title: daf-2(e1370)_on Control RNAi_Fraction2_group4


title: T7-SAGE transcriptome of cleft epithelial cells of embryonic mouse salivary glands

status: Public on Jun 17 2010

type: SAGE

anchor: NlaIII

city: Suita

first: Takayoshi

last: Sakai

state: Osaka

address: 1-8 Yamadaoka

department: Oral-Facial Disorders

country: Japan

institute: Osaka Univ Grad Sch Dent

description: Mus musculus embryonic submandibular salivary glands from embryonic day 12.5 embryos were laser microdissected to isolate epithelial cells from regions adjacent to forming clefts or from the peripheral end bud region.  The isolated region-specific samples were then subjected to T7-SAGE transcriptome analysis.

data_processing: SAGE 2000 software from http://www.sagenet.org

molecule: total RNA

organism: Mus musculus

source_name: Embryonic submandibular salivary gland

extract_protocol: Protocol as published in: Sakai T, Larsen M, Yamada KM. Microanalysis of gene expression in tissues using T7-SAGE: serial analysis of gene expression after high-fidelity T7-based RNA amplification. Curr Protoc Cell Biol. 2002 Nov;Chapter 19:Unit 19.3.

tag: cell type

value: laser microdissected epithelial cells adjacent to cleft of embryonic salivary gland


title: daf-2(e1370)_on Control RNAi_Fraction1_group4

type: RNA

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

country: USA

institute: Buck Institute for Research on Aging

description: The control RNAi is ‘empty’ vector L4440 RNAi feeding vector plasmid (1999 Firelab vector kit) transformed HT115(DE3).  The empty vector RNAi was used as the food source for our array experiment.

hyb_protocol: Hybridization was carried out using a Lucidea Slide Pro machine. All wash solutions were made using Ambion Pre-Made Solutions (Nuclease-free Water, 20% SDS and 20XSSC) and filtered sterilized with a 500ml, 0.22uM filter unit. All C. elegans arrays from the Washington University in St. Louis Genomic Sequencing Center arrive pretreated; no blocking step was necessary. To prepare the aRNA sample for hybridization, the labeled aRNA sample was brought up to a volume with Nuclease-free water and Dextran Sulfate/ Hybe Buffer mix was added to the aRNA sample. The mixture was warmed to 50oC. Using a Hamilton syringe the labeled sample was loaded into the Lucidea chamber. The hybridization program was run for 16hrs at 42oC with a cycling speed of 10µl/sec every 30 minutes. The array was then washed at a speed of 50ul/sec with the following wash buffers in succession: 2X SSC +0.1% SDS (warmed to 42oC for 1st wash solution), 2X SSC, 0.2XSSC, and a 95% ethanol drying step.

scan_protocol: The array slide was loaded into a Perkin Elmer Scan Array Express 2-Laser Scanner. A QuickScan was performed, which scans the first 3-4 rows of the array. A surface calibration was then performed using the Spot Report control spots on the array. After surface calibration, the PMT and POW settings were adjusted to have the control spots match in intensity. The array was then scanned. Images were quantitated using GenePix 5.0 software package which overlays the GAL file (provided by the Washington University in St. Louis Genomic Sequencing Center) on the two array TIFF images (Cy3 and Cy5).  Pixels per spot, per channel were counted by the software and a gpr file was generated.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003)

organism: Caenorhabditis elegans

source_name: Wild type (N2)_pooled mix

label_protocol: Each sample, including the reference pool, was subjected to two rounds of linear amplification using the MessageAmp kit from Ambion for the first round and the Amino Allyl Message Amplification II kit from Ambion for the second round. After amplification, each sample was assessed for yield and overall quality via Bioanlayzer (Agilent) and Nanodrop. Samples that did not pass QC were discarded, and not used in the final analysis. Post Labeling Reactive Dyes (Cy3 and Cy5) from Amersham were used in conjunction with the reagents and protocol from the Ambion Amino Allyl Message Amplification II Kit to label the aRNA.  5ug of aRNA plus aRNA spike were labeled (aRNA Spike: equal amounts of the 10 Stratagene Spot Repot Spikes were combined and then amplified 1 round, to make an aRNA Spot Report Spike mix). All controls were labeled with the Cy3 dye and all experimental samples were labeled with the Cy5 dye. The Cy3 and Cy5 sample pairs were combined and purified.

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

tag: strain

tag: tissue

value: whole organism

source_name: daf-2(e1370) on Control RNAi

tag: fraction

value: Fraction 1 - ribosomal and free RNA

tag: group

value: Group 4


title: small RNA_chip_F7_leaf2

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description:
small RNA
A total of 12 hybridization intensities in three biological replicates per a species were obtained, and log values of hybridization intensities were used for normalization and statistical analysis.

hyb_protocol: After prehybridization, the chip was hybridized to small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C. Posthybridization washes were done sequentially once each with 6XSSPET and 3XSSPET and twice with 0.5XSSPET.

scan_protocol: Hybridized chip was scanned using a Genepix 4000B (Molecular Devices, Sunnyvale, CA), and data were extracted using software provided by CombiMatrix (Mukilteo, WA).

data_processing: If the hybridization intensities of a miRNA were not significantly higher than the background signals, the miRNA was considered to be not expressed.

organism: Arabidopsis arenosa x Arabidopsis thaliana

source_name: Young Leaf

label_protocol: Small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C.

extract_protocol: Small RNAs were enriched from total RNA using mirRVana isolation kit (Ambion, Austin, TX).

tag: sample type

value: F7 progeny of A. thaliana and A. arenosa hybrid

value: Young Leaf


title: LV_DCM

city: Baltimore

first: Nikolai

middle: M

last: Soldatov

address: 5600 Nathan Shock Drive

institute: National Institute on Aging, NIH

description: Labeling, hybridization, and data extraction were performed at the Gene Expression and Genomics Unit, National Institute on Aging, NIH (Baltimore, MD).

hyb_protocol: The Cy3-labeled cDNA (5 μg) was incubated at 98ºC for 2 min in the presence of 10X blocking agent (Agilent Technologies, Wilmington, DE) and mixed with 2X HI-RPM Hybridization Buffer (Agilent).  Samples were loaded on to 4x44K custom Human Ion Channel SpliceArrays (ExonHit Therapeutics, Gaithersburg, MD) and hybridized for 17 h at 65º C using Agilent Sure-Hyb chambers. Arrays were washed first at room temperature with Agilent’s Gene Expression Wash Buffer #1 and then at elevated temperature (~31º C) using Gene Expression Wash Buffer #2.

scan_protocol: The arrays were scanned using Agilent’s Microarray Scanner (Model #G2565A).

data_processing: The images were analyzed using Agilent’s Feature Extraction Software v9.5 and processed by ExonHit Therapeutics using Partek Genomics Suite. The data headings present in the raw data output (.txt) files and the algorithms used to calculate the values are explained in the Feature Extraction manual.

organism: Homo sapiens

source_name: Human ventricular myocytes

label_protocol: Each sample was incubated in the dark at 37ºC for 1 h with 120 U Terminal Deoxynucleotidyl Transferase Recombinant Enzyme and Terminal Transferase Buffer (Promega, Madison, WI), and 2.4 nmol Cy-3 dUTP (Amersham Biosciences, Little Chalfont Buckinghamshire, England).  The samples were then denatured at 70ºC for 10 min and purified by Microcon YM-30 Filter device.

extract_protocol: Cellular RNA was extracted using the PicoPure RNA isolation kit (Arcturus). The 3'-end non-bias proportional RNA amplification was carried out using the TransPlex™ Whole Transcriptome Amplification kit (Rubicon Genomics, Ann Arbor, MI).

treatment_protocol: Left ventricle tissue samples were obtained from material resected from the explanted heart of an dilated cardiomyopathy patient undergoing cardiac transplantation according to routine clinical protocols. Samples were washed in 4°C saline, immersed in Tissue-Tek OCT compound (EMS, Hatfield, Pennsylvania), flash frozen in liquid nitrogen and stored at -80˚C until use. Ventricular myocytes were identified in serial 7-8-µm thick cryostat sections using the RNA-preserving quick (10 s) staining by Eosin Y (Sigma-Aldrich, St. Louis, MO). Cells were laser-capture microdissected with the Arcturus PixCell II system and collected.

tag: disease state

value: dilated cardiomyopathy

value: left ventricle

value: myocytes

tag: age

value: 41 yo

tag: gender

value: male

tag: tissue status

value: freshly resected tissue sample


title: small RNA_chip_F7_leaf1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group3

source_name: daf-2(e1370) Heat Shocked on Control RNAi

value: Fraction 2 - light polysomes

value: Group 3

tag: treatment

value: Heat Shocked


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group3


title: chronic.3

city: Hefei

first: Wei

last: Lan

state: Anhui

address: 96#, Jinzhai Road

department: School of Life Science

country: China

institute: University of Science and Technology of China

hyb_protocol: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 20ul hybridization buffer containing 3 x SSC, 0.2% SDS and 15% formamide. The arrays were hybridized at 42℃ overnight and washed with two consecutive solutions (0.2% SDS, 2xSSC at 42C for 4 min, and 0.2xSSC for 4 min at room temperature).

scan_protocol: The miRNA arrays were scanned with a confocal LuxScan 10K/A scanner at CapitalBio Corp.

data_processing: The images obtained were analyzed using LuxScan 3.0 image analysis package. The raw miRNA expression data were quantile-normalized to correct for between-sample variations.

label_protocol: 4ug miRNA from each sample was labeled with 500ng 5'-phosphate-cytidyl-uridyl-cy3 with 2 units T4 RNA ligase. The labeling reaction was performed at 4℃ for 2 hours.

extract_protocol: Total RNA from the three cell models was isolated using Trizol reagent. Low-molecular-weight RNA (<200nt) was isolated from 20 ug total RNA using the PEG method (Thomson, J.M., Parker, J., Perou, C.M., Hammond, S. M., 2004, Nat Methods 1, 47-53).

