title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3691

first: Maarten

last: Fornerod

department: Gene Regulation

institute: Netherlands Cancer Institute

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 7,542 probes was used for analyses. Signals were not background-subtracted, normalized between arrays using the ÒvsnÓ procedure of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Various contrasts of the Lam TSA microarray experiment can be extracted using the multifactorial capabilities of the limma package

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the presence of TSA

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 100 nanomolar Trichostatin A (TSA) for 24h proir to lysis.

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Dam plus TSA

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the absence of TSA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam minus TSA


title: MouseBloodNotInfected3LPSInflammation

status: Public on Aug 29 2006

type: RNA

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

country: USA

institute: Washington University in St. Louis

description:
UNKOWN
Gene expression data

data_processing: The data were analyzed with dChip

label: biotin

molecule: total RNA

organism: Mus musculus

tag: Tissue

value: Blood

tag: Type

value: NotInfected

tag: Batch

tag: Group

value: LPS

tag: Phenotype

value: Inflammation


title: XZ_colWhole_HMBDH_04_F0115_06242005.CEL

status: Public on Aug 30 2006

type: genomic

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: Enriched for CG-methylated DNA

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: Gene chip data files were processed using TileMap and KS method.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: whole palnt tissue w/o root, 40 days

label_protocol: The genomic DNA in the samples was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1 h at 37 degrees C.

growth_protocol: Plants were grown on soil under continuous illumination for 40 days at 25 degrees C

extract_protocol: genomic DNA was isolated from whole plant tissues using DNAeasy kit following instructions from the manufacturer (QIAGEN) instruction

treatment_protocol: Untreated

tag: Enriched for CG-methylated DNA


title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3690

city: Amsterdam

country: Netherlands

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodNotInfected1LPSInflammation

description:
UNKOWN
Gene expression data


title: E. coli D1 #1

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: Hybridization of genomic DNA from E. coli strain D1

data_processing: Standard Affymetrix procedure

label: terminal labeling with biotinylated Affymetrix GeneChip DNA Labeling Reagent

organism: Escherichia coli

label_protocol: see section 3 (Prokaryotic Sample and Array Processing) of the Affymetrix GeneChip Expression Analysis manual

growth_protocol: overnight in Luria-Bertani (LB) broth with continuous agitation

extract_protocol: Qiagen Genomic Tip 500/G (Qiagen, Hilden, Germany) and the Genomic DNA Buffer set (Qiagen)

tag: serotype O175:H16


title: E. coli EDL933 #2

description: Hybridization of genomic DNA from E. coli EDL933

tag: serotype O157:H7


title: E. coli 3538 #3

description: Hybridization of genomic DNA from E. coli strain 3538


title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3689

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam, grown in the presence of TSA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 100 nanomolar Trichostatin A (TSA) for 24h proir to lysis.

tag: Dam-Lam plus TSA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 100 nanomolar Trichostatin A (TSA) for 24h proir to lysis.


title: XZ_colWhole_HMBDL_02_F0217_05052005.CEL

description: Depleted for CG-methylated DNA

tag: Depleted for CG-methylated DNA


title: E. coli 3538 #2


title: XZ_colWhole_mCIPE_06_F0445_12222005.CEL

description: Enriched for methylated DNA at all sequenced contexts


title: E. coli phage 3538 #1

extract_protocol: DNA were extracted and purified as described by Muniesa et al. (2003). Shiga toxin 2-converting bacteriophages associated with clonal variability in Escherichia coli O157:H7 strains of human origin isolated from a single outbreak. Infect Immun 71, 4554-4562.

treatment_protocol: Induced from E. coli strain 3538 with mitomycin C

tag: phage DNA


title: MouseBloodInfected3CLPSeptic

description:
UNKOWN
Gene expression data

value: Infected

value: CLP

value: Septic


title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3688

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodInfected2CLPSeptic

description:
UNKOWN
Gene expression data


title: E. coli D1 #3


title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3687

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam, grown in the absence of TSA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam-Lam minus TSA


title: E. coli phage 3538 #2


title: Embryonic Drosophila cells, Kc167 cells, Lam TSA DamID, array 3686

description: Embryonic Drosophila cells, Kc167 cells


title: E. coli K-12 W3110 #1

description: Hybridization of genomic DNA from E. coli strain K-12 isolate W3110

tag: Isolate W3110 of K-12 strain


title: MouseBloodInfected3CLP+ABXSeptic

description:
UNKOWN
Gene expression data

value: CLP+ABX


title: MouseBloodInfected2CLP+ABXSeptic

description:
UNKOWN
Gene expression data


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3465

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 7,542 probes was used for analyses. Signals were not background-subtracted, normalized between arrays using the ÒvsnÓ procedure of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Various contrasts of the Lam ecdysone microarray experiment can be extracted using the multifactorial capabilities of the limma package

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the presence of Ecdysone

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 1 micromolar Ecdysone for 24h proir to lysis.

tag: Dam plus Ecdysone

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the absence of Ecdysone

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam minus Ecdysone


title: MouseBloodInfected1CLP+ABXSeptic

description:
UNKOWN
Gene expression data


title: XZ_colWhole_HMBDH_03_F0117_06242005.CEL

description: Enriched for CG-methylated DNA


title: XZ_colWhole_HMBDH_02_F0216_05052005.CEL

description: Enriched for CG-methylated DNA


title: MouseBloodNotInfected5NormalControl

description:
UNKOWN
Gene expression data

value: Normal

value: Control


title: XZ_colWhole_HMBDL_04_F0116_06242005.CEL

description: Depleted for CG-methylated DNA


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3637

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3463

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam, grown in the presence of Ecdysone

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 1 micromolar Ecdysone for 24h proir to lysis.

tag: Dam-Lam plus Ecdysone

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam, grown in the absence of Ecdysone

tag: Dam-Lam minus Ecdysone


title: MouseBloodInfected5CLP+ABXSeptic

description:
UNKOWN
Gene expression data

tag: Tissue


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3443

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3464

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3442

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 1 micromolar Ecdysone for 24h proir to lysis.


title: MouseBloodNotInfected5SalineControl

description:
UNKOWN
Gene expression data

tag: Type

value: Saline


title: MouseBloodNotInfected5ShamControl

description:
UNKOWN
Gene expression data

tag: Batch

value: Sham


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3441

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodInfected5CLPMildSeptic

description:
UNKOWN
Gene expression data

tag: Group

value: CLPMild


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3436

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3434

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodNotInfected2LPSInflammation

description:
UNKOWN
Gene expression data

tag: Phenotype


title: E. coli 3538 #1


title: MouseBloodNotInfected4ShamControl

description:
UNKOWN
Gene expression data


title: MouseBloodInfected1CLPSeptic

description:
UNKOWN
Gene expression data


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX TSA DamID, array 3695

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam_delta_CaaX, grown in the presence of TSA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. Lam_delta_CaaX was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 100 nanomolar Trichostatin A (TSA) for 24h proir to lysis.

tag: Dam-Lam_delta_CaaX plus TSA

tag: Dam plus TSA


title: MouseBloodInfected4CLP+ABXSeptic

description:
UNKOWN
Gene expression data


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX DamID, replicate 2968

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 8,484 probes was used for analyses. Signals were background-subtracted, normalized within arrays using ÒlowessÓ and between arrays using ÒaquantileÓ procedures of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Ratios Lam-Dam/Dam were log base 2-transformed and normalized to the median value of the entire array

