title: Rectal Colon Biopsy_SD52966_IBS-D [GP602R_81_127_SS103062]

description: Sample name: GP602R_81_127_SS103062


title: Rectal Colon Biopsy_SD52964_IBS-D [GP602R_78_132_SS103059]

status: Public on Jul 13 2012

type: RNA

city: Stevenage

first: Fiona

middle: M

last: Kelly

state: HERTS

address: GunnelsWood Road

department: Biopharm R&D

country: United Kingdom

institute: GlaxoSmithKline

description: Sample name: GP602R_78_132_SS103059

hyb_protocol: The fragmented and labeled cDNA was hybridized to U133plus2.0 GeneChips® in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,)

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip® Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Samples were separated into separate technical batches and balanced for disease and gender. Each pair of biopsies was allocated to the same batch. Within each batch, samples were randomised.  The chip quality was assessed using Microarray Gene Chip Operating Suite 5 (MAS5) normalised data (normalised to a target intensity of 150) and Principle Component Analysis (PCA) performed in Umetrics SIMCA-P+ 11.5For statistical analysis of gene expression, all probe sets were normalised using the Rosetta Resolver version 5.1 group processing pipeline 15. The normalised data set was imported to SAS version 9.1, the data from two biopsies per donor averaged and the statistically analysed using a linear mixed models. The data set was modelled for disease group, gender, technical batches and the disease:gender interaction and estimates of fold change and P values between disease groups determined. A final intensity threshold was applied (keep genes >25 intensity in any disease group) to the data to remove genes with low detection levels. (Weng L. Rosetta error model for gene expression analysis.Bioinformatics. 2006 May 1;22(9):1111-21. Epub 2006 Mar 7.)

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Rectal Colon Biopsy

label_protocol: 50ng of total RNA was processed to Biotin-labeled cDNA using the NuGEN Ovation™ RNA Amplification System.

extract_protocol: Total RNA was extracted from rectal biopsy samples that had been preserved in RNAlater (Ambion, Applied Biosystems, Warrington, UK) using a Polytron type homogeniser (YellowLine DI 25 Basic) and 1ml TriZol reagent (Invitrogen, Paisley, UK). RNA was purified using RNeasy mini-columns (Qiagen, Valencia, CA) including on-column DNAse-1 step and elution in water

treatment_protocol: Subjects underwent sigmoidoscopy without bowel preparation. Biopsies were obtained using endoscopic biopsy forceps and immersed in formalin for histopathology or RNAlater for RNA extraction and gene expression analysis.

tag: tissue

value: Rectal Colon Biopsy

tag: gender

value: M

tag: subject identifier

tag: disease

value: IBS-D

tag: batch


title: Rectal Colon Biopsy_SD52964_IBS-D [GP602R_77_133_SS103058]

description: Sample name: GP602R_77_133_SS103058


title: Rectal Colon Biopsy_SD52962_IBS-D [GP602R_74_50_SS103055]

description: Sample name: GP602R_74_50_SS103055


title: Glioblastoma_gbm-0221

city: Beijing

first: Wei

last: Zhang

address: No.6 Tiantan Xili, Dongcheng District

department: Glioma Center, Department of Neurosurgery

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina BeadReader

data_processing: The data were background subtracted and normalized using quantile normalization with Illumina BeadStudio software v3.1

source_name: Human glioblastoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total RNA was extracted with mirVana miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer’s protocol. Quality control was performed with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Houston, TX).

tag: patient population

value: Chinese

value: brain

tag: disease state

value: primary glioblastoma multiform (brain tumor)

tag: tumor grade

value: WHO grade 4

tag: patient age

tag: patient gender

value: male


title: Glioblastoma_gbm-0218


title: Glioblastoma_gbm-0210

value: female


title: Glioblastoma_gbm-0205


title: Glioblastoma_gbm-0222


title: Glioblastoma_gbm-0195


title: Glioblastoma_gbm-0214


title: Glioblastoma_gbm-0188


title: Rectal Colon Biopsy_SD52961_IBS-D [GP602R_72_16_SS103053]

description: Sample name: GP602R_72_16_SS103053

value: F


title: Glioblastoma_gbm-0203


title: Rectal Colon Biopsy_SD52961_IBS-D [GP602R_71_10_SS103052]

description: Sample name: GP602R_71_10_SS103052


title: Rectal Colon Biopsy_SD52959_IBS-D [GP602R_68_94_SS103049]

description: Sample name: GP602R_68_94_SS103049


title: Rectal Colon Biopsy_SD52960_IBS-D [GP602R_69_106_SS103050]

description: Sample name: GP602R_69_106_SS103050


title: Rectal Colon Biopsy_SD52963_IBS-D [GP602R_75_83_SS103056]

description: Sample name: GP602R_75_83_SS103056


title: Glioblastoma_gbm-0169


title: Glioblastoma_gbm-0178


title: Glioblastoma_gbm-0172


title: Rectal Colon Biopsy_SD52959_IBS-D [GP602R_67_88_SS103048]

description: Sample name: GP602R_67_88_SS103048


title: Glioblastoma_gbm-0161


title: Glioblastoma_gbm-0160


title: Glioblastoma_gbm-0168


title: Rectal Colon Biopsy_SD52960_IBS-D [GP602R_70_111_SS103051]

description: Sample name: GP602R_70_111_SS103051


title: Rectal Colon Biopsy_SD52962_IBS-D [GP602R_73_49_SS103054]

description: Sample name: GP602R_73_49_SS103054


title: Glioblastoma_gbm-0144


title: Rectal Colon Biopsy_SD52958_IBS-D [GP602R_66_115_SS103047]

description: Sample name: GP602R_66_115_SS103047


title: Rectal Colon Biopsy_SD52958_IBS-D [GP602R_65_112_SS103046]

description: Sample name: GP602R_65_112_SS103046


title: Rectal Colon Biopsy_SD52954_IBS-D [GP602R_57_42_SS103038]

description: Sample name: GP602R_57_42_SS103038


title: Rectal Colon Biopsy_SD52952_IBS-D [GP602R_54_29_SS103035]

description: Sample name: GP602R_54_29_SS103035


title: Glioblastoma_gbm-0182


title: Rectal Colon Biopsy_SD52953_IBS-D [GP602R_56_90_SS103037]

description: Sample name: GP602R_56_90_SS103037


title: Glioblastoma_gbm-0139


title: Rectal Colon Biopsy_SD52952_IBS-D [GP602R_53_36_SS103034]

description: Sample name: GP602R_53_36_SS103034


title: Rectal Colon Biopsy_SD52951_IBS-D [GP602R_52_21_SS103033]

description: Sample name: GP602R_52_21_SS103033


title: Rectal Colon Biopsy_SD52954_IBS-D [GP602R_58_40_SS103039]

description: Sample name: GP602R_58_40_SS103039


title: Glioblastoma_gbm-0126


title: Glioblastoma_gbm-0156


title: Glioblastoma_gbm-0058


title: Glioblastoma_gbm-0102


title: Glioblastoma_gbm-0024


title: Glioblastoma_gbm-0088


title: Glioblastoma_gbm-0100


title: Glioblastoma_gbm-0011


title: Glioblastoma_gbm-0013


title: Rectal Colon Biopsy_SD52953_IBS-D [GP602R_55_74_SS103036]

description: Sample name: GP602R_55_74_SS103036


title: Glioblastoma_gbm-0124


title: Rectal Colon Biopsy_SD52951_IBS-D [GP602R_51_15_SS103032]

description: Sample name: GP602R_51_15_SS103032


title: Glioblastoma_gbm-0001


title: Rectal Colon Biopsy_SD52950_HV [GP602R_49_75_SS103030]

description: Sample name: GP602R_49_75_SS103030

value: HV


title: Rectal Colon Biopsy_SD52947_HV [GP602R_43_5_SS103024]

description: Sample name: GP602R_43_5_SS103024


title: Rectal Colon Biopsy_SD52945_HV [GP602R_40_118_SS103021]

description: Sample name: GP602R_40_118_SS103021


title: Rectal Colon Biopsy_SD52949_HV [GP602R_48_122_SS103029]

description: Sample name: GP602R_48_122_SS103029


title: Rectal Colon Biopsy_SD52946_HV [GP602R_41_56_SS103022]

description: Sample name: GP602R_41_56_SS103022


title: Rectal Colon Biopsy_SD52948_HV [GP602R_46_43_SS103027]

description: Sample name: GP602R_46_43_SS103027


title: Rectal Colon Biopsy_SD52946_HV [GP602R_42_63_SS103023]

description: Sample name: GP602R_42_63_SS103023


title: Rectal Colon Biopsy_SD52950_HV [GP602R_50_82_SS103031]

description: Sample name: GP602R_50_82_SS103031


title: Rectal Colon Biopsy_SD52971_IBS-D [GP602R_91_110_SS103072]

description: Sample name: GP602R_91_110_SS103072


title: Rectal Colon Biopsy_SD52948_HV [GP602R_45_46_SS103026]

description: Sample name: GP602R_45_46_SS103026


title: Rectal Colon Biopsy_SD52949_HV [GP602R_47_128_SS103028]

description: Sample name: GP602R_47_128_SS103028


title: Rectal Colon Biopsy_SD52947_HV [GP602R_44_6_SS103025]

description: Sample name: GP602R_44_6_SS103025


title: Rectal Colon Biopsy_SD52945_HV [GP602R_39_113_SS103020]

description: Sample name: GP602R_39_113_SS103020


title: Rectal Colon Biopsy_SD52944_HV [GP602R_38_55_SS103019]

description: Sample name: GP602R_38_55_SS103019


title: Rectal Colon Biopsy_SD52942_HV [GP602R_34_4_SS103015]

description: Sample name: GP602R_34_4_SS103015


title: Rectal Colon Biopsy_SD52943_HV [GP602R_36_117_SS103017]

description: Sample name: GP602R_36_117_SS103017


title: Rectal Colon Biopsy_SD52941_HV [GP602R_32_124_SS103013]

description: Sample name: GP602R_32_124_SS103013


title: Rectal Colon Biopsy_SD52942_HV [GP602R_33_13_SS103014]

description: Sample name: GP602R_33_13_SS103014


title: Rectal Colon Biopsy_SD52943_HV [GP602R_35_105_SS103016]

description: Sample name: GP602R_35_105_SS103016


title: Rectal Colon Biopsy_SD52941_HV [GP602R_31_140_SS103012]

description: Sample name: GP602R_31_140_SS103012


title: Rectal Colon Biopsy_SD52939_HV [GP602R_28_33_SS103009]

description: Sample name: GP602R_28_33_SS103009


title: Rectal Colon Biopsy_SD52940_HV [GP602R_29_104_SS103010]

description: Sample name: GP602R_29_104_SS103010


title: Rectal Colon Biopsy_SD52940_HV [GP602R_30_103_SS103011]

description: Sample name: GP602R_30_103_SS103011


title: Rectal Colon Biopsy_SD52939_HV [GP602R_27_37_SS103008]

description: Sample name: GP602R_27_37_SS103008


title: DAOY-MXD3-2

type: genomic

city: Sacramento

first: Gustavo

middle: A.