tag: cell line


title: chronic.1


title: daf-2(e1370)_on Control RNAi_Fraction2_group3


title: chronic.4


title: chronic.2


title: small RNA_chip_A_arenosa_leaf9

organism: Arabidopsis arenosa

value: Arabidopsis arenosa


title: daf-2(e1370)_on Control RNAi_Fraction3_group3

value: Fraction 3 - heavy polysomes


title: small RNA_chip_A_arenosa_leaf8


title: small RNA_chip_A_arenosa_leaf6


title: daf-2(e1370)_on Control RNAi_Fraction1_group3


title: acute.4

source_name: HepG2 transfected with a 1.3 full-length HBV genome


title: small RNA_chip_A_arenosa_leaf5


title: daf-2(e1370)_on Control RNAi_Fraction3_group2

value: Group 2


title: small RNA_chip_A_arenosa_leaf4


title: daf-2(e1370)_on Control RNAi_Fraction2_group2

value: whole organism


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group1

value: Group 1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group2

value: Fraction 1 - ribosomal and free RNA


title: small RNA_chip_A_arenosa_leaf7


title: daf-2(e1370)_on Control RNAi_Fraction1_group2


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction3_group4

source_name: Wild type (N2) Heat Shocked on Control RNAi

value: Group 4


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group2


title: daf-2(e1370)_on Control RNAi_Fraction2_group1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group1


title: daf-2(e1370)_on Control RNAi_Fraction1_group1


title: small RNA_chip_A_arenosa_leaf3

value: Young Leaf


title: normal.4


title: normal.3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction1_group4


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction2_group4


title: Wild type (N2)_on Control RNAi_Fraction3_group4

source_name: Wild type (N2) on Control RNAi


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group2


title: acute.2

value: HepG2 transfected with a 1.3 full-length HBV genome


title: acute.3


title: small RNA_chip_A_arenosa_leaf1


title: Wild type (N2)_on Control RNAi_Fraction1_group4


title: acute.1


title: normal.1


title: daf-2(e1370)_on Control RNAi_Fraction3_group1


title: small RNA_chip_A_thaliana_leaf9

organism: Arabidopsis thaliana

value: Arabidopsis thaliana 4x


title: Erythrocytes Poly(I:C) reverse 3

city: Cerdanyola del Vallès

first: Davínia

middle: Morera

last: Capdevila

address: Edifici Biociències, ala sud

department: Biologia cel.lular, Immunologia i Fisiologia

country: Spain

institute: Universitat Autònoma de Barcelona

description: Erythrocytes control vs Poly(I:C) treated. Dye swap reverse. Biological replicate 3 of 3

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, stimulated and control cDNA were labeled with Cy3 and Cy5 respectively, and for the second array dye assignment was reversed. All samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA fraction V, 5x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2x SSC (3 min) and 0.2x SSC (3 min) and hybridized overnight in cocktail containing 1.3x Denhardt’s, 3x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning and image processing was performed with AlphaScan 3.0 Microarray Scanner (Alpha Innotech). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing:
The measurements in spots were filtered by criteria I/B = 3 and (I-B)/(SI+SB) = 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalizations was performed using AI_2200 Alpha Innotech Alpha Ease Software version number v.3.1.2.
To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes.

organism: Oncorhynchus mykiss

source_name: Primary culture isolated trout erythrocytes

label_protocol: cDNA Cy5 or Cy3 Labelling with Cy5-dCTP or Cy3-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

growth_protocol: Trout erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 18 ºC and 5% CO2.

extract_protocol: RNA was extracted with Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) following the manufacture instructions with minor modifications. The RNA was stored at -80 ºC in ethanol 70% until use.

treatment_protocol: Erythrocytes were stimulated with LPS from E. coli (serotype 026:B6, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, each treatment had their own control plate. All culture plates were incubated for 24h.

value: Primary culture erythrocytes

value: control


title: normal.2


title: small RNA_chip_A_arenosa_leaf2


title: small RNA_chip_A_thaliana_leaf8


title: small RNA_chip_A_thaliana_leaf7


title: Erythrocytes Poly(I:C) reverse 2

description: Erythrocytes control vs Poly(I:C) treated. Dye swap reverse. Biological replicate 2 of 3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction3_group3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction2_group3


title: Wild type (N2)_on Control RNAi_Fraction2_group4


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction1_group3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction3_group2


title: Wild type (N2)_on Control RNAi_Fraction2_group3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction2_group2


title: Erythrocytes Poly(I:C) direct 2

description: Erythrocytes control vs Poly(I:C) treated. Dye swap direct. Biological replicate 2 of 3


title: Wild type (N2)_on Control RNAi_Fraction3_group2


title: Wild type (N2)_on Control RNAi_Fraction1_group3


title: Erythrocytes Poly(I:C) reverse 1

description: Erythrocytes control vs Poly(I:C) treated. Dye swap reverse. Biological replicate 1 of 3


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction1_group2


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction3_group1


title: Wild type (N2)_on Control RNAi_Fraction3_group3


title: Erythrocytes Poly(I:C) direct 3

description: Erythrocytes control vs Poly(I:C) treated. Dye swap direct. Biological replicate 3 of 3


title: Wild type (N2)_on Control RNAi_Fraction1_group2


title: small RNA_chip_A_thaliana_leaf6


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction1_group1


title: Wild type (N2)_on Control RNAi_Fraction2_group2


title: small RNA_chip_A_thaliana_leaf4


title: Erythrocytes Poly(I:C) direct 1

description: Erythrocytes control vs Poly(I:C) treated. Dye swap direct. Biological replicate 1 of 3


title: small RNA_chip_A_thaliana_leaf5


title: Wild type (N2)_on Control RNAi_Fraction2_group1


title: small RNA_chip_A_thaliana_leaf3


title: Wild type (N2)_on Control RNAi_Fraction3_group1


title: small RNA_chip_A_thaliana_leaf1


title: Erythrocytes LPS reverse 3

description: Erythrocytes control vs LPS treated. Dye swap reverse. Biological replicate 3 of 3

value: lipopolysaccharide (LPS)


title: Erythrocytes LPS reverse 2

description: Erythrocytes control vs LPS treated. Dye swap reverse. Biological replicate 2 of 3


title: Erythrocytes LPS direct 3

description: Erythrocytes control vs LPS treated. Dye swap direct. Biological replicate 3 of 3


title: small RNA_chip_A_thaliana_leaf2


title: Erythrocytes LPS direct 1

description: Erythrocytes control vs LPS treated. Dye swap direct. Biological replicate 1 of 3


title: PBMCs rep.13

city: Hamburg

first: Christoph

last: Ogrodowczyk

address: Falkenried 94

department: Institute for Neural Signal Transduction

country: Germany

institute: ZMNH

hyb_protocol: Oligonucleotides were spotted on poly-L lysine coated glass slides using a spotting robot (TECAN) and then crosslinked by uv irradiation. Each oligonucleotide occurred four times in each array. Blocking, hybridization and staining were as described (Battaglia et al., 2000; Diehl et al., 2001). Hybridization chambers were from Monterey Industries.

scan_protocol: Fluorescent images of hybridized microarrays were obtained using an arrayWoRx microarray scanner (Applied Precision).Images were analyzed with ScanAlyze (http://rana.lbl.gov/EisenSoftware.htm).

data_processing:
Fluorescence ratios were stored in a custom data base, and normalized data were extracted from this data base for further analysis with Array Assist (Stratagene). Array data were filtered by selecting genes that were present on at least 75% of the arrays, had a spot diameter of ≥ 25 μm and a signal of ≥ 200 in each channel. Genes were represented four times on the arrays.
Normalization and analysis was performed using Excel. Intensities of activated cells were divided by those of unactivated cells. The ratio was normalized against the ratio derived by control genes (aeI, CE11, DD1B).

source_name: PBMCs

label_protocol: Fluorescent cDNA probes for stimulated and unstimulated samples were prepared by reverse transcription of mRNAs with aminoallyl-dUTP followed by Cy3 and Cy5 labelling according to the manufacturer’s protocol (Invitrogen; Amersham Pharmacia Biotech).

extract_protocol: Trizol RNA isolation following manufectureres guidlines

treatment_protocol: Buffy coats were separated in Ficoll gradient, supernatant was discarded and layer containing PBMCs carefully collected

value: PBMCs

tag: activation status

value: unactivated

value: activated


title: Wild type (N2)_on Control RNAi_Fraction1_group1


title: PBMCs rep.14


title: Erythrocytes LPS reverse 1

description: Erythrocytes control vs LPS treated. Dye swap reverse. Biological replicate 1 of 3


title: PBMCs rep.5


title: PBMCs rep.7


title: PBMCs rep.1


title: PBMCs rep.8


title: PBMCs rep.10


title: PBMCs rep.9


title: PBMCs rep.4


title: Wild type (N2)_Heat Shocked_on Control RNAi_Fraction2_group1

value: Fraction 2 - light polysomes

value: Heat Shocked


title: PBMCs rep.6


title: PBMCs rep.2


title: PBMCs rep.3


title: Day 7 replicate 4 dyeswap

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: Technical replicate 2 of 2, Biological replicate 4 of 4. Control pool untreated.

hyb_protocol: The mix was overlaid with a coverslip and hybridised at 47°C for 12–24 h in a humidified atmosphere to Sanger Hver 1.3.1 cDNA microarrays (as part of the CRUK/LICR Microarray Consortium, contain 9930 sequence-validated cDNA clones representing approximately 6000 unique sequences). Microarrays were washed sequentially with 2x SSC, 0.1x SSC/0.1% SDS, and 0.1x SSC and were air-dried by briefly spinning in a centrifuge to remove excess liquid.

scan_protocol: Fluorescent images of hybridised microarrays were captured using a ScanArray Express 3.0 scanner (Perkin Elmer) and ScanArray software

data_processing: background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data was lowess normalized using the bioconductor package limma

source_name: Reference Control

label_protocol: Cy3- and Cy5-labelled probes were coprecipitated with 16µg human Cot 1 DNA (Invitrogen) and 8µg polyA (Sigma). The pellets were resuspended in 8 µl of H2O and 40 µl of hybridization buffer (5 X SSC, 6 X Denhardt’s solution, 60mM Tris HCl pH7.6, 0.12% sarkosyl, 48% formamide) boiled for 5 min and cooled at room temperature for 10 min.

growth_protocol: Total RNA extracted using Qiagen RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions

extract_protocol: Total RNA (100ug), spiked with bacterial-RNA mixture for control was used to prepare direct Cy3- and Cy5-labelled first-strand cDNA probes using a single-base anchored oligo dT17 primer (Sigma) and Superscript II reverse transcriptase (Invitrogen). Unincorporated nucleotides were removed using QIAquick PCR purification kit (QIAGEN)

treatment_protocol: All animals received E2. On day 0, animals were randomly allocated to tamoxifen (2.5 mg released over 60 days, Innovative Research of America) or E2 -only control groups

value: ZR75-1 xenograft


title: PBMCs rep.12


title: PBMCs rep.11


title: Erythrocytes LPS direct 2

description: Erythrocytes control vs LPS treated. Dye swap direct. Biological replicate 2 of 3


title: Day 14 replicate 1 dyeswap

description: Technical replicate 2 of 2, Biological replicate 1 of 2. Control pool untreated.


title: Day 14 replicate 1

description: Technical replicate 1 of 2, Biological replicate 1 of 2. Control pool untreated.


