title: CCRF-CEM cells prednisolone 100uM at 4h

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description:
The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly.
The CCRF-CEM (ALL) cell line was used as the model, it was obtained from the European Collection of Cell Cultures (ECACC). The CCRF-CEM cell line, a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)
The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: Microarray data were normalized by the default procedure of the CodeLink software, i.e. spot intensities were divided by the global median (global median normalization). Normalized data were extracted, pre-processed and sorted with Microsoft Excel ®. For further data analysis the Matlab ® (The Mathworks Inc.) computing environment was used.

source_name: CCRF-CEM cells prednisolone 100uM at 4h

label_protocol: CodeLink Expression Assay protocol

growth_protocol: The T-Lymphoblastic Leukemia CCRF-CEM were grown in RPMI-1640 medium supplemented with 2mM L-Glutamine and Streptomycin/Penicillin 100 U/ml (Gibco), 15% FBS (Gibco) at 37 oC, 5% CO2 and ~100% humidity. Cells were allowed to grow to ~900-1.500×10^3 cells/ul for CCRF-CEM.

extract_protocol: RNA was isolated with Trizol (Invitrogen Inc.) according to the manufacturer’s instructions. RNA was further processed with RQ1 DNase (Promega Inc. Madison, WI, USA) as described by the manufacturer and then it was cleaned-up with the RNEasy Mini kit (#74104, QIAGEN Inc.). The amount of RNA isolated was measured with a NanoDrop 2000 (Thermo Scientific Inc.) spectrophotometer and RNA integrity was estimated by 2% agarose gel electrophoresis. Samples with a 1.8 to 2.0 A260/A280 ratio were selected. In addition, those that empirically showed a twice as bright 28S band than the 18S band on the gel were utilized. 2 μg of RNA from each sample was used.

treatment_protocol: 100uM Prednisolone

tag: cell line

value: CCRF-CEM (ALL)

tag: origin

value: peripheral blood

value: 2 year old

value: Caucasian female

tag: diagnosis

value: lymphosarcoma which progressed later on to acute leukemia

value: 100uM Prednisolone


title: CCRF-CEM control at 4h kit

status: Public on May 11 2011

type: RNA

description:
The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly.
The CCRF-CEM (ALL) cell line was used as the model, it was obtained from the European Collection of Cell Cultures (ECACC). The CCRF-CEM cell line, a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)
The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).
This sample was tested and hybridized with an alternative kit (TargetAmp from Epicentre) in order to account for variations due to the methodology per se.

molecule: total RNA

organism: Homo sapiens

source_name: CCRF-CEM cells with no treatment at 4h

treatment_protocol: No treatment

tag: age

tag: gender

tag: treatment

value: No treatment


title: 9_10 Yqdel_control

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

country: United Kingdom

institute: University of Kent

description:
Control for sample 4421347024_B
4421347024_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization was performed with BeadStudio (Illumina) - software package now renamed GenomeStudio

label: biotin

organism: Mus musculus

source_name: Mouse testis

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

extract_protocol: RNA was extracted with TRI reagent (Sigma), followed by clean-up with QIAGEN RNeasy MinElute kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 2 months

tag: y gene complement

value: Sry absent

tag: transgene

value: Sry

tag: number pooled


title: CCRF-CEM cells prednisolone 700uM at 4h

source_name: CCRF-CEM cells prednisolone 700uM at 4h

treatment_protocol: 700uM Prednisolone

value: 700uM Prednisolone


title: XSxrAY#X_2mo

value: Yq absent


title: CCRF-CEM control at 4h


title: CCRF-CEM cells prednisolone 10nM at 4h

source_name: CCRF-CEM cells prednisolone 10nM at 4h

treatment_protocol: 10nM Prednisolone

value: 10nM Prednisolone


title: Wildtype_control_rep3

description:
Normal controls for shSLY, 2/3 Yqdel and XSxrAY#X genotypes
4421347011_F

value: 8 weeks

value: Complete


title: CCRF-CEM cells prednisolone 1uM at 4h

source_name: CCRF-CEM cells prednisolone 1uM at 4h

treatment_protocol: 1uM Prednisolone

value: 1uM Prednisolone


title: CCRF-CEM control at 4h pool

description:
The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly.
The CCRF-CEM (ALL) cell line was used as the model, it was obtained from the European Collection of Cell Cultures (ECACC). The CCRF-CEM cell line, a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)
The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).
This included a pool of untreated CCRF-CEM cells from various experiments at 4h. This was performed in order to account for the variations due to cell culture conditions.


title: 17d_wildtype_rep2

extract_protocol: RNA was extracted with TRI reagent (Sigma). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For the spermatid samples, purified round spermatids were isolated by centrifugal elutriation.

value: 17 dpp


title: CCRF-CEM cells 2uM MG132 at 4h

source_name: CCRF-CEM cells 2uM MG132 at 4h

treatment_protocol: 2uM MG132

value: CCRF-CEM (ALL)

value: 2uM MG132


title: 17d_wildtype_rep3


title: CCRF-CEM cells MG132 200nM at 4h

source_name: CCRF-CEM cells MG132 200nM at 4h

value: peripheral blood

value: 2 year old


title: shSLY3_rep1

value: shSLY RNAi construct


title: CCRF-CEM cells prednisolone 10uM at 4h

source_name: CCRF-CEM cells prednisolone 10uM at 4h

treatment_protocol: 10uM Prednisolone

value: Caucasian female

value: lymphosarcoma which progressed later on to acute leukemia

value: 10uM Prednisolone


title: CCRF-CEM cells 20uM MG132 at 4h

source_name: CCRF-CEM cells 20uM MG132 at 4h


title: shSLY3_rep2


title: 17d_wildtype_rep1


title: 17d_sh367_rep2


title: Spermatids_wildtype rep2

source_name: Mouse round spermatids


title: Spermatids_2_3Yqdel_rep2

value: 2/3 Yq deleted


title: 17d_sh367_rep1


title: Anaplastic meningioma NCH_q_1099

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

hyb_protocol: We used a custom 60-mer amino modified oligo- array, containing 912 probes, a lot of which specific for genes commonly altered in cancer. The hybridization mix consisted of human COT-1 DNA, yeast tRNA (0.22 μg/μl, Sigma, St. Louis, MO), 3X SSC, 0.1% SDS, and 40% formamide in a final volume of 28 μl. Before hybridization, the cDNA microarray epoxydic slides were washed in HCl 1mM, then in KCl 100mM, and the blocked in blocking buffer (Tris-HCl pH 9.0, Ethanolamine 50 mM, SDS 0,1%) Hybridization was carried out at 42 °C overnight in an hybridization chamber. Before scanning, slides were washed in 2X SSC with 0.1% SDS for 10 min at 60°C, then in 2X SSC, and  finally in 0.2X SSC, sequentially for 10 min. Hybridized arrays were scanned at 10 μm resolution on a ArrayScanner 428 (Affimetrix) at variable gain to obtain maximal signal intensities with minimal background. Resulting images were analyzed via GeneSpring (Agilent) as described in the manufacturer’s manual.

data_processing: The images were combined and processed using the ScanAnalyze program (written by Michael Eisen, http://rana.Stanford.EDU/software/) and the positions on the images were assigned to grid coordinates for the matching of spot identity with average pixel intensity at that region. Background corrected, log converted intensity ratios were determined for each element of the array. The image processing analysis also extracted information regarding spot quality and assigned a quality score to each ratio measurement. The definition of the quality metric was based on the notion that unreliable data points usually result from weak target intensity, high local background, small target area, and inconsistent target intensity within a given target. Implementation of the quality metric enabled unified and universally applicable data filtering before downstream higher-level data analysis. ScanAlyze data was imported in GeneSpring and GenePattern for further elaboration (Silicon Genetics, Redwood City, CA). To import data a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. Parameters are not numerical but define the sample nature or tissue type. The normalization of each sample was performed dividing each signal intensity by the 50th- percentile of all genes in that array. The normalization of each gene between samples was performed on the median of signal intensity of that gene in the reference sample. Genes were also analyzed using GeneSpring for differential expression between sample classes. The software allow the data filtering upon signal intensity and detection value. To select differentially expressed genes we used several approaches: for two class matching we utilized the Scatter Plot selecting the genes with an expression fold >2. To identify differentially expressed genes in a multi class match we calculated the log2 of normalized data. In this way over-expressed genes was the ones with a value >0, while the down-expressed was the ones with a value <0. For statistical validation we used t-test with a p-value of 0.01

source_name: meningioma tissue

label_protocol: RNA amplification and labelling RNA was amplified by means of Whole Transcriptome Amplification (WTA) (Sigma-Aldrich) following manufacturer instructions. The WTA process involves two steps. In the first step, sample RNA is reverse transcribed with substantially non-self-complementary primers composed of a semi-degenerate 3’ end and a universal 5’ end. As polymerization proceeds, displaced single strands serve as new templates for primer annealing and extension. The resultant Omniplex® cDNA library, composed of random, overlapping fragments flanked by universal end sequence, is then amplified by PCR with the universal primer to produce WTA product. Product size ranges from 100–1000 bases when amplifying intact RNA, and typically smaller for degraded RNA. For RNA amplification a modification to the amplification step of the WTA protocol was performed consisting in the substitution of the 10mM dNTP mix of the mix with the 10mM dNTP labelling mix containing Cy3-labelled-dCTP.

extract_protocol: RNA extraction  Tumor and adjacent normal tissues were macro-dissected from 10 micron formalin-fixed, paraffin-embedded (FFPE) tissue sections. Using 3-4 sections for each sample, total RNA was extracted using TRIzol LS reagent (Invitrogen).

tag: sex

value: F

tag: type

value: Anaplastic

tag: grade

value: Grade III

tag: mib-1 labeling indices

tag: recurrence (years)

tag: location

value: Convexity

tag: survival (years)

value: Normal meningal tissue


title: Spermatids_2_3Yqdel_rep1

value: 8 weeks


title: Spermatids_sh367_rep2

treatment_protocol: Purified round spermatids were isolated by centrifugal elutriation.


title: Spermatids_sh367 rep2

value: Complete


title: Wildtype_control_rep1

description:
Normal controls for shSLY, 2/3 Yqdel and XSxrAY#X genotypes
4421347011_B


title: Spermatids_wildtype_rep3


title: Anaplastic meningioma NCH_q_1033

scan_protocol: Hybridized arrays were scanned at 10 μm resolution on a ArrayScanner 428 (Affimetrix) at variable gain to obtain maximal signal intensities with minimal background. Resulting images were analyzed via GeneSpring (Agilent) as described in the manufacturer’s manual.

