title: F50_cortex_Hy3_Total RNA 2

status: Public on Mar 16 2010

city: Frederiksberg C

first: Agnieszka

last: Podolska

address: Grønnegårdsvej 3 2nd floor

department: Department of Basic Animal and Veterinary Sciences

country: Denmark

institute: Faculty of Life Sciences, University of Copenhagen,

description: F50_cortex_Hy3_Total RNA

hyb_protocol: The miRCURY™ LNA microRNA Microarray version 9.2 was used for the array studies. Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland), for 16 hours followed by stringent washes.

scan_protocol: Subsequently, slides were dried and scanned. The analysis were performed using the relevant GenePix® Array Lists (GAL files) www.exiqon.com. The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA), to generate Tagged Image File Format (TIFF) images. The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.

data_processing: The text files, generated by Imagene v.7.0, were imported into the R environment (R Development Core Team (2007). The importing and pre-processing of data was performed using the Linear Models for Microarray Data (LIMMA) package [25]. The “normexp” background correction method [25] was applied. The intensities were then LOG 2 transformed and normalized, using the LIMMA implementation in quantile normalization. The intensities of four intra slide replicates were used to calculate average intensities of each hybridization signal. The data were filtered, firstly to include only human and porcine microRNA (hsa and ssc microRNAs, respectively) and secondly to exclude the probes which: a) showed little or no variation; b) their intensities in all cases were close to the background c) had more than 5 not available values; d) had range of linear intensities exceeding 100. The final, filtered data set consisted of intensity values for 240 probes (see supplementary data for complete list).

organism: Sus scrofa

source_name: F50_cortex_Total RNA

label_protocol: A total of 200 ng and 1μg of the small RNA and total RNA fraction was used for each sample, respectively. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.

extract_protocol: The small and total RNA fractions were isolated from the individual tissues using the miRVana™ microRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) and TRI REAGENT® (Molecular Research Center, Inc., USA), respectively


title: Adult_cerebellum_Hy3_Small fraction

type: other

description: Adult_cerebellum_Hy3_Small fraction

molecule: other

source_name: Adult_cerebellum_Small fraction

tag: tissue


title: F100_cerebellum_Hy3_Small fraction

description: F100_cerebellum_Hy3_Small fraction

source_name: F100_cerebellum_Small fraction


title: F50_cerebellum_Hy3_Small fraction

description: F50_cerebellum_Hy3_Small fraction

source_name: F50_cerebellum_Small fraction


title: Mutant lumbar spinal cord end-stage disease

type: RNA

city: London

first: ANDREA

last: MALASPINA

state: England

address: 4 Newark Street

department: Neuroscience

country: United Kingdom

institute: Institute of Cell and Molecular Science

description: thoracic cord

hyb_protocol: 500 ng from each of the RNA pools were hybridised simultaneously to Brad-chip arrays, using a standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol, Illumina Bead-Chip Reader

data_processing: Output files were processed using the Gene Expression BeadStudio 3.2.6, with background subtraction

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat spinal cord

label_protocol: cRNA labeling was performed with 750 ng of pooled RNA, using the Ambion Total Prep kit. cRNA purity and labelling was checked using the Nanodrop and Agilent bioanalyser.

extract_protocol: RNA was extracted from the spinal cord samples using the SV total RNA isolation system (Promega, UK). RNA quantification was performed using a Nanodrop ND-1000 spectrophotometer and quality was checked using the Agilent bioanalyser system (Agilent).

tag: strain

value: Sprague-Dawley

tag: age

value: 10 weeks

tag: gender

value: female

tag: genotype

value: G93A SOD1

value: lumbar spinal cord

tag: disease state

value: end-stage disease


title: Wild type lumbar spinal cord pre-symptomatic

description: thoracic cord

value: wild type

value: pre-symptomatic


title: F100_cortex_Hy3_Small fraction

description: F100_cortex_Hy3_Small fraction

source_name: F100_cortex_Small fraction


title: Mutant lumbar spinal cord pre-symptomatic

description: thoracic cord


title: non_vasculature_retina_control.rep2

status: Public on Mar 17 2010

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: USA

institute: Genentech

hyb_protocol: Agilent's In situ Hybridization kit

scan_protocol: Agilent DNA microarray scanner

data_processing: Rosetta Resolver Feature Extraction Version 8.5.1.1 Linear & LOWESS normalized

organism: Mus musculus

source_name: 8814_NVR control

label_protocol: Agilent's Low input RNA Linear Amp kit

extract_protocol: RNA was extracted using the Arcturus PicoPure kit (MDS Analytical Technologies, #KIT0204) according to manufacturers instructions.  RNA quality was assessed using an Agilent 2100 Bioanalyzer.

tag: cell type

value: non vasculature retina control

tag: replicate

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740100

tag: reference

value: Universal Mouse Reference RNA (Stratagene Catalog #740100)


title: Mutant lumbar spinal cord disease-onset

description: thoracic cord

value: disease-onset


title: Adult_cortex_Hy3_Small fraction

description: Adult_cortex_Hy3_Small fraction

source_name: Adult_cortex_Small fraction


title: TAX577001_HDPP

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Samples were hybridized and washed as previously described (PMID:17334996).

scan_protocol: Hybridized and washed arrays were scanned using an Agilent G2565AA Scanner.

data_processing: Image data was analyzed using GenePix Pro 4.0. Result files were loaded into BASE (http://base.thep.lu.se) where they were filtered, lowess normalized and imputed for missing values using Weighted nearest neighbour imputation (WENNI). Probes were subsequently merged based on probe id and each probe was next median centered across the entire data set of consisting of 586 additional tumors (n=644 tumors in total). Hierarchical clustering was performed using pearson correlation and complete linkage in MeV (www.tm4.org). SAM analysis was performed in MeV (www.tm4.org).

organism: Homo sapiens

source_name: Breast carcinoma

label_protocol: Fluorescently labeled cDNA targets for hybridization were prepared from 5ug of total RNA using the Corning Pronto Plus System 6 kit.

extract_protocol: Total RNA was extracted from fresh frozen tissue using Trizol (Invitrogen) followed by Rneasy Midi purification (Qiagen). RNA integrity was evaluated using the Agilent Bioanalyzer 2100 system (Agilent).

tag: er

tag: histological grade

tag: node status (1=pos)

tag: hierarchical cluster

source_name: Universal Human reference RNA

value: Universal Human reference RNA, Stratagene


title: TAX577423_HDPP


title: TAX577275_HDPP


title: TAX577446_HDPP


title: TAX577485_HDPP


title: Wild type lumbar spinal cord disease-onset

description: thoracic cord


title: Wild type lumbar spinal cord  end-stage disease

description: thoracic cord


title: TAX577002_HDPP


title: F50_cortex_Hy3_Small fraction

description: F50_cortex_Hy3_Small fraction

source_name: F50_cortex_Small fraction


title: TAX577490_HDPP


title: F50_cortex_Hy3_Total RNA

description: F50_cortex_Hy3_Total RNA


title: TAX577544_HDPP


title: TAX577522_HDPP


title: TAX577492_HDPP


title: F50_cortex_Hy5_Small fraction

description: F50_cortex_Hy5_Small fraction


title: F50_cortex_Hy5_Total RNA 2

description: F50_cortex_Hy5_Total RNA


title: Adult_cerebellum_Hy5_Total RNA

description: Adult_cerebellum_Hy5_Total RNA

source_name: Adult_cerebellum_Total RNA


title: Adult_cortex_Hy5_Total RNA

description: Adult_cortex_Hy5_Total RNA

source_name: Adult_cortex_Total RNA


title: TAX577419_HDPP


title: F100_cerebellum_Hy5_Total RNA

description: F100_cerebellum_Hy5_Total RNA

source_name: F100_cerebellum_Total RNA


title: TAX577571_HDPP


title: TAX577498_HDPP


title: TAX577515_HDPP


title: TAX577012_HDPP


title: TAX577569_HDPP


title: TAX577014_HDPP


title: NAc DTx4+10 2

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description: Replicate 2 of 5.

hyb_protocol: Arrays were hybridized at 37C for 18h in a shaking incubator, and stained with streptavidin-Alexa 647.

scan_protocol: Arrays were scanned with Axon GenePixPro 4000B (Molecular Devices, Axon Instruments, Union City, CA). Images were processed using CodeLink Expression Analysis Software.

data_processing: Normalized values represent median global normalization method, i.e., background-subtracted raw intensity/median intensity of all spots on the array. Genespring Gx 7.3 was used for normalization.

source_name: nucleus accumbens, 10-day abstinence

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample.

extract_protocol: Tri-Reagent/BCP (Molecular Research Center, Cincinnati, OH).  Cleanup with Qiagen Rneasy final step (Valencia, CA).

treatment_protocol: No cocaine, or 10 days of cocaine self-administration followed by 1, 10 or 100 days of enforced abstinence.

value: nucleus accumbens

tag: experimental group

value: cocaine abstinence 10 day

value: male


title: F50_cerebellum_Hy5_Total RNA

description: F50_cerebellum_Hy5_Total RNA

source_name: F50_cerebellum_Total RNA


title: TAX577015_HDPP


title: TAX577223_HDPP


title: F100_cortex_Hy5_Total RNA

description: F100_cortex_Hy5_Total RNA

source_name: F100_cortex_Total RNA


title: NAc DTx4+10 5

description: Replicate 5 of 5.


title: NAc DTx4+10 4

description: Replicate 4 of 5.


title: NAc DTx4+10 1

description: Replicate 1 of 5.


title: NAc DTx4+10 3

description: Replicate 3 of 5.


title: TAX577421_HDPP


title: TAX577214_HDPP


title: wt, biological replicate 2

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: mb20080624yspt1fr_02_wildtype_SPB76_2wk_16.6.2008_267p60_228_(Sp20b_M_v04).CEL

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

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

data_processing: An R-based script, available on request, was used for the analysis. Values were normalized with justRMA() function from R/Bioconductor package affy using standard parameters.

organism: Schizosaccharomyces pombe

source_name: wild type

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

growth_protocol: Strains were grown at 30°C in YES (Yeast Extract with Supplements)

extract_protocol: RNA was isolated from cells collected at OD600=0.5 using the hot phenol method

tag: genome/variation


title: H3K9me2 in Kc cells, sch20080514dtr2

type: genomic

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

description: Di-methylation of Lysine 9 of Histone H3 in Kc cells.