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam_delta_CaaX-Lam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. Lam_delta_CaaX was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam-Lam_delta_CaaX (EXPERIMENTAL)

tag: Dam (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX TSA DamID, array 3693

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam_delta_CaaX, grown in the absence of TSA

tag: Dam-Lam_delta_CaaX minus TSA


title: MouseBloodNotInfected4LPSInflammation

description:
UNKOWN
Gene expression data


title: MouseBloodInfected5CLPSeptic

description:
UNKOWN
Gene expression data


title: MouseBloodNotInfected4NormalControl

description:
UNKOWN
Gene expression data


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX DamID, replicate 2966

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam


title: MouseBloodInfected4CLPMildSeptic

description:
UNKOWN
Gene expression data


title: 15Mm.108

city: Indianapolis

first: Hosein

last: Kouros-Mehr

state: IN

address: 533 Merrill St.

department: Oncology

institute: Eli Lilly

description: Total RNA from GATA-3flox/flox; WAP-rtTA-Cre compared to GATA-3flox/+; WAPrtTA-Cre after dox treament

data_processing: Lowess print-tip normalization (Acuity 4.0)

source_name: GATA-3flox/+; WAP-rtTA-Cre

tag: Whole mammary gland RNA after doxycycline adminstration

source_name: GATA-3flox/flox; WAP-rtTA-Cre


title: Embryonic Drosophila cells, Kc167 cells, Lam DamID, replicate 2955

description: Embryonic Drosophila cells, Kc167 cells"

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 8,485 probes was used for analyses. Signals were background-subtracted, normalized within arrays using ÒlowessÓ and between arrays using ÒaquantileÓ procedures of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Ratios Lam-Dam/Dam were log base 2-transformed and normalized to the median value of the entire array

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam

tag: Dam-Lam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX DamID, replicate 2962

description: Embryonic Drosophila cells, Kc167 cells


title: 15Mm.105


title: F201 E+HS 1st rep

city: Columbia

first: Sachin

middle: S

last: Bhusari

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

description: experimental mouse exposed to E+, HS were sacrificed to extract liver RNA and labeled with Cy5 and reference RNA labeled with Cy3.

source_name: liver of mouse exposed to E+ and HS

label_protocol: indirect labeling

treatment_protocol: Liver tissue obtained from mice exposed to endophyte-infected (E+) fescue and heat stress (HS) for a peroid of 14d.

tag: Strain:ICR inbred mice, age

value: 45d old, liver tissue

source_name: Univ mouse reference RNA

tag: RNA extracted from 11 different mouse cell lines.


title: F201 E+HS SD

description: experimental mouse exposed to E+, HS were sacrificed to extract liver RNA and labeled with Cy3 and reference RNA labeled with Cy5.

source_name: Liver of mouse exposed to E+ and HS

tag: strain ICR, inbred mice, age 45d, liver tissue


title: Embryonic Drosophila cells, Kc167 cells, Lam DamID, replicate 2945

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodInfected4CLPSeptic

description:
UNKOWN
Gene expression data


title: M221 E+HS 1st rep

source_name: Liver from mouse exposed to E+ and HS.

tag: ICR inbred mice strain, 45d old, liver tissue.

tag: RNA extracted from 11 different cell lines.


title: Embryonic Drosophila cells, Kc167 cells, Lam DamID, replicate 2921

description: Embryonic Drosophila cells, Kc167 cells


title: F231 E+HS 1st rep

source_name: Liver from Mouse exposed to E+ and HS

tag: Strain

value: ICR inbred mice, age 45d old, liver tissue.

tag: RNA extracted from 11 different mice cell lines.


title: MouseBloodNotInfected4SalineControl

description:
UNKOWN
Gene expression data

tag: Tissue

tag: Type

tag: Batch


title: F231 E+HS swap dye

source_name: Liver from mouse exposed to E+, HS.


title: Embryonic Drosophila cells, Kc167 cells, Lam DamID, replicate 2907

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX TSA DamID, array 3694

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam-Lam_delta_CaaX plus TSA

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the presence of TSA


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX TSA DamID, array 3692

description: Embryonic Drosophila cells, Kc167 cells


title: MouseBloodInfected1CLPMildSeptic

description:
UNKOWN
Gene expression data

tag: Group

tag: Phenotype


title: Embryonic Drosophila cells, Kc167 cells, Kc expression profiling, replicate 3459

type: mixed

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 8,485 probes was used for analyses. Signals were not background-subtracted, normalized between arrays using ÒvsnÓ procedures of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Ratios mRNA/genomic DNA are log base 2-transformed and normalized to the median value of the entire array

source_name: Embryonic Drosophila cells, Kc167 cells

label_protocol: cDNA was labelled using ULS technology(Kreatech, Biotechnology).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the sample preparation protocol of the Netherlands Cancer Institute microarray facility web site. mRNA was amplified using T7-mRNA amplification system (Invitrogen).

tag: mRNA (EXPERIMENTAL)

label_protocol: DNA was digested with DpnII and labelled using ULS technology (Kreatech, Biotechnology).

extract_protocol: genomic DNA was extracted using DNeasy DNA extraction kit (Qiagen).

tag: genomic DNA (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, Lam_delta_CaaX DamID, replicate 2967

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam-Lam_delta_CaaX (EXPERIMENTAL)

tag: Dam (REFERENCE)


title: F232 E+HS 1st rep

source_name: liver from mouse exposed to E+, HS

tag: Strain ICR inbred mice, age 45d, liver tissue

source_name: Universal mouse reference RNA


title: F232 E+HS 3rd rep swap dye

source_name: Liver from mice exposed to E+ and HS.

value: ICR inbred mice, age 45 d old, liver tissue.

tag: extracted from 11 different mouse cell lines.


title: M203 E+HS 3rd rep swap dye

source_name: M203 mouse exposed to E+ and HS

tag: ICR inbred strain, age 45d old, liver tissue.


title: MouseBloodNotInfected5LPSInflammation

description:
UNKOWN
Gene expression data


title: Embryonic Drosophila cells, Kc167 cells, Kc expression profiling, replicate 3458

description: Embryonic Drosophila cells, Kc167 cells


title: M203 E+HS 2nd rep

source_name: Mouse liver treated with E+ and HS


title: Myotubes_rep2, chip HG-U133A

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: The goal is to study the genome-wide mapping of histone modifications in differentiating human primary myoblasts.

scan_protocol: GeneArray 2500 scanner

data_processing: MicroArray Suite 5.0

label: Biotin

organism: Homo sapiens

source_name: myotubes

growth_protocol: Cultured in SKGM-2 media

extract_protocol: RNA prep method: RNeasy

tag: Fetal skeletal myoblasts


title: Embryonic Drosophila cells, Kc167 cells, Ecdysone expression profiling, replicate 3452

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 7,542 probes was used for analyses. Signals were not background-subtracted, normalized between arrays using ÒvsnÓ procedures of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Ratios are log base 2-transformed and normalized to the median value of the entire array

source_name: Embryonic Drosophila cells, Kc167 cells, grown in presence of Ecdysone

tag: Ecdysone (EXPERIMENTAL)

tag: Absence of Ecdysone (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, Ecdysone expression profiling, replicate 3451

description: Embryonic Drosophila cells, Kc167 cells


title: M203 E+HS 1st rep

source_name: Liver tissue from mice challanged with E+, HS

tag: Strain ICR inbred mice, age 45 d, liver tissue.

tag: RNA extracted from 11 different mouse cell lines.


title: M234 E+HS 3rd rep swap dye

description: This is the 3rd replicate for this sample done in swap dye design with experimental mouse RNA labeled with Cy3 (532) and reference RNA labeled with Cy5(635).

