title: VdG66

description:
Replicate 2
idat file: 9256321012

value: VCaP

value: Prostate Cancer Cell Line


title: VdG46

status: Public on Feb 24 2016

type: RNA

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

country: USA

institute: The University of Illinois at Chicago

description:
Replicate 3
idat file: 9257302051

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: VCaP, 48hrs MDV3100

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

growth_protocol: Cells grown in their respective growth media with 10% FBS and Pen/Strep.  Cells were treated either with DMSO vehicle (Parental Untreated); 10uM MDV3100/Enzalutamide for 48 hours (48hrs MDV3100), or for at least 6 months in 10uM MDV3100 (MDV3100-Resistant)

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

treatment_protocol: Cells were treated with vehicle (DMSO), or 10uM enzalutamide and RNA extracted directly from plate.

tag: cell line

tag: tissue


title: VdG10

description:
Replicate 4
idat file: 9257302001


title: 546775_A07_532

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkey.

hyb_protocol: Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA (see www.nimblegen.com).

data_processing: The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.)

organism: Macaca fascicularis

source_name: kidney, female, China / Mainland Southeast Asia

label_protocol: Labeling was performed using 10 ng of total RNA as input following the standard operating protocol on a Biomek FXp workstation (Beckman Coulter Inc., Brea, CA, USA) with the NuGen Ovation Pico WTA System V2 (NuGEN Technologies, Inc., SanCarlos, CA, USA; see http://www.nugeninc.com). Cy3 labeling of cDNA was performed with the Roche NimbleGen One Color DNA Labeling Kit according to manufacturer's instructions (NimbleGen Systems Inc., Madison, WI USA; see www.nimblegen.com).

growth_protocol: Tissue samples were supplied by contract research organizations and taken from untreated animals of GLP drug-safety studies in accordance with current animal welfare standards. Tissues were stored at -80°C until RNA extraction.

extract_protocol: Tissues were homogenized in tubes prefilled with 1.4 mm ceramic beads and Qiagen's lysis reagent RLT using a FastPrep-24 instrument (MP Biomedicals, Solon, OH, USA). Total RNA from lysates was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Untreated

value: kidney

tag: gender

value: female

tag: age

value: 3 years

tag: weight

value: ~4 kg

tag: origin

value: China / Mainland Southeast Asia

tag: monkey identifier


title: 545248_A06_532

source_name: kidney, female, Vietnam

value: Vietnam


title: Whole Blood + IFN-g 24hrs (3)

city: Thousand Oaks

first: Mara

last: Campbell

state: CA

address: 1 Amgen Center Drive

institute: Amgen

description: Loop design

hyb_protocol: Overnight hybridizations at 650C per manufacturer’s instructions

scan_protocol: All arrays were scanned on the Agilent Surescaner Scanner (Agilent p/n G2600D). Agilent Scan Control Software version 9.1.5.1 was used for array scanning. Array files were processed using Agilent Feature Extraction software 11.0.1.1.

data_processing: Extracted feature intensities for each channel on each array were processed separately by subtracting the lower 0.1th percentile from all intensities and then taking the log base 2. The transformed intensities were mapped using a non-linear function to a proprietary target density to ensure the distributions of the intensities were comparable between arrays and channels. Samples were processed in batches that roughly corresponded to samples from individual cohorts but with a small number of samples repeated between batches to allow estimation and removal of additive linear effects of batch and channel. Finally, replicates of any identical sequences on the array were averaged to produce values called gene intensities. Supplied data tables includes normalized log base 2 intensities.

label: Cy3, Cy5

source_name: healthy volunteer

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color (Agilent Cat # 5188-5340) per manufacturer’s instructions.

extract_protocol: Total RNA was isolated from PAXgene whole blood tubes (BD Cat # 762165) using the PAXgene RNA Kit. (Qiagen Cat # 762164) on the Qiacube automated sample prep system

treatment_protocol: Blood from healthy volunteers (n=4) was collected into sodium heparin tubes, and then untreated or treated with 294 pM recombinant human IFN-γ for 0, 24, or 48 hours with incubation at 37oC, 5 % CO2. The blood was then added to PAXgene tubes and processed for RNA purification. Twenty six subjects with stable, mild to moderate SLE were administered placebo or a single dose of AMG 811 ranging from 2 mg to 180 mg SC or 60 mg IV. Whole blood PAXgene tube samples were collected from all cohorts at baseline, day-1 (pre-dose), and at days 15, 56, and end of study (EOS) after treatment Arrays were hybridized in a Loop design.

value: Whole Blood

tag: subject number

value: Healthy volunteer 3

tag: subject id

tag: treatment day

tag: dose


title: 546775_A05_532


title: 545247_A04_532


title: Whole Blood + IFN-g 24hrs (2)

description: Loop design

value: Healthy volunteer 2


title: Whole Blood + IFN-g 3 (Time 0)

description: Loop design


title: 545247_A01_532

source_name: kidney, male, Philippines

value: male

value: Philippines


title: Whole Blood + IFN-g 2 (Time 0)

description: Loop design


title: Whole Blood + IFN-g 48hrs (1)

description: Loop design

value: Healthy volunteer 1


title: VdG20

description:
Replicate 1
idat file: 9257302016


title: 545248_A10_532

value: 5.5 years

value: ~6 kg


title: VdG80

description:
Replicate 2
idat file: 9255013011


title: VdG32

description:
Replicate 4
idat file: 9257302030

source_name: LNCaP, Parental Untreated

value: LNCaP


title: VdG15

description:
Replicate 2
idat file: 9257302016


title: 546767-MAFA_PH_2-vs-MAFA_MU_ref

type: genomic

description: array CGH fluorescence intensity ratio of Cy3-labeled DNA fragments  from test samples (ch1) relative to Cy5-labeled DNA fragments from the reference (ch2)

hyb_protocol: Hybridization was performed with 34 ug of Cy3- and 34 ug of Cy5-labeled DNA for 72 h at 42°C following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Microarray drying and scanning was performed in an ozone-free NoZone workspace consisting of a NoZone enclosure and a NoZone ozone scrubber (AlphaMetrix Biotech GmbH, Rödemark, Germany). For scanning a NimbleGen MS200 Microarray Scanner was used at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing:
array CGH probe intensities were subjected to LOESS spatial correction (Smyth GK, Speed TP (2003): Normalization of cDNA microarray data. Methods), background correction, and q-spline normalization (Workman et al. (2002): A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol) as implemented in the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI). In addition, the GC base pair content of each probe (120405_Cynomolgus5_CGH_UX1.gcstats) was used for the generation of waviness corrected, normalized array CGH probe intensity ratios as implemented in the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI). Copy number changes were identified with the segMNT v1.1 algorithm (Molla M (2007): Novel Uses for Machine Learning and Other Computational Methods for the Design and Interpretation of Genetic Microarrays. In PhD thesis University of Wisconsin-Madison Department of Computer Sciences) with a min. number of 5 probes per segment as implemented into the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI).
normalized log2 (test=ch1/reference=ch2) ratio per probe for raw data file and log2 segmentation value for processed data file

molecule: genomic DNA

label_protocol: 500 ng of DNA from one animal tissue at a time and 500 ng of reference DNA - pooled DNA from blood specimens of 25 male Cynomolgus monkeys - were used for labeling by an isothermal Klenow fill-in reaction with either Cy3 or Cy5 random nonamer primer using the Roche NimbleGen Dual color labeling kit according to manufacturer's instructions (Roche NimbleGen, Inc., Madison, WI). Labeling Hybridization Controls were spiked-in as quality controls for copy number variation detection (Roche NimbleGen, Inc., Madison, WI).

growth_protocol: Tissue and blood samples were supplied by contract research organizations and taken from untreated animals of GLP drug-safety studies in accordance with current animal welfare standards. Tissues were stored at -80°C until DNA extraction.

extract_protocol: Spleen tissues were homogenized in tubes prefilled with 1.4 mm ceramic beads and QiaGen’s lysis reagent ALT using a FastPrep-24 instrument (MP Biomedicals, Solon, OH, USA) and then incubated with Proteinase K at 55°C for 1 h followed by RNAse A treatment at 25°C for 2 min (Qiagen Inc., Valencia, CA). Blood specimens (0.2 ml) were incubated at 70°C for 10 min in QiaGen’s lysis reagent ALT with Proteinase K and RNAse A. Genomic DNA from lysates was extracted using the QIAamp Mini kit (Qiagen Inc., Valencia, CA, USA).  DNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Ch1: DNA recovered from fresh frozen tissue from untreated Cynomolgus monkey

value: Female

value: 6.8 years

value: ~ 5 kg

treatment_protocol: Ch2 reference DNA:  pooled DNA from blood specimens of 25 male Cynomolgus monkeys

value: Male

value: 3-10 years

tag: weigth

value: Mauritius


title: Whole Blood + IFN-g 48hrs (2)

description: Loop design


title: VdG25

description:
Replicate 4
idat file: 9257302030

source_name: VCaP, MDV3100-Resistant

value: VCaP

value: Prostate Cancer Cell Line


title: ΔglcB PQ 1mM 2

city: Anam-Dong, Seungbuk-Ku

first: Sungeun

last: Ahn

state: Seoul

address: Anamro

department: molecular microbiology

country: South Korea

institute: Korea university

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).

organism: Pseudomonas aeruginosa PAO1

source_name: PQ 1mM

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: Overnight culture was diluted 1:100 in 5 mL LB medium at 37°C with aeration.

