title: SCL60_Control_0_h_Replicate 4

description: Sample name: 61

tag: agent

tag: time point (h)

tag: labelling batch


title: Ampelisca ER 10% rep5

status: Public on Dec 21 2012

type: RNA

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

country: USA

institute: US Environmental Protection Agency

hyb_protocol: Sample placement on the slides was randomized.  Due to the large number of samples, hybridizations were carried out over two consecutive days.  Hybridizations were done according to the manufacturer’s protocol (v 6.5: part number G4140-90040, Agilent).  Following hybridizations and washing, the arrays were immersed in drying and stabilization solution (Agilent), and covered with ozone barrier slide covers.

scan_protocol: Two single pass scans were conducted (10% and 100% PMT) at 5 mm resolution, using an Agilent G2565BA scanner, and combined using the scanner's dual-scan software. Dual-scanning merges two 16-bit images to form a 20 bit image, and serves to increase the potential dynamic range of the scan.

data_processing: Raw data files were imported into R. Data from arrays displaying substantial technical issues apparent in MA-plots, spatial plots, or an analysis of the agreement between replicated probes were removed. Median (across pixels) non-background corrected probe intensities were quantile normalized (BM Bolstad et al., 2003). Technical replicates for a given biological sample were replaced with a single virtual array in which probe intensity was the median of the intensity of the corresponding probe in those technical replicate arrays. Intensities for probes replicated within each array (ESTs are represented by either 2 or 22 identical probes per array) were summarized as the median intensity of the replicate probes. Data from control probesets was removed.

molecule: total RNA

organism: Ampelisca abdita

source_name: 10% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

label_protocol: Ninety ng of total RNA was labeled with cyanine 3-labeled CTP using the One-color Low Input Quick Amp Labeling kit (Agilent, Santa Clara, CA) according to the manufacturer’s protocol (v 6.5: part number G4140-90040).  Labeled RNAs were purified using RNeasy mini spin columns (Qiagen) and the yield and specific activity were determined using a Nanodrop-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).  If cRNA yield was below 0.825 mg or the specific activity was below 6 pmol per mg cRNA, another tube from the same exposure vessel was extracted and labeled.  If none existed, a new labeling reaction with the original extract was conducted.

growth_protocol: A. abdita were field collected from the Narrow River, Narragansett, RI (N 41 26.921’, W 71 27.515’; May 2011) and juvenile organisms that passed through a 1.0  mm screen, but were retained on a 0.7 mm screen were selected for the experiments.  During holding and acclimation, amphipods were fed cultured algae (Tetraselmis suecica), and held in LIS reference sediment at 20 + 2 oC for at least 24 h prior to testing.

extract_protocol: Total RNA from each tube of organisms was separately isolated using TriReagent (MRC Research, Cincinnati, OH) according to the manufacturer’s protocol and genomic contamination was removed (DNA-free, Life Technologies, Grand Island, NY).  RNA purity and quality were assessed using 260:280 ratios and glyoxal gel electrophoresis.

treatment_protocol: Each exposure replicate consisted of 20 g  of sediment and 60 ml of overlying reconstituted seawater (Ho, 2000; U.S.EPA, 2007). Ten amphipods were added to each replicate. All tests were seven-day, static, aerated exposures using 30 ppt reconstituted seawater. Two initial toxicity tests were performed to determine the concentration of ER that caused 30-40% mortality in organisms, one covering a high (100%, 75%, 50% and 25% ER) and another the low range (50%, 25%, 12.5%, 6.25%, 3.13% and 1.56% ER). The initial TIE was performed on a mixture of 10:90 ER to LIS sediment to ensure that the manipulations would not be overwhelmed by the toxicants in ER. TIE manipulations included additions of: (1) coconut charcoal to assess organic toxicity, (2) cation resin to assess metal toxicity, and (3) zeolite to assess ammonia toxicity (U.S.EPA, 2007). Operational controls were performed for each manipulation using LIS sediment. No significant mortality was observed using the 10% ER sediment sample, therefore a second TIE was performed as described above except a 40:60 ER to LIS sediment mixture was used. Upon test termination, the amphipods were sieved through a 0.5 mm screen and enumerated. Missing organisms were considered dead. For all exposures except the model toxicant exposures, but including the high and low toxicity tests, as well as the 10% ER TIE and 40% ER TIE:  live organisms from each replicate were divided into groups of no more than three organisms, placed in a microcentrifuge tube, immediately frozen in liquid nitrogen and stored at -80 deg C until analyzed. For the model toxicant exposures all surviving organisms from an exposure replicate (jar) were placed in a single tube and snap-frozen in liquid nitrogen. Only a single tube from each exposure replicate (exposure replicates started with 10 amphipods) was used for microarray analysis. The remaining tubes were saved and were used if technical issues arose.  Each sample name in the samples section of the metadata matrix and in the processed data matrix represents the organisms from one tube.

tag: treatment (short label)

tag: control group for this treatment/batch

value: LIS 10%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: FALSE


title: Ampelisca ER 10% rep2


title: Ampelisca ER 10% rep3


title: Ampelisca ER 10% rep4


title: Ampelisca ER 10% rep1


title: SCL60_Treated_24_h_Replicate 3

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: Sample name: 45

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadArray

label: biotin

organism: Homo sapiens

source_name: SCL60 (responsive GnRH receptor-transfected HEK293 cells)

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: HEK293 and SCL60 cells were grown in DMEM 10% FCS + P/S. SCL60 cells were supplemented with G418 (0.5mg/ml). Tissue culture plates were coated with a diluted Matrigel solution (200ul Matrigel per 6ml media, 37C for 1-2h, remove excess before gently adding cells) to assist cell adherence.

extract_protocol: Absolutely RNA miniprep kit (Stratagene).

treatment_protocol: 100nM Triptorelin (Sigma)

tag: cell line

tag: gnrhr

value: High

value: Triptorelin

tag: chip#

tag: hybridisation batch


title: Ampelisca ER 1.56% rep3

source_name: 1.56% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: treatment (short label)

value: b


title: SCL60_Control_24_h_Replicate 3

description: Sample name: 53

tag: agent

value: Control

tag: time point (h)

tag: labelling batch


title: SCL60_Control_8_h_Replicate 2

description: Sample name: 23


title: SCL60_Treated_2_h_Replicate 3

description: Sample name: 59


title: SCL60_Treated_8_h_Replicate 3

description: Sample name: 46


title: SCL60_Treated_24_h_Replicate 2

description: Sample name: 33


title: HEK293_Control_1_h_Replicate 3

description: Sample name: 51

source_name: HEK293 (unresponsive parental cells)

value: Undetectable


title: HEK293_Treated_1_h_Replicate 3

description: Sample name: 48


title: SCL60_Control_24_h_Replicate 4

description: Sample name: 75


title: GSC-Replicate 1

status: Public on Dec 20 2012

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

hyb_protocol: After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0). The samples were hybridized on a hybridization station. 200 or 400 ng of total RNA from sample and universal reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark). The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed green signal/processed red signal. Agilent software was used (Genespring GX9). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Isolated from glioma tissue

label_protocol: After RNA quality control in order to assess the integrity of the RNA, its content of small RNA, and its concentration, the samples were labeled using miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias.

extract_protocol: Total RNA extracted using Exiqon kit following manufacturer's instructions

tag: tissue source

value: glioma tissue

tag: cell type

value: Glioma stem cells (GCS)

source_name: Universal Reference

tag: sample type

value: a mixture of 20 different tissue RNAs


title: GSC-Replicate 3


title: NSC-Replicate 2

source_name: Isolated from foetal brain (LONZA)

value: foetal brain tissue (LONZA)

value: Neural Stem Cells (NSC)


title: HEK293_Treated_24_h_Replicate 3

description: Sample name: 41


title: HEK293_Control_24_h_Replicate 3

description: Sample name: 54


title: GSC-Replicate 2


title: NSC-Replicate 3


title: NSC-Replicate 1


title: HEK293_Control_24_h_Replicate 4

description: Sample name: 76


title: Ampelisca ER 1.56% rep2

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: SCL60_Treated_1_h_Replicate 4

description: Sample name: 68

tag: cell line

tag: gnrhr


title: SCL60_Treated_2_h_Replicate 4

description: Sample name: 70

tag: chip#

tag: hybridisation batch


title: Non-producer culture - fermentation 2- time point 1

city: Brisbane

first: Stefanie

last: Dietmair

state: QLD

address: Bldg 75

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description: Sample 20

hyb_protocol: Hybridisation was performed according to the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed according to the standard Illumina scanning protocol.

data_processing:
The data from Genome studio was imported into GeneSpring version 11.5.1 (Agilent), log2 transformed and quantile normalised without baseline transformation. See Data table below.
A filter was applied to remove probes which were not expressed in 12/24 samples (the lower cut-off of the detection p-value was set to > 0.99).  See 'filtered_processed_data_matrix.txt' supplementary file on Series record.

label_protocol: The RNA was amplified and labelled using the Illumina TotalPrep RNA Amplification kit (IL1791, Ambion/Applied Biosystems, Austen, USA) according to the manufacturer's instructions.