title: Day 7 replicate 2 dyeswap

description: Technical replicate 2 of 2, Biological replicate 2 of 4. Control pool untreated.


title: Day 7 replicate 4

description: Technical replicate 1 of 2, Biological replicate 4 of 4. Control pool untreated.


title: Day 7 replicate 3

description: Technical replicate 1 of 2, Biological replicate 3 of 4. Control pool untreated.


title: Day 7 replicate 3 dyeswap

description: Technical replicate 2 of 2, Biological replicate 3 of 4. Control pool untreated.


title: Day 14 replicate 2

description: Technical replicate 1 of 2, Biological replicate 2 of 2. Control pool untreated.


title: Day 7 replicate 2

description: Technical replicate 1 of 2, Biological replicate 2 of 4. Control pool untreated.


title: Day 14 replicate 2 dyeswap

description: Technical replicate 2 of 2, Biological replicate 2 of 2. Control pool untreated.


title: Day 7 replicate 1 dyeswap

description: Technical replicate 2 of 2, Biological replicate 1 of 4. Control pool untreated.


title: Day 4 replicate 1 dyeswap

description: Technical replicate 2 of 2, Biological replicate 1 of 5. Control pool untreated.


title: Day 4 replicate 3

description: Technical replicate 1 of 2, Biological replicate 3 of 5. Control pool untreated.


title: Day 4 replicate 2 dyeswap

description: Technical replicate 2 of 2, Biological replicate 2 of 5. Control pool untreated.


title: Day 4 replicate 4 dyeswap

description: Technical replicate 2 of 2, Biological replicate 4 of 5. Control pool untreated.


title: Day 4 replicate 5

description: Technical replicate 1 of 2, Biological replicate 5 of 5. Control pool untreated.


title: Day 2 replicate 2 dyeswap


title: Day 4 replicate 1

description: Technical replicate 1 of 2, Biological replicate 1 of 5. Control pool untreated.


title: Day 7 replicate 1

description: Technical replicate 1 of 2, Biological replicate 1 of 4. Control pool untreated.


title: Day 4 replicate 5 dyeswap

description: Technical replicate 2 of 2, Biological replicate 5 of 5. Control pool untreated.


title: T47D-pHUSH-Elf5-shRNA_progesterone_doxycycline_rep3

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

country: Australia

institute: Garvan Institute of Medical Research

description:
Cells pooled from three wells
HuGene-1_0-st-v1.r3.pgf

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: raw data from the 9 CEL files was normalised in a single batch using Affymetrix Power Tools, on all probesets, using the PLIER algorithm. Specifically, the plier-gcbg-sketch analysis option was used. Data has been log-base-2 transformed. Aray Quality Control was carried out in the Expression Console (Affymetrix), and NUSE and RLE signal boxplots were very similar across arrays. Differential expression was assessed using limma and the Benjamini-Yekutieli correction for multiple testing

label: biotin

label_protocol: standard Affymetrix protocol

growth_protocol: T47D-EcoR and T47D-pHUSH-Elf5-shRNA cells were cultured as monolayers in RPMI 1640 medium (Invitrogen, VIC, Au) supplemented with 10% Tet System Approved Fetal Bovine Serum (Clontech, Palo Alto, CA, USA), 10 mg/mL insulin (Actrapid, Novo Nordisk, Baulkham Hills, NSW, Australia), 50 μg/ml penicillin/streptomycin (Invitrogen) and 20 μg/ml Gentamicin (Pfizer, Bentley, WA, Au). T47D-pHUSH-Elf5-shRNA cells were maintained in the presence of Puromycin at a concentration of 2μg/ml.

extract_protocol: Total RNA was extracted using the RNeasy Minikit (Qiagen, Doncaster, Vic., Australia) as described in the manufacturer’s instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: T47D-EcoR cells for retroviral infection were generated as described in (1). A retroviral single vector system that enables Doxycycline regulated RNAi (pHUSH) expression was obtained from Genentech Inc., San Francisco, USA (2), and the shRNA Elf5-pHUSH constructs were generated according to the methods detailed (2). Elf5 repression was achieved by treatment with Doxycycline at 0.1 μg/ml (Clontech, Palo Alto, CA, USA). Progesterone stimulation experiments involved treating cells with 10 nM ORG2058 (Amersham Australia).                                                                                1. Musgrove EA, Hunter L-JK, Lee CSL, Swarbrick A, Hui R, Sutherland RL 2001 Cyclin D1 overexpression induces progestin resistance in T-47D breast cancer cells despite p27-Kip1 association with cyclin E-Cdk2. J Biol Chem 276:47675-47693                                                                                2. Gray D, Hoeflich K, Peng L, Gu Z, Gogineni A, Murray L, Eby M, Kljavin N, Seshagiri S, Cole M, Davis D 2007 pHUSH: a single vector system for conditional gene expression. BMC Biotechnol 7:61

value: 10nM progesterone (ORG2058 [Amersham Australia]) and 0.1μg/ml doxycycline (Clontech, Palo Alto, CA, USA) for four days


title: Day 4 replicate 2

description: Technical replicate 1 of 2, Biological replicate 2 of 5. Control pool untreated.


title: Day 1 replicate 2 dyeswap

description: Technical replicate 2 of 2, Biological replicate 2 of 4. Control pool untreated.


title: Day 1 replicate 4 dyeswap

description: Technical replicate 2 of 2, Biological replicate 4 of 4. Control pool untreated.


title: T47D-pHUSH-Elf5-shRNA_progesterone_doxycycline_rep1


title: Day 1 replicate 3 dyeswap

description: Technical replicate 2 of 2, Biological replicate 3 of 4. Control pool untreated.


title: T47D-pHUSH-Elf5-shRNA_ethanol vehicle only_rep3

source_name: T47D-pHUSH-Elf5-shRNA, ethanol vehicle only

value: Ethanol vehicle only


title: T47D-pHUSH-Elf5-shRNA_progesterone_rep2

source_name: T47D-pHUSH-Elf5-shRNA, progesterone

value: 10nM progesterone (ORG2058 [Amersham Australia]) for four days

value: T47D-pHUSH-Elf5-shRNA, progesterone


title: Day 2 replicate 2

description: Technical replicate 1 of 2, Biological replicate 2 of 2. Control pool untreated.


title: Day 1 replicate 4

description: Technical replicate 1 of 2, Biological replicate 4 of 4. Control pool untreated.


title: Day 2 replicate 1

description: Technical replicate 1 of 2, Biological replicate 1 of 2. Control pool untreated.


title: Day 2 replicate 1 dyeswap

description: Technical replicate 2 of 2, Biological replicate 1 of 2. Control pool untreated.


title: T47D-pHUSH-Elf5-shRNA_progesterone_doxycycline_rep2


title: Day 1 replicate 1


title: T47D-pHUSH-Elf5-shRNA_progesterone_rep3


title: T47D-pHUSH-Elf5-shRNA_ethanol vehicle only_rep2

value: T47D-pHUSH-Elf5-shRNA, ethanol vehicle only


title: T47D-pHUSH-Elf5-shRNA_progesterone_rep1


title: Day 1 replicate 3

description: Technical replicate 1 of 2, Biological replicate 3 of 4. Control pool untreated.


title: enteropathy associated T cell lymphoma

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: reference DNA is pooled DNA from the blood of 18 healthy individuals

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. Values represent normalized log2 ratio (Cy3/Cy5).

molecule: genomic DNA

source_name: T cell lymphoma CV406-2705

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA from a cell pelet of the T cell lymphoma (>10exp6) was isolated by using the Wizard Genomic DNA Purification Kit (Promega, A1120)

tag: disease stage

value: T cell lymphoma

source_name: female reference DNA

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: reference


title: T47D-pHUSH-Elf5-shRNA_ethanol vehicle only_rep1


title: Day 1 replicate 2

description: Technical replicate 1 of 2, Biological replicate 2 of 4. Control pool untreated.


title: Day 1 replicate 1 dyeswap

description: Technical replicate 2 of 2, Biological replicate 1 of 4. Control pool untreated.


title: Sle1a R3

status: Public on Jun 16 2010

city: Oklahoma City

first: Igor

last: Dozmorov

state: OK

address: 825 NE 13th Street

department: Arthritis & Immunology

institute: OMRF

description: exp B1a replicate 3

hyb_protocol: hybridization to Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: scanned on an Affymetrix GeneChip Analysis System GC3000 7G.

data_processing:
All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Two-step normalization procedure (1). The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”.     The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.

source_name: CD4+ T cells from B6.Sle1a.1 mice

label_protocol: cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

extract_protocol: RNA was extracted with the Qiagen RNeasy Micro Kit.

tag: genotype/variation

value: female

value: experimental


title: Sle1a R2

description: exp B1a replicate 2


title: Sle1a R1

description: exp B1a replicate 1


title: Sle1a R4

description: exp B1a replicate 4


title: B6 Control R4

description: control B1a replicate 4

source_name: CD4+ T cells from B6 mice

value: wild type

value: control


title: NDR1KO_Tumorcells_05

city: Basel

first: Brian

middle: Arthur

last: Hemmings

address: Maulbeerstrasse 66

department: Growth Control

country: Switzerland

institute: Friedrich-Miescher Institute

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: raw values were GC-RMA normalized using the gcrma package from R/Bioconductor; for analysis with Expressionist, normalized expression values were transformed into linear space (i.e. 2^x) using R. Log2 transformed VALUES are included in the data table below.

source_name: Thymus, treated (ENU;100mg/kg), Tumor

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

extract_protocol: Total RNA was extracted using Trizol and further purified using RNeasy kit (Qiagen) according to the manufacturer's instructions.

value: Thymus

value: N-ethyl-N-nitrosourea (ENU) 100mg/kg

tag: disease status

value: tumor


title: mRNA of IBT-HGG072, Anaplastic PXA, 7 years

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

description: Gene expression data from pediatric HGG patient.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: brain of 7 years