value: Olfactory groove


title: Anaplastic meningioma NCH_q_1105


title: Anaplastic meningioma NCH_q_1065

value: Atipic

value: Grade II

value: Parasagittal


title: Anaplastic meningioma NCH_q_1062

value: Supresellar


title: Anaplastic meningioma NCH_q_1007

value: M


title: Anaplastic meningioma NCH_q_1049


title: Spermatids_sh367_rep1

value: shSLY RNAi construct


title: Anaplastic meningioma NCH_q_1035

value: Sphenoid wing


title: Spermatids_shSLX1_rep1

value: shSLX RNAi construct


title: Spermatids_shSLX1_rep2


title: Spermatids_wildtype_rep4


title: Spermatids_wildtype_rep2


title: Anaplastic meningioma NCH_q_1070


title: Spermatids_sh367 rep1


title: Atypical meningioma NCH_q_1009

value: clivius


title: Atypical meningioma NCH_q_980

value: F

value: Intraventricular


title: Atypical meningioma NCH_q_1024


title: Atypical meningioma NCH_q_1116


title: Atypical meningioma NCH_q_1030


title: Tumor alone 2

status: Public on May 12 2011

city: Singapore

first: Siew-Min

last: Ong

address: 8A Biomedical Grove, Immunos Level 4

country: Singapore

institute: Singapore Immunology Network (SIgN)

description: Biological replicate 2

data_processing: The data were normalised using quantile normalisation with R/Bioconductor

source_name: cell line

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

growth_protocol: Spheroids were cultured in IMDM with 5% human serum for 8 days

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

tag: cell type

value: tumor cell


title: 17d_sh367_rep3

value: 17 dpp


title: Atypical meningioma NCH_q_1080

value: Normal meningal tissue


title: Atypical meningioma NCH_q_1003

value: Falx


title: Atypical meningioma NCH_q_1026


title: Atypical meningioma NCH_q_1051


title: Spermatids_wildtype_rep1

value: 8 weeks


title: Atypical meningioma NCH_q_1010

value: Posterior fossa


title: Atypical meningioma NCH_q_1038

value: Atipic

value: Olfactory groove


title: Atypical meningioma NCH_q_1047

value: Grade II

value: Convexity


title: Typical meningioma NCH_q_1097


title: Typical meningioma NCH_q_1022

value: M


title: Typical meningioma NCH_q_940


title: Typical meningioma NCH_q_1063

value: Supresellar


title: Typical meningioma NCH_q_1061


title: Typical meningioma NCH_q_1106


title: Typical meningioma NCH_q_1039

value: Tipic

value: Grade I


title: Typical meningioma NCH_q_1072

value: Parasagittal


title: Typical meningioma NCH_q_1048

value: F


title: Typical meningioma NCH_q_1031


title: Typical meningioma NCH_q_1093

value: Sphenoid wing


title: Atypical meningioma NCH_q_1004


title: Typical meningioma NCH_q_1066


title: Typical meningioma NCH_q_1059


title: Typical meningioma NCH_q_1005


title: Typical meningioma NCH_q_1008


title: Typical meningioma NCH_q_977


title: Typical meningioma NCH_q_1028


title: Typical meningioma NCH_q_1046


title: Typical meningioma NCH_q_1021


title: Typical meningioma NCH_q_1103


title: Typical meningioma NCH_q_1023


title: Typical meningioma NCH_q_1079


title: Typical meningioma NCH_q_1020


title: Typical meningioma NCH_q_1001


title: Typical meningioma NCH_q_1091


title: Typical meningioma NCH_q_1050


title: Typical meningioma NCH_q_1095

value: optic nerve


title: Typical meningioma NCH_q_968


title: Typical meningioma NCH_q_995


title: Typical meningioma NCH_q_1067


title: Typical meningioma NCH_q_1060


title: Typical meningioma NCH_q_1068


title: Typical meningioma NCH_q_1036


title: Typical meningioma NCH_q_1058


title: Typical meningioma NCH_q_1019


title: Spermatids_wildtype rep1

value: Complete


title: Anaplastic meningioma NCH_q_839

value: Anaplastic

value: Grade III

value: Normal meningal tissue


title: Anaplastic meningioma NCH_q_868


title: Typical meningioma NCH_q_932


title: Anaplastic meningioma NCH_q_802


title: Typical meningioma NCH_q_1006

value: Falx


title: Typical meningioma NCH_q_975


title: Anaplastic meningioma NCH_q_874


title: Typical meningioma NCH_q_1102


title: Anaplastic meningioma NCH_q_831


title: Anaplastic meningioma NCH_q_818


title: Anaplastic meningioma NCH_q_804

value: Atipic

value: Posterior fossa


title: Typical meningioma NCH_q_1014


title: Atypical meningioma NCH_q_885

value: Grade II


title: Atypical meningioma NCH_q_793


title: Atypical meningioma NCH_q_778


title: Anaplastic meningioma NCH_q_834


title: Atypical meningioma NCH_q_799

value: Intraventricular


title: Atypical meningioma NCH_q_779

value: M


title: Atypical meningioma NCH_q_849


title: Atypical meningioma NCH_q_816


title: Atypical meningioma NCH_q_820

value: Convexity


title: Atypical meningioma NCH_q_807

value: Supresellar


title: Anaplastic meningioma NCH_q_776


title: Typical meningioma NCH_q_791


title: Atypical meningioma NCH_q_749

value: Olfactory groove


title: Typical meningioma NCH_q_866


title: Atypical meningioma NCH_q_772


title: Typical meningioma NCH_q_832


title: Atypical meningioma NCH_q_773


title: Typical meningioma NCH_q_709

value: Parasagittal


title: Atypical meningioma NCH_q_795

value: F


title: Typical meningioma NCH_q_841

value: Tipic

value: Grade I


title: Typical meningioma NCH_q_808


title: Typical meningioma NCH_q_872


title: Typical meningioma NCH_q_830


title: Typical meningioma NCH_q_817


title: Typical meningioma NCH_q_875

value: Sphenoid wing


title: Typical meningioma NCH_q_993


title: Typical meningioma NCH_q_770


title: Typical meningioma NCH_q_862

value: clivius


title: Typical meningioma NCH_q_835


title: Typical meningioma NCH_q_800


title: Typical meningioma NCH_q_774


title: Typical meningioma NCH_q_746


title: Typical meningioma NCH_q_797


title: Typical meningioma NCH_q_815


title: Typical meningioma NCH_q_777


title: Typical meningioma NCH_q_790


title: Typical meningioma NCH_q_792


title: Typical meningioma NCH_q_789


title: Typical meningioma NCH_q_860


title: Typical meningioma NCH_q_829


title: Typical meningioma NCH_q_819


title: Typical meningioma NCH_q_848


title: Typical meningioma NCH_q_871


title: Typical meningioma NCH_q_783


title: Typical meningioma NCH_q_775


title: Typical meningioma NCH_q_762


title: Typical meningioma NCH_q_864


title: Typical meningioma NCH_q_764


title: Typical meningioma NCH_q_737


title: Typical meningioma NCH_q_827


title: Typical meningioma NCH_q_788


title: Typical meningioma NCH_q_805


title: Typical meningioma NCH_q_701


title: Typical meningioma NCH_q_744


title: Anaplastic meningioma NCH_q_645

value: Anaplastic

value: Grade III


title: Anaplastic meningioma NCH_q_651

value: Normal meningal tissue


title: Anaplastic meningioma NCH_q_579

value: Falx


title: Typical meningioma NCH_q_836


title: Anaplastic meningioma NCH_q_595


title: Anaplastic meningioma NCH_q_608


title: Anaplastic meningioma NCH_q_553

value: Atipic


title: Atypical meningioma NCH_q_570

value: Grade II


title: Anaplastic meningioma NCH_q_611


title: Atypical meningioma NCH_q_662


title: Atypical meningioma NCH_q_576

value: Posterior fossa


title: Atypical meningioma NCH_q_549


title: Atypical meningioma NCH_q_526


title: Atypical meningioma NCH_q_572


title: Atypical meningioma NCH_q_556


title: Atypical meningioma NCH_q_550

value: M


title: Anaplastic meningioma NCH_q_581


title: Atypical meningioma NCH_q_555

value: Convexity


title: Atypical meningioma NCH_q_584


title: Atypical meningioma NCH_q_597


title: Atypical meningioma NCH_q_593

value: optic nerve


title: Typical meningioma NCH_q_568


title: Typical meningioma NCH_q_643

value: Supresellar


title: Typical meningioma NCH_q_828


title: Atypical meningioma NCH_q_626


title: Typical meningioma NCH_q_486

value: Parasagittal


title: Typical meningioma NCH_q_607

value: F


title: THP1_Untreated_24hr_rep2

first: Koon Yeow

last: Leow

address: 21 Lower Kent Ridge Road

institute: NUS

hyb_protocol: Hybridization procedure is according to the standard protocol provided by Illumina; no deviation from the protocols were noted.

scan_protocol: Scanning procedure is according to the standard protocol recommended by Illumina; no deviation from the protocols was noted.

data_processing: The non-normalised matrix was obtained from Illumina Genomestudio. The quality of the microarray data was also determined using Illumina Genomestudio. Data is normalised using Illumina Genome Studio. Average normalisation was the algorithm used for normalisation.

label: Biotin

label_protocol: RNA amplification was conducted using Illumina TotalPrep RNA amplifcation kit. Integrity of the cRNA was verified using Bioanalyser prior to hybridization.

extract_protocol: RNA was extracted with a RNA extraction kit.

value: THP-1 dervied macrophages


title: Typical meningioma NCH_q_609

value: Olfactory groove


title: THP1_Variant SAA1(p.Gly72Asp)_24hr_rep1

source_name: THP1_Variant SAA1(p.Gly72Asp)_24hr


title: THP1_Untreated_24hr_rep1


title: THP1_Variant SAA1(p.Gly72Asp)_24hr_rep2


title: THP1_Wildtype SAA1_24hr_rep2

source_name: THP1_Wildtype SAA1_24hr


title: Typical meningioma NCH_q_652


title: Typical meningioma NCH_q_585

value: Tipic

value: Grade I


title: THP1_Untreated_8hr_rep1


title: THP1_Wildtype SAA1_24hr_rep1


title: THP1_Untreated_8hr_rep2


title: THP1_Variant SAA1(p.Gly72Asp)_8hr_rep2

source_name: THP1_Variant SAA1(p.Gly72Asp)_8hr


title: Typical meningioma NCH_q_618


title: THP1_Wildtype SAA1_8hr_rep2

source_name: THP1_Wildtype SAA1_8hr


title: THP1_Variant SAA1(p.Gly72Asp)_8hr_rep1


title: THP1_Wildtype SAA1_8hr_rep1


title: Anaplastic meningioma NCH_q_616

value: Anaplastic


title: Y 6881 389T

city: Columbus

first: Jeff

middle: J

last: Palatini

state: Ohio

address: 460 West 12th Ave.

country: USA

institute: The Ohio State University

description: The OSUCCC miRarray v4.0 comprises miRs and ncRNA from various organisms. Only the mature forms of Human miRs were analyzed in this study.