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

treatment_protocol: Exponential phase cell was used for microarray analysis. In case of paraquat treatment, 1mM concentration of paraquat was added on exponential phase cell for 15min.

tag: strain

value: ΔPA0482 transposon insertion mutant

tag: treatment

value: 1mM PQ


title: Whole Blood + IFN-g 24hrs (1)

description: Loop design

value: Whole Blood


title: ΔglcB control 2

source_name: LB control

value: LB broth


title: 545248_A11_532

source_name: kidney, female, Philippines

value: kidney

value: female

value: 6.6 years

value: ~5 kg

value: Philippines


title: ΔaceA PQ 1mM 2

value: ΔPA2634 transposon insertion mutant


title: ΔaceA control 2


title: 545247_A08_532

value: 6.8 years


title: 545247_A05_532

value: 5.5 years


title: VdG82

description:
Replicate 3
idat file: 9255013011

source_name: LNCaP, 48hrs MDV3100

value: LNCaP


title: 543016_A01_532

source_name: heart, male, Mauritius

value: heart

value: male

value: 4 years


title: VdG79

description:
Replicate 1
idat file: 9255013011

value: Prostate Cancer Cell Line


title: Whole Blood + IFN-g 1 (Time 0)

description: Loop design

value: Healthy volunteer 1


title: VdG48

description:
Replicate 4
idat file: 9257302051


title: MPA01 PQ 1mM 2

value: 1mM PQ


title: VdG13

description:
Replicate 1
idat file: 9257302016


title: VdG23

description:
Replicate 4
idat file: 9257302016

source_name: LNCaP, MDV3100-Resistant


title: MPA01 control 2


title: ΔglcB PQ 1mM 1

value: ΔPA0482 transposon insertion mutant


title: VdG57

description:
Replicate 2
idat file: 9256321010


title: VdG11

description:
Replicate 2
idat file: 9257302001


title: 543052_A02_532

value: Mauritius


title: VdG69

description:
Replicate 3
idat file: 9256321012


title: 543016_A12_532


title: 544133_A09_532


title: VdG36

description:
Replicate 1
idat file: 9257302030


title: 544133_A01_532

source_name: heart, female, Mauritius

value: ~4 kg


title: ΔglcB control 1

value: LB broth


title: ΔaceA control 1


title: VdG67

description:
Replicate 3
idat file: 9256321012

source_name: LAPC-4, MDV3100-Resistant


title: MPA01 PQ 1mM 1


title: VdG16

description:
Replicate 4
idat file: 9257302016


title: MPA01 control 1


title: 546775_A02_532

value: kidney

value: 6.5 years

value: ~6 kg


title: VdG52

description:
Replicate 2
idat file: 9256321010


title: ΔaceA PQ 1mM 1

value: ΔPA2634 transposon insertion mutant


title: lacZ_UAS-dpp_rep3

city: Santiago de Chile

first: Calixto

last: Dominguez

state: Región Metropolitana

address: Zanartu 1482

department: Center for Bioinformatics and Genome Biology

country: Chile

institute: Fundación Ciencia y Vida

description: cDNA samples from UAS-dpp embryos were tagged with Cy5 and compared with samples tagged with Cy3 from UAS-lacZ expresed embryos

hyb_protocol: Two independent control (nos-Gal4>lacZ) and experimental (nos-Gal4>UAS-dpp) samples (biological replicates) were hybridized onto nine slides, and dye-swap replicates were conducted in the first hybridization. Oligonucleotide D. melanogaster microarrays were purchased from Microarray Inc. and contained 14,593 probes designed from the Gadfly release 3.1 database, they represent 13,664 genes and 17,899 transcripts. Oligonucleotides corresponding to genes coding for the spikes RNAs were randomly distributed in different blocks throughout the array. Microarrays were pre-washed in 50 mL of  pre-hybridization buffer (5 × SSC, 0.1% SDS, 0.1% BSA Fraction V) for 60 min at 42 ˚C, then 5 times in ddH2O for 1 min at room temperature. After the pre-washing, microarrays were dried by centrifugation. Then, microarrays were hybridized with labelled probes in a hybridization solution containing 20% formamide, 5X SSC and 0.1% SDS. Hybridized slides were sequentially washed 4 times by 15 min in 2X SSC, 0.1%SDS, 4 times by 5 min in0.1× SSC, 0.1% SDS and then rinsed 4 times by 1 min in 0.1X SSC.

scan_protocol: Images were processed using the software ScanArray Express (Perkin Elmer) to align both channels at different PTM gain. Image quality was assessed by q.com descriptors included within the R function. Additionally, control spots (spike controls, empty spots and random oligomers) were analysed separately to distinguished high quality hybridized slides.

data_processing: Data from selected slides were processed to remove noise using normexp, normalized by block with loess  and differentially expressed genes were identified  using the statistical R package LIMMA. LIMMA is able to estimates the coefficients of the contrast matrix between the conditions and fits a linear model for each gene. Estimation of significance is based on a hypothesis test that uses the statistical t-moderate associated to p-value. In addition, a Bayesian statistical analysis was included which is based on the calculation of the posterior probability estimated from prior probability conditionality. P values were adjusted by the method of Benjamini and Hochberg to control the rate of false values. Genes with statistically significant changes in expression (adjusted P-value < 0.05) were selected.

organism: Drosophila melanogaster

source_name: Expression lacZ in 5-7 staged embryos

label_protocol: To prepare the fluorescent probes, total RNA was amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Texas) following the manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 1µg of total RNA and then converted into ddcDNA. The amino allyl aRNA was obtained by in vitro transcription with amino allyl UTP nucleotide. 5 µg of this aRNA was coupled with NHS-activated Cy3 or Cy5 dyes (Amersham). Labelled aRNA was purified using QIAquick columns (Qiagen), yield and specific activity of each probe was determined by absorption spectroscopy. Pairs of Cy3 and Cy5 labeled aRNA probes (2.5 µg/probe) were pooled, fragmented (Ambion RNA Fragmentation Reagent) and hybridized to the D. melanogaster microarrays. The experimental samples were tagged with Cy5 and the control samples with Cy3 and dye swapped.

growth_protocol: Adults were grown at 22 ºC on standard cornmeal, molasses, agar and yeast medium

extract_protocol: Total RNA from nos-Gal4>lacZ, nos-Gal4>UAS-dpp embryos (N=100-200) at late stage 5 (cellularization) to stage 7 (gastrulation) of development was extracted as described in Zuñiga et al. (BMC Biology. 7:61, 2009). For microarray experiments, 50 pg of the spikes mRNAs were added to each RNA preparation prior to labelling. The three spikes genes were Bacillus subtilis tryptophan operon, trpCDEF (ATCC 87485), diaminopimelate decarboxylase gene lysA (ATCC 87482) and dihydrodipicolinate reductase gene, dapB, (ATCC 87486). Each vector consists of bacterial cDNA cloned into the XhoI and BamHI sites of a modified pBluescript II-KS+ vector in which a poly(dA) stretch follows the BamHI restriction site. From each vector, RNA transcripts containing a poly(A) tract were generated using the Riboprobe Combination System (Promega).

treatment_protocol: Flies carrying UAS-dpp have been described (FlyBase, http://flybase.bio. indiana.edu/), they were crossed to a Gal4 driver in which the Gal4 protein is expressed under the control of the maternal gene nanos promoter (P{GAL4-nos.NGT}40).

tag: genotype/variation

tag: development stage

value: Embryo stage 5-7

source_name: Overexpression ectopic Dpp in 5-7 staged embryos


title: 543048_A10_532

source_name: heart, female, Vietnam

value: female

value: 3 years

value: Vietnam


title: 543052_A11_532

value: heart


title: 544133_A10_532

source_name: heart, female, China / Mainland Southeast Asia

value: China / Mainland Southeast Asia


title: 543016_A02_532

value: 4 years


title: VdG31

description:
Replicate 4
idat file: 9257302030

source_name: LAPC-4, Parental Untreated

value: Prostate Cancer Cell Line


title: VdG26

description:
Replicate 1
idat file: 9257302030


title: 543052_A10_532


title: lacZ_UAS-dpp_rep2


title: VdG45

description:
Replicate 4
idat file: 9257302051

source_name: LAPC-4, 48hrs MDV3100


title: lacZ_UAS-dpp_rep1


title: 543048_A07_532


title: 543016_A03_532

source_name: heart, male, Vietnam

value: male

value: ~5 kg


title: VdG81

description:
Replicate 3
idat file: 9255013011


title: UAS-dpp_LacZ_rep6

description: cDNA samples from UAS-dpp embryos were tagged with Cy3 and compared with samples tagged with Cy5 from UAS-lacZ expresed embryos


title: 544133_A07_532


title: VdG60

description:
Replicate 3
idat file: 9256321010


title: VdG70

description:
Replicate 1
idat file: 9256321012


title: 543048_A06_532


title: UAS-dpp_LacZ_rep5


title: UAS-dpp_LacZ_rep3


title: UAS-dpp_LacZ_rep4


title: 544133_A08_532

source_name: heart, male, Philippines

value: Philippines


title: UAS-dpp_LacZ_rep2


title: 543016_A08_532

value: 5.5 years


title: VdG59

description:
Replicate 2
idat file: 9256321010


title: VdG4

description:
Replicate 1
idat file: 9257302001


title: 546775_A09_532

source_name: kidney, female, China / Mainland Southeast Asia

value: ~4 kg


title: VdG68

description:
Replicate 4
idat file: 9256321012

source_name: CWR-R1, Parental Untreated


title: UAS-dpp_LacZ_rep1


title: 543016_A09_532


title: KBC5_miRNA-4_0

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC5

hyb_protocol: Samples were hybridized on the Affymetrix 4.0 microarrays overnight.

