skin_R2

value: skin adjacent to B16-F10 Mouse Melanoma xenograft


title: MM_044: CD138_selected_plasma_cells_presentation


title: MM_040: CD138_selected_plasma_cells_presentation


title: MM_043: CD138_selected_plasma_cells_presentation


title: MM_042: CD138_selected_plasma_cells_presentation


title: MM_041: CD138_selected_plasma_cells_presentation


title: MM_039: CD138_selected_plasma_cells_presentation


title: B16-F10_Skin_R1


title: LOX IMVI_Skin_R3

description: Gene expression data from skin adjacent to LOX IMVI human melanoma xenograft

source_name: LOX IMVI

value: LOX IMVI


title: MM_036: CD138_selected_plasma_cells_presentation


title: MM_037: CD138_selected_plasma_cells_presentation

value: Trizol


title: Mouse universal RNA__R3


title: H3K4me2 in the female germ cells at 15.5 dpc

description:
FGC.H3K4me2
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 15.5 dpc female germ cells

value: female


title: NCI-H522_Skin_R3

description: Gene expression data from skin adjacent to NCI-H522 Human lung adenocarcinoma xenograft


title: LOX IMVI_Skin_R1

value: skin adjacent to LOX IMVI human melanoma xenograft


title: H3K4me2 in the female germ cells at 13.5 dpc

description:
FGC.H3K4me2_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 13.5 dpc female germ cells

value: germ cells

source_name: Input DNA from 13.5 dpc female germ cells


title: NCI-H522_Skin_R1

value: skin adjacent to NCI-H522 Human lung adenocarcinoma xenograft


title: NCI-H522_Skin_R2


title: LOX IMVI_Skin_R2


title: COLON-26_Tumor_R3

description: Gene expression data from COLON-26 Mouse Colon cancer xenograft

value: Tumor

value: COLON-26 Mouse Colon cancer xenograft


title: MM_038: CD138_selected_plasma_cells_presentation

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

source_name: pre-treatment bone marrow


title: MM_035: CD138_selected_plasma_cells_presentation


title: MM_033: CD138_selected_plasma_cells_presentation


title: MM_032: CD138_selected_plasma_cells_presentation


title: COLON-26_Tumor_R1


title: B16-F10_Tumor_R3

description: Gene expression data from B16-F10 Mouse Melanoma xenograft

value: B16-F10 Mouse Melanoma xenograft


title: MM_027: CD138_selected_plasma_cells_presentation

value: myeloma cells


title: MM_025: CD138_selected_plasma_cells_presentation

value: AllPrep


title: MM_030: CD138_selected_plasma_cells_presentation


title: MM_029: CD138_selected_plasma_cells_presentation


title: MM_028: CD138_selected_plasma_cells_presentation


title: H3K4me2 in the male germ cells at 13.5 dpc

description:
MGC.H3K4me2_13
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me2 ChIP DNA from 13.5 dpc male germ cells

value: anti-H3K4me2 (Millipore 07-030, lot# DAM1570816)


title: B16-F10_Tumor_R2


title: MM_024: CD138_selected_plasma_cells_presentation


title: NCI-H522_Tumor_R2

description: Gene expression data from NCI-H522 Human lung adenocarcinoma xenograft


title: B16-F10_Tumor_R1


title: LOX IMVI_Tumor_R2

description: Gene expression data from LOX IMVI Human Melanoma xenograft

value: LOX IMVI Human Melanoma xenograft


title: LOX IMVI_Tumor_R3


title: MM_023: CD138_selected_plasma_cells_presentation


title: MM_022: CD138_selected_plasma_cells_presentation


title: H3K36me3 in the female germ cells at 15.5 dpc

description:
FGC.H3K36me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K36me3 ChIP DNA from 15.5 dpc female germ cells

value: anti-H3K36me3 (21st Century NB21-1253, lot# B2)


title: NCI-H522_Tumor_R1

value: NCI-H522 Human lung adenocarcinoma xenograft


title: MM_019: CD138_selected_plasma_cells_presentation

value: RLT


title: MM_017: CD138_selected_plasma_cells_presentation


title: MM_018: CD138_selected_plasma_cells_presentation


title: H3K4me1 in the male germ cells at 15.5 dpc

description:
MGC.H3K4me1
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me1 ChIP DNA from 15.5 dpc male germ cells

value: CF1 x TgOG2

value: male

value: anti-H3K4me1 (Abcam ab8895, lot# GR43806-1)

source_name: Input DNA from 15.5 dpc male germ cells


title: MM_021: CD138_selected_plasma_cells_presentation


title: PBMCs_HV9_LPS unprimed

city: Lyon

first: Florence

last: Frager

address: 5 place d'arsonval

department: LCR HCL-biomérieux

institute: biomerieux

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000.

