title: E. coli-CHIR-090-rep1

status: Public on Oct 20 2009

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St Jude Children's Research Hospital

description: Gene expression data from E. coli cells treated with CHIR-090.

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

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Escherichia coli

source_name: E. coli treated with CHIR-090

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: E. coli strain MG1655 was grown in Luria broth to mid-log phase with an OD at 600 nm of 0.6

extract_protocol: Total RNA was isolated using Ambion RNAqueous purification kit according to the manufacturer's instructions and the purified RNA sample was treated with Turbo Dnase (Ambion).

treatment_protocol: E. coli cells was treated with CHIR-090 (1µg/ml) or equal volume of DMSO solvent

value: K12 derivative MG1655


title: Sample 9

status: Public on Oct 21 2009

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

country: USA

institute: NIDDK/NIH

hyb_protocol: Affymetrix standard hyb  protocol

scan_protocol: Affymetrix standard scan  protocol

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: STAT5 WT

label_protocol: Affymetrix standard label  protocol

growth_protocol: In NIDDK growth core lab protocol

extract_protocol: TRIzol reagent

tag: tissue

value: mammary

tag: genotype

value: STAT5 WT


title: Aspergillus niger, glycerol, biological rep1

city: Göteborg

first: Margarita

last: Salazar Peña

address: Kemigården 4

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from A. niger grown in batch cultivations

hyb_protocol: Approximately 15 mg of fragmented cRNA was hybridized for 16 hr at 45 °C on the 3AspergDTU Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Agilent GeneArrayÒ Scanner 3000. Scanned probe array images (.DAT files) were converted into .CEL files using the Affymetrix GeneChip Operating Software.

data_processing: Affymetrix CEL data files were preprocessed using the statistical language R version 2.7.1 and Bioconductor version 2.2. Normalization was performed using the qspline algorithm and gene expression indexes were calculated from the PM probes with the median polish summary method. All statistical preprocessing methods were implemented in affy package using R scripts and limma package.

organism: Aspergillus niger

source_name: Fungal  biomass

label_protocol: Biotin-labeled cRNA was prepared from approximately 5 mg of total RNA according to the protocol described in the Affymetrix GeneChipÒ Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).

growth_protocol: Aspergillus nidulans, Aspergillus oryzae and Aspergillus niger were grown in batch cultivations.

extract_protocol: A. niger and A. nidulans total RNA was isolated using the Qiagen RNeasy Mini Kit according to the protocol for isolation of total RNA from plant and fungi. A. oryzae total RNA was purified by using the Promega RNAgents Total RNA Isolation system following manufacturer’s recommendations.

treatment_protocol: Fungal biomass from each of the Aspergillus fermentation replicates was harvested in the mid exponential phase of growth, filtered, washed, dryed by squeezing, frozen in liquid nitrogen and stored at -80 °C until further processing.

tag: strain


title: MEF_h3k4me3_ip_ptip_rep1

type: genomic

city: Kansas City

first: Pengfei

last: Wang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute

hyb_protocol: 5ug each Cy3- and Cy5- labeled DNA were hybridized to the arrays for 24hrs at 65C and 20RPM

scan_protocol: Arrays were scanned with the Agilent G2565CA Microarray Scanner System

data_processing: Scanned images were quantified using Agilent Feature Extraction v 10.5.1.1, with feature extraction protocol ChIP_105_Dec08. Data was read into R. Data was median normalized within array.

molecule: genomic DNA

source_name: Mouse embryonic fibroblast cell line, Ptip-/-, H3K4me3 IP

label_protocol: Agilent Mammalian ChIP-on-chip Protocol v10.0 (GenomicDNA kit plus)

growth_protocol: DMEM with 10% FBS

extract_protocol: Approximately ~ 3-5 x 10^8 cells were harvested and cross-linked with 1% formaldehyde. Phenol-chloroform was used to extract DNA. See protocol (Lee, T. et al. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748 (2006).)

treatment_protocol: Chromatin Immunoprecipitation with H3K4me3

tag: cell type

value: mouse embryonic fibroblasts (MEF)

tag: antibody

value: H3K4me3 (homemade)

value: Ptip-/-

source_name: Mouse embryonic fibroblast cell line, Ptip-/-, whole cell extract

treatment_protocol: No treatment


title: Cells transduced with vector expressing Mouse testis library (MCF10A LIB 1 Unselected)

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Transduced with vector expressing Mouse testis library

hyb_protocol: 1500 ng of cRNA was hyb on mouse-6 for 16-20 hours. Array washing was performed using wash buffer; an high strincengy temp wash was performed at 55C for 30 minutes. Arrays were stained with SA-Cy3

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Data are summarized with beadstudio 1.5.1.3 and intentionally not normalized to preserve the asymmetry due to selection and enrichment of a limited number of transcripts.

label: biotin-SA Cy3

organism: Homo sapiens

source_name: MCF10A LIB 1 Unselected

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit introducing  the following variations: 20 ug of total RNA using pFB specific primer starting from

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

tag: cell line


title: E. coli-CHIR-090-rep3

tag: agent


title: E. coli-CHIR-090-rep2


title: MEF_h3k4me3_ip_wt_rep5

source_name: Mouse embryonic fibroblast cell line, wt, H3K4me3 IP, rep3

value: wt

source_name: Mouse embryonic fibroblast cell line, wt, whole cell extract


title: MEF_h3k4me3_ip_men1_rep2

data_processing: Scanned images were quantified using Agilent Feature Extraction v 10.1.1, with feature extraction protocol ChIP-v1_10_Apr09. Data was read into R. Data was median normalized within array.

source_name: Mouse embryonic fibroblast cell line, Men1-/-, H3K4me3 IP

source_name: Mouse embryonic fibroblast cell line, Men1-/-, whole cell extract


title: MEF_h3k4me3_ip_wt_rep4

source_name: Mouse embryonic fibroblast cell line, wt, H3K4me3 IP, rep2


title: mll_h3_arrayhalf1_rep2

hyb_protocol: 5 ug each Cy3- and Cy5- labeled DNA were hybridized to the arrays for 40hrs at 65C and 20RPM.

data_processing: Scanned images were quantified using Agilent Feature Extraction v 9.5.3.1, with feature extraction protocol ChIP-v1_95_May07. Data was read into R. Data was median normalized within array and aquantile normalized between arrays.

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, H3 IP

treatment_protocol: Chromatin Immunoprecipitation with H3

value: H3 (ab1791, Abcam)

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, whole cell extract


title: mll_k4me3_arrayhalf1_rep2

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, H3K4me3 IP

value: H3K4me3 (ab8580, Abcam)


title: wt_h3_arrayhalf1_rep2

source_name: Mouse embryonic fibroblast cell line, wt, H3 IP


title: wt_k4me3_arrayhalf1_rep2

source_name: Mouse embryonic fibroblast cell line, wt, H3K4me3 IP


title: E. coli-DMSO-rep2

description: Gene expression data from E. coli cells treated with DMSO only.

source_name: E. coli treated with DMSO as a control

value: DMSO


title: MEF_h3k4me3_ip_wt_rep3


title: mll_k4me3_arrayhalf1_rep1


title: wt_h3_arrayhalf1_rep1


title: E. coli-DMSO-rep1


title: wt_k4me3_arrayhalf1_rep1


title: MEF_h3k4me3_ip_wt_rep2

source_name: Mouse embryonic fibroblast cell line, wt, H3K4me3 IP, rep1


title: mll_k4me3_arrayhalf2_rep2


title: Wild-type cells, not selected (MCF10A WTB Uns)

description: Wild-type MCF10A cells, not selected

hyb_protocol: 1500 ng of cRNA was hyb on human-6 V2 for 16-20 hours. Array washing was performed using wash buffer; an high strincengy temp wash was performed at 55C for 10 minutes. Arrays were stained with SA-Cy3

data_processing: Data were summarized and rank-invariant normalized using the Illumina Beadstudio software (ver. 1.5.1.3).

source_name: MCF10A, wt B cells no selection

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit.


title: mll_h3_arrayhalf2_rep2


title: MEF_h3k4me3_ip_mll3_rep1

source_name: Mouse embryonic fibroblast cell line, Mll3-/-, H3K4me3 IP

source_name: Mouse embryonic fibroblast cell line, Mll3-/-, whole cell extract


title: wt_pol2_rep2

hyb_protocol: 5ug each Cy3- and Cy5- labeled DNA were hybridized to the arrays for 78hrs at 65C and 20RPM

source_name: Mouse embryonic fibroblast cell line, wt, PolII IP, rep3

treatment_protocol: Chromatin Immunoprecipitation with PolII

value: RNA Pol II CTD (homemade)


title: mll_h3_arrayhalf1_rep1


title: AALE-Vector + shTBK1, biological rep3

city: La Jolla

first: Pablo

last: Tamayo

state: CA

address: 3855 Health Sciences Drive MC 0658

department: Moores Cancer Center

institute: UCSD

description: Gene expression data from vector expression/TBK1 suppression

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on U133A Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The data were scanned using Affymetrix Gene Chip Scanner 3000

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file    annotate probes  yes

source_name: Vector expression/TBK1 suppression

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

growth_protocol: AALE cells (Lundberg et al., Oncogene 2002;21:4577) expressing oncogenic KRAS or vector alone were grown in serum free SABM media with supplements using standard culture conditions.