scan_protocol: Washing, staining and scanning of the arrays was performed using the Command Console, and the spike-in analysis of control oligonucleotides was evaluated using the Expression Console.

data_processing: Data were analyzed using the recommended Transcriptome Analysis Console (TAC) software from Affymetrix. Only human microRNAs were included in the analysis, resulting in reduced data set of 6,631 rows.

source_name: superficial temporal artery tissue

label_protocol: Following the manufacturer’s protocol, 130ng of total RNA was labeled with the FlashTag Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA). To confirm efficient labeling the ELOSA QC assay (Affymetrix, Santa Clara, CA) was performed.

growth_protocol: Human samples of cerebral aneurysm and superficial temporal arteries were extracted surgically from patients undergoing craniotomy for cerebral aneurysms.

extract_protocol: After successful clipping of the aneurysm, the dome was resected with the use of micro-scissors and bayonetted forceps (not used before during the case) and was placed immediately into a vial containing RNAlater solution (Ambion, Austin, TX) to protect RNA from degradation. The vials were immediately frozen to -80 °C. Small RNA was then size selected with mirVana miRNA isolation kit.

tag: subject status

tag: subject/sample id

value: superficial temporal artery (STA) tissue


title: KBC8_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC8

value: patients undergoing craniotomy for cerebral aneurysms

tag: tissue


title: KBC7_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC7


title: 544133_A02_532

tag: gender


title: 543016_A05_532

source_name: heart, female, Philippines

tag: age


title: VdG53

description:
Replicate 3
idat file: 9256321010

tag: cell line


title: VdG6

description:
Replicate 1
idat file: 9257302001


title: KBC3_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC3


title: KBC15_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC15


title: RAW 264.7, LPS 1

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

country: Germany

institute: TWINCORE

hyb_protocol: GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit P/N 702808 Rev. 6

scan_protocol: Affymetrix® GeneChip® Command Console® User Manual (P/N 702569).

data_processing: The data were preprocessed, normalised and analysed using the GCRMA and limma packages from R/Bioconductor software environment. The CDF was used according to GPL18802 and submitted the unique list of IDs and their expression values.

organism: Mus musculus

source_name: RAW264.7 Macrophages

label_protocol: The Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays Part Number 4425209 Rev. C 09/2009

growth_protocol: The murine RAW264.7 macrophage cell line was cultured in DMEM medium (Invitrogen, Life Technologies, Carlsbad, California) with 10% Fetal Bovine Serum (FBS), 0.1mg/mL streptomycin (Invitrogen, Life Technologies, Carlsbad, California) and 100U/mL penicillin (Invitrogen, Life Technologies, Carlsbad, California).

extract_protocol: Total RNA was purified from cultured cells using the Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: For the experiments, lipopolysaccharide (LPS, Sigma) was used at a final concentration of 10ng/mL.

tag: cell type

value: RAW264.7 Macrophages


title: 544133_A04_532

value: 6.6 years

tag: weight

tag: origin

tag: monkey identifier


title: RAW 264.7, LPS 3


title: KBC16_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC16


title: RAW 264.7, LPS 2


title: KBC14_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC14


title: RAW 264.7, Control 3


title: VdG30

description:
Replicate 2
idat file: 9257302030


title: RAW 264.7, Control 2


title: VdG63

description:
Replicate 4
idat file: 9256321012

source_name: CWR-R1, 48hrs MDV3100


title: KBC12_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC12


title: VdG12

description:
Replicate 3
idat file: 9257302001


title: VdG28

description:
Replicate 1
idat file: 9257302030


title: VdG8

description:
Replicate 4
idat file: 9257302001

source_name: CWR-R1, MDV3100-Resistant


title: RAW 264.7, Control 1


title: VdG17

description:
Replicate 3
idat file: 9257302016


title: VdG22

description:
Replicate 2
idat file: 9257302016


title: KBC11_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC11


title: KBC10_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Superficial temporal artery sample KBC10


title: VdG2

description:
Replicate 3
idat file: 9257302001

source_name: LNCaP, Parental Untreated

value: LNCaP


title: KB_20_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB20

source_name: cerebral aneurysm tissue

value: cerebral aneurysm tissue


title: VdG75

description:
Replicate 2
idat file: 9255013011


title: VdG33

description:
Replicate 1
idat file: 9257302030


title: KB5_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB5


title: 543052_A08_532

value: female

value: 6.8 years


title: KB8_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB8


title: LNCaP_normoxia_2_Scr

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA and samples were hybridized on Agilent Human Gene Expression 4x44K v2 Microarray Kit, AMDID 026652.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 5um scan resolution

data_processing: Data was processed with Agilent Feature Extraction 10.10, quantile normalized and analyzed in Agilent GeneSpring 11.

label_protocol: Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0

growth_protocol: Standard procedures for LNCaP cells.

extract_protocol: Qiagen RNeasy kit

treatment_protocol: 24 h hypoxia (1% O2)

tag: condition

value: normoxia

tag: replicate

tag: sirna

value: Scr

tag: group

value: Sh Scr N

tag: ID


title: High Zinc + Negative Control siRNA (rep2)

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description:
replicate 2
101723-11

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using GeneSpring GX (v11, Agilent). Raw data were transformed using a log2 transformation, and normalized with the quantile normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

source_name: Caco-2 Control siRNA 150µM Zinc

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

growth_protocol: Human epithelial colonic adenocarcinoma, Caco-2, cells were grown in Dulbeco’s Modified Eagle medium, containing 10% (v/v) fetal calf serum; 60 μg/ml gentamycin and 1% (v/v) non essential amino acids (Sigma).

extract_protocol: Total RNA prepared using Trizol reagent [Invitrogen] following manufacturer’s protocol, RNA integrity checked using Agilent Bioanalyser.

treatment_protocol: Cells were transfected with oligonucleotides using lipofectamine RNAiMAX (Invitrogen) according to manufacturer's instructions.

value: Negative Control siRNA (ON-TARGETplus Non-targeting siRNA #1; Thermo Scientific)

tag: zinc concentration


title: KB4_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB4


title: LNCaP_normoxia_3_Scr


title: LNCaP_normoxia_1_Scr


title: KB6_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB6


title: LNCaP_hypoxia_3_Scr

value: hypoxia

value: Sh Scr H


title: KB3_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB3


title: LNCaP_normoxia_3_Rb

value: Rb

value: Sh Rb N


title: High Zinc + Negative Control siRNA (rep3)

description:
replicate 3
101723-12

value: Human epithelial colonic adenocarcinoma, Caco-2


title: LNCaP_normoxia_1_Rb


title: High Zinc + Negative Control siRNA (rep1)

description:
replicate 1
101723-10


title: Low Zinc + Negative Control siRNA (rep2)

description:
replicate 2
101723-08

source_name: Caco-2 Control siRNA 3µM Zinc


title: KB7_miRNA-4_0

description: Affymetrix GeneChip miRNA array 4.0 for Cerebral Aneurysm sample KB7


title: LNCaP_hypoxia_2_Rb

value: Sh Rb H


title: High Zinc + MTF1 siRNA (rep3)

description:
replicate 3
101723-06

source_name: Caco-2 MTF1 siRNA 150µM Zinc

value: MTF1 siRNA (ON-TARGETplus, Thermo Scientific)


title: OVCA429 with shGRHL2 OV429_shG210_2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: GRHL2 knockdown

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Gene 2.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0002 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

source_name: Ovarian cancer cell line OVCA429

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

growth_protocol: Cells were grown in DMEM 10% FBS, 37°C in 5% CO2, 3µg/ml puromycin

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

treatment_protocol: Cells were infected with shRNAs (control and GRHL2-targeting shRNAs) by lentivirus, followed by puromycin selection.

tag: shconstruct


title: LNCaP_hypoxia_1_Scr


title: Low Zinc + Negative Control siRNA (rep1)

description:
replicate 1
101723-07


title: OVCA429 with shGRHL2 OV429_shG212_1

description: GRHL2 knockdown


title: High Zinc + MTF1 siRNA (rep2)

description:
replicate 2
101723-05


title: Stealth-D3 vs Stealth-CTR cells (dye-swap)

city: Naples

first: Monica

last: Dentice

address: Via S. Pansini 5

department: Department of Clinical Medicine and Surgery

country: Italy

institute: University of Naples "Federico II"

description:
Each channel represents: transfected BCC cells, pool of 3 different experiments
Slide13768401 1192A cy5 vs 1192B cy3
1192A = Stealth-D3 transfected BCC cells, 1192B = Stealth-ctr transfected BCC cells

hyb_protocol: miRCURY LNA (TM) microRNA Array microarray kit instruction manual v9.2

scan_protocol: Scanner=GenePix 4000B [92213]

data_processing:
Genepix software package was used to generate an intensity value for each probe by taking the median spot intensity and subtracting the median local background. Bad spots or areas of the array with obvious defects were manually flagged. Flagged spots were not included in subsequent analyses.
LOWESS normalized, background subtracted data obtained from log2 of processed Cy5 signal/processed Cy3 signal. Agilent software was used.

