title: Differentially expressed genes by knocking down of MMP14-1 in EBC-1

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

source_name: si-MMP14-1 transfected cell line


title: 549618A08 - SXB49_87 vs SXB49_86

status: Public on Jul 04 2017

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: The objective is to better understand the adaptive response of the wheat plant to an elevated mean temperature. Besides the morphological and ecophysiological responses, the changes in the expression of genes are investigated. Two genotypes (SxB49 and SxB139) are subjected to two different temperature regimes during the lag-phase of the developing grains. The profiling of the accumulation of gene transcripts throughout 12 developmental stages is carried out using a custom-designed 12x135K Roche NimbleGen gene expression microarray comprising the most recent NCBI wheat contig assembly and annotation (about 45 000 unigenes). This should permit both the identification of differentially expressed genes after heat treatment and the comparison of the behaviours of two wheat genotypes (SxB139 and SxB49).

hyb_protocol: SXB49_86 Cy5 / SXB49_87 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Triticum aestivum

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: seed - Plants were grown under semi-controlled conditions in containers 2m2 and 0.5 m deep each, covered by transparent enclosures under natural light. Water was daily supplied but the water statute of the plants was not measured. The mean temperature of one container was set at 19°C and corresponded to the control samples. The mean temperature of a second container was set at 27°C and corresponded to the heat-treated samples. The elevated temperature was applied at Anthesis and lasted for 15 days after anthesis (15DAA), then it was lowered back to 19°C as for the control samples. To obtain a mean temperature of 19 °C on a daily basis, the temperature of the container was set at 21°C between 6am30 and 10pm30 and 15°C otherwise. To obtain a mean temperature of 27°C during the lag-phase, the containers were maintained at 29°C from 6am30 to 10pm30 and 23°C for the rest.

treatment_protocol: Name:Heat-treated - environmental treatment - temperature,temperature:time 250day . 250°Cd, see Table “RNA extracted”

tag: triticum aestivum (serix babax rils)  -  dev.stage (boyes et al. plant cell 2001)

treatment_protocol: no treatment


title: 549618A02 - SXB49_80 vs SXB49_77

hyb_protocol: SXB49_77 Cy5 / SXB49_80 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Differentially expressed genes by knocking down of MYO1B-2 in SAS

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

organism: Homo sapiens

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

value: SAS

tag: cell type

value: oral squamous cell carcinoma

tag: transfection

value: no transfection

source_name: si-MYO1B-2 transfected cell line


title: 549616A09 - SXB139_65 vs SXB139_68

hyb_protocol: SXB139_68 Cy5 / SXB139_65 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549618A05 - SXB49_85 vs SXB49_88

hyb_protocol: SXB49_88 Cy5 / SXB49_85 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP37degree-4

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

description:
Genotypes of spore of Spo11 enriched DNA
KZIP37-4

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°.

scan_protocol: We acquired the microarray images with a GenePix 4000B scanner and analyzed the images with the GenePix Pro 6.0 software

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: cell culture of strain KZ5, Spo11 enriched

label_protocol: The Spo11p-enriched DNA was then PCR amplified and the PCR products were labeled with Cy5-dUTP using Invitrogen Bioprime Array CGH Genome Labeling Module using the kit protocol. Non-enriched genomic DNA that had been amplified was labeled with Cy3-dUTP and was used as a control for the CGH microarrays (Agilent custom ChIP-on-Chip 8x15k array G4499A).

growth_protocol: To induce Spo11-catalyzed DSBs, strain KZ5 cells collected from 5 mL YPD were cultured in 200 mL pre-sporulation medium at 30ºC for 16 h and all the cells were transferred into 200 mL sporulation medium at 14ºC (48 h), 30ºC (24 h) and 37ºC (24 h), respectively.

extract_protocol: Genomic DNA from KZ5 cells was isolated from meiotic and pre-meiotic cells (from pre-sporulation medium) by using a method described by Mieczkowski et al. (2006, Mol Cell Biol).

treatment_protocol: Yeast cells were collected after culture in sporulation medium for 24-48 hours.

tag: strain

tag: temperature

tag: sample type

value: Spo11 enriched DNA

source_name: cell culture of strain KZ5, Non-Spo11 enriched

value: Non-Spo11 enriched


title: 549616A04 - SXB139_51 vs SXB139_50

hyb_protocol: SXB139_50 Cy5 / SXB139_51 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A10 - SXB139_68 vs SXB139_65

hyb_protocol: SXB139_65 Cy5 / SXB139_68 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A11 - SXB139_90 vs SXB139_91

hyb_protocol: SXB139_91 Cy5 / SXB139_90 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A06 - SXB139_84 vs SXB139_81

hyb_protocol: SXB139_81 Cy5 / SXB139_84 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A02 - SXB139_52 vs SXB139_49

hyb_protocol: SXB139_49 Cy5 / SXB139_52 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A03 - SXB139_50 vs SXB139_51

hyb_protocol: SXB139_51 Cy5 / SXB139_50 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A09 - SXB139_92 vs SXB139_89

hyb_protocol: SXB139_89 Cy5 / SXB139_92 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A01 - SXB139_49 vs SXB139_52

hyb_protocol: SXB139_52 Cy5 / SXB139_49 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A04 - SXB139_75 vs SXB139_74

hyb_protocol: SXB139_74 Cy5 / SXB139_75 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A07 - SXB139_82 vs SXB139_83

hyb_protocol: SXB139_83 Cy5 / SXB139_82 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A10 - SXB139_89 vs SXB139_92

hyb_protocol: SXB139_92 Cy5 / SXB139_89 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A03 - SXB139_74 vs SXB139_75

hyb_protocol: SXB139_75 Cy5 / SXB139_74 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A08 - SXB139_83 vs SXB139_82

hyb_protocol: SXB139_82 Cy5 / SXB139_83 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549537A12 - SXB139_91 vs SXB139_90

hyb_protocol: SXB139_90 Cy5 / SXB139_91 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP30degree-4

description:
Genotypes of spore of Spo11 enriched DNA
KZIP30-4


title: KZIP37degree-1

description:
Genotypes of spore of Spo11 enriched DNA
KZIP37-1


title: 549537A05 - SXB139_81 vs SXB139_84

hyb_protocol: SXB139_84 Cy5 / SXB139_81 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP30degree-3

description:
Genotypes of spore of Spo11 enriched DNA
KZIP30-3


title: KZIP37degree-2

description:
Genotypes of spore of Spo11 enriched DNA
KZIP37-2


title: KZIP37degree-3

description:
Genotypes of spore of Spo11 enriched DNA
KZIP37-3


title: 549537A01 - SXB139_73 vs SXB139_76

hyb_protocol: SXB139_76 Cy5 / SXB139_73 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP30degree-1

description:
Genotypes of spore of Spo11 enriched DNA
KZIP30-1

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°.


title: 549537A02 - SXB139_76 vs SXB139_73

hyb_protocol: SXB139_73 Cy5 / SXB139_76 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A11 - SXB139_42 vs SXB139_43

hyb_protocol: SXB139_43 Cy5 / SXB139_42 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP30degree-2

description:
Genotypes of spore of Spo11 enriched DNA
KZIP30-2


title: 549418A12 - SXB139_43 vs SXB139_42

hyb_protocol: SXB139_42 Cy5 / SXB139_43 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A10 - SXB139_44 vs SXB139_41

hyb_protocol: SXB139_41 Cy5 / SXB139_44 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A09 - SXB139_41 vs SXB139_44

hyb_protocol: SXB139_44 Cy5 / SXB139_41 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: KZIP14degree-1

description:
Genotypes of spore of Spo11 enriched DNA
KZIP14-1


title: KZIP14degree-2

description:
Genotypes of spore of Spo11 enriched DNA
KZIP14-2


title: PDX MAP-IC-A23-NB-1 H3K27ac, ChIP-seq

status: Public on Jul 01 2017

type: SRA

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

library_source: genomic

data_processing:
ChIP-seq: Alignment with Bowtie2, default options
ChIP-seq: Quality filtering: Q > 20; duplicates kept
ChIP-seq: Peak calling with HMCan v1.30
ChIP-seq: Renormalization of wig profiles among all H3K27ac samples with an in-house R script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to renormalized signal; score in .bed files correspond to the likelihood of a region to be enriched in H3K27ac or to be a binding site of a TF
RNA-seq:TopHat2 v2.0.643 with the following parameters: global alignment, no mismatch in the 22 bp seed, up to three mismatches in the read, library type fr-firststrand
Genome_build: hg19/GRCh37

source_name: PDX MAP-IC-A23-NB-1

growth_protocol:
ChIP-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).
RNA-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).