last: Barisone

state: CA

department: Internal Medicine

country: USA

institute: University of California Davis Health System

description: ChIP-chip HA-MXD3 stable DAOY cell line anti-HA, experiment 2

hyb_protocol: Thirteen µg of the test and reference samples were combined, vacuum-dried, resuspended in array hybridization buffer (Nimblegen) and hybridized to Human HG18 RefSeq 385K promoter arrays (Nimblegen) for 16-20 hrs according to manufacturer’s instructions in a MAUI station (BioMicro) at 42°C.

scan_protocol: Arrays were scanned on an Axon 4000B scanner using the following settings: wavelengths 532 (Cy3) and 635 (Cy5); 532 PMT Gain=690; 635 PMT Gain=750; Power=100%; Pixel size=5 µm; Lines to average=1; Focus position=0 µm.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.2 ChIP data extraction.

molecule: genomic DNA

source_name: HA ChIP DNA from DAOY cells expressing HA-MXD3

label_protocol: DNA was amplified using the GenomePlex WGA4 kit (Sigma). DNA fragments were labeled by Klenow extension using 9-mer random Cy3-primers for total (unenriched) input and Cy5-primers for immunoprecipitated material. One µg of DNA and primers (1 O.D./42 µl) were denatured at 98°C for 10 min and incubated with Klenow (50 U/µl, New England Biolabs) and 1 mM dNTP at 37°C for 2 hrs. After stopping the reaction with 50 mM EDTA, DNA was precipitated with isopropanol and resuspended in H2O.

extract_protocol: 107 cells were fixed with 1% formaldehyde for 10 min at room temperature, followed by addition of glycine (125 mM final concentration) for 5 min. Fixed cells were collected with a cell-scraper, washed once with phosphate buffered saline (PBS) and either used immediately or snap-frozen and stored at -80°C. Fixed cells were homogenized in 5 mM Pipes pH 8.0, 85 mM KCl, 1% NP40 and pelleted nuclei were lysed in 50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS. DNA was fragmented to ~200 bp. Chromatin was pre-cleared with washed (2 mM EDTA, 20 mM Tris-HCL pH 8.0 twice, followed by boiling for 30 min in PBS, 3% SDS, 10 % 2-mercaptoethanol, followed by 2 washes in 2 mM EDTA, 20 mM Tris-HCL pH 8.0), blocked (1 mg/ml sperm salmon DNA, 1 mg/ml BSA, overnight 4°C) Staphilococcus aureus cells (Calbiochem cat# 507862) and immunoprecipitated overnight at 4°C with mouse anti-HA (Covance, cat# MMS-101R) and secondary rabbit anti-mouse IgG (MP Biomedicals, cat# 55436) antibodies. Immune complexes were pulled down with blocked Staphilococcus aureus cells for 15 min at room temperature, washed twice with 2 mM EDTA, 20 mM Tris-HCL pH 8.0 and 4 more times with 100 mM Tris-HCl pH 8.0, 0.5 M LiCl, 5% NP-40, 5% Deoxycolic acid. Complexes were eluted twice with 1% SDS, 50 mM NaHCO3 for 15 min at room temperature. Cross-linking was reversed by adding NaCl to 0.2 M and incubating at 67°C overnight. DNA was purified using QIAquick PCR purification kit (Qiagen) and quantified with the Quant-iT PicoGreen assay (Invitrogen).

tag: cell line

value: DAOY

tag: cell type

value: medulloblastoma

tag: genotype/variation

value: overexpressing HA tagged MXD3

tag: chip antibody

value: anti-HA

tag: chip antibody vendor

value: Covance

tag: chip antibody catalog #

source_name: total input DNA from DAOY cells expressing HA-MXD3

tag: transgene


title: Rectal Colon Biopsy_SD52938_HV [GP602R_25_71_SS103006]

description: Sample name: GP602R_25_71_SS103006

tag: tissue


title: DAOY-MXD3-1

description: ChIP-chip HA-MXD3 stable DAOY cell line anti-HA, experiment 1


title: Rectal Colon Biopsy_SD52937_HV [GP602R_24_139_SS103005]

description: Sample name: GP602R_24_139_SS103005

tag: gender


title: Rectal Colon Biopsy_SD52937_HV [GP602R_23_138_SS103004]

description: Sample name: GP602R_23_138_SS103004

tag: subject identifier


title: Rectal Colon Biopsy_SD52938_HV [GP602R_26_73_SS103007]

description: Sample name: GP602R_26_73_SS103007

tag: disease


title: Rectal Colon Biopsy_SD52936_HV [GP602R_21_84_SS103002]

description: Sample name: GP602R_21_84_SS103002

tag: batch


title: Rectal Colon Biopsy_SD52936_HV [GP602R_22_77_SS103003]

description: Sample name: GP602R_22_77_SS103003


title: Genomic DNA blood Family12 mother

city: Leuven

first: Caroline

last: Robberecht

address: Herestraat 49

country: Belgium

institute: Catholic University Leuven

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the GeneChip Scanner 3000 7G.

data_processing:
SNP copy number analysis was performed using ‘‘Copy Number Analyzer for Genechip (CNAG) version 2.0’’ or the ‘‘Copy Number Analysis Tool’’ (CNAT4.0.1; Affymetrix) and the Genotyping Console™ Software (Affymetrix, Inc.). SNP probe intensities were analyzed by GTYPE 4.1 (Affymetrix) using the dynamic model45 with stringency P0.12. To determine the parental origin of the DNA copy number aberrations by a SNP-cluster strategy, normalized SNP A- and B-allele intensities as well as SNP genotype calls were computed using Affymetrix power tools (APT-1.10.1) in combination with the Birdseed command(Korn et al. 2008). Besides the described trio datasets, in-house produced Affymetrix 250K SNP NspI data from 102 additional DNA-samples were co-processed for accurate SNP-cluster and genotype determination. Subsequently, the probe-intensities and genotype calls for SNPs within the regions of interest were retrieved for all DNA-samples and interpreted by custom R-code (http://www.r-project.org/) in which patient and parental SNP-probe intensities are visualized in the Birdseed SNP-clusters from the 102 individuals.
Computed genotypes are provided in the CHP files

label: biotin

source_name: genomic DNA isolated from blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Standard Autopure LS or phenol-chlorophorm extraction

tag: individual

value: Family12 mother

value: blood


title: Rectal Colon Biopsy_SD52935_HV [GP602R_19_130_SS103000]

description: Sample name: GP602R_19_130_SS103000

value: Rectal Colon Biopsy

value: M


title: Rectal Colon Biopsy_SD52935_HV [GP602R_20_126_SS103001]

description: Sample name: GP602R_20_126_SS103001


title: Rectal Colon Biopsy_SD52933_HV [GP602R_16_69_SS102997]

description: Sample name: GP602R_16_69_SS102997


title: Rectal Colon Biopsy_SD52934_HV [GP602R_18_30_SS102999]

description: Sample name: GP602R_18_30_SS102999


title: Rectal Colon Biopsy_SD52934_HV [GP602R_17_32_SS102998]

description: Sample name: GP602R_17_32_SS102998


title: Genomic DNA blood Family11 father

description: Hybridized to 250K_Nsp

value: Family11 father


title: Genomic DNA blood Family12 father

description: Hybridized to 250K_Nsp

value: Family12 father


title: Genomic DNA blood Family10 mother

description: Hybridized to 250K_Nsp

value: Family10 mother


title: Genomic DNA blood Family11 mother

description: Hybridized to 250K_Nsp

value: Family11 mother


title: Genomic DNA blood Family10 father

description: Hybridized to 250K_Nsp

value: male

value: Family10 father


title: Rectal Colon Biopsy_SD52933_HV [GP602R_15_51_SS102996]

description: Sample name: GP602R_15_51_SS102996

value: F


title: Genomic DNA blood Family10 Patient10

description: Hybridized to 250K_Nsp

value: Family10 Patient10


title: Genomic DNA blood Family12 Patient12

description: Hybridized to 250K_Nsp

value: female

value: Family12 Patient12


title: Genomic DNA blood Family9 mother

description: Hybridized to 250K_Nsp

value: Family9 mother


title: Genomic DNA blood Family8 mother

description: Hybridized to 250K_Nsp

value: Family8 mother


title: Genomic DNA blood Family11 Patient11

description: Hybridized to 250K_Nsp

value: Family11 Patient11


title: Rectal Colon Biopsy_SD52932_HV [GP602R_13_9_SS102994]

description: Sample name: GP602R_13_9_SS102994

value: HV


title: Genomic DNA blood Family9 father

description: Hybridized to 250K_Nsp

value: Family9 father

value: blood


title: Rectal Colon Biopsy_SD52931_HV [GP602R_12_102_SS102993]

description: Sample name: GP602R_12_102_SS102993

value: Rectal Colon Biopsy

value: M


title: wild type seedling, biological rep2

first: Liguo

address: South Zhongguancun Street

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from three-week-old wild type seedling

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome 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 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.

organism: Oryza sativa

source_name: Wild type seedling three weeks old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Surface-sterilized seeds of the wild type and Epi-df plants were soaked in water for 3 d and then placed in artificial soil for three weeks.