growth_protocol: Producer and non-producer cells were cultivated in 1.5 L of Freestyle 293 Expression Medium in a 3 L Applikon bioreactor (Z611000220, Applikon Biotechnologies, The Netherlands). Stirrer speed was 150 rpm, temperature was maintained at 37°C, pH was controlled at 7.0 and pO2 at 50% air saturation. Duplicate samples for transcriptomics (total RNA) were taken approximately 30, 43, 51 and 67 hours after inoculation of the bioreactor.

extract_protocol: Total RNA was extracted using an RNeasy Midi Kit (75144, Qiagen, Doncaster, Australia) according to the manufacturer’s instructions including on-column digestion of DNA (79254, Qiagen).

treatment_protocol: Approximately 5 x 106 cells were removed from the bioreactor and centrifuged at 200 rcf for 2 min. The supernatant was discarded and the cell pellet frozen in liquid nitrogen and stored at -80°C until extraction of RNA which was performed one day after sampling.

tag: genotype/variation

value: non-producing parent

tag: time

value: time point 1

tag: chip nr


title: Non-producer culture - fermentation 2- time point 4

description: Sample 23

value: time point 4


title: SCL60_Treated_8_h_Replicate 4

description: Sample name: 73

tag: agent

tag: time point (h)

tag: labelling batch


title: Non-producer culture - fermentation 1- time point 4

description: Sample 22


title: Producer culture - fermentation 1- time point 4

description: Sample 16

value: recombinant protein producer


title: Producer culture - fermentation 1- time point 1

description: Sample 13


title: Producer culture - fermentation 2- time point 4

description: Sample 17


title: Producer culture - fermentation 2- time point 1

description: Sample 14


title: Non-producer culture - fermentation 2- time point 2

description: Sample 8

value: time point 2


title: Non-producer culture - fermentation 1- time point 3

description: Sample 10

value: time point 3


title: Producer culture - fermentation 3- time point 1

description: Sample 15


title: Producer culture - fermentation 3- time point 4

description: Sample 18


title: Non-producer culture - fermentation 3- time point 2

description: Sample 9


title: Non-producer culture - fermentation 3- time point 4

description: Sample 24


title: Non-producer culture - fermentation 2- time point 3

description: Sample 11


title: Non Producer culture - fermentation 1- time point 2

description: Sample 7


title: Non-producer culture - fermentation 3- time point 1

description: Sample 21


title: Non Producer culture - fermentation 1- time point 1

description: Sample 19


title: Non-producer culture - fermentation 3- time point 3

description: Sample 12


title: Producer culture - fermentation 3- time point 3

description: Sample 6


title: Producer culture - fermentation 2- time point 2

description: Sample 2


title: Ampelisca ER 1.56% rep1

tag: treatment (short label)

tag: control group for this treatment/batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: FALSE


title: Producer culture - fermentation 2- time point 3

description: Sample 5

tag: cell line


title: Producer culture - fermentation 3- time point 2

description: Sample 3


title: Producer culture - fermentation 1- time point 2

description: Sample 1


title: PBMC_C9-8w_rep1

city: MARSEILLE

first: El Chérif

last: Ibrahim

address: 27 Bd Jean Moulin

country: France

institute: Aix Marseille Université-CNRS

description: Gene expression of control PBMCs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul 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 (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization using limma R/bioconductor package (v.2.16.4).

source_name: Control_PBMC_8 wk

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 8-10ml venous peripheral blood from fasting patients and healthy controls were collected during 7am and 9am. PBMCs were separeted by Ficoll gradient centrifugation.Total RNA was isolated using the mirVanai Kit (Ambion) according to manufacturer's recommendation. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: status

value: control

tag: gender

value: male

tag: age

tag: treatment

value: No treatment

tag: sample collection

value: 8 weeks later after clinical remission


title: PBMC_C8-0w_rep1

description: Gene expression of control PBMCs

source_name: Control_PBMC_1 wk

value: 1st week (during a severe episode of depression)


title: PBMC_C5-8w_rep1

description: Gene expression of control PBMCs

value: female


title: PBMC_C4-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_C7-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_C4-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_C2-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_P9-8w_rep1

description: Gene expression of MDE PBMCs

source_name: MDE_PBMC_8 wk

value: major depressive episode (MDE)

value: Duloxetine, Comipranime, Lithium, Benzodiazepine

tag: hamilton depression rating scale with 17 items (hdrs-17)


title: PBMC_P8-8w_rep1

description: Gene expression of MDE PBMCs


title: Producer culture - fermentation 1- time point 3

description: Sample 4

tag: genotype/variation

tag: time

tag: chip nr


title: PBMC_C6-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_C9-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_C6-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_C3-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_C7-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_C5-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_P9-0w_rep1

description: Gene expression of MDE PBMCs

source_name: MDE_PBMC_1 wk


title: PBMC_C1-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_P8-0w_rep1

description: Gene expression of MDE PBMCs

value: Venlafaxine, Mirtazapine, Aripiprazole


title: PBMC_P7-8w_rep1

description: Gene expression of MDE PBMCs


title: PBMC_C1-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_C8-8w_rep1

description: Gene expression of control PBMCs


title: PBMC_C2-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_P6-8w_rep1

description: Gene expression of MDE PBMCs

value: Milnacipram, Mirtazapine, Fluoxetine


title: PBMC_P7-0w_rep1

description: Gene expression of MDE PBMCs

value: Comipranime, Fluoxetine, Venlafaxine, Amisulpride, Benzodiazepine


title: PBMC_C3-0w_rep1

description: Gene expression of control PBMCs


title: PBMC_P5-8w_rep1

description: Gene expression of MDE PBMCs

value: Duloxetine, Mirtazapine, Lithium, Aripiprazole, Benzodiazepine


title: PBMC_P5-0w_rep1

description: Gene expression of MDE PBMCs

value: Duloxetine, Mirtazapine, Benzodiazepine


title: Chimpanzee cerebellum adult 5

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description:
C5cereb
Gene expression of Chimpanzee cerebellum adult 5

hyb_protocol: Hybridization to Affymetrix® Human Exon 1.0 ST arrays was carried out following standard Affymetrix protocols.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Prior to expression data analysis, we masked all probes that did not match reference human genomes perfectly (hg18) and did not map to a unique location. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared the signal intensity for each probe to a distribution of signal intensities of the antigenomic probes with the same GC content. Antigenomic probes are specifically designed by Affymetrix to provide an estimate of the non-specific background hybridization. The probe signal was classified as detected above background if its intensity was larger than the 95% percentile of the background probes with the same GC content. If more than 80% of probes and at least ten probes per transcript were detected, the transcript signal was classified as detected for each sample. To further remove any possible systematic experimental differences between the arrays, we performed a PM-GCBG correction and quantile normalization. Prior to the normalization, all intensities were base-two-logarithm transformed. The intensities of transcripts were summarized by median polish method
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.all.ps

organism: Pan troglodytes

source_name: Dissected chimpanzee post-mortem cerebellar cortex

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland).

tag: tissue

value: cerebellar cortex


title: Chimpanzee cerebellum adult 3

description:
C3cereb
Gene expression of Chimpanzee cerebellum adult 3


title: PBMC_P4-8w_rep1

description: Gene expression of MDE PBMCs


title: PBMC_P3-8w_rep1

description: Gene expression of MDE PBMCs

value: Escitalopram


title: Rhesus cerebellum adult 1

description:
R1cereb
Gene expression of Rhesus cerebellum adult 1

organism: Macaca mulatta

source_name: Dissected Rhesus Macaque post-mortem cerebellar cortex


title: PBMC_P3-0w_rep1

description: Gene expression of MDE PBMCs


title: Chimpanzee cerebellum adult 2

description:
C2cereb
Gene expression of Chimpanzee cerebellum adult 2


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 5

city: Gainesville

first: Sunil

last: Joshi

state: Florida

address: 1600 S W Archer Road

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

description: HLP- AP Med 5

hyb_protocol: Standard Illumina hybridization protocol used.

scan_protocol: Standard Illumina scaning protocol used.

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

organism: Rattus norvegicus

source_name: Hydroxy-L-Proline + Apocynin treated medulla_28d

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean up and Dnase 1 treatment with QIAGEN RN easy mini kit  according to protocol provided with the kit. Quality control was  performed with Agilent Bioanalyzer.

