title: 006/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135197

source_name: post-mortem brain tissue, individual ID 006/09, cerebellar cortex


title: 021/05_cerebellar cortex

status: Public on Aug 29 2014

type: RNA

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

description: This entry supercedes previous accession: GSM1135256

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using Affymetrix Power Tools 1.14.3. Arrays were pre-processed using RMA quantile normalization with background correction. Gene level summary signals were generated by calculating the Winsorized mean (10% and 90%) of all probe sets annotated to a transcript.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: Core_adapted_from_netaffyx31
Transcript assignments are based on genome build hg19
Core exons only are included in this analysis

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: post-mortem brain tissue, individual ID 021/05, cerebellar cortex

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal labelling kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, UK). cDNA synthesis and amplification were performed using the Ambion┬«WT Expression Kit (Ambion, UK).

treatment_protocol: Not applicable.

tag: individual id

tag: brain region

value: cerebellar cortex

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

tag: Cause of death

value: pulmonary embolism

tag: Sex

value: Female

tag: age at death (in years)

tag: post-mortem interval (in hours)

tag: ancestry

value: European

tag: brain ph

tag: rin


title: 017/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135265

source_name: post-mortem brain tissue, individual ID 017/08, cerebellar cortex

value: Other


title: 020/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135273

source_name: post-mortem brain tissue, individual ID 020/07, cerebellar cortex


title: 032/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135210

source_name: post-mortem brain tissue, individual ID 032/10, cerebellar cortex

value: Male


title: 016/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135233

source_name: post-mortem brain tissue, individual ID 016/07, cerebellar cortex


title: 036/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135262

source_name: post-mortem brain tissue, individual ID 036/09, cerebellar cortex


title: 021/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135188

source_name: post-mortem brain tissue, individual ID 021/10, cerebellar cortex


title: 006/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135275

source_name: post-mortem brain tissue, individual ID 006/10, cerebellar cortex


title: 92_10_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 92_10, cerebellar cortex

value: Sun Health Research Institute

value: multisystem failure


title: 002/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135282

source_name: post-mortem brain tissue, individual ID 002/10, cerebellar cortex


title: 037/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135223

source_name: post-mortem brain tissue, individual ID 037/08, cerebellar cortex


title: 010/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135280

source_name: post-mortem brain tissue, individual ID 010/10, cerebellar cortex


title: 97_02_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 97_02, cerebellar cortex


title: 014/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135190

source_name: post-mortem brain tissue, individual ID 014/09, cerebellar cortex


title: 97_45_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 97_45, cerebellar cortex


title: 97_37_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 97_37, cerebellar cortex


title: 96_44_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 96_44, cerebellar cortex


title: 95_27_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_27, cerebellar cortex


title: 92_32_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 92_32, cerebellar cortex


title: 95_03_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_03, cerebellar cortex

value: Respiratory failure


title: 97_17_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 97_17, cerebellar cortex


title: 031/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135250

source_name: post-mortem brain tissue, individual ID 031/09, cerebellar cortex

value: Ischaemic heart disease


title: 009/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135263

source_name: post-mortem brain tissue, individual ID 009/07, cerebellar cortex


title: 030/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135251

source_name: post-mortem brain tissue, individual ID 030/09, cerebellar cortex


title: 035/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135241

source_name: post-mortem brain tissue, individual ID 035/06, cerebellar cortex


title: 032/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135270

source_name: post-mortem brain tissue, individual ID 032/09, cerebellar cortex


title: 019/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135203

source_name: post-mortem brain tissue, individual ID 019/10, cerebellar cortex


title: 006/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135272

source_name: post-mortem brain tissue, individual ID 006/08, cerebellar cortex


title: 015/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135198

source_name: post-mortem brain tissue, individual ID 015/10, cerebellar cortex


title: 034/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135253

source_name: post-mortem brain tissue, individual ID 034/09, cerebellar cortex


title: 030/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135264

source_name: post-mortem brain tissue, individual ID 030/06, cerebellar cortex


title: 018/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135260

source_name: post-mortem brain tissue, individual ID 018/07, cerebellar cortex


title: 021/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135236

source_name: post-mortem brain tissue, individual ID 021/09, cerebellar cortex


title: 016/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135201

source_name: post-mortem brain tissue, individual ID 016/10, cerebellar cortex


title: 023/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135212

source_name: post-mortem brain tissue, individual ID 023/10, cerebellar cortex


title: 027/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135269

source_name: post-mortem brain tissue, individual ID 027/09, cerebellar cortex


title: 018/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135207

source_name: post-mortem brain tissue, individual ID 018/10, cerebellar cortex


title: 016/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135215

source_name: post-mortem brain tissue, individual ID 016/08, cerebellar cortex


title: 004/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135278

source_name: post-mortem brain tissue, individual ID 004/10, cerebellar cortex


title: 011/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135191

source_name: post-mortem brain tissue, individual ID 011/09, cerebellar cortex


title: 014/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135211

source_name: post-mortem brain tissue, individual ID 014/10, cerebellar cortex


title: 024/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135224

source_name: post-mortem brain tissue, individual ID 024/08, cerebellar cortex


title: 038/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135214

source_name: post-mortem brain tissue, individual ID 038/09, cerebellar cortex


title: 001/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135283

source_name: post-mortem brain tissue, individual ID 001/10, cerebellar cortex


title: 012/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135268

source_name: post-mortem brain tissue, individual ID 012/08, cerebellar cortex


title: 023/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135222

source_name: post-mortem brain tissue, individual ID 023/09, cerebellar cortex


title: 009/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135231

source_name: post-mortem brain tissue, individual ID 009/09, cerebellar cortex


title: 028/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135271

source_name: post-mortem brain tissue, individual ID 028/09, cerebellar cortex


title: 040/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135221

source_name: post-mortem brain tissue, individual ID 040/08, cerebellar cortex


title: 004/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135234

source_name: post-mortem brain tissue, individual ID 004/06, cerebellar cortex


title: 033/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135258

source_name: post-mortem brain tissue, individual ID 033/09, cerebellar cortex


title: 007/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135218

source_name: post-mortem brain tissue, individual ID 007/08, cerebellar cortex


title: 008/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135279

source_name: post-mortem brain tissue, individual ID 008/10, cerebellar cortex


title: 002/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135206

source_name: post-mortem brain tissue, individual ID 002/08, cerebellar cortex


title: 022/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135196

source_name: post-mortem brain tissue, individual ID 022/06, cerebellar cortex


title: 018/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135194

source_name: post-mortem brain tissue, individual ID 018/08, cerebellar cortex


title: 026/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135247

source_name: post-mortem brain tissue, individual ID 026/08, cerebellar cortex


title: 004/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135248

source_name: post-mortem brain tissue, individual ID 004/08, cerebellar cortex


title: 026/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135229

source_name: post-mortem brain tissue, individual ID 026/09, cerebellar cortex


title: 038/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135232

source_name: post-mortem brain tissue, individual ID 038/08, cerebellar cortex


title: 043/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135267

source_name: post-mortem brain tissue, individual ID 043/06, cerebellar cortex


title: 003/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135274

source_name: post-mortem brain tissue, individual ID 003/08, cerebellar cortex


title: 011/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135276

source_name: post-mortem brain tissue, individual ID 011/10, cerebellar cortex


title: 031/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135217

source_name: post-mortem brain tissue, individual ID 031/08, cerebellar cortex


title: 024/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135225

source_name: post-mortem brain tissue, individual ID 024/09, cerebellar cortex


title: 013/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135246

source_name: post-mortem brain tissue, individual ID 013/09, cerebellar cortex


title: 025/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135239

source_name: post-mortem brain tissue, individual ID 025/08, cerebellar cortex


title: 007/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135277

source_name: post-mortem brain tissue, individual ID 007/10, cerebellar cortex


title: 017/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135244

source_name: post-mortem brain tissue, individual ID 017/07, cerebellar cortex


title: 016/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135245

source_name: post-mortem brain tissue, individual ID 016/09, cerebellar cortex


title: 026/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135261

source_name: post-mortem brain tissue, individual ID 026/07, cerebellar cortex


title: 015/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135208

source_name: post-mortem brain tissue, individual ID 015/09, cerebellar cortex


title: 018/05_cerebellar cortex

description: This entry supercedes previous accession: GSM1135259

source_name: post-mortem brain tissue, individual ID 018/05, cerebellar cortex


title: 020/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135249

source_name: post-mortem brain tissue, individual ID 020/08, cerebellar cortex


title: 017/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135192

source_name: post-mortem brain tissue, individual ID 017/09, cerebellar cortex


title: 025/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135216

source_name: post-mortem brain tissue, individual ID 025/10, cerebellar cortex


title: 015/07_cerebellar cortex

description: This entry supercedes previous accession: GSM1135227

source_name: post-mortem brain tissue, individual ID 015/07, cerebellar cortex


title: 028/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135213

source_name: post-mortem brain tissue, individual ID 028/10, cerebellar cortex


title: 025/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135220

source_name: post-mortem brain tissue, individual ID 025/09, cerebellar cortex

value: Cardiac


title: 013/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135204

source_name: post-mortem brain tissue, individual ID 013/10, cerebellar cortex


title: 06_53_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 06_53, cerebellar cortex


