title: Rrm3-Flag WT

description: GAL::YRA1 Rrm3 exp1 and exp2

source_name: Rrm3-Flag ChIP DNA from WRBb-9B, asynchronous culture

value: WRBb-9B+ pRS413-GAL::YRA1

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG + pRS413-GAL::YRA1


title: WT HA-Yra1

status: Public on Mar 11 2016

type: genomic

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: HA-Yra1 exp1 and exp2

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: HA-Yra1 ChIP DNA from W303-A1, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in minimal medium + Glucose 2%  to mid-log phase at 30°C. In samples with Rrm3-Flag ChIP, yeast cells were grown minimal medium + Galactose 2%

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-HA polyclonal antibody (Abcam) was used for ChIP. Anti-FLAG M2 monoclonal (Sigma-Aldrich)

tag: strain

tag: genotype

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from W303-1A+ pRS413-GAL::YRA1


title: E23_Bl007_BRP009

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: Image data was analyzed using Genomestudio with genotyping module (Illumina). The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0.75. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG). The data is provided as family stuctures, i.e. a BRP family for each cross.

organism: Bos taurus

source_name: Blastomere

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The zygotes were transferred to synthetic oviductal fluid (SOF) supplemented with essential and non-essential amino acids (SOFaa), 0.4% BSA and ITS (5 µg/ml insulin, 5 µg/ml transferrin and 5 ng/ml selenium). In vitro culture (IVC) occurred in 4-well dishes in 20 µL drops (1 per donor cow) covered with mineral oil. Embryos were incubated at 38.5°C in 5% CO2, 5% O2 and 90% N2.

extract_protocol: The isolated blastomeres were placed immediately on dry ice and stored in -20oC for 30 minutes prior to whole genome amplification (WGA). WGA was performed on the day of blastomere isolation. DNA from single blastomeres was whole-genome amplified using commercial MDA kits (REPLI-g Single Cell Kit, Qiagen and GenomiPhiV2, GE Healthcare Biosciences). MDA amplification with GenomiPhiV2 was performed as described previously (Spits et al. 2006, Nat Protoc). MDA amplification of single blastomeres with the single-cell Repli-g kit was performed according to the manufacturer’s instructions for the fast 3-hour protocol. WGA products were purified using SPRI-beads (AMPure) at 0.8x of total reaction volume.

treatment_protocol: The embryos were treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, P88110, Sigma-Aldrich in TCM-199) and were subsequently washed in TCM-199 with 10% FBS followed by Ca+2/Mg+2 free PBS with 0.05% BSA to stimulate blastomere dissociation. Subsequently, the zona-free embryos were washed in Ca+2/ Mg+2 free PBS with 0.1% PVP (wash medium) and were transferred onto a petri dish for blastomere dissociation. Blastomere pick-up and tubing was performed with the use of a mouth-pipetting system using a 75μm capillary.

tag: dna sample

value: Single Cell

tag: wga

value: MDA (GenomiPhiV2)


title: E05_Bl003_BRP008

description: DNA extracted from single blastomere derived from cleavage stage day-2post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: E22_Bl001_BRP009

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified byGenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: Father_BRP008

description: DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen).

source_name: Semen

value: Multi cell


title: E05_Bl004_BRP008


title: Grandmother_BRP008

description: DNA extracted from a large amount of cells derived from the cow's ovarian tissue using DNeasy Blood and Tissue kit (Qiagen).

source_name: Ovarian tissue


title: E05_Bl002_BRP008


title: E05_Bl001_BRP008


title: E22_Bl006_BRP009


title: E04_Bl003_BRP008

description: DNA extracted from single blastomere derived from cleavage stage day-2post-insemination, in vitro produced embryo and subsequently whole genome amplified byGenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: E04_Bl002_BRP008


title: Mother_BRP007


title: E04_Bl001_BRP008


title: COB59 control cortex

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen) as per manufacturer’s instructions. DNA was then purified and concentrated using the DNA Clean & Concentrator kit (Zymo Research).

tag: Sex

value: M

tag: disease status

value: Control

tag: tissue

value: Cortex

tag: hd allele cag repeat number

tag: wt allele cag repeat number

tag: age of death

tag: age of disease onset

tag: age of disease onset percentile

tag: post-mortem interval (pmi)

tag: years with hd

tag: sentrix id

tag: sentrix position

tag: sentrix row


title: E04_Bl004_BRP008


title: HDB159 HD cortex

value: Huntington's Disease (HD)

value: Mean


title: E23_Bl004_BRP009


title: HDB166 HD cortex

value: F

value: Late


title: HDB119 HD cortex


title: Father_BRP007


title: E07_Bl003_BRP007


title: E07_Bl004_BRP007


title: COB20_30 control cortex


title: HDB167 HD liver

value: Liver


title: Grandfather_BRP006


title: E21_Bl009_BRP006


title: E07_Bl001_BRP007


title: Grandfather_BRP007


title: Grandmother_BRP006


title: Reprogrammed CWR-22rv1#3

type: RNA

first: Shawn

last: Anderson

address: 2660 Oak Street

institute: Vancouver Prostate Centre

description: Gene expression in reprogrammed CWR-22rv1 cell line.

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004).

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings.

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities. Analysis via GeneSpring Version 12.0, quantile normalization.

molecule: total RNA

source_name: CWR-22rv1 prostate cancer cells, reprogrammed cell line

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: Parental cells were grown in phenol-red-free medium supplemented with 10% FBS, whereas reprogrammed cells were grown in our custom stem-transition medium (STM).

extract_protocol: RNA was extracted from cell lines using Qiagen RNeasy kit, according to the manufacturer’s instructions.

tag: source cell line

tag: parental/reprogrammed state

value: reprogrammed


title: Reprogrammed CWR-22rv1#2


title: COB51 control cortex


title: Reprogrammed CWR-22rv1#1


title: COB125 control cortex


title: HDB165 HD cortex

value: Early


title: Father_BRP006

tag: dna sample


title: Parental CWR-22rv1#3

description: Gene expression in parental CWR-22rv1 cell line.

source_name: CWR-22rv1 prostate cancer cells, parental cell line

value: parental


title: E21_Bl007_BRP006

tag: wga


title: E21_Bl008_BRP006


title: E07_Bl002_BRP007


title: HDB176 HD liver

tag: Sex


title: E21_Bl006_BRP006


title: E21_Bl004_BRP006


title: Reprogrammed VCaP#3

description: Gene expression in reprogrammed VCaP cell line.

source_name: VCaP prostate cancer cells, reprogrammed cell line

value: VCaP


title: Normal_Normal-93

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

country: USA

institute: Janssen R&D

description: Sample name: 5500254226354081915641_101406.A05

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 8.

source_name: Whole blood, normal

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer's protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Using PAXgene Blood RNA tubes, whole blood was collected from 16 patients with hidradenitis suppurativa and 10 healthy normal subjects. Samples in PAXgene tubes were placed upright at room temperature for 2 hours and then stored at -80oC until RNA preparation.

tag: subject id

tag: disease state

value: Healthy

value: Whole blood


title: Parental CWR-22rv1#1


title: E21_Bl005_BRP006

value: Single Cell


title: Parental CWR-22rv1#2


title: Normal_Normal-87

description: Sample name: 5500254226354081915641_101406.E09

tag: tissue


title: Normal_Normal-88

description: Sample name: 5500254226354081915641_101406.E07


title: Grandmother_BRP007


title: HDB162 HD liver

tag: disease status

tag: hd allele cag repeat number

tag: wt allele cag repeat number


title: E13_Bl003_BRP006

value: MDA (GenomiPhiV2)


title: COB51 control liver

tag: age of death

tag: age of disease onset

tag: age of disease onset percentile


title: E21_Bl002_BRP006


title: Reprogrammed VCaP#2


title: HDB167 HD cortex

tag: post-mortem interval (pmi)

tag: years with hd

tag: sentrix id


title: Normal_Normal-86

description: Sample name: 5500254226354081915641_101406.C11


title: E13_Bl002_BRP006


title: Reprogrammed VCaP#1

tag: source cell line


title: E21_Bl003_BRP006


title: E13_Bl004_BRP006


title: Parental VCaP#2

description: Gene expression in parental VCaP cell line.

source_name: VCaP prostate cancer cells, parental cell line

tag: parental/reprogrammed state


title: Parental VCaP#3


title: E21_Bl001_BRP006

tag: dna sample


title: E13_Bl001_BRP006

tag: wga


title: Grandmother_BRP005

value: Multi cell


title: COB 22_52 control cortex

tag: Sex

value: M

tag: sentrix position

tag: sentrix row


title: HDB119 HD liver

tag: tissue


title: Normal_Normal-15

description: Sample name: 5500254226354081915641_101406.F10

tag: subject id

tag: disease state


title: Normal_Normal-68

description: Sample name: 5500254226354081915641_101406.B09


title: Normal_Normal-120

description: Sample name: 5500254226354081915641_101406.B11


title: HDB176 HD cortex

tag: disease status

tag: hd allele cag repeat number

tag: wt allele cag repeat number


title: Normal_Normal-119

description: Sample name: 5500254226354081915641_101406.A10


title: HDB162 HD cortex

tag: age of death

tag: age of disease onset

tag: age of disease onset percentile


title: Parental VCaP#1


title: Reprogrammed LAPC4#3

description: Gene expression in reprogrammed LAPC4 cell line.

source_name: LAPC4 prostate cancer cells, reprogrammed cell line


title: Mother_BRP006


title: Grandfather_BRP005


title: Normal_Normal-115

description: Sample name: 5500254226354081915641_101406.F02


title: Reprogrammed LAPC4#1


title: Parental LAPC4#3

description: Gene expression in parental LAPC4 cell line.

source_name: LAPC4 prostate cancer cells, parental cell line


title: Mother_BRP005

description: DNA extracted from a large amount of cells derived from the cow's ovarian tissue using DNeasy Blood and Tissue kit (Qiagen).