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

value: seedling

tag: variety

value: japonica

tag: genotype

value: wild type

tag: age

value: three-week-old


title: wild type seedling, biological rep3


title: Epi-df seedling, biological rep3

description: Gene expression data from three-week-old Epi-df seedling

source_name: Epi-df seedling three weeks old

value: Epi-df


title: Genomic DNA blood Family7 mother

description: Hybridized to 250K_Nsp

value: Family7 mother


title: Genomic DNA blood Family9 Patient9

description: Hybridized to 250K_Nsp

value: Family9 Patient9


title: wild type seedling, biological rep1


title: H4-930choline

city: Ithaca

first: Xinyin

last: Jiang

state: NY

address: 241 Kinzelberg Hall, Cornell University

department: Nutritional Sciences

institute: Cornell University

hyb_protocol: Cy3-labelled aRNA 825ng was fragmented at 60°C for 30 minutes in a reaction volume of 55μL containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. After fragmentation, the samples were cooled on ice for 1 minute. The 2XGEx Hybridization buffer HI-RPM of 55 μL was added to the fragmented sample mixtures.  The sample mixtures prepared above (100μL) was used to hybridized to Agilent Whole Human Gene Expression Microarray 4×44K with an Agilent Microarray Hybridization Chamber (G2534A). Microarray hybridization was performed at 65℃ for 17 hours in the hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent Scanner G2505C using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using protocol GE1_105_Dec08 and Grid: 014850_D_20070820 to obtain background subtracted and spatially detrended Processed Signal intensities. The probesets with signal detected (gBGSubSignal intensity >0) in over 75% of the samples were retained for further processing, otherwise they were excluded from the dataset (which led to data reduction in the processed matrix file). There were 36001 out of the 41108 probesets in the  GPL6480 platform that passed the filtering criteria and were retained for further processing. For these 36001 probesets, the gBGSubSignal values were log2 transformed and median normalized to get the final normalized data used for between group analyses.

source_name: placenta_930 mg choline/d_12 wks

label_protocol: Antisense RNA amplification and cyanine 3 labeling was performed with an Amino Allyl MessageAmp II aRNA amplification kit (Ambion Inc., Grand island, NY) using 1000ng input total RNA according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The RNAlater stablized placental samples were homogenized with a homogenizer in 1mL TRIzol® Reagent (Invitrogen, Grand Island, NY) for RNA extraction. Total RNA was purified via a commercially available kit (RNeasy Mini kit, Qiagen, Valencia, CA) with on-column DNase digestion. The concentration and quality of the isolated RNA was assayed with a NanoDrop® ND-1000 instrument (Thermo,Wilmington, DE). For RNA quality, a value higher than 1.8 for the ratio of 260 to 280 was deemed acceptable. The integrity of the RNA samples was further determined using an Agilent 2100 Bioanalyzer (Agilent Technologies,Santa Clara, CA). Only samples of an RNA Integrity Number (RIN) >8.0 were included for microarray.

treatment_protocol: Healthy third trimester (gestational week 26-29) pregnant women were randomized to a 12-week choline controlled feeding study. The participants  consumed  either 480 (n=6) or 930 (n=6) mg choline/d for 12 weeks. The placenta samples were obtained within 90 minutes after the delivery of the babies in the hospital.  After removing the amniotic sac, the placenta was visually divided into four quadrants. Full thickness biopsies (0.5cm*0.5cm*placenta depth) were obtained from the center of each quadrant, rinsed with PBS and either flash frozen in liquid nitrogen or immersed in RNAlater (Qiagen, Valencia, CA, USA).

tag: participants group

value: healthy third trimester (gestational week 26-29) pregnant women

value: placenta

tag: gender of baby

value: male

tag: mode of delivery

value: vaginal

tag: gestational age at delivery

tag: choline intake for 12 weeks

value: 930 mg/d for 12 wks


title: Genomic DNA blood Family8 father

description: Hybridized to 250K_Nsp

value: Family8 father


title: Epi-df seedling, biological rep1


title: Genomic DNA blood Family6 father

description: Hybridized to 250K_Nsp

value: Family6 father


title: H5-930choline


title: Genomic DNA blood Family8 Patient8

description: Hybridized to 250K_Nsp

value: female

value: Family8 Patient8

value: blood


title: Genomic DNA blood Family7 Patient7

description: Hybridized to 250K_Nsp

value: Family7 Patient7


title: Epi-df seedling, biological rep2

value: seedling

value: japonica


title: Genomic DNA blood Family6 mother

description: Hybridized to 250K_Nsp

value: Family6 mother


title: Genomic DNA blood Family7 father

description: Hybridized to 250K_Nsp

value: Family7 father


title: Rectal Colon Biopsy_SD52930_HV [GP602R_10_59_SS102991]

description: Sample name: GP602R_10_59_SS102991

value: Rectal Colon Biopsy

value: M

value: HV


title: H3-930choline

value: healthy third trimester (gestational week 26-29) pregnant women

value: placenta


title: Amniocytes Family6 Patient6

description: Hybridized to 250K_Nsp

source_name: genomic DNA isolated from amniocytes

value: male

value: Family6 Patient6

tag: cell type

value: Amniocytes


title: Genomic DNA blood Family5 father

description: Hybridized to 250K_Nsp

value: Family5 father


title: Rectal Colon Biopsy_SD52931_HV [GP602R_11_99_SS102992]

description: Sample name: GP602R_11_99_SS102992


title: Genomic DNA blood Family5 mother

description: Hybridized to 250K_Nsp

value: female

value: Family5 mother


title: H6-930choline

value: vaginal

value: 930 mg/d for 12 wks


title: H2-930choline


title: H1-930choline


title: Rectal Colon Biopsy_SD52930_HV [GP602R_9_62_SS102990]

description: Sample name: GP602R_9_62_SS102990


title: L4-480choline

source_name: placenta_480 mg choline/d_12 wks


title: L5-480choline


title: preadipocytes_Day14_rep3

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Sample name: Day14_4053_F
preadipocytes differentiated for 14 days

hyb_protocol: An aliquot of 1.5 micrograms of amplified products were loaded onto Illumina Human HT-12 Beadchips and hybridized at 58ºC for 17 hours, washed and incubated with straptavidin-Cy3 to detect biotin-labeled cRNA on the arrays.

scan_protocol: Arrays were scanned using a BeadArray Reader under standard Illumina protocols.

data_processing: Background subtracted and quantile normalized gene expression values were calculated using Illumina BeadStudio Software.

source_name: subcutaneous preadipocytes

label_protocol: Two hundred nanograms of total RNA were amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, Cat# IL1791) following the manufacturer’s instructions. The first strand cDNA was synthesized by incubating RNA with T7 oligo(dT) primer and reverse transcriptase mix at 42 ºC for 2 hours.  RNase H and DNA polymerase master mix were immediately added into the reaction mix following reverse transcription and were incubated for 2 hours at 16 ºC to synthesize second strand cDNA. In vitro transcription was performed and biotinylated cRNA was synthesized by a 16-hour amplification with dNTP mix containing biotindUTP and T7 RNA polymerase. Amplified cRNA was subsequently purified and the concentration was measured by NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE).

extract_protocol: Total RNA was prepared using RNeasy (Qiagen, CA).  RNA was purified on a Qiagen Mini spin column.

treatment_protocol: Confluent cells were differentiated using growth media supplemented with 100 nM human insulin, 0.250 mM 3-isobutyl-1-methylxanthine (IBMX), 500 nM dexamethasone, and 3 uM rosiglitazone

value: subcutaneous preadipocytes

tag: treatment protocol

value: differentiation protocol

tag: time

value: 14 days


title: L6-480choline

tag: tissue


title: preadipocytes_Day14_rep4

description:
Sample name: Day14_4054_B
preadipocytes differentiated for 14 days

tag: gender


title: L2-480choline


title: L3-480choline


title: L1-480choline

value: C-section


title: Genomic DNA blood Family5 Patient5

description: Hybridized to 250K_Nsp

value: Family5 Patient5

value: blood


title: preadipocytes_Day14_rep2

description:
Sample name: Day14_4053_D
preadipocytes differentiated for 14 days


title: Genomic DNA blood Family4 Patient4

description: Hybridized to 250K_Nsp

value: Family4 Patient4


title: Genomic DNA blood Family4 father

description: Hybridized to 250K_Nsp

value: Family4 father


title: preadipocytes_Day7_rep3

description:
Sample name: Day7_4054_F
preadipocytes differentiated for 7 days

value: 7 days


title: HeLa cells treated with heat and mock

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cDNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: RMA using the GeneChip Analysis Suite.

source_name: Human cervical carcinoma HeLa cells, heat and mock

label_protocol: 100 ng of total RNA was used to synthesize cDNA with an Ambion® WT Expression Kit.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA.

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h. Two days after transfection, the cells were placed in water bath at 44°C for 60 min (heat treatment) and were incubated at 37°C for 6 h.

tag: cell line

value: HeLa

value: cervical carcinoma

tag: morphology

value: epithelial-like

tag: treatment

value: heat and mock


title: HeLa cells treated with siRNA for DNA-PK

source_name: Human cervical carcinoma HeLa cells, DNA-PK siRNA

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing siRNA for DNA-PK and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h. Two days after transfection, the cells were placed in water bath at 37°C for 60 min (heat treatment) and were incubated at 37°C for 6 h.

value: female

value: DNA-PK siRNA


title: HeLa cells treated with heat and negative control siRNA

source_name: Human cervical carcinoma HeLa cells, heat and negative control siRNA

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing negative control siRNA and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h. Two days after transfection, the cells were placed in water bath at 44°C for 60 min (heat treatment) and were incubated at 37°C for 6 h.

value: heat and negative control siRNA


title: Genomic DNA blood Family3 father

description: Hybridized to 250K_Nsp

value: male

tag: individual

value: Family3 father


title: HeLa cells treated with negative control siRNA

source_name: Human cervical carcinoma HeLa cells, negative control siRNA

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing negative control siRNA and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h. Two days after transfection, the cells were placed in water bath at 37°C for 60 min (heat treatment) and were incubated at 37°C for 6 h.

value: negative control siRNA


title: HeLa cells treated with heat and siRNA for DNA-PK

source_name: Human cervical carcinoma HeLa cells, heat and DNA-PK siRNA

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing siRNA for DNA-PK and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h. Two days after transfection, the cells were placed in water bath at 44°C for 60 min (heat treatment) and were incubated at 37°C for 6 h.

value: heat and DNA-PK siRNA


title: Genomic DNA blood Family4 mother

description: Hybridized to 250K_Nsp

value: Family4 mother


title: preadipocytes_Day7_rep2

description:
Sample name: Day7_4053_B
preadipocytes differentiated for 7 days

value: subcutaneous preadipocytes

value: differentiation protocol


title: fkh2-S2A 2

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

hyb_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

data_processing: Raw data (CEL files) was imported into ArrayStar 4, per-gene normalized to median and filtered on flags.

