title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [2hFreq_LISAdata]

status: Public on Apr 07 2017

type: RNA

city: New York

first: Frederique

last: Ruf-Zamojski

state: NY

address: 1468 Madison Avenue

department: Neurology

country: USA

institute: Mount Sinai Medical Center

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8

data_processing:
Results were exported as cycle threshold (Ct) values, and Ct values of target genes were normalized to those of housekeeping gene (HKG) RPS11 (ribosomal protein S11; NM_013725.4). Data were expressed as relative Copy numbers by using the formula, Copy Number = 2500 X 1.93(Ct value of Rps11 - Ct value of gene of interest). No fold changes were calculated.
In the non-normalized data matrix, each Biological Sample N appears in 3 columns with the headers 'SAMPLE N-1', 'SAMPLE N-2', and 'SAMPLE N-3', which correspond to 3 qPCR replicates.
In the Sample data tables, the Copy Number of each Biological Sample was derived from the median Ct value of its 3 qPCR replicates.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: pituitary gonadotrope-derived cells, vehicle-pulsed, 2h period, 4-pulse collection

label_protocol: After reverse-transcription of 1 mg of RNA with the Affinity Script reverse-transcriptase (Agilent, Santa Clara, CA), samples were diluted 1:20 in molecular biology grade H2O (Cellgro, Manassas, VA). Later, SYBR Green qPCR assays were performed (40 cycles) in an ABI Prism 7900HT thermal cycler (Applied Biosystems, Foster City, CA) using 5ml of cDNA template and 5ml of master mix containing the specific primers for the targeted gene, Platinum®Taq DNA polymerase, and the required qPCR buffer, according to manufacturer’s recommendations. Three technical qPCR replicates were run for each biological replicate.

growth_protocol: LβT2 cells were seeded on each tissue culture-treated coverslip and were grown for two days in DMEM supplemented with 10% FBS. Cells were incubated in DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES overnight before the pulse experiment.

extract_protocol: Coverslips were collected with forceps directly in the chamber and placed immediately in 360 ml guanidium thiocyanate RNA lysis buffer (4M guanidium thiocyanate, 25mM sodium citrate pH 7, 0.5% sarcosyl [N-lauroyl sarcosine], and 0.1M 2-mercaptoethanol). Total RNA was isolated with the “Absolutely RNA 96 microprep” kit (Agilent, Santa Clara, CA) according to the manufacturer's protocol, subjected to an ethanol precipitation to remove salts, and resuspended in elution buffer (Agilent, Santa Clara, CA). RNA concentrations were determined with Quant-iT RiboGreen RNA reagent (Invitrogen, Carlsbad, CA) using a fluorescence microplate reader (SpectraMax M3, Molecular Devices, Sunnyvale, CA).

treatment_protocol: Coverslips were placed in inert coverslip racks and pulse patterns were achieved by moving racks among GnRH, wash and resting solutions in chambers maintained at 37°C in a water bath.

tag: cell line

tag: cell type

value: immortalized gonadotrope cells


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2

source_name: pituitary gonadotrope-derived cells, GnRH-pulsed, 2h period, 4-pulse collection


title: CCP2_WT

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

country: China

institute: Institute of Biophysics, CAS

description:
This is wild-type CHILPs
3´105 CHILPs were isolated from WT or CCP2-deleted mice by FACS

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

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

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

label: biotin

source_name: WT CHILPs

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to The GeneChip® WT Terminal Labeling and Hybridization User Manual

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

tag: genotype

value: Wild-type


title: mESC control (unexposed), biological rep3

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: The values of individual probes belonging to one probe set in .CEL files were summarized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software v.1.3 (Affymetrix), which comprises of convolution background correction, quantile normalization, and median polish summarization.

source_name: mESC control, 24 h after EB formation

label_protocol: The total RNA samples (50 ng each) were labeled using the GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Pluripotent C57BL/6 mouse ESCs were seeded on 0.1% gelatin-coated flasks, and maintained at 37 °C in a 5% CO2 humidified incubator at standard densities (i.e., between 5×104/cm2 and 5×105/cm2) in ESGRO Complete Plus Clonal Grade Medium (EMD Millipore). The medium contains leukemia inhibitory factor (LIF), bone morphogenic protein 4 (BMP-4), and a glycogen synthase kinase-3b inhibitor (GSK3b-I) to help maintain pluripotency and self-renewal of the ESCs. Cells were passaged every 2-3 days (when reaching 60% confluence) with ESGRO Complete Accutase (EMD Millipore) at about 1:6 ratio.

extract_protocol: EBs were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: ESC differentiation cultures were exposed from the EB stage on day 3 for 24 h to 5.0 µg/ml 20 nm AgNPs or 5.0 µg/ml Ag+.

tag: strain

value: embryonic stem cell

tag: treatment

value: control, 24 h after EB formation


title: T6E ICN1-DMSO-rep 2

city: Boston

first: Eric

middle: A

last: Severson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The .CEL files were imported into R using the oligo package. Data were analyzed in R and batch effects were corrected with ComBat. Differential expression was assessed in R using the limma package.

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

treatment_protocol: Cells were treated with DMSO or 1 uM of Compound E, a gamma secretase inhibitor, for 6 hours.

tag: transfected with

value: intracellular Notch 1 (ICN1)

tag: treated with

value: DMSO for 6hrs


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: T6E R1984A-DMSO-rep 1

value: dimerization-defective intracellular Notch 1(R1984A)


title: CCP2_KO

description:
This is CCP2-deficient CHILPs
3´105 CHILPs were isolated from WT or CCP2-deleted mice by FACS

source_name: CCP2-deficient CHILPs

value: CCP2 knockout


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: T6E ICN1-DMSO-rep 3


title: mESC exposed to 5.0 µg/ml AgNPs, biological rep3

source_name: mESC exposed to 5.0 µg/ml AgNPs for 24 h

value: 5.0 µg/ml AgNPs for 24 h


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep5 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: mESC control (unexposed), biological rep2


title: mESC control (unexposed), biological rep1


title: T6E ICN1-DMSO-rep 1


title: T6E ICN1-GSI-rep 2

value: gamma secretase inhibitor (GSI) for 6hrs


title: T6E DNMAML-GSI-rep 3

value: dominant negative MAML (DNMAML)


title: T6E DNMAML-GSI-rep 2


title: mESC exposed to 5.0 µg/ml AgNPs, biological rep2


title: mESC exposed to 5.0 µg/ml AgNPs, biological rep1


title: mESC exposed to 5.0 µg/ml Ag+, biological rep2

source_name: mESC exposed to 5.0 µg/ml Ag+ for 24 h

value: 5.0 µg/ml Ag+ for 24 h


title: mESC exposed to 5.0 µg/ml Ag+, biological rep3


title: T6E DNMAML-DMSO-rep 1


title: T6E MigR1-DMSO-rep 3

value: empty MigR1 vector


title: T6E MigR1-DMSO-rep 2


title: T6E MigR1-GSI-rep 2


title: T6E DNMAML-DMSO-rep 2


title: T6E MigR1-GSI-rep 1


title: T6E DNMAML-DMSO-rep 3


title: T6E DNMAML-GSI-rep 1


title: T6E MigR1-GSI-rep 3


title: mESC exposed to 5.0 µg/ml Ag+, biological rep1


title: WAT_LFD_Sucnr1KO_rep4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: Epidydimal white adipose tissue, SUCNR1 knockout mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 4