title: 020/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135199

source_name: post-mortem brain tissue, individual ID 020/10, cerebellar cortex


title: 022/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135230

source_name: post-mortem brain tissue, individual ID 022/09, cerebellar cortex


title: 99_14_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 99_14, cerebellar cortex


title: 07_28_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 07_28, cerebellar cortex


title: 010/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135195

source_name: post-mortem brain tissue, individual ID 010/09, cerebellar cortex


title: 04_19_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 04_19, cerebellar cortex


title: 039/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135205

source_name: post-mortem brain tissue, individual ID 039/06, cerebellar cortex


title: 95_26_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_26, cerebellar cortex

value: Cancer


title: 96_13_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 96_13, cerebellar cortex


title: 97_14_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 97_14, cerebellar cortex


title: 09_56_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 09_56, cerebellar cortex


title: 04_05_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 04_05, cerebellar cortex


title: 08_88_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 08_88, cerebellar cortex


title: 94_35_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 94_35, cerebellar cortex


title: 96_32_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 96_32, cerebellar cortex


title: 95_21_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_21, cerebellar cortex

value: cerebrovascular accident


title: 98_34_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 98_34, cerebellar cortex


title: 98_27_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 98_27, cerebellar cortex


title: 96_03_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 96_03, cerebellar cortex


title: 02_06_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 02_06, cerebellar cortex


title: 05_10_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 05_10, cerebellar cortex


title: 03_28_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 03_28, cerebellar cortex


title: Par_MB 270

status: Public on Jun 02 2014

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

description: Gene expression data from a medulloblastoma tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Primary medulloblastoma tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: age

tag: gender

value: M

tag: histology

value: LCA


title: MB102

value: F

value: desmoplastic


title: MB59


title: MB101


title: nch1020


title: e231/12

value: mben


title: MB125


title: MB20

value: classic


title: MB126


title: nch480


title: nch394


title: MB127


title: e845/10


title: MB75


title: r-46429


title: t01-11423

value: medulloblastoma, NOS


title: MB68


title: e393/04


title: MB77


title: t90


title: e1012/11


title: 4m64


title: e173/10


title: bttb 723


title: t07-03091


title: 1960


title: nch443


title: tc615


title: 3103823


title: MB72


title: MB74


title: MB63


title: MB62


title: ps-07-003036


title: MB61


title: MB60


title: MB53


title: MB3


title: MB22


title: MB29


title: 5m6


title: MB56


title: MB23


title: 5m9


title: 5m16


title: 5m17


title: 2m8


title: 2m9


title: 5m8


title: 2m16


title: 2m17


title: 5m18


title: 5m13


title: 2m21


title: 1m5


title: 1m9


title: 1m31


title: 1m12


title: The bottom side-derived PSC2 in monoculture

status: Public on Feb 25 2014

city: BALTIMORE

first: Kenji

last: Fujiwara

state: MD

address: 1650 Orleans Street

department: Oncology

country: USA

institute: Johns Hopkins University SOM

description: SAMPLE 4

hyb_protocol: We used a HumanHT-12v4 Expression BeadChip (Illumina, San Diego, CA) for these analyses.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation with IlluminaGUI in R

label: Biotin

source_name: Human pancreatic stellate cells 2

label_protocol: Probe cDNA was amplified and labeled with an Illumina total prep RNA amplification kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol

extract_protocol: Total RNA was extracted from cultured cells using the High Pure RNA Isolation Kit (Roche Diagnostics, Mannheim, Germany) and DNase I (Roche Diagnostics) treatment according to the manufacturer's instructions.

tag: tissue

value: Human surgical pancreatic tissues

tag: cell type

value: pancreatic stellate


title: βcat(ex3)osb vs WT(C57BL/J) replicate 1

status: Public on Jan 21 2014

type: genomic

city: New York

first: Stavroula

last: Kousteni

state: NY

address: 650 West 168th Street

department: Physiology and Cellular Biophysics

institute: Columnia University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
The data was further analyzed/filtered using Agilent Genomic Workbech with the following parameters;
Genome: mm9
Aberration Algorithm: ADM-1
Threshold: 6.0
Fuzzy Zero: OFF
GC Correction: OFF
Centralization (legacy): ON
Centralization (legacy) Bin Size: 10
Centralization (legacy) Threshold: 6.0
Diploid Peak Centralization: ON
Manually Reassign Peaks: OFF
Combine Replicates (Intra Array): OFF
Combine Replicates (Inter Array): OFF
Array Level Filter: NONE
Aberration Filter:  ( Minimum Number of Probes for Amplification >= 3 AND Minimum Size (Kb) of Region for Amplification >= 0.0 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 3 AND Minimum Size (Kb) of Region for Deletion >= 0.0 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )
Feature Level Filter: NONE
Design Level Filter: NONE
Genomic Boundary: OFF
Show Flat Intervals: OFF

molecule: genomic DNA

organism: Mus musculus

source_name: WT_spleen myeloid cells

label_protocol: 5 μL of Random Primer was added to 26 μLof 2 μg gDNA. Then 3 µL of labeling master mix, containg Cyanine 3-dUTP or Cyanine 5-dUTP was added.

growth_protocol: Mice were fed a normal powdered diet that contained all the required nutrients (20% protein, 3.0 ppm Folic Acid, 51 mcg/kg B12 from PicoLab Rodent Diet 20, Cat. Nu. 5053). Folate and B12 levels in their blood were normal (folate > 24 ng/ml and B12 > 1,000 pg/ml) confirming adequate intake of critical nutrients.

extract_protocol:
Extraction was performed with the PureLink Genomic DNA Mini Kit ® from INVITROGEN. Cat. No: k1820-01.
The genomic DNA is eluted using PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA)

tag: strain background

tag: genotype/variation

value: wild type

value: 5 weeks

value: female

value: spleen myeloid cells

source_name: βcat(ex3)osb_spleen myeloid cells


title: βcat(ex3)osb vs WT(C57BL/J) replicate 3


title: βcat(ex3)osb vs WT(C57BL/J) replicate 2


title: c.FoxO1.2

hyb_protocol: 12.5mg  of aRNA was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the MAS5 algorithm

source_name: Osteoblast specific FoxO1 deleted mice

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

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

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

value: indeterminante

tag: background strain

value: osteoblasts

value: 2-3 days

value: Osteoblast specific FoxO1 deleted


title: The top side-derived PSC2 in monoculture

description: SAMPLE 3


title: The bottom side-derived PSC1 with pancreatic cancer cells

description: SAMPLE 2

source_name: Human pancreatic stellate cells 1


title: CD166- Panc-1 cells

description: SAMPLE 4

hyb_protocol: We used a Human HT-12v4 Expression BeadChip (Illumina, San Diego, CA) for these analyses.