title: Parental LAPC4#2


title: Reprogrammed LAPC4#2


title: Hidradenitis_Patient 9

description: Sample name: 5500254226354081915641_101406.C04

source_name: Whole blood, hidradenitis

value: Patient 9

value: Hidradenitis suppurativa


title: Normal_Normal-54

description: Sample name: 5500254226354081915641_101406.B06


title: Father_BRP005

description: DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen).


title: Parental LAPC4#1


title: Hidradenitis_Patient 6

description: Sample name: 5500254226354081915641_101406.A04

value: Patient 6


title: Reprogrammed LNCaP#2

description: Gene expression in reprogrammed LNCaP cell line.

source_name: LNCaP prostate cancer cells, reprogrammed cell line

value: LNCaP


title: Hidradenitis_Patient 8

description: Sample name: 5500254226354081915641_101406.C01

value: Patient 8


title: Reprogrammed LNCaP#3


title: Hidradenitis_Patient 4

description: Sample name: 5500254226354081915641_101406.F04

value: Patient 4


title: Hidradenitis_Patient 5

description: Sample name: 5500254226354081915641_101406.H01

value: Patient 5


title: Hidradenitis_Patient 3

description: Sample name: 5500254226354081915641_101406.F06

value: Patient 3


title: Parental LNCaP#3

description: Gene expression in parental LNCaP cell line.

source_name: LNCaP prostate cancer cells, parental cell line


title: Hidradenitis_Patient 2

description: Sample name: 5500254226354081915641_101406.D08

value: Patient 2


title: E20_Bl004_BRP005

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: Hidradenitis_Patient 19

description: Sample name: 5500254226354081915641_101406.H03

value: Patient 19


title: Parental LNCaP#2

value: parental


title: COB05 control cortex

value: Control

value: Cortex

tag: post-mortem interval (pmi)

tag: years with hd

tag: sentrix id


title: Parental LNCaP#1

tag: source cell line

tag: parental/reprogrammed state


title: E20_Bl003_BRP005

tag: dna sample

value: Single Cell

tag: wga


title: Hidradenitis_Patient 17

description: Sample name: 5500254226354081915641_101406.F03

value: Patient 17

value: Whole blood


title: Hidradenitis_Patient 18

description: Sample name: 5500254226354081915641_101406.B04

value: Patient 18


title: Hidradenitis_Patient 16

description: Sample name: 5500254226354081915641_101406.E06

value: Patient 16


title: Hypoxia_20h_S11

city: Lund

first: Mattias

last: Belting

address: Barngatan 2B

department: Department of Oncology

country: Sweden

institute: Lund Univercity

description:
Hypoxia 20h replicate 2
Sample 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE2 followed by further analysis in R statistical programming environment.

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Labeling Kit for Illumina arrays

growth_protocol: HeLa cells maintained in DMEM, 4.5 g/L glucose (Thermo scientific), supplemented with 10% foetal bovine serum (FBS, Sigma-Aldrich), 1% penicillin-streptomycin (Sigma–Aldrich), 1% L-glutamine (Sigma-Aldrich).

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (Qiagen) and quantified with Nanodrop spectrophotometer (Saveen Werner). RNA integrity was verified on an Agilent 2100 Bioanalyzer, and microarray experiments were performed at the Swegene Center for Integrative Biology, Lund University, using the Illumina Human HT-12 v4 Expression BeadChip.

treatment_protocol: Medium was changed to serum free (SF) (DMEM 4.5 g/L glucose, 1% penicillin-streptomycin, 1% L-glutamine) followed by 6 h or 20 h incubation at 21% oxygen or 1% oxygen.

value: cervix

tag: cell line

value: HeLa

tag: disease

value: adenocarcinoma


title: E20_Bl001_BRP005

value: MDA (GenomiPhiV2)


title: Hidradenitis_Patient 15

description: Sample name: 5500254226354081915641_101406.G07

tag: subject id

value: Patient 15

value: Hidradenitis suppurativa

tag: tissue


title: Hypoxia_20h_S12

description:
Hypoxia 20h replicate 3
Sample 12


title: Reprogrammed LNCaP#1

value: LNCaP

value: reprogrammed


title: E19_Bl007_BRP005


title: E19_Bl005_BRP005


title: E19_Bl004_BRP005


title: E19_Bl006_BRP005


title: Normixa_20h_S9

description:
Normoxia 20h replicate 3
Sample 9


title: Hidradenitis_Patient 12

description: Sample name: 5500254226354081915641_101406.D02

value: Patient 12

tag: disease state


title: Hidradenitis_Patient 13

description: Sample name: 5500254226354081915641_101406.H06

value: Patient 13


title: Hypoxia_20h_S10

description:
Hypoxia 20h replicate 1
Sample 10


title: E19_Bl008_BRP005


title: Normoxia_20h_S8

description:
Normoxia 20h replicate 2
Sample 8


title: E20_Bl002_BRP005


title: E20_Bl005_BRP005


title: Normoxia_20h_S7

description:
Normoxia 20h replicate 1
Sample 7


title: Hypoxia_6h_S5

description:
Hypoxia 6h replicate 2
Sample 5


title: Hypoxia_6h_S6

description:
Hypoxia 6h replicate 3
Sample 6


title: Hidradenitis_Patient 10

description: Sample name: 5500254226354081915641_101406.C10

value: Patient 10


title: Hidradenitis_Patient 1

description: Sample name: 5500254226354081915641_101406.G03

value: Patient 1


title: Hypoxia_6h_S4

description:
Hypoxia 6h replicate 1
Sample 4


title: ESC derived EBs after 18h of differentiation in the presence of 1.88µM GSK-J5 (vehicle compound) in EB medium

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: Gene expression data from ESC derived EBs of 18h of differentiation in the presence of GSK-J5

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Mouse Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

organism: Mus musculus

source_name: vehicle control-treated ESC derived EBs from R1 background

label_protocol: 100ng of total RNA were amplified with the WT Expression Kit (Ambion), followed by ssDNA labeling with the WT Terminal Labeling Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: For ESC differentiation, feeder-depleted ESC (separation via 0.1% gelatin-coated plates, incubated for 45 min at 37°C) were cultured in ESC medium with LIF-withdrawal in bacteriological Petri dishes and incuated for 18h in a 37°C, 5% CO2 incubator in the presence of EB medium only, DMSO, GSK-J5 or GSK-J4 (both 1,88 µM).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: For harvest, EBs were transferred to 15 ml Falcon tubes and allowed to sediment. Medium was replaced by Trypsin/EDTA followed by 3 min incuation at 37°C. Dissociation of EBs was done by pipetting up and down.

tag: treatment

value: R1 mouse ESC line


title: ESC derived EBs after 18h of differentiation in the presence of 1.88µM GSK-J4 (KDM6 specific inhibitor) in EB medium

description: Gene expression data from ESC derived EBs of 18h of differentiation in the presence of GSK-J4

source_name: inhibitor-treated ESC derived EBs from R1 background


title: ESC derived EBs after 18h of differentiation in the presence of DMSO in EB medium

description: Gene expression data from ESC derived EBs of 18h of differentiation in the presence of DMSO


title: Normoxia_6h_S2

description:
Normoxia 6h replicate 2
Sample 2


title: Normoixa_6h_S3

description:
Normoxia 6h replicate 3
Sample 3


title: ESC derived EB after 18h of differentiation in the presence of EB medium

description: Gene expression data from ESC derived EBs of 18h of differentiation

source_name: untreated ESC derived EBs from R1 background


title: YRA1∆i, biological rep. 3

description: Gene expression data from mid-log yeast cells in minimal medium galactose (2%)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 1.5-fold expression change compared to wild-type strain with a p-value FDR < 0.01, were considered as altered. Expression values were obtained with the anti-log of RMA values

source_name: Total RNA from W303 cells overexpressing YRA1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was growing in minimal medium supplemented with raffinose and shifted for four hours to galactose (2%)

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)

tag: strain

value: W303-1A + pRS413::GAL-YRA1∆i

tag: genotype


title: E11_Bl004_BRP005

description: DNA extracted from single blastomere derived from cleavage stage day-2post-insemination, in vitro produced embryo and subsequently whole genome amplified byGenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).

source_name: Blastomere

value: Single Cell


title: E19_Bl001_BRP005


title: E19_Bl003_BRP005


title: E19_Bl002_BRP005


title: Grandfather_BRP004

description: DNA extracted from a large amount of cells derived from the bull's semen using DNeasy Blood and Tissue kit (Qiagen).

source_name: Semen

value: Multi cell


title: YRA1∆i, biological rep. 2


title: YRA1∆i, biological rep. 1


title: LNCaP-NE#3

description: Gene expression in LNCaP-NE cell line.

hyb_protocol: Samples were hybridized with Affymetrix.ExonExprChip.HuGene-1_0-st-v1_na30_1_hg19_2010-01-22 (GeneChip® Human Gene 1.0 ST Array).