hyb_protocol: Samples were hybridized in 6X SSPE/30% Formamide at 25 C for 18 hours

scan_protocol: Arrays were stained with Streptavidin-Alexa 647 conjugate (Invitrogen/Molecular Probes) and scanned at 10um resolution at 635nm with qred laser at 100% Power and 800 PMT. Data extracted with GenePix 6.0.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed quantiles normalization method to selected human miR genes and quantified using GenePix 6.0 and analyzed with BRB-array Tools

source_name: Hapatocellular Carcinoma (HCC) Cells

label_protocol: Biotinylated random octamers were used to reverse transcribe 2ug of total RNA into biotinylated cDNA

growth_protocol: HCC cell lines (HepG2, C3A, Hep3B, Huh7, PLC/PRF/5, SNU-387, SNU-423, SNU-449, SNU-475) were cultured as recommended by ATCC.

extract_protocol: Total RNA of HCC tissue samples and HCC cell lines were extracted using Tri-Reagent and TRIZOL respectively in accordance with manufacturer’s instructions.

treatment_protocol: HCC tissue samples were fresh-frozen in liquid nitrogen after surgery and kept at −80 ℃. Frozen tissue samples were homogenized using the Tissue Ruptor (QIAGEN) before RNA extraction.

value: Hapatocellular Carcinoma (HCC) Cells

tag: p53 mutation status

value: WT p53


title: Typical meningioma NCH_q_649

value: Sphenoid wing

value: Normal meningal tissue


title: Y 6879 342T


title: Y 6880 383T


title: Typical meningioma NCH_q_547


title: Y 6883 400T


title: Y 6884 420T


title: Typical meningioma NCH_q_594


title: Typical meningioma NCH_q_612


title: Y 6878 272T


title: Typical meningioma NCH_q_639


title: Y 6866 43T


title: Typical meningioma NCH_q_577


title: Y 6868 440T


title: Y 6870 444T


title: Typical meningioma NCH_q_605


title: Y 6864 438T


title: Typical meningioma NCH_q_551


title: Y 6877 128T


title: Typical meningioma NCH_q_523


title: Y 6854 427T


title: Y 6852 426T


title: Typical meningioma NCH_q_574


title: Typical meningioma NCH_q_592


title: Y 6848 424T


title: Typical meningioma NCH_q_554

value: Falx


title: Typical meningioma NCH_q_567


title: Y 6842 417T


title: Y 6840 416T


title: Typical meningioma NCH_q_569


title: Typical meningioma NCH_q_566


title: Y 6856 429T


title: Y 6838 415T


title: Y 6836 399T


title: Typical meningioma NCH_q_637


title: Typical meningioma NCH_q_596


title: Typical meningioma NCH_q_552


title: Y 6832 394T


title: Typical meningioma NCH_q_648


title: Typical meningioma NCH_q_539


title: Y 6844 418T


title: Typical meningioma NCH_q_606


title: Typical meningioma NCH_q_560

value: Posterior fossa


title: Y 6828 390T


title: Y 6830 391T


title: Typical meningioma NCH_q_625


title: Y 6834 397T


title: Typical meningioma NCH_q_641


title: Y 6824 386T


title: Typical meningioma NCH_q_541

value: M


title: Typical meningioma NCH_q_478


title: Y 6822 385T


title: B6

city: charlottesville

first: qian

last: wang

state: virginia

address: 480 Ray C Hunt Drive

department: radiology

institute: university of virginia

hyb_protocol: Following fragmentation, cRNA were hybridized to mouse arrays MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the the Affymetrix Scanner 3000

data_processing: The data were analyzed using the Gene Chip Operating System.

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were weaned onto a chow diet at 3 weeks of age.

extract_protocol: Total RNA was extracted from the liver using a Qiagen kit.

treatment_protocol: Mice were started with a Western diet at 6 weeks of age and maintained on the diet for 12 weeks.

tag: strain

value: C57BL/6 apoE-/- mice

tag: disease state

value: Hyperglycemia

tag: diet

value: western


title: Failed Adjacent Stroma Sample 27 from an Ovary Exhibiting a Malignant Tumor

city: Charlotte

first: Timothy

middle: L

last: Tickle

state: NC

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: University of North Carolina at Charlotte

description:
This was not included in the matrix because this cel file did not pass quality control during the development of this data set. It was not possible to successfully resample this tissue and so was removed from this study. We provide this cel file for research as one sees fit.
probe_group_file:HuEx-1_0-st-v2.na31.hg19.probeset.csv
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: The Affymetrix recommended hybridization cocktail was optimized for Nugen cDNA products, specifically with respect to the use of Human Exon 1.0 ST arrays (Affymetrix, Inc.) and Nugen’s Ovation products (see FL-Ovation™ cDNA Biotin Module V2 Users Guide, Appendix A.1).

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

data_processing: The matrix values provided were creating using the Partek® Genomics Suite™ implementation of GC-RMA, core-exon probes only (using only samples indicated as "Experimental" as opposed to "Replicate" or "Failed").

source_name: Ovarian stroma (from an ovary with a malignant tumor)

label_protocol: ST-cDNA was fragmented and labeled with the FL-Ovation™ cDNA Biotin Module V2 kit (NuGEN Technologies Inc).

growth_protocol: After collection by a clinician, ovary samples were placed in a gamma radiation-sterilized 50ml tubes with approximately 7.5ml of Hank’s Balanced Salt solution (Invitrogen Co.). Samples were transferred to a standard sized cryomold (Sakura Finetek USA), covered with Optimal Cutting Temperature (OCT) compound (Sakura Finetek USA), frozen on dry ice, and stored at -80°C.

extract_protocol: RNA extraction was performed using a PicoPure® RNA Isolation kit (Applied Biosystems, Life Technologies, Co.). Complimentary DNA (cDNA) generation and amplification was performed using the Whole Transcriptome WT-Ovation™ Pico RNA Amplification System Kit (NuGEN Technologies Inc.). Complementary DNA was converted to be compatible with exon chips using the WT-Ovation Exon™ Module (NuGEN Technologies Inc).

treatment_protocol: Cryomold samples were serially sectioned in a Leica CM 1850 UV Cryostat (Leica Microsystems Inc.). The HistoGene LCM Frozen Section Staining kit (MDS Analytical Technologies) was used to prepare fresh frozen samples for LCM. Samples were microdissected using a PixCell IIe instrument or an ArcturusXT™ Laser Microdissection instrument (Applied Biosystems, Life Technologies, Co.) using CapSure® HS LCM caps. When available, normal epithelium, tumor, adjacent stroma (to tumor), and distal stroma (to tumor) were separately collected from each section.

tag: tissue

value: Ovarian stroma

tag: patient

tag: pathology

value: Serous Carcinoma

tag: experimental status

value: Failed Sample


title: Failed Adjacent Stroma Sample 27 from an Ovary Exhibiting a Malignant Tumor_2


title: Ch1ABC

value: Bglu3 congenic mice


title: Failed Distal Stroma Sample 12 from an Ovary Exhibiting a Malignant Tumor

description:
This was not included in the matrix because this cel file did not pass quality control during the development of this data set. The tissue this cel file was derived from was resampled, passed quality control, and was used in the experiment as a different cel file. We provide this cel file for research as one sees fit.
probe_group_file:HuEx-1_0-st-v2.na31.hg19.probeset.csv
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: Failed Tumor Sample 17 from an Ovary Exhibiting a Malignant Tumor

source_name: Ovarian tumor (from an ovary with a malignant tumor)

value: Malignant ovarian tumor


title: WT rep3

city: Philadelphia

first: Cara

middle: Michele

last: Winter

address: 421 Curie Blvd.

institute: University of Pennsylvania

description: D9 35S::LFY-GR vs WT seedling expression array, 4 biological reps

hyb_protocol: Hybridization to the Affymetrix Arabidopsis ATH1 array was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.

scan_protocol: Scanning was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.

data_processing: Microarray data were processed using Bioconductor packages in R. Data were gcRMA normalized (Wu et al., 2004). Non-specific filtering was performed with the MAS5.0 algorithm for genes that were ‘Present’ in at least 2 of 4 arrays in at least one treatment group (genotype) (McClintick and Edenberg, 2006). Differentially expressed genes were identified using LIMMA (Smyth, 2004).

organism: Arabidopsis thaliana

source_name: D9 WT (Ler) dex treated seedling RNA

label_protocol: RNA was amplified and labeled using NuGEN's Ovation™ RNA kits according to the manufacturer's instructions.

growth_protocol: Seeds cold-treated for 7 days at 4°C were grown in inductive conditions (continuous light or 16 hour long-day light conditions) at 23°C at a fluence rate of 45 μmol/m2 sec on 0.5x Murashige and Skoog plates

extract_protocol: RNA was extracted from four independent pools of apices using TRI-Reagent followed by column purification (RNeasy kit; QIAGEN).

treatment_protocol: 35S::LFY-GR and WT seedlings were treated with 10uM dexamethasone, 0.1% ethanol, for 4 hours essentially as described (Wagner et al., 1999).

tag: genotype/variation

value: wild type (Ler)

value: shoot apices

tag: age

value: 9-day-old seedlings


title: B6 chow

source_name: aorta

treatment_protocol: Mice continued with a chow diet or switched onto a Western diet at 4 weeks of age and maintained on the diet for 2 weeks.