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

treatment_protocol: Cells were infected with TBK1- or GFP-specific lentivirally delivered shRNAs for 4 hours, puromycin selection was initiated 24 hours post-infection, then RNA was harvested 48 hours post-infection.

value: Immortalized lung epithelial cells


title: mll_pol2_rep2

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, PolII IP, rep4


title: MEF_h3k4me3_ip_wt_rep1

source_name: Mouse embryonic fibroblast cell line, wt, whole cell extract


title: MK10

city: Osaka, Suita City

first: Kunihiko

last: Hiramatsu

address: 2-2, Yamadaoka

department: Bone and Cartilage Biology

country: Japan

institute: Osaka University

description: mice adult dermal fibroblasts

hyb_protocol: 10 mg of fragmented cRNAs were hybridized to Affymetrix 430 2.0 GeneChip arrays at 45C for 16 hour. Genechips were washed and stained using an Affymetrix Fluidics station 450.

scan_protocol: GeneChips were scanned using a Genechip scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Induced chondrogenic cell line "MK-10" from mouse dermal fibroblasts

label_protocol: Biotin-labeled cRNA was obtained from 250 ng of total RNA with MessageAmp III RNA Amplification Kit (Ambion).

growth_protocol: Induced cell lines were cultured in DMEM supplemented with 10% FBS

extract_protocol: Total RNAs were extracted using Rneasy Mini Kits (Qiagen, Santa Clarita, CA).

treatment_protocol: Induced cell lines were detached with 0.25% trypsin-EDTA (GIBCO) and collected.

value: dermal fibroblasts

tag: gender

value: male

tag: age

value: 6 months


title: MK7

description: mice adult dermal fibroblasts

source_name: Induced chondrogenic cell line "MK-7" from mouse dermal fibroblasts


title: HEK293E cells, TDP-43 siRNA, replicate 4

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner.

data_processing: The data were analysed using GC-RMA for background correction, normalization and probe summarization using the Bioconductor package gcrma with default values.

source_name: HEK cells transfected with TDP-43 siRNA, 24h after transfection

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: HEK293E cells were grown in Dulbecco’s modified Eagle medium (DMEM) (Biochrom) supplemented with 10% fetal bovine serum (PAA) at 37°C under humidified 5% CO2/air

extract_protocol: RNA  was extracted by using RNeasy Mini Kit (Qiagen) following manufacturers instructions for animal cells.

treatment_protocol: Cells were transiently transfected three consecutive days using HiPerfect with 5nmol scrambled (both Qiagen) or TDP-specific  siRNAs (5’-CAATAGCAATAGACAGTTA-3’) and cultivated for 24h.


title: wt_k4me3_arrayhalf2_rep2


title: wt_h3_arrayhalf2_rep2


title: mll_h3_arrayhalf2_rep1

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, H3 IP


title: mll_pol2_rep1

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, PolII IP, rep2

value: RNA Pol II CTD (ab5408, Abcam)

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, whole cell extract


title: E. coli-DMSO-rep3


title: MK5

description: mice adult dermal fibroblasts

source_name: Induced chondrogenic cell line "MK-5" from mouse dermal fibroblasts


title: HEK293E cells, TDP-43 siRNA, replicate 3


title: MEF_h3k4me3_ip_men1_rep1

source_name: Mouse embryonic fibroblast cell line, Men1-/-, H3K4me3 IP

source_name: Mouse embryonic fibroblast cell line, Men1-/-, whole cell extract


title: MEF_h3k4me3_ip_mll3_rep2


title: HEK293E cells, scrambled siRNA, replicate 4

source_name: HEK cells transfected with scrambled siRNA, 24h after transfection


title: Pregnant_12

city: Frederiksberg

first: Esben

last: Oestrup

address: Groennegaardsvej 7

department: Department of Basic Animal and Veternary Sciences

country: Denmark

institute: University of Copenhagen

description: Gene expression data from pregnant animals

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

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 with Autoloader and Barcode reader

data_processing: Data were processed using the Robust Multi-Array (RMA) normalization in the BioConductor package affy for R. Significance analysis was performed using the BioConductor package “Linear Models for Microarray Data” (LIMMA). Cut-off values were set to two-fold difference in expression values and a false discovery rate (FDR) of 1%.

label: Biotin

organism: Sus scrofa

source_name: Endometrium, pregnant sow, Day 14 after insemination

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

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s recommendations. An additional RNA selective precipitation was made using ammonium acetate.

treatment_protocol: The uteri were removed upon slaughter and each uterine horn was flushed with PBS containing 1% fetal calf serum, and subsequently opened longitudinally at the anti-mesometrial side. The sites of embryonic attachment were macroscopically visual in the endometrium on the mesometrial side in form of hyperemic zones. Samples of the endometrium (lamina epithelialis, lamina propria and tela submucosa, but not tunica muscularis) were isolated from proximal (the end close to the ovaries), intermedial, and distal (next to the corpus uteri)) sections of each uterine horn. Samples were taken from the endometrium of the non-pregnant animals at comparable locations. Tissue samples were transferred to RNAlater (Ambion, Huntingdon, Cambridgeshire, UK) . Samples in RNAlater were incubated overnight at 4°C and stored at -80°C until further processing.

value: Yorkshire (YY)

value: Endometrium

value: Female

tag: pregnancy status

value: Pregnant


title: wt_pol2_rep1

source_name: Mouse embryonic fibroblast cell line, wt, PolII IP, rep1

value: mouse embryonic fibroblasts (MEF)


title: Pregnant_10

value: Landrace (LL)


title: HEK293E cells, TDP-43 siRNA, replicate 2


title: HEK293E cells, TDP-43 siRNA, replicate 1


title: mll_h3_rep1


title: HEK293E cells, scrambled siRNA, replicate 3


title: mll_k4me3_arrayhalf2_rep1

source_name: Mouse embryonic fibroblast cell line, Mll1-/-, H3K4me3 IP


title: HEK293E cells, scrambled siRNA, replicate 2


title: wt_k4me3_rep2

source_name: Mouse embryonic fibroblast cell line, wt, H3K4me3 IP

value: H3K4me3 (homemade antibody)


title: Non-pregnant_9

description: Gene expression data from non-pregnant animals

source_name: Endometrium, non-pregnant sow, Day 14 after insemination

value: Non-pregnant


title: mll_k4me3_rep2


title: HEK293E cells, scrambled siRNA, replicate 1


title: PPAR KO_DEHP 1150_123

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

description:
PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from  PPAR(alpha)-null mouse liver treated with DEHP

hyb_protocol: following Affymetrix protocol

scan_protocol: The fluorescence intensities were measured with Affymetrix GeneChip scanner 3000 with 7G upgrade

data_processing: The intensity data files (.cel files) were loaded to Rosetta Resolver (Rosetta Biosoftware, Seattle, WA) for analysis.

source_name: liver, PPAR KO_DEHP 1150_123

label_protocol: Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification kit protocol.

growth_protocol: Food (LabDiet 5001, PMI Nutrition International, St. Louis, MO) and municipal tap water were provided ad libitum.  Animal facilities were controlled for temperature (20°C–24°C) and relative humidity (40%–60%) and kept under a 12-h light-dark cycle.

extract_protocol: Total RNA was isolated and purified from mouse livers according to the mirVana™ miRNA isolation kit (Ambion, Austin, TX)    The integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer (Agilent, Foster City, CA), and RNA quantity was determined using a Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: Wild-type and PPAR(alpha)-null mice were given four daily gavage doses of DEHP (1150 mg/kg/bw/day) in corn oil or corn oil alone.

tag: genotype/variation

value: PPAR KO

tag: treatment

value: DEHP


title: Pregnant_8


title: mll_k4me3_rep1

value: H3K4me3 (ab8580, Abcam)


title: wt_h3_rep1

source_name: Mouse embryonic fibroblast cell line, wt, H3 IP

value: H3 (ab1791, Abcam)

value: wt

source_name: Mouse embryonic fibroblast cell line, wt, whole cell extract


title: PPAR KO_DEHP 1150_121

description:
PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from PPAR(alpha)-null mouse liver treated with DEHP

source_name: liver, PPAR KO_DEHP 1150_121


title: Non-pregnant_7


title: Non-pregnant_11


title: wt_k4me3_rep1


title: PPAR KO_ctr_118

description:
PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from PPAR(alpha)-null mouse liver

source_name: liver, PPAR KO_ctr_118

value: control


title: wt_h3_arrayhalf2_rep1


title: wt_k4me3_arrayhalf2_rep1


title: PPAR KO_ctr_117

source_name: liver, PPAR KO_ctr_117

value: male


title: Pregnant_6


title: PPAR KO_ctr_116

source_name: liver, PPAR KO_ctr_116


title: PPAR KO_DEHP 1150_122

source_name: liver, PPAR KO_DEHP 1150_122


title: Non-pregnant_5


title: MK4

description: mice adult dermal fibroblasts

source_name: Induced chondrogenic cell line "MK-4" from mouse dermal fibroblasts

value: dermal fibroblasts

value: 6 months


title: Pregnant_4

value: Yorkshire (YY)


title: PPAR WT_DEHP 1150_58

description:
PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from wildtype mouse liver treated with DEHP

source_name: liver, PPAR WT_DEHP 1150_58

value: PPAR WT


title: R1881

type: SAGE

anchor: NlaIII

city: Vancouver

first: Marianne

middle: D.

last: Sadar

state: British Columbia

address: 675 W. 10th Ave

department: Genome Sciences Centre

country: Canada

institute: British Columbia Cancer Agency

description: LongSAGE libraries were constructed with 5ug of total RNA using the Invitrogen I-SAGE Long kit.

source_name: Cell line

growth_protocol: LNCaP human prostate cancer cells were maintained in RPMI-1640 media supplemented with 10% v/v fetal bovine serum, 100 units/mL penicillin and 100 units/mL streptomycin.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions.

treatment_protocol: 1 x 106 LNCaP cells were seeded in 10 cm-diameter dishes. The next day, cells were serum starved for 48 hours and then treated for 16 hours with 10 nM synthetic androgen R1881.

value: LNCaP

value: vehicle


title: PPAR WT_DEHP 1150_59

source_name: liver, PPAR WT_DEHP 1150_59


title: MEF_mll_wt_rep3

hyb_protocol: 825 ng each Cy3- and Cy5-labeled cRNA was hybridized to the array for 17 hours at 65 C and 10 RPM.

data_processing: Scanned images were quantified using Agilent Feature Extraction v 10.1.1, with feature extraction protocol GE2-v5_10_Apr08. Data was read into R. Data was loess normalized within arrays and aquantile normalized between arrays.

source_name: Mouse embryonic fibroblast cell line, Mll1-/-

label_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp Labeling). Version 5.7, March 2008.

growth_protocol: MEF cells were grown on DMEM with 10% FBS.

extract_protocol: RNA was extracted using Qiagen RNA mini kit.

value: mouse embryonic fibroblasts (MEF)

value: Mll-/-

source_name: Mouse embryonic fibroblast cell line, wt


title: PPAR WT_ctr_52

description:
PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from wildtype mouse liver

source_name: liver, PPAR WT_ctr_52


title: MEF_mll_wt_rep1


title: PPAR WT_ctr_53

source_name: liver, PPAR WT_ctr_53


title: Non-pregnant_1

source_name: Endometrium, non-pregnant sow, Day 14 after insemination

value: Endometrium

value: Female


title: MEF_mll_wt_rep4


title: PPAR WT_ctr_54

source_name: liver, PPAR WT_ctr_54


title: Vehicle

treatment_protocol: 1 x 106 LNCaP cells were seeded in 10 cm-diameter dishes. The next day, cells were serum starved for 48 hours and then treated for 16 hours with vehicle (ethanol; final concentration 2.85 x 10%).

value: R1881 androgen


title: PPAR KO_ctr_115

source_name: liver, PPAR KO_ctr_115

value: PPAR KO


title: PPAR WT_DEHP 1150_57

source_name: liver, PPAR WT_DEHP 1150_57

value: DEHP


title: glp-1_control_2008_rep2

status: Public on Oct 19 2009

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Non-UVC exposed nematodes were submitted to the same process, except for the UVC dose.

