title: Kidney_lupus NZB/W (30 weeks old) rep1

description:
Sample name: 30wks1_BG3RL
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)

tag: disease state

value: non-proteinuric

value: 30 weeks old

value: Whole kidney


title: Kidney from lupus NZB/W mouse, rep6

status: Public on Dec 31 2014

type: RNA

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

country: USA

institute: University of Michigan

description:
Young6_grp1_M6
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by the GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using the GenePattern pipeline: The RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization, and Combat for batch correction within the NZB/W mouse model and the NZW/BXSB mouse model.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Kidney from prenephritic mouse, NZB/W, 6 weeks old

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

growth_protocol: None.

extract_protocol: Total RNA was isolated using Trizol and the manufacturer's instructions.

treatment_protocol: None.

tag: strain

value: NZB/W

tag: age

value: 6 weeks

tag: disease status

value: prenephritic, non-proteinuric

tag: tissue

value: whole kidney


title: Non-recurrence_patient-27_SCC_str

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description: Sample 58.

hyb_protocol: Hybridizations and washes were performed according to the Exiqon® miRCURY™ LNA microRNA Array Instruction manual using an HS4800 hybridization station (Tecan®, Grödig, Austria). This work was performed as a commercial service by Exiqon®.

scan_protocol: Arrays were scanned using the G2565BA Microarray Scanner System (Agilent®), and image analysis was carried out using the ImaGene™ software (version 9; BioDiscovery®, Hawthorne, CA). This work was performed as a commercial service by Exiqon®.

data_processing:
Raw Hy3™ and Hy5™ signal data for all 136 arrays were processed together in R (version 2.15.1) using the limma Bioconductor package (version 3.12.3) on Mac OS X 10.6.8. Briefly, background signals were adjusted for using the 'normexp' method with 'offset' value of 10. Array data was then subjected to within-array global loess normalization with a 'span' value of 1/3. This was followed by between-array 'quantile' normalization. Probe-set summarization for Hy3™/Hy5™ ratio values (test RNA/reference RNA) was then performed, using the mean value from replicate probe-spots when the maximum was <1.5x minimum value, using the median value otherwise.

Raw data files:
1_Exiqon*:  Hy3
0_Exiqon*: Hy5

organism: Homo sapiens

source_name: Non-recurrence case, patient-27, SCC, stromum

label_protocol: The miRCURY™ LNA microRNA Hi-Power Labeling kit from Exiqon® was used to label 350 ng of test RNA with the Cy3-like Hy3™ dye. The reference RNA (350 ng) was similarly labeled with the Cy5-like Hy5™ dye. Artificial small RNAs were spiked in to test and reference RNA samples before labeling. This work was performed as a commercial service by Exiqon®.

growth_protocol: Formalin-fixed and paraffin-embedded, resected, stage I, human lung cancer tumor tissue samples were provided by the Department of Pathology of Roswell Park Cancer Institute, Buffalo, NY, USA.

extract_protocol: Total RNA was extracted from microdissectates using the FFPE RNA Purification kit (catalog# 25300, Norgen-Biotek®, Thorold, ON, Canada) following the kit manufacturer's guidelines. The kit uses silicon carbide spin-columns. The extracted RNA preparations were not treated with DNase. The low-range Quant-iT™ Ribogreen assay (Life Technologies®, Carlsbad, CA) was used to estimate RNA concentration using yeast tRNA as the standard. Refer to Patnaik et al., BMC Research Notes, 2012, 5:40 (PMID 22260539) for details on RNA isolation and quantitation. The reference RNA, a human 'universal reference total RNA,' was obtained by Exiqon® from Ambion® (catalog# AM6000; Austin, TX).

treatment_protocol: Laser capture microdissection was performed to isolate epithelial or stromal compartments of tumors using hematoxylin-eosin-stained tissue sections. Refer to Patnaik et al., BMC Research Notes, 2012, 5:40 (PMID 22260539) for details on tissue section preparation and microdissection.

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

value: N

tag: histology

value: SCC

tag: gender

value: M

tag: race

value: White

value: current

value: S

source_name: Reference RNA

tag: sample type

value: reference


title: P21

type: SRA

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

library_source: transcriptomic

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing using the Picard ExtractIlluminaBarcodes algorithm.
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC hg19 RepeatMasker track (downloaded March 14, 2011).
Remaining reads are aligned using TopHat2 (default parameters except for --mate-inner-dist (average size with adapters 355, range 268-465, measured for each sample individually) --mate-std-dev 100 --library-type fr-firststrand --keep-fasta-order --no-coverage-search) to the human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences) together with 80,884 transcript annotations from the UCSC knownGenes table (downloaded September 10, 2012).
Cufflinks v2.1.1 is used to calculate expression levels, fragments per kilobase of exon per million mapped reads (FPKM), using default settings except --frag-bias-correct --multi-read-correct --library-type fr-firststrand --compatible-hits-norm.
Gene expression data were pre-processed by collapsing on 27,979 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, performing a log2 transformation, and centering the gene expression values by subtracting the row-wise (gene) median (calculated across the 49 primary data sets) from the values in each row of data.
Subtyping was performed on the normalized expression matrix using the genefu R package and the published gene lists PAM50, Sorlie and Hu.
Genome_build: Human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences).

molecule: polyA RNA

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 instrument.

value: primary breast tumor

tag: ht12 subtype pam50

value: Basal

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Negative

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: tp53 mutations


title: Non-recurrence_patient-25_BAC_str

description: Sample 54.

source_name: Non-recurrence case, patient-25, BAC, stromum

tag: tissue

value: bronchioloalveolar carcinoma stroma

tag: patient

tag: recurrence

tag: histology

value: BAC

value: F

value: former


title: Non-recurrence_patient-26_AC_epi

description: Sample 55.

source_name: Non-recurrence case, patient-26, AC, epithelium

value: adenocarcinoma epithelia

value: AC

tag: gender

tag: race

value: E

tag: sample type


title: AN3CA human endometrium adenocarcinoma cell line, treated cell line 1

city: Helsinki

first: Johanna

last: Lotsari-Salomaa

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

description: MMR-deficient

hyb_protocol: The slides were hyridized in 2X Hi-RPM Hybridization Buffer for 20 hours in +55 ̊C in the Microarray Hybridization Chamber.

scan_protocol: After hybridization the slides were washed and scanned on an Agilent Technologies DNA Microarray G2505C Scanner. Signal intensities of fluorescence were calculated by Agilent's Feature Extraction software (version 10.7.3.1). Microarrays were investigated in duplicates for each cell lines.

data_processing:
GeneSpring GX software (version 11.0.2, Agilent Technologies) was used for miRNA data analysis. Data was normalized by quantile normalization.
Statistically significant differentially expressed miRNA were identified by T-test unpaired combined with the Benjamini and Hochberg correction for multiple testing and using filters based on p-value cut-off 0.05 and fold change cut-off +/- 2.00.

label_protocol: Agilent's human miRNA arrays (8x15K from Agilent Technologies, G4470B) containing 723 human and 76 human viral miRNAs sources from the Sanger miRBase, v.10.1 were used according to the protocol. 100 ng of RNA were used in Microarrays and samples were labelled with Cyanine3-pCp (Cy3).

growth_protocol: All cell lines were purchased from the American Type Culture Collection (Rockville, MD, USA) or JCRB and cultured according to the suppliers' protocol.

extract_protocol: Total RNA was extracted with miRNAeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol:
Cells were treated with 5 uM 5-aza-2' deoxycytidine (5-Aza, Sigma, A3656) for 96 hours and with 200nM trichostatin (TSA, Sigma, T1952) for 18 hours. All treatments were performed in duplicates.
The efficiency of the drug treatments was confirmed by expressional (Taqman) and methylation (SALSA MS-MLPA ME001-C1 Tumor Suppressor-1 kit, MRC-Holland, Amsterdam, the Netherlands) analyses of selected tumor suppressor genes in all cell lines, as well as by IHC analysis of MLH1 in RKO.

tag: cell line

value: ATCC HTB-111

value: uterus

tag: treatment

value: cultured with 5-Aza and TSA


title: Kidney from lupus NZB/W mouse, rep3

description:
Young3_grp1_M3
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).

tag: strain

value: NZB/W

tag: age

value: 6 weeks

tag: disease status

value: prenephritic, non-proteinuric

value: whole kidney


title: P20

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: Normal

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status


title: T84 human colon carcinoma cell line, untreated cell line 2

description: MMR-proficient

value: ATCC CCL-248

tag: tissue

value: colon


title: P19

value: LumB

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: Kidney from lupus NZB/W mouse, rep4

description:
Young4_grp1_M4
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).


title: Non-recurrence_patient-25_BAC_epi

description: Sample 53.

source_name: Non-recurrence case, patient-25, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

tag: patient

tag: recurrence

value: N

tag: histology

value: BAC

tag: gender

value: F

tag: race

value: White

value: former

tag: sample type

value: reference


title: P18

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: pik3ca mutations

tag: runx1 mutations


title: Non-recurrence_patient-24_SCC_str

description: Sample 52.

source_name: Non-recurrence case, patient-24, SCC, stromum

value: squamous cell carcinoma stroma

value: SCC

value: never

value: S


title: Kidney from lupus NZB/W mouse, rep2

description:
Young2_grp1_M2
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).