source_name: Human pancreatic cancer cell lines

extract_protocol:
For cell separation, we incubated magnetic microbeads conjugated with anti-PE reagent (Miltenyi Biotec) to labeled cells for 15 minutes at 4 °C. Labeled cells were isolated by passing the suspension through an AutoMACS PRO separator (Miltenyi Biotec). Unlabeled cells were negatively selected and collected by the depletion method through the AutoMACS PRO separator.
Total RNA was extracted from cultured cells using the High Pure RNA Isolation Kit (Roche Diagnostics, Mannheim, Germany) and DNase I (Roche Diagnostics) treatment according to the manufacturer's instructions. The quality of the RNA samples was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: Pancreatic cancer cell

tag: cell line


title: a.wt.3

source_name: Wt mice


title: βcat(ex3)osb vs WT(C57BL/J) replicate 4


title: The top side-derived PSC2 with pancreatic cancer cells

description: SAMPLE 5


title: c.FoxO1.1


title: b.bcat.3

source_name: Osteoblast specific beta-catenin expressed mice

value: Osteoblast specific beta-catenin constitutively expressed


title: βcat(ex3)osb vs WT(C57BL/J) replicate 5


title: CD166+ Panc-1 cells

description: SAMPLE 3


title: a.wt.4


title: CD166- SW1990 cells

description: SAMPLE 2


title: The top side-derived PSC1 with pancreatic cancer cells

description: SAMPLE 1


title: c.FoxO1.3


title: b.bcat.1


title: a.wt.1


title: a.wt.2


title: b.bcat.2


title: CD166+ SW1990 cells

description: SAMPLE 1


title: The bottom side-derived PSC2 with pancreatic cancer cells

description: SAMPLE 6


title: EPN_859_1

status: Public on Aug 30 2013

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Primary

value: brain tumor (ependymoma)


title: EPN_80_1


title: EPN_700_1


title: EPN_393_1


title: EPN_392_1


title: EPN_507_1


title: NORMAL-605-Cerebellum

status: Public on Aug 25 2013

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
Gene expression data from surgical tumor sample of normal brain
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.

source_name: normal brain (cerebellum)

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

tag: disease state

value: normal

value: cerebellum


title: EPN_110_1


title: EPN_811_1


title: EPN_419_1


title: EPN_64_1


title: EPN_492_1


title: EPN_812_1


title: EPN_691_1

description:
included_in_corresponding_manuscript:no
Gene expression data from surgical tumor sample of ependymoma


title: EPN_723_1


title: EPN_195_1


title: EPN_364_1


title: NORMAL-514-Cerebellum


title: EPN_246_1


title: MED-925

description:
Gene expression data from surgical tumor sample of medulloblastoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

source_name: brain tumor (medulloblastoma)

value: brain tumor

value: medulloblastoma


title: MED-801b


title: MED-877


title: MED-898


title: MED-719


title: MED-791


title: MED-797


title: EPN_483_1


title: MED-676


title: MED-B40


title: MED-613


title: MED-330


title: MED-437


title: MED-0945


title: MED-801


title: MED-288


title: MED-277


title: MED-258


title: MED-254


title: MED-529


title: MED-262


title: MED-565


title: CTRL_CBM_12

status: Public on Jun 12 2013

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

institute: German Cancer Research Center

source_name: Normal cerebellum RNA (commercial source)

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: Normal cerebellum control

tag: brain location

value: Cerebellum

tag: age at diagnosis (years)

value: Male

tag: dna methylation subgroup

tag: mapk hit

value: Pilocytic astrocytoma:N/A


title: CTRL_CBM_15


title: CTRL_CBM_10

value: Fetal


title: CTRL_CBM_11

value: Female


title: CTRL_CBM_14

value: Adult


title: CTRL_CBM_13


title: CTRL_CBM_07


title: CTRL_CBM_08


title: Proliferation [gene expression]

status: Public on Apr 11 2013

city: San Francisco

first: Abhinav

last: Nellore

state: CA

address: 513 Parnassus Avenue

institute: UCSF

description: SAMPLE 8

hyb_protocol: Hybridization was perfomed on a Maui Hybridization System

scan_protocol: Scanning was done on a GenePix 4000B scanner according to standard Nimblegen protocols

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the DEVA package, version 1.2.1
Sample data table contains RMA-normalized, averaged gene-level signal intensity (i.e. values in the 'PM_AVG' conlumn in processed data .calls file)

source_name: cell culture

label_protocol: Labeling was performed according to standard Nimblegen Protocols

growth_protocol: SVZ cells were grown in monolayer in proliferation media. At passage 5-7, cells were switched to media without growth factors for indicated timepoints (1,2,4 days)

extract_protocol: Total RNA was isolated with trizol reagent and amplified with Whole Transcriptome Amplification Kit (Thermo).

treatment_protocol: For FACS isolated cells, total SVZ was dissected and subjected to the FACS protocol detailed in Pastrana, et al 2009

value: Proliferating SVZ-NSC monolayers


title: CTRL_CBM_09


title: 2d_diff [gene expression]

description: SAMPLE 10

value: SVZ-NSCs two day in differentiation media


title: 4d_diff [gene expression]

description: SAMPLE 11

value: SVZ-NSCs four day in differentiation media


title: 1d_diff [gene expression]

description: SAMPLE 9

value: SVZ-NSCs one day in differentiation media


title: Astro_1 [gene expression]

description: SAMPLE 6

source_name: Mouse Brain_niche astrocytes (astros)

value: FACS isolated niche astrocytes


title: NB [gene expression]

description: SAMPLE 5

source_name: Mouse Brain_neuroblast (NB)

value: FACS isolated neuroblasts


title: Astro_2 [gene expression]

description: SAMPLE 7


title: TA_2 [gene expression]

description: SAMPLE 4

source_name: Mouse Brain_transit amplifying cells (TA)

value: FACS isolated transit amplifying cells


title: TA_1 [gene expression]

description: SAMPLE 3


title: SVZ_NSCs_2 [gene expression]

description: SAMPLE 2

source_name: Mouse Brain_activated stem cells (NSCs)

value: FACS isolated SVZ stem cells


title: 4d_diff [lncRNA Array]

description: SAMPLE 12

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the DEVA package, version 1.2.1
Sample data table contains RMA-normalized, averaged gene-level signal intensity (i.e. values in the 'EXPRS' column in processed data *RMA.calls file)


title: Proliferation_2 [lncRNA Array]

description: SAMPLE 9


title: MED-186

value: brain tumor


title: Proliferation_1 [lncRNA Array]

description: SAMPLE 8


title: SVZ_NSCs_1 [gene expression]

description: SAMPLE 1


title: NB [lncRNA Array]

description: SAMPLE 5


title: Astro_1 [lncRNA Array]

description: SAMPLE 6


title: 2d_diff [lncRNA Array]

description: SAMPLE 11


title: 1d_diff [lncRNA Array]

description: SAMPLE 10


title: SVZ_NSCs_2 [lncRNA Array]

description: SAMPLE 2


title: TA_2 [lncRNA Array]

description: SAMPLE 4


title: Astro_2 [lncRNA Array]

description: SAMPLE 7


title: SVZ_NSCs_1 [lncRNA Array]

description: SAMPLE 1


title: CC134_100909

status: Public on Dec 31 2012

city: Changsha

first: Chao

last: Chen

address: 110 Xiangya Road

country: China

institute: Central South University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

data_processing: The data were analyzed by RMA using Affymetrix Expression Console with default analysis settings.

source_name: cerebellum from brain, unaffected control

label_protocol: GeneChip® WT Sense Target Labeling and Control Reagents.

extract_protocol: RNAs were extracted from the cerebellum of 144 samples using the RNeasy Mini kit (Qiagen, Valencia, CA). The concentration and A260/A280 ratio were measured on the NanoDrop spectrophotometer. The 28S:18S rRNA ratio and RNA Integrity Number (RIN) were measured using an RNA LabChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Only RNA samples with a RIN >7 were used for the expression profiling.

value: cerebellum

tag: disease status

value: unaffected

tag: post-mortem interval (pmi)

tag: Sex

value: F

tag: ph


title: CC140_103009

tag: age


title: CC140_111109

tag: tissue


title: CC124_102109

value: M


title: CC117_111809


title: CC117_100909


title: CC125_102109


title: CC117_102109


title: TA_1 [lncRNA Array]

description: SAMPLE 3

tag: cell type


title: CC132_100909


title: CC117_111109


title: CC117_103009


title: CC101_102309


title: CC123_102109


title: CC109_102309


title: CC94_111809


title: CC96_103009


title: CC97_103009


title: CC93_111809


title: CC88_111109


title: CC108_102309


title: CC117_102309


title: CC92_111809


title: CC100_102109


title: CC77_100909


title: CC82_111809


title: CC87_111109


title: CC80_111109


title: CC73_111109


title: CC75_100909


title: CC81_111109


title: CC67_111109


title: CC62_111109


title: CC60_111809


title: CC46_103009


title: CC47_103009


title: CC68_111109


title: CC50_111809


title: CC44_102309


title: CC55_111809


title: CC29_102109


title: CC45_102309


title: CC39_102309


title: CC48_103009


title: CC27_102109


title: CC23_100909


title: CC13_100909


title: CC8_100909


title: CC17_100909


title: CC26_103009


title: human sporadic medulloblastoma tumor_HMED12

status: Public on Oct 27 2012

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

description: Gene expression data of human medulloblastoma tumor tissue

hyb_protocol: Following fragmentation,  2 ug cRNA was hybridized for 16 hr at 45°C on Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 2500.

