title: BJ iPS cells, 4d, cholesterol deficient, biological replicate 2

description:
BJ_4day_2
Control iPS cells removed from mTeSR1 media, 4 days culture


title: BJ iPS cells, 5d, cholesterol deficient, biological replicate 3

status: Public on Sep 18 2015

type: RNA

city: Sioux Falls

first: Kevin

middle: R

last: Francis

state: SD

department: Cellular Therapies

country: USA

institute: Sanford Research

description:
BJ_5day_3
Control iPS cells removed from mTeSR1 media, 5 days culture

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Standard manufacturing protocols were followed for preparation of arrays, washes, and sample loading.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software. GCRMA background correction was applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BJ iPS cells_5d_cholesterol deficient

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Control (BJ) and SLOS (A2) iPS cell lines cultured in cholesterol rich conditions (0 hr) were transferred to cholesterol deficient conditions.  RNA was isolated after 2, 3, 4, 5, and 7 days cholesterol deficient culture.

extract_protocol: Samples were collected by scraping and snap frozen in dry ice. All RNA samples were prepared using PicoPure RNA isolation kit. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Cholesterol rich pluripotent  culture consisted of human ES cell media (including 20% KOSR, 7.5 ng/mL bFGF) on a MEF feeder layer.  Cholesterol deficient culture was performed in mTeSR1 defined pluripotent conditions devoid of feeders.

tag: cell line

value: BJ

tag: cell type

value: Human iPS cells

tag: genotype/vairation

value: wild-type (control)

tag: cultured in

value: cholesterol deficient condition

tag: time point

value: 5 days


title: BJ iPS cells, 4d, cholesterol deficient, biological replicate 1

description:
BJ_4day_1
Control iPS cells removed from mTeSR1 media, 4 days culture

source_name: BJ iPS cells_4d_cholesterol deficient

value: 4 days


title: BJ iPS cells, 3d, cholesterol deficient, biological replicate 4

description:
BJ_3day_4
Control iPS cells removed from mTeSR1 media, 3 days culture

source_name: BJ iPS cells_3d_cholesterol deficient

value: 3 days


title: ILD sample 86

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

institute: University of Pittsburgh

description:
LT211379RL
6-digit tissue label
micro RNA

hyb_protocol: Hybridized to Agilent-021827 or Agilent-031181 miRNA arrays according to Agilent instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: Probes from the two arrays were matched using gene symbols, and loess normalization was applied using affy package in R. Probes whose mean value of normalized expression (loess normalization) was less than 1.7 were filtered.

source_name: flash frozen lung tissues, ILD

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the QuickAmp kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).

growth_protocol: Not applicable.

extract_protocol: 30 ug of whole lung was homogenized with Trizol, and then total RNA was extracted using the QiaCube system (Qiagen, Valencia CA).

treatment_protocol: Not applicable.

tag: tissue

value: lung

tag: disease status

value: interstitial lung disease (ILD)

tag: scaled bmi

tag: scaled age


title: ILD sample 84

description:
LT206871LU
6-digit tissue label
micro RNA


title: ILD sample 85

description:
LT207073RU
6-digit tissue label
micro RNA


title: BJ iPS cells, 5d, cholesterol deficient, biological replicate 1

description:
BJ_5day_1
Control iPS cells removed from mTeSR1 media, 5 days culture


title: ILD sample 83

description:
LT206005RL
6-digit tissue label
micro RNA


title: BJ iPS cells, 3d, cholesterol deficient, biological replicate 3

description:
BJ_3day_3
Control iPS cells removed from mTeSR1 media, 3 days culture


title: BJ iPS cells, 3d, cholesterol deficient, biological replicate 1

description:
BJ_3day_1
Control iPS cells removed from mTeSR1 media, 3 days culture


title: BJ iPS cells, 2d, cholesterol deficient, biological replicate 4

description:
BJ_2day_4
Control iPS cells removed from mTeSR1 media, 2 days culture

source_name: BJ iPS cells_2d_cholesterol deficient

value: 2 days


title: BJ iPS cells, 3d, cholesterol deficient, biological replicate 2

description:
BJ_3day_2
Control iPS cells removed from mTeSR1 media, 3 days culture


title: BJ iPS cells, 2d, cholesterol deficient, biological replicate 3

description:
BJ_2day_3
Control iPS cells removed from mTeSR1 media, 2 days culture


title: ILD sample 80

description:
LT201348LL
6-digit tissue label
micro RNA


title: ILD sample 79

description:
LT196309RL
6-digit tissue label
micro RNA


title: ILD sample 78

description:
LT195522RU
6-digit tissue label
micro RNA


title: BJ iPS cells, 0hr, cholesterol rich, biological replicate 4

description:
BJ_0hr_4
Control iPS cells removed from MEF feeders, 20% KOSR medium

source_name: BJ iPS cells_0hr_cholesterol rich

value: cholesterol rich condition


title: BJ iPS cells, 2d, cholesterol deficient, biological replicate 2

description:
BJ_2day_2
Control iPS cells removed from mTeSR1 media, 2 days culture


title: BJ iPS cells, 2d, cholesterol deficient, biological replicate 1

description:
BJ_2day_1
Control iPS cells removed from mTeSR1 media, 2 days culture


title: ILD sample 73

description:
LT191618LU
6-digit tissue label
micro RNA


title: BJ iPS cells, 0hr, cholesterol rich, biological replicate 3

description:
BJ_0hr_3
Control iPS cells removed from MEF feeders, 20% KOSR medium


title: BJ iPS cells, 0hr, cholesterol rich, biological replicate 1

description:
BJ_0hr_1
Control iPS cells removed from MEF feeders, 20% KOSR medium


title: ILD sample 77

description:
LT195207LL
6-digit tissue label
micro RNA


title: BJ iPS cells, 0hr, cholesterol rich, biological replicate 2

description:
BJ_0hr_2
Control iPS cells removed from MEF feeders, 20% KOSR medium


title: ILD sample 71

description:
LT184241RL
6-digit tissue label
micro RNA


title: ILD sample 72

description:
LT191087RM
6-digit tissue label
micro RNA


title: ILD sample 76

description:
LT195188RL
6-digit tissue label
micro RNA


title: ILD sample 74

description:
LT191675RL
6-digit tissue label
micro RNA


title: ILD sample 75

description:
LT195011RL
6-digit tissue label
micro RNA


title: ILD sample 70

description:
LT178790LL
6-digit tissue label
micro RNA


title: ILD sample 69

description:
LT175399RU
6-digit tissue label
micro RNA


title: ILD sample 65

description:
LT167906LL
6-digit tissue label
micro RNA


title: ILD sample 81

description:
LT201831RU
6-digit tissue label
micro RNA


title: ILD sample 64

description:
LT167891LU
6-digit tissue label
micro RNA


title: ILD sample 82

description:
LT204935LL
6-digit tissue label
micro RNA


title: ILD sample 66

description:
LT168094RL
6-digit tissue label
micro RNA


title: ILD sample 63

description:
LT166111RU
6-digit tissue label
micro RNA


title: ILD sample 68

description:
LT173946RL
6-digit tissue label
micro RNA


title: ILD sample 62

description:
LT158795LL
6-digit tissue label
micro RNA


title: ILD sample 60

description:
LT152615RL
6-digit tissue label
micro RNA


title: ILD sample 61

description:
LT155318RL
6-digit tissue label
micro RNA


title: ILD sample 67

description:
LT168902RM
6-digit tissue label
micro RNA


title: ILD sample 56

description:
LT143944LL
6-digit tissue label
micro RNA


title: ILD sample 58

description:
LT151370RL
6-digit tissue label
micro RNA


title: ILD sample 55

description:
LT139601RU
6-digit tissue label
micro RNA


title: ILD sample 59

description:
LT151513LL
6-digit tissue label
micro RNA


title: ILD sample 57

description:
LT147610LL
6-digit tissue label
micro RNA


title: ILD sample 54

description:
LT135390LL
6-digit tissue label
micro RNA


title: ILD sample 177

description:
LT269381RU
6-digit tissue label
micro RNA


title: ILD sample 178

description:
LT275526RU
6-digit tissue label
micro RNA


title: ILD sample 174

description:
LT230142RL
6-digit tissue label
micro RNA


title: ILD sample 172

description:
LT217339RL
6-digit tissue label
micro RNA


title: ILD sample 173

description:
LT222702LL
6-digit tissue label
micro RNA


title: ILD sample 170

description:
LT205707LL
6-digit tissue label
micro RNA


title: TW22_D8 KO Th1_3

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse MoGene-2_0-st microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

organism: Mus musculus

source_name: Tcf7 deficient Th1 cells

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Mice were infected with LCMV

tag: infection

value: LCMV

value: SMARTA CD4 Tcells

tag: cell type (separated by facs)

value: Th1 cells

tag: genotype/variation

value: Tcf7 deficient


title: non-irradiated primary tumor

city: Seoul

first: SuJin

last: Jang

address: 215-4, Gongneung-dong, Nowon-gu

country: South Korea

institute: KIRAMS

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Quantile normalization: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies) The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. The selected gProcessedSignal value was transformed by logarithm and normalized by quantile method, resulting in 18,502 data rows.

organism: Rattus norvegicus

source_name: non-ɣ-irradiation primary tumor tissue from rat glioma (C6-L cell) xenograft model

