title: ChIP-chip of RNA Pol II from cells at 3 hr in meiosis

description: RNA Pol II ChIP chip in meiotic cells

source_name: ChIP of RNA Pol II

value: RNA Pol II (8WG16, MMS-126R, Covance)


title: ChIP-chip of RNA Pol II from exponentially growing cells

status: Public on Dec 13 2012

type: genomic

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: RNA Pol II ChIP chip in exponentially growing cells

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then the ratios from replicate #1 and replicate #2 were averaged, and the resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For exponentially growing cells, cells were grown in rich medium (YPD) to a density of 2.107 cells/ml.

extract_protocol: 10ml (2*108 cells) were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 0.8 µg of monoclonal 9E10 anti-Myc (Santa Cruz) or 2 µg of mouse monoclonal M2 anti-FLAG (Sigma) or 2 µl of monoclonal 8WG16 (Covance) and 30 µl protein G magnetic beads suspension (New England Biolabs)

tag: strain

tag: growth condition

value: YPD

tag: chip antibody

source_name: Whole cell extract

label_protocol: 1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling


title: ChIP-chip of Rec8-Flag from cells at 4 hr in meiosis

description: Rec8-Flag ChIP chip in meiotic cells

source_name: ChIP of Rec8-Flag

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 4 hr in meiosis

value: at 4 hr in meiosis

value: anti-Flag M2 antibody (F1804, Sigma)


title: ChIP-chip of Spp1-Myc from exponentially growing cells

description: Spp1-Myc ChIP chip in exponentially growing cells

source_name: ChIP of Spp1-Myc

value: 9E10 anti-Myc (sc-40, Santa Cruz)


title: ChIP-chip of Spp1-Myc from cells at 3 hr in meiosis

description: Spp1-Myc ChIP chip in meiotic cells

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 3 hr in meiosis

value: at 3 hr in meiosis


title: RP1186-B4-48H-29C

type: RNA

city: University Park

first: Nicholas

last: Polato

state: PA

address: 208 Mueller Lab

department: Biology

country: USA

institute: Penn State University

description: This sample was not used for analysis after initial normalization. A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.

hyb_protocol: Samples were resuspended in the appropriate tracking control and hybridization solution master mix was added following manufacturer’s instructions (Roche NimbleGen). Following two 5-minute incubations at 95°C and 42°C, the mixer was attached to the array and hybridization solutions were added according to the manufacturer’s instructions. Hybridization was performed while mixing overnight at 42°C in a MAUI hybridization instrument (BioMicro Systems, UT). Hybridized slides were washed according to the manufacturer’s instructions (Roche NimbleGen), and spun at 1000 RPM for 3 minutes in a 50 ml conical tube filled with N2 gas. Dried slides were placed in fresh tubes with 2.5 ml of DyeSaver (Genisphere Inc.) and rotated for 45 seconds to coat the slide. A final spin at 700 RPM for 3 seconds removed excess DyeSaver.

scan_protocol: Scanning was performed with an Axon GenePix 4000B

data_processing: Raw probe intensities were read into R for analysis in the Bioconductor package LIMMA (Smyth 2005; R_Development_Core_Team 2008). Probe intensities were normalized within arrays using lowess normalization, and between arrays using the Aquantile normalization method which ensures that the average intensities have the same empirical distribution across arrays (Yang and Thorne 2003).

molecule: total RNA

organism: Acropora palmata

source_name: Acropora palmata larval culture

label_protocol: To prepare samples for microarray hybridization, one cycle of amplification was per-formed on 1ug of each RNA sample using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Life Technologies, AM1753) following the manufacturer’s protocol.  Dye coupling of 15 ug of aRNA was performed with Cy3 or Cy5 (GE Health Care, RPN5661), and subsequently purified according to the Ambion Kit instructions. For each pair of samples that were to be hy-bridized to the same array, 2µg each of the Cy3 and Cy5 labeled sample were combined and fragmented using RNA Fragmentation Reagents (Ambion, AM8740) according the manufactur-er’s instructions, then dried down completely in a speed-vac.

growth_protocol: Gametes from multiple parent colonies were collected during the 2009 mass spawning event on the reef off of Rincon, Puerto Rico. The genotypic identity of each colony targeted for gamete collection was determined using microsatellite markers (Baums, Hughes et al. 2005). Batch cultures, consisting of four genotypically distinct parents each, were generated by combining sperm and eggs from selected parent colonies. After fertilization (one hour), the zygotes were rinsed with filtered sea water and transferred to temperature controlled aquaria.