extract_protocol:
ChIP-seq: Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones or transcription factors according to the supplier's protocol (Diagenode )
ChIP-seq: llumina sequencing libraries were prepared from ChIP and input DNAs using the TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, DNA were subjected to consecutive steps of end-repair, dA-tailing and ligation to TruSeq indexed Illumina adapters. Size-selection was performed only for the H3K27ac ChIP (100 – 600 bp). After a final amplification step, the resulting DNA libraries were quantified using a qPCR method (KAPA library quantification kit) and sequenced on the Illumina HiSeq2500 instrument (rapid run mode; single reads 100 nts).
RNA-seq: Total RNA was extracted from fresh cells or frozen tumors using TRIzol® Reagent (Invitrogen), or AllPrep DNA/RNA Mini Kit (Qiagen) or NucleoSpin RNA kit (Macherey-Nagel; for the SK-N-SH cell line treated with chemotherapy). All samples were subjected to quality control on a Bioanalyzer instrument and only RNA with RIN (RNA Integrity Number) > 6 were used for sequencing.
RNA-seq: RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows performing a strand-specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2 x 50 cycles (paired-end reads 50 nts) for all samples (except SH-EP, 2 x 100; Pair1-Relapse and Pair3-Relapse, 2 x 75; Pair2-Relapse, 2 x 150). Sequencing was performed with the Illumina HiSeq2500 instrument (high output mode).

treatment_protocol:
RNA-seq: Cells were not treated unless it is specified
RNA-seq: Treatment of cell lines with chemotherapy: SK-N-SH cells were plated in 6-well plates and then treated with cisplatin (7.5 µM) or doxorubicin (100 nM) for 7 days, medium and drugs were changed every 2 days. RNAs were extracted using NucleoSpin RNA kit (Macherey-Nagel).
RNA-seq: Doxycycline-inducible shRNA systems: PHOX2B-specific short hairpin RNAs sh1783 (5’-CCGGTGGAAGGCAGAAACCATTAAA- CTCGAGTTTAATGGTTTCTGCCTTCCATTTTTG-3’) and sh1437 (5’-CCGGAGTAATCG- CGCTAAGAATAAACTCGAGTTTATTCTTAGCGCGATTACTTTTTTG-3’) were selected from Sigma Mission shRNA library and cloned into the pLKO-Tet-On all-in-one system46 (Addgene). Lentiviral particles were produced in HEK293T cells and CLB-GA cells were infected as previously described4. SH-SY5Y cells were incubated with viral particules for 48 hours without polybrene. Selection with puromycin (Invitrogen) at 400 ng/ml or 1 µg/ml, respectively, was performed 24 h after infection and maintained during all culture experiments, for CLB-GA and SH-SY5Y cells, respectively. PHOX2B knockdown efficacy was assessed by Western blot 24 h/48 h/96 h after the addition of doxycycline (100 ng/ml or 1 μg/ml). For colony formation assays, 6x104 transduced cells were plated at day 0 in 6-well dishes and stained with crystal violet at day 11.

value: Neuroblastoma PDX

tag: chip antibody

value: ab4729 (rabbit polyclonal, Abcam)

tag: treatment


title: PDX MAP-GR-B25-NB-1 H3K27ac, ChIP-seq

source_name: PDX MAP-GR-B25-NB-1


title: KZIP14degree-3

description:
Genotypes of spore of Spo11 enriched DNA
KZIP14-3


title: 549418A01 - SXB139_25 vs SXB139_28

hyb_protocol: SXB139_28 Cy5 / SXB139_25 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: PDX MAP-GR-A99-NB-1 H3K27ac, ChIP-seq

source_name: PDX MAP-GR-A99-NB-1


title: PDX HSJD-NB011 H3K27ac, ChIP-seq

source_name: PDX HSJD-NB011


title: 549418A03 - SXB139_26 vs SXB139_27

hyb_protocol: SXB139_27 Cy5 / SXB139_26 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: PDX IGR-N835 H3K27ac, ChIP-seq

source_name: PDX IGR-N835


title: PDX IGR-NB8 H3K27ac, ChIP-seq

source_name: PDX IGR-NB8


title: 549418A02 - SXB139_28 vs SXB139_25

hyb_protocol: SXB139_25 Cy5 / SXB139_28 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: MDS_BM_GFPplus_430

city: New York

first: Kimihito

middle: Cojin

last: Kawabata

state: NY

department: Medicine

country: USA

institute: Weill-Cornell Medicine

description: Gene expression data from BMCs from an MDS-like BMT recipient mouse. GFP-positive control

hyb_protocol: Hybridized to Affymetrix Mouse Expression array 430A, which contains 45000 probe sets for 39000 transcripts and variants from over 34000 well-characterized mouse genes (Affymetrix).

scan_protocol: After washing and staining, the arrays were scanned on the GeneChip system confocal scanner (Affymetrix).

data_processing: Using Genespring software the data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Normalized expression data was filtered on expression (3 - 120543).

label: biotin

organism: Mus musculus

source_name: Mouse BMC in BMT using EZH2-Mt transgene

label_protocol: Double-stranded cDNA was synthesized from 5 μg of total RNA with oligo (dT)24 T7 primer, amplified with T7 RNA polymerase up to approximately 50 μg of cRNA,

growth_protocol: BMCs were harvested from sacrificed BMT-recipient mice.

extract_protocol: BMCs were lysed in TRIZOL, then added 200 microL of chloroform, and centrifuged. Upper layer was subjected to RNA extraction using Rneasy miniculumns using a manufactures protocol.

treatment_protocol: For harvesting RNA from BMCs of MDS-like mice transplanted with BMCs-expressing EZH2-Mt, wholc BMCs were sorted into GFP-positive and -negative fractions.

tag: tissue

value: bone marrow

tag: transgene

tag: sorting

value: GFP-positive


title: BMT_mock_3_430

description: Gene expression data from BMCs from a BMT recipient mouse transplanted with control BMC-expressing mock

source_name: Mouse BMC in BMT using Mock control transgene

value: mock

value: No


title: BMCs_ser2_1_Exp_430

description: Gene expression data from BMCs from a BMT recipient mouse transplanted with BMC-ABCG2

source_name: Mouse BMC in BMT using ABCG2 transgene


title: MDS_BM_GFPminus_430

description: Gene expression data from BMCs from an MDS-like BMT recipient mouse. GFP-negative control

value: GFP-negative


title: BMCs_ser2_2_Exp_430


title: BMT_mock_2_430


title: BMT_mock_1_430


title: KZIP14degree-4

description:
Genotypes of spore of Spo11 enriched DNA
KZIP14-4


title: 549418A04 - SXB139_27 vs SXB139_26

description: The objective is to better understand the adaptive response of the wheat plant to an elevated mean temperature. Besides the morphological and ecophysiological responses, the changes in the expression of genes are investigated. Two genotypes (SxB49 and SxB139) are subjected to two different temperature regimes during the lag-phase of the developing grains. The profiling of the accumulation of gene transcripts throughout 12 developmental stages is carried out using a custom-designed 12x135K Roche NimbleGen gene expression microarray comprising the most recent NCBI wheat contig assembly and annotation (about 45 000 unigenes). This should permit both the identification of differentially expressed genes after heat treatment and the comparison of the behaviours of two wheat genotypes (SxB139 and SxB49).

hyb_protocol: SXB139_26 Cy5 / SXB139_27 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Melanoma UACC cell line 647_2

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC647_2

hyb_protocol: Resuspended samples are denatured, then hybridized to locus-specific 50-mer oligonucleotides which are attached to 1-micron beads on the BeadChip.  These 50-mer probes stop one base before the location of interest.  Enzymatic single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates tagged nucleotides on the BeadChip, which are subsequently fluorophore-labeled during staining. The fluorescent label determines the genotype call for the sample.