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was isolated from tissue or cell using RNAeasy Mini Kit (Qiagen, Valencia, CA, USA)

tag: host strain

value: BALB/c nu/nu nude mice

tag: age

value: 6 weeks

value: non-ɣ-irradiation primary tumor tissue

value: 6 weeks after rat glioma cell xenograft


title: TW23_D8 WT TFH_3

source_name: WT TFH cells

value: TFH cells

value: WT


title: ɣ-irradiation primary tumor

source_name: ɣ-irradiation primary tumor tissue from rat glioma (C6-L cell) xenograft model

value: ɣ-irradiation primary tumor tissue

value: 6 weeks after ɣ-irradiation


title: metastatic tumor (lung nodule No.3)

description: N_Metastatic Tumor 3

source_name: metastatic lung nodule from rat glioma (C6-L cell) xenograft model

value: metastatic lung nodule


title: TW24_D8 WT Th1_3

source_name: WT Th1 cells


title: metastatic tumor (lung nodule No.2)

description: N_Metastatic Tumor 2


title: TW21_D8 KO TFH_3

source_name: Tcf7 deficient TFH cells


title: ILD sample 169

description:
LT203446LL
6-digit tissue label
micro RNA

value: lung


title: ILD sample 167

description:
LT203006LL
6-digit tissue label
micro RNA

value: interstitial lung disease (ILD)


title: A549_RELB kd(2)_RELB si(2)_rep3

city: Edinburgh

first: Simon

last: Wilkinson

address: Crewe Road South

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: siRNA: Hs_RELB_4 Predesigned siRNA, Qiagen

hyb_protocol: Standard Illumina hybridization protocol (18 h)

scan_protocol: Standard Illumina scanning protocol (Illumina HiScan)

data_processing: The data were normalised by VST transformation and RSN normalisation using lumi in R. Reverse transformed normalised values are provided in Matrix normalized dataset.

source_name: A549 non-small cell lung cancer cell line, siRNA transfected 72 h

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Cat# AMIL1791) was used according to manufacturer's instructions. Labelled cRNA was quality controlled using an Agilent 2100 Bioanalyser.

growth_protocol: Cells were grown in DMEM + 10% FCS, 5% CO2

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit and DNA digestion performed according to manufacturers instructions. Total RNA was quality controlled using an Agilent 2100 Bioanalyser.

treatment_protocol: Subconfluent, log-phase cells were plated the day prior to treatment. Then they were transfected with 10 nM siRNA (complexed with Oligofectamine) for 24 h, and replated to allow outgrowth for a further 48 h.

tag: treatment

value: siRNA Hs_RELB_4 Predesigned siRNA, Qiagen


title: ILD sample 171

description:
LT211455LU
6-digit tissue label
micro RNA


title: TW20_D8 WT Th1_2


title: TW19_D8 WT TFH_2


title: TW18_D8 KO Th1_2


title: metastatic tumor (lung nodule No.1)

description: N_Metastatic Tumor 1


title: TW17_D8 KO TFH_2


title: TW15_D8 WT TFH_1


title: A549_RELB kd_RELB si_rep3

description: siRNA: Hs_RELB_3 Predesigned siRNA, Qiagen

value: siRNA Hs_RELB_3 Predesigned siRNA, Qiagen


title: TW16_D8 WT Th1_1

value: LCMV


title: TW14_D8 KO Th1_1

value: SMARTA CD4 Tcells


title: A549_ctrl_NTC2_rep3

description: siRNA:  Qiagen control siRNA catalogue number # 1022076

value: siRNA  Qiagen control siRNA catalogue number # 1022076


title: A549_ATG5 kd_ATG5 si_rep3

description: siRNA: siGenome duplex 004374-03, Dharmacon

value: siRNA siGenome duplex 004374-03, Dharmacon


title: ILD sample 168

description:
LT203431RL
6-digit tissue label
micro RNA


title: A549_ULK1 kd_ULK1 si_rep3

description: siRNA: Hs_ULK1_5 Validated siRNA, Qiagen

value: siRNA Hs_ULK1_5 Validated siRNA, Qiagen


title: A549_ctrl_NTC1_rep3

description: siRNA:  siGENOME Non-Targeting siRNA #1, Dharmacon catalogue number # D-001210-01-50

value: siRNA  siGENOME Non-Targeting siRNA #1, Dharmacon catalogue number # D-001210-01-50


title: TW13_D8 KO TFH_1

value: Tcf7 deficient


title: A549_ATG5 kd(2)_ATG5 si(2)_rep3

description: siRNA target: GCAACTCTGGATGGGATTG

value: siRNA target GCAACTCTGGATGGGATTG


title: ILD sample 163

description:
LT180758RM
6-digit tissue label
micro RNA


title: ILD sample 166

description:
LT188510RM
6-digit tissue label
micro RNA


title: ILD sample 161

description:
LT168219RL
6-digit tissue label
micro RNA


title: ILD sample 160

description:
LT166493RM
6-digit tissue label
micro RNA


title: PGC-1alpha B-02-1

city: Kyoto

first: Yukino

last: Hatazawa

address: 1-5 Hangi-cho, Shimogamo, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-014868 Whole Mouse Genome Microarray 4 × 44K G4122F was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1-v5_95_Feb07 and Grid: 014868_D_20070207) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

source_name: PGC-1alpha B(02-1 line)

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of transgenic and wild-type control mice. RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany). Samples from wild-type and transgenic mice (N = 5 for each group) were pooled before use.

value: skeletal muscle

tag: gendar

value: male


title: PGC-1alpha B-03-2

source_name: PGC-1alpha A(03-2 line)


title: ILD sample 158

description:
LT159457LL
6-digit tissue label
micro RNA


title: ILD sample 159

description:
LT163657RL
6-digit tissue label
micro RNA


title: WT

source_name: WT


title: PGC-1alpha A-E

source_name: PGC-1alpha A(E line)


title: ILD sample 155

description:
LT154455RU
6-digit tissue label
micro RNA


title: ILD sample 162

description:
LT171905RL
6-digit tissue label
micro RNA


title: ILD sample 154

description:
LT139008LU
6-digit tissue label
micro RNA


title: ILD sample 92

description:
LT227135RL
6-digit tissue label
micro RNA


title: ILD sample 153

description:
LT133029RM
6-digit tissue label
micro RNA


title: ILD sample 152

description:
LT128262RU
6-digit tissue label
micro RNA


title: ILD sample 151

description:
LT121014LL
6-digit tissue label
micro RNA


title: ILD sample 150

description:
LT119300LU
6-digit tissue label
micro RNA


title: A549_ATG5 kd(2)_ATG5 si(2)_rep2

description: siRNA target: GCAACTCTGGATGGGATTG


title: A549_RELB kd_RELB si_rep2

description: siRNA: Hs_RELB_3 Predesigned siRNA, Qiagen


title: A549_ctrl_NTC2_rep2

description: siRNA:  Qiagen control siRNA catalogue number # 1022076


title: A549_RELB kd(2)_RELB si(2)_rep1

description: siRNA: Hs_RELB_4 Predesigned siRNA, Qiagen


title: A549_ATG5 kd_ATG5 si_rep2

description: siRNA: siGenome duplex 004374-03, Dharmacon


title: A549_RELB kd_RELB si_rep1


title: A549_RELB kd(2)_RELB si(2)_rep2


title: A549_ctrl_NTC1_rep2

description: siRNA:  siGENOME Non-Targeting siRNA #1, Dharmacon catalogue number # D-001210-01-50


title: A549_ULK1 kd_ULK1 si_rep1

description: siRNA: Hs_ULK1_5 Validated siRNA, Qiagen


title: A549_ULK1 kd_ULK1 si_rep2


title: ILD sample 149

description:
LT118098LU
6-digit tissue label
micro RNA


title: A549_ATG5 kd(2)_ATG5 si(2)_rep1

description: siRNA target: GCAACTCTGGATGGGATTG


title: A549_ctrl_NTC1_rep1


title: A549_ctrl_NTC2_rep1


title: ILD sample 148

description:
LT112491RM
6-digit tissue label
micro RNA


title: ILD sample 145

description:
LT107185RU
6-digit tissue label
micro RNA


title: ILD sample 143

description:
LT100654RL
6-digit tissue label
micro RNA


title: ILD sample 144

description:
LT105618RL
6-digit tissue label
micro RNA


title: ILD sample 147

description:
LT109321RL
6-digit tissue label
micro RNA


title: ILD sample 142

description:
LT093665LI
6-digit tissue label
micro RNA


title: ILD sample 140

description:
LT090283LL
6-digit tissue label
micro RNA


title: ILD sample 139

description:
LT089958RL
6-digit tissue label
micro RNA


title: A549_ATG5 kd_ATG5 si_rep1


title: ILD sample 137

description:
LT072789RU
6-digit tissue label
micro RNA


title: ILD sample 136

description:
LT066309LL
6-digit tissue label
micro RNA


title: ILD sample 138

description:
LT083491LU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 39

city: Buffalo

first: kaiyu

last: Jiang

state: NY

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr on Affymetrix human EXON 1.0 ST  array or GeneChip™ miRNA 1.0 array following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner

data_processing: Expression summary values from Affymetrix Exon and miRNA arrays were generated using RMA software in the “Affy” package of Bioconductor in the R statistical computing environment

source_name: neutrophil RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA)

