title: Forward Trans Expt 2 - MBY38 + Dox 6 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 6 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 2 - MBY38 + Dox 5 hrs

status: Public on Dec 12 2012

type: RNA

city: San Antonio

first: David

last: Kadosh

state: TX

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

country: USA

institute: University of Texas Health Science Center at San Antonio

description: No additional information.

hyb_protocol: Sample Hybridization Protocol Other: Hybridization was performed by adding 48 uL of secondary hybridization solution to the slide under a supported glass coverslip and carried out at 65 C for 3 hr. at high humidity in the dark. At hybridization termination, arrays were gently submerged into 2X SSC, 0.2% SDS (at 65 C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. To prevent fluorophore degradation, the arrays were treated with Dyesaver (Genisphere).

scan_protocol: ScanArray Scanning Protocol Other: Arrays were scanned using a ScanArray Express HT (Serial No.: 680078) microarray scanner along with ScanArray Express 2.00 image analysis software.

data_processing:
Forward Transition Expt Data Processing
Calculation Method: Microarray data was normalized using the Lowess method (Y.H. Yang, 2001) and filtered using Partek software to only include spots showing a median signal intensity >200 and signal-to-noise ratio >2. The forward yeast-pseudohyphal-hyphal transition time course experiment was repeated twice (two independent biological replicates). For each biological replicate experiment, the median signal ratio (ratio of the median signal intensity of each spot) for the zero time point versus reference was first determined based on 3 technical replicates (one of which was performed using reverse fluors) using cDNA from the same total RNA preparation. Next, the signal ratio for each time point sample versus reference was divided by the median signal ratio for the zero time point versus reference.

molecule: total RNA

organism: Candida albicans

source_name: Forward Transition Expt - Cy3 Reference Sample

label_protocol:
Cy3 Labeling Protocol
Other: Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 uL), 3DNA capture reagent with Cy5 (2.5 uL), SDS-based hybridization buffer (vial 6-Genisphere) (26 uL), and RNase/DNnase-free water (21 uL). The secondary hybridization solution was incubated in the dark at 80 C for 10 min., then at 50 C for 15 min.

extract_protocol:
Hot Acid Phenol Extraction Protocol
Other: RNA was isolated from C. albicans cells using the hot acid phenol method. Total RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.

tag: strain

tag: genotype/variation

tag: other

value: Forward Transition Pooled Reference:Equal aliquots of the 21 sample RNAs (Dox dosage of 1.0 ug/ml (n=11) or 0 ug/ml (n=10) at time points from 0 to 10 hours) were combined to create a pooled reference sample.

source_name: Forward Transition Expt - MBY38 + Dox 5 hrs - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 uL), 3DNA capture reagent with Cy5 (2.5 uL), SDS-based hybridization buffer (vial 6-Genisphere) (26 uL), and RNase/DNnase-free water (21 uL). The secondary hybridization solution was incubated in the dark at 80 C for 10 min., then at 50 C for 15 min.

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 2 - MBY38 + Dox 8 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 8 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 2 - MBY38 + Dox 7 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 7 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 2 - MBY38 + Dox 3 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 3 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 2 - MBY38 + Dox 2 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 2 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 D8 Acute  3

city: Philadelphia

first: Alison

last: Crawford

state: PA

address: 421 Curie Blvd, BRB

department: Microbiology

institute: University of Pennsylvania

description: 3265_14042B_4CD4A8 _MoGene1.0ST

hyb_protocol: Hybridization was performed on Affymetrix hybridization oven 640 for 16 hours.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector.

label: biotin

organism: Mus musculus

source_name: CD4 D8 Acute

label_protocol: RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

extract_protocol: LCMV-specific CD8 T cells were FACS-purified based on CD8+, CD4-, CD44hi, DbGP33-41 tetramer. LCMV-specific CD4 T cells were FACS-purified based on CD8-, CD4+, CD44hi, I-Ab66-77 tetramer. Cells were sorted directly into TRIzol LS. RNA was isolated by phenol chloroform extraction. Concentrations of total RNA were determined using a Nanodrop spectrophotometer

treatment_protocol: C57BL/6J mice were infected with LCMV Armstrong or LCMV clone 13. At various days post infection, LCMV-specific CD4 and CD8 T cells were purified on a BD Aria sorter.

tag: tissue

value: spleen


title: CD4 D15 Acute

description: 3265_14043_1C4A15 _MoGene1.0ST

source_name: CD4 D15 Acute


title: tomato fruits_Lycb-1 transgenic_rep1

city: wuhan

first: Fei

last: Guo

address: shizishan

country: China

institute: Huazhong Agricultural Univesity

hyb_protocol: The labelled cDNA was hybridized overnight with the microarray at 42ºC.

scan_protocol: The arrays were scanned with a LuxScan 10KA confocal laser scanner. Images analysed by ImaGene image analysis software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Solanum lycopersicum

source_name: Lycb-1 transgenic ripe fruits

label_protocol: Total RNA (5µg) and T7-Oligo (dT)15 (Boya, China) was employed to reverse transcribe double-stranded cDNA, using a DNA Synthesis kit (Promega, USA), and then transcribed into cRNA using the T7 RiboMAX Express Large Scale RNA Production System (Promega, USA). A 2µg aliquot of cRNA was combined with random primer 9 (New England Biolabs, USA) and 200µ/µl M-MLV (Invitrogen, USA) to synthesize produce cDNA. Finally, a 2µg sample of the cDNA was combined with Klenow polymerase (Takara, Japan), random primer 9, and final concentrations of 120 µM dATP, dGTP and dTTP, 60µM dCTP and 40 µM of both Cy5- and Cy3-dCTP, to produce Cy5/Cy3-labelled cDNA.