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

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

tag: disease

value: Anaplastic PXA

value: 7 years


title: B6 Control R3

description: control B1a replicate 3


title: NDR1KO_Tumorcells_06


title: NDR1KO_Tumorcells_07


title: NDR1KO_Tumorcells_04


title: NDR1HT_Tumorcells_07


title: NDR1KO_Tumorcells_02

value: male


title: B6 Control R2

description: control B1a replicate 2


title: mRNA of OT-HGG029, Anaplastic Oligodendroglioma, 10.7 years

source_name: brain of 10.7 years

value: Anaplastic Oligodendroglioma

value: 10.7 years


title: B6 Control R1

description: control B1a replicate 1


title: mRNA of OT-HGG155, Anaplastic Oligodendroglioma, 6.2 years

source_name: brain of 6.2 years

value: 6.2 years


title: mRNA of IBT-HGG081, Anaplastic PXA, 19 years

source_name: brain of 19 years

value: 19 years


title: NDR1KO_Tumorcells_03


title: NDR1KO_Tumorcells_01


title: NDR1HT_Tumorcells_06


title: mRNA of AA-HGG080, Anaplastic Astrocytoma, 12 years

source_name: brain of 12 years

value: Anaplastic Astrocytoma

value: 12 years


title: mRNA of OT-HGG021, Anaplastic Oligodendroglioma, 22.7 years

source_name: brain of 22.7 years

value: 22.7 years


title: mRNA of OT-HGG069, Anaplastic Oligodendroglioma, 1.6 years

source_name: brain of 1.6 years

value: 1.6 years


title: mRNA of OT-HGG007, Anaplastic Oligodendroglioma, 16.7 years, Post-ALL

source_name: brain of 16.7 years

value: 16.7 years; Other:Post-ALL


title: NDR1HT_Tumorcells_04


title: mRNA of AA-HGG082, Anaplastic Astrocytoma, 5 years

source_name: brain of 5 years

value: 5 years


title: NDR1HT_Tumorcells_05

value: female


title: mRNA of AA-HGG073, Anaplastic Astrocytoma, 6 years

source_name: brain of 6 years

value: 6 years


title: NDR1HT_Tumorcells_01

value: Thymus

value: N-ethyl-N-nitrosourea (ENU) 100mg/kg


title: mRNA of AA-HGG063, Anaplastic Astrocytoma, 2 years

source_name: brain of 2 years

value: 2 years


title: NDR1HT_Tumorcells_03

value: tumor


title: mRNA of AA-HGG097, Anaplastic Astrocytoma, 9 years

source_name: brain of 9 years

value: 9 years


title: NDR1WT_Tumorcells_05

value: NDR1+/+ (wild type)


title: mRNA of AA-HGG079, Anaplastic Astrocytoma, 23 years, Post-ALL

source_name: brain of 23 years

value: 23 years; Other:Post-ALL


title: mRNA of AA-HGG060, Anaplastic Astrocytoma, 2.75 years

source_name: brain of 2.75 years

value: 2.75 years


title: mRNA of AA-HGG045, Anaplastic Astrocytoma, 5 days old

source_name: brain of 5 days old

value: 5 days old


title: NDR1HT_Tumorcells_02


title: NDR1WT_Tumorcells_04


title: NDR1WT_Tumorcells_03


title: mRNA of AA-HGG024, Anaplastic Astrocytoma, 7.5 years

source_name: brain of 7.5 years

value: Anaplastic Astrocytoma

value: 7.5 years


title: mRNA of GBV-HGG048, Glioblastoma variant, 3.6 years

source_name: brain of 3.6 years

value: Glioblastoma variant

value: 3.6 years


title: mRNA of GBV-HGG160, Glioblastoma variant, 14.3 years

source_name: brain of 14.3 years

value: 14.3 years


title: NDR1WT_Tumorcells_02

source_name: Thymus, treated (ENU;100mg/kg), Tumor


title: NDR1KO_Thymocytes_M_02

source_name: Thymus, untreated, normal

value: male

value: normal


title: NDR1KO_Thymocytes_M_01


title: mRNA of GBV-HGG050, Glioblastoma variant, 9.2 years, Post-ALL

source_name: brain of 9.2 years

value: 9.2 years; Other:Post-ALL


title: mRNA of GBV-HGG083, Glioblastoma variant, 8 years

source_name: brain of 8 years

value: 8 years


title: NDR1HT_Thymocytes_M_02

value: Thymus


title: NDR1WT_Tumorcells_01

value: female

value: N-ethyl-N-nitrosourea (ENU) 100mg/kg


title: mRNA of GBM-HGG162, Glioblastoma, 13.5 years

source_name: brain of 13.5 years

value: Glioblastoma

value: 13.5 years


title: NDR1KO_Thymocytes_F_01


title: NDR1HT_Thymocytes_F_02


title: mRNA of GBM-HGG157, Glioblastoma, 14.8 years

source_name: brain of 14.8 years

value: 14.8 years


title: mRNA of GBM-HGG154, Glioblastoma, 3.8 years

source_name: brain of 3.8 years

value: 3.8 years


title: mRNA of GBM-HGG158, Glioblastoma, 10.7 years

source_name: brain of 10.7 years

value: 10.7 years


title: NDR1HT_Thymocytes_F_01


title: NDR1WT_Thymocytes_M_02

value: NDR1+/+ (wild type)


title: NDR1WT_Thymocytes_F_01


title: NDR1WT_Thymocytes_M_01


title: mRNA of GBM-HGG085, Glioblastoma, 10 years

source_name: brain of 10 years

value: 10 years


title: mRNA of GBM-HGG140, Glioblastoma, 3 years

source_name: brain of 3 years

value: 3 years


title: sorted-R5 cells, repl 2

city: Cambridge

first: Shilpa

middle: Manohar

last: Hattangadi

state: MA

address: 9 Cambridge Center

department: Lodish Lab

institute: Whitehead Institute (WIBR)

description: Expression profiling for each successive stage of erythroid development

hyb_protocol: Labeled samples were hybed onto the Affymetrix GeneChip Mouse Genome 430 2.0 microarray (mouse 3' whole genome mouse microarray).

scan_protocol: Slides were scanned on the GeneChip scanner 3000 7G and then processed with the Affymetrix Gene Chip Operating System (GCOS) v 1.1.1

data_processing:
Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method (trimmed mean set to 150), then the replicates were compared to each other using Limma linear-fit modeling using Bioconductor and R.
Additional supplementary file (available on the Series record) contains Log2ratio of each stage against R2 (first erythroid-committed, erythroid-specific stage) or MAS 5.0 signal intensity are included (as labelled in matrix). P-values for significant differences between stage and control stage (R2) are included as well.

source_name: E14.5 C57/Bl6 fetal livers

label_protocol: Reverse-transcribed with Invitrogen Superscript II and then labeled with Cy5 using the Micromax ASAP labeling kit.

growth_protocol: Freshly isolated fetal livers were stained with anti-Ter119 and CD71 antibodies and FACS-sorted for each successive stage of development (Zhang, et al. Blood. 2003 Dec 1; 102(12):3938-46).

extract_protocol: Each set of replicates was extracted on the same date, using the Qiagen RNAeasy Micro Kit for smaller numbers of cells.

treatment_protocol: Cells were sorted into Qiagen RNA easy extraction buffer directly and then frozen for extraction on a later date.

tag: cell type

value: fetal liver cells

tag: developmental stage

tag: differentiation stage


title: NDR1WT_Thymocytes_F_02

tag: tissue

tag: strain


title: NDR1HT_Thymocytes_M_01


title: mRNA of GBM-HGG153, Glioblastoma, 13.1 years

source_name: brain of 13.1 years

value: 13.1 years


title: mRNA of GBM-HGG159, Glioblastoma, 13.1 years, Post-medulloblastoma

value: 13.1 years; Other:Post-medulloblastoma


title: mRNA of GBM-HGG077, Glioblastoma, 4 years, Diffuse pontine glioma

source_name: brain of 4 years

value: 4 years; Other:Diffuse pontine glioma


title: mRNA of GBM-HGG146, Glioblastoma, 12 years

source_name: brain of 12 years

value: 12 years


title: mRNA of GBM-HGG093, Glioblastoma, 11.25 years

source_name: brain of 11.25 years

value: 11.25 years


title: mRNA of GBM-HGG145, Glioblastoma, 14 years

source_name: brain of 14 years

value: 14 years


title: mRNA of GBM-HGG144, Glioblastoma, 19 years

source_name: brain of 19 years

value: 19 years


title: mRNA of GBM-HGG084, Glioblastoma, 1 years

source_name: brain of 1 years

value: 1 years


title: sorted-R4 cells, repl 1


title: sorted-R2 cells, repl 2


title: mRNA of GBM-HGG059, Glioblastoma, 14.3 years

source_name: brain of 14.3 years

value: Glioblastoma

value: 14.3 years


title: sorted-R3 cells, repl 3


title: sorted-R2 cells, repl 3


title: sorted-R1 cells, repl 2


title: sorted-R3 cells, repl 2


title: granule neuron precursors, biological replicate 2

description: Gene expression data from purified granule neuron precursors.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array Mouse 430 v2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: cerebellum of six days old pups

value: cerebellum

value: 6 days old

value: granule neuron precursor cells

tag: genome/variation


title: mRNA of GBM-HGG056, Glioblastoma, 4.7 years

source_name: brain of 4.7 years

value: 4.7 years


title: mRNA of GBM-HGG031, Glioblastoma, 1.2 years

source_name: brain of 1.2 years

value: 1.2 years


title: mRNA of GBM-HGG023, Glioblastoma, 9.9 years

source_name: brain of 9.9 years

value: 9.9 years


title: mRNA of GBM-HGG046, Glioblastoma, 1 month years

source_name: brain of 1 month years

value: 1 month years


title: mRNA of GBM-HGG061, Glioblastoma, 14.08 years

source_name: brain of 14.08 years

value: 14.08 years


title: sorted-R2 cells, repl 1

value: fetal liver cells


title: mRNA of GBM-HGG054, Glioblastoma, 10.9 years

source_name: brain of 10.9 years

value: 10.9 years


title: mRNA of GBM-HGG028, Glioblastoma, 19.8 years, Post-Germinoma

source_name: brain of 19.8 years

value: 19.8 years; Other:Post-Germinoma


title: sorted-R5 cells, repl 1

source_name: E14.5 C57/Bl6 fetal livers


title: sorted-R3 cells, repl 1


title: Atoh1 engineered Medulloblastoma, biological replicate 1

description: Gene expression data from Atoh1 engineered Medulloblastoma, replicate 1.

source_name: mouse cerebellum

tag: disease model

value: medulloblastoma


title: mRNA of GBM-HGG026, Glioblastoma, 19.8 years, Post-ALL

tag: age

value: 19.8 years; Other:Post-ALL


title: granule neuron precursors, biological replicate 1


title: Gli1 engineered Medulloblastoma, biological replicate 3

description: Gene expression data from Gli1 engineered Medulloblastoma, replicate 3.


title: Gli1 engineered Medulloblastoma, biological replicate 2

description: Gene expression data from Gli1 engineered Medulloblastoma, replicate 2.


title: granule neuron precursors, biological replicate 3


title: sorted-R1 cells, repl 1


title: mRNA of GBM-HGG047, Glioblastoma, 7.3 years, Diffuse pontine glioma

source_name: brain of 7.3 years

value: 7.3 years; Other:Diffuse pontine glioma


title: Atoh1 engineered Medulloblastoma, biological replicate 3

description: Gene expression data from Atoh1 engineered Medulloblastoma, replicate 3.