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

data_processing:
Analysis via GeneSpring Version 12.0, quantile normalization - log2.
Summarization Algorithm: ExonRMA16
Confidence level: ALL
Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1_na30_1_hg19_2010-01-22
Normalization: Quantile
Baseline Transformation: None

source_name: LNCaP prostate cancer cells, transdifferentiated neuroendocrine-like cell line

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

growth_protocol: Parental LNCaP were grown in phenol-red-free medium supplemented with 10% CSS and 10pM R1881, and transdifferentiated neuroendocrine LNCaP were grown 15 days in phenol-red-free medium supplemented with 10% CSS.

tag: parental/ne-like state

value: transdifferentiated neuroendocrine-like


title: WT, biological rep. 3

source_name: Total RNA from W303 cells without YRA1 overexpression


title: E11_Bl003_BRP005

description: DNA extracted from single blastomere derived from cleavage stage day-2post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: LNCaP-NE#2

description: Gene expression in LNCaP-NE cell line.


title: WT, biological rep. 2


title: Normoxia_6h_S1

description:
Normoxia 6h replicate 1
Sample 1

value: cervix


title: WT, biological rep. 1


title: LNCaP-NE#1

description: Gene expression in LNCaP-NE cell line.


title: E11_Bl002_BRP005


title: Grandmother_BRP004

description: DNA extracted from a large amount of cells derived from the cow's ovarian tissue using DNeasy Blood and Tissue kit (Qiagen).

source_name: Ovarian tissue


title: Mother_BRP004


title: E11_Bl001_BRP005


title: LNCaP#1

description: Gene expression in parental LNCaP cell line.

value: parental


title: GPM6A+mesothelial cells (MC) isolated from biliary fibrosis

city: Los Angeles

first: Kinji

last: Asahina

state: CA

address: 1333 San Pablo Street

department: Pathology

institute: University of Southern California

description:
AI013
Gene expression data from cells in adult mouse liver

hyb_protocol: Following fragmentation, 3.75 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array in the GeneChip Hybridization Oven 640. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymerix GeneArray® Scanner.

data_processing: The data were analyzed with Partek Genomics Suite software with RMA normalization.

source_name: Purified cells from adult mouse liver

label_protocol: Biotinylated probes were synthesized from 20 ng total RNA using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen).

extract_protocol: Total RNA was extracted with RNAqueous Micro (Ambion).

tag: strain background

tag: genotype/variation

value: Col1a1-GFP transgenic

tag: age

value: adult

value: liver

tag: cell type

value: GPM6A+mesothelial cells


title: LNCaP#2

tag: source cell line

value: LNCaP


title: E18_Bl006_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).

value: MDA (GenomiPhiV2)


title: Father_BRP004


title: SAMP8, Kurozu-containing CE2 diet administrated for 5 weeks, biological rep4

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation,  1 µg of labeled cDNA (10 ng/µl) were hybridized for 17 hr at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Robust Multi-array Average (RMA), using the statistical language R (R-3.1.0) and Bioconductor 2.14.

source_name: left side of hippocampus resion excised from brain of SAMP8 mouse

label_protocol: Labeled cDNA was obtained from 50 ng of purified total RNA using a Ambion WT Expression Kit and a GeneChip WT Terminal Labeling (Ambion, Austin, TX, USA and Affymetrix, Santa Clara, CA, USA, respectively).

extract_protocol:
The left side of the hippocampus region was excised from brain.
Total RNA was isolated from the tissues with RNeasy Mini Kit (Qiagen, Valencia, CA, USA), in accordance with the manufacturer’s instructions.

tag: gender

value: Male

value: hippocampus

value: 17 weeks


title: VitaminA+ hepatic stellate cells (HSC) isolated from biliary fibrosis

description:
AI014
Gene expression data from cells in adult mouse liver

value: VitaminA+ hepatic stellate cells


title: Portal fibroblasts (PFs) isolated from sham operation

description:
AI011
Gene expression data from cells in adult mouse liver

value: Portal fibroblasts


title: E18_Bl005_BRP004

tag: dna sample


title: HLaC78 multicellular spheroids for 72hrs

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

data_processing: Data were preprocessed in the R v3.1.1 environment with Bioconductor package affy; background correction, normalization and probeset summary were performed with the rma command using default parameter settings.

source_name: HLaC78_spheroid culture

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol:
HLaC78 cells cultured for 72h as spheroid
HLaC78 cells were cultured in RPMI 1640medium supplemented with 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA of HLaC78 monolayer and spheroidal cell cultures was isolated with the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Tumour spheroids were generated by seeding 5000 cells in ultra-low-attachment T75 flasks (Corning, Amsterdam, Netherlands).

value: larynx carcinoma cell line

tag: cultured in

value: multicellular spheroids for 72hrs

tag: rin

tag: hyb date


title: LNCaP#3


title: GPM6A+mesothelial cells (MC)

value: GPM6A+mesothelial cells (MC)


title: VitaminA-GFP+ cells

source_name: Purified cells from adult Col1a1-GFP mouse liver

value: VitaminA-GFP+ cells


title: SAMP8, Kurozu-containing CE2 diet administrated for 5 weeks, biological rep1


title: E17_Bl005_BRP004

value: Single Cell

tag: wga


title: LL-37-replicate 3

city: Hsinchu

first: Pei-Wen

last: Tsai

address: Kuang-Fu Rd.

country: Taiwan

institute: National Tsing Hua University

description: Gene expression after 0.5 h LL-37 treatment in RPMI

hyb_protocol: 0.6 μg of Cy3-labeled cRNA was fragmented to an average size of about 50–100 nucleotides by incubation in fragmentation buffer at 60oC for 30 min. The fragmented labeled cRNA was then hybridized to the C. albicans oligo microarray (Agilent Technologies) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned using an Agilent microarray scanner (Agilent Technologies).

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies). Normalization and expression analysis was performed by using GeneSpring GX 11.5 (Agilent Technologies). Data analysis was conducted with JMP Genomics (SAS Institute Inc., Cary, NC). The array-to-array correlation heat map was first processed among the ten arrays, which hybridized with 5 replicate samples from cells with or without LL-37 treatment. It revealed that the correlation of each microarray pair was mostly above 0.98 and indicated no intensity-dependent structures. Genes considered to be significantly responsed to LL-37 treatment were based on an average expression level change of ≥ 1.32-fold to control cells (average ratio of five independent replicates) and the p-value less than 0.01.

organism: Candida albicans

label_protocol: For cRNA synthesis, 1 μg total RNA was amplified using a Quick-Amp Labeling kit (Agilent Technologies) and labeled with Cy3 (PerkinElmer, Life Sciences) by in vitro transcription reactions.

growth_protocol: Cells were grown in YPD medium at 30°C overnight and subsequently diluted into fresh YPD medium to an OD600 = 0.5. After 3 h of incubation, cells were washed and then treated with or without 5 ug/ml LL-37 in RPMI for 30 min.

extract_protocol: Total RNAs were isolated with Trizol® Reagent (Ambion, Inc., Carlsbad, CA) combining the shaking at 5,000 rpm for 15 sec with a MagNA Lyser System (Roche Applied Science, Indianapolis, IN) and glass beads. After solubilization, phase separation was performed by adding chloroform and centrifugation. The total RNAs were subsequently purified by RNeasy Mini Kit (Qiagen, Germany). Purified RNAs were quantified at OD260nm using a ND-1000 spectrophotometer (Thermo Scientific Pierce) and the RNA quality was examined using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with RNA 6000 nano labchip kit (Agilent Technologies).

value: with 5 ug/ml LL-37 in RPMI for 30 min


title: E18_Bl003_BRP004


title: E18_Bl004_BRP004


title: SAMP8, control CE2 diet administrated for 5 weeks, biological rep4

tag: tissue


title: LL-37-replicate 4

treatment_protocol: Cells were grown in YPD medium at 30°C overnight and subsequently diluted into fresh YPD medium to an OD600 = 0.5. After 3 h of incubation, cells were washed and then treated with or without 5 ug/ml LL-37 in RPMI for 30 min.


title: E17_Bl003_BRP004


title: E18_Bl001_BRP004


title: VitaminA+ hepatic stellate cells (HSC)

value: Col1a1-GFP transgenic

value: VitaminA+ hepatic stellate cells (HSC)


title: E17_Bl001_BRP004


title: E17_Bl006_BRP004


title: SAMP8, Kurozu-containing CE2 diet administrated for 5 weeks, biological rep2


title: HLaC78 2D monolayer for 72hrs

source_name: HLaC78_monolayer culture

growth_protocol:
HLaC78 cells cultured for 72h as monolayer
HLaC78 cells were cultured in RPMI 1640medium supplemented with 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

tag: cell line

value: 2D monolayer for 72hrs


title: E18_Bl002_BRP004


title: E17_Bl004_BRP004


title: LL-37-replicate 5

tag: treatment


title: LL-37-replicate 2

tag: strain


title: SAMP8, Kurozu-containing CE2 diet administrated for 5 weeks, biological rep3


title: E16_Bl004_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-3post-insemination, in vitro produced embryo and subsequently whole genome amplified byGenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: LL-37-replicate 1


title: control-replicate 5

description: Gene expression after 0.5 h in RPMI


title: E16_Bl006_BRP004


title: Portal fibroblasts (PFs) isolated from biliary fibrosis

description:
AI012
Gene expression data from cells in adult mouse liver

value: adult

value: liver


title: SAMP8, control CE2 diet administrated for 5 weeks, biological rep2


title: E16_Bl003_BRP004

value: MDA (GenomiPhiV2)


title: wild-type mice, biological rep3

city: Gothenburg

first: Adil

last: Mardinoglu

state: Gothenburg

address: Kemivägen 10

department: Department of Biology and Biological Engineering

institute: Chalmers University of Technology

description: Gene expression data from bone marrow–derived macrophages

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

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

data_processing: Raw probe intensity values were background corrected, normalized with quantile normalization, transformed to the log2 scale, and summarized into probesets using the Robust Multichip Analysis algorithm. The data were analyzed with Piano R package.

source_name: Macrophages from wild-type mice cultured at normoxy conditions

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: Vimentin-deficient and wild-type littermates on C57BL/6 background were housed in a pathogen-free barrier facility and fed rodent chow.