hyb_protocol: Approximately 6-10μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
Tiling arrays were analyzed using MAT (Model-based Analysis of Tiling-array) software (Johnson et al. 2006). The bandwith was set to 1000bp for replication timing analysis, and 200bp for H3K27me3, H3K9me2, and transcription data. MAT scores were extracted from the BAR files generated using the Python script ‘Bar2Wig.py’ kindly provided by Wei Li (Harvard University). Data from the Wiggle files were reformatted using Perl for subsequent analysis in R.
HMM_based_differentially replicating regions_Kc-HP1.txt: Hidden Markov Model segmentation of replication timing differences between Kc and HP1 kd cells (HMM switch.type, difference between Comparison 1 and Comparison 1 of GSE13328), including a cutoff for strong replication timing differences (significant replication timing switch). Transcription differences (Comparison 2), replication timing (Comparison 1 and Comparison  1 of GSE13328), HP1 binding, H3K27me3 (Comparison 3), H3K9me2 (Comparison 4), numer of repeats, and repeat density (percentage of sequence covered by repeats) within HMM based regions are included (as average signal within HMM based region).

label: Biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 2K9-ChIP DNA

label_protocol: Samples (6-10μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Drosophila Kc cells were kept in HyQ-SFX (Hyclone).

extract_protocol: We sorted cells into S-phase fractions on the basis of DNA content using Fluorescent Activated Cell Sorting (FACS). We collected 60,000 cells from each fraction directly into lysis buffer. DNA was purified, sonicated, denatured and immunoprecipitated with an antibody specific for BrdU (Becton Dickinson) as described (Schubeler et al. 2002), but with two consecutive rounds of immunoprecipitation to increase specificity. RNA was isolated from cells using Trizol (Invitrogen) and subsequently purified using an RNeasy kit (QIAGEN). For hybridization to Affymetrix tiling arrays, we made double-stranded cDNA by performing two rounds of cDNA synthesis using random primers and addition of 2 mM dUTPs using the GeneChip® WT Double-Stranded cDNA Synthesis Kit (Affymetrix). ChIP for H3K27me3 and H3K9me2 was carried out as described (Bell et al. 2007).To obtain sufficient target DNA for microarray hybridization, we amplified the denatured and immunoprecipitated DNA as described (Schubeler et al. 2002).

treatment_protocol: Double stranded RNA (dsRNA) was prepared from a PCR product spanning the entire HP1 coding region, generated with primers containing a T7 RNA Polymerase binding site using the MEGASCRIPT T7 In Vitro Transcription Kit (Ambion, Cat.No. AM1334). The RNA was purified and heated to 70○C for 10 minutes and slowly cooled down to room temperature for about 30 minutes to enhance annealing. 50μg of dsRNA was added to 106 cells every 2nd day and 8 days after initial addition of dsRNA cells were harvested and the efficiency of HP1 reduction was estimated by western blot analysis using a monoclonal α-HP1 antibody.

tag: female, embryonic origin

source_name: Input DNA


title: TAX577422_HDPP


title: TAX577435_HDPP


title: TAX577065_HDPP


title: NAc DTx4+1 5

description: Replicate 5 of 5.

source_name: nucleus accumbens, 1-day abstinence

value: cocaine abstinence 1 day


title: TAX577171_HDPP


title: NAc DTx4+1 4

description: Replicate 4 of 5.


title: NAc DTx4+1 2

description: Replicate 2 of 5.


title: TAX577436_HDPP


title: H3K27me3 in Kc cells, sch20080807dtr2

description: Tri-methylation of Lysine 27 of Histone H3 in Kc cells.

source_name: 3K27-ChIP DNA


title: TAX577040_HDPP


title: H3K9me2 in Kc cells

data_processing: Tiling arrays were analyzed using MAT (Model-based Analysis of Tiling-array) software (Johnson et al. 2006). The bandwith was set to 1000bp for replication timing and nascent DNA analysis, and 300bp for H4K16ac , RNA Polymerase II and transcription data. MAT scores were extracted from the BAR files generated using the Python script ‘Bar2Wig.py’ kindly provided by Wei Li (Harvard University). Data from the Wiggle files were reformatted using Perl for subsequent analysis in R.

extract_protocol: Protocol based on Fatemi et al., (Fatemi et al, 2005) with minor modifications. Drosophila cells were suspended in 1ml cold RSB (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.25% NP-40) and placed on ice for 3 min, followed by cold centrifugation for 5 min at 3000 rpm. Next, nuclei were washed twice with 1x M.SssI methylation buffer (10mM Tris-HCl pH 7.9, 50 mM NaCl, 10mM MgCl2, 0.3 M sucrose, freshly added 1mM DTT and Complete protease inhibitor (Roche)). Finally, nuclei were resuspended in 1x M.SssI buffer to a concentration of 5x107 nuclei/ml. In vitro methylation was performed at ambient temperature with 100 ul nuclei (5x106 nuclei) and adding 1ul 32mM SAM, 15ul SssI (60U) and 34ul water to a final volume of 150ul. The reaction was terminated by addition of 2x Bradley buffer and Proteinase K and incubation at 55°C. Fully methylated DNA served as control and was obtained by repeatedly treating genomic DNA with M.SssI and SAM for 3h (Schubeler et al, 2001). MeDIP was performed as previously described (Weber et al., 2007) using 2 ug sonicated (300-1000 bp) genomic DNA as starting material and 2 ug antibody against 5-methylcytidine (Eurogentec, BI-MECY-1000). Mouse monoclonal antibodies against H3K36me2 as previously described (Bell et al. 2008). H3K4me3 (gift from Bryan Turner, described in Schubeler et al., 2004), H3K36me3 (Abcam ab9050), H4K16ac (Upstate 07-329), 5-methylcytidine (Eurogentec, BI-MECY-1000).

tag: antibody

value: female, embryonic origin


title: TAX577042_HDPP


title: NAc DTx4+1 3

description: Replicate 3 of 5.

value: Sprague-Dawley

tag: tissue


title: H3K27me3 in Kc cells


title: NAc DTx4+1 1

description: Replicate 1 of 5.

tag: strain


title: TAX577053_HDPP


title: NAc Naïve 5

description: Replicate 5 of 5.

source_name: nucleus accumbens, naïve

value: Naïve


title: F50_cortex_Hy5_Total RNA

description: F50_cortex_Hy5_Total RNA

source_name: F50_cortex_Total RNA


title: TAX577039_HDPP


title: accessibility of Kc cells

description: Chromatin accessibility in S2 cells as measured by MeDIP-footprint.

source_name: 3-5min methylated DNA

source_name: fully methylated DNA


title: TAX577052_HDPP

source_name: Breast carcinoma

source_name: Universal Human reference RNA


title: TAX577048_HDPP


title: TAX577354_HDPP


title: TAX577047_HDPP


title: NAc Naïve 4

description: Replicate 4 of 5.


title: TAX577331_HDPP


title: TAX577022_HDPP


title: TAX577279_HDPP


title: NAc Naïve 3

description: Replicate 3 of 5.


title: NAc Naïve 2

description: Replicate 2 of 5.


title: TAX577280_HDPP


title: NAc Naïve 1

description: Replicate 1 of 5.


title: TAX577033_HDPP


title: TAX577034_HDPP


title: mPFC DT4+100 6

description: Replicate 6 of 6.

source_name: medial prefrontal cortex, 100-day abstinence

value: medial prefrontal cortex

value: cocaine abstinence 100 day


title: TAX577281_HDPP


title: TAX577193_HDPP


title: TAX577036_HDPP


title: TAX577146_HDPP


title: mPFC DT4+100 4

description: Replicate 4 of 6.


title: mPFC DT4+100 3

description: Replicate 3 of 6.


title: TAX577116_HDPP


title: TAX577128_HDPP


title: TAX577129_HDPP


title: TAX577327_HDPP


title: TAX577088_HDPP


title: TAX577302_HDPP


title: mPFC DT4+100 5

description: Replicate 5 of 6.


title: TAX577289_HDPP


title: TAX577277_HDPP


title: TAX577305_HDPP


title: mPFC DT4+1 4

description: Replicate 4 of 6.

source_name: medial prefrontal cortex, 1-day abstinence


title: TAX577290_HDPP


title: TAX577057_HDPP


title: transcript levels in Kc and HP1 knockdown cells, sch20070412dtr

description: Total RNA was measured in Kc cells with and without HP1 knockdown.

source_name: random-primed cDNA from total RNA of Kc cells

source_name: random-primed cDNA from total RNA from Cl8 cells

value: total RNA from HP1 knockdown cells


title: mPFC Naïve 5

description: Replicate 5 of 6.

source_name: medial prefrontal cortex, naïve


title: mPFC DT4+1 5

description: Replicate 5 of 6.


title: replication timing of Kc cells after knockdown of HP1, sch20070411dtr

description: The timing of DNA replication in Kc cells after HP1 knockdown.

source_name: early replicating DNA

value: cells in early S phase

source_name: late replicating DNA

value: genomic DNA of cells in late S phase


title: mPFC DT4+100 2

description: Replicate 2 of 6.


title: TAX577284_HDPP


title: mPFC DT4+1 1

description: Replicate 1 of 6.


title: mPFC DT4+100 1

description: Replicate 1 of 6.


title: accessibility of S2 cells

description: Chromatin accessibility in Kc cells as measured by MeDIP-footprint.

value: male, embryonic origin


title: mPFC DT4+1 6

description: Replicate 6 of 6.


title: mPFC DT4+1 2

description: Replicate 2 of 6.


title: TAX577049_HDPP


title: mPFC Naïve 6

description: Replicate 6 of 6.


title: mPFC DT4+1 3

description: Replicate 3 of 6.


title: mPFC Naïve 4

description: Replicate 4 of 6.


title: mPFC Naïve 1

description: Replicate 1 of 6.


title: mPFC Naïve 3

description: Replicate 3 of 6.


title: H3K36me3 in Kc cells

description: Tri-methylation of Lysine 36 of Histone H3 in Kc cells.

source_name: 3K36-ChIP DNA


title: H3K4me3 in Kc cells

description: Tri-methylation of Lysine 4 of Histone H3 in Kc cells.

source_name: 3K4-ChIP DNA

source_name: Input DNA


title: HOTAIR EZH2 promoter 2

city: Stanford

first: Rajnish

last: Gupta

address: CCSR Room 2155

institute: Stanford University

description: EZH2 ChIP DNA from MDA-MB-231 HOTAIR

hyb_protocol: Labeled DNA was hybridized to Nimblegen promoter arrays according to standard Nimblegen protocols

scan_protocol: Slides were scanned using a Axon 4000B scanner

data_processing: Experimental/input (Cy5/C3) ratio files were generated and peaks filtered with FDR less than or equal to 0.2

source_name: EZH2 ChIP DNA from MDA-MB-231 HOTAIR

label_protocol: Amplified DNA was labeled according to standard Nimblegen protocols

extract_protocol: Genomic DNA was isolated from MDA-MB-231 Vector or HOTAIR cells and amplifed using the Sigma Whole Genome Amplification Kit

tag: cell line

tag: ab


title: Control_D-47 [miRNA]

status: Public on Mar 15 2010

city: Cambridge

first: Matthew

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

institute: MRC Cancer Cell Unit

description: Biological replicate 7 of 8

hyb_protocol: Test and reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA array platform version 9.2 (Exiqon, Vedbaek, Denmark), according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., Santa Clara, CA, USA), followed by image analysis using ImaGene 7.0 software (BioDiscovery, Inc., El Segundo, CA, USA).

data_processing:
The resultant .txt files were processed using the Bioconductor package limma in the statistical software environment R. Within-array normalization was performed using the global loess method and between-array normalization using the Aquantile method.
VALUE = Post global loess normalization log2 ratios (test/reference)

source_name: Developmental fetal ovary control

label_protocol: Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark). Microarrays were hybridized using a Tecan HS4800 hybridization station (Tecan, Grödig, Austria)

growth_protocol: Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.