data_processing: Data normalization was done using  GCRMA algorithm in the Bioconductor package (v 2.1) of the R statistical environment (http://www.bioconductor.org)

source_name: human medulloblastoma tumor tissue

label_protocol: 100 ng total RNA was reverse transcribed, amplified, and labeled with biotin using the whole transcript sense target labeling kit as per the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was extracted from tumor tissues using the mirVANA kit ( Ambion, Austin, TX, USA) , as per the manufacturer’s protocol after ensuring at least 80% tumor cell content.The RNA was further purified using RNeasy columns (Qiagen,Valencia, CA, USA), for removing genomic DNA contamination if at all . RNAs having more than 7.0 RIN value and no detectable genomic DNA contamination were used for the analysis.

tag: gender

value: male

tag: age (yr)

tag: tumor grade (histological)

value: IV

tag: molecular subgroup

value: Group 3


title: human sporadic medulloblastoma tumor_HMED8

value: female

value: WNT


title: CC32_102109


title: human sporadic medulloblastoma tumor_HMED15

value: Group 4


title: human sporadic medulloblastoma tumor_HMED18


title: human sporadic medulloblastoma tumor_HMED22

value: SHH


title: human sporadic medulloblastoma tumor_HMED7


title: human sporadic medulloblastoma tumor_HMED14


title: human sporadic medulloblastoma tumor_HMED11


title: human sporadic medulloblastoma tumor_HMED10


title: human sporadic medulloblastoma tumor_HMED17


title: human sporadic medulloblastoma tumor_HMED13


title: human sporadic medulloblastoma tumor_HMED20


title: human sporadic medulloblastoma tumor_HMED16


title: human sporadic medulloblastoma tumor_HMED3


title: human sporadic medulloblastoma tumor_HMED9


title: human sporadic medulloblastoma tumor_HMED2


title: human sporadic medulloblastoma tumor_HMED5


title: human sporadic medulloblastoma tumor_HMED6


title: human sporadic medulloblastoma tumor_HMED1


title: Primary medulloblastoma sample_MB-1158

status: Public on Jul 27 2012

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

institute: German Cancer Research Center (DKFZ)

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: Signal estimates for Gene Level Analysis were determined using Affymetrix Expression Console (1.1) and default paramters.  Samples were analyzed in three separate batches according to medulloblastoma subgroup affilliation:  SHH, Group 3, and Group 4.

source_name: Primary medulloblastoma

label_protocol: As directed by Affymetrix using 400ng total RNA as starting material.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values ≥7 were included in the study.

tag: histology

value: Classic

tag: subgroup


title: Primary medulloblastoma sample_MB-1127

value: LCA


title: Primary medulloblastoma sample_MB-1193


title: Primary medulloblastoma sample_MB-1139


title: Primary medulloblastoma sample_MB-874


title: Primary medulloblastoma sample_MB-793


title: Primary medulloblastoma sample_MB-886


title: Primary medulloblastoma sample_MB-1140


title: Primary medulloblastoma sample_MB-819

value: Medulloblastoma


title: Primary medulloblastoma sample_MB-765


title: Primary medulloblastoma sample_MB-1132


title: Primary medulloblastoma sample_MB-1181

value: Desmoplastic


title: Primary medulloblastoma sample_MB-864


title: Primary medulloblastoma sample_MB-1143


title: Primary medulloblastoma sample_MB-791


title: Primary medulloblastoma sample_MB-696


title: Primary medulloblastoma sample_MB-663


title: Primary medulloblastoma sample_MB-664


title: Primary medulloblastoma sample_MB-680


title: Primary medulloblastoma sample_MB-641


title: Primary medulloblastoma sample_MB-646


title: Primary medulloblastoma sample_MB-648


title: Primary medulloblastoma sample_MB-642


title: Primary medulloblastoma sample_MB-638


title: Primary medulloblastoma sample_MB-634


title: Primary medulloblastoma sample_MB-632


title: Primary medulloblastoma sample_MB-620


title: Primary medulloblastoma sample_MB-628


title: Primary medulloblastoma sample_MB-640


title: Primary medulloblastoma sample_MB-635


title: Primary medulloblastoma sample_MB-586


title: Primary medulloblastoma sample_MB-405


title: Primary medulloblastoma sample_MB-142


title: Primary medulloblastoma sample_MB-106


title: Primary medulloblastoma sample_MB-378


title: Primary medulloblastoma sample_MB-1148


title: Primary medulloblastoma sample_MB-1003


title: Primary medulloblastoma sample_MB-1213


title: Primary medulloblastoma sample_MB-548


title: Primary medulloblastoma sample_MB-1094


title: Primary medulloblastoma sample_MB-1208


title: Primary medulloblastoma sample_MB-306


title: Primary medulloblastoma sample_MB-1276


title: Primary medulloblastoma sample_MB-391


title: Primary medulloblastoma sample_MB-948


title: Primary medulloblastoma sample_MB-322


title: Primary medulloblastoma sample_MB-356


title: Primary medulloblastoma sample_MB-216


title: Primary medulloblastoma sample_MB-1188


title: Primary medulloblastoma sample_MB-136


title: SJMB037

status: Public on Jul 06 2012

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: primary tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 v2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.  Natural log start stransfomation was perfomed in STATA/SE 11.2.

source_name: Medulloblastoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: Isolation was performed using RNA STAT-60, according to the manufacturer's instructions. Briefly, tissue samples were homogenized in the STAT-60 using teflon homogenizers. Chloroform was added and the samples centrifuged. The upper layer (aqueous phase) was removed to a fresh tube and the RNA precipitated with isopropanol. Following centrifugation, the RNA pellet was washed once in 75% ethanol, then the air-dried pellet resuspended in DEPC-treated water.