organism: Schizosaccharomyces pombe

source_name: fkh2-S2A mutant

label_protocol: Labeling was performed according to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

growth_protocol: Yeast cells were grown to mid-log phase in rich medium (YEL)

extract_protocol: RNA was isolated from mid-log phase cultures according to Xue et al. 2004 (Yeast 21(1):25-39).

tag: strain

value: fkh2-S2A mutant


title: preadipocytes_Day14_rep1

description:
Sample name: Day14_4028_F
preadipocytes differentiated for 14 days

value: 14 days


title: HeLa cells treated with mock

source_name: Human cervical carcinoma HeLa cells, mock

treatment_protocol: HeLa cells, a human cervical carcinoma cell line, were cultured at 37°C. The cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co.) containing Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C for 6 h (mock-treated). Two days after transfection, the cells were placed in water bath at 37°C for 60 min (control) and were incubated at 37°C for 6 h.

value: mock


title: HUES6 replicate 2

city: La Jolla

first: Jason

last: Nathanson

address: 2880 Torrey Pines Rd, Rm 3807

department: Cellular and Molecular Medicine

institute: University of Californa San Diego

description: Gene expression data from Human Embryonic Stem cell (replicate 2)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: HuGene-1.0-st were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl  us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111  02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110  RA.CEL CM081110RB.CEL CM081110RC.CEL )

source_name: ES, HUES6

label_protocol: standard Affymetrix protocol

growth_protocol: iPSCs and HUES6 were grown in mTeSR media at 37oC in a humidified atmosphere at 5% CO2. Fibroblasts were maintained in DMEM containing 15% Fetal Bovine Serum also at 37oC in a humidified atmosphere at 5% CO2.

extract_protocol: Total RNA was extracted using Trizol according manufacturer's instructions.

treatment_protocol: Fibroblasts were detached from tissue flasks using trypsin and iPSCs and HUES6 were detached manually. After that, cells were collected with media, centrifuged and ressuspended in Trizol.

tag: sample type

value: F,embryonic


title: Genomic DNA blood Family3 mother

description: Hybridized to 250K_Nsp

value: Family3 mother

value: blood


title: HUES6 replicate 1

description: Gene expression data from Human Embryonic Stem cell (replicate 1)


title: H1 replicate 2

source_name: ES, WA01


title: HUES6 replicate 3

description: Gene expression data from Human Embryonic Stem cell (replicate 3)


title: Genomic DNA blood Family3 Patient3

description: Hybridized to 250K_Nsp

value: Family3 Patient3


title: H1 replicate 3


title: preadipocytes_Day7_rep1

description:
Sample name: Day7_4028_D
preadipocytes differentiated for 7 days

value: female

value: 7 days


title: preadipocytes_Day4_rep4

description:
Sample name: Day4_7013_E
preadipocytes differentiated for 4 days

value: 4 days


title: fkh2-S2A 1

scan_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

tag: genotype


title: fkh2delta 2


title: fkh2delta 1


title: H1 replicate 1


title: WT-iPSC clone 2, replicate 3

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 2, replicate 3)

source_name: iPSC, AG09319

value: iPSC derived from AG09319

tag: clone

value: WT-iPSC clone 2


title: Glioblastoma_gbm-0525

data_processing: The data were background subtracted and normalized using average normalization with Illumina BeadStudio software v3.1

source_name: Human glioblastoma

tag: patient population

value: Chinese

value: brain

tag: disease state

value: primary glioblastoma multiform (brain tumor)

tag: tumor grade

value: WHO grade 4

tag: patient age

tag: patient gender

value: male


title: preadipocytes_Day4_rep3

description:
Sample name: Day4_4042_C
preadipocytes differentiated for 4 days

tag: cell type

value: subcutaneous preadipocytes

tag: treatment protocol

value: differentiation protocol


title: Genomic DNA blood Family2 father

description: Hybridized to 250K_Nsp

source_name: genomic DNA isolated from blood

value: Family2 father

tag: tissue


title: Glioblastoma_gbm-0549


title: WT-iPSC clone 2, replicate 2

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 2, replicate 2)


title: Wild type 1

source_name: wild type

value: wild type


title: Genomic DNA blood Family2 Patient2

description: Hybridized to 250K_Nsp

tag: gender

value: Family2 Patient2


title: preadipocytes_Day3_rep3

description:
Sample name: Day3_4042_A
preadipocytes differentiated for 3 days

tag: time

value: 3 days


title: Glioblastoma_gbm-0547


title: WT-iPSC clone 1, replicate 3

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 1, replicate 3)

value: WT-iPSC clone 1


title: Genomic DNA blood Family2 mother

description: Hybridized to 250K_Nsp

value: female

value: Family2 mother

value: blood


title: Glioblastoma_gbm-0439


title: Glioblastoma_gbm-0409


title: preadipocytes_Day3_rep2

description:
Sample name: Day3_4054_C
preadipocytes differentiated for 3 days


title: preadipocytes_Day4_rep1

description:
Sample name: Day4_4028_B
preadipocytes differentiated for 4 days

value: 4 days


title: preadipocytes_Day4_rep2

description:
Sample name: Day4_4054_E
preadipocytes differentiated for 4 days


title: WT-iPSC clone 1, replicate 2

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 1, replicate 2)

value: iPSC derived from AG09319


title: Wild type 2


title: preadipocytes_Day3_rep4

description:
Sample name: Day3_7013_D
preadipocytes differentiated for 3 days


title: Genomic DNA blood Family1 father

description: Hybridized to 250K_Nsp

value: Family1 father


title: WT-iPSC clone 2, replicate 1

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 2, replicate 1)

value: WT-iPSC clone 2


title: Glioblastoma_gbm-0401

value: Chinese

value: brain

value: primary glioblastoma multiform (brain tumor)


title: preadipocytes_Day3_rep1

description:
Sample name: Day3_4053_E
preadipocytes differentiated for 3 days

value: subcutaneous preadipocytes


title: Genomic DNA blood Family1 mother

description: Hybridized to 250K_Nsp

value: Family1 mother


title: Glioblastoma_gbm-0370

value: WHO grade 4

value: male


title: CSB-iPSC clone 3, replicate 3

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 3, replicate 3)

source_name: iPSC, GM10903

value: iPSC derived from GM10903

value: CSB-iPSC clone 3


title: CSB-iPSC clone 2, replicate 3

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 2, replicate 3)

value: CSB-iPSC clone 2


title: preadipocytes_Day2_rep4

description:
Sample name: Day2_7013_C
preadipocytes differentiated for 2 days

value: female

value: differentiation protocol

value: 2 days


title: CSB-iPSC clone 3, replicate 2

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 3, replicate 2)


title: preadipocytes_Day2_rep3

description:
Sample name: Day2_4054_A
preadipocytes differentiated for 2 days


title: CSB-iPSC clone 2, replicate 1

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 2, replicate 1)


title: preadipocytes_Day2_rep2

description:
Sample name: Day2_4053_C
preadipocytes differentiated for 2 days


title: preadipocytes_Day2_rep1

description:
Sample name: Day2_4028_E
preadipocytes differentiated for 2 days


title: Glioblastoma_gbm-0371


title: Glioblastoma_gbm-0342


title: Glioblastoma_gbm-0308


title: Glioblastoma_gbm-0366


title: CSB-iPSC clone 1, replicate 3

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 1, replicate 3)

value: CSB-iPSC clone 1


title: preadipocytes_Day1_rep4

description:
Sample name: Day1_7013_B
preadipocytes differentiated for 1 day

value: 1 day


title: CSB-iPSC clone 2, replicate 2

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 2, replicate 2)


title: CSB-iPSC clone 3, replicate 1

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 3, replicate 1)


title: preadipocytes_Day1_rep3

description:
Sample name: Day1_4042_D
preadipocytes differentiated for 1 day


title: Glioblastoma_gbm-0346


title: Glioblastoma_gbm-0324


title: Genomic DNA blood Family1 Patient1

description: Hybridized to 250K_Nsp

value: Family1 Patient1

value: blood


title: preadipocytes_Day1_rep2

description:
Sample name: Day1_4053_A
preadipocytes differentiated for 1 day


title: WT-iPSC clone 1, replicate 1

description: Gene expression data from iPSCs clone derived from normal fibroblasts (clone 1, replicate 1)

value: iPSC derived from AG09319

value: WT-iPSC clone 1


title: CSB-iPSC clone 1, replicate 1

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 1, replicate 1)


title: preadipocytes_Day0_rep4

description:
Sample name: Day0_7013_A
undifferentiated preadipocytes

value: undifferentiated

value: control


title: CSB-FB replicate 3

description: Gene expression data from CS fibroblasts (replicate 3)

source_name: Fibroblast, GM10903

tag: cell line


title: s3068

city: Vancouver

first: Martin

middle: Richard

last: Jones

state: BC

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Segmentation analysis based on the DNACopy package. Segmentation GFF file. Genome annotation GFF file

organism: Caenorhabditis elegans

source_name: homozyogus mutants generated in the rol-3(s1040) genetic background

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

growth_protocol: Nematodes were grown at 200C on 150mm NGM agar plates seeded with Escherichia coli strain OP50.

extract_protocol: Animals were harvested and treated with a standard protienase K digestion. Samples were extracted using a standard phenol/chloroform protocol, treated with RNAse A for 1 hour and subjected to a second round of phenol/chloroform extraction. DNA was resuspended in water and quantified.

tag: organism

value: whole animal, mixed stage

source_name: strain BC6637 (rol-3(s1040)) - control


title: s3071

hyb_protocol: see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.