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

value: ripe fruits

value: Lycb-1 transgenic

source_name: Wild type ripe fruits

value: Wild type


title: Forward Trans Expt 2 - MBY38 + Dox 0 hrs - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Forward Transition Expt - Cy5 Reference Sample

source_name: Forward Transition Expt - MBY38 + Dox 0 hr - Cy3

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 D8 Acute  2

description: 3265_14042A_4CD4A8 _MoGene1.0ST


title: CD4 D15 Acute  3

description: 3265_14046_4C4A15 _MoGene1.0ST


title: Forward Trans Expt 2 - MBY38 + Dox 4 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 4 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 D8 Acute  1

description: 3265_14041_3CD4A8 _MoGene1.0ST


title: tomato fruits_Lycb-1 transgenic_rep2


title: CD4 D15 Acute  1

description: 3265_14044_2C4A15 _MoGene1.0ST


title: CD4 D15 Acute  2

description: 3265_14045_3C4A15 _MoGene1.0ST


title: tomato fruits_Lycb-1 transgenic_rep3


title: Forward Trans Expt 2 - MBY38 + Dox 1 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 1 hr - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 D6 Acute  2

description: 3265_14037_3CD4A6 _MoGene1.0ST

source_name: CD4 D6 Acute


title: Forward Trans Expt 2 - MBY38 + Dox 0 hrs - repeat 1

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 0 hr - Cy5


title: CD4 D8 Acute

description: 3265_14040_2CD4A8 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + no Dox 10 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 10 hrs - Cy5

treatment_protocol:
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 D6 Acute  1

description: 3265_14036_2CD4A6 _MoGene1.0ST


title: Low zinc replicate 3 array 1

city: Columbus

first: Amanda

middle: Jane

last: Bird

state: OH

address: 1787 Neil Avenue

department: Human Nutrition and Molecular Genetics

institute: The Ohio State University

hyb_protocol: Arrays hybridized with unlabelled total RNA at 65C for 17 hours, washed, then labeled with primary mouse monoclonal anti-RNA/DNA hybrid antibody, washed again, and finally labeled using Cy3-labeled goat anti-mouse antibody.

scan_protocol: Arrays scanned on an Agilent G2505B scanner at 5 micron resolution

data_processing: Image data processed in Agilent Feature Extraction software version 9.5.1.1, which provides spatially-detrended intensity data for each feature.

organism: Schizosaccharomyces pombe

source_name: S. pombe grown in low zinc conditions

label_protocol: See hybridization protocol.

growth_protocol: S. pombe was grown to exponential phase in Edinburgh minimal medium before transfer to a zinc-limiting medium (LZM) that contained a 0.003 mM zinc supplement (low zinc or LZM3) or a 3 mM zinc supplement (high zinc or LZM3000).  LZM contains the metal ion chelators EDTA and Na Citrate (see Zhao and Eide, (1997), Mol. Cell, Biol. 17:5044-5052 for more details.

extract_protocol: Total RNA was extracted using hot acidic phenol.

treatment_protocol: Cells were grown in LZM with the appropriate zinc supplement for 4 hrs before harvesting.

tag: zinc concentration

value: low zinc or LZM3


title: Forward Trans Expt 2 - MBY38 + Dox 0 hrs - repeat 2

description: No additional information.

source_name: Forward Transition Expt - Cy3 Reference Sample


title: Toxin_r1

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
TOX_1
4514

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: The data were analyzed with dCHIP

organism: Homo sapiens

source_name: toxin treated_500ng/mL_4hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip 3' IVT Express Kit Affymetrix).

growth_protocol: Whole blood was collected by venous puncture from healthy human volunteers into 8mL vacutainer tubes containing Ficoll (BD Biosciences). The study followed US Department of Health and Human Services guidelines and was approved by the University of Florida Institutional Review Board. Whole blood was incubated with a monocyte negative selection antibody (Stem Cell Technologies) for 20 min., centrifuged 1700 x g for 25 minutes at RT, no brake over Ficoll, re-suspended in 10mL RPMI (Mediatech) complete media, centrifuged at 250 x g for 9 min. to remove platelets,  and re-suspended to 7-9 x 105 cells/mL in RPMI.

extract_protocol: Total RNA was harvested using the RNeasy RNA Isolation kit  standard protocol (Qiagen, Valencia, CA)

treatment_protocol: Purified monocytes were incubated at 37°C with 500ng/mL lethal toxin for 4 hours.

tag: gender

value: male

tag: age

value: 52 year-old

tag: volunteer group

value: whole blood

tag: cell type

value: monocytes


title: CD4 Naïve 3

description: 3265_14034_04CD4N _MoGene1.0ST

source_name: CD4 Naïve


title: CD4 D6 Acute

description: 3265_14035_1CD4A6 _MoGene1.0ST


title: Low zinc replicate 1 array 1


title: Forward Trans Expt 1 - MBY38 + no Dox 9 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 9 hrs - Cy5

treatment_protocol:
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Control_r4

description:
CON_4
4519

source_name: Control

value: 36 year-old


title: High zinc replicate 2 array 1

source_name: S. pombe grown in high zinc conditions

value: high zinc or LZM3000


title: Toxin_r2

description:
TOX_2
4516

value: female

value: 24 year-old


title: Toxin_r3

description:
TOX_3
4518

value: 31 year-old


title: CD4 Naïve 2

description: 3265_14033_03CD4N _MoGene1.0ST


title: Control_r3

description:
CON_3
4517


title: Toxin_r4

description:
TOX_4
4520


title: High zinc replicate 1 array 1


title: Low zinc replicate 2 array 1


title: High zinc replicate 3 array 1


title: Forward Trans Expt 1 - MBY38 + no Dox 5 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 5 hrs - Cy5

treatment_protocol:
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + no Dox 4 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 4 hrs - Cy5

treatment_protocol:
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + no Dox 8 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 8 hrs - Cy5

treatment_protocol:
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + no Dox 6 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 6 hrs - Cy5

treatment_protocol:
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + no Dox 7 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 7 hrs - Cy5

treatment_protocol:
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD4 Naïve

description: 3265_14031_01CD4N _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + no Dox 2 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 2 hrs - Cy5

treatment_protocol:
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.

value: Dosage Expt Pooled Reference Protocol:Equal aliquots of the 12 sample RNAs (Dox dosage:20 ug/mL, 1 ug/mL, 0.4 ug/mL, 0.35 ug/mL, 0.3 ug/mL, 0.25 ug/mL, 0.2 ug/mL, 0.15 ug/mL, 0.1 ug/mL, 0.05 ug/mL, 0.02 ug/mL, 0 ug/mL ) were combined to create a pooled reference sample.


