title: Sensory Neurons_CFA paw injected_rep3

city: Milwaukee

first: Andy

last: Weyer

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description:
Sample name: CFA Paw 3
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.

hyb_protocol: 2.3 ug of fragmented and labeled ss-cDNA was hybridized to GeneChips overnight for 16 hours at 45 degrees C with rotation speed 60 rpm. Chips were then washed and stained using an Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Chip data from .CEL files was imported into Partek Genomics Suite and data was normalized using RMA background corrections. All chips were imported simultaneously for normalization purposes and to allow comparison between chips.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0st-v1.r4.mps

source_name: Large diameter CGRP-positive sensory neurons projecting to skin, CFA injected into paw

label_protocol: 50 ng total RNA was amplified using the Affymetrix GeneChip WT cDNA synthesis and amplification kit. All cDNA synthsis, biotinylation of cRNA, fragmentation, and labeling was performed according to the manufacturer's instructions

growth_protocol: Sensory neurons from the lumbar 2-5 dorsal root ganglia (DRG) on the experimental side were obtained after killing the mouse. DRGs were then enzymatically and mechanically dissociated into a single cell suspension. This suspension was then sorted into large diameter (>26.9 um) neurons and then based on expression of GFP (under the Calcitonin Gene-Related Peptide promoter) and Wheat Germ Agglutinin-AF647 (retrograde tracer injected into the gastrocnemius muscle or saphenous nerve 5 days before sacrifice of the mouse).

extract_protocol: Starting with the whole cell lysate within the Trizol, RNA was isolated using the Purelink Microkit (Life Technologies) according to the manufacturer's instructions and stored in water at -20 degrees C

treatment_protocol: Large diameter sensory neurons were sorted based on expression of CGRP directly into Trizol

value: large diameter sensory neurons projecting to skin

tag: cgrp status of cell

value: CGRP Positive

value: CFA injected into paw


title: BPH-infested Xiushui 11 shoots, biological rep 3

status: Public on Nov 06 2015

type: RNA

city: Hangzhou

first: Gongyin

last: Ye

state: Zhejiang

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Oryza sativa

source_name: BPH-infested Xiushui 11 shoots

label_protocol: Double strand cDNA was synthesized from total RNA. After cleanup, biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Rice seeds were germinated and grown in a controlled chamber at 30°C in the light and 25°C in the dark under a 16:8 h light: dark regime. The relative humidity was maintained at 85%. Three weeks later, rice seedlings of similar sizes were transplanted into glass tubes (38 × 250 mm) covered with nylon mesh, with one tube per seedling. The glass tube was filled with 5 ml nutrient solution, which was renewed every 3 days.

extract_protocol: Frozen rice shoots were homogenized in liquid nitrogen using a mortar and pestle. Total RNA was extracted using Trizol regent according to the supplier‟s recommendation (Invitrogen, Karlsruhe, Germany).

treatment_protocol: For BPH treatment, 10 second-instar nymphs were infested onto each 30-day-old seedling. After 72 h, the BPH nymphs were carefully removed and rice shoots of both BPH-infested and non-infested plants were sampled for microarray analysis. There were four treatments: Xiushui 11-non infested, Xiushui 11-BPH infested, KMD2-non infested, KMD2-BPH infested.

tag: line

value: parental rice line Xiushui 11

tag: treatment

value: BPH-infested 72h

tag: tissue

value: shoot


title: intermediate-state cells-rep1

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from Sox1-GFP-positive cells at day 6 of OKSM-induced astrocyte reprogramming.

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: The probe set signals were calculated with the robust multi-array average (RMA) algorithm implemented in GeneSpring GX 12.6 software (Agilent Technologies).

organism: Mus musculus

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: Astrocytes were maintained in DMEM/F12 with 10% fetal bovine serum (FBS). NSCs were maintained in DMEM/F12 medium supplemented with N2 (25 mg/ml insulin , 100 mg/ml apo-transferrin, 20 nM progesterone, 100 mM putrescine and 30 nM sodium selenite), 20 ng/ml basic FGF (bFGF) and  20 ng/ml EGF. The cells undergoing reprogramming were cultured in standard mouse ESC medium containing 15% ES-FBS and 1000 U/ml LIF. Mature iPSCs were cultured on feeder layers of mitomycin C-treated MEFs in mouse ESC medium containing 15% ES-FBS or 15% KnockOut Serum Replacement (KSR) and 1500 U/ml LIF.

extract_protocol: Total RNAs were extracted using Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

treatment_protocol: Astocytes (Sox1-GFP-negative cells) were infected with retroviruses encoding the four transcription factors (Oct4, Klf4, Sox2 and c-Myc).

tag: genotype

value: Sox1-GFP reporter (Sox1+/-)

tag: cell type


title: non-infested KMD2 shoots, biological rep 1

source_name: non-infested KMD2 shoots

value: Bt rice line KMD2

value: non-infested


title: non-infested Xiushui 11 shoots, biological rep 1

source_name: non-infested Xiushui 11 shoots


title: iPSCs from astrocytes-rep2

description: Gene expression data from mature iPSCs established from Sox1-GFP astrocytes.

source_name: mature iPSCs establised from astrocytes

value: mature iPSCs establised from astrocytes


title: BPH-infested KMD2 shoots, biological rep 3

source_name: BPH-infested KMD2 shoots


title: Sensory Neurons_Saline paw injected_rep2

country: USA

description:
Sample name: Saline Paw 2
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.

source_name: Large diameter CGRP-positive sensory neurons projecting to skin, saline injected into paw

tag: strain

value: saline injected into paw


title: Sensory Neurons_CFA paw injected_rep2

description:
Sample name: CFA Paw 2
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Sensory Neurons_Saline paw injected_rep3

description:
Sample name: Saline Paw 3
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Sensory Neurons_Saline paw injected_rep1

description:
Sample name: Saline Paw 1
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: BPH-infested KMD2 shoots, biological rep 1


title: BPH-infested Xiushui 11 shoots, biological rep 1


title: Sensory Neurons_Saline muscle injected_rep1

description:
Sample name: Saline Muscle 1
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.

source_name: Large diameter CGRP-negative sensory neurons projecting to muscle, Saline injected into muscle

value: large diameter sensory neurons projecting to muscle

value: CGRP Negative

value: Saline injected into muscle


title: Sensory Neurons_CFA paw injected_rep1

description:
Sample name: CFA Paw 1
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Sensory Neurons_Saline muscle injected_rep3

description:
Sample name: Saline Muscle 3
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Sensory Neurons_Acid muscle injected_rep1

description:
Sample name: Acid Muscle 1
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.

source_name: Large diameter CGRP-negative sensory neurons projecting to muscle, Acid injected into muscle

value: Acid injected into muscle


title: Sensory Neurons_Acid muscle injected_rep2

description:
Sample name: Acid Muscle 2
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Sensory Neurons_Acid muscle injected_rep3

description:
Sample name: Acid Muscle 3
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: normal8 [mRNA]

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

description: Gene expression of adjacent normal tissue 8

hyb_protocol: For the expression arrays Cy-3-labeled cRNA was hybridized according to the manual One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5, May 2010) from Agilent Technologies.

scan_protocol: The slides were scanned immediately after washing on the Agilent Microarray Scanner G2565C using protocol GE1_107_Sep09 for the expression microarrays and protocol.

data_processing: The scanned images were analyzed using Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters. The expression profiles were backgroundcorrected and quantile normalized for mRNA. Filtering of controls, unannotated genes and low expressed probes was done.

organism: Homo sapiens

source_name: Fresh frozen tumor

label_protocol: mRNA was labeled with Cy-3 according to the manual One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5, May 2010) from Agilent Technologies, using 100 ng total RNA as input.

extract_protocol: Total RNA was isolated from cell pellets using mirVana kit (Ambion/Life Technologies) according to the manufacturer’s instructions. Total RNA was eluted in 100 µl H2O, concentration measured on NanoDrop ND-1000.

value: adjacent normal tissue


title: normal11 [mRNA]

description: Gene expression of adjacent normal tissue 11


title: normal7 [mRNA]

description: Gene expression of adjacent normal tissue 7


title: normal2 [mRNA]

description: Gene expression of adjacent normal tissue 2


title: normal10 [mRNA]

description: Gene expression of adjacent normal tissue 10


title: Sensory Neurons_CFA muscle injected_rep1

description:
Sample name: CFA Muscle 1
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.