title: mRNA of GBM-HGG020, Glioblastoma, 13.8 years, Post-ALL

source_name: brain of 13.8 years

value: 13.8 years; Other:Post-ALL


title: Atoh1 engineered Medulloblastoma, biological replicate 2

description: Gene expression data from Atoh1 engineered Medulloblastoma, replicate 2.


title: mRNA of GBM-HGG010, Glioblastoma, 17.8 years

source_name: brain of 17.8 years

value: Glioblastoma

value: 17.8 years


title: mRNA of GBM-HGG014, Glioblastoma, 7 years

source_name: brain of 7 years

value: 7 years


title: mRNA of GBM-HGG008, Glioblastoma, 16.5 years

source_name: brain of 16.5 years

value: 16.5 years


title: Gli1 engineered Medulloblastoma, biological replicate 1

description: Gene expression data from Gli1 engineered Medulloblastoma, replicate 1.

value: cerebellum


title: mRNA of GBM-HGG005, Glioblastoma, 16.5 years


title: mRNA of GBM-HGG006, Glioblastoma, 6.3 years

source_name: brain of 6.3 years

value: 6.3 years


title: NDR1KO_Thymocytes_F_02

source_name: Thymus, untreated, normal

value: Thymus

tag: gender

value: female

value: normal


description: Gene expression data from GNPs expressing Math1 DNA-binding mutant treated with Tamoxifen for 4 hours.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array 430 v2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

tag: treatment group

value: Tamoxifen for 4 hrs

value: granule neuron progenitor cells

value: expressing Math1 DNA-binding mutant (negative control)


description: Gene expression data from GNPs expressing Math1-ER treated with Tamoxifen for 8 hours.

value: Tamoxifen for 8 hrs

value: expressing Math1-ER


title: mRNA of GBM-HGG001, Glioblastoma, 5.8 years

source_name: brain of 5.8 years

value: 5.8 years


description: Gene expression data from GNPs expressing Math1-ER with no Tamoxifen treatment.

value: no tamoxifen

value: medulloblastoma


title: mRNA of GBM-HGG151, Glioblastoma, 8.9 years, Post-Ependymoma

source_name: brain of 8.9 years

value: Glioblastoma

value: 8.9 years; Other:Post-Ependymoma


title: MS25_5B_MEK5_220307

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: MEK5D-transfected HUVEC

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA)

data_processing: Fluorescent signals were detected by the GeneChip Scanner 3000 and recorded and computed by GeneChip Operating Software (GCOS) version 1.4 (Affymetrix)

label: SAGE

source_name: HUVEC monolayer

value: HUVEC


title: MS25_5A_LV_220307

description: empty vector transfected HUVEC

scan_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA)


title: MS25_4B_MEK5_220307

description: MEK5D-transfected HUVEC

label_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA)


description: Gene expression data from GNPs expressing Math1-ER treated with Tamoxifen for 24 hours.

value: Tamoxifen for 24 hrs


title: MS25_4A_LV_220307

description: empty vector-transfected HUVEC

extract_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA)


description: Gene expression data from GNPs expressing Math1-ER treated with Tamoxifen for 4 hours.

value: cerebellum


title: mRNA of GBM-HGG027, Glioblastoma, 9.7 years, Post-ALL

source_name: brain of 9.7 years

value: 9.7 years; Other:Post-ALL


title: K12 12H replicate dye-swap 3

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

description: Macrophages treated with PGN K12 12H Replicate 6

hyb_protocol: The slides were pretreated with 1% BSA fraction V, 5× SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60°C in a cocktail containing 1.3 × Denhardt's, 3 × SSC 0.3% SDS, 0.67 μg/μL polyade- nylate and 1.4 μg/μL yeast tRNA. After hybridization slides were washed at room temperature in 0.5 × SSC and 0.1% SDS (15 min), 0.5 × SSC and 0.01% SDS (15 min), and twice in 0.06 × SSC (2 and 1 min, respectively).

scan_protocol: Scanning was performed with Alphascan (High Performance Dual-Laser Scanner for Microaray Slides from Alpha innotech) and images were processed with VisionLite (ThermoSpectronic). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Kuopiochip and Dyaswapanalized software were used.

source_name: Primary culture Trout hematopoietic macrophages

label_protocol: Microarray analyses were conduced in pooled samples with equal inputs of RNA from twelve individuals (3 pool for condition and time point 1, 6, and 12 h). A dye swap design of hybridization was applied. In analyses of infected immune cells, the non-infected cells were used as a control. Each sample was analyzed with two slides. The control and test samples (15 μg RNA in each) were labelled with respectively Cy3-dUTP and Cy5-dUTP (Amersham Pharmacia, Little Chalfont, UK) for the first slide and dye assignment was reversed for the second slide (test and control cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed). The fluorescent dyes were incorporated in cDNA using the SuperScript III reverse transcriptase (Invitrogen) and Oligo (dt) primer (promega). The cDNA synthesis was performed at 50°C for 2 hours in a 20 μL reaction volume, following RNA degradation with 0.2 M NaOH at 37°C for 15 min and alkaline neutralization with 0.6 M Hepes. Labelled cDNA was purified with Microcon YM30 (Milli- pore, Bedford, MA, USA).

growth_protocol: The experimental protocols used for head kidney isolation have been reviewed and approved by the Ethics and Animal Welfare Committee of the Universitat Autonoma de Barcelona, Spain. After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.

extract_protocol: Total RNA was extracted from cell cultures using 1 mL of TriReagent (Molecular Research Center) per well cell culture, following the manufacturer’s instructions. Quantification was carried out with a Nanodrop1000 (Thermo Scientific) and the quality of the RNA was checked with a Bioanalyzer (Agilent technologies). Total RNA (2 μg) was used to synthesize cDNA with SuperScript III Transcriptase (Invitrogen) and oligo-dT primer (Promega).

treatment_protocol: Macrophages isolated of twelve animals were stimulated with PGN O111:B4 and K12 E. coli strain. The stimulated macrophages was conduced since 1, 6 until 12 h. The individuals RNA was grouped in three pools by each time point (1, 6, and 12 h) and PGNs (N = 72 animals). The transcriptomic response was analyzed by microarray assay, and divided in three experimental time points named early (1 h), median (6 h) and late stage (12 h). The analysis was carried out with common gen expressed between the three pools. The q-PCR validation assay was conduced whit mRNA of individuals in the late stage.

value: cultured hematopoietic macrophages

tag: treatment

value: DAP-PGN from K12

tag: time

tag: sample type

value: untreated uninfected


title: K12 12H replicate dye-swap 1

description: Macrophages treated with PGN K12 12H Replicate 4

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.


title: MS25_3B_MEK5_220307

description: MEK5D-transfected HUVEC

tag: cell line


title: K12 6H replicate dye-swap 2

description: Macrophages treated with PGN K12 6H Replicate 5


title: genomic DNA of OT-HGG029, Anaplastic Oligodendroglioma, 10.7 years old

description: tissue from pediatric HGG patient.

hyb_protocol: Hybridizations were performed according the standard Affymetrix protocol from 250 ng genomic DNA.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA.

data_processing: The data was first analyzed with dChipSNP to extract un-normalized signal intensity.  The data was then normalized using reference normalization with selected diploid chromosomes within each sample.

source_name: brain of 10.7 years old

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k array manual 701930 Rev.3, Affymetrix).

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

value: Anaplastic Oligodendroglioma

value: 10.7 years old


title: MS25_3A_LV_220307

description: empty vector transfected HUVEC


title: K12 6H replicate dye-swap 1

description: Macrophages treated with PGN K12 6H Replicate 4


title: K12 1H replicate dye-swap 2

description: Macrophages treated with PGN K12 1H Replicate 5


title: genomic DNA of OT-HGG021, Anaplastic Oligodendroglioma, 22.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 22.7 years old

value: 22.7 years old


title: genomic DNA of IBT-HGG081, Anaplastic PXA, 19 years old

description: tissue from pediatric HGG patient.

source_name: brain of 19 years old

value: Anaplastic PXA

value: 19 years old


title: genomic DNA of AA-HGG156, Anaplastic Astrocytoma, 13.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 13.2 years old

value: Anaplastic Astrocytoma

value: 13.2 years old


title: genomic DNA of IBT-HGG072, Anaplastic PXA, 7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7 years old

value: 7 years old


title: genomic DNA of OT-HGG155, Anaplastic Oligodendroglioma, 6.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6.2 years old

value: 6.2 years old


title: genomic DNA of OT-HGG007, Anaplastic Oligodendroglioma, 16.7 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 16.7 years old

value: 16.7 years old; Other:Post-ALL


title: B4 12H replicate dye-swap 3

description: Macrophages treated with PGN B4 12H Replicate 6

value: DAP-PGN from O111:B4


title: genomic DNA of OT-HGG069, Anaplastic Oligodendroglioma, 1.6 years old

description: tissue from pediatric HGG patient.

source_name: brain of 1.6 years old

value: 1.6 years old


title: genomic DNA of AA-HGG080, Anaplastic Astrocytoma, 12 years old

description: tissue from pediatric HGG patient.

source_name: brain of 12 years old

value: 12 years old


title: genomic DNA of AA-HGG097, Anaplastic Astrocytoma, 9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 9 years old

value: 9 years old


title: genomic DNA of AA-HGG094, Anaplastic Astrocytoma, 0.42 years old

description: tissue from pediatric HGG patient.

source_name: brain of 0.42 years old

value: 0.42 years old


title: genomic DNA of AA-HGG087, Anaplastic Astrocytoma, 20 years old

description: tissue from pediatric HGG patient.

source_name: brain of 20 years old

value: 20 years old


title: genomic DNA of AA-HGG073, Anaplastic Astrocytoma, 6 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6 years old

value: 6 years old


title: B4 12H replicate dye-swap 2

description: Macrophages treated with PGN B4 12H Replicate 5

value: cultured hematopoietic macrophages

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.

value: untreated uninfected


title: K12 1H replicate dye-swap 3

description: Macrophages treated with PGN K12 1H Replicate 6

value: DAP-PGN from K12


title: genomic DNA of AA-HGG079, Anaplastic Astrocytoma, 23 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 23 years old

value: 23 years old; Other:Post-ALL


title: genomic DNA of AA-HGG060, Anaplastic Astrocytoma, 2.75 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.75 years old

value: Anaplastic Astrocytoma

value: 2.75 years old


title: B4 12H replicate dye-swap 1

description: Macrophages treated with PGN B4 12H Replicate 4


title: genomic DNA of AA-HGG082, Anaplastic Astrocytoma, 5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 5 years old

value: 5 years old


title: genomic DNA of AA-HGG063, Anaplastic Astrocytoma, 2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2 years old

value: 2 years old


title: genomic DNA of AA-HGG052, Anaplastic Astrocytoma, 8.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 8.5 years old

value: 8.5 years old


title: genomic DNA of AA-HGG045, Anaplastic Astrocytoma, 5 days old

description: tissue from pediatric HGG patient.