data_processing: Value is the Normalized value of log2(F532/F635)

source_name: Mouse liver exposed to E+ and HS

label_protocol: Indirect labeling

treatment_protocol: Liver RNA extracted from Mice exposed to Endophyte-infected (E+) fescue and Heat stress (HS) for 14 d.

tag: Strain ICR inbred mice, 45 d old, liver tissue

tag: RNA extracted from 11 different cell lines.


title: Myotubes_rep1, chip HG-U133A

molecule: nuclear RNA


title: Myoblasts_rep3, chip HG-U133A

molecule: cytoplasmic RNA

source_name: myoblasts


title: M234 E+HS 2nd rep

description: This is the 2nd replicate for this sample.

data_processing: Value is the Normalized value of log2(F635/F532)

source_name: Mouse Liver exposed to E+ and HS

tag: ICR inbred strain, Male, 45d old, liver


title: M234 E+HS 1ts rep

description: This is the 1st replicate for this sample.

source_name: Mouse liver RNA exposed to E+ and HS labeled with Cy5

tag: Inbred ICR mice, 45 d old, Male, Liver


title: Myoblasts_rep2, chip HG-U133A


title: Embryonic Drosophila cells, Kc167 cells, Ecdysone expression profiling, replicate 3426

description: Embryonic Drosophila cells, Kc167 cells

label_protocol: cDNA was labelled using ULS technology(Kreatech, Biotechnology)

extract_protocol: Total RNA was extracted using TRIzol reagent according to the sample preparation protocol of the Netherlands Cancer Institute microarray facility web site. mRNA was amplified using T7-mRNA amplification system (Invitrogen)


title: Myoblasts_rep1, chip HG-U133A

description: The goal is to study the genome-wide mapping of histone modifications in differentiateing human primary myoblasts.


title: F232 E+HS 2nd rep

source_name: Liver from mouse exposed to E+, HS

tag: Strain

value: ICR inbred, age:45d old, liver tissue.

source_name: Univ mouse reference RNA


title: Hoxb1 mutant E10.5, rep 2 (M6)

status: Public on Aug 28 2006

city: Salt Lake City

first: Petr

last: Tvrdik

state: UT

department: Human Genetics

institute: University of Utah

description: Transcriptional profiling was done in Hoxb1 mutant  E10.5 embryos in tissues primarily consisting of rhombomere 4 and surrounding branchial arches.

data_processing: Bioconductor affy package

source_name: Rhombomere 4 segments dissected from mutant embryonic hindbrains

tag: The r4 segments with surrounding branchial arch tissues were carefully dissected from mutant or wild type E10.5 embryos, separately pooled in TRIZOL (Invitrogen), snap frozen on dry ice and stored at  –80º C.


title: Hoxb1 mutant E10.5, rep 3 (M8)


title: Hoxb1 wt E10.5, rep 2 (W6)

source_name: Rhombomere 4 segments dissected from normal embryonic hindbrains

tag: The r4 segments with surrounding branchial arch tissues were  carefully dissected from mutant or wild type E10.5 embryos, separately pooled in TRIZOL (Invitrogen), snap frozen on dry ice and stored at  –80º C.


title: Myotubes_rep3, chip HG-U133A


title: WC1 gammadelta T cell vs Reference, #3

status: Public on Aug 26 2006

city: Amherst

first: Seth

last: Blumerman

state: MA

address: Paige Laboratory

institute: University of Massachusetts, Amherst

description: Comparing leptospiral antigen-responsive WC1+ gammadelta T cells to reference of unstimulated PBMC.  Antigen-stimulated cells were cultured 6 days with leptospiral antigen and proliferating cells isolated by FACS.  Reference RNA from total PBMC, ex vivo and unstimulated, pooled RNA from 3 control animals.

data_processing: LOWESS normalization using PROC LOESS

organism: Bos taurus

source_name: WC1+ gammadelta T cell, animal 3

tag: Amplified RNA generated from total RNA isolated from FACS purified antigen-responsive WC1+ gammadelta T cells

source_name: Reference

tag: RNA from total PBMC, unstimulated cells (pool from 3 animals)


title: CD4 alphabeta T cell vs reference, #3

description: Comparing leptospiral antigen-responsive CD4+ alphabeta T cells to reference of unstimulated PBMC.  Antigen-stimulated cells were cultured 6 days with leptospiral antigen and proliferating cells isolated by FACS.  Reference RNA from total PBMC, ex vivo and unstimulated, pooled RNA from 3 control animals.

source_name: CD4+ alphabeta T cell, animal 3

tag: Amplified RNA generated from total RNA isolated from FACS purified antigen-responsive CD4+ alphabeta T cells


title: WC1 gammadelta T cell vs Reference

source_name: WC1+ gammadelta T cell, animal 1


title: Hoxb1 wt E10.5, rep 1 (W5)


title: WC1 gammadelta T cell vs Reference, #2

source_name: WC1+ gammadelta T cell, animal 2


title: Hoxb1 wt E10.5, rep 3 (W8)


title: CD4 alphabeta T cell vs WC1 gammadelta T cell, #3

description: Comparing leptospiral antigen-responsive CD4+ alphabeta T cells versus WC1+ gammadelta T cells. Cells were cultured 6 days with antigen and proliferating cells isolated by FACS.


title: WC1 gammadelta T cell vs CD4 alphabeta T cell, #2

source_name: CD4+ alphabeta T cell, animal 2


title: Hoxb1 mutant E10.5, rep 1 (M5)


title: Embryonic Drosophila cells, Kc167 cells, Ecdysone expression profiling, replicate 3450

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells


title: simultaneous activation of heat shock and oxidative stress pathways by celastrol-celastrol I

city: Houston

first: Kevin

middle: A

last: Morano

state: TX

address: 6431 Fannin St, MSB 1.300

department: Microbiology and Molecular Genetics

institute: UT Medical School at Houston

description: celastrol over DMSO only hybridization by UT Southwestern Core Facility

data_processing: expression ratios from background-corrected signal normalized to median

organism: Saccharomyces cerevisiae

source_name: 10 micromolar celastrol treatment for one hour

tag: 10 micromolar celastrol (in DMSO) treatment for one hour at pH 7.2

source_name: DMSO treatment for one hour

tag: DMSO treatment for one hour at pH 7.2


title: CD4 alphabeta T cell vs reference, #2


title: Embryonic Drosophila cells, Kc167 cells, Ecdysone expression profiling, replicate 3427

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, grown in presence of Ecdysone


title: Simultaneous activation of heat shock and oxidative stress pathways by celastrol-heat shock I

description: heat shock over control temperature hybridization by UT Southwestern Core Facility

source_name: heat shock (39 deg for 30 min)

tag: heat shock (39 deg for 30 min)

source_name: heat shock control (30 deg for 30 min)

tag: heat shock control (30 deg for 30 min)


title: Donor MK11 thrombopoietin + nicotinamide Day 10 rep2

status: Public on Aug 25 2006

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: Primary human hematopoietic stem cell culture directed toward megakaryocytic differentiation with or without nicotinamide supplementation