source_name: Large diameter CGRP-negative sensory neurons projecting to muscle, CFA injected into muscle

value: CFA injected into muscle


title: S. cerevisiae_evolved_h9_tRNA_rep3

city: Aveiro

first: Ana

middle: Rita

last: Bezerra

address: Campus Universitário Santiago

department: Health Sciences

country: Portugal

institute: University of Aveiro

description: gene expression of mistranslating yeast after lab evolution

hyb_protocol: To prepare hybridization, 1.65 μg of Cy3-labeled cRNAs were mixed with the fragmentation mix (Blocking Agent and Fragmentation Buffer) and incubation lasted for 30 minutes at 60 ºC. Finally, GEx Hybridization Buffer HI-RPM was added and the preparation was assembled in the custom made Agilent arrays (yeast G4813A). Slides were prepared using Agilent gasket slides according to the manufacturer instructions. Each hybridization was carried out for 17 hours at 65ºC, in an Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 60%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 016322_D_F_20130122) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

source_name: evolved lineage h9, mistranslating, replicate 3

label_protocol: Labeling was performed using the Agilent protocol for One-Color MicroarrayBased Gene Expression Analysis Quick Amp Labeling v5.7 (Agilent Technologies). cDNA was synthesized from 600 ng of total RNA using Agilent T7 Promoter Primer and T7 RNA Polymerase Blend and labeled with Cyanine 3-CTP. Labeled cDNA was purified with RNAeasy mini spin columns (QIAGEN) to remove residual Cyanine 3-CTP. Dye incorporation and quantification was monitored using the Nanodrop 1000 Spectrophotometer.

growth_protocol: Ancestor and evolved lineages grew in liquid media (SC-leucine)

extract_protocol: Total RNA was extracted using the hot-phenol method. Total RNA samples were treated with DNaseI (Amersham Biosciences) according to the commercial enzyme protocol and quantification and quality control was performed using the Agilent 2100 Bioanalyzer system.

treatment_protocol: A 20-week-long laboratory experimental evolution (SC-leucine) was carried in lineages B3, D11 and H9. 1ul of stationary phase cultures were transferred to fresh media every second days using handheld pintools.

tag: evolution step

value: evolved

tag: plasmid

value: Ser-tRNACAG


title: normal4 [mRNA]

description: Gene expression of adjacent normal tissue 4


title: normal12 [mRNA]

description: Gene expression of adjacent normal tissue 12


title: normal6 [mRNA]

description: Gene expression of adjacent normal tissue 6


title: Sensory Neurons_Saline muscle injected_rep2

description:
Sample name: Saline Muscle 2
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: normal5 [mRNA]

description: Gene expression of adjacent normal tissue 5


title: normal9 [mRNA]

description: Gene expression of adjacent normal tissue 9


title: Sensory Neurons_CFA muscle injected_rep3

description:
Sample name: CFA Muscle 3
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Duodenum_8 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 8

value: duodenal adenocarcinoma type


title: Sensory Neurons_CFA muscle injected_rep2

description:
Sample name: CFA Muscle 2
Transgenic mice that have Green Fluorescent Protein inserted under the Calcitonin Gene-Related Peptide promoter . The reference for this mouse line is: McCoy, E. S.; Taylor-Blake, B.; Zylka, M. J. CGRPα-Expressing Sensory Neurons Respond to Stimuli That Evoke Sensations of Pain and Itch. PloS one 2012, 7.


title: Duodenum_5 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 5


title: Duodenum_10 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 10


title: normal1 [mRNA]

description: Gene expression of adjacent normal tissue 1


title: normal3 [mRNA]

description: Gene expression of adjacent normal tissue 3


title: Duodenum_7 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 7


title: S. cerevisiae_evolved_h9_tRNA_rep2

source_name: evolved lineage h9, mistranslating, replicate 2


title: S. cerevisiae_evolved_h9_tRNA_rep1

source_name: evolved lineage h9, mistranslating, replicate 1


title: Duodenum_2 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 2


title: Duodenum_6 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 6


title: Duodenum_1 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 1


title: Duodenum_4 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 4


title: S. cerevisiae_evolved_h9_empty vector_rep3

description: gene expression of non-mistranslating yeast after lab evolution

source_name: evolved lineage h9, non-mistranslating, replicate 3

value: empty


title: ampullaI_7 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 7

value: ampulla intestinal type


title: S. cerevisiae_evolved_h9_empty vector_rep2

source_name: evolved lineage h9, non-mistranslating, replicate 2


title: S. cerevisiae_evolved_d11_empty vector_rep2

source_name: evolved lineage d11, non-mistranslating, replicate 2


title: S. cerevisiae_evolved_d11_tRNA_rep3

description: gene expression of mistranslating yeast after lab evolution

source_name: evolved lineage d11, mistranslating, replicate 3


title: S. cerevisiae_evolved_d11_empty vector_rep3

source_name: evolved lineage d11, non-mistranslating, replicate 3


title: ampullaI_6 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 6


title: S. cerevisiae_evolved_d11_tRNA_rep1

source_name: evolved lineage d11, mistranslating, replicate 1


title: S. cerevisiae_evolved_d11_empty vector_rep1

source_name: evolved lineage d11, non-mistranslating, replicate 1


title: S. cerevisiae_evolved_b3_tRNA_rep3

source_name: evolved lineage b3, mistranslating, replicate 3


title: S. cerevisiae_evolved_d11_tRNA_rep2

source_name: evolved lineage d11, mistranslating, replicate 2


title: Duodenum_3 [mRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 3


title: ampullaI_4 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 4


title: S. cerevisiae_evolved_h9_empty vector_rep1

source_name: evolved lineage h9, non-mistranslating, replicate 1


title: ampullaI_5 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 5


title: ampullaI_1 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 1


title: ampullaI_3 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 3


title: S. cerevisiae_evolved_b3_tRNA_rep1

source_name: evolved lineage b3, mistranslating, replicate 1


title: ampullaP_8 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 8

value: ampulla pancreatobiliary type


title: ampullaP_5 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 5


title: ampullaI_2 [mRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 2


title: S. cerevisiae_evolved_b3_empty vector_rep2

source_name: evolved lineage b3, non-mistranslating, replicate 2


title: S. cerevisiae_evolved_b3_tRNA_rep2

source_name: evolved lineage b3, mistranslating, replicate 2


title: ampullaP_6 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 6

source_name: Fresh frozen tumor


title: S. cerevisiae_non-evolved_tRNA_rep3

description: gene expression of mistranslating yeast

source_name: ancestor, mistranslating, replicate 3

value: ancestor


title: ampullaP_7 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 7


title: S. cerevisiae_non-evolved_tRNA_rep1

description: gene expression of mistranslating yeast

source_name: ancestor, mistranslating, replicate 1


title: S. cerevisiae_non-evolved_empty vector_rep2

description: gene expression of non-mistranslating yeast

source_name: ancestor, non-mistranslating, replicate 2


title: S. cerevisiae_non-evolved_tRNA_rep2

description: gene expression of mistranslating yeast

source_name: ancestor, mistranslating, replicate 2


title: S. cerevisiae_non-evolved_empty vector_rep1

source_name: ancestor, non-mistranslating, replicate 1


title: bileduct_8 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 8

value: bile duct adenocarcinoma


title: ampullaP_3 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 3


title: ampullaP_2 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 2


title: ampullaP_4 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 4


title: bileduct_6 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 6


title: ampullaP_1 [mRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 1


title: bileduct_3 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 3


title: elevated CO2, high light, stationary, series B, rep 2

city: Seattle

first: Justin

last: Ashworth

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: Array slides were hybridized according to the standard Agilent protocol for 8x60k custom array slides.

scan_protocol: Array slides were scanned using an Agilent slide scanner.

data_processing: Data were processed from Agilent files using the limma package in R, including background correction, loess (within-array) and 'Aquantile' (between-array) normalization.

organism: Thalassiosira pseudonana

source_name: T. pseudonana batch culture

label_protocol: Total RNA was amplified and labeled using the Agilent Quick-Amp labeling kit (two-color).

growth_protocol: 2L batch cultures of artificial seawater medium with reduced nitrate (100 uM) and 80 uM silicic acid were equilibrated to normal or elevated CO2 levels by bubbling with co2 enrich air, and then innoculated with Thalassiosira pseudonana cells at 2x10^5 cells/mL starting cell density. Cells were grown under constant light for approximately three days, after which cultures reached a stationary cell density (~2x10^6/cells/mL) and both free nitrate and silicic acid levels were exhausted (completely incorporated into cells).

extract_protocol: Cells (3x10^7 cells, volume dependent on cell culture density) were harvested by filtration, flash frozen, and then total RNA was extracted using the mirVANA extraction kit.