source_name: brain of 5 days old

value: 5 days old


title: K12 1H replicate dye-swap 1

description: Macrophages treated with PGN K12 1H Replicate 4

source_name: Primary culture Trout hematopoietic macrophages


title: K12 6H replicate dye-swap 3

description: Macrophages treated with PGN K12 6H Replicate 6


title: B4 6H replicate dye-swap 1

description: Macrophages treated with PGN B4 6H Replicate 4

value: DAP-PGN from O111:B4


title: B4 6H replicate dye-swap 2

description: Macrophages treated with PGN B4 6H Replicate 5


title: B4 6H replicate dye-swap 3

description: Macrophages treated with PGN B4 6H Replicate 6


description: tissue from pediatric HGG patient.

value: Anaplastic Oligodendroglioma

value: 1.6 years old


title: K12 12H replicate dye-swap 2

description: Macrophages treated with PGN K12 12H Replicate 5


title: genomic DNA of IBT-HGG081, Anaplastic PXA, 19 years old

description: tissue from pediatric HGG patient.

source_name: brain of 19 years old

value: Anaplastic PXA

value: 19 years old


title: genomic DNA of GBV-HGG160, Glioblastoma variant, 14.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.3 years old

value: Glioblastoma variant

value: 14.3 years old


description: tissue from pediatric HGG patient.

source_name: brain of 6.2 years old

value: 6.2 years old


title: B4 1H replicate dye-swap 2

description: Macrophages treated with PGN B4 1H Replicate 5

value: cultured hematopoietic macrophages

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.

value: untreated uninfected


title: K12 12H replicate 3

description: Macrophages treated with PGN k12 12H Replicate 3

value: DAP-PGN from K12


title: B4 1H replicate dye-swap 3

description: Macrophages treated with PGN B4 1H Replicate 6


title: B4 1H replicate dye-swap 1

description: Macrophages treated with PGN B4 1H Replicate 4


title: genomic DNA of GBV-HGG055, Glioblastoma variant, 8.1 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 8.1 years old

value: 8.1 years old; Other:Post-ALL


title: K12 12H replicate 2

description: Macrophages treated with PGN K12 12H Replicate 2


title: K12 12H replicate 1

description: Macrophages treated with PGN K12 12H Replicate 1


description: tissue from pediatric HGG patient.

source_name: brain of 16.7 years old

value: 16.7 years old; Other:Post-ALL


title: genomic DNA of IBT-HGG072, Anaplastic PXA, 7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7 years old

value: 7 years old


title: genomic DNA of AA-HGG156, Anaplastic Astrocytoma, 13.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 13.2 years old

value: Anaplastic Astrocytoma

value: 13.2 years old


description: tissue from pediatric HGG patient.

source_name: brain of 12 years old

value: 12 years old


title: genomic DNA of GBV-HGG083, Glioblastoma variant, 8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 8 years old

value: 8 years old


description: tissue from pediatric HGG patient.

value: 5 years old


title: genomic DNA of GBV-HGG048, Glioblastoma variant, 3.6 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3.6 years old

value: 3.6 years old


title: K12 6H replicate 3

description: Macrophages treated with PGN K12 6H Replicate 3


title: genomic DNA of GBM-HGG158, Glioblastoma, 10.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 10.7 years old

value: Glioblastoma

value: 10.7 years old


title: genomic DNA of GBM-HGG162, Glioblastoma, 13.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 13.5 years old

value: 13.5 years old


description: tissue from pediatric HGG patient.

value: 2 years old


title: genomic DNA of AA-HGG094, Anaplastic Astrocytoma, 0.42 years old

description: tissue from pediatric HGG patient.

source_name: brain of 0.42 years old

value: 0.42 years old


title: genomic DNA of GBV-HGG050, Glioblastoma variant, 9.2 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 9.2 years old

value: Glioblastoma variant

value: 9.2 years old; Other:Post-ALL


title: genomic DNA of GBM-HGG159, Glioblastoma, 13.1 years old, Post-medulloblastoma

description: tissue from pediatric HGG patient.

source_name: brain of 13.1 years old

value: 13.1 years old; Other:Post-medulloblastoma


title: genomic DNA of AA-HGG024, Anaplastic Astrocytoma, 7.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7.5 years old

value: 7.5 years old


title: K12 6H replicate 2

description: Macrophages treated with PGN K12 6H Replicate 2

source_name: Primary culture Trout hematopoietic macrophages

value: cultured hematopoietic macrophages

value: DAP-PGN from K12

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.

value: untreated uninfected


title: K12 6H replicate 1

description: Macrophages treated with PGN K12 6H Replicate 1


title: genomic DNA of OT-HGG021, Anaplastic Oligodendroglioma, 22.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 22.7 years old

value: Anaplastic Oligodendroglioma

value: 22.7 years old


title: genomic DNA of AA-HGG087, Anaplastic Astrocytoma, 20 years old

description: tissue from pediatric HGG patient.

source_name: brain of 20 years old

value: Anaplastic Astrocytoma

value: 20 years old


title: genomic DNA of GBM-HGG154, Glioblastoma, 3.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3.8 years old

value: Glioblastoma

value: 3.8 years old


title: K12 1H replicate 3

description: Macrophages treated with PGN K12 1H Replicate 3


title: genomic DNA of AA-HGG079, Anaplastic Astrocytoma, 23 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 23 years old

value: 23 years old; Other:Post-ALL


title: genomic DNA of GBV-HGG004, Glioblastoma variant, 10.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 10.2 years old

value: 10.2 years old


title: genomic DNA of GBM-HGG157, Glioblastoma, 14.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.8 years old

value: 14.8 years old


title: genomic DNA of AA-HGG097, Anaplastic Astrocytoma, 9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 9 years old

value: 9 years old


title: genomic DNA of AA-HGG045, Anaplastic Astrocytoma, 5 days old

description: tissue from pediatric HGG patient.

source_name: brain of 5 days old

value: 5 days old


title: genomic DNA of AA-HGG060, Anaplastic Astrocytoma, 2.75 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.75 years old

value: 2.75 years old


title: genomic DNA of OT-HGG029, Anaplastic Oligodendroglioma, 10.7 years old

description: tissue from pediatric HGG patient.

value: 10.7 years old


title: genomic DNA of AA-HGG073, Anaplastic Astrocytoma, 6 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6 years old

value: 6 years old


title: genomic DNA of GBV-HGG048, Glioblastoma variant, 3.6 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3.6 years old

value: Glioblastoma variant

value: 3.6 years old


title: genomic DNA of GBV-HGG160, Glioblastoma variant, 14.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.3 years old

value: 14.3 years old


title: K12 1H replicate 2

description: Macrophages treated with PGN K12 1H Replicate 2

value: cultured hematopoietic macrophages

value: DAP-PGN from K12

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.

value: untreated uninfected


description: tissue from pediatric HGG patient.

value: 9.2 years old; Other:Post-ALL


title: genomic DNA of GBM-HGG153, Glioblastoma, 13.1 years old

description: tissue from pediatric HGG patient.

value: Glioblastoma

value: 13.1 years old


title: genomic DNA of GBM-HGG151, Glioblastoma, 8.9 years old, Post-Ependymoma

description: tissue from pediatric HGG patient.

source_name: brain of 8.9 years old

value: 8.9 years old; Other:Post-Ependymoma


title: genomic DNA of GBV-HGG055, Glioblastoma variant, 8.1 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 8.1 years old

value: 8.1 years old; Other:Post-ALL


title: genomic DNA of AA-HGG052, Anaplastic Astrocytoma, 8.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 8.5 years old

value: Anaplastic Astrocytoma

value: 8.5 years old


title: genomic DNA of GBM-HGG162, Glioblastoma, 13.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 13.5 years old

value: 13.5 years old


title: genomic DNA of GBM-HGG145, Glioblastoma, 14 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14 years old

value: 14 years old


title: genomic DNA of GBM-HGG159, Glioblastoma, 13.1 years old, Post-medulloblastoma

description: tissue from pediatric HGG patient.

source_name: brain of 13.1 years old

value: 13.1 years old; Other:Post-medulloblastoma


title: genomic DNA of GBV-HGG083, Glioblastoma variant, 8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 8 years old

value: Glioblastoma variant

value: 8 years old


title: genomic DNA of GBM-HGG158, Glioblastoma, 10.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 10.7 years old

value: 10.7 years old


title: genomic DNA of GBM-HGG146, Glioblastoma, 12 years old

description: tissue from pediatric HGG patient.

source_name: brain of 12 years old

value: 12 years old


title: genomic DNA of GBM-HGG154, Glioblastoma, 3.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3.8 years old

value: 3.8 years old


title: B4 12H replicate 2

description: Macrophages treated with PGN B4 12H Replicate 2

source_name: Primary culture Trout hematopoietic macrophages

value: cultured hematopoietic macrophages

value: DAP-PGN from O111:B4

value: After anesthetizing the fish in 3-aminobenzoic acid ethyl ester (0.1 g/L), animals were sacrificed and the head kidney was dissected. Trout macrophages were isolated as previously described (MacKenzie et al., 2003). Before stimulation, differentiated macrophages were incubated in serum free medium for 3 h. For stimulation, the medium of each well was removed and fresh medium containing the indicated concentrations of PGN were added and the cultures were incubated for the indicated times.


title: K12 1H replicate 1

description: Macrophages treated with PGN K12 1H Replicate 1

value: DAP-PGN from K12

value: untreated uninfected


title: B4 12H replicate 3

description: Macrophages treated with PGN B4 12H Replicate 3


title: genomic DNA of GBM-HGG144, Glioblastoma, 19 years old

description: tissue from pediatric HGG patient.

source_name: brain of 19 years old

value: Glioblastoma

value: 19 years old


title: genomic DNA of GBM-HGG157, Glioblastoma, 14.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.8 years old

value: 14.8 years old


title: B4 6H replicate 1

description: Macrophages treated with PGN B4 6H Replicate 1


title: B4 6H replicate 2

description: Macrophages treated with PGN B4 6H Replicate 2


title: B4 6H replicate 3

description: Macrophages treated with PGN B4 6H Replicate 3


title: B4 12H replicate 1

description: Macrophages treated with PGN B4 12H Replicate 1


title: genomic DNA of GBM-HGG143, Glioblastoma, 8 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

value: 8 years old; Other:Diffuse pontine glioma


title: B4 1H replicate 3

description: Macrophages treated with PGN B4 1H Replicate 3


description: tissue from pediatric HGG patient.