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: SUCNR1+/- mice on a C57BL/6 background were a kind gift from Amgen. The animals were intercrossed to yield homozygous wild-type and SUCNR1-/- offspring as determined by genotyping. All mice were housed under specified pathogen-free conditions.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Male mice, aged between 8-10 wks, were fed a semi-synthetic low fat diet for 16 weeks. At the age 24-26 wks, mice were killed and epidydimal white adipose tissue was removed.

tag: sexe

value: male

tag: strain/background

tag: age


title: PoAF-patients12

city: shenyang

first: huishan

last: wang

state: liaoning

address: No.83, Wenhua Road

department: Department of Cardiovascular Surgery

institute: General Hospital of Shenyang Military Area Command

description:
circular RNAs expression before cardiac surgery
[P20S](normalized)

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.value definitionNormalized signal intensityextract protocolTrizol extraction of total RNA was performed according to the manufacturer's instructions.

organism: Homo sapiens

extract_protocol: total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method

treatment_protocol: Plasma of patients with postoperative atrial fibrilltion and Patients without postoperative atrial fibrilltion were detected the expression of circular RNAs.

tag: subject status

value: patients with postoperative atrial fibrilltion (PoAF)

tag: gender

tag: tissue

value: plasma

tag: molecule subtype

value: circular RNA


title: WAT_LFD_WT_rep2

source_name: Epidydimal white adipose tissue, wild-type (C57BL/6) mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 2


title: WAT_LFD_Sucnr1KO_rep2

source_name: Epidydimal white adipose tissue, SUCNR1 knockout mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 2


title: WAT_LFD_WT_rep3

source_name: Epidydimal white adipose tissue, wild-type (C57BL/6) mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 3


title: PoAF-patients7

description:
circular RNAs expression before cardiac surgery
[P9S](normalized)

label_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven


title: PoAF-patients9

description:
circular RNAs expression before cardiac surgery
[P11S](normalized)


title: PoAF-patients10

description:
circular RNAs expression before cardiac surgery
[P12S](normalized)


title: WAT_LFD_Sucnr1KO_rep3

source_name: Epidydimal white adipose tissue, SUCNR1 knockout mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 3


title: PoAF-patients15

description:
circular RNAs expression before cardiac surgery
[P30S](normalized)

value: female


title: PoAF-patients14

description:
circular RNAs expression before cardiac surgery
[P23S](normalized)


title: T6E MigR1-DMSO-rep 1


title: PoAF-patients13

description:
circular RNAs expression before cardiac surgery
[P22S](normalized)


title: PoAF-patients11

description:
circular RNAs expression before cardiac surgery
[P15S](normalized)


title: WAT_LFD_Sucnr1KO_rep1

source_name: Epidydimal white adipose tissue, SUCNR1 knockout mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 1


title: WAT_LFD_WT_rep1

source_name: Epidydimal white adipose tissue, wild-type (C57BL/6) mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 1


title: PoAF-patients5

description:
circular RNAs expression before cardiac surgery
[P7S](normalized)


title: WT-NT

city: shanghai

first: Hui

last: Xiao

address: 320 Yueyang Road, Life Science Research Building B

institute: Institut Pasteur of Shanghai

description: Gene expression in WT pDCs

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 using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

source_name: WT pDCs

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

growth_protocol: Bone marrow cells from CXXC5 WT and KO mice were differentiated with FLT3L for 6 days

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with Agilent Microarray Scanner (Agilent p/n G2565BA).

value: bone marrow derived pDCs

value: 8 weeks

tag: genotype/variation

value: Wildtype pDCs


title: PoAF-patients8

description:
circular RNAs expression before cardiac surgery
[P10S](normalized)


title: no-PoAF-patient14

description:
circular RNAs expression before cardiac surgery
[N22S](normalized)

value: patients without postoperative atrial fibrilltion (no-PoAF)


title: PoAF-patients4

description:
circular RNAs expression before cardiac surgery
[P5S](normalized)


title: PoAF-patients6

description:
circular RNAs expression before cardiac surgery
[P8S](normalized)


title: PoAF-patients1

description:
circular RNAs expression before cardiac surgery
[P1S](normalized)


title: no-PoAF-patient8

description:
circular RNAs expression before cardiac surgery
[N13S](normalized)


title: no-PoAF-patient10

description:
circular RNAs expression before cardiac surgery
[N16S](normalized)


title: no-PoAF-patient2

description:
circular RNAs expression before cardiac surgery
[N2S](normalized)


title: no-PoAF-patient4

description:
circular RNAs expression before cardiac surgery
[N4S](normalized)


title: no-PoAF-patient7

description:
circular RNAs expression before cardiac surgery
[N11S](normalized)


title: no-PoAF-patient15

description:
circular RNAs expression before cardiac surgery
[N24S](normalized)


title: no-PoAF-patient5

description:
circular RNAs expression before cardiac surgery
[N6S](normalized)


title: PoAF-patients2

description:
circular RNAs expression before cardiac surgery
[P2S](normalized)


title: no-PoAF-patient3

description:
circular RNAs expression before cardiac surgery
[N3S](normalized)


title: no-PoAF-patient1

description:
circular RNAs expression before cardiac surgery
[N1S](normalized)


title: PoAF-patients3

description:
circular RNAs expression before cardiac surgery
[P3S](normalized)


title: KO-CpG-A

description: Sorted cells were stimulated with CpG-A(2ug/ml) for 3 hours

source_name: CXXC5-deficient pDCs

value: CXXC5-deficient pDCs


title: KO-NT

description: Gene expression in CXXC5-deficient pDCs


title: no-PoAF-patient12

description:
circular RNAs expression before cardiac surgery
[N19S](normalized)


title: WT-CpG-A


title: no-PoAF-patient11

description:
circular RNAs expression before cardiac surgery
[N17S](normalized)


title: no-PoAF-patient6

description:
circular RNAs expression before cardiac surgery
[N10S](normalized)


title: no-PoAF-patient13

description:
circular RNAs expression before cardiac surgery
[N21S](normalized)


title: HFD, flux, replicate 8

status: Public on Apr 06 2017

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with Ozone-barrier slides.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: HFD, flux, replicate 8

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Cy-3 labelled samples were pooled on an equimolar basis and served as reference pool; this comprised all samples, including control group, present in the SuperSeries GSE53805.

extract_protocol: Total RNA was isolated from epididymal whiet adipose tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: C57BL/6JOlaHsd wildtype male mice were acclimatized in the facility by feeding purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks, followed by 12 weeks BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into 2 treatment groups: i) control group which remained at thermoneutrality for 5 days, and ii) 5 days at normal housing temperatures (22C degrees), while continously in an indirect calorimetry system. On day 6, 2 hours after food removal at the start of the light phase, mice were killed immediately after taking them out of the indirect calorimetry system by decapitation. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen.

value: adult

value: epididymal white adipose tissue

source_name: reference pool


title: HFD, flux, replicate 9

source_name: HFD, flux, replicate 9


title: HFD, flux, replicate 4

source_name: HFD, flux, replicate 4


title: HFD, flux, replicate 7

source_name: HFD, flux, replicate 7


title: HFD, flux, replicate 10

source_name: HFD, flux, replicate 10


title: HFD, flux, replicate 5

source_name: HFD, flux, replicate 5


title: HFD, DFO injected, replicate 3

source_name: HFD, DFO injected, replicate 3

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Cy-3 labelled samples were pooled on an equimolar basis and served as reference pool; this comprised all samples, including the control group, present in the SuperSeries GSE53805.