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÆ Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

organism: Caenorhabditis elegans

source_name: Young adult (24 h post-vulval crescent L4 stage) whole nematodes were reared at 25°C in control conditions, experiment carried out in 2008

label_protocol: Starting with 100ng of total RNA, biotin-labeled cRNA was produced using the Affymetrix Amplification Two-Cycle Target labeling kit according to manufacturer's protocol.

extract_protocol: Young adult (24 h post-vulval crescent L4 stage) nematodes were reared at 25°C and exposed to 50 J/m2 UVC radiation on K-agar plates without food as  described (Meyer et al., 2007 Genome Biology 8:R70), placed on OP50-seeded plates for 2 h 45 minutes, washed off plates and rinsed with K-medium 3 times (~5 minutes each) by allowing settling, resuspending, settling again, etc. Nematodes were frozen by dripping 3,000-5,000 pelleted worms suspended in about 500 ul K-medium into liquid nitrogen, and stored at -80°C. The pellets were ground into fine powder with a liquid nitrogen-cooled mortar and pestle and RNA was extracted using an RNeasy kit (Qiagen, Valencia, CA, USA). RNA was quantified with a NanoDrop Fluorospectrometer (NanoDrop Technologies, Wilmington, DE, USA) and analyzed for integrity with a BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: glp-1 point mutant (JK1107 strain)


title: N2_UV_2008_rep1

description: UVC radiation exposures were performed in a CL-1000 Ultraviolet Crosslinker (UVP, Upland, CA, USA) with an emission peak at 254 nm. Worms were plated such that they did not shiled each other, and there was no significant K medium remaining at the time of

source_name: Young adult (24 h post-vulval crescent L4 stage) whole nematodes were reared at 25°C and exposed to 50 J/m2 UVC radiation then frozen 3h later, experiment carried out in 2008

value: N2 (ancestral) wildtype strain


title: MEF_mll_wt_rep2

value: wt


title: N2_UV_2008_rep2


title: glp-1_control_2008_rep1


title: Pregnant_2

source_name: Endometrium, pregnant sow, Day 14 after insemination

value: Pregnant


title: PPAR WT_ctr_55

source_name: liver, PPAR WT_ctr_55

value: male

value: control


title: N2_control_2008_rep2


title: PPAR WT_DEHP 1150_56

source_name: liver, PPAR WT_DEHP 1150_56


title: xpa-1_UV_2008_rep2

value: xpa-1 deletion mutant (strain RB864, outcrossed 3 times)


title: N2_control_2008_rep1


title: Non-pregnant_3

value: Yorkshire (YY)

value: Non-pregnant


title: xpa-1_UV_2008_rep1


title: glp-1_UV_2007_rep2

hyb_protocol: 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

source_name: Young adult (24 h post-vulval crescent L4 stage) whole nematodes were reared at 25°C and exposed to 50 J/m2 UVC radiation then frozen 3h later, experiment carried out in 2007

label_protocol: Starting with 500pg of total RNA, biotin-labeled cRNA was produced using the Epicentre Biotechnologies TargetAmp 2-Round aRNA Amplification Kit 2.0 according to manufacturer's protocol with the exception that 10ul biotin-UTP was incorporated in place of 3.6ul unlabeled UTP, and final product was eluted in 25ul water.


title: Cdx2+/-Cdx4-/- replicate 1

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: According to Agilent guidelines

scan_protocol: According to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction (V9.5.3, Agilent technologies).

source_name: Posterior parts of 5 somite embryos (n=10)

label_protocol: According to Agilent guidelines

extract_protocol: Posterior tissues from pools of 10 embryos of each genotype were pooled and stored in RNAlater (Ambion, cat. AM1924). RNAs were purified using a kit from Qiagen (Cat 74104).

value: wildtype


title: xpa-1_control_2008_rep2


title: xpa-1_control_2008_rep1


title: xpa-1_control_2007_rep1

source_name: Young adult (24 h post-vulval crescent L4 stage) whole nematodes were reared at 25°C in control conditions, experiment carried out in 2007


title: P28 +/+;CrxpNrl retina, biological rep3

first: Douglas

last: Forrest

address: 10 Center Drive

department: Clinical Endocrinology Branch

institute: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

description: 2 retina from one mouse

hyb_protocol: 15ug of biotinylated-cRNA was hybridized to GeneChip Mouse Genome 430 2.0 arrays according to GeneChip Expression Analysis Techinical Manual (Affymetrix, P/N 701021 Rev. 5).

scan_protocol: GeneChip arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The Robust Multichip Average (RMA) method was used for background correction, quantile normalization, and summarization of expression scores.

source_name: P28 +/+;CrxpNrl retina

label_protocol: 5ug of total RNA was used as the starting material for GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Mouse retina were dissected from day 14 and day 28 mouse eyes.

extract_protocol: Each sample consists of 2 retina from one mouse and was snap frozen on dry ice. Total RNA was isolated with Trizol (Invitrogen).

value: retina

value: +/+;CrxpNrl


title: N2_UV_2007_rep1


title: P28 Rorb-/-;CrxpNrl retina, biological rep1

description: 2 retina from one mouse

source_name: P28 Rorb-/-;CrxpNrl retina

value: Rorb-/-;CrxpNrl


title: xpa-1_UV_2007_rep2


title: P28 Rorb-/-;CrxpNrl retina, biological rep4

description: 2 retina from one mouse


title: Cdx2+/-Cdx4-/- replicate 2


title: glp-1_control_2007_rep2


title: Cdx2+/-Cdx4-/- replicate 1 dyeswap


title: glp-1_control_2007_rep1


title: Cdx2+/-Cdx4-/- replicate 2 dyeswap


title: xpa-1_UV_2007_rep1


title: P28 Rorb-/-  retina, biological rep3

description: 2 retina from one mouse

source_name: P28 Rorb-/- retina

value: Rorb-/-


title: N2_UV_2007_rep2


title: P28 +/+;CrxpNrl retina, biological rep2

description: 2 retina from one mouse


title: P28 +/+;CrxpNrl retina, biological rep1

description: 2 retina from one mouse


title: P28 Rorb-/-  retina, biological rep4

description: 2 retina from one mouse


title: P28 Rorb-/-;CrxpNrl retina, biological rep2

description: 2 retina from one mouse


title: P28 Rorb-/- retina, biological rep1

description: 2 retina from one mouse


title: P28 Rorb-/-;CrxpNrl retina, biological rep3

description: 2 retina from one mouse


title: P28 Rorb-/-  retina, biological rep2

description: 2 retina from one mouse


title: glp-1_UV_2007_rep1


title: P28 +/+ retina, biological rep4

description: 2 retina from one mouse

source_name: P28 +/+ retina


title: xpa-1_control_2007_rep2


title: WT_pBAD_ArcZ_BR3

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description: Intensity ratios of RNA (channel 2) divided by DNA (channel 1) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios.

organism: Salmonella enterica

source_name: Reference genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/Safety/Microarrays/default.html#protocols

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

tag: reference

value: Salmonella enterica serovar Typhimurium SL1344 genomic DNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Strain SL1344 was transformed with plasmids pKP4-13 (pBAD-ArcZ) and grown in liquid culture inoculated 1:100 from an overnight culture to an OD600 of 1.5. Expression from the pBAD promoter was induced with L-arabinose (0.2% final concentrations) for 10 min.

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: cell (plasmid)

value: Salmonella enterica serovar Typhimurium SL1344 (pKP4-13)


title: N2_control_2007_rep2


title: P28 +/+ retina, biological rep1

description: 2 retina from one mouse


title: N2_control_2007_rep1


title: P28 +/+ retina, biological rep2

description: 2 retina from one mouse


title: glp-1_UV_2008_rep1


title: P28 +/+ retina, biological rep3

description: 2 retina from one mouse


title: WT_pBAD_ArcZ_BR2


title: P14 Rorb-/-;CrxpNrl retina, biological rep2

description: 2 retina from one mouse

source_name: P14 Rorb-/-;CrxpNrl retina


title: arcZ_pArcZ_BR3

growth_protocol: Strain JVS-0082 (ΔarcZ) was transformed with plasmid pKP48-1 (parcZ), and grown in liquid culture inoculated 1:100 from an overnight culture for 6h after cells had reached an OD600=2.0 to reach late stationary phase

value: Salmonella enterica serovar Typhimurium SL1344 delta arcZ (pKP48-1)


title: P14 Rorb-/-;CrxpNrl retina, biological rep4

description: 2 retina from one mouse


title: arcZ_pArcZ_BR1


title: arcZ_pJV300_BR3

growth_protocol: ArcZ deletion mutant was grown in liquid culture inoculated 1:100 from an overnight culture for 6h after cells had reached an OD600=2.0 to reach late stationary phase.

value: Salmonella enterica serovar Typhimurium SL1344 delta arcZ (pJV300)


title: WT_pBAD_CTRL_BR1

growth_protocol: Strain SL1344 was transformed with plasmids pKP8-35 (pBAD-control) and grown in liquid culture inoculated 1:100 from an overnight culture to an OD600 of 1.5. Expression from the pBAD promoter was induced with L-arabinose (0.2% final concentrations) for 10 min.

value: Salmonella enterica serovar Typhimurium SL1344 (pKP8-35)


title: arcZ_pArcZ_BR2


title: P14 +/+;CrxpNrl retina, biological rep4

description: 2 retina from one mouse

source_name: P14 +/+;CrxpNrl retina


title: P14 Rorb-/-;CrxpNrl retina, biological rep3

description: 2 retina from one mouse


title: glp-1_UV_2008_rep2

value: glp-1 point mutant (JK1107 strain)


title: WT_pBAD_CTRL_BR3


title: arcZ_pJV300_BR2


title: WT_pBAD_ArcZ_BR1


title: WT_pBAD_CTRL_BR2


title: P14 +/+;CrxpNrl retina, biological rep2

description: 2 retina from one mouse


title: P14 +/+;CrxpNrl retina, biological rep1

description: 2 retina from one mouse


title: P14 Rorb-/-;CrxpNrl retina, biological rep1

description: 2 retina from one mouse


title: P14 +/+;CrxpNrl retina, biological rep3

description: 2 retina from one mouse


title: P14 Rorb-/-  retina, biological rep4

description: 2 retina from one mouse

source_name: P14 Rorb-/-  retina


title: P14 Rorb-/-  retina, biological rep3

description: 2 retina from one mouse


title: arcZ_pJV300_BR1


title: P14 +/+ retina, biological rep2

description: 2 retina from one mouse

source_name: P14 +/+ retina


title: WT_pJV300_BR2

growth_protocol: Strain was grown in liquid culture inoculated 1:100 from an overnight culture for 6h after cells had reached an OD600=2.0 to reach late stationary phase.