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

value: neutrophils

tag: disease

value: Healthy control


title: Neutrophils, Healthy control, Biological replicate 40


title: Neutrophils, Healthy control, Biological replicate 38


title: Neutrophils, Healthy control, Biological replicate 37


title: ILD sample 135

description:
LT056301LL
6-digit tissue label
micro RNA


title: ILD sample 134

description:
LT056024RL
6-digit tissue label
micro RNA


title: ILD sample 133

description:
LT055841LL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 35


title: Neutrophils, Healthy control, Biological replicate 36


title: Neutrophils, Healthy control, Biological replicate 34


title: ILD sample 131

description:
LT048637LL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 33


title: ILD sample 130

description:
LT047521RL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 43


title: Neutrophils, Healthy control, Biological replicate 32


title: ILD sample 132

description:
LT049193LU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 41


title: ILD sample 129

description:
LT024857LU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 42


title: ILD sample 128

description:
LT013743LL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 31


title: Neutrophils, Healthy control, Biological replicate 30


title: ILD sample 1

description:
LT142933RU
6-digit tissue label
micro RNA


title: COPD sample 135

description:
LT291673RM
6-digit tissue label
micro RNA

source_name: flash frozen lung tissues, COPD

value: chronic obstructive pulmonary disease (COPD)


title: Neutrophils, Healthy control, Biological replicate 29


title: Neutrophils, Healthy control, Biological replicate 28


title: COPD sample 134

description:
LT282467LL
6-digit tissue label
micro RNA

value: lung


title: Neutrophils, Healthy control, Biological replicate 27


title: Neutrophils, Healthy control, Biological replicate 26


title: Neutrophils, Healthy control, Biological replicate 24


title: COPD sample 132

description:
LT271851LU
6-digit tissue label
micro RNA


title: COPD sample 131

description:
LT265199LU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 23


title: Neutrophils, Healthy control, Biological replicate 25


title: COPD sample 130

description:
LT206010LU
6-digit tissue label
micro RNA


title: COPD sample 129

description:
LT204017RL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 22


title: COPD sample 128

description:
LT193936RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 21


title: Neutrophils, Healthy control, Biological replicate 20


title: COPD sample 127

description:
LT184347RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 18


title: Neutrophils, Healthy control, Biological replicate 38


title: COPD sample 126

description:
LT174536LU
6-digit tissue label
micro RNA


title: COPD sample 125

description:
LT161707RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 19


title: Neutrophils, Healthy control, Biological replicate 39


title: COPD sample 124

description:
LT152979LL
6-digit tissue label
micro RNA


title: COPD sample 123

description:
LT150340LU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 17


title: Neutrophils, Healthy control, Biological replicate 14


title: Neutrophils, Healthy control, Biological replicate 15


title: COPD sample 122

description:
LT147658RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 16


title: COPD sample 120

description:
LT144462RU
6-digit tissue label
micro RNA


title: COPD sample 119

description:
LT131432RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 13


title: COPD sample 133

description:
LT282031RU
6-digit tissue label
micro RNA


title: COPD sample 118

description:
LT127070RL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 12


title: COPD sample 117

description:
LT125775RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 10


title: Neutrophils, Healthy control, Biological replicate 11


title: Neutrophils, Healthy control, Biological replicate 9


title: COPD sample 114

description:
LT110408RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 8


title: Neutrophils, Healthy control, Biological replicate 5


title: Neutrophils, Healthy control, Biological replicate 7


title: COPD sample 115

description:
LT112339LI
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 4


title: COPD sample 121

description:
LT145162RM
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 6


title: COPD sample 113

description:
LT100984RL
6-digit tissue label
micro RNA


title: COPD sample 112

description:
LT081077RU
6-digit tissue label
micro RNA


title: COPD sample 111

description:
LT075917RU
6-digit tissue label
micro RNA


title: COPD sample 110

description:
LT070021RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 3


title: COPD sample 109

description:
LT060406RL
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 2


title: COPD sample 108

description:
LT059865RU
6-digit tissue label
micro RNA


title: COPD sample 107

description:
LT056627RU
6-digit tissue label
micro RNA


title: Neutrophils, Healthy control, Biological replicate 1


title: Neutrophils, Cystic Fibrosis, Biological replicate 8

value: Cystic Fibrosis


title: COPD sample 106

description:
LT051993RU
6-digit tissue label
micro RNA


title: COPD sample 116

description:
LT113077LL
6-digit tissue label
micro RNA


title: Neutrophils, Cystic Fibrosis, Biological replicate 7


title: Neutrophils, Cystic Fibrosis, Biological replicate 14


title: Neutrophils, Cystic Fibrosis, Biological replicate 13


title: Neutrophils, Cystic Fibrosis, Biological replicate 6


title: COPD sample 104

description:
LT046180RU
6-digit tissue label
micro RNA


title: COPD sample 105

description:
LT051568RU
6-digit tissue label
micro RNA


title: COPD sample 103

description:
LT038591LU
6-digit tissue label
micro RNA


title: Neutrophils, Cystic Fibrosis, Biological replicate 10


title: Neutrophils, Cystic Fibrosis, Biological replicate 11


title: Neutrophils, Cystic Fibrosis, Biological replicate 4


title: Neutrophils, Cystic Fibrosis, Biological replicate 5


title: Neutrophils, Cystic Fibrosis, Biological replicate 9


title: Neutrophils, Healthy control, Biological replicate 10


title: Neutrophils, Cystic Fibrosis, Biological replicate 3


title: Neutrophils, Cystic Fibrosis, Biological replicate 2


title: COPD sample 101

description:
LT026458RL
6-digit tissue label
micro RNA


title: COPD sample 100

description:
LT010491LL
6-digit tissue label
micro RNA


title: Neutrophils, Cystic Fibrosis, Biological replicate 1


title: Neutrophils, Patient, JIA, Biological replicate 38

value: Juvenile idiopathic arthritis


title: COPD sample 98

description:
LT001098RU
6-digit tissue label
micro RNA


title: COPD sample 99

description:
LT007392RU
6-digit tissue label
micro RNA


title: COPD sample 102

description:
LT032775RU
6-digit tissue label
micro RNA


title: Neutrophils, Patient, JIA, Biological replicate 36


title: Neutrophils, Healthy control, Biological replicate 1


title: Neutrophils, Patient, JIA, Biological replicate 35


title: Cell culture time-point at 84h - Ciological rep C

city: Umeå

first: Edouard

last: Pesquet

address: Umeå University

department: Department of Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

description: Progression of tracheary element secondary cell wall deposition at 84h

hyb_protocol: 15µg of cRNA were hybridized for 16h at 45°C and then wahsed in GeneChip Fluidics Station 450 according to the standard Affymetrix protocol (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

scan_protocol: Scanning was performed using GeneChip 3000 according to the standard Affymetrix protocol (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

data_processing: Data was processed using RMA normalization and analysis using R (performed by Johannes Hanson)

organism: Arabidopsis thaliana

source_name: Differentiating Arabidopsis cell culture time-point at 84h - Ciological rep C

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

growth_protocol: Arabidopsis habituated cell suspension cultures were grown in 1x MS liquid pH 5.7 complemented with b5 vitamins and 3% sucrose

extract_protocol: Total RNA were extracted from frozen cell cultures using the Trizol reagent methods - repeated twice (according to manufacturer's instruction)

treatment_protocol: Tracheary element differentiation was triggered by incubating 7-days old cells into fresh MS liquid medium pH 5.7 b5 vitamins 3% sucrose complmented with 6µg/ml NAA, 1µg/ml BAP and 4µM epibrassinolides (see Pesquet et al., Current Biology 2010 for details).

tag: ecotype

value: inducible pluripotent cells


title: Neutrophils, Cystic Fibrosis, Biological replicate 12

tag: cell type


title: Cell culture time-point at 96h - Ciological rep C

description: Completion of tracheary element secondary cell wall deposition and preparation of programmed cell death and post-mortem lignification at 96h

source_name: Differentiating Arabidopsis cell culture time-point at 96h - Ciological rep C


title: Neutrophils, Patient, JIA, Biological replicate 34


title: Cell culture time-point at 72h - Ciological rep C

description: Progression of tracheary element secondary cell wall deposition at 72h

source_name: Differentiating Arabidopsis cell culture time-point at 72h - Ciological rep C


title: Cell culture time-point at 60h - Ciological rep C

description: Initiation of tracheary element secondary cell wall deposition at 60h

source_name: Differentiating Arabidopsis cell culture time-point at 60h - Ciological rep C


title: Cell culture time-point at 48h - Ciological rep C

description: Progression of tracheary element differentiation prior to secondary cell wall deposition at 48h

source_name: Differentiating Arabidopsis cell culture time-point at 48h - Ciological rep C


title: Neutrophils, Patient, JIA, Biological replicate 31


title: Neutrophils, Patient, JIA, Biological replicate 33


title: Neutrophils, Patient, JIA, Biological replicate 32


title: Neutrophils, Patient, JIA, Biological replicate 30


title: Cell culture time-point at 36h - Ciological rep C

description: Initial step of tracheary element differentiation at 36h

source_name: Differentiating Arabidopsis cell culture time-point at 36h - Ciological rep C


title: Cell culture time-point at 24h - Ciological rep C

description: Loss of cell division, initiation of cell expansion and tracheary element differentiation at 24h

source_name: Differentiating Arabidopsis cell culture time-point at 24h - Ciological rep C


title: Neutrophils, Patient, JIA, Biological replicate 37


title: Cell culture time-point at 12h - Ciological rep C

description: Loss of cell division, initiation of cell expansion at 12h

source_name: Differentiating Arabidopsis cell culture time-point at 12h - Ciological rep C