scan_protocol: The Illumina iScan scans the BeadChips at two wavelengths to detect the fluorescent label, creating image files that are converted into genotype calls based on the detected fluorescence.

data_processing: Genomic DNA extracted from melanoma cell lines was genotyped using Illumina Infinium human OmniExpress array

label: C-Bio and A-DNP

source_name: Melanoma UACC cell line

label_protocol: 200ng of genomic DNA, quantitated using Quant-iT™ PicoGreen dsDNA Reagent (ThermoFisher Scientific, Waltham, MA, USA) is denatured and neutralized, then isothermally amplified by whole-genome amplification.  The amplified product is enzymatically fragmented, then precipitated and re-suspended.

growth_protocol: Melanoma cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

extract_protocol: Genomic DNA was isolated from melanoma cells using Qiagen DNeasy Blood and Tissue kit

tag: disease state

value: Melanoma

value: Skin


title: Melanoma UACC cell line 1093

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1093


title: Melanoma UACC cell line 558_2

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC558_2


title: Melanoma UACC cell line 3379

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3379


title: Melanoma UACC cell line 3371

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3371


title: Melanoma UACC cell line 3361

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3361


title: Melanoma UACC cell line 2512

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2512


title: Melanoma UACC cell line 3093

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3093


title: Melanoma UACC cell line 3291

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3291


title: Melanoma UACC cell line 952

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC952


title: Melanoma UACC cell line 3395

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3395


title: Melanoma UACC cell line 2659

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2659


title: Melanoma UACC cell line 2994

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2994


title: Melanoma UACC cell line 2993

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2993


title: Melanoma UACC cell line 3312

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3312


title: Melanoma UACC cell line 502

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC502


title: Melanoma UACC cell line 2851

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2851


title: Melanoma UACC cell line 3090

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3090


title: Melanoma UACC cell line 3476

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3476


title: Melanoma UACC cell line 3020

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3020


title: Melanoma UACC cell line 91

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC91


title: Melanoma UACC cell line 3074

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3074


title: Melanoma UACC cell line 2837

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2837


title: Melanoma UACC cell line 612_2

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC612_2


title: Melanoma UACC cell line 3337

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3337


title: Melanoma UACC cell line 612

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC612


title: Melanoma UACC cell line 3211

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC3211


title: Melanoma UACC cell line 2876

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2876


title: Melanoma UACC cell line 2972

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2972


title: Melanoma UACC cell line 2641

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2641


title: Melanoma UACC cell line 2610

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2610


title: Melanoma UACC cell line 2496

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2496


title: Melanoma UACC cell line 2534

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2534


title: Melanoma UACC cell line 2528

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2528


title: Melanoma UACC cell line 1729

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1729


title: Melanoma UACC cell line 2404

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2404


title: Melanoma UACC cell line 2545

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2545


title: Melanoma UACC cell line 1940

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1940


title: Melanoma UACC cell line 1816

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1816


title: Melanoma UACC cell line 2427

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2427


title: Melanoma UACC cell line 1389

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1389


title: Melanoma UACC cell line 1592

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1592


title: Melanoma UACC cell line 1113

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1113


title: Melanoma UACC cell line 1469

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1469


title: Melanoma UACC cell line 2331

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC2331


title: Melanoma UACC cell line 1509

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1509


title: Melanoma UACC cell line 1241

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1241


title: Melanoma UACC cell line 1451

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1451


title: Melanoma UACC cell line 1190

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1190


title: Melanoma UACC cell line 1316

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1316


title: Melanoma UACC cell line 1237

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1237


title: Melanoma UACC cell line 1120

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1120


title: Melanoma UACC cell line 1118

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1118


title: control heat inact NHS chip11

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN727 cells stimulated with sera cancer patient

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProd package in Bioconductor.

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

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

treatment_protocol: Gene expression was accomplished by culturing PBMCs for 9 hours at 37°C in 5% CO2 with media supplemented with sera of cervical cancer patients from either local or metastatic group.The cultures were prepared in a Costar 24-well plate (Corning, St Louis, MO), using 12 wells per condition (500,000 cells/well in 300 µl of RPMI 1640 medium plus 200 µl of patient-derived serum). In addition to the 5 serum samples from patients with non-recurrent local disease and the 5 samples from patients with metastatic cervical SCC, we created an 11th co-culture that contained cancer-free human serum as a control. After culture total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

value: UPN727 cells

tag: source of serum used for treatment

value: cancer-free human serum as a control.


title: Melanoma UACC cell line 1097

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1097


title: Melanoma UACC cell line 1265

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1265


title: Melanoma UACC cell line 1649

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1649


title: Melanoma UACC cell line 1308

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC1308


title: 430P Chip6

source_name: UPN727 cells stimulated with sera cancer patient

value: SCCA Grade 2 Stage Ib2 negative lymph nodes


title: Melanoma UACC cell line 903

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC903


title: 409P Chip8

value: SCCA Grade 3 Stage Ib1 positive lymph nodes


title: 311P Chip5


title: 1304P Chip9

value: SCCA Grade 3 Stage Ib2 positive lymph nodes


title: 1327P Chip10

value: SCCA Grade 2 Stage Ib1 negative lymph nodes


title: 405P Chip3


title: Melanoma UACC cell line 929

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC929


title: 402P Chip2

value: SCCA Grade 2 Stage Ib2 positive lymph nodes


title: Melanoma UACC cell line 827

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC827


title: 709P Chip4


title: NF54 stage IV/V gametocytes treated with 10 x IC50 of MMV390048 and harvested 48 h post expt initiation (LG, 48h, T048)

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

description:
NF54 Mixed Stage asexual parasites and stage II-V gametocytes with and without MMV390048 and MMV642943 treatment
NF54 stage IV/V gametocytes treated with 10 x IC50 of MMV390048 and harvested 48 h post experiment initiation
LG, 48h, T048

hyb_protocol: Kafsak BFC, Painter HJ, Llinas M,  New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community. Malar J. 2012; 11:187

scan_protocol: Axon GenePix 4000B Scanner. Images were quantified using GenePix Pro 5.1 (Acuity) software.

data_processing: GenePix Pro 5.1 (Acuity) was used for background subtraction and the Bioconductor, limma, and marray packages in R 3.2.3 were used for within and between-slide normalisation

organism: Plasmodium falciparum

source_name: NF54 48h T048 RNA

growth_protocol:
P. falciparum (NF54) parasites were maintained with shaking at 37°C in human erythrocytes, suspended at 5% hematocrit in complete culture medium [RPMI 1640 medium (Sigma-Aldrich) supplemented with 25 mM HEPES (Sigma-Aldrich), 20 mM D-glucose (Sigma-Aldrich), 200 μM hypoxanthine (Sigma-Aldrich), 0.2% (w/v) sodium bicarbonate, 24 μg/ml Gentamycin (Sigma-Aldrich) and 0.5% (w/v) AlbuMAX II] under hypoxic conditions (90% N2, 5% O2, and 5% CO2). Parasite development was monitored with light microscopy through Giemsa staining and parasites were synchronized (>95% synchronization) by two consecutive treatments with 5% D-sorbitol. Gametocytes were maintained in complete culture medium under hypoxic conditions. Residual asexual parasites were eliminated from culture with 2 consecutive days of N-acetylglucosamine (50 mM) treatment.
[gametocyte cultivation] Reader J, Botha, M, Theron J, Lauterbach SB, Rossouw C, Engelbrecht D, Wepener M, Smit A, Leroy D, Mancama D, Coetzer TL, Birkholtz L, Nowhere to hide: interrogating different metabolic parameters of Plasmodium falciparum gametocytes in a transmission blocking drug discovery pipeline towards malaria elimination. Malar J, 2015. 14: p. 213.

extract_protocol: Total RNA was isolated from untreated and treated asexual parasite and late gametocyte samples using a combination of TriZol reagent and the Qiagen RNeasy kit according to the manufacturer's instructions. RNA integrity, purity and quantity were determined by agarose gel electrophoresis and spectrophotometry. RNA was stored at -70°C.