value: Salmonella enterica serovar Typhimurium SL1344 (pJV300)


title: WT_pJV300_BR1


title: P14 +/+ retina, biological rep4

description: 2 retina from one mouse


title: WT_pJV300_BR3


title: P14 Rorb-/-  retina, biological rep2

description: 2 retina from one mouse


title: P14 Rorb-/- retina, biological rep1

description: 2 retina from one mouse

source_name: P14 Rorb-/- retina


title: P14 +/+ retina, biological rep3

description: 2 retina from one mouse


title: P14 +/+ retina, biological rep1

description: 2 retina from one mouse


title: 9.30.04 18 Untreated 3

status: Public on Oct 18 2009

city: Palo Alto

first: Alexander

last: Red Eagle

address: 3230 CCSR

institute: Alexander Red Eagle

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56357.gif

hyb_protocol: hybridized for 16 hours

scan_protocol: Agilent scanner model G2505A

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)

source_name: E17.5 Reference

label_protocol: A common reference was generated using e17.5 C57Bl/6 embryos. 30ug of either reference or macrophage RNA was labeled with Cy3 and Cy5 (Amersham) and hybridized to Stanford Functional Genomics Facility mouse cDNA microarrays for 16 hours.

extract_protocol: Qiagen's RNeasy Kit

value: e17.5 C57Bl/6 embryos

source_name: 18 Untreated 3

growth_protocol: HoxA9 immortalized ES cell derived myeloid precursors were created and differentiated as in Odegaard et al, 2007. After expansion, macrophages were differentiated for 8 days in the presence of MCSF in 20% L929 conditioned media with 2.5% bovine serum albumin in low glucose media.

value: PPARd -/-

value: differentiated macrophages


title: 9.30.04 J1 Untreated 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56324.gif

source_name: J1 Untreated 1

label_protocol: 30ug of either reference or macrophage RNA was labeled with Cy3 and Cy5 (Amersham) and hybridized to Stanford Functional Genomics Facility mouse cDNA microarrays for 16 hours.

value: WT


title: 9.30.04 J1 Untreated 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56325.gif

source_name: J1 Untreated 2

value: Wt


title: 9.30.04 18 Untreated 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56354.gif

source_name: 18 Untreated 2


title: 9.30.04 J1 Untreated 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56326.gif

source_name: J1 Untreated 3


title: FL051_Mapping250K_Nsp

status: Public on Oct 17 2009

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
Clinical information of primary lymphoma samples subjected to SNP arrays analysis can be found in Supplementary Table 1 of the associated publication.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).

source_name: lymphoma primary specimen

label_protocol: Affymetrix standard protocol

extract_protocol: standard DNA extraction using PUREGENE DNA extracting kit (Gentra, USA)

tag: disease state

value: non-Hodgkin's lymphoma (NHL), Primary


title: 9.30.04 18 Untreated 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56353.gif

label_protocol: HoxA9 immortalized ES cell derived myeloid precursors were created and differentiated as in Odegaard et al, 2007. After expansion, macrophages were differentiated for 8 days in the presence of MCSF in 20% L929 conditioned media with 2.5% bovine serum albumin in low glucose media.

source_name: 18 Untreated 1


title: FL019_Mapping250K_Nsp


title: DLBCL059_Mapping250K_Nsp


title: DLBCL062_Mapping250K_Nsp


title: FL048_Mapping250K_Nsp


title: DLBCL056_Mapping250K_Nsp


title: FL043_Mapping250K_Nsp


title: FL046_Mapping250K_Nsp


title: DLBCL053_Mapping250K_Nsp


title: DLBCL052_Mapping250K_Nsp


title: DLBCL051_Mapping250K_Nsp


title: DLBCL047_Mapping250K_Nsp


title: DLBCL049_Mapping250K_Nsp


title: DLBCL058_Mapping250K_Nsp


title: DLBCL048_Mapping250K_Nsp


title: FL044_Mapping250K_Nsp


title: DLBCL057_Mapping250K_Nsp


title: DLBCL046_Mapping250K_Nsp


title: DLBCL045_Mapping250K_Nsp


title: FL042_Mapping250K_Nsp


title: DLBCL042_Mapping250K_Nsp


title: DLBCL055_Mapping250K_Nsp


title: FL045_Mapping250K_Nsp


title: DLBCL043_Mapping250K_Nsp


title: FL040_Mapping250K_Nsp


title: FL047_Mapping250K_Nsp


title: DLBCL040_Mapping250K_Nsp


title: DLBCL044_Mapping250K_Nsp


title: DLBCL016_Mapping250K_Nsp


title: DLBCL028_Mapping250K_Nsp


title: DLBCL037_Mapping250K_Nsp


title: DLBCL039_Mapping250K_Nsp


title: FL041_Mapping250K_Nsp


title: DLBCL054_Mapping250K_Nsp


title: DLBCL036_Mapping250K_Nsp


title: FL038_Mapping250K_Nsp


title: FL037_Mapping250K_Nsp


title: DLBCL035_Mapping250K_Nsp


title: DLBCL038_Mapping250K_Nsp


title: DLBCL012_Mapping250K_Nsp


title: DLBCL019_Mapping250K_Nsp


title: FL021_Mapping250K_Nsp


title: DLBCL034_Mapping250K_Nsp


title: DLBCL020_Mapping250K_Nsp


title: FL033_Mapping250K_Nsp


title: DLBCL030_Mapping250K_Nsp


title: DLBCL017_Mapping250K_Nsp


title: DLBCL033_Mapping250K_Nsp


title: MALT070_Mapping250K_Nsp


title: MALT080_Mapping250K_Nsp


title: DLBCL015_Mapping250K_Nsp


title: MALT078_Mapping250K_Nsp


title: MALT079_Mapping250K_Nsp


title: DLBCL014_Mapping250K_Nsp


title: DLBCL013_Mapping250K_Nsp


title: MALT062_Mapping250K_Nsp


title: DLBCL041_Mapping250K_Nsp


title: FL020_Mapping250K_Nsp


title: MALT076_Mapping250K_Nsp


title: MALT075_Mapping250K_Nsp


title: MALT077_Mapping250K_Nsp


title: MALT072_Mapping250K_Nsp


title: MALT056_Mapping250K_Nsp


title: MALT086_Mapping250K_Nsp


title: MALT083_Mapping250K_Nsp


title: MALT071_Mapping250K_Nsp


title: MALT084_Mapping250K_Nsp


title: MALT051_Mapping250K_Nsp


title: MALT060_Mapping250K_Nsp


title: MALT058_Mapping250K_Nsp


title: MALT063_Mapping250K_Nsp


title: MALT059_Mapping250K_Nsp


title: MM-239_miRNA

status: Public on Oct 30 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from multiple myeloma patient MM-239

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55°C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 9.5 software (Agilent Technologies) was used to obtain the microarray raw data. The human miRNAs included in the platform were annotated according to Sanger miRBase Release 12.0.

data_processing: After discarding non-human miRNAs, the data were normalized using the Aroma Light package for Bioconductor. To overcome scaling biases due to background subtraction, the data were converted to obtain positive values throughout the dataset, at a minimum value of 1.

source_name: Multiple myeloma patient MM-239

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) to the 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37°C for 30 min. The labeled RNA was purifed on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA).

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was >90% in all cases.

tag: disease status

value: multiple myeloma patient

tag: sex

value: F

tag: age at diagnosis (years)

tag: stage (durie-salmon)

value: nd

tag: monoclonal component

value: Gk

tag: tc classification

tag: related gene expression profiling (gep) data available (geo id)

tag: related genome-wide dna analysis data available (geo id)


title: SOD1G93A spinal cord at D126, biological rep 1

city: Washington

first: Bruce

last: Lerman

state: DC

address: 111 Michigan Ave NW

department: Research Center for Genetic  Medicine

institute: Children's National Medical Center

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: PLIER algorithm

source_name: SOD1G93A spinal cord at D126

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

growth_protocol: Mice were sacrificed at various ages, including 28,42,56,70,98,112, and 126 days of age

tag: tissue

value: spinal cord

tag: genotype

value: 126 days


title: SOD1G93A spinal cord at D126, biological rep 3

tag: age


title: SOD1G93A spinal cord at D112, biological rep 3

source_name: SOD1G93A spinal cord at D112

value: 112 days


title: MALT064_Mapping250K_Nsp


title: MALT065_Mapping250K_Nsp


title: MALT053_Mapping250K_Nsp


title: MALT055_Mapping250K_Nsp


title: SOD1G93A spinal cord at D112, biological rep 1


title: MALT054_Mapping250K_Nsp


title: SOD1G93A spinal cord at D112, biological rep 2


title: MALT074_Mapping250K_Nsp


title: MALT085_Mapping250K_Nsp


title: SOD1G93A spinal cord at D70, biological rep 3

source_name: SOD1G93A spinal cord at D70

value: 70 days


title: SOD1G93A spinal cord at D98, biological rep 3

source_name: SOD1G93A spinal cord at D98

value: 98 days


title: MALT061_Mapping250K_Nsp


title: SOD1G93A spinal cord at D98, biological rep 2


title: SOD1G93A spinal cord at D98, biological rep 1


title: SOD1G93A spinal cord at D70, biological rep 2


title: MALT069_Mapping250K_Nsp


title: SOD1G93A spinal cord at D70, biological rep 1


title: SOD1G93A spinal cord at D56, biological rep 3

source_name: SOD1G93A spinal cord at D56

value: 56 days


title: MALT073_Mapping250K_Nsp


title: MALT067_Mapping250K_Nsp


title: SOD1G93A spinal cord at D56, biological rep 2


title: MALT087_Mapping250K_Nsp


title: SOD1G93A spinal cord at D42, biological rep 1

source_name: SOD1G93A spinal cord at D42

value: 42 days


title: SOD1G93A spinal cord at D56, biological rep 1


title: MALT066_Mapping250K_Nsp


title: SOD1G93A spinal cord at D42, biological rep 3


title: SOD1G93A spinal cord at D42, biological rep 2


title: SOD1G93A spinal cord at D126, biological rep 2


title: MALT081_Mapping250K_Nsp


title: SOD1G93A spinal cord at D28, biological rep 2

source_name: SOD1G93A spinal cord at D28

value: 28 days


title: SOD1G93A spinal cord at D28, biological rep 3


title: HDLM2_Mapping250K_Nsp


title: MALT052_Mapping250K_Nsp


title: control spinal cord at D126, biological rep 2

source_name: control spinal cord at D126

value: wild-type


title: control spinal cord at D112, biological rep 3

source_name: control spinal cord at D112


title: SOD1G93A spinal cord at D28, biological rep 1


title: MALT057_Mapping250K_Nsp


title: control spinal cord at D112, biological rep 1


title: control spinal cord at D98, biological rep 3

source_name: control spinal cord at D98


title: control spinal cord at D70, biological rep 3

source_name: control spinal cord at D70


city: Tarrytown

first: Wen

last: Fury

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling

institute: Regeneron Pharmaceuticals, Inc.