tag: strain

value: NZB/W

tag: age

value: 6 weeks

tag: disease status

value: prenephritic, non-proteinuric

value: whole kidney


title: T84 human colon carcinoma cell line, untreated cell line 1

description: MMR-proficient

tag: cell line

value: ATCC CCL-248

tag: tissue

value: colon

tag: treatment


title: T84 human colon carcinoma cell line, treated cell line 2

description: MMR-proficient

value: cultured with 5-Aza and TSA


title: Recurrence_patient-23_BAC_str

description: Sample 50.

source_name: Recurrence case, patient-23, BAC, stromum

value: bronchioloalveolar carcinoma stroma

tag: patient

value: Y

value: current


title: P17

value: primary breast tumor

value: LumA

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: arid1a mutations


title: P16

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: Normal

tag: ht12 subtype hu

value: LumB

tag: pik3ca mutations

tag: tp53 mutations


title: SW480 human colon adenocarcinoma cell line, untreated cell line 2

description: MMR-proficient

tag: cell line

value: ATCC CCL-228

tag: tissue

tag: treatment


title: SW480 human colon adenocarcinoma cell line, untreated cell line 1

description: MMR-proficient


title: T84 human colon carcinoma cell line, treated cell line 1

description: MMR-proficient


title: Recurrence_patient-23_BAC_epi

description: Sample 49.

source_name: Recurrence case, patient-23, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

tag: patient

tag: recurrence

tag: histology

value: BAC

tag: gender

value: F

tag: race

value: White

value: E

tag: sample type

value: reference


title: Recurrence_patient-22_AC_str

description: Sample 48.

source_name: Recurrence case, patient-22, AC, stromum

value: adenocarcinoma stroma

value: AC

value: S


title: P15

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: map3k1 mutations


title: P14

tag: tissue

tag: ht12 subtype pam50

value: Basal

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: lymphocyte content (1

tag: atm mutations

tag: tbl1xr1 mutations


title: SW480 human colon adenocarcinoma cell line, treated cell line 2

description: MMR-proficient

tag: cell line

value: colon

tag: treatment

value: cultured with 5-Aza and TSA


title: rtr-2_vs_wt_rep4

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 5um resolution in Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) and spots quantified with Feature Extraction software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were LOWESS-nomalized (intra-array normalization) followed by adjustment of their quantiles (inter-array normalization).

organism: Arabidopsis thaliana

source_name: wt inflorescence apices

label_protocol: 1 ug of total RNA was amplified with aRNA MessageAmp II kit (Ambion) and 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled either with Cy3 or Hype5 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, GE Heathcare). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion)

growth_protocol: Seeds were sown in soil, vernalized for 2 days at 4ºC and then transfered to a growth chamber under a 14 h light:10 hours dark cycle for 32 days  (bolts shorter that 1 cm). Then the inflorescence shoot apices from 11 plants of each genotype were collected in each experiment. The experiment was repeated 12 times indepedently. Each sample for RNA extraction and microarray hybridization was a pool from three independent experiments (33 plants in total for each wild ype mutant comparison).

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

tag: ecotype

value: Col

value: Inflorescence apices

tag: genotype

value: wildtype

source_name: rtr-2 inflorescence apices


title: Kidney from lupus NZB/W mouse, rep1

description:
Young1_grp1_M1
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).

tag: strain

value: NZB/W

tag: age

value: 6 weeks

tag: disease status

value: prenephritic, non-proteinuric

value: whole kidney


title: P13

value: primary breast tumor

value: Normal

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade


title: SW480 human colon adenocarcinoma cell line, treated cell line 1

description: MMR-proficient

value: ATCC CCL-228

tag: tissue


title: Non-recurrence_patient-21_AC_str

description: Sample 46.

source_name: Non-recurrence case, patient-21, AC, stromum

value: adenocarcinoma stroma

tag: patient

tag: recurrence

value: N

tag: histology

value: AC

tag: gender

value: M

tag: race

value: White

value: former

tag: sample type

value: reference


title: RKO human colon carcinoma, untreated cell line 2

description: MMR-deficient

tag: cell line

value: ATCC CRL-2577

value: colon

tag: treatment


title: rtr-2_vs_wt_rep3

tag: ecotype

value: Col

value: Inflorescence apices

tag: genotype

value: wildtype


title: Recurrence_patient-22_AC_epi

description: Sample 47.

source_name: Recurrence case, patient-22, AC, epithelium

value: adenocarcinoma epithelia

value: Y

value: F

value: current

value: E


title: Non-recurrence_patient-20_AS_str

description: Sample 44.

source_name: Non-recurrence case, patient-20, AS, stromum

value: adenosquamous carcinoma stroma

value: AS

value: S


title: rtr-2_vs_wt_rep2


title: RKO human colon carcinoma, untreated cell line 1

description: MMR-deficient


title: Non-recurrence_patient-20_AS_epi

description: Sample 43.

source_name: Non-recurrence case, patient-20, AS, epithelium

value: adenosquamous carcinoma epithelia

value: N

value: M


title: P10

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: Positive

value: Negative

tag: tumor cell content (1

tag: lymphocyte content (1

tag: tp53 mutations


title: RKO human colon carcinoma, treated cell line 2

description: MMR-deficient

value: ATCC CRL-2577

tag: tissue

value: colon

value: cultured with 5-Aza and TSA


title: Non-recurrence_patient-19_SCC_epi

description: Sample 41.

source_name: Non-recurrence case, patient-19, SCC, epithelium

value: squamous cell carcinoma epithelia

tag: patient

tag: recurrence

tag: histology

value: SCC

value: White

value: former

value: reference


title: RKO human colon carcinoma, treated cell line 1

description: MMR-deficient


title: HCT116 human colon carcinoma, untreated cell line 2

description: MMR-deficient

value: ATCC CCL-247


title: P12

value: Basal

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: rb1 mutations


title: P9

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: Normal


title: P8

value: LumB

tag: ht12 subtype hu

tag: rna-seq subtype pam50


title: rtr-2_vs_wt_rep1

tag: ecotype

value: Col

value: Inflorescence apices

tag: genotype

value: wildtype


title: Non-recurrence_patient-21_AC_epi

description: Sample 45.

source_name: Non-recurrence case, patient-21, AC, epithelium

value: adenocarcinoma epithelia

value: N

value: AC

tag: gender

value: M

tag: race

value: E

tag: sample type


title: Recurrence_patient-18_SCC_str

description: Sample 40.

source_name: Recurrence case, patient-18, SCC, stromum

tag: tissue

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

value: Y

value: F

value: S

source_name: Reference RNA


title: P7

source_name: Primary breast tumor

value: primary breast tumor

value: LumA

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

value: Negative

tag: tumor cell content (1

tag: lymphocyte content (1


title: P11

tag: ht12 subtype pam50

value: Basal

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: pik3ca mutations


title: AM vs. MePR-2B, replicate 2

city: naples

first: marco

last: miceli

address: De crecchio,7

country: Italy

institute: Second University of Naples

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 2 of 2. AM vs. MePR-2B.

hyb_protocol: Two-color microarray-based gene expression analysis with tecan hs pro protocol. Gene expression hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: Agilent Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS and Quantile normalizations.

source_name: AM (amniocytes)

label_protocol: Two-color microarray-based gene expression analysis with tecan hs pro protocol. RNA Spike-in Kit two color (Agilent p/n 5188-5279) and Quick Amp Labeling Kit, Two color (Agilentp/n 5190-0444).

growth_protocol: AM (amniocytes), MePR-0A, MePR-2B and MePR-3A were cultured in RPMI 1640 containing 20% decomplemented FBS.

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

treatment_protocol: Primary amniocytes were infected with lentiviral vector producted in HEK293-FT. The method was: The VSV-G-pseudotyped lentiviral vectors were generated in 150-mm tissue culture dishes by transient co-transfection with 1) the VSV-G-expressing construct pCMV-VSV-G (Invitrogen, USA) (66μg), 2) the packaging construct pCMVΔR8.2 (addgene) (48μg), and 3) the lentiviral vector plasmids (pSin hTERT or Psin E6-E7) (66μg) into sub-confluent 293FT cells (Invitrogen) by calcium phosphate precipitation (Clontech, Calphos Mammalian Transfection Kit). The supernatant containing the virus was produced in HEK-293FT, collected, filtered and used to infect primary amniocytes.

tag: cell type

value: primary amniocytes

source_name: MePR-2B (immortalized AM-derived fibroblastoid cell line)

tag: cell line

value: immortalized AM-derived fibroblastoid cells


title: AM vs. MePR-3A, replicate 1

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 1 of 2. AM vs. MePR-3A.

source_name: MePR-3A (immortalized AM-derived fibroblastoid cell line)


title: HCT116 human colon carcinoma, untreated cell line 1

description: MMR-deficient

value: ATCC CCL-247

value: colon

tag: treatment


title: AM vs. MePR-2B, replicate 1

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 1 of 2. AM vs. MePR-2B.


title: Recurrence_patient-18_SCC_epi

description: Sample 39.

source_name: Recurrence case, patient-18, SCC, epithelium

value: squamous cell carcinoma epithelia

tag: histology

value: SCC

tag: gender

tag: race

value: White

value: former

tag: sample type

value: reference


title: AM vs. MePR-0A, replicate 1

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 1 of 2. AM vs. MePR-0A.

source_name: MePR-0A (immortalized AM-derived epitheloid cell line)

value: immortalized AM-derived epitheloid cells


title: Recurrence_patient-17_SCC_str

description: Sample 38.