data_processing: Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affymetrix package of the Bioconductor microarray analysis environment (http://www.bioconductor.org).

source_name: PBMCs

label_protocol: 125 ng of total RNA were reverse transcribed and labeled using the WT ovation RNA amplification system (Nugen) according to manufacturer’s instructions.

extract_protocol: Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen, Hilden, Germany). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen). RNA was eluted in 30 µl. RNA quality was assessed on a bioanalyser (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7. RNA quantity was determined for each sample using a Qubit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: PBMCs were isolated from citrated venous blood by Ficoll-Paque density gradient centrifugation  and washed with PBS while the remaining red blood cells were lysed. Cells were cultured in 24-well plates at 2.106 cells/ml in X-Vivo 20 Medium . To induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of  2ng/ml LPS and incubated overnight at 37 °C and 5% CO2 (15 hours). Following a washing step, PBMCs were incubated for an additional 24 hours in the presence or absence (control group stimulated or not with LPS) of rIFN-γ1b. Finally, cells were stimulated a second time by adding 100ng/ml of LPS for another 6 hours.

tag: culture condition

value: LPS unprimed


title: MM_016: CD138_selected_plasma_cells_presentation


title: PBMCs_HV9_medium

value: medium


title: H3K4me1 in the female germ cells at 15.5 dpc

description:
FGC.H3K4me1
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K4me1 ChIP DNA from 15.5 dpc female germ cells

value: germ cells

value: female


title: COLON-26_Tumor_R2

value: Tumor


title: PBMCs_HV9_LPS primed

value: LPS primed


title: PBMCs_HV9_LPS primed+IFNg

value: LPS primed + IFNg


title: PBMCs_HV7_medium


title: MM_020: CD138_selected_plasma_cells_presentation

value: myeloma cells


title: H3K36me3 in the male germ cells at 15.5 dpc

description:
MGC.H3K36me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K36me3 ChIP DNA from 15.5 dpcmale germ cells


title: PBMCs_HV7_LPS primed+IFNg


title: PBMCs_HV7_LPS primed


title: PBMCs_HV7_LPS unprimed


title: H3K27me3 in the male germ cells at 15.5 dpc

description:
MGC.H3K27me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K27me3 ChIP DNA from 15.5 dpc male germ cells

value: anti-H3K27me3 (Millipore 07-449, lot# DAM1387952)


title: MM_015: CD138_selected_plasma_cells_presentation

value: Trizol


title: PBMCs_HV6_LPS primed+IFNg


title: PBMCs_HV6_LPS primed


title: MM_011: CD138_selected_plasma_cells_presentation

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, RNA extracted using Qiagen RNA/DNA kit and small RNA enriched

value: RNA/DNA kit


title: H3K27me3 in the female germ cells at 15.5 dpc

description:
FGC.H3K27me3
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).

source_name: H3K27me3 ChIP DNA from 15.5 dpc female germ cells

source_name: Input DNA from 15.5 dpc female germ cells


title: MM_010: CD138_selected_plasma_cells_presentation

value: AllPrep


title: MM_013: CD138_selected_plasma_cells_presentation


title: MM_014: CD138_selected_plasma_cells_presentation


title: MM_012: CD138_selected_plasma_cells_presentation


title: MM_008: CD138_selected_plasma_cells_presentation


title: MM_007: CD138_selected_plasma_cells_presentation


title: PBMCs_HV5_LPS primed+IFNg


title: PBMCs_HV6_LPS unprimed


title: MM_006: CD138_selected_plasma_cells_presentation


title: PBMCs_HV3_LPS primed+IFNg


title: PBMCs_HV5_medium


title: MM_031: CD138_selected_plasma_cells_presentation


title: PBMCs_HV5_LPS primed


title: MM_034: CD138_selected_plasma_cells_presentation


title: MM_005: CD138_selected_plasma_cells_presentation


title: PBMCs_HV3_LPS primed


title: MM_009: CD138_selected_plasma_cells_presentation


title: PBMCs_HV5_LPS unprimed


title: MM_004: CD138_selected_plasma_cells_presentation


title: PBMCs_HV3_medium


title: PBMCs_HV3_LPS unprimed


title: PBMCs_HV6_medium


title: MM_003: CD138_selected_plasma_cells_presentation


title: MM_002: CD138_selected_plasma_cells_presentation


title: PBMCs_HV2_LPS primed+IFNg


title: PBMCs_HV2_LPS primed


title: PBMCs_HV2_LPS unprimed


title: MM_001: CD138_selected_plasma_cells_presentation


title: MM_026: CD138_selected_plasma_cells_presentation


title: HO-1 AdPNP 18 hrs_3

status: Public on Jul 30 2013

city: Jacksonville

first: Catherine

last: Dumur

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 18 hours_replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The human melanoma cell line HO-1 was maintained in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen Life Technologies) supplemented with 10% fetal bovine serum (FBS; Sigma) and 5% penicillin/streptomycin (Gibco).