description: Kawasaki_IVIG study_study#3246_3.42 yr female_IVIG responder_after IVIG

hyb_protocol: Cyanine 3 and Cyanine 5 labeled cRNAs were hybridized to the Agilent G4112F Human Whole Genome Oligo Arrays per the manufacturer's instructions except for the following modification: cRNAs containing 300 pmol of Cyanine 3 and 150 pmol of Cyanine 5 were used and the hybridization was done at 70oC.  Hybridized microarrays were washed according to the manufacturer's protocol.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner.

data_processing: Agilent Feature Extraction Software (v9.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: IVIG responder_after IVIG

label_protocol: Aminoallyl cRNA was produced from 1 ug of total RNA using Fluorescent Linear Amplification Kit (Agilent Technologies) and aminoallyl UTP.  Cyanine 3 or Cyanine 5 was chemically conjugated to amninoallyl cRNA using Cyanine 3 or Cyanine 5 NHS ester (GE Life Sciences).

extract_protocol: Blood was obtained using Paxgene Blood RNA System, (PreanalytiX GmbH, 8634 Hombrechtikon, CH). PAXgene tubes were stored at 4°C C for no more than 5 days and RNA was purified according to the manufacturer's instructions

value: female

value: IVIG responder_after IVIG

value: whole blood

source_name: human blood common reference


title: control spinal cord at D112, biological rep 2


description: Kawasaki_IVIG study_study#3237_0.33 yr male_IVIG non responder_after IVIG

source_name: IVIG non responder_after IVIG

value: male

value: IVIG non responder_after IVIG


description: Kawasaki_IVIG study_study#3253_4 yr female_IVIG non responder_after IVIG

value: 4 yr


title: control spinal cord at D126, biological rep 3


title: control spinal cord at D70, biological rep 2


description: Kawasaki_IVIG study_study#3228_1.58 yr male_IVIG responder_after IVIG


title: control spinal cord at D98, biological rep 1


title: control spinal cord at D98, biological rep 2


description: Kawasaki_IVIG study_study#3261_4.92 yr female_IVIG non responder_after IVIG


title: control spinal cord at D70, biological rep 1


title: control spinal cord at D126, biological rep 1


description: Kawasaki_IVIG study_study#3265_2 yr male_IVIG non responder_after IVIG

value: 2 yr


description: Kawasaki_IVIG study_study#3227_2 yr male_IVIG responder_after IVIG


description: Kawasaki_IVIG study_study#3268_1.7 yr male_IVIG non responder_after IVIG


title: control spinal cord at D56, biological rep 3

source_name: control spinal cord at D56


description: Kawasaki_IVIG study_study#3208_5.33 yr female_IVIG responder_after IVIG


description: Kawasaki_IVIG study_study#3251_1.58 yr female_IVIG non responder_after IVIG


description: Kawasaki_IVIG study_study#3205_3.92 yr female_IVIG responder_after IVIG


title: control spinal cord at D42, biological rep 3

source_name: control spinal cord at D42


title: control spinal cord at D56, biological rep 2


description: Kawasaki_IVIG study_study#3147_1.08 yr male_IVIG responder_after IVIG


description: Kawasaki_IVIG study_study#3177_0.33 yr male_IVIG non responder_after IVIG


description: Kawasaki_IVIG study_study#3120_3.46 yr female_IVIG responder_after IVIG


description: Kawasaki_IVIG study_study#3200_4.19 yr male_IVIG non responder_after IVIG


description: Kawasaki_IVIG study_study#3098_2.25 yr female_IVIG responder_after IVIG


title: control spinal cord at D42, biological rep 2


description: Kawasaki_IVIG study_study#3174_9 yr female_IVIG responder_after IVIG

value: 9 yr


description: Kawasaki_IVIG study_study#3157_3.16 yr male_IVIG responder_after IVIG


title: control spinal cord at D28, biological rep 3

source_name: control spinal cord at D28

value: spinal cord


title: control spinal cord at D56, biological rep 1


title: control spinal cord at D28, biological rep 2


description: Kawasaki_IVIG study_study#3268_1.7 yr male_IVIG non responder_Acute

source_name: IVIG non responder_Acute

value: IVIG non responder_Acute


title: control spinal cord at D42, biological rep 1


description: Kawasaki_IVIG study_study#3237_0.33 yr male_IVIG non responder_Acute


title: control spinal cord at D28, biological rep 1


description: Kawasaki_IVIG study_study#3251_1.58 yr female_IVIG non responder_Acute


description: Kawasaki_IVIG study_study#3246_3.42 yr female_IVIG responder_Acute

source_name: IVIG responder_Acute

value: IVIG responder_Acute


description: Kawasaki_IVIG study_study#3265_2 yr male_IVIG non responder_Acute


description: Kawasaki_IVIG study_study#3146_0.33 yr female_IVIG responder_after IVIG


title: MALT082_Mapping250K_Nsp

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
Clinical information of primary lymphoma samples subjected to SNP arrays analysis can be found in Supplementary Table 1 of the associated publication.

source_name: lymphoma primary specimen

value: non-Hodgkin's lymphoma (NHL), Primary


description: Kawasaki_IVIG study_study#3253_4 yr female_IVIG non responder_Acute


title: Planktonic 9B norm

city: San Marcos

first: Robert

middle: JC

last: McLean

state: TX

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

description: The overall protocols for RNA purification and gene array analysis are spelled out in detail in a publication by Arnold et al., J. Bacteriol. 183: 2178-2186, 2001.

hyb_protocol: Sigma-Genosys gene array manufacturer protocol was followed.

scan_protocol: 100-um resolution using a Fujix phosphorimager

data_processing: Visag-HDG Analyzer software (RM Lupton Inc) was used.  Data were normalized to the total intensity on the image.

source_name: Planktonic, MOPS

label_protocol: Reverse transcription with 33P-CTP was performed.

growth_protocol: E. coli MG1655 biofilm and planktonic cells were grown in serine-limited chemostat for 4 or 6 days.

extract_protocol: Water-saturated phenol extraction, enzymatic removal of proteins, and re-extraction with phenol and ethanol was used to extract RNA.

treatment_protocol: Biofilm and planktonic cells were removed from chemostat and placed into ice-cold phenol-ethanol mixture.

tag: strain

tag: cell type

value: planktonic


title: MALT068_Mapping250K_Nsp


title: Biofilm 9A norm

source_name: Biofilm culture, MOPS

value: biofilm


title: #3228_1.58 yr male_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3228_1.58 yr male_IVIG responder_Acute


title: #3227_2 yr male_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3227_2 yr male_IVIG responder_Acute


description: Kawasaki_IVIG study_study#3208_5.33 yr female_IVIG responder_Acute


title: #3235_5 yr male_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3235_5 yr male_IVIG responder_Acute

value: 5 yr


description: Kawasaki_IVIG study_study#3261_4.92 yr female_IVIG non responder_Acute


title: Biofilm 8A norm


title: Planktonic 8B norm


description: Kawasaki_IVIG study_study#3205_3.92 yr female_IVIG responder_Acute


description: Kawasaki_IVIG study_study#3200_4.19 yr male_IVIG non responder_Acute


description: Kawasaki_IVIG study_study#3146_0.33 yr female_IVIG responder_Acute


title: OVCA429-MAGP2, Biological rep2

city: Boston

last: Birrer

state: MA

address: 70 Blossom Street

department: Medicine

institute: MGH

description: Gene expression data from OVCA429 cells.

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).

data_processing:
Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Dr. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis. Only those probe sets present in greater than 50% of the arrays and displaying a variance in the top 50th percentile were evaluated. Differentially expressed genes were identified by a univariate t-test (P<0.01 and fold-change>1.5). A random-variance model was selected to permit information sharing among probe sets.

The differentially expressed genes are available in the file 'GSE18373_diff_exp_OVCA429.txt', which is linked to the Series GSE18373 record as a supplementary file.

source_name: OVCA429 cell line, untreated

label_protocol: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.

growth_protocol: OVCA429 were grown in RPMI-1640 supplemented with 10% FBS, 2mM glutamine and penicillin/streptomycin (Invitrogen). HUVECs were grown in EBM supplemented with 2% FBS and EGM-2 MV SingleQuots.

extract_protocol: Rneasy Mini Kit, Qiagen.

treatment_protocol: recMAGP2 treated and untreated cell lines.

tag: cell line

tag: treatment

value: untreated cells


title: #3174_9 yr female_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3174_9 yr female_IVIG responder_Acute


title: #231_4.47 yr female_healthy controls

description: Kawasaki_IVIG study_study#231_4.47 yr female_healthy controls

source_name: healthy controls

value: healthy controls


title: OVCA429-MAGP2, Biological rep1


description: Kawasaki_IVIG study_study#3098_2.25 yr female_IVIG responder_Acute

value: female


title: #225_2.14 yr male_healthy controls

description: Kawasaki_IVIG study_study#225_2.14 yr male_healthy controls


title: #228_0.91 yr female_healthy controls

description: Kawasaki_IVIG study_study#228_0.91 yr female_healthy controls


title: OVCA429+MAGP2, Biological rep1

source_name: OVCA429 cell line, MAGP2 treated

value: recombinant MAGP2


title: OVCA429-MAGP2, Biological rep3


title: #3147_1.08 yr male_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3147_1.08 yr male_IVIG responder_Acute

value: whole blood


title: #3157_3.16 yr male_IVIG responder_Acute

description: Kawasaki_IVIG study_study#3157_3.16 yr male_IVIG responder_Acute

value: male


title: #223_1.54 yr male_healthy controls

description: Kawasaki_IVIG study_study#223_1.54 yr male_healthy controls


title: HUVEC-MAGP2, Biological rep3

description: Gene expression data from HUVEC cells.

data_processing:
Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Dr. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis. Only those probe sets present in greater than 50% of the arrays and displaying a variance in the top 50th percentile were evaluated. Differentially expressed genes were identified by a univariate t-test (P<0.01 and fold-change>1.5). A random-variance model was selected to permit information sharing among probe sets.