tag: genotype

value: Atherosclerosis

value: chow


title: Ch9 Western

value: Ath29 congenic mice

value: Resistance to atherosclerosis


title: Typical meningioma NCH_q_514

tag: sex

value: F

tag: type

value: Tipic

tag: grade

value: Grade I

value: Intraventricular

value: Normal meningal tissue


title: Y 6814 367T

value: Hapatocellular Carcinoma (HCC) Cells

value: WT p53


title: B6 Western

value: C57BL/6 apoE-/- mice

value: western


title: Failed Distal Stroma Sample 11 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian stroma

value: Serous Carcinoma

value: Failed Sample


title: Y 6812 366T


title: WT rep1

value: wild type (Ler)

value: shoot apices

value: 9-day-old seedlings


title: LFYGR rep4

source_name: D9 35S::LFY-GR dex treated seedling RNA


title: Typical meningioma NCH_q_614

tag: mib-1 labeling indices

tag: recurrence (years)

tag: location

value: Falx


title: Typical meningioma NCH_q_613

value: M

value: Olfactory groove

tag: survival (years)


title: LFYGR rep3


title: LFYGR rep2


title: WT rep4


title: WT rep2


title: Y 6816 370T

tag: cell type

tag: p53 mutation status


title: Y 6810 358T


title: Typical meningioma NCH_q_582

value: Tipic

value: Convexity


title: Failed Distal Stroma Sample 10 from an Ovary Exhibiting a Malignant Tumor


title: Failed Normal Epithelium Sample 4 from an Ovary Exhibiting a Malignant Tumor

source_name: Ovarian normal epithelium (from an ovary with a malignant tumor)

value: Ovarian normal epithelium


title: LFYGR rep1


title: Failed Normal Epithelium Sample 3 from an Ovary Exhibiting a Malignant Tumor


title: Y 6808 357T


title: Failed Adjacent Stroma Sample 23 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian stroma (from an ovary with a benign tumor)

value: Serous Cystadenofibroma


title: Y 6806 355T

value: Hapatocellular Carcinoma (HCC) Cells


title: Typical meningioma NCH_q_521

value: F

value: Grade I

value: Normal meningal tissue


title: Typical meningioma NCH_q_565


title: Y 6796 337T

value: WT p53


title: Failed Tumor Sample 17 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian tumor (from an ovary with a benign tumor)

value: Benign ovarian tumor


title: Typical meningioma NCH_q_604

value: Parasagittal


title: Typical meningioma NCH_q_837

value: Supresellar


title: Failed Tumor Sample 15 from an Ovary Exhibiting a Benign Tumor

value: Failed Sample


title: Ch9 chow

value: Ath29 congenic mice

tag: disease state

value: Resistance to atherosclerosis

tag: strain

tag: diet

value: chow


title: Anaplastic meningioma NCH_q_428

value: Anaplastic

value: Grade III

value: Falx

source_name: Normal meninge tissue


title: Failed Distal Stroma Sample 10 from an Ovary Exhibiting a Benign Tumor

tag: tissue

value: Ovarian stroma

tag: patient

tag: pathology


title: Anaplastic meningioma NCH_q_399

source_name: meningioma tissue

tag: age

value: Sphenoid wing


title: Y 6794 335T

value: Hapatocellular Carcinoma (HCC) Cells


title: Anaplastic meningioma NCH_q_362

value: F


title: Anaplastic meningioma NCH_q_434

value: M

value: Convexity


title: Failed Normal Epithelium Sample 4 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian normal epithelium (from an ovary with a benign tumor)

value: Ovarian normal epithelium

value: Serous Cystadenofibroma

tag: experimental status


title: Y 6788 332T

value: WT p53


title: Y 6792 334T


title: day 6 adults, biological rep 3

city: Cambridge

first: Matthew

last: Youngman

state: MA

address: 77 Massachusetts Ave. (68-440D)

department: Biology

institute: MIT

description: Gene expression data from a synchronized population of 6-day-old adult C. elegans grown on E. coli strain OP50 in the presence of FUDR

hyb_protocol: Samples were hybridized to GeneChip C. elegans genome microarrays at 45˚C for 16 h.

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

data_processing: Absent/present calls were generated by analyzing the data with Microarray Suite version 5 (MAS5.0).  Processed arrays were normalized and expression values output using GCRMA (Wu and Irizarry, Nature Biotechnol., 2004).

organism: Caenorhabditis elegans

source_name: C. elegans d6 adults

label_protocol: RNA was quantified and quality confirmed using an Agilent 2100 Bioanalyzer.  100 ng of total RNA was amplified and labeled using the NuGen Ovation RNA amplification v2 kit.

growth_protocol: Eggs derived from bleach-treated gravid adult C. elegans were hatched in M9 buffer and starved overnight at 20˚C to yield a developmentally synchronized population of L1 larvae. L1 larvae were then dropped to NGM (Nematode Growth Medium) plates seeded with E. coli strain OP50 and incubated at 20˚C.  After 2 days, animals had reached the L4 larval stage and were split into two groups.  RNA was prepared immediately from the first group, as described below, for hybridization to microarrays.  The second group of L4s was transferred to OP50-seeded NGM plates containing 0.05 mg/mL FUDR (to prevent hatching of eggs) by chunking.  These animals were aged at 20˚C and harvested at either day 6 or day 15 of adulthood for RNA extraction.  This protocol was performed in triplicate to produce three independent biological replicates for microarray analysis.

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

treatment_protocol: Animals were harvested by flooding NGM plates with M9 buffer, collected into a 15 mL tube and allowed to settle.  After removing most of the supernatant, animals were transferred to a cryovial and resuspended in 1 mL Trizol.  After vortexing to disrupt corpses, samples were flash frozen in liquid nitrogen and stored at -80˚ C until RNA was extracted.

value: Bristol N2

value: day 6 adult

value: whole worm


title: day 15 adults, biological rep 2

description: Gene expression data from a synchronized population of 15-day-old adult C. elegans grown on E. coli strain OP50 in the presence of FUDR

source_name: C. elegans d15 adults

value: day 15 adult


title: day 15 adults, biological rep 3


title: Anaplastic meningioma NCH_q_391

tag: sex

value: Normal meningal tissue


title: day 15 adults, biological rep 1


title: Y 6782 328T


title: Failed Normal Epithelium Sample 1 from an Ovary Exhibiting a Benign Tumor

value: Failed Sample


title: Anaplastic meningioma NCH_q_378

tag: type

value: Anaplastic

value: Grade III

value: Supresellar


title: Replicate Tumor Sample 14 from an Ovary Exhibiting a Malignant Tumor

description:
This was not included in the matrix because this cel file represented a feature (replication) of the experimental design not used in the final analysis after quality control. We provide this cel file to augment the cel files used in analysis as one sees fit.
probe_group_file:HuEx-1_0-st-v2.na31.hg19.probeset.csv
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

value: Malignant ovarian tumor

value: Papillary Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)

value: Replicate Sample


title: day 6 adults, biological rep 2


title: Y 6776 322T

value: Hapatocellular Carcinoma (HCC) Cells


title: day 6 adults, biological rep 1


title: Anaplastic meningioma NCH_q_394

value: F

value: Atipic

tag: grade

value: Grade II

value: Sphenoid wing


title: Y 6786 331T

value: WT p53


title: L4 larvae, biological rep2

description: Gene expression data from a synchronized population of L4 larval stage C. elegans grown on E. coli strain OP50

source_name: C. elegans L4 larvae

value: Bristol N2

value: whole larva


title: L4 larvae, biological rep3


title: Y 6778 325T


title: Replicate Normal Epithelium Sample 6 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian normal epithelium

value: Serous Carcinoma


title: Replicate Distal Stroma Sample 9 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian stroma

value: Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Anaplastic meningioma NCH_q_364

tag: mib-1 labeling indices

value: Falx

value: Normal meningal tissue


title: Replicate Adjacent Stroma Sample 24 from an Ovary Exhibiting a Malignant Tumor


title: Y 6772 319T


title: Replicate Adjacent Stroma Sample 24 from an Ovary Exhibiting a Benign Tumor

value: Papillary Serous Cystadenofibroma


title: Y 6774 321T


title: Replicate Tumor Sample 16 from an Ovary Exhibiting a Benign Tumor

value: Benign ovarian tumor

value: Serous Cystadenofibroma


title: Atypical meningioma NCH_q_445

tag: recurrence (years)

value: Posterior fossa


title: Y 6770 316T

value: Hapatocellular Carcinoma (HCC) Cells


title: Replicate Distal Stroma Sample 7 from an Ovary Exhibiting a Benign Tumor

value: Replicate Sample


title: Replicate Normal Epithelium Sample 4 from an Ovary Exhibiting a Benign Tumor


title: Atypical meningioma NCH_q_309

value: F

value: Atipic

value: Grade II

tag: location


title: Atypical meningioma NCH_q_353

value: Convexity

tag: survival (years)


title: Atypical meningioma NCH_q_359

value: Supresellar


title: Y 6760 308T

tag: cell type

value: WT p53


title: Y 6764 310T

tag: p53 mutation status


title: Atypical meningioma NCH_q_338

value: M


title: Atypical meningioma NCH_q_332

value: Sphenoid wing


title: Y 6758 307T


title: Y 6766 312T


title: S6-/-_24 hrs

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: replicate 1

data_processing: rank invariant normalization performed by Illumina's GenomeStudio software

source_name: Mouse Embryonic Fibroblast

label_protocol: Cy5 cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: MEFs were generated from 13.5-day-old embryos using standard methods and propagated in DMEM (Invitrogen) plus 15% FBS. MEFs were passaged a total of four times before TNF-α treatment

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) from mouse embryonic fibroblasts.  RNA was labeled with Cy5 and hybridized to whole genome mouse bead arrays (Illumina).

treatment_protocol: Cells were  treated with TNF-α (20 ng/mL) for the indicated times.

tag: genotype

value: Sirt6 -/-

tag: treatment

value: TNF-α for 24 hrs

value: MEF


title: Atypical meningioma NCH_q_409

value: Normal meningal tissue


title: S6-/-RelA-/-_24 hrs

description: replicate 1


title: S6-/-RelA-/-_0min

description: replicate 1

value: TNF-α for 0 min


title: Y 6750 302T

source_name: Hapatocellular Carcinoma (HCC) Cells


title: Y 6752 304T


title: S6-/-RelA-/-_1.5 hrs

description: replicate 1

value: TNF-α for 1.5 hrs


title: Atypical meningioma NCH_q_333


title: S6-/-RelA-/-_6 hrs

description: replicate 1

value: TNF-α for 6 hrs


title: Y 6746 205T

value: Hapatocellular Carcinoma (HCC) Cells


title: S6-/-_0min

description: replicate 1


title: S6-/-_6 hrs

description: replicate 1


title: Anaplastic meningioma NCH_q_336


title: Atypical meningioma NCH_q_355

value: Posterior fossa


title: Y 6742 202T


title: S6-/-_1.5 hrs

description: replicate 1


title: L4 larvae, biological rep1

tag: strain

value: Bristol N2

value: whole larva


title: Y 6744 204T


title: Atypical meningioma NCH_q_339

value: F

value: Atipic

value: Grade II

value: Olfactory groove


title: Atypical meningioma NCH_q_380

value: Supresellar


title: Atypical meningioma NCH_q_367

value: Parasagittal


title: Y 6740 199T

value: WT p53


title: WT_24 hrs

description: replicate 1

value: Wild type

value: TNF-α for 24 hrs


title: Y 6738 198T


title: WT_6 hrs

description: replicate 1

value: MEF


title: Atypical meningioma NCH_q_376

value: clivius

value: Normal meningal tissue


title: Adjacent Stroma Sample 29 from an Ovary Exhibiting a Malignant Tumor

description:
Partek® Genomics Suite™ derived GC-RMA, core-exon probes only
probe_group_file:HuEx-1_0-st-v2.na31.hg19.probeset.csv
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

data_processing: The matrix values provided were creating using the Partek® Genomics Suite™ implementation of GC-RMA, core-exon probes only (using only samples indicated as Experimental as opposed to Replicate or Failed).