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

growth_protocol: Grown in X-VIVO20 serum-free media with 100 ng/mL thrombopoietin, 37degC, 5% CO2

extract_protocol: Agilent RNA isolation mini-kit

treatment_protocol: 6.25 mM nicotinamide added on day 5, cultured to day 10

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 19, African American

source_name: Universal Reference RNA

tag: Pooled RNA from 10 human cell lines


title: Simultaneous activation of heat shock and oxidative stress pathways by celastrol-heat shock II


title: Donor MK11 thrombopoietin + nicotinamide Day 10 rep1


title: Donor MK11 thrombopoietin + nicotinamide Day 08 rep2

treatment_protocol: 6.25 mM nicotinamide added on day 5, cultured to day 8


title: Donor MK11 thrombopoietin + nicotinamide Day 06 rep2

treatment_protocol: 6.25 mM nicotinamide added on day 5, cultured to day 6


title: Donor MK11 thrombopoietin + nicotinamide Day 06 rep1


title: Donor MK11 thrombopoietin + nicotinamide Day 08 rep1


title: CD4 alphabeta T cell vs reference

source_name: CD4+ alphabeta T cell, animal 1


title: Donor MK11 thrombopoietin Day 10 rep2

source_name: Donor MK11 thrombopoietin Day 10

treatment_protocol: Cultured 10 days


title: WC1 gammadelta T cell vs CD4 alphabeta T cell, #3


title: Donor MK11 thrombopoietin Day 08 rep2

source_name: Donor MK11 thrombopoietin Day 08

treatment_protocol: Cultured 8 days


title: Donor MK11 thrombopoietin Day 10 rep1


title: simultaneous activation of heat shock and oxidative stress pathways by celastrol-celastrol II

tag: 10 micromolar celastrol (in DMSO) treatment for one hour at pH 7.5

tag: DMSO treatment for one hour at pH 7.5


title: Donor MK11 thrombopoietin Day 06 rep2

source_name: Donor MK11 thrombopoietin Day 06

treatment_protocol: Cultured 6 days


title: CD4 alphabeta T cell vs WC1 gammadelta T cell, #2


title: Donor MK11 thrombopoietin Day 08 rep1


title: Donor MK11 Pre-treat Day 5 rep2

source_name: Donor MK11 Pre-treat Day 5

treatment_protocol: Cultured 5 days


title: Donor MK11 thrombopoietin Day 06 rep1


title: Donor MK11 Pre-treat Day 5 rep1


title: Donor MK09 thrombopoietin + nicotinamide Day 10 rep2

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 21, African American


title: Donor MK09 thrombopoietin + nicotinamide Day 08 rep1


title: WC1 gammadelta T cell vs CD4 alphabeta T cell

description: Comparing leptospiral antigen-responsive CD4+ alphabeta T cells versus WC1+ gammadelta T cells.  Cells were cultured 6 days with antigen and proliferating cells isolated by FACS.


title: Donor MK09 thrombopoietin + nicotinamide Day 06 rep1


title: Donor MK09 thrombopoietin + nicotinamide Day 10 rep1


title: Donor MK09 thrombopoietin + nicotinamide Day 06 rep2


title: CD4 alphabeta T cell vs WC1 gammadelta T cell

tag: Amplified RNA generated from total RNA isolated from FACS purified antigen-responsive CD4+ gammadelta T cells


title: Donor MK09 thrombopoietin Day 10 rep2

source_name: Donor MK09 thrombopoietin Day 10


title: Donor MK09 thrombopoietin Day 10 rep1


title: Donor MK09 thrombopoietin + nicotinamide Day 08 rep2


title: Donor MK09 thrombopoietin Day 08 rep2

source_name: Donor MK09 thrombopoietin Day 08


title: Donor MK09 thrombopoietin Day 08 rep1


title: Donor MK09 thrombopoietin Day 06 rep1

source_name: Donor MK09 thrombopoietin Day 06


title: Donor MK09 Pre-treat Day 5 rep1

source_name: Donor MK09 Pre-treat Day 5


title: Donor MK09 Pre-treat Day 5 rep2


title: Donor MK09 thrombopoietin Day 06 rep2


title: S5.9_2_1/3R clavicular line

city: Stanford

first: Howard

last: Chang

address: CCSR 2142

department: Dermatology

institute: Stanford University

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58378.gif; format: GIF

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

source_name: 2 cm below umb, 1/3 lat R clavicular line

source_name: Stratagene + skin samples

tag: Stratagene + skin samples


title: S5.16_1cm_BLW_2Lmid

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs//58376.gif; format: GIF

source_name: 1 cm below umb, 2 cm L of midline

tag: 1 cm below umb, 2 cm L of midline


title: FL3

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58372.gif; format: GIF

source_name: Fetal Lung Fibroblasts (howards old ones) sample 3


title: S97-1_D_upper_arm

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58409.gif; format: GIF

source_name: S97.1 upper arm, dorsal

tag: S97.1 upper arm, dorsal

source_name: Strratagene

tag: Strratagene


title: Foreskin (BLS8)

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58375.gif; format: GIF

source_name: Foreskin fibroblasts BLS8

tag: Foreskin fibroblasts BLS8


title: S5.11_1cm_blw_umb_R2cm

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58404.gif; format: GIF

source_name: S5.11 1 cm below umb, 2 cm R of midline

tag: S5.11 1 cm below umb, 2 cm R of midline


title: S1.3_1/3 proximal_R med arm,

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58374.gif; format: GIF

source_name: R medial upper arm, 1/3 proximal

tag: R medial upper arm, 1/3 proximal


title: S97-8i_D_4th_digit

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58406.gif; format: GIF

source_name: s97-8 dorsal 4th digit

tag: s97-8 dorsal 4th digit


title: mek1pppC_bio3_tc2_hour18

first: Ezgi

last: Booth

address: S430, One Baylor Plaza

institute: Baylor College of Medicine

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 18 hrs of development labeled with Cy5.

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer's recommended protocol as indicated below.Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65°C. Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

scan_protocol: The arrays were scanned with a ScanArrayLite scanner (Perkin Elmer) according to the manufacturer's recommended protocol. PMT and Laser settings were not recorded.All images were processed with the ImaGene software package (BioDiscovery, Inc.).

data_processing: After quantiation the normalization is implemented in 6 distinct steps: thresholding, quantile adjustment of single channel values, bias adjustment, averaging of on-chip replicates, by-signal-size variance estimation and scaling of the final values using the estimated by-signal-size variance. For more details see Van Driessche, et al.(2005). "Epistasis analysis with global transcriptional phenotypes" Nat Genet 37(5):471-7.

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum_mek1-pppC-

label_protocol: Total RNA (10 µg) was mixed with 1 µg of labeled [dT(18)] primer in 13 µl of water, incubated at 70°C for 10 minutes and on ice for 2-5 minutes. Reaction buffer (Gibco-BRL), 0.1M DTT, 0.5 mM of each dNTP and 200U Superscript II (Gibco-BRL) were added and the reaction was incubated at 42°C for 2 hours. Experimental RNA samples were labeled with Alexa 647 primers and the reference RNA sample was labeled with Cy3. Both of the primers were HPLC-purified by the manufacturer (Operon Technologies). Reverse transcription reactions were terminated with 0.1M EDTA. RNA was degraded by adding 0.3 N NaOH and incubating at 60°C for 20 minutes. The reaction was neutralized with 0.4 M Tris.HCl pH7.6. Labeled cDNA was purified by ethanol precipitation, resuspended in 10 µl of DDW and mixed with 130 µl of PerfectHybTM Plus Hybridization buffer (SIGMA H-7033).