treatment_protocol: all samples are untreated tissues

value: 5yrs 9mos

value: Male

tag: ethnic

value: Black

tag: m stage

value: MB-CL


title: SJMB013

description: primary tumor

value: 5yrs 1mos

value: White

value: MB-DN


title: SJMB124

description: primary tumor

value: 10yrs 3mos


title: SJMB034

description: primary tumor

value: 10yrs 10mos

value: Hispanic


title: SJMB137

description: primary tumor

value: WNT

value: 8yrs 5mos


title: SJMB069

description: primary tumor

value: 11yrs 8mos

value: MB-AN


title: SJMB040

description: primary tumor

value: 8yrs 2mos

value: Female


title: SJMB085

description: primary tumor

value: 6yrs 11mos


title: SJMB131

description: primary tumor

value: U

value: 9yrs 1mos

value: Asian

value: MB-Myo


title: SJMB082

description: primary tumor

value: 3yrs 11mos

value: Male

value: MB-CL


title: SJMB089

description: primary tumor

value: SHH

value: 4yrs 1mos

value: White

value: MB-DN


title: SJMB027

description: primary tumor

value: 9yrs 10mos


title: SJMB090

description: primary tumor

value: 12yrs 2mos


title: SJMB139

description: primary tumor

value: WNT

value: 8yrs 4mos


title: SJMB122

description: primary tumor

value: 5yrs 0mos


title: SJMB071

description: primary tumor

value: 12yrs 1mos


title: SJMB036

description: primary tumor

value: 6yrs 4mos

value: Female

value: Black


title: SJMB038

description: primary tumor

value: 8yrs 8mos


title: SJMB079

description: primary tumor

value: 5yrs 9mos

value: Asian Indian


title: SJMB114

description: primary tumor

value: 9yrs 2mos

value: Pacific Islander

value: MB-CL


title: SJMB094

description: primary tumor

value: 5yrs 2mos

value: Male

value: Hispanic


title: SJMB008

description: primary tumor

value: 13yrs 7mos

value: White

value: MB-AN


title: SJMB129

description: primary tumor

value: WNT

value: 8yrs 5mos

value: other


title: SJMB080

description: primary tumor

value: 5yrs 10mos


title: SJMB039

description: primary tumor

value: 8yrs 2mos


title: SJMB117

description: primary tumor

value: 6yrs 11mos


title: SJMB081

description: primary tumor

value: 7yrs 1mos

value: Female


title: SJMB078

description: primary tumor

value: 9yrs 2mos


title: SJMB031

description: primary tumor


title: SJMB010

description: primary tumor

value: 6yrs 9mos

value: Black


title: SJMB004

description: primary tumor

value: SHH

value: 8yrs 9mos

value: MB-CL


title: SJMB011

description: primary tumor

value: 8yrs 8mos

value: Male


title: SJMB093

description: primary tumor

value: 11yrs 7mos

value: White

value: MB-AN


title: SJMB033

description: primary tumor

value: 16yrs 8mos


title: SJMB032

description: primary tumor

value: 12yrs 11mos

value: Asian


title: SJMB003

description: primary tumor

value: 7yrs 0mos

value: MB-DN


title: SJMB091

description: primary tumor

value: 6yrs 2mos

value: Hispanic


title: SJMB073

description: primary tumor

value: U

value: 10yrs 10mos

value: MB-Myo


title: SJMB087

description: primary tumor

value: 3yrs 2mos


title: SJMB068

description: primary tumor

value: SHH

value: Female

value: MB-CL


title: SJMB064

description: primary tumor

value: 5yrs 0mos

value: Male


title: SJMB070

description: primary tumor

value: 11yrs 9mos

value: White

value: MB-AN


title: SJMB088

description: primary tumor

value: 4yrs 3mos


title: SJMB035

description: primary tumor

value: 6yrs 4mos


title: SJMB063

description: primary tumor

value: 3yrs 8mos


title: SJMB067

description: primary tumor

value: 10yrs 0mos

value: Asian Indian


title: SJMB028

description: primary tumor

value: WNT

value: 11yrs 7mos


title: SJMB118

description: primary tumor

value: SHH OUTLIER

value: 8yrs 4mos

value: Black

value: MB-DN


title: SJMB104

description: primary tumor

value: 13yrs 5mos

value: Female

value: Hispanic

value: MB-CL


title: SJMB107

description: primary tumor

value: SHH

value: 16yrs 1mos

value: White


title: SJMB006

description: primary tumor

value: 3yrs 4mos

value: Male

value: MB-AN


title: SJMB055

description: primary tumor

value: 8yrs 7mos


title: SJMB025

description: primary tumor

value: 12yrs 11mos


title: SJMB030

description: primary tumor


title: SJMB021

description: primary tumor


title: SJMB023

description: primary tumor

value: 5yrs 5mos


title: SJMB024

description: primary tumor

value: 6yrs 9mos


title: SJMB101

description: primary tumor

value: 11yrs 9mos


title: SJMB052

description: primary tumor

value: 4yrs 8mos


title: SJMB017

description: primary tumor

value: 10yrs 10mos


title: SJMB050

description: primary tumor

value: 5yrs 2mos


title: SJMB009

description: primary tumor

value: 9yrs 4mos


title: SJMB016

description: primary tumor

value: 7yrs 9mos

value: Female

value: Asian Indian


title: SJMB097

description: primary tumor

value: 4yrs 11mos

value: MB-CL


title: SJMB051

description: primary tumor

value: WNT

value: 9yrs 1mos

value: White


title: SJMB020

description: primary tumor

value: 8yrs 9mos

value: Male

value: Hispanic

value: MB-AN


title: SJMB015

description: primary tumor

value: 8yrs 1mos


title: SJMB084

description: primary tumor

value: 14yrs 8mos


title: SJMB014

description: primary tumor

value: 9yrs 2mos


title: SJMB048

description: primary tumor

value: 9yrs 8mos

value: other


title: SJMB019

description: primary tumor

value: 8yrs 8mos


title: SJMB043

description: primary tumor

value: 8yrs 3mos

value: Black


title: SJMB018

description: primary tumor

value: 8yrs 4mos


title: SJMB001

description: primary tumor

value: 6yrs 6mos

value: Female

value: MB-CL


title: SJMB012

description: primary tumor

value: SHH

value: 8yrs 6mos

value: Asian

value: MB-DN


title: SJMB045

description: primary tumor

value: 9yrs 0mos

value: White


title: medulloblastoma_21

status: Public on Dec 31 2011

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

hyb_protocol: The resultant labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000 7G plus.

data_processing: The data were analyzed with Bioconductor in R statistical software.

source_name: fresh frozen tissue

label_protocol: amplified and labeled according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript Sense Target Labeling protocol

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy Mini kit (Hilden, Germany).

value: medulloblastoma

value: F

tag: age(month)

value: Desmoplastic

tag: seeding(metastasis)

value: N

tag: death

value: alive


title: medulloblastoma_29

value: M


title: medulloblastoma_26

value: Classic

value: Y

value: death


title: medulloblastoma_16


title: medulloblastoma_12


title: medulloblastoma_28

value: Anaplastic


title: medulloblastoma_23


title: medulloblastoma_13


title: medulloblastoma_24


title: medulloblastoma_31


title: medulloblastoma_10


title: medulloblastoma_15


title: medulloblastoma_14


title: medulloblastoma_25


title: medulloblastoma_20


title: medulloblastoma_11


title: medulloblastoma_17


title: medulloblastoma_18


title: H1581

status: Public on Jun 18 2012

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

value: lung cancer cell line

tag: cell line

tag: atcc alias

value: Large Cell

tag: race

value: Caucasian


title: medulloblastoma_07

tag: Sex


title: medulloblastoma_27

tag: tissue


title: medulloblastoma_06


title: medulloblastoma_08


title: medulloblastoma_19


title: medulloblastoma_04


title: medulloblastoma_05


title: medulloblastoma_03


title: medulloblastoma_01


title: medulloblastoma_09


title: Human - cerebellar cortex - 94 days old

status: Public on Dec 09 2011

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 94 days old human individual
Hsa_94days_batch2

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >70% of human, chimpanzee or macaque individuals.

source_name: Dissected Human post-mortem cerebellar cortex

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cerebellar cortex.

tag: age

value: 94 days

value: m

value: cerebellar cortex of the brain

tag: post-mortem interval (hours)

tag: rna integrity number (rin)

tag: batch


title: Human - cerebellar cortex - 9277 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 9277 days old human individual
Hsa_9277days_batch1

value: 9277 days

tag: gender


title: Human - cerebellar cortex - 8364 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 8364 days old human individual
Hsa_8364days_batch2

value: 8364 days


title: Human - cerebellar cortex - 32120 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 32120 days old human individual
Hsa_32120days_batch1


title: Human - cerebellar cortex - 35770 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 35770 days old human individual
Hsa_35770days_batch2


title: Human - cerebellar cortex - 35770 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 35770 days old human individual
Hsa_35770days_batch1


title: Human - cerebellar cortex - 28692 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 28692 days old human individual
Hsa_28692days_batch2

value: f


title: Human - cerebellar cortex - 3912 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 3912 days old human individual
Hsa_3912days_batch2

value: 3912 days


title: Human - cerebellar cortex - 4 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 4 days old human individual
Hsa_4days_batch1

value: 4 days


title: Human - cerebellar cortex - 787 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 787 days old human individual
Hsa_787days_batch2

value: 787 days


title: Human - cerebellar cortex - 2 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 2 days old human individual
Hsa_2days_batch2

value: 2 days


title: Human - cerebellar cortex - 24090 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 24090 days old human individual
Hsa_24090days_batch1


title: Human - cerebellar cortex - 32850 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 32850 days old human individual
Hsa_32850days_batch2


title: Human - cerebellar cortex - 19 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 19 days old human individual
Hsa_19days_batch2

value: 19 days


title: Human - cerebellar cortex - 19457 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 19457 days old human individual
Hsa_19457days_batch1