title: Neutrophils, Patient, JIA, Biological replicate 28


title: Cell culture time-point at 96h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 96h - biological rep B


title: Neutrophils, Patient, JIA, Biological replicate 27


title: Cell culture time-point at 0h - Ciological rep C

description: Undifferentiated actively dividing pluripotent cells at 0h

source_name: Differentiating Arabidopsis cell culture time-point at 0h - Ciological rep C


title: Neutrophils, Patient, JIA, Biological replicate 26


title: Neutrophils, Patient, JIA, Biological replicate 29


title: Cell culture time-point at 84h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 84h - biological rep B


title: Neutrophils, Healthy control, Biological replicate 27


title: Neutrophils, Cystic Fibrosis, Biological replicate 5


title: Cell culture time-point at 60h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 60h - biological rep B


title: Neutrophils, Patient, JIA, Biological replicate 23


title: Cell culture time-point at 72h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 72h - biological rep B


title: Neutrophils, Healthy control, Biological replicate 2


title: Neutrophils, Patient, JIA, Biological replicate 25


title: Neutrophils, Patient, JIA, Biological replicate 22


title: Neutrophils, Patient, JIA, Biological replicate 24


title: Cell culture time-point at 24h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 24h - biological rep B


title: Neutrophils, Patient, JIA, Biological replicate 28


title: Cell culture time-point at 36h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 36h - biological rep B


title: Neutrophils, Patient, JIA, Biological replicate 21

source_name: neutrophil RNA


title: Neutrophils, Patient, JIA, Biological replicate 20


title: Cell culture time-point at 12h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 12h - biological rep B


title: Neutrophils, Cystic Fibrosis, Biological replicate 15


title: Neutrophils, Patient, JIA, Biological replicate 19


title: Cell culture time-point at 0h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 0h - biological rep B


title: Cell culture time-point at 48h - biological rep B

source_name: Differentiating Arabidopsis cell culture time-point at 48h - biological rep B


title: Neutrophils, Patient, JIA, Biological replicate 18


title: Neutrophils, Cystic Fibrosis, Biological replicate 7


title: Cell culture time-point at 84h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 84h - biological rep A


title: Cell culture time-point at 96h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 96h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 17


title: Cell culture time-point at 72h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 72h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 23


title: Neutrophils, Patient, JIA, Biological replicate 16


title: Neutrophils, Patient, JIA, Biological replicate 15


title: Cell culture time-point at 36h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 36h - biological rep A


title: Cell culture time-point at 48h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 48h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 30


title: Cell culture time-point at 60h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 60h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 13


title: Neutrophils, Patient, JIA, Biological replicate 22


title: Neutrophils, Patient, JIA, Biological replicate 14


title: Neutrophils, Patient, JIA, Biological replicate 21


title: Cell culture time-point at 24h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 24h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 20


title: Neutrophils, Patient, JIA, Biological replicate 12


title: Cell culture time-point at 12h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 12h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 11


title: Neutrophils, Patient, JIA, Biological replicate 9


title: Neutrophils, Patient, JIA, Biological replicate 10


title: PRMT1 knockout complemented rep2

city: Tampa

first: Elena

last: Suvorova

state: Florida

address: 3720 Spectrum Blvd

department: Internal Medicine

institute: University of South Florida

hyb_protocol: Fragmented cRNA (5μg) was hybridized to the Toxoplasma gondii Affymetrix microarray according to standard hybridization protocols (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html).

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

data_processing: Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies). Several filers were applied to raw RMA value list, which resulted in reduction of number of probe ID: (1) reads with raw RMA values 50 and below were considered background, (2) probe reads corresponding to the host (human) cell contamination and (3) orphan probes that are not affiliated with ORFs in newly annotated genome(toxoDB) were identifed and removed from the list. Resulted reduced list was further processed. t-Test on the final list was run in order to identify genes with significantly greater than random variation in RNA abundance across the data grouped by genotype.  Variances were calculated using cross-gene error model, with a p-value cutoff 0.1, and multiple testing correction: Benjamini and Hochberg False Discovery Rate.

organism: Toxoplasma gondii

source_name: complemented PRMT1 knockout strain

label_protocol: A total of 500ng starting RNA was used to produce biotinilated cRNA using the Affymetrix One-Cycle Kit (Affymetrix).

growth_protocol: Toxoplasma gonidii strains were grown in HFF monolayers at 37oC for 32 hours in DMEM supplemented with 1%FBS and 1xPSA.

extract_protocol: RNA was extracted from parasites using the RNeasy kit and DNase I treatment (Qiagen).   RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Parasites were separated by filtration and collected by centrifugation.

value: PRMT1 knockout complemented with RFP-tagged PRMT1 protein (C)

tag: developmental stage

value: tachyzoite


title: Neutrophils, Patient, JIA, Biological replicate 18


title: PRMT1 knockout complemented rep3


title: Cell culture time-point at 0h - biological rep A

source_name: Differentiating Arabidopsis cell culture time-point at 0h - biological rep A


title: Neutrophils, Patient, JIA, Biological replicate 7


title: PRMT1 knockout complemented rep1


title: PRMT1 knockout rep2

source_name: PRMT1 knockout strain

value: PRMT1 knockout (K)


title: Neutrophils, Patient, JIA, Biological replicate 5


title: Neutrophils, Patient, JIA, Biological replicate 6


title: PRMT1 knockout rep1


title: Neutrophils, Patient, JIA, Biological replicate 4


title: Neutrophils, Patient, JIA, Biological replicate 3


title: PRMT1 knockout rep3


title: Neutrophils, Patient, JIA, Biological replicate 16


title: parent strain rep2

source_name: parent strain

value: RH-hxgprt parent strain (W)


title: Arectinib-resistant clone2 cells

city: Okayama

first: Hideko

last: Isozaki

address: 2-5-1 Shikatacho

department: Department of Hematology, Oncology and Respiratory Medicine

institute: Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences

description: Biological replicate 1 of 3. Alectinib-resistant H2228 cells.

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: The base medium for these cell lines is RPMI-1640 Medium. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Parental cells were cultured with increasing concentrations of alectinib, starting with the IC50, to establish the alectinib-resistant lines. Doses were increased in a stepwise pattern when normal cell proliferation resumed. Fresh drug was added every 96 h. Resistant cells began to grow in 1 μM alectinib after 5 months of culture with the drug. Each clone was derived using a single-cell cloning method.

tag: gender

value: female

tag: cell line


title: parent strain rep3


title: Arectinib-resistant clone3 cells

tag: tissue


title: Neutrophils, Patient, JIA, Biological replicate 2


title: Neutrophils, Patient, JIA, Biological replicate 8


title: parent strain rep1


title: Arectinib-resistant clone1 cells


title: Neutrophils, Patient, JIA, Biological replicate 1


title: Neutrophils, Patient, JIA, Biological replicate 13


title: Parental cells

description: Biological replicate 1 of 1. Parental H2228 cells.


title: aCGH_PDX_primary RCC

type: genomic

first: Kyu-Tae

address: Irwon-Ro 81

department: Samsung Genome Institute

institute: Samsung Medical Center

description: Reference human male DNA labeled with Cy3, purchased from Promega (catalog no. G1471)

hyb_protocol: Labeled Test (Cy5) and Reference (Cy3) DNA samples were paired and co-hybridized to the SurePrint G3 Human CGH Microarrays, 4×180K (Agilent®) at 67 °C, 20rpm for 24hrs, then washed at room temperature by using the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol (V7.3, 2014). The hybridized array was immediately scanned with an Agilent Microarray Scanner (Agilent Technologies, Inc.)

scan_protocol: CGH data were extracted from scanned images (TIFF files) using Feature Extraction software (v11.0.1.1).

data_processing: Extracted signals from the scanned microarray image were translated into log10 ratios of the Cy3(green) labeled normal DNA and Cy5(red) labeled test DNA signals in each of all probes, allowing us to measure DNA copy number changes in the experiments using Agilent Genomic Workbench v7.0.4.0 software.  Feature extraction was used to extract foreground signal for background subtraction and to correct dye biases for LOWESS normalization. To reduce biased signals between arrays, data was normalized using the limma package (Ritchie et al., Bioinformatics 2007) implemented in R environment. For the overlapped probe ID in the matrix, corresponding values were averaged.

molecule: genomic DNA

source_name: PDX, primary RCC

label_protocol: DNA labeling and hybridization were performed by using the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol (V 7.3, 2014). Briefly, 500ng of genomic DNA was digested with Alu1 and Rsa1 restriction enzymes at 37°C for two hours and then random primers were added. Test and Reference DNA samples were then labeled with Cy5-dUTP and Cy3-dUTP respectively, by incubation with Exo-Klenow at 37°C for a further two hours. Excess nucleotides were removed using Agilent Purification Columns. After purification, the labeled DNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA) that measuring A260 (for DNA), A550 (for Cy5) and A649 (for Cy3) was used for determination of DNA and fluorophore concentrations.

growth_protocol: This study was carried out in accordance with the principles of the Declaration of Helsinki, and approved by The Samsung Medical Center (Seoul, Korea) Institutional Review Board (IRB) (no. 2010-04-004). A participant in this study gave written informed consent for research and publication of the results. Animal experiments were conducted in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals and within the protocols approved by the appropriate IRB at the Samsung Medical Center.

extract_protocol: gDNAs were prepared using QIAamp® DNA Mini kit (QIAGEN, CA, USA). For the quality control, DNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), and by 1% agarose gel electrophoresis.