The differentially expressed genes are available in the file 'GSE18373_diff_exp_HUVEC.txt', which is linked to the Series GSE18373 record as a supplementary file.

source_name: HUVEC cell line, untreated

value: HUVEC


title: #229_4.09 yr female_healthy controls

description: Kawasaki_IVIG study_study#229_4.09 yr female_healthy controls


description: Kawasaki_IVIG study_study#3177_0.33 yr male_IVIG non responder_Acute


title: HUVEC-MAGP2, Biological rep2

description: Gene expression data from HUVEC cells.


title: #224_1.65 yr female_healthy controls

description: Kawasaki_IVIG study_study#224_1.65 yr female_healthy controls


title: OVCA429+MAGP2, Biological rep3


title: HUVEC-MAGP2, Biological rep1

description: Gene expression data from HUVEC cells.


title: #226_0.39 yr female_healthy controls

description: Kawasaki_IVIG study_study#226_0.39 yr female_healthy controls


title: OVCA429+MAGP2, Biological rep2


title: HUVEC+MAGP2, Biological rep3

description: Gene expression data from HUVEC cells.

source_name: HUVEC cell line, MAGP2 treated


title: NKTDC_205

city: Milan

first: simone

last: caielli

address: Via olgettina, 60

institute: San Raffaele Scientific Institute

hyb_protocol: Test arrays are relatively inexpensive and used as assessment tools for determining target quality and labelling efficiency. In our experience, for Two-Cycle Target Labelling Assay, it is not necessary to test each reaction, but about 30% of the samples. Fragmented cRNA from two samples was hybridized to the test arrays for 16 hours at 45°C. The test array was then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station.

scan_protocol: The arrays were scanned using GeneChip Scanner 3000.

data_processing: The images were analyzed using GCOS and comparison analyses were carried out according to the instructions provided by Affymetrix.

source_name: nkt modulated DC

label_protocol: Two-Cycle Target Labelling Assay Biotinylated cRNA was prepared and fragmented according to the Affymetrix protocol. Very strict quality control measures were applied during the target preparation procedures. cRNA before and following fragmentation was analysed by Agilent Bioanalyzer. Typical cRNA products examined on an Agilent 2100 Bioanalyzer have a size range from 500nt to 2500nt with a peak around 1000nt. The expected amount of cRNA obtained should be above 10 times more than the amount of starting total RNA material.

extract_protocol: Total RNA was extracted following the double extraction protocol: RNA isolation by acid thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure. RNA purity was assessed by spectrophotometer (Nanodrop): 260/280 and 260/230 ratios were evaluated. If the 260/280 and 260/230 ratios are < of 1.9, RNA samples are ethanol precipitated and, the values given in table 1, report the values obtained following ethanol precipitation. Total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated. The RIN ranges from 1 (totally degraded RNA) to 10 (completely intact RNA).

value: bone marrow dendritic cells


title: Genomic uninduced IRN342 #2

status: Public on Oct 16 2009

city: Cambridge

first: Alan

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

institute: MIT

hyb_protocol: Sample were hybridized as described in Auchtung etal. 2005 PNAS 102:12554-9.

scan_protocol: Arrays were scanned and analyzed with GenePix Pro 3.0 (Axon Instruments).

data_processing: Cy3 and Cy5 signals for each spot were normalized to the total Cy3 and Cy5 signals of the array. The total signal for each channel was calculated by summing the values of the total signals for each spot, which was calculated by multiplying the mean signal intensity (per pixel) by the number of pixels.

organism: Bacillus subtilis

source_name: uninduced IRN342

label_protocol: Samples were prepared for microarray analysis by labelling aliquots of the HaeIII digested genomic DNA with aminoallyl-dUTP using 13 U Sequenase (USB) and 5 μg random nonamer. The labelled samples were purified, conjugated to Cy3 or Cy5, and hybridized to microarrays.

growth_protocol: 37C Minimal 1% D-glucose

extract_protocol: Cells from 5 ml of culture (OD600~1) were resuspended in 0.3 ml of A buffer (1998, Lin and Grossman, Cell, 92:675-685) containing 1 mg/ml lysozyme, lysed by incubation at 37°C for 30 min, followed by room temperature additions of 3 µl 100 mg/ml RNase A for 5 min, 0.3 ml 2 x IP buffer (1998, Lin and Grossman) for 5 min, then addition of 15 µl 10% SDS and 3 µl Proteinase K (Qiagen, stock solution ≥600 mAU/ml) at 37°C for 30 min. Cell lysates were extracted twice, once with phenol:chloroform:isoamyl alcohol (1:1:48) and once with chloroform alone. Genomic DNA was precipitated from 0.5 ml of extracted lysate by addition of 15 µl of 5M NaCl and 1.25 ml of cold (-20°C) ethanol and resuspended in 10mM Tris-HCl 0.1mM EDTA pH 8.For microarray analysis, genomic DNA was digested with HaeIII, run on MinElute PCR Purification columns, washed twice with PB, once with PE (Qiagen), then eluted with water.

value: uninduced IRN342

source_name: AG174 Reference

growth_protocol: 37C Minimal 1% D-glucose to T0; add 200 micrograms per ml Cam 2 hours

value: AG174 Reference


title: Genomic uninduced IRN342 #1


title: Genomic RapI-induced attR- ICEBs1 #1

source_name: RapI-induced CAL108

growth_protocol: 37C Minimal 1% D-glucose, induced with 1mM IPTG for 1 hour

value: RapI-induced CAL108


title: Genomic RapI-induced nicK- ICEBs1 #2

source_name: RapI-induced CAL306

value: RapI-induced CAL306


title: Genomic RapI-induced attR- ICEBs1 #2


title: Genomic RapI-induced nicK- ICEBs1 #1


title: #221_2.95 yr male_healthy controls

description: Kawasaki_IVIG study_study#221_2.95 yr male_healthy controls

source_name: human blood common reference


title: ChIP enrichment DnaC RapI-induced CAL635

source_name: DnaC immunoprecipitated DNA

label_protocol: Samples were prepared for microarray analysis by labelling aliquots of the resuspended immunoprecipitated DNA or total control DNA with aminoallyl-dUTP using 13 U Sequenase (USB) and 5 μg random nonamer. The labelled samples were purified, conjugated to Cy3 or Cy5, and hybridized to microarrays.

growth_protocol: 30C Minimal 1% L-arabinose, induced with 1% xylose 2 hours

extract_protocol: Chromatin immunoprecipitation (ChIP) of DNA bound to epitope-tagged and untagged proteins was done essential as described (1998, Lin and Grossman, Cell, 92:675-685; 2007, Breier and Grossman, Molecular Microbiology, 64:703-718).

value: RapI-induced CAL635

source_name: total control DNA


title: ChIP enrichment PolC-GFP RapI-induced CAL879

source_name: PolC-GFP immunoprecipitated DNA

value: RapI-induced CAL879


title: #222_0.82 yr female_healthy controls

description: Kawasaki_IVIG study_study#222_0.82 yr female_healthy controls


title: NKTDC_204


title: HUVEC+MAGP2, Biological rep2

description: Gene expression data from HUVEC cells.


title: IDC_202

source_name: immature DC


title: Genomic RapI-induced WT ICEBs1 #2

source_name: RapI-induced JMA168

value: RapI-induced JMA168


title: HUVEC+MAGP2, Biological rep1

description: Gene expression data from HUVEC cells.


title: Genomic RapI-induced WT ICEBs1 #1


title: ChIP enrichment Myc-PcrA RapI-induced CAL992

source_name: Myc-PcrA immunoprecipitated DNA

value: RapI-induced CAL992


title: Genomic uninduced WT B.subtilis #2


title: ChIP enrichment Ssb-GFP RapI-induced CAL635

source_name: Ssb-GFP immunoprecipitated DNA


title: Genomic uninduced WT B.subtilis #1


title: Genomic RapI-induced recF pcrA +pcrBA B.subtilis #3

source_name: RapI-induced CAL1148

value: RapI-induced CAL1148


title: IDC_201


title: Control_4h_rep2

city: Toulouse

first: Stéphane

last: VISPE

address: 3 Rue des Satellites

country: France

institute: Laboratoires Pierre Fabre

description: Sample corresponding to untreated cells. Measurement after 4h. Replicate 2.

hyb_protocol: 1650 ng of cyanine 3-labelled amplified RNA are hybridised at 65°C for 17 hours

scan_protocol: Scanning is performed with the Agilent scanner using default parameters for 4x44 K formats. For an XDR extraction, two image files (.tif) are generated, one noted H (high, PMT 100) and the other one noted L (low, PMT 10)

data_processing: Data are extracted with the Feature Extraction 9,1 software (Agilent Technologies). This software reads and processes raw microarray image files to prepare them for analysis. Feature extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. The software finds microarray grids, determines feature intensities, rejects outliers, and calculates statistical confidences

source_name: A549 cell line isolated from a human non small cell lung cancer, treated in vitro with various concentrations of triptolide

label_protocol: Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) generates fluorescent cRNA with 500ng of total RNA. In this procedure, samples are labelled with cyanine 3. A primer containing poly dT and a T7 polymerase promoter is annealed to the poly A+ RNA. Reverse transcriptase is added to the reaction to synthesize the first and second strands of cDNA. Next, cRNA are synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine-labelled CTP.

growth_protocol: A549 cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum, penicillin (65 µg/ml) and streptomycin (100 µg/ml).

extract_protocol: RNA extraction was performed using TRIzol reagent (Invotrogen). Total RNA were dissolved in 20 µl of Rnase-free water and qualified using the NanoDrop ND-1000 Spectrophotometer

treatment_protocol: A549 cells were seeded in 75cm2 plates up to 70% confluence before exposure to various concentrations of triptolide for 1, 2 and 4 hours before RNA was extracted.

tag: gender

value: lung cancer


title: Control_4h_rep3

description: Sample corresponding to untreated cells. Measurement after 4h. Replicate 3.


title: Genomic RapI-induced recF pcrA +pcrBA B.subtilis #1


title: Control_4h_rep1

description: Sample corresponding to untreated cells. Measurement after 4h. Replicate 1.


title: Genomic RapI-induced recF pcrA B.subtilis #3

source_name: RapI-induced CAL1175

value: RapI-induced CAL1175


title: Genomic RapI-induced recF pcrA +pcrBA B.subtilis #2


title: 0,45_4h_rep3

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 4h. Replicate 3.