source_name: Recurrence case, patient-17, SCC, stromum

tag: tissue

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

value: Y

value: M

value: Asian


title: P6-replicate

value: primary breast tumor

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: tumor cell content (1


title: HCT116 human colon carcinoma, treated cell line 2

description: MMR-deficient

value: cultured with 5-Aza and TSA


title: AM vs. MePR-0A, replicate 2

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 2 of 2. AM vs. MePR-0A.

tag: cell type

value: primary amniocytes


title: AM vs. MePR-3A, replicate 2

description:
MePR cell lines are lentiviral-transfected with hTERT and E6-E7.
Biological replicate 2 of 2. AM vs. MePR-3A.

tag: cell line

value: immortalized AM-derived fibroblastoid cells


title: P6

tag: ht12 subtype pam50

value: Basal

tag: pgr status

value: Negative

tag: erbb2 status

tag: nottingham grade

tag: lymphocyte content (1

tag: chek2 mutations

tag: nf1 mutations


title: Recurrence_patient-17_SCC_epi

description: Sample 37.

source_name: Recurrence case, patient-17, SCC, epithelium

tag: tissue

value: squamous cell carcinoma epithelia

tag: patient

tag: recurrence

tag: histology

tag: gender

tag: race

value: E

tag: sample type


title: HCT15 human colon adenocarcinoma, untreated cell line 2

description: MMR-deficient

value: ATCC CCL-225

value: colon

tag: treatment


title: Non-recurrence_patient-16_BAC_str

description: Sample 36.

source_name: Non-recurrence case, patient-16, BAC, stromum

value: bronchioloalveolar carcinoma stroma

value: N

value: BAC

value: White

value: former

value: S

value: reference


title: P5-replicate

value: primary breast tumor

value: LumB

tag: ht12 subtype sorlie

value: LumA

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: tumor cell content (1

tag: tp53 mutations


title: P5

tag: ht12 subtype pam50

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: lymphocyte content (1

tag: setd2 mutations


title: HCT15 human colon adenocarcinoma, untreated cell line 1

description: MMR-deficient

tag: cell line

tag: tissue


title: P4

value: Basal


title: HCT15 human colon adenocarcinoma, treated cell line 2

description: MMR-deficient

tag: treatment

value: cultured with 5-Aza and TSA


title: P3

tag: ht12 subtype sorlie

value: Negative

tag: erbb2 mutations


title: 5_N

city: Paris

first: Anne

last: Janin

address: 1 Av C Vellefaux

country: France

institute: University Paris 7, INSERM, APHP

hyb_protocol: 1.65 µg Cy3-labeled fragmented cRNA was hybridized overnight at 65 °C to Agilent Whole Human Genome Oligo Microarrays 4x44K

scan_protocol: Fluorescence signals were detected using Agilent’s Microarray Scanner

data_processing: RMA Normalisation was performed using BRB-Array Tools version 4.1.0 and Bioconductor packages with the Open Source R software.

source_name: human renal tumor spheres, normoxic

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using Agilent Quick labeling kit. The yields of cRNA and the dye-incorporation rate were measured with ND-1000 Spectrophotometer (NanoDrop, LabTech, France). The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridisation Kit.

growth_protocol: Isolated cells were placed in a low-attachment six-well plate at a density of 2000 to 5000 cells per well, and cultured in a serum-free DMEM-F12 high glucose medium (Gibco) supplemented with 2% B27 NeuroMix (PAA, France), 0,4% foetal bovine serum (PAA, France), 5 µg/mL Insulin (Sigma, France), 6.25 ng/mL epidermal growth factor (Tebu Bio, France) and 12.5ng/mL fibroblast growth factor (Tebu Bio, France). Carcinoma spheres were obtained after 5 to 21 days.

extract_protocol: Total RNA was extracted from carcinoma tissue using RNeasy Mini Kit (Qiagen, France), quantified on NanoDrop and qualified on Bio-Rad ExperionTM Automated Electrophoresis Station (BioRad, France)

treatment_protocol: The spheres were maintained in a humidified chamber (37°C, 5% CO2), either under normoxia (20% O2), or hypoxia (1% O2).

tag: tissue type

value: human renal tumor spheres

tag: growth condition

value: normoxic


title: HCT15 human colon adenocarcinoma, treated cell line 1

description: MMR-deficient

value: ATCC CCL-225

value: colon


title: Non-recurrence_patient-16_BAC_epi

description: Sample 35.

source_name: Non-recurrence case, patient-16, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

tag: patient

tag: recurrence

value: N

tag: histology

tag: gender

value: M

tag: race

value: E

tag: sample type


title: Non-recurrence_patient-15_AC_str

description: Sample 34.

source_name: Non-recurrence case, patient-15, AC, stromum

value: adenocarcinoma stroma

value: AC

value: F

value: White

value: former

value: S


title: Recurrence_patient-14_AC_str

description: Sample 32.

source_name: Recurrence case, patient-14, AC, stromum

value: Y

value: reference


title: 5_Hyx

source_name: human renal tumor spheres, hypoxic

value: hypoxic


title: HCT116 human colon carcinoma, treated cell line 1

description: MMR-deficient

value: ATCC CCL-247

value: cultured with 5-Aza and TSA


title: Non-recurrence_patient-15_AC_epi

description: Sample 33.

source_name: Non-recurrence case, patient-15, AC, epithelium

value: adenocarcinoma epithelia


title: P1

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype hu

value: LumB

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: tumor cell content (1


title: Tm_2

source_name: human renal tumor xenograft, nude mouse

tag: tissue type

value: human renal tumor xenograft

value: nude mouse


title: 1_Hyx

value: human renal tumor spheres

tag: growth condition


title: Tm_1


title: Recurrence_patient-13_AC_str

description: Sample 30.

source_name: Recurrence case, patient-13, AC, stromum

tag: tissue

value: adenocarcinoma stroma

tag: patient

value: AC

value: M

value: White

value: current

source_name: Reference RNA


title: Primary melanoma_76

first: Göran

last: Jönsson

address: Scheelevägen 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation. Features present in <80% of assays were discarded (presence defined as detection p‐value < 0.01), leaving 12,379 features for further analysis. After log2 transformation, the data were adjusted for plate by median centering each feature to zero.Reporters with standard deviation (SD) across the replicates of at least 0.3 in at least 50% of the replicated samples were excluded (n=3,447). Replicate samples were merged by average. Missing values have been imputed by k‐nearest neighbor imputation (k=10), using the R package impute. Using principal componenet analysis (PCA) the variation of  PC1 and PC3 were removed since these were strongly associated with technical variables. Hence, the processed data represent log(2) values adjusted for technical variation.

source_name: Primary melanoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extractedusing the FFPE Roche kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: normal

tag: mutation status

tag: thickness

tag: histology

tag: clark

tag: number of replicates


title: Recurrence_patient-14_AC_epi

description: Sample 31.

source_name: Recurrence case, patient-14, AC, epithelium

tag: recurrence

value: Y

tag: gender

tag: race

value: former

value: E

tag: sample type

value: reference


title: 1_N

value: normoxic


title: normal retina at 16 wks, biological rep1

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13086_G5128_miRNA.CEL

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

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

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted miRNAs; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe sets for positive and negative controls were examined in Expression Console, and Facility quality control parameters were confirmed to fall within normal ranges.  Probes for each targeted miRNA were averaged and inter-array normalization performed using the Robust Multichip Analysis (RMA) algorithm

organism: Canis lupus familiaris

source_name: Retinal miRNAs from a normal dog at 16 wks of age

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: Retinas were obtained from age-matched normal and XLPRA2-mutant dogs with a common genetic background that were maintained at the Retinal Disease Studies Facility (RDSF) in Kennett Square, Pennsylvania, and housed under 12 hour cyclic light conditions. To avoid potential fluctuations in retinal gene expression with time of the day, the eyes were collected at a single time period (noon). Both eyes were enucleated following intravenous anesthesia with sodium pentobarbital, and the dogs were euthanatized after enucleation with a barbiturate overdose. Retinas were collected within 1-2 minutes after enucleation, flash frozen in liquid nitrogen, and stored at -80°C until use. The research was conducted in full compliance with the ARVO Resolution on the Use of Animals in Ophthalmic and Vision Research

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

value: retina

tag: disease status

tag: age

value: 16 wks


title: normal retina at 16 wks, biological rep4

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3162_12802_2354_microRNA.CEL


title: P2

source_name: Primary breast tumor

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

value: Normal

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

value: Negative

tag: erbb2 status

tag: nottingham grade

tag: lymphocyte content (1

tag: map3k1 mutations

tag: pik3ca mutations

tag: smad4 mutations


title: normal retina at 16 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13087_G5129_miRNA.CEL

tag: tissue


title: normal retina at 16 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13088_G5130_miRNA.CEL

tag: disease status


title: Non-recurrence_patient-12_AC_str

description: Sample 28.

source_name: Non-recurrence case, patient-12, AC, stromum

value: adenocarcinoma stroma

tag: patient

tag: recurrence

value: N

tag: histology

value: AC

tag: gender

value: F

tag: race

value: S

tag: sample type


title: Primary melanoma_74

value: nevus

tag: mutation status

tag: thickness

tag: clark

tag: number of replicates


title: XLPRA2 retina at 16 wks, biological rep1

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13083_Z196_miRNA.CEL

source_name: Retinal miRNAs from a XLPRA2-mutant dog at 16 wks of age

tag: age


title: Kidney from lupus NZW/BXSB mouse, rep4

description:
8wks4_PK87RU
Gene expression data from NZW/BXSB prenephritic kidney (8 weeks old, non-proteinuric).