treatment_protocol: Cells were grown under normal (~400ppm) or elevated (~800ppm) CO2 levels. Experiments were also repeated twice each at normal and elevated light levels.

tag: light level

value: normal light

tag: phase

value: mid-log

tag: co2 level

value: normal co2

value: high light

value: stationary

value: elevated


title: bileduct_4 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 4


title: elevated CO2, high light, stationary, series A, rep 3


title: bileduct_7 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 7


title: bileduct_2 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 2


title: elevated CO2, high light, stationary, series B, rep 1


title: bileduct_5 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 5


title: elevated CO2, high light, stationary, series A, rep 2


title: elevated CO2, high light, stationary, series A, rep 1


title: elevated CO2, high light, stationary, series B, rep 3


title: PDAC_49 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 49

value: pancreatic ductal adenocarcinoma


title: normal CO2, high light, stationary, series B, rep 1

value: normal


title: PDAC_48 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 48


title: PDAC_52 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 52


title: bileduct_1 [mRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 1


title: PDAC_51 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 51


title: PDAC_47 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 47


title: normal CO2, high light, stationary, series B, rep 2


title: PDAC_44 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 44


title: elevated CO2, high light, exponential, series B, rep 1

value: exponential


title: normal CO2, high light, stationary, series A, rep 2


title: PDAC_45 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 45


title: elevated CO2, high light, exponential, series A, rep 3


title: PDAC_41 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 41


title: normal CO2, high light, stationary, series B, rep 3


title: PDAC_40 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 40


title: normal CO2, high light, stationary, series A, rep 3


title: normal CO2, high light, stationary, series A, rep 1


title: elevated CO2, high light, exponential, series B, rep 2


title: PDAC_46 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 46


title: PDAC_43 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 43


title: PDAC_37 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 37


title: elevated CO2, high light, exponential, series A, rep 1


title: elevated CO2, high light, exponential, series B, rep 3


title: normal CO2, high light, exponential, series B, rep 2


title: PDAC_39 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 39


title: elevated CO2, high light, exponential, series A, rep 2


title: normal CO2, high light, exponential, series B, rep 3


title: PDAC_36 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 36


title: PDAC_38 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 38


title: normal CO2, high light, exponential, series B, rep 1


title: PDAC_35 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 35


title: normal CO2, high light, exponential, series A, rep 3


title: normal CO2, high light, exponential, series A, rep 2


title: normal CO2, high light, exponential, series A, rep 1


title: PDAC_33 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 33


title: PDAC_26 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 26


title: elevated CO2, normal light, stationary, series B, rep 2


title: elevated CO2, normal light, stationary, series A, rep 3


title: elevated CO2, normal light, stationary, series B, rep 3


title: normal CO2, normal light, stationary, series B, rep 2


title: PDAC_30 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 30


title: PDAC_24 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 24


title: PDAC_27 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 27


title: PDAC_34 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 34


title: PDAC_31 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 31


title: normal CO2, normal light, stationary, series B, rep 3


title: normal CO2, normal light, stationary, series B, rep 1


title: elevated CO2, normal light, stationary, series B, rep 1


title: PDAC_32 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 32


title: S. cerevisiae_evolved_b3_empty vector_rep1

description: gene expression of non-mistranslating yeast after lab evolution

source_name: evolved lineage b3, non-mistranslating, replicate 1

value: evolved


title: PDAC_21 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 21


title: elevated CO2, normal light, stationary, series A, rep 2


title: normal CO2, normal light, stationary, series A, rep 3


title: PDAC_20 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 20


title: PDAC_23 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 23


title: elevated CO2, normal light, stationary, series A, rep 1


title: PDAC_25 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 25


title: PDAC_28 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 28


title: PDAC_22 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 22


title: normal CO2, normal light, stationary, series A, rep 1


title: elevated CO2, normal light, exponential, series B, rep 1


title: PDAC_19 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 19


title: elevated CO2, normal light, exponential, series B, rep 2


title: elevated CO2, normal light, exponential, series B, rep 3


title: elevated CO2, normal light, exponential, series A, rep 3


title: PDAC_14 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 14


title: elevated CO2, normal light, exponential, series A, rep 1


title: normal CO2, normal light, exponential, series B, rep 2


title: PDAC_15 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 15


title: normal CO2, normal light, stationary, series A, rep 2


title: PDAC_11 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 11


title: PDAC_17 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 17


title: normal CO2, normal light, exponential, series A, rep 1


title: elevated CO2, normal light, exponential, series A, rep 2


title: normal CO2, normal light, exponential, series B, rep 1


title: PDAC_18 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 18


title: normal CO2, normal light, exponential, series A, rep 2


title: PDAC_9 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 9


title: PDAC_10 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 10


title: normal CO2, normal light, exponential, series A, rep 3


title: PDAC_16 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 16


title: PDAC_8 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 8


title: PDAC_6 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 6


title: PDAC_7 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 7


title: PDAC_12 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 12


title: normal CO2, normal light, exponential, series B, rep 3


title: PDAC_5 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 5


title: PDAC_3 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 3


title: PDAC_2 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 2


title: PDAC_13 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 13


title: PDAC_4 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 4


title: PDAC_1 [mRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 1


title: gDNA_CD8_Graves_rep37

type: genomic

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

hyb_protocol: The hybridization protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina. PDF is available on the series record.

scan_protocol: The scanning protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina. PDF is available on the series record.

data_processing: Data preprocessing and quality control analyses were performed in R (http://www.r-project.org/) with the Bioconductor package minfi [1], using the original IDAT ﬁles. The dataset was split by cell type into CD4+ and CD8+ datasets. Cross-hybridizing and SNP-containing probes that are listed in [2] and probes with a detection p-value >0.01 were removed before normalization. The datasets were normalized with the stratified quantile normalization method described in [3] and implemented in minfi. The normalized signal intensities were converted to M-values [4]. Prior to finding differentially methylated sites, the methylation values of each CpG site were corrected by fitting a linear model with age, sex, methylation bead array chip and array row on the chip as covariates. The model residuals were used for differential methylation analysis with the R package “seqlm” (https://github.com/raivokolde/seqlm) by applying the statistical test to single CpG sites (argument max_dist=1). Single CpGs with a false discovery rate (FDR) <0.005 and an absolute methylation difference of >0.5 were considered as differentially methylated and used in downstream analyses.     1. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics, 2014;30:1363-9.  2. Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013;8:203-9.  3. Touleimat N, Tost J. Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics, 2012;4:325-41.  4. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics, 2010;11:587.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Genomic DNA, CD8 cells, Graves' patient

label_protocol: The labeling protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina. PDF is available on the series record.

extract_protocol: Peripheral blood mononuclear cells were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD8+ T-cells and CD4+ T cells were purified by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. The cell populations were collected and stored as cell pellets in a -80°C freezer. Genomic DNA was isolated from the purified cell pellets using the QIAmp DNA Mini Kit (Qiagen) according to the manufacturer's protocol. The purity and concentrations of the DNA samples were measured by NanoDrop ND-1000 spectrophotometry (Thermo Scientific) and Qubit fluorometry (Life Technologies). Five hundred nanograms of genomic DNA were treated with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research Corporation) according to the manufacturer’s instructions. Further steps t process  Infinium® HumanMethylation450 BeadChips (hybridization, labeling and scanning of arrays) were performed according to instructions given by Illumina. PDF is available on the series record.

value: blood

tag: gender

value: Female

tag: age

value: CD8 T cells

tag: diagnosis

value: Graves' Patient


title: RNA_CD8_Graves_rep15

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The preprocessing steps and quality control of the datasets were performed directly on the IDAT files of the expression arrays using the Bioconductor package “limma” [1]. The expression arrays were given weights as described in [2] and implemented in “limma”. Age and the expression bead array chip were considered as covariates and the sample group was the variable of interest in a linear regression model that was used in the arrayWeights() function. To test for differential expression between healthy controls and GD patients, age and the expression bead array chip were included in a linear regression model as covariates to test for differential expression with the “limma” software. Genes with the FDR adjusted p-value < 0.1 and a fold change >1.5 were considered to be differentially expressed.    1. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol, 2004;3:Article3.  2. Ritchie ME, Diyagama D, Neilson J, van Laar R, Dobrovic A, Holloway A et al. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics, 2006;7:261.

label: Biotin

source_name: Total RNA, CD8, Graves' patient

label_protocol: RNA was labeled and amplified using the TargetAmp- Nano Labeling Kit for the Illumina Expression BeadChip (Epicentre Biotechnologies) using SuperScript III Reverse Transcriptase (Life Technologies). The material was purified with the RNeasy MinElute Cleanup Kit (Qiagen) and RNA quality was assessed using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit.