title: Control_r1

description:
CON_1
4513


title: Forward Trans Expt 1 - MBY38 + no Dox 3 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 3 hrs - Cy5

treatment_protocol:
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D30 Chronic  1

description: 3265_14028_2C8C30 _MoGene1.0ST

source_name: CD8 D30 Chronic


title: CD8 D30 Chronic

description: 3265_14027_1C8C30 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 7 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 7 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D30 Chronic  3

description: 3265_14030_4C8C30 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 5 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 5 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D30 Chronic  2

description: 3265_14029_3C8C30 _MoGene1.0ST

treatment_protocol: C57BL/6J mice were infected with LCMV Armstrong or LCMV clone 13. At various days post infection, LCMV-specific CD4 and CD8 T cells were purified on a BD Aria sorter.


title: Forward Trans Expt 1 - MBY38 + Dox 9 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 9 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + Dox 10 hrs

description: No additional information.

source_name: Forward Transition Expt - Cy3 Reference Sample

source_name: Forward Transition Expt - MBY38 + Dox 10 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D8 Chronic  2

description: 3265_14021_3CD8C8 _MoGene1.0ST

source_name: CD8 D8 Chronic


title: CD8 D15 Chronic

description: 3265_14023_1C8C15 _MoGene1.0ST

source_name: CD8 D15 Chronic


title: Forward Trans Expt 1 - MBY38 + no Dox 1 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + no Dox 1 hr - Cy5

treatment_protocol:
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Control_r2

description:
CON_2
4515

source_name: Control


title: CD8 D8 Chronic  3

description: 3265_14022_4C8CA8 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 4 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 4 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + Dox 8 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 8 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D8 Chronic  1

description: 3265_14020_2CD8C8 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 2 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 2 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + Dox 6 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 6 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D15 Chronic  2

description: 3265_14025_3C8C15 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 3 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 3 hrs - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D15 Chronic  3

description: 3265_14026_4C8C15 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 1 hrs

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 1 hr - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: CD8 D15 Chronic  1

description: 3265_14024_2C8C15 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 0 hrs - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Forward Transition Expt - Cy5 Reference Sample

source_name: Forward Transition Expt - MBY38 + Dox 0 hr - Cy3

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 1.0 ug/mL
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.


title: Forward Trans Expt 1 - MBY38 + Dox 0 hrs - repeat 2

description: No additional information.

source_name: Forward Transition Expt - MBY38 + Dox 0 hr - Cy5


title: CD8 D6 Chronic  2

description: 3265_14017_3CD8C6 _MoGene1.0ST

source_name: CD8 D6 Chronic


title: CD8 D6 Chronic  3

description: 3265_14018_4CD8C6 _MoGene1.0ST


title: CD8 D8 Chronic

description: 3265_14019_1CD8C8 _MoGene1.0ST


title: CD8 D6 Chronic

description: 3265_14015_1CD8C6 _MoGene1.0ST


title: CD8 D6 Chronic  1

description: 3265_14016_2CD8C6 _MoGene1.0ST


title: CD8 D30 Acute  1

description: 3265_14012_2C8A30 _MoGene1.0ST

source_name: CD8 D30 Acute


title: CD8 D30 Acute  3

description: 3265_14014_4C8A30 _MoGene1.0ST


title: CD8 D30 Acute

description: 3265_14011_1C8A30 _MoGene1.0ST


title: Forward Trans Expt 1 - MBY38 + Dox 0 hrs - repeat 1

description: No additional information.

source_name: Forward Transition Expt - Cy3 Reference Sample


title: Dosage Expt 2 - MBY38 + 0 ug/ml Dox

description: No additional information.

data_processing:
Dosage Expt Data Processing
Calculation Method: Microarray data was normalized using the Lowess method (Y.H. Yang, 2001) and filtered using Partek software to only include spots showing a median signal intensity >200 and signal-to-noise ratio >2. The UME6 dosage experiment was performed using two independent biological replicates. In each biological replicate experiment, the median signal ratio (ratio of the median signal intensity of each spot) for the 20 ug/mL Dox sample versus reference sample was first determined based on three technical replicates (one of which was performed using reverse fluors) using cDNA prepared from the same total RNA preparation. Next, the signal ratio of each Dox concentration sample versus reference was divided by the median signal ratio of the 20 ug/mL Dox sample versus reference.

source_name: Dosage Expt - Cy3 Reference Sample

source_name: Dosage Expt - MBY38 - no Dox - Cy5

treatment_protocol:
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .02 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .02 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.02 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .05 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .05 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.05 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .1 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .1 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.1 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: CD8 D30 Acute  2

description: 3265_14013_3C8A30 _MoGene1.0ST


title: Dosage Expt 2 - MBY38 + .15 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .15 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.15 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: CD8 D15 Acute  3

description: 3265_14010_4C8A15 _MoGene1.0ST

source_name: CD8 D15 Acute


title: Dosage Expt 2 - MBY38 + .2 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .2 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.2 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .25 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .25 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.25 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .3 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .3 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.3 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + .4 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .4 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.4 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: Dosage Expt 2 - MBY38 + 20 ug/ml Dox - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Dosage Expt - Cy5 Reference Sample

source_name: Dosage Expt - MBY38 + 20 ug/ml Dox - Cy3

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: CD8 D15 Acute  2

description: 3265_14009_3C8A15 _MoGene1.0ST

treatment_protocol: C57BL/6J mice were infected with LCMV Armstrong or LCMV clone 13. At various days post infection, LCMV-specific CD4 and CD8 T cells were purified on a BD Aria sorter.


title: CD8 D8 Acute  3

description: 3265_14006_4CD8A8 _MoGene1.0ST

source_name: CD8 D8 Acute


title: Dosage Expt 2 - MBY38 + 20 ug/ml Dox - repeat 2

description: No additional information.

source_name: Dosage Expt - MBY38 + 20 ug/ml Dox - Cy5


title: CD8 D8 Acute  2

description: 3265_14005_3CD8A8 _MoGene1.0ST


title: CD8 D8 Acute  1

description: 3265_14004_2CD8A8 _MoGene1.0ST


title: Dosage Expt 2 - MBY38 + 20 ug/ml Dox - repeat 1

description: No additional information.


title: Dosage Expt 2 - MBY38 + .35 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .35 ug/ml Dox - Cy5