treatment_protocol: C57BL/6JOlaHsd wildtype male mice were acclimatized in the facility by feeding purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks, followed by 12 weeks BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into 2 treatment groups: i) control group which remained under normoxia, and ii) 5 days daily injections with iron chelator Desferrioxamine (DFO; 100mg/kg body weight). On day 6, after 2 hours food removal at the start of the light phase, mice were decapitated. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen.


title: HFD, flux, replicate 1

source_name: HFD, flux, replicate 1


title: HFD, DFO injected, replicate 10

source_name: HFD, DFO injected, replicate 10


title: HFD, DFO injected, replicate 8

source_name: HFD, DFO injected, replicate 8


title: HFD, DFO injected, replicate 4

source_name: HFD, DFO injected, replicate 4


title: HFD, flux, replicate 6

source_name: HFD, flux, replicate 6


title: HFD, DFO injected, replicate 6

source_name: HFD, DFO injected, replicate 6


title: HFD, DFO injected, replicate 2

source_name: HFD, DFO injected, replicate 2


title: HFD, DFO injected, replicate 7

source_name: HFD, DFO injected, replicate 7


title: HFD control, normoxia, replicate 5

source_name: HFD control, normoxia, replicate 5

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Cy-3 labelled samples were pooled on an equimolar basis and served as reference pool; this comprised all samples present in the SuperSeries GSE53805.

treatment_protocol: C57BL/6JOlaHsd wildtype male mice were acclimatized in the facility by feeding purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks, followed by 12 weeks BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into 2 treatment groups: i) control group which remained under normoxia for 5 days, and ii) 5 days oxygen restriction to 13% ambient oxygen. On day 6, after 2 hour food removal at the start of the light phase, mice were killed immediately after taking them out of the indirect calorimetry system by decapitation. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen.


title: HFD control, normoxia, replicate 3

source_name: HFD control, normoxia, replicate 3


title: HFD control, normoxia, replicate 7

source_name: HFD control, normoxia, replicate 7

source_name: reference pool


title: HFD control, normoxia, replicate 4

source_name: HFD control, normoxia, replicate 4


title: HFD, flux, replicate 3

source_name: HFD, flux, replicate 3


title: HFD control, normoxia, replicate 8

source_name: HFD control, normoxia, replicate 8


title: HFD control, normoxia, replicate 2

source_name: HFD control, normoxia, replicate 2


title: CLL022-postRS-RT

type: genomic

city: Chicago

first: Carrie

last: Fitzpatrick

state: IL

address: 5841 S Maryland Ave

institute: University of Chicago

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix Molecular Diagnostic Software (AMDS version 1.1).  Copy number values for individual probes is extracted and converted to an intensity data (CEL) file by and subsequently converted graphical, tabular and segmental data files (CYCHP for CytoScan, OSCHP for OncoScan) using Affymetrix Chromosome Analysis Suite (ChAS 3.0) software. Estimation of ploidy and aberrant call percentage in OSCHP files is calculated using the TuScan algorithm.

label: Biotin

molecule: genomic DNA

source_name: CLL022_lymph node

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh tissue, peripheral blood or bone marrow at defined time points during treatment and/or disease course using the Qiagen DNA Blood Mini Kit or QIAmp DNA for FFPE tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Qubit fluorometer or PicoGreen and agarose gel electrophoresis.

value: ibrutinib-relapsed CLL  patients

tag: subject id

tag: disease stage

value: LN-richter transformation

value: lymph node


title: HFD, DFO injected, replicate 9

source_name: HFD, DFO injected, replicate 9


title: HFD, flux, replicate 2

source_name: HFD, flux, replicate 2


title: no-PoAF-patient9

description:
circular RNAs expression before cardiac surgery
[N15S](normalized)


title: Control (7018844094_G)

city: Berlin

first: Joscha

last: Griger

address: Robert-Rössle-Strasse 10

country: Germany

institute: Max Delbrück Centre for Molecular Medicine

description:
7018844094_G
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using Partek Genomics suite.

source_name: Control, limb myogenic progenitor cells

label_protocol: Biotinylated cRNA was synthesized using the Ambion Illumina TotalPrep RNA amplification kit

extract_protocol: RNA was obtained with Trizol according to manufacturers instruction.

value: Control

value: VCAM31+CD31-CD45-Sca1- limb myogenic progenitor cells


title: coShp2 (7018844094_F)

description:
7018844094_F
SAMPLE 11

source_name: coShp2, limb myogenic progenitor cells


title: HFD control, normoxia, replicate 10

source_name: HFD control, normoxia, replicate 10

value: male


title: coShp2 (7018844094_B)

description:
7018844094_B
SAMPLE 9


title: Control (7018844093_F)

description:
7018844093_F
SAMPLE 5


title: coShp2 (7018844093_G)

description:
7018844093_G
SAMPLE 6


title: HFD, DFO injected, replicate 1

source_name: HFD, DFO injected, replicate 1


title: HFD control, normoxia, replicate 9

source_name: HFD control, normoxia, replicate 9


title: HFD, DFO injected, replicate 5

source_name: HFD, DFO injected, replicate 5


title: CLL022-postCLL-RT

value: LN-CLL


title: MDA-MB-231 cell line, WA treated

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description: MDA-MB-231 treated with 700 nM Withaferin A

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Beta-values were normalized using the Illumina custom normalization. Probes with detection p-values < 0.0001, on sex chromosomes or overlapping with SNPs were removed.
Unmethylated and methylated signal intensities

label: Cy5 and Cy6

source_name: MDA-MB-231 cell line, WA

label_protocol: Standard Illumina Protocol

growth_protocol: The MDA-MB-231 and MCF-7 cell lines, purchased from American Type Culture Collection (Manassas, VA, USA), were cultivated in high glucose (4,5 g/L) Dulbecco’s Modified Eagle Medium with 10% Foetal Bovine Serum, 2 mM L-Glutamine, 1 mM Sodium Pyruvate MEM, 50 IU/mL Penicillin and 50 µg/mL Streptomycin. The MDA-MB-231 cell line was additionally supplemented with 1% MEM Non-Essential Amino Acids. Each cell line was maintained at 37°C in the humidified atmosphere containing 5% CO2 until 80-90% confluence.

extract_protocol: Genomic DNA was extracted with Dneasy Blood & Tissue kit (Qiagen).

treatment_protocol: Induction experiments with WA, 2 x 10^4 viable MDA-MB-231 cells/cm2 and 5.3 x 10^3 viable MCF-7 cells/cm2 were plated in an appropriate cell culture flask/plate 24 hours before the treatment. Every 24 hours, Withaferin A (700nM) or DMSO controls (final concentration 0,0035% if not otherwise stated) diluted in a fresh medium were added for a total time of 72 hours. At that time point, cells were harvested with 0.05% Trypsin/EDTA solution, washed with 1x PBS and collected for further analysis.