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

treatment_protocol: Nil; pre-treatment

tag: tumor composition

tag: anatomical site

value: Ovary

tag: gender

value: Female

tag: age (yrs)

tag: tumor stage

value: Pooled human RNA from 20 anatomical sites


title: Control_D-48 [miRNA]

description: Biological replicate 8 of 8

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX

tag: reference


title: Vector H3K27 promoter 2

description: H3K27 ChIP DNA from MDA-MB-231 Vector

source_name: H3K27 ChIP DNA from MDA-MB-231 Vector


title: Vector EZH2 promoter 2

description: EZH2 ChIP DNA from MDA-MB-231 Vector

source_name: EZH2 ChIP DNA from MDA-MB-231 Vector


title: Control_D-46 [miRNA]

description: Biological replicate 6 of 8

source_name: Developmental fetal yolk sac control

value: Yolk sac


title: TAX577420_HDPP

source_name: Breast carcinoma

tag: er

tag: histological grade

source_name: Universal Human reference RNA

value: Universal Human reference RNA, Stratagene


title: UMC-iPSC-C6

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: Gene expression data from UMC iPSC cell line C6

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: iPSCs from umbilical cord mesenchymal cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Human iPSCs and H9 were cultured on Matrigel using mTeSR1 medium. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No special treatment during the culture.

tag: tissue source

value: umbilical cord

tag: cell type

value: induced pluripotent stem cells (iPSCs)


title: UMC-iPSC-C1

description: Gene expression data from UMC iPSC cell line C1.


title: HOTAIR H3K27 promoter 2

description: H3K27 ChIP DNA from MDA-MB-231 HOTAIR

source_name: H3K27 ChIP DNA from MDA-MB-231 HOTAIR


title: AMC-iPSC-C22

description: Gene expression data from AMC iPSC cell line C22.

source_name: iPSCs from amniotic mesenchymal cells

value: placenta


title: Control_D-45 [miRNA]

description: Biological replicate 5 of 8


title: AMC-iPSC-C28

description: Gene expression data from AMC iPSC cell line C28.


title: Vector SUZ12 promoter 2

description: SUZ12 ChIP DNA from MDA-MB-231 Vector

source_name: SUZ12 ChIP DNA from MDA-MB-231 Vector


title: HOTAIR SUZ12 promoter 2

description: SUZ12 ChIP DNA from MDA-MB-231 HOTAIR

source_name: SUZ12 ChIP DNA from MDA-MB-231 HOTAIR


title: H9-ESC

description: Gene expression data from ES cell line H9.

source_name: embryonic stem cells

value: embryonic stem cells (ESC)


title: Control_N-43 [miRNA]

description: Biological replicate 3 of 8

source_name: Normal post-pubertal testis control

value: Testis

value: Male


title: Control_N-44 [miRNA]

description: Biological replicate 4 of 8

source_name: Normal post-pubertal ovary control


title: Control_N-41 [miRNA]

description: Biological replicate 1 of 8

source_name: Normal pre-pubertal testis control


title: Cell line_CL-40 [miRNA]

description: Biological replicate 6 of 6

source_name: Cell line 2102Ep

value: Cell line


title: Cell line_CL-39 [miRNA]

description: Biological replicate 5 of 6

source_name: Cell line TCam-2


title: Control_N-42 [miRNA]

description: Biological replicate 2 of 8

source_name: Normal pre-pubertal ovary control

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Benign germ cell tumor_IT-29 [miRNA]

description: Biological replicate 1 of 6

source_name: Immature teratoma replicate 1

value: Pure

value: Immature


title: Cell line_CL-36 [miRNA]

description: Biological replicate 2 of 6

source_name: Cell line GCT44


title: Cell line_CL-35 [miRNA]

description: Biological replicate 1 of 6

source_name: Cell line Tera-2


title: Benign germ cell tumor_IT-30 [miRNA]

description: Biological replicate 2 of 6

source_name: Immature teratoma replicate 2


title: Benign germ cell tumor_IT-31 [miRNA]

description: Biological replicate 3 of 6

source_name: Immature teratoma replicate 3

value: Abdominal


title: Cell line_CL-38 [miRNA]

description: Biological replicate 4 of 6

source_name: Cell line 1411H


title: Vector SUZ12 promoter 1

description: SUZ12 ChIP DNA from MDA-MB-231 Vector

source_name: Input DNA


title: HOTAIR H3K27 promoter 1

description: H3K27 ChIP DNA from MDA-MB-231 HOTAIR

source_name: H3K27 ChIP DNA from MDA-MB-231 HOTAIR


title: Malignant germ cell tumor_EC-28 [miRNA]

description: Biological replicate 3 of 3

source_name: Embryonal carcinoma replicate 3


title: Trichoderma reesei QM6a CGH self hybridization

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

description: Biological replicate 1.

hyb_protocol: The two samples were then mixed together and hybridised according to the oligo aCGH/ChIP-on-Chip hybridisation kit (Agilent).

scan_protocol: Array was read using a GenePix 4000B scanner (Molecular Devices) and the signal analysis was done using the GenePix Pro 6.1 software.

data_processing: Data pretreatment was applied on each result file to discard GenePix flag and saturating spots. The data were normalised without background subtraction by the global Lowess method performed with the Goulphar software (Lemoine, 2006).

label: Alexa 555

organism: Trichoderma reesei

source_name: Genomic DNA extracted from wil type (QM6a).

label_protocol: Four µg of genomic DNA were labelled with Alexa 555 using the BioPrime Total aCGH labelling kit (Invitrogen).

extract_protocol: Chromosomal DNA from T. reesei QM6a strain was prepared as described previously (Seidl, 2008, PMID: 18620557).

label: Alexa 647

label_protocol: Four µg of genomic DNA were labelled with Alexa 647 using the BioPrime Total aCGH labelling kit (Invitrogen).


title: Benign germ cell tumor_MT-34 [miRNA]

description: Biological replicate 6 of 6

source_name: Mature teratoma replicate 3

value: Mixed, within yolk sac tumor

value: Mature


title: Benign germ cell tumor_MT-32 [miRNA]

description: Biological replicate 4 of 6

source_name: Mature teratoma replicate 1

value: Sacrococcygeal


title: Timepoint1b_CP_rep3

city: Rochester

first: Atta

last: Behfar

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Gene expression data from stem cells following combinatorial growth factor stimulation

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Stem cells following combinatorial growth factor stimulation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell culture derived from inner cell mass of murine blastocysts.

extract_protocol: Extraction of total RNA using the Invitrogen Micro-to-Midi kit, performed according to the manufacturer's instructions.

value: cardopoietic cell (CP)


title: Benign germ cell tumor_MT-33 [miRNA]

description: Biological replicate 5 of 6

source_name: Mature teratoma replicate 2

value: Ovary

value: Female

value: Pooled human RNA from 20 anatomical sites


title: Timepoint2_CM_rep3

value: cardiomyocyte (CM)


title: Vector H3K27 promoter 1

description: H3K27 ChIP DNA from MDA-MB-231 Vector

source_name: H3K27 ChIP DNA from MDA-MB-231 Vector


title: Timepoint1b_CP_rep2


title: HOTAIR SUZ12 promoter 1

description: SUZ12 ChIP DNA from MDA-MB-231 HOTAIR

source_name: SUZ12 ChIP DNA from MDA-MB-231 HOTAIR


title: HOTAIR EZH2 promoter 1

description: EZH2 ChIP DNA from MDA-MB-231 HOTAIR

source_name: EZH2 ChIP DNA from MDA-MB-231 HOTAIR


title: Vector EZH2 promoter 1

description: EZH2 ChIP DNA from MDA-MB-231 Vector

source_name: EZH2 ChIP DNA from MDA-MB-231 Vector


title: Malignant germ cell tumor_Sem-18 [miRNA]

description: Biological replicate 6 of 13

source_name: Seminoma replicate 6

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Malignant germ cell tumor_Sem-24 [miRNA]

description: Biological replicate 12 of 13

source_name: Seminoma replicate 12


title: Malignant germ cell tumor_Sem-21 [miRNA]

description: Biological replicate 9 of 13

source_name: Seminoma replicate 9

value: Metastasis from gonadal primary


title: Malignant germ cell tumor_Sem-25 [miRNA]

description: Biological replicate 13 of 13

source_name: Seminoma replicate 13


title: Malignant germ cell tumor_EC-26 [miRNA]

description: Biological replicate 1 of 3

source_name: Embryonal carcinoma replicate 1


title: Malignant germ cell tumor_Sem-22 [miRNA]

description: Biological replicate 10 of 13

source_name: Seminoma replicate 10


title: Malignant germ cell tumor_Sem-23 [miRNA]

description: Biological replicate 11 of 13

source_name: Seminoma replicate 11


title: Malignant germ cell tumor_Sem-19 [miRNA]

description: Biological replicate 7 of 13

source_name: Seminoma replicate 7


title: Malignant germ cell tumor_Sem-17 [miRNA]

description: Biological replicate 5 of 13

source_name: Seminoma replicate 5


title: AP: in vivo vs in vitro Rep4 (Dye swap)

city: Cairo

first: Ramy

middle: Karam

last: Aziz

address: Qasr-El-Einy Street

department: Microbiology and Immunology

country: Egypt

institute: Faculty of Pharmacy, Cairo University

hyb_protocol: Genisphere 3DNA Array 900TM protocol (Genisphere, http://www.genisphere.com/array_detection_900.html)

scan_protocol: Scanner=GenePix 4000B [83743]; FocusPosition=0; LinesAveraged=2; room temperature

data_processing: GenePixPro 4.0 and GeneSpring 7 to output genelists

label: Alexa Fluor 546, Genisphere Dendrimers

organism: Streptococcus pyogenes

source_name: 5448 AP, in vivo

label_protocol: Genisphere 3DNA Dendrimers followed by post-hybridization labeling with an equal mixture of Alexa Fluor 546 or 647 post-hybridization

growth_protocol: In vitro: Bacteria were grown in Todd Hewitt broth supplemented with 1.5% yeast extract for either 12h or (mostly) 18h; In vivo: Overnight in vitro culture was washed in phosphate-buffer saline and injected in sterile Teflon chambers implanted under mice skin

extract_protocol: RNA was extracted with QIAgen RNeasey kit after the bacteria were beaten with beads; RNA was treated with DNase until no contaminating genomic DNA was detected; RNA was purified and concentrated with QIAgen RNeasy Microelute.