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:2','time point:18 hr'

extract_protocol: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: Dbelowknee

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56676.gif; format: GIF

source_name: S101-43 L  leg, dorsal, below knee

tag: S101-43 L  leg, dorsal, below knee

source_name: Stratagene

tag: Stratagene


title: Vaboveknee

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56673.gif; format: GIF

source_name: L  leg, ventral above knee (S101-22)

tag: L  leg, ventral above knee (S101-22)


title: mek1pppC_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 12 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:2','time point:12 hr'


title: FL2

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56672.gif; format: GIF

source_name: Fetal Lung Amplified

tag: Fetal Lung Amplified


title: A14.5_mid_abdomen

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58416.gif; format: GIF


title: S5.6_1cm_abv_umb_L2cm

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58403.gif; format: GIF

source_name: 1 cm above umbilicus, 2 cm L to midline

tag: 1 cm above umbilicus, 2 cm L to midline


title: mek1pppC_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 6 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:2','time point:6 hr'


title: S97-4_V_forearm

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58407.gif; format: GIF

source_name: s97-4 forearm, ventral

tag: s97-4 forearm, ventral


title: mek1pppC_bio3_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:2','time point:0 hr'


title: A14.1_Rscalp

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58383.gif; format: GIF

source_name: A14.1 right scalp

tag: A14.1 right scalp


title: D_foot

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56674.gif; format: GIF

source_name: S101-45 L  foot dorsal ball of foot

tag: S101-45 L  foot dorsal ball of foot


title: Vbelowknee

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56679.gif; format: GIF

source_name: S101-23 L  leg,ventral, below knee

tag: S101-23 L  leg,ventral, below knee


title: S5.17_suprapubic_2cmL

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58381.gif; format: GIF

source_name: S15. 17 suprapubic, 2 cm L of midline

tag: S15. 17 suprapubic, 2 cm L of midline


title: Vfoot

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56678.gif; format: GIF

source_name: S101-25 L  foot, dorsum, over dorsalis pedis VENTRAL


title: mek1pppC_bio3_tc1_hour12

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:1','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: Daboveknee

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56677.gif; format: GIF

source_name: S101-42 L leg,dorsal above knee

tag: S101-42 L leg,dorsal above knee


title: mek1pppC_bio3_tc1_hour18

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:1','time point:18 hr'


title: A17.2_mid_abdomen

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58388.gif; format: GIF

source_name: A17.2 mid abdomen

tag: A17.2 mid abdomen


title: Prostate_stromal

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58408.gif; format: GIF

source_name: prostate stromal

tag: prostate stromal

source_name: Strratagene

tag: Strratagene


title: mek1pppC_bio3_tc1_hour0

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:1','time point:0 hr'


title: A17.1_chest

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58384.gif; format: GIF

source_name: A17.1 chest

tag: A17.1 chest

tag: Stratagene


title: mek1pppC_bio2_tc2_hour12

source_name: Dictyostelium discoideum_mek1-pppC-

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:2','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1pppC_bio2_tc2_hour6

extract_protocol:
RNA samples prepared from developing mek1-pppC- cells at 6 hr using TRIZOL(Invitrogen)
)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:2','time point:6 hr'


title: S5.4_1 cm_subxyphoid_2 cm L to midline

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58377.gif; format: GIF

source_name: 1 cm sub-xyhpoid, 2 cm L to midline

tag: 1 cm sub-xyhpoid, 2 cm L to midline

source_name: Stratagene + skin samples

tag: Stratagene + skin samples


title: Dachilies

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56675.gif; format: GIF

source_name: S101-44 L  leg, dorsal, over achilles tendon

source_name: Stratagene


title: A17.3_low_abdomen

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58385.gif; format: GIF

source_name: A17.3 lower abdomen

tag: A17.3 lower abdomen


title: mek1pppC_bio2_tc2_hour0

extract_protocol:
RNA samples prepared from developing mek1-pppC- cells at 0 hr using TRIZOL(Invitrogen)
)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:2','time point:0 hr'


title: A12.3_L_scalp

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58414.gif; format: GIF

source_name: A12.3 Left Scalp

tag: A12.3 Left Scalp


title: mek1pppC_bio2_tc1_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 18 hrs of development labeled with Cy5.

extract_protocol: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1pppC_bio2_tc1_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 12 hrs of development labeled with Cy5.

extract_protocol: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:1','time point:12 hr'


title: A14.2_middle scalp

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58382.gif; format: GIF

source_name: A14.2 middle scalp

tag: A14.2 middle scalp


title: S97-5i_D_1st_digit

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58405.gif; format: GIF

source_name: s97 dorsal 1st digit

tag: s97 dorsal 1st digit


title: mek1pppC_bio2_tc1_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 6 hrs of development labeled with Cy5.

extract_protocol: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:1','time point:6 hr'

tag: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)


title: S5.1_1cm_subXyph_R2cm

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58415.gif; format: GIF


title: mek1pppC_bio2_tc1_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 0  hrs of development labeled with Cy5.

extract_protocol: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:1','time point:0 hr'


title: mek1pppC_bio1_tc2_hour18

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1pppC_bio1_tc2_hour12

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:2','time point:12 hr'


title: mek1pppC_bio1_tc2_hour6

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:2','time point:6 hr'


title: mek1pppC_bio1_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 0 hrs of development labeled with Cy5.

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:2','time point:0 hr'


title: mek1pppC_bio1_tc1_hour18

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: BLS10

description:
Simple annotation: Skin, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58380.gif; format: GIF


title: mek1pppC_bio1_tc1_hour12

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:1','time point:12 hr'


title: mek1smkA_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-smkA- strain from 12 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_mek1-smkA-

extract_protocol: RNA samples prepared from developing mek1-smkA- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:2','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1pppC_bio1_tc1_hour0

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'


title: mek1smkA_bio3_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-smkA- strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-smkA- cells at 0 hr using TRIZOL(Invitrogen)


title: mek1smkA_bio3_tc2_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-smkA- strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-smkA- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:2','time point:18 hr'

source_name: Dictyostelium discoideum_mek1-smkA


title: mek1smkA_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-smkA- strain from 6 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-smkA- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:2','time point:6 hr'


title: mek1pppC_bio1_tc1_hour6

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'


title: mek1smkA_bio3_tc1_hour18

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio3_tc1_hour12

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:1','time point:12 hr'


title: mek1smkA_bio3_tc1_hour0

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:1','time point:0 hr'


title: mek1smkA_bio2_tc2_hour18

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio3_tc1_hour6

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:3','technical replication:1','time point:6 hr'


title: mek1smkA_bio2_tc2_hour12

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:2','time point:12 hr'


title: mek1smkA_bio2_tc1_hour18

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio2_tc2_hour0

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:2','time point:0 hr'


title: mek1smkA_bio2_tc1_hour12

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:1','time point:12 hr'


title: mek1smkA_bio1_tc2_hour12

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:2','time point:12 hr'

extract_protocol: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio1_tc2_hour6

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:2','time point:6 hr'


title: mek1smkA_bio1_tc2_hour18

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:2','time point:18 hr'


title: mek1smkA_bio2_tc1_hour0

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:1','time point:0 hr'


title: mek1smkA_bio1_tc1_hour18

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio2_tc1_hour6

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:1','time point:6 hr'


title: mek1smkA_bio1_tc2_hour0


title: smkA_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with smkA- strain from 6 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_smkA-

extract_protocol: RNA samples prepared from developing smkA- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:2','time point:6 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio3_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with smkA- strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing smkA- cells at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:2','time point:0 hr'


title: mek1smkA_bio1_tc1_hour0

tag: 'strain:mek1-smkA1', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'

extract_protocol: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)


title: mek1smkA_bio1_tc1_hour6

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'


title: smkA_bio3_tc1_hour6

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:1','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with smkA- strain from 12 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing smkA- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:2','time point:12 hr'


title: smkA_bio2_tc2_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with smkA- strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing smkA- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio3_tc1_hour18