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

treatment_protocol: Lentiviral constructs (pGIPZ) expressing GFP were purchased from Open Biosystems that either contained non-silencing short hairpin RNA (shRNA) or shRNAs against hPNPaseold-35. For the overexpression experiments, the Adenovirus empty vector (Ad.vec) was used as a control. For all adenoviral experiments, 1x105 cells were grown in 6 cm dishes and infected after 24 hours with Ad.vec or Ad.hPNPaseold-35 at a final m.o.i of 5000vp/cell diluted in 1ml of serum free media. After 6 hours of infection with shaking every 15 minutes, complete media was added and cells were harvested at the required time points (e.g., 36 hours post-infection) for microarray analysis, RNA or protein isolation.


title: HO-1 AdPNP 18 hrs_2

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 18 hours_replicate 2


title: HO-1 AdPNP 36 hrs_2

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 36 hours_replicate 2


title: HO-1 AdPNP 18 hrs_1

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 18 hours_replicate 1


title: HO-1 AdVec 36 hrs_2

source_name: Human HO-1 melanoma cells infected with Adenovirus empty vector for 36 hours_replicate 2


title: HO-1 AdPNP 36 hrs_3

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 36 hours_replicate 3


title: HO-1 AdPNP 36 hrs_1

source_name: Human HO-1 melanoma cells infected with Adenoviresexpressing hPNPaseold-35 for 36 hours_replicate 1


title: PBMCs_HV2_medium


title: NCI-H522_Tumor_R3

value: NCI-H522 Human lung adenocarcinoma xenograft


title: LOX IMVI_Tumor_R1

source_name: LOX IMVI

value: LOX IMVI

value: LOX IMVI Human Melanoma xenograft


title: HO-1 AdVec 36 hrs_1

source_name: Human HO-1 melanoma cells infected with Adenovirus empty vector for 36 hours_replicate 1


title: HO-1 AdVec 36 hrs_3

source_name: Human HO-1 melanoma cells infected with Adenovirus empty vector for 36 hours_replicate 3


title: HCC69N-Sty

city: shanghai

first: Zeguang

last: Han

address: No.351,Guoshoujing Rd.,Zhangjiang Hi-Tech Park

country: China

institute: Chinese National Genome Center at Shanghai

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 array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

source_name: hepatocellular carcinoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from hepatocellular carcinoma and their adjacent liver tissues using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: disease state

value: hepatocellular carcinoma

tag: sample id


title: HCC65N-Sty

description: Hybridized to 250K_Sty


title: HCC71N-Sty

description: Hybridized to 250K_Sty


title: HCC63N-Sty

description: Hybridized to 250K_Sty


title: HCC67N-Sty

description: Hybridized to 250K_Sty


title: HCC47N-Sty

description: Hybridized to 250K_Sty


title: HCC51N-Sty

description: Hybridized to 250K_Sty


title: HCC43N-Sty

description: Hybridized to 250K_Sty


title: HCC15N-Sty

description: Hybridized to 250K_Sty


title: HCC77N-Sty

description: Hybridized to 250K_Sty


title: HCC75N-Sty

description: Hybridized to 250K_Sty


title: HCC45N-Sty

description: Hybridized to 250K_Sty


title: HCC53N-Sty

description: Hybridized to 250K_Sty


title: HCC39N-Sty

description: Hybridized to 250K_Sty


title: HCC21N-Sty

description: Hybridized to 250K_Sty


title: HCC17N-Sty

description: Hybridized to 250K_Sty


title: HCC49N-Sty

description: Hybridized to 250K_Sty


title: HCC79N-Sty

description: Hybridized to 250K_Sty


title: HCC19N-Sty

description: Hybridized to 250K_Sty


title: HCC55N-Sty

description: Hybridized to 250K_Sty


title: HCC61N-Sty

description: Hybridized to 250K_Sty


title: HCC27N-Sty

description: Hybridized to 250K_Sty


title: HCC35N-Sty

description: Hybridized to 250K_Sty


title: HCC13N-Sty

description: Hybridized to 250K_Sty


title: HCC25N-Sty

description: Hybridized to 250K_Sty


title: HCC73N-Sty

description: Hybridized to 250K_Sty


title: HCC121N-Sty

description: Hybridized to 250K_Sty


title: HCC41N-Sty

description: Hybridized to 250K_Sty


title: HCC125N-Sty

description: Hybridized to 250K_Sty


title: HCC23N-Sty

description: Hybridized to 250K_Sty


title: HCC123N-Sty

description: Hybridized to 250K_Sty


title: HEK293, stable PRL-1 transfectant, biological replicate 2

city: Indianapolis

first: Carmen

middle: M.