extract_protocol: Embryos for the microarray experiment were sampled at 24, 48, and 72 hours (only samples from batch 2 were available at 72h) and preserved in RNAlater (Ambion, TX) followed by storage at -80°C. Total RNA was extracted from approximately 30-100 larvae from each sample using the RNeasy Mini Kit (Qiagen, CA). Quality and concentration of total RNA was as-sessed on an Agilent 2100 Bioanalyzer to ensure that high molecular weight RNA was present.

treatment_protocol: Larvae were reared at a control temperature (27°C) or elevated temperature (29°C). Replicates of each batch culture (n = 2) were kept in separate 1L plastic containers (with mesh sides to allow for water exchange). Plastic 1 L containers (n = 10) were suspended in replicate 45L polycarbonate bins (n = 4) at each temperature (n = 2). Water in each bin was circulated with an aquarium pump and changed daily with filtered sea water preheated to the target temperature. Temperatures were maintained within ±1°C with ¼ hp aquarium chillers (Current USA, CA) and monitored with HOBO data loggers (Onset Co., MA).

tag: tissue type

value: larval culture

tag: batch

value: batch 4

tag: age

value: 48 hours

tag: temperature


title: RP597-B2-48H-27C

description: A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.

value: batch 2


title: RP1102-B2-48H-29C


title: Naïve, rep1

city: Mississippi State

first: Teresia

last: Buza

state: Mississippi

address: 240 Wise Center Drive

department: Basic Sciences

institute: Mississippi State University

description: Global gene expression in peritoneal macrophages without LPS challenge or SMD pretreatment (Naïve)

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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 with a target intensity value of 500 for normalization.

label: biotin

organism: Mus musculus

source_name: Naïve

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 7.5μg total RNA using the Affymetrix one cycle labeling kit.

growth_protocol: Experimental mice were housed in filter top shoebox cages with 5 mice per cage in a temperature (70-78°F) and humidity (40-60%) controlled environment. Mice were housed and used in accord with NIH and Mississippi State University regulations.

extract_protocol: RNA extraction Trizol method for isolation

treatment_protocol: Mice were anesthetized with halothane and 50 µl of SMD solution was placed on the nares before the treatment.

value: C57Bl/6 x C3H F1

tag: gender

value: female

tag: tissue

value: peritoneal macrophages


title: RP1177-B5-48H-27C-Cy3

description: Used a Cy5 replicate of sample RP1177. A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.

value: batch 5


title: RP1188-B4-48H-29C


title: RP1178-B3-48H-27C

value: batch 3


title: RP1103-B2-48H-29C


title: RP1174-B5-48H-27C


title: LPS+SMD at 300mg/kg, biological rep2

description: Global gene expression in peritoneal macrophages 2.0 hrs after LPS challenge and SMD pretreatment at 300mg/kg

source_name: Mice challenged with LPS and SMD pretreatment at 300mg/kg


title: LPS+SMD at 200mg/kg, biological rep3

description: Global gene expression in peritoneal macrophages 2.0 hrs after LPS challenge and SMD pretreatment at 200mg/kg

source_name: Mice challenged with LPS and SMD pretreatment at 200mg/kg


title: LPS+SMD at 300mg/kg, biological rep3


title: RP1169-B4-48H-27C


title: LPS+SMD at 100mg/kg, biological rep3

description: Global gene expression in peritoneal macrophages 2.0 hrs after LPS challenge and SMD pretreatment at 100mg/kg

source_name: Mice challenged with LPS and SMD pretreatment at 100mg/kg


title: Naïve, rep2


title: RP1189-B5-48H-29C


title: LPS+SMD at 200mg/kg, biological rep2


title: RP1168-B3-48H-27C


title: LPS+SMD at 300mg/kg, biological rep1


title: RP1162-B2-72H-29C

value: 72 hours


title: RP1177-B5-48H-27C-Cy5

description: Used a Cy3 replicate of sample RP1177 because a batch 2 sample for this condition was not available. A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.


title: RP1190-B3-48H-29C


title: LPS+SMD at 200mg/kg, biological rep1


title: RP1161-B2-72H-29C


title: RP1175-B4-48H-27C


title: Smoke rep 2

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software

source_name: Adult ovary from cigarette smoke exposed mouse

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: All experimental procedures involving the use of animals were performed with the approval of the University of Newcastle’s Animal Care and Ethics Committee (ACEC). Specific pathogen-free adult female (6-week-old) C57BL/6 mice were obtained from the animal services unit and maintained according to the recommendations prescribed by the ACEC. Mice were housed under a controlled lighting regime (16L:8D) at 21–22°C and supplied with food and water ad libitum.

extract_protocol: Total RNA (approximately 3 µg) was isolated from adult ovaries using a QIAGEN RNeasy Mini Kit (Hilden, Germany) in accordance with the manufacturer’s recommendations.