title: Human - cerebellar cortex - 5105 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 5105 days old human individual
Hsa_5105days_batch1

value: 5105 days


title: Human - cerebellar cortex - 196 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 196 days old human individual
Hsa_196days_batch1

value: 196 days


title: Human - cerebellar cortex - 29200 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 29200 days old human individual
Hsa_29200days_batch1


title: Human - cerebellar cortex - 443 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 443 days old human individual
Hsa_443days_batch2

value: 443 days


title: Human - cerebellar cortex - 1630 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 1630 days old human individual
Hsa_1630days_batch2

value: 1630 days


title: Human - cerebellar cortex - 2 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 2 days old human individual
Hsa_2days_batch1


title: Human - cerebellar cortex - 2922 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 2922 days old human individual
Hsa_2922days_batch1

value: 2922 days


title: Human - cerebellar cortex - 21204 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 21204 days old human individual
Hsa_21204days_batch2


title: HSB187_CBC_L [gene-level]

status: Public on Oct 27 2011

city: New Haven

first: Feng

last: Cheng

state: CT

address: 333 Cedar Street SHM C338

department: Neurobiology

institute: Yale University

hyb_protocol: Microarrays were hybridized at 45 °C for 16–24 hours, washed and stained using an Affymetrix FS450 fluidics station, according to manufacturer recommendations. Microarrays were scanned on a GeneChip Scanner 3000 and visually inspected for hybridization artefacts. Exon chip analysis was performed using Affymetrix Power Tools 1.12.0. Probe level data was summarized into probe set level data using the Robust Multichip Average (RMA) background correction algorithm in combination with an R-script. The raw image files (.DAT files) were analyzed using Affymetrix GeneChip Operating Software to generate CEL files.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing:
Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction, quantile normalization, mean probe set summarization, and log2 transformation. Only high-quality core probe sets, as defined by Affymetrix, were included because theyalways have reliable annotations from RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org). It is noted that thedatasets were annotated according to the UCSC human genome hg19 reference sequence (http://genome.ucsc.edu/cgi-bin/hgGateway).Besides,105,271 core probes (within 62,448 prob sets) contained common SNPswas removed because SNP-containing probe sets may lead to reduced signal intensity and result in spurious results. These probes were defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is basedon the dbSNPdatabase (version 129, April 2008) andSNPinprobe_1.0 database. Removal of SNP-affected probes was accomplished in Partek program.Probe sets and gene intensities was summarized only on those probes not affected by SNPs.Finally, a total of 17,565 genes (transcript clusters) were surveyed for downstream analysis.
probe group file: HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Exon array hybridizations were performed at the Yale Center for Genome Analysis and at Gene Logic Inc. (Gaithersburg, MD). Reverse transcription (RT) was performed to generate cDNA from total RNA using RT primers designed using an oligonucleotide matching algorithm. For the selective cDNA synthesis, the Ambion WT Expression kit (Ambion) was used in combination with the GenechipWT Terminal Labeling and Controls Kit (Affymetrix) for target preparation, according to manufacturer recommendations. PolyA controls were added to the input RNA to measure efficiency of target amplification. Fragmented and labelled second cycle cDNA (5.5 μg) was added to a hybridization cocktail prior to loading of 200 μl onto individual Affymetrix Human Exon 1.0 ST arrays.

extract_protocol: A bead mill homogenizer (Bullet Blender, Next Advance) was used to lyse the pulverized tissue. Each pulverized tissue sample was transferred to a chilled safe-lock microcentrifuge tube (Eppendorf). A mass of chilled stainless steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue was added to the tube. Two volumes of Buffer RLT (Qiagen) were added to the tissue and beads. Samples were mixed in the Bullet Blender for 1 min at a speed of six. Samples were visually inspected to confirm desired homogenization and then incubated at 37 °C for five min. Buffer RLT was added up to 0.6 ml, and samples were mixed in the Bullet Blender for 1 min. Total RNA was extracted using a non-phenolic procedure (RNeasy Plus Mini Kit, Qiagen), followed by DNase treatment (TURBO DNase, Ambion) as per manufacturers’ instructions. Optical density values of extracted RNA were measured using a NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was determined for each sample using Bioanalyzer RNA 6000 Nano Kit or Bioanalyzer RNA 6000 Pico Kit (Agilent), depending upon the total amount of RNA.

treatment_protocol: This study was conducted using postmortem human brain specimens from tissue collections at the Department of Neurobiology at Yale University School of Medicine and the Clinical Brain Disorders Branch of the National Institute of Mental Health. Additional specimens were procured from the Human Fetal Tissue Repository at the Albert Einstein College of Medicine (AECOM), the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, the Birth Defects Research Laboratory at the University of Washington, Advanced Bioscience Resources Inc. and the MRC-Wellcome Trust Human Developmental Biology Resource at the Institute of Human Genetics, University of Newcastle, UK. Tissue was collected after obtaining parental or next of kin consent and with approval by the institutional review boards at the Yale University School of Medicine, the National Institutes of Health, and at each institution from which tissue specimens were obtained. Specimens range in age from 5.7 post-conceptual weeks (PCW) to over 80 years. Of 57 post-mortem brain specimens included in this study, 24 were obtained with either left or right hemisphere, and 33 were obtained with both hemispheres. Embryonic and fetal age was extrapolated based on the date of the mother’s last menstruation, characteristics of the fetus noted upon ultrasonographic scanning, foot length of the fetus, and visual inspection.

tag: brain code

tag: region

value: CBC

tag: hemisphere

value: L

value: F

tag: Stage

tag: postmortem interval

tag: ph

tag: rna integrity number


title: Human - cerebellar cortex - 14309 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 14309 days old human individual
Hsa_14309days_batch2

value: m

value: cerebellar cortex of the brain


title: HSB194_CBC_R [gene-level]

value: R

value: M

value: 37 PCW


title: HSB187_CBC_R [gene-level]


title: HSB185_URL_L [gene-level]

value: URL

value: 6 PCW


title: HSB182_CBC_L [gene-level]


title: HSB194_CBC_L [gene-level]


title: HSB174_CBC_L [gene-level]

value: 8 Y


title: HSB185_URL_L [exon-level]

data_processing:
Partek Genomics Suite version 6.5 (Partek Incorporated, St. Louis, MO, USA) was used to normalize raw exon array data and to summarize expression of the probe set and transcript cluster. Affymetrix CEL files that passed QC analyses were imported into Partek Genomics Suite using the default Partek settings: RMA background correction114, quantile normalization, mean probe set summarization, and log2-transformation. Only high-quality core probe sets, as defined by Affymetrix, were included. These high-quality core probe sets have reliable annotations from RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org). Datasets were annotated according to the UCSC human genome hg19 reference sequence (http://genome.ucsc.edu/cgi-bin/hgGateway). 105,271 core probes (within 62,448 probe sets out of 230,918 core probe sets) contained SNPs defined in the probe group file HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf provided by Affymetrix, which is based on the dbSNP database (version 129, April 2008) and SNPinprobe_1.0 database. The gene and exon expression were evaluated twice, with one evaluation excluding SNP-containing probe sets. The Pearson correlation analysis was performed to compare gene and exon expression levels of the data with and without SNP-containing probe sets. Almost all of the correlation coefficients (98.8%) for all 1,340 samples were within the range of 0.980-0.995 for genes and 0.975-0.995 for exons, suggesting that SNP-containing probe sets have a very minimal effect on measured expression levels (Supplementary Fig.6). Nevertheless, we removed SNP-containing probe sets during the normalization step in the Partek program to be control for SNP-related confounding effects. The median of all individual probe sets of one transcript cluster was used as the estimate of gene expression values. To filter out low expression signals (including noise or poorly hybridized probes), which may lead to false positives, detection above background (DABG) P-values of exon probe sets and transcript clusters were calculated using Affymetrix power tools (APT, http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).
The expression level for all core probe sets within an exon were averaged to obtain an expression value for the exon, and the median of all exons within one gene (transcript cluster) was used as the estimate of gene expression.