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 0.35 ug/ml
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In all experiments cells were grown under non-filament-inducing conditions: yeast extract-peptone-dextrose (YEPD) medium at 30°C. For the experiment in which C. albicans morphologies were examined in static culture in response to UME6 dosage, a saturated overnight culture of the tetO-UME6 (MBY38) strain was diluted into 50 mL of YEPD medium plus various concentrations of Doxycycline (Dox) (20, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.02 and 0 µg/mL) and grown overnight at 30°C to OD600 = 1.0. Cells were then harvested for RNA extraction.


title: CD8 D8 Acute

description: 3265_14003_1CD8A8 _MoGene1.0ST


title: CD8 D6 Acute  1

description: 3265_14000_2CD8A6 _MoGene1.0ST

source_name: CD8 D6 Acute


title: CD8 D6 Acute

description: 3265_13999_1CD8A6 _MoGene1.0ST


title: CD8 D6 Acute  3

description: 3265_14002_4CD8A6 _MoGene1.0ST


title: Dosage Expt 1 - MBY38 + .02 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - Cy3 Reference Sample


title: Trigeminal Ectoderm + FGF2 rep 1

city: Houston

first: Andrew

last: Groves

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Differential gene expression was analyzed using Bioconductor’s Limma package (www.bioconductor.org) and probes ranked by fold up-regulation using Excel. A cut off value of 2-fold up-regulation was selected to generate the otic and FGF-specific gene sets.

label: Biotin

organism: Gallus gallus

source_name: Stage 8 Chick Trigeminal ectoderm, Cultured 18 hours + 50ng/ml FGF2

label_protocol: RNA was amplified and biotinylated using the Two-Cycle cDNA synthesis kit and IVT labeling kit (Affymetrix)

growth_protocol: Samples 5 and 6 were grown in DMEM/F12 + N2 supplements. Samples 7 and 8 were grown in the same conditions + 50ng/ml FGF2. Samples 5-8 were cultured in collagen gels for 18 hours

extract_protocol: Cells lysis was performed using QIAshredder columns (Qiagen) and RNA isolated using the RNeasy Micro kits (Qiagen) according to the manufacturer’s protocols, although the DNAseI step was omitted and an additional RNA cleanup step was employed.

treatment_protocol: Samples 5-8 were grown in defined medium +/- FGF2. Samples 1-4 were freshly dissected from chick embryos

tag: condition

value: Trigeminal Ectoderm + FGF2

tag: growth protocol

value: grown in DMEM/F12 + N2 supplements + 50ng/ml FGF2


title: Lateral Ectoderm rep 2

source_name: Stage 10 Chick lateral ectoderm, freshly dissected

value: Lateral Ectoderm


title: Lateral Ectoderm rep 1


title: Trigeminal Ectoderm - FGF2 rep 2

source_name: Stage 8 Chick Trigeminal ectoderm, Cultured 18 hours

value: Trigeminal Ectoderm - FGF2

value: grown in DMEM/F12 + N2 supplements


title: Trigeminal Ectoderm + FGF2 rep 2


title: CD8 D15 Acute  1

description: 3265_14008_2C8A15 _MoGene1.0ST

value: spleen


title: Otic Ectoderm rep 1

source_name: Stage 10 Chick Otic ectoderm, freshly dissected

value: Otic Ectoderm


title: CD8 D6 Acute  2

description: 3265_14001_3CD8A6 _MoGene1.0ST


title: CD8 Naïve 3

description: 3265_13998_04CD8N _MoGene1.0ST

source_name: CD8 Naïve


title: Trigeminal Ectoderm - FGF2 rep 1


title: Dosage Expt 1 - MBY38 + 0 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 - no Dox - Cy5


title: Dosage Expt 1 - MBY38 + .1 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .1 ug/ml Dox - Cy5


title: Dosage Expt 1 - MBY38 + .05 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .05 ug/ml Dox - Cy5


title: Mice fed with a  n-3 PUFA-depleted diet and returned on a control diet during the last 10 days of experiment

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: gene expression data from mice fed with n-3 PUFA depleted diet and returned on a control diet during the last 10 days of experiment

hyb_protocol: cRNA was hybridized to mouse genome 430 2.0 array (Affymetrix, Santa Clara, USA)

scan_protocol: Affymetrix standard protocol

data_processing: The MAS5 algorithm was run using GCOS® Affymetrix software as follows: the scaling factor using all probe sets was set to 100, the normalize factor was set to 1 and the baseline comparison was done on the CT diet hybridization samples

source_name: liver tissue

label_protocol: Biotin-labeled cRNA was synthesized using GeneChip IVT labelling kit (Affymetrix, Santa Clara, USA)

growth_protocol: Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of 4 mice per cage at 22°C in a 12 h light/dark cycle and given free access to diet and water.   After an acclimatisation period of 1 week, mice were fed a control (CT) (D08041805, Research Diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research Diets, New Brunswick, USA) for 112 days ad libitum. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. Ten days before the end of the experiment, DEF mice were divided into three groups: DEF, DEF/FOS and DEF/CT mice. The DEF mice were still fed with the n-3 PUFA depleted diet (DEF). The DEF/FOS mice were still fed the DEF diet and were supplemented for 10 days with fructooligosaccharides (DEF/FOS). FOS (Beneo P95 gift from Orafti; Tienen, Belgium) was added to tap water in a concentration adequate to reach an intake of 0.25g of FOS per day. For DEF/CT mice, the DEF diet was replaced by the CT diet during the last 10 days of treatment. At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively).

extract_protocol: Total RNA was isolated from liver tissue using the TriPure reagent (Roche, Basel, Switzerland). RNA quality was checked using Bioanalyzer (Agilent). Equal amounts RNA from each mice (n = 4 to 8 mice per group) were pooled within each group.Double-stranded cDNA was synthesized from total RNA using the One-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA).

treatment_protocol: At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively). The liver tissue was immediately clamped in liquid N2 and kept at -80°C until analysis.

tag: treatment

value: deficient diet + control diet during the last 10 days of treatment

value: liver

value: male


title: CD8 Naïve 2

description: 3265_13997_03CD8N _MoGene1.0ST


title: Dosage Expt 1 - MBY38 + .15 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .15 ug/ml Dox - Cy5


title: CD8 Naïve 1

description: 3265_13996_02CD8N _MoGene1.0ST


title: Dosage Expt 1 - MBY38 + .2 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .2 ug/ml Dox - Cy5


title: Otic Ectoderm rep 2


title: CD4 Naïve 1

description: 3265_14032_02CD4N _MoGene1.0ST

source_name: CD4 Naïve


title: Dosage Expt 1 - MBY38 + .3 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .3 ug/ml Dox - Cy5


title: CD8 Naïve

description: 3265_13995_01CD8N _MoGene1.0ST


title: Dosage Expt 1 - MBY38 + .35 ug/ml Dox

description: No additional information.