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

treatment_protocol: Femur was cleaned from muscle and tissue and bone marrow was flushed out using DMEM containing 2% heat inactivated fetal calf serum (FCS). Isolated marrow was washed with PBS containing 10 mM EDTA, red blood cells were lysed in 2% acetic acid, washed once more in PBS EDTA and plated in high-glucose DMEM supplemented with 10% FCS, 1% HEPES, 1% glutamine, 1% gentamicin, 0.01% β-mercaptoethanol, and 10% whole supernatant of cell line CMG14-12 as a source of mouse M-CSF.

value: macrophages

value: C57BL/6 background

tag: genotype

value: wild-type


title: control-replicate 4

description: Gene expression after 0.5 h in RPMI


title: SAMP8, control CE2 diet administrated for 5 weeks, biological rep3

value: Male

value: hippocampus

value: 17 weeks


title: control-replicate 3

description: Gene expression after 0.5 h in RPMI


title: SAMP8, control CE2 diet administrated for 5 weeks, biological rep1


title: wild-type mice, biological rep1


title: E16_Bl002_BRP004


title: E16_Bl005_BRP004


title: wild-type mice, biological rep2


title: SAMR1, control CE2 diet administrated for 5 weeks, biological rep2

source_name: left side of hippocampus resion excised from brain of SMR1 mouse


title: Vimentin-deficient mice, biological rep3

source_name: Macrophages from vimentin-deficient mice cultured at normoxy conditions

value: vimentin-deficient


title: Vimentin-deficient mice, biological rep2


title: control-replicate 2

description: Gene expression after 0.5 h in RPMI


title: control-replicate 1

description: Gene expression after 0.5 h in RPMI


title: SAMR1, control CE2 diet administrated for 5 weeks, biological rep3


title: SAMR1, control CE2 diet administrated for 5 weeks, biological rep4


title: E10_Bl004_BRP004


title: Vimentin-deficient mice, biological rep1


title: Adult mouse liver

source_name: Adult mouse liver

value: wild type


title: SAMR1, control CE2 diet administrated for 5 weeks, biological rep1


title: Oryza rufipogon-120mM_rep2

status: Public on Mar 10 2016

city: Mymensingh

first: Mohammad

middle: Rashed

last: Hossain

address: Factulty of Agriculture (East Building)

department: Genetics and Plant Breeding

country: Bangladesh

institute: Bangladesh Agricultural University

description: Gene expression in 120mM NaCl stressed (for 48 hrs)_16 day old_whole rice seedling

hyb_protocol: Cy3-labelled cRNA (1.65 ug) was fragmented at 60°C for 30 minutes by 11.0 µL of 10x blocks and 2.2 µL of fragmentation buffer in a reaction volume of 55 uL as per the manufacturer’s instructions. After that, 55 µL 2 x GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4x44K Microarray (product G2519F; Design ID-015241) for 17 h at 650C in an Agilent hybridization rotisserie. Microarrays were then washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with GE Wash buffer 2 (Agilent), for 10 s with 100% acetonitrile followed by another wash in a stabilising and drying solution for 30 s.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides at ‘Profile AgilentG3_GX_1Color’.

data_processing: Data were acquired from the scanned images using Agilent feature extraction software version 9.5.3 to obtain background subtracted and spatially detrended Processed Signal intensities. After the successful completion of extraction, the QC report for each extraction set was critically evaluated and the features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: Whole seedling, 120mM NaCl, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using the ‘One color - Low Input Quick Amplification Labeling Protocol v.6.5, May 2010’ (available from www.agilent.com/chem/dnamanuals-protocols) according to the manufacturer’s (Agilent) instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  The incorporation of Cy3 dye and the yield of cRNA were checked with the NanoDrop ND-1000 VIS spectrophotometer (v. 3.2.1).

growth_protocol: Seeds were heat treated at 48°C for 5 d, then sterilized with 1% sodium hypochlorite and incubated on pre-soaked filter paper in a sterile petridish at 20°C for 48 h. Germinated seeds were transferred to test tubes filled with Yoshida nutrient medium (Yoshida et al., 1976) for seedling establishment for 7 d and then the seedlings were transferred to aluminum foil wrapped 250 mL conical flasks. Individual seedlings were held in place using a sponge bung in each flask and roots were suspended in nutrient solution. Flasks were maintained in a growth room with 16/8 h photoperiod, 28/20°C day/night temperature, 70-75% relative humidity and average 290 μmol m-2 s-1 photosynthetic photon flux.

extract_protocol: RNA extractions were carried out using the QIAGEN RNeasy Plant Mini Kit from the 16 day old fresh whole seedlings (including root and shoot). For seedlings weighing more than the recommended starting material (100 mg), representative sections (tip, middle and basal portion) of root, stem and leaves of each seedling were kept using sterile scissors. RNA was quantified using a Nanodrop ND-1000 VIS spectrophotometer (v. 3.2.1) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Seedlings in flasks were challenged with 0 & 120 mM NaCl in Yoshida nutrient medium (with additional CaCl2 added at a molar concentration ratio of 1:6) with three replicates per treatment. Half strength salt stress was applied at 13 d after emergence and after another 24 h the full strength stress was applied. The pH of the nutrient solution was maintained at 5.0 on a daily basis and the solution was renewed every week.

tag: organism (germplasm accession)

value: Oryza sativa (IRGC 105390)

value: whole seedling

value: 16 days after emergence

tag: stress level

value: 120 mM NaCl

tag: stress duration

value: 48 hrs


title: Oryza rufipogon-120mM_rep1

source_name: Whole seedling, 120mM NaCl, replicate 1

tag: age


title: E10_Bl003_BRP004

value: Single Cell


title: Oryza rufipogon-0mM_rep3

description: Gene expression in unstressed_16 day old_whole rice seedling

source_name: Whole seedling, 0mM NaCl, replicate 3

value: 0 mM NaCl


title: Oryza latifolia-0mM_rep2

source_name: Whole seedling, 0mM NaCl, replicate 2

value: Oryza sativa (IRGC 100965)


title: Oryza rufipogon-120mM_rep3

source_name: Whole seedling, 120mM NaCl, replicate 3


title: Oryza latifolia-120mM_rep1


title: Oryza latifolia-120mM_rep2


title: Oryza rufipogon-0mM_rep1

source_name: Whole seedling, 0mM NaCl, replicate 1


title: Oryza rufipogon-0mM_rep2


title: Oryza latifolia-120mM_rep3


title: Oryza latifolia-0mM_rep1


title: E16_Bl001_BRP004

source_name: Blastomere

value: MDA (GenomiPhiV2)


title: Nipponbare-120mM_rep3

value: Oryza sativa (IRGC 117274)


title: Nipponbare-0mM_rep3


title: Nipponbare-120mM_rep1


title: E10_Bl002_BRP004


title: Nipponbare-0mM_rep1


title: Banikat-120mM_rep3

value: Oryza sativa (IRGC 67720)


title: Banikat-120mM_rep1


title: Banikat-0mM_rep3


title: Nipponbare-0mM_rep2


title: E10_Bl001_BRP004


title: BRRIdhan 29-120mM_rep2

value: Oryza sativa (IRTP 15241)


title: BRRIdhan 29-120mM_rep1


title: BRRIdhan 29-0mM_rep1


title: E17_Bl002_BRP004


title: E09_Bl001_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-2 post insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: BRRIdhan 29-0mM_rep3


title: IR58-0mM_rep2

value: Oryza sativa (IRGC 63492)


title: IR58-120mM_rep1


title: E09_Bl003_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-2post insemination,  in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: E09_Bl004_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-2 post-insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: PSBRc50-120mM_rep3

value: Oryza sativa (IRGC 99706)


title: IR58-120mM_rep2


title: 5FU+SB431542

city: Pisa

first: Roberto

last: Giovannoni

address: Via Derna, 1

department: Biology

country: Italy

institute: University of Pisa

description:
Test
StepOne Plus instrument (Applied Biosystems)

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: HCT116p53KO colorectal carcinoma cell line, 5FU+SB431542

label_protocol: PCR assays were performed using the 84 genes Human TGF-β Signaling Targets RT2 array (Cat. N. PAHS-235ZA, Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 1ug total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (StepOne Plus, Applied Biosystems) with 40 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: CellSperse™ solution was used to recover cells grown on Cultrex®, following manufacturer instructions. RNeasy® Mini Kit (Qiagen) was used to extract total RNA from cells grown on a thin layer of Cultrex®. RNA samples were treated with DNase to ensure elimination of genomic DNA. At the end of the procedure, the RNA concentration was measured with Nanodrop 2000 (Thermo Scientific) and samples were checked for RNA quality and integrity by 1.5% agarose gel electrophoresis in denaturing conditions. One microgram of extracted RNA was then converted to cDNA by using the RT2 First Strand Kit (Qiagen) according to manufacturer’s instructions.

value: HCT116p53KO drug-resistant colon carcinoma cells


title: Banikat-0mM_rep1


title: Banikat-120mM_rep2


title: IR58-120mM_rep3


title: IR58-0mM_rep1


title: Banikat-0mM_rep2


title: 5FU

description:
Test/Control
StepOne Plus instrument (Applied Biosystems)

source_name: HCT116p53KO colorectal carcinoma cell line, 5FU


title: PSBRc50-120mM_rep1


title: Nipponbare-120mM_rep2


title: BRRIdhan 29-0mM_rep2


title: NT

description:
Control
StepOne Plus instrument (Applied Biosystems)

source_name: HCT116p53KO colorectal carcinoma cell line, NT

value: Control


title: Oryza latifolia-0mM_rep3


title: 5FU+LiCl

source_name: HCT116p53KO colorectal carcinoma cell line, 5FU+LiCl


title: E16_Bl008_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-3 in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).


title: PSBRc50-0mM_rep1


title: PSBRc50-0mM_rep2


title: Pokkali-120mM_rep3

value: Oryza sativa (IRGC 108921)


title: Control cells when cultured in the absence of 4mM H2O2, replicate 2

city: Singapore

first: Hefang

last: Geng

address: 62 Nanyang Drive, School of Chemical & Biomedical Engineering, Nanyang Technological University

country: Singapore

institute: Nanyang Technological University

description: Gene expression when OD600 of cell culture reached 1.0

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was applied for the hybridization process. To ensure the accuracy of the collected data, Agilent G2545A Hybridization Calibration Procedure (p/n G2545-90002,  version A1 or higher) was performed.

scan_protocol: Slides were scanned immediately after washing on SureScan microarray scanner using one color scan setting for 8x15k array slides

data_processing:
Agilent Genespring GX software was used for raw data analysis and p-values were calculated with unpaired Student t-test
Normalized signal intensity, using the 75th percentile signal value for inter-array comparisons. Compared to the median or 50th  percentile signalsignal value, the 75th percentile of all of non-control probes on the microarray is a more robust and representative  value of the overall microarray signal.

source_name: Saccharomyces cerevisiae cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Yeast cells were grown in YPD medium supplemented with/without 4mM H2O2

extract_protocol: Total RNA was extracted with RNeasy® Mini Kit and RNase-Free DNase Set following manufacture's instructions. RNA quality and integrity was verified by gel electrophoresis, as well as by measuring 260/230 ratios with a NanoDrop 1000 spectrophotometer (Thermo Scientific, USA).