tag: cell line

value: 700 nM Withaferin A


title: MCF-7 cell line, DMSO treated

description: MCF-7 treated with solvent control DMSO

label: Cy5 and Cy3

source_name: MCF-7 cell line, DMSO

value: DMSO


title: HFD control, normoxia, replicate 6

source_name: HFD control, normoxia, replicate 6


title: CLL017-RSLN-RT

source_name: CLL017_lymph node

value: richter transformation


title: Breast tumor tissue, ER+_Z048T

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Tumor

data_processing:
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.
For the normalization it uses the average of four housekeeping genes: EIF2B1, ELF1, and UBB
Raw data were normalised and fold changes analysed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.

label: FAM

source_name: Breast tumor tissue, ER+

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in  ViiA7 Real-Time PCR System produced by Life technologies (Carlsbad, CA) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)

tag: tissue type

value: Tumor


title: Breast tumor tissue, ER+_Z062T

description: Tumor


title: Control (7018844093_B)

description:
7018844093_B
SAMPLE 2

tag: cell type


title: Control (7018844094_A)

description:
7018844094_A
SAMPLE 8


title: Control (7018844094_E)

description:
7018844094_E
SAMPLE 10


title: coShp2 (7018844093_H)

description:
7018844093_H
SAMPLE 7


title: coShp2 (7018844093_C)

description:
7018844093_C
SAMPLE 3


title: coShp2 (7018844094_H)

description:
7018844094_H
SAMPLE 13


title: WAT_LFD_WT_rep4

source_name: Epidydimal white adipose tissue, wild-type (C57BL/6) mouse, after 16 weeks on a semi-synthetic low fat diet, replicate 4


title: coShp2 (7018844093_E)

description:
7018844093_E
SAMPLE 4


title: HFD control, normoxia, replicate 1

source_name: HFD control, normoxia, replicate 1

tag: strain

source_name: reference pool


title: Breast tumor tissue, ER+_Z045T

description: Tumor


title: Breast tumor tissue, ER+_Z042T

description: Tumor


title: Breast tumor tissue, ER+_Z043T

description: Tumor


title: Breast tumor tissue, ER+_Z037T

description: Tumor


title: Breast tumor tissue, ER+_Z056T

description: Tumor


title: Breast tumor tissue, ER+_Z033T

description: Tumor


title: Control (7018844093_A)

description:
7018844093_A
SAMPLE 1


title: Breast tumor tissue, ER+_Z039T

description: Tumor


title: MCF-7 cell line, WA treated

description: MCF-7 treated with 700 nM Withaferin A

label: Cy5 and Cy5

source_name: MCF-7 cell line, WA

tag: treatment


title: Breast tumor tissue, ER+_Z006T

description: Tumor


title: Breast tumor tissue, ER+_Z032T

description: Tumor


title: Breast tumor tissue, ER+_Z026T

description: Tumor


title: Breast tumor tissue, ER+_Z027T

description: Tumor


title: Breast tumor tissue, ER+_Z041T

description: Tumor


title: Breast tumor tissue, ER-_Z144T

description: Tumor

source_name: Breast tumor tissue, ER-


title: Breast tumor tissue, ER+_Z004T

description: Tumor


title: Breast tumor tissue, ER-_Z125T

description: Tumor


title: Breast tumor tissue, ER+_Z005T

description: Tumor


title: Breast tumor tissue, ER-_Z137T

description: Tumor


title: Breast tumor tissue, ER-_Z111T

description: Tumor


title: MDA-MB-231 cell line, DMSO treated

description: MDA-MB-231 treated with solvent control DMSO

label: Cy5 and Cy4

source_name: MDA-MB-231 cell line, DMSO


title: Breast tumor tissue, ER+_Z047T

description: Tumor


title: Breast tumor tissue, ER-_Z046T

description: Tumor


title: Breast tumor tissue, ER-_Z036T

description: Tumor


title: Breast tumor tissue, ER-_Z054T

description: Tumor


title: Breast tumor tissue, ER-_Z070T

description: Tumor


title: Breast tumor tissue, ER-_Z038T

description: Tumor


title: Breast tumor tissue, ER-_Z057T

description: Tumor


title: Breast non-tumor tissue_Z032V

description: Non-tumor

source_name: Breast non-tumor tissue

value: Non-tumor


title: Breast non-tumor tissue_Z042V

description: Non-tumor


title: Breast tumor tissue, ER-_Z124T

description: Tumor


title: Breast non-tumor tissue_Z004V

description: Non-tumor


title: Breast non-tumor tissue_Z037V

description: Non-tumor


title: Breast non-tumor tissue_Z041V

description: Non-tumor


title: Breast tumor_M398T

data_processing:
For the normalization it uses the average of three housekeeping genes: EIF2B1, ELF1 and UBB
Target gene signals normalized to housekeeping genes; Ct_Target/Ct_HKGmean

source_name: Breast tumor

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in  ViiA7 Real-Time PCR System produced by Life technologies (Carlsbad, CA) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

tag: age (years)

tag: menopause

value: post

tag: histology (1=idc, 0=other)

tag: grade

tag: Stage

value: I

tag: pt

tag: pn

value: unknown

tag: relapse (0=no, 1=yes)

tag: dfs (months)


title: Breast non-tumor tissue_Z036V

description: Non-tumor


title: Breast non-tumor tissue_Z046V

description: Non-tumor


title: Breast tumor_M394T


title: Breast tumor_M396T


title: Breast tumor tissue, ER-_Z028T

description: Tumor


title: Breast non-tumor tissue_Z006V

description: Non-tumor


title: Breast tumor_M399BT


title: Breast tumor_M384T

value: pre


title: Breast non-tumor tissue_Z038V

description: Non-tumor


title: Breast non-tumor tissue_Z043V

description: Non-tumor


title: Breast tumor_M362T


title: Breast tumor_M365T


title: Breast tumor_M369T


title: Breast tumor_M381T


title: Breast tumor_M367T


title: Breast tumor_M389T


title: Breast tumor_M359T

value: IIIA


title: Breast tumor_M348AT


title: Breast tumor_M375T

value: IIB


title: Breast tumor_M380T


title: Breast tumor_M336AT

value: IIA


title: Breast tumor_M330T


title: Breast tumor_M328BT


title: Breast tumor_M357AT


title: Breast tumor_M329T


title: Breast tumor_M318T


title: Breast tumor_M366T


title: Breast tumor_M322T


title: Breast tumor_M360T


title: Breast tumor_M316T


title: Breast tumor_M326T


title: Breast tumor_M338T


title: Breast tumor_M315T


title: Breast tumor_M385T


title: Breast tumor_M325T


title: Breast tumor_M314T


title: Breast tumor_M310T


title: Breast tumor_M323T


title: Breast tumor_M321T


title: Breast tumor_M358T


title: Breast tumor_M332T


title: Breast tumor_M342T


title: Breast tumor_M337T


title: Breast tumor_M307T


title: Breast tumor_M297T


title: Breast tumor_M308T


title: Breast tumor_M305T


title: Breast tumor_M277T


title: Breast tumor_M304T


title: Breast tumor_M294T


title: Breast tumor_M279T


title: Breast tumor_M272T


title: Breast tumor_M266T


title: Breast tumor_M290T


title: Breast tumor_M301T


title: Breast tumor_M284T


title: Breast tumor_M259T


title: Breast tumor_M262T


title: Breast tumor_M291T


title: Breast tumor_M257T


title: Breast tumor_M275T


title: Breast tumor_M255T


title: Breast tumor_M240T

value: IIIB


title: Breast tumor_M289T


title: Breast tumor_M248T


title: Breast tumor_M251T


title: Breast tumor_M298T


title: Breast tumor_M246T


title: Breast tumor_M261T


title: Breast tumor_M258T


title: Breast tumor_M233T


title: Breast tumor_M267T


title: Breast tumor_M235T


title: Breast tumor_M234T


title: Breast tumor_M244T


title: Breast tumor_M229T


title: Breast tumor_M250T


title: CLL022-post-RL

source_name: CLL022_peripheral blood

tag: subject status

value: ibrutinib-relapsed CLL  patients

tag: subject id

tag: disease stage

value: Ibrutinib relapse, post richter transformation

tag: tissue

value: peripheral blood


title: Breast tumor_M230T

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)