tag: tissue

value: Ovarian stroma

value: Papillary Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)

value: Experimental Sample


title: Y 6736 182T

value: Hapatocellular Carcinoma (HCC) Cells


title: Adjacent Stroma Sample 28 from an Ovary Exhibiting a Malignant Tumor

tag: patient

value: Serous Carcinoma


title: Typical meningioma NCH_q_351

value: F


title: WT_0min

description: replicate 1

value: TNF-α for 0 min


title: Adjacent Stroma Sample 26 from an Ovary Exhibiting a Malignant Tumor

tag: pathology


title: WT_1.5 hrs

description: replicate 1

value: TNF-α for 1.5 hrs


title: Typical meningioma NCH_q_426

tag: age

value: Atipic

value: Grade II


title: Adjacent Stroma Sample 25 from an Ovary Exhibiting a Malignant Tumor

tag: experimental status


title: placenta - trisomic - female - 4

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Each hybridization mixture was made up from 1.1 µg Test (Cy3) and 1.1 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of the appropriate sample tracking control (STC, Roche Nimblegen) was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 95°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto a 12x135k Mus musculus microarray (Catalog no. 05543797001, Design 090901 MM9 EXP HX12) containing 44,170 genes with 3 probes per target gene. Microarrays were hybridized for 20 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen). Afterwards, the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0

scan_protocol: Slides were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

data_processing: Raw microarray signal data were normalised in R (www.r-project.org), using a four step approach {Baken, 2006 74 /id}: (1) natural log-transformation, (2) quantile normalisation of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate oligo spots. Normalised data for the resulting 44170 oligonucleotides were further analysed in R and Microsoft Excel.

source_name: placenta

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: To obtain Ts1Cje and wildtype fetuses for RNA isolation, female C3H/HeNHsd mice of 8-10 weeks of age were bred with male B6EiC3SnF1/J mice (control group) or male B6EiC3Sn-Ts(16C-tel)1Cje1 mice with genotype Ts/+ (Down group). After mating during the night, females were separated in the morning, at timepoint day E0.5, from the male and feasible vaginal plugs were scored.

extract_protocol: RNA was extracted from placenta and fetal liver using the miRNeasy kit (Qiagen). RNA concentrations were measured using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The integrity of the RNA samples was investigated with the BioAnalyzer (Agilent Technolgies, Amstelveen, The Netherlands) using the RNA nano 6000 kit (Agilent Technologies) yielding RIN-values ≥ 9.6.

treatment_protocol: Females were sacrificed on time point day E15.5 using CO2/O2. From pregnant mice the complete embryo strand was collected and every single embryo was processed further. Placenta and fetal liver were collected for RNA extraction and paws were collected for DNA extraction and genotyping. All tissues were immediately frozen in liquid nitrogen and stored at -80 °C until further processing.

value: placenta

source_name: common placenta reference

tag: sample type

value: reference


title: placenta - trisomic - female - 6


title: placenta - trisomic - female - 7


title: Y 6732 179T

value: WT p53


title: Adjacent Stroma Sample 24 from an Ovary Exhibiting a Malignant Tumor

source_name: Ovarian stroma (from an ovary with a malignant tumor)

value: Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Tumor Sample 20 from an Ovary Exhibiting a Malignant Tumor

source_name: Ovarian tumor (from an ovary with a malignant tumor)

value: Malignant ovarian tumor


title: Adjacent Stroma Sample 22 from an Ovary Exhibiting a Malignant Tumor


title: Adjacent Stroma Sample 23 from an Ovary Exhibiting a Malignant Tumor


title: Typical meningioma NCH_q_269

tag: sex

value: M

tag: type

value: Olfactory groove


title: Y 6720 129T


title: Typical meningioma NCH_q_435

tag: grade

tag: mib-1 labeling indices

value: Posterior fossa

value: Normal meningal tissue


title: Y 6726 169T


title: Typical meningioma NCH_q_392

tag: recurrence (years)

tag: location

value: Convexity


title: Y 6730 174T

tag: cell type

value: Hapatocellular Carcinoma (HCC) Cells


title: Typical meningioma NCH_q_390

value: Sphenoid wing

tag: survival (years)


title: Y 6724 165T

tag: p53 mutation status


title: Y 6718 127T


title: Typical meningioma NCH_q_368

value: F

value: Tipic

value: Grade I


title: Typical meningioma NCH_q_401


title: placenta - trisomic - female - 1

tag: genotype


title: placenta - trisomic - male - 5


title: placenta - trisomic - male - 2


title: Y 6882 398T

value: Mutant p53


title: placenta - trisomic - male - 4


title: placenta - trisomic - female - 2


title: placenta - trisomic - female - 3


title: Typical meningioma NCH_q_432


title: Y 6876 102T


title: placenta - trisomic - male - 3


title: Typical meningioma NCH_q_330

value: optic nerve


title: Tumor Sample 19 from an Ovary Exhibiting a Malignant Tumor

value: Serous Carcinoma

value: Experimental Sample


title: placenta - trisomic - male - 6

value: placenta

value: reference


title: Y 6712 108T

value: WT p53


title: placenta - trisomic - male - 1


title: Distal Stroma Sample 13 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian stroma


title: Tumor Sample 17 from an Ovary Exhibiting a Malignant Tumor

value: Malignant ovarian tumor


title: Tumor Sample 18 from an Ovary Exhibiting a Malignant Tumor


title: Typical meningioma NCH_q_395

value: Parasagittal


title: Y 6875 99T


title: Tumor Sample 15 from an Ovary Exhibiting a Malignant Tumor


title: Tumor Sample 14 from an Ovary Exhibiting a Malignant Tumor

value: Papillary Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Tumor Sample 16 from an Ovary Exhibiting a Malignant Tumor

value: Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Distal Stroma Sample 12 from an Ovary Exhibiting a Malignant Tumor


title: Distal Stroma Sample 11 from an Ovary Exhibiting a Malignant Tumor


title: Y 6874 97T

value: Hapatocellular Carcinoma (HCC) Cells


title: Y 6873 81T


title: Typical meningioma NCH_q_422

value: Posterior fossa

value: Normal meningal tissue


title: Typical meningioma NCH_q_377

value: F

value: Tipic


title: Typical meningioma NCH_q_360

value: Grade I


title: Y 6872 79T

value: Mutant p53


title: Typical meningioma NCH_q_388

value: M

value: Supresellar


title: Y 6862 437T


title: Y 6858 432T


title: Y 6860 436T


title: Typical meningioma NCH_q_306

value: Convexity


title: Typical meningioma NCH_q_334

value: Falx


title: Distal Stroma Sample 10 from an Ovary Exhibiting a Malignant Tumor

value: Serous Carcinoma

value: Experimental Sample


title: placenta - control - female - 4

value: placenta

value: wild type

value: reference


title: placenta - control - female - 5


title: placenta - control - female - 6


title: placenta - control - female - 1


title: placenta - control - female - 3


title: placenta - control - male - 5


title: placenta - control - female - 2


title: Y 6850 425T


title: Distal Stroma Sample 8 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian stroma


title: Distal Stroma Sample 9 from an Ovary Exhibiting a Malignant Tumor

value: Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Distal Stroma Sample 7 from an Ovary Exhibiting a Malignant Tumor

value: Papillary Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Normal Epithelium Sample 6 from an Ovary Exhibiting a Malignant Tumor

value: Ovarian normal epithelium


title: Y 6818 371T

value: Hapatocellular Carcinoma (HCC) Cells


title: Typical meningioma NCH_q_337

value: F

value: Tipic

value: Sphenoid wing

value: Normal meningal tissue


title: Typical meningioma NCH_q_350

value: Grade I


title: Typical meningioma NCH_q_357

value: M

value: Intraventricular


title: Typical meningioma NCH_q_375


title: placenta - control - male - 6


title: Y 6804 354T

value: Mutant p53


title: Y 6826 387T


title: Y 6802 353T


title: Y 6798 341T


title: Typical meningioma NCH_q_352

value: Olfactory groove


title: Typical meningioma NCH_q_349


title: placenta - control - male - 4

value: placenta


title: placenta - control - male - 3

value: wild type


title: Y 6790 333T


title: Typical meningioma NCH_q_389

value: Parasagittal


title: placenta - control - male - 2

value: reference


title: Normal Epithelium Sample 1 from an Ovary Exhibiting a Malignant Tumor

value: Not Tumorous

value: Experimental Sample


title: fetal liver - trisomic - female - 7

source_name: fetal liver

value: fetal liver

source_name: common fetal liver reference


title: Normal Epithelium Sample 3 from an Ovary Exhibiting a Malignant Tumor

source_name: Ovarian normal epithelium (from an ovary with a malignant tumor)

value: Ovarian normal epithelium

value: Serous Carcinoma


title: Normal Epithelium Sample 5 from an Ovary Exhibiting a Malignant Tumor


title: Adjacent Stroma Sample 25 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian stroma (from an ovary with a benign tumor)

value: Ovarian stroma

value: Serous Cystadenofibroma


title: Y 6780 326T

value: Hapatocellular Carcinoma (HCC) Cells


title: fetal liver - trisomic - female - 6


title: Typical meningioma NCH_q_420

value: Tipic

value: Grade I

value: Normal meningal tissue


title: Typical meningioma NCH_q_408

value: F


title: Y 6784 330T

value: Mutant p53


title: Typical meningioma NCH_q_379

value: Posterior fossa


title: Y 6768 314T


title: Normal Epithelium Sample 2 from an Ovary Exhibiting a Malignant Tumor

value: Papillary Serous Carcinoma (with Fallopian Tube Carcinoma Co-occurrence)


title: Adjacent Stroma Sample 24 from an Ovary Exhibiting a Benign Tumor

value: Papillary Serous Cystadenofibroma


title: Y 6762 309T


title: fetal liver - trisomic - female - 4

value: reference


title: Y 6756 306T


title: Adjacent Stroma Sample 22 from an Ovary Exhibiting a Benign Tumor


title: Adjacent Stroma Sample 23 from an Ovary Exhibiting a Benign Tumor


title: Typical meningioma NCH_q_343

value: Parasagittal


title: Adjacent Stroma Sample 21 from an Ovary Exhibiting a Benign Tumor

value: Experimental Sample


title: fetal liver - trisomic - female - 3

value: fetal liver


title: Y 6748 295T


title: fetal liver - trisomic - female - 1


title: Y 6734 180T


title: Typical meningioma NCH_q_431


title: Y 6728 172T


title: Typical meningioma NCH_q_335

value: Sphenoid wing


title: placenta - control - male - 1

value: placenta

value: wild type


title: fetal liver - trisomic - female - 2


title: Typical meningioma NCH_q_424


title: fetal liver - trisomic - male - 6


title: Tumor Sample 21 from an Ovary Exhibiting a Malignant Tumor

value: Malignant ovarian tumor


title: fetal liver - trisomic - male - 4


title: fetal liver - trisomic - male - 5


title: Typical meningioma NCH_q_322

value: M

value: Falx


title: Tumor Sample 19 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian tumor (from an ovary with a benign tumor)