label_protocol: miRCURY LNA (TM) microRNA Array Power Labeling Kit

growth_protocol: BCC cells were cultured under low calcium conditions with 8% Ca2+-chelated fetal bovine serum and keratinocyte growth factor

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Next we purifed with the RNeasy MinElute Cleanup Kit.

treatment_protocol: BCC cells were transfected with D3-stealth and ctr-stealth oligos and harvested 48 hours following the transfection.

value: BCC cell line G2N2C

tag: transfection

value: Stealth-ctr


title: High Zinc + MTF1 siRNA (rep1)

description:
replicate 1
101723-04


title: OVCA429 with shGRHL2 OV429_shG212_3

description: GRHL2 knockdown


title: Low Zinc + Negative Control siRNA (rep3)

description:
replicate 3
101723-09


title: LNCaP_normoxia_2_Rb

value: LNCaP


title: LNCaP_hypoxia_1_Rb


title: Low Zinc + MTF1 siRNA (rep3)

description:
replicate 3
101723-03

source_name: Caco-2 MTF1 siRNA 3µM Zinc


title: LNCaP_hypoxia_2_Scr


title: OVCA429 with shGRHL2 OV429_shG212_2

description: GRHL2 knockdown


title: OVCA429 with shNon control OV429_shNon_2

description: Control

value: shNon


title: LNCaP_hypoxia_3_Rb


title: Low Zinc + MTF1 siRNA (rep2)

description:
replicate 2
101723-02


title: OVCA429 with shGRHL2 OV429_shG210_1

description: GRHL2 knockdown


title: mice treated with cisplatin

status: Public on Feb 23 2016

city: Beijing

first: Chong

last: Li

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Gene expression data from tumors with drug treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: tumor tissue

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

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

tag: protocol

value: LNCaP cells were subcutaneously injected into backs of NOD/SCID mice

tag: treatment

value: mice treated with cisplatin

value: tumor


title: Stealth-D3 vs Stealth-CTR cells

description:
Each channel represents: transfected BCC cells, pool of 3 different experiments
Slide13768400 1192A cy3 vs 1192B cy5
1192A = Stealth-D3 transfected BCC cells, 1192B = Stealth-ctr transfected BCC cells


title: C57/BL6 fed with MCD diet during 3 weeks before PH70%  and continuous with the same diet for other 2 weeks 4

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

country: Spain

institute: IIB ALBERTO SOLS

description:
MCD1_2_4_T15
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH

hyb_protocol: Preparation of probes and hybridization was performed as described One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies. Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60C for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65C for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37C (1 minute)

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project. Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: C57/BL6 fed with MCD diet during 3 wks after that we developed 70% PH and continuous with the same diet for other two wks

label_protocol: RNA was labeled with Cy3 by using the SuperScript indirect cDNA labeling system (invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were done with livers from diferent treated animals. Total RNA was extracted from livers at final treatment period. The CHD animals were fec on standard diet for during 3 weeks. MCD animals were fed on methionine and choline deficient (MCD) diet during 3 weeks. CG49  were fed on standard diet and treated during 2 weeks with 4,4 mg/kg/day of dual agonist of GLP1R/GCGR every two days. MG49 animals were fed on MCD diet during 3 weeks, after first week were treated with 4,4 mg/kg/day of dual agonist of GLP1R/GCGR every two days. T15 refeers to livers from animals sacrified 2 weeks after partial hepatectomy (70%) and treated before and after PH with the same diet and treatment were recipt the same diet and treatments

extract_protocol: Total RNA was isolated from livers frozen in liquid nitrogen with Trizol® reagent (Invitrogen, Madrid, Spain) and purified using the RNeasy midi Kit from Qiagen according to manufacturer’s instructions. Quality of the RNA samples was ensured in a Bioanalyzer 2100.

tag: strain

tag: gender

value: male

tag: tissue

value: liver

tag: sample group

value: methyl and choline deficient diet during 3 wks after that we developed 70% partial hepatectomy and continuous with the same diet for other two wks


title: C57/BL6 fed with MCD diet during 3 weeks before PH70%  and continuous with the same diet for other 2 weeks 3

description:
MCD1_2_3_T15
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH


title: C57/BL6 fed with chow diet treated with dual agonist of GLP1R/GCGR  during 2 weeks before and after 70% PH 4

description:
CG491_1_4_T15
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals

source_name: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR during two wks and two wks after 70 % PH treated with dual agonist

value: standard diet treated with dual agonist of GLP1R/GCGR during two wks and two wks after 70 % partial hepatectomy treated with dual agonist


title: C57/BL6 fed MCD diet (1w).After were fed with same diet and treated with dual agonist during 2w before and after 70%PH 3

description:
MG49-1_2_3_T15
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH

source_name: C57/BL6 fed with MCD diet during 3 wks and treated with dual agonist of GLP1R/GCGR during two wks after that were hepatectomized (70%PH) and continuous with the same diet and treatment

value: methyl and choline deficient diet during 3 wks and treated with dual agonist of GLP1R/GCGR during two wks after that were hepatectomized (70%PH) and continuous with the same diet and treatment


title: C57/BL6 fed MCD diet (1w).After were fed with same diet and treated with dual agonist during 2w before and after 70%PH 4

description:
MG49-1_2_4_T15
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH


title: C57/BL6 fed with chow diet treated with dual agonist of GLP1R/GCGR  during 2 weeks before and after 70% PH 2

description:
CG491_1_2_T15
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals


title: mice treated with vehicle PBS

description: Gene expression data from tumors with PBS treatment

value: mice treated with vehicle


title: C57/BL6 fed MCD diet (1w).After were fed with same diet and treated with dual agonist during 2w before and after 70%PH 1

description:
MG49-1_2_1_T15
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH


title: C57/BL6 fed MCD diet (1w).After were fed with same diet and treated with dual agonist during 2w before and after 70%PH 2

description:
MG49-1_2_2_T15
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH


title: C57/BL6 fed with MCD diet during 3 weeks before PH70%  and continuous with the same diet for other 2 weeks 2

description:
MCD1_2_2_T15
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH


title: C57/BL6 fed with chow diet treated with dual agonist of GLP1R/GCGR  during 2 weeks before and after 70% PH 3

description:
CG491_1_3_T15
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals


title: C57/BL6 fed with chow diet treated with dual agonist of GLP1R/GCGR  during 2 weeks before and after 70% PH 1

description:
CG49_1_1_T15
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals


title: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy 4

description:
CHD1_1_4_T15
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy

source_name: C57/BL6 fed with standard diet two wks after 70 % PH

value: standard diet two wks after 70 % partial hepatectomy


title: NGFR_4

city: Berlin

first: Christian

last: Regenbrecht

address: Chariteplatz 1

department: Tumor stem cells

institute: Charité University Medicine Berlin, Germany

description: NGFR-GFP transfected A375 cells, rep1

data_processing: Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization.

label: BIOTIN

source_name: Melanoma cells

growth_protocol: Cells were grown in Tumor-growth medium Quantum 263 or Lebovitz medium (L15) in absence or presence of serum supplemented with penecilin and streptomycin. Transfected cells were stably selected in presence of G418 (100-300 µg/ml.

extract_protocol: RNA isolation from frozen cell pellets was performed with the RNeasy Mini Kit (Qiagen,Germany), following the manufacturers protocol. Reverse transcription of 500 ng - 2.5 μg RNA was performed with SuperScript VILO cDNA synthesis kit (Invitrogen, Germany) and diluted to a final volume of 50 μl , followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. RIN-values were in a range of 9.6 - 10.0

treatment_protocol: Cells were expanded under in vitro conditions

tag: cell type

value: A375 cells


title: NGFR_5

description: NGFR-GFP transfected A375 cells, rep2


title: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy 3

description:
CHD1_1_3_T15
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy


title: C57/BL6 fed with MCD diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks 3

description:
MG49-1_2_3
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet

source_name: C57/BL6 fed with MCD diet during 3 wks and treated with dual agonist of GLP1R/GCGR during two wks

value: methyl and choline deficient diet during 3 wks and treated with dual agonist of GLP1R/GCGR during two wks


title: C57/BL6 fed with MCD diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks 4

description:
MG49-1_2_4
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet


title: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy 2

description:
CHD1_1_2_T15
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy


title: GFP_3

description: GFP transfected A375 cells, rep3


title: NGFR_3

description: NGFR transfected cells, rep3

value: cell strain (T20/02) established from a patient-derived lymph node metastasis


title: GFP_1

description: GFP transfected A375 cells, rep1


title: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy 1

description:
CHD1_1_1_T15
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy


title: NGFR_6

description: NGFR-GFP transfected A375 cells, rep3


title: C57/BL6 fed with MCD diet during 3 weeks before PH70%  and continuous with the same diet for other 2 weeks 1

description:
MCD1_2_1_T15
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH


title: GFP_2

description: GFP transfected A375 cells, rep2


title: VdG43

description:
Replicate 2
idat file: 9257302051

tag: cell line

value: Prostate Cancer Cell Line


title: NGFR_1

description: NGFR transfected cells, rep1


title: C57/BL6 fed with MCD diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks 1