treatment_protocol: Twenty-one C57BL/6 5 week old female mice were simultaneously exposed to cigarette smoke [twelve 3R4F reference cigarettes (University of Kentucky, USA) twice/day, 2.7 mg particulate matter, five times per week, for 12-18 weeks] using a custom-designed and purpose-built nose-only, directed flow inhalation and smoke-exposure system (CH Technologies, NJ, USA) housed in a fume and laminar flow hood. Each exposure lasted 60 minutes. Control mice received room air.

value: Ovary

tag: genetic background

tag: treatment

value: cigarette smoke


title: RP1156-B2-72H-27C


title: RP1187-B5-48H-29C


title: RP1157-B2-72H-27C


title: Smoke rep 3


title: LPS+SMD at 100mg/kg, biological rep1


title: RP567-B4-24H-29C

value: 24 hours


title: Control rep 1

source_name: Adult ovary from room air exposed mouse

value: control


title: LPS, biological rep3

description: Global gene expression in peritoneal macrophages after LPS challenge

source_name: Mice challenged with LPS


title: RP1295-B2-24H-27C


title: Smoke rep 1


title: Control rep 2


title: LPS, biological rep2


title: Control rep 3


title: Tumor_M3_GFP+

city: Durham

first: Yun

last: Zhang

state: North Carolina

address: 308 Research Dr., C215 LSRC

department: Pharmacology and Cancer Biology

institute: Duke University

description: Test, repeat 3

data_processing: For the normalization, we used the house keepting gene β-actin. Target gene signals normalized to β-actin signal as 2^-deltaCt, where deltaCt = (Ct_Target − Ct_β-actin).

label: SYBR Green

source_name: GFP positive 4T1 tumor cells isolated from xenograft tumors initiated using 4T1 cells with pri-miR-126 overexpression

label_protocol: We utilized a SYBR-based real-time PCR to quantify mature miRNA expression (Quantobio Technology). cDNA were synthesized using superscript III reverse transcriptase (Invitrogen) with oligo dT as the primer.

growth_protocol: Control and pri-miR-126 overexpression 4T1 cells were maintained in RPMI 1640 medium with 10% fetal bovine serum and 1% penicillin/streptomycin. Tumor cells were inoculated into the mammary fat pad of 6~8 week old female BALB/c mice following an established protocol. 10 days later, tumors were excised, treated with collagenase, and GFP positive cells were sorted out for RNA isolation.

extract_protocol: The total RNA of cells was isolated with the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions.

value: miR-126/126* overexpression

tag: cell line


title: Tumor_M2_GFP+

description: Test, repeat 2


title: control_AIM2 negative

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: Gene expression data from mock-transfected HCT116 cells, showing absent AIM2 expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome 133 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

data_processing: a CustomCDF file was used to annoatate the microarrays ( http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp, version 10). The data were quantile normalized and analyzed with JMP Genomics based on mixed model ANOVA.

organism: Homo sapiens

source_name: mock-transfected HCT116 cells showing absent AIM2 expression

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: All cell lines were grown in RPMI 1640 (Invitrogen, Life Technologies, Karlsruhe, Germany) supplemented with 10% FCS, 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: RNA was extracted using RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Construction of subclones D1 and B8 and control was described in Patsos et al., 2009.

tag: aim2 expression

value: absent expression


title: D1_AIM2 positive

description: Gene expression data from transfected HCT116 cells, subclone D1, showing persistent AIM2 expression

source_name: transfected HCT116 cells with persistent AIM2 expression

tag: sub-clone

value: persistent expression


title: RP574-B4-24H-29C

value: larval culture


title: RP1182-B3-48H-29C


title: B8_AIM2 positive

description: Gene expression data from transfected HCT116 cells, subclone B8, showing persistent AIM2 expression


title: EP602-B2-24H-29C


title: LPS, biological rep1


title: suspended melanoma

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

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

label: Biotin

source_name: suspended culture cells

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

growth_protocol: The cells were maintained in DMEM medium supplemented with 10% (v/v) FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin under 5% CO2 with 100% humidity at 37 degree

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: The suspended cells were derived from adherent cells by plating  onto sterile plastic dishes at the density of 4x10^5 cells per 10 ml under the same culture medium as adherent culture did.


title: adherent melanoma

source_name: adherent culture cells


title: Tumor_M1_GFP+

description: Test, repeat 1


title: RP553-B5-24H-27C


title: Tumor_C3_GFP+

description: Control, repeat 3

source_name: GFP positive 4T1 tumor cells isolated from xenograft tumors initiated using 4T1 cells with control vector


title: RP560-B5-24H-27C


title: Tumor_C1_GFP+

description: Control, repeat 1


title: Tumor_C2_GFP+

description: Control, repeat 2


title: MCF10CA1a.cl1 M-IV

description: high metastatic potential

data_processing:
For the normalization, it used the small RNA U6. Target gene signals normalized to U6 signal as 2^-deltaCt, where deltaCt = (Ct_Target − Ct_U6).
Fold Change worksheet reports M-IV/M-II, M-III/M-II and M-IV/M-III ratios.