treatment_protocol: Synchronised ring-stage (~6 hours post merozoite invasion) parasites (5% haematocrit, ~10% parasitaemia) were incubated with 10 x IC50 of MMV390048 or MMV642943. Untreated parasite cultures were maintained in parallel. Parasite cultures were removed at 48 hours post-treatment, washed once with twice with 1 x PBS and pelleted parasitised erythrocytes were stored at -70°C. For gametocyte cultures (1-3% gametocytaemia) were treated with 10 x IC50 of MMV390048 or 10 x IC50 of MMV642943. Untreated gametocyte cultures were maintained in parallel. After 48 hours of treatment, parasites were isolated from host erythrocytes by density gradient (Nycoprep) centrifugation. Parasite pellets were washed three times with 1x PBS and stored at -70°C.

tag: time (after treatment)

source_name: NF54 Mixed Stage asexual parasites, stage II-V gametocytes treated with MMV390048, MMV642943 and untreated asexual parasite, stage II-V gametocyte reference pool

value: Reference


title: NF54 stage IV/V gametocytes remained untreated and were harvested 48 h post expt initiation (LG, 48h, UT943)

description:
NF54 Mixed Stage asexual parasites and stage II-V gametocytes with and without MMV390048 and MMV642943 treatment
NF54 stage IV/V gametocytes remained untreated and were harvested 48 h post experiment initiation
LG, 48h, UT943

source_name: NF54 48h Untreated RNA

label_protocol: Kafsak BFC, Painter HJ, Llinas M,  New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community. Malar J. 2012; 11:187

value: control


title: NF54 stage IV/V gametocytes remained untreated and were harvested 48 h post expt initiation (LG, 48h, UT048)

description:
NF54 Mixed Stage asexual parasites and stage II-V gametocytes with and without MMV390048 and MMV642943 treatment
NF54 stage IV/V gametocytes remained untreated and were harvested 48 h post experiment initiation
LG, 48h, UT048


title: SATaARPE19_Rep3

city: Guangzhou

first: Lili

last: Gong

state: Guangdong

address: Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description:
Gene expression data from GFP-Satllite alpha transfected ARPE19 cells
 Retinal pigment epithelia cell line

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: GFP-SATalpha transfected ARPE19 cells

label_protocol: Total RNAs were amplified, biotin labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Affymetrix, #902416).

growth_protocol: ARPE19 cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/ streptomycin.

extract_protocol: RNA was extracted using RNeasy mini kit, (QIAGEN, #P/N74104).

treatment_protocol: ARPE19 cells cultured in 6-well plates were transfected with 2.5 ug GFP or GFP-satellite alpha plasmids/well. Transfection was conducted in triplicate in each condition.


title: 539P Chip1


title: NF54 asexual ring-stage parasites remained untreated and harvested 48 h post expt initiation (A48, UT)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites remained untreated and harvested 48 h post experiment initiation
A48, UT

source_name: NF54 Mixed Stage asexual parasites treated with MMV390048, MMV642943 and untreated asexual parasite Reference Pool


title: NF54 stage IV/V gametocytes treated with 10 x IC50 of MMV642943 and harvested 24 h post expt initiation (LG, 48h, T943)

description:
NF54 Mixed Stage asexual parasites and stage II-V gametocytes with and without MMV390048 and MMV642943 treatment
NF54 stage IV/V gametocytes treated with 10 x IC50 of MMV642943 and harvested 24 h post experiment initiation
LG, 48h, T943

source_name: NF54 T943 48h RNA


title: GFPARPE19_Rep1

description:
Gene expression data from GFP transfected ARPE19 cells
 Retinal pigment epithelia cell line

source_name: GFP transfected ARPE19 cells


title: GFPARPE19_Rep3


title: SATaARPE19_Rep2


title: NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV642943 and harvested 48 h post expt initiation (A48,T943)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV642943 and harvested 48 h post experiment initiation
A48,T943


title: NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV390048 and harvested 48 h post expt initiation (A24,T048)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV390048 and harvested 48 h post experiment initiation
A24,T048

source_name: NF54 24h T048 RNA


title: NF54 asexual ring-stage parasites remained untreated and harvested 24 h post expt initiation (A24,UT)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites remained untreated and harvested 24 h post experiment initiation
A24,UT

source_name: NF54 24h Untreated RNA


title: NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV390048 and harvested 24 h post expt initiation (A48,T048)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV390048 and harvested 24 h post experiment initiation
A48,T048


title: MAM IgG rep3

status: Public on Jun 30 2017

city: Houston

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

description: Gene expression data from myeloma-associated macrophages treated with IgG antibody ctrl 3

hyb_protocol: Fragmented and labeled ss-cDNA was hybridyzed for 16 hr at 45°C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed using the Robust Multiarray Average and differentially expressed genes between two groups were identified by R/Bioconductor using limma package.

label_protocol: Total RNA was labeled using the GeneChip WT PLUS Reagent Kit.

growth_protocol: We cultured murine bone marrow (BM)-derived monocytes from 3 C57BL/KaLwRij mice in the presence of M-CSF for 7 days to generate BM-derived Macrophages (BMDMs).

extract_protocol: Total RNA of BMDMs was extracted with RNeasy Mini kit (Qiagen).

treatment_protocol: BMDMs were cocultured with murine myeloma 5TGM1-luc cells overnight and treated with 0.5 nM anti-mouse CSF1R antibody or IgG antibody control for 3 days.

value: murine bone marrow derived macrophages cocultured with myeloma cells


title: 417P Chip7

description: Gene expression data from UPN727 cells stimulated with sera cancer patient


title: MAM CS7 rep3

description: Gene expression data from myeloma-associated macrophages treated with CSF1R antibody 3


title: MAM CS7 rep2

description: Gene expression data from myeloma-associated macrophages treated with CSF1R antibody 2


title: NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV642943 and harvested 24 h post expt initiation (A24,T943)

description:
NF54 Mixed Stage asexual parasites with and without MMV390048 and MMV642943 treatment
NF54 asexual ring-stage parasites treated with 10 x IC50 of MMV642943 and harvested 24 h post experiment initiation
A24,T943

source_name: NF54 T943 24h RNA


title: MAM IgG rep2

description: Gene expression data from myeloma-associated macrophages treated with IgG antibody ctrl 2


title: MAM IgG rep1

description: Gene expression data from myeloma-associated macrophages treated with IgG antibody ctrl 1


title: AAV-HBV/AAV-HDV rep 2

city: Pamplona

first: Gloria

last: Gonzalez-Aseguinolaza

state: Does Not Apply

address: Av PioXII 55

department: Gene Therapy

country: Spain

institute: FIMA, CIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

label: Biotin

source_name: AAV-HBV/AAV-HDV

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Anaimals received a single intravenous injection of AAV-HBV or AAV-HBV, or AAV-HBV + AAV-HDV or AAV-Luc

tag: gender

value: male

tag: age

value: 11 week-old

tag: injected with

value: AAV-HBV/AAV-HDV

value: liver


title: AAV-HDV rep 2

source_name: AAV-HDV

value: AAV-HDV


title: AAV-HBV/AAV-HDV rep 3


title: AAV-HBV rep 1

source_name: AAV-HBV

value: AAV-HBV


title: AAV-Luc rep 3

source_name: AAV-Luc

value: AAV-Luc


title: AAV-HBV/AAV-HDV rep 1


title: AAV-HBV rep 2


title: Melanoma UACC cell line 647

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC647

value: Melanoma

value: Skin


title: DR261

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

description: fraction: promoter

scan_protocol: Array was scanned on an Affymetrix GeneChip Scanner 3000.

data_processing:
Hybridization was performed with an Affymetrix GeneChip Promoter 1.0R array.
The resulting processed data are generated by the Affymetrix Tiling Analysis Software.

label_protocol: Then, 3.5 mg (7 mL) of MBD-Biotin Protein was added to 10 mL Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

growth_protocol: Peripheral blood leukocytes was collected from patinets and control.

extract_protocol: One microgram of genomic DNA was sonicated to produce fragments ranging from 100 to 500 bp.