tag: strain

value: Wistar

value: 28 days

tag: tissue source

value: Kidney

value: renal medulla

tag: diet group

value: regular diet with 5% HLP and 4 mmol Apocynin


title: PBMC_P2-8w_rep1

description: Gene expression of MDE PBMCs

value: Duloxetine, Lithium

value: 8 weeks later after clinical remission


title: Human cerebellum adult 5

description:
H5cereb
Gene expression of Human cerebellum adult 5

source_name: Dissected human post-mortem cerebellar cortex


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 4

description: HLP- AP Med 4

value: male


title: PBMC_P1-8w_rep1

description: Gene expression of MDE PBMCs

value: major depressive episode (MDE)

value: female

value: Electro-convulsivo-therapy, Mirtazapine, Aripiprazole, Hydroxyzine


title: PBMC_P2-0w_rep1

description: Gene expression of MDE PBMCs

value: Duloxetine, Mirtazapine, Lithium

value: 1st week (during a severe episode of depression)


title: Chimpanzee cerebellum adult 1

description:
C1cereb
Gene expression of Chimpanzee cerebellum adult 1


title: PBMC_P1-0w_rep1

description: Gene expression of MDE PBMCs

value: Venlafaxine, Olanzapine, Aripiprazole, Benzodiazepine


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 6

description: HLP- AP Med 6


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 3

description: HLP- AP Med 3


title: Apocynin treated medulla at 28 days rep 6

description: AP Med 6

source_name: Apocynin treated medulla_28d

value: regular diet with 4 mmol Apocynin to drink


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 2

description: HLP- AP Med 2


title: Human cerebellum adult 4

description:
H4cereb
Gene expression of Human cerebellum adult 4

value: cerebellar cortex


title: Hydroxy-L-Proline + Apocynin treated medulla at 28 days rep 1

description: HLP- AP Med 1


title: Human cerebellum adult 3

description:
H3cereb
Gene expression of Human cerebellum adult 3


title: Apocynin treated medulla at 28 days rep 4

description: AP Med 4


title: Human cerebellum adult 2

description:
H2cereb
Gene expression of Human cerebellum adult 2


title: Apocynin treated medulla at 28 days rep 2

description: AP Med 2


title: Apocynin treated medulla at 28 days rep 1

description: AP Med 1


title: Apocynin treated medulla at 28 days rep 3

description: AP Med 3


title: Control-2

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

description: Cells transfected with control ( pcDNA3.1 (+))

hyb_protocol: Samples were hybridized to the Affymetrix Human Exon 1.0 ST array for 16 hours at 45°C following manufacturer’s instructions. Hybridized arrays were then washed and stained on a GeneChip Fluidics 450 workstation (Affymetrix) using the FS450_0001 protocol.

scan_protocol: The arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Data were processed using Partek Genomics Suite version 6.5 (Partek Inc.). Probe-signal intensities were sketch normalized using a subset of the 1.4 million probe sets. Transcript expression was summarized by using a robust multiarray average method (RMA) with the core set of well annotated exons (~200,000).

source_name: human gastric cancer cell line (AGS)

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

growth_protocol: AGS cells were grown in 90% RPMI 1640 medium (biological industries) supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum (biological industries). Cells were cultured at 37 ℃ in an incubator with controlled humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Plus Kits according to the manufacturers protocol. RNA purity was confirmed by spectrophotometry (A260/A280 ratio) and capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent).

treatment_protocol: Cells transfected with pcDNA3.1 (+)/AnxA4 and control (empty vector) using Lipofectamine 2000 (Invitrogen) following the manufacturer's instructions.

value: AGS

value: transfected with empty vector


title: Hydroxy-L-Proline treated medulla at 28 days rep 3

description: HLP Med 3

source_name: Hydroxy-L-Proline treated medulla_28d

value: Wistar

value: 28 days

value: regular diet supplemented with 5% Hydroxy-L-Proline (HLP)


title: Hydroxy-L-Proline treated medulla at 28 days rep 5

description: HLP Med 5

value: Kidney

value: renal medulla


title: Control medulla at 28 days rep 4

description: Control Med 4

source_name: Control medulla_28d

value: regular rat chow diet


title: AnxA4 overexpression-2

description: Cells transfected with control ( pcDNA3.1 (+)/AnxA4)

value: transfected with pcDNA3.1 (+)/AnxA4


title: Human cerebellum adult 1

description:
H1cereb
Gene expression of Human cerebellum adult 1


title: Control medulla at 28 days rep 2

description: Control Med 2

value: male


title: Control medulla at 28 days rep 6

description: Control Med 6


title: Hydroxy-L-Proline treated medulla at 28 days rep 4

description: HLP Med 4


title: Apocynin treated medulla at 28 days rep 5

description: AP Med 5


title: Control medulla at 28 days rep 5

description: Control Med 5


title: Hydroxy-L-Proline treated medulla at 28 days rep 2

description: HLP Med 2


title: Hydroxy-L-Proline treated medulla at 28 days rep 1

description: HLP Med 1


title: Hydroxy-L-Proline treated medulla at 28 days rep 6

description: HLP Med 6


title: Control-1


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 6

description: HLP- AP Cor 6

source_name: Hydroxy-L-Proline + Apocynin treated cortex_28d

value: renal cortex

value: regular diet with 5% HLP and 4 mmol Apocynin


title: Control medulla at 28 days rep 1

description: Control Med 1


title: AnxA4 overexpression-1


title: Control medulla at 28 days rep 3

description: Control Med 3


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 4

description: HLP- AP Cor 4


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 3

description: HLP- AP Cor 3


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 2

description: HLP- AP Cor 2


title: Apocynin treated cortex at 28 days rep 6

description: AP Cor 6

source_name: Apocynin treated cortex_28d


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 5

description: HLP- AP Cor 5


title: PBMC_P6-0w_rep1

description: Gene expression of MDE PBMCs

value: major depressive episode (MDE)

value: Milnacipram, Mirtazapine


title: Hydroxy-L-Proline + Apocynin treated cortex at 28 days rep 1

description: HLP- AP Cor 1


title: Apocynin treated cortex at 28 days rep 5

description: AP Cor 5


title: Apocynin treated cortex at 28 days rep 4

description: AP Cor 4


title: Apocynin treated cortex at 28 days rep 1

description: AP Cor 1


title: Apocynin treated cortex at 28 days rep 3

description: AP Cor 3


title: Hydroxy-L-Proline treated cortex at 28 days rep 6

description: HLP Cor 6

source_name: Hydroxy-L-Proline treated cortex_28d


title: Hydroxy-L-Proline treated cortex at 28 days rep 2

description: HLP Cor 2


title: Hydroxy-L-Proline treated cortex at 28 days rep 4

description: HLP Cor 4


title: Hydroxy-L-Proline treated cortex at 28 days rep 5

description: HLP Cor 5


title: Apocynin treated cortex at 28 days rep 2

description: AP Cor 2


title: Hydroxy-L-Proline treated cortex at 28 days rep 1

description: HLP Cor 1


title: Hydroxy-L-Proline treated cortex at 28 days rep 3

description: HLP Cor 3


title: Control cortex at 28 days rep 6

description: Control Cor 6

source_name: Control cortex_28d


title: OV4936_CGH

type: genomic

city: Oslo

first: Aslaug

last: Helland

address: Hospital Radiumhospitalet

department: Dept of Genetics

country: Norway

institute: Institute for Cancer Research, Oslo University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43879.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

source_name: universal reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 54 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Chimpanzee cerebellum adult 4

description:
C4cereb
Gene expression of Chimpanzee cerebellum adult 4

value: cerebellar cortex


title: Control cortex at 28 days rep 3

description: Control Cor 3

value: Wistar

tag: gender

tag: age


title: Control cortex at 28 days rep 2

description: Control Cor 2

value: 28 days


title: OV4275_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43185.gif

value: 48 years


title: Control cortex at 28 days rep 5

description: Control Cor 5

value: Kidney


title: Control cortex at 28 days rep 1

description: Control Cor 1


title: NCFM-Polydestrose vs Isomaltulose

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description: NCFM-Polydestrose vs Isomaltulose

hyb_protocol: Prior to hybridization, oligoarray slides were prehybridized in a buffer containing 0.1% (wt/vol) SDS (Invitrogen), 0.1% (wt/vol) bovine serum albumin (Invitrogen), and 5X SSC (1X SSC is 0.15 M NaCl plus 0.015 M sodium citrate; Invitrogen) at 42C for 1 hr, then rinsed by submerging 5 times in sterile distilled water, twice in isopropanol, and spin-dry. Pairwise Cy3- and Cy5-labeled probes were dried with a Vacufuge speed-vacuum system (Epperdorf, Westbury, NY) and resuspended in a total volume of 48-50 µl of hybridization buffer containing 5X SSC, 5X Denhardt’s solution (Invitrogen), 30% (vol/vol) formamide, 0.1% SDS, and 200 µg/ml of salmon sperm DNA (Invitrogen). The resulting probe mixtures were incubated at 95°C for 2 min and hybridized to the oligoarrays for 18-20 hrs at 42C. Post-hybridized arrays were first washed in pre-warmed (42C) washing buffer containing 1X SSC and 0.03% SDS, followed by a second wash in washing buffer containing 0.5X SSC and 0.03% SDS at room temperature. Subsequently, the arrays were washed in 0.2X SSC followed by a final wash in 0.05X SSC. Each washing step was performed for 5 min.

scan_protocol: Fluorescence intensities were acquired at 10-µm per pixel resolution by using a ScanArray 4000 Microarray Scanner (Packard Biochip BioScience; Biochip Technologies LLC) and stored as TIFF image files. Signal intensities (stored as TIFF image files) were quantified, the background was subtracted, and data were normalized by using the QuantArray 3.0 software package (Perkin-Elmer).

data_processing: Median values were calculated for all ORFs and the data was log2 transformed before being imported into SAS JMP Genomics (SAS institute Inc, Cary, NC) for all 12 samples described in study. The data was quantile normalized and ANOVA was performed using Bonferroni correction (α=0.05) to identified statistically significant and differentially up-regulated genes to each carbohydrate growth condition.