title: genomic DNA of GBM-HGG095, Glioblastoma, 5 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 5 years old

value: 5 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG093, Glioblastoma, 11.25 years old

description: tissue from pediatric HGG patient.

source_name: brain of 11.25 years old

value: 11.25 years old


title: genomic DNA of GBM-HGG142, Glioblastoma, 4 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4 years old

value: 4 years old


title: B4 1H replicate 2

description: Macrophages treated with PGN B4 1H Replicate 2


title: genomic DNA of GBM-HGG153, Glioblastoma, 13.1 years old

description: tissue from pediatric HGG patient.

value: 13.1 years old


title: genomic DNA of GBM-HGG085, Glioblastoma, 10 years old

description: tissue from pediatric HGG patient.

source_name: brain of 10 years old

value: 10 years old


description: tissue from pediatric HGG patient.


title: B4 1H replicate 1

description: Macrophages treated with PGN B4 1H Replicate 1


title: genomic DNA of GBM-HGG151, Glioblastoma, 8.9 years old, Post-Ependymoma

description: tissue from pediatric HGG patient.

source_name: brain of 8.9 years old

value: 8.9 years old; Other:Post-Ependymoma


title: genomic DNA of GBM-HGG098, Glioblastoma, 10 years old

description: tissue from pediatric HGG patient.


title: genomic DNA of GBM-HGG084, Glioblastoma, 1 years old

description: tissue from pediatric HGG patient.

source_name: brain of 1 years old

value: 1 years old


title: genomic DNA of GBM-HGG068, Glioblastoma, 4.8 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 4.8 years old

value: 4.8 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG077, Glioblastoma, 4 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

value: 4 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG099, Glioblastoma, 11.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 11.5 years old

value: 11.5 years old


title: genomic DNA of GBM-HGG140, Glioblastoma, 3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3 years old

value: 3 years old


title: genomic DNA of GBM-HGG066, Glioblastoma, 3.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 3.3 years old

value: 3.3 years old


title: genomic DNA of GBM-HGG067, Glioblastoma, 2.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.3 years old

value: 2.3 years old


title: genomic DNA of GBM-HGG056, Glioblastoma, 4.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4.7 years old

value: Glioblastoma

value: 4.7 years old


title: genomic DNA of GBM-HGG065, Glioblastoma, 12.75 years old

description: tissue from pediatric HGG patient.

source_name: brain of 12.75 years old

value: 12.75 years old


title: genomic DNA of GBM-HGG061, Glioblastoma, 14.08 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.08 years old

value: 14.08 years old


title: genomic DNA of GBM-HGG059, Glioblastoma, 14.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.3 years old

value: 14.3 years old


title: genomic DNA of GBM-HGG057, Glioblastoma, 12.3 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 12.3 years old

value: 12.3 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG051, Glioblastoma, 5.6 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 5.6 years old

value: 5.6 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG054, Glioblastoma, 10.9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 10.9 years old

value: 10.9 years old


title: genomic DNA of GBM-HGG044, Glioblastoma, 2.9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.9 years old

value: 2.9 years old


title: genomic DNA of GBM-HGG053, Glioblastoma, 4.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4.3 years old

value: 4.3 years old


title: genomic DNA of GBM-HGG031, Glioblastoma, 1.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 1.2 years old

value: 1.2 years old


title: genomic DNA of GBM-HGG046, Glioblastoma, 1 month years old

description: tissue from pediatric HGG patient.

source_name: brain of 1 month years old

value: 1 month years old


title: genomic DNA of GBM-HGG027, Glioblastoma, 9.7 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 9.7 years old

value: 9.7 years old; Other:Post-ALL


title: genomic DNA of GBM-HGG028, Glioblastoma, 19.8 years old, Post-Germinoma

description: tissue from pediatric HGG patient.

source_name: brain of 19.8 years old

value: 19.8 years old; Other:Post-Germinoma


title: genomic DNA of GBM-HGG043, Glioblastoma, 7.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7.7 years old

value: 7.7 years old


title: genomic DNA of GBM-HGG030, Glioblastoma, 4.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4.2 years old

value: 4.2 years old


title: genomic DNA of GBM-HGG047, Glioblastoma, 7.3 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 7.3 years old

value: 7.3 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG067, Glioblastoma, 2.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.3 years old

value: Glioblastoma

value: 2.3 years old


title: WT Chd7  replicate 1

city: Cleveland

first: Mike

middle: Paul

last: Schnetz

state: OH

address: 10900 Eulid Ave

department: Genetics

institute: Case Western Reserve University

description: replicate 1

hyb_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions

scan_protocol: Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays were scanned according to the manufacturer’s instructions.

data_processing:
Raw data were background subtracted and quantile normalized using Illumina Bead Studio software version 3
Unnormalized data are signal intensity with background subtracted; normailized data are signal intensity with background subtracted and quantile normalized using Illumina Bead Studio software

source_name: mouse ES cells

growth_protocol: ES cells were cultured using feeder MEFs according to standard procotols.

extract_protocol: Total RNA was isolated using Trizol.  The ratio of ES to feeder cells was estimated at 5:1.

value: mouse ES cells

tag: genotype/variation

value: WT Chd7


title: Acid shocked pH 2 10 min, rep 4

city: Logan

first: Jeff

last: Broadbent

state: UT

department: NFS

institute: Utah State University

hyb_protocol: Done according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using RMA as the normilization method.

organism: Lacticaseibacillus paracasei ATCC 334

source_name: Acid shocked pH 2 10 min, rep 4

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

growth_protocol: Bacterial strain and growth conditions.  L. casei ATCC ATCC 334 (American Type Culture Collection, Rockville, MD.) was maintained in a laboratory collection as a glycerol stock at -80oC and propagated at 37oC in MRS broth (Difco Laboratories, Detroit, MI).  Working cultures were prepared from stock cultures through two successive transfers (0.1% inocula) in MRS broth at 37oC for 17 h.

extract_protocol: RNA isolation.  Cell pellets were thawed at room temperature, then carefully suspended in 1 ml of lysozyme solution (20 mg/ml in TE buffer) that also contained 20 Units of mutanolysin (Sigma, St. Louis, MO) and 75 ml of rifampicin (25 mg/ml in methanol).  This mixture was incubated at 37oC for 15 minutes in a shaker incubator at 240 rpm, then total RNA was isolated from each of the cell samples using the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, CA) following procedures recommended by the vendor except for the following modifications:

treatment_protocol: Cell treatments for transcriptome studies.  Cells were grown in batch culture with pH control as described above, then six 50 ml samples were aseptically harvested into sterile 200 ml centrifuge bottles and administered one of six treatments designated as control 1 (C1), control 2 (C2), acid adapted 1 (AA1), acid adapted 2 (AA2), acid shocked (AS), and acid adapted-acid shocked (AA-AS).  For C1, cells were immediately suspended in 100 ml of RNAprotect reagent (QIAGEN, Inc., Valencia,, CA) plus 900 mL rifampicin (25 mg/ml in methanol) (Sigma, St. Louis, MO), mixed by vortex for 15 s then incubated for 10 min at room temperature.

value: ATCC 334

value: Acid shocked pH 2 10 min


title: Heterozygous Chd7 Null replicate 3

description: replicate 3

label_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions

value: Heterozygous Chd7 Null


title: Acid adapted pH 4.5, 20 min, acid shocked pH 2, 10 min, rep 4

scan_protocol: Done according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

value: Acid adapted pH 4.5, 20 min acid shocked pH 2, 10 min


title: genomic DNA of GBM-HGG056, Glioblastoma, 4.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4.7 years old

value: 4.7 years old


title: Heterozygous Chd7 Null replicate 2

description: replicate 2


title: Acid adapted pH 4.5 20 min, rep 4

source_name: Acid adapted pH 4.5 20 min, rep 4

value: Acid adapted pH 4.5 20 min


title: genomic DNA of GBM-HGG023, Glioblastoma, 9.9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 9.9 years old

value: 9.9 years old


title: Homozygous Chd7 Null replicate 1

description: replicate 1

value: Homozygous Chd7 Null


description: tissue from pediatric HGG patient.

value: 4.3 years old


title: Heterozygous Chd7 Null replicate 1

description: replicate 1


title: genomic DNA of GBM-HGG022, Glioblastoma, 14.1 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.1 years old

value: 14.1 years old


title: MMTV-Wnt/ILK tumor rep2

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

country: Canada

institute: British Columbia Cancer Agency

description: RMA expression value derived from ArrayAssist version 5.0 software; core-exon and gene level analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the CTAG Facility of the British Columbia Cancer Agency, Vancouver, BC, Canada.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix)

data_processing: CEL files were processed using ArrayAssist 5.0.  Targets showing absolute fold change greater than 1.5 and p-value < 0.05 were assessed for further investigation.

source_name: Mammary tumor tissue from double-transgenic MMTV-Wnt/ILK mouse.

label_protocol: Total RNA was extracted from snap frozen tumor tissue using the GeneChip Whole Transcript (WT) Sense Target (ST) Labeling Assay (Affymetrix) as per manufacturer’s recommendations before being hybridized to a GeneChip Mouse Exon 1.0 ST Array (Affymetrix).

growth_protocol: Nulliparous females were monitored bi-weekly for the appearance of a small palpable tumor nodule in the mammary fat pads.

extract_protocol: 1 μg of RNA  was  used  as  starting  material  and  rRNA  reduced  using  the  RiboMinus Transcriptome Isolation Kit (Invitrogen) as per Affymetrix recommendations.

value: mammary fat pad

value: female

tag: parity

value: nulliparous

tag: transgenic strain

value: MMTV-Wnt/ILK


title: Acid adapted pH 4.5 5 min, rep4

source_name: Acid adapted pH 4.5 5 min, rep4

value: Acid adapted pH 4.5 5 min


title: genomic DNA of GBM-HGG020, Glioblastoma, 13.8 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 13.8 years old

tag: disease

value: Glioblastoma

value: 13.8 years old; Other:Post-ALL


description: tissue from pediatric HGG patient.

value: 7.3 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG051, Glioblastoma, 5.6 years old, Diffuse pontine glioma

description: tissue from pediatric HGG patient.

source_name: brain of 5.6 years old

value: 5.6 years old; Other:Diffuse pontine glioma


title: genomic DNA of GBM-HGG019, Glioblastoma, 14.4 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.4 years old

value: 14.4 years old


title: Homozygous Chd7 Null replicate 2

description: replicate 2

tag: cell type

value: mouse ES cells


description: tissue from pediatric HGG patient.