source_name: Kidney from prenephritic mouse, NZW/BXSB, 8 weeks old

tag: strain

value: NZW/BXSB

value: 8 weeks

value: prenephritic, non-proteinuric

value: whole kidney


title: normal retina at 7 wks, biological rep4

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3162_12801_2045_microRNA.CEL

source_name: Retinal miRNAs from a normal dog at 7 wks of age

value: retina

value: normal

value: 7 wks


title: Primary melanoma_284


title: XLPRA2 retina at 16 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13085_Z248_miRNA.CEL

value: 16 wks


title: Primary melanoma_222

value: melanoma

value: Sporadic

value: NM


title: Primary melanoma_219


title: XLPRA2 retina at 16 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13084_Z371_miRNA.CEL


title: Primary melanoma_238


title: Primary melanoma_230


title: Non-recurrence_patient-10_AC_epi

description: Sample 23.

source_name: Non-recurrence case, patient-10, AC, epithelium

value: adenocarcinoma epithelia

value: White

value: never

value: E

value: reference


title: Primary melanoma_274


title: Non-recurrence_patient-10_AC_str

description: Sample 24.

source_name: Non-recurrence case, patient-10, AC, stromum

value: adenocarcinoma stroma

value: N

value: AC

value: F

value: S


title: Recurrence_patient-11_SCC_str

description: Sample 26.

source_name: Recurrence case, patient-11, SCC, stromum

value: squamous cell carcinoma stroma

value: Y

value: SCC

value: M

value: former


title: Non-recurrence_patient-12_AC_epi

description: Sample 27.

source_name: Non-recurrence case, patient-12, AC, epithelium


title: normal retina at 7 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13081_651_miRNA.CEL

value: retina

value: normal

value: 7 wks


title: Recurrence_patient-11_SCC_epi

description: Sample 25.

source_name: Recurrence case, patient-11, SCC, epithelium

value: squamous cell carcinoma epithelia

value: White


title: Primary melanoma_149


title: normal retina at 7 wks, biological rep1

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13080_649_miRNA.CEL


title: Non-recurrence_patient-9_BAC_str

description: Sample 22.

source_name: Non-recurrence case, patient-9, BAC, stromum

value: bronchioloalveolar carcinoma stroma

value: BAC

value: current


title: Non-recurrence_patient-9_BAC_epi

description: Sample 21.

source_name: Non-recurrence case, patient-9, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

value: N

value: E

value: reference


title: normal retina at 7 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13082_652_miRNA.CEL


title: Recurrence_patient-8_SCC_str

description: Sample 20.

source_name: Recurrence case, patient-8, SCC, stromum

value: squamous cell carcinoma stroma

value: S


title: XLPRA2 retina at 7 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13078_Z321_2_miRNA.CEL

source_name: Retinal miRNAs from a XLPRA2-mutant dog at 7 wks of age


title: Primary melanoma_213

source_name: Primary melanoma

value: melanoma

value: Sporadic

value: SSM


title: XLPRA2 retina at 7 wks, biological rep4

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13079_Z323_2_miRNA.CEL

value: retina


title: Primary melanoma_148

value: nevus


title: XLPRA2 retina at 7 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13077_Z320_miRNA.CEL

value: 7 wks


title: XLPRA2 retina at 7 wks, biological rep1

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13089_Z318_miRNA.CEL


title: Recurrence_patient-8_SCC_epi

description: Sample 19.

source_name: Recurrence case, patient-8, SCC, epithelium

value: squamous cell carcinoma epithelia

value: Y

value: SCC

value: M

source_name: Reference RNA


title: Primary melanoma_135

value: Mucosal


title: Primary melanoma_147


title: Non-recurrence_patient-7_SCC_str

description: Sample 18.

source_name: Non-recurrence case, patient-7, SCC, stromum

value: F

value: White

value: former


title: Primary melanoma_298


title: Primary melanoma_297


title: Non-recurrence_patient-7_SCC_epi

description: Sample 17.

source_name: Non-recurrence case, patient-7, SCC, epithelium

value: N

value: E

value: reference


title: Non-recurrence_patient-6_SCC_epi

description: Sample 15.

source_name: Non-recurrence case, patient-6, SCC, epithelium

value: never


title: Non-recurrence_patient-6_SCC_str

description: Sample 16.

source_name: Non-recurrence case, patient-6, SCC, stromum

value: squamous cell carcinoma stroma

value: S


title: Recurrence_patient-4_AC_str

description: Sample 14.

source_name: Recurrence case, patient-4, AC, stromum

value: adenocarcinoma stroma

value: AC


title: XLPRA2 retina at 3 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13073_Z238_miRNA.CEL

source_name: Retinal miRNAs from a XLPRA2-mutant dog at 3 wks of age

value: retina

value: 3 wks


title: normal retina at 3 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13075_V11615_miRNA.CEL

source_name: Retinal miRNAs from a normal dog at 3 wks of age

value: normal


title: Non-recurrence_patient-3_SCC_str

description: Sample 12.

source_name: Non-recurrence case, patient-3, SCC, stromum

value: SCC


title: normal retina at 3 wks, biological rep1

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13074_V11614_miRNA.CEL


title: Primary melanoma_121

value: melanoma

value: Sporadic

value: SSM


title: ir-aoc coronatine treatment_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) 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: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: ir-aoc coronatine treatment, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata Utah ir-aoc plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Floral buds at 4 DAP (4 days after corolla protruded and appeared outside sepals) of ir-aoc (silenced for ALLENE OXIDE CYCLASE)- treated with ctrl (control) or 1µM COR (coronatine) solution - were harvested on the morning before flowers would open. Flowers were dissected and 3 biological replicates of each tissue (complete corolla, style and gynoecium tissues) were collected. Individual replicates were obtained from 20+ flowers of each 2 plants.

value: floral buds

tag: treatment

value: 1µM COR (coronatine) solution


title: Primary melanoma_294


title: ir-aoc coronatine treatment_rep2

source_name: ir-aoc coronatine treatment, replicate 2


title: Non-recurrence_patient-3_SCC_epi

description: Sample 11.

source_name: Non-recurrence case, patient-3, SCC, epithelium

value: squamous cell carcinoma epithelia

value: N

value: F

value: White

value: former


title: XLPRA2 retina at 3 wks, biological rep1

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13071_Z234_miRNA.CEL


title: Primary melanoma_295


title: Primary melanoma_296


title: normal retina at 3 wks, biological rep3

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13076_V11616_miRNA.CEL


title: normal retina at 3 wks, biological rep4

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3162_12800_2411_microRNA.CEL


title: Recurrence_patient-4_AC_epi

description: Sample 13.

source_name: Recurrence case, patient-4, AC, epithelium

value: adenocarcinoma epithelia

value: Y

value: never

value: E

value: reference


title: XLPRA2 retina at 3 wks, biological rep2

description:
miRNA expression data from canine retinal samples at different ages
Raw data file: 3199_13072_Z235_miRNA.CEL

value: retina

value: 3 wks


title: Non-recurrence_patient-2_SCC_str

description: Sample 10.

source_name: Non-recurrence case, patient-2, SCC, stromum

value: squamous cell carcinoma stroma

value: SCC

value: M

value: current

value: S


title: Primary melanoma_292

value: melanoma

value: Sporadic


title: Primary melanoma_291

value: SSM


title: ir-aoc control treatment_rep1

source_name: ir-aoc control treatment, replicate 1

value: floral buds

value: control


title: ir-aoc coronatine treatment_rep1

source_name: ir-aoc coronatine treatment, replicate 1

value: 1µM COR (coronatine) solution


title: ir-aoc control treatment_rep2

source_name: ir-aoc control treatment, replicate 2


title: Primary melanoma_290

source_name: Primary melanoma


title: ir-aoc control treatment_rep3

source_name: ir-aoc control treatment, replicate 3


title: Non-recurrence_patient-1_SCC_str

description: Sample 8.

source_name: Non-recurrence case, patient-1, SCC, stromum

value: N

value: F

value: White

source_name: Reference RNA


title: Primary melanoma_293


title: Primary melanoma_289


title: Recurrence_patient-62_SCC_epi_tech-rep2b

description:
Sample 6.
Technical duplicate for sample 143.

source_name: Recurrence case, patient-62, SCC, epithelium

value: squamous cell carcinoma epithelia

value: Y

value: former

value: E

value: reference


title: Primary melanoma_288


title: Primary melanoma_287


title: Non-recurrence_patient-2_SCC_epi

description: Sample 9.

source_name: Non-recurrence case, patient-2, SCC, epithelium

value: SCC

value: M


title: Primary melanoma_286


title: Non-recurrence_patient-1_SCC_epi

description: Sample 7.

source_name: Non-recurrence case, patient-1, SCC, epithelium

value: current


title: Recurrence_patient-62_SCC_epi_tech-rep2

description:
Sample 5.
Technical duplicate for sample 127.


title: MCF7-EV-rep5

city: Ankara

first: Ayse

middle: Elif

last: Erson-Bensan

state: Cankaya

address: Universiteler Mah. No:1

department: Biology

country: Turkey

institute: METU

description: Gene expression data from empty vector transfected MCF7 cells

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

scan_protocol: GeneChips were scanned using the Scanner GCS 3000.

data_processing: Data was RMA normalized using R/Bioconductor

source_name: Empty vector stably transfected MCF-7

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

growth_protocol: MCF7-125 and MCF7-EV stably transfected cells were grown in DMEM medium supplied with 10% FBS, 1% Penicillin/Streptomycin and 250ug/mL G418. Cell lines were grown as monolayers and were incubated at 37oC with 95% humidified air and 5% CO2.