organism: Lactobacillus acidophilus NCFM

source_name: Lactobacillus acidophilus NCFM Polydextrose

label_protocol: Reverse transcription and fluorescent labeling of identical amounts (20 µg) of purified RNA was performed with the SuperScript™ Indirect cDNA Labeling System for DNA Microarrays (Invitrogen, Carlsband, CA) according to the manufacturer’s directions except 6 µg of random primers (Invitrogen) were used for each 30 µl in the first strand cDNA synthesis reaction. Labeled cDNA samples were coupled with mono-reactive Cy3 or Cy5 dyes (GE Healthcare Bio-Sciences Corp., Piscataway, NJ).

growth_protocol: NCFM was grown in fresh 1% (w/v) carbohydrate supplemented SSM with a 1% inoculum from an overnight culture for a total of five subcultured passages. Aliquots of cells were collected at OD600 0.3-0.5 (early log-phase) by quick centrifugation at room temperature. Cell pellets were flash-frozen in ethanol-dry ice bath and stored at -80 C.

extract_protocol: Total RNA isolation, DNase-treatment and RNA purification were performed essentially as described previously (Goh et al., 2006 Appl. Environ. Microbiol. 72:7518-30).

tag: growth condition

value: Early logarithmic growth phase grown on polydextrose

source_name: Lactobacillus acidophilus NCFM Isomaltulose

value: Early logarithmic growth phase grown on isomaltulose


title: A549 minus SER 24hr DMSO.104

city: Cambridge

first: Charles

last: Kung

state: MA

address: 38 Sidney St., Suite 2

institute: Agios Pharmaceuticals

hyb_protocol: standard Affymetix protocol

scan_protocol: standard Affymetix protocol

data_processing: Data were processed using RMA (Gentleman et al., 2004; Irizarry et al., 2003), and differential expression was assessed using the limma package in Bioconductor (Gentleman et al., 2004; Smyth, 2004).  Pathway and transcription factor analyses were conducted using the sigpathway algorithm (Tian et al., 2005), Pathway Studio (Ariadne Genomics) and the MetaCore web application (GeneGo Inc).

source_name: A549 minusSER 24hr DMSO

label_protocol: standard Affymetix protocol

growth_protocol: A549 cells were grown in RPMI media and switched to BME+NEAA media with or without serine 24 hours prior to compound treatment (1 uM 16 or DMSO).  Samples were harvested in triplicate at 0, 1.5, 6, and 24 hours post compound addition, and hybridized to Affymetrix HG-U219 GeneChips.

extract_protocol: Trizol

tag: cell line

tag: media

value: NEAA minus Serine

tag: treatment

value: DMSO


title: NCFM-Isomaltulose vs Glucose

description: NCFM-Isomaltulose vs Glucose

source_name: Lactobacillus acidophilus NCFM Glucose

value: Early logarithmic growth phase grown on glucose


title: PBMC_P4-0w_rep1

description: Gene expression of MDE PBMCs

source_name: MDE_PBMC_1 wk

tag: status

value: male

value: Duloxetine, Mirtazapine, Benzodiazepine

tag: hamilton depression rating scale with 17 items (hdrs-17)

tag: sample collection

value: 1st week (during a severe episode of depression)


title: NCFM-Beta-glucan vs Polydextrose

description: NCFM-Beta-glucan vs Polydextrose

source_name: Lactobacillus acidophilus NCFM Beta-Glucan oligomers

value: Early logarithmic growth phase grown on beta-glucans


title: Liver_NOPAC72

city: Milan

first: Marco

last: Ranzani

address: via olgettina 58

department: TIGET

country: Italy

institute: HSR-TIGET

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 100 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip mouse 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console, R and Bioconductor (RMA normalization).

organism: Mus musculus

source_name: Non-tumoral liver from control mouse

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

extract_protocol: Total RNA including small RNAs from tumoral masses and normal liver was isolated with the miRNeasy Mini Kit (Qiagen)

treatment_protocol: Newborn mice were administered LV.ET.LTR. Mice were euthanized if sick or at different time point according to the genetic model. Liver masses were sampled for nucleic acid analyses.

tag: tissue

value: non-tumoral liver

tag: strain

tag: genotype/variation

value: Pten flox/flox AlbCre

tag: ccl4 administration

value: N


title: A549 minus SER 24hr DMSO.103

tag: time


title: Control cortex at 28 days rep 4

description: Control Cor 4

tag: tissue source

value: renal cortex

tag: diet group

value: regular rat chow diet


title: NCFM-Lactitol vs Beta-glucan

description: NCFM-Lactitol vs Beta-glucan

source_name: Lactobacillus acidophilus NCFM Lactitol

value: Early logarithmic growth phase grown on lactitol


title: OV3887_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43136.gif

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 72 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Liver_N120

value: wild type


title: A549 minus SER 24hr DMSO.102

tag: cell line

tag: media

value: NEAA minus Serine

tag: treatment

value: DMSO


title: Liver_N151

tag: tissue

value: Y


title: Liver_N150

tag: strain


title: A549 minus SER 24hr compound16 1uM.99

source_name: A549 minusSER 24hr compound16 1uM

value: compound16 1uM


title: NCFM-Gentiobiose vs Lactitol

description: NCFM-Gentiobiose vs Lactitol

source_name: Lactobacillus acidophilus NCFM Gentiobiose

tag: growth condition

value: Early logarithmic growth phase grown on gentiobiose


title: OV4044_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43883.gif

tag: age

value: 40 years


title: OV3581_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43886.gif

value: 66 years


title: NCFM-Isomaltose vs Gentiobiose

description: NCFM-Isomaltose vs Gentiobiose

source_name: Lactobacillus acidophilus NCFM Isomaltose

value: Early logarithmic growth phase grown on isomaltose


title: OV3546_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44831.gif

scan_protocol: Scanner Model: GenePix 4000B


title: OV3337_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43884.gif

value: 64 years


title: OV3485_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43885.gif

value: 69 years


title: A549 minus SER 24hr compound16 1uM.101

tag: time


title: A549 minus SER 24hr compound16 1uM.100


title: Liver_NOPAC73

value: non-tumoral liver

tag: genotype/variation

value: Pten flox/flox AlbCre

tag: ccl4 administration

value: N


title: NCFM-Stachyose vs Isomaltose

description: NCFM-Stachyose vs Isomaltose

source_name: Lactobacillus acidophilus NCFM Stachyose

value: Early logarithmic growth phase grown on stachyose


title: NCFM-Panose vs Stachyose

description: NCFM-Panose vs Stachyose

source_name: Lactobacillus acidophilus NCFM Panose

value: Early logarithmic growth phase grown on panose


title: Liver_N74

value: Cdkn2a-/- Ifnar1-/-


title: A549 plus SER 24hr DMSO.98

source_name: A549 plusSER 24hr DMSO

value: NEAA


title: OV4064_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44829.gif

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 77 years

value: serous


title: Liver_N31


title: Liver_N102


title: OV3654_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs//43880.gif

value: 60 years

tag: tumor histology


title: NCFM-GOS vs Raffinose

description: NCFM-GOS vs Raffinose

source_name: Lactobacillus acidophilus NCFM GOS

value: Early logarithmic growth phase grown on GOS

source_name: Lactobacillus acidophilus NCFM Raffinose

value: Early logarithmic growth phase grown on raffinose


title: HCC_TDOPAC14

source_name: Hepatocellular carcinoma induced by LV.ET.LTR insertional mutagenesis

value: hepatocellular carcinoma


title: A549 plus SER 24hr DMSO.96

value: DMSO


title: NCFM-Raffinose vs Panose

description: NCFM-Raffinose vs Panose


title: A549 plus SER 24hr DMSO.97


title: OV4398_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43422.gif

source_name: universal reference

value: 52 years

tag: grade of tumor


title: NCFM-Cellobiose vs GOS

description: NCFM-Cellobiose vs GOS

source_name: Lactobacillus acidophilus NCFM Cellobiose

value: Early logarithmic growth phase grown on cellobiose


title: HCC_T102A

description: cis retrieved: Braf


title: OV4004_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43882.gif

value: 56 years

tag: event (alive=1, dead=2)


title: OV3859_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43877.gif

value: 43 years

tag: progression (no progression=1, progression=2)


title: HCC_TB159

description: cis retrieved: Sos1

value: wild type

value: Y


title: HCC_TBOPAC12

value: Pten flox/flox AlbCre

value: N


title: A549 plus SER 24hr compound16 1uM.95

source_name: A549 plusSER 24hr compound16 1uM

value: NEAA

value: compound16 1uM


title: NCFM-Glucose vs Cell

description: NCFM-Glucose vs Cell

source_name: Lactobacillus acidophilus NCFM Glucose

value: Early logarithmic growth phase grown on glucose


title: A549 minus SER 6hr DMSO.67

source_name: A549 minusSER 6hr DMSO

value: NEAA minus Serine


title: HCC_TD161

description: cis retrieved: Rtl1; Sos1


title: A549 plus SER 24hr compound16 1uM.93


title: A549 minus SER 6hr DMSO.68


title: A549 minus SER 6hr compound16 1uM.65

source_name: A549 minusSER 6hr compound16 1uM


title: Genomic DNA from lymphoblastoid B cells (LCLs), H7.2

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

description:
H7.2
DNA methylation profile of B cells after EBV infection.

hyb_protocol: Bisulfite conversion of DNA samples was done using the EZ DNA methylation kit (Zymo Research, Orange, CA). After bisulfite treatment, the remaining assay steps were identical to those of the Infinium Methylation Assay, using reagents and conditions supplied and recommended by Illumina.