title: Glioblastoma_gbm-0225

value: Chinese

value: brain

value: primary glioblastoma multiform (brain tumor)

value: WHO grade 4


title: s3069


title: Glioblastoma_gbm-0203

value: male


title: Glioblastoma_gbm-0292


title: preadipocytes_Day1_rep1

description:
Sample name: Day1_4028_C
preadipocytes differentiated for 1 day

source_name: subcutaneous preadipocytes

value: subcutaneous preadipocytes

value: female


title: Glioblastoma_gbm-0255


title: CSB-iPSC clone 1, replicate 2

description: Gene expression data from iPSCs clone derived from CS fibroblasts (clone 1, replicate 2)

value: iPSC derived from GM10903


title: CSB-FB replicate 2

description: Gene expression data from CS fibroblasts (replicate 2)


title: preadipocytes_Day0_rep5

description:
Sample name: Day0_7013_F
undifferentiated preadipocytes


title: preadipocytes_Day0_rep3

description:
Sample name: Day0_4042_B
undifferentiated preadipocytes


title: preadipocytes_Day0_rep1

description:
Sample name: Day0_4028_A
undifferentiated preadipocytes


title: Glioblastoma_gbm-0222


title: CSB-FB replicate 1

description: Gene expression data from CS fibroblasts (replicate 1)


title: s3070


title: s3067


title: s3072


title: RCK8 LMO2 transfected, biological replicate 4

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: The microarrays were scannedusing a GenePix 4000A scanner (Molecular Devices) and the resulting images were analyzed with the software package GenePix Pro.

data_processing: Data were analyzed using the rma function of Bioconductor with custom CDF file mapping to Entrez gene from Brainarray (version 14)

source_name: RCK8 DLBCL_LMO2 transfected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Cell lines were grown in RPMI 1640 medium (Mediatech, Inc. Herdon, VA), supplemented with 10% fetal bovine serum, 2 mM glutamine (GIBCO BRL, Grand Island, NY), and penicillin/streptomycin (Mediatech, Inc. Herdon, VA)

extract_protocol: Total cellular RNA was isolated from transfected cells using the Trizol reagent (Invitrogen) according to the manufacturer’s instructions

treatment_protocol: pIREShrGFP II LMO2 plasmids were constructed using standard molecular biology methods and used for generation of the Rck8 LMO2 stable transfected cell line

value: RCK8 DLBCL

value: diffuse large B cell lymphoma

tag: transfected with

value: pIREShrGFP II-LMO2 plasmid


title: preadipocytes_Day0_rep2

description:
Sample name: Day0_4054_D
undifferentiated preadipocytes


title: Glioblastoma_gbm-0178


title: Glioblastoma_gbm-0182


title: RCK8 LMO2 transfected, biological replicate 3


title: RCK8 LMO2 transfected, biological replicate 2


title: DAOY

description: SAMPLE 8

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data was average-normalized and background substracted using Illumina BeadStudio.

source_name: DAOY cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Cells were grown according to ATCC guidelines. Stable cell lines were selected and maintained in standard medium with 800 µg/ml G418.

extract_protocol: RNA was extracted using Qiagen Rneasy kit according to manufacturer's instruction. RNA quality was checked with Agilent Bioanalizer.

tag: cell line background

value: DAOY

value: medulloblastoma

tag: genotype/variation

value: parental cell line control


title: DAOY-control stable 2

description: SAMPLE 7

source_name: DAOY cells_transgenic_control

value: vector only control

tag: transgene

value: pHM6 (vector only)


title: RCK8 LMO2 transfected, biological replicate 1


title: Glioblastoma_gbm-0172


title: RCK8 control, biological replicate 1

source_name: RCK8 DLBCL_control

value: control pIREShrGFP II plasmid


title: RCK8 control, biological replicate 2


title: DAOY-MXD3 stable 5

description: SAMPLE 5

source_name: DAOY cells_transgenic_MXD3

value: MXD3 stable transgenic


title: DAOY-control stable 1

description: SAMPLE 6


title: DAOY-MXD3 stable 4

description: SAMPLE 4


title: RCK8 control, biological replicate 4


title: 3B4.15_Dex_treated_rep3

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

description: This sample is of Dexamethasone treated 3B4.15 T hybridoma cells It is the third of three  treated biological replicates used in this experiment, each from separate flasks.

hyb_protocol: Hybridization was performed by Nimblegen systems following their standard operating protocol. See www.nimblegen.com

scan_protocol: Scanning  was performed by the Sabanci University Nanotechnology Research and Application Center (SUNUM http://sunum.sabanciuniv.edu/) following their standard operating protocol and instructions for NimbleGen arrays. See www.nimblegen.com

data_processing: The raw data were processed using the ANAIS software (Simon, A., and Biot, E. (2010) Bioinformatics 26, 2468-2469). Array quality was assessed at the probe level. Values for 3 probes for each gene in each array were combined to summarize gene expression from probe sets. RMA background normalization and quantile normalization were performed for intra- and inter-array normalization respectively. Genes with signal intensities above a 95% random threshold were chosen for further studies. Differentially expressed genes were obtained based on the following criteria: Fold-change ≥ 2.5 and ANOVA p-value ≤ 0.01. Hierarchical clustering was applied to the top 500 differentially expressed genes with Genesis software (Sturn, A., Quackenbush, J., and Trajanoski, Z. (2002) Bioinformatics 18, 207-208).

organism: Mus musculus

source_name: 3B4.15 T_Dexamethasone treated for 16hr

label_protocol: cDNA was  labeled with Cy-3, according to the manufacturer’s protocols (Roche-Nimblegen).

growth_protocol: 3B4.15 T hybridoma cells grown in 5% CO2 at 37C in RPMI-1640 medium supplemented with 10% fetal calf serum, 100 unit/ml penicillin/streptomycin, 2 mM L-glutamine, 1x MEM vitamins/non-essential amino acids, and 50 μM β−mercaptoethanol.

extract_protocol: Total RNA was extracted using Tri-Reagent  (Sigma), RNA quality was confirmed on an RNA 6000 Nano chip (AGT-5067-1511) in an Agilent Bioanalyzer. Double stranded cDNA was generated using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: 3B4.15 T hybridoma cells, either mock treated (Ethanol) or treated with 1 μM Dexamethasone (Sigma) for 16 hours.

value: 3B4.15 T hybridoma cells

tag: treated with

value: 1 μM Dexamethasone for 16hr


title: 3B4.15_mock_treated_rep3

description: This sample is of mock treated 3B4.15 T hybridoma cells It is the third of three mock treated biological replicates used in this experiment, each from separate flasks.

source_name: 3B4.15 T_mock treated

value: Ethanol (mock)


title: DAOY-MXD3 stable 3

description: SAMPLE 3


title: 3B4.15_mock_treated_rep2

description: This sample is of mock treated 3B4.15 T hybridoma cells It is the second of three mock treated biological replicates used in this experiment, each from separate flasks.


title: 3B4.15_Dex_treated_rep2

description: This sample is of Dexamethasone treated 3B4.15 T hybridoma cells It is the second of three  treated biological replicates used in this experiment, each from separate flasks.


title: RCK8 control, biological replicate 3


title: 3B4.15_mock_treated_rep1

description: This sample is of mock treated 3B4.15 T hybridoma cells It is the first of three mock treated biological replicates used in this experiment, each from separate flasks.


title: DAOY-MXD3 stable 2

description: SAMPLE 2


title: 3B4.15_Dex_treated_rep1

description: This sample is of Dexamethasone treated 3B4.15 T hybridoma cells It is the first of three  treated biological replicates used in this experiment, each from separate flasks.


title: Wild type 3

status: Public on Jul 12 2012

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

scan_protocol: Standard Illumina scanning protocol

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

source_name: Wild type

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were anesthetized with isoflurane at 3PM and subcutaneous adipose tissues were immediately snap frozen in liquid nitrogen.

tag: strain

value: FVB

value: Male

tag: age

value: 12 weeks

value: Subcutaneous adipose tissue

tag: genetic variant

value: Wild type


title: 1

city: Wuhan

first: Lei

state: Hubei

address: 1095# Jiefang Avenue

institute: Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: primary cultured hepatocytes isolated from the livers of healthy mice

data_processing: The data were normalized using Cubic Spline normalisation in genomestudio

source_name: hepatocytes

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ambion Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol. Quality control was performed with Polyacrylamide gel electrophoresis.

value: BALB/c

value: healthy

value: 10 months

value: male

value: liver

value: hepatocytes


title: MitoNEET-transgenic 3

source_name: MitoNEET-transgenic

value: MitoNEET-transgenic


title: MitoNEET-transgenic 2


title: MitoNEET-transgenic 1


title: 4

description: primary cultured oval cells isolated from the livers of HBV transgenic mice

source_name: oval cells

value: HBV transgenic

value: oval cells


title: 2

description: primary cultured oval cells isolated from the livers of healthy mice


title: Wild type 1


title: DAOY-MXD3 stable 1

description: SAMPLE 1

value: DAOY

value: medulloblastoma

value: MXD3 stable transgenic


title: 3

description: primary cultured hepatocytes isolated from the livers of HBV transgenic mice


title: wt-blood-gr1-low-1

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description:
WT_BD_Gr1_Lo_5
healthy donor, dendritic cell, Gr1 low,Mus musculus,blood,dendritic cell,Gr1 low,total RNA,biotin

hyb_protocol: According to BeadChip array manufacturer's protocol.

data_processing: Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered.

source_name: healthy donor, dendritic cell, Gr1 low

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis.

extract_protocol: RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per manufacturer's specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in a microarray assay.

value: blood

value: dendritic cell

tag: cell subtype

value: Gr1 low

tag: genotype

value: wildtype

tag: disease state


title: ID patient 9

city: Amsterdam

first: Els

last: Voorhoeve

address: De Boelelaan 1117

department: Clinical Genetics

country: Netherlands

institute: VU medical center

hyb_protocol: Following standard manufacturer's procedures

scan_protocol: Arrays were scanned at 5-μm resolution using the GenePix4000B scanner and images where extracted by NimbleScan 2.0 extraction software

data_processing: Each array data set was imported into R (www.r-project.org; Ihaka et al., 1996) for normalization. The normalize.qspline method from the affy Bioconductor package was used to normalize the signal intensities of the test vs. reference. (see for further details, Rebecca R. Selzer1 et al., 2005)

source_name: DNA patient 9

label_protocol: The Patient DNA was labeled with Cy5 and the reference DNA with Cy3, as described by Rebecca R. Selzer1 et al., 2005

extract_protocol: Genomic DNA was extracted from  peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: Lymfocytes

tag: disease

value: intellectual disability/autism

value: female

value: developemental delay aged 1 year and 7 months

source_name: reference GM15724 from Coriell

tag: reference

value: male reference DNA


title: CR013

city: Kansas City

first: Douglas

middle: C

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

hyb_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols

data_processing: All statistical analyses were performed using statistical software: SPSS, Partek (Partek, Inc. St Louis, Mo.). Robust Multichip Analysis (RMA) was used for background correction followed by quantile normalization with baseline transformation to the median of the control samples

label: FlashTag Biotin HSR

source_name: right ventricle_TOF

growth_protocol: Tissues samples obtained during patient surgery were immediately de-identified and frozen.