label_protocol: We utilized a SYBR-based real-time PCR to quantify mature miRNA expression (Quantobio Technology). E. coli polyA polymerase was employed to add adenines at the 3' end of RNA molecules lacking a polyA tail. Following oligo dT annealing, a universal tag was attached to the 3' end of cDNAs during the cDNA synthesis using superscript III reverse transcriptase (Invitrogen). With this universal tag, qPCR was performed with miRNA-specific forward primers and a universal reverse primer mix.

growth_protocol: The cells were cultured in vitro for three days. M-II were cultured in DMEM/F12 medium containing 5% horse serum, 10 ug/ml insulin, 20 ng/ ml EGF, 500 ng/ml hydrocortisone and 100 ng/ml cholera toxin. M-III and M-IV were cultured in DMEM/F12 medium containing 5% horse serum.

extract_protocol: The total RNA of cells was isolated with the miRVana extraction kit (Ambion) according to the manufacturer's instructions.

tag: phenotype

value: high metastatic potential


title: inducible clone, biological replicate1

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 1.CEL

hyb_protocol: Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline

growth_protocol: The growth of each inducible clone was performed in medium deprived of Tetracycline for 48 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted

extract_protocol: Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

value: mouse Embryonic Stem (ES)  cells


title: EP606-B2-24H-29C

value: batch 2


title: MCF10CA1h M-III

description: low metastatic potential

value: low metastatic potential


title: MCF10AT1 M-II

description: benign

value: benign


title: CTL, biological replicate 3

description:
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 3.CEL

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: inducible clone, biological replicate2

description:
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 2.CEL


title: inducible clone, biological replicate3

description:
Gene expression data from mouse inducible ES stable clone
Raw data file: induction 3.CEL


title: RP564-B3-24H-27C


title: RP557-B3-24H-27C


title: CTL, biological replicate 1

description:
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 1.CEL


title: shE13, biological replicate2

description:
Gene expression data from mouse specific gene knock-down ES stable clone
Raw data file: shE13 2.CEL

hyb_protocol: Biotinylated cRNAs were then generated, using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.

source_name: specific gene knock-down ES cell line

growth_protocol: The growth of each clone was performed in mouse ES standard conditions and the total RNA was extracted

treatment_protocol: The stable knock-down cell line was generated by using the short-hairpin RNA strategy.


title: shE13, biological replicate1

description:
Gene expression data from mouse specific gene knock-down ES stable clone
Raw data file: shE13 1.CEL


title: CTL, biological replicate 2

description:
Gene expression data from mouse inducible ES stable control clone
Raw data file: CTL 2.CEL


title: RP566-B5-24H-29C

description: A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.

source_name: Acropora palmata larval culture


title: shE13, biological replicate 3

description:
Gene expression data from mouse specific gene knock-down ES stable clone
Raw data file: shE13 3.CEL


title: shCTL, biological replicate 2

description:
Gene expression data from mouse knock-down ES stable control clone
Raw data file: shCTL 2.CEL

source_name: knock-down ES stable cell line control


title: RP573-B5-24H-29C


title: hypo-norm_rep4

status: Public on Dec 12 2012

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

description: biological replicate 4 of 6

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Following instructions of GenePix 4000B Array Scanner; extract intensity information using GenePix Pro 6

data_processing: Background corrected and LOWESS normalized; R plus limma package

organism: Locusta migratoria

source_name: hypoxia-treated locusts

label_protocol: 40 µg of total RNA were primed with 2.5 µl of 2 µg/µl oligo(dT) at 68°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM aa-dUTP

growth_protocol: 30 centidegree, light:dark=14h:10h, wheat bran as food

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Simulated 4km altitude hypoxia

value: thoratic flight muscle

source_name: locusts in normoxia


title: hypo-norm_rep3

description: biological replicate 3 of 6


title: hypo-norm_rep2

description: biological replicate 2 of 6


title: RP568-B3-24H-29C

description: This sample was not used for analysis after initial normalization. A batch extract from 30-100 coral larvae derived from the same set of four parent colonies from Rincon, Puerto Rico, and raised at a common temperature for a specified time since fertilization.