description:
MG49-1_2_1
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet


title: Mock_2

description: untransfected cells, rep2


title: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR  during two weeks 3

description:
CG49-1_1_3
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

source_name: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR during two wks


title: Mock_3

description: untransfected cells, rep3


title: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR  during two weeks 2

description:
CG49-1_1_2
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

value: standard diet treated with dual agonist of GLP1R/GCGR during two wks


title: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR  during two weeks 1

description:
CG49-1_1_1
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated


title: T101 iPSC

city: novato

first: Ying

last: Pei

state: ca

address: 8001 redwood blvd

institute: Buck Institute

description: replicate 6

source_name: GBA patient line fibroblast

tag: diagnosis

value: Parkinsons disease

value: Human skin fibroblast


title: C57/BL6 fed with standard diet treated with dual agonist of GLP1R/GCGR  during two weeks 4

description:
CG49-1_1_4
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated


title: C57/BL6 fed with methyl and choline deficient diet during 3 weeks 2

description:
MCD1_2_2
Biological replicate 2 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

source_name: C57/BL6 fed with MCD diet during 3 wks

value: methyl and choline deficient diet during 3 wks


title: S110 iPSC

description: replicate 8

source_name: PARKIN patient line #3  fibroblast


title: Sample_AN01125_ba9_22

type: SRA

city: San Francisco

first: Donna

middle: M

last: Werling

address: 1550 4th St., Room RH 447

institute: UCSF

library_source: transcriptomic

data_processing:
Aligned to the Human reference genome assembly GRCh37.73 using Tophat2 {v2.0.9, Trapnell:2012gg} as follows:  tophat -o outputfolder -g 10 -p 8 -r 99 --no-novel-juncs -G GRCh37.73.gtf hg19bowtieindex pairedread1.fastq pairedread2.fastq  Aligned reads were sorted and reads mapped to different chromosomes were removed from the BAM file using samtools v0.1.19.
Quantification of gene expression levels with HTSeq (v.0.6.1) with a union exon model as follows:  python -m HTSeq.scripts.count --stranded=no --mode=union --type=exon --quiet inputfile.sam --GTF GRCh37.73.gtf >> outputfolder
Calculated FPKM values from count level data as follows: datFPM <- sweep(log2(datExpr + 1), 2, log2(apply(datExpr,2,sum)/10^6))
Normalized FPKM values for GC content biases using the cqn package in R, and log2-transformed the normalized FPKM values.
Filtered out genes with < 1 FPKM in 50% of both male and female samples.
Quantile normalized FPKM values for remaining genes.
Genome_build: hg19
Supplementary_files_format_and_content: Log2-transformed and quantile normalized FPKM values generated in R from count-level data generated by HTSeq

source_name: Post-mortem brain tissue

extract_protocol:
Approximately 100mg of tissue across the cortical region of interest was isolated from each sample for up to two RNA extractions using the miRNeasy kit (Qiagen). The best RNA extraction based on RIN was used for RNA-seq.
Ribosomal RNA was depleted from 2ug total RNA with the Ribo-Zero Gold kit (Epicentre). Remaining RNA was then size selected with AMPure XP beads (Beckman Coulter) and resuspended in 8.5 ul of Illumina resuspension buffer and an additional 8.5 ul of 2x EPF buffer. Subsequent steps followed the Illumina TruSeq protocol (starting at page 84 of the sample prep v2 guide, no changes). After this protocol was followed, libraries were quantified with the Quant-iT PicoGreen assay (Life Technologies) and validated on an Agilent 2200 TapeStation system. Libraries were pooled to multiplex 24 samples per lane using Illumina barcodes, and each pool was sequenced six times on a HiSeq2000/2500 instrument using high output mode with standard chemistry and protocols for 50bp paired end reads. Most libraries were sequenced across two sequencing cores at UCLA. Read quality was similar across both core facilities, and reads across six lanes for each sample were pooled after demultiplexing (with Casava v1.8) for downstream analysis.

tag: brainid

tag: regionid

value: CTL

tag: age

tag: Sex

value: M

tag: rin

tag: brainbank

value: ATP

tag: pmi


title: C57/BL6 fed with methyl and choline deficient diet during 3 weeks 3

description:
MCD1_2_3
Biological replicate 3 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

value: male

value: liver


title: Sample_AN15088_ba9_1st

value: F

tag: primarycauseofdeath

value: Heart Attack


title: NGFR_2

description: NGFR transfected cells, rep2


title: C57/BL6 fed with standard diet 4

description:
CHD1_1_4
Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet

source_name: C57/BL6 fed with standard diet

value: standard diet


title: C57/BL6 fed with MCD diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks 2

description:
MG49-1_2_2
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet


title: Sample_AN01410_ba9_67


title: C57/BL6 fed with methyl and choline deficient diet during 3 weeks 4

description:
MCD1_2_4
Biological replicate 4 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet


title: Mock_1

description: untransfected cells, rep1


title: B119 iPSC

description: replicate 7

source_name: PARKIN patient line #2  fibroblast


title: K20 iPSC

description: replicate 5

source_name: LRRK2 patient line #2 fibroblast


title: Sample_AN10679_ba9_1st


title: Sample_UMB5079_ba9_2nd

value: NICHD


title: C57/BL6 fed with methyl and choline deficient diet during 3 weeks 1

description:
MCD1_2_1
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet


title: Sample_AN08161_ba9_1st

value: Multisystem Failure


title: K25 iPSC

description: replicate 4

source_name: LRRK2 patient line #1 fibroblast


title: A6 iPSC

description: replicate 1

source_name: SNCA patient line fibroblast


title: Y9 iPSC

description: replicate 3

source_name: Control fibroblast

value: healthy (control)


title: I3 iPSC

description: replicate 2

source_name: PARKIN patient line #1 fibroblast


title: C57/BL6 fed with standard diet 1

description:
CHD1_1_1
Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet


title: Sample_AN19760_ba9_25

value: Unknown


title: Sample_AN15566_ba9_28


title: Sample_UMB5168_ba9_2nd


title: Sample_AN17425_ba9_1st

tag: secondarycauseofdeath

value: Heart Disease


title: C57/BL6 fed with standard diet 3

description:
CHD1_1_3
Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet


title: C57/BL6 fed with standard diet 2

description:
CHD1_1_2
Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet


title: GP25_MM7_16H

city: Irapuato

first: José

last: Ruiz-Herrera

state: Guanajuato

address: Libramiento Norte Carretera Irapuato León Kilómetro 9.6, Carretera Irapuato León.

department: Ingeniería Genética

country: Mexico

institute: CINVESTAV, Irapuato, México

description: Single mutant strain delta-gcn5 grown at pH 7

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.)

organism: Mycosarcoma maydis

source_name: Ustilago maydis mutant monomorphic strain (a2b2 delta-gcn5 ) pH 7

label_protocol: Synthesis and labeling of cDNA were performed by Roche  NimbleGen Inc.

growth_protocol: U. maydis WT strain and the mutants CL211 and GP25 were recovered from minimal medium (MM; Holliday, 1974) pH 7 and inoculated into 500 ml MM adjusted to pH 3, pH 7 and pH 9.  Incubation under shaking conditions of 150 rpm at 28 ºC for 16 h.

extract_protocol: RNA was isolated from three independent cell cultures (biological replicates) using the Trizol method (Invitrogen, Carlsband, CA, USA) following the manucfactures´s instructions and purified with QIAGEN columns. RNA concentrations were messured by absorbance at 260 nm with Nanodrop (Termo Scientific, Waltham, MA, USA), and its integrity was observed by electrophoresis in denaturing agarose gels.

treatment_protocol: Cell were recovered by centifugation

tag: genotype

value: Mutant delta-gcn5

tag: phenotype

value: mycelium-monomorphic

tag: accession


title: CL211_MM7_16H

description: Single mutant strain delta-ubc2 grown at pH 7

source_name: Ustilago maydis mutant monomorphic strain (a2b2 delta-ubc2) pH 7

value: Mutant delta-ubc2

value: yeast-monomorphic


title: GP25_MM3_16H

description: Single mutant strain delta-gcn5 grown at pH 3

source_name: Ustilago maydis mutant monomorphic strain (a2b2 delta-gcn5 ) pH 3


title: stem region from gall midge challenged rice plant, biological replicate 3

city: New Delhi

first: Suresh

last: Nair

address: Aruna Asaf Ali Marg

department: Plant Molecular Biology Group

country: India

institute: International Centre for Genetic Engineering and Biotechnology (ICGEB)

description: Gene expression data from gall midge challenged rice plants

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

organism: Oryza sativa

source_name: Stem region of gall midge challenged rice plants

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

growth_protocol: The RP2068-18-3-5 seeds were sown in 4 rows, 5 cm apart, with 25 plants in each row, in plastic trays (60 x 30 x 30 cm) that were filled with puddle nutrient enriched soil under greenhouse conditions

extract_protocol: 1 cm tissue from the stem region, from the insect feeding site in gall midge infested plants and corresponding region from control plants, were excised at three different time points i.e. 24 hours after infestation (24 hai),  48hai and 72hai. Plant tissues from all three time points were pooled and total RNA was extracted. Plants from 3 trays represented three independent biological replicates. RNA extraction was carried out using Plant Total RNA Miniprep Kit (mdi Membrane Technologies, USA) as per manufacturer’s instructions.