description: Kawasaki_IVIG study_study#3120_3.46 yr female_IVIG responder_Acute

source_name: IVIG responder_Acute

value: female

value: IVIG responder_Acute


title: 0,15_4h_rep2

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 4h. Replicate 2.


title: Genomic RapI-induced recF B.subtilis #3

source_name: RapI-induced CAL1174

value: RapI-induced CAL1174


title: 0,45_4h_rep2

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 4h. Replicate 2.

value: male


title: 0,15_4h_rep3

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 4h. Replicate 3.


title: Genomic RapI-induced recF B.subtilis #2


title: 0,05_4h_rep3

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 4h. Replicate 3.


title: 0,45_4h_rep1

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 4h. Replicate 1.


title: Genomic RapI-induced recF B.subtilis #1


title: 0,05_4h_rep2

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 4h. Replicate 2.


title: Control_2h_rep3

description: Sample corresponding to untreated cells. Measurement after 2h. Replicate 3.


title: 0,05_4h_rep1

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 4h. Replicate 1.


title: Genomic RapI-induced recF pcrA B.subtilis #2


title: Genomic RapI-induced WT B.subtilis #2

source_name: RapI-induced CAL1173

value: RapI-induced CAL1173


title: Control_2h_rep1

description: Sample corresponding to untreated cells. Measurement after 2h. Replicate 1.


title: Genomic RapI-induced WT B.subtilis #3

source_name: AG174 Reference


title: Genomic RapI-induced recF pcrA B.subtilis #1


title: Genomic RapI-induced WT B.subtilis #1


title: 0,45_2h_rep3

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 2h. Replicate 3.


title: 0,15_4h_rep1

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 4h. Replicate 1.


title: Control_2h_rep2

description: Sample corresponding to untreated cells. Measurement after 2h. Replicate 2.


title: 0,45_2h_rep2

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 2h. Replicate 2.


title: Patient6S

city: Gothenburg

first: Mikael

last: Benson

address: Smorslottsgatan

department: Paediatrics

institute: Queen Silvia Children's Hospital

hyb_protocol: 1.50 ug of mRNA was hybridized to Illumina’s Sentrix Human-6 Expression BeadChips (cat no BD-25-101) at 55 C overnight (18,5 h) according to Illumina BeadStation 500X –protocol, Revision F.

scan_protocol: Hybridization was detected with 1 ug/ml Cyanine3-streptavidine, Amersham Biosciences (cat no 146065). Chips were scanned with Illumina BeadArray Reader PMT 625 and the numerical results were extracted with Bead Studio v1.5.1.34 without any normalization or background subtraction.

data_processing: Data was normalized using the rank invariant method.

source_name: Allergen-challenged CD4+ cells

label_protocol: Biotinylate RNA was prepared using Ambion's Illumina RNA TotalPrep Amplification kit (cat no IL1791, http://www.ambion.com/techlib/prot/fm_IL1791.pdf)

growth_protocol: PBMCs were prepared by centrifugation on Ficoll-Hypaque, washed and stimulated in microtiter wells with grass pollen extract (ALK-Abelló A/S, Hörsholm, Denmark; 100 ug/mL) and cell culture medium at a density of 106 cells/mL in a total volume of 2 mL per well. After seven days of incubation at 37 oC and 5 % CO2 the CD4+ cells were enriched from the allergen-challenged PBMCs by using anti-CD4-coated paramagnetic microbeads and a MACS system according to the instructions of the manufacturer (Miltenyi Biotech GmbH, Bergisch Gladbach, Germany).

extract_protocol: 200 ug of total RNA was prepared using Ambion's Illumina RNA TotalPrep Amplification kit (cat no IL1791, http://www.ambion.com/techlib/prot/fm_IL1791.pdf)

treatment_protocol: PBMCs were cultured with diluent (PBS) or diluent with 100 ug grass pollen extract (ALK-Abelló A/S, Hörsholm, Denmark).

value: CD4+ cells

tag: condition

value: Allergen-challenged

tag: subject


title: 0,15_2h_rep3

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 2h. Replicate 3.


title: 0,45_2h_rep1

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 2h. Replicate 1.


title: Patient7S


title: Patient7C

source_name: Unchallenged CD4+ cells

value: Unchallenged


title: 0,15_2h_rep2

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 2h. Replicate 2.


title: 0,15_2h_rep1

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 2h. Replicate 1.


title: 0,05_2h_rep3

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 2h. Replicate 3.


title: 0,05_2h_rep2

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 2h. Replicate 2.


title: Patient6C


title: Patient4S


title: Patient4C


title: Control_1h_rep2

description: Sample corresponding to untreated cells. Measurement after 1h. Replicate 2.


title: Hypertrophic-3

city: University Park

first: Paul

middle: A

last: Bartell

state: PA

address: 205 Henning Bldg.

department: Poultry Science

institute: Penn State University

description: Pooled isolated hypertrophic chondrocytes.

hyb_protocol: Hybridized to Affymetrix GeneChip Chicken Genome Arrays for 16 h at 45°C; washing with Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Affymetrix GCS3000 Scanner.

data_processing: Expression analysis was performed using GeneSifter software (VizXLab). CEL data were subjected to a Robust Multichip Average (RMA) to adjust for background and quantile normalization. Pairwise t-test analysis was performed to identify genes that are differentially expressed in proliferative versus hypertrophic chondrocytes. All genes were subjected to a filter of 3-fold change in gene expression, with a P value of 0.05 deemed significant. P values were adjusted for multiple testing comparisons using Benjamini and Hochberg method in order to control the false discovery rate.

organism: Gallus gallus

source_name: Tibiotarsus growth plate, hypertrophic chondrocytes

label_protocol: Affymetrix One Cycle Target Labeling Kit according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).

growth_protocol: Hypertrophic chondrocytes from 1-day-old chicks; proliferative chondrocytes from 3-week-old chicks.

extract_protocol: RLT Lysis buffer followed by RNeasy Mini-Kit.

treatment_protocol: Not Applicable.

value: Tibiotarsus growth plate

value: Chondrocytes

tag: chondrocyte type

value: Hypertrophic

value: 1 day


title: 0,05_2h_rep1

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 2h. Replicate 1.


title: Hypertrophic-1


title: 0,45_1h_rep3

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 1h. Replicate 3.


title: Control_1h_rep1

description: Sample corresponding to untreated cells. Measurement after 1h. Replicate 1.


title: 0,45_1h_rep1

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 1h. Replicate 1.


title: Control_1h_rep3

description: Sample corresponding to untreated cells. Measurement after 1h. Replicate 3.


title: Hypertrophic-2


title: Hypertrophic-4


title: Proliferative-4

description: Pooled isolated proliferative chondrocytes.

source_name: Tibiotarsus growth plate, proliferative chondrocytes

value: Proliferative

value: 3 weeks


title: 0,15_1h_rep2

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 1h. Replicate 2.


title: Proliferative-1


title: Proliferative-2


title: 0,45_1h_rep2

description: Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 1h. Replicate 2.


title: 0,15_1h_rep3

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 1h. Replicate 3.


title: Proliferative-3


title: 0,15_1h_rep1

description: Sample corresponding to a treatment of 0,15µM of triptolide. Measurement after 1h. Replicate 1.


title: 0,05_1h_rep3

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 1h. Replicate 3.


title: 0,05_1h_rep1

description: Sample corresponding to a treatment of 0.05µM of triptolide. Measurement after 1h. Replicate 1.


title: 0,05_1h_rep2

description: Sample corresponding to a treatment of 0,05µM of triptolide. Measurement after 1h. Replicate 2.


title: mural (38_2640_m)

status: Public on Oct 15 2009

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description: Gene expression profile of human granulosa

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductor software based on R language

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (WT cDNA Synthesis and Amplification Kit).

growth_protocol: Frozen in liquid nitrogen

extract_protocol: RNeasy Micro and Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Ovum pick-up (OPU) for IVF, 36h aftre hCG administration. Mural granulosa cells from OPU fluid, cumuls cells collected 4h after OPU during oocyte denudation.

value: mural granulosa


title: mural (39_2703_m)


title: mural (40_2733_m)


title: mural (35_661_m)


title: mural (32_2001_m)


title: mural (36_2573_m)


title: mural (34_1247_m)


title: mural (33_2725_m)


title: mural (29_2596_m)


title: mural (31_2350_m)


title: mural (25_2411_m)


title: mural (23_2508_m)


title: mural (30_2177_m)


title: mural (22_2689_m)


title: cumulus (20_2733_c)

value: cumulus granulosa


title: cumulus (18_2640_c)


title: mural (24_2599_m)


title: mural (28_2586_m)


title: mural (21_2545_m)


title: cumulus (16_2573_c)


title: mural (27_2738_m)


title: mural (26_1452_m)


title: cumulus (14_1247_c)


title: cumulus (12_2001_c)


title: Patient8_4weeks_posthealing

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

institute: University of Washington

description: Patient 8_4weeks_posthealing

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Human skin biopsy

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.

value: skin


title: cumulus (11_2350_c)


title: cumulus (15_661_c)


title: cumulus (10_2177_c)


title: cumulus (19_2703_c)


title: FEAT transgenic mouse, normal liver

city: Fukuoka

first: Atsushi

last: Takahashi

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

description: To evaluate whether hepatocellular carcinomas (HCCs) that developed in FEAT transgenic mice recapitulate genetic events that occur in human HCCs, we analyzed the amplification (gain) or deletion (loss) of genomic regions (copy number alterations) using array-CGH.

hyb_protocol: Agilent Oligo aCGH Hybridization Kit (5188-5220) Agilent oligo aCGH Wash Buffer Kit (5188-5226) Agilent Hybridization Chamber Gasket Slides (G2534-60003)

scan_protocol: Micro Array Scanner (Agilent Technologies)

data_processing: Feature Extraction using default setting for CGH-v4_91 protocol (ex. Dye Normalization, linear) (Agilent Technologies) CGH analytics 3.4 (Agilent Technologies). Features with signal intensity < 100 were removed using Tools_Feature Lvel Filters.