tag: clone

tag: isolate

label: Alexa Fluor 647, Genisphere Dendrimers

source_name: 5448 AP, in vitro


title: AP: in vitro vs in vivo Rep4


title: Malignant germ cell tumor_Sem-20 [miRNA]

description: Biological replicate 8 of 13

source_name: Seminoma replicate 8


title: AP: in vivo vs in vitro Rep3 (Dye swap)


title: Malignant germ cell tumor_Sem-16 [miRNA]

description: Biological replicate 4 of 13

source_name: Seminoma replicate 4

value: Central nervous system


title: H3K36me2 in Kc cells

description: Di-methylation of Lysine 36 of Histone H3 in Kc cells.

source_name: 2K36-ChIP DNA

tag: antibody

value: female, embryonic origin

source_name: Input DNA


title: adult_Control_Testis-5 [mRNA]

description: GEO reference number: GSM72499

hyb_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014

data_processing: Pre-processing of microarray .cel (CEL) files (including background correction and normalization) was performed using the Bioconductor package Robust Multi-Array Average (RMA) in the statistical software environment R.

source_name: Normal gonadal control replicate 5 of 5

value: Testis

tag: developmental stage

value: adult


title: Timepoint1_ES-LIF(-)_rep3

description: Gene expression data from stem cells following growth factor withdrawal

source_name: Stem cells following growth factor withdrawal

value: ES-LIF(-)


title: mPFC Naïve 2

description: Replicate 2 of 6.

source_name: medial prefrontal cortex, naïve

tag: strain

value: Sprague-Dawley

tag: tissue

value: medial prefrontal cortex

tag: experimental group

value: Naïve

value: male


title: Control_ES-LIF(+)_rep3

description: Gene expression data from naïve stem cells

source_name: Naïve murine stem cells

value: ES-LIF(+)


title: adult_Control_Testis-4 [mRNA]

description: GEO reference number: GSM72498

scan_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014

source_name: Normal gonadal control replicate 4 of 5

tag: tumor composition

value: Male


title: adult_Control_Testis-3 [mRNA]

description: GEO reference number: GSM72497

source_name: Normal gonadal control replicate 3 of 5

label_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014

tag: anatomical site


title: Malignant germ cell tumor_Sem-15 [miRNA]

description: Biological replicate 3 of 13

source_name: Seminoma replicate 3

value: Pure

tag: gender

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Malignant germ cell tumor_Sem-14 [miRNA]

description: Biological replicate 2 of 13

source_name: Seminoma replicate 2

tag: age (yrs)


title: AP: in vivo vs in vitro Rep2


title: Malignant germ cell tumor_Sem-13 [miRNA]

description: Biological replicate 1 of 13

source_name: Seminoma replicate 1

value: Ovary

tag: tumor stage


title: AP: in vitro vs in vivo Rep3


title: AP: in vitro vs in vivo Rep1


title: adult_Control_Testis-2 [mRNA]

description: GEO reference number: GSM72496

source_name: Normal gonadal control replicate 2 of 5

growth_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014


title: WT: in vitro vs in vivo Rep4

source_name: 5448 WT, in vitro

source_name: 5448 WT, in vivo


title: Malignant germ cell tumor_YST-12 [miRNA]

description: Biological replicate 12 of 12

source_name: Yolk sac tumor replicate 12

value: Vagina

value: Female

tag: reference


title: WT: in vivo vs in vitro Rep3 (Dye swap)


title: adult_Malignant germ cell tumor_Seminoma-12 [mRNA]

description: GEO reference number: GSM72485

source_name: Seminoma replicate 12 of 12

extract_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014


title: Placenta_Spike_Pool6_Exiqon

status: Public on Mar 18 2010

city: Austin

first: Sachin

last: Sah

state: TX

address: 2150 Woodward St, Suite 100

institute: Asuragen Inc.

description:
Hy5 raw data file: 0_Exiqon_13764702_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764702_S01_Cropped.txt

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.

scan_protocol: Arrays were scanned as per Exiqons protocols.

data_processing: Log ratios between the Hy3/Hy5 have been provided along with the normalized independent Hy3 and Hy5 signals. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Human Placenta_Spike_Pool6

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit

extract_protocol: Total RNA was extracted from placental tissue using the miRVana Isolation Kit (Ambion). Protocol was used in such a way that small RNAs were retained.

value: Placenta

source_name: Human Placenta Pools_1-7


title: TonsilPoolCD3-3

city: Houston

first: Carl

last: Allen

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

description: Project: Cell-Specific Gene Expression in Langerhans Cell Histiocytosis.

hyb_protocol: Biotinylated cDNA was hybridized for 16 hours at 45oC at 60 revolutions per minute.  The chips were processed in the fluidic station using the FS450_004 wash and stain protocol.

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

data_processing: Normalization and probe set summarization was done in BRB-Arraytools (v3.7).  The dataset is an unfiltered list.

source_name: Sorted CD3+ Cells from 5 pooled tonsils (presumably normal).

label_protocol: Amplified cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module v2 (Nugen).

extract_protocol: RNA was extracted with PicoPure RNA Isolation Kit (Molecular Devices).  Quality was verified with the Agilent 6000 Picochip.  RNA was then amplified with the WT-Ovation Pico System (Nugen).

value: tonsils


title: Malignant germ cell tumor_YST-11 [miRNA]

description: Biological replicate 11 of 12

source_name: Yolk sac tumor replicate 11

value: Pooled human RNA from 20 anatomical sites


title: TonsilPool-CD3-2


title: adult_Control_Testis-1 [mRNA]

description: GEO reference number: GSM72495

source_name: Normal gonadal control replicate 1 of 5

treatment_protocol: As per published paper: Korkola et al, Cancer Research 2006:66;820-7; PMID 16424014


title: adult_Malignant germ cell tumor_Seminoma-10 [mRNA]

description: GEO reference number: GSM72467

source_name: Seminoma replicate 10 of 12


title: TonsilPool4-CD3-4


title: TonsilPool-CD3-1


title: WT: in vitro vs in vivo Rep3


title: WT: in vivo vs in vitro Rep2 (Dye swap)


title: Skin CD207-9

source_name: Control Skin - Sorted Epidermal CD207+ Cells

value: skin


title: adult_Malignant germ cell tumor_Seminoma-9 [mRNA]

description: GEO reference number: GSM72457

source_name: Seminoma replicate 9 of 12

value: Testis


title: Malignant germ cell tumor_YST-9 [miRNA]

description: Biological replicate 9 of 12

source_name: Yolk sac tumor replicate 9


title: adult_Malignant germ cell tumor_Seminoma-11 [mRNA]

description: GEO reference number: GSM72473

source_name: Seminoma replicate 11 of 12

value: adult


title: WT: in vitro vs in vivo Rep2


title: Malignant germ cell tumor_YST-8 [miRNA]

description: Biological replicate 8 of 12

source_name: Yolk sac tumor replicate 8

value: Mixed, within mature teratoma

value: Sacrococcygeal

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Malignant germ cell tumor_YST-6 [miRNA]

description: Biological replicate 6 of 12

source_name: Yolk sac tumor replicate 6


title: Skin-CD207-8


title: Skin-CD207-7


title: Malignant germ cell tumor_YST-5 [miRNA]

description: Biological replicate 5 of 12

source_name: Yolk sac tumor replicate 5


title: Malignant germ cell tumor_YST-10 [miRNA]

description: Biological replicate 10 of 12

source_name: Yolk sac tumor replicate 10


title: WT: in vivo vs in vitro Rep1 (Dye swap)

source_name: 5448 WT, in vivo

source_name: 5448 WT, in vitro


title: WT: in vitro vs in vivo Rep1


title: adult_Malignant germ cell tumor_Seminoma-5 [mRNA]

description: GEO reference number: GSM72452

source_name: Seminoma replicate 5 of 12


title: adult_Malignant germ cell tumor_Seminoma-6 [mRNA]

description: GEO reference number: GSM72453

source_name: Seminoma replicate 6 of 12


title: adult_Malignant germ cell tumor_Seminoma-8 [mRNA]

description: GEO reference number: GSM72456

source_name: Seminoma replicate 8 of 12


title: adult_Malignant germ cell tumor_Seminoma-7 [mRNA]

description: GEO reference number: GSM72454

source_name: Seminoma replicate 7 of 12


title: adult_Malignant germ cell tumor_Seminoma-4 [mRNA]

description: GEO reference number: GSM72439

source_name: Seminoma replicate 4 of 12


title: Malignant germ cell tumor_YST-4 [miRNA]

description: Biological replicate 4 of 12

source_name: Yolk sac tumor replicate 4


title: In vivo: AP vs WT Rep6/ Dye swap

source_name: 5448 AP, in vivo


title: In vivo: WT vs AP Rep5


title: adult_Malignant germ cell tumor_Seminoma-3 [mRNA]

description: GEO reference number: GSM72405

source_name: Seminoma replicate 3 of 12


title: Skin-CD207-3

source_name: Control Skin - Sorted Epidermal CD207+ Cells


title: Skin-CD207-4


title: Skin-CD207-5


title: Skin-CD207-2


title: Skin-CD207-6


title: adult_Malignant germ cell tumor_Seminoma-2 [mRNA]

description: GEO reference number: GSM72404

source_name: Seminoma replicate 2 of 12


title: Malignant germ cell tumor_YST-3 [miRNA]

description: Biological replicate 3 of 12

source_name: Yolk sac tumor replicate 3


title: In vivo: WT vs AP Rep4


title: Malignant germ cell tumor_YST-1 [miRNA]

description: Biological replicate 1 of 12

source_name: Yolk sac tumor replicate 1

value: Central nervous system

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: In vivo: AP vs WT Rep6/ Duplicate