title: Dosage Expt 1 - MBY38 + .25 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .25 ug/ml Dox - Cy5


title: Dosage Expt 1 - MBY38 + .4 ug/ml Dox

description: No additional information.

source_name: Dosage Expt - MBY38 + .4 ug/ml Dox - Cy5


title: Mice fed with a n-3 PUFA-depleted diet and supplemented with FOS during the last 10 days of experiment

description: gene expression data from mice fed with n-3 PUFA depleted diet and supplemented with FOS during the last 10 days of experiment

value: deficient diet + FOS supplementation during the last 10 days of treatment


title: Highly pathogenic avian influenza infected RIG-I transfected DF-1 cell RNA replicate 2

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Biological replicate 2 of 2. Highly pathogenic avian influenza infected RIG-I transfected DF-1 cell

hyb_protocol: Microarray hybridization was performed at 65°C for 18 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 3μm resolution, and the array data was extracted with Agilent feature extraction software using the GE2_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used along with LOWESS normalization

label_protocol: 500ng of total RNA were labeled (Cy3, control sample; Cy5, test sample) according to Agilent's labeling protocol

growth_protocol: PCR amplification and standard cloning techniques were used to insert the duck RIG-I gene into the pCDNA 3.1. Either RIG-I or empty pcDNA 3.1 plasmid was transfected into the chicken embryonic fibroblast cell line, DF-1.

extract_protocol: Total RNA as extracted using Trizol and Rneasy columns following manufacturer's instructions

treatment_protocol: Post-transfection, cells were infected with low pathogenic avian influenza A/mallard/British Columbia/500/2005 (H5N2) or infected with highly pathogenic avian influenza A/Viet Nam/1203/2004 (H5N1)

tag: infection

tag: transfection

value: RIG-I

tag: cell line

value: DF-1 cells (chicken embryonic fibroblasts)

source_name: Untransfected, uninfected DF-1 cell reference RNA

value: uninfected

value: untransfected


title: Highly pathogenic avian influenza infected empty vector transfected DF-1 cell RNA replicate 1

description: Biological replicate 1 of 2. Highly pathogenic avian influenza infected empty vector transfected DF-1 cell.

value: highly pathogenic avian influenza A/Viet Nam/1203/2004 (H5N1)

value: empty vector


title: Dosage Expt 1 - MBY38 + 20 ug/ml Dox - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Dosage Expt - Cy5 Reference Sample

value: Dosage Expt Pooled Reference Protocol:Equal aliquots of the 12 sample RNAs (Dox dosage:20 ug/mL, 1 ug/mL, 0.4 ug/mL, 0.35 ug/mL, 0.3 ug/mL, 0.25 ug/mL, 0.2 ug/mL, 0.15 ug/mL, 0.1 ug/mL, 0.05 ug/mL, 0.02 ug/mL, 0 ug/mL ) were combined to create a pooled reference sample.

source_name: Dosage Expt - MBY38 + 20 ug/ml Dox - Cy3


title: Highly pathogenic avian influenza infected RIG-I transfected DF-1 cell RNA replicate 1

description: Biological replicate 1 of 2. Highly pathogenic avian influenza infected RIG-I transfected DF-1 cell


title: Dosage Expt 1 - MBY38 + 20 ug/ml Dox - repeat 2

description: No additional information.

source_name: Dosage Expt - Cy3 Reference Sample

source_name: Dosage Expt - MBY38 + 20 ug/ml Dox - Cy5


description: Gene expression profiling from untreated Gastrointestinal neuroendocrine cell line

hyb_protocol: Affymetrix standard

scan_protocol: GCOS

data_processing: RMA normalization using default setting (rma-gene-default) with Expression Console v 1.1.2800.19935

label_protocol: Affymetrix standard

growth_protocol: Tumor cells cultured in medium and incubated at 37˚C with 5% CO2

extract_protocol: PARIS Kit ( Ambion )

treatment_protocol: Octreotide 1µM

value: tumor cell line Established from a primary multifocal ileal neuroendocrine tumors

tag: treatment time


title: Low pathogenic avian influenza infected RIG-I transfected DF-1 cell RNA replicate 3

description: Biological replicate 3 of 3. Low pathogenic avian influenza infected RIG-I transfected DF-1 cell.

value: low pathogenic avian influenza A/mallard/British Columbia/500/2005 (H5N2)


title: Low pathogenic avian influenza infected RIG-I transfected DF-1 cell RNA replicate 2

description: Biological replicate 2 of 3. Low pathogenic avian influenza infected RIG-I transfected DF-1 cell.


title: Ileum neuroendocrine cell line, 10 months

description: Gene expression profiling from untreated Ileum  neuroendocrine cell line

source_name: Ileum  neuroendocrine cell line

value: tumor cell line Established from liver metastasis from a patient with a primary ileum neuroendocrine tumor

value: 10 Months


title: Pancreatic neuroendocrine cell line

description: Gene expression profiling from untreated Pancreatic neuroendocrine cell line

source_name: Pancreatic neuroendocrine cell line

value: tumor cell line Established from a human pancreatic islet cell carcinoma

value: QGP


title: Ileum neuroendocrine cell line, 16 months

value: 16 Months


title: Highly pathogenic avian influenza infected empty vector transfected DF-1 cell RNA replicate 2

description: Biological replicate 2 of 2. Highly pathogenic avian influenza infected empty vector transfected DF-1 cell.


title: Low pathogenic avian influenza infected empty vector transfected DF-1 cell RNA replicate 3

description: Biological replicate 3 of 3. Low pathogenic avian influenza infected empty vector transfected DF-1 cell.


title: Dosage Expt 1 - MBY38 + 20 ug/ml Dox - repeat 1

description: No additional information.


title: Low pathogenic avian influenza infected empty vector transfected DF-1 cell RNA replicate 2

description: Biological replicate 2 of 3. Low pathogenic avian influenza infected empty vector transfected DF-1 cell.