title: RP576-B3-24H-29C


title: RP1293-B2-24H-27C


title: RP561-B4-24H-27C

value: batch 4


title: LPS+SMD at 100mg/kg, biological rep2

description: Global gene expression in peritoneal macrophages 2.0 hrs after LPS challenge and SMD pretreatment at 100mg/kg

source_name: Mice challenged with LPS and SMD pretreatment at 100mg/kg

value: C57Bl/6 x C3H F1

value: female

value: peritoneal macrophages


title: RP555-B4-24H-27C


title: hypo-norm_rep1

description: biological replicate 1 of 6


title: hypo-norm_rep5

description: biological replicate 5 of 6


title: hypo-norm_rep6

description: biological replicate 6 of 6


title: T-ALL-SNP-#99

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

hyb_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

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 500.

source_name: RNA extracted from T-lineage ALL

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases at diagnosis.

extract_protocol: Total RNA extraction (Trizol)

value: leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type

value: T-lineage ALL


title: T-ALL-SNP-#90

scan_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: T-ALL-SNP-#89

label_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: T-ALL-SNP-#88


title: T-ALL-SNP-#92


title: T-ALL-SNP-#85


title: T-ALL-SNP-#74


title: T-ALL-SNP-#75


title: T-ALL-SNP-#87


title: T-ALL-SNP-#79

source_name: RNA extracted from T-lineage ALL and early thymic progenitor immunophenotype


title: T-ALL-SNP-#73


title: T-ALL-SNP-#91

value: T-lineage ALL and early thymic progenitor immunophenotype


title: Other-SNP-#116

source_name: RNA extracted from B-precursor ALL with miscellaneous karyotype


title: T-ALL-SNP-#71


title: T-ALL-SNP-#80


title: Other-SNP-#122

value: B-precursor ALL with miscellaneous karyotype


title: T-ALL-SNP-#77


title: Hyperdip47-50-SNP-#38

source_name: RNA extracted from B-precursor ALL with low hyperdiploid karyotype


title: Other-SNP-#113


title: shCTL, biological replicate 1

description:
Gene expression data from mouse knock-down ES stable control clone
Raw data file: shCTL 1.CEL


title: Other-SNP-#99


title: Other-SNP-#110


title: Other-SNP-#102


title: Pseudodip-SNP-#08

source_name: RNA extracted from B-precursor ALL with pseudodiploid karyotype


title: Other-SNP-#147

source_name: RNA extracted from tumor with alteration of ERG

value: tumor with alteration of ERG


title: T-ALL-SNP-#101


title: Other-SNP-#141


title: Other-SNP-#140


title: Other-SNP-#159


title: Other-SNP-#125


title: Other-SNP-#129


title: Other-SNP-#152

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with CRLF2 rearrangement

value: childhood ALL with CRLF2 rearrangement


title: TEL-AML1-SNP-#88

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: Other-SNP-#100


title: TEL-AML1-SNP-#114

value: childhood ALL with ETV6-RUNX1 rearrangement


title: Other-SNP-#101


title: Other-SNP-#112


title: MLL-SNP-#03

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement

value: childhood ALL with MLL rearrangement


title: Down-SNP-#20


title: MLL-SNP-#29


title: Other-SNP-#126


title: TEL-AML1-SNP-#87


title: TEL-AML1-SNP-#76


title: TEL-AML1-SNP-#84


title: TEL-AML1-SNP-#23


title: TEL-AML1-SNP-#85


title: TEL-AML1-SNP-#58


title: E2A-PBX1-SNP-#35

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with TCF3-PBX1 rearrangement


title: Other-SNP-#108


title: TEL-AML1-SNP-#77


title: E2A-PBX1-SNP-#34

value: childhood ALL with TCF3-PBX1 rearrangement


title: TEL-AML1-SNP-#78


title: E2A-PBX1-SNP-#24


title: E2A-PBX1-SNP-#32


title: Hyperdip>50-SNP-#167

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype


title: E2A-PBX1-SNP-#25


title: Hyperdip>50-SNP-#160

value: childhood ALL with high hyperdiploid karyotype


title: Hyperdip>50-SNP-#158


title: Control Expt - PCY87 + no Dox - repeat 6 - Rev. fluor.

city: San Antonio

first: David

last: Kadosh

state: TX

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

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: GenePix and ScanArray Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4000B (Serial No.: 82713) microarray scanner along with ScanArray Express 2.00 image analysis software.

data_processing:
Dox Control 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. For the experiment to determine the effect of Dox alone on C. albicans global gene expression, signal ratios for the minus Dox sample versus reference were divided by signal ratios for the 20 ug/mL Dox sample versus reference. This experiment was performed using 5 independent biological replicates. Three of the biological replicates were labeled using normal fluors, one of which was repeated as a technical replicate using reverse fluors. Two of the 5 biological replicates were performed using reverse fluors.

organism: Candida albicans

source_name: Dosage Expt - Cy5 Reference Sample

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.