treatment_protocol: Genomic DNA was extracted from peripheral blood leukocytes by using the Genomic DNA extraction kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

value: Blood

tag: disease


title: DR259

description: fraction: promoter

hyb_protocol: Hybridization was performed with an Affymetrix GeneChip Promoter 1.0R array.


title: DR240

description: fraction: promoter


title: DR218

description: fraction: promoter


title: AAV-HDV rep 1


title: AAV-HBV rep 3


title: DN279

description: fraction: promoter


title: DN322

description: fraction: promoter


title: DR227

description: fraction: promoter


title: DN246

description: fraction: promoter


title: MAM CS7 rep1

description: Gene expression data from myeloma-associated macrophages treated with CSF1R antibody 1


title: Melanoma UACC cell line 383

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC383


title: SATaARPE19_Rep1

description:
Gene expression data from GFP-Satllite alpha transfected ARPE19 cells
 Retinal pigment epithelia cell line

tag: cell line


title: AAV-Luc rep 1


title: AAV-HDV rep 3


title: DN228

description: fraction: promoter


title: DN230

description: fraction: promoter


title: AAV-Luc rep 2


title: Melanoma UACC cell line 62

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC62


title: DN073

description: fraction: promoter


title: DN060

description: fraction: promoter


title: DN020

description: fraction: promoter


title: DN184

description: fraction: promoter


title: 33071

description: fraction: promoter

value: Normal


title: 33069

description: fraction: promoter


title: 66070

description: fraction: promoter


title: DN192

description: fraction: promoter


title: 33068

description: fraction: promoter


title: Melanoma UACC cell line 457

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC457


title: 33067

description: fraction: promoter


title: Melanoma UACC cell line 558

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC558


title: FrvA induced vs uninduced_120 min

city: Ithaca

first: Hualiang

last: Pi

address: 125 Wing Dr.

department: Microbiology

institute: Cornell University

hyb_protocol: Equal amount (250 pmol) of labeled cDNA was combined plus hybridization buffer (2X = 50% form amide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.). Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

label: Alexa Fluor 555

organism: Bacillus subtilis

source_name: IPTG induced

label_protocol: Total RNA were then treated with Turbo-DNAse (Thermo Fisher Scientific) to remove any possible DNA contamination, and then reverse transcribed using SuperScript™ Indirect cDNA Labeling System (Thermo Fisher Scientific) into cDNA. cDNA was aliquoted and labelled with either fluorescent dye 555 or dye 647, and hybridized to microarray slides containing 60 nt oligonucleotides for each coding region according to laboratory protocol.

growth_protocol: Cells (WT Pspac-frvA) were grown in LB medium amended with 10 µM to an OD600 of ∼0.25 and divided into two 1 L flasks, one treated with 1 mM IPTG and the other untreated. Aliquots of 40 ml of cell culture were harvested from both flasks at different time-points.

extract_protocol: Total RNA was extracted using an acidic phenol-based method.

treatment_protocol: To induce expression of FrvA, 1 mM IPTG was added into one flask while the other was left untreated as a control.

tag: genotype

value: Pspac-frvA

tag: background strain

label: Alexa Fluor 647

source_name: uninduced


title: FrvA induced vs uninduced_OD600~0.6


title: FrvA induced vs uninduced_180 min


title: FrvA induced vs uninduced_20 min


title: FrvA induced vs uninduced_30 min


title: Melanoma UACC cell line 285

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC285

source_name: Melanoma UACC cell line


title: FrvA induced vs uninduced_60 min


title: FrvA induced vs uninduced_0 min


title: Melanoma UACC cell line 257

description:
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC257


title: fur null vs WT OD600~0.5

source_name: fur null mutant

tag: strain

value: fur null

source_name: WT

value: wildtype


title: Non-pregnant islets #3

city: Mölndal

first: Alex-Xianghua

last: Zhou

state: - If in U.S, Select a State -

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca R&D Gothenburg

hyb_protocol: Fragmented and labeled cDNA probes were hybridized with Invitrogen™ NCode™ non-coding RNA arrays

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C).

data_processing: Signal intensity was normalized for expression analysis. Primer sequences were BLASTed against a database generated from the transcript sequences of all transcripts in the ab initio annotation. Only hits that were unique and perfect (60 nt at 100% match) were considered valid.

organism: Mus

source_name: Pancreatic islets, non-pregnant mice

label_protocol: SuperScript® Indirect RNA Amplification System with Alexa Fluor® reactive dye decapacks

extract_protocol: Immediately after isolation, total islet RNA was extracted with Stratagene RNA kit (Life Technologies).

treatment_protocol: Mouse islets were isolated from non-pregnant mice or dams at gestational day 14.5. Islets from 3-4 mice were pooled to collect at least 500 islets per sample.

value: Female

value: 6-8 weeks

tag: gestational status

value: non-pregnant

value: Pooled pancreatic islets


title: GFPARPE19_Rep2

description:
Gene expression data from GFP transfected ARPE19 cells
 Retinal pigment epithelia cell line


title: Pregnant islets #3

source_name: Pancreatic islets, pregnant mice at gestational day 14.5

value: pregnant, gestational day 14.5


title: Pregnant islets #1


title: Pregnant islets #2


title: Non-pregnant islets #2


title: siCYLD + ALK5 inhibitor

status: Public on Jun 29 2017

city: Kumamoto

first: Satoru

last: Shinriki

state: 日本 (Japan)

address: 1-1-1, Honjo, Chuo-ku

institute: Kumamoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GCS3000 System (Affymetrix).

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

source_name: SAS cells treated with ALK5 inhibitor after transfection with CYLD siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Extraction of total RNA by RNeasy Mini Kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: SAS cells transfected with siRNA were cultured for 2 days and treated with DMSO or ALK5 inhibitor for 48 h in serum-free medium.

value: SAS

tag: cell type

value: oral squamous cell caricnoma cell line


title: siCtrl, rep2

source_name: SAS cells transfected with CYLD siRNA


title: Non-pregnant islets #1


title: siCYLD, rep1

source_name: SAS cells transfected with control siRNA


title: siCtrl, rep1


title: siCYLD, rep2


title: MA7

city: Pune

first: Richa

last: Ashma

state: Maharashtra

address: Assistant Professor, Center for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune – 411007

country: India

institute: Savitribai Phule Pune University

hyb_protocol: Agilent’s In situ Hybridzation kit 5190-6420

scan_protocol: The images were manually verified and found to be devoid of uneven hybridization, streaks, blobs and other artifacts. Hybridization across the slide was done based on number of feature that were “g is PosAndSignif” which indicates feature is positive and significantly above background.

data_processing: The raw data generated by microarray hybridization was intra array normalized using Genespring GX software. For inter-array normalization, median of 4 normal subjects and 4 osteoporosis females across all genes (spots / entity) was considered. From the entity of osteoporosis, the median value of normal was subtracted. This normalized data was used for log2fold change (FC) calculation

source_name: Osteoclast precursors derived from PBMCs

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA using the Agilent Quick-Amp labeling Kit

growth_protocol: PBMCs were isolated from whole blood vials by fractionating on Hypaque 1077. Isolated PBMCs were resuspended in 1 ml of isolation buffer and cell count was taken. An average of ~ 1.5× 107 cells/ml were obtained and subjected for CD14+ sorting using Dynabeads® CD14 positive isolation kit (Invitrogen) following manufacturer’s protocol.

extract_protocol: Total RNA was isolated from these CD14+ cells using Trizol reagent (life technologies) and was purified using RNeasy mini kit (Quigene). RNA quality and concentration was determined using Nanodrop and 1% agarose gel electrophoresis. RNA integrity was checked by assessing ratio of 18s and 28s ribosomal RNA intensity peaks (Agilent 2100 Expert Bioanalyzer).

treatment_protocol: The osteoporotic and non-osteoporotic conditions were decided using WHO guidelines stating T score above -1 SD is non-osteoporotic and below -2.5 SD is osteoporotic condition

tag: Stage

value: Postmenopause

tag: normal - osteoporosis

value: osteoclast precursors


title: MA13

value: Osteoporosis


title: siCtrl + ALK5 inhibitor

source_name: SAS cells treated with ALK5 inhibitor after transfection with control siRNA


title: MA11


title: MA5


title: MA3


title: MA9


title: MA15


title: MA1


title: 367205 Exp2

city: Miami

first: Tongyu

last: Wikramanayake

state: FL

address: 1600 NW 10th Avenue, RMSB 2023A

department: Dermatology and Cutaneous Surgery

institute: University of Miami Miller School of Medicine

hyb_protocol: Biotinylated cRNA samples are fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the surface of microarrays enclosed in custom hybridization chambers. Constant rotation in a Robbins Scientific hybridization oven is utilized to achieve uniform sample dispersion across the array surface by bubble/ gravity mixing. This gravity mixing process allows ORB to minimize inter-sample variation due to hybridization as well as non-specific background, while maximizing signal intensity for low abundance RNAs. After 16-18 hours of hybridization, microarray slides are washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen), and scanned using an Axon GenePix 4000B scanner.