description: Gene expression profiling from untreated Bronchopulmonary neuroendocrine cell line

value: tumor cell line Derived from a human pulmonary carcinoid tumor


description: Gene expression profiling from untreated Atypical bronchopulmonary neuroendocrine cell line

value: tumor cell line Derived from human pulmonary carcinoid tumors


title: Low pathogenic avian influenza infected RIG-I transfected DF-1 cell RNA replicate 1

description: Biological replicate 1 of 3. Low pathogenic avian influenza infected RIG-I transfected DF-1 cell.


title: Low pathogenic avian influenza infected empty vector transfected DF-1 cell RNA replicate 1

description: Biological replicate 1 of 3. Low pathogenic avian influenza infected empty vector transfected DF-1 cell.


title: Ileum neuroendocrine cell line, + octreotide 10 months

description: Gene expression profiling from Ileum  neuroendocrine cell line treated with octreotide 1µM

value: Octreotide 1µm


title: Ileum neuroendocrine cell line, + octreotide 16 months


title: A1KD_2

status: Public on Dec 11 2012

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: Gene Expression

hyb_protocol: 600 ng of cRNA (specific activity >10.0 pmol Cy3/ug cRNA) per channel per array spot (8 per slide) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, 1 volume of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 8x60k gene expression arrays (G4858A-028004) 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)(both without Triton added).

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array Scan resolution 3 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE2-105_Dec08 with the cognate G4858A-028004 grid file to obtain background subtracted and spatially detrended Processed Signal intensities. Processed Signal Intensities were expressed as a ratio to the 75th percentile value (control probes excluded) and median centered for each array and log2 transformed. Only probes tagged by Feature Extraction as above background in all constituents of a sample triplicate or duplicate set in at least one condition were considered for further analysis. After background filtering, probes values were collapsed by the GeneName column from the Feature Extraction output to condense multiple reads of the same gene. To correct for slide batch effects (each slide = 8 arrays) the R ComBat package (Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007) was employed using the universal reference (technical replicates) array on each slide upon which a universal replicate was hybridized along with each condition treating each array as a different batch.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug total RNA using the One-Color Low-Input QuickAmp 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-1000 Spectrophotometer.

extract_protocol: Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions. RNA quality was assessed using an Aglient Bioanalyzer

value: lung fibroblasts

value: HOXA1 knockdown


title: SCR_3

description: Gene Expression

value: Scramble siRNA


title: A1KD_3

description: Gene Expression


title: SCR_1

description: Gene Expression


title: SCR_2

description: Gene Expression


title: A1KD_1

description: Gene Expression


title: Neg Control, Total lysate replicate 1

city: Chicago

first: Xiaowei

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Human Gene 1.0 ST chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner

data_processing: The data were analyzed with RMA analysis using Expression Console software (v1.1) with global scaling as normalization method.

source_name: H4_Neg Control_total lysate

label_protocol: Ambion WT expression kit was used along with the standard Affymetrix protocol.

growth_protocol: Human H4 (Glioneuronal phenotype) cells were cultured and harvested 48 hours post miRNA transfection [Arnstein, P.et al (1974) J Natl Cancer Inst, 52, 71-84.]

extract_protocol: RNA was obtained according to two separate protocols; (1) anti-Argonaute co-immunoprecipitation with monoclonal antibody 2A8 [Nelson PT, et al (2007) 13:1787-92]; or (2) total RNA in the lysate.  For detailed protocol, see Wang WX et al, RNA (2010) 16:394-404.  Trizol LS extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Individual miRNA mimics or a negative control RNA were transfected into H4 cells.

value: glioneuronal cells

tag: transfected with

value: negative control miRNA from Ambion

tag: sample type

value: total lysate (total input RNA)


title: Mut M1, Total lysate replicate 2

source_name: H4_Mut M1_total lysate

value: miR-107-mut1 (miRNA-like molecule)


title: Neg Control, Total lysate replicate 3


title: Mut M2, Total lysate replicate 2

source_name: H4_Mut M2_total lysate

value: mir-107-mut2 (miRNA-like molecule)


title: Mut M2, Total lysate replicate 1


title: miR-320, Total lysate replicate 3

source_name: H4_miR-320_total lysate

value: miR-320 (control miRNA)


title: miR-195, Total lysate replicate 3

source_name: H4_miR-195_total lysate


title: Mut M2, Total lysate replicate 3


title: Neg Control, Total lysate replicate 2


title: miR-195, Total lysate replicate 1


title: miR-320, Total lysate replicate 2


title: Mut M1, Total lysate replicate 1


title: miR-195, Total lysate replicate 2


title: miR-16, Total lysate replicate 1

source_name: H4_miR-16_total lysate


title: Mut M1, Total lysate replicate 3


title: miR-320, Total lysate replicate 1


title: miR-16, Total lysate replicate 2


title: CD8 D15 Acute

description: 3265_14007_1C8A15 _MoGene1.0ST

source_name: CD8 D15 Acute

value: spleen


title: miR-15b, Total lysate replicate 2

source_name: H4_miR-15b_total lysate

value: miR-15b (anti-sense control miRNA)


title: miR-15b, Total lysate replicate 1


title: miR-16, Total lysate replicate 3


title: Neg Control, IP replicate 2

source_name: H4_Neg Control_IP

value: RIP-chip

tag: ip antibody

value: anti-Argonaute (anti-AGO) monoclonal antibody generated in Dr. Nelson's lab


title: miR-103, Total lysate replicate 2

source_name: H4_miR-103_total lysate


title: miR-15b, Total lysate replicate 3


title: Mut M2, IP replicate 3

source_name: H4_Mut M2_IP


title: miR-107, Total lysate replicate 3

source_name: H4_miR-107_total lysate


title: miR-103, Total lysate replicate 3


title: Neg Control, IP replicate 1


title: miR-320, IP replicate 3


title: Mut M2, IP replicate 2


title: miR-103, Total lysate replicate 1


title: Mut M2, IP replicate 1


title: miR-107, Total lysate replicate 2


title: miR-107, Total lysate replicate 1


title: Mut M1, IP replicate 1

source_name: H4_Mut M1_IP


title: Neg Control, IP replicate 3


title: miR-320, IP replicate 2


title: Mut M1, IP replicate 3


title: miR-195, IP replicate 3


title: Mut M1, IP replicate 2


title: miR-195, IP replicate 1


title: miR-320, IP replicate 1


title: miR-16, IP replicate 3


title: TMD8_8h_VRPR_4

city: New York

first: Lorena

last: Fontan

state: NY

address: 1300 York Ave

department: Medicine

institute: Weill Cornell Medical College

description: TMD8 z-VRPR-fmk 8h rep4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and quantile normalized with Partek Genome Suite