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: genotype/variation

tag: other

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: Control Expt - PCY87 + no Dox - Cy3

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.

treatment_protocol:
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In order to determine the effect of Dox alone on C. albicans global gene expression, the PCY87 control strain was grown to saturation and diluted into 50 mL YEPD medium in the presence or absence of 20 µg/mL Dox. These cultures were grown overnight at 30°C and cells were harvested for RNA preparation at OD600 = 1.0.


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 5 - Rev. fluor.

description: No additional information.

tag: strain

source_name: Control Expt - PCY87 + 20 ug/ml Dox - Cy3

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: Overnight
Treatment temperature: 30 C
In-vitro treatment: In order to determine the effect of Dox alone on C. albicans global gene expression, the PCY87 control strain was grown to saturation and diluted into 50 mL YEPD medium in the presence or absence of 20 µg/mL Dox. These cultures were grown overnight at 30°C and cells were harvested for RNA preparation at OD600 = 1.0.


title: Control Expt - PCY87 + no Dox - repeat 5 - Rev. fluor.

description: No additional information.


title: Control Expt - PCY87 + no Dox - repeat 4

description: No additional information.

source_name: Dosage Expt - Cy3 Reference Sample

source_name: Control Expt - PCY87 + no Dox - Cy5


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 2

description: No additional information.

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.

source_name: Control Expt - PCY87 + 20 ug/ml Dox - Cy5


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 3 - Rev. fluor.

description: No additional information.


title: Control Expt - PCY87 + no Dox - repeat 2

description: No additional information.


title: Control Expt - PCY87 + no Dox - repeat 3 - Rev. fluor.

description: No additional information.


title: Hyperdip>50-SNP-#152


title: Hyperdip>50-SNP-#132


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 4

description: No additional information.


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 6 - Rev. fluor.

description: No additional information.


title: Hyperdip>50-SNP-#139


title: Hyperdip>50-SNP-#163


title: Hyperdip>50-SNP-#133


title: Control Expt - PCY87 + 20 ug/ml Dox - repeat 1

description: No additional information.


title: Control Expt - PCY87 + no Dox - repeat 1

description: No additional information.


title: Hyperdip>50-SNP-#124


title: Hyperdip>50-SNP-#129


title: Hyperdip>50-SNP-#116


title: Reverse Trans Expt 2 - MBY38 + no Dox 10 hrs

description: No additional information.

scan_protocol: GenePix Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4000B (Serial No.: 82713) microarray scanner along with GenePix Pro 6.0.1.25 image analysis software (Molecular Devices, Sunnyvale, CA).

data_processing:
Reverse 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 reverse hyphal-pseudohyphal-yeast transition time course experiment was repeated twice (2 independent biological replicates). For each biological replicate, first separate median signal ratios (ratio of the median signal intensity of each spot) for +Dox and -Dox zero time point versus reference were determined based on 3 technical replicates each (one of which was performed using reverse fluors) using cDNA from the same total RNA preparation. Next, signal ratios for each time point sample versus reference were divided by the signal ratio for the corresponding zero time point versus reference.

source_name: Reverse Transition Expt - Cy3 Reference Sample

value: Reverse Transition Pooled Reference:Equal aliquots of the 22 sample RNAs (Dox dosage of 20 ug/ml (n=11) or 0 ug/ml (n=11) at time points from 0 to 10 hours) were combined to create a pooled reference sample.

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

treatment_protocol:
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 8 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 7 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 9 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Hyperdip>50-SNP-#134


title: Reverse Trans Expt 2 - MBY38 + no Dox 6 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 5 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Hyperdip>50-SNP-#136


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

description: No additional information.

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

treatment_protocol:
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 3 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 2 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Hyperdip>50-SNP-#109

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype


title: Hyperdip>50-SNP-#115


title: Hyperdip>50-SNP-#121


title: Reverse Trans Expt 2 - MBY38 + no Dox 0 hrs - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Reverse Transition Expt - Cy5 Reference Sample

source_name: Reverse Transition Expt - MBY38 + no Dox 0 hr - Cy3

treatment_protocol:
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 0 hrs - repeat 2

description: No additional information.

source_name: Reverse Transition Expt - MBY38 + no Dox 0 hr - Cy5


title: Hyperdip>50-SNP-#113


title: Hyperdip>50-SNP-#104


title: Hyperdip>50-SNP-#107


title: Reverse Trans Expt 2 - MBY38 + no Dox 0 hrs - repeat 1

description: No additional information.


title: Hyperdip>50-SNP-#82


title: Reverse Trans Expt 2 - MBY38 + Dox 10 hrs

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + no Dox 4 hrs

description: No additional information.