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) at 10 uM using 650 PMT and a 635 nM wavelength.

data_processing:
Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. Spot intensities were transformed by taking the base 2 logarithm of each value. The spot intensities were then normalized by subtracting the 70th percentile of the spot intensities of all non-control rat probes and adding back a scaling factor (grand mean of 70th percentile). After removing data for low quality spots, control sequences, and non-rat probes, 39,033 rat probe intensities remained. The rat probes intensities were filtered to identify all probes with intensity above a normalized threshold (log2 (5* standard deviation of raw local background) + mean of log2-transformed negative controls), to arrive at 16,198 probes above threshold in all samples from at least one treatment group (CTRL, EXP).  For statistical analysis, samples were binned into two treatment groups (CTRL, EXP). The log2-transformed and normalized spot intensities for the 16,198 detectable probes were examined for differences between the treatment groups by 1-way ANOVA using National Institute of Ageing (NIA) Array Analysis software. This ANOVA was conducted using the Bayesian Error Model and 10 degrees of freedom. The statistical significance was determined using the False Discovery Rate (FDR) method.  A total of 3,239 probes showed significant differences with P<0.05 and FDR (false discovery rate) less than 0.1.   Data for the 3,239 significant and detectable probes were clustered using Cluster 3.0 software. The data was pre-processed by three consecutive rounds of gene median centering. Data was then hierarchically clustered using centered correlation as the similarity metric and average linkage as clustering method. Intensity scale shown is arbitrary.
Raw data was background-subtracted, log2-transformed and normalized.

organism: Rattus norvegicus

source_name: rat skin wound

label_protocol: Ocean Ridge Biosciences (ORB) has chosen in vitro transcription based-incorporation of biotinylated UTP for production of amplified and labeled complementary RNA (cRNA). First, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence is used to prime reverse transcription catalyzed by Superscript II (Invitrogen). Double-stranded cDNA is prepared from the 1st strand product by the method of Gubler & Hoffman, and purified on a PCR purification column (Qiagen). The double- stranded cDNA is then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion) and including biotin-16-UTP in the reaction mixture. Using their optimized variation of Van Gelder's method, they routinely obtain between 25-60 micrograms of biotinylated cRNA from each microgram of total RNA, depending on tissue of origin.

extract_protocol: Total RNA was extracted with TriZol Reagent (Life Technologies, Grand Island, NY) and purified with the RNeasy micro kit (Qiagen), and sent to Ocean Ridge Biosciences (ORB, Palm Beach Gardens, FL) for microarray analysis using the Rat MI-Ready array from Microarrays Inc.

treatment_protocol: A 3-mm incisional wound was made on the dorsum of Long-Evans rat pups 3 days after birth.  Thirty-six hours later, skin specimens were collected from the wound sites (wound) and corresponding sites of unwounded rat pups (control).

value: Long-Evans

tag: sample group

value: wounded

tag: tissue

value: skin


title: 367210 Exp3


title: 368382 Exp4


title: 367202 ctrl3

source_name: rat skin

value: control


title: Sample88

first: James

last: Lupski

address: One Baylor plaza

department: MHG

institute: BCM

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

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: DNA extracted from whole blood

label_protocol: 0.9 ug genomic DNA of CMA samples and reference samples were digested with AluI and RsaI for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for CMA DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN, USA) according to the manufacturer's protocal.

value: whole bood

tag: targeting loci

value: M

source_name: reference sample


title: Sample87


title: 367203 ctrl4


title: Sample81


title: 367201 ctrl2


title: Sample89


title: 366670 ctrl1


title: Sample83

value: F


title: 367204 Exp1


title: Sample86


title: Sample82


title: Sample77


title: Sample75


title: Sample84


title: Sample74


title: Sample76


title: Sample80


title: Sample71

value: YWHAE


title: Sample78


title: Sample65

value: FANCA


title: Sample72


title: Sample79


title: Sample73


title: Sample63


title: Sample68


title: Sample85


title: Sample70


title: Sample66


title: Sample69


title: Sample64


title: Sample67


title: Sample55


title: Sample60


title: Sample59


title: Sample52


title: Sample58


title: Sample61


title: Sample48


title: Sample50


title: Sample56


title: Sample46


title: Sample57


title: Sample39


title: Sample62


title: Sample49


title: Sample53


title: Sample43


title: Sample44


title: Sample47


title: Sample51


title: Sample45


title: Sample35


title: Sample54


title: Sample36


title: Sample40


title: Sample42


title: Sample41


title: Sample34


title: Sample38


title: Subject: Mouse7 Group: WT

city: Boston

first: Niroshana

last: Anandasabapathy

state: MA

address: 221 Longwood Ave

department: Dermatology

institute: Brigham and Women's Hospital

hyb_protocol: Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Five micrograms of material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.

scan_protocol: Scanning is carried out on an Affymetrix Model 7000 scanner with autoloader. The Affymetrix AGCC v3.2 operating system controls the Model 7000 scanner and data acquisition functions. AGCC maintains the mediated first level data analysis and desktop data management for the entire GeneChip System

data_processing: RMA (using oligo package from R/Bioconductor).

source_name: migDC, WT

label_protocol: The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.  Quantification of the samples is carried out on a NanoDrop 1000 UV Reader.

extract_protocol: For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation Pico WTA System V2 (P/N 3302).  Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process.

treatment_protocol: migDCs were flow sorted from n=3 individual IFNgR1-/-, IL27Ra-/-, and C57Bl/6 control mice after collagenase D digestion of pooled skin draining LNs on IAIEhi CD11cint selection following size and live/dead exclusion

tag: subject

tag: group

value: WT

tag: genotype/variation

value: migDC


title: Subject: Mouse9 Group: WT


title: Subject: Mouse8 Group: WT


title: Sample30

tag: gender


title: Subject: Mouse5 Group: IL27r

source_name: migDC, IL27r


title: Sample33


title: Sample25


title: Sample37


title: Sample32


title: Sample31


title: Subject: Mouse6 Group: IL27r


title: Subject: Mouse3 Group: IFNgr1

source_name: migDC, IFNgr1


title: Sample20


title: Sample29


title: Sample17


title: Sample28


title: Subject: Mouse4 Group: IL27r


title: Sample26


title: Sample22


title: Sample21


title: Sample27


title: Sample18


title: Sample24


title: Sample10


title: Sample13


title: Subject: Mouse1 Group: IFNgr1


title: Subject: Mouse2 Group: IFNgr1


title: Sample11


title: Sample2


title: Sample4


title: Sample3


title: Sample16


title: Sample19


title: Sample23


title: Sample15


title: Sample5


title: Sample7


title: Sample8


title: Sample12


title: Sample14


title: Sample6


title: Sample1


title: Sample9


title: Pig 40 ESMG

status: Public on Jun 28 2017

city: Durham

first: Katherine

last: Garman

state: NC

address: 905 S LaSalle

institute: Duke University

description: RMA expression value derived from Expression Console software; rma-gene-full analysis

hyb_protocol: Samples were hybridized with GeneChip Porcine Exon 1.0 ST Arrays (Affymetrix) and scanned at the Duke Microarray Core Facility.