title: HSB187_CBC_L [exon-level]


title: HSB194_CBC_R [exon-level]


title: HSB175_CBC_L [gene-level]


title: HSB183_CBC_L [exon-level]


title: HSB175_CBC_L [exon-level]


title: HSB182_CBC_L [exon-level]


title: HSB187_CBC_R [exon-level]


title: HSB194_CBC_L [exon-level]


title: HSB173_CBC_L [gene-level]

value: 3 Y


title: HSB174_CBC_L [exon-level]


title: HSB171_CBC_L [exon-level]

value: 10 PMonth


title: HSB172_CBC_L [exon-level]


title: HSB171_CBC_L [gene-level]


title: HSB172_CBC_L [gene-level]


title: HSB183_CBC_L [gene-level]


title: HSB159_CBC_R [gene-level]

value: 22 PCW


title: HSB159_CBC_R [exon-level]


title: HSB159_CBC_L [exon-level]


title: HSB159_CBC_L [gene-level]


title: HSB155_CBC_R [gene-level]

value: 35 PCW


title: HSB173_CBC_L [exon-level]


title: HSB156_CBC_R [exon-level]


title: HSB156_CBC_R [gene-level]


title: HSB150_CBC_R [gene-level]

value: 12 PCW


title: HSB155_CBC_L [gene-level]


title: HSB156_CBC_L [gene-level]


title: HSB149_CBC_R [gene-level]

value: 13 PCW


title: HSB149_CBC_L [gene-level]

value: CBC


title: HSB155_CBC_R [exon-level]


title: HSB156_CBC_L [exon-level]

value: L


title: HSB155_CBC_L [exon-level]

value: F


title: HSB150_CBC_L [gene-level]


title: HSB149_CBC_L [exon-level]


title: HSB149_CBC_R [exon-level]


title: HSB148_URL_R [exon-level]

value: 9 PCW


title: medulloblastoma_22

value: medulloblastoma

tag: age(month)

tag: histology

value: Anaplastic

tag: seeding(metastasis)

value: N

tag: death

value: alive


title: HSB150_CBC_R [exon-level]

value: R

tag: Sex


title: HSB148_URL_L [exon-level]

value: URL

value: M

tag: age


title: HSB150_CBC_L [exon-level]


title: HSB148_URL_L [gene-level]


title: HSB148_URL_R [gene-level]


title: HSB145_CBC_R [gene-level]


title: HSB145_CBC_L [gene-level]


title: HSB144_CBC_R [gene-level]


title: HSB144_CBC_L [gene-level]


title: HSB142_CBC_R [gene-level]


title: HSB143_CBC_R [gene-level]

value: 2 Y


title: HSB143_CBC_L [gene-level]


title: HSB145_CBC_L [exon-level]


title: HSB141_CBC_L [gene-level]

value: 8 Y


title: HSB143_CBC_R [exon-level]


title: HSB144_CBC_R [exon-level]


title: HSB143_CBC_L [exon-level]


title: HSB142_CBC_L [gene-level]


title: HSB142_CBC_R [exon-level]


title: HSB139_CBC_L [exon-level]

value: 4 PMonth


title: HSB136_CBC_L [exon-level]


title: HSB145_CBC_R [exon-level]


title: HSB141_CBC_L [exon-level]


title: HSB144_CBC_L [exon-level]


title: HSB136_CBC_R [exon-level]


title: HSB142_CBC_L [exon-level]


title: HSB135_CBC_L [gene-level]


title: HSB139_CBC_L [gene-level]


title: HSB136_CBC_L [gene-level]


title: HSB136_CBC_R [gene-level]


title: HSB133_CBC_L [gene-level]


title: HSB132_CBC_L [gene-level]


title: HSB132_CBC_R [gene-level]


title: HSB126_CBC_R [gene-level]


title: HSB131_CBC_L [gene-level]

value: 6 PMonth


title: HSB127_CBC_L [gene-level]


title: HSB126_CBC_L [gene-level]


title: HSB132_CBC_R [exon-level]


title: HSB126_CBC_R [exon-level]


title: HSB124_CBC_R [exon-level]


title: HSB135_CBC_L [exon-level]


title: HSB130_CBC_L [exon-level]


title: HSB127_CBC_L [exon-level]


title: HSB132_CBC_L [exon-level]


title: HSB124_CBC_L [exon-level]


title: HSB123_CBC_L [gene-level]


title: HSB131_CBC_L [exon-level]


title: HSB122_CBC_L [gene-level]

value: 1 Y


title: HSB124_CBC_R [gene-level]


title: HSB126_CBC_L [exon-level]


title: HSB122_CBC_R [gene-level]


title: HSB124_CBC_L [gene-level]


title: HSB121_CBC_L [exon-level]


title: HSB122_CBC_L [exon-level]


title: HSB130_CBC_L [gene-level]


title: HSB121_CBC_R [exon-level]


title: HSB119_CBC_L [exon-level]


title: HSB118_CBC_R [exon-level]

value: 4 Y


title: HSB122_CBC_R [exon-level]

value: CBC


title: HSB121_CBC_R [gene-level]


title: HSB121_CBC_L [gene-level]

value: L


title: HSB123_CBC_L [exon-level]


title: HSB119_CBC_L [gene-level]


title: HSB118_CBC_R [gene-level]


title: HSB112_URL_R [gene-level]

value: 8 PCW


title: HSB113_CBC_L [gene-level]

value: F

value: 12 PCW


title: HSB113_CBC_L [exon-level]


title: HSB112_URL_L [gene-level]


title: HSB113_CBC_R [exon-level]


title: HSB133_CBC_L [exon-level]


title: HSB113_CBC_R [gene-level]


title: HSB112_URL_L [exon-level]


title: HSB112_URL_R [exon-level]


title: HSB111_CBC_R [gene-level]


title: HSB107_CBC_R [gene-level]

value: 21 PCW


title: HSB107_CBC_L [gene-level]


title: HSB111_CBC_R [exon-level]


title: HSB105_CBC_L [gene-level]


title: HSB106_CBC_R [gene-level]


title: HSB106_CBC_L [gene-level]


title: HSB107_CBC_R [exon-level]


title: HSB106_CBC_R [exon-level]


title: HSB103_CBC_L [gene-level]

value: 13 PCW


title: HSB107_CBC_L [exon-level]


title: HSB105_CBC_L [exon-level]


title: HSB104_URL_LR [gene-level]

value: LR

value: 5.7 PCW


title: HSB106_CBC_L [exon-level]


title: HSB103_CBC_R [gene-level]

value: R


title: HSB102_CBC_R [gene-level]


title: HSB104_URL_LR [exon-level]

value: URL

value: M


title: HSB102_CBC_L [exon-level]


title: HSB103_CBC_L [exon-level]


title: HSB103_CBC_R [exon-level]


title: HSB98_CBC_NA [gene-level]

value: 19 PCW


title: HSB100_CBC_L [gene-level]


title: HSB102_CBC_L [gene-level]


title: HSB102_CBC_R [exon-level]


title: HSB100_CBC_L [exon-level]


title: HSB100_CBC_R [gene-level]


title: HSB100_CBC_R [exon-level]


title: HSB97_CBC_L [gene-level]

value: 17 PCW


title: HSB99_CBC_NA [exon-level]


title: HSB97_CBC_R [exon-level]


title: HSB97_CBC_R [gene-level]


title: HSB98_CBC_NA [exon-level]


title: HSB97_CBC_L [exon-level]


title: HSB96_CBC_NA [exon-level]

value: 16 PCW


title: HSB92_CBC_R [gene-level]


title: HSB96_CBC_NA [gene-level]


title: HSB99_CBC_NA [gene-level]


title: Primary medulloblastoma MDT-MB-49

status: Public on Sep 14 2010

hyb_protocol: As directed by the manufacturer.

scan_protocol: As directed by the manufacturer.

data_processing:
Affymetrix CEL files were imported into Affymetrix Expression Console (Version 1.1) and gene-level analysis (CORE content) was performed.  Arrays were quantile normalized (sketch) and summarized using PLIER with PM-GCBG background correction.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: As directed by the manufacturer.

extract_protocol: Trizol method as directed by the manufacturer.