value: primary renal cell carcinoma

tag: tissue source

value: patient-derived xenograft

source_name: Human Genomic DNA: Male (#cat: G1471, Promega)

tag: control type

value: Reference human male DNA


title: aCGH_patient_metastatic RCC

source_name: patient, metastatic RCC

value: metastatic renal cell carcinoma

value: patient


title: HOXA9/MEIS1.6

status: Public on Sep 17 2015

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

hyb_protocol: Biotin labeled cDNA was hybridized to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA) using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

scan_protocol: Hybridized arrays were washed using the GeneChip Fluidics Station 450 (Affymetrix) using protocol FS450_001 and scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Exon array data were processed using an R/Bioconductor package, as previously described (Okoniewski and Miller, 2008). Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm (Irizarry et al., 2003). Probesets annotated in Ensembl murine genome build 66 as “exonic” and not “multitarget”, with their expression values, were extracted in CSV file format. The CSV file was used to calculate “gene level summaries”, which represent the mean expression of all exonic probesets mapping to each Ensembl annotated gene (see metadata file).
MoEx-1_0-st-v1.r2.pgf

source_name: Flow sorted murine CD117+Gr1+ BM AML cells

label_protocol: The cDNA was then fragmented and biotin labeled using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

extract_protocol: RNA was extracted using QIAshredder spin columns and an RNeasy Plus Micro kit (Qiagen, Manchester, UK). RNA quality was confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Next cDNA amplification of 40ng RNA was performed using the Ovation Pico WTA System V2 (NuGEN, San Carlos, CA), according to manufacturer’s instructions.

value: BM AML cells

tag: transduction


title: HOXA9/FOXC1.4


title: HOXA9/MEIS1.2


title: HOXA9/MEIS1.7


title: HOXA9/FOXC1.2


title: HOXA9/FOXC1.1


title: aCGH_patient_primary RCC

source_name: patient, primary RCC


title: HOXA9/MTV.1


title: HOXA9/MTV.2


title: HOXA9/MTV.4


title: aCGH_PDX_metastatic RCC

source_name: PDX, metastatic RCC


title: HMDS66D

city: Leeds

first: Catherine

last: Cargo

address: Beckett Street

department: HMDS

institute: Leeds Cancer Centre

description:
MDS5q-_diagnostic_66
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto CytoSNP-12 BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Data was visualised in Illumina KaryoStudio, using the HumanCytoSNP-12v2-0_L.bpm manifest file, and copy number changes were detected using cnvPartition 3.0.7 and confirmed 'by eye'

label: Cy3 and Cy5

source_name: bone marrow, MDS5q-, diagnostic

label_protocol: upto 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using denaturation/neutralization/amplification master mixes (MA1, MA2, MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from EDTA blood or marrow, or from stored smears, was performed using proteinase K and Qiagen miniprep kits.

value: Female

value: Bone marrow

tag: disease state

value: Myelodysplastic syndrome (5q-)


title: HMDS69P

description:
AML_pre-diagnostic_69
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

source_name: bone marrow, pre-diagnostic

value: Pre-diagnostic


title: HMDS65

description:
AML_diagnostic_65
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

source_name: bone marrow, AML, diagnostic

value: Male

value: Acute myeloid leukaemia


title: HMDS67P

description:
AML_pre-diagnostic_67
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS69D

description:
AML_diagnostic_69
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: Croatian20

city: Oxford

first: George

last: Busby

state: OXON

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics

hyb_protocol: Followed Illumina Standrd Protocol

scan_protocol: Followed Illumina Standrd Protocol

data_processing: Image was analysed using Illumina GenomeStudio v2009.2.0.29803

source_name: saliva

label_protocol: Followed Illumina Standrd Protocol

extract_protocol: Extraction of genomic DNA from saliva and blood using common laboratory protocols.

value: male

tag: ethnicity

value: Croatian


title: HMDS68D

description:
AML_diagnostic_68
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS67D

description:
AML_diagnostic_67
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: Croatian3


title: HMDS66P

description:
MDS5q-_pre-diagnostic_66
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS64

description:
RCMD_diagnostic_64
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

source_name: bone marrow, RCMD, diagnostic

value: Refractory cytopenia with multilineage dysplasia


title: Croatian17


title: Croatian8


title: Croatian9


title: Croatian19


title: Croatian4


title: Croatian11


title: Croatian18


title: Croatian6


title: Croatian2


title: Croatian12


title: Croatian15


title: Croatian10


title: Croatian14


title: Croatian16


title: HMDS68P

description:
AML_pre-diagnostic_68
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS60

description:
RCMD_diagnostic_60
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: Croatian13


title: HMDS63D

description:
AML_diagnostic_63
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: Croatian1


title: HMDS59D

description:
RAEB_diagnostic_59
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

source_name: bone marrow, RAEB, diagnostic

value: Refractory anaemia with excess blasts


title: Croatian7


title: Croatian5


title: HMDS58P

description:
RAEB_pre-diagnostic_58
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS62

description:
RAEB_diagnostic_62
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS59P

description:
RAEB_pre-diagnostic_59
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS56P

description:
AML_pre-diagnostic_56
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS58D

description:
RAEB_diagnostic_58
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS56D

description:
AML_diagnostic_56
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS63P

description:
AML_pre-diagnostic_63
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS53D

description:
RAEB_diagnostic_53
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS61

description:
RAEB_diagnostic_61
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS53P

description:
RAEB_pre-diagnostic_53
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS55D

description:
RCMD_diagnostic_55
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS57

description:
RCMD_diagnostic_57
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS51P

description:
AML_pre-diagnostic_51
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS54

description:
RCMD_diagnostic_54
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS50D

description:
AML_diagnostic_50
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS50P

description:
AML_pre-diagnostic_50
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS49P

description:
AML_pre-diagnostic_49
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS55P

description:
RCMD_pre-diagnostic_55
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS51D

description:
AML_diagnostic_51
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS52P

description:
AML_pre-diagnostic_52
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS52D

description:
AML_diagnostic_52
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS47P

description:
RAEB_pre-diagnostic_47
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS46

description:
RCMD_diagnostic_46
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS48

description:
RCMD_diagnostic_48
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS44

description:
RAEB_diagnostic_44
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS47D

description:
RAEB_diagnostic_47
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS43D

description:
RAEB_diagnostic_43
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS49D

description:
AML_diagnostic_49
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS45

description:
RAEB_diagnostic_45
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS39D

description:
RCMD_diagnostic_39
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS41

description:
RCMD_diagnostic_41
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS42P

description:
RCMD_pre-diagnostic_42
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS42D

description:
RCMD_diagnostic_42
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS33D

description:
RCMD_diagnostic_33
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS38

description:
RCMD_diagnostic_38
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS33P

description:
RCMD_pre-diagnostic_33
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS30P

description:
AML_pre-diagnostic_30
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS40P

description:
RCMD_pre-diagnostic_40
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS30D

description:
AML_diagnostic_30
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS35P

description:
RCMD_pre-diagnostic_35
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS39P

description:
RCMD_pre-diagnostic_39
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS29P

description:
AML_pre-diagnostic_29
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS40D

description:
RCMD_diagnostic_40
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS35D

description:
RCMD_diagnostic_35
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS31D

description:
AML_diagnostic_31
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS43P

description:
RAEB_pre-diagnostic_43
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS34D

description:
AML_diagnostic_34
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS34P

description:
AML_pre-diagnostic_34
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS36

description:
RCMD_diagnostic_36
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS29D

description:
AML_diagnostic_29
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS32

description:
RAEB_diagnostic_32
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS31P

description:
AML_pre-diagnostic_31
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS28

description:
RCMD_diagnostic_28
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS37P

description:
RCMD_pre-diagnostic_37
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS27

description:
RAEB_diagnostic_27
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS37D

description:
RCMD_diagnostic_37
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS24

description:
RCMD_diagnostic_24
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS20

description:
RAEB_diagnostic_20
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS25

description:
RAEB_diagnostic_25
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS21

description:
AML_diagnostic_21
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS23

description:
RAEB_diagnostic_23
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS19D

description:
RAEB_diagnostic_19
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: resFOP(cl2)-MSC

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

description: Gene expression data from human mesenchymal stromal cells derived from PSCs through neural crest cell lineage

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing:
Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA algorithm.
Normalized expression signals were calculated from Affymetrix CEL files with the RMA algorithm implemented in the GeneSpring 12.6.1

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: Cells were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).