source_name: TMD8 z-VRPR-fmk

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: lymphoma


title: miR-16, IP replicate 1


title: miR-15b, IP replicate 3


title: miR-195, IP replicate 2


title: miR-16, IP replicate 2


title: miR-103, IP replicate 2


title: miR-107, IP replicate 1


title: miR-15b, IP replicate 2


title: miR-107, IP replicate 2


title: TMD8_8h_2_3

description: TMD8 MI-2 8h rep3

source_name: TMD8 MI-2


title: TMD8_8h_2_2

description: TMD8 MI-2 8h rep2


title: HBL_1_8h_2_2

description: HBL-1 MI-2 8h rep2

source_name: HBL-1 MI-2


title: TMD8_8h_ve2

description: TMD8 vehicle 8h rep2

source_name: TMD8 vehicle


title: TMD8_8h_ve4

description: TMD8 vehicle 8h rep4


title: TMD8_8h_ve3

description: TMD8 vehicle 8h rep3


title: HBL_1_8h_ve3

description: HBL-1 vehicle 8h rep3

source_name: HBL-1 vehicle


title: miR-107, IP replicate 3


title: miR-103, IP replicate 1


title: TMD8_8h_2_1

description: TMD8 MI-2 8h rep1


title: miR-103, IP replicate 3


title: HBL_1_8h_VRPR_4

description: HBL-1 z-VRPR-fmk 8h rep4

source_name: HBL-1 z-VRPR-fmk


title: miR-15b, IP replicate 1


title: HBL_1_8h_ve2

description: HBL-1 vehicle 8h rep2


title: HBL_1_8h_2_3

description: HBL-1 MI-2 8h rep3


title: TMD8_8h_ve1

description: TMD8 vehicle 8h rep1


title: MIA PaCa-2_MeTA

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in MIA PaCa-2 cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MIA PaCa-2, MeTA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MIA PaCa-2 cells were grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen).

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MIA PaCa-2 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

value: pancreatic cancer cell line

tag: source gender

value: male

tag: source age

value: MIA PaCa-2

value: Transcriptional activating fragment with a methyl-CpG binding domain


title: HBL_1_8h_ve4

description: HBL-1 vehicle 8h rep4


title: HBL_1_8h_2_1

description: HBL-1 MI-2 8h rep1


title: PANC-1_MeTA

description: Gene expression in PANC-1 cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

source_name: PANC-1, MeTA

growth_protocol: PANC-1 cells were grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen).

treatment_protocol: PANC-1 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.


title: PANC-1_Vec

description: Gene expression in PANC-1 cells transfected with pcDNA6/myc-His vector

source_name: PANC-1, Vector

treatment_protocol: PANC-1 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

value: Vector


title: MIA PaCa-2_Vec

description: Gene expression in MIA PaCa-2 cells transfected with pcDNA6/myc-His vector

source_name: MIA PaCa-2, Vector

treatment_protocol: MIA PaCa-2 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.


title: HBL_1_8h_ve1

description: HBL-1 vehicle 8h rep1


title: AsPC-1_MeTA

description: Gene expression in AsPC-1 cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

source_name: AsPC-1, MeTA

growth_protocol: A human pancreatic cancer cell line AsPC-1 was grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen).

treatment_protocol: AsPC-1 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

value: female


title: AsPC-1_Vec

description: Gene expression in AsPC-1 cells transfected with pcDNA6/myc-His vector

source_name: AsPC-1, Vector

treatment_protocol: AsPC-1 cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.


title: HPDE_MeTA

description: Gene expression in HPDE cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

source_name: HPDE, MeTA

growth_protocol: An immortal cell line derived from normal human pancreatic ductal epithelium (HPDE) was grown in HuMedia-KG2 (KURABO).

treatment_protocol: HPDE cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

value: normal pancreatic ductal epithelial cell line

value: HPDE


title: S-group bone 4 weeks postsurgery rep2

city: Guangzhou

first: DaoZhang

last: Cai

state: GuangDong

department: Orthopaedics

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Gene expression proﬁles of subchondral bone at 4 weeks after sham-operation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarrays (G4131F) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: subchondral bone,sham operation,4 weeks postsurgery

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Temperature 20-22℃, Humidity 55±5%, Specified rat pathogen free conditions, 12 hours light/dark cycle, Water ad libitum, Nutrients MF-Oriental Yeast-Japan, Housed in cages according to Chinese legislation.

extract_protocol: Total RNA of the subchondral bone was extracted using E.Z.N.A Total RNA Kit Ⅱ (Omega Bio-Tek, Inc., USA), according to the manufacturer's instructions, including a DNase digestion step. The quantity and quality of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE) and the agarose gel electrophoresis.

treatment_protocol: Animals were equally divided into two groups: experimental group (E-Group) and sham-operated group (S-Group). The right knee joints of the E-Group rats underwent open surgery, involved in both medial meniscectomy and medial collateral ligament (MCL) transaction with micro-scissors. The right knee joints of the S-Group rats were carried out with a sham operation, via a similar incision, without operations of the medial meniscus and the medial collateral ligament. Animals were killed at 1, 2, and 4 weeks postsurgery. After exarticulation of the right knee joints of the rats, the femurs were fracted from the epiphyseal plate quickly, and the femoral condyles were frozen in liquid nitrogen until subchondral bone separation and total RNA extraction. The articular cartilage and epiphyseal plate tissue of the femur condyle sample were cleared away with a micro-electric burnish implement with drill to obtain subchondral bone.