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

data_processing: BeadStudio software v3.2 as recommended by Illumina.

label: Cy5 and Cy3

source_name: Lymphoblastoid B cells

label_protocol: Standard Illumina protocol.

extract_protocol: Viable peripheral blood mononuclear cells (PBMCs) were isolated using LymphoprepTM density gradient centrifugation. Resting B cells were isolated by positive selection using CD19 MicroBeads (Miltenyi Biotec), or by depletion using the B Cell Isolation Kit (Miltenyi Biotec). Isolated B cells were immortalized with the supernatant of the EBV producer cell line B95.8 for the methylation studies.

tag: gender

value: female

tag: cell type

value: lymphoblastoid B cells

tag: ebv infection

value: yes

tag: sample type

value: Bcell immortalized


title: Genomic DNA from lymphoblastoid B cells (LCLs), H6.2

description:
H6.2
DNA methylation profile of B cells after EBV infection.


title: Genomic DNA from lymphoblastoid B cells (LCLs), H5.2

description:
H5.2
DNA methylation profile of B cells after EBV infection.


title: HCC_TA161

description: cis retrieved: Rtl1

value: hepatocellular carcinoma


title: HCC_TC161

description: cis retrieved: Rtl1


title: HCC_TA159

description: cis retrieved: Rtl1


title: HCC_T148

description: cis retrieved: Rtl1


title: A549 minus SER 6hr DMSO.66

tag: cell line

tag: media

tag: treatment

value: DMSO


title: Genomic DNA from lymphoblastoid B cells (LCLs), H4.2

description:
H4.2
DNA methylation profile of B cells after EBV infection.

value: male


title: ieSCs (from MEFs)-2 (YB14)

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description:
gene expression after 2 weeks of dox removal
YB14

hyb_protocol: Standard Agilent Protocol

scan_protocol: Standard Agilent Protocol

data_processing: Quantile Normalization using limma R package

source_name: ieSCs (from MEFs)-2

label_protocol: Standard Agilent Protocol

growth_protocol: Cells were grown 2 weeks in the absent of dox in F12/DMEM medium in 20% O2 and 5% CO2

extract_protocol: Qiagen Rneasy kit  Cat-74106

tag: background strain

value: Congenic, homo R26-M2rtTA strain

value: embryonic Sertoli-like cells

tag: transgene

value: Nr5a1, Wt1, Dmrt1, Gata4, Sox9


title: Genomic DNA from lymphoblastoid B cells (LCLs), H3.2

description:
H3.2
DNA methylation profile of B cells after EBV infection.


title: ieSCs (from female TTFs)-2 (YB13)

description:
gene expression after 2 weeks of dox removal
YB13

source_name: ieSCs (from female TTFs)-2


title: MEFs (YB12)

description:
gene expression after 2 weeks of culture
YB12

source_name: MEFs

value: MEFs

value: no


title: HCC_T160

description: cis retrieved: Rtl1

tag: tissue

tag: strain

value: wild type

value: Y


title: Genomic DNA from lymphoblastoid B cells (LCLs), H2.2

description:
H2.2
DNA methylation profile of B cells after EBV infection.


title: A549 minus SER 6hr compound16 1uM.64

tag: time

value: compound16 1uM


title: A549 minus SER 6hr compound16 1uM.63


title: HCC_T120A

description: cis retrieved: Rtl1

tag: genotype/variation

tag: ccl4 administration

value: N


title: ieSCs (from MEFs)-1 (YB10)

description:
gene expression after 2 weeks of dox removal
YB10

source_name: ieSCs (from MEFs)-1


title: A549 plus SER 6hr DMSO.61

source_name: A549 plusSER 6hr DMSO

value: NEAA


title: Genomic DNA from B cells, H7.1

description:
H7.1
DNA methylation profile of B cells before EBV infection.

source_name: CD19 cells

value: female

value: CD19 cells

value: Bcell


title: A549 plus SER 6hr DMSO.62


title: ieSCs (from MEFs)-2 (YB6)

description:
gene expression after 2 weeks of dox removal
YB6


title: A549 plus SER 24hr compound16 1uM.94


title: HCC_TE161

description: cis retrieved: Fign; Sos1


title: A549 plus SER 6hr DMSO.60


title: A549 plus SER 6hr compound16 1uM.59

source_name: A549 plusSER 6hr compound16 1uM


title: ieSCs (from female TTFs)-1 (YB9)

description:
gene expression after 2 weeks of dox removal
YB9

source_name: ieSCs (from female TTFs)-1


title: HCC_TEOPAC14

description: cis retrieved: Rtl1

value: Pten flox/flox AlbCre


title: Genomic DNA from B cells, H6.1

description:
H6.1
DNA methylation profile of B cells before EBV infection.


title: Genomic DNA from B cells, H5.1

description:
H5.1
DNA methylation profile of B cells before EBV infection.


title: HCC_TB161

description: cis retrieved: Fign

value: hepatocellular carcinoma


title: A549 plus SER 6hr compound16 1uM.58


title: ieSCs (from female TTFs)-2 (YB5)

description:
gene expression after 2 weeks of dox removal
YB5


title: HCC_TB157

description: cis retrieved: Fign


title: MEFs (YB4)

description:
gene expression after 2 weeks of culture
YB4


title: Genomic DNA from B cells, H3.1

description:
H3.1
DNA methylation profile of B cells before EBV infection.


title: A549 plus SER 6hr compound16 1uM.57


title: ieSCs (from MEFs)-1 (YB2)

description:
gene expression after 2 weeks of dox removal
YB2


title: Genomic DNA from B cells, H4.1

description:
H4.1
DNA methylation profile of B cells before EBV infection.


title: A549 minus SER 1.5hr DMSO.56

source_name: A549 minusSER 1.5hr DMSO

value: NEAA minus Serine

value: DMSO


title: HCC_TOPAC11

description: cis retrieved: Fign

source_name: Hepatocellular carcinoma induced by LV.ET.LTR insertional mutagenesis


title: Genomic DNA from B cells, H2.1

description:
H2.1
DNA methylation profile of B cells before EBV infection.

value: male


title: ieSCs (from female TTFs)-1 (YB1)

description:
gene expression after 2 weeks of dox removal
YB1

value: Congenic, homo R26-M2rtTA strain

value: embryonic Sertoli-like cells


title: HCC_TCOPAC14

description: cis retrieved: Fign


title: Mature Sertoli cells (YB16)

description:
gene expression after 2 weeks of culture
YB16

source_name: Mature Sertoli cells

growth_protocol: MEFs (NWD) were grown for 1 month  in F12/DMEM medium supplemented with 2mg/ml dox and were cultured in 20% O2 and 5% CO2. Immature Sertoli, mature Sertoli and MEFs were cultured for 3 days in DMEM 10%FBS and collected.

treatment_protocol: no treatment

value: Mature Sertoli (8 weeks)


title: Transcriptome WT_Col_II vs nerd1-1_Col_II

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

description: Transcriptome analysis

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biases. Normalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.

organism: Arabidopsis thaliana

source_name: RNA nerd1-1_Col_II

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, 1 ug of total RNA were amplified with one round of in vitro transcription 10h at 37°C using the MessageAmp™ II aRNA Amplification Kit (Ambion). Double stranded cDNA synthesis was then performed on 2 ug of aRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).

growth_protocol: Aerial parts of 21 day-old plants grown in soil, 16 hours photoperiod.

extract_protocol: nerd1-1_Col_II:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.

tag: ecotype

tag: age

value: 21 days

value: aerial parts

extract_protocol: WT_Col_II:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.


title: HCC_TAOPAC29

description: cis retrieved: Fign


title: Transcriptome nerd1-1_Col_I vs WT_Col_I

description: Transcriptome analysis

source_name: RNA WT_Col_I

extract_protocol: WT_Col_I:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.

extract_protocol: nerd1-1_Col_I:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.


title: A549 minus SER 1.5hr DMSO.54


title: HCC_T102B

description: cis retrieved: Fign

value: Cdkn2a-/- Ifnar1-/-


title: Immature Sertoli cells (YB15)

description:
gene expression after 2 weeks of dox removal
YB15

source_name: Immature Sertoli cells

value: Immature Sertoli cells (19 dpc)

value: no


title: MEFs (NWD) (YB10)

source_name: MEFs (NWD-infected)

value: MEFs after infection of Nr5a1, Wt1 and Dmrt1

value: Nr5a1, Wt1, Dmrt1


title: Uterine leiomyoma tumor 954T Secretory

city: Botucatu

first: Priscila

middle: Daniele Ramos

last: Cirilo

state: SP

address: Distrito de Rubião Junior S/N

department: Genética

country: Brazil

institute: Instituto de Biociências de Botucatu

description: Tumor sample Cy5-labeled mixed with reference sample Cy3-labeled

hyb_protocol: The labeling efficiency of the samples was obtained based on the ratio pmol / uL concentration of dye in mg / uL. The reference and test samples with similar efficiencies were combined. Was added to each reaction Human Cot DNA, 2X and 10X Blocking Agent Hi-RPM Hybridization Solution. The reaction was denatured at 95 ° C for 3 min and incubated at 37 ° C for 30min. The samples were applied onto the 4x44 k (Agilent) slides and kept at 65 ° C at 20rpm for 24 hours.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: Agilent Feature Extraction Software version (v.10.1.1.1) was used for background subtraction and LOWESS normalization.