extract_protocol: Peripheral blood mononuclear cells were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD8+ T-cells and CD4+ T cells were purified by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. The cell populations were collected and stored as cell pellets in a -80°C freezer. RNA was extracted from the purified T-cells using the miRNeasy Mini Kit combined with the recommended RNase-free DNase I treatment (both from Qiagen). RNA was concentrated using the Heraeus vacuum centrifugation system without heating. RNA quality was assessed using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit.

tag: diagonsis


title: RNA_CD8_Graves_rep16


title: RNA_CD8_Graves_rep14


title: RNA_CD8_Graves_rep13


title: gDNA_CD8_Graves_rep31


title: RNA_CD8_Graves_rep12


title: gDNA_CD8_Graves_rep32


title: gDNA_CD8_Graves_rep34

value: Male


title: gDNA_CD8_Graves_rep33


title: gDNA_CD8_Graves_rep35


title: gDNA_CD8_Graves_rep28


title: RNA_CD8_Graves_rep11


title: gDNA_CD8_Graves_rep27


title: gDNA_CD8_Graves_rep22


title: gDNA_CD8_Graves_rep24


title: gDNA_CD8_Graves_rep30


title: gDNA_CD8_Graves_rep26


title: gDNA_CD8_Graves_rep18


title: gDNA_CD8_Graves_rep23


title: gDNA_CD8_Graves_rep36


title: gDNA_CD8_Graves_rep13


title: gDNA_CD8_Graves_rep16


title: gDNA_CD8_Graves_rep21


title: gDNA_CD8_Graves_rep20


title: gDNA_CD8_Graves_rep15


title: gDNA_CD8_Graves_rep14


title: gDNA_CD8_Graves_rep17


title: gDNA_CD8_Graves_rep29


title: gDNA_CD8_Graves_rep19


title: RNA_CD8_Graves_rep6


title: gDNA_CD8_Graves_rep12


title: RNA_CD8_Graves_rep8


title: RNA_CD8_Graves_rep3


title: gDNA_CD8_Graves_rep25


title: RNA_CD8_Graves_rep10


title: RNA_CD8_Graves_rep7


title: RNA_CD8_Graves_rep5


title: RNA_CD8_Graves_rep2


title: RNA_CD8_Graves_rep1


title: RNA_CD8_Graves_rep4


title: RNA_CD8_Graves_rep9


title: RNA_CD8_Control_rep7

source_name: Total RNA, CD8, healthy control

value: Healthy


title: RNA_CD8_Control_rep5


title: RNA_CD8_Control_rep8


title: RNA_CD8_Control_rep4


title: RNA_CD8_Control_rep2


title: gDNA_CD8_Graves_rep11


title: RNA_CD8_Control_rep3


title: gDNA_CD8_Graves_rep5


title: gDNA_CD8_Graves_rep3


title: gDNA_CD8_Graves_rep4


title: RNA_CD4_Graves_rep15

source_name: Total RNA, CD4, Graves' patient

value: CD4 T cells


title: RNA_CD8_Control_rep1


title: gDNA_CD8_Graves_rep7


title: gDNA_CD8_Graves_rep2


title: RNA_CD8_Control_rep6


title: RNA_CD4_Graves_rep13


title: gDNA_CD8_Control_rep31

source_name: Genomic DNA, CD8 cells, healthy control


title: RNA_CD4_Graves_rep14


title: gDNA_CD8_Graves_rep10


title: gDNA_CD8_Graves_rep6


title: gDNA_CD8_Graves_rep8


title: RNA_CD4_Graves_rep12


title: gDNA_CD8_Control_rep26


title: gDNA_CD8_Control_rep24


title: gDNA_CD8_Graves_rep1


title: RNA_CD4_Graves_rep9


title: RNA_CD4_Graves_rep10


title: gDNA_CD8_Graves_rep9


title: gDNA_CD8_Control_rep25


title: gDNA_CD8_Control_rep29


title: gDNA_CD8_Control_rep30


title: RNA_CD4_Graves_rep8


title: RNA_CD4_Graves_rep11


title: gDNA_CD8_Control_rep28


title: RNA_CD4_Graves_rep7


title: RNA_CD4_Graves_rep6


title: gDNA_CD8_Control_rep27


title: gDNA_CD8_Control_rep23


title: gDNA_CD8_Control_rep22


title: RNA_CD4_Graves_rep5


title: gDNA_CD8_Control_rep21


title: RNA_CD4_Graves_rep1


title: gDNA_CD8_Control_rep19


title: RNA_CD4_Graves_rep3


title: gDNA_CD8_Control_rep18


title: RNA_CD4_Graves_rep4


title: RNA_CD4_Control_rep6

source_name: Total RNA, CD4, healthy control


title: RNA_CD4_Control_rep5


title: RNA_CD4_Control_rep8


title: RNA_CD4_Control_rep9


title: gDNA_CD8_Control_rep16


title: gDNA_CD8_Control_rep17


title: gDNA_CD8_Control_rep14


title: RNA_CD4_Control_rep3


title: RNA_CD4_Graves_rep2


title: RNA_CD4_Control_rep7


title: BEH-TBPH con 4

city: Gaithersburg

first: Leona

middle: Dance

last: Scanlan

state: MD

address: 100 Bureau Dr

institute: NIST

scan_protocol: 16-bit GenePix 4000B microarray scanner with 5-micron resolution and features, edited with GenePix Pro 6.0

data_processing: Regression analysis in GenePixPro, subsequent analysis as in Loguinov 2004, with a “Treatment vs. Control”  design. Global normalization with loess was applied to the data. The file log2_values_treatment_v_control.xlsx contains the normalized log2 ratios for each treatment vs control, summarized across the replicates.

organism: Daphnia magna

source_name: BEH-TBPH solvent (DMSO) control

label_protocol: as per Agilent Low-Input Quick-Amp one-color array kit and protocol. 200 ng total RNA starting material.

growth_protocol: Grew daphnids in COMBO growth medium. Fed and changed media three times per week; 8 hours dark and 16 hours light per day.

extract_protocol: Phenol and chloroform extraction (Trizol) with handheld homogenizer

treatment_protocol: Exposed to 1/10 LC50 concentrations of FR or to solvent control. Also exposed to four additional FM500 concentrations.

value: whole organism

tag: developmental stage

value: adult

value: 2 weeks old


title: gDNA_CD8_Control_rep13


title: gDNA_CD8_Control_rep20


title: RNA_CD4_Control_rep4


title: BEH-TBPH con 3

hyb_protocol: as per Agilent Low-Input Quick-Amp one-color array kit and protocol.