title: Cell line_CL-37 [miRNA]

description: Biological replicate 3 of 6

source_name: Cell line PA-1

value: Cell line


title: Skin-CD207-11


title: In vitro: WT vs AP Rep3

source_name: 5448 WT, in vitro, 18h

source_name: 5448 AP, in vitro, 18h


title: In vivo: WT vs AP Rep1

source_name: 5448 WT, in vivo


title: adult_Malignant germ cell tumor_YST-8 [mRNA]

description: GEO reference number: GSM72477

source_name: Yolk sac tumor replicate 8 of 8


title: In vivo: WT vs AP Rep2


title: In vitro: AP vs WT Rep3 (Dye swap)


title: Skin-CD207-12


title: adult_Malignant germ cell tumor_Seminoma-1 [mRNA]

description: GEO reference number: GSM72398

source_name: Seminoma replicate 1 of 12


title: adult_Malignant germ cell tumor_YST-7 [mRNA]

description: GEO reference number: GSM72474

source_name: Yolk sac tumor replicate 7 of 8


title: Skin-CD207-10


title: In vitro: AP vs WT Rep2 (Dye swap)


title: adult_Malignant germ cell tumor_YST-5 [mRNA]

description: GEO reference number: GSM72447

source_name: Yolk sac tumor replicate 5 of 8


title: adult_Malignant germ cell tumor_YST-6 [mRNA]

description: GEO reference number: GSM72469

source_name: Yolk sac tumor replicate 6 of 8


title: Skin-CD207-1


title: adult_Malignant germ cell tumor_YST-4 [mRNA]

description: GEO reference number: GSM72431

source_name: Yolk sac tumor replicate 4 of 8


title: LCH-P-CD3-14

source_name: Langerhans Cell Histiocytosis - Sorted Peripheral CD3+ Cells

value: blood


title: In vitro: WT vs AP Rep2


title: LCH-P-CD3-7


title: LCH-P-CD3-11


title: In vivo: AP vs WT Rep3/ Dye swap

source_name: 5448 AP, in vivo


title: In vitro: AP vs WT 12 h (Dye swap)

source_name: 5448 AP, in vitro, 12h


title: In vitro: AP vs WT Rep1 (Dye swap)


title: LCH-P-CD3-9


title: In vitro: WT vs AP Rep1


title: adult_Malignant germ cell tumor_YST-2 [mRNA]

description: GEO reference number: GSM72416

source_name: Yolk sac tumor replicate 2 of 8


title: LCH-P-CD3-3


title: adult_Malignant germ cell tumor_YST-1 [mRNA]

description: GEO reference number: GSM72401

source_name: Yolk sac tumor replicate 1 of 8


title: Control_N-44 [mRNA]

hyb_protocol: Target cRNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) at Geneservice Ltd (Cambridge Science Park, Cambridge, UK), formerly MRC Geneservice. Briefly, spike controls were added to 15 µg fragmented cRNA before overnight hybridization with the Genechip Human Genome U133A arrays (Affymetrix).

scan_protocol: Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner.

data_processing: The array, once scanned, was used to generate an image file (with the extension .dat). GeneChip Operating Software (GCOS) was then used to compute cell intensity data from the image file and this data was saved in a file with the extension .cel. The .cel (CEL) files were provided by Geneservice Ltd and used for subsequent data analysis. Pre-processing of microarray data (including background correction and normalization) was performed using the Bioconductor package Robust Multi-Array Average (RMA) in the statistical software environment R.

source_name: Normal gonadal control replicate 3 of 3

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA in a one-cycle target labeling procedure, with minor modifications from the manufacturer’s recommendations available at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx. Briefly, 10 µg of cleaned total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 10-fold amplification of RNA.

tag: tumor type

value: control

value: Postpubertal ovary


title: adult_Malignant germ cell tumor_YST-3 [mRNA]

description: GEO reference number: GSM72430

source_name: Yolk sac tumor replicate 3 of 8

value: Pure

value: Male


title: In vitro: WT vs AP 12 h

source_name: 5448 WT, in vitro, 12h


title: Malignant germ cell tumor_Sem-25 [mRNA]

description: GEO reference number: GSM267503

source_name: Seminoma replicate 6 of 6

value: Seminoma

value: Ovary


title: LCH-CD3-11

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD3+ Cells

value: Langerhans cell histiocytosis lesion


title: LCH-P-CD3-2


title: Malignant germ cell tumor_EC-26 [mRNA]

source_name: Embryonal carcinoma replicate 1 of 1

value: Embryonal carcinoma

value: Metastasis from gonadal primary


title: Benign germ cell tumor_MT-34 [mRNA]

source_name: Mature teratoma replicate 1 of 1

value: Mature teratoma

value: Mixed, within yolk sac tumor

value: Female

value: Mature


title: LCH-CD3-9


title: LCH-CD3-14


title: Control_N-41 [mRNA]

source_name: Normal gonadal control replicate 1 of 3

value: Prepubertal testis


title: LCH-P-CD3-6


title: LCH-CD3-7


title: LCH-CD3-8


title: Malignant germ cell tumor_Sem-23 [mRNA]

description: GEO reference number: GSM267504

source_name: Seminoma replicate 4 of 6


title: LCH-CD3-12


title: LCH-CD3-6


title: Malignant germ cell tumor_Sem-24 [mRNA]

description: GEO reference number: GSM267500

source_name: Seminoma replicate 5 of 6


title: Malignant germ cell tumor_EC-27 [miRNA]

description: Biological replicate 2 of 3

source_name: Embryonal carcinoma replicate 2

value: Testis

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX

value: Pooled human RNA from 20 anatomical sites


title: LCH-CD3-5


title: Malignant germ cell tumor_Sem-13 [mRNA]

description: GEO reference number: GSM267501

source_name: Seminoma replicate 1 of 6


title: Malignant germ cell tumor_YST-11 [mRNA]

description: GEO reference number: GSM267521

source_name: Yolk sac tumor replicate 10 of 10

value: Yolk sac tumor


title: Malignant germ cell tumor_YST-10 [mRNA]

description: GEO reference number: GSM267515

source_name: Yolk sac tumor replicate 9 of 10


title: Malignant germ cell tumor_Sem-14 [mRNA]

description: GEO reference number: GSM267505

source_name: Seminoma replicate 2 of 6

value: Central nervous system


title: LCH-CD3-3


title: LCH-CD3-4


title: LCH-CD3-1


title: LCH-CD207-7

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD207+ Cells


title: Malignant germ cell tumor_YST-8 [mRNA]

description: GEO reference number: GSM267523

source_name: Yolk sac tumor replicate 8 of 10

value: Mixed, within mature teratoma

value: Sacrococcygeal


title: Malignant germ cell tumor_YST-7 [mRNA]

description: GEO reference number: GSM267508

source_name: Yolk sac tumor replicate 7 of 10

value: Pure

value: Male


title: Malignant germ cell tumor_Sem-15 [mRNA]

description: GEO reference number: GSM267506

source_name: Seminoma replicate 3 of 6

value: Seminoma


title: LCH-CD207-3

value: Langerhans cell histiocytosis lesion


title: NSCB_CGH_385K_314_WA01

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

hyb_protocol: 7.9.1. Set the Roche NimbleGen Hybridization System 12 to 48°C. With the cover closed, allow at least 3 hours for the temperature to stabilize. 7.9.2. Hybridization Solution Master Mix per Chip 7.9.2.1. Thaw Alignment Oligo on ice, protected from light. 7.9.2.2. Add 11.8µl 2X Hybridization Buffer to 0.2ml PCR tube. 7.9.2.3. Add 4.7µl Hybridization Component A. 7.9.2.4. Add 0.5µl Alignment Oligo. Total amount of solution is 17.0µl. 7.9.2.5. Vortex to mix. 7.9.2.6. Briefly centrifuge samples using a tabletop centrifuge and keep on ice, protected from light. 7.9.3. Combine Test and Reference DNA Samples 7.9.3.1. Quantify each sample using the NanoDrop as described in SOP-SS-001 7.9.3.2. Combine 6µg each of test and reference labeled DNA in a PCR tube and bring to total volume of 5µl with VWR water. The combined volume of the test and reference samples must not exceed 5.0µl. Each of the labeled samples must fall within the concentration range of 2400-3400/ml. 7.9.3.2.1. If the concentration of the labeled sample is low, dehydrate the labeled sample in the SpeedVac at high heat for 3 minutes with tube lids open. Monitor the volume of sample to prevent complete dehydration. 7.9.3.2.2. If the concentration is still too low, reprecipitate starting from the second DNA precipitation (do NOT add 11.5ul of 5M NaCl) and rehydrate the pellet in a smaller volume of VWR water. 7.9.3.2.3. If the concentration of either sample is greater than 3400 µg/ml, dilute with VWR water to achieve the acceptable concentration range. 7.9.3.3. Add 13µl Hybridization Solution Master Mix to combined labeled DNA. 7.9.3.4. Vortex the samples for 20 seconds and quickly centrifuge in tabletop centrifuge. Keep samples protected from light. 7.9.3.5. Place samples in 95ºC thermocycler for 5 minutes. 7.9.3.6. Briefly vortex and centrifuge samples. 7.9.3.7. Quickly transfer the 0.2ml PCR tubes to the Roche NimbleGen Hybridization System 12 sample block (pre-heated to 48°C) for at least 5 minutes before sample loading. 7.9.4. Prepare X1 Mixer 7.9.4.1. Prepare X1 mixer according to NimbleGen™ Arrays User Guide (CGH Analysis v5.0). 7.9.5. Load Sample 7.9.5.1. Quickly transfer labeled DNA sample from PCR tube in 48ºC sample block to a 2.0 ml tube. 7.9.5.2. Dispense 18µl of sample into the bottom X1 mixer hole using a Gilson Microman M100 pipette. 7.9.5.3. Dry any excess sample from X1 mixer holes using a Kimwipe. 7.9.5.4. Seal top and bottom X1 mixer holes with mixer port seals. 7.9.5.5. Close the bay clamp. 7.9.5.6. Dampen humid cover with Millipore water and place over bays. Humid covers must be kept damp throughout hybridization. 7.9.5.7. Close the Roche NimbleGen Hybridization System 12 lid. 7.9.5.8. Turn on the Mixing Panel on the Hybridization System, set the mix mode to B, and press the mix button to start mixing. 7.9.5.9. Confirm that the Hybridization System recognizes the slide in each occupied bay by indicator light turning green. 7.9.5.10. Hybridize the sample to the array(s) for 40-42 hours at 48°C. 7.10. Sample Storage 7.10.1. Label the remaining labeled DNA according to the following format: 7.10.2. Store labeled DNA samples at -20C in “CGH Labeled Samples” box for up to two weeks. 7.11. Array Washing 7.11.1. Turn on GenePix 4000B to warm up lasers prior to beginning wash procedure. 7.11.2. Disassemble and wash arrays according to NimbleGen™ Arrays User Guide (CGH Analysis v5.0) with the following exceptions: 7.11.2.1. Heat both Wash Buffer I solutions to 42ºC. 7.11.2.2. Agitate array in Wash Buffer I for 3 minutes. 7.11.2.3. Follow 1 minute agitation in Wash Buffer 2 with a 2 minute incubation. 7.11.3. Perform washes protecting arrays from light and ozone. 7.11.4. Place array in corresponding case and wrap case in aluminum foil. 7.11.4.1. Label with CGH number. 7.11.5. Scan arrays immediately after washing (ref: SOP-CH-309). 7.12. Array Storage 7.12.1. Store scanned arrays in the dessicator.