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:1','time point:18 hr'


title: smkA_bio3_tc1_hour0


title: smkA_bio2_tc2_hour12

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:2','time point:12 hr'


title: smkA_bio2_tc2_hour6

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:2','time point:6 hr'


title: smkA_bio2_tc2_hour0

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:2','time point:0 hr'


title: smkA_bio2_tc1_hour18

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: mek1smkA_bio2_tc2_hour6

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:2','technical replication:2','time point:6 hr'


title: smkA_bio2_tc1_hour6

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:1','time point:6 hr'


title: smkA_bio2_tc1_hour12

tag: strain:smkA-'development:filter','biological replication:2','technical replication:1','time point:12 hr'


title: smkA_bio2_tc1_hour0

tag: 'strain:smkA-'development:filter','biological replication:2','technical replication:1','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio1_tc2_hour6

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:2','time point:6 hr'

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:2','time point:0 hr'


title: mek1smkA_bio1_tc1_hour12

tag: 'strain:mek1-smkA-', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'


title: smkA_bio3_tc2_hour18

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio1_tc2_hour18

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio1_tc1_hour18

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:1','time point:18 hr'


title: smkA_bio1_tc1_hour12

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:1','time point


title: smkA_bio1_tc1_hour6

tag: 'strain:smkA-'development:filter','biological replication:1','technical replication:1','time point:6 hr'


title: smkA_bio1_tc2_hour0


title: smkA_bio3_tc1_hour12

tag: 'strain:smkA-'development:filter','biological replication:3','technical replication:1','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: smkA_bio1_tc1_hour0

tag: strain:smkA-'development:filter','biological replication:1','technical replication:1','time point:0 hr'


title: pppC_bio3_tc2_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 18 hrs of development labeled with Cy5

source_name: Dictyostelium discoideum_pppC-

extract_protocol: RNA samples prepared from developing pppC- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:2','time point:18 hr'


title: pppC_bio3_tc1_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 18 hrs of development labeled with Cy5.

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:1','time point:18 hr'


title: pppC_bio3_tc1_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 6 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing pppC- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:1','time point:6 hr'


title: pppC_bio3_tc1_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 12 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing pppC- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:1','time point:12 hr'


title: pppC_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 12 hrs of development labeled with Cy5

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:2','time point:12 hr'


title: pppC_bio3_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 0 hrs of development labeled with Cy5

extract_protocol: RNA samples prepared from developing pppC- cells at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:2','time point:0 hr'


title: pppC_bio3_tc1_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 0 hrs of development labeled with Cy5.

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:1','time point:0 hr'


title: pppC_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with pppC- strain from 6 hrs of development labeled with Cy5

tag: 'strain:pppC-', 'development:filter','biological replication:3','technical replication:2','time point:6 hr'


title: mek1pppC_bio3_tc1_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 6 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_mek1-pppC

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:3','technical replication:1','time point:6 hr'


title: pppC_bio2_tc2_hour12

tag: 'strain:pppC-', 'development:filter','biological replication:2','technical replication:2','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: pppC_bio2_tc2_hour6

tag: 'strain:pppC-', 'development:filter','biological replication:2','technical replication:2','time point:6 hr'


title: pppC_bio2_tc2_hour0

tag: 'strain:pppC-', 'development:filter','biological replication:2','technical replication:2','time point:0 hr'


title: pppC_bio2_tc2_hour18

source_name: Dictyostelium discoideum_pppC

tag: 'strain:pppC-', 'development:filter','biological replication:2','technical replication:2','time point:18 hr'


title: mek1pppC_bio2_tc2_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with mek1-pppC- strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing mek1-pppC- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:mek1-pppC-', 'development:filter','biological replication:2','technical replication:2','time point:18 hr'


title: pppC_bio2_tc1_hour18

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: pppC_bio2_tc1_hour6

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:2','time point:6 hr'


title: pppC_bio2_tc1_hour12

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:2','time point:12 hr'


title: pppC_bio2_tc1_hour0

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:2','time point:0 hr'


title: pppC_bio1_tc2_hour18


title: pppC_bio1_tc1_hour18

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: pppC_bio1_tc2_hour6


title: pppC_bio1_tc1_hour12

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:1','time point:12 hr'


title: pppC_bio1_tc1_hour6

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'


title: pppC_bio1_tc2_hour12


title: pppC_bio1_tc1_hour0

tag: 'strain:pppC-', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: pppC_bio1_tc2_hour0


title: Mek_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 6 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_Mek1-

extract_protocol: RNA samples prepared from developing Mek1- cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:2','time point:6 hr'


title: Mek_bio3_tc2_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing Mek1- cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:2','time point:18 hr'


title: Mek_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 12 hrs of development labeled with Cy5

extract_protocol: RNA samples prepared from developing Mek1- cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:2','time point:12 hr'


title: Mek_bio3_tc1_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 12 hrs of development labeled with Cy5.

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:1','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: Mek_bio3_tc1_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with Mek1- strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing Mek1- cells at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:1','time point:0 hr'


title: Mek_bio3_tc1_hour18

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:1','time point:18 hr'


title: Mek_bio2_tc2_hour18

tag: 'strain:Mek1-', 'development:filter','biological replication:2','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: Mek_bio2_tc2_hour12

tag: 'strain:Mek1-', 'development:filter','biological replication:2','technical replication:2','time point:12 hr'


title: Mek_bio2_tc1_hour18

tag: 'strain:Mek1-', 'development:filter','biological replication:2','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: Mek_bio3_tc2_hour0

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:2','time point:0 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: Mek_bio3_tc1_hour6

tag: 'strain:Mek1-', 'development:filter','biological replication:3','technical replication:1','time point:6 hr'


title: Mek_bio2_tc2_hour0


title: Mek_bio2_tc1_hour12

tag: strain:Mek1-', 'development:filter','biological replication:2','technical replication:1','time point:12 hr'

extract_protocol: samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)


title: Mek_bio2_tc2_hour6

tag: 'strain:Mek1-', 'development:filter','biological replication:2','technical replication:2','time point:6 hr'


title: Mek_bio2_tc1_hour0

tag: strain:Mek1-', 'development:filter','biological replication:2','technical replication:1','time point:0 hr'


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-6 (2 ng/ml) and LPS (100 ng/ml), biol. rep2 T45

city: Memphis

first: Peter

middle: J

last: Murray

state: TN

address: 332 Nth Lauderdale

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: BMDMs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BMDMs differentiated from bone marrow in mCSF (CSF-1).  Samples grown fro 7 days and rested in complete DMEM for 1 hr prior to Trizol processing

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

treatment_protocol: LPS 45 minutes

tag: Time point 45 minutes post-stimulation

tag: IL-10-/- 129xC57BL/6 genetic background


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-6 (2 ng/ml) and LPS (100 ng/ml), biol. rep1 T45


title: Mek_bio1_tc2_hour18

tag: strain:Mek1-', 'development:filter','biological replication:1','technical replication:2','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep2 T180

treatment_protocol: LPS 180 minutes

tag: Time point 180 minutes post-stimulation


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep1 T180


title: Mek_bio1_tc2_hour12

tag: strain:Mek1-', 'development:filter','biological replication:1','technical replication:2','time point:12 hr'


title: Mek_bio1_tc2_hour6


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep2 T45


title: Mek_bio1_tc2_hour0

tag: strain:Mek1-', 'development:filter','biological replication:1','technical replication:2','time point:0 hr'


title: DTG_heart_on6w/off2w_rep3_chip430B

city: Boston

first: Stephan

last: Schiekofer

address: 700 Albany Street, W611

department: Molecular Cardiology

institute: Boston University School of Medicine

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 6 weeks of Akt induction followed by 2 weeks of Akt repression