source_name: Uterine leoimyoma tumor sample

label_protocol: Tumor and reference samples (500ng) to the labeling using Bioprime CGH Labeling Kit Module (Invitrogen) according to manufacturer's specifications. DNA were submitted to a random enzymatic digestion step in reaction containing ultra-pure sterile water, 2.6 ul of 10x buffer, 0.2 ul BSA, 0.5 ml of each enzyme (AluI and RsaI) totaling 26μL. The reactions were incubated at 37 ° C for 2 hours, 65 ° C for 20min and kept on ice throughout the procedure. Were added 20μL of the reaction Random Primer (Invitrogen), and then the samples were denatured at 95 ° C for 5 min and transferred to ice. The reference and test samples were labeled with 1.5 ul of Cy3 and Cy5 dCTPs, respectively added to 5μL of dNTP mix and 1μL of Exo-Klenow enzyme. The labeling reaction was performed at 37 ° C for 2hours, 65 ° C for 10min and kept on ice during the reaction. The samples were purified on mini-cellulose columns (Microcon YM-30, Millipore) and resuspended in 21μL of TE (Tris-EDTA) 1x pH = 8.0 (Prodimol).

extract_protocol: Genomic DNA from 51 ULs was isolated by the standard procedure using sodium dodecyl sulphate/proteinase K digestion followed by phenol-chloroform extraction and ethanol precipitation. The samples were treated with 20 µg/mL RNaseA (Sigma-Aldrich, St. Louis, MO, USA).

tag: phase

value: secretory menstrual cycle

value: Uterine leoimyoma tumor

value: female

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-3 (green).


title: HCC_T31

description: cis retrieved: Braf

value: hepatocellular carcinoma

value: N


title: A549 minus SER 1.5hr DMSO.55

value: NEAA minus Serine

value: DMSO


title: MEFs (YB9)

value: Congenic, homo R26-M2rtTA strain

value: MEFs


title: A549 minus SER 1.5hr compound16 1uM.52

source_name: A549 minusSER 1.5hr compound16 1uM

value: compound16 1uM


title: Mature Sertoli cells (YB8)

description:
gene expression after 2 weeks of dox removal
YB8

value: Mature Sertoli (8 weeks)


title: HCC_T74

description: cis retrieved: Braf


title: Transcriptome WT_Col_I vs nerd1-1_Col_I

description: Transcriptome analysis

source_name: RNA nerd1-1_Col_I

value: 21 days

value: aerial parts


title: nerd1-1_Col_II_IP vs WT_Col_II_IP

description: Methylome analysis

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after ChIP and directly from input chromatin was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

extract_protocol: WT_Col_II_IP:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

tag: antibody

tag: vendor

extract_protocol: nerd1-1_Col_II_IP:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: Uterine leiomyoma tumor 729TC Secretory

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

tag: gender

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-5 (green).


title: A549 minus SER 1.5hr compound16 1uM.51


title: A549 plus SER 1.5hr DMSO.50

source_name: A549 plusSER 1.5hr DMSO

value: NEAA


title: Uterine leiomyoma tumor 722TC Secretory

tag: sample type

value: reference commercial genomic DNA (Promega)


title: Uterine leiomyoma tumor 729TB Secretory


title: Transcriptome nerd1-1_Col_II vs WT_Col_II

description: Transcriptome analysis

source_name: RNA WT_Col_II


title: Immature Sertoli cells (YB7)

description:
gene expression after 2 weeks of culture
YB7

tag: cell type

value: Immature Sertoli cells (19 dpc)

value: no


title: WT_Col_II_IP vs nerd1-1_Col_II_IP

description: Methylome analysis

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biasesNormalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.

extract_protocol: WT_Col_II:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: MEFs (NWD) (YB2)

value: MEFs after infection of Nr5a1, Wt1 and Dmrt1

value: Nr5a1, Wt1, Dmrt1


title: A549 minus SER 1.5hr compound16 1uM.53

tag: cell line

tag: media


title: A549 plus SER 1.5hr DMSO.49

tag: treatment


title: Uterine leiomyoma tumor 844TB Proliferative

value: proliferative menstrual cycle

value: Uterine leoimyoma tumor

value: female


title: MEFs (YB1)

source_name: MEFs

tag: background strain

tag: transgene


title: A549 plus SER 1.5hr compound16 1uM.48

source_name: A549 plusSER 1.5hr compound16 1uM


title: Uterine leiomyoma tumor 684T Secretory

value: secretory menstrual cycle

tag: tissue


title: Uterine leiomyoma tumor 722TA Secretory


title: WT_Col_I_IP vs nerd1-1_Col_I_IP

description: Methylome analysis

extract_protocol: nerd1-1_Col_I_IP:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after ChIP and directly from input DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

extract_protocol: WT_Col_I:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.


title: A549 plus SER 1.5hr compound16 1uM.47

tag: time


title: Bos taurus_biceps brachii_C47

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

description: Sample of bovine biceps brachii muscle

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R2.11.1 statistical software

label: Cyanine 3

organism: Bos taurus

source_name: Bovine biceps brachii samples collected at the slaughterhouse

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: sample id

value: Bos taurus muscle, C47

tag: status

value: negative control


title: A549 plus SER 1.5hr compound16 1uM.46


title: A549 minus SER 0hr DMSO.19

source_name: A549 minusSER 0hr DMSO

value: NEAA minus Serine

value: DMSO


title: Bos taurus_biceps brachii_C46

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, C46


title: A549 minus SER 0hr DMSO.21


title: Uterine leiomyoma tumor 642TB Secretory


title: Bos taurus_biceps brachii_C48

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C48


title: Uterine leiomyoma tumor 683TA Secretory


title: Bos taurus_biceps brachii_C41

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C41


title: nerd1-1_Col_I_IP vs WT_Col_I_IP

description: Methylome analysis

extract_protocol: WT_Col_I_IP:10ug. DNA was extracted using the Qiagen MaxiPrep kit (Qiagen) and sonicated using a Diagenode Bioruptor. Immunoprecipitation was done on 1.5µg of DNA (IP fraction) and 150ng serves as INPUT DNA. First, IP fraction was denaturated by incubating 10 minutes at 95°C and 2 minutes on ice in 600µl of buffer 1 (10 mM Tris HCl pH 7.5, 500 mM NaCl, 1 mM EDTA). Immunoprecipitation was performed by adding 5µg of 5mC antibody (Diagenode, cat n° MAb-006-500) to denatured IP fraction and incubating overnight at 4°C with gentle agitation. Forty microliters of washed M280 Dynabeads (Invitrogen) were added to the IP fraction and incubated at 4°C for 4 hr with gentle agitation. Supernatant was collected in a new tube (Supernatant fraction). Three hundred microliters of buffer 1 were added to IP tube and incubated 10 min at room temperature with gentle agitation. This first wash was added to Supernatant fraction. Then IP fraction was washed three times by gentle mixing for 10 min at room temperature with 600 ml of buffer 1. To elute, IP fraction was incubated 1 hour at 42°C with 300µl of buffer 2 (30mM Tris HCl pH: 8.0) and 7µl of Proteinase K (NEB, 20µg/µl). DNA from the Supernatant an IP fractions was recovered by phenol-chloroform extraction and ethanol precipitation.

tag: ecotype

value: 21 days

value: aerial parts


title: YB16

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Quantile normalization using limma R package

source_name: Mature Sertoli (8 week-old mouse testis)

label_protocol: standard Agilent protocol

growth_protocol: For ieSCs samples (2%FBS in DME medium and 2mg/ml doxycyclin) for MEFs, TTFS, immature and mature Sertoli cells (10%FBS in DME). The 14.5 dpc male gonad was not cultured at all.

extract_protocol: Total RNA was extracted using the RNAEASY kit (Qiagen) following the manufacture's recommendation.

treatment_protocol: The ieSCs were cultured for 6 months, the MEFs and the TTFs were cultured for 3 passages. The immature and mature sertoli cells were cultured for 3 and 7 days respectivly.