tag: tissue type


title: Breast tumor_M226T

tag: age (years)


title: Breast tumor_M218T

tag: menopause


title: CLL024-post-Rel

source_name: CLL024_bone marrow

value: Ibrutinib relapse

value: bone marrow


title: Breast tumor_M224T

tag: histology (1=idc, 0=other)


title: CLL021-post-Rel

source_name: CLL021_peripheral blood


title: Breast tumor_M205T

tag: grade


title: Breast tumor_M200T

tag: Stage


title: Breast tumor_M184T

tag: pt


title: CLL024-pre-PreIbr

value: Pre-ibrutinib treatment


title: CLL022-pre-PreIbr

source_name: CLL022_bone marrow


title: Breast tumor_M214T

tag: pn


title: CLL021-pre-PreIbr

source_name: CLL021_bone marrow


title: Breast tumor_M216T

tag: relapse (0=no, 1=yes)


title: CLL020-C1-Rel

source_name: CLL020_peripheral blood


title: Breast tumor_M199T

tag: dfs (months)


title: Breast tumor_M202T


title: Breast tumor_M187T


title: Breast tumor_M182T


title: Breast tumor_M192T


title: Breast tumor_M175T


title: CLL019-A2-PreIbr

source_name: CLL019_bone marrow

tag: subject status


title: CLL019-C-Rel1

source_name: CLL019_peripheral blood

tag: subject id


title: Breast tumor_M195T


title: CLL015-C-Rel1

source_name: CLL015_peripheral blood

tag: disease stage


title: CLL017-A-PreIbr

source_name: CLL017_bone marrow

tag: tissue


title: CLL017-B-Rel1


title: Breast tumor_M174T

tag: er (0=negative, 1= positive)


title: CLL020-A-PreIbr

source_name: CLL020_bone marrow


title: CLL015-A-PreIbr


title: CLL012-A-PreIbr

source_name: CLL012_bone marrow


title: Breast tumor_M169T

tag: pr (0=negative, 1= positive)


title: Breast tumor_M160T

tag: her2 (0=negative, 1= positive)


title: CLL012-D-Rel

source_name: CLL012_peripheral blood


title: Breast tumor_M168T

tag: tissue type


title: Breast tumor_M215T

tag: age (years)


title: CLL011-RSLN-RT

source_name: CLL011_peripheral blood

value: richter transformation


title: Breast tumor_M170T

tag: menopause

value: Tumor


title: Breast tumor_M152T

tag: histology (1=idc, 0=other)


title: Breast tumor_M155T

tag: grade


title: Breast tumor_M149T


title: CLL011-B-Resp1

source_name: CLL011_bone marrow

value: Responding time point 1


title: CLL015-B-Resp


title: CLL011-C-Resp2

value: Responding time point 2


title: Breast tumor_M103T

value: post

tag: Stage

value: I


title: Breast tumor_M164T

tag: pt

value: unknown


title: CLL011-D-Rel


title: CLL011-A-PreIbr


title: Breast tumor_M172T

tag: pn


title: Breast tumor_M111T

tag: relapse (0=no, 1=yes)


title: Breast tumor_M098T

tag: dfs (months)


title: Breast tumor_M097T


title: Breast tumor_M100T


title: Breast tumor_M084T


title: Breast tumor_M154T


title: Breast tumor_M079T


title: Breast tumor_M080T


title: Breast tumor_M071T


title: Cap_Nudt16_rep2

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

country: Spain

institute: IDIBELL

description: m3G/m7G-capped RNA transcripts

hyb_protocol: Hybridization, washing and staining were performed using Agilent system instruments and protocols.

scan_protocol: After washing, microarrays were scanned using an Agilent microarray scanner (Agilent Technologies).

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software. Background correction and quantile array normalization was performed using limma library in R software.

source_name: Cell line MOLT-4

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using Agilent protocol.

extract_protocol: Total RNA from mock-transfected or NUDT16-overexpressing MOLT-4 cells was extracted using Trizol Reagent. 20 μg of total RNA was used per cap-immunoprecipitation reaction. The RNA eluate was then hybridized onto expression microarrays

tag: cell line

tag: vector


title: Breast tumor_Z133T

source_name: Breast tumor


title: Breast tumor_M076T


title: Breast tumor_M068T


title: Cap_Nudt16_rep1

description: m3G/m7G-capped RNA transcripts


title: Cap_Mock_rep1

description: m3G/m7G-capped RNA transcripts

value: mock


title: Cap_Nudt16_rep3

description: m3G/m7G-capped RNA transcripts


title: Breast tumor_Z128T


title: Cap_Mock_rep3

description: m3G/m7G-capped RNA transcripts


title: Breast tumor_Z127T


title: Breast tumor_Z116T


title: Breast tumor_Z131T


title: Breast tumor_M065T


title: Breast tumor_Z114T


title: Breast tumor_M033T


title: Breast tumor_Z136T

value: pre


title: Breast tumor_Z112T


title: Breast tumor_Z119T

value: IIA


title: Breast tumor_Z121T


title: Breast tumor_M086T


title: Breast tumor_Z130T


title: Breast tumor_Z118T


title: Breast tumor_Z117T


title: Breast tumor_Z110T


title: Breast tumor_Z107T


title: Breast tumor_Z115T


title: Breast tumor_Z103T


title: Breast tumor_Z120T


title: Cap_Mock_rep2

description: m3G/m7G-capped RNA transcripts


title: Breast tumor_Z98T


title: Breast tumor_Z102T


title: Breast tumor_Z85T


title: Breast tumor_Z92T


title: Breast tumor_Z104T


title: Breast tumor_Z83T


title: Breast tumor_Z100T


title: Breast tumor_Z82T


title: Breast tumor_Z96T

value: IIB


title: Breast tumor_Z78T


title: Breast tumor_Z99T


title: Breast tumor_Z93T


title: Breast tumor_Z84T


title: Breast tumor_Z95T


title: Breast tumor_Z109T


title: Breast tumor_Z108T


title: Breast tumor_Z74T


title: Breast tumor_Z73T

value: IIIA


title: Breast tumor_Z72T


title: Breast tumor_Z79T


title: BU2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in the UBALD1 transfected cells from primary undifferentiated carcinoma thyroid tissues of a 78y old female

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 12.0.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas, Biological Theory 2016.

source_name: Stably transfected with UBALD1 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 2