source_name: normal liver, FEAT transgenic mouse

label_protocol: Agilent Genomic DNA Labeling Kit PLUS (5188-5309)

extract_protocol: Minced tissues in 2-ml microfuge tubes were suspended in 1 ml ice-cold TEN buffer (50 mM TrisHCl, pH 8.0, 1 mM EDTA, pH 8.0, and 100 mM NaCl) and gently mixed with 150 µl of 10% SDS.  Twenty-five microliters of 20 mg/ml proteinase K was added and the tissues were incubated overnight at 50°C.  Next, 1 ml TE Saturated Phenol (NIPPON GENE) was added, the samples were rotated for 1 h at room temperature, and the aqueous phase was recovered by centrifuging at 8000 rpm for 15 min at 15°C.  After the phenol extraction was repeated, the aqueous phase was collected and 1 ml chloroform:isoamyl alcohol was added.  The mixture was rotated for 1 h at room temperature and the aqueous phase was recovered by centrifuging at 3000 rpm for 10 min at 15°C.  Genomic DNA was precipitated by adding 2 ml ethanol precooled at -20°C and gently mixed by swirling.  The precipitate was transferred with a Pasteur pipette into a 1.5-ml microfuge tube containing 1 ml 70% ethanol and centrifuged at 15000 rpm for 5 min at 4°C.  The pellet was resuspended in 200 µl TE buffer41 and dissolved by rotating overnight at room temperature.  The DNA concentration was determined by measuring the absorbance at 260 nm using a spectrophotometer (DU 800; Beckman Coulter).  The quality of DNA was assessed by electrophoresis of 200 ng DNA on a 0.8% agarose gel containing 0.5 µg/ml ethidium bromide.  Only DNA preparations without smearing were used for labeling and hybridization.

tag: genome/variation

value: FEAT transgenic mouse

value: 13 months

value: liver

tag: disease status

value: normal

source_name: normal liver

value: wild type

value: 6 months


title: Patient8_control_for_4weeks_posthealing

description: Patient 8_control


title: Patient2_2weeks_posthealing

description: Patient 2_2weeks_posthealing


title: cumulus (13_2725_c)


title: TG16 HCC

source_name: hepatocellular carcinoma (HCC), FEAT transgenic mouse

value: male

value: 20 months

value: hepatocellular carcinoma (HCC)

tag: tumor stage

value: multiple tumors in liver


title: Patient3_2weeks_posthealing

description: Patient 3_2weeks_posthealing


title: cumulus (8_2586_c)


title: cumulus (9_2596_c)


title: cumulus (7_2738_c)


title: Patient3_control_for_2weeks_posthealing

description: Patient 3_control


title: Patient2_control_for_2weeks_posthealing

description: Patient 2_control


title: C57BL/6 normal liver

source_name: normal liver, C57BL/6


title: Patient3_4weeks_posthealing

description: Patient 3_4weeks_posthealing


title: TG18 HCC

value: 18.5 months

value: multiple liver tumors, lung metastasis


title: cumulus (6_1452_c)


title: 18-15-6 HCC

scan_protocol: Micro Array Scanner (Agilent Technologies) Feature Extraction (Agilent Technologies)

value: 12 months

value: localized in liver


title: cumulus (5_2411_c)


title: Patient3_control_for_4weeks_posthealing

description: Patient 3_control


title: Patient2_newly_healed

description: Patient 2_newly_healed


title: 18-8 HCC

value: 22 months


title: 1-9 HCC

value: 16 months

value: tumors in the right and left lobe of liver


title: 16-4 HCC

value: FEAT transgenic mouse

value: 21 months

value: liver tumor only


title: Fuso + 25% saliva + lysine B

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

description: standard 49 format custom GeneChip

hyb_protocol: The hybridization and washing procedures were performed similarly as recommended in the GeneChip® Expression Analysis Technical Manual with some minor modifications. The hybridization buffer consisted of 1x MES buffer (100 mM morpholineethanesulfonic acid [MES], 1M NaCl, 20 mM EDTA, 0.01% Tween-20), 50 pM B2 control oligo, 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, and the fragmented, labeled cDNA in a total volume of 200 µL.  The hybridization solution was then loaded into the microarray cartridge and mixed for 16 hr at 60 rpm and 47°C in an Affymetrix hybridization oven. After the incubation period, the hybridization solution was removed and the array was washed and stained in the Affymetrix Fluidics Station 450 using a slightly modified script of the standard wash script file “ProkGE-WS2v3-450”, which increased the wash stringency from 45°C to 47°C. The staining solution consisted of 3 different MES buffers each in a 600 µL total volume. The first consisted of 1x MES buffer, 2 mg/mL BSA, and 10 µg/mL streptavidin, the second consisted of 1x MES buffer, 2 mg/mL BSA, 0.1 mg/mL goat IgG, and 5 µg/mL biotin anti-streptavidin, and the third solution consisted of 1x MES buffer, 2 mg/mL BSA, and 10 µg/mL streptavidin-phycoerythrin (Molecular Probes, Eugene, OR).

scan_protocol: The GeneChips® were scanned at 570 nM using an Affymetix 7G laser scanner.

data_processing: Analysis of signal intensities was performed using the GeneChip® operating system software (GCOS) ver. 1.4 and gene expression data were compared using the GCOS batch analysis function. Normalization procedures are performed directly by the software using a script designed by Affymetrix and provided with the F. nucleatum custom array.  This eliminates user bias during the normalization procedure.

organism: Fusobacterium nucleatum

source_name: bacteria

label_protocol: 32 µL of  fragmented cDNA was labeled with the BioArray terminal labeling kit (Enzo, New York, NY) in a total volume of 50 µL containing 10 µL 5x buffer, 5 µL 10x CoCl2, and 2 µL terminal deoxynucleotide transferase. The reaction was incubated at 37°C for 60 min.

growth_protocol: Cells were first grown to stationary phase in Columbia broth, which was then used as a starter culture to inoculate SDM cultures. Stationary phase cells were diluted 1:100 in 20 mL of SDM and grown 16 hrs overnight to late log phase (OD600 0.7 – 0.9).  The following day, the cells were centrifuged and resuspended to OD600 0.5 – 0.6 in either 25 mL SDM, SDM + 25% saliva, or SDM + 25% saliva and 50 mM L-lysine.  Next, the cells were prewarmed to 37°C before incubating anaerobically for 90 min. at 37°C. Every 15 – 20 min., the non-aggregating cultures (SDM and SDM + saliva/lysine) were gently agitated to maximize separation between the cells and prevent any settling.

extract_protocol: After the assay period, the cells were immediately centrifuged at 4°C in a prechilled refrigerated centrifuge. Cell pellets were resuspended in 500 µL chilled TE buffer on ice. Next, the cells were placed in a 70°C waterbath and 900 µL preheated acidic phenol (pH 4.3) was immediately added to the cultures followed by SDS to a final concentration of 1% wt/vol.  The mixture was incubated for 5 minutes before removing, adding 400 µL chloroform, and centrifuging. The mixture was further phenol/chloroform extracted 3 times before the RNA was precipitated and resuspended in 90 µL RNase-free water + 10 µL DNase buffer. DNase was added to the samples and incubated at 37°C for 45 minutes. Finally, the samples were further purified with Qiagen RNeasy MinElute spin columns according to the manufacturer’s protocol and eluted in RNase-free water. The resulting RNA integrity was confirmed by the presence of clearly defined rRNA bands in agarose gels and later quantified for concentration by OD260 readings.

value: atcc 25586 wild type

tag: aggregation status

value: dispersed


title: Fuso + 25% saliva A

description: standard 49 format custom GeneChip

value: aggregated


title: Fuso + 25% saliva + lysine A

description: standard 49 format custom GeneChip


title: Patient3_lesion

description: Patient 3_lesion

value: skin


title: Fuso B

description: standard 49 format custom GeneChip


title: Patient2_control_for_newly_healed

description: Patient 2_control


title: Patient7_lesion

description: Patient 7_lesion


title: cumulus (4_2599_c)

value: cumulus granulosa


title: Fuso A

description: standard 49 format custom GeneChip


title: Patient2_lesion

description: Patient 2_lesion


title: Patient3_newly_healed

description: Patient 3_newly_healed


title: Fuso + 25% saliva B

description: standard 49 format custom GeneChip


title: Patient1_lesion

description: Patient 1_lesion


title: Patient3_control

description: Patient 3_control


title: cumulus (2_2689_c)


title: cumulus (3_2508_c)


title: Patient3_control_for_newly_healed

description: Patient 3_control


title: Patient2_control

description: Patient 2_control


title: cumulus (1_2545_c)


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3B RNAi (expression), replicate 2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

description: change in expression after H3.3B RNAi

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel at 10 um resolution using a suitable scan area.

data_processing: Images of the expression arrays were analyzed using Agilent Feature Extraction Software version 9.5.1.1. Mean spot intensities without background subtraction were used to normalize with subarray loess and calculate weighted average ratios per reporter by a NKI platform adjusted Rosetta error model (Weng L. et al., Bioinformatics (2006)), tuned by self-self hybridizations. These mean, normalized data without spike-in control oligos are represented in the Supplementary data file 'Expression_norm.txt' together with associated A and p values. The matrix data table contains normalized  values before weighed averaging of duplicate REPORTER_IDs and replicate samples.

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, H3.3B RNAi

label_protocol: 1 µg of RNA was labeled with 0.3 µl of ULS-Cy5 or 1 µl of ULS-Cy3 label using the ULS labeling system from Kreatech. Details can be found at the website of the NKI Central Microarray Facility (http://cmfdb.nki.nl/process/protocolView).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul H3.3B dsRNA.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Contaminating gDNA was degraded using DNaseI (1 unit/µg RNA), 15 min. at room temperature).

treatment_protocol: Cells were stored in Trizol at -80°C.

source_name: Embryonic Drosophila cells, Kc167 cells, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA.


title: Treated Worm-13 13 day (PMT 450)

status: Public on Oct 14 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A8_SL2
PMT: 450

hyb_protocol: 600 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 350/450/510 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 016423_D_20070410.gal to obtain signal intensities.  Non-uniform spots and spots with a signal intensity outside the linear range were flagged.  Signal intensity was converted into relative RNA concentration based on the linear standard curve of spike-in RNAs.  The relative RNA concentration was normalized to the median value on each array.

organism: Eisenia fetida

source_name: whole organism

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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.

growth_protocol: Earthworms were kept in moistened sphagnum peat (pH 6.5–7.5, moisture content 50%) and fed ad libitum on a diet of with Magic Worm Food (Carolina Biological Supply).

extract_protocol: Total RNA was extracted from RNAlater-ICE fixed worms using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adults bearing clitelum and weighing 0.4~0.5 g were pulled out of the culture and allowed to depurate overnight prior to being exposed to CL-20 on filter paper (0.2 ug/cm2). Worms were snap-frozen upon experimental termination.

tag: protocol

value: 6 days treatment, 7 days recovery

tag: agent

value: whole organism


title: Treated Worm-16 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A4_SL3
PMT: 450

tag: tissue