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification:
Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization:
CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

source_name: WA01 DNA476

label_protocol:
7.7.1. Cy3/Cy5 Labeling
7.7.1.1. Verify that the DNA concentration is between 25 and 30ng/ul for all test and reference samples.
7.7.1.2. Thaw the Cy3/Cy5 random nonamers on ice, protected from light.
7.7.1.3. Add 1µg of sonicated test DNA to 40 µl Cy3 dye. Bring to volume in 80 µl VWR water. Repeat for all test samples to be labeled.
7.7.1.4. Add 1 µg of sonicated reference DNA to 40 µl Cy5 dye. Bring to volume in 80 µl VWR water. Repeat for all reference samples to be labeled.
7.7.1.5. Vortex and quickly centrifuge test and reference DNA samples.
7.7.1.6. Incubate samples for 10 minutes at 98ºC protecting from light.
7.7.1.7. Rapidly transfer samples to an ice-water bath for 5 minutes protecting from light.
7.7.1.8. Prepare 20µl of the following aha-dNTP/Klenow Master Mix for each test and reference sample.
7.7.1.8.1. aha-dNTP/Klenow Master Mix per Sample
7.7.1.8.1.1. Thaw all reagents and aha-dNTP/Klenow master mix on ice.
7.7.1.8.1.2. Add 9µl VWR water to 0.2ml PCR tube.
7.7.1.8.1.3. Add 10µl 50X aha-dNTP Mix.
7.7.1.8.1.4. Add 1µl Klenow (50U/µl). DO NOT vortex. Total amount of solution is 20µl.
7.7.1.9. Add 20μl of the aha-dNTP/Klenow Master Mix to each of the cooled samples. Keep on ice.
7.7.1.10. Pipette to mix (15 times). DO NOT vortex.
7.7.1.11. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.12. Incubate the samples for 2 hours 15 minutes at 37°C in thermocycler protected from light.
7.7.1.13. Remove samples from thermocycler, keep at room temperature. Heat thermocycler to 98ºC. Place samples back into thermocycler and incubate for 10 minutes at 98ºC.
7.7.1.14. Rapidly transfer samples to an ice-water bath for 5 minutes protecting samples from light.
7.7.1.15. Add 1 µl of Klenow (50U/µl) to each sample.
7.7.1.16. Pipette to mix (15 times). DO NOT vortex.
7.7.1.17. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.18. Place samples in thermocycler at 37ºC for overnight amplification.
7.7.2. First DNA Precipitation
7.7.2.1. Set Roche Nimblegen Hybridization System 12 to 48ºC if proceeding to hybridization in the same day to allow for at least 3 hours of stabilization.
7.7.2.2. Cool centrifuge to 4ºC.
7.7.2.3. Add 10µl of 0.5M EDTA to each sample to stop the overnight amplification reaction.
7.7.2.4. Add 11.5 µl of 5M NaCl to each sample, then vortex for 10 seconds.
7.7.2.5. Briefly centrifuge samples using a tabletop centrifuge.
7.7.2.6. Transfer each sample into a 1.5ml tube containing 200 µl of isopropanol.
7.7.2.7. Vortex samples for 20 seconds.
7.7.2.8. Incubate at room temperature for 10 minutes, protected from light.
7.7.2.9. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.2.10. Aspirate supernatant.
7.7.2.11. Rinse pellet with 500µl of 80% ice-cold ethanol. As you rinse, gently wash pellet from tube wall.
7.7.2.12. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.2.13. Aspirate supernatant.
7.7.2.14. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.2.15. Proceed to Alexa Fluor Labeling or store labeled samples at -20°C, protected from light.
7.7.2.15.1. Frozen samples are stable for up to 2 weeks at -20ºC.
7.7.3. Alexa Fluor Labeling
7.7.3.1. Thaw one vial of Alexa Fluor 555 dye per Cy3-labeled test DNA sample on ice. Keep protected from light.
7.7.3.2. Thaw one vial of Alexa Fluor 647 dye per Cy5-labeled reference DNA sample on ice. Keep protected from light.
7.7.3.3. Thaw Alexa Fluor Labeling Buffer on ice.
7.7.3.4. Add 5 µl VWR water to each DNA sample.
7.7.3.5. Place samples in thermocycler at 42ºC for 5 minutes.
7.7.3.6. Add 3 µl Labeling Buffer to each DNA sample.
7.7.3.7. Vortex and quickly centrifuge DNA samples.
7.7.3.8. Add 2 µl DMSO to one of the vials of Alexa Fluor dye (either 555 or 647).
7.7.3.9. Vortex for 10 seconds to dissolve Alexa Fluor dye.
7.7.3.10. Immediately add 8 µl of corresponding DNA to the dissolved dye.
7.7.3.11. Pipette up and down to further dissolve dye pellet, replace lid and vortex briefly to mix.
7.7.3.12. Incubate at room temperature, protected from light for 1 hour.
7.7.3.13. Repeat steps 7.7.3.8.-7.7.3.12 for each Cy-labeled DNA to be labeled with Alexa Fluor dyes.
7.7.4. Second DNA Precipitation
7.7.4.1. Add 100 µl VWR water to each labeled DNA sample.
7.7.4.2. Add 11.5 µl of 5M NaCl to each sample.
7.7.4.3. Vortex for 10 seconds.
7.7.4.4. Briefly centrifuge samples using a tabletop centrifuge.
7.7.4.5. Transfer each sample into 1.5ml tubes containing 200 µl each of isopropanol.
7.7.4.6. Vortex samples for 20 seconds.
7.7.4.7. Incubate at room temperature for 10 minutes, protected from light.
7.7.4.8. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.4.9. Aspirate supernatant.
7.7.4.10. Add 500µl of 80% ice-cold ethanol to the pellet and gently wash pellet from tube wall by pipetting.
7.7.4.11. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.4.12. Aspirate supernatant.
7.7.4.13. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.4.14. Proceed to ‘Specific Activity Calculation’ or store labeled samples at -20°C, protected from light. Frozen samples are stable for up to 2 weeks at -20ºC.

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.

value: human embryonic stem (hES)

tag: cell line


title: Malignant germ cell tumor_YST-6 [mRNA]

description: GEO reference number: GSM267514

source_name: Yolk sac tumor replicate 6 of 10


title: Malignant germ cell tumor_YST-7 [miRNA]

description: Biological replicate 7 of 12

source_name: Yolk sac tumor replicate 7


title: Malignant germ cell tumor_YST-4 [mRNA]

description: GEO reference number: GSM267520

source_name: Yolk sac tumor replicate 4 of 10

value: Ovary


title: Malignant germ cell tumor_YST-3 [mRNA]

description: GEO reference number: GSM267513

source_name: Yolk sac tumor replicate 3 of 10


title: LCH-CD207-9

extract_protocol: RNA was extracted with PicoPure RNA Isolation Kit (Molecular Devices).  Quality was verified with the Agilent 6000 Picochip.  RNA was then amplified with the WT-Ovation Pico System (Nugen)


title: LCH-CD207-2


title: LCH-CD207-6


title: Malignant germ cell tumor_YST-5 [mRNA]

description: GEO reference number: GSM267518

source_name: Yolk sac tumor replicate 5 of 10


title: LCH-CD207-8


title: Malignant germ cell tumor_YST-2 [miRNA]

description: Biological replicate 2 of 12

source_name: Yolk sac tumor replicate 2


title: NSCB_CGH_385K_309_WA09


title: Control_N-43 [mRNA]

source_name: Normal gonadal control replicate 2 of 3

value: control

value: Postpubertal testis


title: NSCB_CGH_385K_313_WA09


title: NSCB_CGH_385K_306_WA01


title: NSCB_CGH_385K_307_BG03


title: NSCB_CGH_385K_301_WA01


title: LCH-CD207-15


title: LNCaP - 28days

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

country: Japan

institute: SHIMA Institution for Quantum Medicine

description: LNCaP 28days

hyb_protocol: hybridization buffer : 50% formamide-6 x SSC-0.2% SDS-5 x denhardt’s-0.2 mg/ml denatured salmon sperm, hybridization : at 70°C for 16 h, washing : three times with 2× SSC, 0.2% SDS at 65°C for 10 min, and rinsed once with 0.05 × SSC at room temperature

scan_protocol: Scanned on an GMS 428 arrayer (Affymetrix Inc) Images were quantified using ImaGene version 6.0  (Biodiscovery Inc., CA, USA)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data analysis was performed using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland).

source_name: prostate cancer cell line LNCaP - exposed to RB - 28 days

label_protocol: 4 µg of total RNA were labeled with Cy3 or Cy5 monoreactive dyes (Amersham, Buckinghamshire, UK) using RNA Transcript SureLABEL™ Core Kit (TaKaRa Bio) according to the manufacture’s instructions

growth_protocol: The DU145, PC-3 and LNCaP cell lines were obtained from American Type Culture Collection (Manassas, VA, USA). DU145 cells were maintained in minimum essential medium supplemented with 10% heat-inactivated fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin G and 0.1 mM non-essential amino acids in an atmosphere of 5% CO2 at 37°C. PC-3 and LNCaP cells were maintained in F-12K medium and RPMI medium with the same supplements, respectively.

extract_protocol: Total RNA extracted using Trizol (Invitrogen, CA) and purified using RNeasy kit (QIAGEN, Hilden, Germany) following manufacturer's instructions

treatment_protocol: Cells were passaged several times in log phase cultures.  Experimental dishes were sandwiched with RBs.  Another sets of dishes as reference samples were cultured without RBs.

value: LNCaP

value: male

source_name: prostate cancer cell line LNCaP - control - 28 days


title: Malignant germ cell tumor_YST-1 [mRNA]

description: GEO reference number: GSM267525

source_name: Yolk sac tumor replicate 1 of 10


title: NSCB_CGH_385K_300_WA01


title: NSCB_CGH_385K_299_WA09


title: LNCaP - 21days

description: LNCaP 21days

source_name: prostate cancer cell line LNCaP - exposed to RB - 21 days

source_name: prostate cancer cell line LNCaP - control - 21 days


title: Malignant germ cell tumor_YST-2 [mRNA]

description: GEO reference number: GSM267524

source_name: Yolk sac tumor replicate 2 of 10

value: Female


title: NSCB_CGH_385K_305_TE06


title: LCH-CD207-14

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD207+ Cells


title: NSCB_CGH_385K_297_WA09


title: PC-3 - 28days

description: PC-3 28days

source_name: prostate cancer cell line PC-3 - exposed to RB - 28 days

source_name: prostate cancer cell line PC-3 - control - 28 days


title: LCH-CD207-13


title: LCH-CD207-12


title: LCH-CD207-11


title: d0-d3 (M. sedula prior to inoculation vs M. sedula 3 days after inoculation on CuFeS2)

city: Raleigh

first: Kathryne

middle: Sherlock

last: Auernik

state: NC

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description: Scatterplots of signal intensities are reviewed to check for balance between channels.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a Packard BioChip Scanarray 4000 scanner containing 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards.