last: Dumaual

state: IN

address: 723 West Michigan St., Room SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

description: PRL-1 Overexpressing

data_processing:
Raw threshold cycle (Ct) values were obtained using Sequence Detection System (SDS) Software v2.4 (Applied Biosystems).  Ct values greater than or equal to 40 were set to 40 and were considered not detectable.
Among 4 reference genes tested, B2M, 18S, GAPDH, and UBC, 18S was found to be the most stable across the sample set according to analysis with DataAssist Software v2.0 (Applied Biosystems).  Therefore, 18S was used as the endogenous control.
For comparative statistics, the raw data files were processed with Partek Genomics Suite version 6.12.0531 using default parameters and 18S as the endogenous control.  Mean normalized Ct values for each assay over all biological replicates (n = 2) for both the experimental comparison groups (HEK293-PRL-1 and HEK293-vector) were calculated.
Differential expression between the two comparison groups was calculated using the comparative Ct (deltadeltaCt) method
Matrix normalized worksheet reports signals normalized to 18S
Fold Change worksheet reports Fold_Change of PRL-1 overexpressing sample group (P1_) versus baseline of empty vector sample group (EV_) calculated using 2^-ddCt where ddCt = [(Normalized Ct_HEK293-PRL-1) - (Normalized Ct_HEK293-vector)]

label: FAM

source_name: HEK293 cells stably transfected with pcDNA4-PRL-1

label_protocol: Reverse transcription was performed from 1ug total RNA using the Invitrogen SuperScript III First-Strand Synthesis System.  The resulting cDNA was used as a template for qRT-PCR analysis of 184 TaqMan assays arrayed on two custom TaqMan Array 96-well Plates (Applied Biosystems).  100ng cDNA was added to each well of the custom array plates and was amplified by PCR on an Applied Biosystems 7900HT Fast Real-Time PCR System following the manufacturer's guidelines (2 min at 50C; 10 min at 95C; 40 cycles of 15 sec at 95C and 1 min at 60C).

growth_protocol: HEK293 cells stably overexpressing PRL-1 or transfected with empty pcDNA4 vector were grown in 100mm plates in DMEM supplemented with 10% (v/v) fetal bovine serum, 50 units/ml penicillin, and 50ug/ml streptomycin.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Life Technologies) and further purified with a Qiagen Rneasy Mini Kit, following the manufacturers' instructions for both.  Following extraction, the isolated total RNA was then treated with DNase I.


title: HEK293, empty pcDNA4 vector, biological replicate 2

description: Control

source_name: HEK293 cells stably transfected with empty pcDNA4 vector


title: HEK293, stable PRL-1 transfectant, biological replicate 1

description: PRL-1 Overexpressing


title: HEK293, empty pcDNA4 vector, biological replicate 1

description: Control


title: SHAE004_Mock_84h_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Human airway epithelium cultures (HAE) were generated by provision of an air-liquid interface for 6 to 8 weeks to form well-differentiated , polarized cultures that resemble in vivo pseudo-stratified mucociliary epithelium.

extract_protocol: At 0, 12, 24, 36, 48, 60, 72, 84 and 96 hours post-infection (hpi) (SARS viruses) or 0, 6, 12, 18, 24, 36 and 48 hpi (H1N1) triplicate/quadruplicate wells of infected cells or mock infected were washed with 1X PBS and lysed directly with 1 ml of Trizol (Invitrogen) according to the manufacturer’s recommendation.  The resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative PCR (qPCR) and microarray analyses.

treatment_protocol: Cells were seeded in 6-well plates (1 x 10e6 cells/well) two days prior to infection.  Immediately preceding infection, cell monolayers were washed with fresh medium and inoculated with either SARS viruses (MOI = 2) or A/CA/04/2009 (MOI = 1) and subsequently incubated at 37°C for 40 minutes.  Mock-infected controls were inoculated with culture medium only.  Following the incubation, cell monolayers were washed 3X with 1X PBS and fresh medium was added to the wells prior to time 0.