treatment_protocol: After 15 days, plants in 3 trays were exposed to GMB1 females (n=25) and males (n=10) and plants in other 3 trays were left un-exposed but all trays were treated alike. The former represent infested tissues or treated samples (RP-I) and latter represent uninfested or control samples (RP-UI). After 48h of insect release, all the trays were transferred to humidity chamber (>90% relative humidity) and were maintained there to facilitate egg hatching and maggot establishment. Each tray served as an independent biological replicate.


title: 544130_A11_532_RMA

city: Basel

first: Morgane

last: Ravon

address: Grenzacherstrasse

institute: Hoffman-La Roche

description: MSC-PKCM

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
Background corrected, quantile normalized and RMA normalized probe intensities followed by average signal intensity calculation and log2 transformation.

organism: Sus scrofa

source_name: pig Mesenchymal Stem Cells, Kras+/G12D, p53R167H/R167H, cMyc overexpression  (pool 67/1.1)

label_protocol: Labeling was performed using 1ug of total RNA as input. Cy3 labeling of cDNA was performed with  the Roche NimbleGen One Color DNA Labeling Kit according to manufacturer's instructions (NimbleGen Systems Inc., Madison, WI USA. (See www.nimblegen.com).

growth_protocol: RNA was obtained from cell lysates derived from MSCs and sarcomas cells.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) . DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Genetic modification of porcine MSCs via TP53 and KRAS gene targeted mutations.

value: Mesenchymal Stem Cells

tag: genotype/variation


title: stem region from gall midge challenged rice plant, biological replicate 2


title: CL211_MM3_16H

description: Single mutant strain delta-ubc2 grown at pH 3

source_name: Ustilago maydis mutant monomorphic strain (a2b2 delta-ubc2) pH 3


title: 544130_A12_532_RMA

description: MSC-PKC

source_name: pig Mesenchymal Stem Cells, Kras+/G12D, p53R167H/R167H  (clone 67/1.4)


title: 544130_A09_532_RMA

description: WT-MSC

source_name: pig Mesenchymal Stem Cells (100209)

value: WT


title: 544130_A10_532_RMA

description: MSC-PK

source_name: pig Mesenchymal Stem Cells, Kras+/-, p53-/-  (clone 67)


title: stem region from gall midge challenged rice plant, biological replicate 1


title: 544130_A05_532_RMA

description: MSC-PKCM

value: Kras+/G12D, p53R167H/R167H, cMyc overexpression


title: stem region from control rice plant, biological replicate 3

description: Gene expression data from rice plants

source_name: Stem region of rice plants


title: 544130_A04_532_RMA

description: MSC-PK

source_name: pig Mesenchymal Stem Cells, Kras+/-, p53-/-  (clone 39)


title: FB2_MM9_16H

description: Wild-type strain Ustilago maydis (a2b2) grown at pH 9

source_name: Ustilago maydis wild-type strain (a2b2) pH 9

value: Wild-type

value: Normal


title: 1 N.mas5-Signal

city: shijiazhuang

first: li

last: lei

address: jiankang road

institute: hebei medical university

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix Microarray Suite version 5.0

source_name: SGC-7901 cells treated with periplocin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: SGC-7901 cells were treated with 100ng/ml periplocin for 24h at 37 ºC in a humidified incubator with 5% CO2.

value: gastric cancer cell line SGC-7901

tag: agent

value: periplocin


title: C3H_WNT3_sample_3

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

hyb_protocol: Arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.3μg of biotinylated target, at 45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: RMA

source_name: C3H cells, WNT3a stimulated

label_protocol: 100ng of total RNA were used to perform target preparation using the WT Expression Kit (Life Technologies). 5.5 μg of each fragmented cDNA was end-labeled with biotin

growth_protocol: DMEM 10% FBS 1% pen-strep

extract_protocol: Total RNA extraction with RNAeasy mini kit (Qiagen) .

treatment_protocol: subconfluent C3H10T1/2 cells in 60mm plates stimulated with 0.1uM recombinant Wnt3a  for 24hrs.

tag: expression

tag: stimulation


title: 544130_A08_532_RMA

description: WT-MSC

hyb_protocol: Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

source_name: pig Mesenchymal Stem Cells (170910)

tag: cell type


title: B N.mas5-Signal

source_name: SGC-7901 cells were untreated

tag: cell line

value: control


title: 544130_A06_532_RMA

description: MSC-PKC

source_name: pig Mesenchymal Stem Cells, Kras+/G12D, p53R167H/R167H  (clone 67/1.3)


title: stem region from control rice plant, biological replicate 1

description: Gene expression data from rice plants


title: C3H_WNT3_control_3

source_name: C3H cells, control

value: PBS


title: C3H_WNT3_control_2


title: stem region from control rice plant, biological replicate 2

description: Gene expression data from rice plants


title: Low Zinc + MTF1 siRNA (rep1)

description:
replicate 1
101723-01

source_name: Caco-2 MTF1 siRNA 3µM Zinc

tag: sirna

value: MTF1 siRNA (ON-TARGETplus, Thermo Scientific)

tag: zinc concentration

value: Human epithelial colonic adenocarcinoma, Caco-2


title: 544130_A07_532_RMA

description: MSC-PK

source_name: pig Mesenchymal Stem Cells, Kras+/-, p53-/-  (clone 82)


title: C3H_WNT3_control_1


title: OVCA429 with shNon control OV429_shNon_1

description: Control

source_name: Ovarian cancer cell line OVCA429

tag: shconstruct

value: shNon


title: 544130_A03_532_RMA

description: MSC-PKC

source_name: pig Mesenchymal Stem Cells, Kras+/G12D, p53R167H/R167H  (clone 67/1.1)


title: C3H_WNT3_sample_2


title: FB2_MM3_16H

description: Wild-type strain Ustilago maydis (a2b2) grown at pH 3

source_name: Ustilago maydis wild-type strain (a2b2) pH 3


title: FB2_MM7_16H

description: Wild-type strain Ustilago maydis (a2b2) grown at pH 7

source_name: Ustilago maydis wild-type strain (a2b2) pH 7


title: 544130_A02_532_RMA

description: MSC-PKCM

source_name: pig Mesenchymal Stem Cells, Kras+/G12D, p53R167H/R167H, cMyc overexpression  (pool 67/1.1)


title: C3H_SS18SSX_sample

source_name: C3H cells expressing SYTSSX


title: C3H_SS18SSX_control

source_name: C3H cells, empty vector

value: empty vector


title: 544060_A11_532_RMA

description: poSARCO

source_name: primary porcine tumor cells SMJ192

value: primary tumor cells SMJ192


title: 544060_A12_532_RMA

description: WT-MSC


title: LUC control knockdown CD34+/CD71- cord blood derived cells, biological replicate 3

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

hyb_protocol: Samples were hybridized to Human Gene 1.0 ST arrays (Affymetrix) at the Biomedical Informatics Core (Washington University in St. Louis)

scan_protocol: Samples were scanned at the Biomedical Informatics Core (Washington University in St. Louis)

data_processing:
RMA-summarized gene-level expression values computed using Affymetrix Expression Console.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

label_protocol: Nugen Encore Biotin kit protocol

growth_protocol: Cord blood mononuclear cells were isolated, CD34+ cells purified by autoMACS, and preconditioned overnight in X-vivo 15 media supplemented with 50ng/mL SCF, IL3, FLT3L and TPO. The following day media was replaced with erythroid differentiation media (SFEM media with SCF [25ng/mL], IL6 [10ng/mL], IL3 [10ng/mL], EPO [0.5U/mL]) for 4 more days.

extract_protocol: Day 5 cells were stained with CD34, glycophorin A and CD71 for FACS sorting. CD34+/CD71- cells were sorted directly into TRIzol LS (Life Technologies) and RNA was extracted using standard protocols. cDNA was prepared using the PicoSL Ovation system (NuGen). Samples were hybridized to Human Gene 1.0 ST arrays.

treatment_protocol: Cells were transduced with lentiviral vectors (pLKO.1) harboring a luciferase control shRNA or HSPA9 knockdown shRNA after overnight preconditioning. One day later, puromycin selection was begun and maintained until cell sorting.

tag: tissue source

value: human cord blood

value: CD34+ cells

tag: transduced with

value: shLUC

tag: cell subpopulation


title: HSPA9 knockdown CD34+/CD71- cord blood derived cells, biological replicate 4


title: LUC control knockdown CD34+/CD71- cord blood derived cells, biological replicate 1


title: 544130_A01_532_RMA

description: WT-MSC

source_name: pig Mesenchymal Stem Cells (030309)

value: Mesenchymal Stem Cells


title: HSPA9 knockdown CD34+/CD71- cord blood derived cells, biological replicate 1


title: LUC control knockdown CD34+/CD71- cord blood derived cells, biological replicate 4


title: 544060_A09_532_RMA

description: WT-MSC

source_name: pig Mesenchymal Stem Cells (100209)

value: WT


title: HSPA9 knockdown CD34+/CD71- cord blood derived cells, biological replicate 2


title: 544060_A05_532_RMA

description: WT-MSC


title: HSPA9 knockdown CD34+/CD71- cord blood derived cells, biological replicate 3


title: 544060_A02_532_RMA

description: WT-MSC


title: C3H_WNT3_sample_1

source_name: C3H cells, WNT3a stimulated


title: 544060_A03_532_RMA

description: WT-MSC


title: 544060_A06_532_RMA

description: poSARCO


title: LUC control knockdown CD34+/CD71- cord blood derived cells, biological replicate 2


title: VND7 plants with DEX treatment at T48, biological rep3

status: Public on Feb 22 2016

city: Melbourne

first: Zheng

address: Grattan Street,  Parkville, Victoria

country: Australia

institute: The University of Melbourne

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The obtained ATH1 chip and expression data (CEL files) were quality control checked, and evaluated using the Robin software package. RNA levels measured by high-throughput technique RNA microarray Affymetrix ATH1 and the probe-sets were redefined according to (Dai et al., 2005). The expression levels of probe sets were then estimated by GC-robust multi-array (GCRMA) analysis using R package gcrma.