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: BCPAP cells protocol described in: Fabien N. Fusco A. Santoro M. Barbier Y. Dubois PM. Paulin C. (1994) Description of a human papillary thyroid-carcinoma cell-line—morphologic study and expression of tumoral markers. Cancer. 73:2206–2212. 8505C cells protocol described in: Ito T, Seyama T, Hayashi Y, Hayashi T, Dohi K, Mizuno T, Iwamoto K, Tsuyama N, Nakamura N, Akiyama M. (1994). Establishment of 2 human thyroid-carcinoma cell-lines (8305c, 8505c) bearing p53 gene-mutations. Int J Oncol. 4(3):583-6.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Cells were cultured in Rosswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS), penicillin 10,000 IU/mL, streptomycin 10 mg/mL, and 2 mM L-glutamine. Cells were stably transfected using pLX304 lentiviral vector (marker blasticidin, V5 epitope tag) with the ORF clone of UBALD1 (UBA-like domain containing 1), ORF clone accession number BC012018.1, BC062534.1. The clone was produced by the shRNA Core Facility of the Albert Einstein College of Medicine (Catalog # HsCD00436146, https://www.einstein.yu.edu/research/shared-facilities/shrna/resources).

tag: Sex

value: female

tag: age

value: 78 years old

tag: cell type

tag: transfection

value: thyroid gland


title: AU2

description: Gene expression in the UBALD1 transfected cells from papillary carcinoma with local and lymph node metastasis of a 76y old female

source_name: Stably transfected with UBALD1 BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 2

value: 76 years old

value: AU=BCPAP

tag: tissue


title: BU4

source_name: Stably transfected with UBALD1 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 4


title: AU3

source_name: Stably transfected with UBALD1 BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 3


title: Breast tumor_Z105T

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)

tag: tissue type


title: BU3

source_name: Stably transfected with UBALD1 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 3


title: Patient_1_circRNA expression profiles in adjacent normal mucosae

city: Jinan

first: shengda

last: cao

state: Shandong Province

address: wenhua west road

department: ENT

institute: Qilu hospital

hyb_protocol: The labeled circRNAs were hybridized onto the Agilent human circRNA Array (V1.0)  (Agilent Technologies, Santa Clara, USA). The slides were rotated at a speed of 20rpm and a temperature of at 42℃ in a Agilent Hybridization Oven overnight.

scan_protocol: After being washed, arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies, Santa Clara, USA).

data_processing:
Raw data was extracted from scanned images by Agilent Feature Extraction software (version 11.0.1.1). GeneSpring software (V13.0) (Agilent ) was used for the microarray data analysis, including data summarization, normalization and quality control. After normalization of the raw data, low intensity filtering was performed.
The circRNAs with at least 4 out of 8 samples flagged in “detected” were selected for further analysis. CircRNAs with fold change absolute ≥ 2.0 and P vlaue < 0.05 were selected and considered as differentially expressed ones with statistic significance.

source_name: adjacent normal mucosae

label_protocol: Extracted total RNA were treated with Rnase R (Epicentre, Madison, USA) to get rid of linear RNA. Subsequently, the enriched circRNAs were amplified and transcribed into fluorescent circRNAs using random primers according to directions of CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China)

growth_protocol: Samples were not cultured in vitro.

extract_protocol: Total RNA was extracted from samples using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to manufacter’s protocol.

treatment_protocol: Tissue samples were immediately frozen in liquid nitrogen and then transferred to - 80℃ for long-term storage.

value: adjacent normal mucosae


title: Patient_4_circRNA expression profiles in hypopharyngeal carinoma tissue

source_name: hypopharyngeal carinoma tissue

value: hypopharyngeal carinoma tissue


title: Breast tumor_Z66T

tag: age (years)

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade

value: Tumor


title: BU1

source_name: Stably transfected with UBALD1 8505C cells purchased from DSMZ in Braunschweig, Germany_ Replicate 1


title: Patient_3_circRNA expression profiles in adjacent normal mucosae


title: Breast tumor_Z77T

tag: Stage

tag: pt

tag: pn

tag: relapse (0=no, 1=yes)


title: AU4

source_name: Stably transfected with UBALD1 BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 4

tag: Sex


title: WT vascular_CEP1 treatment_rep1

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

country: Japan

institute: Nagoya University

description:
Aragene-0544
Vascular tissues of WT cotyledons grown on the medium containing 1 uM CEP1 for 8 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing:
Data procession was performed with Expression Console Version 1.3 (Affymetrix).
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.0.187

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Approximately 100 seeds were sown on Murashige-Skoog (MS) medium solidified using 1.0% agar in 13 × 10 cm plastic plates and incubated for 8 days at 22°C with continuous light.

extract_protocol: Twenty cotyledons of 8-day-old seedlings were harvested and immersed in 1 ml of the enzyme solution (0.75% Cellulase Onozuka R-10 (Yakult), 0.25% Macerozyme R-10 (Yakult), 0.4 M mannitol, 5 mM MES-KOH (pH 5.6), 8 mM CaCl2) in 1.5-ml tube and sonicated 3-5 times for 5 sec each with a Bioruptor UCD-250 (Cosmo Bio, Japan). Macerated cotyledons were spread on a Petri dish and vascular tissues were manually collected under a stereomicroscope. Isolated vascular tissues were directly dropped into 450 ul RLT buffer provided in an RNeasy Plant Mini Kit (QIAGEN) in 1.5-ml tubes and the RNA was isolated.

treatment_protocol: For peptide treatment, CEP1 peptide was added to the culture medium at 1 uM throughout the growth period.

tag: genotype/variation

value: Wild type

tag: treated with

value: 1 uM CEP1

value: Vascular tissues of cotyledons


title: Breast tumor_Z94T

value: post

value: I

value: unknown

tag: dfs (months)


title: Breast tumor_Z68T

value: pre

value: IIA


title: Patient_3_circRNA expression profiles in hypopharyngeal carinoma tissue

tag: tissue


title: Breast tumor_Z76T

tag: er (0=negative, 1= positive)


title: Patient_2_circRNA expression profiles in adjacent normal mucosae


title: Breast tumor_Z88T

tag: pr (0=negative, 1= positive)


title: 904 TGF

status: Public on Apr 05 2017

city: Cardiff

first: Donald

middle: James

last: Fraser

state: Wales

address: Heath Park Campus

department: School of Medicine

country: United Kingdom

institute: Cardiff University

hyb_protocol: 3D-Gene antisense-miRNA oligo chips were hybridized with the resulting labeled miRNAs.

scan_protocol: The chips were rigorously washed prior fluorescent signal scanner by ScanArray Lite Scanner and analyzed using GenePix Pro software.

data_processing: The software considers a valid spot any probe hybridization which signal intensity is greater than the mean intensity of the background signal plus 2 standard deviations. A normalization step for each specific miRNA adjusted median value is subsequently performed. This will identify and remove sources of systematic variation within arrays correcting for spatial and dye bias. The relative miRNAs expression level is determined by comparing the mean signal intensity of the real hybridizated spots with their average value across the microarray experiment.

source_name: Peritoneal Mesothelial Cells

label_protocol: A final 500 ng of total RNA from each sample was labeled with Cy5 using the Label IT miRNA labeling kit.

growth_protocol: Human peritoneal mesothelial cells (HPMCs) were obtained from omental donors undergoing abdominal surgery, with ethical approval and informed consent for use of their omentum for research purposes. ells were cultured in Earle’s M199 medium with 10% FBS. Experiments were performed on second passage cells at 80-90% confluence, growth arrested for 24 h before treatment.

extract_protocol: HPMCs were lysed in TRI reagent (Ambion, Life Technologies), and RNA was extracted as recommended by the manufacturer. RNA quality and concentration assessment were performed using 1 μl of sample (˂500 ng/μl) Agilent 2100 Bioanalyzer.