tag: tissue

value: subchondral bone

value: sham surgery

tag: time

value: 4 weeks postsurgery

tag: strain

value: Sprague Dawley


title: S-group bone 2 weeks postsurgery rep2

description: Gene expression proﬁles of subchondral bone at 2 weeks after sham-operation

source_name: subchondral bone,sham operation,2 weeks postsurgery

tag: gender

tag: age

value: 2 weeks postsurgery


title: S-group bone 2 weeks postsurgery rep4


title: S-group bone 2 weeks postsurgery rep5


title: S-group bone 4 weeks postsurgery rep4


title: S-group bone 4 weeks postsurgery rep1


title: S-group bone 2 weeks postsurgery rep3


title: S-group bone 4 weeks postsurgery rep5


title: S-group bone 2 weeks postsurgery rep1


title: S-group bone 1 week postsurgery rep1

description: Gene expression proﬁles of subchondral bone at 1 week after sham-operation

source_name: subchondral bone,sham operation,1 week postsurgery

value: 1 week postsurgery


title: S-group bone 1 week postsurgery rep3


title: E-group bone 4 weeks postsurgery rep4

description: Gene expression proﬁles of subchondral bone at 4 weeks postsurgery

source_name: subchondral bone,operation,4 weeks postsurgery

value: medial meniscectomy and medial collateral ligament transection


title: S-group bone 1 week postsurgery rep2


title: S-group bone 1 week postsurgery rep4


title: S-group bone 1 week postsurgery rep5


title: HPDE_Vec

description: Gene expression in HPDE cells transfected with pcDNA6/myc-His vector

source_name: HPDE, Vector

treatment_protocol: HPDE cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

tag: cell type


title: S-group bone 4 weeks postsurgery rep3


title: E-group bone 4 weeks postsurgery rep5


title: Monocyte#5

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

country: France

institute: INSERM

description: purified CD14 monocyte

hyb_protocol: RNA were hybridized for 16 hr at 45C on Affymetrix HGU133 plus 2.0 panGenome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Raw data were log (base 2)-transformed and normalized by RMA.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in vitro cell culture in complete culture medium (RPMI 1640 + 10% fetal calf serum)

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

treatment_protocol: cell samples were purified from the cell culture on the basis of CD14 or CD163 phenotypes

tag: disease state

value: Healthy donor

value: purified CD14 monocyte


title: Monocyte#4

description: purified CD14 monocyte


title: MOF, rep3

type: genomic

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: Chip-chip S2 cells MOF

hyb_protocol: performed by imaGenes (www.imagenes-bio.de)

data_processing: raw signals of all channels in all replicate arrays were log2 transformed and quantile normalized in R/Bioconductor.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Input DNA

growth_protocol: Cells were grown in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).

value: none, input DNA

source_name: MOF IP DNA

value: MOF SA 4897


title: Monocyte#1

description: purified CD14 monocyte


title: E-group bone 4 weeks postsurgery rep1

value: male

tag: treatment


title: Monocyte#3

description: purified CD14 monocyte


title: E-group bone 4 weeks postsurgery rep3


title: E-group bone 4 weeks postsurgery rep2


title: E-group bone 2 weeks postsurgery rep5

description: Gene expression proﬁles of subchondral bone at 2 weeks postsurgery

source_name: subchondral bone,operation,2 weeks postsurgery


title: Monocyte#2

description: purified CD14 monocyte


title: E-group bone 2 weeks postsurgery rep4


title: MOF, rep5

description: Chip-chip S2 cells MOF

scan_protocol: performed by imaGenes (www.imagenes-bio.de)


title: E-group bone 2 weeks postsurgery rep2


title: NLC#9

description: purified nurse-like cell

value: chronic lymphocytic leukemia

value: purified nurse-like cell


title: MSL3, rep1

description: Chip-chip S2 cells MSL3

label_protocol: performed by imaGenes (www.imagenes-bio.de)

source_name: MSL3 IP DNA

value: MSL3, R74


title: NLC#5

description: purified nurse-like cell


title: NLC#8

description: purified nurse-like cell


title: NLC#10

description: purified nurse-like cell


title: NLC#6

description: purified nurse-like cell


title: E-group bone 1 week postsurgery rep5

description: Gene expression proﬁles of subchondral bone at 1 week postsurgery

source_name: subchondral bone,operation,1 week postsurgery


title: E-group bone 2 weeks postsurgery rep3


title: NLC#7

description: purified nurse-like cell


title: MLE, rep1

description: Chip-chip S2 cells MLE

source_name: MLE IP DNA

value: MLE, 6E11


title: MLE, rep2

description: Chip-chip S2 cells MLE


title: E-group bone 2 weeks postsurgery rep1


title: MOF, rep2

description: Chip-chip S2 cells MOF


title: E-group bone 1 week postsurgery rep4


title: MLE, rep3

description: Chip-chip S2 cells MLE


title: MOF, rep1

description: Chip-chip S2 cells MOF


title: NLC#4

description: purified nurse-like cell


title: NLC#3

description: purified nurse-like cell


title: NLC#2

description: purified nurse-like cell


title: MOF, rep4

description: Chip-chip S2 cells MOF


title: MLE, rep4

description: Chip-chip S2 cells MLE

value: MLE, guinea pig #17


title: NLC#1

description: purified nurse-like cell


title: CL1-5 biological repeat 2

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CL1-5

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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.

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were cultured in RPMI basal media supplemented with 10 % of fetal bovine serum and 1% penicillin/streptomycin.

tag: parental cell line

value: Lung adenocarcinoma

tag: cell population

value: highly invasive


title: E-group bone 1 week postsurgery rep1

value: subchondral bone


title: MEL_Ldb1KD_uninduced_rep2

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

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

data_processing: Bioconductor/R (R 2.15.2); affy (1.36.0) and limma (3.14.1) packages; Mouse430_2_Mm_ENTREZG cdf (brainarray v.16.0)

source_name: MEL_Ldb1 shRNA knockdown_uninduced

growth_protocol: Cells cultured in DMEM supplemented with 10% fetal bovine serum

extract_protocol: RNA was prepared from 2e6 cells using the Rneasy Plus Mini Kit (Qiagen). One microgram of RNA was reverse transcribed with random hexamers using the Superscript III first-strand synthesis system as suggested by the manufacturer (Invitrogen).

treatment_protocol: Uninduced MEL cells were differentiated by incubating 2.5e5 cells/ml with 1.5-2% DMSO; cells were stably transformed with either control or Ldb1 shRNA from Open Biosystems.

tag: strain background

value: BALB/c

value: Murine erythroidleukema (MEL) cells

tag: genotype/variation

value: Ldb1 shRNA knockdown


title: MEL_control_uninduced_rep1

source_name: MEL_control knockdown_uninduced

value: control