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 48h

label_protocol: RNA was labeled with biotin.

growth_protocol: Arabidopsis thaliana plant lines (Col-0) that harbor a dexamethasone (DEX)-inducible pH35GVGR Gateway-based construct containing VND7-VP16-GR under the control of a 35S promoter were used. T3 seeds (~15-20 mg) were surface sterilized (10 min, 3% Na-hypochlorite) and washed five times with 1 ml of sterilized water each time. Seeds were added to 100 ml liquid MS medium supplemented with 1% sucrose (3.9 g/l Murashige & Skoog minerals including vitamins (Duchefa), adjusted with 0.45 g/l MES buffer and KOH to pH 5.7-5.8). Cultures were grown at 23°C for six days in the dark with 80 rpm in 250 ml flasks on a GFL 3017 shaker (GFL, Burgwedel, Germany).

extract_protocol:
Flasks were decanted over filter paper and washed 3 times with sterilized distilled H2O, dried on tissue paper, flash frozen, ball milled (Retsch 1-3 min, 30 Hz) and stored at -80°C until further use.
Total RNA was isolated using RNeasy Kits (Qiagen, Hilden, Germany) following the manufacturer's instruction.

treatment_protocol: The cultures were induced by using a final concentration of 10 µM dexamethasone (DEX) per flask and further cultivated for the time course experiment. Cultures were harvested at indicated time points after induction (1, 3, 6, 9, 12, 24, 30, 48 h) and at time point zero (0). Uninduced cultures (DMSO instead of DEX) served as controls for each time point, and thus, 48 microarray analyses for 8 time points (3 biological reps) for +/- induced VND7-VP16-GR cultures, and 3 arrays for time 0h.

tag: ecotype/background

tag: vector

tag: tissue

value: hypocotyl

tag: treatment

value: dexamethasone (DEX)

tag: time after induction


title: VND7 plants with DEX treatment at T48, biological rep1


title: VND7 plants with DEX treatment at T48, biological rep2


title: VND7 plants with DEX treatment at T30, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 30h


title: 544060_A08_532_RMA

description: WT-MSC

tag: genotype/variation


title: VND7 plants with DEX treatment at T30, biological rep1


title: VND7 plants with DEX treatment at T30, biological rep2


title: VND7 plants with DEX treatment at T24, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 24h


title: VND7 plants with DEX treatment at T24, biological rep2


title: 544060_A01_532_RMA

description: poSARCO


title: VND7 plants with DEX treatment at T24, biological rep1


title: VND7 plants with DEX treatment at T12, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 12h


title: VND7 plants with DEX treatment at T12, biological rep1


title: VND7 plants with DEX treatment at T9, biological rep1

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 9h


title: VND7 plants with DEX treatment at T9, biological rep3


title: VND7 plants with DEX treatment at T3, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 3h


title: VND7 plants without DEX treatment at T48, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 48h

value: DMSO


title: VND7 plants with DEX treatment at T9, biological rep2


title: VND7 plants without DEX treatment at T48, biological rep3


title: VND7 plants without DEX treatment at T30, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 30h


title: VND7 plants without DEX treatment at T30, biological rep1


title: VND7 plants with DEX treatment at T3, biological rep1


title: VND7 plants with DEX treatment at T1, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 1h


title: VND7 plants with DEX treatment at T6, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, DEX, 6h


title: VND7 plants with DEX treatment at T6, biological rep3


title: VND7 plants with DEX treatment at T3, biological rep3


title: VND7 plants without DEX treatment at T48, biological rep1


title: VND7 plants with DEX treatment at T1, biological rep2


title: VND7 plants without DEX treatment at T30, biological rep2


title: VND7 plants with DEX treatment at T6, biological rep1


title: VND7 plants with DEX treatment at T12, biological rep2


title: VND7 plants without DEX treatment at T24, biological rep1

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 24h


title: VND7 plants with DEX treatment at T1, biological rep1


title: VND7 plants without DEX treatment at T24, biological rep3


title: VND7 plants without DEX treatment at T12, biological rep1

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 12h


title: VND7 plants without DEX treatment at T24, biological rep2


title: VND7 plants without DEX treatment at T9, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 9h


title: VND7 plants without DEX treatment at T12, biological rep2


title: VND7 plants without DEX treatment at T12, biological rep3


title: VND7 plants without DEX treatment at T6, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 6h


title: VND7 plants without DEX treatment at T6, biological rep3


title: VND7 plants without DEX treatment at T6, biological rep1


title: VND7 plants without DEX treatment at T9, biological rep3


title: VND7 plants without DEX treatment at T1, biological rep1

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 1h


title: CiPEHR_warmed_rep5

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

hyb_protocol: The labeled DNA was resuspended in 10 µL hybridization solution containing 2.68 µL sample tracking control (Roche NimbleGen, Inc., Madison, WI, USA), 40% formamide, 25% SSC, 1% SDS, 1.6% Cy3 labeled alignment oligo, 1.6% Cy5-labeled alignment oligo and 2% Cy5-labeled common oligonucleotide reference standard target (NimbleGen). After denaturing at 95°C for 5 min, the mixtures were spun down and kept at 42°C to be deposited onto the glass microarray. GeoChip 4.2 slides were synthesized by NimbleGen in a 12-plex format (i.e., 12 arrays per glass slide). An HX12 mixer (NimbleGen) was affixed onto the array using a Precision Mixer Alignment Tool (NimbleGen). The array was preheated at 42°C in the 12-Bay MAUI Hybridization System (BioMicro Systems, Inc., Salt Lake City, UT, USA) for at least 5 min before the samples were loaded onto the array. Hybridizations were performed on the MAUI Hybridization System at 42°C in the presence of 40% formamide for about 16 hours with mixing. Then the mixers were removed from the slides while soaking in buffer I. The slides were manually washed in buffer I for 120 s, in buffer II for 60 s and in buffer III for 15 s and spun to dry in a NimbleGen slide spinner. All washing buffers were provided by NimbleGen.

scan_protocol: The dried microarray was scanned with a laser power of 100% and a photomultiplier (PMT) gain of 100% by a MS 200 Microarray Scanner (NimbleGen) at 532 nm and 635 nm. NimbleScan software version 2.5 (NimbleGen) was used to grid the images. After gridding, every spot (containing one unique probe) on the GeoChip array was fixed into a 7 × 7 pixel square and was adjacent to four blank equal-sized squares (void spaces). The probe signal was then calculated as the average intensity of the center 5 × 5 pixels for each spot, and the background noise signal was the average void intensity for each spot. The signal and background intensity report was generated also in NimbleScan software.

data_processing: Raw data from NimbleScan were submitted to the Microarray Data Manager on our website (http://ieg.ou.edu/microarray/) and analyzed using the data analysis pipeline with the following major steps: (i) Raw signal intensities (Cy3 channel, barcode_position_532.exp.ftr file) on each array were multiplied by a normalization weight I, which is the ratio of the maximum average universal standard intensity (Cy5 channel, barcode_position_635.ctr.ftr) among all the samples divided by the average universal standard intensity of each array; (ii) The signal intensities on each array were further multiplied by a normalization weight II, which is the ratio of the maximum total raw intensity (Cy3 channel) among all the samples divided by the total raw intensity of each array; (iii) Spots with  SNR (signal to noise ratio, noise defined as the averaged pixel intensity of the area between two adjacent spots, barcode_position_532.void.ftr file) ≥2 were considered as positive. Otherwise they were treated as negative spots with 0 value (iv) Spots with signal intensity lower than 1000 were not considered as positive and were removed in subsequent analysis; (v) If a probe appeared in only one-third or fewer of the samples in one treatment group (two out of six samples), it was removed from that group before any further analyses; (vi) Signal intensities plus 1 were transformed to their natural logarithm; and (vii) The mean ratio in each sample was calculated by dividing the transformed signal intensity of each probe by the average transformed signal intensity for all detected probes in each sample. Altogether, a total of 48,188 functional gene probes were detected across all samples in this study. Since data could be very sparse with many 0 values, this could change data structure and affect subsequent data analysis. To reduce sparsity, original signal intensity instead of 0 were used for spots with SNR between 1.5 and 2.0.