treatment_protocol: miRNA expression was measured in control samples and after 1 ng/ml of TGF-β1 treatment for 48 h. TGF-β1-driven MMT was confirmed in all samples by analysis of the eight molecular markers previously described (data not shown).

value: Omentum

tag: treatment

value: 1 ng/ml TGF-β1 for 48 h


title: 909 TGF


title: Breast tumor_Z75T

tag: her2 (0=negative, 1= positive)

tag: tissue type


title: Patient_2_circRNA expression profiles in hypopharyngeal carinoma tissue


title: CLL020-C-RSLNL-RT

source_name: CLL020_lymph node

tag: subject status

value: ibrutinib-relapsed CLL  patients

tag: subject id

tag: disease stage

value: richter transformation

value: lymph node


title: Breast tumor_Z69T

tag: age (years)

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade

tag: Stage

value: IIB


title: 901 TGF


title: 900 TGF


title: Patient_4_circRNA expression profiles in adjacent normal mucosae

value: adjacent normal mucosae


title: Breast tumor_Z67T

tag: pt

tag: pn

tag: relapse (0=no, 1=yes)


title: Breast tumor_Z64T

tag: dfs (months)


title: Breast tumor_Z65T

tag: er (0=negative, 1= positive)


title: 900 Con

tag: tissue

value: Control


title: 901 Con

tag: treatment


title: AU1

source_name: Stably transfected with UBALD1 BCPAP cells purchased from DSMZ in Braunschweig, Germany_Replicate 1

tag: Sex

value: female

tag: age

value: 76 years old

tag: cell type

value: AU=BCPAP

tag: transfection

value: thyroid gland


title: 904 Con


title: 909 Con


title: cepr1-1 vascular_rep1

description:
Aragene-0545
Vascular tissues of cepr1-1 cotyledons grown on the medium for 8 days

tag: genotype/variation

value: cepr1-1 mutant

value: Vascular tissues of cotyledons


title: Bart19-14_8 vs. HK-1

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

description: Bart19-14_8 vs. HK-1

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. ImaGene feature extraction: Features were extracted using ImaGene software from BioDiscovery.

data_processing: Genes, no bg corr, hybset spec. dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

source_name: 293T-ISRE-mCherry, MaHo_Bart19-14

label_protocol: Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNase Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNaseH (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul.  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems)  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.  * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.  Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script:  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

growth_protocol: Growth of cell lines: Cell lines HK-1 or 293T were grown and maintained in, respectively, Roswell Park Memorial Institute medium or Dulbecco's modified Eagle medium (RPMI 1640 or DMEM; Life Technologies), both supplemented with 10% FCS (Sigma), 2 mM L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin. 293T-ISRE-mCherry reporter cells were generated by lentivirus transduction of 293T cells with pSicoR-ISRE-mCherry; single clones were prepared by limiting dilution.

extract_protocol: RNA extraction from cell lines: 1. Add 1 ml Trizol per 5 x10^6 cells in suspension (1 ml Trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.  2. Incubate 5 min at room temperature.  3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.  4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.  5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml Trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.   6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column).  7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer).   8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.  9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at room temperature! DNase treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.  10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.  11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.  12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).  13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ.  14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Treatment of cell lines: 293T-ISRE-mCherry cells were lentivirally transduced to coexpress miR-BART16 and the miR-BART19-14 helper cluster or the helper cluster alone as control. Transduced cells were subsequently selected by blasticidin for two weeks. Details: EBV miRNAs were expressed from the lentiviral expression vector pCCLsin.PPT.pA.CTE.4xscrT.eGFP.mCMV.hPGK.NGFR (kindly provided by Dr Luigi Naldini, San Raffaele Scientific Institute, Milan, Italy), which was adapted by introducing an intron into the eGFP gene, replacing the minimal CMV promoter by the human EF1a promoter and replacing the NGFR gene by a blasticidin resistance marker. The miRNAs were cloned into the eGFP intron in this vector, which we will address as pLenti-Blast-eGFPintron, to allow high miRNA expression and eGFP fluorescence simultaneously. A detailed map of the pLenti-Blast-eGFPIntron vector will be provided on request. To express the BART miRNAs cluster called BART cluster1 in this study, we PCR-amplified the genomic regions of miR-BART3-6 (BART3, 4, 1, 15, 5, 16, 17 and 6) and miR-BART21-18 (BART21 and 18) from genomic DNA isolated from EBV+ cells (Akata strain), and combined these in the intron of the pLenti-Blast-eGFPintron vector. For expression of the individual BART16 pre-miRNA, ~250 bp encompassing miR-BART16 was PCR amplified from genomic DNA. To boost miRNA expression for the microarray gene expression analysis, the BART16 pre-miRNA sequence was combined with a helper miRNA cluster containing miR-BART19, 20, 13 and 14 (miRNAs not present in BART cluster 1).

tag: cell line

tag: transduction

source_name: HK-1, MaHo-refpool

value: MaHo-refpool


title: HK-1 vs. Bart19-14_4

description: HK-1 vs. Bart19-14_4


title: Kidney_Si repleted_replicate 1

hyb_protocol: Hybridization of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA v2.36.0, applying the Emperical Bayes (EB) estimate to estimate background levels.

organism: Rattus norvegicus

source_name: Kidney, Si repleted diet [4.1 mg Si/kg body weight/day], after 26 weeks of intervention

label_protocol: The Affymetrix One-cycle Target Labeling Assay was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix. A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Weanling (21 d old) female Sprague–Dawley rats (B&K Universal Ltd; Hull, UK) were separated into eight plastic cages with stainless-steel-grid bases (North Kent Plastics, Rochester, UK) with five rats per cage. After acclimatization for three days on a standard pelleted rodent feed (chow, B&K Rat and Mouse Standard Diet; B&K Universal Ltd) and drinking water (tap water), rats were divided into three dietary groups.

extract_protocol: Left kidneys were ground in liquid nitrogen and total RNA was extracted with the Qiagen RNeasy Maxi kit for microarray and quantitative PCR analysis. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Rats were fed diets very low in Si (Si-deplete group [0.17 mg Si/kg body weight/day], n=10), moderately high in Si (Si-replete group [4.1 mg Si/kg/day], n=8), or high in Si (Si-high reference group [standard chow pellets; 18.5 mg Si/kg/day], n=5)  for 26 weeks. For microarray analysis four rats from the Si-deplete and four rats from the Si-replete group were selected. Following their harvest, kidneys were frozen and stored at -80C.