treatment_protocol: The cells were collected by centrifugation and washed twice with ddH2O.

tag: genotype/variation

value: Control cells

tag: growth phase

value: Exponential Phase


title: Mutant cells when cultured in the presence of 4mM H2O2, replicate 2

value: TFIIB mutant cells


title: Mutant cells when cultured in the absence of 4mM H2O2, replicate 1


title: Treated rat kidney_6day_rep5

city: Shanghai

first: Ze'an

last: Zhang

address: Room 1403, No. 1 Building, Cai Lun Road

country: China

institute: Shanghai University of Traditional Chinese Medicine

description:
miRNA expression after 6days in AAI-treated wistar rat kidney tissue.
78

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: Treated rat kidney, 6 days

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Male Wistar rats with 80-100 g body weight, were treated with 40mg Aristolochic acid I/kg body weight by i.p. for 6 days; vehicle control rats were treated with PEG400 (PEG400:dH2O=1:1) using the same schedule as for the AAI-treated rats. On day 2, day 4 and day 6, collected 5 kidneys in each group and time point to prepare for microarry analysis.

value: Wistar

tag: gender

value: male

value: AAI

tag: time

value: 6 days

value: kidney


title: Pokkali-0mM_rep2

value: whole seedling

value: 16 days after emergence

value: 0 mM NaCl


title: Pokkali-120mM_rep1

value: 120 mM NaCl

value: 48 hrs


title: triple_60_min_BA_rep1

city: Freising

first: Quirin

middle: Ludwig

last: Ranftl

address: Emil-Ramann-Straße 4

department: Wissenschaftszentrum Weihenstephan

institute: TU München

description: Gene expression of whole seedlings at day 14

hyb_protocol: The probes were hybridized in rotating hybridization chambers (Agilent Technologies) and incubated at 65 °C for 17 h overnight in a hybridization oven. Subsequently, the arrays were washed according to manufacturer’s instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v1_107_Sep09 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: 14 days-old seedlings, replicate 1

label_protocol: Cy3-labeled cRNA was prepared from 150 ng total RNA

growth_protocol: Seedlings were grown in 120 µE white light on 1/2 MS medium for 10 days in continious light

extract_protocol: RNA was prepared using the Machery-Nagel Nucleo Spin RNA Plant Kit.

treatment_protocol: 20 µM 6-BA (6-Benzylaminopurine) for 60 min.

tag: ecotype

value: gata16 gata17 gata17l


title: Pokkali-0mM_rep1


title: Pokkali-120mM_rep2


title: Treated rat kidney_6day_rep4

description:
miRNA expression after 6days in AAI-treated wistar rat kidney tissue.
75


title: Treated rat kidney_6day_rep3

description:
miRNA expression after 6days in AAI-treated wistar rat kidney tissue.
74


title: Control cells when cultured in the absence of 4mM H2O2, replicate 1


title: Treated rat kidney_6day_rep2

description:
miRNA expression after 6days in AAI-treated wistar rat kidney tissue.
72


title: Control cells when cultured in the presence of 4mM H2O2, replicate 2


title: Control cells when cultured in the presence of 4mM H2O2, replicate 1


title: Mutant cells when cultured in the presence of 4mM H2O2, replicate 1


title: E09_Bl002_BRP004

description: DNA extracted from single blastomere derived from cleavage stage day-2post insemination, in vitro produced embryo and subsequently whole genome amplified by GenomiPhiV2 (GE Healthcare) as per Spits et al (Nat Protoc. 2006;1(4):1965-70. doi:10.1038/nprot.2006.326).

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

data_processing: Image data was analyzed using Genomestudio with genotyping module (Illumina). The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0.75. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG). The data is provided as family stuctures, i.e. a BRP family for each cross.

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

extract_protocol: The isolated blastomeres were placed immediately on dry ice and stored in -20oC for 30 minutes prior to whole genome amplification (WGA). WGA was performed on the day of blastomere isolation. DNA from single blastomeres was whole-genome amplified using commercial MDA kits (REPLI-g Single Cell Kit, Qiagen and GenomiPhiV2, GE Healthcare Biosciences). MDA amplification with GenomiPhiV2 was performed as described previously (Spits et al. 2006, Nat Protoc). MDA amplification of single blastomeres with the single-cell Repli-g kit was performed according to the manufacturer’s instructions for the fast 3-hour protocol. WGA products were purified using SPRI-beads (AMPure) at 0.8x of total reaction volume.

tag: dna sample

value: Single Cell

value: MDA (GenomiPhiV2)


title: triple_60_min_BA_rep3

source_name: 14 days-old seedlings, replicate 3


title: triple_mock_rep2

source_name: 14 days-old seedlings, replicate 2


title: triple_mock_rep3


title: Treated rat kidney_6day_rep1

description:
miRNA expression after 6days in AAI-treated wistar rat kidney tissue.
71


title: triple_60_min_BA_rep2


title: Tumor27

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

institute: Heidelberg University Hospital

description: DNA was enriched for hypermethylated fractions by Methyl-CpG Immunoprecipitation (MCIp)

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Scanning raw data were processed using the statistical environment R. Background correction and log2 transformation were performed according to the NormExp method with offset = 50 (Ritchie et al., Bioinformatics 2007). Intensity-based LOESS normalization was applied to rank-invariant probes and negative controls in order to reduce technical noise between samples (Tseng et al., Nucleic Acids Res 2001). For intra-array normalization, log-intensity ratios (M-value) and log-intensity averages (A-values) were scaled to have the same median-absolute value across the array.

source_name: glioblastoma tissue

label_protocol: Highly methylated glioblastoma and normal brain control DNA were labeled with Alexa Fluor 5 and Alexa Fluor 3, respectively.

growth_protocol: Not applicable

extract_protocol: Tumor tissue was snap-frozen and stored at -80°C until further processing. DNA was extracted with the QIAmp DNA Mini Kit (Qiagen) from samples found eligible in terms of tumor cell content (>60%) and necrosis (<20%). Analyte concentration and quality were determined using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent). For enrichment of hypermethylated DNA fractions, Methyl-CpG-binding domain (MBD)-Fc protein was produced and MCIp performed as previously described (Schilling et al., Genomics 2007). Briefly, 75 µg of MBD-Fc protein was coupled to 50 µl SIMAG protein A magnetic beads (Chemicell) at 4°C overnight. After binding of 2 µg sonicated DNA, the DNA was eluted with increasing NaCl concentrations (300-1000 mM) using the MagnetoPure-Micro bead separator (Chemicell). Lowly and highly methylated DNA was eluted at the lowest and highest concentrations, respectively. DNA enrichment was monitored by real-time PCR targeting known unmethylated and methylated DNA regions.

value: short-term survivor (STS)

tag: tissue type

value: glioblastoma

source_name: normal brain tissue

value: normal brain


title: Treated rat kidney_4day_rep5

description:
miRNA expression after 4days in AAI-treated wistar rat kidney tissue.
70

source_name: Treated rat kidney, 4 days

value: 4 days


title: wild type (Col-0)_2_60_min_BA_rep3

value: wild type


title: triple_mock_rep1


title: wild type (Col-0)_2_60_min_BA_rep2


title: Treated rat kidney_4day_rep4

description:
miRNA expression after 4days in AAI-treated wistar rat kidney tissue.
69

value: Wistar

value: male


title: Tumor29


title: Tumor25


title: Tumor22


title: Tumor28


title: Pokkali-0mM_rep3

description: Gene expression in unstressed_16 day old_whole rice seedling

source_name: Whole seedling, 0mM NaCl, replicate 3

value: Oryza sativa (IRGC 108921)


title: Tumor20


title: Tumor23


title: Tumor21


title: Treated rat kidney_4day_rep3

description:
miRNA expression after 4days in AAI-treated wistar rat kidney tissue.
68

value: AAI

value: kidney


title: Tumor24


title: wild type (Col-0)_2_mock_rep3


title: wild type (Col-0)_2_60_min_BA_rep1


title: Treated rat kidney_4day_rep2

description:
miRNA expression after 4days in AAI-treated wistar rat kidney tissue.
67


title: Tumor26


title: Treated rat kidney_4day_rep1

description:
miRNA expression after 4days in AAI-treated wistar rat kidney tissue.
66


title: wild type (Col-0)_2_mock_rep2


title: Tumor19


title: Tumor18


title: quintuple_60_min_BA_rep3

source_name: 10 days-old seedlings, replicate 3

value: gnc gnl gata16 gata17 gata17l


title: PSBRc50-0mM_rep3

value: Oryza sativa (IRGC 99706)

value: whole seedling

value: 16 days after emergence

value: 0 mM NaCl


title: Treated rat kidney_2day_rep5

description:
miRNA expression after 2days in AAI-treated wistar rat kidney tissue.
65

source_name: Treated rat kidney, 2 days

value: 2 days


title: Tumor17


title: Treated rat kidney_2day_rep4

description:
miRNA expression after 2days in AAI-treated wistar rat kidney tissue.
64


title: Treated rat kidney_2day_rep3

description:
miRNA expression after 2days in AAI-treated wistar rat kidney tissue.
63


title: Treated rat kidney_2day_rep2

description:
miRNA expression after 2days in AAI-treated wistar rat kidney tissue.
62


title: Mutant cells when cultured in the absence of 4mM H2O2, replicate 2

description: Gene expression when OD600 of cell culture reached 1.0

value: TFIIB mutant cells

value: Exponential Phase


title: Tumor15

value: short-term survivor (STS)

value: glioblastoma


title: Tumor11

value: long-term survivor (LTS)

value: normal brain


title: Tumor14


title: wild type (Col-0)_2_mock_rep1

description: Gene expression of whole seedlings at day 14

value: wild type


title: Tumor12


title: Treated rat kidney_2day_rep1

description:
miRNA expression after 2days in AAI-treated wistar rat kidney tissue.
61

value: Wistar

value: male


title: Tumor16


title: Tumor9


title: quintuple_mock_rep2

source_name: 10 days-old seedlings, replicate 2


title: Tumor13


title: Tumor10


title: quintuple_60_min_BA_rep2


title: quintuple_60_min_BA_rep1

source_name: 10 days-old seedlings, replicate 1


title: Control rat kidney_6day_rep5

description:
miRNA expression after 6days in PEG400-treated wistar rat kidney tissue.
15

source_name: Control rat kidney, 6 days

value: control

value: 6 days


title: Tumor3


title: Control rat kidney_6day_rep4

description:
miRNA expression after 6days in PEG400-treated wistar rat kidney tissue.
14

value: kidney


title: CD4 T-LA-3

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: gene expression data

hyb_protocol: 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit). Next cDNAs were fragmented, biotinylated, and hybridized to the GeneChip MoGene-2_0-st Arrays (Affymetrix WT Terminal Labeling Kit).