extract_protocol: RNA was extracted from ~10 mg of frozen tissue from right ventricle using a mirVana microRNA isolation kit (Applied Biosystems/Ambion, Austin, TX) according to manufactures instruction

treatment_protocol: All tissue samples removed during surgery were excised by the performing surgeon for clinical indications utilizing standard of care procedures.

tag: group

value: infant with nonsyndromic tetralogy of Fallot (TOF)

tag: tissue

value: right ventricular myocardium


title: GE003

scan_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols

source_name: right ventricle_control

value: control (normally developing infants)


title: GE002

label_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols


title: pdc-3

description:
pDC_3
Healthy donor,Mus musculus,plasmacytoid dendritic cell,total RNA,biotin

scan_protocol: According to BeadChip array manufacturer's protocol.

source_name: healthy donor, plasmacytoid dendritic cell

value: plasmacytoid dendritic cell

tag: gender

value: male

value: healthy


title: GE001


title: wt-blood-gr1-high-3

description:
WT_BD_Grl_hi_3
healthy donor, dendritic cell, Gr1 high,Mus musculus,blood,dendritic cell,Gr1 high,total RNA,biotin

source_name: healthy donor, dendritic cell, Gr1 high

value: Gr1 high


title: CR003


title: wt-blood-gr1-high-2

description:
WT_BD_Grl_hi_2
healthy donor, dendritic cell, Gr1 high,Mus musculus,blood,dendritic cell,Gr1 high,total RNA,biotin


title: spleen-cd4-1

description:
Spleen_CD4_-1
healthy donor, dendritic cell, CD4,Mus musculus,spleen,dendritic cell,CD4,total RNA,biotin

source_name: healthy donor, dendritic cell, CD4

value: spleen


title: pdc-4

description:
pDC_4
Healthy donor,Mus musculus,plasmacytoid dendritic cell,total RNA,biotin

value: blood


title: pdc-2

description:
pDC_2
Healthy donor,Mus musculus,plasmacytoid dendritic cell,total RNA,biotin


title: wt-blood-gr1-low-2

description:
WT_BD_Gr1_Lo_4
healthy donor, dendritic cell, Gr1 low,Mus musculus,blood,dendritic cell,Gr1 low,total RNA,biotin

value: dendritic cell


title: Wild type 2

value: FVB

value: Male

value: 12 weeks

value: Subcutaneous adipose tissue

value: Wild type


title: spleen-cd4-3

description:
Spleen_CD4_-3
healthy donor, dendritic cell, CD4,Mus musculus,spleen,dendritic cell,CD4,total RNA,biotin

value: wildtype


title: pdc-1

description:
pDC_1
Healthy donor,Mus musculus,plasmacytoid dendritic cell,total RNA,biotin


title: spleen-cd8-3

description:
Spleen_CD8_-3
healthy donor, dendritic cell, CD10,Mus musculus,spleen,dendritic cell,CD10,total RNA,biotin

source_name: healthy donor, dendritic cell, CD10


title: spleen-cd8-1

description:
Spleen_CD8_-1
healthy donor, dendritic cell, CD8,Mus musculus,spleen,dendritic cell,CD8,total RNA,biotin

source_name: healthy donor, dendritic cell, CD8


title: spleen-cd4-2

description:
Spleen_CD4_-2
healthy donor, dendritic cell, CD4,Mus musculus,spleen,dendritic cell,CD4,total RNA,biotin


title: wt-blood-gr1-high-1

description:
WT_BD_Grl_hi_1
healthy donor, dendritic cell, Gr1 high,Mus musculus,blood,dendritic cell,Gr1 high,total RNA,biotin


title: spleen-cd8-2

description:
Spleen_CD8_-2
healthy donor, dendritic cell, CD9,Mus musculus,spleen,dendritic cell,CD9,total RNA,biotin

source_name: healthy donor, dendritic cell, CD9


title: LabCR047


title: LabCR042


title: LabCR057


title: CR023


title: CR018


title: LabCR055


title: LabCR010


title: LabCR025


title: LabCR039


title: LabCR020


title: LabCR012


title: LabCR024


title: LabCR022


title: GE009


title: GE008


title: GE007


title: LabCR-016


title: lung_1918 PCT1_d8_rep4

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling after 8 days 1918 PCT1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from harvested lungs using Trizol/phenol chloroform extraction followed by precipitation.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Balb/c mice exposed via intranasal inoculation of either wild-type 1918 influenza virus or 1918 FS or 1918 PCT1 for 3,5 or 8 days.

value: Balb/c

value: Lung

tag: virus strain

tag: time p.i.

value: day 8


title: FH68

source_name: right ventricle_fetal

value: fetal heart samples

value: right ventricular myocardium


title: Day 4.5

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: 190 Kaiyuan Ave. Science City

department: Stem Cell

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Science

description: Gene expression after 4.5 day of reprogramming

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

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

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

source_name: 4.5 day of reprogramming

label_protocol: Total RNA was amplified and labeled with Cyanine (Cy3) by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: MEF cells were cultured in DMEM supplemented with 10% FBS and NEAA, penicillin/streptomycin, L-glutamine

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Retrovirus containing supernant was collected 24 hr and 48 hr after Plat-E cells were transfected with pMXs-based retroviral vectors. 1) Oct4 and Klf4 containing retrovirus was delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6.

value: Mouse Embryonic Fibroblast isolated from 13.5 day mouse embryos which carrying the Oct4-GFP transgenic allele

tag: time

value: 4.5 day of reprogramming

tag: cell passage

value: two passages after isolation


title: GE005

value: control (normally developing infants)


title: Day 6

description: Gene expression after 6 day of reprogramming

source_name: 6 day of reprogramming

value: 6 day of reprogramming


title: FH46


title: MEF

description: Gene expression after 0 day of reprogramming

source_name: 0 day of reprogramming

value: 0 day of reprogramming


title: FH01


title: lung_1918 FS_d8_rep4

description: Gene expression profiling after 8 days 1918 FS


title: lung_1918 PCT1_d8_rep2


title: Day 3

description: Gene expression after 3 day of reprogramming

source_name: 3 day of reprogramming

value: 3 day of reprogramming


title: GE004


title: Day 1.5

description: Gene expression after 1.5 day of reprogramming

source_name: 1.5 day of reprogramming

value: 1.5 day of reprogramming


title: lung_1918 FS_d8_rep3


title: lung_1918 PCT1_d8_rep3


title: lung_1918 PCT1_d8_rep1


title: lung_1918 FS_d8_rep1


title: WT-3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: MAS 5.0

organism: Escherichia coli

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

growth_protocol: E. coli cultutures were grown in M9 media using standard protocol, to log phase (OD600 of 0.7-0.8)

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

treatment_protocol: No treatment, just comparison of RNAs from wild type and mutant.

value: wild type


title: lung_Mock_d8_rep4

description: Gene expression profiling of uninfected

source_name: Mock

value: PBS

value: Day 8


title: WT-2


title: lung_1918 FS_d8_rep2


title: ID patient 13

description: hybridized to array Agilent 105k

scan_protocol: Scanned on an Agilent scanner

data_processing: Data analysis using Genomic Workbench Standard Edition 5.0.14, the Admin-2 algorithm was used for calculation of log2 ratio's and for CNV-calling a minimum of 3 probes for deletions and 5 probes for duplications was taken into account.

source_name: DNA patient 13

label_protocol: As per manufacturer (Agilent)

growth_protocol: not applicable

value: lymfocytes

value: intellectual disability/autism

value: female

value: adult

source_name: sex matched DNA control pool of at least 10 different healthy individuals


title: ID patient 5

description: hybridized to array Agilent 105k

source_name: DNA patient 5

value: male

value: child

value: sex matched DNA control pool of at least 10 different healthy individuals


title: Skin_Normal_13

city: Rochester

middle: A

last: Plager

state: MN

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

hyb_protocol: standard Affymetrix protocols

scan_protocol: Hybridized microarrays were scanned in the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed using Affymetrix Microarray Suite to quantify and scale the fluorescence data. Data analyses to identify differential transcription used GeneSpring GX 9.0 software (Agilent).

organism: Canis lupus familiaris

source_name: Skin, healthy

label_protocol: standard Affymetrix protocols

extract_protocol: After removal from RNAlater, each skin specimen was frozen in liquid nitrogen, placed in ice-cold TRIzol (Invitrogen, Carlsbad, CA), and immediately shattered and homogenized with a Polytron homogenizer (Brinkmann Instruments, Westbury, NY).  Total RNA was isolated using the TRIzol Plus RNA Purification System (Invitrogen) according to the manufacturer’s protocol.