tag: genotype/variation

value: wild type


title: YB15

source_name: Immature Sertoli (19 dpc embro testis)

value: Immature Sertoli (19 dpc embro testis)


title: YB12

source_name: ieSCs (derived fromMEFs)

value: ieSCs (derived from MEFs)

value: Nr5a1, Wt1, Dmrt1, Gata4 and Sox9

value: transdifferentiated cells


title: Uterine leiomyoma tumor 631TC Proliferative

tag: phase

value: proliferative menstrual cycle

value: Uterine leoimyoma tumor

value: female

value: reference commercial genomic DNA (Promega)


title: Bos taurus_biceps brachii_C45

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C45

value: negative control


title: Bos taurus_biceps brachii_C44

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, C44


title: A549 minus SER 0hr DMSO.20

extract_protocol: Trizol

value: NEAA minus Serine

value: DMSO


title: YB13

source_name: ieSCs (derived from TTFs)

value: ieSCs (derived from TTFs)


title: Uterine leiomyoma tumor 683TB Secretory

value: secretory menstrual cycle


title: YB14

source_name: 14.5 dpc male gonad

value: 14.5 dpc male gonad

value: wild type


title: Uterine leiomyoma tumor 631TA Proliferative


title: Uterine leiomyoma tumor 722TB Secretory


title: YB10

source_name: TTFs

value: TTFs

value: tdTomato


title: YB9

value: MEFs

value: Empty vector


title: Bos taurus_biceps brachii_C23

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C23


title: A549 minus SER 0hr compound16 1uM.18

source_name: A549 minusSER 0hr compound16 1uM

value: compound16 1uM


title: Uterine leiomyoma tumor 630T 1 Proliferative

source_name: Uterine leoimyoma tumor sample

value: proliferative menstrual cycle

value: Uterine leoimyoma tumor

value: female

value: reference commercial genomic DNA (Promega)


title: A549 minus SER 0hr compound16 1uM.17


title: YB8

value: Mature Sertoli (8 week-old mouse testis)


title: Bos taurus_biceps brachii_C22

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, C22

value: negative control


title: A549 minus SER 0hr compound16 1uM.16

value: NEAA minus Serine


title: A549 plus SER 0hr DMSO.15

source_name: A549 plusSER 0hr DMSO

value: NEAA

value: DMSO


title: YB7

value: Immature Sertoli (19 dpc embro testis)

value: wild type


title: Bos taurus_biceps brachii_C24

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C24


title: A549 plus SER 0hr DMSO.13


title: Bos taurus_biceps brachii_C17

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C17


title: Uterine leiomyoma tumor 317T 3 Secretory

value: secretory menstrual cycle


title: Bos taurus_biceps brachii_C20

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C20


title: Bos taurus_biceps brachii_C21

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C21


title: YB5

value: ieSCs (derived from TTFs)

value: Nr5a1, Wt1, Dmrt1, Gata4 and Sox9

value: transdifferentiated cells


title: YB6

value: 14.5 dpc male gonad


title: Bos taurus_biceps brachii_K12

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, K12


title: A549 plus SER 0hr DMSO.14


title: YB2

value: TTFs

value: tdTomato


title: Uterine leiomyoma tumor 317T 1 Secretory

value: Uterine leoimyoma tumor

value: female

value: reference commercial genomic DNA (Promega)


title: A549 plus SER 0hr compound16 1uM.11

source_name: A549 plusSER 0hr compound16 1uM

value: NEAA

value: compound16 1uM


title: Uterine leiomyoma tumor 307T 2 Proliferative

value: proliferative menstrual cycle

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-5 (green).


title: Uterine leiomyoma tumor 307T 1 Proliferative


title: Bos taurus_biceps brachii_C18

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, C18

value: negative control


title: Uterine leiomyoma tumor 629TA Secretory

value: secretory menstrual cycle


title: A549 plus SER 0hr compound16 1uM.12


title: Uterine leiomyoma tumor 317T 2 Secretory


title: YB1

value: MEFs

value: Empty vector

value: wild type


title: Bos taurus_biceps brachii_K10

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, K10


title: Uterine leiomyoma tumor 304T Proliferative


title: A549 preSwitch.3

source_name: A549 preSwitch

value: full Media (pre Media Switch)


title: A549 plus SER 0hr compound16 1uM.10


title: A549 preSwitch.2


title: Uterine leiomyoma tumor 301T 3 Proliferative


title: Bos taurus_biceps brachii_K11

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, K11


title: Bos taurus_biceps brachii_K7

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, K7


title: Bos taurus_biceps brachii_K8

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, K8


title: Uterine leiomyoma tumor 301T 2 Proliferative

value: Uterine leoimyoma tumor

value: female


title: Uterine leiomyoma tumor 303T Secretory

value: reference commercial genomic DNA (Promega)


title: Uterine leiomyoma tumor 301T 1 Proliferative


title: iPS_KH2-SC_MEF_1-6 [miRNA]

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description:
Sample 17
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

hyb_protocol: Each hybridized on Exiqon BWA 0.5.9 arrays against a pool of all the samples.

scan_protocol: Samples were scanned as a service by Exiqon using their inhouse protocol

data_processing: Samples were loess normalized and probes with more than 3 missing values were removed from further consideration. Other missing data were imputed using a KNN method

source_name: Sorted cells

label_protocol: Each sample was labeled using the miRCURY™ Hy3™/Hy5™ power labelling kit

growth_protocol: Mouse Embryonic fibroblast (MEFF) cultures were established from E13.5 embryos from a reprogrammable mice strain carrying one copy of the OKSM cassette and Rosa26-M2rtTA allele (het/het) or carrying two copies of the OKSM cassette and Rosa26-M2rtTA allele (ho/ho). Reprogramming was performed in ESC medium (KODMEM with 15% FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, b-mercaptoethanol and 1000 U/ml LIF) in the presence of doxycycline.

extract_protocol: RNA was isolated using the miRNeasy Mini Kit (QIAGEN)

treatment_protocol: Harvested cells were incubated with antibodies against Thy1.2 (PE conjugated, 53-2.1, eBiosciences) and SSEA-1 (mouse IgM, MC-480, Developmental Hybridoma Bank) for 20 minutes. Cells were washed in PBS and then incubated for 20 minutes with APC conjugated anti mouse IgM, (eBioscience) and Pacific Blue-conjugated streptavidin (Invitrogen). The cells were washed in PBS, resuspended in propidium iodide 5% FBS/PBS solution and passed through a 40mm cell strainer to achieve single cell suspension. Cells were sorted on a FACSAria (BD Biosciences ) and/or analysed in a LSRII (BD Bioscience).  For analysis and/or sorting of intermediates, cells were stained with Thy1.2 and SSEA1 antibodies and sorted or analyzed as indicated.

tag: strain

tag: time after induction [days]

tag: cell stage

value: iPS

value: NEG

value: POS

tag: gfp

source_name: a pool of all the samples

value: reference


title: iPS_KH2-SC_MEF_1-3 [miRNA]

description:
Sample 18
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

tag: sample type


title: iPS_KH2-SC_MEF_1-5 [miRNA]

description:
Sample 16
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: Uterine leiomyoma tumor 629TB Secretory

value: secretory menstrual cycle

tag: gender


title: Bos taurus_biceps brachii_269

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 269

value: unknown corticosteroids treatment


title: Bos taurus_biceps brachii_270

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 270


title: Uterine leiomyoma tumor 300TB Secretory


title: Bos taurus_biceps brachii_265

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 265


title: A549 preSwitch.1

tag: cell line

tag: media

value: full Media (pre Media Switch)


title: Day12_Thy- M2 [miRNA]

description:
Sample 13
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: Intermediates


title: Day12_SSEA1+ M2 [miRNA]

description:
Sample 14
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: Bos taurus_biceps brachii_81

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, 81


title: Bos taurus_biceps brachii_263

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 263


title: Day12_Thy+ M2 [miRNA]

description:
Sample 12
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: Bos taurus_biceps brachii_266

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 266


title: Uterine leiomyoma tumor 300TA Secretory

value: Uterine leoimyoma tumor

value: female


title: Uterine leiomyoma tumor 1002 Secretory

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-3 (green).


title: Uterine leiomyoma tumor 1005 Proliferative

value: proliferative menstrual cycle

value: reference commercial genomic DNA (Promega)


title: Day9_SSEA1+ M2 [miRNA]

description:
Sample 11
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: NEG

value: POS


title: Uterine leiomyoma tumor 947 Proliferative


title: Day9_Thy- M2 [miRNA]

description:
Sample 10
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: reference


title: Bos taurus_biceps brachii_79

description: Sample of bovine biceps brachii muscle

source_name: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, 79


title: Uterine leiomyoma tumor 901 Proliferative


title: Day9_Thy+ M2 [miRNA]

description:
Sample 9
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: Bos taurus_biceps brachii_78

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 78

value: unknown corticosteroids treatment


title: Bos taurus_biceps brachii_60

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 60


title: Bos taurus_biceps brachii_76

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 76


title: Day6_SSEA1+ M2 [miRNA]

description:
Sample 8
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: Intermediates


title: Uterine leiomyoma tumor 855 Secretory

value: secretory menstrual cycle


title: Day6_Thy- M2 [miRNA]

description:
Sample 7
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: Bos taurus_biceps brachii_61

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, 61


title: F9 shVector, biological rep2

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

description: Gene expression data from F9 shVector cells, biological rep2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Hybridization signals were retrieved and normalized, followed by differential expression analysis and statistical analysis using GeneSpring Analysis Platform GX 11 (Agilent Technologies).

source_name: F9 shVector, biological rep2

label_protocol: Standard Affymetrix protocol

growth_protocol: F9 embryonic carcinoma cells were obtained from ATCC and maintained using recommended culture conditions.