value: Benign ovarian tumor

value: Serous Cystadenofibroma


title: Tumor Sample 18 from an Ovary Exhibiting a Benign Tumor


title: Tumor Sample 17 from an Ovary Exhibiting a Benign Tumor


title: Typical meningioma NCH_q_324

value: Tipic

value: Grade I

source_name: Normal meninge tissue

value: Normal meningal tissue


title: Y 6714 109T

value: Hapatocellular Carcinoma (HCC) Cells

value: Mutant p53


title: fetal liver - trisomic - male - 3

value: reference


title: fetal liver - trisomic - male - 2


title: Y 6710 96T


title: Typical meningioma NCH_q_261

source_name: meningioma tissue

value: F


title: Tumor Sample 16 from an Ovary Exhibiting a Benign Tumor

value: Experimental Sample


title: fetal liver - trisomic - male - 1

value: fetal liver


title: Tumor Sample 14 from an Ovary Exhibiting a Benign Tumor

value: Simple Serous Cysts


title: Adjacent Stroma Sample 20 from an Ovary Exhibiting a Benign Tumor

value: Ovarian stroma


title: Y 6708 92T


title: Distal Stroma Sample 13 from an Ovary Exhibiting a Benign Tumor

value: Simple Cyst


title: Typical meningioma NCH_q_396

value: Sphenoid wing


title: Y 6706 88T


title: Y 6704 83T


title: Distal Stroma Sample 12 from an Ovary Exhibiting a Benign Tumor

value: Papillary Serous Cystadenofibroma


title: Y 6702 35T


title: Typical meningioma NCH_q_365


title: Typical meningioma NCH_q_387

value: Falx


title: Typical meningioma NCH_q_397


title: Typical meningioma NCH_q_297

value: Supresellar


title: fetal liver - control - female - 5

value: wild type


title: fetal liver - control - female - 4


title: Typical meningioma NCH_q_304

value: Tipic

value: Posterior fossa


title: fetal liver - control - female - 2


title: Distal Stroma Sample 11 from an Ovary Exhibiting a Benign Tumor

value: Serous Cysts


title: Distal Stroma Sample 8 from an Ovary Exhibiting a Benign Tumor

value: Serous Cystadenofibroma


title: Distal Stroma Sample 9 from an Ovary Exhibiting a Benign Tumor


title: fetal liver - control - female - 6


title: Distal Stroma Sample 7 from an Ovary Exhibiting a Benign Tumor


title: fetal liver - control - female - 3


title: Distal Stroma Sample 10 from an Ovary Exhibiting a Benign Tumor


title: fetal liver - control - female - 1


title: Normal Epithelium Sample 5 from an Ovary Exhibiting a Benign Tumor

source_name: Ovarian normal epithelium (from an ovary with a benign tumor)

value: Ovarian normal epithelium

value: Not Tumorous


title: fetal liver - control - male - 5

value: reference


title: fetal liver - control - male - 6


title: Distal Stroma Sample 6 from an Ovary Exhibiting a Benign Tumor

value: Experimental Sample


title: Typical meningioma NCH_q_348

value: F

value: Grade I

value: Convexity

value: Normal meningal tissue


title: Aspergillus fumigatus in response to Artemisinin exposure (Biol rep 1)

city: Delhi

first: Santosh

middle: Kumar

last: Upadhyay

state: Delhi

address: Near Jubilee Hall, Mall Road Delhi

department: Allergy and infectious Disesases

country: India

institute: Institute of Genomics and Integrative Biology

description:
Biological replicate and Dye swap of sample 1
Gene expression profile of Aspergillus fumigatus in response to Artemisinin exposure (Biological replicate 1)

hyb_protocol: The whole-genome A. fumigatus microarray slides (version 2) were obtained from the J. Craig Venter Institute (Rockville, MD). Each of the slides was prehybridized with prehybridization buffer (5× SSC, 0.1% SDS, 1% bovine serum albumin) for 1 h at 42 °C. The slides were washed thrice with Milli-Q-purified water for 5 min, followed by 2 min of washing in isopropyl alcohol. The slides were then removed from isopropyl alcohol and immediately centrifuged at 700 rpm for 10 min at room temperature and subjected to a hybridization process.Labeled cDNAs in hybridization buffer were mixed and heated at 94 °C for 5 min before being loaded onto the array slides. The slides were covered with a 24- by 50-mm glass coverslip (Erie Scientific Company, Portsmouth, NH) and kept in hybridization chamber (Corning, St. Louis, MO) at 42 °C for 16 to 18 h to prevent evaporation (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

scan_protocol: After hybridization, the slides were processed as per the protocol of the Micromax TSA labeling kit and scanned in both the Cy3 and the Cy5 channels with a model 4200 Axon Instruments scanner with a 10-µm resolution. Each of the signals was converted into a resolution of 16 bits per pixel.

data_processing: TIFF images were analyzed using GenePix Pro 6.0 software. The signal intensity value of each spot was reduced by the local background level for each spot. Diagnosis and normalization of microarray data (DNMAD) program (http://dnmad.bioinfo.cnio.es/) was used for print-tip loess normalization of microarray data . M-values obtained from this program were converted to fold modulation. Genes having less than 3 spots in 2 dye swap slides were discarded and only those having their all fold change values (from 3 or 4 replicates in 2 slides; as each target has been spotted twice in each slide) within a coefficient of variation ± 0.5 were used for analysis. Gene expression ratios of ≥2 (fold upregulation or downregulation) in both replicates (dye swap) were considered to be differentially expressed genes.

organism: Aspergillus fumigatus

source_name: Aspergillus fumigatus treated with Artemisinin

label_protocol: Total RNA (7 µg) from A. fumigatus treated with solvent control or artemisinin was reverse transcribed separately using fluorescein-labeled dCTP or biotin-labeled dCTP from Micromax TSA labeling kits (Perkin Elmer, Wellesley, MA). Labeled cDNA was purified by isopropanol precipitation per the protocol of the Micromax TSA labeling kit. Each of the purified labeled cDNAs was dissolved in 20 μl of hybridization buffer (50% formamide, 5× sodium citrate-sodium chloride [SSC; 1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% SDS, and 300 μg salmon sperm DNA. A dye swap experiment with two biological replicates was performed to ensure the reproducibility of each gene expression pattern

growth_protocol: A. fumigatus strain Af293 culture was maintained on Sabouraud dextrose agar (SDA) (4.7 g/liter; Himedia, Mumbai, India) slants. Spores were harvested from A. fumigatus culture (after 72 h) growing on SDA by using phosphate buffer saline (PBS) with 0.05% Tween 20 (PBST), centrifuged at 10,000 rpm for 10 min at 4 °C, and washed with PBS twice. Conidia were then allowed to swell in PBS containing Ca2+ and Mg2+ for 1 h, followed by a viability count (numbers of CFU/ml) on SDA plates by a hemocytometer.

extract_protocol: DNA-free total RNA was isolated from A. fumigatus by using RNeasy plant minikits (Qiagen, GmbH, Hilden, Germany). Fungal pellets stored at -70 degree C were crushed using a mortar and pestle separately in the presence of liquid nitrogen. The cell powder was resuspended in 2 ml of RLT lysis buffer provided with the RNeasy plant mini kit and centrifuged at 10,000 rpm for 2 min, followed by further steps for isolation of total RNA, including treatment with RNase-free DNase, as described in the kit protocol. Gel electrophoresis of total RNA revealed intact 28S and 18S ribosomal bands and no genomic DNA contamination. RNA concentration was determined spectrophotometrically by measuring absorption at 260 nm with a Lambda Bio 20 UV–visible-light spectrophotometer (Perkin Elmer, Wellesley, MA)

treatment_protocol: The fungal spores were cultured for 48 h (log phase) and then treated with solvent control or artemisinin for 3 h. The fungal culture thus analyzed was homogenous containing mycelia. Culture flasks containing 100 ml of RPMI 1640 medium (with L-glutamine and sodium bicarbonate) (Sigma, St. Louis, MO) were inoculated with A. fumigatus spores (1 × 106/ml), and incubated at 37 °C for 48 h. Solvent control (DMSO) or artemisinin MIC50 amount was added to separate flasks and incubated at 37 °C for 3 h. A. fumigatus was scraped from the culture flasks and pelleted at 4 °C by centrifugation at 18,000 rpm for 10 min.

tag: strain

tag: treatment

value: Culture flasks containing 100 ml of RPMI 1640 medium (with L-glutamine and sodium bicarbonate) (Sigma, St. Louis, MO) were inoculated with A. fumigatus spores (1 × 106/ml), and incubated at 37 °C for 48 h. After this Artemisinin (MIC50 amount) was added and incubated at 37 °C for 3 h. A. fumigatus was scraped from the culture flasks and pelleted at 4 °C by centrifugation at 18,000 rpm for 10 min. Total RNA (7 µg) from this sample was reverse transcribed using biotin-labeled dCTP from Micromax TSA labeling kits (Perkin Elmer, Wellesley, MA). Labeled cDNA was purified by isopropanol precipitation per the protocol of the Micromax TSA labeling kit.

source_name: Aspergillus fumigatus treated with DMSO

value: Culture flasks containing 100 ml of RPMI 1640 medium (with L-glutamine and sodium bicarbonate) (Sigma, St. Louis, MO) were inoculated with A. fumigatus spores (1 × 106/ml), and incubated at 37 °C for 48 h. After that DMSO (an equivalent volume, as used to dissolve the MIC50 amount of Artemisinin) was added and incubated at 37 °C for 3 h. A. fumigatus was scraped from the culture flasks and pelleted at 4 °C by centrifugation at 18,000 rpm for 10 min. Total RNA (7 µg) from this sample was reverse transcribed using florescin-labeled dCTP from Micromax TSA labeling kits (Perkin Elmer, Wellesley, MA). Labeled cDNA was purified by isopropanol precipitation per the protocol of the Micromax TSA labeling kit.


title: Normal Epithelium Sample 4 from an Ovary Exhibiting a Benign Tumor

tag: tissue

tag: patient


title: fetal liver - control - male - 4

value: fetal liver


title: fetal liver - control - male - 2


title: fetal liver - control - male - 3


title: p19Arf-null Hepatocyte-3

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

description: p19Arf-null hepatocytes are proliferative homogenous epithelial cells

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data was normalized by Quantile.

source_name: Primary hepatocyte isolated from p19Arf-null mouse

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: For TTF and MEF, cells are cultured in DMEM with 10% FBS. For iHep and hepatocytes, cells are cultured in modified Block's medium.

extract_protocol: Total RNA was isolated from cells by Trizol (Invitrogen) following manufacturer's introductions.

treatment_protocol: For iHep cell induction, p19Arf-null TTFs were infected with lentiviruses expressing 3 liver enriched transcription factors.