title: gDNA_CD8_Control_rep9


title: BEH-TBPH con 2


title: BEH-TBPH 4

source_name: BEH-TBPH exposed 0.091 mg/L


title: BEH-TBPH 3


title: BEH-TBPH 2


title: penta con 4

source_name: PentaBDE solvent (DMSO) control


title: gDNA_CD8_Control_rep3


title: gDNA_CD8_Control_rep8


title: gDNA_CD8_Control_rep6


title: gDNA_CD8_Control_rep4


title: gDNA_CD8_Control_rep12


title: BEH-TBPH 1


title: gDNA_CD8_Control_rep5


title: gDNA_CD8_Control_rep7


title: penta con 2


title: penta con 1


title: RNA_CD4_Control_rep10


title: gDNA_CD8_Control_rep15


title: penta 4

source_name: PentaBDE exposed 0.0058 mg/L


title: RNA_CD4_Control_rep1


title: gDNA_CD4_Graves_rep33

source_name: Genomic DNA, CD4 cells, Graves' patient


title: gDNA_CD8_Control_rep11


title: penta 3


title: RNA_CD4_Control_rep2


title: BEH-TBPH con 1


title: gDNA_CD4_Graves_rep29


title: gDNA_CD8_Control_rep1


title: gDNA_CD8_Control_rep2


title: gDNA_CD4_Graves_rep32


title: gDNA_CD4_Graves_rep34


title: penta 2


title: octa con 4

source_name: OctaBDE solvent (DMSO) control


title: gDNA_CD4_Graves_rep36


title: gDNA_CD4_Graves_rep30


title: gDNA_CD4_Graves_rep27


title: octa con 3


title: octa con 2


title: octa con 1


title: penta 1


title: penta con 3


title: octa 3

source_name: OctaBDE exposed 0.396 mg/L


title: octa 2


title: octa 4


title: BZ54 con 4

source_name: BZ54 solvent (DMSO) control


title: octa 1


title: BZ54 con 3


title: BZ54 con 2


title: gDNA_CD4_Graves_rep31


title: gDNA_CD4_Graves_rep28


title: BZ54 3

source_name: BZ54 exposed 0.05 mg/L


title: BZ54 con 1


title: gDNA_CD4_Graves_rep26


title: BZ54 4


title: BZ54 1


title: BEHP con 4

source_name: BEHP solvent (DMSO) control


title: BZ54 2


title: BEHP con 3


title: gDNA_CD8_Control_rep10


title: BEHP con 2


title: gDNA_CD4_Graves_rep25


title: gDNA_CD4_Graves_rep21


title: BEHP con 1


title: BEHP 4

source_name: BEHP exposed 0.331 mg/L


title: gDNA_CD4_Graves_rep23


title: BEHP 2


title: BEHP 3


title: gDNA_CD4_Graves_rep35


title: gDNA_CD4_Graves_rep22


title: gDNA_CD4_Graves_rep9


title: BEHP 1


title: gDNA_CD4_Graves_rep7


title: sip4-del-1-a

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: wild type

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: sip4-del-1-b


title: gDNA_CD4_Graves_rep3


title: gDNA_CD4_Graves_rep6


title: gDNA_CD4_Graves_rep5


title: gDNA_CD4_Graves_rep20


title: gDNA_CD4_Graves_rep10


title: TPhP con 3

source_name: TPhP solvent (DMSO) control


title: gDNA_CD4_Graves_rep8


title: gDNA_CD4_Graves_rep17


title: nrg2-del-1-b


title: gDNA_CD4_Graves_rep2


title: gDNA_CD4_Graves_rep18


title: gDNA_CD4_Control_rep31

source_name: Genomic DNA, CD4 cells, healthy control


title: gDNA_CD4_Graves_rep1


title: nrg2-del-1-a


title: nrg1-del-2-a


title: gDNA_CD4_Graves_rep15


title: nrg1-del-2-b


title: gDNA_CD4_Graves_rep16


title: gDNA_CD4_Graves_rep19


title: gDNA_CD4_Control_rep30


title: gDNA_CD4_Graves_rep13


title: gDNA_CD4_Graves_rep24


title: TPhP 3

source_name: TPhP exposed 0.053 mg/L


title: gDNA_CD4_Graves_rep12


title: gDNA_CD4_Graves_rep14


title: gDNA_CD4_Graves_rep11


title: TPhP con 2


title: gDNA_CD4_Control_rep27


title: TPhP 2


title: msn2-del-2-b


title: gDNA_CD4_Control_rep29


title: TPhP 1


title: msn2-del-2-a


title: gDNA_CD4_Control_rep26


title: gis1-del-1-b


title: gDNA_CD4_Graves_rep4


title: cat8-del-1-b


title: gDNA_CD4_Control_rep24


title: gDNA_CD4_Control_rep28


title: FM550 0.243 M4

source_name: FM550 exposed 0.243 mg/L


title: gDNA_CD4_Control_rep25


title: TPhP con 1


title: TPhP 4


title: FM550 0.243 M2


title: FM550 0.243 M3


title: FM550 0.243 M1


title: gDNA_CD4_Control_rep23


title: gis1-del-1-a


title: snt1-del-1-a

data_processing:
as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only  dye-bias corrections for yeast.
limma, A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth.    The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.


title: tod6-del-1-a


title: sum1-del-1-a


title: FM550 0.0486 M4

source_name: FM550 exposed 0.0486 mg/L


title: nhp6b-del-3-b


title: FM550 0.0486 M3


title: sum1-del-1-b


title: nhp6a-del-1-b


title: tod6-del-1-b


title: isw2-del-1-b


title: msn4-del-1-b


title: FM550 0.0486 M2


title: gDNA_CD4_Control_rep22


title: snt1-del-1-b


title: FM550 0.0486 M1


title: dot6-del-1-b


title: gDNA_CD4_Control_rep21


title: nhp6b-del-3-a


title: rph1-del-2-a


title: msn4-del-1-a


title: FM550 0.0486 U4

source_name: FM550 exposed 0.0486 μg/L


title: gDNA_CD4_Control_rep20


title: dot6-del-1-a


title: rph1-del-2-b


title: FM550 0.0486 U1


title: FM550 0.0486 U3


title: FM550 0.243 U4

source_name: FM550 exposed 0.243 μg/L


title: FM550 0.243 U3


title: FM550 0.0486 U2


title: FM550 0.243 U2


title: gDNA_CD4_Control_rep19


title: FM550 0.0486 N4

source_name: FM550 exposed 0.0486 ng/L


title: FM550 0.0486 N2


title: isw2-del-1-c


title: FM550 C4

source_name: FM550 solvent (DMSO) control


title: FM550 0.243 U1


title: gDNA_CD4_Control_rep18


title: FM550 C3


title: FM550 C2


title: gDNA_CD4_Control_rep14


title: FM550 0.0486 N1


title: FM550 C1


title: gDNA_CD4_Control_rep13


title: gDNA_CD4_Control_rep17


title: gDNA_CD4_Control_rep16


title: normal5 [miRNA]

description: Gene expression of adjacent normal tissue 5

hyb_protocol: miRNA microarrays Cy-3-labeled cRNA was hybridized according to the manual miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (version 2.4, September 2011) from Agilent Technologies.

data_processing: The scanned images were analyzed using Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters. The expression profiles was RMA normalized for miRNA expression data. Filtering of controls, unannotated genes and low expressed probes was done.

source_name: Fresh frozen tumor

label_protocol: miRNA was labeled with Cy-3 according to the manual miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (version 2.4, September 2011) from Agilent Technologies, using 200 ng total RNA as input.

value: adjacent normal tissue


title: normal4 [miRNA]

description: Gene expression of adjacent normal tissue 4


title: normal3 [miRNA]

description: Gene expression of adjacent normal tissue 3


title: normal6 [miRNA]

description: Gene expression of adjacent normal tissue 6


title: gDNA_CD4_Control_rep12


title: gDNA_CD4_Control_rep9


title: normal2 [miRNA]

description: Gene expression of adjacent normal tissue 2


title: gDNA_CD4_Control_rep11


title: normal1 [miRNA]

description: Gene expression of adjacent normal tissue 1


title: Duodenum_10 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 10

value: duodenal adenocarcinoma type


title: 171_preserved

city: Leiden

first: Wouter

middle: den

last: Hollander

address: Einthovenweg 20

department: Molecular Epidemiology

institute: LUMC

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Inhouse quality control pipeline, takes into account color bias and the different probe types.

label: Cy3 and Cy5

source_name: Preserved cartilage

label_protocol: standard Illumina protocol

extract_protocol: DNA was isolated using Promega Wizard Genomic DNA Purification kits

tag: joint

value: Hip

tag: Sex

value: Preserved cartilage


title: 221_preserved

value: Knee


title: Duodenum_9 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 9


title: gDNA_CD4_Control_rep10


title: gDNA_CD4_Control_rep7


title: gDNA_CD4_Control_rep1


title: gDNA_CD4_Control_rep4


title: Duodenum_8 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 8


title: 227_preserved


title: gDNA_CD4_Control_rep6


title: gDNA_CD4_Control_rep2


title: 227_lesioned

source_name: Lesioned cartilage

value: Lesioned cartilage


title: 216_lesioned


title: gDNA_CD4_Control_rep8

value: blood


title: FM550 0.0486 N3


title: gDNA_CD4_Control_rep3

value: Female


title: Duodenum_7 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 7


title: Duodenum_6 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 6


title: 131_lesioned


title: gDNA_CD4_Control_rep5


title: 170_preserved


title: Ly6Cmed myeloid cells 24h incisional wound replicate 3

city: Kingston

first: Nader

last: Ghasemlou

state: Ontario

address: 18 Stuart Street, room 754

country: Canada

institute: Queen's University

description: Gene expression data from CD11b+Ly6G-Ly6Cmed cells

hyb_protocol: Affymetrix GeneChip Hybridization control kit and the Affymetrix GeneChip Hybridization, wash, stain kit was used to hybridize samples to Affymetrix Mouse Gene ST 2.0 GeneChips, fluidics performed on the Affymetrix Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 7G (Affymetrix).

data_processing: The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cells sorted from plantar portion of the hindpaw, 24h after incision

label_protocol: RNA was amplified into cDNA using the Applause WT-Amp ST System expression kit (NuGEN), with Poly-A controls from the Affymetrix Genechip Eukaryotic Poly-A RNA control kit (Affymetrix, Santa Clara, CA, USA). The Affymetrix Genechip WT Terminal labeling kit was used for fragmentation and biotin labeling.