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

tag: cell line

tag: transfected with

value: pSUPER empty vector (control)


title: MCF7-EV-rep3


title: Recurrence_patient-44_AC_epi_tech-rep2

description:
Sample 4.
Technical duplicate for sample 91.

source_name: Recurrence case, patient-44, AC, epithelium

tag: tissue

value: adenocarcinoma epithelia

value: AC


title: irJAZd_2h_Wound+Os elicitation_rep3

description: Gene expression after 2 hr of elicitation with oral secretions from Manduca sexta larvae

source_name: irJAZd leaves, 2h, oral secretion elicitation, replicate 3

growth_protocol: Seeds from N. attenuata Utah wild type and ir-JAZd plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of Manduca sexta oral secretions diluted 1/5 (v/v) in water.

tag: genotype/variation

value: irJAZd

value: leaves


title: MCF7-EV-rep4


title: irJAZd_2h_Wound+Os elicitation_rep2

source_name: irJAZd leaves, 2h, oral secretion elicitation, replicate 2


title: MCF7-EV-rep2


title: WT vs DyvrHG

city: Wageningen

first: Mark

middle: de

last: Been

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 300ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to the Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA using the extended dynamic range scan mode, according to the Agilent protocol.

data_processing: Lowess-normalization, performed with Agilent Feature Extract software.

organism: Bacillus cereus ATCC 14579

source_name: WT mid-exp (iv)

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

growth_protocol: B. cereus ATCC 14579 (WT) cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm).

extract_protocol: RNA was extracted as described by Van Schaik et al., 2007

source_name: DyvrHG mid-exp (ii)

growth_protocol: B. cereus delta-yvrHG cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm).

value: delta-yvrHG


title: WT vs DyufLM

description: No extra description.

source_name: WT mid-exp (ii)

source_name: DyufLM mid-exp (ii)

growth_protocol: B. cereus delta-yufLM cells were grown to mid-exponential growth phase (OD600 = 0.5-0.6) (BHI, 30 degrees Celcius, 200 rpm).

value: delta-yufLM


title: DyvrHG vs WT

description: No extra description.

source_name: DyvrHG mid-exp

source_name: WT mid-exp (iii)


title: irJAZd_2h_Wound+Os elicitation_rep1

source_name: irJAZd leaves, 2h, oral secretion elicitation, replicate 1


title: Primary melanoma_285

source_name: Primary melanoma

value: melanoma


title: WT_2h_Wound +Os elicitation_rep1

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 1

value: wild type


title: DyufLM vs WT

description: No extra description.

source_name: DyufLM mid-exp

source_name: WT mid-exp


title: WT_2h_Wound +Os elicitation_rep2

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 2


title: WT_2h_Wound +Os elicitation_rep3

source_name: wild type leaves, 2h, oral secretion elicitation, replicate 3


title: MCF7-EV-rep1

source_name: Empty vector stably transfected MCF-7


title: Non-recurrence_patient-28_SCC_epi_tech-rep2

description:
Sample 3.
Technical duplicate for sample 59.

source_name: Non-recurrence case, patient-28, SCC, epithelium

value: squamous cell carcinoma epithelia

tag: patient

value: N

value: White

source_name: Reference RNA


title: N. attenuata_nectary_stage 2_Rep2

description: late development orange nectary (stage2)

source_name: Utah accession, nectary, stage 2

growth_protocol: Wild type, Nicotiana attenuata seedlings were transferred to 1L pots with sand to facilitate sampling of roots. Plants were watered by flood irrigation system with 200 g CaNO34H2O, 200 g Flory B1 in 400 L water and grown in the glasshouse at 26 - 28oC under 16 h supplemental light from Master Sun-T PIA Agro 400 or Master Sun-T PIA Plus 600 W Na lights (Philips, Turnhout, Belgium)

extract_protocol: Total RNA was extracted from nectary using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: no treatment

value: nectary


title: N. attenuata_nectary_stage 2_Rep3


title: N. attenuata_nectary_stage 2_Rep1


title: Primary melanoma_283

value: NM


title: Recurrence_patient-13_AC_epi

description: Sample 29.

source_name: Recurrence case, patient-13, AC, epithelium

tag: recurrence

value: Y

value: E

value: reference


title: Non-recurrence_patient-1_SCC_epi_tech-rep2

description:
Sample 1.
Technical duplicate for sample 7.

source_name: Non-recurrence case, patient-1, SCC, epithelium

tag: histology

value: SCC

value: F

value: current


title: MCF7-mir125b-rep3

description: Gene expression data from hsa-mir-125b transfected MCF7 cells

source_name: mir-125b stably transfected MCF-7


title: Primary melanoma_278

value: SSM


title: Primary melanoma_279


title: MCF7-mir125b-rep4


title: Non-recurrence_patient-12_AC_epi_tech-rep2

description:
Sample 2.
Technical duplicate for sample 27.

source_name: Non-recurrence case, patient-12, AC, epithelium

value: adenocarcinoma epithelia

value: AC

tag: gender

value: former


title: MCF7-mir125b-rep2


title: Primary melanoma_280

value: melanoma


title: Primary melanoma_281

value: Sporadic


title: Primary melanoma_282


title: N. attenuata_nectary_stage 1_Rep3

description: early development white nectary (stage1)

source_name: Utah accession, nectary, stage 1


title: N. attenuata_nectary_stage 1_Rep2


title: N. attenuata_nectary_stage 1_Rep1


title: ovary Ov_W3_rep1

city: Tokyo

first: Toru

last: Togawa

address: Sakurajyosui 3-25-40, Setagaya-ku

department: Integrated Sciences in Physics and Biology

country: Japan

institute: Nihon University

hyb_protocol: The hybridization was performed using Agilent Gene Expression Hybridization kit.  1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer and 2x Blocking Agent followed by adding 55 ul of 2x GE Hybridization Buffer HI-RPM to stop the fragmentation.  The mixture was hybridized with the microarrays in a Hybridization oven for 17 hours at 65˚C.  After hybridization, microarrays were washed with GE Wash Buffer 1 at room temperature for 1 min and with GE Wash Buffer 2 at 37˚C for 1 min, and then microarrays were dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B; system G2565BA) using one color scan setting for 4x44k formats (Scan area, 61x21.6 mm; Scan resolution, 5um; Dye channel, Green) with eXtended Dynamic Range option (XDR Hi, Green PMT 100%; XDR Lo, Green PMT 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) with protocol GE1-v5_95_Feb07.  If the Processed Signal intensities were lower than 0.01, the signal intensities were transformed to 0.01.  Probes on this DNA microarray are biased to genes expressed in a specific organ, so signal intensities of probes from one particular probe set which is from genome-wide gene prediction Gene Model were used for the normalization (Those probes are named CUST_xxxx_PI394957839).  Signal intensities of probes for Gene Models were extracted from a whole data set of each microarray, and their median was calculated.  The signal intensities of all probes were divided by that median as normalization.

organism: Bombyx mori

source_name: ovary, day-10 5th instar larva, replicate 1

label_protocol: cRNA synthesis, amplification, and labeling with Cy3 were performed with Low RNA Input Fluorescent Linear Amplification Kit (Agilent) with 200 ng of starting total RNA.  Cy3-labeled cRNA was purified with RNeasy Mini Kit (Qiagen).

growth_protocol: A commercial strain, Kinsyu x Showa, was used for microarray analyses.  Larvae were reared at 25˚C on mulberry leaves until the developmental stages to be analyzed.

extract_protocol: Larvae were dissected in PBS under a binocular microscope, and isolated CC-CA complexes were immediately homogenized in the lysis buffer of RNeasy Kit (Qiagen).  Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacture’s instructions from tissues.

value: ovary

tag: developmental stage

value: day-10 5th instar (3 days after the beginning of wandering) larva


title: corpora cardiaca-corpora allata complex CC-CA_V4_rep1

source_name: corpora cardiaca-corpora allata complex, day-4 5th instar larva, replicate 1

value: corpora cardiaca-corpora allata complex

value: day-4 5th instar larva


title: SCC8

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

hyb_protocol: Biotin-labeled cRNA was hybridized on Human Genome U133A 2.0 array according to the manufacturer’s recommendation

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

data_processing: Raw data were analyzed using the RMA package, available within Bioconductor.

source_name: skin squamous cell carcinoma

label_protocol: The resulting cDNAs were used for preparation of biotin-labeled antisense cRNA

extract_protocol: 15 μg total RNA from normal epidermis and  SCC lesions (all from different patients) were used for RNA probe preparation and hybridization to gene chips (Human Genome U133A 2.0 array; Affymetrix) according to the manufacturer’s recommendations

treatment_protocol: Human SCC samples were obtained with Massachusetts General Hospital institutional approval as discarded material during Mohs micrographic surgery. For controls, normal skin was shaved very superficially with a #15 scalpel blade with minimal dermal contamination.

tag: disease state

value: skin squamous cell carcinoma


title: testis Ts_W3_rep1

source_name: testis, day-10 5th instar larva, replicate 1

value: testis


title: SCC4


title: SCC9


title: salivary gland SalG_IV2_rep1

source_name: salivary gland, day-2 4th instar larva, replicate 1

value: salivary gland

value: day-2 4th instar larva


title: SCC3


title: ir-CDPK4/5_stem_rep2

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. All controls and replicated probes are averaged. Log transformation was done. 75 percentile normalization was performed (keeping the controls in the list). BASELINE transformation was done. Controls were removed from the list.