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

treatment_protocol:
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 2 - MBY38 + Dox 9 hrs

description: No additional information.

source_name: Reverse Transition Expt - Cy3 Reference Sample

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: High zinc replicate 3 array 2

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 high 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: high zinc or LZM3000


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: High zinc replicate 2 array 2


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: 882-1

city: HOUSTON

first: Zhengxin

last: Jiang

state: Texas

address: ONE BAYLOR PLAZA

department: MOLECULAR AND HUMAN GENETICS

institute: BAYLOR COLLEGE OF MEDICINE

description: Zic3 flox/y; Sox2-cre

hyb_protocol: Biotinylated cRNAs were hybridized onto Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) per manufacturer’s instructions.

scan_protocol: Hybridized BeadChips were scanned by iScan (Illumina) per manufacturer’s instructions.

data_processing: Data were quantile normalized and background subtracted in Genome Studio (Illumina)

source_name: Heart

label_protocol: In vitro transcription and labeling was performed using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion).

extract_protocol: Total RNAs were extracted and purified using RNeasy Mini Kit (QIAGEN) in accordance with the prescribed protocol provided with the kit. Spectrophotometry (NanoDrop-1000 Spectrophotometer, Thermo Fisher Scientific) and microfluidic electrophoresis (Experion Automated Electrophoresis System, Bio-Rad Laboratories) were used for RNA quality control.

value: Male

value: Embryonic heart

tag: Stage

value: Zic3 flox/y; Sox2-cre


title: 1493-1

description: Zic3 -/y

value: Zic3 -/y


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: ZJGXZ3_1191-2

description: Zic3 -/y


title: 913-1

description: Zic3 flox/y; Sox2-cre


title: Low zinc replicate 1 array 2

source_name: S. pombe grown in low zinc conditions

value: low zinc or LZM3


title: ZJGXZ3_1191-3

description: Zic3 -/y


title: ZJGXZ3_1235-8

description: Zic3 -/y


title: 882-2

description: Zic3 flox/y; Sox2-cre


title: High zinc replicate 1 array 2


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

description: No additional information.

source_name: Reverse Transition Expt - Cy5 Reference Sample

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


title: 1322-3

description: Zic3 -/y


title: ZJGXZ3_628-4

description: Zic3 flox/y; Sox2-cre


title: ZJGXZ3_754-4

description: Zic3 flox/y; Sox2-cre


title: Low zinc replicate 3 array 2


title: Low zinc replicate 2 array 2


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

description: No additional information.

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

treatment_protocol:
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: 741-4

description: Zic3 flox/y

value: Zic3 flox/y


title: ZJGXZ3_754-2

description: Zic3 flox/y; Sox2-cre


title: 741-3

description: Zic3 flox/y


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

description: No additional information.

source_name: Reverse Transition Expt - Cy3 Reference Sample

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

treatment_protocol:
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 1 - MBY38 + no Dox 0 hrs - repeat 3 - Rev. fluor.

description: No additional information.

source_name: Reverse Transition Expt - MBY38 + no Dox 0 hr - Cy3

treatment_protocol:
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 1 - MBY38 + no Dox 0 hrs - repeat 2

description: No additional information.

source_name: Reverse Transition Expt - MBY38 + no Dox 0 hr - Cy5


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

description: No additional information.

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

treatment_protocol:
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Reverse Trans Expt 1 - MBY38 + no Dox 0 hrs - repeat 1

description: No additional information.


title: WT-5

description: Zic3 +/y

source_name: Heart

value: Zic3 +/y


title: ZJGXZ3_E15-4

description: Zic3 +/y


title: 680-5

description: Zic3 flox/y


title: ZJGXZ3_628-1

description: Zic3 flox/y


title: Wildtype_male_4

city: Brisbane

first: Melissa

middle: Helen

last: Little

state: Queensland

address: Carmody Rd, St. Lucia

department: Institute for Molecular Bioscience

institute: The University of Queensland

description: SAMPLE 8

data_processing: The data were vst transformed and rsn normalised with lumi in R

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

extract_protocol: RNA was extracted with the use of a QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: wild type

value: adult

value: male

value: kidney

value: CD31+ MACS sorted endothelial cells


title: ZJGXZ3_678-5

description: Zic3 flox/y


title: WT-2

description: Zic3 +/y


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 9 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: WT-1

description: Zic3 +/y


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 8 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Hyperdip>50-SNP-#117

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype

value: leukemic cells obtained from bone marrow or blood at diagnosis


title: ZJGXZ3_678-4

description: Zic3 flox/y


title: Crim1_male_4

description: SAMPLE 7

value: Crim1KST264/KST264 mutant


title: ZJGXZ3_E15-6

description: Zic3 +/y


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 10 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


title: Wildtype_female_3

description: SAMPLE 6

value: female


title: Crim1_female_3

description: SAMPLE 5


title: Wildtype_male_2

description: SAMPLE 4


title: Crim1_male_2

description: SAMPLE 3


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

description: No additional information.

value: Reverse Transition Pooled Reference:Equal aliquots of the 22 sample RNAs (Dox dosage of 20 ug/ml (n=11) or 0 ug/ml (n=11) at time points from 0 to 10 hours) were combined to create a pooled reference sample.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 4 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

source_name: Reverse Transition Expt - Cy3 Reference Sample

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 5 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 6 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 3 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 2 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 0 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.