extract_protocol: Cells were sorted directly into QIAzol and then snap-frozen. RNA was extracted using the RNEasy Lipid Tissue kit, per manufacturer's protocol.

treatment_protocol: 24h after incisional wound in C57BL/6 mice, the plantar hindpaw was removed and a single-cell suspension made of the cells. Cells were sorted by flow cytometry to select for CD11b+Ly6G- cells, and then classified by Ly6C expression.

value: male

value: 8 weeks old

tag: sorted cells

value: Ly6C med


title: 216_preserved

tag: tissue


title: Ly6Cmed myeloid cells 24h incisional wound replicate 2


title: Duodenum_4 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 4


title: 131_preserved

value: Male


title: 170_lesioned


title: 135_preserved


title: Ly6Clow myeloid cells 24h incisional wound replicate 3

description: Gene expression data from CD11b+Ly6G-Ly6Clow cells

value: Ly6C low


title: Ly6Cmed myeloid cells 24h incisional wound replicate 1


title: Duodenum_3 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 3


title: Duodenum_5 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 5


title: gDNA_CD4_Control_rep15

value: CD4 T cells

value: Healthy


title: Duodenum_1 [miRNA]

description: Gene expression of fresh frozen duodenal adenocarcinoma type patient 1


title: Ly6Clow myeloid cells 24h incisional wound replicate 2


title: ampullaI_6 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 6

value: ampulla intestinal type


title: Ly6Clow myeloid cells 24h incisional wound replicate 1


title: 213_lesioned


title: ampullaI_4 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 4


title: ampullaI_7 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 7


title: 221_lesioned


title: ampullaI_3 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 3


title: 171_lesioned


title: ampullaI_2 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 2


title: ampullaI_1 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 1


title: Ly6Chi myeloid cells 24h incisional wound replicate 3

description: Gene expression data from CD11b+Ly6G-Ly6Chi cells

value: Ly6C high


title: 213_preserved

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits


title: 135_lesioned


title: ampullaP_7 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 7

value: ampulla pancreatobiliary type


title: ampullaI_5 [miRNA]

description: Gene expression of fresh frozen ampulla intestinal type patient 5


title: ampullaP_6 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 6


title: ampullaP_8 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 8


title: Ly6Chi myeloid cells 24h incisional wound replicate 1


title: 126_lesioned


title: Ly6Chi myeloid cells 24h incisional wound replicate 2


title: ampullaP_4 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 4


title: ampullaP_3 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 3


title: ampullaP_5 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 5


title: 122_lesioned


title: ampullaP_2 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 2


title: ampullaP_1 [miRNA]

description: Gene expression of fresh frozen ampulla pancreatobiliary type patient 1


title: bileduct_7 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 7

value: bile duct adenocarcinoma


title: bileduct_8 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 8


title: 122_preserved


title: 212_preserved


title: 212_lesioned


title: bileduct_6 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 6


title: bileduct_5 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 5


title: bileduct_4 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 4


title: 103_lesioned


title: bileduct_3 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 3


title: 125_preserved


title: bileduct_2 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 2


title: 125_lesioned

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits


title: 103_preserved


title: 207_lesioned


title: 198_lesioned

value: Hip


title: PDAC_52 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 52

value: pancreatic ductal adenocarcinoma


title: 98_lesioned


title: bileduct_1 [miRNA]

description: Gene expression of fresh frozen bile duct adenocarcinoma patient 1


title: PDAC_51 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 51


title: PDAC_50 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 50


title: 98_preserved

value: Preserved cartilage


title: 207_preserved

value: Knee


title: 89_preserved


title: 198_preserved


title: 89_lesioned

value: Lesioned cartilage


title: PDAC_48 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 48


title: PDAC_47 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 47


title: PDAC_46 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 46


title: PDAC_49 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 49


title: 185_lesioned


title: PDAC_45 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 45


title: 185_preserved


title: 86_lesioned

value: Female


title: 86_preserved


title: PDAC_43 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 43


title: 181_lesioned


title: 244_preserved


title: 245_lesioned


title: 81_preserved


title: PDAC_42 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 42


title: PDAC_40 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 40


title: PDAC_41 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 41


title: PDAC_38 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 38


title: 245_preserved


title: 81_lesioned


title: PDAC_39 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 39


title: 181_preserved


title: PDAC_44 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 44


title: 244_lesioned

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits


title: PDAC_36 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 36


title: 180_preserved


title: PDAC_35 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 35


title: 180_lesioned


title: PDAC_37 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 37


title: PDAC_33 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 33


title: 237_lesioned


title: PDAC_32 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 32


title: PDAC_31 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 31


title: PDAC_29 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 29


title: PDAC_34 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 34


title: PDAC_28 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 28


title: PDAC_30 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 30


title: 78_lesioned


title: 233_lesioned


title: PDAC_24 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 24


title: PDAC_23 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 23


title: 237_preserved


title: 78_preserved


title: PDAC_19 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 19


title: PDAC_20 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 20


title: 159_lesioned


title: 158_lesioned


title: PDAC_16 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 16


title: PDAC_18 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 18


title: PDAC_27 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 27


title: PDAC_17 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 17


title: 126_preserved

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits


title: 159_preserved


title: PDAC_22 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 22


title: PDAC_21 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 21


title: PDAC_25 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 25


title: PDAC_13 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 13


title: PDAC_14 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 14


title: 233_preserved


title: 77_lesioned


title: PDAC_26 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 26


title: PDAC_12 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 12


title: PDAC_11 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 11


title: 77_preserved


title: PDAC_15 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 15


title: 158_preserved


title: PDAC_9 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 9


title: PDAC_10 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 10


title: PDAC_8 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 8


title: PDAC_6 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 6


title: HLE_449abc_2

city: Hannover

first: Maria

last: Sandbothe

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

hyb_protocol: 0.6 µg Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in fragmentation buffer and blocking agent (both Agilent) following the manufacturer’s instructions. Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture. Samples were hybridized to SurePrint G3 Human Gene Expression v2 8x60K Microarrays (Agilent) for 17 hours at 65°C in a rotating 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the profile „AgilentHD_GX_1Color“ (Scan area 61x21.6 mm, resolution 3 µm).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain processed signal intensities.

source_name: HLE, 50nM miR-449abc, 48h, replicate 2

label_protocol: RNA of three biological replicates per microarray was pooled. 50 ng of pooled RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent) following the manufacturer’s instructions. Cy3-labeling efficiency was analyzed utilizing a nanophotometer.

growth_protocol: The HCC cell line HLE was cultured in DMEM containing 10% FCS, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin.

extract_protocol: To isolate RNA, cells were lysed in Qiazol Lysis Reagent and total RNA including miRNAs was isolated with the miRNeasy Mini Kit (both Qiagen). RNA quality was routinely determined using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: For transient overexpression of miRNAs, cells were transfected with 50 nM miScript miRNA mimics (Qiagen, Hilden, Germany). MiRNA mimics for miR-449a, miR-449b, and miR-449c were either single transfected or cotransfected in equimolar amounts (16.7 nM each).  For transfection, HiPerFect Transfection Reagent (Qiagen) was used and Allstars Negative Control (Qiagen) served as negative control.

tag: cell line

value: HLE

value: hepatocellular carcinoma

tag: construct


title: PDAC_4 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 4


title: 73_lesioned


title: PDAC_2 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 2


title: PDAC_5 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 5


title: PDAC_3 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 3


title: PDAC_7 [miRNA]

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 7


title: HLE_449c_2

source_name: HLE, 50nM miR-449c, 48h, replicate 2

tag: cell type


title: HLE_449abc_1

source_name: HLE, 50nM miR-449abc, 48h, replicate 1


title: HLE_449a_2

source_name: HLE, 50nM miR-449a, 48h, replicate 2


title: HLE_449c_1

source_name: HLE, 50nM miR-449c, 48h, replicate 1


title: Treated_replicate2

status: Public on Nov 05 2015

city: Chicago

first: Douglas

middle: David

last: Thomas

state: IL

address: 900 S Ashland Ave Room 3306

department: Medicinal Chemistry & Pharmacognosy

institute: University of Illinois at Chicago

description: Sample name: mRNA_D3

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining using fluidics script FS450_0002.

scan_protocol: Microarray chips were read on the GeneChip® Scanner 3000 7G with AGCC version 4.0.0.1567.

data_processing: RMA in affy R package

label_protocol: Samples were labeled using the Affymetrix GeneChip® 3' IVT Expression Kit as per manufacturer's protocols.