value: male-neutered

tag: age (years)

tag: breed

value: Golden Retriever

tag: disease severity

value: Not applicable

tag: biopsy site

value: scapula

tag: medications


title: Skin_Normal_8

value: female-spayed

value: Labrador Retriever

value: inner thigh


title: Skin_Normal_12

value: para-lumbar region


title: lung_1918 wild-type_d8_rep3

description: Gene expression profiling after 8 days 1918

source_name: 1918 wt Day 8

tag: strain

value: Balb/c

value: Lung

value: 1918 wild-type


title: Skin_Normal_11

value: Gordon Setter


title: lung_1918 PCT1_d5_rep2

description: Gene expression profiling after 5 days 1918 PCT1

value: day 5


title: lung_1918 wild-type_d8_rep4

value: Day 8


title: Skin_Normal_6

value: flank area


title: Skin_Normal_7

value: Greyhound


title: Skin_Normal_5

value: commissure of the mouth


title: Skin_Normal_4

value: male-neutered

value: Labrador mix


title: lung_1918 wild-type_d8_rep1


title: lung_1918 PCT1_d5_rep1


title: lung_1918 PCT1_d5_rep4


title: lung_1918 wild-type_d5_rep3

description: Gene expression profiling after 5 days 1918

source_name: 1918 wt Day 5

value: Day 5


title: lung_1918 wild-type_d5_rep4


title: Skin_Normal_2

value: Pug

value: Not applicable

value: caudal aspect shoulder


title: Skin_Normal_3

value: female-spayed

value: Shih tzu

value: caudal to the shoulder


title: gss-3

tag: genotype

value: gss mutant


title: gss-1


title: lung_Mock_d8_rep3

description: Gene expression profiling of uninfected

value: Balb/c

value: Lung

value: PBS


title: gss-2


title: Skin_AcuteLesionalAD_13

source_name: Skin, acute lesional atopic dermatitis

value: Bichon Frise

value: inner thigh


title: lung_1918 wild-type_d5_rep1

value: 1918 wild-type


title: lung_1918 FS_d5_rep4

description: Gene expression profiling after 5 days 1918 FS


title: Skin_AcuteLesionalAD_12

value: Labrador Retriever

value: cranial aspect of the shoulder


title: lung_Mock_d8_rep2

description: Gene expression profiling of uninfected

value: Day 8


title: lung_1918 wild-type_d5_rep2

value: Day 5


title: lung_1918 wild-type_d8_rep2


title: Skin_Normal_1

value: English Setter


title: lung_1918 FS_d5_rep3


title: lung_1918 PCT1_d5_rep3

value: day 5


title: Skin_AcuteLesionalAD_10

value: West Highland White Terrier

value: groin region

value: Simplicef 100mg SID; Hydroxyzine 25mg BID


title: Skin_AcuteLesionalAD_11

value: male-intact

value: Old English Sheepdog

value: cranial elbow


title: lung_1918 FS_d5_rep2

value: Balb/c

value: Lung


title: WT-1

value: wild type


title: lung_1918 FS_d5_rep1


title: Skin_AcuteLesionalAD_8

value: male-neutered

value: American Staffordshire Terrier

value: flank region


title: lung_1918 wild-type_d3_rep3

description: Gene expression profiling after 3 days 1918

source_name: 1918 wt Day 3

value: 1918 wild-type

value: Day 3


title: Skin_Normal_10

value: Labrador Retriever

value: Not applicable

value: cranial aspect of shoulder


title: lung_1918 wild-type_d3_rep4


title: lung_Mock_d8_rep1

description: Gene expression profiling of uninfected

value: PBS

value: Day 8


title: Skin_AcuteLesionalAD_7

value: female-spayed

value: para-lumbar region


title: ID patient 14

description: hybridized to SNP array affymetrix 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner

data_processing: The relative DNA copy numbers at the SNP/CNV loci from the Affymetrix platforms were determined by comparison of the normalised array signal intensity data for the proband’s DNA sample against the HapMap270 reference file provided by Affymetrix, using Genotyping Console or ChAS software (default settings). (see Laura Bernardini et. al., 2010)

source_name: DNA patient 14

label_protocol: As per manufacturer (Affymetrix)

tag: cell type

value: lymphocyte

value: intellectual disability/autism

value: female

tag: age

value: toddler


title: Skin_AcuteLesionalAD_6

value: commissure of the mouth


title: Skin_Normal_9

value: male-neutered

value: West Highland White Terrier

value: groin region


title: Skin_AcuteLesionalAD_9

value: medial thigh


title: Skin_AcuteLesionalAD_5

value: Shih tzu

value: lateral chest

value: Simplicef 50mg SID; antihistamine


title: Skin_AcuteLesionalAD_1

value: English Setter

value: scapula

value: Cephalexin 750mg BID


title: Skin_AcuteLesionalAD_3

value: female-spayed

value: German Shepherd

value: axillary region


title: Skin_AcuteLesionalAD_4

value: Soft Coat Wheat Terrier

value: lumbar region


title: Skin_NonlesionalAD_13

source_name: Skin, nonlesional atopic dermatitis

value: Bichon Frise

value: inner thigh


title: Skin_AcuteLesionalAD_2

value: Pug

value: Marbofloxacin 55mg SID


title: Skin_NonlesionalAD_12

value: Labrador Retriever

value: cranial aspect of the shoulder


title: lung_1918 PCT1_d3_rep4

description: Gene expression profiling after 3 days 1918 PCT1

value: Balb/c

value: Lung

value: day 3


title: lung_1918 FS_d3_rep2

description: Gene expression profiling after 3 days 1918 FS

value: Day 3


title: lung_1918 PCT1_d3_rep3


title: lung_1918 FS_d3_rep3


title: lung_1918 wild-type_d3_rep2

value: 1918 wild-type


title: lung_1918 PCT1_d3_rep1


title: blood cells

city: Graz

first: Carina

last: Fischer

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

description:
MNC
MNC.birdseed-v2.chp
Hybridized to SNP 6.0

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files (generated by Affymetrix GeneChip Command Console Software version 1.1) were processed by Genotyping Console using the birdseed v2 algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: blood cells

growth_protocol: Iscove/RPMI 1:4 containing 10% FBS (fetal bovine), 1% ITS (Insulin, Transferin, Selenium), 2 mM glutamine and 1% Pen/Strep (Penicillin/Streptomycin). Incubation was carried out at 37°C in a humidified atmosphere of 5 % CO2.

extract_protocol: Genomic DNA was extracted from cells or cryo tissue using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Spectrophotometer (Microcuvette)

value: blood cells


title: lung_1918 wild-type_d3_rep1


title: lung_1918 PCT1_d3_rep2


title: tumor

description:
Chordoma (TU)
14417.birdseed-v2.chp
Hybridized to SNP 6.0

source_name: tumor

value: chordoma tumor


title: ID patient 10

description: hybridized to SNP array affymetrix 6.0

source_name: DNA patient 10

value: lymphocyte

tag: disease

value: intellectual disability/autism

value: female

value: toddler


title: lung_1918 FS_d3_rep1


title: Skin_NonlesionalAD_10

value: female-spayed

value: West Highland White Terrier

value: groin region

value: Simplicef 100mg SID; Hydroxyzine 25mg BID


title: Skin_NonlesionalAD_9

value: Labrador Retriever

value: medial thigh


title: PCa_Pool_3_R2

city: Mexico City

first: Mauricio

last: Rodriguez-Dorantes

state: Distrito Federal

address: Periferico Sur 4124

department: Research

country: Mexico

institute: National Institute Of Genomic Medicine

description:
Tumor
PCa_3.2
microRNA profiling

data_processing:
For normalization we used as the average of the  the endogenous small nuclear RNAs (snRNAs): MammU6 and U48
Target microRNAs signals were normalized to endogenous snRNAs ; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_snRNAs)]
Normalized microRNAs signal was compared between Pca and BPH groups , using Mann-Whitney U test. All analisys were done using bioconductor packages (HTqPCR, gplots, ) of the R programing enviroment.

label: FAM

source_name: Prostate Cancer

label_protocol: In total, we formed 3 pools from BPH specimens and 3 from PCa, each pool containing 100 ng of RNA. RT and preamplification reactions were carried out using a GeneAmp PCR system 9700 (Applied Biosystems). For the Megaplex RT reaction, the TaqMan® MicroRNA reverse transcription kit and the Megaplex™ RT primers, human pool A v2.0 (Applied Biosystems) were used. RT product was use as imput for the preamflification reaction, performed with the Preamp Master Mix and the Megaplex 10X preamp primer mix ( Applied Biosystems). PCR was performed using the TaqMan Array Human MicroRNA set v.2.1card A and and amplification signal  was detected using the 7900 FAST real time thermal cycler ( Applied Biosystems).

extract_protocol: RNA extraction  was performed according to easymini kit manufacturer's guideline (Qiagen, Inc)

value: Prostate Cancer

tag: activation agent

value: Tumor

tag: sample type

value: Urine


title: PCa_Pool_3_R1

description:
Tumor
PCa_3.1
microRNA profiling


title: Skin_NonlesionalAD_11

tag: gender

value: male-intact

value: Old English Sheepdog

value: cranial elbow


title: PCa_Pool_3_R3

description:
Tumor
PCa_3.3
microRNA profiling


title: PCa_Pool_2_R2

description:
Tumor
PCa_2.2
microRNA profiling


title: PCa_Pool_2_R1

description:
Tumor
PCa_2.1
microRNA profiling


title: PCa_Pool_1_R3

description:
Tumor
PCa_1.3
microRNA profiling


title: lung_1918 FS_d3_rep4

value: Balb/c

tag: tissue

value: Lung

tag: virus strain

value: Day 3


title: PCa_Pool_2_R3

description:
Tumor
PCa_2.3
microRNA profiling


title: PCa_Pool_1_R2

description:
Tumor
PCa_1.2
microRNA profiling


title: Skin_NonlesionalAD_8

value: male-neutered

value: American Staffordshire Terrier

value: flank region


title: Skin_NonlesionalAD_7

value: female-spayed

value: para-lumbar region


title: chordoma cell line p5

description:
MUG-ChorI_p5
Chrodom_III+5.birdseed-v2.chp
Hybridized to SNP 6.0

source_name: chordoma cell line p5

value: chordoma cell line p5

tag: cell line


title: BPH_Pool_3_R1

description:
Control
BPH_3.1
microRNA profiling

source_name: Benign Prostate Hyperplasia

value: Benign Prostate Hyperplasia

value: Control


title: 713T2

city: Cambridge

first: Manway

last: Liu

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

description: 2.5 mg/Kg BW + 18 mg/Kg BW

hyb_protocol: Biotinylated cRNA was hybridized to Illumina MouseRef8v2 bead chips.

scan_protocol: Gene expression matrices were scanned using Illumina iSCAN Control Software.

data_processing: Data was quantile normalized with background subtraction using Illumina BeadStudio.

source_name: Tumor

label_protocol: The integrity of the RNA was measured using a Bioanalyser and RIN values > 7-8 were considered adequate to proceed further with total RNA transcription into cRNA using the Illumina Total Prep RNA amplification kit (Ambion) following the manufacturer’s protocol.

growth_protocol: C57Bl/6 mice were obtained from Jackson laboratories. At two weeks of age, male mice were injected intraperitoneally with 50 mg/kg BW of diethylnitrosamine (DEN) (Sigma).

extract_protocol: Total RNA from all the samples was purified using the Qiagen RNeasy purification kit following the manufacturer’s protocol.

treatment_protocol: At ~44 weeks of age, the animals (n=9-10) were gavaged twice daily for 28 days with the specified doses of RAD001 and/or BEZ235. The mice were starved for three hours prior to sacrifice and received their last dose of RAD001 at the time starvation or BEZ235 1 hour before sacrifice.