tag: strain

value: Sprague-Dawley

tag: gender

value: 29 weeks

tag: stress

value: control (Si repleted diet)

value: kidney


title: Patient_1_circRNA expression profiles in hypopharyngeal carinoma tissue

value: hypopharyngeal carinoma tissue


title: WT vascular_control_rep1

description:
Aragene-0543
Vascular tissues of WT cotyledons grown on the medium for 8 days

value: Wild type


title: Kidney_Si repleted_replicate 2


title: Kidney_Si deprived_replicate 2

source_name: Kidney, Si deprived diet [0.17 mg Si/kg body weight/day], after 26 weeks of intervention

value: Si deprived diet


title: Kidney_Si repleted_replicate 3


title: S534Aun1

city: New York

first: Robert

middle: F

last: Schwabe

address: 1150 st Nicholas Av

department: Medicine

institute: Columbia University

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

source_name: Liver from Nfkb S534A mice in a C57Bl6/J genetic background

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Roche) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Exon 10 of p65 gene was sub-cloned in TOPO plasmid (Life Technologies, Carlsbad, CA), and S534A mutation was induced using a 2 single point mutagenesis strategy using Quick-Change Mutagenesis kit (Stratagene, La Jolla, CA) thus generating a codon modification from TCC (Serine) to GCA (Alanine). Sequential rounds of homologous recombination allowed us to introduce the mutated exon 10, a FRT-Neo-FRT-LoxP and DTA cassette on a bacterial artificial chromosome thus generating the p65 S534A knock-in targeting construct. The FNFL cassette conferred G418 resistance during gene targeting in PTL1 embryonic stem cells (ESCs), and the DTA cassette provided autonomous negative selection to reduce random integration. After transfection, two ESC clones were identified by PCR screening, and injected in C57Bl6J blastocysts and produce germline chimeras. Chimeras were mated with mice expressing Flipase (FLPe) in order to excise the Neo cassette after FRT sites recombination. The offspring were screened for the targeted allele without the neo cassette and the FLPe transgene.  Following five backcrosses to C57Bl6/J, mice were interbred to generate homozygosity. Mice that were treated  with LPS were treated with 1mg/kg LPS.

value: Male

value: Liver


title: S534Aun2


title: Kidney_Si repleted_replicate 4


title: Kidney_Si deprived_replicate 3


title: S534Aun4


title: S534ALPS1mg3

source_name: Liver treated with 1mg/kg LPS from Nfkb S534A mice in a C57Bl6/J genetic background


title: S534ALPS1mg4


title: wtLPS1mg3

source_name: Liver from WT C57Bl6/J mice treated with 1mg/kg LPS


title: S534ALPS1mg2


title: S534Aun3


title: Kidney_Si deprived_replicate 1


title: HK-1 vs. Bart16+Bart19-14_3

description: HK-1 vs. Bart16+Bart19-14_3


title: wtLPS1mg4


title: S534ALPS1mg1


title: wtLPS1mg1


title: Bart16+Bart19-14_7 vs. HK-1

description: Bart16+Bart19-14_7 vs. HK-1


title: wtLPS1mg2


title: wtun3

source_name: Untreated liver from WT C57Bl6/J mice


title: wtun4


title: Kidney_Si deprived_replicate 4


title: wtun1


title: wtun2


title: WT1-1

source_name: Liver from WT C57Bl6/J mice treated with 1µg/kg LPS

treatment_protocol: Exon 10 of p65 gene was sub-cloned in TOPO plasmid (Life Technologies, Carlsbad, CA), and S534A mutation was induced using a 2 single point mutagenesis strategy using Quick-Change Mutagenesis kit (Stratagene, La Jolla, CA) thus generating a codon modification from TCC (Serine) to GCA (Alanine). Sequential rounds of homologous recombination allowed us to introduce the mutated exon 10, a FRT-Neo-FRT-LoxP and DTA cassette on a bacterial artificial chromosome thus generating the p65 S534A knock-in targeting construct. The FNFL cassette conferred G418 resistance during gene targeting in PTL1 embryonic stem cells (ESCs), and the DTA cassette provided autonomous negative selection to reduce random integration. After transfection, two ESC clones were identified by PCR screening, and injected in C57Bl6J blastocysts and produce germline chimeras. Chimeras were mated with mice expressing Flipase (FLPe) in order to excise the Neo cassette after FRT sites recombination. The offspring were screened for the targeted allele without the neo cassette and the FLPe transgene.  Following five backcrosses to C57Bl6/J, mice were interbred to generate homozygosity. Mice that were treated  with LPS were treated with 1µg/kg LPS.

tag: background strain

tag: genotype

value: wild type


title: WT4-4


title: S534A-4-8

source_name: Liver treated with 1µg/kg LPS from Nfkb S534A mice in a C57Bl6/J genetic background

value: Nfkb S534A


title: s04


title: Human male embryo 11

city: México

first: Esther

last: Lopez-Bayghen

address: Av. IPN 2508 San Pedro Zac

department: Toxicología

country: Mexico

institute: Cinvestav-IPN

description:
65588-2
Biological replicate 11 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)

hyb_protocol: Samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Scanned on an Innopsys InnoScan 710 laser scan.

data_processing: Images were imported as .tiff and analyzed using BlueFuse Multi 4.3(25799) Software.

source_name: Trophectoderm human embryo cells

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Whole Genome Amplification performed with Sureplex following manufacturer's instructions.

value: Human embryo trophectoderm cells biopsied at day 5 by conventional method

source_name: Human reference DNA

tag: sample type

value: SureRef reference DNA


title: WT3-3


title: WT2-2


title: S534A-3-7


title: s01


title: S534A-1-5


title: Human male embryo 7

description:
57567-4
Biological replicate 7 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 3

description:
57834-4
Biological replicate 3 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: s02


title: Human male embryo 4

description:
70775-1
Biological replicate 4 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: S534A-2-6


title: s03


title: Human male embryo 10

description:
70088-6
Biological replicate 10 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 6

description:
55045-1
Biological replicate 6 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 8

description:
62429-8
Biological replicate 8 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 9

description:
70088-4
Biological replicate 9 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 5

description:
29139-5
Biological replicate 5 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human female embryo 6

description:
70642-5
Biological replicate 6 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human female embryo 8

description:
46526-4
Biological replicate 8 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human female embryo 5

description:
65199-2
Biological replicate 5 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 559665A09 - GRWSB_3 vs GRWWB_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: GRWWB_3 Cy5 / GRWSB_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Lathyrus oleraceus

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Growth conditions (1-2-3-4):           1  Media   perlite:sand (vol:vol 3:1)  hygrometry   50%  Temperature   15°C night ; 18°C day  Light   16h photoperiod

treatment_protocol: Name:GRWW - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 100percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.

value: Pisum sativum L  - harvest date:03-02-14

treatment_protocol: Name:GRWS - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 50percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.


title: Human female embryo 3

description:
64493-4
Biological replicate 3 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 559665A11 - GRWSB_4 vs GRWWB_4

hyb_protocol: GRWWB_4 Cy5 / GRWSB_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 559665A12 - GRWWB_4 vs GRWSB_4

hyb_protocol: GRWSB_4 Cy5 / GRWWB_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Human female embryo 9

description:
57567-2
Biological replicate 9 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human female embryo 7

description:
46526-2
Biological replicate 7 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 559665A10 - GRWWB_3 vs GRWSB_3

hyb_protocol: GRWSB_3 Cy5 / GRWWB_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Human female embryo 10

description:
71313-3
Biological replicate 10 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human male embryo 2

description:
57834-2
Biological replicate 2 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 559665A03 - GRWWA_4 vs GRWSB_4

hyb_protocol: GRWSB_4 Cy5 / GRWWA_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Pisum sativum L  - harvest date:27-01-14


title: 549559A12 - GRWWA_2 vs GRWSB_2

hyb_protocol: GRWSB_2 Cy5 / GRWWA_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 549559A10 - GRWWA_1 vs GRWSB_1

hyb_protocol: GRWSB_1 Cy5 / GRWWA_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Human female embryo 1

description:
31521-2
Biological replicate 1 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)