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

data_processing: Data was processed using Affymetrix Software; specifically Expression Console build 1.4.1.46 and Transcriptome Analysis Console 3.0 software

organism: Sus scrofa

source_name: control pig esophagus

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Spheroids were cultured in growth factor reduced Matrigel overlaid with Advanced DMEM/F12 containing 10mM HEPES, B27, N2, and 50ng/ml recombinant human EGF.

extract_protocol: ESMG and Squamous tissues were processed for RNA with the Qiagen Rneasy Universal Mini Kit. Spheroid RNA was isolated using a Qiagen Rneasy Micro Kit.

value: ESMG


title: 04_A549_Comp.2_02

city: Kyoto

first: Zutao

last: Yu

state: Kyoto

address: Kyoto University Kitashirakawa-Oiwakecho, Sakyo, Department of Chemistry,  Graduate School of Science

department: Science, chemistry

institute: Kyoto University

description: Gene expression data from Comp.2-treated cells (on day 2)

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48°C on Human Gene ST Array Strip. Strip was washed and stained in the Fluidics Station of GeneAtlas System.

scan_protocol: Strip was scanned using the Imaging Station.

data_processing: The data were analyzed with Expression Console 1.3.1 and Transcriptome Analysis Console 2.0 using RMA.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: A549 cell meidum in ATCC-formulated DMEM medium, fetal bovine serum (Sigma FBS) to a final concentration of 10% and L-glutamine to a final percentage of 2 mM, at 37°C, 5% CO2

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 24 hs from plating, the cells were treated with vehicle or 2 µM of 664-PIP and RNA was extracted after 2 days

value: adenocarcinomic human alveolar basal epithelial cells

tag: treatment

value: Comp.2  (2 µM)

tag: time

value: Day 2


title: Pig 39 Squmaous

value: Squamous


title: Pig 2 Spheroids

source_name: ESMG derived spheroids in vitro

value: Spheroids


title: 05_A549_Comp.4_01

description: Gene expression data from Comp.4-treated cells (on day 2)

tag: cell line

value: Comp.4  (2 µM)


title: 06_A549_Comp.4_02


title: Pig 40 Squamous


title: Pig 1 Spheroids


title: 02_A549_vehicle_02

description: Gene expression data from control cells (on day 2)

value: non (vehicle only)


title: 03_A549_Comp.2_01


title: HBEC4_high_mobility

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description:
cells selected through a series of transwell insert
H4-HM

hyb_protocol: As recommended by manufacturer (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) and scanned at the UCLA Microarray Core Facility

data_processing: RMA expression value derived from Expression Console software; gene-level analysis

source_name: HBEC4, high mobility subpopulation

growth_protocol: Grown in Keratinocyte medium supplemented with 30ug/ml Bovine Pituitary Extract (BPE) and 0.2ng/ml recombinant Epidermal Growth Factor (EGF), all from Invitrogen (#17005-042).

extract_protocol: Total RNA was extracted using Qiagen's Rneasy Mini Kit according to the manufacturer's instructions.

value: Human bronchial epithelial cells immortalized with hTERT and hCDK4

tag: cell mobility

value: high mobility subpopulation

tag: patient age

tag: patient gender

value: Female

tag: patient smoking status

value: Smoker

tag: patient diagnosis

value: With lung cancer as cells isolated from large airway

tag: p53-shrna,kras v12

value: no

tag: snail oe


title: Pig 37 Squamous


title: Pig 3 Spheroids


title: HBEC3_unselected

description:
unselected population
H3

source_name: HBEC3, unselected population

label_protocol: As recommended by manufacturer (Affymetrix)

tag: cell type

value: unselected population

value: No lung cancer as cells isolated from large airway


title: HBEC3_high_mobility

description:
cells selected through a series of transwell insert
H3-HM

source_name: HBEC3, high mobility subpopulation


title: HBEC4_SnailOE_high_mobility

description:
cells selected through a series of transwell insert
H4S-HM

source_name: HBEC4 SNAIL OE, high mobility subpopulation

value: yes


title: Pig 39 ESMG

tag: tissue

value: ESMG


title: HBEC4_unselected

description:
unselected population
H4

source_name: HBEC4, unselected population


title: Pig 37 ESMG


title: HBEC3_p53_KRAS_unselected

description:
unselected population
H3PK

source_name: HBEC3 p53 KRAS, unselected population


title: HBEC3_SnailOE_unselected

description:
unselected population
H3S

source_name: HBEC3 SNAIL OE, unselected population


title: HBEC3_p53_KRAS_high_mobility

description:
cells selected through a series of transwell insert
H3PK-HM

source_name: HBEC3 p53 KRAS, high mobility subpopulation


title: HBEC4_SnailOE_unselected

description:
unselected population
H4S

source_name: HBEC4 SNAIL OE, unselected population


title: 01_A549_vehicle_01

value: adenocarcinomic human alveolar basal epithelial cells


title: HBEC3_SnailOE_high_mobility

description:
cells selected through a series of transwell insert
H3S-HM

source_name: HBEC3 SNAIL OE, high mobility subpopulation


title: HBEC3_p53_KRAS_SnailOE_high_mobility

description:
cells selected through a series of transwell insert
H3PKS-HM

source_name: HBEC3 p53 KRAS SNAIL OE, high mobility subpopulation


title: MMVE003_MOCK_48HRS_RNA_D

status: Public on Jun 27 2017

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 4

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 5 PFU.

tag: virus

value: MOCK


title: MMVE003_icMERS_48HRS_RNA_E

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 48h, bioreplicate 5

value: icMERS


title: MMVE003_MOCK_48HRS_RNA_B

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 2


title: MMVE003_MOCK_48HRS_RNA_E

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 5


title: MMVE003_icMERS_48HRS_RNA_C

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 48h, bioreplicate 3


title: MMVE003_icMERS_48HRS_RNA_A

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 48h, bioreplicate 1


title: MMVE003_icMERS_48HRS_RNA_D

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 48h, bioreplicate 4


title: MMVE003_MOCK_36HRS_RNA_B

source_name: Primary human microvascular endothelial cells, mock-inoculated, 36h, bioreplicate 2


title: HBEC3_p53_KRAS_SnailOE_unselected

description:
unselected population
H3PKS

source_name: HBEC3 p53 KRAS SNAIL OE, unselected population


title: MMVE003_MOCK_36HRS_RNA_C

source_name: Primary human microvascular endothelial cells, mock-inoculated, 36h, bioreplicate 3


title: MMVE003_MOCK_48HRS_RNA_C

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 3


title: MMVE003_MOCK_48HRS_RNA_A

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 1


title: MMVE003_icMERS_48HRS_RNA_B

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 48h, bioreplicate 2


title: MMVE003_MOCK_24HRS_RNA_A

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 1


title: MMVE003_icMERS_36HRS_RNA_E

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 36h, bioreplicate 5


title: MMVE003_MOCK_24HRS_RNA_C

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 3


title: MMVE003_MOCK_24HRS_RNA_E

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 5


title: MMVE003_icMERS_36HRS_RNA_D

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 36h, bioreplicate 4


title: MMVE003_MOCK_36HRS_RNA_D

source_name: Primary human microvascular endothelial cells, mock-inoculated, 36h, bioreplicate 4


title: MMVE003_MOCK_24HRS_RNA_D

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 4


title: MMVE003_icMERS_24HRS_RNA_C

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 24h, bioreplicate 3


title: MMVE003_MOCK_36HRS_RNA_A

source_name: Primary human microvascular endothelial cells, mock-inoculated, 36h, bioreplicate 1


title: MMVE003_icMERS_36HRS_RNA_B

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 36h, bioreplicate 2


title: MMVE003_MOCK_36HRS_RNA_E

source_name: Primary human microvascular endothelial cells, mock-inoculated, 36h, bioreplicate 5