scan_protocol: scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control(all from Affymetrix, Santa Clara, CA).

data_processing:
Expression data were normalized, background-corrected, and summarized using the RMA algorithm
Data were log-transformed (base 2) for subsequent statistical analysis

label: Biotin

source_name: CD4 T-LA-3

extract_protocol: Total RNA was extracted from CD4 and CD8 cells by using RNeasy kit (Qiagen, Germantown, , MD, USA)

treatment_protocol: Splenocyte was cultured with or without 50μM linoleic acid for 24 hrs. CD4+ and CD8+ T cells were sorted, treated samples labeled with LA, control samples labeled with CTR.

tag: protocol

value: Splenocyte was cultured with 50μM linoleic acid

tag: sorted cell type

value: CD4 T cell


title: Control rat kidney_6day_rep3

description:
miRNA expression after 6days in PEG400-treated wistar rat kidney tissue.
13

tag: tissue


title: CD8 T-LA-3

description: gene expression data

source_name: CD8 T-LA-3

label_protocol: 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit). Next cDNAs were fragmented, biotinylated, and hybridized to the GeneChip MoGene-2_0-st Arrays (Affymetrix WT Terminal Labeling Kit).

growth_protocol: Splenocyte was cultured with or without 50μM linoleic acid for 24 hrs. CD4+ and CD8+ T cells were sorted

value: CD8 T cell


title: quintuple_mock_rep1

value: gnc gnl gata16 gata17 gata17l


title: CD8 T-LA-2

description: gene expression data

source_name: CD8 T-LA-2


title: Tumor8

description: DNA was enriched for hypermethylated fractions by Methyl-CpG Immunoprecipitation (MCIp)


title: Tumor4


title: gnc gnl_60_min_BA_rep3

value: gnc gnl


title: gnc gnl_60_min_BA_rep1


title: gnc gnl_60_min_BA_rep2


title: Control rat kidney_6day_rep1

description:
miRNA expression after 6days in PEG400-treated wistar rat kidney tissue.
11

tag: treatment


title: Control rat kidney_6day_rep2

description:
miRNA expression after 6days in PEG400-treated wistar rat kidney tissue.
12

tag: strain


title: Tumor6


title: Tumor2


title: Tumor5


title: Tumor7


title: gnc gnl_mock_rep1

tag: genotype


title: CD8 T-LA-1

description: gene expression data

source_name: CD8 T-LA-1


title: Tumor1


title: gnc gnl_mock_rep2


title: PSBRc50-120mM_rep2

description: Gene expression in 120mM NaCl stressed (for 48 hrs)_16 day old_whole rice seedling

source_name: Whole seedling, 120mM NaCl, replicate 2

tag: organism (germplasm accession)

value: Oryza sativa (IRGC 99706)

value: whole seedling

value: 16 days after emergence

value: 120 mM NaCl

value: 48 hrs


title: CD4 T-CTR-1

description: gene expression data

source_name: CD4 T-CTR-1

value: Splenocyte was cultured without linoleic acid


title: wild type (Col-0)_1_60_min_BA_rep1

source_name: 14 days-old seedlings, replicate 1

value: wild type


title: gnc gnl_mock_rep3

source_name: 14 days-old seedlings, replicate 3


title: CD4 T-CTR-2

description: gene expression data

source_name: CD4 T-CTR-2


title: CD4 T-CTR-3

description: gene expression data

source_name: CD4 T-CTR-3


title: CD8 T-CTR-1

description: gene expression data

source_name: CD8 T-CTR-1


title: wild type (Col-0)_1_60_min_BA_rep3


title: My5/CRBN

status: Public on Mar 09 2016

city: scottsdale

first: qinqin

last: xu

state: arizona

address: 13400 E shea blvd

institute: mayo clinic arizona

description:
Control
OCI-My5 is the original MM cell line, low level of CRBN.

data_processing:
Data analyses were performed with QIAGEN online software (http://pcrdataanalysis.sabiosciences.com/mirna/arrayanalysis.php, MIHS-3001Z).
Non-normalized file reports raw Ct. Linked as supplementary file on Series record.
Fold-change file reports test/control. Linked as supplementary file on Series record.

label: SYBR green

source_name: My5/CRBN multiple myeloma cells, control

label_protocol: Reverse transcription was performed with the miScript II RT kit (QIAGEN), according to the protocol provided by QIAGEN. Quantitative analysis of miRNA was performed with the miScript SYBR Green PCR Kit (QIAGEN) and miScript miRNA PCR Arrays (QIAGEN).

growth_protocol: Human multiple myeloma (MM) cell lines were maintained in RPMI-1640 medium (Thermo Scientific) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Scientific) and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated from cells with the miRNeasy Mini kit (QIAGEN), according to the protocol provided by QIAGEN.

treatment_protocol: 1. pCDH.puro.EIF2C2.42.4 or EIF2C2-shRNA constructs were used to make lentiviral particles, according to the routine method. 2. EIF2C2 knockdown or overexpressing cells were constructed using lentiviral particles according to the routine method. 3. Cells cultured in 6 cm plates were treated with 0 or 10µM lenalidomide for 72 or 120hrs.

tag: original cell line

tag: cell line

tag: cell type

value: multiple myeloma (MM) cell line, high level of CRBN

tag: overexpression

tag: knockdown


title: My5/CRBN/EIF2C2

description:
Test, EIF2C2 overexpress
OCI-My5 is the original MM cell line, low level of CRBN.

source_name: My5/CRBN multiple myeloma cells, EIF2C2 overexpression


title: My5/LV/sh72

description:
Test, EIF2C2 knockdown
OCI-My5 is the original MM cell line, low level of CRBN.

source_name: My5/LV multiple myeloma cells, EIF2C2 knockdown

value: multiple myeloma (MM) cell line, low level of CRBN


title: My5/LV+Len72hrs

description:
Test, treatment with lenalidomide 72hours
OCI-My5 is the original MM cell line, low level of CRBN.

source_name: My5/LV multiple myeloma cells, lenalidomide for 72hours

value: lenalidomide for 72hours


title: My5/CRBN/sh72

source_name: My5/CRBN multiple myeloma cells, EIF2C2 knockdown


title: My5/LV/EIF2C2+Len72hrs

description:
Test, EIF2C2 overexpress and treatment with lenalidomide 72hours
OCI-My5 is the original MM cell line, low level of CRBN.

source_name: My5/LV multiple myeloma cells, EIF2C2 overexpression, lenalidomide for 72hours


title: My5/CRBN+Len72hrs

source_name: My5/CRBN multiple myeloma cells, lenalidomide for 72hours


title: My5/CRBN/EIF2C2+Len72hrs

source_name: My5/CRBN multiple myeloma cells, EIF2C2 overexpression, lenalidomide for 72hours


title: My5/LV/EIF2C2

source_name: My5/LV multiple myeloma cells, EIF2C2 overexpression


title: My5/LV

source_name: My5/LV multiple myeloma cells, control


title: My5/LV+Len120hrs

description:
Test, treatment with lenalidomide 120hours
OCI-My5 is the original MM cell line, low level of CRBN.

source_name: My5/LV multiple myeloma cells, lenalidomide for 120hours

value: lenalidomide for 120hours


title: My5/CRBN+Len120hrs

source_name: My5/CRBN multiple myeloma cells, lenalidomide for 120hours


title: WT1

city: Suita

first: Koichi

last: Hasegawa

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

description: SAMPLE 4

hyb_protocol: Labeled cRNA samples were loaded onto CodeLinkTM Mouse Whole Genome Microarray glass slides (Applied Microarrays) and hybridized at 37℃/300 rpm for 18 hours.

scan_protocol: Arrays were scanned with GenePix 4400A (Molecular Devices).

data_processing: Array images were analyzed using CodeLinkTM Expression Analysis Software v5.0 (Applied Microarrays). Data were normalized by quantile normalization method.

source_name: Cortical neurons

label_protocol: Total RNA (1μg ) was labeled using MessageAmpTM II-Biotin Enhanced Kit (AM1791, Ambion) according to the manufacture’s protocol.

growth_protocol: Primary cortical neurons were incubated at 37℃ in humidified atmosphere of 5% CO2 and 95% air for four days.

extract_protocol: Total RNA was extracted from primary cortical neurons with TRI Reagent.