growth_protocol: MDA-MB-231 human triple negative breast cancer cells were obtained from American Type Culture Collection (ATCC) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a controlled environment (37°C and 5% CO2).

extract_protocol: RNA was extracted using the RNAqueous 4PCR kit (Ambion) as per manufacturer's protocols.

treatment_protocol: For conducting experiments, cells were grown to 80% confluency and serum starved overnight prior to treatment with 500uM DETA/NO for 24 hours.

value: triple negative breast adenocarcinoma

tag: agent

value: DETA/NO


title: HLE_449b_2

source_name: HLE, 50nM miR-449b, 48h, replicate 2


title: HLE_449b_1

source_name: HLE, 50nM miR-449b, 48h, replicate 1


title: HLE_NC_2

source_name: HLE, 50nM Allstars Negative Control, 48h, replicate 2

value: negative control


title: Untreated_replicate2

description: Sample name: mRNA_C2

value: control


title: 73_preserved

description: DNA was BS treated using Zymo EZ-96 DNA Methylation kits


title: Treated_replicate1

description: Sample name: mRNA_D2


title: HLE_449a_1

source_name: HLE, 50nM miR-449a, 48h, replicate 1


title: HLE_NC_1

source_name: HLE, 50nM Allstars Negative Control, 48h, replicate 1


title: Cell_WSN_DMSO_12h_rep1

city: fuzhou

first: xiaojuan

last: chi

address: cangshan NO:15

institute: Fujian Agriculture and Forestry University

description: Gene expression of WSN infected cells treated with DMSO for 12h

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cells, WSN infection, DMSO 12h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent p/n 5190-2305)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-2000 Spectrophotometer.

growth_protocol: A549 cells were maintained in Dulbecco’s modified Eagle’s medium(DMEM) containing 10% fetal calf serum(FCS) supplemented with penicillin (100U/ml) and streptomycin (100μg /ml) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: A549 cells infected with WSN virus were treated with or without the compound L435 (0.2 ug/ml) for 12 h.

tag: treatment


title: Cell_WSN_DMSO_12h_rep2

source_name: cells, WSN infection, DMSO 12h, replicate 2

value: WSN infected cells treated with DMSO for 12h


title: Cell_WSN_DMSO_12h_rep3

source_name: cells, WSN infection, DMSO 12h, replicate 3


title: Untreated_replicate1

description: Sample name: mRNA_C1


title: rodZ/pCA24N vs. rodZ/pCA24N-RodZ

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

description: Biological replication 1 of 1

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

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

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).

organism: Escherichia coli

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).

growth_protocol: Overnight cultures were inoculate in 250 ml of LB medium for OD600=0.5

extract_protocol: After culturing each cells, bacterial cells were distrupted with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) and Rnase free-DNase I treatment (Qiagen)

treatment_protocol: And then, cells were exposed to 1 mM IPTG for additional 6 h.

tag: strain

tag: genotype/variation

value: rodZ gene deleted mutant

tag: transfection

value: empty vector pCA24N

value: pCA24N-RodZ for RodZ overexpression


title: Cell_WSN_L435_12h_rep2

description: Gene expression of WSN infected cells treated with L435 for 12h

source_name: cells, WSN infection, L435 12h, replicate 2


title: non-treated control_4h

city: Chiba

first: Toshio

last: Hattori

address: 2-870-1, Sakaecho-Nishi, Matsudo

department: Maxillofacial Surgery

institute: Nihon University School of Dentistry at Matsudo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) 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 (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: temporomandibular joint, synovium, 4hr, 0 ng/ml

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.

extract_protocol: Total cellular RNA from FLS was extracted using the RNeasy Mini Kit, (Qiagen, Valencia, CA, USA), and was then stored at -80 °C until use.

value: synovium

tag: gender

value: female


title: Cell_Mock_rep2

description: Gene expression of mock infected cells

source_name: cells, Mock, replicate 2

value: mock infected cells


title: Cell_Mock_rep1

description: Gene expression of mock infected cells

source_name: cells, Mock, replicate 1


title: Cell_Mock_rep3

description: Gene expression of mock infected cells

source_name: cells, Mock, replicate 3


title: Mutant_males_RT_In(1)BM2(reinverted)_replicate 2

city: Pune

first: Priyanka

last: Guru

address: Ganeshkind road

department: Interdisciplinary School of Health Sciences

country: India

institute: Savitribai Phule Pune University

description: Gene expression in In(1)BM2(reinverted) males at room temperature  (24°C±1)

hyb_protocol: Cy3 labelled cRNA was fragmented and hybridized onto oligonucleotide-based whole genome DNA microarrays (Drosophila, 4x44 K, Agilent Technologies, Palo Alto, CA) for 16 hours at 65°C.The arrays were subsequently washed with gene expression wash buffers according to the manufacturer’s hybridization protocol (Agilent Oligo Microarray Kit, Agilent Technologies,CA).

scan_protocol: The slides were scanned with Agilent microarray scanner (G2505B) using one colour scan setting for 4x44 K array slides (scan resolution 5μm, dye channel was set to green, green PMT was set to 100%).

data_processing: The images were processed with Agilent’s feature extraction software (10.5)(Agilent, Palo Alto, CA). GeneSpring GX 11.0 Software was used for normalization. Percentile shift normalization was used.

organism: Drosophila melanogaster

source_name: In(1)BM2(reinverted) males, room temperature, replicate 2

label_protocol: Cy3 labelled cRNA was prepared using Agilent Quick-Amp labelling Kit (Agilent, Palo Alto, CA).

growth_protocol: Flies were reared on standard corn-yeast-molases medium at 24°C

extract_protocol: RNA was extracted from 15 males using the TRIzol method followed by purification using RNeasy mini kit (Qiagen, Germany).

treatment_protocol: Exposure to cold shock at 12±1°C for 4 hours

value: adult flies

value: male


title: BW25113 WT/pCA24N vs. rodZ/pCA24N

description: Biological replication 1 of 1

source_name: BW25113 WT/pCA24N

value: control strain


title: Cell_WSN_L435_12h_rep3

source_name: cells, WSN infection, L435 12h, replicate 3

value: WSN infected cells treated with L435 for 12h


title: Wild_type_male_RT_Oregon R_replicate1

description: Gene expression in Oregon R males at room temperature (24°C±1)

source_name: Oregon R males, room temperature, replicate 1

value: Oregon R


title: Mutant_males_RT_In(1)BM2(reinverted)_replicate 1

source_name: In(1)BM2(reinverted) males, room temperature, replicate 1


title: Wild_type_male_RT_Oregon R_replicate2

source_name: Oregon R males, room temperature, replicate 2


title: Mutant_males_CS_In(1)BM2(reinverted)_replicate 1

description: Gene expression in In(1)BM2(reinverted) males after 4 hours cold shock at 12°C±1

source_name: In(1)BM2(reinverted) males, cold shock, replicate 1


title: treated with IL-17A _4h

source_name: temporomandibular joint, synovium, 4hr, 10 ng/ml IL-17A

tag: age


title: Wild_type_male_CS_Oregon R_replicate1

description: Gene expression in Oregon R males after 4 hours cold shock at 12°C±1

source_name: Oregon R males, cold shock, replicate 1


title: 282_C

city: Columbus

first: Hamdy

last: Awad

state: Ohio

address: 410 W 10th Avn.

department: Anesthesiology

institute: Ohio State University

description: Gene expression in caudal region of spinal cord 24 hours after aortic cross clamping

hyb_protocol: Labeled cRNA targets were hybridized to Affymetrix GeneChip® Mouse Genome 430 array for 16 h at 45 °C rotating at 60rpm. The arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: Arrays were scanned using the using the GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were imported to the BRB-Arraytools software developed by Dr. Richard Simon and the BRB-Arraytools Development team, normalized using the robust multichip analysis (RMA) procedure and log 2 transform.

source_name: Spinal cord 24 hours post aortic cross clamping caudal region

label_protocol: A 2ug aliquot of total RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences). Then, 15ug of labeled cRNA was fragmented following the manufacturer's instructions.

growth_protocol: Wild-type C57Bl/6 mice 10-12 weeks old, obtained from Jackson Laboratories were housed at the Ohio State University Animal Facility with food and water available ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were submitted to either sham-surgery or aortic cross-clamping for 7.5 minutes.

value: Spinal cord


title: Cell_WSN_L435_12h_rep1

source_name: cells, WSN infection, L435 12h, replicate 1


title: 282_R

description: Gene expression in rostral region of spinal cord 24 hours after aortic cross clamping

source_name: Spinal cord 24 hours post aortic cross clamping rostral region


title: Mutant_males_CS_In(1)BM2(reinverted)_replicate 2

source_name: In(1)BM2(reinverted) males, cold shock, replicate 2


title: 281_R


title: 283_R


title: Wild_type_male_CS_Oregon R_replicate2

source_name: Oregon R males, cold shock, replicate 2


title: 281_C


title: 283_C


title: Treated_replicate2

description: Sample name: miRNA_D2

hyb_protocol: The GeneChip® Hybridization, Wash, and Stain Kit was used as per manufacturer’s protocols. The GeneChip® Fluidics Station 450 was used for washing and staining with fluidics script FS450_0002.

data_processing: RMA  in Partek

label_protocol: Samples were labeled using the Affymetrix FlashTag™ Biotin HSR RNA Labeling Kit as per manufacturer's protocols.