title: MMVE003_icMERS_24HRS_RNA_E

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 24h, bioreplicate 5


title: MMVE003_icMERS_36HRS_RNA_A

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 36h, bioreplicate 1


title: MMVE003_icMERS_24HRS_RNA_A

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 24h, bioreplicate 1


title: MMVE003_icMERS_36HRS_RNA_C

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 36h, bioreplicate 3


title: MMVE003_icMERS_24HRS_RNA_B

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 24h, bioreplicate 2


title: MMVE003_MOCK_24HRS_RNA_B

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 2


title: MMVE003_icMERS_12HRS_RNA_A

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 12h, bioreplicate 1


title: MMVE003_icMERS_12HRS_RNA_E

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 12h, bioreplicate 5


title: MMVE003_icMERS_24HRS_RNA_D

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 24h, bioreplicate 4


title: MMVE003_icMERS_12HRS_RNA_B

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 12h, bioreplicate 2


title: MMVE003_MOCK_12HRS_RNA_D

source_name: Primary human microvascular endothelial cells, mock-inoculated, 12h, bioreplicate 4


title: MMVE003_MOCK_12HRS_RNA_C

source_name: Primary human microvascular endothelial cells, mock-inoculated, 12h, bioreplicate 3


title: MMVE003_MOCK_12HRS_RNA_B

source_name: Primary human microvascular endothelial cells, mock-inoculated, 12h, bioreplicate 2


title: MMVE003_MOCK_12HRS_RNA_E

source_name: Primary human microvascular endothelial cells, mock-inoculated, 12h, bioreplicate 5


title: MMVE003_icMERS_12HRS_RNA_C

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 12h, bioreplicate 3


title: MMVE003_MOCK_12HRS_RNA_A

source_name: Primary human microvascular endothelial cells, mock-inoculated, 12h, bioreplicate 1


title: MMVE003_MOCK_0HRS_RNA_C

source_name: Primary human microvascular endothelial cells, mock-inoculated, 0h, bioreplicate 3


title: MMVE003_MOCK_0HRS_RNA_E

source_name: Primary human microvascular endothelial cells, mock-inoculated, 0h, bioreplicate 5


title: MMVE003_MOCK_0HRS_RNA_A

source_name: Primary human microvascular endothelial cells, mock-inoculated, 0h, bioreplicate 1


title: MMVE003_icMERS_0HRS_RNA_D

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 0h, bioreplicate 4


title: MMVE003_icMERS_0HRS_RNA_E

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 0h, bioreplicate 5


title: MMVE003_icMERS_0HRS_RNA_C

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 0h, bioreplicate 3


title: MMVE003_icMERS_0HRS_RNA_A

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 0h, bioreplicate 1


title: MMVE003_icMERS_0HRS_RNA_B

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 0h, bioreplicate 2


title: MMVE003_MOCK_0HRS_RNA_B

source_name: Primary human microvascular endothelial cells, mock-inoculated, 0h, bioreplicate 2


title: MMVE003_MOCK_0HRS_RNA_D

source_name: Primary human microvascular endothelial cells, mock-inoculated, 0h, bioreplicate 4


title: MHAE003_MOCK_48HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 5

value: Primary human airway epithelial cells

value: Mock


title: MHAE003_icMERS_48HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 5


title: MHAE003_icMERS_48HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 4


title: MHAE003_MOCK_48HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 1


title: MHAE003_icMERS_48HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 3


title: MHAE003_MOCK_48HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 3


title: MHAE003_icMERS_48HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 2


title: MHAE003_MOCK_36HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 4


title: MHAE003_icMERS_48HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 1


title: MHAE003_MOCK_36HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 5


title: MHAE003_MOCK_36HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 3


title: MHAE003_MOCK_48HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 4


title: MHAE003_icMERS_36HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 4


title: MHAE003_MOCK_24HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 5


title: MMVE003_icMERS_12HRS_RNA_D

source_name: Primary human microvascular endothelial cells, icMERS-inoculated, 12h, bioreplicate 4


title: MHAE003_icMERS_36HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 3


title: MHAE003_icMERS_36HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 5


title: MHAE003_MOCK_36HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 1


title: MHAE003_icMERS_36HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 2


title: MHAE003_MOCK_24HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 4


title: MHAE003_icMERS_36HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 1


title: MHAE003_MOCK_24HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 1


title: MHAE003_icMERS_24HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 5


title: MHAE003_icMERS_24HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 4


title: MHAE003_MOCK_24HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 2


title: MHAE003_MOCK_24HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 3


title: MHAE003_MOCK_12HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 3


title: MHAE003_MOCK_12HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 5


title: MHAE003_MOCK_12HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 4


title: MHAE003_MOCK_48HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 2


title: MHAE003_icMERS_24HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 2


title: MHAE003_icMERS_24HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 1


title: MHAE003_MOCK_12HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 1


title: MHAE003_MOCK_12HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 2


title: MHAE003_icMERS_24HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 3


title: MHAE003_icMERS_12HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 4


title: MHAE003_icMERS_12HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 1


title: MHAE003_icMERS_12HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 2


title: MHAE003_icMERS_0HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 5


title: MHAE003_MOCK_0HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 3


title: MHAE003_icMERS_12HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 3


title: MHAE003_MOCK_0HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 2


title: MHAE003_MOCK_0HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 4


title: MHAE003_MOCK_0HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 5


title: MHAE003_MOCK_0HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 1


title: MHAE003_icMERS_0HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 2


title: MFB003_MOCK_48HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 4

value: primary fibroblasts


title: MHAE003_icMERS_12HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 5


title: MHAE003_icMERS_0HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 4


title: MFB003_MOCK_48HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 3


title: MFB003_MOCK_36HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 5


title: MFB003_MOCK_36HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 4


title: MHAE003_icMERS_0HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 1


title: MFB003_MOCK_36HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 1


title: MFB003_icMERS_48HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 5


title: MFB003_MOCK_48HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 2


title: MFB003_icMERS_48HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 4


title: MFB003_icMERS_48HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 1


title: MFB003_MOCK_36HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 2


title: MFB003_MOCK_36HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 3


title: MFB003_icMERS_48HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 2


title: MFB003_MOCK_48HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 5


title: MFB003_icMERS_36HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 5


title: MFB003_icMERS_48HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 3


title: MFB003_icMERS_36HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 1


title: MFB003_icMERS_36HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 2


title: MFB003_MOCK_24HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 5


title: MFB003_MOCK_48HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 1


title: MHAE003_icMERS_0HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 3


title: MFB003_icMERS_36HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 4


title: dorsolateral prostate miR32

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

description: technical replicate 1

hyb_protocol: The labeled RNA was purified using Quiagen Rneasy mini spin columns and quantified using NanoDrop UV-VIS Spectrophotometer ver. The hybridization was performed in Agilent 2X GE Hybridization Buffer HI-RPM according to Agilent guidelines in Agilent hybridization oven at 65 degrees C 10rpm for 19 hours.

scan_protocol: Scanned on Agilent scanner G2565CA. Images were quantified using Agilent Feature Extraction ver. 11.0.1.1

data_processing: As a quality filtering step, only probes detected in both arrays were included (flog flitering in Genespring software) and the remaining data was normalized by sample wise median removal.

source_name: Mouse, dorsolateral prostate

label_protocol: 100ng of total RNA were labeled using the Agilent Low Input Quick Amp labeling kit according to the manufacturer’s protocol

growth_protocol: Dorsolateral prostates of FVB/N mice collected at 6 months of age

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: FVB/N

value: dorsolateral prostate

tag: age

value: 6 months

tag: genotype

value: wild type

value: ARR2PB-miR32 transgenic


title: ventral prostate miR32

description: technical replicate 1

data_processing: As a quality filtering step, only probes detected in both arrays (per tissue) were included (flog flitering in Genespring software) and the remaining data was normalized by sample wise median removal.

source_name: Mouse, ventral prostate

growth_protocol: Ventral prostates or Dorsolateral prostates of FVB/N mice collected at 6 months of age

value: FBV/N

value: ventral prostate


title: ventral prostate miR32 dye-swap replicate

description: technical replicate 2 (dye swap)


title: MFB003_MOCK_24HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 2


title: dorsolateral prostate miR32 dye-swap replicate

description: technical replicate 2 (dye swap)


title: MFB003_MOCK_24HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 3


title: MFB003_icMERS_24HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 4


title: MFB003_icMERS_24HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 3


title: MFB003_MOCK_24HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 4


title: MFB003_icMERS_24HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 5


title: MFB003_MOCK_24HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 1


title: MFB003_icMERS_24HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 1