source_name: ircDPK4/5 stem

growth_protocol: Seeds from N. attenuata wild type and ir-CDPK4/5 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted fromstems using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Stems were harvested and immediately frozen in liquid nitrogen, tissue was grinded.

value: 41 days

value: stem


title: WT_stem_rep3

source_name: wild type stem

value: wild type


title: Malpighian tubule MT_IV2_rep1

source_name: Malpighan tubule, day-2 4th instar larva, replicate 1

value: Malpighan tubule


title: ir-CDPK4/5_stem_rep3


title: Primary melanoma_276

source_name: Primary melanoma

tag: mutation status

value: NM


title: ir-CDPK4/5_stem_rep1


title: MCF7-mir125b-rep1


title: epidermis Ep_IV2_rep1

source_name: epidermis, day-2 4th instar larva, replicate 1

value: epidermis


title: Primary melanoma_275

tag: thickness


title: SCC2


title: Primary melanoma_271

value: normal

tag: clark


title: mid gut MG_IV2_rep1

source_name: mid gut, day-2 4th instar larva, replicate 1

value: mid gut


title: WT_stem_rep2


title: Primary melanoma_272

value: melanoma

tag: number of replicates


title: SCC12


title: Primary melanoma_270

value: SSM


title: SCC13


title: Primary melanoma_273

value: Sporadic


title: Primary melanoma_269


title: WT_stem_rep1

tag: age


title: brain Br_IV2_rep1

source_name: brain, day-2 4th instar larva, replicate 1

value: brain


title: SCC11


title: SCC10


title: corpora cardiaca-corpora allata complex CC-CA_IV2_rep2

source_name: corpora cardiaca-corpora allata complex, day-2 4th instar larva, replicate 2

value: corpora cardiaca-corpora allata complex


title: AscKO_lung_Sp_24h

city: Kyoto

first: Kohsuke

last: Tsuchiya

address: Yoshida Konoe-cho, Sakyo-ku

department: Microbiology

institute: Kyoto University

description: Gene expression in the lung 24 h after intranasal infection with Streptococcus pneumoniae

hyb_protocol: Hybridization was done by using Gene Expression Hybridization Kit (Agilent).

scan_protocol: Slides were scanned on an Agilent DNA Microarray Scanner G2565CA.

data_processing: Data were obtained using Agilent Feature Extraction software.

source_name: Lung, Streptococcus pneumoniae, 24h

label_protocol: Cy3-labeled cRNAs were synthesized using Low Input Quick Amp Labeling Kit One-Color (Agilent, Santa Clara, CA).

extract_protocol: Total RNAs were extracted from whole lungs using TRIzol Reagent (Life Technologies, Carlsbad, CA) followed by cleanup using NucleoSpin RNA Clean-up (MACHEREY-NAGEL, Düren, Germany). Total RNA samples from two mice per group were mixed before analysis.

treatment_protocol: Mice were infected intranasally with 5*10^7 CFU of Streptococcus pneuminiae. After 24 h, the lungs were perfused with 10 ml of PBS and then collected.

value: Lung

tag: strain

value: male

value: 9 weeks

value: Asc-/-


title: fat body FB_IV2_rep1

source_name: fat body, day-2 4th instar larva, replicate 1

value: fat body

value: day-2 4th instar larva


title: Casp1KO_lung_Sp_24h

source_name: Lung, Streptococcus pneumoniae, intranasal infection, 24h


title: WT_lung_Sp_24h

value: female

value: wild type


title: prothoracic gland PG_IV2_rep1

source_name: prothoracic gland, day-2 4th instar larva, replicate 1

value: prothoracic gland


title: EP 48 hrs

city: Trivandrum

first: Ajay

last: Kumar

state: Kerala

address: Thycaud P.O.

department: Molecular Microbiology

country: India

institute: Rajiv Gandhi Centre for Biotechnology

description:
Cells treated with EPMC for 48 hrs
US83000164_251994310013_S01_GE1_105_Dec08_2_2

hyb_protocol: The labeled cRNA samples were hybridized onto Agilent Custom Mycobacterium tuberculosis 8x15k slide format (Genotypic Technology Pvt. Ltd, Bangalore). Six hundred ng of Cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent). Hybridization was carried out in Agilent’s Surehyb Chambers at 65 ºC for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers and scanned using the Agilent Microarray Scanner at 5 micron resolution.

scan_protocol: Slide was scanned using Agilent Scanner

data_processing: Feature extracted data was analyzed using GeneSpring GX version 10 software (Agilent, Palo Alto, CA). (Gene based Analysis) Normalization of the data was done in GeneSpring GX using the 75th percentile shift and Normalization to Specific Samples. Genes showing upregulation and downregulation by one fold and above among the test samples compared to untreated control samples were identified. Differentially regulated genes were clustered using hierarchical clustering based on Pearson coefficient correlation algorithm to identify significant gene expression patterns.

organism: Mycobacterium tuberculosis H37Rv

source_name: EP 48 hrs

label_protocol: The RNA samples were labeled using Quick Amp Kit PLUS (Agilent, Palo Alto, CA) using cy3 CTP.

extract_protocol: The isolation of RNA was carried out using RNAspin mini Kit (GE Lifesciences) as per the protocol provided by the manufacturer. Finally the RNA was eluted in 60 µl of RNase-free water and stored frozen at -80 °C until use.  Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA).

treatment_protocol: M. tuberculosis H37Rv cells were grown to an OD580 of 0.6 in Middlebrooks 7H9 broth (Difco BBL) containing 0.5% (v/v) glycerol, 0.05% (v/v) Tween-80 and supplemented with 10% (v/v) OADC.The culture was aliquoted to sterile screw cap tubes. EPMC was added to make a final concentration of 2.42 mM (5 X MIC). Isoniazid at 1.45 µM served as a positive control. Untreated control consisted of the bacterial culture treated with no drug but only with dimethyl formamide (DMF) which was used to dissolve EPMC.

tag: treatment

value: Cells treated with EPMC

tag: time


title: SCC1

value: skin squamous cell carcinoma


title: Primary melanoma_268


title: corpora cardiaca-corpora allata complex CC-CA_IV2_rep1

source_name: corpora cardiaca-corpora allata complex, day-2 4th instar larva, replicate 1


title: Primary melanoma_267


title: EP 24 hrs

description:
Cells treated with EPMC for 24 hrs
US83000164_251994310013_S01_GE1_105_Dec08_2_1

source_name: EP 24 hrs


title: Primary melanoma_266

value: NM


title: INH 48 hrs

description:
Cells treated with isoniazid for 48 hrs
US83000164_251994310013_S01_GE1_105_Dec08_1_4

source_name: INH 48 hrs

value: Cells treated with isoniazid


title: Normal skin 1

source_name: normal skin

value: normal skin


title: INH 24 hrs

description:
Cells treated with isoniazid for 24 hrs
US83000164_251994310013_S01_GE1_105_Dec08_1_3

source_name: INH 24 hrs


title: Primary melanoma_263

value: melanoma


title: Primary melanoma_262

value: Sporadic


title: Normal skin 3


title: Primary melanoma_265

value: SSM


title: Liver B6 SHIVA mouse 3

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 40µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Liver RNA, SHIVA, 24 hours fasting

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA total using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from liver using Trizol and then further purified with Qiagen purification columns.

treatment_protocol: Female mice (8-12 weeks old) were fasted for 24 hours prior to harvesting liver.

tag: strain/background

tag: genotype

value: Sox17 mutation

value: liver

value: 8-12 weeks

value: fasting for 24 hr


title: Primary melanoma_261

tag: tissue


title: Nlrp3KO_lung_Sp_24h

value: Lung

value: male

value: 9 weeks

tag: genotype/variation


title: Primary melanoma_264


title: fracture hematoma, old rat, rigid fixation, biological rep 2

city: Berlin

first: Andrea

last: Ode

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

description:
PD_11_Signal
pooled total RNA from three animals

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat GeneChip Array 230 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip System confocal scanner 3000

data_processing: Raw data were analyzed with the Affymetrix GeneChip Operating Software (GCOS 1.2). The data were normalized to a global intensity of 500.

organism: Rattus norvegicus

source_name: fracture hematoma_old rat_rigid fixation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-3 ug total RNA.

treatment_protocol: Using an anterolateral approach, the left femur was osteotomized at the midshaft, distracted to a gap of 1.5 mm and externally fixated. The distance between fixator and bone (offset) was set to 7.5 mm in the rigid configuration and 15 mm in the semi-rigid configuration.

value: Sprague–Dawley rat

value: 52 wks; old

tag: fixation stability

value: rigid

value: fracture hematoma

tag: timepoint

value: 3d post-osteotomy


title: Liver B6 SHIVA mouse 4

tag: gender

value: female


title: fracture hematoma, young rat, rigid fixation, biological rep 3

description:
PD_09_Signal
pooled total RNA from three animals

source_name: fracture hematoma_young rat_rigid fixation

value: 12 wks; young


title: Normal skin 2

value: normal skin


title: fracture hematoma, old rat, rigid fixation, biological rep 1

description:
PD_10_Signal
pooled total RNA from three animals


title: Liver B6 SHIVA mouse 2


title: Primary melanoma_260

source_name: Primary melanoma

value: melanoma

tag: histology


title: Ctrl 24 hrs

description:
Untreated control taken at 24 hours
US83000164_251994310013_S01_GE1_105_Dec08_1_1

source_name: Ctrl 24 hrs

value: Untreated control


title: Ctrl 48 hrs

description:
Untreated control taken at 48 hrs
US83000164_251994310013_S01_GE1_105_Dec08_1_2

source_name: Ctrl 48 hrs


title: 1uM Bexarotene_rep3

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: Gene expression data from mesenchymal GBM cell line with 1uM Bexarotene treatment

hyb_protocol: After fragmentation, the biotin-labeled cRNAs were hybridized for 16 h at 45°C, according to the standard Affymetrix protocols.