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides are quantitated, data from all slides in loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001)].

organism: Metallosphaera sedula

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy3 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol: Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2) and 10g/L chalcopyrite, with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2.

extract_protocol: At harvest, cells were quickly chilled and then centrifuged at 9510 x g for 15 minutes at 4C. RNA was extracted using Trizol (Invitrogen) and purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Harvest of cells occurred 3 days after inoculation onto 10g/L chalcopyrite.

value: Metallosphaera sedula whole cells

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy5 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 7.3 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these autotrophic conditions in DSMZ 88 media.

treatment_protocol: Harvest of final passage occurred 1 day after inoculation into media (no chalcopyrite present).


title: DU145 - 21days

description: DU145 21days

source_name: prostate cancer cell line DU145 - exposed to RB - 21 days

source_name: prostate cancer cell line DU145 - control - 21 days


title: LCH-CD207-10


title: LCH-CD3-2

source_name: Langerhans Cell Histiocytosis Lesion - Sorted CD3+ Cells


title: NSCB_CGH_385K_298_ES01


title: LCH-CD207-1


title: NSCB_CGH_385K_293_WA09


title: DU145 - 28days

description: DU145 28days

source_name: prostate cancer cell line DU145 - exposed to RB - 28 days

source_name: prostate cancer cell line DU145 - control - 28 days


title: d0-d9 (M. sedula prior to inoculation vs M. sedula 9 days after inoculation on CuFeS2)

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC.

growth_protocol: Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2) and 10g/L chalcopyrite (300mL working volumes in 1L bottles), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2.

treatment_protocol: Harvest of cells occurred 9 days after inoculation onto 10g/L chalcopyrite.


title: NSCB_CGH_385K_296_WA09


title: PC-3 - 21days

description: PC-3 21days

source_name: prostate cancer cell line PC-3 - exposed to RB - 21 days

source_name: prostate cancer cell line PC-3 - control - 21 days


title: d3-d9 (M. sedula 3 days after inoculation on CuFeS2 vs M. sedula 9 days after inoculation on CuFeS2)


title: INA-6 (after Co-Culture with BMSCs)_replicate2

status: Public on Mar 14 2010

city: Boston

first: Constantine

middle: S.

last: Mitsiades

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on Human Genome 133 plus2 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Standard Affymetrix Scanner protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files processed/normalized using DNA-Chip Analyzer (dChip) to generate probeset-level signal intensity data..

source_name: INA-6 cells after co-culture with HS-5 BMSCs

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

growth_protocol: Human multiple myeloma (MM) cell lines (MM.1S, MM.1R, INA-6) stably expressing green fluorescent protein (GFP) were cultured in vitro either alone or in the presence of the human bone marrow stromal cell line HS-5 (ie, BMSCs) for 24hrs. Fluorescence activated cell sorting was used to separate the GFP+ MM cells from GFP- stromal cells. The gene expression profiles of MM cells after their co-culture with stromal cells  were compared with the profiles of MM cells cultured alone.

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

value: multiple myeloma (MM) cell line INA-6

tag: culture conditions of tumor cells (growth protocol)

value: co-cultured with BMSCs


title: INA-6 (after Co-Culture with BMSCs)_replicate1


title: INA-6 (cultured alone)_replicate2

source_name: INA-6 cells cultured alone

value: cultured alone


title: High　Temperature during Grain Filling of Rice, Biological Replicate 2, Dye Swap 2

city: Joetsu

first: Hiromoto

last: Yamakawa

state: Niigata

address: Inada 1-2-1

department: Hokuriku Research Center

institute: National Agricultural Research Center

description: US22502590_251524111384_S01_GE2-v4_95_Feb07_1_4.txt

hyb_protocol: Fluorescently labeled targets were hybridized to Agilent rice 44-K oligo DNA microarrays (Agilent Technologies). The hybridization and washing were performed according to the manufacturer’s instructions.

scan_protocol: Hybridized microarrays were scanned using an Agilent Microarray Scanner (Agilent Technologies).

data_processing: Feature Extraction software (version 9.1; Agilent Technologies) was employed for the data extraction and normalization processes. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer's instructions.

organism: Oryza sativa

source_name: High temperature, Replicate 2

label_protocol: Total RNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit (Agilent Technologies).

growth_protocol: Rice (Oryza sativa ssp. japonica) ‘Nipponbare’ was grown at 27°C/22°C (12-h-day/12-h-night photoperiod) until flowering in a plant incubator (model FLI-301NH; Eyela, Tokyo, Japan) equipped with a sodium lamp, which allows illumination at an intensity of 560 µmol photons m-2 s-1. Six plants were grown in a plastic container (15 × 10 × 6 cm) filled with 600 ml of rice nursery culture soil (containing 0.15 g each of nitrogen, phosphate, and potassium), and each plant was restricted to the main culm by the removal of tillers. Approximately 15 to 20 d before heading, 3 g of a fertilizer (containing 0.18 g nitrogen, 0.24 g phosphate, 0.18 g potassium, and 0.06 g magnesium) was supplied per container.

extract_protocol: Total RNA was extracted from 12 developing caryopses harvested from 25°C/20°C- and 33°C/28°C-treated plants using the method of Chang et al. (1993) (3 biologically independent replicates, each). The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Five days after flowering (DAF), the plants were transferred to either a 33°C/28°C or 25°C/20°C chamber for high temperature or control treatment, respectively, and then the temperature was maintained at 25°C/20°C from 20 DAF to maturity. Ten and 12 DAF for high temperature and control plots, respectively, developing caryopses were detached from the ear at midday (6 h after illumination was started), immediately frozen in liquid nitrogen, and stored at -80°C.

tag: experimental condition

value: high temperature

source_name: Control, Replicate 2


title: High　Temperature during Grain Filling of Rice, Biological Replicate 3, Dye Swap 2

description: US22502590_251524111385_S02_GE2-v5_95_Feb07_1_2.txt

source_name: High temperature, Replicate 3

source_name: Control, Replicate 3


title: High　Temperature during Grain Filling of Rice, Biological Replicate 2, Dye Swap 1

description: US22502590_251524111384_S01_GE2-v4_95_Feb07_1_3.txt


title: NSCB_CGH_385K_292_WA09

tag: cell type


title: High　Temperature during Grain Filling of Rice, Biological Replicate 3, Dye Swap 1

description: US22502590_251524111385_S02_GE2-v5_95_Feb07_1_1.txt


title: MM1R (after Co-Culture with BMSCs)_replicate2

source_name: MM1R cells after co-culture with HS-5 BMSCs

value: multiple myeloma (MM) cell line MM.1R


title: INA-6 (cultured alone)_replicate1


title: High　Temperature during Grain Filling of Rice, Biological Replicate 1, Dye Swap 2

description: US22502590_251524111384_S01_GE2-v4_95_Feb07_1_2.txt

source_name: High temperature, Replicate 1

source_name: Control, Replicate 1


title: MM1R (cultured alone)_replicate2

source_name: MM1R cells cultured alone


title: MM1R (after Co-Culture with BMSCs)_replicate1


title: High　Temperature during Grain Filling of Rice, Biological Replicate 1, Dye Swap 1

description: US22502590_251524111384_S01_GE2-v4_95_Feb07_1_1.txt


title: NSCB_CGH_385K_291_WA09


title: MM1R (cultured alone)_replicate1


title: BRD7#4 knockdown vector +Ras

city: Amsterdam

first: Jarno

last: Drost

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: The Netherlands Cancer Institute

description: mRNA expression data from BJ primary fibroblasts expressing pRS-BRD7#4 vector and RasV12

hyb_protocol: According to Illumina IntelliHyb protocol: Whole-Genome Gene Expression; Direct Hybridization (Assay Guide); Chips used: Sentrix(r) HumanWG-6 v3 Expression Beadchip.

scan_protocol: The BeadChip is scanned on the Illumina BeadArray Reader, according to Illumina settings.

data_processing: BeadChip array data quality control was performed using Illumina BeadStudio software. Transcript average intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor. Average transcript intensities were log2 transformed and normalized by quantile method.

source_name: BJ cells + pRS-BRD7#4+ Ras

label_protocol: RNA amplification+biotin labeling: Illumina(r) TotalPrep(tm) RNA Amplification Kit (Cat# AMIL1791); Extra: We started the protocol by adding 1ul T7 primer to the 11ul sample (input 350 ng) and incubate this for 10 minutes at 70 degrees Celsius, then let sample come to RT then place on ice. In the next step (adding the first strand mix) we left out the T7 primer and followed the protocol as described in the manual.

treatment_protocol: BJ/ET/RASV12ER cells containing BRD7#4 knockdown vector were cultured in the presence (+RASV12) of 4OHT for 10 days. mRNA levels were determined by microarray.

value: BJ

value: foreskin fibroblasts

tag: oncogene expression

tag: vector


title: MM1S (cultured alone)_replicate2

source_name: MM1S cells cultured alone

value: multiple myeloma (MM) cell line MM.1S


title: empty vector +Ras

description: mRNA expression data from BJ primary fibroblasts expressing pRS control vector and RasV12

source_name: BJ cells + pRS + Ras

treatment_protocol: BJ/ET/RASV12ER cells containing control vector were cultured in the presence (+RASV12) of 4OHT for 10 days. mRNA levels were determined by microarray.