organism:
Bacteria
Archaea
Eukaryota
Viruses

source_name: soil microbial metagenome in soil warming group

label_protocol: For each sample, 1µg DNA was diluted to a volume of 25 μL and was mixed with 20 μL random primers (Invitrogen by Life Technologies, Grand Island, NY, USA), denatured at 99.9°C for 5 min and immediately chilled on ice. Then, 2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL fluorescent dye Cy-3 dUTP (GE Healthcare UK Limited, Buckinghamshire, UK) and 80 U of the large Klenow fragment (Imer Inc., CA, USA) were added to the denatured DNA. The 50 μL mixture was incubated at 37°C for 6 hours, followed by heating at 95°C for 3 min. Labeled DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Cy-3 dye concentration was measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Products). The labeled DNA was then dried in a Savant SPD1010 SpeedVac concentrator system (Thermo Fisher Scientific) at 45°C for 45 min.

growth_protocol: uncultured

extract_protocol: Soil DNA was extracted using a PowerMax Soil DNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol.  DNA quality was assessed based on spectrometry absorbance at wavelengths of 230 nm, 260 nm and 280 nm detected by a NanoDrop ND1000 Spectrophotometer (NanoDrop Technologies Inc., now NanoDrop Products by Thermo Fisher Scientific). The 260/280 nm absorbance ratios were around 1.8, and 260/230 nm ratios were greater than 1.7.  Finally, DNA was quantified with Pico Green using a FLUOstar OPTIMA fluorescence plate reader (BMG LabTech, Jena, Germany) and used for gene array labeling and sequencing library preparation.

treatment_protocol: snow pile warmed soil

tag: soil origin

value: Akaska acidic tundra

organism: synthetic construct

source_name: synthesized common oligonucleotide reference standard

tag: sequence

tag: molecule subtype

value: single stranded oligonucleotide


title: CiPEHR_control_rep3

source_name: soil microbial metagenome in control group

treatment_protocol: untreated natural soil


title: VND7 plants without DEX treatment at T3, biological rep3

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 3h


title: CiPEHR_warmed_rep2


title: CiPEHR_warmed_rep6


title: CiPEHR_warmed_rep3


title: VND7 plants without DEX treatment at T3, biological rep2


title: VND7 plants without DEX treatment at T1, biological rep3


title: CiPEHR_warmed_rep4


title: CiPEHR_control_rep6


title: CiPEHR_warmed_rep1


title: CiPEHR_control_rep4


title: VND7 plants without DEX treatment at T3, biological rep1


title: CiPEHR_control_rep1


title: VND7 plants without DEX treatment at T0, biological rep2

source_name: Arabidopsis thaliana plants harboring VND7 inducible vectors, without DEX, 0h


title: VND7 plants without DEX treatment at T0, biological rep3


title: VND7 plants without DEX treatment at T9, biological rep1


title: Empty vector plants with DEX treatment at T24, biological rep3

source_name: Arabidopsis thaliana plants harboring empty vectors, with DEX, 24h


title: VND7 plants without DEX treatment at T0, biological rep1


title: VND7 plants without DEX treatment at T1, biological rep2


title: CiPEHR_control_rep2


title: CiPEHR_control_rep5


title: Empty vector plants with DEX treatment at T12, biological rep3

source_name: Arabidopsis thaliana plants harboring empty vectors, with DEX, 12h


title: Empty vector plants with DEX treatment at T24, biological rep1


title: Empty vector plants with DEX treatment at T24, biological rep2


title: Empty vector plants with DEX treatment at T12, biological rep1


title: Empty vector plants with DEX treatment at T12, biological rep2


title: Empty vector plants with DEX treatment at T9, biological rep3

source_name: Arabidopsis thaliana plants harboring empty vectors, with DEX, 9h


title: Empty vector plants with DEX treatment at T9, biological rep2


title: Empty vector plants with DEX treatment at T9, biological rep1


title: G266_DMSO_5

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

description: total RNA isolated from cell cultures

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
CEL files generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) were imported into ChipInspector software, version 21 (El Dorado Database version: E30R1410 Genomatix GmbH). Differential expression was analyzed using the group-wise exhaustive analysis with false discovery rate set to zero and 10-significant probe minimum coverage. The differential gene expression was analyzed comparing total RNA of 11 controls (DMSO, 6 ZMTA and 5 G266 cell line samples ) to  14 treatments (AZA, 7 per each cell line) using the group-wise exhaustive analysis with False Discovery Rate set to zero and 10-significant probe minimum coverage.
In the file Mixed_ZMTZ_G266_AZAvsControl.txt are the significance results obtained by ChipInspector.
The differential expression was analyzed using the group-wise exhaustive analysis i.e., treatment samples group compare to Controls samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol.
The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).

organism: Taeniopygia guttata

source_name: G266 cells

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Cells were cultured in DMEM high glucose medium (Life Technologies 41965039) supplemented with 10% heat inactivated fetal bovine serum (Life Technologies 102070106), 2% heat inactivated chicken serum (Life Technologies 15140122) and 1% penicillin streptomycin (Life Technologies 15070063). The cultures were maintained at 37°C, 5% CO2 and 95-98% humidity.

extract_protocol: Total RNA was extracted from AZA- and DMSO-treated G266 and ZFTMA cell lines using Trizol and the RNeasy mini kit (Qiagen 74106),  according to the manufacturer’s instructions. RNA concentrations were measured using Nanodrop 1000 (Thermo Fisher Scientific).

treatment_protocol: Cells were treated for 72 hours with a 500 nM concentration of AZA (= demethylation treatment, Sigma-Aldrich A3656) or  DMSO as a solvent control. Both AZA and DMSO inductions were repeated every 24 hours, as AZA is known to be relative unstable in aqueous solution.

tag: gender

value: male

tag: origin

value: tumoral

value: dimethyl sulfoxide

tag: duration of treatment

value: 72 hours


title: G266_DMSO_4

description: total RNA isolated from cell cultures

tag: cell line


title: G266_DMSO_3

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_6

description: total RNA isolated from cell cultures

source_name: ZFTMA cells

value: female

value: ZFTMA


title: G266_DMSO_1

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_5

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_4

description: total RNA isolated from cell cultures


title: Empty vector plants without DEX treatment at T24, biological rep1

source_name: Arabidopsis thaliana plants harboring empty vectors, without DEX, 24h


title: G266_DMSO_2

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_3

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_1

description: total RNA isolated from cell cultures


title: ZFTMA_DMSO_2

description: total RNA isolated from cell cultures


title: G266_AZA_7

description: total RNA isolated from cell cultures


title: Empty vector plants without DEX treatment at T24, biological rep3


title: Empty vector plants without DEX treatment at T24, biological rep2


title: Empty vector plants without DEX treatment at T12, biological rep2

source_name: Arabidopsis thaliana plants harboring empty vectors, without DEX, 12h


title: Empty vector plants without DEX treatment at T12, biological rep3


title: Empty vector plants without DEX treatment at T9, biological rep3

source_name: Arabidopsis thaliana plants harboring empty vectors, without DEX, 9h


title: Empty vector plants without DEX treatment at T9, biological rep2


title: G266_AZA_6

description: total RNA isolated from cell cultures


title: G266_AZA_5

description: total RNA isolated from cell cultures


title: G266_AZA_4

description: total RNA isolated from cell cultures


title: Empty vector plants without DEX treatment at T12, biological rep1


title: G266_AZA_2

description: total RNA isolated from cell cultures


title: G266_AZA_1

description: total RNA isolated from cell cultures


title: G266_AZA_3

description: total RNA isolated from cell cultures


title: ZFTMA_AZA_7

description: total RNA isolated from cell cultures


title: Empty vector plants without DEX treatment at T9, biological rep1


title: ZFTMA_AZA_5

description: total RNA isolated from cell cultures


title: ZFTMA_AZA_6

description: total RNA isolated from cell cultures


title: ZFTMA_AZA_4

description: total RNA isolated from cell cultures


title: ZFTMA_AZA_3

description: total RNA isolated from cell cultures


title: ZFTMA_AZA_2

description: total RNA isolated from cell cultures


title: TA1626_OE_2

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

description: overexpression

hyb_protocol: Hybridization was performed using a GeneChip Hybridization Oven 640 overnight at 45°C. Microarray washing and staining was done using a GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Probe level analysis including background subtraction and quantile normalization took placed with the Robust Multi Array Average Algorithm (RMA) using the Affymetrix Expression Console Software 1.3

label_protocol: Labeling took place following Affymetrix protocol

growth_protocol: Lineage negative cells were isolated from bone marrow and cultured  for 24 hours before isolation of total RNA

extract_protocol: Qiagen Rneasy kit

value: bone marrow

value: OE


title: TA1626_OE_1

description: overexpression


title: ZFTMA_AZA_1

description: total RNA isolated from cell cultures


title: PA2685_KO_2

description: knockout

value: KO


title: K562 shKDM2B_2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Human leukemia cell lines were maintained in IMDM supplemented with 10% FBS

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells were infected with shKDM2B and RNA harvested after 6 days


title: GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep4

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 4 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1

hyb_protocol: On each two-colour microarray 825 ng of cRNA from GO exposed cells (Cy5) and 825 ng of cRNA from control cells (Cy3) were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Equus caballus

source_name: GO-treated equine satellite cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation 0,125 µM GO was added and cells were incubated for 24h. Because GO is insoluble in water DMSO (0,04µl/ml) was used as a vehicle. Control medium contained DMSO in the same dose as in GO treated cells. DMSO - Dimethyl sulfoxide.

tag: age

value: 3rd day of differentiation

tag: satellite cell origin

value: m. semitendinosus muscle


description: Biological replicate 1 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1