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: heart tissue

label_protocol: standard Affymetrix procedures

extract_protocol: Ultraspec(TM)-II RNA Isolation System

tag: Strain

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:20 weeks, Tissue:heart tissue


title: Mek_bio1_tc1_hour18

tag: strain:Mek1-', 'development:filter','biological replication:1','technical replication:1','time point:18 hr'

extract_protocol: Extract Protocol RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)

tag: 'strain:AX4', 'development:filter','biological replication:1','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_on6w/off2w_rep1_chip430B


title: DTG_heart_on6w_rep3_chip430B

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 6 weeks of Akt induction

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:18 weeks, Tissue:heart tissue


title: DTG_heart_on6w/off2w_rep2_chip430B


title: DTG_heart_on6w_rep2_chip430B


title: IL-10-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2 T180


title: IL-10-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1 T180


title: DTG_heart_on6w_rep1_chip430B


title: DTG_heart_on2w/off2d_rep4_chip430B

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 2 weeks of Akt induction followed by 2 days of Akt repression

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:14 weeks + 2 days, Tissue:heart tissue


title: IL-10-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2 T45


title: Mek_bio1_tc1_hour6

tag: 'strain:Mek1-', 'development:filter','biological replication:1','technical replication:1','time point:6 hr'

extract_protocol: RNA samples prepared from vegetative wild type cells and from 6 developmental times (0, 3, 6, 12, 17, 24 hours) using TRIZOL(Invitrogen)


title: DTG_heart_on2w/off2d_rep3_chip430B


title: DTG_heart_on2w/off2d_rep2_chip430B


title: IL-10-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1 T45


title: DTG_heart_on2w/off2d_rep1_chip430B


title: DTG_heart_on2w_rep4_chip430B

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice after 2 weeks of Akt induction

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:14 weeks, Tissue:heart tissue


title: DTG_heart_on2w_rep3_chip430B


title: Mek_bio1_tc1_hour0

tag: 'strain:Mek1-', 'development:filter','biological replication:1','technical replication:1','time point:0 hr'


title: KAX3_bio3_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 12 hrs of development labeled with Cy5.

source_name: Dictyostelium discoideum_KAX3

extract_protocol: RNA samples prepared from developing KAX3 cells at 12 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:2','time point:12 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_on2w_rep2_chip430B


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-6 (2 ng/ml) and LPS (100 ng/ml), biol. rep1 T45

tag: IL-6-/- 129xC57BL/6 genetic background


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-6 (2 ng/ml) and LPS (100 ng/ml), biol. rep2 T45


title: LightResponse-Rep3 (Swap)

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

description: For preparation of RNA for the microarray studies, all replicate for the induced (collected 30 min. after exposure to a 5 min pulse of white light) and non-induced (dark) mycelia was isolated using RNeasy kits (Qiagen Inc. Valencia, CA, USA).

hyb_protocol: Ten micrograms of total RNA for each sample were reverse transcribed and labelled with Cy3 or Cy5 using CyScribe First Strand cDNA Labelling Kit (Amersham Biosciences, Piscataway, NJ, USA). The labelled products were purified with GFX purification columns (CyScribe GFX Purification Kit, Amersham Biosciences). The slides were placed in pre-hybridization solution (1% BSA, 5X SSC, and 0.1% SDS at 45?C) for 2 hours to eliminate non-specific interactions, and then rinsed with 0.1X SSC (22-25?C for 5 min) and HPLC grade water. Each slide was hybridized with a combination of untreated and treated labelled probes at 45?C for 14-16 h in a humidified hybridization chamber (Corning, Acton, MA, USA). After hybridization, the slides were washed once in solutions 1-4 (wash solution 1: 2x SSC, 0.1% SDS at 45?C; wash solution 2: 0.1x SSC, 0.1% SDS; wash solution 3: 0.1x SSC; wash solution 4: 0.01x SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation in a conical tube for 5 min at 1600 rpm. Three independent replicates of each mycelial treatment, RNA isolation and labelling, and microarray hybridization were performed. To estimate ?system noise? that may be due to differences in Cy-dye labelling between samples, we performed a ?self-to-self? hybridization, where the same control sample was labelled separately with Cy5 and Cy3, and then hybridized.

data_processing: Data normalization was performed using the GeneSpring 6.1 software package (Silicon Genetics, Redwood, CA, USA) applying the Cross-gene-error-model in combination with a one-way ANOVA (significance level set at p>0.05).  The background fluorescence median values that were less than zero were set to zero and subjected to intensity-dependent LOWESS (locally weighted scatter plot smoother) normalization, in which 20% of the data was used for smoothing (Clevel & Devlin 1998; Yang et al., 2001). This normalization was used to account for differences in overall intensity between slides. Each experimental result was interpreted as the average of the three biological replicates and their corresponding swap replicate. Gene expression profiles were required to be present in all three of the data sets. A signal-to-control channel ratio > 1.8 and a probability t test P<0.05 was defined as up-regulation by the light stimulus. A signal-to-control channel ratio < 0.667 and a probability t test P<0.05 was defined as down-regulation.

organism: Trichoderma atroviride

source_name: LightResponse-Ref-Label (Cy5)-Rep3B

label_protocol:
This protocol can be used to prepare Cy3 or Cy5 labelled cDNA from purified total eukaryotic RNA. In one standard reaction, 2.5 -25 ug of total RNA can be reverse transcribed into fluorescently labelled cDNA. We utilized 10 ug of total RNA in our experiments for each of the conditions (induced mycelia collected 30 min. after exposure to a 5 min pulse of white light and non-induced mycelia growth in total darkness). The final volume recommended for the labelling reaction is 20 ul after addition of all reaction components, therefore, to anneal primers, the volumes corresponding to total RNA (10 ug) and anchored oligo(dT) (2.5 ug) should be adjusted to 11 ul. This reaction mixture it is incubated at 70?C for 5 min and subsequently let the reaction mixture cool at room temperature for 10 minutes allow the primers to anneal with the total RNA template. Finally the labelling components for the reaction added in the following order: 4 ul for the 5x CyScript buffer, 2 uL 0.1 M DTT, 1 uL dUTP nucleotide mix, 1 uL dUTP CyDye-labelled nucleotide (Cy3 or Cy5), and 1 uL SuperScript II reverse transcriptase, and the reaction mix incubated at 42?C for 1.5 hours. All the components before mentioned for the reactions from total RNA can be reverse transcribed into fluorescently labelled cDNA form part of the CyScribe First-Strand cDNA labelling kit (cat. Number: RPN6201, Amersham Biosciences).
It is necessary to remove the RNA template for the each sample before the hybridization, from the single-stranded cDNA to promote hybridization of the cDNA probe to immobilized microarray targets and to minimize hybridization with complementary RNA in solution. Removal of unincorporated CyDye-nucleotides is also necessary for minimizing hybridization background and for improving the sensitivity of detection of low abundance targets. The removal of RNA can be achieved in two steps. First RNA is degraded into short oligomers with alkaline treatment (adding 2 uL of 2.5 M NaOH into each microcentrifuge tube containing labelling reactions and incubating the samples at 37?C for 15 min, subsequently we add 10 uL of 2 M HEPES to neutralize the pH). Then these short oligomers, as well as unincorporated nucleotides, are removed with spin chromatography columns. We use CyScribe GFX Purification kit (Cat. Number: 27-9606-02, Amersham Biosciences). Labelled cDNA tightly bound to the CyScribe GFX column was eluted in 60 ul elution buffer (provided with the kit).