title: HMDS17D

description:
RCMD_diagnostic_17
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS14

description:
RCMD_diagnostic_14
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS22

description:
RCMD_diagnostic_22
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: resFOP(cl1)_2-MSC

value: human mesenchymal stromal cells derived from PSCs through neural crest cell lineage


title: HMDS19P

description:
RAEB_pre-diagnostic_19
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: FOP(cl1)_2-MSC


title: resFOP(cl1)_1-MSC


title: HMDS16

description:
RAEB_diagnostic_16
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS11D

description:
RCMD_diagnostic_11
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS8

description:
RCMD_diagnostic_8
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS15

description:
RCMD_diagnostic_15
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: FOP(cl2)-MSC


title: HMDS9

description:
RCMD_diagnostic_9
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS13

description:
AML_diagnostic_13
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS26

description:
RCMD_diagnostic_26
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS17P

description:
RCMD_pre-diagnostic_17
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS4P

description:
AML_pre-diagnostic_4
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: TIG120-4f1-MSC


title: FOP(cl1)-MSC


title: resFOP(cl2)-NCC

description: Gene expression data from human neural crest cells derived from PSCs


title: HMDS4D

description:
AML_diagnostic_4
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS12P

description:
RCMD_pre-diagnostic_12
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: resFOP(cl1)-NCC

value: human neural crest cells derived from PSCs


title: HMDS10

description:
RAEB_diagnostic_10
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: 414C2-MSC

description: Gene expression data from human mesenchymal stromal cells derived from PSCs through neural crest cell lineage


title: HMDS3

description:
AML_diagnostic_3
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS7

description:
RAEB_diagnostic_7
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS5D

description:
RCMD_diagnostic_5
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: FOP(cl1)-NCC


title: FOP(cl2)-NCC


title: HMDS6

description:
RCMD_diagnostic_6
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: TIG120-4f1-NCC


title: HMDS1

description:
AML_diagnostic_1
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS12D

description:
RCMD_diagnostic_12
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS2

description:
AML_diagnostic_2
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: FOP(cl2)-iPSC

description: Gene expression data from human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: 414C2-NCC


title: resFOP(cl2)-iPSC


title: TIG120-4f1-iPSC


title: FOP(cl1)-iPSC


title: resFOP(cl1)-iPSC


title: 414C2-iPSC


title: HMDS11P

description:
RCMD_pre-diagnostic_11
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: HMDS5P

description:
RCMD_pre-diagnostic_5
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).


title: B6 mouse2

city: Houston

first: Simanta

last: Pathak

address: 3605 Cullen Blvd

institute: University of Houston

description: SAMPLE 5

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina MouseWG-6 V2 Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScanSQ scanner

data_processing: The data is analyzed using Illumina GenomeStudio software (framework version 2011.1; Gene expression module version 1.9.0)

source_name: WT_spleen B-cell

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

growth_protocol: freshly isolated splenic B cells were used to extract total mRNA

extract_protocol: Total RNAs were isolated with Trizol reagent (Invitrogen)

tag: strain background

tag: genotype/variation

value: wild type

value: mouse spleen B-cell


title: Sle2 mouse3

description: SAMPLE 3

source_name: Sle2_spleen B-cell

value: Sle2 (B6.Sle2)

tag: stain info

value: congenic strain that harboring the Sle2 locus from Chromosome 4 of NZM2410 strain in a B6 background


title: B6 mouse3

description: SAMPLE 6


title: B6 mouse1

description: SAMPLE 4


title: Sle2 mouse2

description: SAMPLE 2


title: Sle2 mouse1

description: SAMPLE 1


title: Allo Veh SHORT (8762536017_A)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scaning protocol

data_processing: Data were loaded and background corrected with BeadStudio. The resulting matrix was VST transformed and RSN normalized with lumiT and lumiN functions from lumi package in R.

source_name: prostate tumor/tissue

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were treated dailly for 5 consecutive days with the indicated drugs and prostate tumor/tissues harvested the fifth day

tag: strain

value: NU/J

value: Allografted NPK tumors in Athymic nude mice

tag: treatment

value: vehicle

tag: duration

value: SHORT

value: prostate tumor/tissue


title: Allo RAPPD SHORT (8762536023_B)

value: RAPPD


title: Allo RAPPD SHORT (8762536023_E)


title: Allo RAPPD SHORT (8762536023_C)


title: NPK RAPPD SHORT (5644841006_E)

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+ (NPK mice)


title: Allo RAPPD SHORT (8762536023_D)


title: NPK RAPPD SHORT (5644841006_B)


title: NPK RAPPD SHORT (5644841006_C)


title: NPK RAPPD SHORT (5644841006_A)


title: Allo Veh SHORT (8762536016_A)


title: HMDS18

description:
AML_diagnostic_18
Genomic DNA extracted from bone marrow was genotyped using HumanCytoSNP-12 v2.0 BeadChip (Illumina).

value: Male

value: Bone marrow

value: Acute myeloid leukaemia


title: Allo Veh SHORT (8762536023_A)


title: NPK Veh SHORT (5645107002_E)


title: NPK Veh SHORT (5645107002_A)


title: NPK Docetaxel SHORT (5644841056_D)

value: Docetaxel


title: NPK Docetaxel SHORT (5644841056_B)


title: NPK Veh LONG (5535696014_E)

value: LONG


title: NPK Veh SHORT (5645107002_C)


title: NPK Veh LONG (5535696014_A)


title: NPK Veh SHORT (5645107002_D)


title: NPK Doxetaxel SHORT (5644841056_E)


title: NPK Docetaxel SHORT (5644841056_A)


title: NPK RAPPD LONG (5003139027_E)


title: NPK Veh SHORT (5645107002_B)


title: NPK Docetaxel SHORT (5644841056_C)


title: NPK Veh LONG (5535696014_C)


title: NPK RAPPD SHORT (5644841006_D)


title: NPK RAPPD LONG (5535696020_F)


title: NPK RAPPD LONG (5003139027_D)


title: NPK RAPPD LONG (5535696014_F)


title: Wild_type LONG (5003139006_C)

source_name: prostate tissue

value: Wildtype

value: prostate tissue


title: Wild_type LONG (5003139006_B)


title: NPK Veh LONG (5535696020_D)


title: NPK RAPPD LONG (5003139027_F)


title: NPK Veh LONG (5535696020_B)


title: Wild_type LONG (5003139006_A)


title: wt3

city: Bethesda

first: Sugata

last: Manna

state: Maryland

address: 37 Convent Dr. Room 3032A

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

description: wild-type mature CD4 SP thymocytes, Biological Replicate 3

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Data were processed using Partek software using RMA Background Correction and  Quantile Normalization

label_protocol: Not provided

extract_protocol: Total RNA from mature CD4 thymocytes was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Mature Va2hi CD24lo CD4 SP thymocytes

tag: genotype

value: Wild type

tag: tcr transgene

value: OT-II


title: dKO1

description: dKO mature CD4 SP thymocytes, Biological Replicate 1

tag: cell type


title: dKO2

description: dKO mature CD4 SP thymocytes, Biological Replicate 2


title: dKO3

description: dKO mature CD4 SP thymocytes, Biological Replicate 3


title: wt1

description: wild-type mature CD4 SP thymocytes, Biological Replicate 1


title: wt2

description: wild-type mature CD4 SP thymocytes, Biological Replicate 2


title: L_DM_Wt_OD-023_v_L2_DM_744-1_Tpt-1

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

hyb_protocol: Hybridization was performed as described before. N. S. Baliga et al., Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14, 1025–1035 (2004).

scan_protocol: Arrays were scanned in ScanArray (Perkin‐Elmer) and spot finding was done using Feature Extraction (Agilent Technologies).

data_processing: Normalization and statistical analysis were performed as described before. Agilent Feature Extraction file for the dye flip experiment includes dye_flip in its name.

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Dv DVU0744::Tn5 and Mm coculture, 2nd syntrophic condition, Early Log

label_protocol: Labeling was performed as described before. N. S. Baliga et al., Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14, 1025–1035 (2004).

growth_protocol: Syntrophic co-cultures of Methanococcus and either Desulfovibrio wild type or DVU0744::Tn5 mutant strains were grown in 200 ml bottles with 50 ml culture media in replicates. Growth was performed under anaerobic conditions at 37 C. The anoxic environment was created by filling the headspace with 80% N2 and 20% CO2 gas mixtures.

extract_protocol: Cells in the anaerobic Balch tubes were centrifuged at 2500 rpm for 10 minutes and then taken into anaerobic chamber for harvesting cell pellets. Cell pellets were immediately flash-frozen in liquid nitrogen and stored at -80C before RNA extraction and sample preparation. Total RNA extraction was performed with MasterPure Complete DNA and RNA Purification kit (Epicentre Technologies, Madison, WI) per manufacturer’s instructions. Ambion DNA-free kit (Life Technologies, Grand island, NY) was used to ensure DNA-free samples for array analysis. Quality and purity of RNA samples were determined with a Bioanalyzer, gel electrophoresis and PCR.

treatment_protocol: Cells were initially grown in syntrophic growth medium (L) until they reach to early log phase (OD600 ~ 0.15). At this stage 5 ml of cultures were withdrawn with syringes and injected into anaerobic empty Balch tubes for sampling via centrifugation. In the meantime, another 0.5 ml of samples were withdrawn and transferred into sulfate-respiration growth media (LS). Sampling was repeated when cells reached mid-log (OD600 ~ 0.3) phase. The same sampling schedule was repeated for sulfate respiration growth following the first syntrophic growth and for second syntrophic growth following sulfate respiration.