value: Human airway epithelium cells (HAE)

tag: infection code

value: Mock

tag: sample material

value: cells

tag: timepoint

tag: biological replicate


title: HCC113N-Sty

description: Hybridized to 250K_Sty


title: HCC117N-Sty

description: Hybridized to 250K_Sty


title: HCC119N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_96h_2


title: HCC11N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_96h_1


title: HCC115N-Sty

description: Hybridized to 250K_Sty


title: HCC109N-Sty

description: Hybridized to 250K_Sty


title: HCC101N-Sty

description: Hybridized to 250K_Sty

tag: sample type


title: SHAE004_Mock_72h_1


title: SHAE004_Mock_84h_2


title: HCC127N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_84h_1


title: HCC111N-Sty

description: Hybridized to 250K_Sty


title: HCC105N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_60h_3


title: SHAE004_Mock_96h_3


title: HCC103N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_72h_3


title: HCC107N-Sty

description: Hybridized to 250K_Sty


title: SHAE004_Mock_36h_3


title: SHAE004_Mock_60h_2


title: SHAE004_Mock_48h_2


title: SHAE004_Mock_48h_3


title: SHAE004_Mock_24h_3


title: SHAE004_Mock_36h_2


title: SHAE004_Mock_18h_2


title: SHAE004_Mock_6h_2


title: SHAE004_Mock_60h_1


title: SHAE004_Mock_0h_2


title: SHAE004_icSARS_96h_1

value: icSARS


title: SHAE004_Mock_12h_1


title: SHAE004_Mock_24h_1


title: SHAE004_Mock_0h_3


title: SHAE004_Mock_6h_1


title: SHAE004_Mock_24h_2


title: SHAE004_Mock_12h_2


title: SHAE004_Mock_18h_1


title: SHAE004_Mock_0h_1


title: SHAE004_Mock_36h_1


title: SHAE004_Mock_6h_3


title: SHAE004_Mock_12h_3


title: SHAE004_Mock_48h_1


title: SHAE004_icSARS_96h_3


title: SHAE004_icSARS_96h_2


title: SHAE004_icSARS_84h_2


title: SHAE004_icSARS_84h_3


title: SHAE004_icSARS_72h_1


title: SHAE004_icSARS_72h_2


title: SHAE004_icSARS_48h_3


title: SHAE004_icSARS_84h_1


title: SHAE004_icSARS_72h_3


title: SHAE004_icSARS_60h_2


title: SHAE004_icSARS_48h_2


title: SHAE004_icSARS_36h_1


title: SHAE004_icSARS_48h_1


title: SHAE004_Mock_72h_2


title: SHAE004_icSARS_12h_2


title: SHAE004_icSARS_36h_3


title: SHAE004_Mock_18h_3


title: SHAE004_icSARS_0h_2


title: SHAE004_icSARS_24h_3


title: SHAE004_icSARS_12h_3


title: SHAE004_icSARS_60h_3


title: SHAE004_icSARS_60h_1


title: SHAE004_icSARS_0h_1


title: SHAE004_icSARS_12h_1


title: SHAE004_icSARS_36h_2


title: SHAE004_icSARS_24h_2


title: SHAE004_H1N1_48h_3


title: SHAE004_icSARS_24h_1


title: SHAE004_H1N1_48h_1


title: SHAE004_H1N1_48h_2


title: SHAE004_icSARS_0h_3


title: SHAE004_H1N1_36h_1


title: SHAE004_H1N1_36h_2


title: SHAE004_H1N1_36h_3


title: SHAE004_H1N1_24h_3


title: SHAE004_H1N1_18h_3


title: SHAE004_H1N1_24h_1


title: SHAE004_H1N1_24h_2


title: SHAE004_H1N1_12h_1


title: SHAE004_H1N1_0h_3


title: SHAE004_H1N1_12h_3


title: SHAE004_H1N1_12h_2


title: SHAE004_H1N1_6h_1


title: SHAE004_dORF6_96h_2


title: SHAE004_H1N1_18h_2


title: SHAE004_dORF6_72h_2


title: SHAE004_dORF6_84h_3


title: SHAE004_H1N1_0h_1


title: SHAE004_H1N1_6h_2


title: SHAE004_dORF6_60h_3


title: SHAE004_dORF6_96h_1


title: SHAE004_dORF6_72h_1


title: SHAE004_dORF6_84h_1


title: SHAE004_dORF6_84h_2


title: SHAE004_dORF6_72h_3


title: SHAE004_dORF6_96h_3


title: SHAE004_dORF6_60h_2


title: SHAE004_H1N1_6h_3


title: SHAE004_H1N1_18h_1