value: ICR

value: brain

value: cortical neuron

value: wildtype

tag: developmental stage

value: embryonic day 14.5


title: wild type (Col-0)_1_mock_rep3

source_name: 14 days-old seedlings, replicate 3


title: CD4 T-LA-1

description: gene expression data

source_name: CD4 T-LA-1

value: Splenocyte was cultured with 50μM linoleic acid

value: CD4 T cell


title: KO2

description: SAMPLE 2

value: necdin knockout


title: CD4 T-LA-2

description: gene expression data

source_name: CD4 T-LA-2


title: wild type (Col-0)_1_60_min_BA_rep2

source_name: 14 days-old seedlings, replicate 2


title: WT2

description: SAMPLE 5


title: WT3

description: SAMPLE 6


title: CD8 T-CTR-2

description: gene expression data

source_name: CD8 T-CTR-2

value: CD8 T cell


title: KO3

description: SAMPLE 3


title: wild type (Col-0)_1_mock_rep1

source_name: 14 days-old seedlings, replicate 1


title: KO1

description: SAMPLE 1


title: wild type (Col-0)_1_mock_rep2


title: prostate_RP_b9close_J

city: San Diego

first: Elai

last: Davicioni

address: 10355 Science Center Dr

institute: GenomeDx Biosciences

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE, prostate, normal, RP

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: At CSMC and UCSF, tumor tissues were sampled from FFPE biopsy cores by dissecting a portion of the tumor tissue directly from the blocks in the areas corresponding to marked areas on each H&E slide using a sterile biopsy punch tool, and then extracting RNA as described below. The histologically benign peripheral zone glandular tissue was sampled in an analogous manner. Benign tissues were defined as adjacent to tumor (benign adjacent) when they were within 1mm to 5 mm of the tumor.  Benign contralateral tissues were obtained from a biopsy core from the opposite side of the prostate relative to the primary tumor site, and from as far away from any other tumor or high grade PIN areas as possible. For each case, RP tissue was punched in the same manner at locations matching those where the biopsy punches were taken for each tissue type (tumor, benign adjacent to tumor, and benign contralateral to tumor). Benign contralateral to tumor in RPs was taken at least 1 cm away from any other tumor or high grade PIN areas. At UHN, both biopsy and RP specimens were sliced  as 4 μm thick unstained sections and the areas of interest were macrodissected (scraped) from the slides for nucleic acid extraction. Six unstained sections were used to collect biopsy tissue and four to collect RP tissue. RP tissue was sampled in locations matching the location of tumor in the biopsy cores. Total RNA was extracted and purified using the RNeasy FFPE kit (Qiagen, Valencia, CA). RNA was amplified and labeled using the Ovation WTA FFPE system (NuGen, San Carlos, CA).

treatment_protocol: Not Applicable

value: normal

value: RP

tag: location

value: adjacent

tag: patient

value: J


title: prostate_RP_tumor_DD

source_name: FFPE, prostate, tumor, RP

value: tumor

value: DD


title: prostate_BX_tumor_EE

source_name: FFPE, prostate, tumor, BX

value: BX

value: EE


title: BARC-2_4dpi_BErhcJ_rep2

city: Fuchu

first: Michiko

last: YASUDA

state: Tokyo

address: 3-5-8 Saiwaicho

department: International Environmental and Agricultural Science

institute: Tokyo University of Agriculture and Technology

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 4 days after inoculation.
BErhcJ_4d_2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to Agilent G. max (Soybean) Oligo Microarray 4x44K (arrayID:016772) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After hybridization, the microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides at two laser power settings (100% and 10%).

data_processing: The scanned images were analyzed with Agilent’s Feature Extraction Software (v 10.7.3.1) to obtain background subtracted and spatially detrended Processed Signal intensities. The data were then normalized subjected to 75 percentile normalization and log2 transformation using data analysis tools Subio Basic Plug-in (Subio Inc. Tokyo, Japan).

organism: Glycine max

source_name: BARC-2, 4dpi, BErhcJ, replicate 2

label_protocol: Each RNA sample (0.2 ug) was labeled with Cyanine-3 (Cy3) fluorescent dye, using Agilent’s Quick Amp Labeling Kit. The cRNA product was purified with RNeasy mini spin columns (QIAGEN, Hilden, Germany).

growth_protocol: Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. RNA was extracted from the roots at 2 days and 4 days after inoculation with B. elkanii USDA61 (WT) and its typeIII mutant, BErhcJ.

extract_protocol: RNA was prepared using the Qiagen RNeasy plant mini-kit (Qiagen, Hilden, Germany), following the manufacturer's instructions. The protocol includes an on-column DNase digestion. RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: Seeds of soybeans (Glycine max L. cv. BARC-2) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to the seed pack (Daiki Rika Co. Ltd., Shiga, Japn) with nitrogen-free medium. One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BerhcJ (1 x 106 CFU/plant, respectively) . To determine the gene expression, RNA was extracted from the roots at 4 days after inoculation for Enrei and 8 days after inoculation for En1282, respectively.

value: root

tag: cultivar

tag: inoculant

value: BErhcJ

tag: days post inoculation


title: BARC-2_4dpi_USDA61_rep2

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 4 days after inoculation.
WT_4d_2

source_name: BARC-2, 4dpi, USDA61, replicate 2

value: WT


title: prostate_RP_b9close_T

value: T


title: prostate_RP_b9close_E

value: E


title: BARC-2_2dpi_BErhcJ_rep2

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 2 days after inoculation.
BErhcJ_2d_2

source_name: BARC-2, 2dpi, BErhcJ, replicate 2


title: BARC-2_4dpi_BErhcJ_rep3

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 4 days after inoculation.
BErhcJ_4d_3

source_name: BARC-2, 4dpi, BErhcJ, replicate 3


title: prostate_BX_tumor_Q

value: Q


title: prostate_RP_tumor_C

value: C


title: prostate_RP_b9away_M

value: contralateral

value: M


title: prostate_BX_b9away_M

source_name: FFPE, prostate, normal, BX

value: normal


title: BARC-2_4dpi_USDA61_rep1

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 4 days after inoculation.
WT_4d_1

source_name: BARC-2, 4dpi, USDA61, replicate 1


title: prostate_BX_b9away_T


title: prostate_BX_tumor_H

value: H


title: BARC-2_2dpi_BErhcJ_rep1

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 2 days after inoculation.
BErhcJ_2d_1

source_name: BARC-2, 2dpi, BErhcJ, replicate 1


title: BARC-2_4dpi_BErhcJ_rep1

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 4 days after inoculation.
BErhcJ_4d_1

source_name: BARC-2, 4dpi, BErhcJ, replicate 1


title: BARC-2_2dpi_USDA61_rep3

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 2 days after inoculation.
WT_2d_3

source_name: BARC-2, 2dpi, USDA61, replicate 3


title: prostate_BX_tumor_T


title: BARC-2_2dpi_BErhcJ_rep3

description:
Gene expression in Rj4 soybean roots inoculated with BErhcJ at 2 days after inoculation.
BErhcJ_2d_3

source_name: BARC-2, 2dpi, BErhcJ, replicate 3


title: BARC-2_2dpi_USDA61_rep2

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 2 days after inoculation.
WT_2d_2

source_name: BARC-2, 2dpi, USDA61, replicate 2


title: prostate_BX_b9away_D

value: D


title: prostate_RP_b9away_O

value: RP

value: O


title: prostate_RP_tumor_P

value: tumor

value: P


title: BARC-2_2dpi_USDA61_rep1

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 2 days after inoculation.
WT_2d_1

source_name: BARC-2, 2dpi, USDA61, replicate 1


title: BARC-2_4dpi_USDA61_rep3

description:
Gene expression in Rj4 soybean roots inoculated with USDA61 at 4 days after inoculation.
WT_4d_3

source_name: BARC-2, 4dpi, USDA61, replicate 3


title: prostate_RP_b9away_B

value: B


title: prostate_RP_tumor_I

value: I


title: prostate_BX_b9close_T

value: BX

value: adjacent


title: CD8 T-CTR-3

description: gene expression data

source_name: CD8 T-CTR-3

tag: protocol

value: Splenocyte was cultured without linoleic acid

tag: sorted cell type

value: CD8 T cell


title: prostate_BX_b9close_S

tag: tissue

value: S


title: prostate_BX_tumor_BB

value: BB


title: prostate_BX_tumor_V

value: V


title: prostate_BX_b9close_H


title: prostate_BX_b9away_E

value: contralateral

value: E


title: prostate_RP_b9close_L

source_name: FFPE, prostate, normal, RP

value: normal

value: L


title: prostate_BX_b9close_O


title: prostate_RP_b9close_B

value: RP


title: prostate_BX_b9away_W

value: W


title: prostate_RP_b9away_N

value: N


title: prostate_BX_b9away_O

value: O


title: prostate_RP_tumor_E

source_name: FFPE, prostate, tumor, RP

value: tumor


title: prostate_BX_b9away_R

value: R


title: prostate_BX_b9close_A

value: BX

value: A


title: prostate_RP_tumor_J

value: J


title: prostate_BX_b9close_V

value: adjacent


title: prostate_RP_b9close_K

value: K


title: prostate_BX_b9close_Q

value: Q


title: prostate_BX_tumor_AA

source_name: FFPE, prostate, tumor, BX

value: AA


title: prostate_RP_tumor_H

value: H


title: prostate_RP_b9close_F

value: F


title: prostate_BX_b9away_K

value: normal

value: contralateral


title: prostate_RP_tumor_R

value: RP


title: prostate_BX_tumor_Y

value: Y


title: prostate_RP_b9away_H


title: prostate_RP_tumor_L

value: L


title: prostate_BX_b9away_J


title: prostate_RP_b9close_Q


title: prostate_RP_b9away_L


title: prostate_RP_tumor_M

value: M


title: prostate_RP_tumor_X

value: tumor

value: X


title: prostate_RP_b9away_I

value: I


title: prostate_BX_b9away_L

value: BX


title: prostate_BX_b9close_W

value: W


title: prostate_BX_tumor_F


title: prostate_RP_b9away_G

value: G


title: prostate_RP_tumor_FF

value: FF


title: prostate_RP_b9away_S

value: S


title: prostate_BX_b9away_B

value: B


title: prostate_RP_tumor_T

value: T


title: prostate_RP_tumor_AA

value: AA


title: prostate_BX_b9away_X

value: normal


title: prostate_RP_b9away_K

value: contralateral

value: K


title: prostate_RP_b9away_P

value: RP

value: P


title: prostate_RP_tumor_S


title: prostate_BX_b9away_F

value: F


title: prostate_RP_b9close_U

value: adjacent

value: U


title: prostate_BX_tumor_P

value: tumor


title: prostate_BX_b9away_C

value: BX

value: C


title: prostate_RP_tumor_Y

value: Y


title: prostate_BX_b9away_I

value: I


title: prostate_BX_tumor_O

value: O


title: Petstore_7

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan Beadarray Reader

data_processing: The data were normalised using quantile normalisation using preprocessCore in R and batch-normalized using the ComBat algorithm through GenePattern