source_name: brain of 1 month years old

value: 1 month years old


title: genomic DNA of GBM-HGG044, Glioblastoma, 2.9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 2.9 years old

value: 2.9 years old


title: MMTV-Wnt/ILK tumor rep3


title: genomic DNA of GBM-HGG026, Glioblastoma, 19.8 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 19.8 years old

value: 19.8 years old; Other:Post-ALL


title: genomic DNA of GBM-HGG014, Glioblastoma, 7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7 years old

value: 7 years old


title: MMTV-Wnt/ILK tumor rep4


title: MMTV-Wnt tumor rep2

source_name: Mammary tumor tissue from MMTV-Wnt-1 mouse.


title: genomic DNA of GBM-HGG010, Glioblastoma, 17.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 17.8 years old

value: 17.8 years old


title: MMTV-Wnt tumor rep3


title: Contol, no treatment, Rep4

source_name: Contol, no treatment, Rep4

value: ATCC 334

value: Contol, no treatment,


title: Acid adapted pH 4.5, 20 min, acid shocked pH 2, 10 min, rep 3

value: Acid adapted pH 4.5, 20 min acid shocked pH 2, 10 min


title: MMTV-Wnt tumor rep4

value: mammary fat pad

value: female

value: nulliparous


title: MMTV-Wnt tumor rep1


title: genomic DNA of GBM-HGG012, Glioblastoma, 11 years old

description: tissue from pediatric HGG patient.

source_name: brain of 11 years old

value: Glioblastoma

value: 11 years old


title: Contol, no treatment, Rep3

source_name: Contol, no treatment, Rep3


title: genomic DNA of GBM-HGG043, Glioblastoma, 7.7 years old

description: tissue from pediatric HGG patient.

source_name: brain of 7.7 years old

value: 7.7 years old


title: genomic DNA of GBM-HGG003, Glioblastoma, 6.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6.5 years old

value: 6.5 years old


title: genomic DNA of GBM-HGG031, Glioblastoma, 1.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 1.2 years old

value: 1.2 years old


title: genomic DNA of GBM-HGG028, Glioblastoma, 19.8 years old, Post-Germinoma

description: tissue from pediatric HGG patient.

value: 19.8 years old; Other:Post-Germinoma


title: MMTV-Wnt/ILK tumor rep1

source_name: Mammary tumor tissue from double-transgenic MMTV-Wnt/ILK mouse.

value: MMTV-Wnt/ILK


title: Acid adapted pH 4.5 5 min, rep3

source_name: Acid adapted pH 4.5 5 min, rep3

value: Acid adapted pH 4.5 5 min


title: Acid adapted pH 4.5 20 min, rep 3

source_name: Acid adapted pH 4.5 20 min, rep 3

value: Acid adapted pH 4.5 20 min


title: Acid adapted pH 4.5, 20 min, acid shocked pH 2, 10 min, rep 2


title: Acid shocked pH 2 10 min, rep 2

source_name: Acid shocked pH 2 10 min, rep 2

value: Acid shocked pH 2 10 min


title: genomic DNA of GBM-HGG030, Glioblastoma, 4.2 years old

description: tissue from pediatric HGG patient.

source_name: brain of 4.2 years old

value: 4.2 years old


title: Acid shocked pH 2 10 min, rep 3

source_name: Acid shocked pH 2 10 min, rep 3

value: ATCC 334


title: genomic DNA of GBM-HGG027, Glioblastoma, 9.7 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 9.7 years old

value: 9.7 years old; Other:Post-ALL


title: genomic DNA of GBM-HGG008, Glioblastoma, 16.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 16.5 years old

value: 16.5 years old


title: genomic DNA of GBM-HGG005, Glioblastoma, 16.5 years old

description: tissue from pediatric HGG patient.


description: tissue from pediatric HGG patient.

source_name: brain of 19.8 years old

value: 19.8 years old; Other:Post-ALL


title: L3/L4 stage whole animal reference, rep3

city: Nashville

first: William

middle: Clay

last: Spencer

address: 465 21st Ave S

department: Cell & Developmental Biology

institute: Vanderbilt University

description: RNA amplified by NuGEN WT-Pico system and labeled by FL-Ovation cDNA Biotin Module V2

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: All data was background adjusted and quantile normalized using RMA.

source_name: Caenorhabditis elegans larvae at L3/L4 stage

label_protocol: Samples were amplified and labeled using NuGEN WT-Pico amplification and FL-Ovation cDNA Biotin Module V2 kits following the manufacturer's protocol.

growth_protocol: Animals were grown at 25C on 150 mm 8P plates inoculated with the E. coli strain Na22

extract_protocol: The reference sample RNA was isolated from whole animal lysates using Trizol following the RNA isolation protocol from Watson, et al., 2008.

value: whole animal

tag: development stage


title: genomic DNA of GBM-HGG006, Glioblastoma, 6.3 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6.3 years old

value: 6.3 years old


title: Acid adapted pH 4.5 20 min, rep 2

source_name: Acid adapted pH 4.5 20 min, rep 2


description: tissue from pediatric HGG patient.

source_name: brain of 7 years old

value: Glioblastoma

value: 7 years old


title: genomic DNA of GBM-HGG019, Glioblastoma, 14.4 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.4 years old

value: 14.4 years old


title: Acid adapted pH 4.5 5 min, rep2

source_name: Acid adapted pH 4.5 5 min, rep2


title: Acid shocked pH 2 10 min, rep 1

source_name: Acid shocked pH 2 10 min, rep 1


title: L3/L4 stage whole animal reference, rep2

tag: tissue


title: genomic DNA of GBM-HGG001, Glioblastoma, 5.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 5.8 years old

value: 5.8 years old


title: Acid adapted pH 4.5, 20 min, acid shocked pH 2, 10 min, rep 1

tag: strain

value: Acid adapted pH 4.5, 20 min acid shocked pH 2, 10 min


title: Contol, no treatment, Rep2

source_name: Contol, no treatment, Rep2

value: Contol, no treatment,


title: Contol, no treatment, Rep1

source_name: Contol, no treatment, Rep1


title: genomic DNA of GBM-HGG022, Glioblastoma, 14.1 years old

description: tissue from pediatric HGG patient.

source_name: brain of 14.1 years old

value: 14.1 years old


title: Acid adapted pH 4.5 5 min, rep1

source_name: Acid adapted pH 4.5 5 min, rep1

value: Acid adapted pH 4.5 5 min


title: L3/L4 stage whole animal reference, rep1


title: genomic DNA of GBM-HGG010, Glioblastoma, 17.8 years old

description: tissue from pediatric HGG patient.

source_name: brain of 17.8 years old

value: 17.8 years old


title: PVD and OLL neurons, biological rep3

molecule: polyA RNA

extract_protocol: poly(A) RNA was isolated from PVD and OLL neurons as described (Von Stetina, et al. 2007).

value: PVD and OLL neurons


title: genomic DNA of GBM-HGG012, Glioblastoma, 11 years old

description: tissue from pediatric HGG patient.

source_name: brain of 11 years old

value: 11 years old


title: Acid adapted pH 4.5 20 min, rep 1

source_name: Acid adapted pH 4.5 20 min, rep 1

value: ATCC 334

value: Acid adapted pH 4.5 20 min


title: genomic DNA of GBM-HGG023, Glioblastoma, 9.9 years old

description: tissue from pediatric HGG patient.

source_name: brain of 9.9 years old

value: 9.9 years old


title: genomic DNA of GBM-HGG020, Glioblastoma, 13.8 years old, Post-ALL

description: tissue from pediatric HGG patient.

source_name: brain of 13.8 years old

value: 13.8 years old; Other:Post-ALL


title: patient 10, tumor liver

status: Public on Jun 15 2010

city: Tokyo

first: satow

last: reiko

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

hyb_protocol: cRNA probes were hybridized to Human Exon 1.0 ST arrays (Affymetrix), as instructed by the supplier

scan_protocol: scanned by GeneChip Scanner 3000

data_processing: Data analysis was carried out using the ArrayAssist software (Version 5.5.1, Stratagene, La Jolla, CA) and HuEx-1_0-st-v2.r2.dt1.hg18.core.mps for primary analysis.

source_name: tumor liver from patient 10

label_protocol: One µg of total RNA was converted to end-labeled cRNA using the Whole Transcript Sense Target Labeling kit (Affymetrix, Santa Clara, CA)

tag: Age

tag: Sex

value: male

tag: Diagnosis

value: hepatitis B and C


title: patient 8, tumor liver

source_name: tumor liver from patient 8

value: hepatitis C


title: patient 5, tumor liver

source_name: tumor liver from patient 5


title: patient 6, tumor liver

source_name: tumor liver from patient 6


description: tissue from pediatric HGG patient.

source_name: brain of 6.3 years old

value: Glioblastoma

tag: age

value: 6.3 years old


title: PVD and OLL neurons, biological rep2

source_name: Caenorhabditis elegans larvae at L3/L4 stage


description: tissue from pediatric HGG patient.

source_name: brain of 16.5 years old

value: 16.5 years old


title: patient 4, tumor liver

source_name: tumor liver from patient 4

value: hepatitis B


title: patient 1, tumor liver

source_name: tumor liver from patient 1


description: tissue from pediatric HGG patient.


title: patient 3, tumor liver

source_name: tumor liver from patient 3


title: patient 5, non-tumor liver

source_name: non-tumor liver from patient 5


title: PVD and OLL neurons, biological rep1


title: patient 6, non-tumor liver

source_name: non-tumor liver from patient 6


title: patient 2, non-tumor liver

source_name: non-tumor liver from patient 2


title: patient 2, tumor liver

source_name: tumor liver from patient 2


title: patient 9, non-tumor liver

source_name: non-tumor liver from patient 9


title: patient 7, non-tumor liver

source_name: non-tumor liver from patient 7


title: genomic DNA of GBM-HGG003, Glioblastoma, 6.5 years old

description: tissue from pediatric HGG patient.

source_name: brain of 6.5 years old

value: 6.5 years old


title: patient 10, non-tumor liver

source_name: non-tumor liver from patient 10


title: patient 1, non-tumor liver

source_name: non-tumor liver from patient 1


title: patient 8, non-tumor liver

source_name: non-tumor liver from patient 8


title: patient 7, tumor liver

source_name: tumor liver from patient 7


title: patient 3, non-tumor liver

source_name: non-tumor liver from patient 3


description: tissue from pediatric HGG patient.

source_name: brain of 5.8 years old

value: 5.8 years old


title: patient 4, non-tumor liver

source_name: non-tumor liver from patient 4