value: empty pRS


title: MM1S (after Co-Culture with BMSCs)_replicate1

source_name: MM1S cells after co-culture with HS-5 BMSCs


title: p53 knockdown vector +Ras

description: mRNA expression data from BJ primary fibroblasts expressing pRS-p53 vector and RasV12

source_name: BJ cells + pRS-p53 + Ras

treatment_protocol: BJ/ET/RASV12ER cells containing p53 knockdown vector were cultured in the presence (+RASV12) of 4OHT for 10 days. mRNA levels were determined by microarray.


title: BRD7#1 knockdown vector +Ras

description: mRNA expression data from BJ primary fibroblasts expressing pRS-BRD7#1 vector and RasV12

source_name: BJ cells + pRS-BRD7#1 + Ras

treatment_protocol: BJ/ET/RASV12ER cells containing BRD7#1 knockdown vector were cultured in the presence (+RASV12) of 4OHT for 10 days. mRNA levels were determined by microarray.


title: MM1S (after Co-Culture with BMSCs)_replicate2


title: MM1S (cultured alone)_replicate1


title: SPurpuratus_SanDiego_Individual42

status: Public on Mar 13 2010

city: Pacific Grove

first: Melissa

last: Pespeni

address: 120 Oceanview Blvd.

department: Biology

description: ch1 (Cy3) was restriction digested, ch2 (Cy5) was treated as control.

hyb_protocol: DNA was hybridized to Agilent 244K custom arrays using Agilent's aCGH hybridization buffer kit, hyb chambers, oven, and aCGH Wash Buffers I and II following Agilent aCGH protocols.

scan_protocol: Arrays were scanned using the Axon GenePix Scanner 4000B. Images were quantified using Agilent's Feature Extraction software (9.5.3).

data_processing:
Data were processed using Feature Extraction default settings: LOWESS normalized and background subtracted resulting in log2 of processed Red signal : processed Green signal.
Data from triplicate features on a single array showed very low variation and were averaged in further analyses. GE, GL, and UP probes centered on cut sites (X) are presented in the Series GSE20857 data table.

organism: Strongylocentrotus purpuratus

source_name: Tube foot tissue

label_protocol: DNA was labeled and purified using the BioPrime labeling kit (Invitrogen) and Cy-dyes (Amersham) following manufacturers instructions.

growth_protocol: Animals were collected from the field, then maintained in common garden conditions in flow-through outdoor aquaria at the Hopkins Marine Station in Monterey, CA.

extract_protocol: Genomic DNA was extracted using Nucleospin extraction protocols (Macherey & Nagel).

tag: developmental stage

value: adult

tag: test

value: restriction digested DNA

value: not restriction digested DNA


title: SPurpuratus_SanDiego_Individual50


title: SPurpuratus_SanDiego_Individual32


title: SPurpuratus_SanDiego_Individual36


title: SPurpuratus_SanDiego_Individual46


title: SPurpuratus_SanDiego_Individual48


title: SPurpuratus_SanDiego_Individual30


title: Ishikawa Hcells, dosed with egf, harvested at 24 hr, rep2

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

description: Gene expression data from human endometrial adenocarcinoma cell line 24 hr dosed with EGF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133 2.0+ Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: type I endometrial adenocarcinoma cell line 24 hr dosed with EGF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Hec50co cells and Ishikawa Hcells were cultured in DMEM containing 10% FBS substitute and 2mM L-Glutamine and 1x antibiotic-antimycotic solution.

extract_protocol: Qiagen RNeasy used for total RNA extraction and was performed according to manufacture's instructions.

treatment_protocol: The two different tissue culture cell lines were dosed with 0.1% DMSO (vehicle=undosed) or with 1uM gefitinib, or with 30ng/ml EGF for 12 or 24 hours then the cells were harvested and total RNA extracted and purified.

tag: tissue type

value: Type I endometrial adenocarcinoma

value: Ishikawa H


title: Ishikawa Hcells, dosed with iressa, harvested at 24 hr, rep1

description: Gene expression data from human endometrial adenocarcinoma cell line 24 hr dosed with Iressa

source_name: type I endometrial adenocarcinoma cell line 24 hr dosed with Iressa


title: SPurpuratus_SanDiego_Individual34


title: Ishikawa Hcells, undosed, harvested at 24 hr, rep2

description: Gene expression data from human endometrial adenocarcinoma cell line 24 hr undosed (DMSO)

source_name: type I endometrial adenocarcinoma cell line 24 hr undosed (DMSO)


title: SPurpuratus_SanDiego_Individual40


title: Ishikawa Hcells, dosed with iressa, harvested at 24 hr, rep2


title: SPurpuratus_BoilerBay_Individual37


title: SPurpuratus_BoilerBay_Individual23


title: SPurpuratus_BoilerBay_Individual33


title: SPurpuratus_BoilerBay_Individual25


title: Ishikawa Hcells, dosed with iressa, harvested at 12 hr, rep2

description: Gene expression data from human endometrial adenocarcinoma cell line 12 hr dosed with Iressa

source_name: type I endometrial adenocarcinoma cell line 12 hr dosed with Iressa


title: SPurpuratus_BoilerBay_Individual35


title: Ishikawa Hcells, dosed with iressa, harvested at 12 hr, rep1


title: SPurpuratus_BoilerBay_Individual27


title: Ishikawa Hcells, dosed with egf, harvested at 24 hr, rep1


title: SPurpuratus_SanDiego_Individual38


title: SPurpuratus_BoilerBay_Individual19


title: SPurpuratus_BoilerBay_Individual21


title: Ishikawa Hcells, dosed with egf, harvested at 12 hr, rep2

description: Gene expression data from human endometrial adenocarcinoma cell line 12 hr dosed with EGF

source_name: type I endometrial adenocarcinoma cell line 12 hr dosed with EGF


title: Hec50co cells, dosed with iressa, harvested at 24 hr, rep2

source_name: type II endometrial adenocarcinoma cell line 24 hr dosed with Iressa

value: Type II endometrial adenocarcinoma


title: Ishikawa Hcells, undosed, harvested at 12 hr, rep1

description: Gene expression data from human endometrial adenocarcinoma cell line 12 hr undosed (DMSO)

source_name: type I endometrial adenocarcinoma cell line 12 hr undosed (DMSO)


title: Ishikawa Hcells, undosed, harvested at 12 hr, rep2


title: SPurpuratus_BoilerBay_Individual29


title: Hec50co cells, dosed with iressa, harvested at 24 hr, rep1


title: Hec50co cells, dosed with egf, harvested at 24 hr, rep2

source_name: type II endometrial adenocarcinoma cell line 24 hr dosed with EGF


title: Ishikawa Hcells, undosed, harvested at 24 hr, rep1


title: LRPPRC knockdown4, biological replicate 2

first: Vishal

middle: M

last: Gohil

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

description:
Gene expression data from LRPPRC knockdown 4 cell line, with only 81% expression of LRPPRC compared to control.
4.2

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 from Affymetrix.

data_processing: The expression data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.

source_name: MCH58 LRPPRC knockdown cell line 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: MCH58 LRPPRC knockdown cells were grown in DMEM high glucose media which was supplemented with 10% fetal bovine serum, 1X penicillin, glutamine and streptomycin, 2 µg/ml puromycin and 50 µg/ml uridine at 37°C.

extract_protocol: Total RNA was extracted from approximately 2 million cells with Qiagen RNAeasy mini kit as per the kit protocol.

treatment_protocol: Immortalized MCH58 human fibroblasts (200,000) grown in a 6-well dish were infected with 30 µl lentiviral supernatant for each of the seven hairpins. 24 hours post infection, cells were selected by adding 2 µg/ml puromycin. The selected cells were passaged 3 times, approximately 9-10 days post infection before extracting total RNA.

value: fibroblasts

tag: sirna

value: LRPPRC

tag: lrpprc expression vs. control


title: LRPPRC knockdown6, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 6 cell line, with only 9% expression of LRPPRC compared to control.
6.2

source_name: MCH58 LRPPRC knockdown cell line 6


title: Hec50co cells, dosed with egf, harvested at 24 hr, rep1


title: LRPPRC knockdown6, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 6 cell line, with only 9% expression of LRPPRC compared to control.
6.1


title: LRPPRC knockdown3, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 3 cell line, with only 69% expression of LRPPRC compared to control.
3.1

source_name: MCH58 LRPPRC knockdown cell line 3


title: SPurpuratus_BoilerBay_Individual31


title: Hec50co cells, dosed with egf, harvested at 12 hr, rep2

source_name: type II endometrial adenocarcinoma cell line 12 hr dosed with EGF


title: LRPPRC knockdown7, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 7 cell line, with only 58% expression of LRPPRC compared to control.
7.1

source_name: MCH58 LRPPRC knockdown cell line 7


title: Hec50co cells, undosed, harvested at 24 hr, rep2

source_name: type II endometrial adenocarcinoma cell line 24 hr undosed (DMSO)


title: LRPPRC knockdown2, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 2 cell line, with only 33% expression of LRPPRC compared to control.
2.2

source_name: MCH58 LRPPRC knockdown cell line 2


title: LRPPRC knockdown5, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 5 cell line, with only 100% expression of LRPPRC compared to control.
5.1

source_name: MCH58 LRPPRC knockdown cell line 5


title: Hec50co cells, dosed with iressa, harvested at 12 hr, rep2

source_name: type II endometrial adenocarcinoma cell line 12 hr dosed with Iressa


title: LRPPRC knockdown3, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 3 cell line, with only 69% expression of LRPPRC compared to control.
3.2


title: LRPPRC knockdown7, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 7 cell line, with only 58% expression of LRPPRC compared to control.
7.2


title: Hec50co cells, dosed with egf, harvested at 12 hr, rep1


title: Hec50co cells, undosed, harvested at 12 hr, rep1

source_name: type II endometrial adenocarcinoma cell line 12 hr undosed (DMSO)


title: Hec50co cells, undosed, harvested at 24 hr, rep1


title: Hec50co cells, undosed, harvested at 12 hr, rep2


title: LRPPRC knockdown1, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 1 cell line, with only 20% expression of LRPPRC compared to control.
1.2

source_name: MCH58 LRPPRC knockdown cell line 1


title: LRPPRC knockdown1, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 1 cell line, with only 20% expression of LRPPRC compared to control.
1.1


title: LRPPRC knockdown5, biological replicate 2

description:
Gene expression data from LRPPRC knockdown 5 cell line, with only 100% expression of LRPPRC compared to control.
5.2


title: LRPPRC knockdown4, biological replicate 1

description:
Gene expression data from LRPPRC knockdown 4 cell line, with only 81% expression of LRPPRC compared to control.
4.1