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen) as per manufacturer's protocols.

value: triple negative breast adenocarcinoma


title: hESC-CM_2Hz_rep1

city: New York

first: Gordana

last: Vunjak-Novakovic

state: NY

department: Biomedical Engineering

institute: Columbia University

description:
replicate 1
111836_2A

data_processing: The data were normalized using quantile scrunch algorithm after Illumina background subtraction by Expression Analysis Inc. (Durham, NC)

source_name: ESC derived cardiomyocytes

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

growth_protocol: Cardiomyocytes were differentiated from human embryonic stem cells as embryoid bodies for 23 days and electrically stimulated for 7 days prior to sample collection

extract_protocol: Cardiomyocytes were flash frozen and sent to Expression Analysis Inc. (Durham, NC) for total RNA extraction and quality control

treatment_protocol: Cardiomyocytes were either unstimulated (control) or stimulated continuously with a 5 V/cm, 2 ms duration pulse at 0.5 Hz, 1 Hz, or 2 Hz for 7 days

value: 30 days

tag: stimulation


title: hESC-CM_1Hz_rep3

description:
replicate 3
111835_1C


title: 280_C

description: Gene expression in caudal of sham mice (surgery but not aortic cross clamping)

source_name: Spinal cord sham caudal region


title: hESC-CM_2Hz_rep3

description:
replicate 3
111838_2C


title: Treated_replicate3

description: Sample name: miRNA_D3

value: DETA/NO


title: 279_R

description: Gene expression in rostral of sham mice (surgery but not aortic cross clamping)

source_name: Spinal cord sham rostral region


title: 278_C


title: 280_R


title: Treated_replicate1

description: Sample name: miRNA_D1


title: hESC-CM_2Hz_rep2

description:
replicate 2
111837_2B


title: 278_R


title: 279_C


title: 277_R


title: hESC-CM_1Hz_rep1

description:
replicate 1
111833_1A


title: Untreated_replicate3

description: Sample name: miRNA_C4

value: control


title: 274_R

description: Gene expression in rostral region of spinal cord 48 hours after aortic cross clamping

source_name: Spinal cord 48 hours post aortic cross clamping rostral region


title: hESC-CM_0.5 Hz_rep3

description:
replicate 3
111832_0.5 C


title: hESC-CM_0.5Hz_rep1

description:
replicate 1
111830_0.5 A


title: 272_C

description: Gene expression in caudal region of spinal cord 48 hours after aortic cross clamping

source_name: Spinal cord 48 hours post aortic cross clamping caudal region


title: 06_KO mTEC

city: Bunkyo

first: Hiroyuki

last: Takaba

state: Tokyo

department: Immunology

institute: University of Tokyo

description: 06_KO mTEC

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CD45-,EpCAM+,CD80hi mTECs sorted from Fezf2 KO thymus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001,Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. (QIAGEN RNeasy)

tag: strain background

value: 3 weeks

value: Fezf2 KO

value: thymus

value: CD45-,EpCAM+,CD80hi Medullary thymic epithelial cells (mTECs)


title: hESC-CM_control_rep3

description:
replicate 3
111829_Con C

value: unstimulated


title: Untreated_replicate2

description: Sample name: miRNA_C3


title: 274_C


title: 272_R


title: Untreated_replicate1

description: Sample name: miRNA_C1


title: 10_KO mTEC

description: 10_KO mTEC


title: colon epithelial cell_CEC-TSC1 KO_DSS_rep1

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

description: mRNAs expression in colon epithelial cells from CEC-TSC1 KO mice treated with DSS for 7 days

hyb_protocol: For hybridization, each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Cat#5188-5242, Agilent) in a Hybridization Oven (Cat#G2545A, Agilent), according to the manufacturer’s instructions.

scan_protocol: After 17 h of hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with a Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent), following the manufacturer’s instructions. Slides were scanned by an Agilent Microarray Scanner (Cat#G2565CA, Agilent) with the following default settings: dye channel, green; scan resolution, 5 μm; PMT 100%, 10%, 16 bit.

data_processing: For data acquisition, data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by the Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: colon epithelial cell, TSC1 KO in CECs, DSS treatment for 7 days, rep1

label_protocol: For RNA amplification and labeling, total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified with an RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Female floxed TSC1 mice (TSC1FL/FL) containing LoxP sites flanking exons 17 and 18 of the TSC1 gene were crossed with male carbonic anhydrase 1 (CA1)-Cre mice, whose expression of Cre recombinase is under control of the CA1 promoter and limited to the epithelial cells of the cecum and colon. The resulting CA1-Cre; TSC1FL/FL (CEC-TSC1 KO) mice are hemizygous for the CA1-Cre transgene and homozygous for the floxed TSC1 allele. All animals were backcrossed for 8 generations onto the C57BL/6 background.

extract_protocol: total RNA of colon epithelial cells from 3 mice were extracted with TRIZOL Reagent and pooled together.

treatment_protocol: Wile type or CEC-specific TSC1 KO mice (about 8-weeks) were treated by 3% dextran sulfate sodium (DSS) FOR 7 days. The mice with resultant colitis were then sacrificed and harvested for colon epithelial cells.

tag: background strain

value: epithelial cell

value: colon

tag: genotype

value: TSC1 KO


title: 276_R


title: 273_C


title: hESC-CM_0.5Hz_rep2

description:
replicate 2
111831_0.5 B


title: 07_KO mTEC

description: 07_KO mTEC


title: hESC-CM_1Hz_rep2

description:
replicate 2
111834_1B


title: 271_C


title: hESC-CM_control_rep2

description:
replicate 2
111828_Con B


title: 09_KO mTEC

description: 09_KO mTEC


title: 273_R


title: hESC-CM_control_rep1

description:
replicate 1
111827_Con A


title: 05_WT mTEC

description: 05_WT mTEC

source_name: CD45-,EpCAM+,CD80hi mTECs sorted from WT thymus

value: wild type


title: 08_KO mTEC

description: 08_KO mTEC


title: H19 deleted ahESC line-2 vs OG-3

city: Beijing

first: Meili

last: Zhang

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: CGH analysis of H19Δ2vs OG-3

hyb_protocol: Hybridization was processed for 40 hr at 65℃ in Agilent hybridization system.  Genechips were washed in 2×SSC (0.2% SDS) at  42 ℃ and in 0.2×SSC at room temperature.

scan_protocol: Arrays were scanned on the Agilent G2565CA Microarray Scanner.

data_processing: The images were processed using Agilent Feature Extraction software (v10.10), which transformed the image signal to digital signal. The data was analyzed using Agilent Genomic Workbench  Software.

source_name: androgenetic haploid ES cells, control

label_protocol: The gDNA samples were labelled using a Agilent SureTag Complete DNA Labeling Kit (5190-4240). Genomic DNA from control sample was lablled with Cy3-dCTP, and DNA from experimental samples were lablled with Cy5-dCTP.

growth_protocol: The cells were cultured in ESC medium supplemented with 15% fetal bovine serum, 1,000 U/ml leukemia inhibitory factor (LIF), 3 M CHIR99021, and 1 M PD0325901.

extract_protocol: Genomic DNA  was extracted using the Wizard Genomic DNA Purification Kit (Promega, A1120) according to the manufacturer’s instructions.

treatment_protocol: ES cells were cultured under normal culture conditions and dissociated with 0.05% Trypsin-EDTA. The harvested cells were then allowed to sit in tissue culture plates for 30-40 min to deplete the feeder cells.

tag: karyotype

value: haploid

value: haploid embryonic stem cells from androgenetic blastocysts (ahESCs)

source_name: H19 deleted (H19Δ) ahESCs


title: 271_R


title: 04_WT mTEC

description: 04_WT mTEC


title: 03_WT mTEC

description: 03_WT mTEC


title: 02_WT mTEC

description: 02_WT mTEC