tag: T. atroviride cultures were grown in the dark for 48 h at 27°C on PDYCA plates and used a pre-inoculum. Mycelial plugs were then placed on a washed cellophane sheet overlying a double layer of filter paper (an 8 cm disk of Whatmann 50 was overlaid on a 7 cm disk of Whatmann 1 filter paper in a Petri dish) soaked in 3 ml PDYCB medium (24 g/l of Potato Dextrose Broth, 2 g/l of Yeast Extract and 1.2 g/l of casein hydrolysate medium, all from DIFCO). Cultures were allowed to grow for further 36h in the dark. Total RNA was isolated from colonies non-induced (kept at all times in the dark). Mycelia were scraped from the surface of the cellophane overlaying the filter paper under red safe-light LEE filter #106 (fluence rate 0.1 mmol/m2s) and immediately frozen in liquid nitrogen for RNA extraction using RNeasy kits (Qiagen Inc. Valencia, CA, USA).

source_name: LightResponse-Test-Label (Cy3)-Rep3B

tag: T. atroviride cultures were grown in the dark for 48 h at 27°C on PDYCA plates and used a pre-inoculum. Mycelial plugs were then placed on a washed cellophane sheet overlying a double layer of filter paper (an 8 cm disk of Whatmann 50 was overlaid on a 7 cm disk of Whatmann 1 filter paper in a Petri dish) soaked in 3 ml PDYCB medium (24 g/l of Potato Dextrose Broth, 2 g/l of Yeast Extract and 1.2 g/l of casein hydrolysate medium, all from DIFCO). Cultures were allowed to grow for further 36h in the dark, and then photoinduced. Total RNA was isolated from colonies that were exposed to white light for five minutes (fluence rate 27 umol/m2s), and placed back in the dark at 27°C for 30 min. Mycelia were scraped from the surface of the cellophane overlaying the filter paper under red safe-light LEE filter #106 (fluence rate 0.1 mmol/m2s) and immediately frozen in liquid nitrogen for RNA extraction using RNeasy kits (Qiagen Inc. Valencia, CA, USA).


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep2 T180


title: LightResponse-Rep3

source_name: LightResponse-Ref-Label (Cy3)-Rep3A

source_name: LightResponse-Test-Label (Cy5)-Rep3A


title: Mek_bio1_tc1_hour12

tag: strain:Mek1-', 'development:filter','biological replication:1','technical replication:1','time point:12 hr'


title: KAX3_bio3_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 6 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 cells at 6 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:2','time point:6 hr'

tag: strain:AX4', 'development:filter','biological replication:3','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: KAX3_bio3_tc2_hour0

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 0 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 cells at 0 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:2','time point:0 hr'


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep1 T180

tag: Time point 180 minutes post-stimulation


title: LightResponse-Rep2 (Swap)

source_name: LightResponse-Ref-Label (Cy5)-Rep2B

source_name: LightResponse-Test-Label (Cy3)-Rep2B


title: KAX3_bio3_tc1_hour18

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 18 hrs of development labeled with Cy5.

extract_protocol: RNA samples prepared from developing KAX3 cells at 18 hr using TRIZOL(Invitrogen)

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:1','time point:18 hr'

tag: 'strain:AX4', 'development:filter','biological replication:3','technical replication:1','time point:0, 3, 6, 12, 17, 24 hr'


title: LightResponse-Rep2

source_name: LightResponse-Ref-Label (Cy3)-Rep2A

source_name: LightResponse-Test-Label (Cy5)-Rep2A


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep2 T45

tag: Time point 45 minutes post-stimulation


title: DTG_heart_on2w_rep1_chip430B

tag: Strain


title: IL-10-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep1 T45

tag: IL-10-/- 129xC57BL/6 genetic background


title: KAX3_bio3_tc1_hour12

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:1','time point:12 hr'


title: IL-6-/- murine bone marrow-derived macrophages stimulated with IL-10 (10 ng/ml) and LPS (100 ng/ml), biol. rep1 T45


title: KAX3_bio3_tc2_hour18

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:2','time point:18 hr'


title: LightResponse-Rep1 (Swap)

data_processing: Data normalization was performed using the GeneSpring 6.1 software package (Silicon Genetics, Redwood, CA, USA) applying the Cross-gene-error-model in combination with a one-way ANOVA (significance level set at p>0.05).  The background fluorescence median values that were less than zero were set to zero and subjected to intensity-dependent LOWESS (locally weighted scatter plot smoother) normalization, in which 20% of the data was used for smoothing (Clevel & Devlin 1998; Yang et al., 2001). This normalization was used to account for differences in overall intensity between slides. Each experimental result was interpreted as the average of the three biological replicates and their corresponding swap replicate. Gene expression profiles were required to be present in all three of the data sets. A signal-to-control channel ratio > 1.8 and a probability t test P<0.05 was defined as up-regulation by the light stimulus. A signal-to-control channel ratio < 0.667 and a probability t test P<0.05 was defined as down-regulation.

source_name: LightResponse-Ref-Label (Cy5)-Rep1B

source_name: LightResponse-Test-Label (Cy3)-Rep1B


title: KAX3_bio3_tc1_hour6

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:1','time point:6 hr''


title: DTG_heart_on6w/off2w_rep3_chip430A


title: DTG_heart_control_rep4_chip430B

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice before Akt induction

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:12 weeks, Tissue:heart tissue


title: IL-6-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2 T180


title: DTG_heart_on6w/off2w_rep2_chip430A


title: KAX3_bio3_tc1_hour0

tag: 'strain:KAX3', 'development:filter','biological replication:3','technical replication:1','time point:0 hr'


title: IL-6-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1 T45

tag: IL-6-/- 129xC57BL/6 genetic background


title: DTG_heart_on6w/off2w_rep1_chip430A


title: IL-6-/- murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep2 T45


title: DTG_heart_control_rep3_chip430B


title: Murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml), biol. rep1 T45


title: DTG_heart_on6w_rep3_chip430A


title: KAX3_bio2_tc2_hour6

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 6 hrs of development labeled with Cy5

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:2','time point:6 hr'

tag: 'strain:AX4', 'development:filter','biological replication:2','technical replication:2','time point:0, 3, 6, 12, 17, 24 hr'


title: DTG_heart_control_rep2_chip430B


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-6 (2 ng/ml), biol. rep2 T45

treatment_protocol: LPS+IL-6 45 minutes


title: KAX3_bio2_tc2_hour0

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:2','time point:0 hr'


title: DTG_heart_control_rep1_chip430B


title: Wild type murine bone marrow-derived macrophages stimulated with LPS (100 ng/ml) and IL-6 (2 ng/ml), biol. rep1 T45


title: KAX3_bio2_tc2_hour12

description: Reference pool collected at 0, 3, 6, 12, 17, 24 hours from development and labeled with Cy3. Sample co-hybridized with KAX3 strain from 12 hrs of development labeled with Cy5

tag: 'strain:KAX3', 'development:filter','biological replication:2','technical replication:2','time point:12 hr'


title: DTG_heart_on6w_rep1_chip430A