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Lentivirus-based shRNA constructs (pLKO.1) that target mose Phf19 gene were obtained from Open Biosystems. pLKO.1-shRNA lentivirus was generated in 293 cells and used according to Open Biosystems protocols. Stable F9 cells were selected by puromycin after pLKO.1-shPhf19 and pLKO.1-shRNA vector control (shVector) lentivirus infection.

tag: shRNA

value: Vector control


title: Uterine leiomyoma tumor 857 Secretory

value: Uterine leoimyoma tumor


title: F9 shPhf19 biological rep1

description: Gene expression data from F9 shPhf19 cells, biological rep1

source_name: F9 shPhf19 biological rep1


title: F9 shPhf19, biological rep2

description: Gene expression data from F9 shPhf19 cells, biological rep2

source_name: F9 shPhf19, biological rep2


title: Uterine leiomyoma tumor 853 Secretory

value: female


title: Bos taurus_biceps brachii_52

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 52


title: F9 shVector, biological rep1

description: Gene expression data from F9 shVector cells, biological rep1

source_name: F9 shVector, biological rep1


title: Bos taurus_biceps brachii_58

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 58


title: Day6_Thy+ M2 [miRNA]

description:
Sample 6
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: NEG


title: Uterine leiomyoma tumor 844 Proliferative

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

value: proliferative menstrual cycle

value: reference commercial genomic DNA (Promega)


title: Bos taurus_biceps brachii_51

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 51


title: Day3_SSEA1+ M2 [miRNA]

description:
Sample 5
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: POS

value: reference


title: Day3_Thy- M2 [miRNA]

description:
Sample 4
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: OVX 34

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: ventricle of ovariectomized female mice receiving placebo treatment for 4 week

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and variance stailization (VSN) as normalization method using vsn2 package

source_name: placebo treatment for 4 week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: female C57BL/6 mice from Harlan- Germany breeding

extract_protocol: RNA was isolated using the Trizol standard protocol, including Dnase digest (Quiagen)

treatment_protocol: female 8 weeks old mice were ovariectomized and received Alzet minipumps 1004 filled up with cyclodextrinated estrogens or placebo solution

tag: age

value: 8 weeks

value: ventricle


title: Uterine leiomyoma tumor 719 Secretory

tag: tissue


title: Bos taurus_biceps brachii_50

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 50

value: unknown corticosteroids treatment


title: Bos taurus_biceps brachii_49

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, 49


title: Day3_Thy+ M2 [miRNA]

description:
Sample 3
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: Intermediates


title: KH2-MEF_m3 [miRNA]

description:
Sample 2
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: MEF


title: CM6X, biological replicate3

city: Columbus

first: Brian

middle: Alexander

last: Kennedy

address: 278 Chittenden AVE

institute: The Ohio State University

description: Dox-Negative, Xrn1-Positive

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix gene chip scanner 3000 7G using AGCC

data_processing: The exon array data was normalized with the standard RMA algorithm from the Oligo package for R from the Bioconductor suite and recorded as log2 expression.

label: Biotin

molecule: cytoplasmic RNA

source_name: U2OS cells stably expressing K294A

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal labeling kit (Affymetrix)

growth_protocol: McCoy's 5A medium with 10% serum at 37oC

extract_protocol: RNA was recovered using trizol (Invitrogen) according to the manufacturer instruction after isolating the cytoplasmic extract from the cells. mRNA isolation using ribominus kit (Invitrogen) and half of the samples were treated with Xrn1 (NEB).

treatment_protocol: Induction with Doxycyline (1 ug/ml) to the samples for 24 h

value: U2OS osteosarcoma

tag: dox

value: Negative

value: Positive


title: Bos taurus_biceps brachii_39

description: Sample of bovine biceps brachii muscle

tag: sample id

value: Bos taurus muscle, 39


title: Uterine leiomyoma tumor 759 Secretory

value: secretory menstrual cycle

value: Uterine leoimyoma tumor

value: female


title: OVX 32


title: Uterine leiomyoma tumor 729 Secretory

value: reference commercial genomic DNA (Promega)


title: Uterine leiomyoma tumor 708 Secretory


title: Bos taurus_biceps brachii_38

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 38

tag: status


title: KH2-MEF_m2 [miRNA]

description:
Sample 1
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.

value: POS

value: NEG

value: reference


title: E2 35

description: ventricle of ovariectomized female mice receiving treatment with the estrogen receptor agonist 17 beta estradiol for 4 week

value: 8 weeks

value: ventricle


title: OVX 33


title: CM4, biological replicate1

description: Dox-Negative, Xrn1-Negative


title: CM5, biological replicate2

description: Dox-Negative, Xrn1-Negative


title: Day12_GFP+ M2 [miRNA]

description:
Sample 15
0_Exiqon* files are channel1 raw data files.
1_Exiqon* files are channel2 raw data files.


title: CM3X, biological replicate3

description: Dox-Positive, Xrn1-Positive


title: Uterine leiomyoma tumor 681 Proliferative

value: proliferative menstrual cycle


title: OVX 31


title: E2 34

source_name: treatment with the estrogen receptor agonist 17 beta estradiol for 4 week


title: OVX 36


title: Uterine leiomyoma tumor 644 Proliferative


title: CM5X, biological replicate2

description: Dox-Negative, Xrn1-Positive


title: Uterine leiomyoma tumor 670 Secretory


title: Bos taurus_biceps brachii_29

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, 29

value: unknown corticosteroids treatment


title: CM4X, biological replicate1

description: Dox-Negative, Xrn1-Positive

value: U2OS osteosarcoma

value: Negative


title: Bos taurus_biceps brachii_37

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 37


title: Uterine leiomyoma tumor 642 Secretory

value: secretory menstrual cycle


title: CM2X, biological replicate2

description: Dox-Positive, Xrn1-Positive

value: Positive


title: CM3, biological replicate3

description: Dox-Positive, Xrn1-Negative


title: Uterine leiomyoma tumor 634 Secretory

value: Uterine leoimyoma tumor

value: female


title: E2 33


title: Uterine leiomyoma tumor 761 Secretory

value: reference commercial genomic DNA (Promega)


title: Bos taurus_biceps brachii_36

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, 36


title: E2 30


title: E2 29


title: CM1, biological replicate1

description: Dox-Positive, Xrn1-Negative


title: Bos taurus_biceps brachii_S57

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, S57

value: suspected for corticosteroids treatment


title: CM2, biological replicate2

description: Dox-Positive, Xrn1-Negative


title: CM6, biological replicate3

description: Dox-Negative, Xrn1-Negative


title: Uterine leiomyoma tumor 631 Proliferative


title: beta 36

description: ventricle of ovariectomized female mice receiving treatment with control solution for 4 week

value: 8 weeks


title: CM1X, biological replicate2

description: Dox-Positive, Xrn1-Positive


title: Uterine leiomyoma tumor 625 Secretory


title: OV3338_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44828.gif

source_name: universal reference

extract_protocol: not provided

tag: reference

value: universal reference

value: Primary tumor, Ovarian

value: 64 years

tag: tumor histology

value: serous

tag: grade of tumor

tag: event (alive=1, dead=2)

tag: progression (no progression=1, progression=2)

tag: overall survival (os, n=months)

tag: progression-free survival (pfs, n=months)


title: Bos taurus_biceps brachii_S54

description: Sample of bovine biceps brachii muscle

value: Bovine biceps brachii samples collected at the slaughterhouse

value: Bos taurus muscle, S54


title: OV4047_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44815.gif

value: 48 years


title: Uterine leiomyoma tumor 630 Proliferative

source_name: Uterine leoimyoma tumor sample

tag: phase

value: proliferative menstrual cycle

tag: sample type


title: Uterine leiomyoma tumor 615 Proliferative

tag: gender


title: beta 33

source_name: treatment with control solution for 4 week

tag: strain

value: ventricle


title: Bos taurus_biceps brachii_S21

description: Sample of bovine biceps brachii muscle

value: Bos taurus muscle, S21


title: OV3417_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44816.gif


title: beta 35


title: beta 31


title: beta 32


title: OV3328_CGH

description: Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44814.gif

value: 57 years


title: alpha 34

description: ventricle of ovariectomized female mice receiving treatment with the estrogen receptor alpha agonist 16 alpha LE2 for 4 week

value: female


title: alpha 33

source_name: treatment with the estrogen receptor alpha agonist 16 alpha LE2 for 4 week


title: Uterine leiomyoma tumor 614 Proliferative

value: Uterine leoimyoma tumor

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-5 (green).


title: iPS_KH2-SC_MEF_1-5 [mRNA]

description: Sample name: KH2-SC_MEFiPS_1-5

hyb_protocol: Samples were hybridized to affymetrix MOE430A arrays using the protocol provided by the supplier

scan_protocol: Arrays were scanned on an affymetrix scanner in according to the manufacturers protocol

data_processing: Data were normalized using robust multi array averaging (RMA) and converted to log2 scale

label_protocol: Samples were labeled with biotin in the standard way

extract_protocol: iPSCs were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Intermidiates cell types were harvest after FACS sorting. Cells were then spun down and the pellet used for isolation of total RNA using the miRNeasy Mini Kit (QIAGEN) without DNase digestion. RNA was eluted from the columns using 50 ml RNase-free water or TE buffer, pH7.5 (10 mM Tris-HCl and 0.1 mM EDTA) and quantified using a Nanodrop (Nanodrop Technologies).

tag: time after induction [days]

tag: cell stage

value: iPS

value: NEG

value: POS

tag: gfp


title: iPS_KH2-SC_MEF_1-3 [mRNA]

description: Sample name: KH2-SC_MEFiPS_1-3


title: iPS_KH2-SC_MEF_1-6 [mRNA]

description: Sample name: KH2-SC_MEFiPS_1-6


title: Day12_GFP+ M2 [mRNA]

description: Sample name: KH197

value: Intermediates