label_protocol: Biotinylated cRNA  were prepared using the Illumina TotalPrep-96 RNA Amplification Kit for High-Throughput RNA Amplification for Array Analysis

extract_protocol: Cells were first homogenized using QIAshredder columns (Qiagen) then RNA was then extracted using RNeasy kit (Qiagen) as per manufacturer’s instructions

tag: strain

value: Unknown

tag: environment

value: Petstore

value: PBMC


title: Petstore_6


title: Petstore_8


title: Petstore_5


title: Petstore_4


title: prostate_RP_b9away_X

value: normal

value: X


title: Petstore_2


title: prostate_BX_tumor_M

value: M


title: Laboratory_8

value: Laboratory


title: Petstore_9


title: Laboratory_3


title: prostate_RP_b9away_R

value: RP

value: contralateral

value: R


title: Laboratory_7


title: Petstore_3


title: prostate_BX_tumor_U

value: U


title: Laboratory_5


title: prostate_RP_b9away_D

value: D


title: prostate_RP_tumor_K

value: tumor

value: K


title: Cohoused_6

value: Cohoused

tag: cohoused with

value: petstore mice


title: Laboratory_4


title: prostate_RP_tumor_V

value: V


title: Cohoused_7


title: prostate_BX_b9close_X

value: BX

value: adjacent


title: Cohoused_5

value: PBMC


title: Petstore_1

value: Unknown

value: Petstore


title: Laboratory_6


title: prostate_BX_tumor_E

value: E


title: Laboratory_2

value: Laboratory


title: Laboratory_1


title: hiPSC-derived ocular surface ectoderm 1

first: Ryuhei

last: Hayashi

address: 2-2 Yamadaoka

institute: Osaka University Graduate School of Medicine

hyb_protocol: standard Agilent protocol

scan_protocol: Microarrays were scanned with SureScan Microarray Scanner G2600D (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software (ver. 11.5.1.1, Agilent) according to the Agilent instruction. The obtained data was normalized by global normalization method.

source_name: hiPSC-derived ocular surface ectoderm

label_protocol: Labeling was performed using Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Palo Alto, CA). Hybridization and washing were performed using Gene Expression Hybridization Kit and Gene Expression Wash Buffers Kit (Agilent). Each procedure was conducted according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted by the QIAZol reagent (Qiagen, Valencia, CA)

value: hiPSCs differentiated for 6 weeks culture

tag: source

value: 201B7 hiPSCs purchased from RIKEN


title: hiPSC-derived ocular surface ectoderm 2


title: prostate_BX_tumor_R

value: R


title: prostate_RP_b9away_Q

value: normal

value: RP

value: contralateral

value: Q


title: prostate_BX_b9close_M

value: M


title: Cohoused_3

value: Cohoused

value: petstore mice


title: prostate_RP_tumor_D

value: tumor

value: D


title: Cohoused_4

value: PBMC


title: prostate_RP_tumor_F

value: F


title: human dermal fibroblasts 2

source_name: Dermal fibroblasts

value: cultivated-dermal fibroblast

value: purchased from ScienceCell


title: prostate_BX_b9close_C

value: BX

value: adjacent

value: C


title: hiPSC-derived ocular surface ectoderm 3

value: hiPSCs differentiated for 6 weeks culture

value: 201B7 hiPSCs purchased from RIKEN


title: human dermal fibroblasts 1


title: Cohoused_2


title: human oral keratninocytes 3

source_name: Oral keratninocytes

value: cultivated-oral mucosal keratinocytes


title: prostate_RP_b9close_P

value: normal

value: RP

value: P


title: human dermal fibroblasts 3


title: Cohoused_1

value: Cohoused


title: human oral keratninocytes 1


title: human corneal epithelial cells 2

source_name: Corneal limbal epithelium

value: cultivated-corneal limbal epithelial cells

value: purchased from Northwest Lions Eye Bank


title: prostate_RP_b9close_G

value: G


title: prostate_BX_tumor_L

value: tumor

value: L


title: human corneal epithelial cells 3


title: prostate_RP_b9close_V

value: V


title: prostate_RP_b9away_W

value: contralateral

value: W


title: human corneal epithelial cells 1


title: human oral keratninocytes 2

value: purchased from ScienceCell


title: hiPSC-derived corneal epithelial cells 4

source_name: hiPSC-derived corneal epithelial cells

value: hiPSC-derived corneal epithelial cells


title: prostate_RP_b9close_C

value: adjacent

value: C


title: hiPSC-derived corneal epithelial cells 3

value: 454E2 hiPSCs purchased from RIKEN


title: prostate_BX_tumor_Z

value: BX

value: Z


title: prostate_BX_b9close_U

source_name: FFPE, prostate, normal, BX

value: normal

value: U


title: prostate_BX_b9close_D

value: D


title: prostate_BX_tumor_S

value: S


title: prostate_RP_b9close_H

value: RP

value: H


title: prostate_BX_b9away_U


title: prostate_RP_tumor_B

value: tumor

value: B


title: prostate_BX_b9close_N

value: N


title: hiPSC-derived corneal epithelial cells 1

value: 201B7 hiPSCs purchased from RIKEN


title: CMM1_Carprofen_6h_rep3

city: Tokyo

first: Kohei

last: Saeki

address: 1-1-1 Yayoi, Bunkyo

institute: The University of Tokyo

description:
Carprofen_3
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

hyb_protocol: The purified cRNAs were quantified and hybridized to the Canine ver. 2 (4 × 44K) array (Agilent Technologies) using the Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's instruction.

scan_protocol: The hybridized array was washed with Gene Expression Wash (Agilent Technologies) and captured using a High-Resolution Microarray Scanner (Agilent Technologies) according to the manufacturer's instruction. Feature Extraction Software (Agilent Technologies) was used to analyze the scanned images.

data_processing: Probe annotation was performed using GeneSpring software (ver. 13.0) (Agilent technology). Data incorporation, preprocessing and quantile normalization were performed using R software (ver. 3.2.2) (R Development Core Team, 2005) and the limma R package (ver. 3.24.15)

organism: Canis lupus familiaris

source_name: CMM1_Carprofen_779 µM_6h

label_protocol: cDNA and Cy3-labeled cRNA were synthesized using Quick Amp Labeling Kit (Agilent Technologies) and RNA Spike-In One-Color Kit (Agilent Technologies) according to the manufacturer's instruction.

growth_protocol: A canine melanoma cell line (CMM1) was maintained at 37°C in a humidified atmosphere of 5% CO2 in RPMI-1640 medium (Wako Pure Chemical Industries Ltd.,Osaka, Japan) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco BRL, NY, USA) and 5 mg/L gentamicin (Sigma-Aldrich, MO, USA).

extract_protocol: Cells were lysed on dish and RNA toal RNA was ourified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. RNA purity and integrity were confirmed with Agilent 2100 Bioanalyzer (Agilent Technologies). The RNA integrity numbers were above 9.0.

treatment_protocol: CMM1 cell line was seeded at 6.3×10^3 cells/cm2. After 24 hours, piroxicam, carprofen and robenacoxib were added at their half maximal inhibitory concentration (779, 116 and 156 microM, respectively). Cells were harvested after another 24 hour-incubation.

tag: cell line

value: canine melanoma cell line

tag: cell line source

value: oral melanoma

tag: treated with

value: carprofen at 779 µMfor 6 h


title: prostate_BX_b9close_F

value: adjacent

value: F


title: prostate_RP_b9close_I

value: I


title: prostate_BX_tumor_K

value: BX

value: K


title: CMM1_Robenacoxib_6h_rep2

description:
Robenacoxib_2
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

source_name: CMM1_Robenacoxib_156 µM_6h

tag: cell type

value: robenacoxib at  156 µMfor 6 h


title: hiPSC-derived corneal epithelial cells 2

value: hiPSC-derived corneal epithelial cells


title: prostate_BX_tumor_D

value: D


title: CMM1_Robenacoxib_6h_rep3

description:
Robenacoxib_3
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: CMM1_Piroxicam_6h_rep3

description:
Piroxicam_3
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

source_name: CMM1_Piroxicam_116 µM_6h

value: piroxicam at 116 µMfor 6 h


title: CMM1_Piroxicam_6h_rep1

description:
Piroxicam_1
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: CMM1_Robenacoxib_6h_rep1

description:
Robenacoxib_1
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: CMM1_Carprofen_6h_rep1

description:
Carprofen_1
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: CMM1_Carprofen_6h_rep2

description:
Carprofen_2
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: prostate_BX_b9close_L

value: normal

value: L


title: prostate_BX_b9away_P

value: contralateral

value: P


title: CMM1_Piroxicam_6h_rep2

description:
Piroxicam_2
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs


title: CMM1_Control_6h_rep1

description:
Control_1
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

value: none (control)


title: CMM1_Control_6h_rep2

description:
Control_2
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

value: canine melanoma cell line


title: CMM1_Control_6h_rep3

description:
Control_3
Gene expression data of canine melanoma cell line after exposure to three different NSAIDs

value: oral melanoma


title: prostate_RP_tumor_U

value: tumor

value: RP

value: U


title: prostate_RP_b9away_C

value: C


title: prostate_BX_b9away_H

value: BX

value: H


title: prostate_BX_b9close_P

value: adjacent


title: prostate_BX_b9close_J

value: J


title: prostate_BX_tumor_A

value: A


title: prostate_BX_b9away_N

value: N


title: prostate_RP_b9away_J

value: normal


title: prostate_BX_tumor_J


title: prostate_RP_b9close_R

value: R


title: prostate_RP_tumor_Q

value: Q


title: prostate_BX_tumor_W

value: W


title: prostate_RP_tumor_GG

value: GG


title: prostate_RP_b9close_O

value: O


title: prostate_RP_tumor_N


title: prostate_RP_tumor_O


title: prostate_RP_b9close_X

value: X


title: prostate_RP_b9close_M

value: M


title: prostate_BX_tumor_I

value: tumor

value: I