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

treatment_protocol:
Treatment type: compound
Agent: Doxycycline (Dox)
Treatment dose: 20.0 ug/mL
Treatment time: 1 hours
Treatment temperature: 30 C
In-vitro treatment: In order to carry out the reverse hyphal-pseudohyphal-yeast transition experiment, the tetO-UME6 strain was grown overnight in 1.5 L YEPD medium at 30°C in the absence of Dox. When the culture reached OD600 ~ 0.01, Dox was added to a concentration of 20 µg/mL and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected immediately prior to the addition of Dox. Over the time course cells were also harvested from an additional control culture in which the tetO-UME6 strain was grown in the same manner but in the absence of Dox.


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

description: No additional information.


title: CD4 D30 Chronic  3

city: Philadelphia

first: Alison

last: Crawford

address: 421 Curie Blvd, BRB

department: Microbiology

institute: University of Pennsylvania

description: 3265_14066_4C4C30 _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.

source_name: CD4 D30 Chronic

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.

value: spleen


title: Forward Trans Expt 2 - MBY38 + no Dox 10 hrs

description: No additional information.

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.

source_name: Forward Transition Expt - Cy3 Reference Sample

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 + 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: Crim1_female_1

description: SAMPLE 1


title: CD4 D30 Chronic

description: 3265_14063_1C4C30 _MoGene1.0ST


title: CD4 D30 Chronic  1

description: 3265_14064_2C4C30 _MoGene1.0ST


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

description: No additional information.

source_name: Reverse Transition Expt - Cy5 Reference Sample

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


title: CD4 D15 Chronic  3

description: 3265_14062_4C4C15 _MoGene1.0ST

source_name: CD4 D15 Chronic


title: CD4 D15 Chronic  1

description: 3265_14060_2C4C15 _MoGene1.0ST


title: Wildtype_female_1

description: SAMPLE 2


title: Forward Trans Expt 2 - 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: CD4 D15 Chronic  2

description: 3265_14061_3C4C15 _MoGene1.0ST


title: Forward Trans Expt 2 - 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: CD4 D8 Chronic  2

description: 3265_14057_3CD4C8 _MoGene1.0ST

source_name: CD4 D8 Chronic


title: CD4 D15 Chronic

description: 3265_14059_1C4C15 _MoGene1.0ST


title: CD4 D8 Chronic  3

description: 3265_14058_4CD4C8 _MoGene1.0ST


title: Forward Trans Expt 2 - 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: CD4 D30 Chronic  2

description: 3265_14065_3C4C30 _MoGene1.0ST


title: CD4 D8 Chronic  1

description: 3265_14056_2CD4C8 _MoGene1.0ST


title: Forward Trans Expt 2 - 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 2 - 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: CD4 D8 Chronic

description: 3265_14055_1CD4C8 _MoGene1.0ST


title: CD4 D6 Chronic  3

description: 3265_14054_4CD4C6 _MoGene1.0ST

source_name: CD4 D6 Chronic


title: Forward Trans Expt 2 - 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: CD4 D6 Chronic  1

description: 3265_14052_2CD4C6 _MoGene1.0ST


title: CD4 D6 Chronic  2

description: 3265_14053_3CD4C6 _MoGene1.0ST


title: Forward Trans Expt 2 - 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: Forward Trans Expt 2 - 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: Forward Trans Expt 2 - 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: CD4 D6 Chronic

description: 3265_14051_1CD4C6 _MoGene1.0ST


title: CD4 D30 Acute  3

description: 3265_14050_4C4A30 _MoGene1.0ST

source_name: CD4 D30 Acute


title: Forward Trans Expt 2 - MBY38 + Dox 9 hrs

description: No additional information.

source_name: Forward Transition Expt - Cy3 Reference Sample

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: CD4 D30 Acute  2

description: 3265_14049_3C4A30 _MoGene1.0ST


title: Forward Trans Expt 2 - MBY38 + Dox 10 hrs

description: No additional information.

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: CD4 D30 Acute  1

description: 3265_14048_2C4A30 _MoGene1.0ST


title: CD4 D30 Acute

description: 3265_14047_1C4A30 _MoGene1.0ST