scan_protocol: An Affymetrix GeneChip Scanner 3000 7G was used to scan the GeneChips

data_processing: The data were analyzed using Affymetrix Expression Console and summarized using the probe logarithmic intensity error algorithm. Background correction and normalization was conducted using Perfect Match and Sketch-Quantile, respectively.

source_name: Human mesenchymal GBM cell line, 1uM Bexarotene treated

label_protocol: Total GBM RNA (250 ng) was used to synthesize biotin-labeled RNA by in vitro transcription, according to the standard Affymetrix protocol.

growth_protocol: Mesenchymal GBM cells were cultured in Neurobasal-A media (Gibco) supplemented with penicillin–streptomycin solution (1%), N2-supplement (0.5%), B-27 supplement (1%), L-glutamine (1%), bFGF (R&D; 0.01%), and EGF (0.1%; Sigma). The cells were cultivated at 37°C in a humidified atmosphere containing 5% CO2.

treatment_protocol: Bexarotene and ATRA were treated a final 1 and 10 µM concentration for 24 hr.

tag: tumor type

value: mesenchymal GBM

tag: cell type

value: Brain tumor primary cell


title: Liver B6 mouse 3

source_name: Liver RNA, WT, 24 hours fasting

value: wildtype

value: liver

value: 8-12 weeks


title: Primary melanoma_259

tag: mutation status

tag: thickness

value: SSM


title: Liver B6 SHIVA mouse 1

value: Sox17 mutation

value: fasting for 24 hr


title: fracture hematoma, young rat, rigid fixation, biological rep 2

description:
PD_08_Signal
pooled total RNA from three animals

value: Sprague–Dawley rat


title: Primary melanoma_258

tag: clark

tag: number of replicates


title: fracture hematoma, young rat, rigid fixation, biological rep 1

description:
PD_07_Signal
pooled total RNA from three animals

tag: strain

tag: age

value: rigid


title: Liver B6 mouse 2

tag: treatment


title: Primary melanoma_257


title: 10uM ATRA_rep3

description: Gene expression data from mesenchymal GBM cell line with 10uM ATRA treatment

source_name: Human mesenchymal GBM cell line, 10uM ATRA treated


title: 10uM Bexarotene_rep3

description: Gene expression data from mesenchymal GBM cell line with 10uM Bexarotene treatment

source_name: Human mesenchymal GBM cell line, 10uM Bexarotene treated


title: fracture hematoma, old rat, rigid fixation, biological rep 3

description:
PD_12_Signal
pooled total RNA from three animals

value: 52 wks; old

value: fracture hematoma


title: Liver B6 mouse 1

tag: strain/background

value: female


title: Primary melanoma_256


title: Th17_3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA from FACS-sorted T cell subsets (see markers above) was isolated by using the allprep DNA/RNA micro kit or RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Ex vivo-isolated spleen and lymph node cells were magnetically enriched for CD4+ cells by using the Miltenyi autoMACS system. The cells were stimulated for 3 hours by PMA (10ng/ml)/Ionomycin (500ng/ml) and then labelled by using a cytokine secretion assay for IL-17A and Interferon g (Miltenyi Biotech). All procedures were performed according to the maunfacturers protocols.

value: Th17 cells

tag: genetic background

value: BALB/c


title: fracture hematoma, old rat, semi-rigid fixation, biological rep 3

description:
PD_06_Signal
pooled total RNA from three animals

source_name: fracture hematoma_old rat_semi-rigid fixation

value: semi-rigid

tag: tissue

value: 3d post-osteotomy


title: fracture hematoma, old rat, semi-rigid fixation, biological rep 1

description:
PD_04_Signal
pooled total RNA from three animals


title: Control (0.1% DMSO)_rep3

description: Gene expression data from mesenchymal GBM cell line (Control)

source_name: Human mesenchymal GBM cell line, 0.1% DMSO

value: mesenchymal GBM


title: 10uM Bexarotene_rep2

value: Brain tumor primary cell


title: fracture hematoma, young rat, semi-rigid fixation, biological rep 3

description:
PD_03_Signal
pooled total RNA from three animals

source_name: fracture hematoma_young rat_semi-rigid fixation

value: 12 wks; young


title: Primary melanoma_255

city: Lund

institute: Lund University

value: melanoma


title: Th1_3

value: Th1 cells


title: fracture hematoma, young rat, semi-rigid fixation, biological rep 2

description:
PD_02_Signal
pooled total RNA from three animals


title: 10uM ATRA_rep2


title: Primary melanoma_277


title: fracture hematoma, old rat, semi-rigid fixation, biological rep 2

description:
PD_05_Signal
pooled total RNA from three animals


title: Primary melanoma_254

value: Sporadic


title: 1uM Bexarotene_rep2


title: GM12878 cells RNA (cDNA) Sty array

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: Qiagen RNeasy isolated RNA was amplified using Affymetrix amplified double stranded cDNA synthesis kit

hyb_protocol: Affymetrix hybridization oven at 49C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.

data_processing:
Analyzing 250K Nsp and 250K Sty chip CEL files by Affymetrix Genotyping Console v4.1, we obtained the probe level intensity data for all match and mismatch probes. We applied quantile normalization to probe level ratios a=PMA/MMA and b=PMB/MMB. Then for each probeset or SNP, we computed the allelic intensities A=max(mean(log2(a)), 0) for allele A and B=max(mean(log2(b)), 0) for allele B based on the normalized ratios a and b. Finally, we obtained the total intensity A+B for each SNP on the 250K Nsp chips and the 250K Sty chips. The intensity data from two kind of chips were combined into one file.
The AplusB8GMs3types.ns.txt matrix file contains the total intensity data. It has 25 columns and 500568 rows. The Affymetrix SNP ids are in the first column. The rest  columns contain 3 assays for each of the 8 CEPH samples.

source_name: GM12878 cells RNA (cDNA) Sty array

label_protocol: Affymetrix standard SNP array protocol

growth_protocol: Cells were grown in RPMI medium 1640 supplemented with 2mM L-glutamine and 15% FBS.

treatment_protocol: Cells were grown to ~80% confluency and colleced after changing the media at -8hrs.

tag: cell line

tag: sample type

value: amplified cDNA from total RNA


title: Th17_1


title: GM12878 cells RNA polymerase ChIP Sty array

type: genomic

description: ChIP DNA amplified using SIGMA WGA2 kit

molecule: genomic DNA

extract_protocol: ChIP DNA amplified using SIGMA WGA2 kit

value: RNA polymerase ChIP DNA


title: Primary melanoma_253

value: NM


title: Th1_2


title: Primary melanoma_252


title: Control (0.1% DMSO)_rep2


title: Th17_2


title: Th1_1


title: GM12802 cells RNA (cDNA) Sty array

source_name: GM12802 cells RNA (cDNA) Sty array

extract_protocol: Qiagen RNeasy isolated RNA was amplified using Affymetrix amplified double stranded cDNA synthesis kit


title: fracture hematoma, young rat, semi-rigid fixation, biological rep 1

description:
PD_01_Signal
pooled total RNA from three animals

value: Sprague–Dawley rat

tag: fixation stability

tag: timepoint


title: Primary melanoma_250

tag: histology


title: 1uM Bexarotene_rep1

tag: tumor type


title: GM12878 cells gDNA Sty array

description: QIAGEN Blood and Cell Culture Midi kit isolated

source_name: GM12878 cells gDNA Sty array

value: genomic DNA


title: 10uM Bexarotene_rep1

tag: cell type


title: GM12802 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: Tnaive_3

source_name: T naive

value: CD4+ T cells


title: Tnaive_1


title: Control (0.1% DMSO)_rep1


title: GM12802 cells gDNA Sty array

source_name: GM12802 cells gDNA Sty array

extract_protocol: QIAGEN Blood and Cell Culture Midi kit isolated


title: GM12740 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: Primary melanoma_249

tag: mutation status


title: Tnaive_2


title: GM12740 cells RNA (cDNA) Sty array

source_name: GM12740 cells RNA (cDNA) Sty array


title: Primary melanoma_251

tag: thickness

value: LMM


title: Primary melanoma_245

tag: clark


title: Primary melanoma_248

value: SSM

tag: number of replicates


title: 10uM ATRA_rep1


title: GM10863 cells RNA (cDNA) Sty array

source_name: GM10863 cells RNA (cDNA) Sty array


title: Tumor_01mgkgd_TPT_3

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: neuroblastoma xenotransplant metronomic topotecan replicate 3

hyb_protocol: 12µg of aRNA were fragmented at 94°C for 35 min, using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to GeneChip®PrimeView™Human Gene Expression Array microarrays. hybridization was done in the GeneChip Hybridization Oven 640.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 7G

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the RMA algorithm

source_name: Neuroblastoma xenotransplant tumor using STA-NB-10 primary cell line, MYCN amplified, in CD1 nude mice

label_protocol: Target labeling and hybridization. For Affymetrix GeneChip 3´ PrimeView analysis, 100 ng total RNA was processed to generate a biotinylated hybridization target using the 3' IVT Amplification Kit Module 1 from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Chip 3´´ IVT Expression kit P/N 703210 Rev. 1, by Affymetrix).

growth_protocol: specific pathogen free animal housing conditions

extract_protocol: total RNA-extraction by using Trizol (Invitrogen, Life Technologies)

treatment_protocol: 0.1 mg/kg/d topotecan in PBS/0.1% DMSO i.p., daily

value: neuroblastoma xenotransplant tumor

tag: host

value: CD1 nude mice


title: GM10863 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: Primary melanoma_247

source_name: Primary melanoma

extract_protocol: RNA was extractedusing the FFPE Roche kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: Primary melanoma_244


title: Tumor_01mgkgd_TPT_1

description: neuroblastoma xenotransplant metronomic topotecan replicate 1


title: GM12740 cells gDNA Sty array

source_name: GM12740 cells gDNA Sty array


title: Tumor_01mgkgd_TPT_2

description: neuroblastoma xenotransplant metronomic topotecan replicate 2


title: wt_20_st_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Bone marrow derived macrophages were differentiated from the cells from femur of the mouse. The cells were differentiated for 7 days using macrophage colony stimulating factor. The differentiated macrophages were used for further experiments.