value: primary hepatocytes

tag: days

value: cultured for 21 days after isolation


title: p19Arf-null Hepatocyte-4


title: Normal Epithelium Sample 2 from an Ovary Exhibiting a Benign Tumor

tag: pathology

tag: experimental status


title: Aspergillus fumigatus in response to Artemisinin exposure (Biol rep 2; also dye swap for sample 1)

description:
Biological replicate and dye swap of sample 2
Gene expression profile of Aspergillus fumigatus in response to Artemisinin exposure (Biological replicate 2; also serves as dye swap experiment for sample 1)

value: Culture flasks containing 100 ml of RPMI 1640 medium (with L-glutamine and sodium bicarbonate) (Sigma, St. Louis, MO) were inoculated with A. fumigatus spores (1 × 106/ml), and incubated at 37 °C for 48 h. After that DMSO (an equivalent volume, as used to dissolve the MIC50 amount of Artemisinin) was added and incubated at 37 °C for 3 h. A. fumigatus was scraped from the culture flasks and pelleted at 4 °C by centrifugation at 18,000 rpm for 10 min. Total RNA (7 µg) from this sample was reverse transcribed using biotin-labeled dCTP from Micromax TSA labeling kits (Perkin Elmer, Wellesley, MA). Labeled cDNA was purified by isopropanol precipitation per the protocol of the Micromax TSA labeling kit.

value: Culture flasks containing 100 ml of RPMI 1640 medium (with L-glutamine and sodium bicarbonate) (Sigma, St. Louis, MO) were inoculated with A. fumigatus spores (1 × 106/ml), and incubated at 37 °C for 48 h. After this Artemisinin (MIC50 amount) was added and incubated at 37 °C for 3 h. A. fumigatus was scraped from the culture flasks and pelleted at 4 °C by centrifugation at 18,000 rpm for 10 min. Total RNA (7 µg) from this sample was reverse transcribed to incorporate florescin-labeled dCTP from Micromax TSA labeling kits (Perkin Elmer, Wellesley, MA). Labeled cDNA was purified by isopropanol precipitation per the protocol of the Micromax TSA labeling kit.


title: Normal Epithelium Sample 3 from an Ovary Exhibiting a Benign Tumor


title: fetal liver - control - male - 1

value: wild type

tag: sample type


title: p19Arf-null Hepatocyte-2


title: p19Arf-null Hepatocyte-1


title: iHep-4

description: iHep single colony shows homogenous epithelial cells

source_name: iHep single colony generated from 3TF transduced p19Arf-null TTF

value: induced hepatocyte (iHep)

tag: protocol

value: cultured for 21 days after induction


title: P3446 10-0

source_name: Hapatocellular Carcinoma (HCC) Cell Lines

value: Hapatocellular Carcinoma (HCC) Cells

tag: cell line

value: SNU-475 Cell Line

value: Mutant p53


title: iHep-3

value: generated from 3TF transduced p19Arf-null TTF


title: P3445 9-0

value: SNU-449 Cell Line


title: P3444 8-0

value: SNU-423 Cell Line


title: iHep-2


title: iHep-1


title: P3443 7-0

value: SNU-387 Cell Line


title: p19Arf-null TTF + 3TF

description: 3TFs tranduced p19Arf-null TTFs generated a mixture of fibroblasts and epithelial cells after 21 days induction

source_name: 3TF transduced p19Arf-null TTF

value: TTF

value: 3TF transduced

value: cultured for 21 days after transfection


title: P3442 6-0

value: PLC/PRF/5 Cell Line


title: p19Arf-null TTF-3

description: p19Arf-null TTFs are flat and elongated cells

source_name: p19Arf-null tail-tip fibroblast

value: cultured for 42 days after isolation


title: Self-Self

type: genomic

city: Buffalo

first: Omer

last: Gokcumen

state: New York

address: 109 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

description: no additional information

hyb_protocol: Test individual DNAs were labeled with Cy5 and co-hybridized with Cy3-labeled DNA from the reference individual (R354) using manufacturer's protocols.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Macaca mulatta

source_name: Blood Whole Genome Extraction - NEPC

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Roughly 6 mL of venous blood was collected in EDTA-Vacutainer tubes during routine physicals in which blood testing was already ongoing. Genomic DNA was then isolated and purified using Flexigene kits (Qiagen, Valencia, CA) following standard manufacturer’s protocol.

value: Blood

tag: subject


title: Mac15

description: no additional information


title: Mac16

description: no additional information


title: RelA_RelA-/-_30min

hyb_protocol: 12 μg of Cy5-labeled ChIP sample and 6 μg of Cy-3 labeled total sample were mixed, dried and resuspended in 40 μL of buffer including hybridization buffer (Nimblegen), alignment oligonucleotides (Nimblegen) and Component A (Nimblegen). The labeled DNA samples were next denatured and hybridized to “MM8” arrays overnight at 42°C. Samples were co-hybridized with input DNA as a reference.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NIMBLESCAN 3.0 extraction software (Nimblegen). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. To normalize across samples, the biweight mean of this log2 ratio was subtracted from each point. ChIP-chip time courses were done twice or more for most time points; representative data from single time courses are shown.

source_name: RelAChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes

label_protocol: Each DNA sample (1 μg) was denatured in the presence of Cy5- or Cy3-labeled randon nonamers and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix (6 mM each in TE buffer) for 2 hours at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8), precipitated with isopropanol, and resuspended in water.

extract_protocol: MEF’s were treated with TNF-α (20 ng/ml) for the indicated times. DNA was cross-linked for 10 minutes with 1% formaldehyde and stopped in 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. Purified chromatin was sonicated to ~500 bp using the Bioruptor (Diagenode, Inc). The lysate was then centrifuged to remove cell debris, diluted 1:2 in IP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.0), precleared for 15 minutes with 10 ml  StaphA beads, and incubated overnight with 5 mg of either anti-Sirt6 (Abcam, ab62739),  RelA (Abcam, ab7971) or Rabbit IgG. After incubation with 10 ml  StaphA beads for 15 minutes at 4C, the immune complexes were collected by centrifugation and washed 2x with Dialysis Buffer (2 mM EDTA, 50 mM Tris-Cl pH 8.0, 0.2% Sarkosyl) and 3x with IP wash buffer (100 mM Tris-Cl pH 9.0, 500 mM LiCl, 1% NP40, 0.1% Deoxycholic Acid). The protein-DNA complexes were eluted from the beads in 100 µl elution buffer (1% SDS, 50 mM NaHCO3) for 15 minutes followed reverse cross-linking by addition of 5M NaCl and incubating overnight at 65C, followed by 100mg/mL RNAseA digestion. DNA was purified with the Ziagen Mini-elute Reaction Cleanup Kit and amplified using the Whole Genome Amplification kit (Sigma) as described by the manufacturer.

treatment_protocol: 30 minutes TNF-alpha

value: RelA-/-

value: Mouse Embryonic Fibroblast

value: TNF-α for 30 mins

source_name: Input DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes


title: P3441 5-0

value: Huh7 Cell Line


title: p19Arf-null TTF-2


title: Mac12

description: no additional information


title: Mac11

description: no additional information


title: P3440 4-0

value: Hapatocellular Carcinoma (HCC) Cells

value: Hep3B Cell Line


title: RelA_WT_15min

source_name: RelAChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes

treatment_protocol: 15 minutes TNF-alpa

value: Wild type

value: TNF-α for 15 mins

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes


title: p19Arf-null TTF-1


title: p19Arf-null MEF

description: p19Arf-null MEFs are flat and elongated cells

source_name: p19Arf-null MEF

value: MEF


title: P3439 3-0

value: C3A Cell Line

value: WT p53


title: RelA_RelA-/-_15min

source_name: RelAChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes

source_name: Input DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes


title: RelA_WT_0min

source_name: RelAChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes

treatment_protocol: 0 minutes

value: TNF-α for 0 min

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes


title: RelA_WT_30min

source_name: RelAChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes


title: Mac9

description: no additional information


title: Sirt6_RelA-/-_30min

source_name: Sirt6ChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes


title: Sirt6_RelA-/-_15min

source_name: Sirt6ChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes


title: Mac14

description: no additional information


title: Sirt6_RelA-/-_60min

source_name: Sirt6ChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 60 minutes

treatment_protocol: 60 minutes TNF alpha

value: TNF-α for 60 mins

source_name: Input DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 60 minutes


title: P3438 2-0

source_name: Hapatocellular Carcinoma (HCC) Cell Lines

value: HepG2 Cell Line


title: Healthy Donor 1

status: Public on May 10 2011

last: gao

address: 138, Yi xue yuan Road

department: Shanghai Medical School

institute: Fudan University

description: Healthy non infected donor 1

hyb_protocol: Cy3-labelled RNAs were heat at 100 °C for 5 minutes in a reaction volume containing 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer  following the manufacturers instructions.  Samples were transfer to ice water baths for 5 min after and then hybridized to Agilent-021827 Human miRNA Microarray (V3) (miRBase release 12.0 miRNA ID version) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray slides were scanned by using the XDR Scan (PMT100, PMT5).(Scan Area  61 x 21.6 mm  ; Scan resolution 5 um; Single pass; eXtended Dynamic range selected ; Green Dye channel ; Green PMT XDR Hi 100% , XDR Lo 5% )

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol miRNA-v1_95_May07) to obtain background subtracted and spatially detrended Processed Signal intensities.  The signal (after background subtraction) was exported directly into the GeneSpring GX9.0 software (Agilent Technologies) for quantile normalization.

source_name: peripheral blood mononuclear cells

label_protocol: 100 ng total RNA (50 ng /ul )were first treat with phosohatase (TakaRa p/n 2250A)at 37 ºC for 30 min .After adding DMSO(Sigma p/n D8418) , samples were heat at 100 ºC for 5-10 min and incubate in ice immediately .Assemble labeling reaction with pCp-Cy3 were then performed by using T4 RNA Ligase at 16ºC for 2h. labeled RNA were then purified by using the Micro Bio spin 6 columns(Bio-Rad p/n 732-6221).

extract_protocol: Total RNA was extracted using the miR VanaTM miRNA isolation kit (Ambion Inc .Austin, Tx) according to the manufacturer’s instructions. RNA quantity and quality was assessed using the Nanodrop 2000 (Thermo Fisher Scientific, Mass) and Agilent 2100 bioanalyzer systems (Agilent Technologies). Samples with a RNA Integrity Number above 7 were used in the study.

treatment_protocol: Peripheral venous blood (10 mL) was drawn from each subject and PBMCs were isolated on Ficoll gradients (GE Health Care, Little Chalfont, U.K); PBMCs were immediately mixed with the miR VanaTM miRNA isolation kit Lysis Buffer (Ambion Inc .Austin, Tx) and frozen at −80°C until RNA was extracted.

tag: disease state

value: Healthy non infected

tag: individual

value: donor 1

value: Peripheral venous blood

value: peripheral blood mononuclear cells

tag: gender

value: Female

tag: age


title: Latent TB 5

description: Latent tuberculosis infection donor  5

value: Latent tuberculosis infection

value: donor  5

tag: cell type

value: Male


title: Latent TB 6

description: Latent tuberculosis infection donor  6

value: donor  6


title: SC5314 cells treated by 10b  vs control SC5314 cells (2)

first: Liang

last: Rong-mei

address: Guohe road 325

institute: smmu

description: compare gene expression profiles of   SC5314  yeast form cells treated by 10b with control SC5314 yeast form cells.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. Two hybridizations were performed by using a reversal fluorescent strategy in one test and control and the other  hybridization without performing reversal fluorescent. The geometric mean  of lowess normalized log2 ratio (test/control) for the two independent experiments was calculated.

organism: Candida albicans

source_name: Yeast form cells treated by 10b

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Candida albicans SC5314 cells were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose).