tag: tissue

value: Primary medulloblastoma

tag: histological subtype

value: Classic

tag: molecular subgroup

value: GroupD


title: Primary medulloblastoma MDT-MB-7

tag: gender

value: SHH


title: Primary medulloblastoma MDT-MB-8

value: Large cell anaplastic

value: GroupC


title: Primary medulloblastoma MDT-MB-48


title: HSB92_CBC_R [exon-level]

tag: brain code

value: CBC


title: Primary medulloblastoma MDT-MB-5

value: F


title: Primary medulloblastoma MDT-MB-6

value: Desmoplastic


title: Primary medulloblastoma MDT-MB-3


title: Primary medulloblastoma MDT-MB-226


title: Primary medulloblastoma MDT-MB-45


title: Primary medulloblastoma MDT-MB-207


title: Primary medulloblastoma MDT-MB-224


title: Primary medulloblastoma MDT-MB-44


title: Primary medulloblastoma MDT-MB-26


title: Primary medulloblastoma MDT-MB-222


title: Primary medulloblastoma MDT-MB-205

value: MBEN


title: Primary medulloblastoma MDT-MB-194


title: Primary medulloblastoma MDT-MB-229


title: Primary medulloblastoma MDT-MB-198


title: Primary medulloblastoma MDT-MB-196


title: Primary medulloblastoma MDT-MB-9


title: Primary medulloblastoma MDT-MB-220


title: Primary medulloblastoma MDT-MB-2


title: Primary medulloblastoma MDT-MB-199


title: Primary medulloblastoma MDT-MB-29


title: Primary medulloblastoma MDT-MB-4


title: Primary medulloblastoma MDT-MB-203


title: Primary medulloblastoma MDT-MB-223


title: Primary medulloblastoma MDT-MB-195


title: Primary medulloblastoma MDT-MB-188


title: Primary medulloblastoma MDT-MB-193


title: Primary medulloblastoma MDT-MB-189


title: Primary medulloblastoma MDT-MB-185


title: Primary medulloblastoma MDT-MB-186


title: Primary medulloblastoma MDT-MB-191

value: WNT


title: Primary medulloblastoma MDT-MB-181


title: Primary medulloblastoma MDT-MB-183


title: Primary medulloblastoma MDT-MB-182


title: Primary medulloblastoma MDT-MB-18


title: Primary medulloblastoma MDT-MB-166


title: Primary medulloblastoma MDT-MB-168


title: Primary medulloblastoma MDT-MB-179


title: Primary medulloblastoma MDT-MB-176


title: Primary medulloblastoma MDT-MB-173


title: Primary medulloblastoma MDT-MB-172


title: Primary medulloblastoma MDT-MB-164


title: Primary medulloblastoma MDT-MB-178


title: Primary medulloblastoma MDT-MB-167


title: Primary medulloblastoma MDT-MB-165


title: Primary medulloblastoma MDT-MB-160


title: Primary medulloblastoma MDT-MB-180


title: Primary medulloblastoma MDT-MB-177


title: Primary medulloblastoma MDT-MB-184


title: Primary medulloblastoma MDT-MB-174


title: Primary medulloblastoma MDT-MB-161


title: Primary medulloblastoma MDT-MB-152


title: Primary medulloblastoma MDT-MB-150


title: Primary medulloblastoma MDT-MB-155


title: Primary medulloblastoma MDT-MB-153


title: Primary medulloblastoma MDT-MB-156


title: Primary medulloblastoma MDT-MB-17


title: Primary medulloblastoma MDT-MB-16


title: Primary medulloblastoma MDT-MB-163


title: Primary medulloblastoma MDT-MB-157


title: Primary medulloblastoma MDT-MB-154


title: Primary medulloblastoma MDT-MB-146


title: Primary medulloblastoma MDT-MB-151


title: Primary medulloblastoma MDT-MB-147


title: Primary medulloblastoma MDT-MB-15


title: Primary medulloblastoma MDT-MB-145


title: Primary medulloblastoma MDT-MB-142


title: Primary medulloblastoma MDT-MB-162


title: Primary medulloblastoma MDT-MB-141


title: Primary medulloblastoma MDT-MB-138


title: Primary medulloblastoma MDT-MB-134


title: Primary medulloblastoma MDT-MB-127


title: Primary medulloblastoma MDT-MB-139


title: Primary medulloblastoma MDT-MB-128


title: Primary medulloblastoma MDT-MB-14


title: Primary medulloblastoma MDT-MB-136


title: Primary medulloblastoma MDT-MB-130


title: Primary medulloblastoma MDT-MB-125


title: Primary medulloblastoma MDT-MB-132


title: Primary medulloblastoma MDT-MB-129


title: Primary medulloblastoma MDT-MB-124


title: Primary medulloblastoma MDT-MB-13


title: Primary medulloblastoma MDT-MB-131


title: Primary medulloblastoma MDT-MB-122


title: Primary medulloblastoma MDT-MB-135


title: Primary medulloblastoma MDT-MB-117


title: Primary medulloblastoma MDT-MB-121


title: Primary medulloblastoma MDT-MB-119


title: Primary medulloblastoma MDT-MB-106


title: Primary medulloblastoma MDT-MB-123


title: Primary medulloblastoma MDT-MB-133


title: Primary medulloblastoma MDT-MB-101


title: Primary medulloblastoma MDT-MB-103


title: Medulloblastoma tumor MB134

status: Public on Feb 02 2009

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

country: France

institute: Institut Curie

hyb_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, California.

data_processing: GC-RMA normalization

source_name: Medulloblastoma tumor

extract_protocol: Total RNAs were isolated using the Trizol Reagent

tag: Patient age at diagnosis

value: 132.4 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB135

scan_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, California.

value: 33.5 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB133

label_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, California.

value: 158.7 months. Histological subtype:classic. CTNNB1 mutation:yes.


title: Primary medulloblastoma MDT-MB-105


title: Primary medulloblastoma MDT-MB-11


title: Medulloblastoma tumor MB136

value: 59.8 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Primary medulloblastoma MDT-MB-118

value: M


title: Primary medulloblastoma MDT-MB-108


title: Primary medulloblastoma MDT-MB-1


title: Medulloblastoma tumor MB122

value: 85.2 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB128

value: 78.1 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Primary medulloblastoma MDT-MB-107

value: Primary medulloblastoma

value: Classic


title: Medulloblastoma tumor MB117

value: 3.4 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB131

value: 130.8 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB124

value: 122.2 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Primary medulloblastoma MDT-MB-110

value: SHH


title: Medulloblastoma tumor MB119

value: 93.4 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB120

value: 108 months. Histological subtype:classic. CTNNB1 mutation:yes.


title: Medulloblastoma tumor MB116

value: 147.1 months. Histological subtype:classic. CTNNB1 mutation:yes.


title: Medulloblastoma tumor MB130

value: 24.5 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB127

value: 67.6 months. Histological subtype:classic. CTNNB1 mutation:yes.


title: Medulloblastoma tumor MB123

value: 36.8 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB118

value: 114.9 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB121

value: 69.7 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB109

value: 63.3 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB107

value: 125.4 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB108

value: 96.1 months. Histological subtype:classic nodular. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB100

value: 91.1 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB102

value: 107.6 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB96

value: 44.1 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB99

value: 98.7 months. Histological subtype:unclassifiable. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB80

value: 96.5 months. Histological subtype:nodular desmoplasic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB112

value: 137.7 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB91

value: 58.6 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB105

value: 11.7 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB106

value: 50.2 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB92

value: 106.4 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB82

value: 41.3 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB95

value: 41.3 months. Histological subtype:large cell/anaplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB81a

value: 109.5 months. Histological subtype:large cell/anaplasic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB87a

value: 87 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB79

value: 36 months. Histology subtype:medullomyoblastoma. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB93

value: 69.9 months. Histological subtype:nodular desmoplastic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB89

value: 134 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma tumor MB125

value: 42.5 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma #427

status: Public on Sep 02 2008

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.

source_name: tumor

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

tag: Gender

value: M

tag: Histology

value: Desmoplastic

tag: Metastatic stage


title: Medulloblastoma #426

value: Classic


title: Medulloblastoma tumor MB101

value: 67 months. Histological subtype:classic nodular. CTNNB1 mutation:no.


title: Medulloblastoma #435

value: F


title: Medulloblastoma #452

value: nd


title: Medulloblastoma #455


title: Medulloblastoma #434


title: Medulloblastoma tumor MB88

value: 113.7 months. Histological subtype:classic. CTNNB1 mutation:no.


title: Medulloblastoma #458


title: Medulloblastoma #424