tag: condition

value: syntrophy

tag: growth phase

value: Early Log

source_name: Dv WT and Mm coculture reference grown syntrophically to Mid Log

value: Mid Log


title: L_DM_Wt_OD-023_v_L2_DM_744-3_Tpt-2

source_name: Dv DVU0744::Tn5 and Mm coculture, 2nd syntrophic condition, Mid Log


title: L_DM_Wt_OD-023_v_L2_DM_Wt-1_Tpt-2

source_name: Dv WT and Mm coculture, 2nd syntrophic condition, Mid Log


title: L_DM_Wt_OD-023_v_L2_DM_Wt-1_Tpt-1

source_name: Dv WT and Mm coculture, 2nd syntrophic condition, Early Log


title: L_DM_Wt_OD-023_v_LS_DM_744-1_Tpt-2

source_name: Dv DVU0744::Tn5 and Mm coculture, sulfate-respiration condition, Mid Log

value: sulfate respiration


title: L_DM_Wt_OD-023_v_L2_DM_Wt-3_Tpt-2


title: L_DM_Wt_OD-023_v_LS_DM_Wt-3_Tpt-2

source_name: Dv WT and Mm coculture, sulfate-respiration condition, Mid Log


title: ΔscnAB_48H_rep2_KA1

city: HangZhou

first: TanJun

last: Wang

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Biochemistry

country: China

institute: Zhejiang University

description: SAMPLE 4

hyb_protocol: Each  Slide  was  hybridized  with  600ng  Cy3-labeled  cRNA  using  Gene  Expression   Hybridization  Kit  (Cat#5188-5242,  Agilent  technologies,  Santa  Clara,  CA,  US)  in   Hybridization  Oven  (Cat#G2545A,  Agilent  technologies,  Santa  Clara,  CA,  US),   according  to  the  manufacturer ’ s  instructions.  After  17  hours  hybridization,  slides   were  washed  in  staining  dishes  (Cat#121,  Thermo  Shandon,  Waltham,  MA,  US)  with Gene  Expression  Wash  Buffer  Kit(Cat#5188-5327,  Agilent  technologies,  Santa  Clara,   CA, US),followed the manufacturer ’ s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara,CA.US).

organism: Streptomyces chattanoogensis

label_protocol: Total  RNA  was  amplified  and  labeled  by  Low  Input  Quick  Amp  Labeling  Kit,   One-Color  (Cat#5190-2305,  Agilent  technologies,  Santa  Clara,  CA,  US),  following  the   manufacturer ’ s  instructions.  Labeled  cRNA  were  purified  by  RNeasy  mini  kit   (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Streptomyces chattanoogensis L10 were cultured at 30℃for 48H in YEME

extract_protocol: Total RNA was isolated using the RNA extract kit (QIAGEN, Germany), according to the manufacturer’s instructions, and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mycelium was collected from YEME culture by centrifugation, discard the supernatant, wash the mycelium twice by PBS buffer.

value: scnA and scnB deleted

tag: developmental stage

value: exponential phase (cultured at 30C for 48hrs)

tag: tissue

value: Mycelium


title: ΔscnAB_48H_rep1_KC2-7

description: SAMPLE 5


title: WT_48H_rep3_WE1

description: SAMPLE 3


title: ΔscnAB_48H_rep3_KC2-9

description: SAMPLE 6


title: L_DM_Wt_OD-023_v_LS_DM_Wt-1_Tpt-2


title: L_DM_Wt_OD-023_v_LS_DM_744-3_Tpt-2


title: L_DM_Wt_OD-023_v_L2_DM_Wt-3_Tpt-1


title: L_DM_Wt_OD-023_v_LS_DM_Wt-3_Tpt-1

source_name: Dv WT and Mm coculture, sulfate-respiration condition, Early Log


title: L_DM_Wt_OD-023_v_L1_DM_Wt-3_Tpt-1

source_name: Dv WT and Mm coculture, 1st syntrophic condition, Early Log


title: L_DM_Wt_OD-023_v_L1_DM_744-3_Tpt-1

source_name: Dv DVU0744::Tn5 and Mm coculture, 1st syntrophic condition, Early Log


title: L_DM_Wt_OD-023_v_LS_DM_744-1_Tpt-1

source_name: Dv DVU0744::Tn5 and Mm coculture, sulfate-respiration condition, Early Log


title: L_DM_Wt_OD-023_v_L2_DM_744-3_Tpt-1


title: L_DM_Wt_OD-023_v_L1_DM_Wt-1_Tpt-2

source_name: Dv WT and Mm coculture, 1st syntrophic condition, Mid Log


title: WT_48H_rep2_WD1

description: SAMPLE 2


title: L_DM_Wt_OD-023_v_LS_DM_Wt-1_Tpt-1


title: L_DM_Wt_OD-023_v_LS_DM_744-3_Tpt-1


title: L_DM_Wt_OD-023_v_L1_DM_Wt-3_Tpt-2


title: Normal human BM monocytes 4

hyb_protocol: Biotin labeled cDNA was hybridized to GeneChip Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA) using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

scan_protocol: Hybridized arrays were washed using the GeneChip Fluidics Station 450 (Affymetrix) using protocol 001 and scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Exon array data were processed using an R/Bioconductor package, as previously described (Okoniewski and Miller, 2008). Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm (Irizarry et al., 2003). Probesets annotated in Ensembl human genome build 54 as “exonic” and not “multitarget”, with their expression values, were extracted in CSV file format. The CSV file was used to calculate “gene level summaries”, which represent the mean expression of all exonic probesets mapping to each Ensembl annotated gene (see metadata file).
HuEx-1_0-st-v2.r2.pgf

source_name: Flow sorted normal primary human monocytes

label_protocol: cDNA amplification of RNA was with the Ovation Pico WTA System (NuGEN) and a WT-Ovation Exon Module kit (NuGEN) was used to generate sense transcript cDNA. The cDNA was then fragmented and biotin labeled using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

value: BM monocytes


title: L_DM_Wt_OD-023_v_L1_DM_744-1_Tpt-1


title: Normal human BM monocytes 2


title: WT_48H_rep1_WC2

description: SAMPLE 1


title: L_DM_Wt_OD-023_v_L1_DM_Wt-1_Tpt-1


title: Normal human BM monocytes 1


title: Normal human BM neutrophils 4

source_name: Flow sorted normal primary human neutrophils

value: BM neutrophils


title: L_DM_Wt_OD-023_v_L1_DM_744-1_Tpt-2

source_name: Dv DVU0744::Tn5 and Mm coculture, 1st syntrophic condition, Mid Log


title: Normal human BM neutrophils 1


title: Normal human BM neutrophils 2


title: L_DM_Wt_OD-023_v_L1_DM_744-3_Tpt-2


title: Normal human BM monocytes 3


title: AN3-CA at C1, biological rep1

first: yeonui

last: Kwak

address: Room#2224,Building L2, Hwarangno 14-gil 5, Seongbuk-Gu

institute: Korea Institute of Science and Technology

description:
AN3-CA_C1-1
gene expression data from the activated state with aFGF stimulation. i.e, after activation of Fibroblast growth factor receptors

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-array Analysis(RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: AN3-CA cells after 18 hr treatment of DMSO in the presence of aFGF stimulus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: AN3-CA cells that were suspended in DMEM supplemented with 10% FBS, 100U/mL penicllin, and 100ug/mL streptomycin, were plated into six  60mm dishes, followed by 18-hr incubation with different conditions C0-C2

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

treatment_protocol: AN3-CA cells were cultured in 6mm dishes for 24hrs, and media was changed to serum-free media treated with DMSO control or cotreated with 300nM AZD4547(or 0.5% DMSO)  in the presence of aFGF(10ng/mL). After 18hr treatment, total RNA was extracted.

value: endometrium

tag: cell line

value: endometrial cancer cell line AN3-CA

value: DMSO in the presence of aFGF stimulus


title: AN3-CA at C1, biological rep2

description:
AN3-CA_C1-2
gene expression data from the activated state with aFGF stimulation. i.e, after activation of Fibroblast growth factor receptors


title: Parasitized by Pales pavida vs control in hemocytes_2

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

institute: National Institute of Agrobiological Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with AgilentExpression Wash Buffer Kit.

scan_protocol: Scanned on an Agilent G2565BA scanner with 5 μm scan resolution.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.1)

organism: Bombyx mori

source_name: control

label_protocol: Total RNA (500 ng each for Cy3 and Cy5) was processed to cRNA using Agilent Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from the tissues using TRIzol reagent (Invitrogen) following manufacturer’s protocol.

treatment_protocol: Day 0 of 5th instar silkworm larvae were offered to the tachnid flies (D. inconspicuoides, E. japonica) in transparent ventilated cages. Silkworm-fly interactions were monitored to ensure only 3 eggs were laid per host. Parasitization  by P. pavida was achieved by inoculating three eggs on to the silkworm’s artificial diet. Parasitized larvae were maintained at 25oC and after 5 days, hemocytes and fat body were collected for extracting RNA.

value: Day 0 of 5th instar silkworm larvae

value: hemocytes

source_name: Parasitized by Pales pavida


title: AN3-CA at C0, biological rep1

description:
AN3-CA_C0-1
gene expression data in the basal state without aFGF stimulation. i.e, before activiation of Fibroblast growth factor receptors

source_name: AN3-CA cells after 18 hr treatment of DMSO in the absence of aFGF stimulus

value: DMSO


title: Parasitized by Pales pavida vs control in hemocytes_1


title: Parasitized by Pales pavida vs control in fat body

value: fat body


title: Dhh1-GFP_YEP_total_rep3

status: Public on Sep 16 2015

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: Detection with S9.6 antibody & Cy3 secondary

hyb_protocol: 5ug of Total RNA or 200ng of IP RNA was fragmented and hybridized to the array according to manufactuers directions for 17h at 65ºC. Arrays were washed in 6x SSPE and 0.005% N-lauronylsarcosine for 1min at RT and then in 0.6x SSPE, 0.005% N-lauronylsarcosine for 1min at 30ºC. Arrays were then incubated in 3 ng/ml S9.6 antibody (ATCC clone HB-8730) for 1hr at 25ºC and washed 4x in SSPE, 0.01% Tween. Primary antibody was detected with a Cy3 conjugated anti-mouse secondary antibody incubated at 6 ng/ml for 1hr at 25ºC followed by 4 washes in SSPE, 0.01% Tween. Prior to scanning, slides were dried by centrifugation 5 minutes at 600 rpm.