value: 48 weeks

tag: treatment


title: chordoma cell line p13

description:
MUG-ChorI_p13
Chordom_III+13_(GenomeWideSNP_6).birdseed-v2.chp
Hybridized to SNP 6.0

source_name: chordoma cell line p13

value: chordoma cell line p13


title: 726T1

description: 2.5 mg/Kg BW + 18 mg/Kg BW

value: Tumor


title: 726T2

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 713T1

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 726T3

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: BPH_Pool_2_R1

description:
Control
BPH_2.1
microRNA profiling

value: Urine


title: BPH_Pool_2_R2

description:
Control
BPH_2.2
microRNA profiling


title: Skin_NonlesionalAD_5

tag: age (years)

value: Shih tzu

value: lateral chest

value: Simplicef 50mg SID; antihistamine


title: Skin_NonlesionalAD_4

tag: breed

value: Soft Coat Wheat Terrier

value: lumbar region


title: BPH_Pool_1_R3

description:
Control
BPH_1.3
microRNA profiling


title: BPH_Pool_1_R2

description:
Control
BPH_1.2
microRNA profiling


title: Skin_NonlesionalAD_3

value: German Shepherd

tag: disease severity

value: axillary region

value: Cephalexin 750mg BID


title: Skin_NonlesionalAD_2

value: female-spayed

value: Pug

tag: biopsy site

value: scapula

value: Marbofloxacin 55mg SID


title: BPH_Pool_1_R1

description:
Control
BPH_1.1
microRNA profiling

value: Benign Prostate Hyperplasia

value: Control


title: Skin_NonlesionalAD_1

value: English Setter

tag: medications


title: Skin_NonlesionalAD_6

value: male-neutered

value: Labrador Retriever

value: commissure of the mouth


title: BPH_Pool_2_R3

description:
Control
BPH_2.3
microRNA profiling

value: Urine


title: 713liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW

source_name: Liver

value: Liver

tag: strain

value: 48 weeks


title: 775T1

description: 2.5 mg/Kg BW + 18 mg/Kg BW

value: Tumor


title: 709liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 764liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 726liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 742liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 775liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 747T1

value: Placebo


title: 747T3


title: 769T3


title: 696T1


title: 710T2


title: 769T4


title: 14-day resting macrophage infection Day 4, rep 2

city: Ithaca

first: Kyle

middle: Herman

last: Rohde

address: Vet. Med. Center, C5 101

department: Microbiology and Immunology

institute: Cornell University

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95762.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis H37Rv

source_name: 2hr no macrophage control

label_protocol: not provided

extract_protocol: Trizol; T7 RNA polymerase amplification

source_name: Day 4 post infection

growth_protocol: Starting OD = 0.05; Elapsed Time = 7 days; OD at Harvest = 0.5 - 0.6; Growth Temperature = 37oC; Static or Shaking = Static; Growth Vessel Volume = 25 cm^2; Media = "Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol"

tag: time

value: 4 d


title: 14-day resting macrophage infection Day 2, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95759.gif

source_name: Day 2 post infection

value: 2 d


title: 747T2


title: 773liver

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: 14-day resting macrophage infection Day 14, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95772.gif

source_name: Day 14 post infection


title: 710T1


title: 14-day resting macrophage infection Day 6, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95763.gif

source_name: Day 6 post infection

value: 6 d


title: 14-day resting macrophage infection Day 12, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95770.gif

source_name: Day 12 post infection


title: 14-day resting macrophage infection Day 10, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95768.gif

source_name: Day 10 post infection


title: 14-day resting macrophage infection Day 8, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95766.gif

source_name: Day 8 post infection

value: 8 d


title: 14-day resting macrophage infection Day 12, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs//95815.gif


title: 14-day resting macrophage infection Day 8, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95765.gif


title: 748T3


title: 748liver


title: 771T1


title: 696liver


title: 744liver


title: 776liver


title: 14-day resting macrophage infection Day 14, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95771.gif


title: 14-day resting macrophage infection Day 6, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95764.gif


title: 14-day resting macrophage infection 2hr, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95758.gif

source_name: 2 hr post infection

value: 2 h


title: 710liver


title: 730T2

description: 10 mg/Kg BW


title: 14-day resting macrophage infection Day 4, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95761.gif


title: 700T2

description: 10 mg/Kg BW


title: 14-day resting macrophage infection Day 2, rep 2

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95760.gif


title: 771liver


title: 14-day resting macrophage infection 2hr, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95757.gif


title: 730T1

description: 10 mg/Kg BW


title: 763T1

description: 10 mg/Kg BW


title: BPH_Pool_3_R2

description:
Control
BPH_3.2
microRNA profiling

tag: cell type


title: PCa_Pool_1_R1

description:
Tumor
PCa_1.1
microRNA profiling

value: Prostate Cancer


title: 724liver

tag: age


title: AMs PR8 4h from donor 46

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

description: Gene expression data from dogs with hemangiosarcoma of different breeds

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 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 background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

source_name: human alveolar macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: human primary cultured cells were used

extract_protocol: RNA was prepared using the RNEasy Mini Kit and QIAshredder columns (QIAGEN, Valencia, CA)

treatment_protocol: influenza virus infection at moi of 0.5

value: primary alveolar macrophages

tag: individual

value: donor 46

tag: infection


title: 763T2

description: 10 mg/Kg BW


title: AMs PR8 24h from donor 46


title: AMs control 24h from donor 46

value: control


title: 732T1

description: 10 mg/Kg BW


title: 727T3

description: 10 mg/Kg BW


title: 773T1

description: 2.5 mg/Kg BW + 18 mg/Kg BW


title: AMs control 4h from donor 46


title: ATII cells control 4h from donor 46

source_name: human alveolar epithelial cells

value: primary alveolar epithelial cells


title: 772T1

description: 10 mg/Kg BW


title: 772T2

description: 10 mg/Kg BW


title: AMs PR8 24h from donor 40

value: donor 40


title: ATII cells PR8 4h from donor 46


title: 700T6

description: 10 mg/Kg BW


title: AMs PR8 4h from donor 40


title: ATII cells PR8 24h from donor 46


title: ATII cells control 24h from donor 46


title: AMs control 4h from donor 40


title: 730liver

description: 10 mg/Kg BW


title: 745liver

description: 10 mg/Kg BW


title: AMs control 24h from donor 40


title: 760liver

description: 10 mg/Kg BW


title: 14-day resting macrophage infection Day 10, rep 1

description:
Simple annotation: Macrophage, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2012-01/95767.gif


title: 763liver

description: 10 mg/Kg BW


title: 697T2

description: 30 mg/Kg BW


title: ATII cells PR8 4h from donor 40


title: 728T1

description: 30 mg/Kg BW


title: 732liver

description: 10 mg/Kg BW


title: ATII cells PR8 24h from donor 40


title: 772liver

description: 10 mg/Kg BW


title: AMs PR8 24h from donor 39

value: donor 39


title: ATII cells control 24h from donor 40


title: 759T2

description: 30 mg/Kg BW


title: ATII cells control 4h from donor 40


title: ID patient 17

description: male with intellectual disability/autism

hyb_protocol: The labeled DNA was hybridized to each array according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned with default settings using the Ilumina iScan

data_processing: Analysis and intra-chip normalization of resulting image files was performed using Illumina's GenomeStudio Module software v.2020.3 with default parameters. CNV alaysis was performed using a multi-algorithm approach as discribed in Pinto et al. Nature 2010, Pubmed ID: 2053469).

source_name: DNA patient 17

label_protocol: DNA was indipendently amplified and labeled according to the manufacturer's protocol.

value: lymfocytes

tag: disease

value: intellectual disability/autism

value: male

value: child


title: 755T1

description: 30 mg/Kg BW

value: Tumor

value: 48 weeks


title: AMs control 4h from donor 39


title: 712T1

description: 30 mg/Kg BW


title: 759T1

description: 30 mg/Kg BW


title: 700liver

description: 10 mg/Kg BW

value: Liver


title: AMs control 24h from donor 39


title: AMs PR8 4h from donor 39


title: 697T1

description: 30 mg/Kg BW


title: 712T4

description: 30 mg/Kg BW


title: ATII cells PR8 24h from donor 39


title: ATII cells PR8 4h from donor 39


title: ATII cells control 4h from donor 39


title: 712T2

description: 30 mg/Kg BW


title: ATII cells control 24h from donor 39


title: 725liver

description: 30 mg/Kg BW


title: 755liver

description: 30 mg/Kg BW


title: 759liver

description: 30 mg/Kg BW


title: Nurr_3minus

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse WG-6 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing:
The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed.
1. Illumina data are loaded into GenomeStudio and produced the raw data automatically. There is no normalization and background correction applied during this process. The data will be automatically normalized in Partek. To avoid shifting the data, Partek doesn't recommend to use background correction. Otherwise the negative intensities in the data will create problems for the following analysis.
2. Data from GenomeStudio is exported in a custom Partek report file for seamless importation into Partek. Gene level option is chosen and the probe intensities are summarized and averaged for the same genes. The intensity is log2 transformed at the same time.
3. After the Partek version data is imported into Partek, there are options for normalization to be chosen. But it is not necessary to use normalization according to Partek. So there is no further background correction and normalization. The user assigned the factor (sample attributes) before ANOVA analysis and did one factor analysis.

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

value: mESC

tag: genotype/variation


title: 693T1

description: 30 mg/Kg BW

tag: tissue


title: Nurr_3plus


title: 697liver

description: 30 mg/Kg BW


title: Pitx_3minus


title: Hes_3minus


title: Pitx_3plus


title: Hes_3plus


title: 712liver

description: 30 mg/Kg BW


title: Smo-deficient OP9 cells, rep1

city: Baltimore

first: Stephen

last: Desiderio

address: 733 N. Broadway

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Gene expression data from Smo-deficient cells

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix Scanner 3000 with 7G upgrade

data_processing:
Affymetrix Expression Suite 1.1
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-algorithm-param-quantification-name = med-polish
affymetrix-algorithm-param-quantification-scale = log2

source_name: Smo-deficient OP9 cells

label_protocol: Affymetrix standard

growth_protocol: Maintained in ATCC-recommended medium at sub-confluency

extract_protocol: Qiagen RNA easy kit


title: Pitx_2minus


title: Smo-deficient OP9 cells, rep2


title: 693liver

description: 30 mg/Kg BW


title: Pitx_2plus


title: Pitx_1minus


title: Pitx_1plus