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: SC5314 cells were cultured to 0.4 - 1.0×106 cells/ml in YPD, then divided into two parts: one was exposed to 10b (10 μM) whereas the other was the control and grown an additional 5–9 h until reaching 0.4 - 1.0×107 cells/ml, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

tag: system

tag: agent

source_name: Control yeast cells

value: untreated


title: SC5314 cells treated by 10b  vs control SC5314 cells (1)


title: Latent TB 4

description: Latent tuberculosis infection donor  4

value: donor  4


title: Healthy Donor 3

description: Healthy non infected donor 3

value: donor 3


title: Latent TB 3

description: Latent tuberculosis infection donor  3

value: donor  3


title: Sirt6_RelA-/-_0min

source_name: Sirt6ChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes

tag: genotype

value: Mouse Embryonic Fibroblast

tag: treatment

source_name: Input DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes


title: Mac6

description: no additional information

source_name: Blood Whole Genome Extraction - NEPC

tag: tissue

value: Blood


title: Mac4

description: no additional information


title: Mac13

description: no additional information


title: Mac8

description: no additional information


title: Mac10

description: no additional information


title: Active TB 6

description: Activr pulmonary tuberculosis patient 6

value: Active pulmonary tuberculosis

value: patient 6


title: Active TB 5

description: Activr pulmonary tuberculosis patient 5

value: patient 5


title: Active TB 4

description: Activr pulmonary tuberculosis patient 4

value: patient 4


title: Active TB 3

description: Activr pulmonary tuberculosis patient 3

value: patient 3

value: Peripheral venous blood


title: Healthy Donor 2

description: Healthy non infected donor 2

value: Healthy non infected

value: donor 2

value: peripheral blood mononuclear cells

value: Female


title: Active TB 1

description: Activr pulmonary tuberculosis patient 1

value: patient 1


title: BA02_heart_active_N03-152

first: Haifang

last: Wang

address: 320 yueyang road

department: CAS-MPG Partner institute for Computational Biology

institute: Shanghai institute for biology science

description: heart tissue from summer active black bear

hyb_protocol: The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Ursus americanus

source_name: heart, summer active

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

tag: tissue type

value: heart

value: male


title: BA02_heart_active_N04-104_rep2


title: Latent TB 1

description: Latent tuberculosis infection donor  1

value: Latent tuberculosis infection

value: donor  1


title: BA02_heart_active_N05-132_rep2


title: BA02_heart_active_N04-104


title: RelA_RelA-/-_0min

source_name: RelAChIP DNA from RelA-/- Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes

value: RelA-/-

value: Mouse Embryonic Fibroblast

value: TNF-α for 0 min


title: Mac7

description: no additional information

value: Blood


title: BA02_heart_hibernating_N07-027

description: heart tissue from hibernating black bear

source_name: heart, hibernating


title: Mac5

description: no additional information


title: BA02_heart_active_N04-113


title: BA02_heart_hibernating_N4-047


title: BA02_heart_active_N05-131


title: BA02_heart_hibernating_N05-035


title: BA02_heart_hibernating_N03-056


title: Active TB 2

description: Activr pulmonary tuberculosis patient 2

value: Active pulmonary tuberculosis

value: patient 2

value: Male


title: BA02_heart_active_N05-132


title: Mac3

description: no additional information


title: BA02_liver_hibernating_N07-027

description: liver tissue from hibernating black bear

source_name: liver, hibernating

value: liver


title: BA02_liver_hibernating_N07-027_rep2


title: BA02_liver_hibernating_N06-030


title: BA02_heart_hibernating_N05-034


title: Sirt6_WT_30min

source_name: Sirt6 ChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 30 minutes

value: Wild type

value: TNF-α for 30 mins


title: Sirt6_WT_60min

source_name: Sirt6 ChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 60 minutes

value: TNF-α for 60 mins

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 60minutes


title: Mac1

description: no additional information


title: BA02_liver_hibernating_N04-047


title: BA02_liver_active_N05-132

description: liver tissue from summer active black bear

source_name: liver, summer active


title: BA02_liver_hibernating_N05-035

source_name: liver,hibernating


title: BA02_liver_hibernating_N05-034


title: BA02_liver_hibernating_N03-056


title: BA02_liver_active_N04-113


title: Sirt6_WT_15min

source_name: Sirt6 ChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes

value: TNF-α for 15 mins

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 15 minutes


title: Mac2

description: no additional information


title: Sirt6_WT_0min

source_name: Sirt6 ChIP DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes

source_name: Input DNA from wildtype Mouse Embryonic Fibroblast cells treated with TNF-alpha for 0 minutes


title: BA02_liver_active_N03-152


title: Latent TB 2

description: Latent tuberculosis infection donor  2

source_name: peripheral blood mononuclear cells

value: donor  2

value: Peripheral venous blood

value: peripheral blood mononuclear cells


title: BA02_liver_active_N04-104

value: male


title: HKI-120-other

city: Helsinki

first: Taru

middle: A

last: Muranen

address: Haartmaninkatu

department: Department of Obstetrics and Gynecology

country: Finland

institute: Helsinki University Central Hospital

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

scan_protocol: Arrays were scanned with Agilent Microarray Scanner (Agilent Technologies) and quality controlled using the GenePix 4.1.1.4 software (Axon instruments)

data_processing: Background correction was done with the normexp method recommended by [PMID: 17720982]. Data was normalized first within arrays with the print-tip loess method and subsequently between arrays with the quantile method. Measurements of replicate reporters were averaged.

source_name: breast tumor tissue

label_protocol: Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6.

extract_protocol: Sections of frozen tumor tissues (roughly 10 – 100 mg) were submerged in liquid nitrogen and homogenized using a mechanical homogenizer, after which the tissue powder was dissolved in 4 ml of TrizolTM. The RNA was then separated into an aqueous phase by adding 800 ml of chloroform followed by centrifugation at 12,000 g at four degrees centigrade for 15 min. Subsequent RNA extraction and purification was performed using the Qiagen RNeasy RNA purification kit (Qiagen Inc., CA, USA).

tag: chek2 1100delc mutation status

value: other

tag: er status (1=positive, o=negative)

tag: family history of breast cancer (1=familial case, 0=sporadic case)

tag: histological subtype

value: ductal

tag: nqo1 rs1800566 genotype

value: CC

source_name: Universal Human RNA

value: reference


title: HKI-119-other

value: lobular

tag: sample type


title: HKI-118-other

tag: disease state


title: NTD spina 1

city: Beijing

first: Liuyan

last: Zhang

address: 4A Dutun Rd., Chaoyang District

institute: Institute of Psychology, Chinese Academy of Sciences

description: A chip was employed for each total RNA sample derived from a pool of spinal cord tissue from fetuses whose mother had been either treated or not treated with RA.

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 mL hybridization solution (3×SSC, 0.2% SDS, 25% formamide, and 5×Denhart’s). DNA was denatured at 95 °C for 3 min prior loading on a microarray, and hybridized 16 h at 42 °C, then washed with 0.2% SDS, 2× SSC at 42 °C for 5 min and 0.2% SSC for 5 min at room temperature.

scan_protocol: A LuxScan 10KA Scanner (Capital Bio) was used to scan arrays, and images were analyzed with LuxScan 3.0 software (Capital Bio).

data_processing: The median average intensity of foreground and background was extracted from the .LSR files. If a spot intensity was zero or negative after background subtraction, it was set at half of the minimum positive corrected intensities in the array. We performed normalization using the spike probes that were previously shown to have a consistent log-ratio. Then, linear model and empirical Bayes smoothing analyses were combined to obtain the statistics value and fold change of each spot. Significant candidates were selected with values of fold change >1.5, which means genes with at least a 1.5-fold change in expression as compared to control samples were considered significant.

source_name: Spinal cord from day 18 fetuses obtained from mothers treated with RA

label_protocol: An aliquot of 5 ug total RNA was used to produce fluorescent dye-labeled cDNA with the Eberwine’s linear RNA amplification method and subsequent enzymatic reactions according to previously published protocols (Guo et al., 2005; Patterson et al., 2006). The labeled DNA was purified with PCR Clean-up NucleoSpin kits (Macherey Nagel, Duren, Germany), re-suspended in Elution buffer, and quantified by UV spectrophotometry. Two samples (NTD and normal control) were labeled with different fluorophores (Cy3 and Cy5 dyes) and hybridized together on a single microarray.

growth_protocol: Male and female C57BL/6J mice (8 weeks of age) were housed in a temperature-controlled (23 ± 2°C) and humidity-controlled (50 ± 5%) animal facility. The mice were maintained on a 12-h light/dark cycle with access to food and water ad libitum.

extract_protocol: The total RNA was isolated using TRIZOL (Invitrogen, Gaithersburg, MD, USA) and purified with the NucleoSpin RNA clean-up kit (Macherey-negel, Germany), according to the manufacturer’s protocol. The quality and concentration of total RNA was assessed using a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and A260, respectively.

treatment_protocol: The female mice were mated at 8 weeks from 9:00 - 11:00 A.M. and the experimenter checked the plugged females at 2:00 P.M. Animals with vaginal plugs were considered to be at 0 days and 0 h (0 d, 0 h) of pregnancy (0 dpc). Pregnant mice were gavage-fed three successive doses of all-trans retinoic acid (RA, 20 mg/kg/dose) suspended in olive oil on day 8 of gestation at 6, 12 and 18 h. Groups of treated and control mice were allowed to survive to day 18 of pregnancy. At the time their uteri were excised, the number of live fetuses with opened or closed neural tubes, as well as the number of dead fetuses, was determined under a dissecting microscope. Embryos were staged by somite number. For the gene expression studies, the spinal cords of 20 fetuses from 11 litters with spina bifida induced by maternal RA treatment were specifically removed. Tissues from 20 normal fetuses, from 5 vehicle-treated litters, were used as controls.

tag: strain

value: spinal cord

tag: developmental stage

value: day 18 fetus

value: maternal retinoic acid (RA) treatment

source_name: Spinal cord from day 18 fetuses obtained from mothers treated with olive oil vehicle

value: maternal olive oil treatment

value: control


title: NTD spina 3


title: HKI-112-other


title: BA02_liver_active_N05-131

value: liver

tag: gender


title: HKI-116-CHEK2