scan_protocol: Agilent G2565CA Microarray Scanner and Feature Extraction software

data_processing: Background signal for each hybridization was measured based on the median intensity from 1,573 array features that do not hybridize to a yeast transcript and subtracted from all features. Signals were then log transformed and pairs of total RNA and IP RNA arrays were normalized by cyclic loess as implemented in the Limma Bioconductor package (. Normalized signals for transcript replicate probes were averaged and transcript levels were thresholded to remove low intensity, high variability signal or high intensity, near saturation signal.

label: No label

organism: Saccharomyces cerevisiae

source_name: Dhh1-GFP total RNA, -Glucose 30min

label_protocol: RNA was not labeled prior to hybridization. RNA:DNA hybrids were detected using the S9.6 monoclonal antibody (ATCC clone HB-8730)

growth_protocol: Cells were grown in 2L rich media (YPD) to log phase (OD600 = 1.0) at which point they were either quickly collected or changed to media without glucose (YEP) for 30 minutes at which point they were collected. Cells were collected by filtration, concentrated into conical tubes by a low speed, 500g centrifugation and flash frozen in liquid nitrogen.

extract_protocol: RNA was extracted from total and IP fractions in parallel. To each fraction an equal volume of 1% SDS, 10mM Tris (pH 7.5) and 1mM EDTA was added followed by a total equal volume of acid phenol (pH 4) and incubated at 65ºC for 60min. Phenol:chloroform extraction was performed on the acqueous phase followed by a precipitation in cold ethanol. Pellets were washed in 70% ethanol, resuspended in TE and stored at -80ºC.

treatment_protocol: Cell pellets were lysed by grinding in a Retsch PM-100 planetary ball mill and pellets and resultant pulvarized cell powder were maintained at -80ºC for the duration of lysis. Cell powder was resuspended in a buffer optimized to maintain RNP complexes and subjected to an anti-GFP immunoprecipitation (IP) protocol using anti-GFP conjugated to magnetic beads. RNA was eluted from a fraction of the beads after the IP by incubating the beads in 1% SDS, 30 mM Hepes (pH 7.4), with protease and RNase inhibitors for 30 minutes at room temperature. RNA was extracted from a small amount of the resuspended cell powder set aside prior to IP (Total RNA) as well as from the fraction eluted off the beads after the IP (IP RNA).

value: YAD49, Dhh1-GFP

value: -glucose

tag: molecule type

value: total RNA


title: Dhh1-GFP_YEP_total_rep2


title: Parasitized by Pales pavida vs control in silkgland dye swap

value: silkgland


title: Parasitized by Exorista japonica vs control in hemocytes

source_name: Parasitized by Exorista japonica


title: Parasitized by Pales pavida vs control in hemocytes dye swap_2


title: Parasitized by Pales pavida vs control in hemocytes dye swap_1


title: Dhh1-GFP_YEP_total_rep1


title: Dhh1-GFP_YEP_total_rep4


title: Parasitized by Drino inconspicuoides vs control in hemocytes dye swap

source_name: Parasitized by Drino inconspicuoides


title: Dhh1-GFP_YEP_ip_rep4

source_name: Dhh1-GFP IP RNA, -Glucose 30 min

value: IP RNA


title: Parasitized by Drino inconspicuoides vs control in hemocytes


title: Parasitized by Pales pavida vs control in fat body dye swap


title: Dhh1-GFP_YEP_ip_rep1


title: Dhh1-GFP_YEP_ip_rep2


title: Parasitized by Exorista japonica vs control in hemocytes dye swap


title: Dhh1-GFP_YEP_ip_rep3


title: Dhh1-GFP_YPD_ip_rep2

source_name: Dhh1-GFP IP RNA, +Glucose

value: +glucose


title: Dhh1-GFP_YPD_total_rep2

source_name: Dhh1-GFP total RNA, +Glucose


title: Dhh1-GFP_YPD_total_rep1


title: GFP_total_rep1

source_name: GFP total RNA, -Glucose

value: YAD393, pTEF-GFP(S65T)


title: GFP_ip_rep1

source_name: GFP IP RNA, -Glucose


title: Normal human BM neutrophils 3


title: 452 EXPT: THP-1 DUST EXTRACT 0.1 3H_2

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Genome Studio v2011.1

label_protocol: Standard Illumina

growth_protocol: Cells were grown in serum or complete medium to ~ 80% confluency.

extract_protocol: RNA was isolated using TRI-Reagent.

treatment_protocol: Cells were serum-straved overnight (16-18 h) and then treated with medium alone or poultry dust. extract


title: 452 EXPT: BEAS2B DUST ETRACT 0.25 1H_1

value: BEAS 2B


title: 452 EXPT: THP-1 CONTROL_2


title: 452 EXPT: THP-1 CONTROL_1


title: 452 EXPT: BEAS2B CONTROL_1


title: 452 EXPT: BEAS2B DUST ETRACT 0.25 3H_1


title: 452 EXPT: THP-1 DUST EXTRACT 0.1 1H_1


title: 452 EXPT: BEAS2B CONTROL_2


title: 452 EXPT: THP-1 DUST EXTRACT 0.1 1H_2


title: 391 EXPT: BEAS2B CONTROL_2


title: 452 EXPT: THP-1 DUST EXTRACT 0.1 3H_1


title: 452 EXPT: BEAS2B DUST ETRACT 0.25 1H_2


title: L_DM_Wt_OD-023_v_L2_DM_744-1_Tpt-2

source_name: Dv DVU0744::Tn5 and Mm coculture, 2nd syntrophic condition, Mid Log

value: syntrophy

value: Mid Log

source_name: Dv WT and Mm coculture reference grown syntrophically to Mid Log

value: Wild type


title: 391 EXPT: BEAS2B DUST EXTRACT 0.25 1H_1


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 29

city: Toronto

first: Sean

middle: Eoin

last: Egan

state: Ontario

address: 686 Bay Street, Room 15-9704

department: Program in Developmental and Stem Cell Biology

country: Canada

institute: The Hosital for Sick Children

description: Gene expression data from R26(H1047R/+);KRas(G12D/+);CreT Poorly differentiated carcinoma

hyb_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek software and absolute expression values were obtained

source_name: Mouse Mammary Tumor B3579 1L

growth_protocol: Samples from independent primary mammary tumors from KRas(G12D/+);CreT, R26(H1047R/+);KRas(G12D/+);CreT, and MMTV-Neu models were harvested into RNAlater and frozen at -80

extract_protocol: Total RNA was extracted with Qiagen RNAeasy kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

value: Primary Mammary Tumor

tag: pathology

value: Poorly differentiated carcinoma


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 27

scan_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

source_name: Mouse Mammary Tumor B3338 5R


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 31

source_name: Mouse Mammary Tumor B3779 4L

label_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: 391 EXPT: BEAS2B CONTROL_1


title: 391 EXPT: BEAS2B DUST EXTRACT 0.25 6H_1


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 28

source_name: Mouse Mammary Tumor B3343 5R


title: 391 EXPT: A549 DUST EXTRACT 0.25 6H_2


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 19

description: Gene expression data from R26(H1047R/+);KRas(G12D/+);CreT Complex adenocarcinoma

source_name: Mouse Mammary Tumor B3431 3L

value: Complex adenocarcinoma


title: AN3-CA at C0, biological rep2

city: Seoul

description:
AN3-CA_C0-2
gene expression data in the basal state without aFGF stimulation. i.e, before activiation of Fibroblast growth factor receptors

value: endometrium

value: endometrial cancer cell line AN3-CA


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 23

source_name: Mouse Mammary Tumor B3343 4R


title: 391 EXPT: A549 DUST EXTRACT 0.25 1H_2


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 18

source_name: Mouse Mammary Tumor B3343 3L


title: 391 EXPT: BEAS2B DUST EXTRACT 0.25 6H_2


title: KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 15

description: Gene expression data from KRas(G12D/+);CreT Complex adenocarcinoma

source_name: Mouse Mammary Tumor B4592 3L


title: 391 EXPT: A549 DUST EXTRACT 0.25 1H_1


title: 391 EXPT: A549 DUST EXTRACT 0.25 6H_1


title: SCM2

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

description: Dye-swap replicate of biological replicate 2

hyb_protocol: Hybridization mixture and washing procedure were prepared and performed according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.

scan_protocol: Array slides were immediately scanned at 5 μm resolution using an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) with the autoscan feature from the default setting. TIFF images were analysed by software  Gene Pix Pro 6.0.

data_processing: FlexArray software version 1.6.3 (http://genomequebec.mcgill.ca/) was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Sus scrofa

label_protocol: 200ng of total RNA with adding of external RNA spike-in was used for aRNA synthesis according to the manual provided by Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) for two-color processing. Antisense RNA (aRNA) labelling with Cy3 and Cy5 was performed according to the kit under ozone free environmental chamber.

extract_protocol: Direct-zol™ RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) was used for RNA extraction with in-column DNase treatment to remove DNA.

treatment_protocol:
Sows were euthanized at day 30 of gestation and embryos were recovered for DNA and RNA extraction.
Embryos were collected at Day 30 post-ovulation from sows submitted to  three different treatment groups such as C group; n= 6,  FE group ; n=3 and SE group; n=3 group. Three males and three females D30E were pooled separately from each sow in each treatment group ending up with 24 distinct biological replicates.

value: Day 30 embryo

tag: Sex

value: male

tag: treatment group

value: Control