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution

data_processing: Data were quantile normalized and log2 transformed using R and Bioconductor package limma.

source_name: Femur (cells were flushed out of femur and differentited into BMDMs for 7 days using MCSF)

label_protocol: For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: animals were housed at the central animal facility of the University Medical Center Göttingen

extract_protocol: mRNA was isolated from bonemarrow derived macrophages. The cells were then transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf)

treatment_protocol: The animals were not treated.

tag: strain

tag: age

value: 8 weeks

tag: Sex

value: Male

value: Bone marrow derived macrophages

tag: genotype

value: wild type

tag: oxygen concentration

value: 20 ox

tag: feeding

value: starved


title: GM10863 cells gDNA Sty array

source_name: GM10863 cells gDNA Sty array

tag: cell line

tag: sample type


title: wt_20_c_3

value: control


title: Primary melanoma_246

data_processing: The data were normalised using cubic spline normalisation. Features present in <80% of assays were discarded (presence defined as detection p‐value < 0.01), leaving 12,379 features for further analysis. After log2 transformation, the data were adjusted for plate by median centering each feature to zero.Reporters with standard deviation (SD) across the replicates of at least 0.3 in at least 50% of the replicated samples were excluded (n=3,447). Replicate samples were merged by average. Missing values have been imputed by k‐nearest neighbor imputation (k=10), using the R package impute. Using principal componenet analysis (PCA) the variation of  PC1 and PC3 were removed since these were strongly associated with technical variables. Hence, the processed data represent log(2) values adjusted for technical variation.

tag: tissue

value: melanoma


title: Primary melanoma_243

value: Sporadic

tag: histology


title: wt_20_c_2


title: Tumor_DMSOcontrol_1

description: neuroblastoma xenotransplant control replicate 1

treatment_protocol: CTRL, PBS/0.1% DMSO i.p., daily


title: wt_20_st_2


title: Tumor_DMSOcontrol_2

description: neuroblastoma xenotransplant control replicate 2


title: wt_20_st_1


title: wt_1_c_3

value: 1 ox


title: wt_20_c_1


title: Tumor_DMSOcontrol_3

description: neuroblastoma xenotransplant control replicate 3


title: TPTshort_CLB-Ma

description: CLB-Ma

source_name: Neuroblastoma cell line, MYCN amplified

growth_protocol: RPMI1640 GlutaMAX medium (Gibco, Life Technologies) supplemented with 1x Penicilin/Streptomycin, Na-Pyruvate, HEPES and 10% FCS (all PAA Laboratories GmbH, Austria) in a CO2 incubator at 37°C

extract_protocol: mRNA-extraction by using the miRNEasy kit (Qiagen)

treatment_protocol: topotecan 5 nM for 5 days

value: CLB-Ma

value: neuroblastoma


title: GM10839 cells RNA (cDNA) Sty array

source_name: GM10839 cells RNA (cDNA) Sty array

value: amplified cDNA from total RNA


title: Primary melanoma_242

value: NM


title: wt_1_c_2


title: GM10839 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit

value: RNA polymerase ChIP DNA


title: GM10839 cells gDNA Sty array

source_name: GM10839 cells gDNA Sty array

value: genomic DNA


title: GM10831 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: Primary melanoma_237

value: SSM


title: TPT_STA-NB10

source_name: Neuroblastoma primary cell line, MYCN amplified

treatment_protocol: topotecan 5 nM for 3 weeks


title: wt_1_c_1

value: 8 weeks


title: Primary melanoma_241

value: LMM


title: Primary melanoma_240


title: GM10831 cells gDNA Sty array

source_name: GM10831 cells gDNA Sty array


title: Primary melanoma_236


title: HU_STA-NB10

treatment_protocol: hydroxyurea 150 µM for 10 weeks


title: Primary melanoma_239


title: ko_20_st_1

value: Male

value: Bone marrow derived macrophages


title: GM07019 cells RNA (cDNA) Sty array

source_name: GM07019 cells RNA (cDNA) Sty array


title: TPT_CLB-Ma

description: CLB-Ma


title: ko_20_st_3

value: 20 ox


title: Primary melanoma_235


title: Fsp_STA-NB10

description: STA-NB-10 purified spontaneous morphologically flat cells

treatment_protocol: untreated


title: ko_20_st_2

value: starved


title: HU_CLB-Ma

description: CLB-Ma

treatment_protocol: hydroxyurea 200 µM for 10 weeks


title: TPTshort_STA-NB10


title: ko_20_c_2

value: control


title: GM10831 cells RNA (cDNA) Sty array

source_name: GM10831 cells RNA (cDNA) Sty array


title: ko_20_c_3


title: Fsp_CLB-Ma

description: CLB-Ma purified spontaneous morphologically flat cells


title: Primary melanoma_234

value: melanoma


title: GM07019 cells gDNA Sty array

source_name: GM07019 cells gDNA Sty array


title: Primary melanoma_233

value: Sporadic

value: Mucosal


title: GM06991 cells RNA (cDNA) Sty array

source_name: GM06991 cells RNA (cDNA) Sty array


title: GM07019 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: Primary melanoma_232


title: Primary melanoma_231


title: GM06991 cells gDNA Sty array

source_name: GM06991 cells gDNA Sty array


title: Primary melanoma_229


title: ko_1_c_2

value: 1 ox


title: CTRL_CLB-Ma

description: CLB-Ma control

value: CLB-Ma

value: neuroblastoma


title: CTRL1_STA-NB10

description: STA-NB-10 control replicate 1


title: ko_1_c_1


title: Primary melanoma_228

value: NM


title: BrdU_STA-NB10

treatment_protocol: bromo-deoxy-uridine 15 µM for 3 weeks


title: CPT_STA-NB10

treatment_protocol: captothecin 3 nM for 3 weeks


title: ko_1_c_3


title: CTRL2_STA-NB10

description: STA-NB-10 control replicate 2


title: Primary melanoma_227


title: GM06991 cells RNA polymerase ChIP Sty array

description: ChIP DNA amplified using SIGMA WGA2 kit

value: RNA polymerase ChIP DNA


title: ko_20_c_1


title: heart/t4

city: Chandigarh

first: madhu

last: khullar

state: Chandigarh

address: Research Block-B

department: Experimental Medicine and Biotechnology

institute: Postgraduate Institute of Medical Education and Research

hyb_protocol: Following labeling, 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48C on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G..

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings). Further normalized data also analysed follwed by differentiall miRNA expression and cluster analysis using  GeneSpring GX12.0 sofware.

source_name: left ventrical/heart

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

growth_protocol: Wistar rats were housed in standard polypropylene cages (2 rats/cage) and maintained under controlled room temperature and humidity with 12/12-hour light-dark cycle.

extract_protocol: Total RNA was isolated using RNeasy mini kit Qiagen.

treatment_protocol: Diabetes in Wistar rats was induced by feeding them with high-fat diet for 4 weeks followed by two Intraperitoneal injection of streptozotocin (STZ, 30mg/kg body weight), at one week interval.Non-diabetic rats was be fed with regular chow for 4 weeks followed by two Intraperitoneal injection of citrate buffer (pH 4.4, 0.05 M at a dose of 0.25 ml/kg body weight), as vehicle, at an interval of one week. Then after both Diabetic and non-diabetic rats were fed on high fat and normal chow diet, respectively and  were sacrificed at 12 weeks after the second STZ injection.   Diabetes in Wistar rats was confirmed by increased fasting blood glucose level (556.25±107.68mg/dl), Total Cholesterol (139.63±55.35mg/dl) & Triglycerides (78.93±21mg/dl), at the time of sacrifice. Intraperitoneal glucose tolerance test (IPGTT) and Intraperitoneal insulin resistance test (IPIRT) confirms glucose tolerance and insulin sensitivity in Diabetic rats.    DCM in Wistar rats was confirmed by the 1.6 fold increased heart to body weight ratio and presence of non-ischemic lesions, interstitial and perivascular fibrosis as well as myocytes atrophy and hypertrophy, on gross and microscopic examination of the heart.

value: heart let ventricle

tag: disease state

value: diabetic cardiomyopathy

tag: gender

value: male

value: Wistar

value: adult


title: BrdU_CLB-Ma

description: CLB-Ma

tag: cell type